Brain Mapping An Encyclopedic Reference (-PUNISHER-)

BRAIN MAPPING
AN ENCYCLOPEDIC
REFERENCE
Volume 1
Acquisition Methods
Methods and Modeling
This page intentionally left blank
BRAIN MAPPING
AN ENCYCLOPEDIC
REFERENCE
Volume 1
Acquisition Methods
Methods and Modeling
EDITOR-IN-CHIEF
ARTHUR W. TOGA
University of Southern California, Los Angeles, CA, USA
SECTION EDITORS
PETER BANDETTINI
National Institute of Mental Health, Bethesda, MD, USA
PAUL THOMPSON
Keck USC School of Medicine, USA
KARL FRISTON
Wellcome Trust Centre for Neuroimaging, London, UK
AMSTERDAM BOSTON HEIDELBERG LONDON

NEW YORK OXFORD PARIS SAN DIEGO
SAN FRANCISCO SINGAPORE SYDNEY TOKYO
Academic Press is an imprint of Elsevier

32 Jamestown Road, London NW1 7BY, UK
525 B Street, Suite 1800, San Diego, CA 92101-4495, USA
225 Wyman Street, Waltham, MA 02451, USA
The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, UK
2015 Elsevier Inc. All rights reserved.
The following articles are US government work in the public domain and are not subject to copyright:
Contrast Agents in Functional Magnetic Resonance Imaging; Distribution of Estrogen Synthase (Aromatase) in the Human Brain; Evolution
of Instrumentation for Functional Magnetic Resonance Imaging; Temporal Resolution and Spatial Resolution of fMRI
The following articles are not part of Elsevier:
Cytoarchitectonics, Receptorarchitectonics, and Network Topology of Language; Expertise and Object Recognition; Hemodynamic and
Metabolic Disturbances in Acute Cerebral Infarction; Inflammatory Disorders in the Brain and CNS; Neuropsychiatry; Primary Progressive
Aphasia; Puberty, Peers, and Perspective Taking: Examining Adolescent Self-Concept Development Through the Lens of Social Cognitive
Neuroscience
No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means electronic,
mechanical, photocopying, recording or otherwise without the prior written permission of the publisher.
Permissions may be sought from Elseviers Science & Technology Rights department in Oxford, UK: phone (44) (0) 1865 843830;
fax (44) (0) 1865 853333; email: permissions@elsevier.com
Alternatively you can submit your request online by visiting the Elsevier website at http://elsevier.com/locate/permissions and selecting
Obtaining permission to use Elsevier material.
Notice
No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability,
negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein.
British Library Cataloguing in Publication Data
A catalogue record for this book is available from the British Library
Library of Congress Cataloging-in-Publication Data
A catalog record for this book is available from the Library of Congress
ISBN: 978-0-12-397025-1
For information on all Elsevier publications
visit our website at store.elsevier.com
15 16
17 18 19
10 9 8 7 6 5 4 3 2 1
Publisher: Lisa Tickner

Acquisitions Editor: Ginny Mills
Content Project Manager: Will Bowden Green
Production Project Manager: Paul Prasad
Cover Designer: Alan Studholme
CONTRIBUTORS
I Aganj
Massachusetts General Hospital, Harvard Medical
School, MA, USA
PA Ciris
Yale University School of Medicine, New Haven,
CT, USA
AL Alexander
University of Wisconsin Madison, Madison, WI, USA
RT Constable
CT, USA
DC Alexander
University College London, London, UK
C Allefeld
Universitatsmedizin Berlin, Berlin, Germany
S Arridge
J Ashburner
UCL Institute of Neurology, London, UK
PA Bandettini
National Institute of Mental Health, Bethesda, MD, USA
GR Barnes
DS Barron
University of Texas Health Science Center at San Antonio,
San Antonio, TX, USA
Bharat Biswal
New Jersey Medical School, Rutgers University,
NJ, USA
DA Boas
Harvard Medical School, Charlestown, MA, USA
G Bruce Pike
University of Calgary, Calgary, AB, Canada
RB Buxton
University of California, San Diego, CA, USA
RJ Cooper
P Coutin-Churchman
University of California at Los Angeles, Los Angeles,
CA, USA
O David
Universite Joseph Fourier, Grenoble, France
JA de Zwart
National Institutes of Health, Bethesda, MD, USA
G Deco
Universitat Pompeu Fabra, Barcelona, Spain
JH Duyn
ES Finn
CT, USA
C Fischer
CEA, Gif-sur-Yvette, France; CATI Multicenter
Neuroimaging Platform, Paris, France
B Fischl
Charlestown, MA, USA
G Flandin
A Cachia
Universite Paris Descartes, Paris, France
PT Fox
University of Texas Health Science Center at San Antonio,
San Antonio, TX, USA; South Texas Veterans Health
Care System, San Antonio, TX, USA
MA Chappell
University of Oxford, Oxford, UK
KJ Friston
vi
Contributors
C Gaser
Jena University Hospital, Jena, Germany
RD Hoge
Universite de Montreal, Montreal, QC, Canada
CR Genovese
Carnegie Mellon University, Pittsburgh, PA, USA
AR Hoy
United States Navy, Falls Church, VA, USA; University of
Wisconsin Madison, Madison, WI, USA
G Gerig
University of Utah, Salt Lake City, UT, USA
JH Gilmore
University of North Carolina, Chapel Hill, NC, USA
DR Gitelman
Professor of Neurology, Chicago Medical School at
Rosalind Franklin University, Park Ridge, IL, USA
RN Gunn
Imanova Ltd, London, UK; Imperial College London,
London, UK; University of Oxford, Oxford, UK
Q Guo
Imanova Ltd, London, UK; AbbVie Translational
Sciences, North Chicago, IL, USA; Kings College
London, London, UK; Imperial College London, London,
UK
A Jasanoff
Massachusetts Institute of Technology, Cambridge, MA,
USA
S Jbabdi
Oxford University Centre for Functional MRI of the Brain
(FMRIB), Oxford, UK
P Jezzard
NK Kasabov
Auckland University of Technology, Auckland, New
Zealand
KN Kay
Stanford University, Stanford, CA, USA; Washington
University, St. Louis, MO, USA
A Hahn
Medical University of Vienna, Vienna, Austria
SJ Kiebel
Technische Universitat Dresden, Dresden, Germany
A Hai
Massachusetts Institute of Technology, Cambridge, MA,
USA
G Kindlmann
University of Chicago, Chicago, IL, USA
M Hamalainen
Aalto University, Espoo, Finland; Massachusetts General
Hospital, Charlestown, MA, USA
N Harel
University of Minnesota Medical School, MN, USA
R Hari
Aalto University, Espoo, Finland
J-D Haynes
Universitatsmedizin Berlin, Berlin, Germany; HumboldtUniversitat zu Berlin, Berlin, Germany
S Heldmann
Fraunhofer MEVIS, Lubeck, Germany
G Helms
Medical Radiation Physics, Lund University, Lund,
Sweden
RN Henson
MRC Cognition and Brain Sciences Unit, Cambridge, UK
PJ Koopmans
N Kriegeskorte
Medical Research Council, Cambridge, UK
F Kurth
UCLA School of Medicine, Los Angeles, CA, USA
R Lanzenberger
Medical University of Vienna, Vienna, Austria
F Lecaignard
Lyon Neuroscience Research Center (CRNL), Lyon,
France; University Lyon 1, Lyon, France; Cermep
Imagerie du vivant, Lyon, France
J Lefe`vre
Aix-Marseille Universite, Marseille, France
C Lenglet
University of Minnesota Medical School, Minneapolis,
MN, USA
GT Herman
City University of New York, New York, NY, USA
JP Lerch
The Hospital for Sick Children, Toronto, ON, Canada;
University of Toronto, Toronto, ON, Canada
L Hernandez-Garcia
University of Michigan, Ann Arbor, MI, USA
KK Leung
Contributors
Z-P Liang
University of Illinois at Urbana-Champaign, Urbana, IL,
USA
K Mueller
Max Planck Institute for Human Cognitive and Brain
Sciences, Leipzig, Germany
MA Lindquist
Johns Hopkins University, Baltimore, MD, USA
JA Mumford
University of Texas, Austin, TX, USA
TT Liu
University of California, San Diego, CA, USA
G Nedjati-Gilani
JD Lopez
Universidad de Antioquia UDEA, Medelln, Colombia
G Operto
E Luders
UCLA School of Medicine, Los Angeles, CA, USA
M Maddah
Cellogy Inc., Menlo Park, CA, USA; SRI International,
Menlo Park, CA, USA
J-F Mangin
E Mark Haacke
Wayne State University, Detroit, MI, USA
J Mattout
Lyon Neuroscience Research Center (CRNL), Lyon,
France; University Lyon 1, Lyon, France
vii
X Papademetris
Yale University School of Medicine, New Haven, CT,
USA
N Papenberg
Fraunhofer MEVIS, Lubeck, Germany
L Parkkonen
Aalto University, Espoo, Finland
M Perrot
RA Poldrack
Stanford University, Stanford, CA, USA
AR McIntosh
Rotman Research Institute, Toronto, ON, Canada;
JR Polimeni
Massachusetts General Hospital, Charlestown, MA, USA;
Harvard Medical School, Boston, MA, USA
RS Menon
The University of Western Ontario, London, ON, Canada
J-B Poline
University of California, Berkeley, CA, USA
MI Miller
A Ponce-Alvarez
Universitat Pompeu Fabra, Barcelona, Spain
D Millett
Hoag Hospital, Newport Beach, CA, USA
V Priesemann
Max Planck Institute for Brain Research, Frankfurt,
Germany
B Misic
Rotman Research Institute, Toronto, ON, Canada;
J Modersitzki
University of Lubeck, Lubeck, Germany; Fraunhofer
MEVIS, Lubeck, Germany
R Moran
Virginia Tech Carilion Research Institute, Roanoke, VA,
USA; Bradley Department of Electrical and Computer
Engineering, Roanoke, VA, USA
O Puonti
Technical University of Denmark, Lyngby, Denmark
Y Rathi
JR Reichenbach
Friedrich-Schiller University, Jena, Germany
GR Ridgway
University of Oxford, Headington, UK; UCL Institute of
Neurology, London, UK
S Mori
Johns Hopkins University School of Medicine, Baltimore,
MD, USA
D Rivie`re
M Muckley
University of Michigan, Ann Arbor, MI, USA
N Roberts
University of Edinburgh, Edinburgh, UK
viii
Contributors
A Roebroeck
Maastricht University, Maastricht, The Netherlands
J Tohka
Tampere University of Technology, Tampere, Finland
MJ Rosa
X Tomas-Fernandez
Harvard Medical School, Boston MA, USA
N Sadeghi
J-D Tournier
Florey Neuroscience Institutes, Heidelberg West, VIC,
Australia
G Sapiro
Duke University, NC, USA
D Scheinost
USA
F Schmitt
Siemens Healthcare, Erlangen, Germany
X Shen
USA
J Shi
Arizona State University, Tempe, AZ, USA
AC Silva
JG Sled
Hospital for Sick Children, Toronto, ON, Canada;
SM Smith
Oxford University Centre for Functional MRI of the Brain
(FMRIB), Oxford, UK
O Sporns
Indiana University, Bloomington, IN, USA
KE Stephan
University of Zurich & Swiss Federal Institute of
Technology (ETH Zurich), Zurich, Switzerland;
JM Stern
University of California at Los Angeles, Los Angeles, CA,
USA
X Tang
BT Thomas Yeo
National University of Singapore, Singapore, Singapore;
Duke-NUS Graduate Medical School, Singapore,
Singapore; Massachusetts General Hospital, Charlestown,
MA, USA
R Todd Constable
USA
NJ Trujillo-Barreto
Institute of Brain, Behaviour and Mental Health, The
University of Manchester, UK
R Turner
Max Planck Institute for Human Cognitive and Brain
Sciences, Leipzig, Germany
D Tward
K Ugurbil
University of Minnesota, Minneapolis, MN, USA
K Uludag
A van der Kouwe
JD Van Horn
K Van Leemput
JF Vargas
Universidad de Antioquia UDEA, Medelln, Colombia
TD Wager
University of Colorado at Boulder, Boulder, CO, USA
LL Wald
Massachusetts General Hospital, Charlestown, MA, USA;
Harvard Medical School, Boston, MA, USA; HarvardMIT Division of Health Sciences and Technology,
Cambridge, MA, USA
BA Wandell
Stanford University, Stanford, CA, USA
Y Wang
Cornell University, New York, NY, USA; Arizona State
University, Tempe, AZ, USA
SK Warfield
Harvard Medical School, Boston MA, USA
C-F Westin
M Wibral
Goethe University, Frankfurt, Germany
Contributors
J Winawer
New York University, New York, NY, USA
MW Woolrich
E Yacoub
University of Minnesota, Minneapolis, MN, USA
L Ying
State University of New York at Buffalo, Buffalo, NY,
USA
Y Zhang
ix
VOLUME 1 TABLE OF CONTENTS

Preface
xv
Editor-in-Chief
xvii
Section Editors
xix
Acknowledgments
xxiii
INTRODUCTION TO ACQUISITION METHODS
Anatomical MRI for Human Brain Morphometry
A van der Kouwe and B Fischl
Obtaining Quantitative Information from fMRI
29
G Bruce Pike and RD Hoge
Contrast Agents in Functional Magnetic Resonance Imaging
37
AC Silva
Diffusion MRI
47
AR Hoy and AL Alexander
Echo-Planar Imaging
53
F Schmitt
Basic Principles of Electroencephalography
75
D Millett, P Coutin-Churchman, and JM Stern
Functional MRI Dynamics
81
K Uludag
Evolution of Instrumentation for Functional Magnetic Resonance Imaging
89
JA de Zwart and JH Duyn
High-Field Acquisition
97
RS Menon
High-Speed, High-Resolution Acquisitions
103
LL Wald and JR Polimeni
Basic Principles of Magnetoencephalography
117
R Hari, L Parkkonen, and M Hamalainen
Molecular fMRI
123
A Hai and A Jasanoff
Pulse Sequence Dependence of the fMRI Signal
131
P Jezzard and PJ Koopmans
Myelin Imaging
137
R Turner
xi
xii
Volume 1 Table of Contents
Functional Near-Infrared Spectroscopy
143
RJ Cooper and DA Boas
Perfusion Imaging with Arterial Spin Labeling MRI
149
TT Liu
Positron Emission Tomography and Neuroreceptor Mapping In Vivo
155
R Lanzenberger and A Hahn
Susceptibility-Weighted Imaging and Quantitative Susceptibility Mapping
161
E Mark Haacke, JR Reichenbach, and Y Wang
Temporal Resolution and Spatial Resolution of fMRI
173
PA Bandettini
MRI and fMRI Optimizations and Applications
183
PA Ciris and R Todd Constable
fMRI at High Magnetic Field: Spatial Resolution Limits and Applications
191
E Yacoub, K Ugurbil, and N Harel
INTRODUCTION TO METHODS AND MODELING
201
Computerized Tomography Reconstruction Methods
203
GT Herman
Pharmacokinetic Modeling of Dynamic PET
209
Q Guo and RN Gunn
Optical Image Reconstruction
217
S Arridge and RJ Cooper
Image Reconstruction in MRI
223
L Ying and Z-P Liang
Artifacts in Functional MRI and How to Mitigate Them
231
L Hernandez-Garcia and M Muckley
Diffusion Tensor Imaging
245
C Lenglet
Probability Distribution Functions in Diffusion MRI
253
Y Rathi and C-F Westin
Q-Space Modeling in Diffusion-Weighted MRI
257
I Aganj, G Sapiro, and N Harel
Fiber Tracking with DWI
265
J-D Tournier and S Mori
Tract Clustering, Labeling, and Quantitative Analysis
271
M Maddah
Tissue Microstructure Imaging with Diffusion MRI
277
G Nedjati-Gilani and DC Alexander
Tissue Properties from Quantitative MRI
287
G Helms
Intensity Nonuniformity Correction
295
JG Sled
Rigid-Body Registration
301
J Tohka
Nonlinear Registration Via Displacement Fields
307
J Modersitzki, S Heldmann, and N Papenberg
Diffeomorphic Image Registration

J Ashburner and MI Miller
315
Lesion Segmentation
xiii
323
SK Warfield and X Tomas-Fernandez
Manual Morphometry
333
N Roberts
Voxel-Based Morphometry
345
F Kurth, E Luders, and C Gaser
Cortical Thickness Mapping
351
JP Lerch
Automatic Labeling of the Human Cerebral Cortex
357
BT Thomas Yeo
Sulcus Identification and Labeling
365
J-F Mangin, M Perrot, G Operto, A Cachia, C Fischer, J Lefe`vre, and D Rivie`re
Tissue Classification
373
K Van Leemput and O Puonti
Tensor-Based Morphometry
383
J Ashburner and GR Ridgway
Surface-Based Morphometry
395
J Shi and Y Wang
Bayesian Multiple Atlas Deformable Templates
401
MI Miller, S Mori, X Tang, D Tward, and Y Zhang
Computing Brain Change over Time
417
GR Ridgway, KK Leung, and J Ashburner
Modeling Brain Growth and Development
429
N Sadeghi, G Gerig, and JH Gilmore
Tract-Based Spatial Statistics and Other Approaches for Cross-Subject Comparison of Local
Diffusion MRI Parameters
437
SM Smith, G Kindlmann, and S Jbabdi
The General Linear Model
465
SJ Kiebel and K Mueller
Contrasts and Inferences
471
JA Mumford and J-B Poline
Analysis of Variance (ANOVA)
477
RN Henson
Convolution Models for FMRI
483
DR Gitelman
Design Efficiency
489
RN Henson
Topological Inference
495
G Flandin and KJ Friston
False Discovery Rate Control
501
CR Genovese
Bayesian Model Inversion
509
MW Woolrich and MA Chappell
Posterior Probability Maps
517
MJ Rosa
Variational Bayes
MA Chappell and MW Woolrich
523
xiv
Bayesian Model Inference
535
NJ Trujillo-Barreto
Models of fMRI Signal Changes
541
RB Buxton
Forward Models for EEG/MEG
549
F Lecaignard and J Mattout
Distributed Bayesian Inversion of MEG/EEG Models
557
JD Lopez, JF Vargas, and GR Barnes
Neural Mass Models
563
O David
The Emergence of Spontaneous and Evoked Functional Connectivity in a Large-Scale

Model of the Brain
571
A Ponce-Alvarez and G Deco
Resting-State Functional Connectivity
581
Bharat Biswal
Effective Connectivity
587
B Misic and AR McIntosh
Granger Causality
593
A Roebroeck
Information Theoretical Approaches
599
M Wibral and V Priesemann
Dynamic Causal Models for fMRI
617
KE Stephan
Dynamic Causal Models for Human Electrophysiology: EEG, MEG, and LFPs
625
R Moran
Graph-Theoretical Analysis of Brain Networks
629
O Sporns
Crossvalidation
635
N Kriegeskorte
Multi-voxel Pattern Analysis
641
C Allefeld and J-D Haynes
Reverse Inference
647
RA Poldrack
Computational Modeling of Responses in Human Visual Cortex
651
BA Wandell, J Winawer, and KN Kay
Meta-Analyses in Functional Neuroimaging
661
MA Lindquist and TD Wager
Integrative Computational Neurogenetic Modeling
667
NK Kasabov
BrainMap Database as a Resource for Computational Modeling
675
DS Barron and PT Fox
Databases
685
JD Van Horn
Methodological Issues in fMRI Functional Connectivity and Network Analysis

ES Finn, D Scheinost, X Shen, X Papademetris, and RT Constable
697
PREFACE
The contributions of brain mapping are self-evident. Perhaps only a few areas of science have been applied as
broadly and deeply as brain mapping. In less than 50 years, it has revolutionized the study of brain structure
and function as well as the practice of clinical neuroscience. The resulting images derived from brain mapping
studies can be found everywhere. They grace the covers of many scientific journals, and even permeate the lay
media. The arresting imagery derived from sophisticated brain mapping methodologies and applied to
previously intractable problems has transformed neuroscience like no other specialty.
Brain mapping is a field that encompasses a wide range of scientific areas from MR physics, molecular
dynamics, and the mathematical modeling of data to the anatomical and physiological measurement of brain
systems and the study of complex cognitive functions. These all have been applied to understand the human
condition in health and disease. Advances have led to new effective treatments in stroke and improved
therapeutic intervention in many diseases affecting the brain. New approaches have enabled measures that
differentiate us as individuals anatomically and functionally. Maps that represent whole populations of people
of a certain age, gender, handedness, suffering from a particular neurological or psychiatric condition or even
genetic cohorts with a particular single nucleotide polymorphism can be created. The utility of these maps as
biomarkers or as guides in clinical trials has become a reality. Brain mapping is as vibrant and dynamic as ever
and increasingly links to other paths of discovery including genetics, proteomics, biologics, and big data.
The creation of this encyclopedia comes at a time that acknowledges the spectacular growth and important
contributions already made and the promise for ever more exciting and significant discoveries. It was just about
20 years ago that the first of the Brain Mapping Trilogy was published with the title, Brain Mapping: The Methods.
At about the same time, a group of brain imaging scientists decided it would be a good idea to form a new
society and the Organization for Human Brain Mapping was born. There are now several journals devoted to
neuroimaging and brain mapping. Other periodicals focused on more general neuroscience invariably include
a considerable number of papers on brain mapping. For the last couple of decades the number of brain
mapping publications grew from around 3200 in 1996 to about 14 000 in 2013, more than a 400% increase!
What a remarkable 20 years it has been. No longer can the breadth of brain mapping be covered in a traditional
text book style. The field has grown just too large.
Given the fact that there are well over 100 000 published papers on brain mapping, an encyclopedic
reference system to navigate these numbers is sorely needed. The three volumes of this encyclopedia fill that
need and consist of a comprehensive collection of thoughtful and informative descriptions of each topic. Well
referenced and written by recognized authorities, each article provides a wealth of information for the novice
and expert alike.
We organized the encyclopedia into seven sections. Volume 1 includes sections entitled Acquisition Methods
edited by Peter Bandettini and another entitled Methods and Modeling edited by Karl Friston and Paul Thompson. Acquisition Methods includes descriptions of magnetic resonance imaging (MRI), functional magnetic
resonance imaging (fMRI), magnetoencephalography (MEG), positron emission tomography (PET), and
near-infrared spectroscopy (NIRS). Most of the articles focus on variations in fMRI acquisition, given the
range and extent of this brain imaging method. However, it is clear that other approaches covered in this section
have lots to offer in the study of brain, each with its own advantages and disadvantages and each method has its
limitations, no one is a panacea. All are highly complementary and benefit from the synergy of multimodal
integration described further in Methods and Modeling. Here, Friston and Thompson selected papers describing advances in analytics built upon novel mathematics for representing and modeling signals, detecting
patterns, and understanding causal effects. These have accelerated the contributions of imaging and brain
xv
xvi
Preface
mapping significantly. Creative applications of random fields to dynamic causal models, graph theory,
networks, and topological measures of connectomes, to chart connections inferred from functional synchrony
or anatomical circuitry. Continuum mechanics fluid flow, differential geometry, and relativity all have been
used to model and manipulate anatomical surfaces in the brain, and to align and compare observations from
whole populations.
Volume 2 includes a section on Anatomy and Physiology edited by Karl Zilles and Katrin Amunts and another
devoted to Systems edited by Marsel Mesulam and Sabine Kastner. In the Anatomy and Physiology section, the
functional, cellular, and molecular basics along with organizational principles of brain structure provide a solid
foundation for models and simulations. This section goes on to provide an overview of brain development
beginning with the evolution of the cerebral cortex as well as embryonic and fetal development of the human
brain. Finally, the last part of this section is dedicated to different brain regions with emphasis focused on
functional systems and a superb lead into Systems. The section on Systems edited by Mesulam and Kastner is
comprised of articles that address the functional anatomy of action, perception, and cognition in multiple
modalities and domains.
Volume 3 contains sections on Cognitive Neuroscience edited by Russ Poldrack and another focused on Social
Cognitive Neuroscience edited by Matthew Lieberman and a third covering Clinical Brain Mapping edited by
Richard Frackowiak. The section on Cognitive Neuroscience covers a broad range of topics on mapping cognitive
functions including attention, learning and memory, decision making, executive function, and language. There
are articles on neuroeconomics, a field that combines neuroscience, psychology, and economics to better
understand the neural mechanisms for decision making. There is also a series of papers on memory, including
episodic memory, familiarity, semantic memory, and nondeclarative forms of learning. Language is covered in
this section as well, with articles on speech perception and production, syntax, semantics, and reading.
Poldrack also included studies of unique populations such as sign language speakers, bilinguals, and individuals with reading disabilities.
The section on Social Cognitive Neuroscience deals with how our brain responds to our social world. There are
papers that chart the different ways in which people respond to the rewards and punishments of social living
such as perceptions of unfair treatment, social rejection, or other negative social influences. There are also
articles describing neural mechanisms for reward and incentive motivation that respond to reinforcers like
money or sexual cues. Another part of this section deals with the concept of self. And another explores the
basic mechanisms of social perception. These articles focus on the perception of faces, bodies, and emotions as
basic cues. Also included are articles about social thinking and attitudinal and evaluative processes that keep
track of what matters to us and who or what we align ourselves with or against. Clinical Brain Mapping provides
numerous examples of the translational value of brain mapping. For example, the time course and cascade of
stroke pathophysiology pointed to the need for hyperacute treatment with thrombolytics. The contribution of
functional imaging first with PET and subsequently with fMRI, forever altered clinical neurology, neurosurgery
and other clinical neuroscience specialties. The ability to perform scans repetitively gave insights into functional
dynamics in the human brain enabling investigations of neurodegenerative disease, psychiatric disorders, and
the efficacy of therapeutic intervention.
Each of these sections stands alone as a comprehensive collection of articles describing the how, why, and
what brain mapping has contributed to these areas. Each article introduces the topic and brings the reader up to
date with the latest in findings and developments. We deliberately structured the encyclopedia so that readers
can peruse the material in any order or concentrate on a particular set of topics from methods to applications.
We kept the articles concise and suggest further reading to those who desire a more extensive review. They are
well referenced and illustrated appropriately.
Together these articles comprise a unique and rich resource for anyone interested in the science of mapping
the brain.
Arthur W. Toga
EDITOR-IN-CHIEF
Arthur W. Toga is the director, Laboratory of Neuro Imaging; director, Institute
of Neuroimaging and Informatics; provost professor, Departments of Ophthalmology, Neurology, Psychiatry, and the Behavioral Sciences, Radiology
and Engineering at the Keck School of Medicine of USC. His research is focused
on neuroimaging, informatics, mapping brain structure and function, and
brain atlasing. He has developed multimodal imaging and data aggregation
strategies and applied them in a variety of neurological diseases and psychiatric
disorders. His work in informatics includes the development and implementation of some of the largest and most widely used databases and data mining
tools linking disparate data from genetics, imaging, clinical and behavior,
supporting global efforts in Alzheimers disease, Huntingtons, and Parkinsons
disease. He was trained in neuroscience and computer science and has written
more than 1000 papers, chapters, and abstracts, including eight books. Recruited to USC in 2013, he directs the
Laboratory of Neuro Imaging. This 110-member laboratory includes graduate students from computer science,
biostatistics, and neuroscience. It is funded with grants from the National Institutes of Health grants as well as
industry partners. He has received numerous awards and honors in computer science, graphics, and neuroscience. Prior to coming to USC he was a distinguished professor of Neurology at UCLA, held the Geffen Chair of
Informatics at the David Geffen School of Medicine at UCLA, associate director of the UCLA Brain Mapping
Division within the Neuropsychiatric Institute, and associate dean, David Geffen School of Medicine at UCLA.
He is the founding editor-in-chief of the journal NeuroImage and holds the chairmanship of numerous
committees within NIH and a variety of international task forces.
xvii
SECTION EDITORS
Peter A. Bandettini is chief of the section on Functional Imaging Methods and
director of the Functional MRI Core Facility at the National Institutes of
Health. He is also editor-in-chief of the journal NeuroImage. He received his
BS from Marquette University in 1989 and his PhD from the Medical College
of Wisconsin in 1994, where he pioneered the development of magnetic
resonance imaging of human brain function using blood oxygenation contrast.
During his postdoctoral fellowship at the Massachusetts General Hospital with
Bruce Rosen, he continued his investigation of methods to increase the interpretability, resolution, and applicability of functional MRI techniques. In
1999, he joined NIMH as an investigator in the Laboratory of Brain and
Cognition and as the director of the NIH Functional MRI Core Facility. In
2001, he was awarded the Scientific Directors Merit Award for his efforts in
establishing the NIH FMRI Core Facility. In 2002, he was conferred the Wiley
Young Investigators Award at the Annual Organization for Human Brain
Mapping meeting. His section on Functional Imaging Methods is currently
developing MRI methods to improve the spatial resolution, temporal resolution, sensitivity, interpretability, and applications of functional MRI. Recently,
his research has focused specifically on improving general methodology for
fMRI applications at 3 and 7 T, investigation of fMRI-based functional connectivity methodology and applications, and investigation of fMRI decoding
methodology and applications. He has published over 120 papers and 20
book chapters and has given over 300 invited presentations. Recently, his
paper Time course EPI of Human Brain Function during Task Activation was
honored by the journal, Magnetic Resonance in Medicine, as one of their 30
papers in the past 30 years that helped shape the field.
Marsel Mesulam is director of Cognitive Neurology and Alzheimers Disease
Center, Northwestern University. He has completed his MD in medicine from
Harvard Medical School in 1972, received his postdoctoral fellow ship from
Harvard University in 1977. He was conferred with Bengt Winblad Lifetime
Achievement Award from Alzheimers Association in 2010 and Lishman Lectureship Award from International Neuropsychiatric Association. His research
interests are neural networks, functional imaging, dementia, cerebral cortex,
and cholinergic pathways. Also he has received Distinguished Career Contribution Award from the Cognitive Neuroscience Society and the Potamkin Prize
from the American Academy of Neurology.
xix
xx
Section Editors
Sabine Kastner is professor at the Princeton Neuroscience Institute and Department of Psychology, Princeton University, Princeton, NJ. She has received her
M.D. from the University of Dusseldorf (Germany) in 1993 and her Ph.D from
the University of Gottingen (Germany) in 1994, and did postdoctoral training at
NIMH. She was conferred with Young Investigator award from the Cognitive
Neuroscience Society (2005), the John Mclean, Jr., Presidential University
Preceptorship from Princeton University (2003), and is a fellow of the American
Psychological Society. Her research interests include the neural basis of visual
perception, attention and awareness, studied in two primate brain models
(monkey and human) with functional brain imaging and electrophysiology.
Richard Frackowiak studied medicine at the University of Cambridge where he
first became interested in the neurosciences. He joined the Medical Research
Councils Cyclotron Unit at Hammersmith Hospital, London, in 1979, under
Professor Terry Jones, who had just installed one of Britains first Positron Emission Tomography (PET) scanners. Richard Frackowiak is director at Department of
Clinical Neuroscience and Head of Service of Neurology, CHUV University Hospital, Lausanne, Switzerland. Frackowiak has won the IPSEN and Wilhelm Feldberg prizes and during the 1990s was the fourth most highly cited British
biomedical scientist. His books include Human Brain Function and Brain Mapping:
The Disorders. He is currently setting up a new Clinical Neuroscience Department
at the University of Lausanne. His research interest has been the functional and
structural architecture of the human brain in health and disease. He has pioneered
the development and introduction of positron emission tomography and magnetic resonance imaging and prosecuted a research programme dedicated to
understanding the organization of human brain functions, but his focus has
been on plasticity and mechanisms for functional recuperation after brain injury
and the patho-physiology of cerebral neurodegenerations. He has become interested in the use of MR-based morphometry especially in the study of genetic
influences on brain disease and in a search for biomarkers and endophenotypes
of neurodegenerative disorders. Most recently he has introduced computerized
image classification for diagnosis and treatment monitoring into clinical science.
Matthew Lieberman received his PhD from Harvard University. Lieberman,
with Kevin Ochsner, coined the term Social Cognitive Neuroscience, an area of
research that integrates questions from the social sciences which the methods
of cognitive neuroscience and has become a thriving area of research.
Lieberman has been a professor at UCLA in the Departments of Psychology,
Psychiatry and Biobehavioral Sciences since 2000. His work uses functional
magnetic resonance imaging (fMRI) to examine the neural bases of social
cognition and social experience. In particular, his work has examined the
neural bases of social cognition, emotion regulation, persuasion, social rejection, self-knowledge, and fairness. His research has been published in top
scientific journals including Science, American Psychologist, and Psychological
Science. His research has been funded by grants from the National Institute of
Mental Health, National Science Foundation, Guggenheim Foundation, and
Defense Advanced Research Projects Agency. His work has received coverage by
HBO, The New York Times, Time magazine, Scientific American, and Discover
Magazine. Lieberman is also the founding editor of the journal Social Cognitive
and Affective Neuroscience and helped create the Social and Affective Neuroscience
Society. Lieberman won the APA Distinguished Scientific Award for Early
Career Contribution to Psychology (2007) and campus wide teaching awards
from both Harvard and UCLA. He is the author of the book Social: Why Our
Brains Are Wired to Connect (finalist for the LA Times Book Prize and winner of
the Society for Personality and Social Psychology Book Prize).
Section Editors
xxi
Karl Zilles, MD, PhD, graduated from the University of Frankfurt, medical
faculty, and received the MD (1971) and the PhD (1977) in anatomy from the
Hannover Medical School, Germany. He was full professor of anatomy and
neuroanatomy at the University of Cologne between 1981 and 1991 and at
the University of Dusseldorf between 1991 and 2012. Additionally, he was
director of the C. & O. Vogt-Brain Research Institute, Dusseldorf, from 1991 to
2012, and of the Institute of Neuroscience and Medicine, Research Center Julich,
Germany, from 1998 to 2012. He is currently JARA senior professor at the
Research Center Julich and at the RWTH Aachen University, Germany. He serves
as editor-in-chief of the journal Brain Structure and Function and was member of
editorial boards of various scientific journals (e.g., NeuroImage). Karl Zilles is
fellow of the German National Academy of Sciences Leopoldina and fellow of
the North-Rhine Westphalia Academy of Science and Arts. His research focus is
on the structural (cyto- and myeloarchitecture), molecular (receptor architecture), and functional (neuroimaging using MRI, fMRI, and PET) organization of
the mouse, rat, nonhuman primate, and human cerebral cortex. He pioneered
brain mapping based on the regional and laminar distribution of transmitter
receptors in the healthy and pathologically impaired human brains and brains
of genetic mouse and models. He recently introduced, together with Katrin
Amunts, Markus Axer, and colleagues, an ultra-high-resolution method for
nerve fiber and fiber tract visualization based on polarized light imaging in the
human, monkey, mouse, and rat brains. He published more than 590 original
articles in nature, science, neuron, brain, and other peer-reviewed journals.
Katrin Amunts, MD, PhD, graduated in 1987 from the Pirogov Medical School
in Moscow, Russia. She received the PhD (1989) in neuroscience, anatomy from
the Institute of Brain Research at the Lumumba University in Moscow, Russia.
After her postdoc at the C. & O. Vogt Institute for Brain Research of the HeinrichHeine-University Dusseldorf, Germany, and at the Institute of Neuroscience and
Medicine, Research Center Julich, she became associate professor for StructuralFunctional Brain Mapping (2004), and full professor at the Department of
Psychiatry, Psychotherapy, and Psychosomatics of the RWTH Aachen University
(2008) as well as director of the Institute of Neuroscience and Medicine (INM-1)
at the Research Centre Julich. Since 2013, she is additionally full professor for
Brain Research and director of the C. & O. Vogt Institute for Brain Research, at the
Heinrich-Heine-University Dusseldorf. She is a member of the editorial board of
Brain Structure and Function. Currently, she is member of the German Ethics
Council and speaker for the programme Decoding the Human Brain of the
Helmholtz Association, Germany. Katrin Amunts is interested in understanding
the relationship between the microstructure of the human brain and functional
systems such as motor control, language, and vision. Although scientists have
been studying brain cytoarchitecture for over 100 years, its importance has
increased rapidly with the advance of modern imaging techniques. This led,
together with Karl Zilles and his team, to the development of a novel, observerindependent and functionally relevant cytoarchitectonic mapping strategy resulting in freely available brain maps comprising approximately 200 areas and
nuclei, as well as the anatomy toolbox software, developed with Simon Eickhoff,
for co-localizing functional activations and cytoarchitectonically defined brain
regions. The Julich atlas JuBrain as a multimodal human brain model will replace
during the next decade the cytoarchitectonic brain atlas, which Korbinian Brodmann published in 1909 (Zilles and Amunts, Nature Reviews Neuroscience,
2010). Recently, the group has provided the first ultra-high resolution model of
the human brain, the BigBrain (Amunts et al., Science, 2013).
xxii
Section Editors
Russell A. Poldrack is Professor of Psychology at Stanford University. He has

previously held academic posts at the University of Texas, UCLA, and Harvard
Medical School. His lab uses the tools of cognitive neuroscience to understand
how decision making, executive control, and learning and memory are implemented in the human brain. They also develop neuroinformatics tools and
resources to help researchers make better sense of data, with involvement in
projects including the Cognitive Atlas, OpenfMRI, Neurosynth, and
Neurovault.
Paul Thompson directs the ENIGMA Consortium, a global alliance of 307

scientists in 33 countries who study ten major diseases ranging from schizophrenia, depression, ADHD, bipolar illness, and OCD, to HIV and addiction.
ENIGMAs genomic screens of over 31 000 peoples brain scans and genomewide data (published in Nature Genetics, 2012; Nature, 2015) bring together
experts from 185 institutions to unearth genetic variants that affect the brain
structure, and discover factors that help or harm the brain. At USC, Thompson
is associate dean for Research at the Keck School of Medicine and a Professor of
Neurology, Psychiatry, Radiology, Pediatrics, Engineering, and Ophthalmology. Thompson also directs the USC Imaging Genetics Center a group of 35
scientists in Marina del Rey, California. His team also studies aging and
Alzheimers disease, as well as brain growth in children. Thompson has an
MA in mathematics and Greek and Latin Languages from Oxford University,
and a PhD in neuroscience from UCLA.
Karl Friston is a theoretical neuroscientist and authority on brain imaging. He
invented statistical parametric mapping (SPM), voxel-based morphometry
(VBM), and dynamic causal modeling (DCM). These contributions were motivated by schizophrenia research and theoretical studies of value-learning
formulated as the dysconnection hypothesis of schizophrenia. Mathematical
contributions include variational Laplacian procedures and generalized filtering for hierarchical Bayesian model inversion. Friston currently works on
models of functional integration in the human brain and the principles that
underlie neuronal interactions. His main contribution to theoretical neurobiology is a free-energy principle for action and perception (active inference).
Friston received the first Young Investigators Award in Human Brain Mapping
(1996) and was elected a fellow of the Academy of Medical Sciences (1999). In
2000, he was president of the International Organization of Human Brain
Mapping. In 2003, he was awarded the Minerva Golden Brain Award and was
elected a fellow of the Royal Society in 2006. In 2008, he received a Medal,
Colle`ge de France and an Honorary Doctorate from the University of York in
2011. He became a fellow of the Society of Biology in 2012 and received the
Weldon Memorial prize and Medal in 2013 for contributions to mathematical
biology.
ACKNOWLEDGMENTS
Sometimes, the scope and structure of a book is clear from the outset, other times it evolves as the outlines are
written or because contributors with different perspectives suggest new and different things. This book
occasionally took on a life of its own, morphing into something greater than the original concept. But that
was because of the hundreds (literally) of people who contributed to it. Working independently and together
we created a one-of-a-kind collection of excellent articles on brain mapping, from data generation to knowledge
about the brain. This collaborative effort is one of the greatest joys in working on project of this magnitude. The
end result is a mix of all this expertise into a single product. While such a process could easily produce chaos, in
this case each editor had a clear vision that complemented the other sections of the book. Each contributor
produced a superb article and collectively they cover the field.
One of the most difficult aspects of this project was limiting the scope because its magnitude kept getting
larger the more we all talked about it. There are so many new areas within brain mapping. There are so many
creative ways to apply the ever increasing number of methods to study the structure and function of brain in
health and disease. This scope further motivated us to create an encyclopedia because the field was not only
ready for such a thing, it needed it.
Many of us who worked on this book have known each other for a long time. Others of you are new
acquaintances, but to each of you I owe my sincerest gratitude. You are among the best and brightest minds in
neuroscience and your participation made this book. Your research and writing will be appreciated by the
readers for many years to come.
In addition to all the contributors writing and editing chapters and sections there are many others who
deserve mention. At the Laboratory of Neuro Imaging at the University of Southern California I am privileged
to have a spectacular staff. Grace Liang-Franco manages the lab with an efficiency and deftness that defies limits.
Sandy, Diana, and Catalina all keep things moving smoothly and professionally so I can work on projects like
this encyclopedia. Thanks to you all. The team at Elsevier has been terrific. They have tolerated the fits and starts
associated with a project like this and helped usher into the world an important and substantial work. Thanks
to Mica Haley, Ashlie Jackman, Will Bowden-Green, Erin Hill-Parks, and many others.
Finally, I always express gratitude to my family. They do not help me write or edit or even read the things I
write but somehow they make it possible. I work at home in the evenings and on weekends, just like many of
you reading this book. I guess I could be doing other things but my family tolerates this behavior and has for
decades. Perhaps they are happy I am preoccupied with academic pursuits. It keeps me busy and out of their
hair. But for whatever the real reason, my wife Debbie, and my children Nicholas, Elizabeth, and Rebecca let me
work on these things and I appreciate them more than can be stated here.
Arthur W. Toga
Los Angeles, CA
xxiii
INTRODUCTION TO ACQUISITION METHODS
Brain imaging can be thought of as evolving along the parallel paths of applications, methods and modeling,
and acquisition techniques. Each plays a fundamental role in shaping the direction and setting the pace of brain
imaging advancement. The field itself has been defined by the depth and quality of interaction between these
paths, as well as a balance of effort for each. For instance, as new methods for data acquisition are developed,
fundamentally new questions about the brain may be asked perhaps at higher temporal or spatial resolution
or with higher sensitivity and new methods, tailored to the specific acquisition method and with the specific
questions or applications in mind, are developed. From this, new clinical applications or new biomarkers may
emerge.
This section, Acquisition Methods, is an overview of the major acquisition methods that have been
developed over the years each with specific capabilities, costs, limitations, and unique potential. A leader
in the field who has pioneered and advanced their particular acquisition method has written each article.
The acquisition methods described in this section include magnetic resonance imaging (MRI), functional
magnetic resonance imaging (fMRI), magnetoencephalography (MEG), positron emission tomography (PET),
near-infrared spectroscopy (NIRS), and electroencphalography (EEG). The bulk of the articles focus on the many
aspects of fMRI acquisition, as, in the past decade, fMRI has become the predominant brain imaging method.
However, a clear message from these articles is that there is no one best method. All the methods not only are
highly complementary but also can stand to benefit substantially from the synergy of multimodal integration.
The advancement of MRI methods has mostly been driven by technological advancements; however, a surprisingly large number of advancements have been in data processing, resulting in novel applications for neuroscience research and headways into wider clinical use. EEG, MEG and PET have also had something of a resurgence
in recent years as the limits inherent to MRI and fMRI have been more clearly delineated.
A didactic and detailed Anatomical MRI for Human Brain Morphometry article begins this section. A method
invented in the late 1970s and implemented in the early 1980s, MRI provides high spatial resolution and soft
tissue contrast without ionizing radiation, making it the modality of choice for structural brain imaging
applications, including human brain morphometry. This article describes the basics of MRI, some perspective
on the field, and useful details for the sophisticated user. Diffusion MRI, advanced in the late 1980s to early
1990s, is a flourishing field that has grown in sophistication and in relevance to neuroscience as it has shed light
on everything from brain connectivity to localization of lesions associated with trauma to the brain. While
Diffusion Tensor Imaging (DTI) has become an accepted clinical procedure, there is no consensus for best
acquisition and the area itself continues to rapidly evolve. A more recently developed MRI-based method,
susceptibility-weighted imaging (See Susceptibility-Weighted Imaging and Quantitative Susceptibility Mapping), derives its contrast from differences in susceptibility between tissue, thus highlighting, among other things,
iron in the tissue and blood, leading to exciting clinical applications and breathtakingly unique and detailed
images of brain anatomy and venous vasculature. The most recently emergent anatomical MRI technique is
myelin imaging (See Myelin Imaging) or myelography, which, like many MRI acquisition methods, is relatively
easy to implement, yet has taken considerable time to develop as our understanding of how brain anatomy and
physiology influence MRI contrast is even after 30 years still growing.
Since its inception in the early 1990s, functional MRI has grown rapidly in popularity, quickly growing to be
the method of choice for neuroscientists who want to noninvasively map systems-level activity in humans. This
success was due to many factors. First, the ubiquity of fMRI-ready scanners in hospitals around the world from
the decade-earlier insurgence of MRI as a powerful clinical tool was a large factor in the rapidity of the growth of
fMRI. Other aspects of fMRI, including the fidelity and repeatability of the functional signal, the complete
noninvasiveness of the method, and the relatively high spatial and temporal resolution also contributed to its
success. As of 2014, over 2500 papers per year are published using fMRI acquisition. Because of this, and
Introduction to Acquisition Methods
because fMRI acquisition is still rapidly evolving and diversifying, many articles in this section are devoted to
this area.
Obtaining quantitative information from fMRI/MRI data (See Obtaining Quantitative Information from
fMRI) outlines the current methods for using blood oxygen level-dependent (BOLD) contrast for obtaining
quantitative measures of oxidative metabolism, perfusion, and blood volume changes with activation. Echo
planar imaging (EPI) (See Echo-Planar Imaging) is the method of choice in part because of its speed but
primarily because of its stability. While fMRI acquisition has evolved over the years, the basic method, EPI, has
stayed mostly the same. The hemodynamic signal changes are a source of intense study as they are so neural
information-rich yet so variable and sensitive to other aspects of brain physiology. FMRI dynamics (See
Functional MRI Dynamics) explores all the temporal aspects of the BOLD signal changes. Though BOLD
has been the functional contrast of choice for brain activation, perfusion contrast (See Perfusion Imaging with
Arterial Spin Labeling MRI) has played an important role over the years and has considerable potential for
addressing questions and perhaps slow temporal scales that BOLD cannot. Functional MRI is not limited to
endogenous contrast. In fact, both human and animal studies have benefited substantially from novel
application of contrast agents (See Contrast Agents in Functional Magnetic Resonance Imaging). Article 13
is devoted to the discussion on the development of fMRI contrast agents for molecular imaging (See Molecular
fMRI). Functional MRI fundamentally is based on the acquisition hardware. Article 9 outlines the evolution of
hardware as well as the cutting edge hardware for fMRI (See Evolution of Instrumentation for Functional
Magnetic Resonance Imaging). The most fundamental piece of MRI and fMRI hardware, the main magnetic
field, continues to increase. Two chapters in this section describe the unique challenges and advantages of highfield acquisition (See High-Field Acquisition and fMRI at High Magnetic Field: Spatial Resolution Limits
and Applications).
Several articles describe the limits and potential of fMRI in terms of speed and resolution from a predominantly pulse sequence perspective (See High-Speed, High-Resolution Acquisitions) and a predominantly
hemodynamic perspective (See Temporal Resolution and Spatial Resolution of fMRI). Two other papers
provide comprehensive perspectives of the decision process and variables associated with choosing for the
optimal pulse sequence and acquisition scheme discussing the trade-offs and several applications (See Pulse
Sequence Dependence of the fMRI Signal, MRI and fMRI Optimizations and Applications).
Lastly, the fields of functional near-infrared spectroscopy (See Functional Near-Infrared Spectroscopy),
PET (See Positron Emission Tomography and Neuroreceptor Mapping In Vivo), EEG (See Basic Principles of
Electroencephalography), and MEG (See Basic Principles of Magnetoencephalography) are all well
described by the leaders and pioneers of each. The article on PET also includes the application of neuroreceptor
mapping. The article on MEG also delves into other electrophysiological techniques including EEG.
Overall, the Acquisition Method section provides useful practical knowledge as the articles are highly
readable and didactic. Importantly, this section also provides a history and a broad perspective of the
technology- and acquisition related-issues that have shaped the field of brain imaging.
Peter A. Bandettini
Anatomical MRI for Human Brain Morphometry

A van der Kouwe and B Fischl, Charlestown, MA, USA
Glossary
B0 The main magnetic field.

Bandwidth The rate at which we read out the signal. Higher
BW means not only less distortion but also lower signal-tonoise ratio (SNR).
EPI Echo planar imaging.
FLAIR Fluid-attenuated inversion recovery. T2-/PDweighted image with an inversion pulse to make the CSF
dark (helps differentiate damaged white matter).
FLASH/SPGR PD-/T1-/T*-weighted
structural imaging
2
(depends on acquisition parameters).
Flip angle Controls T1/PD weighting in FLASH (larger flips
mean more T1 weighting, up to a point).
MPRAGE T1-weighted with enhanced gray matter/white
matter contrast, particularly in the cortex.
PD Density of water protons (linear scale signal).
PSF Point spread function; quantifies the amount and
direction of blurring.
RF Radio frequency.
SAR Specific rate of absorption of RF energy deposited into
the body.
SNR/CNR Signal-to-noise ratio/contrast-to-noise ratio.
Introduction
More than any other imaging modality, MRI provides exquisite
soft tissue contrast that is especially valuable for identifying
anatomy and pathology in the brain. Indeed, one of the earliest
clinical market drivers of MRI, in the early 1980s, was its ability
to definitively and positively diagnose multiple sclerosis (MS).
Before then, MS could only be inferred from the observable
symptoms by eliminating all of the alternative pathologies.
With MRI, the white matter lesions that characterize MS
could be seen directly. With MRI, it also became possible to
collect images of the brain with any slice orientation. Today,
the ability to image with high, isotropic resolution and excellent contrast has enabled reliable and automated brain morphometric analyses.
Fundamental particles such as protons (or hydrogen nuclei
1
H) possess an intrinsic physical property called spin, a quantized form of angular momentum. Like a spinning charged
particle in classical electrodynamics, particles with spin behave
like magnetic dipoles. Groups of particles with spin tend to
align in a static magnetic field, and in the aggregate, they
exhibit classical behavior, like a spinning gyroscope. When
energy is added to the system by an external radio frequency
(RF) pulse with a magnetic component perpendicular to the
static magnetic field, the aggregate magnetic moment is tipped
away from the equilibrium state. MRI derives its signal from
the relaxation of the spins back to their equilibrium state,
during which time they relinquish the absorbed energy and
Brain Mapping: An Encyclopedic Reference
SPACE/CUBE/VISTA 3-D encoding T2-weighted sequences

(can also have T1 weighting).
T1 Longitudinal relaxation time (also called spinlattice
relaxation) or the time constant of the recovery of
magnetization. The dominant imaging contrast for
structural studies.
T2 Transverse relaxation time in spin echo imaging (also
called spinspin relaxation) or the time constant of the
exponential decay of magnetization.
T2* Transverse relaxation time in gradient-echo imaging
(always shorter than T2).
TE Echo time (controls amount of T2/T*
2 weighting).
TI Inversion time (controls amount of T1 weighting).
TR Repetition time (controls amount of T1 weighting).
Transverse (or XY) plane The plane perpendicular
to Z.
TSE Turbo spin echo. T2-/PD-weighted. Helps differentiate
CSF from bone/air and for damaged white matter.
Weighting The dominant source of contrast in an image (e.g.,
T2-weighted has mostly T2 contrast, but PD is always present).
Z-axis The direction of the main magnetic field (along the
bore of the scanner, also called longitudinal).
this can be detected with an RF receiver. Since this process is

fundamental to every NMR experiment, the signal is always
modulated by the number of spins from which the signal is
received. When an image is reconstructed, the image intensity
at each voxel is therefore proportional to the number of spins
in the voxel and the ratio of spins to unit volume is called the
spin density. Since water is ubiquitous in physiological tissue
and water molecules contain two hydrogen nuclei with magnetic spin, the hydrogen nucleus is the most commonly
imaged nucleus in clinical MRI. In this kind of imaging, spin
density is equivalent to proton density (PD) since the hydrogen nucleus is a single proton. Because the density of water is
somewhat constant across brain structures, PD provides a low
level of contrast in brain images. However, by manipulating
the relaxation behavior of the spins using a sequence of RF
pulses and exploiting the timing differences of the process of
spin relaxation in different chemical environments, additional
contrast can be generated (Figure 1).
Particles with spin in a static external magnetic field absorb
energy at a characteristic frequency known as the Larmor frequency (o 2pf), which relates directly to the external magnetic flux density (field strength) B0 by the Larmor equation
o gB0. A particle with spin may thus be induced to absorb
energy by radiating it with an external electromagnetic RF pulse
at the Larmor frequency, and this process is called resonance.
In isolation, the particle might take years to release the energy
spontaneously. However, the particle exists in an environment
or lattice of other particles, and it is induced by this
http://dx.doi.org/10.1016/B978-0-12-397025-1.00001-4
INTRODUCTION TO ACQUISITION METHODS | Anatomical MRI for Human Brain Morphometry
Figure 1 Examples of (top) 5 FLASH (PD-weighted) images, (middle) 30 FLASH (T1-weighted) images, and (bottom) MEMPRAGE (T1-weighted)
images. Note that the amount of weighting depends on the sequence and its associated parameters.
environment to exchange energy, returning to thermodynamic

equilibrium in a matter of seconds. This is a stochastic process,
characterized by a time constant on the order of seconds, called
the spinlattice relaxation time and designated T1. T1 refers to
the average time it takes for 1 1/e (about 63%) of the spins to
return to their equilibrium energy state.
Classically, we observe that in the equilibrium state, the
aggregate magnetic moment is completely aligned with the
principal (longitudinal) axis of the external magnetic field.
Like torque applied to a gyroscope, an external RF pulse tips

the magnetization away from the longitudinal axis. The product of the amplitude and duration of the pulse determines the
tip or flip angle through which the magnetic moment is
driven. For example, a 90 pulse will drive all of the magnetization from the longitudinal axis into the transverse (perpendicular) axis and a 180 pulse (known as an inversion pulse)
will invert the aggregate magnetic moment along the longitudinal axis. T1 is sometimes called the longitudinal relaxation

time because it describes the time taken for 63% of the longitudinal (Mz) component of the aggregate magnetic moment to
recover to its equilibrium value (Mz,eq):
t=T1
Mz t Mz, eq Mz, eq Mz 0 e
[1]
T1 differs with tissue type. In particular, the T1 relaxation

time of gray matter is greater than that of white matter, and the
result is that gray matter appears darker than white matter in
images acquired with pulse sequences designed to provide T1
weighting. Image intensity varies inversely with T1 in T1weighted images. The cerebrospinal fluid (CSF), with substantially greater T1 than gray matter and white matter, usually
appears black in these images. For this reason, T1 images are
preferred for brain morphometry, especially for cortical surface
modeling. T1 provides excellent contrast between the gray
matter and white matter, constraining the model of the inner
surface of the cortex, and excellent contrast between CSF and
gray matter, constraining the model of the outer surface of the
cortex. T1 is not the same everywhere in the cortex, and it
changes with age and disease. T1 also increases with field
strength as fewer protons are available to efficiently exchange
energy with the lattice.
Like a spinning top or gyroscope in a gravitational field, a
perturbed ensemble of spins tipped away from the longitudinal axis tends to precess about the longitudinal axis at the
Larmor frequency, emitting energy as it relaxes back into alignment. In MRI, it is the transverse component (Mxy) of the
magnetization that gives rise to the detected signal. Immediately after excitation, the magnetic moments of all affected
particles with spin precess in phase, creating a coherent transverse magnetic moment. However, neighboring spins interact
with one another, affecting the precession frequency of each,
causing the spins to precess out of phase and resulting in
decoherence of the transverse magnetic moment. This process
takes place with a characteristic time constant, T2, also called
the spinspin relaxation time:
Mxy t Mxy 0et=T2
[2]
Equations [1] and [2] are solutions to the Bloch equations.

In a simple NMR experiment, a sample is placed in a strong
magnetic field (B0) within a solenoid arranged with its axis
perpendicular to the main field. The solenoid is then energized
with a short rectangular pulse at the Larmor frequency of the
nuclei of interest, thus irradiating the sample and tipping the
aggregate magnetization into the transverse plane. Immediately
after excitation, the solenoid starts to receive emitted energy
back from the sample. This is possible because the solenoid is
tuned to the resonant frequency of interest. The emitted signal
is called the free induction decay (FID). Theoretically, the
envelope of the detected FID should follow an exponential
decay with time constant T2. In practice, however, an additional
process causes additional dephasing and decreases the decay
time. Unless the magnetic field is perfectly uniform, neighboring spins will experience slightly different local magnetic fields
and precess at different rates, leading to signal dephasing. The
additional dephasing caused by magnetic field inhomogeneities is described by the time constant T20 . The total observed
decay time due to spinspin dephasing (T2) and local magnetic

field inhomogeneities (T20 )is denoted by T2*:
0
1=T2* 1=T2 1=T2
[3]
Magnetic field inhomogeneities in brain tissue may be

caused by local differences in tissue susceptibilities. These differences are particularly large at tissueair boundaries that
occur near the sinuses and ear canals. In imaging, the amount
of dephasing, and therefore the measured T2*, depends on the
distribution of resonant frequencies within the voxel. In
regions of strong susceptibility change, the resonant frequency
varies sharply across the voxel and dephasing occurs rapidly in
these voxels. To mitigate this effect, MRI scanners are designed
with shim coils that generate small additional magnetic fields
that vary spatially and are intended to correct for inhomogeneities in the field caused by susceptibility effects. The shim
field is adjusted separately for each participant at the start of
each imaging session. Despite careful shim adjustment, T*
2 not
only reflects the underlying tissue T2 but also relates to the
combination of tissue types in the vicinity of the voxel, the size
of the voxel, and the quality of the shim. The local chemical
environment of the protons may also change, affecting T*.
2 This
is the case in blood oxygenation level-dependent (BOLD)
imaging where local susceptibility differences in the environment of blood vessels are exaggerated in the presence of paramagnetic deoxyhemoglobin leading to a decrease in T*
2 relative
to the situation with diamagnetic oxyhemoglobin. In functional imaging, local blood flow increases in regions of
increased neuronal activity, supplying more oxygenated
images, image
blood that increases local T*.
2 In T*-weighted
2
intensity increases with T2*. If particles move around within a
spatially nonuniform magnetic field, they will precess at an
inconstant rate and dephase more quickly relative to their
neighbors. This is the basis of diffusion encoding diffusion
weighted imaging (DWI)/diffusion tensor imaging (DTI), in
which a magnetic field that changes strongly in a particular
direction is imposed deliberately for a short time to induce
dephasing on moving spins before measuring T*.
2 In regions
where particles diffuse faster and over longer distances, in the
direction of the magnetic field gradient, dephasing is greater and
T*
2 is correspondingly shorter. If a number of diffusion directions are interrogated, the preferred diffusion direction will be
that in which T2* is smallest. Deposition of iron in brain structures, such as the basal ganglia, with healthy aging and neurodegenerative disease also causes local changes in susceptibility,
decreasing T2* (Brass, Chen, Mulkern, & Bakshi, 2006; Schenck,
1995; Schenker, Meier, Wichmann, Boesiger, & Valavanis,
1993). However, T2 may also change with age or disease. Unlike
BOLD and diffusion imaging, where T2 is expected to stay the
same for the duration of the experiment, in this case, it is
desirable to separate T2 and T20 , thus separating the intrinsic
tissue T2 from the effect of iron accumulation T20 . It is possible
to measure T2 directly by means of the spin echo experiment.
As previously described, a collection of particles with spin
in equilibrium in a static magnetic field may be tipped by a 90
pulse so that their aggregate magnetic moment is in the transverse plane. Immediately after excitation, all contributing spins
will be in phase but they will decohere with a time constant T*.
2
Those spins experiencing a stronger magnetic field and
therefore precessing faster will accumulate a positive phase

relative to the average. If at a time TE/2 they are exposed to a
180 pulse, their phases will be flipped in the transverse plane,
exactly negating their previous phase relationship. The faster
precessing spins will now have a negative phase relative to the
average. Since they continue to precess faster than the average,
they will accumulate phase relative to the average at the same
rate as before, and after a further time TE after the initial 90
pulse, all spins will once again be in phase and the aggregate
magnetic moment in the transverse plane will peak. The corresponding peak in the detected signal is called a spin echo and
the time TE is the echo time. The 180 pulse is able to negate
or refocus that part of the total signal dephasing (T2*) due to
local magnetic field inhomogeneities (T20 ) and is therefore
called a refocusing pulse. However, it does not negate dephasing due to spinspin interactions (T2). The spinspin interaction is irreversible. Therefore, the envelope of the decay
measured over a range of echo times has the characteristic
time constant of the spinspin relaxation, T2.
The T2 relaxation time of gray matter is greater than that of
white matter, and the result is that gray matter appears brighter
than white matter in T2-weighted images (usually produced
using spin echo sequences). Image intensity varies in proportion to T2 in T2-weighted images. CSF, with substantially greater
T2 than gray matter and white matter, usually appears bright in
these images. Edematous regions and tumors that are highly
vascularized appear bright in T2-weighted images, and these
images are very useful clinically. Fast variants of spin echo are
the most commonly used MRI sequences in clinical practice.
Clinical Imaging Versus Research Imaging

Standard practices in research imaging have evolved to be quite
different from those used by neuroradiologists in direct clinical
care. This has historically been driven by the need for rapid
imaging in the clinic; although with the advent of large-N
phased array receive coils (which we will discuss later) and
the dramatic reduction in scan time that they can provide,
these differences are perhaps now driven more by an established culture rather than technology. The fundamental difference in these two domains is that in research imaging, most
structural MRI acquisitions are 3-D versus the more common

use of 2-D acquisitions by clinicians. We will describe the
technical underpinnings of 2-D versus 3-D later in this article,
but the basic idea in 3-D imaging is that one acquires signal
from the entire imaged object for the entire scan session. This
has a dramatic win in terms of the amount of signal one can
obtain, which directly translates into smaller and importantly
isotropic voxels. That is, in 3-D imaging, we can typically
acquire images with voxels that are the same (or close to the
same) size in all three dimensions (e.g., 1 1 1 mm3 is now
common). In contrast, in 2-D imaging, one only acquires
signal from a single slab (typically a few millimeters thick) at
a time, making it much less efficient. In order to recover
enough signal to make high-quality images, one usually sacrifices resolution in the through-plane direction in order to
obtain high in-plane resolution. Thus, a typical clinical scan
might have voxels that are 0.9 0.9 5 mm3 in size, and the
in-plane resolution may be further interpolated after acquisition. 2-D scans have historically had two important advantages: (1) they can be acquired rapidly, and (2) in contrast to
3-D, in which subject motion at any time during the scan can
corrupt the entire dataset, motion during a 2-D scan will only
affect a small number of slices (both of these advantages have
been significantly reduced by technological advances in 3-D
imaging as will be discussed later in the article). For the purposes of morphometry, these 2-D scans are problematic as they
introduce a directional bias and cannot be resliced accurately
into a different plane. The bias implies that structures that
happen to lie within the high-resolution plane may be
detected, but those that have a substantial through-plane component will be obscured unless they have a large spatial extent.
From a visualization standpoint, 2-D scans will appear to be of
high quality when viewed in the high-resolution plane, but
little can be observed in either of the two perpendicular orientations as shown in Figure 2.
Signal, Noise, and Contrast

In MRI, we control a variety of parameters that allow us to
change the signal we measure (e.g., repetition time (TR), TE,
Figure 2 Clinical T2-weighted TSE scan with high (0.7 0.7 mm2 interpolated to 0.35 0.35 mm2) in-plane resolution (left) and thick (3 mm)
axial slices evident in sagittal view (right).

and flip angle). For example, shortening TE will almost always
decrease the amount of signal decay and hence increase the
absolute value of the signal we measure. However, in morphometric applications, it is almost never the absolute signal level
that we care about, but rather the difference between the signal
of two structures and tissue classes. For example, in the T2weighted image shown in Figure 2, the TE is set to a large value
to enable differences between the gray matter (bright), white
matter (dark), and CSF (very bright) to evolve. Thus, it is
contrast that we care about, as opposed to raw signal. However,
one also needs to be aware of other trade-offs. The first is that
contrast by itself does not tell us anything about how difficult it
would be to discriminate between two tissue classes. For that,
we require a measure of noise, as the difference between classes
must be measured relative to the amount of noise in the
images. This gives rise to the commonly used measure called
the contrast-to-noise ratio or CNR. This is typically defined by
s
mc1 mc2 2
[4]
CNR c1, c2
s2
where mc1 and mc2 are the mean intensities of classes one and two,
respectively (e.g., gray matter and white matter), and s2 is the
variance of the noise. This raises a subtle but important point
how does one measure the noise variance s2? From an MR
physicists point of view, this may be simple draw a region of
interest (ROI) in the background of the image and measure the
variance there. However, if ones goal is segmenting two tissue
classes, this definition will underestimate the difficulty of the
problem. The reason is that any structure within a tissue class, for
example, cortical lamina in the gray matter or blood vessels in
the white matter, will increase the difficulty of segmenting the
two classes. Thus, the variance of interest in the domain of brain
morphometry is usually the within-class variance, even if this
includes interesting signal. This definition of CNR is
s
mc1 mc2 2
CNRc1, c2
[5]
5!s2c1 s2c2
or the square root of the square of the difference in the means
divided by the average of the variances of the two classes. This
measure of CNR implicitly assumes that the noise in the tissue
Figure 3 SPGR (left) versus MPRAGE. Trading off SNR for CNR.
classes is Gaussian-distributed with different means and variances. The multivariate extension of this measure is the Mahalanobis distance, which is the squared difference between the
class means scaled by the inverse of the covariance matrix (see
Duda and Hart, 1973; for an extensive discussion on this type of
modeling). One further point to note is that it is rarely raw CNR
that we care about, but rather how efficiently we can acquire
images with a given CNR. For example, if one sequence yields a
10% increase in CNR relative to another but requires four times
as long to collect, we would normally consider this a poor tradeoff, as we know that in four times the scan time, we could reduce
the noise by a factor of two and therefore improve our CNR by
two. Thus, the measure we use to assess the quality of an MR
sequence is typically CNR per unit time, which is simply the
CNR divided by the square root of the acquisition time. Thus,
longer acquisitions are penalized as they take up valuable scan
time that could otherwise have been used to acquire multiple
images of a shorter type and average them to increase the CNR.
Finally, it is worth pointing out that because it is CNR per unit
time that we ultimately care about in brain morphometry, we
frequently use MR parameters that increase contrast at the price
of reduced signal or increased noise. A common example of this
will be covered later and is shown in Figure 3, which shows a
fast low-angle shot (FLASH) or spoiled gradient-echo (SPGR)
image on the left compared with a magnetization-prepared rapid
gradient-echo (MPRAGE; Mugler & Brookeman, 1990) image on
the right. As can be seen, the FLASH image has very low withinclass variance and hence high signal-to-noise ratio (SNR). Conversely, the MPRAGE allows more within-class noise to achieve a
significantly larger difference between the class means of gray
matter and white matter, thus resulting in better CNR (or CNR
per unit time) than the FLASH scan despite the reduction of
within-class SNR.
Practical Sequences for Brain Morphometry

Spatial Encoding (Slice, Phase, and Frequency Encoding)
The spatial information in an image is encoded through the use
of magnetic field gradients superimposed on the static magnetic
B0
(Direction of main
magnetic field)
Magnetic field without
magnetic field gradients
Magnetic field with

magnetic field gradients
Figure 4 Schematic of magnetic field before (left) and after (right) the application of the magnetic field gradients used to encode spatial location.
The isocenter is shown in red.
field. The longitudinal axis, or main field direction coaxial with

the bore of the magnet, is defined as the Z-direction. Magnetic
field gradients (X, Y, or Z) add magnetic flux in the same direction
as the static magnetic field (Z) as shown in Figure 4. For
example, applying a linear X-gradient adds to the field in
the Z-direction an amount of additional flux that varies as a
function of the distance along the X-axis from the isocenter. In
the negative X-direction, the gradient subtracts from the static
magnetic flux density in the Z-direction. The result is that the
spin magnetic moments precess at a frequency proportional to
the distance along the X-axis and the proportionality constant is
determined by the gradient strength. The isocenter is the origin of
the gradient coordinate system and the point at which the linear
gradients do not add to or subtract from the magnetic field.
If a narrowband RF excitation pulse occurs during a Z
gradient, only a narrow slice of spin magnetic moments in
the XY-plane that resonate at frequencies within the band of
the RF pulse will be excited. In this way, a slice of an object can
be selected and the gradient is called a slice select gradient. By
forming the slice select gradient using multiple gradient axes,
the slice may be oriented in any plane. The normal vector to
the slice specifies the slice encoding direction. The center of the
slice is determined by the center frequency of the RF pulse,
and the thickness of the slice is determined by the bandwidth
(BW) of the RF pulse. The combination of RF pulse and slice
select gradient is called a slice-selective RF pulse. The envelope of the RF pulse waveform determines the profile of the
slice. Achieving a sharper slice profile requires a longer RF
pulse; therefore, selected slices are never perfectly rectangular
in practice, and narrower slices have relatively wider transition regions. In 3-D imaging, a single thick slice may be
subdivided by phase encoding into multiple contiguous slices,
in which case the undivided thick slice is referred to as a slab.
If the entire extent of an object in the slice direction is phaseencoded, the RF pulse need not be slice-selective. In this case,
an RF pulse with no accompanying gradient is used and the
pulse itself can be a short, broadband pulse, typically with a
rectangular envelope. This pulse excites all spins within the
field of the transmit coil and is called a nonselective RF
pulse.
Phase encoding is achieved by briefly pulsing a gradient
after excitation. For example, if the X-gradient is pulsed briefly
after slice-selective excitation in the Z-direction, spins in the
slice that are furthest from the isocenter in the X-direction will
briefly precess faster and gain phase relative to spins closer to
the isocenter and spins in the negative X-direction will precess
slower and lose phase relative to those at the isocenter. The

phase encoding pulse therefore imposes a spatially varying
(linear) offset in the phase of the spins in the X-direction.
The slope of the phase offset is determined by the time integral
of the gradient pulse amplitude, also called the gradient
moment. The slope of the imposed phase offset may be set
up so that the phase passes through multiple 360 transitions
across the field of view in the X-direction. If the total signal
emitted by all of the spins in the slice is now sampled, spins
along the phase encoding direction will interfere constructively
or destructively depending on their spatial arrangement.
Underlying structure that varies sinusoidally with a spatial
frequency that matches that of the 360 transitions will give
rise to a signal formed by constructive interference of the
underlying spin magnetic moments. The phase encoding gradient therefore sets up a sinusoidal basis function that interrogates the spatial distribution of the spins in the X-direction. By
stepping linearly through a range of phase encoding moments,
a range of spatial frequencies is interrogated, that is, the spatial
signal is effectively projected onto a discrete set of Fourier basis
functions. In MRI, this spatial frequency domain is called
k-space. The spatial structure in the X-direction is recovered
simply by Fourier transformation. If a slice is selectively excited
in the Z-direction and phase-encoded in both the X- and
Y-directions, an image of the slice is recovered by 2-D Fourier
transformation and this is the basis of 2-D imaging. For an
Nx Ny image, Nx Ny phase encoding steps are required. The
image resolution is determined by the timeamplitude integral
(moment) of the largest phase encoding gradient and the field
of view is determined by the difference between adjacent phase
encoding steps, that is, the timeamplitude integral of the
phase encoding blips. Specifically, the blip results in a step in
k-space, DK (1/m), that is proportional to the gradient blip
moment, DM (Ts/m), as DK gDM. The step in k-space is
equivalently the reciprocal of the field of view. This simple
pulse sequence has the structure
h
iNx Ny

90z, sel PEx ix PEy iy sample
ix 1 i 1
y
[6]
The time between excitations of the same spins is called the

repetition time and denoted TR. After the 90 excitation, phase
encoding, and signal sampling, it is necessary to wait for the
majority of spins to recover to their equilibrium state, that is,
TR T1, so that all of the longitudinal magnetization can again
be transferred to the transverse plane at the next excitation,

resulting in maximum signal. This experiment results in an
FID, and only a single sample at the beginning of the FID is
necessary after phase encoding to create a PD-weighted image.
The sequence requires Nx Ny TR to encode a single slice. An
entire 3-D volume could be encoded by adding a third phase
encoding loop in the Z-direction and broadening the region of
selectivity of the excitation pulse (or making the pulse nonselective). Clearly, this approach is inefficient. There are several
ways to make it faster.
Instead of phase encoding separately after each excitation,
multiple encoding-sample events can be repeated after a single
excitation:
h
iN y

90z, sel PEy iy readoutx
iy 1
[7]
where
readoutx
PEx 1 sample
x
DPEx ix , ix 1 sampleN
ix 2
[8]
The approach is to impose an initial phase relationship on

the spins such that the spatial frequency at one extreme of
k-space is encoded. This initial gradient PE(1) is called a prewinder. The signal is then sampled repeatedly, each sample
being followed by a small phase encoding gradient pulse
(blip) of opposite sign to the prewinder, stepping the spatial
phase relationship of the spins through all the desired basis
functions of the Fourier transform, that is, across the spatial
frequency range of interest. This procedure is called frequency
encoding. In practice, the blips and samples need not alternate, but can be simultaneous, and are merged into a single
long gradient pulse (readout gradient) with repeated signal
sampling across its duration (the readout). Since all phase
encoding steps in the X-direction have been replaced by a
single readout within each TR, the time to encode a single
slice is reduced to Ny TR. For natural objects, the signal
representing the center of k-space (the average or DC component) is expected to be greatest. This signal is sampled at the
point during the readout when the prewinder and the readout
gradient up to that point integrate to zero. This signal peak,
formed by the preceding gradients and corresponding to the
center of k-space in the readout direction, is called a gradient
echo. The imaging sequence is called a gradient-echo or
gradient-recalled echo (GRE) sequence.
Like the slice encoding direction, the frequency encoding
and phase encoding directions can be oriented arbitrarily by
combining gradient axes. They are almost always perpendicular to one another. A GRE sequence with one phase and one
frequency direction encodes a single slice and is called a 2-D
GRE sequence. This sequence is inefficient because the readout
is much shorter than the required TR and most of the time is
spent waiting for longitudinal relaxation. The sequence can be
made much more efficient by selectively exciting an adjacent,
non-overlapping slice immediately after selectively exciting the
first slice. This sets up a spatially independent 2-D GRE experiment parallel to the first experiment, with the spins in the
second slice relaxing independently of those in the first slice.
Multiple slices may be inserted within the TR to acquire a
complete stack of 2-D slices in the same total time (Ny TR)
and the sequence is still called a 2-D GRE sequence:
h
iNz

90seliz PE iy readoutx
Ny
iz 1 i 1
y
[9]
If the 2-D GRE sequence includes a second phase encoding

loop in the slice encoding direction, instead of multiple separately excited slices, it is called a 3-D GRE sequence. This
sequence has a frequency encoding direction and two phase
encoding directions. The second phase encoding direction
encodes slices of k-space rather than slices of object space,
and this direction is sometimes called the partition direction
where the word partition refers to a slice of k-space. Even with
frequency encoding, this sequence is still inefficient, taking
Ny Nz TR to encode a volume. The efficiency of the 3-D
GRE sequence (and 2-D GRE with few slices) can be improved
greatly by reducing TR, and spoiling is required to prevent
interaction between consecutive regions of excitation.
FLASH or Spoiled GRE

The excitation pulse in each exciteencodereadout event of a
pulse sequence is sometimes referred to as a shot. With a 90
excitation pulse, all of the longitudinal magnetization is transferred to the transverse plane where it can be read out as signal.
It is then necessary to wait for TR T1 so that all of the
magnetization can relax to equilibrium state, ready for the
next shot. Instead of waiting for complete relaxation, another
approach is to tip only a fraction of the available longitudinal
magnetization into the transverse plane every TR using a small
flip angle. If this is done repeatedly, the magnetization reaches
a pseudo steady-state condition in which as much magnetization returns to the longitudinal axis as is tipped into the transverse plane every TR. Compared to the 90 pulse, there is less
signal available in the transverse plane to be read out every TR,
but TR can be much shorter, so this can be done more often.
One concern is that it is now possible for a collection of spin
magnetic moments that were excited during a previous shot
not to have fully decayed by a later readout and to form a
spurious echo. Provided TR is considerably longer than T2*, the
signal will have dephased in the transverse plane due to T*
2
decay (T2* T1) and be unavailable for readout. For shorter
TRs, it is possible to cause deliberate dephasing by applying
a large gradient, called a dephasing or crusher gradient,
after the readout. The dephasing gradient causes the spins
across the slice or slab to precess at vastly different frequencies,
quickly decohering or spoiling the signal (Leupold, Hennig, &
Scheffler, 2008). This technique is called gradient spoiling. To
spoil the potentially interfering signal further, the phase of the
RF excitation pulse is varied with each TR so that magnetization
from previous TRs does not add constructively (Crawley,
Wood, & Henkelman, 1988; Zur, Wood, & Neuringer, 1991).
This technique is called RF spoiling. Combining spoiling
with small, frequent excitation pulses results in an imaging
sequence called SPGR or FLASH. This efficient pulse sequence
is commonly used with 2-D encoding and 3-D encoding for
anatomical imaging.
A closed form solution can be derived for the detected
signal in the spoiled GRE experiment. If the longitudinal magnetization just before the RF pulse with flip angle a is Mz(0),
then the longitudinal magnetization just after the RF pulse is
Mz(0):
10

Mz 0 Mz 0 cos a
[10]
After time TR, the longitudinal magnetization Mz(TR) has

evolved due to T1 decay according to eqn [1]:

[11]
Mz TR Mz 0 eTR=T1 Mz, eq 1 eTR=T1
Let E1 eTR=T1 and insert [10] into [11]:
Mz TR Mz 0 cos aE1 Mz, eq 1 E1
[12]
In the steady state, Mz(0 ) Mz(TR ). The measured signal

from the spoiled GRE sequence at the echo time TE is given by
the transverse magnetization after T2* dephasing, as described
*
by eqn [2], SFLASH Mz 0 sin aeTE=T2 . Solving eqn [12] in
the steady state gives the equation for the signal generated by
the spoiled GRE (FLASH) sequence:
SFLASH PD
sin a1 E1 TE=T2*
e
1 cos aE1
[13]
where PD Mz,eq, because the equilibrium longitudinal magnetization is proportional to the PD. The flip angle yE that
maximizes the signal for a specific TR and T1 is obtained by
finding the root of the derivative of [13] with respect to a for
which the second derivative is negative:

[14]
yE arccos eTR=T1
This flip angle is called the Ernst angle. For the purposes of
brain morphometry, it is important to note that while the Ernst
angle provides maximum signal, it does not necessarily provide maximum contrast. Generally, signal or time is traded for
contrast.
From eqn [13], it is clear that the FLASH signal is influenced
by parameters that depend on the tissue being imaged (PD, T1,
and T*)
2 and on the sequence parameters (TR, TE, and a). For
all sequence parameters, the FLASH image is linearly weighted
by PD. For small flip angles, eqn [13] reduces to
*
SFLASH PDsinaeTE=T2 , that is, there is no T1 weighting when
the flip angle a approaches zero. As a increases, T1 weighting
increases but overall signal decreases when a > yE. Equation [13]
also shows that T2* weighting increases directly with TE, but this
is accompanied by an overall signal decrease. Clearly, it is
necessary to define SNR and CNR before choosing sequence
parameters for any particular application, and it is also useful to
express these quantities per unit time, as explained in Section
Signal, Noise, and Contrast.
SNR, BW, and Distortions in the Readout Direction

Signal and noise are captured by the analog-to-digital converter
(ADC) during the readout. Signal is defined as the current
induced in the receive coils by the spin magnetic moments of
interest. Noise may be induced in the coils by spurious spin
magnetic moments that randomly resonate with the coil due to
physiological or thermal fluctuations in the object. Additional
thermal noise may be introduced by the scanner electronics at
the amplification and RF demodulation stages. The ADC may
add thermal and quantization noise. A complex signal (magnitude and phase or transverse X- and Y-components) is
acquired, and the noise in the complex domain has a Gaussian
distribution. The noise remains Gaussian after complex Fourier

transformation, but the magnitude operation results in Rician
noise in the magnitude images for a single channel. The noise
in the images that are reconstructed by the sum of squares from
an N-channel receive array has a noncentral Chi distribution
with 2N degrees of freedom (Constantinides, Atalar, &
Mcveigh, 1997; Koay & Basser, 2006).
By virtue of the integration process within the ADC electronics during the ADC sampling period or dwell time (Ts), the
integrated signal is proportional to the sampling period,
whereas the standard deviation of the integrated noise is proportional to the square root of the sampling period. The inverse
of the ADC dwell time is the ADC pBW.
Therefore, the SNR
p
relates to the BW as SNR T s 1= BW. Since the image is
formed from the Fourier transform of the readout, each image
pixel is effectively composed of a subband of frequencies from
within the total sampled band. It is therefore sometimes convenient to express the BW in units of sample rate per pixel, for
example, Hertz per pixel. Equivalently, BW per pixel (BWp) is
the reciprocal of the total readout time (Tro) in the case of
frequency encoding, that is, BWp BW/Nro 1/Tro where Nro
is the number of samples in the readout direction and Tro NTs.
While frequency encoding dramatically decreases imaging
time, it introduces distortions in the readout direction. Any
spin magnetic moments resonating at the wrong frequency will
accumulate positive or negative phase across the readout. This
frequency offset is converted into a spatial shift by the Fourier
transform. For example, the resonant frequency of fat is shifted
relatively to water by approximately 3.5 ppm (the fat peak is
relatively broad compared with water). At 1.5 T, the difference
is approximately 225 Hz. If the ADC BW were 225 Hz per
pixel, fat would be shifted in the corresponding image by one
pixel relative to water. At 3 T, the shift would be twice this
amount. Similarly, in regions where the B0 field is offset due to
susceptibility changes, water will resonate at the wrong frequency and be displaced in the image by an amount proportional to the field error and inversely proportional to the
receive BW. Chemical shift and susceptibility distortions are
restricted to the readout direction and are a consequence of the
accumulation of phase during frequency encoding. Echo planar imaging (EPI) is an extension of the frequency encoding
concept in two dimensions, that is, two phase encoding directions are combined into a single EPI readout that traces out a
Cartesian pattern in k-space. As in conventional frequency
encoding, the phase encoding blips in the innermost readout
direction are merged into a single readout gradient, and the
second phase encoding direction is encoded by phase encoding blips between adjacent readouts. Each readout gradient
forms a gradient echo and the time from one line to the next
of the EPI readout is therefore called the echo spacing (ES). Any
B0 errors or chemical shifts give rise to a large accumulation of
spurious phase between the adjacent lines of the Cartesian
readout because the ES is considerably larger than the ADC
dwell time. This is why the chemical shifts and susceptibility
distortions are so dramatic in the phase encoding direction of
images generated by EPI readouts compared with the readout
direction of the simple GRE sequence. There is no such distortion in the phase encoding direction(s) of the GRE sequence,
since the echo time is the same for every line and the ES is
therefore effectively zero (or equivalently, the BW is effectively

infinite) in the phase encoding direction. The phase encoding
direction in 2-D EPI should perhaps be called the slow readout
direction since, strictly speaking, EPI is a 2-D frequency encoding technique. Spiral trajectories are also popular for encoding a
plane and suffer from similar sensitivity to susceptibility artifacts
but the artifacts are blurred in multiple directions.
Frequency encoding may also result in a loss of resolution
due to T*
2 signal decay across the readout. The signal is effectively multiplied in k-space by an exponential decay envelope
or convolved in the object domain by a potentially broadened
point spread function (PSF). If Tro T2*, this effect is negligible,
but for longer readouts (low BW or many sample points like
EPI), it may result in image blurring. While lower BWs result in
worsened chemical shift, susceptibility, and blurring artifacts,
higher BWs result in lower SNR. Higher BWs also require larger
gradients to achieve the same resolution and are thus limited
by the capabilities of the gradient system. Later, we will discuss
how multiecho sequences can be used in brain morphometry
to recover SNR while preserving the beneficial properties of
high-BW imaging.
Optimizing Contrast in FLASH

If time permits, rather than optimizing the parameters for the
FLASH acquisition, it may be worthwhile to collect multiple
11
acquisitions with different parameters and then fit eqn [13] to

estimate PD and T1 directly for each voxel (Segonne et al., 2004).
This is the basis of the DESPOT1 approach (Deoni, Peters, &
Rutt, 2005; Deoni, Rutt, & Peters, 2003). Typically, at least two
FLASH volumes with different flip angles are acquired, spanning
a range around the Ernst angle. Volumes with different TRs could
also be used, but it is usually preferred to have acquisitions with
the same duration. Figure 5 shows the estimated PD and T1
volumes estimated in this way from the acquisitions of Figure 1.
The parameters for these acquisitions were TR 20 ms, a 5 , and
30 . The volumes were acquired with multiple gradient echoes
(TE (1.85 n.2) ms, n 0,. . .,7) and T*
2 can be estimated
from the decay across the multiple readouts following each a
pulse. T2* estimated with a single exponential decay is noisy
because the T*
2 effect is better modeled with multiple complex
exponential decays. Having estimated PD and T1, it is now
possible in principle to simulate the image that would result
from any FLASH sequence parameter selection. Given this information, therefore, it is also possible to calculate the parameters
required for optimal contrast between any tissue classes. For
example, in a group of healthy participants, it was found that a
TR of 20 ms and an a of 22 resulted in good contrast at 3 T
between GM, WM, and CSF.
Once tissue T1 and PD are known for GM, WM, and CSF,
the behavior of the FLASH signal can be predicted. Figure 6
Figure 5 (Top) PD values (arbitrary units) and (bottom) T1 values (ms) derived from the combination of the 5 and 30 FLASH acquisitions
shown in Figure 1. Parameters were estimated by fitting the FLASH signal eqn [13].
12
0.3
WM-GM
GM-CSF
0.2
Contrast (AU)
Signal (AU)
0.8
0.6
WM (T1 = 700 ms)
0.4
GM (T1 = 1000 ms)

CSF (T1 = 3000 ms)
0.2
0
500
1000
1500
0.1
2000
TR (ms)
-0.1
500
1000
1500
2000
TR (ms)
Figure 6 (Left) Typical FLASH contrast curves (signal vs. TR) for GM (blue), WM (red), and CSF (purple). (Right) Contrast curves for WMGM (blue)
and GMCSF (magenta). The dotted lines indicate the maximum difference in signal between WM and GM (blue dotted) and between GM and
CSF (pink dotted).
Figure 7 (Top) Cortical surface showing FLASH flip angle (with TR 20 ms) required to maximize gray matter/white matter contrast across the
cortex (scale varies from 15 to 20 ) in a healthy young volunteer. (Bottom) Inflated surface showing details in the sulci.
shows how the FLASH signal changes with TR for these tissue
classes, and the optimal value can be calculated for each pair of
classes. This argument has been extended to multiecho FLASH
(MEF) acquisitions (Han et al., 2006) where the multidimensional information is valuable in segregating multiple tissue
classes, especially the subcortical brain regions.
Before starting a study, it is worthwhile to consider the
neuroanatomical question to be answered and the population
group(s) of interest. Tissue parameters (PD, T1, and T2) are
known to vary with age and brain region (Hasan, Walimuni,
Kramer, & Frye, 2010; Saito, Sakai, Ozonoff, & Jara, 2009;
Suzuki, Sakai, & Jara, 2006). In neonates, considerable myelination continues until 1224 months of age, and substantial
brain development continues into the third decade of life
(Lebel & Beaulieu, 2011). Parameter values continue to change

with senescence (Salat et al., 2009). Tissue parameters clearly
differ between subcortical structures, but even across the cortical surface in a single subject, the contrast between the gray
matter and underlying white matter varies. Therefore, optimal
parameters can be chosen for age and region of the brain.
Figure 7 shows how the flip angle that maximizes FLASH
contrast between the gray matter and the underlying white
matter varies with cortical region in a healthy young volunteer.
Magnetization-Prepared Rapid Gradient-Echo

Figures 1 and 3 show that a variety of sequences, such as
FLASH and MPRAGE, can be used to generate T1 contrast.
10
9
8
7
6
5
4
3
2
1
0
from TR to TR is affected by the delay time after partition

encoding, and minimizing TR may adversely affect contrast.
There is a nonlinear weighting of the signal across k-space in
the inner phase encoding loop as a consequence of T1 relaxation, and the image is convolved by the Fourier transform of
this weighting. The convolution kernel or PSF is shown in
Figure 8 and results in blurring of the image in the inner
phase encoding loop direction. This effect is analogous to the
T2* decay across the readout, which causes blurring in the
readout direction. Blurring in both cases varies with tissue type.
T2-Weighted Imaging
The basic spin echo experiment consists of a 90 excitation
pulse, followed after a delay TE/2 by a 180 refocusing pulse.
As explained in the introduction, the refocusing pulse reverses
the phase dispersal due to local magnetic field inhomogeneities, resulting in a spin echo at time TE/2 after the refocusing
pulse. The time TE is the spin echo time. The RF pulse refocuses
the T20 component of T2*, leaving only the decay due to spin
spin interactions (T2). This is called the CarrPurcell
experiment, and it has the desirable property that the magnitude of the spin echo is dependent only on T2, a property only
of the sample being examined, independent of the homogeneity of the field:

S PD 1 eTR=T1 eTE=T2 if TR TE
[15]
A sequence structure analogous to multislice 2-D GRE is
used to obtain T2-weighted images. The following is the structure of the 2-D SE sequence that acquires a stack of 2-D slices in
time Ny TR, where the inner loop covers the Nz slices in time
TR and where TR T1 to accommodate T1 recovery between
excitations of the same slice:
h
iNz Ny

90seliz TE=2 180seliz TE=2 PE iy readoutx
iz 1 i 1
y
[16]
The image intensity at each pixel is T2-weighted and easily

modeled using eqn [15]. Figure 9 shows how the signal varies
with TE for WM, GM, and CSF. It can be proven that the
difference between two exponential decay curves, decaying in
time from the same starting value at time zero with only
800
8
Transverse magnetization
Flip angle (degrees)
However, the resulting image contrast is not the same. Moreover, the previous section showed that even with the same
sequence, contrast can be manipulated by adjusting the
sequence parameters. MPRAGE is a variant of the SPGR
sequence specifically designed to enhance T1 contrast between
tissue types. The sequence results in especially good contrast
between the gray matter and white matter, ideal for brain
morphometry.
The MPRAGE sequence is the same as the FLASH sequence
except that a 180 inversion pulse is introduced between slices
and k-space partitions. For example, if there are 176 slices, the
inversion pulse is followed by a gap followed by 176 repetitions of the spoiled GRE sequence kernel (aPEreadout
spoil), which we may refer to as the inner phase encoding
loop, and another gap before the next inversion pulse (sometimes called the delay time). Both gaps are critical to evolve
contrast. The inversion time (TI) is defined as the time between
the middle of the inversion pulse and the partition encoding
step that encodes the centerline of k-space (a gradient echo in
the partition encoding direction). After partition encoding,
there is another gap before the next inversion pulse (as
shown in Figure 8). The TR is redefined as the time between
inversion pulses and therefore includes the gap after the inner
phase encoding loop. The original FLASH TR, or the time
between a pulses, is often called the echo spacing. However,
when there are multiple readouts and therefore multiple gradient echoes between a pulses, as in multiecho MPRAGE
(MEMPRAGE), echo spacing is the time between gradient echoes. Therefore, the time between a pulses may be referred to as
the inter-alpha time.
As the longitudinal magnetization relaxes after the inversion pulse, the signals from different tissue types evolve differentially according to the tissue T1 and the excitation scheme of
the sequence. This process is simulated using the discrete Bloch
equations. Figure 8 shows the excitation structure for a single
TR of the MPRAGE (with typical parameters recommended for
brain morphometry) along with the simulated signal evolution
for white matter, gray matter, and CSF (after a few TRs to
achieve steady state). We choose TI to maximize the separation
between the white matter, gray matter, and CSF. The selection
of TI is critical, but the optimal value is affected by the other
parameters. Although it is tempting to minimize TR to save
time, it is important to note that the steady-state condition
500
1000 1500 2000 2500

Time (ms)
WM(T1 = 700 ms)

GM(T1 = 1000 ms)
CSF(T1 = 3000 ms)
13
WM(T1 = 700 ms)

GM(T1 = 1000 ms)
CSF(T1 = 3000 ms)
700
600
500
400
300
200
2
4
100
0
500
1000 1500 2000 2500

Time (ms)
0
3
0
1
Pixels
Figure 8 (Left) Excitation structure after inversion pulse for a single TR of a standard MPRAGE protocol. (Middle) Evolution of signal transverse
magnetization across a single TR, estimated using discrete Bloch equations. (Right) Corresponding point spread function. Blue, white matter
(T1 700 ms); red, gray matter (T1 1000 ms); magenta, CSF (T1 3000 ms).
14
0.4
Contrast (AU)
0.8
Signal (AU)
0.5
WM (T2 = 70 ms)
GM (T2 = 100 ms)
CSF (T2 = 300 ms)
0.6
0.4
0.2
0
GM-WM
CSF-GM
0.3
0.2
0.1
50
100
150
200
TE (ms)
0
0
50
100
TE (ms)
150
200
Figure 9 Example T2 decay (left) and contrast (right) curves for white matter (WM, blue), gray matter (GM, red), and cerebrospinal fluid
(CSF, magenta).
Long
Proton
density
T2/T2*
TR
Short
poor!
T1
Short
Long
TE
Figure 10 Summary of common MR contrast types and how to generate
them by varying TR and TE in a basic spin echo sequence (T2) and
gradient-echo sequence (T2*).
slightly differing time constants, is maximized when the time is

approximately equal to the time constants. In fMRI, using
gradient-echo imaging, this has the implication that TE should
be chosen approximately equal to the T*
2 in the ROI to maximize BOLD sensitivity. This depends on field strength and
tissue type and may vary across the brain. Similarly, a simple
rule of thumb used in clinical T2 imaging is to maximize
contrast by choosing TE equal to the T2 of the tissue of interest.
Since PD and T2 are close for WM and GM, a value of TE
somewhere between the T2 for WM and GM is expected to
maximize the T2 contrast between these two tissues, and this
corresponds with the simulation in Figure 9.
Equation [15] also explains why with basic spin echo imaging using the SE sequence, a short TE results in more PD
weighting while a longer TE adds T2 weighting. Shortening
TR introduces T1 weighting. This relationship is summarized
in Figure 10. The relationship is qualitatively similar for basic
gradient-echo imaging using the GRE sequence if the dependency on T2 is replaced by T*.
2
T2 imaging using the standard 2-D SE sequence may be
inefficient, depending on the number of slices, because TR
must be long enough for T1 relaxation to occur. One way to

use the additional time is to insert multiple refocusing pulses
after the excitation to form an echo train. The basic NMR
experiment without phase encoding is called the CarrPurcell
MeiboomGill (CPMG) sequence. The peaks of the multiple
spin echoes follow an envelope predicted by the T2 decay time,
and this is the classical sequence for quantitative T2 mapping.
Image formation can be accelerated if varying phase encoding steps are added within the echo train. The multiechoes are
used to encode adjacent lines of k-space rather than to estimate
the T2 decay across a single line of k-space as in the CPMG
experiment. The accelerated imaging sequence is called a fast
spin echo or turbo spin echo (TSE) sequence, and it improves
the sequences efficiency by a factor of the number of PE steps in
each echo train (called the turbo factor), although this must be
traded off against any increase in TR if there are a lot of slices. A
version with 3-D encoding is also possible, but it is uncommon
because it is prone to artifacts and sensitive to motion, and
deposited power (specific absorption rate (SAR) of RF energy)
may be high. The 2-D TSE sequence is among the most common
pulse sequences in clinical use today (Figure 11).
T2-weighted imaging with fluid-attenuated inversion recovery

Due to its long T2 relaxation time, healthy CSF appears bright
in T2-weighted images. However, T2 hyperintensities in brain
tissue are indicative of a wide range of neurological disorders.
It is therefore desirable to suppress the bright signal from
healthy CSF to distinguish regions of pathological T2 prolongation more clearly. Fluids with long T2 can be suppressed
using a technique called fluid-attenuated inversion recovery
(FLAIR). FLAIR is a special case of signal nulling in spin echo
imaging using T1 recovery. A related idea was described earlier
in MPRAGE, where the TI was chosen to maximize the contrast
between GM, WM, and CSF (see Figure 8). If the TI were
chosen instead to be at the point of zero longitudinal magnetization from CSF, there would be no available magnetization
to transfer into the transverse plane (by the alpha pulse) to be
read out as signal and CSF would not appear in the resulting
image. Any tissue class can be nulled in this manner, and the
null point occurs at TI ln(2) T1 ( 0.69 T1). The technique
assumes a narrow range of T1 within the tissue class of interest
and a constrained period of data acquisition around the TI at
each repetition. Multiple consecutive inversion recoveries can
15
Figure 11 Example of a T2-weighted image. (Left) TSE with very bright CSF, bright gray matter and dark white matter. (Right) TSE FLAIR with
attenuated CSF.
be used to null more than one tissue type. For example, a

double inversion recovery sequence has been proposed to
suppress both WM and CSF (Pouwels, Kuijer, Mugler, Guttmann, & Barkhof, 2006; Redpath & Smith, 1994), thus obtaining a segmented image of the cortex based on physics. This
method of segmentation is uncommon, partly because T1 is
not constant all across the cortex or white matter. More relevant for brain morphometry, it is more efficient to use the
acquisition time to collect images that contain all the information necessary to segment multiple tissue classes offline. An
advantage of tissue nulling using physics is that it is effective
within voxels containing a mixture of tissue classes.
As usual, time is traded for contrast, and T2 FLAIR imaging
is relatively inefficient because the T1 recovery time for CSF is
long. Nevertheless, FLAIR is very useful in clinical neuroimaging and the T2 TSE FLAIR sequence is extremely popular in
clinical practice.
Multiecho BW-Matched Imaging

Susceptibility and Gradient Distortion
The main magnetic field (B0) is extremely homogeneous (by
construction), but the introduction of an object with varying
regions of magnetic susceptibility into the field introduces
local inhomogeneities. The MR imaging system includes additional shim coils that correct the inhomogeneities, but they
can only compensate for inhomogeneities that are relatively
smooth in space. The anatomy of the human head results in
inhomogeneities in certain regions that are quite localized and
hard to shim, including regions in the vicinity of the ear canals,
affecting the temporal lobes, and the paranasal sinus regions,
affecting the medial inferior frontal cortex. A B0 field map is
used to quantify these regions (Figure 12). Regions of B0
inhomogeneity, or susceptibility regions, result in signal
dephasing (and dropout in extreme cases) and spatial
distortions. Spatial distortions can be dramatic in EPI and are

relatively underappreciated in anatomical imaging with
MPRAGE or FLASH. However, in brain morphometry, we are
searching for subtle anatomical changes, and even small distortions can dramatically reduce the power of a study. B0related distortions can be corrected offline using the subjectspecific B0 field map (Jezzard & Balaban, 1995) or mitigated
using high-BW multiecho techniques as described in Section
Distortions, SNR, BW, and BW Matching Using Multiecho
Sequences (van der Kouwe, Benner, Salat, & Fischl, 2008).
The other major source of distortion in MRI is spatial nonlinearities in the imaging gradients. Gradient coils are designed
and manufactured with a known level of nonlinearity, and in
general, newer gradient coils have more nonlinearity in order
to facilitate faster switching times and stronger gradients. All
images acquired with the gradient system are therefore distorted in the same known way, independent of sequence and
subject. Consequently, distortions due to gradient nonlinearities are relatively easy to correct offline and a subject-specific
map is not required. Without correction, patient size and positioning relative to isocenter may bias estimated structure sizes,
and this may be especially problematic when a patient group is
consistently positioned differently from the control group, for
example, for reasons of comfort in the scanner.
Distortions, SNR, BW, and BW Matching Using Multiecho

Sequences
B0-related distortions in anatomical imaging can be reduced by
increasing BW, as described in Section SNR, BW, and Distortions in the Readout Direction. However, the reduced distortion comes at the expense of reduced SNR. Decreasing the BW
will recover the SNR, but at the cost of once again increasing
distortion. The contention is resolved if multiple high-BW
echoes are acquired, each with minimal distortion and low
16
SNR, and then recombined to recover the SNR while preserving

the low level of distortion (Deoni et al., 2003; Deoni et al.,
2005; Fischl et al., 2004; van der Kouwe et al., 2008).
Multiecho sequences thus have some advantages over
single-echo ones: (1) they can be relatively undistorted due to
high BW without sacrificing SNR, and (2) they typically yield
some information on anatomically interesting decay parameters such as T2 or T*.
2 An example of this is given in Figure 13,
which shows a PD-weighted FLASH scan (top) and a T1weighted FLASH scan (bottom). The echoes are ordered with
the earliest echo at the left (1.85 ms) and the latest echo at the
right (15.85 ms). One can observe T*
2 decay across the echoes,
as the images get darker as one moves from left to right. Further,
these images are minimally distorted, due to their high BW, and
perhaps more important have almost no differential distortion.
That is, any residual distortions remaining in the T1 and PD are
Figure 12 Field maps showing B0 inhomogeneities in the head. Top, susceptibility region affecting the temporal lobes; bottom, susceptibility region
affecting the medial inferior frontal cortex.
Figure 13 Top: PD-weighted multiecho FLASH (flip angle 5 ). Bottom: T1-weighted multiecho FLASH (flip angle 30 ). TR 20 ms, TE 1.85 n.2 ms
(n 0,. . .,7).

exactly the same, as they have the same geometry (field of view
and matrix size) and matched BW and readout direction. This
greatly increases the utility of this type of data from the standpoint of tissue classification as it implies that they can be exactly
coregistered. In contrast, more standard acquisitions cannot be
accurately registered, which must degrade the accuracy of any
classification procedure, as there will be some locations where
two coregistered voxels will actually represent different tissue
classes due to the differential distortions.
Another interesting fact that can be observed with increasing echo time is that the gray matter/white matter contrast
improves in the PD-weighted image while it decreases in the
T1-weighted images. This is because white matter has a
shorter T2* than gray matter and a lower PD. Thus, white
matter is darker than gray matter at early echo times in the
PD-weighted images and then gets darker faster with increasing TE than gray matter, increasing the difference in intensities between the two classes (i.e., increasing echo time
increases the T*
2 weighting of the images). Conversely, in a
T1-weighted image, white matter with its shorter T1 is brighter
than gray matter at earlier echoes. The shorter T2* of white
matter then decreases image contrast with increasing echo
time, as the white matter signal decays faster than the gray
matter signal, bringing them closer together. Thus, in a typical
T1-weighted sequence, we minimize the echo time (TE) to
maximize contrast, since the T2* weighting induced by the TE
is in the opposite direction of the T1 contrast between the
gray matter and white matter.
The multiecho FLASH scans shown in Figure 13 are an
appealing sequence for morphometry as they are largely undistorted, have no differential distortion, and provide T1-, PD-,
and T2*-weighted image contrast. The multiple contrasts are
of particular importance for segmenting some subcortical
structures that have poor T1-weighted contrast including the
thalamus and the pallidum (Fischl et al., 2004). However, if we
compare the distance of cortical gray matter from the subjacent white matter (i.e., white matter a short distance beneath its
interface with the cortex), we find that the intrinsic CNR of the
MPRAGE is greater than that of even the full 16 images shown
in Figure 13 (Han et al., 2006). This observation led to the
development of a multiecho MPRAGE (MEMPRAGE) sequence
that has the same advantages as the multiecho FLASH scans
high BW, minimal distortion, and some T*
2 information while
retaining the high intrinsic CNR between the cortex and nearby
white matter afforded by the MPRAGE (van der Kouwe et al.,
2008).
A final critical advantage of the multiecho sequences is that
they are more stable for longitudinal studies than typical
single-echo ones. This derives from the higher distortion of
the single-echo sequences. As noted previously, these distortions are predominantly caused by small, local inhomogeneities in the main (B0) magnetic field. The direction of the
distortions thus changes as a function of the orientation of
the head in the bore of the scanner. The result is that unless
extreme care is taken with subject positioning and landmarking, the distortions are in different directions with respect to
the anatomy in different scan sessions, inducing small but
widespread apparent changes in the brain that are actually
differential distortions, thus obscuring possible true changes.
Thus, multiecho sequences provide reduced distortion and
17
additional contrasts relative to the single-echo sequences traditionally used in brain morphometry, and these properties are
especially valuable in longitudinal studies.
Multiecho FLASH
MEF is an example of a sequence where the single long
(low-BW) FLASH readout is easily replaced by multiple short
(high-BW) readouts, thus reducing B0-related distortion while
recovering SNR by combining the images resulting from the
multiechoes. Figure 13 shows that MEF can generate a variety
of contrasts. Since the readouts typically alternate in direction
(i.e., the polarity of the readout gradient switches with each
readout, called bipolar gradients), the resulting distortions in
the readout direction alternate. Areas that are compressed in
the images from odd echoes are stretched in the images from
even echoes and vice versa. Algorithms that model this behavior to derive a displacement map and undistort the images
have been described (Andersson, Skare, & Ashburner, 2003;
Holland, Kuperman, & Dale, 2010). These are more typically
applied to EPI-based images with alternating phase encoding
direction where the scale of the distortions is greater. Chemical
shifts also alternate direction. MEF can be collected with all the
readouts in the same direction (monopolar readout gradients), but the additional rewinder gradient required between
readouts increases echo spacing. With very high resolution
and/or high BW, when the systems peak gradient strength is
used, the rewinder gradient may become as long as the readout, in which case a bipolar acquisition with twice the number
of echoes would be time-equivalent to the monopolar acquisition with rewinder gradients. As long as gradient strength is
not limiting, distortions can be reduced sufficiently by increasing BW so that the difference in distortions between alternate
readouts is negligible.
Since the Mahalanobis distance between classes in the 16-D
observation space will necessarily be greater than or equal to a
subset of the same data (single-echo FLASH, or SEF), provided
the SNR loss per echo is fully compensated by the number of
echoes, it is expected that segmentation routines should perform better on MEF data than on SEF data. Indeed, Han et al.
(2006) showed empirically that the multispectral data from
MEF acquisitions can be exploited to provide better segmentation of subcortical structures using FreeSurfer, while cortical
models based on gray matter/white matter segmentation with
the same software performed better with MPRAGE.
As predicted by eqn [13], the images from the low flip angle
(5 ) acquisition are predominantly PD-weighted, with additional T*
2 weighting increasing with TE. The images from the
higher flip angle (30 ) acquisition are also PD- and T2*weighted but are additionally T1-weighted. By fitting eqn
[13], T1, T2, and T*
2 can be estimated for each pixel. MEF
acquisitions were used to obtain the images shown in Figure 1
and the parameter maps (PD and T1) shown in Figure 5.
Figure 14 shows the T2* parameter map. Note that this method
yields noisy T*
2 maps because the TEs for a typical MEF protocol with a practical TR value are short relative to the expected
T2*, and T2* is better modeled with multiple complex exponential components because multiple tissue components typically
contribute to the signal from a single voxel. Nevertheless,
assuming the model (eqn [13]) accurately describes most of
the MEF signal, the 16-D data can be projected onto three
18
dimensions without loss of information or discriminating

power. In the interest of generality across sequence types
and imaging platforms, multispectral segmentation algorithms
should use parameter maps as input rather than arbitrarily
weighted images (Segonne et al., 2004). This may also include
T2 maps. However, when scanning time is limited, it may not
be possible to collect enough data to estimate tissue parameters, in which case a single scan with the best contrast for the
particular application should be chosen. For cerebral cortical
modeling, multiecho MPRAGE is such a candidate.
Multi-echo-time MPRAGE and multiple TI MPRAGE

MPRAGE was described in Section MPRAGE. This sequence
introduces an inversion pulse and additional timing parameters to the basic FLASH sequence to enhance T1 contrast, in a
flexible way, between selected tissue classes. The MPRAGE
signal can be predicted with a formulation of the Bloch
equations, but a simple analytic expression is not available.

Therefore, the sequence is less suited to parameter mapping
and better suited to specific applications where a shorter protocol is required.
In MPRAGE, like FLASH, B0 inhomogeneities that remain
after shimming result in a time-varying phase offset across the
readout, with resulting spatial distortions. In addition, T*
2
decay across the readout results in broadening of the PSF. If
the single, low-BW readout is replaced with multiple shorter,
high-BW readouts, susceptibility distortion is reduced and
the PSF is narrower in the readout direction, while SNR is
recovered by combining the images resulting from the multiple
readouts (van der Kouwe et al., 2008). This results in greater
power to distinguish morphometric differences, and this is
especially important in longitudinal studies where changes
within patients may be subtle. Figure 15 shows that cortical
surfaces are displaced in the images by an amount that scales
inversely with the ADC BW.

Figure 14 T*
2 map (ms) estimated from 5 to 30 MEF acquisitions using the FLASH signal eqn [13].
2.00
0.505
-0.505
-2.00
Figure 15 Displacement (mm) of the outer cortical surface (positive vs. negative readout gradient) with 195 Hz per pixel MPRAGE (left) and 651 Hz
pixel MEMPRAGE (right).
10
9
8
7
6
5
4
3
2
1
0
Transverse magnetization
Flip angle (degrees)
Although the echo times in MEMPRAGE are typically very

short, they do vary in T2* contrast. Of particular relevance to
brain morphometry, dura mater has a relatively small T2*,
measurable with MEMPRAGE, and can be distinguished from
the adjacent cortical gray matter on this basis (van der Kouwe
et al., 2008). T2* mapping with MEMPRAGE is noisy but feasible. Since the amount of T1 weighting can be varied on the
basis of the MPRAGE or MEMPRAGE protocol, it is also possible to derive a T1 parameter map if two MPRAGE acquisitions
are acquired. For example, two acquisitions with different
TIs would be suitable. An MPRAGE and a FLASH acquisition
would also suffice. In both cases, a Bloch simulation is
required to derive the map and total acquisition time is comparable to the DESPOT method with two FLASH scans.
MP2RAGE is a variant of MPRAGE that accommodates two
TIs in a single scan, that is, two k-space partitions are collected
after each inversion pulse (Marques et al., 2010). The images
resulting from the first inversion have the typical enhanced
MPRAGE contrast, while the images resulting from the second
TI, which is necessarily fairly long, exhibit more FLASH-like
contrast, with a little residual effect of the inversion. The
sequence also allows the two partitions to be encoded with
different flip angles. T1 maps can be estimated from a single
MP2RAGE acquisition. The sequence is gaining popularity at
high field strength, where signal homogeneity is compromised
due to RF transmit field (B
1 ) inhomogeneities. At field
strengths of 7 T or greater, the wavelength of the RF becomes
comparable to the anatomy of interest, contributing to a central brightening effect in head images (Collins, Liu, Schreiber,
Yang, & Smith, 2005). In MP2RAGE, the second image volume
is used as a divisor to flatten the contrast of the first image
volume, thus providing a more homogeneous MPRAGE. It
has been demonstrated that some segmentation algorithms
perform better when operating on these normalized images
(Marques et al., 2010).
Analogous to PSF broadening due to T2* decay across the
readout, T1 recovery across the phase encoding steps after each
inversion pulse in 3-D MPRAGE results in a broadened PSF in
this direction. Acceleration by parallel techniques (GRAPPA/
SENSE/SMASH; Pruessmann, Weiger, Scheidegger, & Boesiger,
1999; Sodickson, 2000; Sodickson & Mckenzie, 2001;
500
1000 1500 2000 2500

Time (ms)
6
5
4
3
2
1
0
1
2
3
4
19
Pruessmann, 2006; Griswold et al., 2002) in the inner phase

encoding loop reduces phase encoding time, thus reducing not
only distortion but also SNR. Each partition encoding block
may be replaced with multiple shorter (accelerated) blocks,
experiencing different TIs, in order to recover SNR when the
volumes corresponding to the various TIs are combined in
image reconstruction. T1 may be estimated by fitting the signal
predicted by the Bloch simulation across TIs (Marques & Gruetter, 2013; Marques et al., 2010). With this approach, total
acquisition time is unaffected by the additional TIs (van der
Kouwe, Tisdall, Bhat, Fischl, & Polimeni, 2014; Figure 16).
For the purposes of automated brain morphometry, a 3-D
encoding T2-weighted imaging sequence with high isotropic
resolution would complement the T1-weighted approaches
already discussed. Unfortunately, the very popular clinical T2weighted sequence, 2-D encoding TSE, is suboptimal for
whole-brain isotropic imaging. Both 2-D TSE and 3-D TSE
suffer from limited echo train length, and therefore, the
phase encoding steps must be split (segmented) across multiple TRs to achieve very high resolutions, resulting in artifacts,
especially in the presence of patient motion. TSE is also limited
by safety constraints on energy deposition (SAR). By replacing
the 180 refocusing pulses with smaller refocusing flip angles
(Hennig, 1988), the echo train length can be increased and T1
contrast is introduced through the combination of spin and
stimulated echoes. If a variable flip angle pulse train is allowed,
SAR can be reduced further, using flip angles as low as 60 , and
contrast can be controlled further. The sequence of flip angles
is optimized for a particular tissue class. Echo train lengths of
hundreds of echoes are feasible, and this enables efficient 3-D
encoding without segmentation artifacts. This sequence is
called SPACE, CUBE, or VISTA. T2 and T1 varieties are
possible. Images resulting from these T2 sequence may additionally exhibit some T1-weighting.
As with regular spin echo and TSE, an additional inversion
pulse followed by the appropriate inversion delay can be used
to attenuate fluid. Figure 17 shows example slices through 3-D
isotropic T2-SPACE and FLAIR T2-SPACE acquisitions. The
bandwidths commonly used for T2-SPACE are high, resulting
in little distortion, and can be conveniently matched to the
bandwidth of MEMPRAGE and MEF.
600
TI = 700 ms
TI = 1400 ms
TI = 2100 ms
500
400
300
200
100
0
500
1000 1500 2000 2500

Time (ms)
0
3
0
1
Pixels
Figure 16 (Left) Excitation structure after inversion for a single TR of a multiple inversion time (TI 700/1400/2100 ms), MEMPRAGE protocol
(TE 1.69/3.55 ms), flip angle 7 , inter-alpha time 6.5 ms, and TR 2.53 s. (Middle) Evolution of signal transverse magnetization across a single TR,
estimated using discrete Bloch equations. (Right) Corresponding point spread function at each TI for tissue with T1 980 ms. Blue, TI 700 ms;
green, TI 1400 ms; magenta, TI 2100 ms.
20
Figure 17 (Top) T2-SPACE; (bottom) FLAIR T2-SPACE.
Getting to High Resolution

Achieving high resolution requires high SNR and high encoding precision. SNR varies in proportion to the volume of the
encoded voxels. For isotropic voxels, therefore, the volume
varies with the cube of the voxel size, that is, doubling the
resolution results in an 8 times reduction in SNR. The following are three approaches to improving SNR:
1. Increase imaging time.
2. Use tighter (closer) fitting coils (and increase the number of
coils if necessary to improve coverage).
3. Increase B0 field strength.
The system hardware, in particular the gradient system, is
usually manufactured with sufficient tolerance to encode very
precisely down to isotropic resolutions of less than 100 mm. At
these resolutions, however, care must be taken to ensure that
the PSF of the resulting images is tightly constrained, that is,
that blurring does not result in an effective resolution less than
the encoded resolution. Long readouts and/or echo trains with
T*
2 or T2 decay across them can result in PSF broadening. For
living human subjects, image blurring and artifacts may result
from physiological noise due to breathing (which introduces
time-varying changes in the B0 field and synchronized bulk

head motion), cardiac activity (which introduces blood flow
artifacts and very small bulk head movements), and bulk head
motions due to patient discomfort or subsidence of the head
supporting material. In living human subjects, minimum coil
size is limited to the size of the head, although arrays with
many elements can be used, and the maximum field strength
has so far been limited to 9.4 T for human imaging, with 7 T
being relatively common in research laboratories. The maximum scanning time that a subject will tolerate varies a lot with
motivation and disease. Currently, however, subjects are likely
to tolerate a scan that is long enough to encode voxels smaller
than the amount they are likely to move during the scan.
Therefore, real-time motion correction during high-resolution
scans is critical.
With tissue samples, the earlier-mentioned suggestions
are easily employed without the difficult problems of physiological noise and real-time motion correction. Figure 18
shows that it is possible to achieve high resolutions revealing
exquisite anatomical detail by scanning for a long time
(10 h) with a small coil (custom-built four-channel array
coil with individual coil diameters of 5 cm) at high field
strength (7 T).
Figure 18 Example of achievable resolution and contrast

(ex vivo human striatum, T2*-weighted FLASH, 7 T, TR/TE 40/20 ms,
flip angle 15 , 150 mm isotropic voxels, bandwidth 30 Hz per
voxel, average of 7 86 min acquisitions or about 10 h of total
scanning using a custom-built four-channel array coil with 5 cm
elements).
Increased Imaging Time

SNR increases with the square root of the imaging time.
Therefore, to double the isotropic resolution and preserve the
SNR per voxel requires 82 or 64 times the imaging time. A
related principle is to keep the ADC open as much of the
time as possible during acquisition. In FLASH imaging, this is
relatively straightforward. As much time as possible of each TR
should be allocated to readouts while minimizing the time
spent phase encoding, slewing the gradients, spoiling the signal, or simply waiting. Spoiling not only wastes time but also,
by definition, destroys available signal. Steady-state free precession (SSFP) sequences avoid spoiling and are not only very
efficient but also very sensitive to B0 inhomogeneities. SSFP
sequences are T2-sensitive and are susceptible to phase interference artifacts. They are uncommon in current routine brain
morphometric studies.
3-D encoding is usually more efficient than 2-D encoding for
large volumes. Although less signal is acquired per shot with 3-D
encoding, because the TR is usually shorter, signal is obtained
from the entire volume at each shot. In consequence, total SNR
for 3-D acquisitions depends only on the total time spent
acquiring data and not on the size of the volume. In other
words, focusing on a region of anatomy to increase SNR per
unit time is not effective in 3-D imaging. An hour spent encoding the whole head in 3-D will result in the same SNR in the
hippocampus as an hour spent encoding only the hippocampus
in 3-D. SNR may in fact be improved by avoiding the slabselective excitation pulse. However, memory limits on the scanner and subject motion may motivate multiple shorter scans
rather than a single long scan. In 2-D imaging, it is well worthwhile to image only that part of the anatomy that is of interest.
Acceleration and Multichannel Arrays

The signal in an MR experiment is almost always received by a
small conductive loop called a receive coil. This coil may or
21
may not be the same as the coil that transmits the RF pulses
into the object to be imaged. In general, there are two rules of
thumb to keep in mind about receive coils. The first is that the
sensitivity of a coil is inversely proportional to its surface area.
The second is that the region of maximum sensitivity extends
to approximately one coil diameter away. Thus, small coils are
extremely sensitive to regions that are close to them but have a
sensitivity profile that decreases rapidly with distance. Conversely, large coils create homogeneous-appearing images as
their sensitivity profiles decrease slowly with distance but have
relatively poor sensitivity over the entire range. Figure 19 gives
examples of the drop-off in sensitivity for different-sized
receive coils, showing that the volume coils have low, but
uniform, sensitivity, while the small coils have very high
sensitivity in proximal regions but a steep drop-off with distance from the coil (Hayes & Axel, 1985; Lawry, Weiner, &
Matson, 1990).
Given that one desires high sensitivity everywhere in the
image, this is another apparent trade-off and one that can also
be avoided, in this case by covering the object to be sampled
with multiple small coils. These multicoil or multichannel
receive coils are known as phased arrays, or sometimes receive
arrays (see Keil and Wald (2013) for a review or Roemer,
Edelstein, Hayes, Souza, and Mueller (1990) for one of the
earliest implementations). Regions that are far from any coil
give rise to noisy image regions, but since there are potentially
many of them (32- and 62-channel arrays for head imaging are
increasingly common), the ensemble of noisy images can be
combined to create a single image that has higher SNR than a
single, large volume coil everywhere in the object (Axel &
Hayes, 1985; Lawry et al., 1990). That is, every coil images
the entire object, and the images are (by construction) as
close to independent as possible. Many techniques have been
devised to optimally combine the images coming from each
channel into a single, high-quality image (De Zwart, van Gelderen, Kellman, & Duyn, 2002; Roemer et al., 1990; Walsh,
Gmitro, & Marcellin, 2000), but they generally rely on a coil
sensitivity map, that is, a spatial map that gives the sensitivity
of each coil at each location in space. The general idea of
the combination is then to weight the images from coils
more strongly in regions in which they have high sensitivity.
As the number of receive coils increases and the coil elements
become smaller, the combined image becomes less uniform,
and the SNR is lowest at the center of the coil, furthest from any
single element. To boost the signal at the center of the coil,
receive array head coils are built to be as tight-fitting to the
head as possible while still accommodating a range of head
sizes. For young children, it is advantageous to use a pediatric
receive array coil.
The fact that receive arrays provide multiple (redundant)
images of the object, even with spatially varying sensitivity,
leads to a second critical advantage of phased arrays over
single-channel coils. The redundancy in the imaging data permits one to accelerate the imaging by skipping part of the
acquisition and then filling in the regions that were not
acquired using the redundancy. As with coil combination,
there are many techniques for accelerated imaging, such as
SENSE, GRAPPA, and SMASH (Griswold et al., 2002; Pruessmann, 2006; Pruessmann et al., 1999; Sodickson, 2000), but
the general idea is the same: some portion, for example, half, of
22
8
a
5
6
4
Relative S/N
Signal-to-noise ratio (arbitrary units)
b
3
c
10
4
14
2
Head
c
a
0
(a)
10
Depth (cm)
0
0.0
15
(b)
5.0
10.0
15.0
Depth (cm)
Figure 19 (a) SNR profile with distance from coil for single-loop coil elements with various diameters. In (a), the labels ad refer to 8 cm surface coil,
10 cm surface coil, 14 cm surface coil, and head coil, respectively. Reproduced with permission from Hayes, C. E., & Axel, L. (1985) Noise performance
of surface coils for magnetic resonance imaging at 1.5 T. Medical Physics, 12, 604607 and Lawry, T. J., Weiner, M. W., & Matson, G. B. (1990) (b)
Computer modeling of surface coil sensitivity. 8, 10 and 14 refer to the number of array elements. Magnetic Resonance in Medicine, 16, 294302.
the acquisition is skipped, resulting in a scan sequence that is

twice as fast but 2 times more noisy than the equivalent
unaccelerated sequence. Note that there are techniques for
accelerating 2-D imaging by acquiring multiple slices at the
same time known as simultaneous multislice or multiband
(Moeller et al., 2010; Norris, Koopmans, Boyacioglu, & Barth,
2011; Setsompop et al., 2012; Souza, Szumowski, Dumoulin,
Plewes, & Glover, 1988; Weaver, 1988) that do not have this
level of noise amplification as they do not skip part of the
acquisition but instead acquire more of the sample/unit time,
greatly increasing the efficiency of the imaging. These techniques make the 2-D imaging closer in terms of efficiency to
fully 3-D imaging. Parallel acceleration has resulted in dramatic decreases in scan time in recent years as large-N array
coils have become more common. An example of this is given
in Figure 20, which shows a 1 mm isotropic resolution scan
acquired in 1 min and 20 s that is of comparable quality to a
12 min scan acquired 1015 years earlier with a volume coil.
The amount of acceleration that can be achieved is theoretically bounded by the number of coils but, in practice, is significantly less than this. Increasing acceleration can lead to
image artifacts and noise amplification particularly in the center of the head, which is a region that is distant from all the coil
elements (Figure 21). Nevertheless, the now common reduction in scan times by factors of 24 has had a huge impact on
our ability to obtain high-quality images of varying times in a
reasonable scan session.
The decision about what field strength is optimal for a given
study can be a complex one, and various factors must be
considered. First among these is that noise is reduced relative
to signal as one moves to higher field in an approximately
linear manner, so a 3 T scanner can be expected to have twice
Figure 20 1 mm isotropic whole head volume acquired in 1 min 20 s,

equivalent to a 14 min acquisition 1214 years ago. TR 12 ms,
TE 4.7 ms, flip angle 15o, bandwidth 130 Hz per pixel, 3 T, 32-channel
array.
the intrinsic SNR as a 1.5 T scanner. Figure 22 shows increasing

SNR with field strength. However, since B0 distortion is also
proportional to field strength, doubling the field also doubles
the magnitude of the distortion. Other factors, such as power
deposition, may also be important (which gets more restrictive
at higher field), but the primary additional dependency that
must be considered is the variation of the intrinsic tissue
parameters with field strength. In general, the following
holds: PD and T2 are independent of field, while T1 grows at
23
Figure 21 The effects of accelerations. From left to right, acceleration factors of 3, 4, 5, and 6 (256 256 matrix, normalized, 8 slices,
single-shot SEEPI, 3 T, 32 channels, 0.9 mm in-plane).
Figure 22 Comparison of TSE at 3 T (left) and 7 T (right) (TSE, 11 echoes, 7 min exam, 20 cm FOV, 512 512, 0.4 0.4 mm, 3 mm thick slices).
SNR for 7 T: WM 65; GM 76. SNR for 3 T: WM 26; GM 34.
higher field and T2* gets shorter at higher field. Since T2* represents signal decay, one might think that this implies that lower
field is beneficial for T2* weighting, but in fact the opposite
is true. The shorter T2* can improve contrast, as shown in
Figure 22, which shows penetrating vessels in the cerebral
cortex with excellent clarity and enhanced anatomical detail
in the hippocampus. The size of the human head represents
a substantial fraction of the RF wavelength at 7 T, and constructive interference within the head results in the characteristic center-brightening effect seen in Figure 23 (Collins et al.,
2005; van de Moortele et al., 2005). With parallel receive coils,
7 T images can be especially inhomogeneous. Both B1 (transmit) inhomogeneities and B1 (receive) inhomogeneities contribute. B1 may be corrected with a receive coil sensitivity map,
as described previously (Brey & Narayana, 1988; Murakami,
Hayes, & Weinberger, 1996; Narayana, Brey, Kulkarni, & Sievenpiper, 1988; Wald et al., 1995). Further advances in parallel
transmit technology may facilitate the shaping of B1 by
enabling efficient spatially varying RF pulses that produce
more homogeneous B1 fields (Curtis, Gilbert, Klassen, Gati,
& Menon, 2012; Setsompop et al., 2009).
High-field imaging is especially sensitive to small differences in tissue magnetic susceptibility (Li et al., 2006). Figure 24
Figure 23 TSE, 11 echoes, 7 min exam, 20 cm FOV, 512 512

(0.4 0.4 mm), 9 slices, 3 mm thick. Image intensity
normalized showing typical bowl-shaped dielectric effects.
24
shows a slice of a FLASH image with considerable T2* (susceptibility) weighting, emphasizing the blood in vessels within the
cortex and subcortical structures.
Motion Correction
The long 3-D encoding scans typically employed for high-quality
brain morphometry are especially sensitive to subject motion
during acquisition. Uncompensated motion during brain imaging degrades the images, introducing a variety of artifacts, including ghosting and blurring, effectively lowering resolution and
image CNR. Even when artifacts are not apparent upon visual
Figure 24 T*-weighted
FLASH collected at 7 T, 0.22 0.22 3 mm3,
2
TR 500 ms, TE 25 ms, BW 30 Hz per pixel, flip angle 35o, acquisition
time 7 min 29 s.
inspection of the images, the derived morphometric measurements are sensitive to the motion. Motion results in spurious and
regionally specific cortical thickness changes, for example, and
this is of particular concern when the control group and patient
group move by a systematically differing amount or in different
ways. Moreover, the pattern of cortical thickness changes introduced by motion may mimic the changes expected in the disorder. Figure 25 shows how cortical thickness measurements are
affected by deliberate subject motion during the scan. These
effects have been shown using various segmentation algorithms
(Reuter, Tisdall, Van Der Kouwe, & Fischl, 2014). Other measurements such as structure volumes may similarly be expected
to be biased by motion during the scan.
Various approaches for correcting head motion in real time
during acquisition have been proposed. Fortunately, if the
nonrigid parts of the head, viz., the lower jaw and neck, are
excluded, the head can be modeled as a single rigid body with
six degrees of freedom. This makes motion detection and correction a far simpler problem in brain imaging, as compared
with nonrigid anatomy such as the heart. Postprocessing
methods may improve image quality, but real-time prospective
methods offer better imaging efficiency and image quality.
Prospective methods may be divided broadly into intrinsic
navigator methods and extrinsic sensor methods. Navigator
methods use the MR signal itself to identify the pose (relative
position and orientation) of the head. Some imaging sequence
types, such as EPI, and some arrangements of radial imaging
can be self-navigating, meaning that the rapidly repeated
images themselves can be used to detect the position of the
head (or other moving anatomy) and correct the next acquisition (Bhat, Ge, Nielles-Vallespin, Zuehlsdorff, & Li, 2011; Thesen, Heid, Mueller, & Schad, 2000). More typically, an
additional short sequence element, or navigator, is interleaved within the main imaging sequence. The navigator represents a snapshot of the head position at regular intervals
throughout the imaging sequence and the position is fed
back to the scanners RF and gradient system to update the
encoded imaging coordinates as the scan proceeds. Navigators
Shake
Free
p = 0.01
p = 0.001
Figure 25 Regions of cortical thinning induced by shaking motion (rotation about the superiorinferior axis) (left) and free motion (including
rotations and translations in a variety of directions) (right). P-values of Wilcoxon signed-rank test are overlaid on the partially inflated cortical surface
model. The figure shows the P-value for a thickness change within each subject, computed for 12 subjects.

can be a simple line in k-space, or projection of the volume, for
measuring translations along a single direction, or a more
complicated trajectory in k-space that can measure translations, rotations, or both, such as orbital navigators (Fu et al.,
1995), spherical navigators (Welch, Manduca, Grimm, Ward,
& Jack, 2002), or cloverleaf navigators (van der Kouwe, Benner,
& Dale, 2006). Three-plane spiral navigators (White et al.,
2010) or full volume navigators (Thesen et al., 2000; Tisdall
et al., 2012) can be used to obtain a low-resolution 3-D snapshot of the brain. Navigators may have to be customized
depending on the imaging sequence in which they are embedded, and they may increase total acquisition time. In the case of
MPRAGE and T2-SPACE and various FLAIR sequences, there
is typically sufficient time spent waiting for recovery during
which there is no signal acquisition for imaging, and navigators with small excitation flip angles can be inserted in these
gaps. Figure 26 shows an MPRAGE collected while a subject
was deliberately moving without motion correction and with
real-time motion correction using volumetric navigators
(Tisdall et al., 2012). Since motion is only estimated once per
navigator and therefore once per TR in the MPRAGE, motion
occurring between navigators may not be corrected until the
next TR. In this case, certain slices of k-space may be corrupted
by motion. Some sequences allow the reacquisition of these
damaged slices of k-space during or at the end of the scan
(Alhamud et al., 2012; Tisdall et al., 2012). This adds to the
total scan time, but is more efficient than collecting two complete scans and choosing the one with less degradation due to
motion, as is often done in studies with patients who may
move. Despite the typically low resolution of the navigator,
estimated motion can be very precise, and a much higherresolution imaging sequence can be driven by a standard navigator. Figure 27 shows a section of a 350 mm isotropic image
acquired during 138 min of imaging with MPRAGE using volumetric navigators to stabilize motion and frequency drift
during the acquisition (Tisdall et al., 2012).
If extrinsic sensors are used, customization of the sequence
is much reduced and motion can be estimated more rapidly
and not necessarily at intervals dictated by the sequence
structure. Optical systems using reflective markers (Zaitsev,
Dold, Sakas, Hennig, & Speck, 2006) or retrograte reflectors
(Andrews-Shigaki, Armstrong, Zaitsev, & Ernst, 2011) can be
25
used to rapidly estimate head pose. The sequence is modified

to track the head position, without affecting total acquisition
time. Correction with prospective optical tracking has
been demonstrated on a slice-by-slice basis (Speck, Hennig, &
Zaitsev, 2006) and even continuously within diffusion gradients
(Herbst et al., 2012). Optical systems require a clear line of
sight between the reflector and the camera(s), and the marker
(s) or reflector(s) must be rigidly attached to the head. An
optical approach using facial geometry for tracking eliminates
the need for a rigidly attached marker (Olesen, Paulsen,
Hojgaard, Roed, & Larsen, 2012; Olesen et al., 2013). Closefitting coils with array elements close to the head offer higher
SNR but obstruct a clear view of the head. Conversely, inductive
sensors require rigid attachment to the head, but require no
clear line of sight. A hybrid navigator approach combines a set
of extrinsic fiducial markers with a simple rapidly acquired navigator that locates the markers and estimates the position and
Figure 27 Zoomed section of axial slice of 138 min MPRAGE

acquisition with 350 mm isotropic resolution, collected with vNav motion
correction in a live volunteer. Image pixelation reflects the encoded image
resolution.
Figure 26 MEMPRAGE from subject performing deliberate motions during an acquisition without motion correction (left) and with real-time
motion correction, frequency drift correction, and reacquisition of damaged sections of k-space using volumetric navigators (right).
26
orientation of the set. Markers may consist of miniature coils

activated by the scanner RF pulses (Muraskin et al., 2013; Ooi,
Aksoy, Maclaren, Watkins, & Bammer, 2013; Thormer et al.,
2012). These methods are more difficult to apply in the clinical
situation due to the additional hardware, calibration, and
markers affixed to the patient. However, in the research setting,
extremely high-resolution imaging is possible under ideal
conditions (Andrews-Shigaki et al., 2011; Schulz et al., 2012;
Zaitsev et al., 2006).
Conclusion
In this article, we have tried to give the reader a basic foundation in the fundamentals of MRI acquisition as it relates to
the goal of quantifying brain structure. We have covered the
most common types of MRI acquisitions including T1-, T2-,
PD-, and T2*-weighted imaging. We have shown examples of
each of these image types and also discussed the theoretical
considerations that cause specific configurations of acquisition
parameters to give rise to images with a particular weighting.
The future of anatomical acquisitions will almost certainly
include pushing the useful resolution that can be acquired.
High resolution is challenging in MRI for two fundamental
reasons. The first is the relationship between SNR and resolution that we discussed earlier halving the linear dimensions of
a voxel results in a factor of 8 times reduction in SNR (0.53),
which requires 82 64 times as much acquisition time to
recover. Thus, even with modern large-N phased array coils,
500 mm isotropic scans are close to the limit of what we have
been able to achieve in living humans at 3 T even in dedicated
scan sessions (<1 h of imaging). Higher-resolution scans
have been acquired with special purpose technology such as
ultrahigh-field scanners, dedicated coils, and acquisition
sequences (see Figure 27 (Tisdall, Polimeni, & van der Kouwe,
2013)). The second limitation is that as the voxels in our images
get smaller, other effects that increase the spatial extent of the
PSF begin to become important. Small subject motions that are
irrelevant for 1 mm images become significant sources of blurring at 350 mm. Similarly, physiological processes such as cardiac and respiratory cycles and the concomitant pulsation of
the brain and the flow of CSF can make the effective resolution
of the scans significantly lower than the voxel size. We expect
these issues will be overcome by the continued development of
more sensitive receive coils, the use of multiple transmit coils to
reduce the dielectric effects that plague ultrahigh-field imaging,
and the inclusion of ever-more sophisticated navigator scans
and/or external tracking devices to measure and remove sources
of distortion and blurring that occur during the scan session.
Acknowledgments
Thanks to Lawrence Wald for several of the images used in this
article and for years of teaching the basics of MRI. Thanks also to
John Kirsch for clarification on many questions related to MR
physics. Support was provided in part by the National Center for
Research Resources (P41RR014075, U24RR021382, and
U24RR021992), the National Cancer Institute (R44CA116980
and R01CA137254), the National Institute on Aging
(R01AG008122 and R01AG022381), the National Institute on

Alcohol Abuse and Alcoholism (R21AA017410 and
R21AA020037), the National Institute of Biomedical Imaging
and
Bioengineering
(R01EB000790,
R21EB002530,
R01EB006758, R21EB008547, and P41EB015896), the Eunice
Kennedy Shriver National Institute of Child Health and Human
Development (R01HD071664), the National Institute on Drug
Abuse (R21/33DA026104), the National Institute of Mental
Health (R21MH084041 and R21MH096559), the National
Institute of Neurological Disorders and Stroke (P01NS035611,
R01NS052585,
R01NS055754,
R01NS070963,
and
R21NS072652), the Fogarty International Center, and the
National Center for Complementary and Alternative Medicine
(U01AT000613 and RC1AT005728). This work was also made
possible by the resources provided by Shared Instrumentation
Grants S10RR019307, S10RR023043, and S10RR023401. Additional support was provided by the Autism and Dyslexia Project
funded by the Ellison Medical Foundation and by the NIH
Blueprint for Neuroscience Research (U01MH093765), part of
the multi-institutional Human Connectome Project. In addition, BF has a financial interest in CorticoMetrics, a company
whose medical pursuits focus on brain imaging and measurement technologies. BFs interests were reviewed and are managed
by Massachusetts General Hospital and Partners HealthCare in
accordance with their conflict of interest policies.
See also: INTRODUCTION TO ACQUISITION METHODS: HighField Acquisition; High-Speed, High-Resolution Acquisitions; MRI and
fMRI Optimizations and Applications; Obtaining Quantitative
Information from fMRI; Susceptibility-Weighted Imaging and
Quantitative Susceptibility Mapping; INTRODUCTION TO
METHODS AND MODELING: Automatic Labeling of the Human
Cerebral Cortex; Computing Brain Change over Time; Cortical
Thickness Mapping; Lesion Segmentation; Manual Morphometry;
Modeling Brain Growth and Development; Sulcus Identification and
Labeling; Surface-Based Morphometry; Tissue Classification; Tissue
Properties from Quantitative MRI; Voxel-Based Morphometry.
References
Alhamud, A., Tisdall, M. D., Hess, A. T., Hasan, K. M., Meintjes, E. M., &
van der Kouwe, A. J. (2012). Volumetric navigators for real-time motion correction
in diffusion tensor imaging. Magnetic Resonance in Medicine, 68, 10971108.
Andersson, J. L., Skare, S., & Ashburner, J. (2003). How to correct susceptibility
distortions in spin-echo echo-planar images: Application to diffusion tensor
imaging. NeuroImage, 20, 870888.
Andrews-Shigaki, B. C., Armstrong, B. S., Zaitsev, M., & Ernst, T. (2011). Prospective
motion correction for magnetic resonance spectroscopy using single camera RetroGrate reflector optical tracking. Journal of Magnetic Resonance Imaging, 33, 498504.
Axel, L., & Hayes, C. (1985). Surface coil magnetic resonance imaging. Archives
Internationales de Physiologie et de Biochimie, 93, 1118.
Bhat, H., Ge, L., Nielles-Vallespin, S., Zuehlsdorff, S., & Li, D. (2011). 3D radial
sampling and 3D affine transform-based respiratory motion correction technique for
free-breathing whole-heart coronary MRA with 100% imaging efficiency. Magnetic
Resonance in Medicine, 65(5), 12691277.
Brass, S. D., Chen, N. K., Mulkern, R. V., & Bakshi, R. (2006). Magnetic resonance
imaging of iron deposition in neurological disorders. Topics in Magnetic
Resonance Imaging, 17, 3140.
Brey, W. W., & Narayana, P. A. (1988). Correction for intensity falloff in surface coil
magnetic resonance imaging. Medical Physics, 15, 241245.
Collins, C. M., Liu, W., Schreiber, W., Yang, Q. X., & Smith, M. B. (2005). Central
brightening due to constructive interference with, without, and despite dielectric
resonance. Journal of Magnetic Resonance Imaging, 21, 192196.

Constantinides, C. D., Atalar, E., & Mcveigh, E. R. (1997). Signal-to-noise
measurements in magnitude images from NMR phased arrays. Magnetic Resonance
in Medicine, 38, 852857.
Crawley, A. P., Wood, M. L., & Henkelman, R. M. (1988). Elimination of transverse
coherences in FLASH MRI. Magnetic Resonance in Medicine, 8, 248260.
Curtis, A. T., Gilbert, K. M., Klassen, L. M., Gati, J. S., & Menon, R. S. (2012).
Slice-by-slice B1 shimming at 7 T. Magnetic Resonance in Medicine, 68,
11091116.
De Zwart, J. A., van Gelderen, P., Kellman, P., & Duyn, J. H. (2002). Application of
sensitivity-encoded echo-planar imaging for blood oxygen level-dependent
functional brain imaging. Magnetic Resonance in Medicine, 48, 10111020.
Deoni, S. C., Peters, T. M., & Rutt, B. K. (2005). High-resolution T1 and T2 mapping of
the brain in a clinically acceptable time with DESPOT1 and DESPOT2. Magnetic
Resonance in Medicine, 53, 237241.
Deoni, S. C., Rutt, B. K., & Peters, T. M. (2003). Rapid combined T1 and T2 mapping
using gradient recalled acquisition in the steady state. Magnetic Resonance in
Medicine, 49, 515526.
Duda, R. O., & Hart, P. E. (1973). Pattern Classification and Scene Analysis. New York:
John Wiley & Sons.
Fischl, B., Salat, D., van der Kouwe, A., Makris, N., Segonne, F., Quinn, B., et al. (2004).
Sequence-independent segmentation of magnetic resonance images. NeuroImage,
23, S69S84.
Fu, Z. W., Wang, Y., Grimm, R. C., Rossman, P. J., Felmlee, J. P., Riederer, S. J., et al.
(1995). Orbital navigator echoes for motion measurements in magnetic resonance
imaging. Magnetic Resonance in Medicine, 34, 746753.
Griswold, M. A., Jakob, P. M., Heidemann, R. M., Nittka, M., Jellus, V., Wang, J., et al.
(2002). Generalized autocalibrating partially parallel acquisitions (GRAPPA).
Magnetic Resonance in Medicine, 47, 12021210.
Han, X., Jovicich, J., Salat, D., van der Kouwe, A., Quinn, B., Czanner, S., et al. (2006).
Reliability of MRI-derived measurements of human cerebral cortical thickness: The
effects of field strength, scanner upgrade and manufacturer. NeuroImage, 32,
180194.
Hasan, K. M., Walimuni, I. S., Kramer, L. A., & Frye, R. E. (2010). Human brain atlasbased volumetry and relaxometry: Application to healthy development and natural
aging. Magnetic Resonance in Medicine, 64, 13821389.
Hayes, C. E., & Axel, L. (1985). Noise performance of surface coils for magnetic
resonance imaging at 1.5 T. Medical Physics, 12, 604607.
Hennig, J. (1988). Multiecho imaging sequences with low refocusing flip angles.
Journal of Magnetic Resonance, 78, 397407.
Herbst, M., Maclaren, J., Weigel, M., Korvink, J., Hennig, J., & Zaitsev, M. (2012).
Prospective motion correction with continuous gradient updates in diffusion
weighted imaging. Magnetic Resonance in Medicine, 67, 326338.
Holland, D., Kuperman, J. M., & Dale, A. M. (2010). Efficient correction of
inhomogeneous static magnetic field-induced distortion in echo planar imaging.
NeuroImage, 50, 175183.
Jezzard, P., & Balaban, R. S. (1995). Correction for geometric distortion in echo planar
images from B0 field variations. Magnetic Resonance in Medicine, 34, 6573.
Keil, B., & Wald, L. L. (2013). Massively parallel MRI detector arrays. Journal of
Magnetic Resonance, 229, 7589.
Koay, C. G., & Basser, P. J. (2006). Analytically exact correction scheme for signal
extraction from noisy magnitude MR signals. Journal of Magnetic Resonance, 179,
317322.
Lawry, T. J., Weiner, M. W., & Matson, G. B. (1990). Computer modeling of surface coil
sensitivity. Magnetic Resonance in Medicine, 16, 294302.
Lebel, C., & Beaulieu, C. (2011). Longitudinal development of human brain wiring
continues from childhood into adulthood. Journal of Neuroscience, 31,
1093710947.
Leupold, J., Hennig, J., & Scheffler, K. (2008). Moment and direction of the spoiler
gradient for effective artifact suppression in RF-spoiled gradient echo imaging.
Li, T. Q., Van Gelderen, P., Merkle, H., Talagala, L., Koretsky, A. P., & Duyn, J. (2006).
Extensive heterogeneity in white matter intensity in high-resolution T2*-weighted
MRI of the human brain at 7.0 T. NeuroImage, 32, 10321040.
Marques, J. P., & Gruetter, R. (2013). New developments and applications of the
MP2RAGE sequencefocusing the contrast and high spatial resolution R1 mapping.
PLoS One, 8, e69294.
Marques, J. P., Kober, T., Krueger, G., van der Zwaag, W., van de Moortele, P. F., &
Gruetter, R. (2010). MP2RAGE, a self bias-field corrected sequence for improved
segmentation and T1-mapping at high field. NeuroImage, 49, 12711281.
Moeller, S., Yacoub, E., Olman, C. A., Auerbach, E., Strupp, J., Harel, N., et al. (2010).
Multiband multislice GE-EPI at 7 tesla, with 16-fold acceleration using partial
parallel imaging with application to high spatial and temporal whole-brain fMRI.
27
Mugler, J. P., 3rd, & Brookeman, J. R. (1990). Three-dimensional magnetizationprepared rapid gradient-echo imaging (3D MP RAGE). Magnetic Resonance in
Medicine, 15, 152157.
Murakami, J. W., Hayes, C. E., & Weinberger, E. (1996). Intensity correction of phasedarray surface coil images. Magnetic Resonance in Medicine, 35, 585590.
Muraskin, J., Ooi, M. B., Goldman, R. I., Krueger, S., Thomas, W. J., Sajda, P., et al.
(2013). Prospective active marker motion correction improves statistical power in
BOLD fMRI. NeuroImage, 68, 154161.
Narayana, P. A., Brey, W. W., Kulkarni, M. V., & Sievenpiper, C. L. (1988).
Compensation for surface coil sensitivity variation in magnetic resonance imaging.
Magnetic Resonance Imaging, 6, 271274.
Norris, D. G., Koopmans, P. J., Boyacioglu, R., & Barth, M. (2011). Power Independent
of Number of Slices (PINS) radiofrequency pulses for low-power simultaneous
multislice excitation. Magnetic Resonance in Medicine, 66, 12341240.
Olesen, O. V., Paulsen, R. R., Hojgaard, L., Roed, B., & Larsen, R. (2012). Motion
tracking for medical imaging: A nonvisible structured light tracking approach. IEEE
Transactions on Medical Imaging, 31, 7987.
Olesen, O. V., Sullivan, J. M., Mulnix, T., Paulsen, R. R., Hojgaard, L., Roed, B., et al.
(2013). List-mode PET motion correction using markerless head tracking: Proof-ofconcept with scans of human subject. IEEE Transactions on Medical Imaging, 32,
200209.
Ooi, M. B., Aksoy, M., Maclaren, J., Watkins, R. D., & Bammer, R. (2013). Prospective
motion correction using inductively coupled wireless RF coils. Magnetic Resonance
in Medicine, 70(3), 639647.
Pouwels, P. J., Kuijer, J. P., Mugler, J. P., 3rd, Guttmann, C. R., & Barkhof, F. (2006).
Human gray matter: Feasibility of single-slab 3D double inversion-recovery highspatial-resolution MR imaging. Radiology, 241, 873879.
Pruessmann, K. P. (2006). Encoding and reconstruction in parallel MRI. NMR in
Biomedicine, 19, 288299.
Pruessmann, K. P., Weiger, M., Scheidegger, M. B., & Boesiger, P. (1999). SENSE:
Sensitivity encoding for fast MRI. Magnetic Resonance in Medicine, 42, 952962.
Redpath, T. W., & Smith, F. W. (1994). Technical note: Use of a double inversion
recovery pulse sequence to image selectively grey or white brain matter. British
Journal of Radiology, 67, 12581263.
Reuter, M., Tisdall, M. D., Van Der Kouwe, A., & Fischl, B. (2014). Head motion in MRI
causes bias in structural brain measurements. In: Annual Meeting of the
Organization for Human Brain Mapping, Hamburg, Germany.
Roemer, P. B., Edelstein, W. A., Hayes, C. E., Souza, O. M., & Mueller, S. P. (1990). The
NMR phased array. Magnetic Resonance in Medicine, 16, 192225.
Saito, N., Sakai, O., Ozonoff, A., & Jara, H. (2009). Relaxo-volumetric multispectral
quantitative magnetic resonance imaging of the brain over the human lifespan:
Global and regional aging patterns. Magnetic Resonance Imaging, 27, 895906.
Salat, D., Lee, S., van der Kouwe, A., Greve, D., Fischl, B., & Rosas, H. (2009). Ageassociated alterations in cortical gray and white matter signal intensity and gray to
white matter contrast. NeuroImage, 48, 2128. http://dx.doi.org/10.1016/j.
neuroimage.2009.06.074.
Schenck, J. F. (1995). Imaging of brain iron by magnetic resonance: T2 relaxation at
different field strengths. Journal of Neurological Sciences, 134, 1018.
Schenker, C., Meier, D., Wichmann, W., Boesiger, P., & Valavanis, A. (1993). Age
distribution and iron dependency of the T2 relaxation time in the globus pallidus and
putamen. Neuroradiology, 35, 119124.
Schulz, J., Siegert, T., Reimer, E., Labadie, C., Maclaren, J., Herbst, M., et al. (2012). An
embedded optical tracking system for motion-corrected magnetic resonance
imaging at 7 T. Magma, 25, 443453.
Segonne, F., Dale, A., Busa, E., Glessner, M., Salvolini, U., Hahn, H., et al. (2004). A
hybrid approach to the skull-stripping problem in MRI. NeuroImage, 22,
11601175.
Setsompop, K., Alagappan, V., Gagoski, B. A., Potthast, A., Hebrank, F., Fontius, U.,
et al. (2009). Broadband slab selection with B1 mitigation at 7 T via parallel
spectral-spatial excitation. Magnetic Resonance in Medicine, 61, 493500.
Setsompop, K., Gagoski, B. A., Polimeni, J. R., Witzel, T., Wedeen, V. J., & Wald, L. L.
(2012). Blipped-controlled aliasing in parallel imaging for simultaneous multislice
echo planar imaging with reduced g-factor penalty. Magnetic Resonance in
Medicine, 67, 12101224.
Sodickson, D. K. (2000). Tailored SMASH image reconstructions for robust in vivo
parallel MR imaging. Magnetic Resonance in Medicine, 44, 243251.
Sodickson, D. K., & Mckenzie, C. A. (2001). A generalized approach to parallel
magnetic resonance imaging. Medical Physics, 28, 16291643.
Souza, S. P., Szumowski, J., Dumoulin, C. L., Plewes, D. P., & Glover, G. (1988). SIMA:
Simultaneous multislice acquisition of MR images by Hadamard-encoded
excitation. Journal of Computer Assisted Tomography, 12, 10261030.
Speck, O., Hennig, J., & Zaitsev, M. (2006). Prospective real-time slice-by-slice motion
correction for fMRI in freely moving subjects. Magma, 19, 5561.
28
Suzuki, S., Sakai, O., & Jara, H. (2006). Combined volumetric T1, T2 and secular-T2
quantitative MRI of the brain: Age-related global changes (preliminary results).
Thesen, S., Heid, O., Mueller, E., & Schad, L. R. (2000). Prospective acquisition
correction for head motion with image-based tracking for real-time fMRI. Magnetic
Thormer, G., Garnov, N., Moche, M., Haase, J., Kahn, T., & Busse, H. (2012).
Simultaneous 3D localization of multiple MR-visible markers in fully reconstructed
MR images: Proof-of-concept for subsecond position tracking. Magnetic Resonance
Imaging, 30, 371381.
Tisdall, M. D., Hess, A. T., Reuter, M., Meintjes, E. M., Fischl, B., &
Van Der Kouwe, A. J. (2012). Volumetric navigators for prospective motion
correction and selective reacquisition in neuroanatomical MRI. Magnetic Resonance
Tisdall, M. D., Polimeni, J. R., & van der Kouwe, A. J. W. (2013). Motion-corrected 350
um isotropic MPRAGE at 3 T using volumetric navigators (vNavs). In: Proceedings of
the International Society for Magnetic Resonance in Medicine, Salt Lake City, UT.
van de Moortele, P. F., Akgun, C., Adriany, G., Moeller, S., Ritter, J., Collins, C. M., et al.
(2005). B(1) destructive interferences and spatial phase patterns at 7 T with a head
transceiver array coil. Magnetic Resonance in Medicine, 54, 15031518.
van der Kouwe, A. J., Benner, T., & Dale, A. M. (2006). Real-time rigid body motion
correction and shimming using cloverleaf navigators. Magnetic Resonance in
Medicine, 56, 10191032.
van der Kouwe, A. J., Benner, T., Salat, D. H., & Fischl, B. (2008). Brain morphometry
with multiecho MPRAGE. NeuroImage, 40, 559569.
van der Kouwe, A. J. W., Tisdall, M. D., Bhat, H., Fischl, B., & Polimeni, J. R. (2014).
Multiple echo and inversion time MPRAGE with inner loop GRAPPA acceleration
and prospective motion correction for minimally distorted multispectral
morphometry. In: 22nd Annual Meeting of the International Society for Magnetic
Resonance in Medicine, Milan, Italy.
Wald, L. L., Carvajal, L., Moyher, S. E., Nelson, S. J., Grant, P. E., Barkovich, A. J., et al.
(1995). Phased array detectors and an automated intensity-correction algorithm for
high-resolution MR imaging of the human brain. Magnetic Resonance in Medicine,
34, 433439.
Walsh, D. O., Gmitro, A. F., & Marcellin, M. W. (2000). Adaptive reconstruction of
phased array MR imagery. Magnetic Resonance in Medicine, 43, 682690.
Weaver, J. B. (1988). Simultaneous multislice acquisition of MR images. Magnetic
Welch, E. B., Manduca, A., Grimm, R. C., Ward, H. A., & Jack, C. R., Jr, (2002).
Spherical navigator echoes for full 3D rigid body motion measurement in MRI.
White, N., Roddey, C., Shankaranarayanan, A., Han, E., Rettmann, D., Santos, J., et al.
(2010). PROMO: Real-time prospective motion correction in MRI using imagebased tracking. Magnetic Resonance in Medicine, 63, 91105.
Zaitsev, M., Dold, C., Sakas, G., Hennig, J., & Speck, O. (2006). Magnetic
resonance imaging of freely moving objects: Prospective real-time motion
correction using an external optical motion tracking system. NeuroImage, 31,
10381050.
Zur, Y., Wood, M. L., & Neuringer, L. J. (1991). Spoiling of transverse magnetization in
steady-state sequences. Magnetic Resonance in Medicine, 21, 251263.
Obtaining Quantitative Information from fMRI

G Bruce Pike, University of Calgary, Calgary, AB, Canada
RD Hoge, Universite de Montreal, Montreal, QC, Canada
Glossary
ASL arterial spin labeling ASL refers to a class of

noninvasive MRI techniques for imaging tissue perfusion. It
uses magnetic labeling (typically inversion) of arterial blood
flowing into the imaging region as an endogenous tracer.
BOLD blood oxygenation level-dependent The term
BOLD was coined by Ogawa et al. (1992) and refers to
intravascular and extravascular T2 and T2* changes that
result from variations in the oxygen saturation of blood. The
BOLD contrast mechanism is widely used for functional
MRI because changes in neuronal activity level normally
result in changes in the postarteriolar blood oxygen
saturation.
cASL continuous arterial spin labeling This is a subclass
of ASL techniques in which the magnetic labeling of blood is
achieved using a long-duration (continuous) low-intensity
radio-frequency excitation.
CBF cerebral blood flow CBF in the context of functional
brain imaging refers to brain tissue perfusion. It is normally
expressed in units of ml 100 ml1 min1.
CBV cerebral blood volume CBV in the context of
functional brain imaging refers to fractional volume of brain
tissue occupied by blood and is often expressed as a
percentage.
CMRO2 cerebral metabolic rate of oxygen CMRO2 is the
rate at which oxygen is consumed by brain tissue. It is
expressed in units of mmol 100 g1 min1.
dHb deoxyhemoglobin Hemoglobin is the ironcontaining metalloprotein found in red blood cells that is
responsible for oxygen transport. In its deoxygenated state, it
is referred to as dHb, and, importantly for BOLD fMRI, it is
paramagnetic and therefore causes focal shortening of T2
and T2* relaxation time constants.
EPI echo-planar imaging EPI is a fast MRI acquisition
technique in which all the data required to reconstruct an
image are collected following a single excitation (single-shot
EPI) or a few excitations (multishot EPI). EPI is the most
widely used fast imaging technique in BOLD fMRI.
GadoliniumDTPA This is a commonly used MRI contrast
agent that is typically injected intravenously and does not
cross the intact bloodbrain barrier. The contrast agent is
paramagnetic and causes a reduction in the relaxation times
(T1, T2, and T2*).
Introduction
MRIs impact on functional brain mapping during the past
quarter century has been profound, and today, fMRI is the
predominant technique used to image brain activity in
humans. The overwhelming majority of fMRI studies exploit
Gradient echo Gradient echo refers to an MRI technique in

which the signal is received without using a refocusing pulse
to correct for static magnetic field inhomogeneities. The
signal decay in a gradient-echo sequence is dependent upon
the T2* relaxation time constant. This is the most common
type of imaging used for BOLD fMRI.
HbO oxyhemoglobin Hemoglobin is the iron-containing
metalloprotein found in red blood cells that is responsible
for oxygen transport. In its oxygenated state, it is referred to
as HbO, and, importantly for BOLD fMRI, it is slightly
diamagnetic, as is brain tissue, and therefore does not alter
the T2 and T2* relaxation time constants of surrounding
tissue.
Hypercapnia This is a condition in which there is an
increased level of carbon dioxide (CO2) in the blood. CO2 is
a potent vasodilator and therefore hypercapnia can be used
to increase CBF without increasing metabolism.
Hypercapnia can be used to calibrate the BOLD fMRI signal.
Hyperoxia This is a condition in which there is an increased
level of oxygen in the blood and can be achieved by inhaling
oxygen at pressures greater than normal atmospheric
pressure. Hyperoxia can be used to calibrate the BOLD fMRI
signal.
M maximal BOLD signal change In the context of
calibrated BOLD imaging, M is the calibration constant. It is
the percent increase in T2*-weighted BOLD MRI signal that
would be observed, from a given baseline condition, upon
complete elimination of all deoxygenated hemoglobin from
brain tissues.
Neurovascular coupling This term refers to the collection
of all mechanisms that link focal changes in neuronal
activity level to subsequent focal changes in CBF.
pASL pulsed arterial spin labeling This is a subclass of
ASL techniques in which the magnetic labeling of blood is
achieved using a brief radio-frequency pulse.
pcASL pseudo-continuous arterial spin labeling This is a
subclass of ASL techniques in which many sequential radiofrequency pulses are used to achieve a pseudo-continuous
magnetic labeling of blood.
Spin echo Spin echo refers to an MRI technique in which a
refocusing pulse is used to correct for static magnetic field
inhomogeneities. The signal decay in a spin-echo sequence
is dependent upon the T2 relaxation time constant.
the blood oxygenation level-dependent (BOLD) contrast

mechanism and are qualitative in nature, providing localization of activity but not a measure of activity level. This is due to
the fact that the BOLD fMRI signal is an indirect and complex
surrogate measure of neuronal activity and its precise interpretation remains controversial. In fact, there are two primary
http://dx.doi.org/10.1016/B978-0-12-397025-1.00002-6
29
30
INTRODUCTION TO ACQUISITION METHODS | Obtaining Quantitative Information from fMRI
issues that complicate the interpretation of the BOLD signal.

The first is the incompletely understood relationship between
changes in neuronal activity and the consequent modulations
in cerebral blood flow (CBF) and volume (neurovascular
coupling) and oxygen metabolism. The second is the fact that
the BOLD contrast mechanism is sensitive to modulations in
the amount of deoxyhemoglobin (dHb) present in a voxel but
the combination of blood flow, blood volume, and oxygen
metabolism changes that produce the change in dHb cannot
be determined from the BOLD signal alone. This article focuses
on this second issue and presents a brief review of the current
state-of-the-art MRI methods for obtaining quantitative measures of CBF, blood volume, and oxygen metabolism for functional brain imaging.
BOLD Contrast
While the transverse magnetization relaxation time constant
(T2) of blood had been shown to depend upon its oxygenation
in 1982 (Thulborn, Waterton, Matthews, & Radda, 1982), it
was a decade later before it was exploited as a contrast mechanism to image brain activity (Kwong et al., 1992; Ogawa et al.,
1992) and Ogawa coined the term BOLD. A fundamental
underpinning of the technique is the fact that the magnetic
properties of hemoglobin significantly change depending
upon whether it is oxygenated or not (Pauling & Coryell,
1936). While oxyhemoglobin (HbO) is slightly diamagnetic,
similar to other brain tissue, dHb is paramagnetic and thus acts
as an endogenous MRI contrast agent that significantly
increases the transverse relaxation rate (i.e., T2 and T2* relaxation times decrease). Combined with the observation that
blood oxygen saturation changes focally with neuronal activity
(Fox & Raichle, 1986), gradient-echo MR imaging with T2*
contrast weighting provides a mechanism to indirectly map
modulations in neuronal activity. While spin-echo imaging
with T2 contrast weighting can also be used for fMRI, the
greater sensitivity and speed of gradient-echo imaging have
resulted in it being the most widely used technique. The final
key ingredient that made BOLD fMRI so ubiquitous is fast
imaging techniques, such as echo-planar imaging (EPI;
Mansfield, 1977), that permit the acquisition of whole-brain
volumes on a timescale similar to the brains hemodynamic
modulations (a few seconds).
To better understand the BOLD signal, one has to consider
how the amount and distribution of dHb within a voxel alter the
T2* relaxation time. This has largely been achieved using vascular
modeling and simulation of the intravascular and extravascular
MR signal evolution (Boxerman et al., 1995). In such a model,
the key physiological parameters that are expected to change
with neuronal activity are the cerebral blood volume (CBV)
and the oxygen saturation (Y) of each vascular compartment
arterial, capillary, and venous. The oxygen saturation is, in turn,
dependent upon the rate of oxygen delivery (proportional to the
product of arterial oxygen saturation Ya and CBF) and the rate
of utilization (cerebral metabolic rate of oxygen consumption
CMRO2). Since Ya is normally quite stable, one is left with three
fundamental physiological parameters that are expected to vary
with neuronal activity level CBF, CBV, and CMRO2. While
precise knowledge of these parameters does not equate to a direct
measure of neuronal activity, they are of enormous value and

interest. CBF and CBV are linked to neuronal activity via the
neurovascular coupling mechanism (Iadecola, 2004), while
CMRO2 is a fundamental neuroenergetic measure of workload
(Hyder & Rothman, 2012). In the sections in the succeeding text,
we outline the primary quantitative MRI methods that have been
developed to measure these three key physiological parameters.
Quantitative fMRI Methods

Cerebral Blood Flow
The brains ability to spatially and temporally regulate its perfusion via neurovascular coupling makes this physiological quantity an obvious target for quantitative fMRI. While CBF can be
measured using a bolus injection of an exogenous contrast agent
and tracer kinetic modeling, this approach is not well suited to
functional imaging because it is invasive, very limited in temporal resolution, and not capable of many repeated measurements. The dominant method for functional perfusion imaging
in humans is arterial spin labeling (ASL see Figure 1), in which
arterial blood water is magnetically labeled (e.g., inverted) in the
upstream vasculature and allowed to flow into the imaging
region and exchange with unlabeled tissue water (Detre, Leigh,
Williams, & Koretsky, 1992; Williams, Detre, Leigh, & Koretsky,
1992). Acquiring two such datasets, with and without upstream
labeling (often called tag and control images), and subtracting
the two produce an image with perfusion-dependent intensity.
Quantitative CBF maps (typically expressed in units of ml
100 ml1 min1) can be derived from these perfusion images
if blood and tissue relaxation times are known and label duration and transit delays are carefully controlled for (Buxton,
2005; Detre, Wang, Wang, & Rao, 2009). While there are
many different implementations of ASL, the methods can generally be classified according to how the magnetic labeling is
performed: pulsed (pASL), continuous (cASL), and pseudocontinuous (pcASL).
Validation of the ASL-based CBF measurement has been
performed using PET (Chen, Wieckowska, Meyer, & Pike,
2008; Feng et al., 2004; Ye et al., 2000) in humans and autoradiography (Ewing, Cao, Knight, & Fenstermacher, 2005) and
microsphere techniques (Walsh, Minematsu, Leppo, & Moore,
1994) in animals. Despite the fact that ASL can provide quantitative CBF measures for functional brain mapping, it has not
been as widely adopted as BOLD fMRI due to technical issues
that have historically limited spatial coverage, temporal resolution, and signal-to-noise ratio (SNR). While improvements
to ASL continue to be developed, its fundamentally lower SNR
means that it is less sensitive than BOLD for qualitative brain
mapping. However, because it is a very specific and quantitative measure, it has been of enormous value in a multitude of
important studies exploring the physiology of neuronal activation and deactivation and the biophysical underpinnings of
the BOLD signal.
Cerebral Blood Volume

CBV changes associated with neuronal activity modulations
are believed to be both active, via the smooth muscle in the
arteriolar wall and vascular pericytes, causing a change in the
Tag
31
Control
Figure 1 Illustration of the arterial spin-labeling (ASL) technique for imaging tissue perfusion. Two sets of images (blue) are acquired, one having an
upstream arterial region labeled (tag e.g., an inversion pulse) and the other not (control). By selecting an appropriate delay between tagging
and imaging, the subtraction of the two datasets produces images where the signal is proportional to perfusion (bottom panel).
arteriolar vascular resistance, and passive, via dilation (constriction) of the venules and veins due to the increase
(decrease) in perfusion pressure (Guyton & Hall, 1996). Volume change at the capillary level is generally thought to be
small with the dominant consequence of upstream regulation
being a change in blood velocity. The active side is driven by a
multitude of neurovascular signaling mechanisms that produce the highly spatially specific response, which is exploited
for functional brain mapping.
While measurement of CBV change was the basis of the first
MRI study to map human brain function (Belliveau et al.,
1991), the technique used was dynamic susceptibility contrast
imaging, which has major shortcomings for functional imaging since it requires bolus injections of gadoliniumDTPA
during rest and stimulation conditions. Steady-state imaging
using long intravascular half-life exogenous contrast agents
(e.g., iron oxide nanoparticle-based agents) alleviates the
requirement for multiple injections and permits dynamic monitoring of CBV changes (Dunn et al., 2004; Kida, Rothman, &
Hyder, 2007; Lu, Soltysik, et al., 2005; Mandeville et al., 1999,
1998; Zhao, Wang, Hendrich, & Kim, 2005; Zhao, Wang,
Hendrich, Ugurbil, & Kim, 2006). However, to date, iron
oxide-based CBV measurements have been limited to animal
studies. Furthermore, this method reflects total blood plasma
volume and does not distinguish between arterial, capillary,

and venous compartments. This is an important point in the
context of understanding and calibrating the BOLD signal since
the primary BOLD effect is the change in dHb content, which is
normally dominated by changes in the postarteriolar vascular
compartments.
Alternate approaches to using an exogenous contrast agent
have been introduced in recent years that have allowed functional CBV mapping and quantitation. The simplest approach,
termed vascular space occupancy (VASO; Lu, Law, et al., 2005),
exploits the T1 relaxation time difference between blood and
tissue using an inversion recovery sequence to null the signal
from blood. Decreases in the residual VASO signal are assumed
to reflect increases in CBV but absolute quantitation requires
knowledge of the baseline CBV. Care must also be taken to
account for the potential influences of inflowing spins
(Donahue, Hua, Pekar, & van Zijl, 2009) and CSF volume
changes (Scouten & Constable, 2008). Furthermore, from the
perspective of BOLD calibration, it is important to note that
VASO is also sensitive to total CBV change. An alternate
approach that is sensitive to deoxygenated CBV (CBVV, primarily capillary and venous compartments) exploits bloods unique
spinspin relaxation properties, as a function of spin-echo
refocusing interval and oxygen saturation (Chen & Pike, 2009;
32
Stefanovic & Pike, 2004; Thulborn et al., 1982; Wright, Hu, &
Macovski, 1991; Zhao, Clingman, Narvainen, Kauppinen, & van
Zijl, 2007) and is termed venous refocusing for volume
estimation (Stefanovic & Pike, 2005). While this technique can
be used as a standalone method for functional brain mapping, it
is a low SNR method and was developed and used primarily to
enhance our understanding of the CBFvenous CBV relationship for the purpose of BOLD signal modeling and calibration.
suited to functional brain mapping since it does not provide

spatial or temporal information.
Mapping CMRO2: Calibrated BOLD

The earliest method for producing images of changes in oxidative metabolism with fMRI signals was introduced by Davis,
Kwong, Weisskoff, and Rosen (1998). The approach, termed
calibrated fMRI, was based on measuring the relation between
the BOLD signal and the purely CBF-weighted signal, provided
by ASL, during application of an external vasodilatory stimulus
that did not alter tissue metabolism. Vasodilation was induced
by adding small amounts of carbon dioxide (CO2) to the air
breathed by subjects, leading to a state of relative hypercapnia.
As CO2 is a potent vasodilator, even the relatively small
amounts added in this calibration procedure (e.g., 5% by
volume) lead to robust changes in BOLD and ASL signals.
The BOLDCBF relation observed during hypercapnia can be
compared to the BOLDCBF relation observed during a task,
with the expectation that any increase in CMRO2 during activation would result in a lower BOLD signal at a given value of
CBF (due to increased conversion of diamagnetic HbO to
paramagnetic dHb associated with increased metabolic
demands). In fact, the BOLDCBF relation observed during
hypercapnia can be fitted to a biophysical model, termed the
dHb dilution model by Hoge et al. (1999a), that describes
fractional changes in the BOLD signal as

!
DBOLD
CMRO2
CBF ab
M 1
CMRO2 j0
BOLD0
CBF0
Cerebral Metabolic Rate of Oxygen

The hemodynamic functional response associated with neurovascular coupling is the key mechanism of detection for many
functional imaging modalities but does not provide direct
information on energetic workload. For neuroenergetics, glucose and oxygen metabolism rates are the primary measures
and the latter is accessible noninvasively via MRI. Outlined in
the succeeding text are the three general approaches to measurement of the CMRO2 using MRI.
Whole-brain CMRO2 measurement

Given basic mass conservation, in the form of the Fick principle
(Figure 2), we can determine that CMRO2 CBF Ca(Ya Yv),
where Ca is the amount of oxygen per unit volume of blood
and Ya and Yv are the arterial and venous oxygen saturation,
respectively (Kety & Schmidt, 1948). Whole-brain CBF can be
measured using ASL or, more simply, using quantitative phasecontrast flow imaging (Pelc, 1995) in the internal carotid and
vertebral arteries. Blood oximetry can be performed in vivo in
macroscopic vessels, such as the sagittal sinus and jugular veins,
using T2 relaxometry (Chen & Pike, 2010a; Lu & Ge, 2008) and
experimental reference data for bloods T2 (Chen & Pike, 2009;
Thulborn et al., 1982; Zhao et al., 2007). This approach has
been used to study whole-brain CMRO2 responses to hyper- and
hypocapnia (Chen & Pike, 2010a), variations across the life
span (Lu et al., 2011), and changes in diseases such as multiple
sclerosis patients (Ge et al., 2012). Although this approach to
oxygen metabolism measurement is fast, robust, and potentially
quite valuable (e.g., assessing vasoactive pharmacological
manipulations or certain clinical conditions), it is not well
where the subscript 0 represents baseline value of a variable, a

relates CBV to CBF changes via the Grubb relationship (CBV/
CBV0 (CBF/CBF0)a) with a having a value in the range of
0.20.4 (Chen & Pike, 2010b; Grubb, Phelps, & Eichling,
1974), and the exponent b represents the nonlinear dependence
of R2* on the concentration of dHb and is normally assumed to
be in the range of 11.5 (Boxerman et al., 1995). The result of
fitting this model to the BOLD and CBF data acquired during
hypercapnia (where CMRO2 is assumed constant; Chen & Pike,
2010a) is the estimation of the calibration constant M, which
represents the maximal BOLD signal increase that would be
observed upon complete elimination of dHb from all vascular
CBF, Ya
Input O2 = CBF Ca Ya
Yv
Return O2 = CBF Ca Yv
CMRO2 = CBF Ca (YaYv)

Figure 2 Illustration of the Fick principle for the MRI-based measurement of the whole-brain CMRO2. CBF can be measured using phase-contrast flow
imaging in the internal carotid and vertebral arteries and Y can be measured using MRI-based oximetry. Ca is the amount of O2 per unit volume of
fully saturated blood (Y 100%).
33
M
CMRO2
BOLD/BOLD0
BOLD/BOLD0
Asymptotic regime
non-linear
regime
CMRO2+
Linear
regime
0
0
(a)
2
3
CBF/CBF0
(b)
2
3
CBF/CBF0
Figure 3 Graphical representation of the dHb dilution model relating BOLD signal, CBF, and CMRO2 (Hoge et al., 1999a). (a) Curve for an iso-metabolic
CBF manipulation such as hypercapnia. (b) Family of curves for different levels of CMRO2 above and below the resting metabolism curve
(dark solid line).
compartments of the tissue (i.e., M is the asymptotic maximal

BOLD signal in Figure 3). Activation-related CMRO2 changes
can then be estimated from the measured BOLD and CBF
signals by inverting the dHb dilution model.
Subsequent calibration methods have used alternatives to
hypercapnia to determine the BOLDCBF relation at baseline
CMRO2. In particular, the technique developed by Bulte and
collaborators at Oxford University (Chiarelli, Bulte, Wise,
Gallichan, & Jezzard, 2007) estimates M by measuring BOLD
signal increases during hyperoxia, which also reduces venous
dHb levels. Additional respiratory measures, which reflect arterial O2 content, are used to model the associated fractional
change in venous dHb concentration instead of relying on a
CBF change as in the Davis hypercapnic method (Mark, Fisher,
& Pike, 2011). Both the original Davis hypercapnic approach
and the hyperoxic variation have since been used in a number
of studies that have provided important information about
vascularmetabolic coupling during sensory stimulation in
the healthy brain (Hoge et al., 1999b), during performance
of executive functions across the human life span (Gauthier
et al., 2013; Mohtasib et al., 2012), and in diseases such as
epilepsy (Stefanovic et al., 2005).
While the original hypercapnic and hypoxic calibration
approaches provide relative quantification in the form of the
percent change in oxygen consumption during a task, they do
not provide absolute quantification of resting CMRO2. Recent
developments have addressed this limitation, allowing absolute quantification of resting CMRO2 in units of mmol
100 g1 min1 (in addition to the M parameter of prior
method) using a combination of hypercapnic and hyperoxic
manipulations (Bulte et al., 2012; Gauthier & Hoge, 2012;
Wise, Harris, Stone, & Murphy, 2013). The ability to quantify
resting CMRO2, in conjunction with other neurovascular
parameters, may have significant implications for studying
pathophysiological mechanisms in neurological diseases such
as Alzheimers and Parkinsons diseases.
Mapping CMRO2: Quantitative BOLD

While calibrated BOLD is a quantitative technique, the term
quantitative BOLD, or simply qBOLD, was coined by He and
Yablonskiy (He & Yablonskiy, 2007). Their technique is based

on a comprehensive multi-compartment brain tissue model
including intracellular water, extracellular water, and intravascular blood, coupled with a detailed analysis of R2*. Specifically, they used multivariate curve fitting of data collected with
a combined gradient-echo and spin-echo sequence to estimate
parameters such as the deoxygenated blood volume (DBV) and
oxygen extraction fraction (OEF), which were shown to be
consistent with literature values (Yablonskiy, 1998). While
the modeling is complex and the number of fitted parameters
large, the technique is of considerable potential interest and
further investigations and validations of the approach are
appearing (Christen et al., 2010; Dickson et al., 2010; He,
Zhu, & Yablonskiy, 2008).
Conclusions
BOLD fMRI has transformed neuroscience research by providing a safe, sensitive, and widely accessible technique to map
brain function. Nonetheless, the BOLD signal is an indirect
measure of neuronal activity with a complex dependence upon
changes in CBF, blood volume, and oxygen consumption. It
has therefore primarily been used as a qualitative technique to
detect where activity occurs. However, MRI methods are now
available to quantitatively measure CBF and volume and when
combined with biophysical models and calibration techniques
can provide quantitative measures of oxygen metabolism.
These techniques are of enormous value in studying the brain
in health and disease because they can provide measures of
both neurovascular and neuroenergetic responses.
Acknowledgments
GBPs work in the area of quantitative fMRI is supported by the
Canadian Institutes of Health Research, the Canadian Foundation for Innovation, Fonds de la recherche en sante du Quebec,
and the Killam Foundation. RDH wishes to acknowledge the
Canadian Institutes for Health Research, the Canadian
34
Foundation for Innovation, the Canadian National Sciences

and Engineering Research Council, and the Quebec Consortium for Drug Discovery. The authors also thank Dr. Erin
Mazerolle for critical reading of this article.
See also: INTRODUCTION TO ACQUISITION METHODS:

Contrast Agents in Functional Magnetic Resonance Imaging; EchoPlanar Imaging; Evolution of Instrumentation for Functional Magnetic
Resonance Imaging; fMRI at High Magnetic Field: Spatial Resolution
Limits and Applications; Functional MRI Dynamics; High-Field
Acquisition; High-Speed, High-Resolution Acquisitions; Molecular
fMRI; MRI and fMRI Optimizations and Applications; Perfusion Imaging
with Arterial Spin Labeling MRI; Pulse Sequence Dependence of the
fMRI Signal; Temporal Resolution and Spatial Resolution of fMRI;
INTRODUCTION TO ANATOMY AND PHYSIOLOGY: Cortical
GABAergic Neurons; The Resting-State Physiology of the Human
Cerebral Cortex; INTRODUCTION TO CLINICAL BRAIN
MAPPING: Cerebral Hemodynamics and Homeostatic Mechanisms;
Cerebral Oxygen Extraction Fraction in Carotid Occlusive Disease:
Measurement and Clinical Significance; INTRODUCTION TO
METHODS AND MODELING: Convolution Models for FMRI; Models
of fMRI Signal Changes.
References
Belliveau, J. W., Kennedy, D. N., McKinstry, R. C., Buchbinder, B. R., Weisskoff, R. M.,
Cohen, M. S., et al. (1991). Functional mapping of the human visual cortex by
magnetic resonance imaging. Science, 254, 716719.
Boxerman, J. L., Bandettini, P. A., Kwong, K. K., Baker, J. R., Davis, T. L., Rosen, B. R.,
et al. (1995). The intravascular contribution to fMRI signal change: Monte Carlo
modeling and diffusion-weighted studies in vivo. Magnetic Resonance in Medicine,
34, 410.
Bulte, D. P., Kelly, M., Germuska, M., Xie, J., Chappell, M. A., Okell, T. W., et al. (2012).
Quantitative measurement of cerebral physiology using respiratory-calibrated MRI.
Neuroimage, 60, 582591.
Buxton, R. B. (2005). Quantifying CBF with arterial spin labeling. Journal of Magnetic
Chen, J. J., & Pike, G. B. (2009). Human whole blood T2 relaxometry at 3 Tesla.
Chen, J. J., & Pike, G. B. (2010a). Global cerebral oxidative metabolism during
hypercapnia and hypocapnia in humans: Implications for BOLD fMRI. Journal of
Cerebral Blood Flow & Metabolism, 30, 10941099.
Chen, J. J., & Pike, G. B. (2010b). MRI measurement of the BOLD-specific flow-volume
relationship during hypercapnia and hypocapnia in humans. Neuroimage, 53,
383391.
Chen, J. J., Wieckowska, M., Meyer, E., & Pike, G. B. (2008). Cerebral blood flow
measurement using fMRI and PET: A cross-validation study. International Journal of
Biomedical Imaging, 2008, 112.
Chiarelli, P. A., Bulte, D. P., Wise, R., Gallichan, D., & Jezzard, P. (2007). A calibration
method for quantitative BOLD fMRI based on hyperoxia. Neuroimage, 37, 808820.
Christen, T., Lemasson, B., Pannetier, N., Farion, R., Segebarth, C., Remy, C., et al.
(2010). Evaluation of a quantitative blood oxygenation level-dependent (qBOLD)
approach to map local blood oxygen saturation. NMR in Biomedicine, 24, 393403.
Davis, T. L., Kwong, K. K., Weisskoff, R. M., & Rosen, B. R. (1998). Calibrated
functional MRI: Mapping the dynamics of oxidative metabolism. Proceedings
of the National Academy of Sciences of the United States of America, 95,
18341839.
Detre, J. A., Leigh, J. S., Williams, D. S., & Koretsky, A. P. (1992). Perfusion imaging.
Detre, J. A., Wang, J., Wang, Z., & Rao, H. (2009). Arterial spin-labeled perfusion MRI
in basic and clinical neuroscience. Current Opinion in Neurology, 22, 348355.
Dickson, J. D., Ash, T. W., Williams, G. B., Harding, S. G., Carpenter, T. A.,
Menon, D. K., et al. (2010). Quantitative BOLD: The effect of diffusion. Journal of
Donahue, M. J., Hua, J., Pekar, J. J., & van Zijl, P. C. (2009). Effect of inflow of fresh
blood on vascular-space-occupancy (VASO) contrast. Magnetic Resonance in
Medicine, 61, 473480.
Dunn, J. F., Roche, M. A., Springett, R., Abajian, M., Merlis, J., Daghlian, C. P., et al.
(2004). Monitoring angiogenesis in brain using steady-state quantification of
DeltaR2 with MION infusion. Magnetic Resonance in Medicine, 51, 5561.
Ewing, J. R., Cao, Y., Knight, R. A., & Fenstermacher, J. D. (2005). Arterial spin
labeling: Validity testing and comparison studies. Journal of Magnetic Resonance
Imaging, 22, 737740.
Feng, C. M., Narayana, S., Lancaster, J. L., Jerabek, P. A., Arnow, T. L., Zhu, F., et al.
(2004). CBF changes during brain activation: fMRI vs. PET. Neuroimage, 22,
443446.
Fox, P., & Raichle, M. (1986). Focal physiological uncoupling of cerebral blood flow
and oxidative metabolism during somatosensory stimulation in human subjects.
Proceedings of the National Academy of Sciences of the United States of America,
83, 11401144.
Gauthier, C. J., & Hoge, R. D. (2012). Magnetic resonance imaging of resting OEF and
CMRO(2) using a generalized calibration model for hypercapnia and hyperoxia.
Gauthier, C. J., Madjar, C., Desjardins-Crepeau, L., Bellec, P., Bherer, L., & Hoge, R. D.
(2013). Age dependence of hemodynamic response characteristics in human
functional magnetic resonance imaging. Neurobiology of Aging, 34, 14691485.
Gauthier, C. J., Madjar, C., Tancredi, F. B., Stefanovic, B., & Hoge, R. D. (2011).
Elimination of visually evoked BOLD responses during carbogen inhalation:
Implications for calibrated MRI. Neuroimage, 54, 10011011.
Ge, Y., Zhang, Z., Lu, H., Tang, L., Jaggi, H., Herbert, J., et al. (2012). Characterizing brain
oxygen metabolism in patients with multiple sclerosis with T2-relaxation-underspin-tagging MRI. Journal of Cerebral Blood Flow & Metabolism, 32, 403412.
Grubb, R. L., Phelps, M. E., & Eichling, J. O. (1974). The effects of vascular changes in
PaCO2 on cerebral blood volume, blood flow and vascular mean transit time. Stroke,
5, 630639.
Guyton, A. C., & Hall, J. E. (1996). Textbook of medical physiology. Philadelphia, PA:
W.B. Saunders.
Hall, E. L., Driver, I. D., Croal, P. L., Francis, S. T., Gowland, P. A., Morris, P. G., et al.
(2011). The effect of hypercapnia on resting and stimulus induced MEG signals.
He, X., & Yablonskiy, D. A. (2007). Quantitative BOLD: Mapping of human cerebral
deoxygenated blood volume and oxygen extraction fraction: Default state. Magnetic
He, X., Zhu, M., & Yablonskiy, D. A. (2008). Validation of oxygen extraction fraction
measurement by qBOLD technique. Magnetic Resonance in Medicine, 60, 882888.
Hoge, R. D., Atkinson, J., Gill, B., Crelier, G. R., Marrett, S., & Pike, G. B. (1999a).
Investigation of BOLD signal dependence on cerebral blood flow and oxygen
consumption: The deoxyhemoglobin dilution model. Magnetic Resonance in
Medicine, 42, 849863.
Hoge, R. D., Atkinson, J., Gill, B., Crelier, G. R., Marrett, S., & Pike, G. B. (1999b).
Linear coupling between cerebral blood flow and oxygen consumption in activated
human cortex. Proceedings of the National Academy of Sciences of the United
States of America, 96, 94039408.
Hyder, F., & Rothman, D. L. (2012). Quantitative fMRI and oxidative neuroenergetics.
Iadecola, C. (2004). Neurovascular regulation in the normal brain and in Alzheimers
disease. Nature Reviews Neuroscience, 5, 347360.
Kety, S. S., & Schmidt, C. F. (1948). The effects of altered arterial tensions of carbon
dioxide and oxygen on cerebral blood flow and cerebral oxygen consumption of
normal young men. Journal of Clinical Investigation, 27, 484492.
Kida, I., Rothman, D. L., & Hyder, F. (2007). Dynamics of changes in blood flow,
volume, and oxygenation: Implications for dynamic functional magnetic resonance
imaging calibration. Journal of Cerebral Blood Flow & Metabolism, 27, 690696.
Kwong, K. K., Belliveau, J. W., Chesler, D. A., Goldberg, I. E., Weisskoff, R. M.,
Poncelet, B. P., et al. (1992). Dynamic magnetic resonance imaging of human brain
activity during primary sensory stimulation. Proceedings of the National Academy of
Sciences of the United States of America, 89, 56755679.
Lu, H., & Ge, Y. (2008). Quantitative evaluation of oxygenation in venous vessels using
T2-Relaxation-Under-Spin-Tagging MRI. Magnetic Resonance in Medicine, 60,
357363.
Lu, H., Golay, X., Pekar, J. J., & Van Zijl, P. C. (2003). Functional magnetic resonance
imaging based on changes in vascular space occupancy. Magnetic Resonance in
Medicine, 50, 263274.
Lu, H., Law, M., Johnson, G., Ge, Y., van Zijl, P. C., & Helpern, J. A. (2005). Novel
approach to the measurement of absolute cerebral blood volume using vascularspace-occupancy magnetic resonance imaging. Magnetic Resonance in Medicine,
54, 14031411.

Lu, H., Soltysik, D. A., Ward, B. D., & Hyde, J. S. (2005). Temporal evolution of the
CBV-fMRI signal to rat whisker stimulation of variable duration and intensity: A
linearity analysis. Neuroimage, 26, 432440.
Lu, H., Xu, F., Rodrigue, K. M., Kennedy, K. M., Cheng, Y., Flicker, B., et al. (2011).
Alterations in cerebral metabolic rate and blood supply across the adult lifespan.
Cerebral Cortex, 21, 14261434.
Mandeville, J. B., Marota, J. J., Ayata, C., Zaharchuk, G., Moskowitz, M. A.,
Rosen, B. R., et al. (1999). Evidence of a cerebrovascular postarteriole windkessel
with delayed compliance. Journal of Cerebral Blood Flow and Metabolism, 19,
679689.
Mandeville, J. B., Marota, J. J., Kosofsky, B. E., Keltner, J. R., Weissleder, R.,
Rosen, B. R., et al. (1998). Dynamic functional imaging of relative cerebral blood
volume during rat forepaw stimulation. Magnetic Resonance in Medicine, 39,
615624.
Mansfield, P. (1977). Multi-planar image formation using NMR spin echoes. Journal of
Physics C, 10, L55L58.
Mark, C. I., Fisher, J. A., & Pike, G. B. (2011). Improved fMRI calibration:
Precisely controlled hyperoxic versus hypercapnic stimuli. NeuroImage, 54,
11021111.
Marrett, S., & Gjedde, A. (1997). Changes of blood flow and oxygen consumption in
visual cortex of living humans. Advances in Experimental Medicine and Biology,
413, 205208.
Mohtasib, R. S., Lumley, G., Goodwin, J. A., Emsley, H. C., Sluming, V., & Parkes, L. M.
(2012). Calibrated fMRI during a cognitive Stroop task reveals reduced metabolic
response with increasing age. Neuroimage, 59, 11431151.
Ogawa, S., Tank, D. W., Menon, R., Ellermann, J. M., Kim, S.-G., Merkle, H., et al.
(1992). Intrinsic signal changes accompanying sensory stimulation: Functional
brain mapping with magnetic resonance imaging. Proceedings of the National
Academy of Sciences of the United States of America, 89, 59515955.
Pauling, L., & Coryell, C. D. (1936). The magnetic properties and structure of
hemoglobin, oxyhemoglobin, and carbonmonoxyhemoglobin. Proceedings of the
National Academy of Sciences of the United States of America, 22, 210216.
Pelc, N. J. (1995). Flow quantification and analysis methods. Magnetic Resonance
Imaging Clinics of North America, 3, 413424.
Scouten, A., & Constable, R. T. (2008). VASO-based calculations of CBV change:
Accounting for the dynamic CSF volume. Magnetic Resonance in Medicine, 59,
308315.
Stefanovic, B., & Pike, G. B. (2004). Human whole-blood relaxometry at 1.5 T:
Assessment of diffusion and exchange models. Magnetic Resonance in Medicine,
52, 716723.
35
Stefanovic, B., & Pike, G. B. (2005). Venous refocusing for volume estimation: VERVE
functional magnetic resonance imaging. Magnetic Resonance in Medicine, 53,
339347.
Stefanovic, B., Warnking, J. M., Kobayashi, E., Bagshaw, A. P., Hawco, C., Dubeau, F.,
et al. (2005). Hemodynamic and metabolic responses to activation, deactivation and
epileptic discharges. Neuroimage, 28, 205215.
Thulborn, K. R., Waterton, J. C., Matthews, P. M., & Radda, G. K. (1982). Oxygenation
dependence of the transverse relaxation time of water protons in whole blood at high
field. Biochimica et Biophysica Acta, 714, 265270.
Walsh, E. G., Minematsu, K., Leppo, J., & Moore, S. C. (1994). Radioactive
microsphere validation of a volume localized continuous saturation perfusion
measurement. Magnetic Resonance in Medicine, 31, 147153.
Williams, D. S., Detre, J. A., Leigh, J. S., & Koretsky, A. P. (1992). Magnetic
resonance imaging of perfusion using spin inversion of arterial water.
89, 212216.
Wise, R. G., Harris, A. D., Stone, A. J., & Murphy, K. (2013). Measurement of OEF and
absolute CMRO: MRI-based methods using interleaved and combined hypercapnia
and hyperoxia. Neuroimage, 83C, 135147.
Wright, G. A., Hu, B. S., & Macovski, A. (1991). Estimating oxygen saturation of blood
in vivo with MR imaging at 1.5 T. Journal of Magnetic Resonance Imaging, 1,
275283.
Yablonskiy, D. A. (1998). Quantitation of intrinsic magnetic susceptibility-related
effects in a tissue matrix. Phantom study. Magnetic Resonance in Medicine, 39,
417428.
Ye, F. Q., Berman, K. F., Ellmore, T., Esposito, G., van Horn, J. D., Yang, Y., et al.
(2000). H(2)(15)O PET validation of steady-state arterial spin tagging cerebral blood
flow measurements in humans. Magnetic Resonance in Medicine, 44, 450456.
Zappe, A. C., Uludag, K., Oeltermann, A., Ugurbil, K., & Logothetis, N. K. (2008). The
influence of moderate hypercapnia on neural activity in the anesthetized nonhuman
primate. Cerebral Cortex, 18, 26662673.
Zhao, J. M., Clingman, C. S., Narvainen, M. J., Kauppinen, R. A., & van Zijl, P. C.
(2007). Oxygenation and hematocrit dependence of transverse relaxation rates of
blood at 3 T. Magnetic Resonance in Medicine, 58, 592597.
Zhao, F., Wang, P., Hendrich, K., & Kim, S. G. (2005). Spatial specificity of cerebral
blood volume-weighted fMRI responses at columnar resolution. Neuroimage, 27,
416424.
Zhao, F., Wang, P., Hendrich, K., Ugurbil, K., & Kim, S. G. (2006). Cortical layerdependent BOLD and CBV responses measured by spin-echo and gradient-echo
fMRI: Insights into hemodynamic regulation. Neuroimage, 30, 11491160.
Contrast Agents in Functional Magnetic Resonance Imaging

AC Silva, National Institutes of Health, Bethesda, MD, USA
Published by Elsevier Inc.
Glossary
Arterial spin labeling (ASL) Refers to the use of

endogenous arterial water as a perfusion tracer in MRI
measurements of blood flow.
Blood oxygenation level dependent (BOLD) The main
source of contrast in functional MRI experiments, in which
the local MR signal varies according to the oxygenation level
of the vasculature.
Continuous ASL (CASL) A form of ASL technique in which
endogenous arterial water is continually labeled prior to
arriving at the organ of interest.
Cerebral blood flow (CBF) The amount of blood flowing
through the cerebral vasculature, expressed in [ml of blood
per 100 g tissue per min].
Cerebral blood volume (CBV) The volume of the cerebral
vasculature, expressed in [ml of blood per 100 g tissue].
Dynamic susceptibility contrast (DSC) A type of MRI
experiment in which a contrast agent is injected into the
vasculature to cause a change in the MRI signal. As blood
carries the contrast agent in the circulation, a dynamic
variation in the MRI signal is produced that allows
measurement of CBF, CBV, and mean transit time (MTT)
from the site of injection to the organ of interest.
Functional MRI (fMRI) A type of MRI experiment in which
brain function is probed by observing the spatiotemporal
changes in MR signal caused by local changes in CBF, CBV,
or BOLD contrast.
Introduction
Since its inception in the early 1990s (Belliveau et al., 1991;
Kwong et al., 1992; Menon et al., 1992; Ogawa, Lee, Kay, &
Tank, 1990; Ogawa, Lee, Nayak, & Glynn, 1990; Ogawa et al.,
1992; Turner, 1992), functional magnetic resonance imaging
(fMRI) has had a tremendous impact in our understanding of
the brain. fMRI measures the regional changes in cerebral
blood flow (CBF), cerebral blood volume (CBV), and blood
oxygenation that occur in response to focal changes in neural
activity. What makes fMRI sensitive to the brain hemodynamics is the clever use of both endogenous and exogenous contrast agents, compounds that change the intrinsic relaxation
rates of blood and tissue, to create a functionally specific signal
directly associated with the physiological quantity of interest.
The purpose of this article is to provide the reader with a
glimpse of the main contrast agents used in fMRI today, with
particular emphasis on the mechanism of contrast and on how
the contrast alters the MRI signal in a way to make it sensitive
to the hemodynamic quantity of interest. In the first session,
the endogenous sources of contrast in fMRI, hemoglobin, and
arterial water are described. Hemoglobin is unique in being the
only endogenous contrast that is sensitive to blood
Gadolinium diethylene-triamine-penta-acetate
(Gd-DTPA) An MRI contrast agent used to cause local
changes in the water relaxation properties and useful to
enhance contrast in the vasculature or to detect lesions in
the brain.
Magnetization transfer (MT) Refers to the transfer of
magnetization due to the exchange of free hydrogen ions in
water with hydrogen ions bound to macromolecules in the
tissue.
Mean transit time (MTT) The average time it takes for the
contrast agent to travel from the site of injection to the organ
of interest.
Pulsed ASL (PASL) A form of ASL technique in which
endogenous arterial water is labeled in discrete intervals
interleaved with image acquisition.
Pseudo-continuous ASL (pCASL) A form of ASL technique
in which endogenous arterial water is labeled by a series of
discrete but contiguous labeling pulses prior to image
acquisition.
Superparamagnetic iron oxide nanoparticles
(SPIO) Nanoparticles of iron oxide that have
superparamagnetic properties and that act as an MRI
contrast agent.
VAscular-Space-Occupancy (VASO) An MRI technique
based on measuring the space occupied by the cerebral
vasculature as a way to estimate CBV.
oxygenation, and it is the source of contrast for BOLD fMRI.

Arterial water, on the other hand, can be used to quantify both
CBF and CBV. The second session addresses the use of exogenously administered contrast agents, such as the paramagnetic
gadolinium chelates, and the superparamagnetic iron oxide
(SPIO) nanoparticles. Gadolinium compounds had an early
and very important role in the development of fMRI and
quickly became a well-established source of contrast for perfusion imaging in clinical practice. SPIO nanoparticles, on the
other hand, are poised to become the exogenous agent of
choice for measurements of CBV, due to their long half-life in
blood.
Intrinsic Contrast Agents in fMRI

Hemoglobin, the Endogenous Source of Contrast for BOLD
fMRI
The source of contrast for BOLD fMRI is hemoglobin,
an oxygen-binding tetramer protein of molecular weight
64 450 Da (Hill, Konigsberg, Guidotti, & Craig, 1962). Hemoglobin has a quaternary structure formed by four subunits
(2 a and 2 b) bound noncovalently (Figure 1(a)). Each
http://dx.doi.org/10.1016/B978-0-12-397025-1.00004-X
37
38
INTRODUCTION TO ACQUISITION METHODS | Contrast Agents in Functional Magnetic Resonance Imaging
CH2
1
CH3
CH2
H3C
N
N
Fe2+
N
CH3
H3C
2
O
(a)
(b)
OH
OH
100
90
80
SO2 (%)
70
60
50
40
30
20
10
0
(c)
20
40
60
PO2 (mmHg)
80
100
120
Figure 1 (a) 3-D structure of the hemoglobin molecule showing the four subunits in different colors. Within each subunit, the heme molecule is
shown in red. (b) Chemical diagram of the heme molecule showing the iron (Fe2) ion (charged atom) in coordination with four nitrogen atoms in the
center of the porphyrin ring. The iron ion reversibly binds an oxygen molecule. (c) Oxygen dissociation curve for hemoglobin, showing the oxygen
saturation (SO2) of hemoglobin as a function of the partial pressure of oxygen (PO2) in blood. Because of the cooperative binding, the affinity of
hemoglobin for oxygen increases as successive molecules of oxygen bind, until the maximum amount of four oxygen molecules per molecule
of hemoglobin is reached. Thus, the oxygen dissociation curve is relatively flat for PO2 > 80 mmHg. As the PO2 decreases, the affinity of hemoglobin
decreases and oxygen is released to tissue.
subunit contains a heme group (Figure 1(b)) and a globin

chain. The heme group is made of a porphyrin ring containing
an iron (Fe) ion in its center. The iron ion, usually in the
ferrous (Fe2) state, is the site of oxygen binding.
Hemoglobin is the main protein in red blood cells (RBC),
making for almost 97% of the RBCs dry weight contents
(Weed, Reed, & Berg, 1963). Its main function is to carry
oxygen from the lungs to all tissues in the body, and it does
so with an oxygen-carrying capacity of 1.37 ml O2 g1
(Dijkhuizen et al., 1977), which is much higher than the
oxygen dissolved in blood plasma. Oxygen binds reversibly
to the heme iron via a cooperative process driven by the partial
saturation of oxygen in which oxygenation of one subunit
induces a conformational change of the entire protein and
increases the binding affinity of the other subunits for oxygen.
As a consequence, hemoglobin becomes rapidly saturated with
oxygen in the lungs, where the partial saturation of oxygen is
high, and it rapidly releases oxygen at the tissues, where the
partial saturation of oxygen is low. This can be well appreciated
in the oxygen dissociation curve for hemoglobin shown in

Figure 1(c). Because of this cooperative binding/unloading
process, hemoglobin exists in the vasculature in two states
only, fully oxygenated (HbO2, oxyhemoglobin) or deoxygenated (Hb, deoxyhemoglobin).
Binding of oxygen changes the magnetic properties of the
heme iron (Pauling & Coryell, 1936). The main property of
interest to BOLD contrast is the susceptibility of blood, which
is strongly determined by the blood oxygenation level Y. It can
be shown that the susceptibility of blood, wblood, can be
expressed as a function of the susceptibility of RBC, wRBC, and
the blood hematocrit Hct by the expression (Spees, Yablonskiy,
Oswood, & Ackerman, 2001; Weisskoff & Kiihne, 1992)
wblood HctwRBC 1 Hctwplasma
[1]
Because the percentage of water in plasma is 93%, the

susceptibility of plasma wplasma 0.722 ppm is only slightly
different than the susceptibility of water, wH2 O 0:719 ppm
39
Blood oxygenation level Y (%)

2
10
20
30
40
50
60
70
80
90
100
35%
40%
cblood (ppm)
45%
50%
55%
6
8
10
12
14
16
Figure 2 Plot of the blood susceptibility Dwblood as a function of the blood oxygenation level Y for several different levels of Hct. The susceptibility
of blood is a direct magnetic indicator of the blood oxygenation level. Changes in local susceptibility with blood oxygenation alter the MRI signal,
forming the basis of the BOLD contrast in fMRI.
(Spees et al., 2001). The susceptibility of RBC, on the other

hand, can be described in terms of the blood oxygenation level
Y as (Spees et al., 2001; Yablonskiy, Sukstanskii, & He, 2013)
(in ppm)
wRBC Y 0:2641 Y 0:736
[2a]
or, relative to the susceptibility of water (in ppm),

DwRBC Y wRBC Y wH2 O 0:2641 Y 0:017
[2b]
In the deoxygenated state (Y 0), the heme Fe ion is

paramagnetic, presenting a positive magnetic susceptibility, relative to that of pure water, DwHb DwRBC(0) 0.247 ppm, due
to the presence of unpaired electrons (Jain, Abdulmalik, Propert,
& Wehrli, 2012; Thulborn, Waterton, Matthews, & Radda, 1982;
Weisskoff & Kiihne, 1992). On the other hand, in the oxygenated state (Y 1), the heme Fe2 ion changes to a low-spin state
and becomes diamagnetic, displaying a very small and negative
magnetic susceptibility, DwHbO2 DwRBC 1 0:017 ppm
(Jain et al., 2012; Thulborn et al., 1982; Weisskoff & Kiihne,
1992). Thus, the magnetic susceptibility of the heme Fe2 ion
serves as an endogenous, intrinsic biomarker of the blood oxygenation level within the tissues. Arterial blood is nearly fully
saturated with oxygen, and thus, hemoglobin is in the diamagnetic, low-spin state. As blood flows through the capillary network, oxygen is released to the tissue, causing hemoglobin to
switch to the paramagnetic, high-spin state as it is carried back to
the systemic circulation by the veins. This forms the basis of the
BOLD fMRI contrast.
Note that the susceptibility of RBC is a linear function of the
blood oxygenation level (eqn [2a] and [2b]). This linear
dependence of wRBC on Y is transmitted to the susceptibility
of blood. Substituting eqn [2] on eqn [1],
wblood Y Hctb0:2641 Y 0:736c
1 Hct0:722
or, relative to the susceptibility of water (in ppm),
[3a]
Dwblood Y wblood Y wH2 O

Hctb0:2641 Y 0:014c 0:003
[3b]
Figure 2 plots Dwblood as a function of the blood oxygenation

level Y for several different levels of Hct. Several conclusions can
be drawn from Figure 2. First, the susceptibility of blood is a
direct magnetic indicator of the blood oxygenation level. Second, within the normal range of blood oxygenation levels, from
65% at the veins to 100% in the arteries, the susceptibility of
blood varies by about 150%. Third, within the normal range of
hematocrits in adult humans (35% at the low end to 55% at
the high end), the susceptibility of blood varies by about 150%,
with higher susceptibilities corresponding to higher hematocrit
values. Finally, the change in local susceptibility with blood
oxygenation alters the MRI signal, and thus, the MRI signal
becomes sensitive to the blood oxygenation level.
The main effects of local changes in susceptibility are to
induce a shift of the resonance frequency Df and to alter the
transverse relaxation rates R2 and R2* (Duyn, 2013; Rosen,
Belliveau, Vevea, & Brady, 1990). Therefore, MRI sequences
sensitive to the transverse relaxation rates are typically used in
BOLD fMRI experiments (Norris, 2006). The two simplest MRI
techniques to sample signal changes induced by local variations in susceptibility are a gradient-echo (GE) sequence and a
spin-echo (SE) sequence. For either sequence, the MRI signal
can be described in terms of a signal attenuation function as
SSE t S0 ej2pDf t eR2 t
SGE t S0 ej2pDf t eR2 *t
R2 R20 R2, Hb , R2 * R20 * R2, Hb *
[4]
where R20(*) are the intrinsic relaxation rates and R2,Hb(*) are
the additional relaxation rates induced by deoxyhemoglobin.
Equation [4] implies that the signal decay can be described
by a simple exponential function, and this ignores contributions of water diffusion through inhomogeneous magnetic
fields and multiple compartment sources of signal dephasing
(Yablonskiy & Haacke, 1994; Yablonskiy et al., 2013).
40
Regardless of what sequence is used to acquire the data, the

total MRI signal will include contributions from both intraand extravascular compartments (Uludag, Muller-Bierl, &
Ugurbil, 2009):
X
CBV i SIV, i
Stotal 1 CBV SEV
i
SEV S0 ej2pDfEV TE eTER20, EV R2, Hb, EV

*
*
SIV, i S0, i ej2pDfIV TE eTER20, IV, i R2, Hb, IV, i
*
[5]
where i denotes the different vascular compartments (arteries,

arterioles, capillaries, venules, and veins). It is important to
separate the intravascular effects caused by RBC in blood
(Thulborn et al., 1982) from the extravascular effects caused
by blood vessels within the surrounding tissue (Ogawa, Lee,
Kay, & Tank, 1990; Ogawa, Lee, Nayak, & Glynn, 1990). For a
single blood vessel of radius R, angled by an angle y with
respect to the main magnetic field B0, the susceptibility effects
shift the water resonance frequency Df inside the blood vessel
(intravascular effects) and at a point of cylindrical coordinates
(r, f) (extravascular effects) by (Ogawa et al., 1993)

1
DfIV gB0 Dwblood Y cos 2 y
3
2
DfEV gB0 Dwblood Y Rr cos 2fsin 2 y
[6]
where g is the gyromagnetic ratio and Dwblood(Y) is the blood

susceptibility given by eqn [3b]. It is important to notice that
the frequency shift induced by local changes in susceptibility is
proportional to the strength of the magnetic field B0, to the
deoxyhemoglobin content (via Dwblood(Y)), and to the radius
of the blood vessel R. For a network of randomly oriented
blood vessels, the voxel signal will integrate across the distribution of vessel orientations.
As blood vessels occupy only a few percent of the voxels
volume, on average, it is reasonable to assume that the tissue
relaxation rates R2,EV(*) will not be significantly affected by the
presence of deoxyhemoglobin (i.e., R2,EV(*) R20,EV(*)). It has
been shown that R20,EV(*) vary linearly with the magnetic field
strength (Uludag et al., 2009). On the other hand, deoxyhemoglobin significantly alters the intravascular relaxation
rates R2,IV and R2,IV*, which have been shown to have a quadratic dependence on Y (Silvennoinen, Clingman, Golay,
Kauppinen, & Van Zijl, 2003; Spees et al., 2001; Thulborn
et al., 1982; Uludag et al., 2009; Yablonskiy et al., 2013;
Zhao, Clingman, Narvainen, Kauppinen, & Van Zijl, 2007):
R2, IV R20, IV C1 Y 2 , R2*, IV R20
* , IV C*1 Y 2
[7]
where C and C* are constants that depend on the concentration

of hemoglobin, hematocrit, and the magnetic field strength.
The amplitude of the MRI signal described by eqn [4] may be
attenuated by two different dephasing mechanisms, one static
and the other dynamic (Norris, 2006; Ogawa et al., 1993;
Yablonskiy & Haacke, 1994). In the static dephasing regime,
spins lose phase coherence via a classical positional mechanism
in the presence of external static spatial field inhomogeneities.
This spin dephasing leads to a signal loss that can be reversed in
the SE sequence but not in the GE sequence. In the dynamic
dephasing regime, spins experience diffusion in the presence of
external static spatial field inhomogeneities, leading to irreversible
dephasing and signal loss. Therefore, the combination of
intravascular and extravascular effects with either static or

dynamic dephasing regimes leads to four main but separate
contrast mechanisms in BOLD fMRI that affect both the magnitude of signal changes and their spatial localization (Boxerman
et al., 1995; Diekhoff et al., 2011; Kim & Ogawa, 2012; Norris,
2006; Ogawa, Menon, Kim, & Ugurbil, 1998; Ogawa et al., 1993;
Uludag et al., 2009; Yablonskiy & Haacke, 1994; Yablonskiy et al.,
2013). The intravascular static dephasing comes about when a
large number of randomly oriented blood vessels within a voxel
experience different frequency offsets DfIV. The intravascular
dynamic dephasing comes from interactions between blood
water within the RBC and that in the plasma. Both intravascular
effects come primarily from venules and veins downstream from
the site of neural activity in the postcapillary vasculature
(Boxerman et al., 1995; Ogawa et al., 1998, 1993; Yablonskiy &
Haacke, 1994). The extravascular dynamic dephasing occurs in
the capillary bed and small venules closest to the site of neural
activity, while the extravascular static dephasing occurs in larger
venules and veins (Boxerman et al., 1995; Kim & Ogawa, 2012;
Ogawa et al., 1998). It is important to notice that while a GRE
sequence is sensitive to all four mechanisms, the SE sequence will
not be sensitive to either the intravascular or the extravascular
static dephasing mechanisms.
Arterial Water, the Endogenous Source of Contrast

for CBF fMRI
The endogenous source of contrast for CBF-based fMRI is
arterial water, which can be magnetically labeled to differentiate its net magnetic polarization from that of brain tissue. As
arterial blood perfuses the tissue (Figure 3), water exchange
occurs, causing a net decrease in magnetization that is proportional to the local CBF rate. Therefore, CBF can be quantified
from the pairwise difference of two images acquired with and
without arterial spin labeling (ASL) (Detre, Leigh, Williams, &
Koretsky, 1992; Williams, Detre, Leigh, & Koretsky, 1992). In
ASL techniques, the lifetime of the label is given by the longitudinal relaxation time constant of arterial water, Tla, which
brings in the advantages of being long sufficient to allow
exchange between arterial water and tissue water prior to the
image acquisition, yet short enough that functional changes in
CBF can be monitored dynamically and repeatedly.
Quantification of CBF using ASL is based on measuring the
longitudinal magnetization in the tissue of interest (e.g., the
brain), considering relaxation, the delivery of new magnetization
by arterial blood flow, and clearance by venous outflow (Barbier,
Lamalle, & Decorps, 2001; Calamante, Thomas, Pell, Wiersma, &
Turner, 1999; Detre et al., 1992), and also loss due to cross
relaxation with tissue macromolecules (Figure 3; Silva, Zhang,
Williams, & Koretsky, 1997; Zhang, Silva, Williams, & Koretsky,
1995; Zhang, Williams, Detre, & Koretsky, 1992). The evolution
of the longitudinal tissue magnetization can be described by the
following Bloch equations (Silva et al., 1997; Zhang et al., 1995):
dMt t M0t Mt t
kfor Mt t krev Mm t f Ma t Mv t

dt
Tlt
0
dMm t Mm Mm t
krev Mm t kfor Mt t
dt
Tlm
[8]
where Mt(t) is the tissue longitudinal magnetization (expressed
per g of tissue), M0t is its equilibrium value, Tlt is the longitudinal
Arterial
water
f Ma(t)
(1-E(f))fMa(t)
Capillary water
fMv(t)
41
Venous
water
E(f)fMa(t)
Tissue water
kfor
krev
Macromolecular
water
Brain tissue
Figure 3 Schematic of the use of arterial water as a perfusion tracer. Within a voxel containing brain tissue and its associated vasculature, a fraction E
(f) of the arterial labeled water crosses the bloodbrain barrier and exchanges with tissue water, while the remaining arterial water flows to the
veins. Tissue water is in exchange with macromolecular protons. Tissue water also crosses the BBB to reach the veins.
relaxation time constant for tissue, Mm(t) is the macromolecules

longitudinal magnetization (expressed per g of tissue), M0m is its
equilibrium value, Tlm is the longitudinal relaxation time constant for macromolecules, f is the blood flow rate, Ma(t) is the
arterial longitudinal magnetization (expressed per ml of arterial
blood), and Mv(t) is the venous longitudinal magnetization
(expressed per ml of venous blood).
Because magnetization in the Bloch equations mentioned
earlier is described in terms of volume of tissue or volume of
blood, at equilibrium, the magnetization of water in blood can
be related to the magnetization of water in tissue as
M0a
M0t
M0v
l
[9]
where l is the tissueblood partition coefficient, expressed in

[(ml of water per g of tissue)/(ml of water per ml of blood)].
The Bloch equations mentioned earlier assume that water is a
freely diffusible tracer, that is, water in blood is in full exchange
with water in tissue. While this seems to be the case in organs
such as the heart or the kidneys over a large range of blood flow
rates, in the brain, the exchange of water between the vasculature
and the parenchyma is limited even at normal resting CBF rates
(Eichling, Raichle, Grubb, & Ter-Pogossian, 1974). Thus, in the
brain, only a fraction E(f) of the arterial water is able to diffuse
out of the vasculature and equilibrate with the exchangeable
water in the brain, while a nonextracted fraction remains confined to the vasculature. The water extraction fraction E(f)
decreases with increasing CBF (Eichling et al., 1974; Herscovitch,
Raichle, Kilbourn, & Welch, 1987; Raichle, Eichling, & Grubb,
1974). When dealing with a (nonfreely) diffusible tracer, eqn [8]
needs to be modified (Figure 3). In this case, the venous water
magnetization can be expressed as the sum of the magnetization
of tissue water that exchanges (i.e., is extracted) to the venous
vasculature and the amount of arterial water magnetization that
does not exchange (i.e., is not extracted) with tissue water:
Mt t
, or
Mv t 1 E f Ma t E f
l

Mt t
Ma t Mv t E f Ma t
l
[10]
Due to the process of ASL, the arterial water may be

expressed as
0
Ma t 1 2a
t M
a ,
t
at a0 exp
Tla
[11]
where a(t) is the degree of labeling. It is important to note that

a(t) expresses both the labeling efficiency a0 at the site of labeling
and the lifetime of the label, given by its relaxation with the
longitudinal relaxation time constant of arterial water, Tla, during
the transit time from the labeling plane to the imaging plane
(Alsop & Detre, 1996). Plugging eqns [9][11] into eqn [8] yields

dMt t
1
f
1 2at E f
M0t
dt
Tlt
l

1
f
dMm t
kfor E f krev Mm t
Mt t
Tlt
l
dt
kfor 0
Mt Mm t
k
kfor Mt t krev Mm t
[12]
rev
Tlm
The solution to eqn [12] needs to consider the specific ASL
technique in use. Generally speaking, ASL MRI techniques can
be implemented either with pulsed labeling (PASL), in which
single or multiple radiofrequency (RF) pulses are employed to
label the arterial water spins, or with continuous labeling
(CASL), in which a long RF pulse is employed in the presence
of a longitudinal field gradient to label the arterial spins
according to the principles of adiabatic fast passage (see
Barbier et al., 2001; Calamante et al., 1999; Detre et al.,
1994; Golay, Hendrikse, & Lim, 2004; Gunther, 2014; Wang
et al., 2002; Williams, 2006; Wong, 2014; Wong, Buxton, &
Frank, 1999; Wu, St Lawrence, Licht, & Wang, 2010 for
reviews). A third approach that labels water spins based on
their velocity is under development (Wong et al., 2006). While
going into details about the different implementations of ASL
techniques is beyond the scope of this work, it is important to
consider the solution of eqn [12] for the case in which a
volume RF coil is used to perform the ASL. In that case, the
labeling RF pulse saturates tissue macromolecules, so that
eqn [12] can be simplified to
42

1
f
Mt t Tlapp M0t
1 2at E f
Tlt
l

t
f
1
1
f
kfor 2at E f e Tlapp
kfor E f
l
Tlapp Tlt
l
[13]
Tlapp is the apparent longitudinal relaxation time for tissue

water accounting for the effects of cross relaxation and for
perfusion. Both cross relaxation and perfusion shorten the
apparent relaxation of tissue water, and therefore, functional
changes in perfusion that happen during a functional task can
be detected with a Tl-sensitive sequence (Kwong et al., 1992).
In the CASL experiment, in which the labeling RF pulse is
applied for a time sufficiently long to allow the tissue magnetization to reach steady state, eqn [13] yields the two steadyand Mlabel
:
state magnetizations Mcontrol
t
t

1
f
Mcontrol
Tlapp M0t
E f
t
T
l
lt

[14]
i
1 h
f
Mlabel
Tlapp M0t
1 2a0 ed=Tla E f
t
Tlt
l
where d is the transit delay from the labeling plane to the
imaging plane. Solving eqn [14] for the flow rate f yields
f
l
Mcontrol Mlabel
t
t
M0t
2a0 ed=Tla E f Tlapp
[15]
While the CASL experiment has a higher signal-to-noise

ratio relative to PASL implementation, the resulting magnetization transfer effects that reduce the available MRI signal
(Mt control < Mt0 ) and limit the acquisition to a single slice parallel to the labeling plane (Silva, Zhang, Williams, & Koretsky,
1995), due to the difficulty in accurately correcting for offresonance saturation of the tissue. To address these issues, a
new approach was devised for CASL that uses pulsed RF and
gradient fields, named pseudocontinuous ASL (PCASL) (Dai,
Garcia, De Bazelaire, & Alsop, 2008). Due to its easier implementation in commercial clinical scanners, PCASL has been
recently recommended as the ASL sequence of choice for clinical applications (Alsop et al., 2014).
Blood Water, the Endogenous Source of Contrast for CBV fMRI

By the same token that arterial water can be used as an endogenous perfusion tracer, as discussed earlier, blood water more
generally can be used to track blood volume. The principle
behind the use of endogenous blood water as a marker of
blood volume (i.e., independently of blood flow velocity) is
again to differentiate the blood magnetization from that of
surrounding tissue. As in ASL, blood water as a blood volume
marker explores differences in the longitudinal relaxation time
constant Tl between blood and tissue (Lu, Golay, Pekar, & Van
Zijl, 2003). In vascular space occupancy (VASO), blood signal
is selectively nulled, so that the remaining signal in the voxel is
proportional to 1 CBV (assuming the total volume of water
in the voxel, intra- and extravascular, is constant) (Lu et al.,
2003). Local increases in blood volume induced by functional
brain activity then lead to a local reduction in the MRI signal,
and thus, the MRI signal becomes sensitive to local blood
volume. The simplest way to null blood signal is to apply a

spatially nonselective inversion RF pulse that inverts the spins
of both blood and tissue water. Following this inversion pulse,
blood and tissue water will recover their respective longitudinal magnetizations with Tlb and Tlt, respectively. Assuming
only blood and tissue make up the voxel composition with
respective relative volumes Vb and (1 Vb), the total MRI
signal at the blood-nulling inversion time t TI following an
inversion RF pulse can be described as

TI
TR
STI Sb TI St TI Sb 0 1 2eTlb e Tlb

TI
TR
St 0 1 2eTlt e Tlt

TI
TR
M0 Vb rb 1 2eTlb e Tlb

TI
TR
M0 1 Vb rt 1 2eTlt e Tlt

TI
TR
0 M0 1 Vb rt 1 2eTlt e Tlt
[16]
where TR is the experiment repetition time, M0 is the total

equilibrium magnetization per unit volume, rb is the blood
proton density (expressed in ml water per ml blood), and rt is
the tissue proton density (expressed in ml water per ml tissue).
Thus, S(TI) (1 Vb).
The fractional functional VASO signal obtained during
functional brain activity is then given by
DS Sact Sbase Vbase Vact
DV
Sbase
1 Vbase
S
1 Vbase
[17]
where Vbase and Vact are the local blood volumes at rest and
during brain activity, respectively. Note that increases in blood
volume are associated with negative VASO signal changes via
the minus sign in eqn [17].
Exogenous Contrast Agents in fMRI

Exogenous paramagnetic agents have had an early and very
important role in the development of fMRI of the brain.
Indeed, the very first human fMRI study used a gadolinium
chelate as a paramagnetic agent sensitive to CBV to measure the
functional response to photic stimulation (Belliveau et al.,
1991). Most exogenous MR contrast agents are intravascular
paramagnetic compounds that change both longitudinal and
transverse relaxation time constants of tissue water via a dipolar interaction between the unpaired electrons within the compounds and the proton nuclear spins in water (Rosen et al.,
1990). Thus, these contrast agents are also referred to as blood
pool or blood volume agents. The presence of the contrast
agent leads to local changes in the longitudinal and transverse
relaxation rates R1 and R2, which are proportional to the contrast agents concentration Ct(t):
R1 t R10 r1 Ct t
R2 t R20 r2 Ct t
[18]
where r1 and r2 are the longitudinal and transverse relaxivities of the contrast agent, respectively, and are dependent

Table 1
43
Relaxivity of gadolinium chelate agents commonly used in clinical MRI

1.5 T
3T
4.7 T
Trade name
Maker
Short name
r1
r2
r1
r2
r1
r2
Magnevist
Gadovist
ProHance
MultiHance
DOTAREM
OMNISCAN
Schering
Schering
Bracco
Bracco
Guerbet
Amersham
Gd-DTPA
Gd-DO3A-butrol
Gd-HP-DO3A
Gd-BOPTA
Gd-DOTA
Gd-DTPA-BMA
4.1
5.2
4.1
6.3
3.6
4.3
4.6
6.1
5.0
8.7
4.3
5.2
3.7
5.0
3.7
5.5
3.5
4.0
5.2
7.1
5.7
11.0
4.9
5.6
3.8
4.7
3.7
5.2
3.3
3.9
4.8
5.9
5.8
10.8
4.7
5.3
Relaxivities expressed in mmol1 s1. Data obtained in plasma at 37 C (Rohrer et al., 2005).
t
on the magnetic field strength. Table 1 lists r1 and r2 for
gadolinium chelates typically used in clinical practice
(Burtea, Laurent, Vander Elst, & Muller, 2008; Rohrer,
Bauer, Mintorovitch, Requardt, & Weinmann, 2005). In
addition to the effects of relaxivity, the contrast agents
have a high magnetic susceptibility that causes additional
dephasing of water spins due to the compartmentalization
of the agent, further affecting the transverse relaxation rates
R2 and R2* (Rosen et al., 1990; Villringer et al., 1988).
CBV t 1
t
1
Ct tdt
Ca tdt
Ct t
CBFt Ca t Rt CBFt

t
tCt tdt
MTTt 1
t
Ct tdt
t
1
Ca tRt tdt
1
[21]
Bolus Tracking Measurements of Cerebral Hemodynamics

Hemodynamic parameters can be determined by tracking the
first pass of an exogenous, paramagnetic intravascular contrast
agent such as gadolinium diethylenetriaminepentaacetate (GdDTPA) through the organ of interest. Typically, the contrast agent
is administered intravenously as a bolus, and thus, the experiments can be referred to as bolus tracking (Ostergaard, 2004).
Bolus-tracking experiments that use Tl-weighted MRI are called
dynamic contrast-enhanced MRI and are used to assess the functional integrity of the bloodbrain barrier via estimation of
vascular permeability (Ferre, Shiroishi, & Law, 2012). Bolustracking experiments that use T2- or T2*-weighted MRI are
referred to as dynamic susceptibility contrast MRI (Ferre et al.,
2012). SE or GE images are rapidly acquired during the passage
of the contrast agent, and the major perfusion-related parameters
CBF, CBV, and mean transit time (MTT) are estimated from
tracer kinetic models based on the use of the central volume
theorem (Calamante, 2013; Calamante et al., 1999). Using
either SE or GE pulse sequences, the MRI signal intensity following contrast agent administration can be determined from the
changes in the transverse relaxation rates as (Rosen et al., 1990)
*
TEDR2 t
St t St 0e
[19]
where TE is the echo time of the experiment.

The concentration of contrast agent can be estimated from
eqns [18] and [19] as

1
St t
ln
[20]
Ct t
r2 TE
St 0
From eqn [20], the hemodynamic parameters CBV, CBF,
and MTT can be quantified as (Barbier et al., 2001; Calamante
et al., 1999; Ostergaard, 2004; Rosen et al., 1990)
where Ca(t) is the arterial concentration of the contrast agent

and R(t) is the tissue residue function, which describes the
fraction of the contrast agent remaining in the tissue at time t
following an instantaneous bolus administration. By definition,
at time t 0, all the contrast agent is in the tissue, that is,
R(0) 1. For a nondiffusible tracer, all the tracer leaves the
tissue after a sufficiently long time, R(1) 0. Thus, R(t)
describes the tissue retention of the contrast agent (Calamante,
2013; Ostergaard, 2004).
According to eqn [21], CBV can be obtained as the ratio of
the areas under the tissue concentrationtime curve and the
arterial concentrationtime curve, also called the arterial input
function (Rosen et al., 1990). On the other hand, CBF must be
obtained via a deconvolution of the tissue concentrationtime
curve with the arterial input function. The deconvolution process can be complex and requires an accurate measurement
of the arterial input function (Calamante, 2013). Finally,
MTT can be obtained from the first moment of the tissue
concentrationtime curve.
Iron Oxide Nanoparticles as an Exogenous CBV Tracer

A main difficulty associated with the use of gadolinium chelates for fMRI is their relatively short blood half-life
(1590 min), which due to a hydrophilic chelating agent
are quickly cleared through the kidneys (Burtea et al.,
2008). The fast clearance of the contrast agent forces multiple
administrations during a single time session, and the functional signal is not stable due to a continuously varying
concentration of the contrast in blood. As an alternative to
gadolinium, iron oxide nanoparticles have significantly longer half-lives than gadolinium chelates (Corot, Robert, Idee,
& Port, 2006), and their concentration in blood following a
44
Table 2
Relaxivity of some iron oxide nanoparticles used in research

1.5 T
3T
4.7 T
Trade name
Maker
Short name
Size (nm)
T1/2 (h)
r1
r2
r1
r2
r1
r2
Endorem
Feridex
Resovist
Sinerem
Combidex
AMAG Pharma
AMI-25
120180
4.5
33
2.7
45
1.2
25
Schering
AMAG Pharma
SHU-555A
AMI-227
60
1530
2.43.6
2436
7.4
9.9
95
65
3.3
160
1.7
118
Half-life in humans (Corot et al., 2006). Relaxivities expressed in mmol1 s1. Data obtained in plasma at 37 C (Rohrer et al., 2005).
single dose is stable during the entire extent of a typical

experimental session.
Iron oxide nanoparticles consist of an iron oxide crystal core
of 410 nm in diameter, such as magnetite (Fe3O4), maghemite
(gFe2O3), or even other ferrites, coated with a biodegradable
hydrophilic polymer layer. When exposed to a magnetic field,
these nanoparticles develop a large magnetic moment. The
hydrophilic coating makes up most of the final nanoparticle
size, and its function is to stabilize the nanoparticle in aqueous
solution. It also has great influence on the half-life and biodistribution of the nanoparticle. Usually, the coating is made of
polymers such as dextrans in several forms, starch, polyethylene
glycol, or 2,3-dimercaptosuccinic acid (Zhao, Zhao, Chen, &
Lan, 2014). SPIO nano particles have a mean hydrodynamic
particle diameter larger than 50 nm. Ultrasmall SPIO (USPIO)
nano particles, on the other hand, have a smaller hydrodynamic
diameter. Table 2 shows the relaxivities of a few SPIO and
USPIO compounds available for research.
The use of iron oxide nanoparticles as an exogenous CBV
tracer uses the steady-state approach. Following an intravenous
injection, the iron oxide nano particles equilibrate quickly
within the plasma volume. CBV can then be calculated using
eqn [19], as
DR2 *

Spost
1
ln
Spre
TE
[22]
where Spre and Spost are the MRI signal intensities before and
after the administration of the contrast agent, respectively.
Once DR2* is obtained, CBV can be calculated assuming the
static dephasing regime (Kim et al., 2013; Yablonskiy &
Haacke, 1994):
DR2 *
CBV
4
p1 HctDwUSPIO gB0 rv
3
[23]
where Hct is the blood hematocrit, DwUSPIO is the susceptibility

difference between arterial blood and water, g is the gyromagnetic ratio, and rv is the blood density.
To quantify the changes in CBV in response to functional
brain stimulation, it is necessary to consider the functional
signals before and after administration of the contrast agent
(Kim et al., 2013). Before administration of the contrast agent,
BOLD
the functional signal DS
SBOLD has only a BOLD contrast:

*
TEBOLD R*2, BOLD
eTHBOLD R20
DSBOLD
sact Sbase S0 e
*
SBOLD
S0 eTHBOLD R20
Sbase

TEBOLD DR*2, BOLD TEBOLD R*20
TEBOLD R*20
e
e
e
R*
eTEBOLD
20

TEBOLD DR*2, BOLD
e
1 TEBOLD DR*2, BOLD
[24]
where TEBOLD is the echo time of the experiment, usually set at
TEBOLD R1* for maximum sensitivity, and DR*2, BOLD depends
20
linearly on the baseline venous CBV, on the magnetic field
strength, and on changes in oxygenation level (Ogawa et al.,
1993). Following administration of the contrast agent, it is
necessary to reset the echo time of the experiment due to the
effect of the contrast agent to increase R*2 :
R*2, USPIO R*2 DR*2, USPIO R*2 r2* Cv CBV
[25]
where r2* is the relaxivity of the contrast agent and Cv is its

USPIO
concentration in blood. The new functional signal DS
SUSPIO has
both BOLD and USPIO contrast contributions (the latter
induced by functional CBV changes):
DSUSPIO
SUSPIO, act SUSPIO, base
SUSPIO
SUSPIO

*
TEUSPIO R*2, USPIO, act
S0, USPIO e
eTEUSPIO R2, USPIO, base
*
S0, USPIO eTEUSPIO R2, USPIO, base

TEUSPIO DR*2, BOLD TEUSPIO Ct r2* DCBV
[26]
From eqns [24] and [26], the fractional CBV changes in

response to functional brain stimulation can be expressed as
1
DSBOLD
1
DSUSPIO

DCBV TEBOLD SBOLD TEUSPIO SUSPIO
CBV
DR*2, USPIO
[27]
Using eqn [27] to calculate CBV changes corrects for the

BOLD contribution to the signal after administration of the
contrast agent. This is particularly important at high magnetic
field strengths (Lu, Scholl, Zuo, Stein, & Yang, 2007).
Conclusions
Endogenous and exogenous contrast agents have a fundamental role in enabling fMRI techniques to probe brain function.

While the underlying signal mechanisms of fMRI are still a
subject of research, the use of specific contrast agents will
help elucidate still to be fully understood issues, such as the
vascular source of contrast, the physiological parameters that
affect quantification of fMRI signals, and the spatiotemporal
specificity of the different fMRI techniques.
The source of BOLD contrast is hemoglobin, which induces
local signal changes that are dependent on the local blood
oxygenation level Y. BOLD contrast has both intravascular
and extravascular contributions. The intravascular contribution can significantly affect the spatial specificity of BOLD
fMRI, but it can be reduced with the use of diffusion-sensitizing
gradients, longer echo times, and higher magnetic field
strengths. The spatial specificity can also improve with the
use of SE techniques that are not sensitive to intra- and extravascular static dephasing mechanisms.
While BOLD contrast depends on a complex interplay
between changes in CBF, CBV, and oxygen consumption,
CBF and CBV can be measured and quantified using both
endogenous and exogenous sources of contrast. Compared to
BOLD contrast, CBF and CBV methods are more sensitive and
specific to changes in neuronal activity, as they have a much
simpler physiological interpretation of their signal source that
translates into better interpretation of both magnitude and
spatiotemporal specificity of signal changes. Therefore, CBF
and CBV fMRI methods are the preferred tools for longitudinal
functional imaging and in clinical applications. The use of
water as an endogenous source of functional contrast has the
main advantages of being noninvasive and allowing repeated
measurements to be performed as often as desired. On the
other hand, exogenous paramagnetic contrast agents have
inherently higher contrast-to-noise ratio due to their high
relaxivity. Iron oxide superparamagnetic nanoparticles, while
not currently available for human use, have significantly longer
half-life than gadolinium chelates and are poised to become
the agent of choice for measurements of CBV.
Acknowledgments
This research was supported by the Intramural Research Program of the NINDS, NIH.
See also: INTRODUCTION TO ACQUISITION METHODS: fMRI at

High Magnetic Field: Spatial Resolution Limits and Applications;
Functional MRI Dynamics; High-Field Acquisition; Molecular fMRI;
MRI and fMRI Optimizations and Applications; Obtaining Quantitative
Information from fMRI; Perfusion Imaging with Arterial Spin Labeling
MRI; Pulse Sequence Dependence of the fMRI Signal; SusceptibilityWeighted Imaging and Quantitative Susceptibility Mapping; Temporal
Resolution and Spatial Resolution of fMRI.
References
Alsop, D. C., & Detre, J. A. (1996). Reduced transit-time sensitivity in noninvasive
magnetic resonance imaging of human cerebral blood flow. Journal of Cerebral
Blood Flow and Metabolism, 16, 12361249.
45
Alsop, D. C., Detre, J. A., Golay, X., Gunther, M., Hendrikse, J., Hernandez-Garcia, L.,
et al. (2014). Recommended implementation of arterial spin-labeled perfusion
MRI for clinical applications: A consensus of the ISMRM perfusion study group
and the European consortium for ASL in dementia. Magnetic Resonance in
Medicine. http://dxdoi.org/10.1002/mrm.25197.
Barbier, E. L., Lamalle, L., & Decorps, M. (2001). Methodology of brain perfusion
imaging. Journal of Magnetic Resonance Imaging, 13, 496520.
Belliveau, J. W., Kennedy, D. N., Jr., Mckinstry, R. C., Buchbinder, B. R.,
Weisskoff, R. M., Cohen, M. S., et al. (1991). Functional mapping of the human
visual cortex by magnetic resonance imaging. Science, 254, 716719.
Boxerman, J. L., Bandettini, P. A., Kwong, K. K., Baker, J. R., Davis, T. L., Rosen, B. R., et al.
(1995). The intravascular contribution to fMRI signal change: Monte Carlo modeling
and diffusion-weighted studies in vivo. Magnetic Resonance in Medicine, 34, 410.
Burtea, C., Laurent, S., Vander Elst, L., & Muller, R. N. (2008). Contrast agents:
Magnetic resonance. Handbook of Experimental Pharmacology, 185, 135165.
Calamante, F. (2013). Arterial input function in perfusion MRI: A comprehensive review.
Progress in Nuclear Magnetic Resonance Spectroscopy, 74, 132.
Calamante, F., Thomas, D. L., Pell, G. S., Wiersma, J., & Turner, R. (1999). Measuring
cerebral blood flow using magnetic resonance imaging techniques. Journal of
Cerebral Blood Flow and Metabolism, 19, 701735.
Corot, C., Robert, P., Idee, J. M., & Port, M. (2006). Recent advances in iron oxide
nanocrystal technology for medical imaging. Advanced Drug Delivery Reviews, 58,
14711504.
Dai, W., Garcia, D., De Bazelaire, C., & Alsop, D. C. (2008). Continuous flow-driven
inversion for arterial spin labeling using pulsed radio frequency and gradient fields.
Detre, J. A., Zhang, W., Roberts, D. A., Silva, A. C., Williams, D. S., Grandis, D. J., et al.
(1994). Tissue specific perfusion imaging using arterial spin labeling. NMR in
Diekhoff, S., Uludag, K., Sparing, R., Tittgemeyer, M., Cavusoglu, M.,
Von Cramon, D. Y., et al. (2011). Functional localization in the human brain:
Gradient-echo, spin-echo, and arterial spin-labeling fMRI compared with
neuronavigated TMS. Human Brain Mapping, 32, 341357.
Dijkhuizen, P., Buursma, A., Fongers, T. M., Gerding, A. M., Oeseburg, B., &
Zijlstra, W. G. (1977). The oxygen binding capacity of human haemoglobin.
Hufners factor redetermined. Pflugers Archiv, 369, 223231.
Duyn, J. (2013). MR susceptibility imaging. Journal of Magnetic Resonance, 229,
198207.
Eichling, J. O., Raichle, M. E., Grubb, R. L., Jr., & Ter-Pogossian, M. M. (1974).
Evidence of the limitations of water as a freely diffusible tracer in brain of the rhesus
monkey. Circulation Research, 35, 358364.
Ferre, J. C., Shiroishi, M. S., & Law, M. (2012). Advanced techniques using contrast
media in neuroimaging. Magnetic Resonance Imaging Clinics of North America, 20,
699713.
Golay, X., Hendrikse, J., & Lim, T. C. (2004). Perfusion imaging using arterial spin
labeling. Topics in Magnetic Resonance Imaging, 15, 1027.
Gunther, M. (2014). Perfusion imaging. Journal of Magnetic Resonance Imaging, 40,
269279.
Herscovitch, P., Raichle, M. E., Kilbourn, M. R., & Welch, M. J. (1987). Positron
emission tomographic measurement of cerebral blood flow and permeabilitysurface area product of water using [15O]water and [11C]butanol. Journal of Cerebral
Hill, R. J., Konigsberg, W., Guidotti, G., & Craig, L. C. (1962). The structure of human
hemoglobin. I. The separation of the alpha and beta chains and their amino acid
composition. The Journal of Biological Chemistry, 237, 15491554.
Jain, V., Abdulmalik, O., Propert, K. J., & Wehrli, F. W. (2012). Investigating the
magnetic susceptibility properties of fresh human blood for noninvasive oxygen
saturation quantification. Magnetic Resonance in Medicine, 68, 863867.
Kim, S. G., Harel, N., Jin, T., Kim, T., Lee, P., & Zhao, F. (2013). Cerebral blood volume
MRI with intravascular superparamagnetic iron oxide nanoparticles. NMR in
Kim, S. G., & Ogawa, S. (2012). Biophysical and physiological origins of blood
oxygenation level-dependent fMRI signals. Journal of Cerebral Blood Flow and
Metabolism, 32, 11881206.
Medicine, 50, 263274.
46
Lu, H., Scholl, C. A., Zuo, Y., Stein, E. A., & Yang, Y. (2007). Quantifying the blood
oxygenation level dependent effect in cerebral blood volume-weighted functional
MRI at 9.4 T. Magnetic Resonance in Medicine, 58, 616621.
Menon, R. S., Ogawa, S., Kim, S. G., Ellermann, J. M., Merkle, H., Tank, D. W., et al.
(1992). Functional brain mapping using magnetic resonance imaging. Signal changes
accompanying visual stimulation. Investigative Radiology, 27(Suppl. 2), S47S53.
Norris, D. G. (2006). Principles of magnetic resonance assessment of brain function.
Journal of Magnetic Resonance Imaging, 23, 794807.
Ogawa, S., Lee, T. M., Kay, A. R., & Tank, D. W. (1990). Brain magnetic
resonance imaging with contrast dependent on blood oxygenation.
Proceedings of the National Academy of Sciences of the United States of
America, 87, 98689872.
Ogawa, S., Lee, T. M., Nayak, A. S., & Glynn, P. (1990). Oxygenation-sensitive contrast
in magnetic resonance image of rodent brain at high magnetic fields. Magnetic
Ogawa, S., Menon, R. S., Kim, S. G., & Ugurbil, K. (1998). On the characteristics of
functional magnetic resonance imaging of the brain. Annual Review of Biophysics
and Biomolecular Structure, 27, 447474.
Ogawa, S., Menon, R. S., Tank, D. W., Kim, S. G., Merkle, H., Ellermann, J. M., et al.
(1993). Functional brain mapping by blood oxygenation level-dependent contrast
magnetic resonance imaging. A comparison of signal characteristics with a
biophysical model. Biophysical Journal, 64, 803812.
Ogawa, S., Tank, D. W., Menon, R., Ellermann, J. M., Kim, S. G., Merkle, H., et al.
Ostergaard, L. (2004). Cerebral perfusion imaging by bolus tracking. Topics in
Pauling, L., & Coryell, C. D. (1936). The magnetic properties and structure of
hemoglobin, oxyhemoglobin and carbonmonoxyhemoglobin. Proceedings
of the National Academy of Sciences of the United States of America, 22, 210216.
Raichle, M. E., Eichling, J. O., & Grubb, R. L.,Jr. (1974). Brain permeability of water.
Archives of Neurology, 30, 319321.
Rohrer, M., Bauer, H., Mintorovitch, J., Requardt, M., & Weinmann, H. J. (2005).
Comparison of magnetic properties of MRI contrast media solutions at different
magnetic field strengths. Investigative Radiology, 40, 715724.
Rosen, B. R., Belliveau, J. W., Vevea, J. M., & Brady, T. J. (1990). Perfusion
imaging with NMR contrast agents. Magnetic Resonance in Medicine, 14, 249265.
Silva, A. C., Zhang, W., Williams, D. S., & Koretsky, A. P. (1995). Multi-slice MRI of rat
brain perfusion during amphetamine stimulation using arterial spin labeling.
Silva, A. C., Zhang, W., Williams, D. S., & Koretsky, A. P. (1997). Estimation of water
extraction fractions in rat brain using magnetic resonance measurement of perfusion
with arterial spin labeling. Magnetic Resonance in Medicine, 37, 5868.
Silvennoinen, M. J., Clingman, C. S., Golay, X., Kauppinen, R. A., & Van Zijl, P. C.
(2003). Comparison of the dependence of blood R2 and R2* on oxygen saturation at
1.5 and 4.7 Tesla. Magnetic Resonance in Medicine, 49, 4760.
Spees, W. M., Yablonskiy, D. A., Oswood, M. C., & Ackerman, J. J. (2001). Water
proton MR properties of human blood at 1.5 Tesla: Magnetic susceptibility, T(1),
T(2), T*(2), and non-Lorentzian signal behavior. Magnetic Resonance in Medicine,
45, 533542.
Turner, R. (1992). Magnetic resonance imaging of brain function. American Journal of

Physiologic Imaging, 7, 136145.
Uludag, K., Muller-Bierl, B., & Ugurbil, K. (2009). An integrative model for neuronal
activity-induced signal changes for gradient and spin echo functional imaging.
Villringer, A., Rosen, B. R., Belliveau, J. W., Ackerman, J. L., Lauffer, R. B.,
Buxton, R. B., et al. (1988). Dynamic imaging with lanthanide chelates in normal
brain: Contrast due to magnetic susceptibility effects. Magnetic Resonance in
Medicine, 6, 164174.
Wang, J., Alsop, D. C., Li, L., Listerud, J., Gonzalez-At, J. B., Schnall, M. D., et al.
(2002). Comparison of quantitative perfusion imaging using arterial spin labeling at
Weed, R. I., Reed, C. F., & Berg, G. (1963). Is hemoglobin an essential structural
component of human erythrocyte membranes? The Journal of Clinical Investigation,
42, 581588.
Weisskoff, R. M., & Kiihne, S. (1992). MRI susceptometry: Image-based measurement
of absolute susceptibility of MR contrast agents and human blood. Magnetic
Williams, D. S. (2006). Quantitative perfusion imaging using arterial spin labeling.
Methods in Molecular Medicine, 124, 151173.
89, 212216.
Wong, E. C. (2014). An introduction to ASL labeling techniques. Journal of Magnetic
Wong, E. C., Buxton, R. B., & Frank, L. R. (1999). Quantitative perfusion imaging using
arterial spin labeling. Neuroimaging Clinics of North America, 9, 333342.
Wong, E. C., Cronin, M., Wu, W. C., Inglis, B., Frank, L. R., & Liu, T. T. (2006).
Velocity-selective arterial spin labeling. Magnetic Resonance in Medicine, 55,
13341341.
Wu, W. C., St Lawrence, K. S., Licht, D. J., & Wang, D. J. (2010). Quantification issues
in arterial spin labeling perfusion magnetic resonance imaging. Topics in Magnetic
Yablonskiy, D. A., & Haacke, E. M. (1994). Theory of NMR signal behavior in
magnetically inhomogeneous tissues: The static dephasing regime. Magnetic
Yablonskiy, D. A., Sukstanskii, A. L., & He, X. (2013). Blood oxygenation leveldependent (BOLD)-based techniques for the quantification of brain hemodynamic
and metabolic properties Theoretical models and experimental approaches. NMR
in Biomedicine, 26, 963986.
Zhang, W., Silva, A. C., Williams, D. S., & Koretsky, A. P. (1995). NMR measurement of
perfusion using arterial spin labeling without saturation of macromolecular spins.
Zhang, W., Williams, D. S., Detre, J. A., & Koretsky, A. P. (1992). Measurement of brain
perfusion by volume-localized NMR spectroscopy using inversion of arterial water
spins: Accounting for transit time and cross-relaxation. Magnetic Resonance in
Medicine, 25, 362371.
Zhao, J. M., Clingman, C. S., Narvainen, M. J., Kauppinen, R. A., & Van Zijl, P. C.
(2007). Oxygenation and hematocrit dependence of transverse relaxation rates of
blood at 3 T. Magnetic Resonance in Medicine, 58, 592597.
Zhao, X., Zhao, H., Chen, Z., & Lan, M. (2014). Ultrasmall superparamagnetic iron
oxide nanoparticles for magnetic resonance imaging contrast agent. Journal of
Nanoscience and Nanotechnology, 14, 210220.
Diffusion MRI*
AR Hoy, United States Navy, Falls Church, VA, USA; University of Wisconsin Madison, Madison, WI, USA
AL Alexander, University of Wisconsin Madison, Madison, WI, USA
Abbreviations
ADC
CHARMED
DBSI
DKI
DSI
Apparent diffusion coefficient

Combined hindered and restricted model of
diffusion
Diffusion basis spectrum imaging
Diffusion kurtosis imaging
Diffusion spectrum imaging
Introduction
Magnetic resonance imaging (MRI) contrast is highly sensitive
to the interaction of MRI-visible water with the local environment. As a fluid, pure water is highly mobile and diffuses
through a process called the Brownian motion that describes
the random motion of water particles in space. This diffusion
process causes the water molecules to exhibit increasing spatial
displacements with time. Einstein (1905) derived the equations describing the Brownian motion. These showed that the
spatialtemporal dependence of diffusion was described by a
Gaussian distribution. Additionally, the mean squared displacement from diffusion, Dx2, increases with the product of
the diffusion coefficient, D, and the diffusion time, t:
Dx2 2nDt
where n is dimensionality of the space (n 3 for three dimensions). Water at 37 C (body temperature) has a diffusion
coefficient of roughly 3 103 mm2 s1 but is sensitive to
temperature and pressure and has isotropic directional
dependence.
Water Diffusion as a Probe of Microstructure

In biological tissues, diffusing water interacts with microstructural features including cellular membranes, myelin sheaths,
and cytoskeletal structures, which hinder and restrict the
Brownian motion exhibited in the absence of these barriers.
These barriers ultimately reduce the diffusion displacements
and corresponding diffusion coefficient. Hindered diffusion
refers to the effects of increased tortuosity from barriers, such
as cellular membranes in the extracellular space, which
impede the diffusion displacements for a given amount of
time. Restricted diffusion occurs when barriers confine the
water motion to a small space such that the maximum diffusion displacements are limited. An important distinction is
?
The views expressed in this article are those of the author and
do not necessarily reflect the official policy or position of the
Department of the Navy, Department of Defense, nor the
U.S. Government.
DTI
EPI
HARDI
HYDI
NODDI
Diffusion tensor imaging

Echo planar imaging
High angular resolution diffusion imaging
Hybrid diffusion imaging
Neurite orientation distribution and density
imaging
that the mean squared displacements increase with diffusion

time for hindered diffusion, but not restricted diffusion.
Further, microstructural features that are either fibrous
(i.e., axons) or elongated (i.e., dendritic processes) will exhibit
anisotropic (not isotropic) water diffusion as a function of
direction. For example, in white matter, which consists of
bundles of long axons, diffusion displacements will be greater
in the direction parallel to the axons than in the perpendicular
direction. Diffusion properties may also be different between
water compartments such as free water (cerebral spinal fluid
and edema) and intracellular, extracellular, and intra-axonal
compartments. The intracellular and intra-axonal compartments will exhibit more restricted diffusion properties;
however, membrane permeability will affect these properties.
Consequently, noninvasive measurement of water diffusion
properties with MRI provides unique opportunities to
probe the density, scale, and organization of the tissue
microstructure.
Sensitivity of MRI to Water Diffusion Using Pulsed

Gradients
Stejskal and Tanner (1965) described the sensitivity of nuclear
magnetic resonance (NMR) signals to diffusion effects when
exposed to pulsed-gradient magnetic fields for example, a pair
of balanced gradient pulses with opposite amplitudes. The first
gradient pulse induces a linear phase dispersion in space across
the sample and the second pulse rephases the magnetization. In
the absence of motion, the phases from both pulses completely
cancel. However, when water moves, the associated magnetization will accumulate the phase that is proportional to the net
displacement. In the case of coherent flow, this phase is proportional to the flow velocity and is the basis for phase contrast
angiography. Conversely, diffusion causes incoherent random
movements that will lead to a dispersion in the displacements
and corresponding phases. This spread in the signal phase from
diffusion causes destructive interference and attenuation of the
image signal. This diffusion-weighting methodology was first
applied to MRI by Le Bihan et al. (1986), which launched the
field of diffusion-weighted (DW) imaging.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00005-1
47
48
INTRODUCTION TO ACQUISITION METHODS | Diffusion MRI

fiber orientations is not known a priori and also varies across the
brain, multiple encoding directions are usually prescribed to
assess the diffusion anisotropy properties. Figure 2 shows the
effect of gradient direction on the measured signal.
180
90
RF
d
Gss
Gp
Gf
Figure 1 Diffusion weighting can be applied in any arbitrary direction
through modulation of the slice-select (red), phase-encoding (green),
and frequency-encoding (blue) diffusion gradients. D is the time between
diffusion-weighting pulses known as the diffusion time and d is the
duration of the pulse.
DW Pulse Sequences
The most common DW pulse sequence is the pulsed-gradient
spin echo where the diffusion-weighting gradient pulses are
placed on both sides of the 180 refocusing pulse; see Figure 1.
Because DW pulse sequences are highly sensitive to motion at
the microscopic scale, most studies use single-shot rapid image
acquisition methods like echo-planar imaging (EPI). While EPI
is very rapid, the spatial resolution is limited. Also, offresonance effects from static magnetic field inhomogeneities
will lead to significant image distortions. Parallel imaging
methods are commonly applied to reduce the amount of EPI
distortion. Multiple shot acquisition methods that may
improve spatial resolution and reduce distortion have also
been developed. However, these methods require navigator
echoes to correct the phase inconsistencies in the data between
shots. Another issue with DW EPI sequences is the residual
eddy currents from the strong DW gradients. Commercial DW
pulse sequences often include an option for bipolar diffusion
gradients with a dual-refocused spin echo sequence (Reese,
Heid, Weisskoff, & Wedeen, 2003); however, that option significantly increases the echo time, which reduces the measurement signal to noise ratio (SNR). Eddy current-induced
distortions may be corrected using retrospective image registration tools that can also correct for head motion.
DW Encoding
Moseley et al. (1990) and Chenevert, Brunberg, and Pipe (1990)
reported that the brain white matter exhibited anisotropic diffusion properties such that the diffusion was greater in the
direction parallel to the white matter tracts than in the perpendicular direction. Because magnetic field gradients vary the magnetic field in a specific direction, the diffusion sensitivity is
encoded along the direction of the gradient. By applying
diffusion weighting in directions both parallel and perpendicular to white matter fiber tracts, the degree of diffusion anisotropy
may be assessed. Since the local direction of the white matter
Apparent Diffusion Coefficient Mapping

As described in the preceding text, the diffusion properties of
water in biological tissues are modulated by cellular barriers,
such as membranes. Since this water diffusion is not described
solely by the Brownian motion phenomena, Le Bihan et al.
(1986) defined the DW MRI signal as having an apparent
diffusion coefficient (ADC) that is different from the diffusion
coefficient of water in the absence of barriers. The ADC may be
either measured in a specific encoding direction or averaged
across directions to mitigate local anisotropic diffusion effects.
Commonly, ADC values are measured in three orthogonal
directions (i.e., ADCx, ADCy, and ADCz) and averaged. Significantly reduced mean ADC is widely used clinically as a marker
of irreversible tissue damage in acute ischemic stroke. Apparent
diffusion along any given direction can be related to the measured signal as follows:

Sb
ln
bD
S0
where S0 is the non-DW signal, Sb is the measured signal for a
given b-value and gradient direction, b is the diffusion weighting in s mm2, and D is the ADC along the applied gradient
direction. For pulsed-gradient diffusion weighting as shown in
Figure 1, the diffusion-weighting b-value is

d
b gGd2 D
3
where g is the gyromagnetic ratio, G is the gradient amplitude,
D is the time between gradient pulses, and d is the pulse
duration. Figure 3 shows the loss of signal that accompanies
an increasing b-value.

In order to describe the anisotropic diffusion phenomena in
biological tissues, Basser, Mattiello, and Le Bihan (1994)
described the diffusion tensor model, which is based upon a
three-dimensional model of Gaussian diffusion displacements.
The diffusion tensor is a 3 3 covariance matrix
0
1
Dxx Dxy Dxz
D @ Dyx Dyy Dyz A
Dzx Dzy Dzz
that describes the three-dimensional distribution of diffusion
displacements based upon the Gaussian diffusion assumption.
This matrix is positive definite (diagonal elements are greater
than zero) and diagonally symmetrical. In this formalism, the
single scalar D is replaced by the diffusion tensor.
The diffusion tensor as shown in the preceding text may be
diagonalized yielding three eigenvalues (l1 > l2 > l3) and their
corresponding orthogonal eigenvectors (e1, e2, and e3). This
allows for visualization of the diffusion tensor as an ellipsoid.
Furthermore, this has led to the definition of several rotationally invariant scalar metrics including fractional anisotropy
49
Figure 2 Signal dependence on gradient direction. All images have the same b-value of 1000 s mm2. From left to right, the gradient directions are
leftright, anteriorposterior, and inferiorsuperior, respectively. The red arrow points out a major WM tract called the corpus callosum. In this slice,
the corpus callosum is oriented primarily leftright and slightly anteriorposterior; thus, there is greater diffusion (hence more attenuation) in the
leftmost image than there is in the rightmost image.
Figure 3 Signal dependence on b-value. All images have the same leftright gradient direction applied. From left to right, the b-values are 0, 500, 1000,
and 1500 s mm2.
(FA), axial diffusivity (DA), radial diffusivity (DR), and mean

diffusivity (MD). Figure 4 shows example images of these
metrics.
l1 l2 l3
MD
3
rs
2
3 l1 MD l2 MD2 l3 MD2
FA
2
l21 l22 l23
l2 l3
DR
2
D A l1
populations in a single voxel cannot be resolved with DTI. As

diffusion weighting increases (b > 2000 s mm2), the departure from Gaussian behavior becomes more evident. Consequently, different formalisms have been introduced to more
fully describe the observed diffusion signal.
With all diffusion models, it is important to consider the
effects of the acquisition. As b-value increases, so does signal
attenuation yielding a smaller SNR. The need to maintain
some minimum SNR may necessitate that larger voxels be
used. Additionally, while more diffusion directions increase
the angular information, it also necessitates a greater scan
time. Choosing a diffusion acquisition and model requires an
analysis of the costs and benefits associated with each.
Beyond the DTI Model

Diffusion tensor imaging (DTI) is inextricably linked to the
assumption of a Gaussian diffusion profile; however, this
assumption does not hold in all cases. Restricted diffusion
does not display Gaussian behavior as compartment size limits
diffusion distance. Likewise, the presence of multiple fiber
High Angular Resolution Diffusion Imaging

High angular resolution diffusion imaging (HARDI) is a
method that treats each voxel as an ensemble of some finite
number of diffusion tensors (Tuch et al., 2002). In this way, the
50
Figure 4 Diffusion metrics shown on an axial slice. These include different displays of FA (a and b) and ADC metrics (c, d, and e). FA can be displayed
as gray scale (a) with intensity determined by the magnitude of anisotropy or as a color-coded image (b) with the primary eigenvalue determining
the displayed color and the brightness determined by FA. In the directional encoding, red is indicative of leftright, green anteriorposterior, and
blue inferiorsuperior. ADCs can be displayed as the MD (c), DA (d), or DR (e). Here, each image is displayed with the same scale.
Gaussian assumption is maintained for any one of the compartments, but any single voxel may contain multiple compartments. This model makes it possible to visualize white matter
pathways, which cross one another while passing through a
single voxel.
Generally, HARDI refers to a class of diffusion methods,
which contain more information than the tensor model. This
includes parametric and nonparametric models. These
methods share a common acquisition with a single b-value
(20004000 s mm2) and many (typically 60100) diffusion directions distributed uniformly over a sphere. The exact
b-value and number of directions are highly dependent on the
chosen model.
Diffusion Kurtosis Imaging

Jensen and colleagues developed diffusion kurtosis imaging
(DKI) (Jensen & Helpern, 2003; Jensen, Helpern, Ramani, Lu,
& Kaczynski, 2005), which utilizes the DTI framework while also
quantifying the departure from Gaussian behavior. This deviation is measured as the kurtosis tensor. The link between DTI and
DKI can be readily seen in the signal equation utilized for DKI:

Sb
1
ln
bD b2 DK
S0
6
where K is the kurtosis tensor. Thus, DKI utilizes an additional
second-order term (in b) to measure deviation from Gaussian
behavior. This definition allows for use of the typical DTI
metrics with additional rotationally invariant apparent kurtosis metrics as well. A truly Gaussian diffusion profile results in a
kurtosis value of zero.
Kurtosis provides information that is complimentary to DTI.
Indeed, white matter and gray matter, which have a similar mean
diffusivity, have a markedly different mean kurtosis. While kurtosis is sensitive to tissue microstructure (Hui, Cheung, Qi, &
Wu, 2008), it cannot easily be tied out to a specific biophysical
property. DTI estimates 6 parameters, while DKI fits 15 independent parameters. DKI also requires the use of two different
b-values with a larger b-value of approximately 2000 s mm2.
Q-Space Imaging: DSI and HYDI

Q-space imaging seeks to fully quantify the diffusion displacement distribution (diffusion propagator) without any assumption about distribution or tissue structure. This is accomplished
by exploiting the Fourier relation between the measured signal
decay and the diffusion propagator:
Z
ED q P s R, Dexpi2pqRdR
where ED(q) is the measured signal as a function of q for a
specific diffusion time (D),P s R, D is the diffusion propagator,
and R is the net displacement. Here, q is related to the b-value,
where q 1/2p (b/D). Q-space is the 3-D space consisting of
the coordinates (qx, qy, and qz) based on the q-value and the
orientation (x, y, and z) of the diffusion gradients used. Callaghan provides an excellent coverage of the foundation and
formalism of q-space imaging (Callaghan, 1991).
Diffusion spectrum imaging (DSI) samples q-space on a
3-D Cartesian grid prior to using a fast Fourier transform to
solve for the diffusion propagator (Wedeen et al., 2000). This
scheme commonly acquires as many as 500 images. To reduce
the necessary number of images, Wu and Alexander proposed a
hybrid diffusion imaging (HYDI) acquisition scheme, which
acquires samples on concentric spherical shells in q-space (Wu
& Alexander, 2007). In addition to acquiring less samples, this
scheme allows reconstructions with DSI, DTI, and various
other reconstruction schemes.
Once the diffusion propagator is known, several quantitative measures can be calculated including the mean displacement distance, the zero displacement probability (P0), and the
kurtosis. However, there are several experimental conditions
that are necessary to accurately measure these quantities. First,
known as the narrow pulse approximation, the diffusion gradient pulse width must be short so that the mean diffusion
distance during the gradient on time is small relative to the
compartment size, l. Second, D must be sufficiently long to
ensure that the water molecules can probe the compartment,
that is, D > l2/2D. Lastly, the signal must be measured until it is
nearly completely decayed.
Hardware limitations ensure that the requisite assumptions, particularly the narrow pulse approximation, are not
met. Consequently, the derived q-space metrics are approximate rather than exact values. The need to acquire many
images leads to a longer acquisition time than most other
diffusion methods. Additionally, the SNR penalty that is inherent with high-b-value/q-value imaging limits the possible
image resolution. Despite these limitations, q-space imaging
provides comprehensive characterization of the diffusion displacement without the need for distribution assumptions or a
priori knowledge of microstructural environment.
Model-Based Diffusion Imaging: CHARMED, NODDI,

and DBSI
In contrast to q-space techniques, there exists a category of
model-based techniques that make a priori assumptions
about the correspondence between microstructure and diffusion signal. In general, these models assign physical meanings,
51
that is, intra- and extra-axonal space, cellularity, CSF contamination, or neurite density, to certain diffusion patterns
or characteristics. Three such techniques will be briefly
introduced.
Assaf, Freidlin, Rohde, and Basser (2004) introduced the
composite hindered and restricted model of diffusion
(CHARMED). This model consists of one extra-axonal compartment and multiple intra-axonal compartments. The extraaxonal compartment is modeled as a diffusion tensor, which is
characteristic of hindered diffusion. Each intra-axonal compartment is characterized by restricted diffusion within a
cylinder.
Neurite orientation dispersion and density imaging
(NODDI) assigns signal to intracellular, extracellular, and
CSF compartments (Zhang, Schneider, Wheeler-Kingshott, &
Alexander, 2012). The intracellular compartment is modeled
as a distribution of highly restricted sticks. A collection of
cylindrically symmetrical tensors models the extracellular compartment. Meanwhile, the CSF compartment is treated as having a fixed isotropic diffusivity.
Diffusion basis spectrum imaging (DBSI) fits a linear combination of a variable number of isotropic and anisotropic
compartments at each voxel (Wang et al., 2011). The anisotropic tensors are considered representative of myelinated and
unmyelinated axons, while the isotropic tensors are hypothesized to be indicative of cells, subcellular structures, and edematous water.
These models are extremely attractive as they provide
meaningful biological explanations for the observed diffusion
phenomena. Typically, these techniques require a higher
b-value, thus, less SNR and a longer acquisition time than
DTI, but less time and greater SNR than q-space techniques.
Improvements in gradient strength and the success of parallel
imaging have made these techniques feasible in a clinical
setting.
Diffusion Time for Probing Restricted Diffusion

It is believed that the axonal space is characterized by restricted
diffusion. The restriction effects are strongly dependent on
diffusion time and the size and shape of the restricting structure. Consider the simplified case of water residing in cylindrical axon with diameter d. When the diffusion time is very short,
the majority of water molecules are uninhibited by the wall,
and thus, they may diffuse freely. As the diffusion time
increases, a greater percentage of the molecules will come in
contact with the walls and the displacement distribution will
deviate from Gaussian behavior. That higher b-values correspond to longer diffusion times aligns well with the observation that non-Gaussian behavior is emphasized in high-b-value
imaging.
Conclusion
Diffusion MR imaging is a flourishing field, which has grown
in complexity and applications since its introduction nearly
52
three decades ago. While DTI has become an accepted clinical

procedure and other models have displayed utility in neuroscience research, there is no consensus on the best model and
acquisition. Understanding the relative strengths and weaknesses associated with each technique is critical when evaluating studies and deciding on protocols.
See also: INTRODUCTION TO METHODS AND MODELING:

Diffusion Tensor Imaging; Fiber Tracking with DWI; Probability
Distribution Functions in Diffusion MRI; Q-Space Modeling in
Diffusion-Weighted MRI; Tensor-Based Morphometry; Tissue
Microstructure Imaging with Diffusion MRI; Tract Clustering, Labeling,
and Quantitative Analysis; Tract-Based Spatial Statistics and Other
Approaches for Cross-Subject Comparison of Local Diffusion MRI
Parameters.
References
Assaf, Y., Freidlin, R. Z., Rohde, G. K., & Basser, P. J. (2004). New modeling and
experimental framework to characterize hindered and restricted water diffusion in
brain white matter. Magnetic Resonance in Medicine, 52, 965978.
Basser, P. J., Mattiello, J., & Le Bihan, D. (1994). MR diffusion tensor spectroscopy and
imaging. Biophysical Journal, 66, 259267.
Callaghan, P. T. (1991). Principles of nuclear magnetic resonance microscopy. Medical
Physics, 19, 1121.
Chenevert, T. L., Brunberg, J. A., & Pipe, J. G. (1990). Anisotropic diffusion in human
white matter: Demonstration with MR techniques in vivo. Radiology, 177, 401405.
Einstein, A. (1905). On the movement of small particles suspended in stationary
liquids required by the molecular-kinetic theory of heat. Annelan der Physik, 17,
549560.
Hui, E. S., Cheung, M. M., Qi, L., & Wu, E. X. (2008). Towards better MR
characterization of neural tissues using directional diffusion kurtosis analysis.
Jensen, J. H. & Helpern, J. A. (2003). Quantifying non-Gaussian water diffusion by
means of pulsed-field-gradient MRI. In Proceedings of the International Society for
Magnetic Resonance in Medicine, p. 2154.
Jensen, J. H., Helpern, J. A., Ramani, A., Lu, H., & Kaczynski, K. (2005). Diffusional
kurtosis imaging: The quantification of non-gaussian water diffusion by means of
magnetic resonance imaging. Magnetic Resonance in Medicine, 53, 14321440.
Le Bihan, D., Breton, E., Lallemand, D., Grenier, P., Cabanis, E., & Laval-Jeantet, M.
(1986). MR imaging of intravoxel incoherent motions: Application to diffusion and
perfusion in neurologic disorders. Radiology, 161, 401407.
Moseley, M. E., Cohen, Y., Kucharczyk, J., Mintorovitch, J., Asgari, H. S.,
Wendland, M. F., et al. (1990). Diffusion-weighted MR imaging of anisotropic water
diffusion in cat central nervous system. Radiology, 176, 439445.
Reese, T. G., Heid, O., Weisskoff, R. M., & Wedeen, V. J. (2003). Reduction of eddycurrent-induced distortion in diffusion MRI using a twice-refocused spin echo.
Stejskal, E. O., & Tanner, J. E. (1965). Spin diffusion measurements: Spin echoes in
the presence of a time-dependent field gradient. Journal of Chemical Physics, 42,
288.
Tuch, D. S., Reese, T. G., Wiegell, M. R., Makris, N., Belliveau, J. W., &
Wedeen, V. J. (2002). High angular resolution diffusion imaging reveals
intravoxel white matter fiber heterogeneity. Magnetic Resonance in Medicine, 48,
577582.
Wang, Y., Wang, Q., Haldar, J. P., Yeh, F.-C., Xie, M., Sun, P., et al. (2011).
Quantification of increased cellularity during inflammatory demyelination. Brain,
134, 35903601.
Wedeen, V., Reese, T., Tuch, D., Weigel, M., Dou, J., Weiskoff, R., et al. (2000).
Mapping fiber orientation spectra in cerebral white matter with Fourier-transform
diffusion MRI. In: Proc. Intl. Sot. Mag. Reson. Med. 8, (p. 5627).
Wu, Y. C., & Alexander, A. L. (2007). Hybrid diffusion imaging. NeuroImage, 36,
617629.
Zhang, H., Schneider, T., Wheeler-Kingshott, C. A., & Alexander, D. C. (2012). NODDI:
Practical in vivo neurite orientation dispersion and density imaging of the human
brain. NeuroImage, 61, 10001016.
Echo-Planar Imaging
F Schmitt, Siemens Healthcare, Erlangen, Germany
Historical Development of Echo-Planar Imaging

Echo-planar imaging (EPI), was invented by Sir Peter Mansfield
in 1977 (Mansfield, 1977) long time before major companies
invested in the development of clinical magnetic resonance
imaging (MRI), which started in honest in 1983. Peter Mansfield
received the Nobel Prize in 2003 for his contribution in the
development of MRI and EPI in particular. His research group
in Nottingham focussed on the technical challenges of image
formation under bipolar gradients. In the late 1980s it eventually
reached the state to be used for abdominal and cardiac imaging
(Howseman et al., 1988) and eventually also for neuro-imaging
(Stehling et al., 1991).
In the mid 1980s Ian Pykett and Richard Rzedzian, both
being trained in Sir Peter Mansfields lab, founded Advanced
NMR (ANMR) which used a 2 T magnet for its EPI development.
In 1987 they published the first in vivo human body imaging
using EPI (Pykett and Rzedzian, 1987). ANMR provided the first
commercially available EPI-only scanner. It was installed at the
Massachusetts General Hospitals (MGH) research center in
Charlestown, MA, USA in 1990. An existing General Electric
Signa 1.5 T scanner was retrofitted with the ANMR Instascan
console and EPI capable gradients driven in a resonance circuit
(Cohen and Weiskoff, 1991). At Siemens EPI activities started in
1987, with the first imaging results in March 1988 (Schmitt,
et al., 1988a,b). However, the results from MGH running an
ANMR EPI scanner spurred the efforts at the other major vendors significantly. This effort resulted in the first EPI scanner
installed in a clinical environment at the Beth Israel Hospital
(BIH) in Boston under Bob Edelmans guidance in summer
1992 (Edelman et al., 1994b; Schmitt et al., 1993).
As EPI is the fastest MRI technique, the early EPI scanners
were primarily dedicated to explore applications in the body
and heart to freeze the motion. Other body organs also have
been explored, such as liver and kidney imaging (Muller et al.,
1994) and even cardiac diffusion (Edelman et al., 1994a,b) has
been tried out. However, it soon turned out that the susceptibility effects at the heart-lung tissue interface or the air in the
bowels were too severe to make this a valuable and acceptable
clinical tool for general whole body applications. While the
MGH primarily focussed on EPI for perfusion and succeeding
to neuro-functional MRI (fMRI), eventually the BIH scanner
was successfully used for early stroke imaging and therefore
opened the door to important clinical use.
The discovery that MRI is feasible to see signal changes
when performing visual tasks was key to the dissemination of
EPI as a method on clinical scanners for the use in neuroscience. Therefore, I describe in short the key events which
are important for understanding the role of EPI in functional
MRI and its technology development.
That blood changes its tranverse relaxation time depending
on oxygenation was shown by Thullborn et al. (1982). Seiji
Ogawa described the blood oxygenation level dependent

(BOLD) effect in 1990 and proposed to apply it for measuring
brain function after activation (Ogawa et al., 1990). His first
mouse imaging data were acquired by using a conventional
gradient-recalled echo (GRE) imaging sequence at a vertical
bore 7 T magnet. In Boston, at the MGH, John Belliveau
(Belliveau et al., 1991) performed the first contrast enhanced
(CE) human in vivo functional MRI experiment using EPI.
While Belliveau focussed on CE methods, Ken Kwong performed the first susceptibility weighted EPI-GRE based
human in vivo experiment in 1991 (Kwong, 2012).
After initial animal experiments, Seiji Ogawa and Kamil
Ugurbil succeeded with human in vivo fMRI on a 4 T scanner
in Kamil Ugurbils MRI lab in Minneapolis in 1991 (Ogawa
et al., 1992). Their initial experiments were based on a conventional T1 weighted two dimensional (2D) GRE technique, called
FISP imaging (Oppelt et al., 1986). They later moved to EPI also.
Besides MGH, other groups also recognized that EPI was
important for fMRI and focussed their efforts on this technology. In 1991, Peter Bandettini and Eric Wong build their own
EPI gradient coil (Bandettini, 2011) and produced their first
fMRI results in fall 1991. In the end, when they published their
work in 1992, it was in fact the first published paper on human
in vivo BOLD fMRI (Bandettini et al., 1992).
About the same time Bob Turner, an early fellow of Sir Peter
Mansfield in Nottingham, skilled in knowledge about EPI and
gradient coil design built his own z-gradient coil, capable of
performing EPI for fMRI at NIH. He first used it for diffusion
weighted imaging, but realized after the MGH results have
been shown that its use for fMRI is essential. His results were
published in 1993 (Turner et al., 1993).
In Bob Shulmans lab at Yale, Andrew Blamire developed
his version of EPI on a 2.1 T whole body scanner running a
Bruker Biospec NMR console. His results have been shown at
the ISMRM 1992 in Berlin (Blamire et al., 1992).
In the mid 1980s Le Bihan et al. realized that diffusion contrast can be utilized for viewing neurological pathologies in
tumors (Le Bihan et al., 1986). About at the time of the raise of
EPI driven fMRI it was also discovered that the combination of
diffusion weighting with EPI as data acquisition module has great
potential for clinical neurological examinations for the detection
of early onset of stroke (Moseley et al., 1990; Warach et al., 1992).
Eventually ANMR was bought by GE which sold about 20
of these scanners before GE started its own EPI development.
By mid-1990 EPI was introduced with their new generation
scanners by all the major MRI vendors and now is a technique
available in many facets on every MRI platform, ranging from
full size whole body human scanners with field strengths from
0.5 T up to 11.7 T to animal scanners at field strength up to
16 T and higher.
For further reading on the history of EPI I suggest (Cohen &
Schmitt, 2013; Mansfield, 2013; Ordidge, 1999).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00006-3
53
54
INTRODUCTION TO ACQUISITION METHODS | Echo-Planar Imaging
Pulse Sequences
The MR signal generation and reception is quite complex and will
not be described in this article. Pulse sequences are the essence of
an MRI machine, as it allows acquiring the data required to
calculate images of the organ on scope. For better understanding
MR imaging methods see Mark Haackes book on Physical principles and sequence design of MRI (Haacke et al., 1999a).
Below, a brief walk from the most basic MR pulse sequence,
the GRE sequence, to the various EPI sequences is given. All
common neuroscience and clinical neurology-related single
shot EPI sequences are described.
The Basic GRE Pulse Sequence

Conventional MR imaging is based on the interaction of the
magnetic moment of proton spins (in water) with static and
dynamic electromagnetic fields. A strong magnet is needed to
create a net polarization of spins which can then be excited with
RF pulses and hence generates the MR signal. Pulsed gradients
(see a typical GRE pulse sequence in Figure 1) are used for slice
selection (SS) and spatial image encoding. The direction of the
three axis gradients are commonly referred to as SS, phase
encoding (PC), and read out (RO) gradient orientation. For SS
an RF-pulse is played out simultaneously with the SS gradient
pulse. The RF-pulse amplitude is commonly expressed with the
so-called excitation flip-angle. If only a single excitation pulse
gets applied, a flip angle of 90 always generates the strongest
MR signal. When driven in steady state, that is, repetitive, the
flip-angle required optimizing contrast and signal-to-noise-ratio
(SNR) for specific applications is lower (1020 ) (Ernst &
Anderson, 1966). This GRE imaging method is also called fast
low angle shot imaging and was invented in 1986 by Haase et al.
(1986).
The gradient echo formation is best explained with the
k-space method. For deeper understanding of the k-space
terminology we suggest (Haacke et al., 1999b). The definition
of k-space is given in eqn [1] below
t
kt g Gt dt
[1]
0
where G(t) defines the time dependent gradient pulse and g the
gyromagnetic ratio (g 42.578 MHz T1). In graphical terms,
the condition of a gradient echo is achieved when the area
under the (negative polarity) pre-phasing lobe of the RO gradient is balanced by the accumulated area under the (positive
polarity) RO gradient pulse. For clarity reasons these two sections are shown shaded in Figure 1. Usually, this coincides
with the time when the maximum signal is detected and is
called echo time (TE). While the SS and read-out gradient pulse
remain constant during the entire imaging process for a 2D
imaging experiment, conventional MRI employs a so-called
phase encoding step. After each repetition time (TR) one
(k-space) data line is acquired and the PC gradient is changing
a bit, by stepping in incremental steps of dGPC 2GPC/N from
GPC to GPC, where N is the matrix size. Total scan time is
therefore N times TR, while TR is defined application specific.
K-space traversal is line by line as shown in Figure 1. The
image is then calculated by a two dimensional Fourier
Transform (2D FT) of the acquired 2D k-space data (commonly called raw data).
The maximum signal can be expressed as
St TE So eTE=T2*
[2]
with So describing the MR signal without T2* relaxation. While

for T2* the following relation holds
1
1
gDBo
T2* T2
[3]
with DBo describing the magnetic flux changes across the voxel
caused by magnetic susceptibility differences of the adjacent
tissue (for fMRI this is the BOLD induced susceptibility effect).
T2* decay is happening asymmetrically across the k-space data
line.
For MR angiographic applications, for example, TE and TR
are kept as short as possible, while for measuring the best
BOLD signal for fMRI one needs to prolong TE quite substantially specific to the field strength of the magnet used. It is
generally established that for 1.5, 3, and 7 T TEs of 40, 30,
and 20 ms are used, respectively, while the repetition time TR is
on the order of seconds to avoid or minimize T1 weighting.
Assuming a matrix size of N 64, which was typically used for
fMRI in the early days, total scan times per image (i.e., slice) are
on the order of 25 min for a stack of slices covering the brain
volume of interest. This takes much too long for performing
useful fMRI experiments. But it can be and was used in the early
times of fMRI as no other faster method like EPI was available
(see above in the history section).
EPI Pulse Sequences

Many variants of EPI are possible providing T1, T2, T2*, and
diffusion weighting. Image acquisition is possible in single shot
and multi shot (i.e., segmented EPI). Here we describe all
relevant single shot EPI techniques only. For better understanding of the segmented techniques we suggest (Wielopolski et al.,
1998). Spiral EPI described by Ahn et al. (1986) which is as fast
as EPI is not described in this article. Contrary to EPI which
mostly uses a rectilinear k-space grid, spiral echo-planar samples the k-space on a spiral trajectory (non rectilinear grid). This
technique is used by some fMRI researcher. For further reading
on this we suggest (Meyer, 1998) as it has not fully made it into
the fMRI.
EPI uses a single shot pulsing scheme, meaning that all kspace data needed to reconstruct a final image gets acquired
after a single excitation pulse. In contrast to this GRE imaging
uses multiple shots to acquire the corresponding image data.
The key to the EPI sequence is the periodic RO gradient pulse
train shown in Figure 2. All k-space data lines are acquired
under this long RO pulse train. K-space traversal is in meander
like fashion as shown in Figure 2. The resulting MR image is
computed by performing a 2D FT similar to the above
described GRE image reconstruction, but some extra steps of
pre-processing of the k-space data are required. In particular kspace resampling, phase corrections and time reversal of every
other data line are required in order to fill the k-space properly.
Due to its alternating acquisition under positive and negative
gradient lobes, EPI is very vulnerable to the so-called Nyquist
55
a
RF
Raw data
Image data
GSS
2D FT
GPC
GRO
RO
Signal
TE
TR
(a)
PC 1
2
.
.
.
.
.
.
t
.
.
.
.
N
et/T2*
K-space
Image space
1..N
K-space trajectory
Figure 1 (a) GRE sequence. Left column: GRE-2D pulse sequence. Note: Condition for a GRE is highlighted in shaded areas of GRO pulse train.
Middle column: typical magnitude raw-data set (above) and rectilinear k-space trajectory (below). Right column: resulting image. (b) 7 T T2* weighted
high-resolution GRE images (1024 1024 matrix size). Left: magnitude image, right: phase image. Note the contrast variations in the phase image
across the optical radiation fiber bundles (see arrows).
EPI-GRE Sequence
or N/2-ghosting artifact which creates double/ghost images
shifted by half the matrix size N and wrapped around in PC
direction. For further reading on EPI image reconstruction we
suggest (Schmitt et al., 1998).
Figure 2 shows the most basic EPI sequence, that is, the
EPI-GRE type which is used for BOLD imaging. The image
is acquired after a single RF-pulse excitation. Shape and
amplitude of PC and the RO gradient pulses are kept
90
RF
RO
PC 1
2
.
.
.
.
.
.
.
.
.
.
N
PC blips
GPC
EPI Readout
Phase Correction
GRO
et/T2*
Signal
GSS
N....1
N+1 .2N
1..N
K-space trajectory
t
(a)
TE
Figure 2 (a) 2D EPI-GRE sequence. Left column: EPI-GRE sequence. MR signal is T2* weighted as indicated in signal trace. Right column: K-space
trajectory is meander like starting from upper right to lower left. Advance in PC direction is generated by little blips in PC direction. (b) Typical 2D
EPI-GRE images through brain taken on a 3 Thead-only MRI system. Scan parameters: Single shot EPI; TE/TR 3000/50 ms; 128 128 matrix size;
48 slices at 3 mm voxel size.

constant during the acquisition of the entire image. What is
established with the PC table in a regular GRE sequence is
accomplished by small gradient pulses (so-called blips)
during the zero crossings of the periodically oscillating RO
gradient pulse train. Typically trapezoidal or sinusoidal
pulse shapes are applied. Although sinusoidal RO gradient
pulses have dominated the early times of EPI (Cohen et al.,
1991; Mansfield et al., 1991; Schmitt et al., 1989), these
days, they are neglected entirely and trapezoidal pulses are
only used. For simplicity we therefore stick to trapezoidal
pulses in all the graphical representations of sequences.
Under each half wave of the RO pulse train, a single kspace data line is acquired. Hence scan time is significantly
shorter, that is, for N 64 and a typical basic frequency of
1 kHz (corresponding to 500 ms per half wave) a total RO
period of 32 ms is achieved. By considering a few milliseconds for the SS the total scan time per slice is below 40 ms,
in case no acceleration methods such as half Fourier imaging (Haacke et al., 1991; Margosian et al., 1986) or parallel
receive, pRX, methods (see succeeding text) are applied. To
cover the entire brain with 3 mm thick slices the resulting
TR is typically on the order of 35 s and therefore the total
scan time is also on the order of 35 s.
Figure 2 resembles a susceptibility weighted 2D multi slice
EPI-GRE sequence which is widely used across different
57
magnet field strength. T2* decay is asymmetric around the

echo center at TE. To optimize for strongest BOLD effects the
TE needs to be adjusted accordingly, as described previously. In
the RO gradient axis, an extra pulsing scheme, the phase correction section, is introduced before the actual EPI readout.
Data acquired under these pulses are used for image reconstruction, to align the trace of echoes and fit the k-space
smoothly before performing the final image reconstruction
via Fourier Transformation. A more detailed description of
the phase corrections for EPI is presented in (Schmitt and
Wielopolski, 1998).
For fMRI a multi slice scheme covering the brain area of
interest is repeated over and over again until the activation
paradigm is finished. Often 500 volumes are acquired resulting
in a total BOLD scan time on the order of 1020 min.
EPI-SE Sequence Type

While the EPI-GRE sequence is highly sensitive to the BOLD
effect from large venous vessels, it however, can mimic activation away from functionally active gray matter (GM) (Olman
et al., 2007). Also, sometimes fMRI experiments request to
separate the BOLD effect of small from large venous vessels at
higher resolution. For this case a so-called Hahn spin-echo
(HSE) (Hahn, 1950) excitation scheme is applied (see Figure 3).
180
90
RF
GSS
RO
PC blips
GPC
1
PC 2
.
.
.
.
.
.
.
.
.
.
N
GRO
t
et/T2
1....N
2N .N+1
K-space trajectory
e|t|/T2*
t
t
TE
(a)
Figure 3 (a) 2D EPI-SE sequence. Left column: EPI-SE sequence. MR signal is T2 weighted as indicated in signal trace. T2* weighting still exists, but is
very minor and occurs only earlier and later to TE. Right column: K-space trajectory is meander like starting from upper left to lower right. Note the
difference in k-space traversal due to 180 HSE refocussing pulse.
(Continued)
58
Figure 3 contd (b-g) Anatomical and functional images from one volunteer taken at 9.4 Tesla. High-resolution anatomical GRE images (b) and (c)
clearly show the veins in both the magnitude and phase representation, respectively. SE-EPI (d) and GRE-EPI (e) have been acquired with 1 mm3
voxel size and show clear activation of the motor and somatosensory cortex (color overlay). Zoomed images of the activation, registered to the
high-resolution anatomical data, are shown in (f) and (g). The locations of the veins are overlaid in blue. The color bar shows the z-score and scaling is
equal in whole brain and zoomed images. Images with permission from MRM and courtesy of Budde, J., Shajan, G., Zaitsev, M., Scheffler, K., &
Pohmann, R. (2014). Functional MRI in human subjects with gradient-echo and spin-echo EPI at 9.4 T. Magnetic Resonance in Medicine, 71, 209218.
Max Planck Institute Tubingen.
A HSE is created with a 90 -t-180 -t-TE RF pulse train. At TE

the susceptibility contrast is zero and the signal is purely T2
weighted and can be expressed as
St TE So eTE=T2
[4]
Susceptibility/T2* weighting is much smaller and is present

only before and after TE and therefore affects the higher spatial
frequency raw-data lines only, as being indicated in Figure 3.
Overall the effects of susceptibility weighting are considered
very small and this technique therefore is better suited for high
resolution fMRI at ultra-high magnetic fields such as 7 T and
above (Budde et al., 2014; Yacoub et al., 2005).
The EPI-HSE excitation scheme is also the basis for diffusion imaging. See succeeding text.
Perfusion Imaging Using EPI

Two types of imaging methods using EPI are available for
qualitative and quantitative perfusion measurement in the
brain. A T2* based CE method using Gadolinium compounds,
such as Gd-DTPA, is commonly used for qualitative evaluation
of perfusion in tumors or stroke. Quantitative blood flow
imaging can be performed with a T1 based method called
arterial spin labeling (ASL).
Dynamic susceptibility contrast perfusion imaging using EPI

Gadolinium bolus imaging is used for qualitative perfusion in
stroke and tumors. To employ this before, during and after
bolus injection of a Gadolinium compound, the entire brain is

repetitively scanned with a multi slice GRE-EPI sequence (b.t.
w. this is the method which was used by Jack Belliveau in his
first CE based fMRI experiment). Sometimes an SE-EPI
sequence is used to highlight effects of smaller vessels (see
preceding text). TEs are ranging between 30 and 50 ms and
50 and 80 ms for a GRE-EPI and SE-EPI acquisition respectively. TR is typically kept below 2 s in order to allow sufficient
time points by covering the entire brain. Total acquisition time
is on the order of 90120 s. Contrast dose is typically
0.10.2 mmol kg1.
On the order of 100 time points are scanned. The time course
of selected voxels in a region of interest, that is, tumor or stroke
lesion, can be used to calculate specific maps reflecting the
physiological state of lesion. Typical maps are relative cerebral
blood volume, relative mean transit time, time to peak, etc.
Arterial input function, information is requested (time course
of a selected arterial vessel) for calculating these maps.
Figure 4 shows the basic time course and the achieved
image contrast during a DSC imaging experiment with administered Gadolinium bolus.
ASL for quantitative perfusion using EPI

MR Imaging can be sensitized to inflowing spins of blood if
these spins have different magnetization state compared to that
of stationary tissue. The technique to achieve this is called
arterial spin labeling introduced by Detre et al. (1992) as continuous ASL, refined by Edelman and Chen (1998) as EPISTAR
and Wong et al. (1997, 1998) as PICORE and QUIPSS. The
inflowing blood exchanges with the tissue water and therefore
changes the tissue magnetization. Based on this effect quantitative perfusion weighted images can be generated by subtracting
labeled and unlabeled inflowing blood signal images. The
strength of the ASL signal changes, DS, as a function of time
and is also dependent on T1 of blood, T1B. It can described as
Signal
t
DSt B0 e T1B
[5]
59
As T1B prolongs with increasing magnetic field, longer data

acquisition times after the tagging pulses can be utilized and
the overall ASL SNR increases with increasing field strength.
This technique can be applied to achieve quantitative blood
flow measurements or even for fMRI of brain activation. Figure 5
shows a principle ASL sequence. Here an EPI-SE version is shown.
A faster method is using an EPI-GRE sequence module as the basic
acquisition scheme. A tagging slap (inversion) is excited in the
neck region followed by an EPI data acquisition covering the entire
brain. Figure 6 shows a functional MRI finger tapping comparison
of BOLD and ASL, acquired at 7 T. The same areas of the cortex are
activated and demonstrated with both techniques.
Diffusion Weighted Imaging Using EPI

The mostly used pulse sequence scheme for diffusion weighting
imaging (DWI) is the so-called StejskalTanner scheme (Stejskal
and Tanner, 1965) which uses an EPI-SE sequence as the basic
imaging module. Additional to the EPI-SE pulse scheme strong
diffusion weighting gradient pulses are placed symmetrically
around the 180 refocussing pulse (see Figure 7). The signal at
echo-time TE with existing diffusion weighting can therefore be
expressed as
DSt TE;b So eTE=T2 ebD
[6]
D describes the tissue dependent diffusion coefficient and b the

strength of the diffusion weighting, described in the simplest
form of rectangular diffusion lobes shown in Figure 7 as

d
[7]
b g2 G2 d2 D
3
Clinical diffusion sequences for exploring early stroke, for
example, use b-weighting of 1000 s mm2. A series of different
b-weighting for a stroke case is shown in Figure 8. It is obvious
that the diffusion contrast peaks at about 1000s mm2. which in
fact is commonly used in clinical routine stroke scanning.
500
450
400
350
300
250
0s
1.5 s
10
3s
4.5 s
20
6s
30
7.5 s
9s
40
Time point
10.5 s 12 s 13.5 s
Figure 4 T2* weighted perfusion time curve. Images shown in insert show the actual time stamps from the bolus arrival until 13.5 s after bolus.
60
HSE-180
Inversion 180
90
t
RF
TI
TE
GSS
GPC
Imaging
slices
Inversion
slab
GRO
Figure 5 2D EPI-ASL sequence. Typically a thick slab in the neck region is inverted and after a wait time of TI an EPI-SE sequence is used to acquire the
flow sensitive MR signal.
Figure 6 Motor task ASL experiment (left) and its corresponding

BOLD fMRI experiment (right) taken at 7 T. Both acquisitions show
activation in the right motor sensory area. Images courtesy Lawrence L.
Wald.
In general, the diffusion coefficient is not a scalar quantity but will exhibit a directional dependence. For example,
water molecules can move rather freely along axonal fibers,
but are restricted in their motion perpendicular to fiber axis.
Thus, a tensor model is commonly applied which sets the
stage for advanced processing techniques like fiber tracking.
It requires a modification of the pulse sequence such that
diffusion lobes are applied in all three gradient directions
and vary in amplitude. Diffusion tensor imaging is one
variant of DWI, allowing to track neuronal fibers. It has
one caveat though; crossing fibers in a single voxel are
beyond the scope of the model and thus cannot be resolved
(Tournier et al., 2013). To overcome this uncertainty the
most general form of diffusion weighting (and processing)

called diffusion spectrum imaging (DSI) or high angular
resolution diffusion imaging (Tuch et al., 1999; Figure 9),
is applied. The latter employs significantly stronger b-weighting, typically 500015 000 s mm2. Conventional clinical
scanners therefore only achieve rather long echo-times
(over 100 ms) for those highly b-weighted scans.
Diffusion imaging is starving for SNR as the MR signal
decays very rapidly with increasing b-value, very strong gradients are therefore needed to achieve short echo-times. Experimental gradient systems performing in such a range have been
developed for the NIH Blueprint for Neuroscience Research
called Human Connectome Project (see Relevant Websites)
(Kimmlingen et al., 2012).
Figure 10 demonstrates what can be accomplished with
very high b-values at short TE. At b-values of
b 10 000 s mm2 still MR signal is visible, not visible at
longer TE. It is also obvious that a better fiber detection is
possible with those high b-weighted at shorter TE (Wedeen et
al., 2012).
Other EPI Sequence Variants Interesting for NeuroScience

Some sequence types which are kind off forgotten and are not
necessarily included in clinical scanners are worth mentioning
as they may provide interesting contrast for particular neuroscience questions.
Inversion recovery-EPI-GRE and Inversion recovery-EPI-SE

T1 contrast is not easily possible with EPI. Standard T1 GRE
sequences use a low flip GRE sequence with as short as
61
180
90
t
RF
TE
GSS
GDiff
GPC
d
d
D
GRO
Figure 7 2D EPI-Diffusion weighted imaging sequence applying the SteijskalTanner diffusion pulsing scheme. The basic sequence is an EPI-SE
sequence with strong diffusion sensitizing gradient lobes (GDiff) between 90 180 pulse and 180 -RO module. These gradient lobes can vary in
amplitude and direction depending on the DTI pulsing scheme. On clinical scanners (Gmax 45 mT m1) with b1000 this pulsing scheme results in
echo-times of about 80100 ms.
b values
s mm2
35
141
318
565
883
possible TR. As the EPI RO train is rather long that method

does not work well for EPI as the TR would be too long and
additionally there is always a strong T2 and T2* weighting
involved. Instead, similar to the MPRAGE sequence (Mugler
& Brookman, 1991) an inversion recovery (IR) 180 pulse is
applied to invert the Mz magnetization. After a certain wait
time, TI, the regular EPI GRE (see Figure A2(a)) or SE (see
Figure A2(b)) pulse scheme is applied. TI is usually set to
null specific tissue type T1, such as fat, WM or, GM. In
principle, form a series of different TIs one can calculate a
T1 image (Ordidge, Gibbs, Chapman, Stehling, & Mansfield,
1990). Figure A2(c) shows a mid-slice series of TI ranging
from 0 to 3800 ms. A TI of about 1200 ms provides great
GR/WM contrast. This TI, for example, can be best used to
overlay fMRI activation maps as the image distortion can be
adjusted the same as for the BOLD sequence, i.e., no misalignment between the BOLD and the anatomical scans is
present.
EPI-GRE-SE
1271
Figure 8 2D multi slice EPI diffusion weighted scanning in patient with

a stroke in left MCA. Left column shows the b-weighting. Common
clinical practice uses a b-value of 1000 s mm2. Images courtesy Steven
Warach, Bob Edelman, BIH.
As mentioned above EPI-GRE used for BOLD is very sensitive

to larger venous vessels, while EPI-SE is more sensitive to
smaller vessels. Normally when exploring these two excitation
methods they are applied consecutively. It can, however, be
combined in one pulse sequence as shown in Figure A3. First
the T2* weighted GRE signal is acquired and after a 180
inversion pulse the T2 (and weakly T2*) weighted HSE signal
180
90
t
RF
TE
GSS
GPC
GRO
Figure 9 2D EPI-DSI sequence with diffusion encoding in three directions. Due to the typically very high b-weightings used in DSI long echo-times in
the excess of 100 ms is resulting. This method is therefore better used in very high performing gradient systems (Gmax > 100 mT m1).
b = 10 000 s mm2, 1.5mm isotropic resolution diffusion weighed images (single direction)
Gmax = 40 mT m1
100 mT m1
300 mT m1
bmax = 10 000 s mm2
10 000 s mm2
10 000 s mm2
15 000 s mm2
Gmax = 40 mT m1
100 mT m1
200 mT m1
300 mT m1
Figure 10 Upper row: Diffusion weighted images (single direction) acquired at Gmax 40 mT m1, 100 mT m1 and 300 mTm1 with
b 10,000 s mm2 and 1.5 mm isotropic resolution. Corresponding TE is 120, 80, 50 ms, respectively. i.e. with increasing available maximum
gradient strength shorter echo times are achieved and hence SNR of the diffusion weighted scans is significantly improved. Data acquired with the 64
channel brain array. Lower row: Effect of gradient strength on diffusion MRI of path crossings. DSI with peak gradients Gmax 40, 100, 200, and
300 mT m1, with mixing time adjusted for constant bmax 10 000 s mm2 are shown in panels 13 (from left to right), and bmax 15 000 in panel 4. As
noted, TEs are minimized for each Gmax. The total number of path solutions identified within the Superior longitudinal fasciculus (SLF; horizontal
green, at center) increases by about 50% from the conventional (40 mT m1) to ultra-high gradient levels. Crossing pathways increase more
dramatically, their count increases by 23x from conventional to intermediate gradient performance (100 mT m1), and an additional 23x gain from
intermediate to the ultra-high gradients (100 vs 300 mT m1). Images courtesy V. Wedeen and L.L. Wald, MGH Martinos Center.

is acquired (Schmitt et al., 1988b). However, due to the long
EPI RO train, a long TE is expected for the SE acquisition,
which results in a low SNR. This method therefore is better
suited for ultra high field imaging at 7 T and above.
EPI Limitations and Caveats

Magnetic Susceptibility and Its Effect on Image Quality
Human tissue has certain magnetic properties which become
relevant when exposed to an external magnetic field, H 0 , produced by the magnet coil winding. In general it can increase or
decrease the magnetic field (the flux) inside the human tissue,
depending on its magnetic properties i.e., dia, para od ferro
magnetic tissue. For further reading on magnetic susceptibility
we suggest (Ernst & Anderson, 1966). The relation between the
magnetic flux, B 0 , (the effective field the tissue is exposed to)
and the external field H 0 is describe with eqn [8]
B 0 m0 1 wH 0
[8]
m and x describe the magnetic permeability and susceptibility

(see also Ernst & Anderson, 1966)
Considering a tissue interface with susceptibility w1 and w2 a
local field inhomogeneity
DB0 w1 w2 B0
[9]
is caused, which results in local image distortion, Dx, and

phase differences, DF, as shown in eqns [10] and [11] below.
Dx
DB0
G
[10]
Significant image artifacts arise due to these local inhomogeneities. For further reading we suggest (Ludeke et al., 1985).
For EPI sequences the relevant gradient axis is the very low
strength equivalent PC gradient. Therefore severe distortions
can be seen in regions of strong susceptibility changes, such as
the eye and nasal sinus. Change of the polarity of the PC
gradient is changing the distortion behavior significantly, that
is, it can either stretch or squeeze those regions (see Figure 11).
This leaves room to optimize EPI accordingly to minimize
distortion effects.
Signal voids due to phase cancelation caused by intra-voxel
signal dephasing is also a common susceptibility-related issue
with EPI, described with eqn [11]
DFgDB0 t
[11]
Especially the nasal sinus regions, the top of frontal lobe

and the region close to the ear canals are prone to signal voids
when using EPI. The appearance of gross signal void susceptibility effects in echo-planar images is demonstrated with varying slice thickness (Figure 12(a)) and TEs (Figure 12(b)).
Obviously these are effects which limit the usability of EPI,
when not counter acted. Thin slices and reasonable short TE is
helpful. Applying in-plane acceleration methods, as described
later in this chapter, is also helping. An example of distortion
minimization is shown in Figure 11(b). Acceleration beyond
R 2 helps to reduce these uncertainties. Also, there are
correction methods known to reduce the susceptibility-caused
63
distortions. These methods need extra scans in order to correct

for static (Jezzard & Balaban, 1995) and dynamic (van Gelderen, de Zwart, & Stareweicz, 2007; Visser, Poser, Bart, & Zwiers,
2012) B0 deterioration. An image example using a similar
(static) technique (Zaitsev, Hennig, & Speck, 2004) is shown
in Figure 11(c). Acquisition parameters are the same as shown
for Figure A2(c). Most recently, methods have been proposed
to compensate for dynamic B0 variations.
Acquisition Speed is Limited by Physiological Effects due

to Peripheral Nerve Stimulation
When gradients are switched with high amplitudes and slewrates physiological side effects, such as peripheral nerve
stimulation (PNS) can occur. This effect was first reported
when applying EPI sequences in humans, causing muscle
twitching at the location of the strongest exposed field
(Figure 13; Budinger et al., 1991; Cohen et al., 1989; Fischer
et al., 1989). One way to mitigate this effect is by shortening
the linearity volume as shown in Figure 13. Head gradients
show the highest PNS thresholds as the gradient field extend is
typically very short (covering the head/brain only).
In general, the PNS threshold expressed in gradient
strength, GTH, is a linear function of the rise time, TRise, when
periodic gradient pulses are applied, such as it is used in EPI.
Sinusoidal and trapezoidal pulse trains result in slightly different slopes of the threshold curves as shown in Figure 14 left,
but still preserve the linear relation of GTH TRise (Irnich,
1993). Interesting to note is the fact that after a certain number
of periods (16 cycles) the thresholds reach a minimum
(Figure 14, right) (Schmitt et al., 1998).
Safe operation is guaranteed by implementing PNS safety
monitors who basically resemble the linear relation of Figure 14
and avoid PNS by staying below this linear threshold curve.
Quality Assurance and Temporal Stability

fMRI exams using EPI-BOLD acquisition is a highly repetitive
process, that is, the same stack of slices covering the brain is
repeated over and over again to follow the excitation paradigm.
Hence time points of each voxel are created and analyzed along
the time axis. Ideally one assumes that everything works perfectly and no extra noise from the MRI machinery or subject
itself is introduced. However, this is not the case. Both, the MRI
scanner and the human brain introduce statistical and systematical changes which need to be considered.
During scanning of the long lasting EPI acquisitions the
gradient system may heats up and expands. That can cause a
frequency drift (f0(t)) as the paradigm progresses. As an
effect a thermal drift in the temporal BOLD signal is visible
which may render an fMRI experiment useless if not counter acted (similar to what can be seen in Figure 15(b) top
left). To solve this the calibration scan (see Figure 2) is used
to extract the frequency drift f0(t) and shift the image
according to its f0 drift. Also, imperfections in shim, gradients and RF electronic may cause sudden changes in the
BOLD signal which are virtually impossible to compensate.
This was a common problem of the early days of fMRI and
now is more or less fixed through careful engineering of the
64

RO
PC
(a)
Figure 11 (a) Susceptibility artefacts. Distortion in eyes and nasal sinus. Polarity of PC gradient is inverted between left and right image, causing
stretching and squeezing of the eyes and nasal sinus region, respectively. (b) 1 mm resolution diffusion-weighted images showing improvement in
frontal lobe susceptibility distortion as acceleration is increased beyond R 2. Images acquired at 3 T with a 32ch head coil. Data courtesy of L.L. Wald,
MGH Martinos Center. (c) Distortion correction of EPI images via PSF deconvolution. EPI-GRE acquisition taken at 7 T with a 32RX head coil.
Slice thickness 1.4 mm; #slices 10; in plane resolution 1.41.4 mm2; FOV 224224; Matrix 160160; Partial Fourier 6/8; GRAPPA factor 3;
TR/TE 5000/25 ms.
30 ms
40 ms
50 ms
60 ms
Figure 12 (a) Susceptibility artefacts. Through-plane signal void as a function of slice thickness. The thicker the slice the more severe the signal voids. Image courtesy Lawrence L. Wald, MGH. (b) Susceptibility
artefacts. In-plane signal void as a function of echo time TE. The longer TE the more the signal voids are pronounced. Therefore BOLD fMRI is a balance between the desired BOLD signal effect and the
accompanying susceptibility aretfacts. Image courtesy Lawrence L. Wald, MGH.
21 ms
(b)
65
66
Bmax
zS
zL
FOVS
Z-gradient
FOVL
GTh(#pulse)
GTh(TRise)
Figure 13 Peripheral nerve stimulation in relation to short and long gradients illustrated with a z-gradient. PNS occur at location of strongest magnetic
flux exposure.
~30%
TRise
N
Th
#periods
Rise
Figure 14 PNS threshold gradient amplitudes as a function of gradient pulse rise time G fct(T ) for sinusoidal and trapezoidal pulse trains (left).
When increasing the numbers of pulses per pulse train, threshold reduces by about 30% and reach a stable value at about 16 periods.
entire gradient chain. However, care must be taken in order

to understand the fidelity of the MRI scanner in use for
fMRI. As the BOLD signal is on the order of a few percent,
overall the temporal stability requirements for performing
good fMRI should not exceed 0.5% peakpeak with thermal
drift compensated.
Clinical MRI exams are less vulnerable to these fluctuations
compared to fMRI scans. Therefore, a daily quality assurance
(QA) procedure is helpful to determine the status of an MRI
scanner when used for fMRI. The evaluation procedure was
introduced by Robert Weisskoff in 1996 (Weisskoff, 1996) and
is now considered the gold standard for performing quality
assurance for fMRI.
It is important to note that the brain itself creates physiological noise which appears in the temporal behavior of the
BOLD signal. This was carefully investigated over the last
decade and can be best understood by reading the publications
of Triantafyllou, Wald et al. (Triantafyllou et al., 2005, 2011)
which describe these phenomena over a range of field strength
of 1.5, 3, and 7 T. To demonstrate the relation of machine
noise and physiological noise see Figure 15. It shows temporal
fMRI signals of white matter (WM), gray matter (GM), and
cerebral spinal fluid (CSF) as well as from a small phantom
attached to the skull. It is obvious that the MRI machine noise,
taken from the phantom, should be smaller than the physiological noise.
Accelerated EPI
EPI is the fastest MRI pulse sequence existing. However, acceleration is still advantageous for a variety of reasons. One
reason for accelerating is to minimize susceptibility artefacts,
that is, distortion and signal voids, as described above. Another
reason is data throughput, that is, how many slices per seconds
can be acquired. This is generally achieved by using knowledge
of the spatial extend of the RF coil profiles of multi-channel
receive coils which are common these days. All major vendors
offer head RX coils with up to 32 RX channels for clinical
scanners now. Experimental coils have been proposed and
introduced offering up to 128 RX channels allowing even
further accelerations in MR imaging (Keil and Wald, 2013;
Wiggins et al., 2009).
Acceleration schemes are basically differentiated by
methods which accelerate the scan time per image (i.e., inplane) or by accelerating the scan time per stack of slices (i.e.,
through-plane). Here we briefly describe these two basic
methods, as they are interwoven into the EPI acquisition.
In-Plane Acceleration
The general terminology for accelerated MR imaging is parallel
imaging, abbreviated as pRX. These methods have been
WM
CSF
PH
GM
(a)
1135
1640
Phantom
Mean signal over ROI
1620
1610
1600
1590
1580
Stability(*)~ 0.5% peakpeak

(*) after detrending
0
50
CSF
1130
1630
100
150
200
Time points
1125
1120
1115
1110
1105
1100
1095
Stability ~ 1.8% peakpeak
1090
250
1085
300
840
250
300
250
300
905
150
200
Time points
GM
835
830
825
820
815 Stability ~ 0.7% peakpeak
(b)
100
910
WM
810
50
50
100
150
200
Time points
900
895
890
885
250
300
880
Stability ~ 1.1% peakpeak

0
50
100
150
200
Time points
Figure 15 (a) Cross sectional EPI-BOLD scan with adjacent phantom to the right taken on a 3T head scanner. Red boxes show 77 pixel
ROIs to be evaluated (see below). Scan parameter are TE 20 ms, TR 2000 ms, matrix size is 6464. (b) Time course evaluation of ROIs
(shown in red in Figure 15 (a)) do reflect MRI scanner noise and physiological noise of an fMRI experiment. Data courtesy of C. Triantafilou
and L. L. Wald, MGH.
67
68
invented at the turn of the last millennium. Pruessmann et al.

(1999) proposed the SENSE method, followed by Sodickson
(2000) who introduced SMASH. The GRAPPA method was
announced by Griswold et al. (2002) and later refined as
CAIPIRHINA (Breuer et al., 2005). Of these techniques
SENSE and GRAPPA are the most commonly used for fMRI.
In-plane acceleration for EPI shortens the RO pulse train. Extra
calibration data need to be acquired to calculate the deconvolution kernel for the SENSE/GRAPPA pRX reconstruction. In-plane SENSE and GRAPPA have the major drawback
that with increasing acceleration signal loss and structured
noise appears, rendering very high acceleration useless. SNR
relates to acceleration R as described in eqn [12], while g
describes the geometry factor, which is coil geometry dependent, and SNRo describes the intrinsic SNR without
acceleration
SNR 0
SNRaccel p
g R
[12]
With current RF coil technology acceleration of up to four

times can work reliably. This is very RF coil performance
dependent also.
Through-Plane Acceleration
Through-plane acceleration has been developed over the recent
35 years and is making very promising advances. These
methods are based on a technique called multi band (MB).
While the MB method exists since the early 2000s (Larkman
et al., 2001) it recently has been refined to allow very high
acceleration rates (Feinberg et al., 2010; Moeller et al., 2010).
Simultaneous multi slice (SMS) in combination with EPI is
based on blipped CAIPHRINHA and provides excellent
through-plane acceleration (Setsompop et al., 2012). The real
advantage of not losing SNR with increasing acceleration, as it
happens with the in-plane methods, is very helpful to maintain
high SNR with high accelerations. Through-plane acceleration
allows high temporal resolution resting state fMRI (rsfMRI) as
it shortens the scan time per stack of slices below a second (see
Figure 16).
For high resolution DSI with very long scan times of
30 min or longer are normal if no acceleration is applied.
Combining in-plane and through-plane acceleration helps
to shorten scan time significantly (Setsompop et al., 2013).
Figure 17 shows results of this technique taken at a 7 T
scanner. Fifteen-fold acceleration is achieved by applying
threefold in-plane (using GRAPPA) with fivefold throughplane SMS acceleration.
Appendix
Technology Development of EPI Capable Gradient Systems
The key specifications of a gradient system is shown in
Figure A1 and is characterized by
(a) the maximum achievable gradient amplitude, Gmax,
measured in magnetic flux variation per meter, that is,
mT m1, which is usually expressed as
Gmax SImax
[13]
with S describing the sensitivity of the gradient coil expressed

in units of gradient strength per current, that is, mT m1 A1
and Imax the current needed to achieve Gmax
(b) how fast one can switch a gradient pulse from zero to
maximum gradient strength, commonly expressed as slew rate
(SR) measured in units of gradient strength per second, that is,
T m1 s1.
SR
dG Gmax
dt T Rise
[14]
Other aspects of importance are

(c) how long one can pulse the gradients before they over
heat. This is generally expressed in something called gradient
power duty cycle (DC) expressed in (%)
t2
Gt 2 dt
100%
DCt1 ; t2 2t1
Gref t2 t1
[15]
(d) the gradient linearity over a certain volume of interest

which defines the geometric imaging fidelity, that is, if the
images is distorted and how much. Ideally the gradient field
should be perfectly linear and can then be described for a
z-gradient as
Bz z Gz
[16]
Note: for MR imaging only the z-component of the magnet

field is important.
MRI gradient performance was very meager at the beginning of MRI (around 1983) compared to these days. Gradient
strength of 1 mT m1 at a SR of 1 T s1 m1 or even lower was
common, while today state of the art whole body scanners of
all major vendors provide at least 40 mT m1 at SRs of
200 T m1 s1. EPI strongly benefits from this increase in performance. In fact, it was EPI which has driven the specification
to these current levels. Another driver for higher gradient specification is EPI based diffusion weighted imaging. Based on
such requests dedicated whole body gradient systems are now
in use providing 300 mT m1 at SR 200 T m1 s1, two orders
of magnitude stronger than the first commercial scanners provided (Kimmlingen et al., 2012).
The key components of a gradient system are the gradient
amplifier and the gradient coil. Gradient amplifiers can be
envisioned as very strong audio amplifiers providing high
output voltages and current in order to drive the specific pulses
through the gradient coil. Electric circuits are characterized by
its resistance (measured in O; 1 O 1 V A1) and inductance
(measured in milli Henry, mH; 1 H Vs/A). The relations
below (eqns [17] and [18]) describe the requirement for voltage and current for driving a trapezoidal gradient pulse
U L
dI
RI
dt
[17]
With U describing the voltage needed to drive a current change

(dI/dt) in a gradient coil of inductance L and resistance R
(Ohms law). Maximum voltage and current for reaching
Gmax at the shortest possible TRise is then expressed as.
(b)
(c)
(d)
69
Figure 16 Multiband through-plane acceleration applied to resting state fMRI at 3 T by using a 32 channel RX head coil. TE 30 ms and 1.6 mm isotropic voxel resolution. (a) Standard fMRI protocol-no
acceleration, TR 6.7 s, flip angle 90 . (b) MultiBand 6 acceleration, PE3, 6/8 PF, TR 6.7 ms, flip angle <90 . (c) MultiBand 6 acceleration, PE3, 6/8 PF, TR 1.1 ms, flip angle <90 . (d) 2 mm isotropic voxels.
MultiBand 6 acceleration, PE3, 7/8 PF, TR 0.74 ms, flip angle <90 . Images courtesy E. Yacoub, K. Ugurbil, D. Feinberg et al. CMRR, Minneapolis.
(a)
70
Figure 17 In-plane (GRAPPA) and through-plane (SMS) acceleration combined results acquired on a 7 T system by using a 32 channel RX
head coil: In total a R15-fold acceleration is achieved. Rin-plane3, Rthrough-plane5. Images courtesy K. Setsompop & J. Polmeni, MGH Martinos
Center.
G(t)
Gmax
t
I(t)
Gmax= S I max
TRise
Imax
V(t) = I(t)RL
dI ( t)
dt
V(t)
V max
V max = I max R + L
t
I max
TRise
Figure A1 Grad-pulse characteristics and specifications.
U max LS
Gmax
RImax
T Rise
[18]
Modern gradient coils have inductance and resistance of about

1 mH and 100 mO, respectively. Sensitivity is on the order of
0.05 mT m1 A1. Thus the maximum output voltage and
current required is on the order of 2000 V and 600900 A,

respectively. This is strongly depending on the gradient coil
design, resulting in lower or higher currents and voltages. For
further reading on understanding gradient systems we suggest
Schmitt (2009).
Inversion 180
71
90
RF
GSS
GPC
GRO
+Mz
Mz/signal
Magnetization Mz
et/T2*
MR signal
1et/T1
Mz
TNULL
TI
TE
(a)
Inversion 180
180
90
RF
GSS
GPC
GRO
0
+Mz
Mz/signal
Magnetization Mz
et/T2
MR signal
1et/T1
Mz
(b)
TNULL
TI
TE
Figure A2 (a) 2D Inversion recovery with EPI-GRE data acquisition sequence. (b) 2D Inversion recovery with EPI-SE data acquisition sequence.
(Continued)
Figure A2 contd (c) Typical image acquired with a 2D inversion recovery with EPI-GRE data acquisition sequence. Note the different TI causes
different contrast between GM and WM.
180
90
RF
GSS
GPC
GRO
et/T2*
et/T2
e(tTE
HSE)/T2*
t
TEGRE
TEHSE
Figure A3 GRE and SE double acquisition EPI sequence.
Acknowledgments
The author is grateful to T. Feiweier for reading and correcting
the manuscript and to H. Meyer for helping with sequence
diagrams. I also deeply appreciate receiving the imaging data
of K. Ugurbil, L.L. Wald, V. Wedeen, E. Yakoub, C. Triantafyllou, M.-H. In, O. Speck, G. Budde, K. Scheffler, R. Pohmann, K.
Setsompop, J. Polimeni, S. Warach, and R. Edelman.
See also: INTRODUCTION TO ACQUISITION METHODS: HighSpeed, High-Resolution Acquisitions.
References
History of EPI
Ordidge, R. (1999). The development of echo-planar imaging (EPI): 19771982.
Magnetic Resonance Materials in Physics, Biology and Medicine, 9, 117121.
Cohen, M. S., & Schmitt, F. (2013). Echo-planar imaging before and after fMRI: A
personal history. NeuroImage, 62, 652659.
Mansfield, P. (2013). The long road to Stockholm The story of MRI An
autobiography. Oxford: Oxford University Press, ISBN: 978-0-19-966454-1.
Cohen, M. S., & Weiskoff, R. M. (1991). Ultra-fast imaging. Magnetic Resonance
Imaging, 9, 137.
Schmitt, F., Fischer, H., & Barfu, H. (1988a). Echo-planar imaging (EPI) erste
Ergebnisse. Siemens Internal Communication.
Schmitt, F., Fischer, H., Bruder, H., et al. (1989). Reconstruction schemes for EPI with
sinusoidal read gradients. Book of abstract SMRI, Los Angeles. Magnetic
Resonance Imaging SMRI, 7(1), P-066.
Schmitt, F., Borth, G., Hagen, U., et al. (1993). A high performance whole body EPIscanner at 1.5 T. Book of abstract SMRI. Magnetic Resonance Imaging Journal, 3,
225.
Muller, M. F., Prasad, P. V., Siewert, B., Nissenbaum, M. A., Raptopoulos, V.,
Lewis, W. D., et al. (1994). Abdominal diffusion mapping using a whole body echo
planar system. Radiology, 190(2), 475478.
Edelman, R. R., Gaa, J., Wedeen, V. J., Loh, E., Hare, J. M., Prasad, P. V., et al. (1994).
In vivo measurement of water diffusion in the human heart. Magnetic Resonance in
Medicine, 32(3), 423428.
Howseman, A. M., Stehling, M. K., Chapman, B., et al. (1988). Improvements in snapshot nuclear magnetic resonance imaging. The British Journal of Radiology, 61,
822828.
Edelman, R. R., Wielopolski, P., & Schmitt, F. (1994). Echo-planar MR imaging.
Radiology, 192, 600612.
Kwong, K. K. (2012). Record of a single fMRI experiment in May of 1991. NeuroImage,
62, 610612.
MR Imaging
Haacke, E. M., Brown, R. W., Thompson, M. R., & Venkatesan, R. (1999a). Magnetic
resonance imaging Physical principles and sequence design. New York: Wiley,
ISBN 0-471-35128-8.
Haacke, E. M., Brown, R. W., Thompson, M. R., & Venkatesan, R. (1999b). The imaging
equation. In Magnetic resonance imaging Physical principles and sequence
design. New York: Wiley, ISBN 0-471-35128-8, Chapter 10.1.1.
Ernst, R. R., & Anderson, W. A. (1966). Application of Fourier transform spectroscopy
to magnetic resonance. Review of Scientific Instruments, 37(1), 93102.
Haase, A., Frahm, J., Matthaei, D., et al. (1986). FLASH imaging. Rapid NMR imaging
using low flip-angle pulses. Journal of Magnetic Resonance, 67, 258266.
Oppelt, A., Graumann, R., Barfuss, H., et al. (1986a). FISP A new fast MRI sequence.
Electromedica, 54, 1518.
Hahn, E. (1950). Spin echoes. Physics Review, 80, 580.
Meyer, C. H. (1998). Spiral echo-planar imaging. In F. Schmitt, M. K. Stehling, & R.
Turner (Eds.), Echo-planar imaging Theory, technique and applications
Magnetic resonance imaging in a fraction of a second. Berlin: Springer3-54063194-1, Chapter 21.
Ahn, C. B., Kim, J. H., & Cho, Z. H. (1986). High speed spiral scan echo planar imaging.
IEEE Transactions on Medical Imaging, 5(1), 25.
Mugler, J. P., & Brookman, J. R. (1991). Rapid three dimensional T1 weighted MR
imaging with the MP-rage sequence. Journal of Magnetic Resonance Imaging, 1,
561567.
73
Echo-Planar Imaging
Physics C: Solid State Physics, 10, L55L58.
Stehling, M. K., Turner, R., & Mansfield, P. (1991). Echo-planar imaging: Magnetic
resonance imaging in a fraction of a second. Science, 254, 4350.
Pykett, I. L., & Rzedzian, R. R. (1987). Instant images of the body by magnetic
resonance. Magnetic Resonance in Medicine, 5, 563571.
Mansfield, P., Harvey, P. R., & Coxon, R. J. (1991). Multi-mode resonant gradient coil
circuit for ultra high speed NMR imaging. Measurement Science and Technology, 2,
10511058.
Wielopolski, P., Schmitt, F., & Stehling, M. K. (1998). Echo-planar imaging pulse
sequences. In F. Schmitt, M. K. Stehling & R. Turner (Eds.), Echo-planar imaging
Theory, technique and applications Magnetic resonance imaging in a fraction of a
second. Berlin: Springer3-540-63194-1 Chapter 4.
Schmitt, F., & Wielopolski, P. (1998). Echo-planar image reconstruction. In F.
Schmitt, M. K. Stehling & R. Turner (Eds.), Echo-planar imaging Theory,
technique and applications Magnetic resonance imaging in a fraction of a second.
Berlin: Springer3-540-63194-1 Chapter 5.
Schmitt, F., Fischer, H., & Ladebeck, R. (1988b). Double acquisition echo-planar
imaging. Book of abstracts SCNMR, Berlin.
Ordidge, R. J., Gibbs, P., Chapman, B., Stehling, M. K., & Mansfield, P. (1990). Highspeed multislice T1 mapping using inversion-recovery echo-planar imaging.
fMRI
Thullborn, K. R., Waterton, J. C., Matthews, P. M., et al. (1982). Oxygenation
field. Biochimica Biophysica Acta, 714, 265270.
Ogawa, S., Lee, T. M., Nayak, A. S., & Tank, D. W. (1990). Brain magnetic resonance
imaging with contrast dependent on blood oxygenation. Proceedings of the National
Academy of Sciences, 87, 98689872.
Ogawa, S., Tank, D. W., Menon, R., et al. (1992). Intrinsic signal changes
accompanying sensory stimulation: Functional brain mapping with magnetic
resonance imaging. Proceedings of the National Academy of Sciences of the United
Belliveau, J. W., Kennedy, D. N., McKinstry, R. C., et al. (1991). Functional mapping of the
human visual cortex by magnetic resonance imaging. Science, 254(5032), 716719.
Oppelt, A., Graumann, R., Barfuss, H., et al. (1986b). FISP A new fast MRI sequence.
Electromedica, 54, 1518.
Bandettini, P. A. (2011). Sewer pipe, wire, epoxy, and finger tapping: The start of fMRI at
the Medical College of Wisconsin. NeuroImage, 62, 620631.
Bandettini, P. A., Wong, E. C., Hinks, R. S., Tokofksy, R. S., & Hyde, J. S. (1992). Time
course EPI of human brain function during task activation. Magnetic Resonance in
Medicine, 25, 390397.
Turner, R., Jezzard, P., Wen, H., et al. (1993). Functional mapping of the human visualcortex at 4 and 1.5 Tesla using deoxygenation contrast EPI. Magnetic Resonance in
Medicine, 29, 277279.
Blamire, A. M., Ogawa, S., Ugurbil, K., et al. (1992). Dynamic mapping of the human
visual-cortex by high-speed magnetic-resonance-imaging. Proceedings of the
Olman, C. A., Inate, S., & Heeger, D. J. (2007). The effect of large veins on spatial localization
with GE BOLD at 3 T: Displacement, not blurring. NeuroImage, 34, 11261135.
Yacoub, E., Van de Moortele, P.-F., Shmuel, A., & Ugurbil, K. (2005). Signal and noise
characteristics of Hahn SE and GE BOLD fMRI at 7 T in humans. NeuroImage, 24,
738750.
Budde, J., Shajan, G., Zaitsev, M., Scheffler, K., & Pohmann, R. (2014). Functional MRI
in human subjects with gradient-echo and spin-echo EPI at 9.4 T. Magnetic
Arterial Spin Labeling
Edelman, R. R., Siewert, B., Darby, D. G., et al. (1994). Qualitative mapping of
cerebral blood-flow and functional localization with echo-planar MR-imaging
and signal targeting with alternating radio-frequency. Radiology, 192,
513520.
Edelman, R. R., & Chen, Q. (1998). EPISTAR MRI: Multi-slice mapping of cerebral
blood flow. Magnetic Resonance in Medicine, 40, 800805.
Wong, E. C., Buxton, R. B., & Frank, L. R. (1997). Implementation of quantitative
perfusion imaging techniques for functional brain mapping using pulsed arterial
spin labeling. NMR in Biomedicine, 10, 237249.
Wong, E. C., Buxton, R. B., & Frank, L. R. (1998). Quantitative imaging of perfusion
using a single subtraction (QUIPSS and QUIPSS II). Magnetic Resonance in
Medicine, 39, 702708.
74
MR Diffusion Imaging
Stejskal, E. O., & Tanner, J. E. (1965). Spin diffusion measurements: Spin echoes in the
presence of time-dependent field gradient. The Journal of Chemical Physics, 42,
288292.
Le Bihan, D., Breton, E., Lallemand, D., et al. (1986). MR imaging of intravoxel
incoherent motions: Application to diffusion and perfusion in neurologic disorders.
Radiology, 161(2), 401407.
Moseley, M. E., Cohen, Y., Kucharczyk, J., et al. (1990). Diffusion-weighted MR imaging of
anisotropic water diffusion in cat central nervous system. Radiology, 176(2), 439445.
Warach, S., Chien, D., Li, W., Ronthal, M., & Edelman, R. R. (1992). Fast magnetic
resonance diffusion weighted imaging of acute human stroke. Neurology, 42,
17171723.
Tournier, J. D., Mori, S., & Leemans, A. (2013). Diffusion tensor imaging and beyond.
Magnetic Resonance in Medicine, 65(6), 15321556.
Tuch, D. S., Weisskoff, R. M., Belliveau, J. W., & Wedeen V. J. (1999). High angular
resolution diffusion imaging of the human brain, Proceedings of the seventh annual
meeting of the ISMRM, Philadelphia, p. 321.
Kimmlingen, R., Eberlein, E., Dietz, P., Kreher, S., et al. (2012). Concept and realization
of high strength gradients for the human connectome project, Proceedings of the
ISMRM 20th annual meeting in Melbourne, Australia, pp. 0696.
Wedeen, V. J., Wald, L. L., Cohen-Adad, J., et al. (2012). In vivo imaging of fiber pathways
of the human brain with ultra-high gradients. Proceedings of the twentieth annual
meeting of the Society of Magnetic Resonance in medicine, Melbourne, p. 6490.
EPI Limitations
Luedeke, K. M., Roeschmann, P., & Tischler, R. (1985). Susceptibility artefacts in NMR
imaging. Magnetic Resonance Imaging, 3, 329343.
Haacke, E. M., Brown, R. W., Thompson, M. R., & Venkatesan, R. (1999). Permeability
and susceptibility. Magnetic Resonance imaging Physical Principles and
Sequence Design (Chapter 25.2). New York: Wiley, ISBN 0-471-35128-8.
Jezzard, P., & Balaban, R. R. (1995). Correction for geometric distortion in echo-planar
images for B0 field variations. Magnetic Resonance in Medicine, 34, 6573.
Visser, E., Poser, B. A., Bart, M., & Zwiers, M. P. (2012). Reference-free unwarping of
EPI data using dynamic off resonance correction with multi acquisition (DOCMA).
van Gelderen, P., de Zwart, J. A., Stareweicz, P., et al. (2007). Real-time shimming to
compensate for respiratory induced Bo fluctuations. Magnetic Resonance in
Medicine, 57, 363368.
Zaitsev, M., Hennig, J., & Speck, O. (2004). Point spread function mapping with parallel
imaging techniques and high acceleration factors: Fast, robust, and flexible method
for echo-planar imaging distortion correction. Magnetic Resonance in Medicine, 52,
11561166.
Cohen, M. S., Weisskoff, R. M., & Kantor, M. L. (1989). Evidence of peripheral nerve
stimulation by time varying magnetic fields, Proceedings of the Radiological Society
of Northern America (RSNA), 75th annual meeting, p. 1188.
Fischer, H., Hentschel, D., Schmitt, F., et al. (1989). Physiological effects by fats
oscillating magnet field gradients, Proceedings of the Radiological Society of
Northern America (RSNA), 75th annual meeting, p. 1189.
Budinger, T. F., Fischer, H., Hentschel, D., et al. (1991). Physiological effects of fast
oscillating magnetic flux gradients. Journal of Computer Assisted Tomography, 15,
909914.
Schmitt, F., Irnich, W., & Fischer, H. (1998). Physiological side effects of fast gradient
switching. In F. Schmitt, M. K. Stehling & R. Turner (Eds.), Echo-planar imaging
Theory, technique and applications Magnetic resonance imaging in a fraction of a
second. Berlin: Springer, ISBN 3-540-63194-1, Chapter 7.
Irnich, W. (1993). Magnetostimulation in MRI, Proceedings of the seventh annual
meeting of the Society of Magnetic Resonance in medicine, New York, p. 1371.
fMRI Quality Assurance
Weisskoff, R. M. (1996). Simple measurement of scanner stability for functional NMR
imaging of activation in the brain. Magnetic Resonance in Medicine, 36, 643645.
Triantafyllou, C., Hoge, R. D., Krueger, G., et al. (2005). Comparison of physiological
noise at 1.5 T, 3 T and 7 T and optimization of fMRI acquisition parameters.
Triantafyllou, C., Polimeni, J. R., & Wald, L. L. (2011). Physiological noise and signalto-noise ratio in fMRI with multi-channel array coils. NeuroImage, 55(2), 597606.
Accelerated MR Imaging
Margosian, P., Schmitt, F., & Purdy, F. (1986). Faster MR imaging: Imaging with half
the data. Health Care Instruments, 1, 195197.
Haacke, E. M., Lindskop, E.-D., & Lin, W. (1991). Partial-Fourier imaging. A fast,
iterative, POCS technique capable of local phase recovery. Journal of Magnetic
Resonance, 2, 126145.
Sodickson, D. K. (2000). Tailored SMASH image reconstructions for robust in vivo

parallel MR imaging. Magnetic Resonance in Medicine, 44, 284289.
Griswold, M. A., Jakob, P. M., Heidemann, R. M., et al. (2002). Generalized
autocalibrating partially parallel acquisitions (GRAPPA). Magnetic Resonance in
Medicine, 47(6), 12021210.
Larkman, D. J., Hajnal, J. V., Herlihy, A. H., et al. (2001). Use of multicoil arrays for
separation of signal from multiple slices simultaneously excited. Journal of
Magnetic Resonance Imaging, 13(2), 313317.
Breuer, F. A., Blaimer, M., Heidemann, R. M., et al. (2005). Controlled aliasing in
parallel imaging results in higher acceleration (CAIPIRINHA) for multi-slice
imaging. Magnetic Resonance in Medicine, 53(3), 684691.
Moeller, S., Yacoub, E., Olman, C. A., et al. (2010). Multiband multislice GE-EPI at 7
tesla, with 16-fold acceleration using partial parallel imaging with application to
high spatial and temporal whole-brain fMRI. Magnetic Resonance in Medicine,
63(5), 11441153.
Feinberg, D. A., Moeller, S., Smith, S. M., et al. (2010). Multiplexed echo planar imaging
for sub-second whole brain fMRI and fast diffusion imaging. PLoS One, 5(12), e15710.
Setsompop, K., Gagoski, B. A., Polimeni, J. R., et al. (2012). Blipped-controlled aliasing
in parallel imaging for simultaneous multislice echo planar imaging with reduced
g-factor penalty. Magnetic Resonance in Medicine, 67(5), 12101224.
Setsompop, K., Kimmlingen, R., Eberlein, E., et al. (2013). Pushing the limits of in vivo
diffusion MRI for the Human Connectome Project. NeuroImage, 80, 220233.
Wiggins, C. G., Polimeni, J. R., Potthast, A., et al. (2009). 96-Channel receive-only head
coil for 3 Tesla: Design optimization and evaluation. Magnetic Resonance in
Medicine, 62(3), 754762.
Gradient Technology
Schmitt, F. (2009). The gradient system. Syllabus ISMRM in Honolulu.
Further Reading
Perfusion Imaging: Contrast Enhanced Susceptibility Weighted Perfusion
Imaging
Rosen, B. R., Belliveau, J. W., Vevea, J. M., & Brady, T. J. (1990). Perfusion contrast
with NMR contrast agents. Magnetic Resonance in Medicine, 14, 249265.
Arterial Spin Labeling
Detre, J. A., Alsop, D. C., Samuels, O. B., Gonzalez-Atavales, J., & Raps, E. C. (1998).
Cerebrovascular reserve testing using perfusion MRI with arterial spin labeling in
normal subjects and patients with cerebrovascular disease, Proceedings of the
ISMRM sixth annual meeting, p. 243.
MR Diffusion Imaging
Wedeen, V. J., Hagmann, P., Tseng, W. Y., et al. (2005). Mapping complex tissue
architecture with diffusion spectrum magnetic resonance imaging. Magnetic
Basser, P. J., & Jones, D. K. (2002). Diffusion-tensor MRI: Theory, experimental design
and data analysis A technical review. NMR in Biomedicine, 15, 456467.
Tuch, D. S., Reese, T. G., Wiegell, M. R., et al. (2002). High angular resolution diffusion
imaging reveals intravoxel white matter fiber heterogeneity. Magnetic Resonance in
Medicine, 48, 577582.
EPI Limitations
Schmitt, F., Wielopolski, P., Fischer, H., & Edelman, R. R. (1994). Peripheral
stimulation and their relation to gradient pulse, Proceedings of the seventh annual
meeting of the society of magnetic resonance in medicine, Philadelphia, p. 102.
Reilly, J. P. (1989). Peripheral nerve stimulation by induced electric currents: Exposure
to time varying magnetic fields. Medical & Biological Engineering & Computing,
27, 101110.
Relevant Websites
http://www.loni.usc.edu/ Laboratory of Neuro Imaging.
http://www.nmr.mgh.harvard.edu/martinos/flashHome.php Martinos Center for
Biomedical Imaging at Massachusetts General Hospital, Human Connectome
Project funded by National Institute of Health.
http://www.humanconnectomeproject.org/.
http://www.neuroscienceblueprint.nih.gov/connectome/ NIH Blueprint: The Human
Connectome Project.
http://www.humanconnectome.org/.
Basic Principles of Electroencephalography

D Millett, Hoag Hospital, Newport Beach, CA, USA
P Coutin-Churchman, University of California at Los Angeles, Los Angeles, CA, USA
JM Stern, University of California at Los Angeles, Los Angeles, CA, USA
Glossary
Craniotomy Surgical procedure to remove a region of skull

and allow access to the brain.
Epilepsy Neurological disorder of seizures due to an
intrinsic predisposition to seizures.
Epileptiform Having features suggestive of epilepsy.
Introduction
Biological Sources of the EEG
Electroencephalography (EEG) is one of the oldest techniques

for mapping the activity of the brain in health and disease and
remains one of the most useful methods in clinical practice.
Fundamentally, it is the graphical depiction of electrical potentials generated by the cerebrum that may occur as brief discharges and ongoing rhythms. EEG not only is most often
recorded from the surface of the head but also may be recorded
from grids of electrodes surgically placed directly on the cerebral surface or from depth electrodes placed within the cerebral
parenchyma. After Berger first described his single-channel
technique for recording the human EEG with needle electrodes
inserted into the scalp (Berger, 1929), physiologists attempted
to localize different EEG rhythms with multichannel recordings in animals (Kornmuller, 1932) and humans (Adrian &
Matthews, 1934). Each rhythm was characterized by its frequency band and was named with a Greek letter: alpha, beta,
theta, delta, and gamma. During the late 1930s, Jasper and
colleagues demonstrated that alpha rhythms are most prominent over the occipital region, while beta rhythms are more
prominent over frontocentral regions (Jasper & Andrews,
1938). Subsequently, EEG recording methods that used closely
spaced electrodes were recommended to better localize the
focal features, including abnormal discharges in patients with
epilepsy (Jasper & Hawke, 1938). Independently, Walter
reported a series of cases in which focal slow waves (delta
activity) predicted the finding of a corresponding structural
lesion at surgery (Walter, 1936). These discoveries form the
foundation for modern EEG, which is typically used to identify
and localize epileptiform abnormalities or assess global and
local cerebral function. One important advance in modern
EEG is its incorporation of digital methods for recording,
storing, and analyzing. Computational techniques provide
analyses to map electrical fields and estimate the localization
of cerebral sources, but visual inspection remains the standard
approach. EEG is one of the most widely used and practical
techniques for clinical brain mapping today because of its high
temporal resolution and applicability in a variety of clinical
and research environments.
Infarction Injury to tissue producing cell death, often due to

insufficient blood supply.
Parenchyma Tissue providing the function of the organ.
Stereotactic Surgical targeting through coordinates in three
spatial dimensions.
The cellular phenomena that give rise to cerebral electrical activity recorded in the EEG were clarified by a series of microelectrode studies that began with animal studies (Li & Jasper, 1953)
and culminated in a series of micro/macro recordings obtained
from epilepsy patients (Morrell, 1961). Results of these investigations have led to the present understanding that the surface
EEG represents a dynamic spatiotemporal summation of extracellular current flow associated with excitatory and inhibitory
postsynaptic potentials (EPSPs and IPSPs) that occur along the
soma, axon, or dendritic tree of pyramidal neurons. Pyramidal
neurons have cell bodies within layer five of the neocortex with
connections within and beyond the neocortex. As such, EEG is
produced by a population of cells within one cellular layer, but
it depicts a reliable measure of widespread brain activity. EEG
generation depends on populations of EPSPs located along an
apical dendrite producing positive current flow into the cell (a
current sink) with and a corresponding extracellular field that is
negatively charged. Passive current flowing out of the soma (a
current source) maintains electrical neutrality of the system.
Together, an extracellular electrical field is produced with a
dipole in a radial orientation and the negative pole directed
toward the cortical surface. These extracellular dipoles are
more sustained and more spatially synchronized than action
potentials mediated by fast sodium channels because of the
PSP durations, and the summation produces an electrical signal
that can be detected at the distance of the scalp. At the cortical
surface, the polarity of this dipole will depend on whether the
excitatory input to the cortex (i.e., the population of EPSPs) is
located in the superficial or deeper layers of the cortex. Furthermore, both simulation models (Cooper, Winter, Crow, et al.,
1965) and simultaneous intracranial and scalp recordings (Tao,
Ray, Hawes-Ebersole, & Ebersole, 2005) have demonstrated that
approximately 6 cm2 of the synchronously active cortex is necessary to generate an epileptiform discharge recorded from scalp
electrodes, and epileptiform discharges are more often associated with even larger areas of up to 20 cm2. For both endogenous rhythms (reviewed by Hughes and Crunelli, 2005) and
epileptiform discharges (Jasper & Droogleever-Fortuyn, 1947),
http://dx.doi.org/10.1016/B978-0-12-397025-1.00007-5
75
76
INTRODUCTION TO ACQUISITION METHODS | Basic Principles of Electroencephalography
thalamocortical networks appear to play a critical role in

entraining these wide areas of the cerebral cortex.
recognized since the beginnings of EEG. The term bipolar refers

to a collection of pairs (called montages) from adjacent electrodes with the resulting output channels arranged in chains
that depict a line of successive electrodes across the scalp.
Bipolar montages commonly include anterior to posterior
chains that represent the electrical activities across regions
from the frontal poles to the occipital poles, transverse chains
that represent electrical activities in the lateral directions, and
circumferential chains that span the frontal and occipital poles
(Figure 2). In contrast, referential montages include collections
of electrode pairs in which each electrode is paired to either
one reference electrode, such as at the vertex, or one of two
similar reference electrodes, such as an ipsilateral ear electrode
(Figure 3). Other referential montages use a mathematical
construct such as an average of all scalp electrodes or an average of the right and left ear electrodes as the comparison. Both
bipolar and referential montages have advantages and disadvantages when determining the location and amplitude of EEG
activity. Bipolar montages are especially useful in locating
smaller electrical fields, such as from focal epileptiform discharges. In contrast, referential montages may depict the wave
contour and amplitude more accurately (depending on the
particular reference employed) and may be more useful in
locating lesions associated with larger electrical fields.
Surface (Scalp) EEG

Surface EEG is a noninvasive, portable, and relatively inexpensive method for detection of both normal and pathological
cerebral activities. Electrical potential recordings obtained
from electrodes affixed to the scalp and often supplemented
with electrodes affixed to the ears, forehead, and cheeks provide a wealth of information about human brain function.
Scalp electrodes are typically located and secured to the surface
of the head in accordance with an approach based on scalp
measurements with electrode location names that are standardized by the International 1020 or 1010 System
(Figure 1). The electrical potential recorded from each electrode is subtracted from the potential at another electrode and
a potential difference (voltage) results. The subtraction is a
differential amplification that minimizes any electrical potential that the electrodes share. As such, noise from noncerebral
electrical potentials is minimized in the EEG. The choice of
which electrodes to include in the pair allows for a variety of
display options, although two basic methods have been
NASION
Fp1
Fp2
F7
F8
F3
F4
FS
ylv1
FZ
A1
C3
T3
CZ
P3
land
F Ro
PZ
A2
C4
T4
P4
T5
T6
O2
O1
INION
Figure 1 International system of electrode placement. Reproduced from Klem, G.H., Luders, H.O., Jasper, H.H., et al. (1999). The ten-twenty electrode
system of the International Federation of Clinical Neurophysiology. Electroencephalography and Clinical Neurophysiology: Supplement 52, 36.

Despite significant improvements provided by digital
recording and processing, there remain limitations to accurate
interpretation of surface EEG. There are a large number of welldescribed normal variants and unusual pathological patterns
that require an experienced reader to avoid false-positive and
Fp1
Fp2
15
19
F7
20
14
13
A1
Fz
F3
T3
F4
F8
16
12
C3
10
11
Cz
C4
77
false-negative interpretations. Accurate localization of focal

abnormalities also is limited because of EEGs intrinsically
poor spatial resolution. It sometimes provides only regional
localization, sometimes to less than a quadrant of the scalp
and occasionally to only a hemisphere. Abnormalities also are
often nonspecific. Nonepileptiform abnormalities manifest as
an abnormal frequency or amplitude and can reflect numerous
types of structural of functional disturbances. Focal abnormalities include infarction, infection, neoplasm, inflammation,
and even a post-seizure state. More generalized abnormalities
may appear in the setting of diffuse brain injury, acute hydrocephalus, encephalopathy, and also a post-seizure state. Epileptiform abnormalities represent a location or region of
irritative activity, indicating a predisposition to epileptic seizures and often indicating a particular type of clinical seizure
and epilepsy. However, these abnormalities are not reliable
indicators of the likelihood of a seizure or whether medications are effective.
A2
T4
Intracranial EEG
21
7
T5
17
P3
Pz
P4
T6
18
22
8
O1
O2
Figure 2 Bipolar montage. Reproduced from Stern, J.M. (2013). Atlas of

EEG patterns (2nd ed.). Philadelphia, PA: Lippincott Williams and Wilkins.
Figure 3
Over a half century ago, long before the development of modern neuroimaging methods, depth electrode recordings were
used to locate the source of seizures in patients undergoing
evaluation for surgical treatment of medication-resistant epilepsy. When combined with advanced imaging techniques,
surface EEG now often provides adequate electrophysiological
data to guide surgical therapy, and the use of intracranial EEG
has shifted to increasingly more complicated forms of epilepsy.
Yet, the use of intracranial EEG continues to be an important
Referential montage. Reproduced from Stern, J.M. (2013). Atlas of EEG patterns (2nd ed.). Philadelphia, PA: Lippincott Williams and Wilkins.
78
technique for the diagnostic evaluation of patients for surgical

treatment. Even when intracranial EEG is necessary, surface
EEG, MRI, and additional neuroimaging methods such as
PET, MEG, and SPECT are important components of the evaluation. Prior to implantation electrodes, these noninvasive
imaging modalities help narrow the localization. Intracranial
EEG then can provide differentiation of two or more potentially epileptic lesions and identify boundaries between an
epileptogenic lesion and the adjacent eloquent cortex.
Intracranial electrodes are divided into two types, each of
which is available in a variety of configurations. The electrodes
are either subdural contacts arranged in grids or strips that are
placed across the cerebral convexity or intraparenchymal
(depth) electrodes that are placed into cerebral tissue orthogonal to the head surface (Figure 4). Subdural contacts consist of
either a grid of two or more electrodes in both row and column
or a strip of several electrodes (Figure 5). The standard subdural contact electrodes are 23 mm in diameter and separated
by 510 mm. Microgrids have electrode contacts that are
1.5 mm in diameter and separated by 4 mm. Both are placed
through a craniotomy with a size depending on the extent of
Figure 4 Depth electrode.
Figure 5 Grid electrode.
cerebral surface that is to be covered. Depth electrode contacts

consist of a series of cuffs along a cylinders length. The standard depth electrode contacts are macro electrodes separated
by 5 or 10 mm, and these may be accompanied by microwire
electrodes deployed from the distal tip that can record single
neuronal units. Depth electrodes are placed through a small
hole using stereotactic navigation to target locations identified
through high-resolution imaging. Common targets include the
mesial temporal lobe, interhemispheric fissure, and periventricular gray matter. By using a collection of depth electrodes,
seizure propagation can be determined in three dimensions
within a cerebral region. This has been termed stereo-EEG
because of the spatial localization. Each type of intracranial
electrode has advantages and disadvantages, so specific clinical
situations have one type that is clinically optimal. Data
obtained from such recordings are used to tailor surgical resections in order to maximize seizure control and minimize the
risk of neurological deficits.
Quantitative Approaches to EEG

The main purpose of EEG in the diagnostic evaluation of
epilepsy is to locate the cerebral source of epileptiform abnormalities because these abnormalities often coincide with epileptogenic regions (Ebersole & Hawes-Ebersole, 2007).
Traditionally, EEG localization has relied on visual identification of the electrode(s) that depicts the local maximum of the
epileptiform discharges electrical field because the discharges
cortical generator is assumed to lie directly beneath the local
maximum of the electrical field. However, in some instances,
the electrical field is quite broad or recurring discharges vary in
their location, and this may be related to the false assumption
that the generator is at the crest of a gyrus below the heads
surface. In fact, discharges also may be generated by the cortex
within the sulci or along cortical surfaces that are within fissures. Surface EEG is insensitive to these fields because of
distance and their orientation away from the scalp, but they
still may occur within the recording. Overall, the ability of
conventional EEG to accurately localize cerebral abnormalities
is complicated and remains controversial (Alarcon, Guy,
Binnie, et al., 1994; Scherg, Bast, & Berg, 1999).
Quantitative approaches to EEG localization exist to improve
the accuracy. A commonly used approach is based on the spatial
distribution of the voltage field over the entire head, which
conveys information about both the source location and also its
dipole orientation. This and similar quantitative methods may
improve the accuracy of EEG source localization by accounting
for the contours in the cortical gyri and sulci that alter the scalp
manifestation of a potential. This is demonstrated by the situation in which two nearby foci each producing an electrical
field perpendicular to the cortical surface project in different
directions because of the cortical ribboning that is between
them. Because the two foci point in different directions, the
head surface maxima are at different scalp locations. The dipole
model may help overcome some of the limitation of visual EEG
inspection by using a vectorial representation illustrating magnitude, location, and orientation. This approach represents the
center of the electrical source and not the spatial distribution or
extent of the generating cortex. The source may be calculated by

determining the location of two simultaneous local maxima on
the scalp. A line connecting these two maxima indicates the
orientation of the sources dipole. The source location along
this line is calculated using each maximums amplitude gradient, with a steeper gradient indicating greater proximity to the
source (Figure 6).
Figure 6 Schematic representation of the surface fields of simulated

dipoles. The dipoles have the same location within the right anterior
parietal lobe but the orientations differ. In the top simulation, the dipole
is pointed radially, and the negative scalp field (in blue) peaks over
centroparietal areas with a steep gradient. The corresponding positive
field (in red) is widely distributed over the lower right scalp. In the bottom
simulation, the dipole is oriented tangentially in an anteroposterior
direction. This produces scalp negative field peaks over midline frontal
areas with a more diffuse gradient and a slight shift to the right.
The corresponding positive field has a steeper gradient over the right
occipital area.
79
The single-dipole solution is complicated when a patient

with focal seizures has multifocal epileptiform discharges that
produce a confusing multitopographic distribution (Alarcon
et al., 1994; Lopes da Silva, 1999). This commonly occurring
problem can be addressed by quantifying the proportion of
separate sources or demonstrating the vicinity of sources that
are producing disparate scalp localizations due to differences
in orientation. Discharges with the same waveform and location are clustered and averaged together, generating a dipole
model of the initial phase of the averaged discharge. The degree
of source concentration of discharges clustered in a given
brain region is then calculated (Figure 7). This approach has
yielded good results in predicting outcome for epilepsy surgery
(Coutin-Churchman, Wu, Chen, et al., 2012; Wilson, Turner,
Emerson, & Scheuer, 1999). However, the approach, as well as
other sophisticated quantitative methods, is highly dependent
on the quality of the raw EEG data.
Despite extensive research on dipole modeling of EEG discharge over the last four decades that has employed many
different methods of computational analyses (Ebersole &
Hawes-Ebersole, 2007; Scherg et al., 1999), a practical clinical
application has remained elusive. Divergent mathematical
models and a lack of standardization in dipole modeling are
major reasons for the technique not being a conventional
clinical approach (Dworetzky & Reinsberger, 2011). In particular, there are significant differences in methods for discharge
identification and physicalmathematical models of the head,
patient populations, and outcomes metrics. Fortunately, there
has been some recent consensus on widely accepted standards
for realistic head models and use of the initial phase of discharges in spatiotemporal dipole modeling (Holmes, Kutsya,
Figure 7 Clustering, quantification, and source localization. The resulting depiction of the dipole region was produced using 2281 epileptiform
discharges from a prolonged EEG recording. Twelve distinct spike clusters with differing morphology, temporal course, and scalp field were estimated.
However, the dipole map shows that all of the clusters are located in the mesiobasal temporal lobes with 72% predominance of the left side.
80
Ojemann, Wilenskya, & Ojemann, 2000). EEG for clinical use

or for brain mapping continues to advance with much of the
progress in data analysis and correlation.
See also: INTRODUCTION TO ACQUISITION METHODS: Basic

Principles of Magnetoencephalography.
References
Adrian, E. D., & Matthews, B. H. C. (1934). The interpretations of potential waves in the
cortex. Journal of Physiology, 81, 440471.
Alarcon, G., Guy, C. N., Binnie, C. D., et al. (1994). Intracerebral propagation of
interictal activity in partial epilepsy: Implications for source localisation. Journal of
Neurology, Neurosurgery, and Psychiatry, 57, 435449.
Berger, H. (1929). Uber das Elektrenkephalogramm des Menschen. Archiv fur
Psychiatrie und Nervenkrankheiten, 87, 527570.
Cooper, R., Winter, A. L., Crow, H. J., et al. (1965). Comparison of subcortical, cortical
and scalp activity using chronically indwelling electrodes in man.
Electroencephalography and Clinical Neurophysiology, 18, 217228.
Coutin-Churchman, P., Wu, J. Y., Chen, L., et al. (2012). Quantification and localization
of EEG interictal spike activity in patients with surgically removed epileptogenic foci.
Clinical Neurophysiology, 123, 471485.
Dworetzky, B. A., & Reinsberger, C. (2011). The role of the interictal EEG in selecting
candidates for resective epilepsy surgery. Epilepsy and Behavior, 20, 167171.
Ebersole, J. S., & Hawes-Ebersole, S. (2007). Clinical application of dipole models in
the localization of epileptiform activity. Journal of Clinical Neurophysiology, 24,
120129.
Holmes, M. D., Kutsya, R. L., Ojemann, G. A., Wilenskya, A. J., & Ojemann, L. M.
(2000). Interictal, unifocal spikes in refractory extratemporal epilepsy predict ictal
origin and postsurgical outcome. Clinical Neurophysiology, 111, 18021808.
Hughes, S. W., & Crunelli, V. (2005). Thalamic mechanisms of EEG alpha rhythms and
their pathological implications. The Neuroscientist, 11, 357372.
Jasper, H. H., & Andrews, H. L. (1938). Electro-encephalography: III. Normal

differentiation of occipital and precentral regions in man. Archives of Neurology and
Psychiatry, 39, 96115.
Jasper, H. H., & Droogleever-Fortuyn, J. (1947). Experimental studies of the functional
anatomy of petit mal epilepsy. Research Publications - Association for Research in
Nervous and Mental Disease, 26, 272298.
Jasper, H. H., & Hawke, W. A. (1938). Electro-encephalography. IV. Localization
of seizures waves in epilepsy. Archives of Neurology and Psychiatry, 39,
885901.
Klem, G. H., Luders, H. O., Jasper, H. H., et al. (1999). The ten-twenty electrode system
of the International Federation of Clinical Neurophysiology. Electroencephalography
and Clinical Neurophysiology. Supplement, 52, 36.
Kornmuller, A. E. (1932). Architektonische Lokalisation bioelektrischer
Erscheinungen auf der Grosshirnrinde. 1. Mitteilung: Untersucheungen am
Kaninchen bei Augenbelichtung. Journal fur Psychologie und Neurologie, 44,
447459.
Li, C. L., & Jasper, H. (1953). Microelectrode studies of the electrical activity of the
cerebral cortex in the cat. Journal of Physiology (London), 121, 117140.
Lopes da Silva, F. (1999). EEG analysis: Theory and practice. In E. Niedermeyer &
F. Lopes da Silva (Eds.), Electroencephalography: Basic principles, clinical
applications and related fields (4th ed., pp.11351164). Baltimore, MD: Williams
& Wilkins.
Morrell, F. (1961). Microelectrode studies in chronic epileptic foci. Epilepsia, 2, 8188.
Scherg, M., Bast, T., & Berg, P. (1999). Multiple source analysis of interictal spikes:
Goals, requirements, and clinical value. Journal of Clinical Neurophysiology, 16,
214224.
Stern, J. M. (2013). Atlas of EEG patterns (2nd ed.). Philadelphia, PA: Lippincott
Williams and Wilkins.
Tao, J. X., Ray, A., Hawes-Ebersole, S., & Ebersole, J. S. (2005). Intracranial EEG
substrates of scalp EEG interictal spikes. Epilepsia, 46, 669676.
Walter, W. G. (1936). The location of cerebral tumours by electro-encephalography.
Lancet, 2, 305308.
Wilson, S. B., Turner, C. A., Emerson, R. G., & Scheuer, M. L. (1999). Spike detection:
II. Automatic, perception-based detection and clustering. Clinical Neurophysiology,
110, 404411.
Functional MRI Dynamics

K Uludag, Maastricht University, Maastricht, The Netherlands
Introduction
In a typical functional neuroimaging experiment, the goal is to
map patterns of neuronal activation while the subject is engaged
in a specific task or is experiencing a sensory stimulus. The fMRI
signal is usually analyzed with the general linear model (GLM)
regressing each voxels time course with the so-called design
matrix (i.e., the experimental design convolved with a hemodynamic response function, HRF; Worsley & Friston, 1995). It is
well known that the hemodynamic response varies between subjects, brain areas, and even neighboring voxels (Handwerker,
Gonzalez-Castillo, DEsposito, & Bandettini, 2012) depending
on basic physiological variables, such as baseline blood oxygenation and volume. To statistically capture various hemodynamic
response shapes, typically two or more basis functions are utilized
(Woolrich, Behrens, & Smith, 2004). For example, an HRF and its
derivative can map hemodynamic responses with different onset
times. The result of this analysis assigns a statistical value to each
voxel indicating activations for positive and deactivations for
negative values. Most fMRI studies do not further examine the
fMRI time course. However, fMRI transients might contain more
valuable information on brain processing (and on nonneuronal
signal sources, such as movement and respiration) than only a
rough indication of the location of the brain area involved in the
task (Buxton, Uludag, Dubowitz, & Liu, 2004).
To appreciate this fact, let us examine the physiological
underpinnings of the fMRI signal: it is directly determined by
the changes in cerebral blood volume (CBV) and blood oxygenation Y, and the latter is determined by cerebral blood flow
(CBF), cerebral metabolic rate of oxygen (CMRO2), and CBV
containing deoxygenated blood (i.e., capillaries and veins;
Uludag et al., 2009). (Note that the fMRI signal, as measured
with standard gradient-echo (GE) or spin-echo (SE) imaging, is
affected not only by the blood oxygenation level-dependent
(BOLD) effect but also directly by the blood volume (Uludag,
Muller-Bierl, & Ugurbil, 2009). Nevertheless, the terms fMRI
and BOLD signals are often used synonymously. Hematocrit
also has a strong influence on the relaxation rate and, hence,
amplitude of the fMRI signal (Silvennoinen, Clingman, Golay,
Kauppinen, & van Zijlv, 2003). However, the change in hematocrit during activation is low. Thus, it is an important variable
for intersubject comparison of the fMRI signal amplitude but
not for assessing the dynamics of the fMRI signal and the
activation patterns within a subject. In Figure 1, the chain of
biophysical events leading to the fMRI signal is illustrated.
Generative models, such as dynamic causal modeling
(Friston, Harrison, & Penny, 2003), might help in disentangling neuronal from vascular effects.
An increase in CMRO2 leads to a decrease in blood oxygenation (hypo-oxygenation) and, hence, in the fMRI signal. In
contrast, an increase in CBF brings oxygenated blood to the
local tissue volume and displaces deoxygenated blood and
therefore leads to hyperoxygenation resulting in an increase
in the fMRI signal. A change in CBV, however, can lead to an

increase or a decrease of the fMRI signal depending on the MRI
parameters utilized. In general, a pure change in CBV affects
the relative contribution of intra- and extravascular MRI signal
(Uludag et al., 2009). Thus, if the intravascular contribution of
the fMRI signal is larger than the extravascular signal, then a
CBV increase induces an increase in the total fMRI signal. This
condition is satisfied for field strengths below 5 T for SE
and 2 T for GE MRI sequences (Uludag et al., 2009).
In total, because of multiple physiological parameters affecting
the fMRI signal, an fMRI signal change cannot be traced back
unambiguously to one of the underlying physiological
variables without further experimental knowledge (Buxton
et al., 2004).
During sensory stimulation or task performance, CBF
changes much more than CBV and CMRO2; as a result, the
oxygen extraction fraction from the blood is reduced and the
venous blood becomes more oxygenated. That is, the CBF
contribution is larger than the CMRO2 and CBV contributions,
leading to a positive fMRI signal change during neuronal activation and a negative signal change during neuronal deactivation. The fMRI transients arise from the fact that these basic
physiological variables can be in temporal imbalance during
rest, activation, and deactivation.
The stimulus-evoked BOLD response has some typical characteristics: it is delayed by 12 s and reaches its maximum after
510 s. In some cases, an initial decrease of the BOLD signal
is observed, called the initial dip (for an overview, see Buxton,
2001; Ugurbil, Toth, & Kim, 2003). After the end of the stimulus, a poststimulus undershoot can often be seen. It is known
that the duration and magnitude of the BOLD signal poststimulus undershoot are dependent on the stimulus type and
duration (e.g., see, Bandettini et al., 1997; Hoge et al., 1999).
In addition, other, less-studied transients can be observed:
onset and offset responses, an initial overshoot, and the negative BOLD response.
Initial Dip
The initial dip, if detected, only lasts less than 2 s (see Figure 2
for illustration) and is usually not detected or reported
(Buxton, 2001; Ugurbil et al., 2003). Its properties, detectability and even that it is of physiological origin and not a measurement or analysis artifact, have been controversially
discussed in both fMRI and optical imaging. The interest in
the initial dip has been sparked by the expectation that it has a
higher effective spatial resolution than the main positive
hemodynamic response, as the changes in blood oxygenation
Y and CBV during the peak response might not be just localized to the neuronally active tissue volume. This effect has been
poetically phrased as watering the entire garden for the sake of
one thirsty flower (Malonek & Grinvald, 1996).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00008-7
81
82
INTRODUCTION TO ACQUISITION METHODS | Functional MRI Dynamics
fMRI signal
Capillary
Blood
flow
Neuronal
response
Energy
75%
Blood
volume
Energy
6%
Synapse
Brain
V
Energy
7%
Neurons
Arriving
spikes
Energy
10%
Deoxy-Hb
content
Astrocyte
CMRO2
Blood oxygenation level-dependent (%)
Figure 1 The chain of physiological and physical events leading to the fMRI signal. Neuronal activity is associated with the cerebral metabolic rate of
oxygen (CMRO2) and induces changes in cerebral blood flow (CBF). The increase in CBF evokes increases in cerebral blood volume (CBV) and changes
the amount of deoxygenated blood. The blood oxygenation and CBV in a localized brain area are detected by the fMRI signal. Courtesy of Martin Havlicek.
2.0
1.5
1000 ms
250 ms
50 ms
5 ms
1.0
0.5
0.0
0.5
15
10
Time (s)
20
25
30
Figure 2 Short, intense visual stimulation evokes detectable initial dip

at 3 T in the visual cortex of healthy human subjects. (Yesilyurt et al.,
2008).
The most prevalent hypothesis for the elusive initial dip is

that CMRO2 starts earlier than the hemodynamic response,
creating an early hypo-oxygenation (i.e., increase in deoxygenated hemoglobin) of the blood (reviewed in Vanzetta, 2006).
Physiologically, this is a plausible hypothesis as oxidative
metabolism in the mitochondria and neurovascular coupling
are largely independent processes. That is, the tissue might
consume energy before the mediators of neurovascular coupling reach the smooth muscles of arterioles and pericytes of
the capillaries. However, currently, it is not possible to directly
measure CMRO2 with high temporal resolution (but see recent
advances in flavoprotein autofluorescence imaging, reviewed
in Vazquez, Masamoto, Fukuda, & Kim, 2010).
Alternatively, an increase in CBV (more specifically arterial
CBV; Uludag, 2010) or a decrease in CBF might cause an initial
dip of the fMRI signal. To the best of our knowledge, nobody
has suggested a decrease in CBF as a possible mechanism for
the initial dip. However, an early increase in arterial CBV is a
possibility: if the initial energy demand of the tissue is met by
glycolysis or the energy consumption is slow compared to

electrophysiological activity and neurovascular coupling, then
it is conceivable that the hemodynamic response (and hence
arterial CBV changes) is actually faster than the CMRO2 change
(or, to be precise, oxygen extraction from the blood). A recent
optical imaging study (Sirotin, Hillman, Bordier, & Das, 2009)
found that, in the early phase of the hemodynamic response,
there is not much change in blood oxygenation but only
in blood volume (corresponding to the total amount of hemoglobin in optical imaging) supporting the idea that there is
an early arterial CBV increase before the change in blood
oxygenation and volume in the capillaries and veins.
Arterial CBV increase leads to an increase of the intravascular water fraction and small changes in the amount of
deoxygenated hemoglobin (i.e., changes in the susceptibility
value). As argued earlier in the text, if the baseline intravascular
relaxation rate is larger than that of the extravascular relaxation
rate, arterial CBV changes have to be associated with an initial
dip (Uludag, 2010). This condition is satisfied for field
strengths 3 T for GE MRI sequence providing evidence why
most studies reporting the initial dip have been performed at
high magnetic fields and not many at 1.5 and 3 T (but see
Yesilyurt, Ugurbil, & Uludag, 2008 in Figure 2).
These two hypotheses have testable consequences: the
CMRO2 hypothesis predicts an initial dip independent of
magnetic field strength because a hypo-oxygenation is always
associated with a decrease in fMRI signal. However, in the arterial CBV hypothesis, a fast arterial CBV response results in magnetic field strength dependence of the initial dip (Uludag, 2010).
An increase in venous CBV also results is field independent
initial dip. However, there is no mechanism in the neurovascular
coupling leading to an increase in venous CBV prior to the
hemodynamic response. Both hypotheses are compatible with
stimulus, brain state, and baseline CBF dependency of the initial
dip. A recent abstract presented at the ISMRM 2014 provided the
first high-resolution fMRI data compatible with the arterial CBV
hypothesis (Yu, Dodd, Silva, & Koretsky, ISMRM 2014).
The initial dip has attracted interest because of potential
higher spatial specificity than the main hemodynamic

response, which for GE MRI acquisition stems mostly from
the draining veins (see Uludag et al., 2009, and references
therein). The hypothesized early CMRO2 increase would
occur in the tissue and thus provide a more accurate localization of brain activity. However, even if the arterial CBV
hypothesis were true, a better localization would also be
achieved if the hemodynamic response in its initial stage is
dominated by small arteries and capillaries. That is, regardless
of whether the early CMRO2 or arterial CBV change hypothesis
is correct, the initial dip (or, in general, the initial phase of the
hemodynamic response) has higher spatial specificity than the
main positive response (Uludag, 2010). Thus, with the help of
the initial dip, a better delineation of functional units in the
brain can be achieved.
Although the scientific community has been interested in
the initial dip from its inception, there is almost no study
utilizing this phenomenon exactly for that purpose. An exception was the study by Kim et al., who showed the spatial
distribution of the initial dip in the cat cortex (Kim, Duong,
& Kim, 2000, and also see Duong, Kim, Ugurbil, & Kim, 2000).
However, this study was criticized because also the sagittal
sinus exhibited an initial dip (Logothetis, 2000), which contradicts its tissue localization. A recent study by Watanabe et al.
has discovered that only the fMRI signals peaking late exhibit
an initial dip (Watanabe, Bartels, Macke, Murayama, &
Logothetis, 2013). The same voxels in trials with earlier maximum fMRI signal do not show an initial dip but, interestingly,
a poststimulus undershoot absent in the trials with long
latency. The same study showed that the point spread function
of the initial dip is lower than the positive response in agreement with the aforementioned study by Sirotin et al. (2009).
Currently, because of the low signal-to-noise ratio and even
absence in many studies, the community has largely lost interest in the initial dip. To utilize the initial dip for higher localization of the activation using MRI, both high temporal
resolution (less than 1 s) and spatial resolution (less than
1 mm) are needed. However, with the advent of high spatial
resolution fMRI studies at 7 T (and higher), it is expected that
the initial dip will be eventually utilized for studying columnar
or laminar level of brain functional organization.
Poststimulus Undershoot
A more common observation is a dip of the fMRI signal below
baseline after the end of the stimulus, referred to as a poststimulus undershoot (one of the most debated issues in fMRI;
Van Zijl, Hua, & Lu, 2012), which can take a long time to resolve
(>30 s; Sadaghiani, Ugurbil, & Uludag, 2009). In block design
experiments, in which the rest period is not sufficiently long
to allow the undershoot to resolve, the effect appears as an
apparent lowering of the baseline after the first stimulus block.
Therefore, it is recommended that the rest periods should be
approximately twice as long as the stimulus duration to fully
allow recovering of the fMRI signal back to baseline.
Zhao et al. found that the poststimulus undershoot with
laminar resolved GE MRI sequence is localized to the tissue in
contrast to the main positive fMRI response (Zhao, Jin, Wang,
& Kim, 2007). In agreement with this study, Sirotin and colleagues had demonstrated with optical imaging that the spatial
83
spread of the poststimulus undershoot (and of the initial signal

changes) is smaller than that of the peak of the positive
response (Sirotin et al., 2009), suggesting that the undershoot
in the tissue reflects active neuronal processes and not just
passive biomechanical aftereffects of the positive response.
Three different explanations of poststimulus undershoot of
the fMRI signal are under discussion: (1) Higher deoxyhemoglobin
content per voxel due to elevated venous CBV: Venous CBV containing most of the deoxyhemoglobin returns to baseline much
slower than CBF (Mandeville et al., 1998). (2) Reduced delivery
of oxygenated hemoglobin: CBF decreases below baseline after the
stimulus termination, possibly due to neuronal inhibition or
reduction of the balanced excitationinhibition activity in the
poststimulus period (Logothetis, Pauls, Augath, Trinath, &
Oeltermann, 2001; Uludag et al., 2004). (3) Sustained production
of deoxygenated hemoglobin: CBF recovers to its baseline prior to
CMRO2; that is, oxygen is still consumed after the stimulation
period has ended (Frahm, Kruger, Merboldt, & Kleinschmidt,
1996; Lu, Golay, Pekar, & Van Zijl, 2004). Hence, oxygen extraction exceeds the basal, prestimulus level, producing a transient
hypo-oxygenation. Note that the different explanations are compatible with each other and can be present at the same time.
Ad 1: Two similar models, the balloon model and the
Windkessel model (Buxton, Wong, & Frank, 1998; Mandeville
et al., 1999), have been proposed to explain this phenomenon
as a slow return of CBV to baseline after the stimulus. Both of
these models are based on the distensibility of the venous
vessels, and the long time constant for CBV to adjust is then
treated as a biomechanical property of the vessels. These
models were motivated by the observation of such a slow
return of CBV in a rat model, corresponding to the duration
of the BOLD poststimulus undershoot and occurring despite a
more rapid return of CBF to baseline.
However, much of this picture is still speculative, although
the resulting model curves often describe experimental fMRI
signal data quite well. In the recent years, more and more
studies have provided experimental evidence that the blood
volume change is dominated by arteries and not by large veins
(Kim & Kim, 2011a, and references therein). (However, note
that in most studies, a capillary vascular compartment is not
explicitly considered. Therefore, to date, it is not clear what the
fractional change and temporal features of capillary CBV
changes are relative to the changes in other vascular compartments and whether the changes attributed to arteriolar CBV
stem in fact from the capillaries.) However, Kim and colleagues
demonstrated that the arterial dominance of CBV changes is
stimulus duration-dependent (Kim & Kim, 2011b). They have
used magnetization transfer-modulated echo-planar imaging
sequence and monocrystalline iron oxide nanoparticle contrast
fMRI in cats and rats to determine the time courses of different
vascular compartments. (However, this method assumes that
the blood oxygenation in the arteries does not change, which is
in contradiction to the findings of the same group using
oxygen-sensitive microelectrode measurements, summarized
in the preceding text (Vazquez et al., 2010).) The main findings
of this study were that (a) CBVa peaks early (time to peak
below 10 s) and declines during stimulation followed by a
poststimulus undershoot indicating CBF deactivation and (b)
CBVv continues to rise during the stimulation period and
declines back to baseline after more than 40 s. Thus, these
84

revealed that a CBF decrease after the stimulation is smaller
(or even absent) than the fMRI signal undershoot. Nevertheless, balloon model calculations show that a small CBF decrease
yields a much larger fMRI signal undershoot. Thus, MRI (and
optical imaging) data indicate that a CBF decrease can be a
contributor to the undershoot (see Figures 3 and 4).
In order to distinguish the fMRI signal undershoot caused by
biomechanical properties of the blood vessels, the CBF poststimulus decrease should be termed poststimulus deactivation.
The time course of neuronal activity and, hence, CBF in the
poststimulus period is state- and stimulus-dependent
(Bandettini et al., 1997). Therefore, the contribution of CBF to
the fMRI signal undershoot is variable and reflects active
Flicker
40
Static
2
30
CBF (%)
Blood oxygenation level-dependent (%)
data predict that the CBV contribution to the undershoot is

larger the longer the stimulus duration and small for short
stimulus durations.
Ad 2: Alternatively, a decrease in CBF might cause an fMRI
signal undershoot. In some studies, CBF drops below baseline
after the stimulus ending (Hoge et al., 1999; Uludag et al.,
2004), presumably due to neuronal inhibition and a corresponding decrease of neural activity in the poststimulus period.
The CBF hypothesis renders the fMRI signal undershoot to be of
neuronal origin, which is compatible with invasive electrophysiological observations in animals: action and local-field potentials often decrease after the stimulus ending. Measuring both
the fMRI signal and CBF using arterial spin labeling has
20
10
0
0
1
10
0
60
120
Time (s)
180
240
60
120
180
Time (s)
240
300
Figure 3 Stimulus dependence of the poststimulus undershoot (Sadaghiani et al., 2009). Static and contrast-reduced flickering checkerboard stimuli
evoke almost the same positive fMRI response in the same voxels (left of the figure). After an initial overshoot, a steady-state value is achieved.
However, the poststimulus undershoot in the fMRI signal is abolished for the static stimulus. In contrast, the CBF for the static stimulus recovers slowly
to baseline, whereas the CBF for the flickering stimulus shows a small deactivation. That is, although the fMRI signal for static stimulus is back to
baseline, the CBF is indicating continuous activation.
Blood volume response
BOLD response
Neuronal transients
Neuronal response
Blood flow response
0 10 20 30 40 50 60 70
Time (s)
0 10 20 30 40 50 60 70
Time (s)
0 10 20 30 40 50 60 70
Time (s)
Blood volume response
BOLD response
0 10 20 30 40 50 60 70
Time (s)
0
Neuronal + vascular transients

0 10 20 30 40 50 60 70
Time (s)
0 10 20 30 40 50 60 70
Time (s)
Figure 4 Exemplary theoretical time courses for neuronal and vascular changes. Neuronal signal can exhibit initial overshoot and poststimulus
deactivation. CBF is a smoothed and delayed version of the neuronal response. CBV can be coupled (upper row) or uncoupled (lower row) from CBF.
In the coupled version, the initial overshoot of the neuronal response is almost completely abolished but the neuronal poststimulus deactivation is
reflected. In the uncoupled version, the BOLD response exhibits also an initial overshoot, which however stems from the CBFCBV uncoupling.
The poststimulus undershoot in the BOLD signal is enhanced as compared to the neuronal deactivation. Courtesy of Martin Havlicek.

tissue processes (Sadaghiani et al., 2009) and not secondary
vascular developments. Thus, the undershoot can provide information on brain function and partition neuronal populations
differentially to the main fMRI response. A recent study using
simultaneous EEG-fMRI demonstrated that the poststimulus
undershoot has electrophysiological correlates independent of
the positive response (Mullinger, Mayhew, Bagshaw, Bowtell, &
Francis, 2013).
Ad 3.: A transient uncoupling of CBF and CMRO2 (Frahm
et al., 1996), with CMRO2 recovering to its baseline value
slower than the CBF, also leads to hypo-oxygenation of the
blood and, hence, to an fMRI undershoot. This again is a
physiologically plausible scenario as the neurovascular coupling is largely independent of oxygen metabolism, and
therefore, the hemodynamic and the metabolic responses to
neuronal activity might be uncoupled. However, currently,
there is only indirect MRI data and no direct dynamic data
on oxygen metabolism supporting this hypothesis. Thus, the
concept of elevated poststimulus CMRO2 comes as hypothesis
to substitute for the persistent elevated CBV explanation or
CBF deactivation as the cause of the fMRI undershoot.
Recently, van Zijl reviewed (Van Zijl et al., 2012) many MRI
data supporting this view showing that data obtained with the
VASO and other CBV techniques exhibit a rapid recovery of
total CBV while fMRI signals proceed to display an undershoot.
However, sustained CMRO2 is not the only explanation of such
data. These data can be reconciled with the aforementioned
two hypotheses if slow venous CBV recovery is compensated
by an arterial CBV undershoot corresponding to the CBF
undershoot (see Kim and Kim, 2011b).
Thus, in summary, the fMRI poststimulus undershoot has
at least two origins (similar view presented in Chen and Pike,
2009): (1) a slow recovery of post-arterial blood volume,
which is always present and larger for long stimulus duration
due to the biomechanical properties of the capillary and
venous vessels, and (2) a CBF undershoot, which seems to be
brain state- and stimulus-dependent, further modulating the
amplitude of the fMRI signal undershoot (Sadaghiani et al.,
2009). (However, a strong opposite view with many supporting data on the poststimulus undershoot main cause being
elevated CMRO2 has been recently presented by Van Zijl et al.
(2012). Thus, methodological subtleties of the different
methods and experimental designs have to be taken into
account in order to resolve the apparent discrepancies.) In
addition, the temporal evolution of the undershoot is baseline
CBF-dependent (Cohen, Ugurbil, & Kim, 2002). However, we
have to be aware that with the current state of the data, the
transient uncoupling between CBF and CMRO2 hypothesis
(Frahm et al., 1996; Lu et al., 2004) cannot be excluded.
Although not suggested by the electrophysiological data
(Logothetis et al., 2001), this mechanism may also be operative together with the venous CBV and CBF contributions.
It is also possible that different mechanisms are applicable
in spatially distinct parts of the cortex and/or the conflicting
observations reflect the different spatial sensitivities and resolutions of the various measurements. Yacoub et al., for example, reported that in the cat visual cortex (area 18), CBV
response measured using iron exogenous oxide particles is
spatially dependent, persisting in the poststimulus period in
the middle layers (layer 4) but returning to baseline rapidly on
85
the cortical surface where pial vessels are located (Yacoub,

Ugurbil, & Harel, 2006). The fMRI response, on the other
hand, displays a poststimulus undershoot in both regions.
They argue that while persistent poststimulus CBV elevation
can account partially for the middle layers, there must be
additional contributions from CMRO2/CBF dynamics to
explain the poststimulus negative BOLD effect. As the veins
are draining the blood from the tissue, altered blood oxygenation of the middle layers will also lead to hypo-oxygenation in
the vein and, hence, to an undershoot. Thus, low-resolution
imaging might mix the effects of brain surface veins and tissue
hemodynamic signals and results in confounded interpretation if a single vascular compartment is assumed.
Other Transients: Onset and Offset Responses

and Initial Overshoot and Negative BOLD Signal
Besides these two well-described transients, other dynamical
features of the fMRI signal for block design experiments have
received less attention, in particular (a) the onset and offset
transients (Uludag, 2008), (b) an initial overshoot before a
steady-state value is reached (Sadaghiani et al., 2009), and (c)
the negative BOLD signal (Shmuel, Augath, Oeltermann, &
Logothetis, 2006). As argued earlier in the text, the standard
analysis in GLM convolves the stimulus design with a canonical basis set of HRFs. The dynamic features (a) and (b), however, cannot be captured with the standard approach and
therefore assigns them a lower statistical value. In the following, we briefly describe these less-studied forms of transients:
(a) A sustained physical stimulus can also evoke phasic
responses in some neuronal populations (Uludag, 2008,
and references therein), as observed in electrophysiology.
Harms and Melcher had, for example, shown that the same
fMRI voxel in the auditory cortex can respond transiently
or be sustained depending on the tone frequency indicating neuronal origin of the phasic responses (Harms &
Melcher, 2002, 2003). Uludag had shown that these transients are mostly positive and can be observed as sole
response in a voxel or can overlap with positive or negative
sustained responses. Simulation results demonstrated that
these phasic responses are most likely of neuronal origin
(Uludag, 2008). Based on the observation of sustained and
phasic responses in the visual cortex, Horiguchi et al. had
suggested that there are two parallel temporal streams of
visual processing (Horiguchi, Nakadomari, Misaki, &
Wandell, 2009). Bandettini and colleagues have shown
that, after averaging a lot of experimental runs, a large
part of the brain responds to the stimulus, with many
voxels responding transiently (Gonzalez-Castillo et al.,
2012). Thus, the same physical stimulus might evoke various types of responses or, in other words, correspond in
fact to many stimuli from the point of view of various
brain areas. In order to capture these responses, either a
more complete basis set of hemodynamic basis functions,
a frequency analysis, or data-driven methods, such as ICA,
should be used. However, cognitive neuroscience studies
using the standard GLM approach mostly overlooked
86
these transient responses and rely on the sustained

responses to characterize brain information processing.
(b) In many fMRI data sets, an initial overshoot is observed
before the signal settles to a new steady-state value (see,
e.g., Sadaghiani et al., 2009). This overshoot is typically
interpreted as neuronal adaptation as similar behavior is
observed for local-field potentials in animal experiments.
However, as eluded in the preceding text, if CBV of the
veins continues to increase after CBF has reached steady
state, then a similar decrease of the fMRI signal after an
initial overshoot is predicted (see, e.g., Figures 3 and 4).
Thus, the settling down to a new steady-state value after an
overshoot can have both neuronal and vascular contributions. The separation of these contributions has yet to be
attempted.
(c) In the beginning of the 2000s, there was a large interest in
the so-called negative BOLD signal. As many analysis software packages and users restricted the results to positive
statistical values, initially, fMRI signal deactivations were
not detected and overlooked. However, negative fMRI signals are often observed close to the activation site surrounding activation or contralaterally to activation sites if
visual or somatosensory stimulation is restricted to one
hemisphere. The former observation was often interpreted
as vascular steal (Devor et al., 2003). That is, it was suggested that the blood delivered to the site of activation is
taken away from the proximal tissue not involved in the
processing in the stimulus. However, except in pathological cases, vascular steal does not exist as the blood flow
regulation is on the level less than 100 mm. Electrophysiological recordings of these negative surround decreases of
the signal have revealed a slight decrease in the neuronal
activity, commonly referred to as lateral surround inhibition (Devor et al., 2007). The seminal paper of Shmuel
et al. has conclusively shown the neuronal origin of the
negative fMRI signal (Shmuel et al., 2006). However, a
comprehensive temporal and spatial characterization of
the negative fMRI signal and its relationship to the positive
response are still lacking.
Summary and Conclusion

The fMRI signal is a complex physiological and physical signal
depending on many physiological contributions (namely,
CBF, CBV, and CMRO2) and MRI acquisition parameters
(e.g., echo time, field strength, and MRI sequence). Thus, the
many fMRI signal transients are ambiguous with respect to
their physiological origin (see Figure 4). However, this complexity, which makes interpretation of the data more difficult,
also allows studying brain function more thoroughly. These
often overlooked transients provide interesting insights into
the complexity of neuronal and vascular responses that can
be utilized to study brain physiology and information processing beyond the standard positive response and the statistical
brain maps.
See also: INTRODUCTION TO ACQUISITION METHODS: EchoPlanar Imaging; fMRI at High Magnetic Field: Spatial Resolution Limits
and Applications; High-Field Acquisition; High-Speed, HighResolution Acquisitions; Obtaining Quantitative Information from fMRI;
Perfusion Imaging with Arterial Spin Labeling MRI; Pulse Sequence
Dependence of the fMRI Signal; Temporal Resolution and Spatial
Resolution of fMRI; INTRODUCTION TO METHODS AND
MODELING: Convolution Models for FMRI; Dynamic Causal Models
for fMRI; Models of fMRI Signal Changes; The General Linear Model.
References
Bandettini, P. A., Kwong, K. K., Davis, T. L., Tootell, R. B., Wong, E. C., Fox, P. T., et al.
(1997). Characterization of cerebral blood oxygenation and flow changes during
prolonged brain activation. Human Brain Mapping, 5, 93109.
Buxton, R. B. (2001). The elusive initial dip. NeuroImage, 13, 953958.
Buxton, R. B., Uludag, K., Dubowitz, D. J., & Liu, T. T. (2004). Modeling the
hemodynamic response to brain activation. NeuroImage, 23(Suppl. 1), S220S233.
Buxton, R. B., Wong, E. C., & Frank, L. R. (1998). Dynamics of blood flow and
oxygenation changes during brain activation: The balloon model. Magnetic
Chen, J. J., & Pike, G. B. (2009). Origins of the BOLD post-stimulus undershoot.
Cohen, E. R., Ugurbil, K., & Kim, S. G. (2002). Effect of basal conditions on the
magnitude and dynamics of the blood oxygenation level-dependent fMRI response.
Journal of Cerebral Blood Flow and Metabolism, 22, 10421053.
Devor, A., Dunn, A. K., Andermann, M. L., Ulbert, I., Boas, D. A., & Dale, A. M. (2003).
Coupling of total hemoglobin concentration, oxygenation, and neural activity in rat
somatosensory cortex. Neuron, 39, 353359.
Devor, A., Tian, P., Nishimura, N., Teng, I. C., Hillman, E. M., Narayanan, S. N., et al.
(2007). Suppressed neuronal activity and concurrent arteriolar vasoconstriction
may explain negative blood oxygenation level-dependent signal. Journal of
Neuroscience, 27, 44524459.
Duong, T. Q., Kim, D. S., Ugurbil, K., & Kim, S. G. (2000). Spatiotemporal dynamics of
the BOLD fMRI signals: Toward mapping submillimeter cortical columns using the
early negative response. Magnetic Resonance in Medicine, 44, 231242.
Frahm, J., Kruger, G., Merboldt, K. D., & Kleinschmidt, A. (1996). Dynamic uncoupling
and recoupling of perfusion and oxidative metabolism during focal brain activation
in man. Magnetic Resonance in Medicine, 35, 143148.
Friston, K. J., Harrison, L., & Penny, W. (2003). Dynamic causal modelling.
Gonzalez-Castillo, J., Saad, Z. S., Handwerker, D. A., Inati, S. J., Brenowitz, N., &
Bandettini, P. A. (2012). Whole-brain, time-locked activation with simple tasks
revealed using massive averaging and model-free analysis. Proceedings of the
Handwerker, D. A., Gonzalez-Castillo, J., DEsposito, M., & Bandettini, P. A. (2012). The
continuing challenge of understanding and modeling hemodynamic variation in
fMRI. NeuroImage, 62, 10171023.
Harms, M. P., & Melcher, J. R. (2002). Sound repetition rate in the human auditory
pathway: Representations in the waveshape and amplitude of fMRI activation.
Journal of Neurophysiology, 88, 14331450.
Harms, M. P., & Melcher, J. R. (2003). Detection and quantification of a wide range of
fMRI temporal responses using a physiologically-motivated basis set. Human Brain
Mapping, 20, 168183.
Hoge, R. D., Atkinson, J., Gill, B., Crelier, G. R., Marrett, S., & Pike, G. B. (1999).
Stimulus-dependent BOLD and perfusion dynamics in human V1. NeuroImage, 9,
573585.
Horiguchi, H., Nakadomari, S., Misaki, M., & Wandell, B. A. (2009). Two temporal
channels in human V1 identified using fMRI. NeuroImage, 47, 273280.
Kim, D. S., Duong, T. Q., & Kim, S. G. (2000). High-resolution mapping of isoorientation columns by fMRI. Nature Neuroscience, 3, 164169.
Kim, T., & Kim, S. G. (2011a). Quantitative MRI of cerebral arterial blood volume. Open
Neuroimaging Journal, 5, 136145.
Kim, T., & Kim, S. G. (2011b). Temporal dynamics and spatial specificity of arterial and
venous blood volume changes during visual stimulation: Implication for BOLD
quantification. Journal of Cerebral Blood Flow and Metabolism, 31, 12111222.
Logothetis, N. (2000). Can current fMRI techniques reveal the micro-architecture of
cortex? Nature Neuroscience, 3, 413414.
Logothetis, N. K., Pauls, J., Augath, M., Trinath, T., & Oeltermann, A. (2001).
Neurophysiological investigation of the basis of the fMRI signal. Nature, 412, 150157.

Lu, H., Golay, X., Pekar, J. J., & Van Zijl, P. C. (2004). Sustained poststimulus elevation
in cerebral oxygen utilization after vascular recovery. Journal of Cerebral Blood Flow
and Metabolism, 24, 764770.
Malonek, D., & Grinvald, A. (1996). Interactions between electrical activity and cortical
microcirculation revealed by imaging spectroscopy: Implications for functional
brain mapping. Science, 272, 551554.
Mandeville, J. B., Marota, J. J., Ayata, C., Zaharchuk, G., Moskowitz, M. A.,
Rosen, B. R., et al. (1999). Evidence of a cerebrovascular postarteriole windkessel
679689.
Mandeville, J. B., Marota, J. J., Kosofsky, B. E., Keltner, J. R., Weissleder, R., Rosen, B. R.,
et al. (1998). Dynamic functional imaging of relative cerebral blood volume during rat
forepaw stimulation. Magnetic Resonance in Medicine, 39, 615624.
Mullinger, K. J., Mayhew, S. D., Bagshaw, A. P., Bowtell, R., & Francis, S. T. (2013).
Poststimulus undershoots in cerebral blood flow and BOLD fMRI responses are
modulated by poststimulus neuronal activity. Proceedings of the National Academy
of Sciences of the United States of America, 110, 1363613641.
Sadaghiani, S., Ugurbil, K., & Uludag, K. (2009). Neural activity-induced modulation of
BOLD poststimulus undershoot independent of the positive signal. Magnetic
Shmuel, A., Augath, M., Oeltermann, A., & Logothetis, N. K. (2006). Negative functional
MRI response correlates with decreases in neuronal activity in monkey visual area
V1. Nature Neuroscience, 9, 569577.
Silvennoinen, M. J., Clingman, C. S., Golay, X., Kauppinen, R. A., & van Zijl, P. C.
(2003). Comparison of the dependence of blood R2 and R2* on oxygen saturation at
Sirotin, Y. B., Hillman, E. M., Bordier, C., & Das, A. (2009). Spatiotemporal precision
and hemodynamic mechanism of optical point spreads in alert primates.
106, 1839018395.
Ugurbil, K., Toth, L., & Kim, D. S. (2003). How accurate is magnetic resonance imaging
of brain function? Trends in Neurosciences, 26, 108114.
Uludag, K. (2008). Transient and sustained BOLD responses to sustained visual
stimulation. Magnetic Resonance Imaging, 26, 863869.
87
Uludag, K. (2010). To dip or not to dip: Reconciling optical imaging and fMRI data.
107, E23, Author reply E24.
Uludag, K., Dubowitz, D. J., Yoder, E. J., Restom, K., Liu, T. T., & Buxton, R. B. (2004).
Coupling of cerebral blood flow and oxygen consumption during physiological
activation and deactivation measured with fMRI. NeuroImage, 23, 148155.
Van Zijl, P. C., Hua, J., & Lu, H. (2012). The BOLD post-stimulus undershoot, one of
the most debated issues in fMRI. NeuroImage, 62, 10921102.
Vanzetta, I. (2006). Hemodynamic responses in cortex investigated with optical imaging
methods. Implications for functional brain mapping. Journal of Physiology Paris,
100, 201211.
Vazquez, A. L., Masamoto, K., Fukuda, M., & Kim, S. G. (2010). Cerebral oxygen delivery
and consumption during evoked neural activity. Frontiers in Neuroenergetics, 2, 11.
Watanabe, M., Bartels, A., Macke, J. H., Murayama, Y., & Logothetis, N. K. (2013).
Temporal jitter of the BOLD signal reveals a reliable initial dip and improved spatial
resolution. Current Biology, 23, 21462150.
Woolrich, M. W., Behrens, T. E., & Smith, S. M. (2004). Constrained linear basis sets
for HRF modelling using Variational Bayes. NeuroImage, 21, 17481761.
Worsley, K. J., & Friston, K. J. (1995). Analysis of fMRI time-series revisitedagain.
Yacoub, E., Ugurbil, K., & Harel, N. (2006). The spatial dependence of the poststimulus
undershoot as revealed by high-resolution BOLD- and CBV-weighted fMRI. Journal
of Cerebral Blood Flow and Metabolism, 26, 634644.
Yesilyurt, B., Ugurbil, K., & Uludag, K. (2008). Dynamics and nonlinearities of the
BOLD response at very short stimulus durations. Magnetic Resonance Imaging, 26,
853862.
Yu, X., Dodd, S. J., Silva, A. C., & Koretsky, A. P. (2014). Mapping the Distinct SingleVessel Vascular Contribution to BOLD and CBV fMRI. Conference Proceedings of
the Annual Meeting of the International Society of magnetic resonance in medicine.
Zhao, F., Jin, T., Wang, P., & Kim, S. G. (2007). Improved spatial localization of poststimulus BOLD undershoot relative to positive BOLD. NeuroImage, 34, 10841092.
Evolution of Instrumentation for Functional Magnetic Resonance Imaging

JA de Zwart and JH Duyn, National Institutes of Health, Bethesda, MD, USA
Glossary
Birdcage coil Conventionally the most common type of

MRI signal detector because of its homogeneous field,
generally also used for signal excitation. It consists of a
cylindrical former, with its axis parallel to the main magnetic
field. There is an end-ring conductor on each end,
interconnected with an even number of wires with the
proper capacitance to form a homogeneous RF field of the
proper frequency.
Gradient slew-rate The time required to ramp, or turn on, a
magnetic field gradient. This is typically expressed per unit of
produced gradient field, in T m1 s1.
Navigator echo An additional signal acquisition in every
shot of the MR imaging pulse sequence, which is encoded in
the exact same way in every shot. Differences between
navigator signals from different shots can therefore be used
to detect undesirable changes, for example due to patient
Introduction
Since the advent of functional MRI (fMRI) in the early 1990s
(Bandettini, Wong, Hinks, Tikofsky, & Hyde, 1992; Kwong,
Belliveau, Chesler, et al., 1992; Ogawa, Lee, Kay, & Tank,
1990), major developments in MRI instrumentation have taken
place that have provided particular benefits for human fMRI and
accelerated its acceptance in the research community. Most notably, improvements in system stability and signal detection hardware, together with increases in gradient switching speed and
magnetic field strength, have significantly increased fMRI spatial
resolution and contrast-to-noise ratio (CNR).
Among the most striking examples of hardware developments that have benefitted fMRI is the gradual transition to
high-magnetic field strength systems. While most human fMRI
was initially performed at systems ranging from 1.5 to 4.0,
7.0 T research systems now have become commonplace in
fMRI research laboratories, and even higher field strengths
(9.4, 10.5, and 11.7 T) are being explored at pioneer sites. At
the same time, gradient switching speeds of clinical MRI systems have improved by more than an order of magnitude,
enabling sophisticated fMRI acquisition techniques, and coil
arrays have improved detection sensitivity severalfold in most
brain regions. Together with improvements in other hardware
and in acquisition and analysis approaches, these developments have led to improved spatial resolution and specificity,
an improved CNR, and a more robust fMRI experiment. In the
following, we will review some of these technological improvements and their specific impact on fMRI research.
Magnetic Field Strength

Apart from an improved intrinsic signal-to-noise ratio (SNR), an
important benefit of stronger magnetic field (B0) is the increased
motion or hardware imperfections, such as magnetic

field drift.
Parallel imaging geometry (g)-factor A measure of the
relative increase in noise (signal variance) in the images
because of the fact that the sensitivity profiles of the coils
used are not perfectly orthogonal and therefore cannot
perfectly unfold aliassed MR images. The g-factor generally
increases with higher acceleration of the imaging
(increased aliassing) and decreases when the number of
coil elements is increased.
T1 relaxation This quantifies the rate at which the
magnetization, on which MR image formation is based,
recovers back to its equilibrium state.
T2* relaxation This parameter reflects the rate of MR signal
decay after excitation due to interactions between different
nuclei (T2 decay) as well as the compound effect of magnetic
field inhomogeneities on a subvoxel scale.
blood oxygen level-dependent (BOLD) contrast that forms the

basis of most fMRI studies. In fact, CNR increases more rapidly
than SNR with increased B0 (Figure 1; Duyn, 2012). Combined
with the reduced contribution of large vessels (Donahue, Hoogduin, Van Zijl, et al., 2011; Ugurbil, Hu, Chen, et al., 1999;
Uludag, Muller-Bierl, & Ugurbil, 2009), increased B0 provides
improved spatial resolution and specificity, in some cases allowing insight into brain activity occurring at the level of cortical
columns (Yacoub, Harel, & Ugurbil, 2008) or layers (Polimeni,
Fischl, Greve, & Wald, 2010). These advantages are described in
more detail in a separate article of this encyclopedia.
Despite the advantages of high field for BOLD fMRI, and
MRI in general, only a small fraction of MRI magnets operate at
high field (here defined as fields greater than 3 T). The primary
reason for this is the increased manufacturing, siting, and
operating cost of high-field magnets. In addition, there are
several technological challenges associated with high-field
MRI that affect the ability to obtain artifact-free images in
most areas of the body, including the brain. Resolving these
issues is an active area of research that may ultimately lead to a
more widespread use of high-field MRI.
Because of the particular BOLD contrast advantages of high
field, a large fraction of the fMRI studies are performed at 3 T or
above. This is in contrast with clinical MRI, which in large part
is done on systems of 1.5 T and below. In fact, fMRI has
contributed to the development of clinical 3 T systems, as
premier fMRI research sites ordered many of the early systems,
at a time when manufacturers were hesitant about the commercial development of high-field MRI. This notion may be
even more true for 7 T systems, whose development was catalyzed by and ran concurrently with the development of fMRI
(Hennig & Speck, 2012). Currently, 3 T systems are common
( 550 systems are installed in the United States alone; http://
www.mriinterventions.com/clearpoint/clearpoint-overview),
http://dx.doi.org/10.1016/B978-0-12-397025-1.00009-9
89
90
INTRODUCTION TO ACQUISITION METHODS | Evolution of Instrumentation for Functional Magnetic Resonance Imaging
and about fifty 7 T systems are installed worldwide. While 3 T

systems have been nearly fully developed for clinical use, the
clinical use of 7 T MRI is only just beginning.
A number of research sites are exploring the feasibility to
perform human fMRI at even higher field strengths. At least 6
MRI systems with fields exceeding 7.0 T are currently under construction, being installed or in operation. The strongest of these
will operate at 11.7 T: A 68 cm bore 11.7 T system is currently
being installed at the National Institutes of Health (NIH) in the
United States (Figure 2), while a 90 cm bore system of the same
strength is being developed for installation at NeuroSpin in
France (Vedrine, Aubert, Beaudet, et al., 2010). These systems
will approach the limit of what is possible with current magnet
15
CNR
SNR
10
10
Field strength (T)
15
20
Figure 1 Estimated dependence of signal-to-noise ratio (SNR) and

contrast-to-noise ratio (CNR) on field strength, normalized to 1 T.
Although both SNR and CNR continue to improve with field strengths of
20 T and beyond, gains in CNR are most prominent. Estimates include
effects of T1 and T2* relaxation. This figure is adapted from Figure 1 in
Duyn, J. H. (2012). The future of ultra-high field MRI and fMRI for study
of the human brain. Neuroimage, 62, 12411248.
technology, as significant further field increases will likely require

the development of new superconductive wire that can carry the
current density necessary for such elevated field strengths.
Another limitation to further magnetic field increases is posed
by a potential interaction with physiological processes, such as
vertigo and nystagmus (Roberts, Marcelli, Gillen, et al., 2011).
Gradients
Since the early days of fMRI, it was realized that an important
factor in the performance of an fMRI system is its ability to
perform rapid image acquisition (Bandettini et al., 1992;
Kwong et al., 1992; Turner, 1992). Rapid imaging not only
facilitates capturing the temporal changes in BOLD signal that
occur in response to brain activation but also reduces the
adverse effects of physiological variability and motion on the
temporal stability of the signal. For this reason, fast imaging
sequences like echo-planar imaging (EPI; Mansfield, 1977) are
generally considered the best choice for functional imaging,
since they provide both high temporal resolution and stability.
Fast imaging however requires rapid switching of the magnetic field gradients that are used for encoding the image
information. In the early 1990s, only a handful of research
MRI systems had EPI capability, as conventional (clinical)
systems had gradient switching rates, strengths, and duty cycles
well below those required for EPI. For this reason, EPI alternatives such as FLASH (Frahm, Bruhn, Merboldt, & Hanicke,
1992), FISP (Ogawa, Tank, Menon, et al., 1992), interleaved
EPI (Butts, Riederer, Ehman, Thompson, & Jack, 1994), and
PRESTO (Van Gelderen, Duyn, Ramsey, Liu, & Moonen, 2012)
were used, albeit generally having inferior fMRI performance.
Because of this, and other developing applications in cardiac,
interventional, and neuro-MRI, there was significant interest in
developing faster gradient systems.
Figure 2 The 11.7 T 68 cm bore magnet during installation at the NIH in Bethesda, MD, USA. This is an Agilent (Magnex Scientific) magnet with
Siemens electronics. It weighs approximately 68 metric tons, is 3.5 m long with a 2 m radius, and is filled with 3 m3 of liquid helium that is kept at 2.4 K
by pumping to a pressure of 5 103 Pa.
Some of the problems that needed to be overcome to
develop high-strength, rapidly switching gradients for clinical
systems were eddy currents, acoustic noise, coil heating, and
the lack of high-current high-voltage gradient amplifiers. Over
the course of the development of fMRI, many of these problems have been resolved or mitigated, resulting in vast
improvements in gradient performance (Cohen & Schmitt,
2012; Schmitt, Stehling, & Turner, 1998).
An early and major factor in the improvement of gradient
performance of clinical MRI systems was the use of active
gradient shielding (Chapman, 1999), which prevented detrimental effects of electrical eddy currents in magnet components on the image quality (Bowtell & Mansfield, 1991).
Other factors include improvements in eddy current compensation, gradient coil cooling, and technology for and cooling of
amplifiers.
As a result of these improvements, gradient performance has
evolved to a level at which gradient switching in whole-body
scanners is limited by the peripheral nerve stimulation threshold
(Reilly, 1989), which is on the order of 200 T m1 s1 (Feldman,
Hardy, Aksel, Schenck, & Chronik, 2009). Gradient strength has
increased by two orders of magnitude since human MR imaging
began, from 2.5 mT m1 in the 1980s (Ahn, Lee, Nalcioglu, &
Cho, 1986) to 300 mT m1 for a state-of-the-art gradient set
developed for the human connectome project (Mcnab, Edlow,
Witzel, et al., 2013). The head-only 11.7 T scanner at NIH is
equipped with an AC88 head-only gradient coil allowing
80 mT m1 amplitude and 200 T m1 s1 maximum slew rate.
Currently, commercially available gradient sets in whole-body
3 T scanners from all three major vendors meet or exceed
50 mT m1 at 200 T m1 s1 (http://www.healthcare.philips.
com/main/products/mri/systems; http://www3.gehealthcare.
com/en/Products/Categories/Magnetic_Resonance_Imaging;
http://usa.healthcare.siemens.com/magnetic-resonanceimaging). The availability of such high-performance gradient
systems on commercial clinical systems has lead to EPI
becoming the default imaging technique for fMRI.
Receive Coil Arrays

Another major development that has occurred over the lifespan of fMRI is that of radiofrequency (RF) coils used for MRI
signal detection. This has affected fMRI in two major ways:
First, it has improved SNR, and, second, it has improved scan
speed. Combined, these improvements can be exploited to
perform fMRI with high temporal or spatial resolution. In the
following, these developments will be discussed briefly.
Sensitivity (SNR) Improvements

Early MRI detectors consisted of single-loop coil or volume
resonator large enough to cover the entire volume of interest.
A landmark paper by Roemer, Edelstein, Hayes, Souza, and
Mueller (1990) showed that, when minimizing coil-to-coil
coupling, arrays of multiple smaller elements could provide
increased SNR over an extended area. For each area in the
object, one has the flexibility to optimally combine the individual coil signals to maximize SNR. Therefore, the focal areas
of high sensitivity near each element can be extended to cover
91
Figure 3 A very early (circa 2001), prototype eight-channel gapped

array for brain imaging built in-house in the Duyn laboratory at the NIH. A
baseball-batting helmet was used as the former; matching circuits are
located on the exterior surface (not visible). It was interfaced to a 1.5 T
General Electric scanner with four receive channels, so only half of its
eight elements could be connected at a time.
much of the object. Unfortunately, adoption of this technology

for fMRI (or brain MRI in general) was delayed for various
reasons, including the resulting inhomogeneous image contrast and SNR, the misconception by many researchers in the
field that SNR in deep brain regions would suffer with these
smaller coils, and the limited number of receiver channels
available at that time.
A major change in the use of multichannel coils was precipitated by the invention of parallel imaging (PI) (Griswold,
Jakob, Heidemann, et al., 2002; Pruessmann, Weiger,
Scheidegger, & Boesiger, 1999; Ra & Rim, 1993; Sodickson &
Manning, 1997), which demonstrated that multielement coil
arrays not only improved SNR but also allowed increased scan
speed (see next section). This set off a still continuing development of MRI scanners with a large number of RF receiver
channels and many-element coil arrays, up to 96 channels for
a dedicated head coil (Wiggins, Polimeni, Potthast, et al.,
2009). For a review, see Keil and Wald (2013). At the same
time, several groups demonstrated that coil arrays allowed
substantial SNR improvements everywhere in the brain (de
Zwart, Ledden, Kellman, Van Gelderen, & Duyn, 2002;
Wiggins, Triantafyllou, Potthast, et al., 2006; Wright & Wald,
1997), including in deep brain regions, primarily because of
the fact that they could be designed to more closely match the
contours of the head and pick up less noise from nonbrain
regions such as the neck and shoulders. This has led to the
development of close-fitting, helmet-like arrays for brain imaging (e.g., Figure 3). For a tight-fitting 16-channel array at 3 T,
this boosted SNR approximately twofold in the center of the
brain compared to a standard product birdcage head coil (de
Zwart, Ledden, Van Gelderen, et al., 2004). As a result, commercial 32-channel brain arrays now available for fMRI on
both 3 and 7 T scanners allow SNR improvements ranging
from 50% to 400%, depending on brain location.
In theory, a larger number of smaller elements augment the
SNR advantage, up to the point where nonsample noise starts
92
140
Whole brain
Brain center
Average SNR
120
100
80
60
40
Average g factor
2.0
1,3
3,1
1.8
1.6
2,3
3,2
1.4
2,2
1,2
2,1
1.2
1.0
0
10
15
20
Number of coil elements

Figure 4 Plots of the measured parallel imaging performance (bottom)
and SNR (top) as a function of the number of coil elements. SNR
averages over the whole brain and over a region in the center of the brain
are shown. Traces in the bottom plot show SENSE g-factor (Pruessmann
et al., 1999) for different combinations of acceleration in readout (r) and
phase-encode direction (p), respectively (shown as an r,p pair next to
each line). This figure is adapted from Figure 3 in de Zwart, J. A., Ledden,
P. J., Van Gelderen, P., et al. (2004). Signal-to-noise ratio and parallel
imaging performance of a 16-channel receive-only brain coil array at 3.0
Tesla. Magnetic Resonance in Medicine, 51, 2226.
to significantly contribute to the measured signal. Since the

ratio between sample and nonsample noise increases with field
strength for a given element size, high-field systems allow for a
larger number of coil elements before this limitation is
encountered. For imaging of the human brain, rough estimates
for this optimum are between 50 and 100 channels for 3 T and
100 and 150 for 7 T.
Scan Speed Improvements

Acceleration of the imaging process with PI techniques
(Griswold et al., 2002; Pruessmann et al., 1999; Ra & Rim,
1993; Sodickson & Manning, 1997) is based on the fact that
the sensitivities of individual elements in an array detector are
distinct across the object. This yields extra spatial information,
which supplements the information obtained from gradient
encoding (Lauterbur, 1973), and therefore allows the latter to
be reduced.
This revolutionary concept changed the way array detectors
were designed and used, prompting MRI manufactures to reengineer the scanner electronics to include more and higherbandwidth receiver channels. The increase in the number of
detector channels augmented the factor (called rate R) by
which the imaging process can be accelerated without substantially increasing image noise. The latter is quantified by the socalled geometry factor, or g-factor, which represents the noise
amplification associated with the image reconstruction process
due to insufficient distinct spatial information in the coil

sensitivity profiles (Pruessmann et al., 1999). This g-factor is
generally lower for arrays with a larger number of elements
but increases with R (Figure 4). Optimal coil design, that
is, element layout and separation, can minimize this
penalty. Increasing PI performance could be a motivation
for increasing the number of coil elements or the degree of
overlap of the elements, beyond what would be optimal from
an SNR perspective.
The synergy of high-field and coil arrays is not only limited
to the fact that at high field, the benefits of decreasing element
size and increasing element count can be extended further, to a
higher element count. Theoretically, increased field strength
also allows higher R-values for the same g-factor. At 7.0 T and
above, rates of around 5 in each image dimension may be
feasible at moderate g-factors (<1.5) with optimized coil arrays
(Wiesinger, Boesiger, & Pruessmann, 2004; Wiesinger, Van De
Moortele, Adriany, et al., 2004).
The ability to accelerate EPI with PI is particularly useful at
high field because of the reduction in T2* (the apparent transverse relation time of the MRI signal). This transverse relaxation (i.e., signal decay) takes place during the EPI signal
acquisition and results in resolution loss. Relaxation effects
can be significantly reduced through the acceleration available
with PI, enabling resolutions in the 1323 mm3 (18 ml) range,
for example, Barry, Strother, Gatenby, and Gore (2011),
Polimeni et al. (2010), Speck, Stadler, and Zaitsev (2008),
and Van Der Zwaag, Francis, Head, et al. (2009).
The scan speed improvements available with PI do not
come entirely for free. Because of noise amplification,
expressed by the g-factor, and because less data are acquired
p
with increasing R, the intrinsic image SNR is reduced by g R.
This may affect the sensitivity of an fMRI experiment, which
depends on signal stability over time. Interestingly, because
this temporal signal stability also depends on factors other
than intrinsic SNR (e.g., physiological noise and subject
motion; Triantafyllou, Hoge, Krueger, et al., 2005), the p
impact
of acceleration on fMRI sensitivity may be well below g R (de

Zwart, Van Gelderen, Kellman, & Duyn, 2002b).
Increases in spatial resolution generally lead to a disproportionate increase in scan time, since not only the number of
samples required to cover an imaging plane increases
quadratically but also the number of slices required for
whole-brain coverage increases. Fortunately, PI not only allows
acceleration of the EPI image acquisition in plane but also can
also be extended to simultaneously acquire multiple slices
(Larkman, Hajnal, Herlihy, et al., 2001; Moeller, Yacoub,
Olman, et al., 2010; Setsompop et al., 2012). This greatly
facilitates the ability to perform whole-brain fMRI at high
resolution and only incurs an SNR penalty equal to the gfactor since the amount of data collected is not reduced in
this method.
Peripheral Hardware
Monitoring of Respiration and Cardiac Cycle
Physiological processes such as heartbeat and respiration affect
the fMRI signals in various ways, resulting in temporal signal
variation that confounds measures of brain activity. Pulsatile
arterial flow related to the heartbeat is directly reflected in the
fMRI signal, as are cerebrospinal fluid flow variations related to
the cardiac (Schroth & Klose, 1992a) and respiratory cycle
(Schroth & Klose, 1992b). The cardiac and respiratory cycles
are also intricately linked with brain perfusion, and changes in
their rates (and also respiration depth) directly affect the BOLD
fMRI signal (Birn, Diamond, Smith, & Bandettini, 2006;
Shmueli, Van Gelderen, de Zwart, et al., 2007). Lastly, respiration also causes magnetic field fluctuations within the brain,
which can similarly result in fMRI signal fluctuations (Raj,
Paley, Anderson, Kennan, & Gore, 2000).
Clinical MRI systems typically come equipped with basic
hardware for monitoring the cardiac and respiratory cycles.
These external signals can be used to correct artifacts, directly
related to either the cardiac and respiratory cycle or changes in
their rate, during postprocessing even if these artifacts are
undersampled in the MRI time-series data, which is the case
in a typical fMRI experiment (Birn et al., 2006; Glover, Li, &
Ress, 2000). Such external physiological monitoring signal can
also be used to adjust magnetic field homogeneity dynamically
to compensate for the effects of respiration (Van Gelderen, de
Zwart, Starewicz, Hinks, & Duyn, 2007), the so-called dynamic
shimming. This requires modification of the scanner hardware
in order to allow dynamic, real-time changes to the scanners
reference frequency and its shim currents.
For fMRI applications, which generally employ single-shot
sequences, both of these approaches mostly serve to improve
temporal stability of the signal, which is the dominant source
of variance in most fMRI experiments, as was discussed in the
preceding text.
Prospective Motion Correction

Patient motion is another source of artifact that negatively
affects fMRI. Motion correction strategies applied during postprocessing of the data are widely used, commonly based on
rigid-body image registration techniques, for example,
Jenkinson, Bannister, Brady, and Smith (2002). However,
these retrospective strategies do not correct all effects of
motion, and some image intensity artifacts may remain. Several prospective motion methods, in which the MR acquisition
is adjusted in real-time to compensate for the motion, have
been proposed. This can be based on additional MR acquisitions in each shot, that is, navigator echoes (Ehman & Felmlee,
1989; Lee, Jack, Grimm, et al., 1996). Disadvantage of such an
approach is that the MR imaging method needs to be modified
and that additional scan time is required. As an alternative, an
external motion tracking system can be implemented. Various
types of hardware have been proposed for this purpose, such as
miniature coils (Derbyshire, Wright, Henkelman, & Hinks,
1998) and cameras (Qin, Van Gelderen, Derbyshire, et al.,
2009; Zaitsev, Dold, Sakas, Hennig, & Speck, 2006).
Shimming
Magnetic field inhomogeneities (in terms of absolute field
deviations over the object) increase at higher magnetic field
strength. They lead to T2* reduction, as well as geometric image
distortions and signal dropouts, especially in the single-shot
images used in fMRI. At low field strength, first-order (linear
over space) field adjustments through shim adjustments would
93
suffice for most applications. Typically, a small additional

shim term can be added to the three imaging gradient coils to
implement this. Commonly, additional dedicated higherorder shim coils are used (Webb & Macovski, 1991), especially
at higher field. Furthermore, methods have been developed in
which different shim settings are used for each acquired slice
(Constable & Spencer, 1999) or to account for dynamic,
mostly respiratory-related changes (Van Gelderen et al.,
2007), as was mentioned in a previous section. Passive shimming has also been applied to compensate the field in known
inhomogeneous areas (Wilson, Jenkinson, & Jezzard, 2002),
but since it is more cumbersome to use and can reduce subject
comfort (Osterbauer, Wilson, Calvert, & Jezzard, 2006), it is
not widely used. Whole-head passive shimming has also been
proposed, in which a subject-specific array of diamagnetic and
paramagnetic particles is placed around the subject (Koch,
Brown, Rothman, & De Graaf, 2006). Since interindividual
variation does not allow a generalized solution that would
benefit most subjects (Heijtel et al., 2009), this approach is
also too impractical for widespread use.
Real-Time fMRI
The vast increases in computational performance over the
lifetime of fMRI not only have made new MR image reconstruction techniques possible but also have led to the development of real-time fMRI, in which fMRI images are
reconstructed on the fly. Immediate availability of the fMRI
activation maps can be used for quality control or planning
successive runs, as was initially suggested (Cox, Jesmanowicz,
& Hyde, 1995). However, the detected BOLD changes can also
be used to provide feedback to the subject on a subsecond
timescale to yield a braincomputer interface. This real-time
fMRI-based neurofeedback has been used to train selfregulation of the local BOLD response in various different
brain areas and to study resulting behavioral effects, such as
modulation of reaction time, pain, linguistic, or emotional
processing (Weiskopf, 2012).
Multimodal Functional Imaging

fMRI suffers from several inherent disadvantages, such as its
low sensitivity, the indirect nature of the contrast mechanism
that exploits changes in vascular parameters to assess neuronal
events, and the relatively low temporal resolution. This low
temporal resolution is a result both of the imaging technique
and of the sluggishness of the vascular response (the basis of
both BOLD- and perfusion-based fMRI), which is on the order
of seconds. Researchers have attempted to address these issues
by trying to more directly assess the electrical events in neurons
in so-called neuronal current fMRI experiments (Bodurka &
Bandettini, 2002), albeit with limited to no tangible success
(Chu, de Zwart, Van Gelderen, et al., 2004), mainly due to the
low level of currents that support brain activity and the relative
insensitivity of fMRI to detect their associated field changes. A
more successful approach has been to combine fMRI with
other established neuroimaging techniques, such as electroencephalography (EEG) and positron-emission topography
(PET), the so-called multimodal fMRI.
94
EEG-fMRI
EEG measures the changing electric field produced by the brain
at approximately a millisecond timescale with reasonably high
sensitivity. Its main disadvantages are poor spatial resolution
and poor sensitivity for deep brain areas, which are further
removed from the electrodes. Combining EEG with fMRI can
to some extent alleviate both these issues (Rosenkranz &
Lemieux, 2010) and potentially yield additional information
about the underlying neuronal circuitry (Liu, de Zwart, Chang,
et al., 2014). However, this is not immediately straightforward,
since changes to EEG hardware and processing are required.
This is because MRI introduces two major artifacts in EEG
signal, both of which are based on an electromotive force
that is induced in the conductive loops formed by the scalp
electrodes (Goldman, Stern, Engel, & Cohen, 2000). The two
major artifact sources are the rapid switching of the field gradients in an MRI experiment (gradient artifact) and the pulsatile blood flow through the scalp (ballistocardiographic
artifact). These artifacts can be orders of magnitude lager than
the cerebral signal of interest, requiring EEG amplifiers with a
high dynamic range. To simplify removal of the gradient artifact, as well as to improve its efficacy, the internal clock of the
EEG system is generally linked to the clock of the MRI system to
assure that EEG data collection is synchronous with the timing
of the MR gradients. Finally, the presence of conductive EEG
leads in the MR bore is a potential safety issue. However,
these issues have been reasonably well addressed (Laufs,
Daunizeau, Carmichael, & Kleinschmidt, 2008), leading to it
being regularly used to study epilepsy in humans (Laufs &
Duncan, 2007).
MRIPET
PET allows for the tracking of radiolabeled isotopes in concentrations far below what would be detectable with MRI alone,
below picomolar range (Judenhofer, Wehrl, Newport, et al.,
2008). This makes PET a sensitive tool to monitor brain
function albeit with its own limitations. MRI on the other
hand can provide excellent soft tissue contrast and is noninvasive, allowing high-resolution (functional) imaging and
spectroscopy. The integration of PET and MRI has been challenging since the PET signal detection is conventionally performed with photon-multiplier tubes, which are sensitive to
magnetic fields. Furthermore, the RF coils used in MRI have to
be made PET-transparent. Significant engineering efforts over
the past few years, including the development of solid-state
PET detectors, have in large part resolved these issues
(Judenhofer et al., 2008), and a fully integrated whole-body
clinical MRI/PET system is currently available as a product
from Siemens. The first results of the application of this methodology to fMRI are currently appearing in literature (Sander,
Hooker, Catana, et al., 2013).
Future Developments
Some of the ongoing developments that have not been discussed in the preceding text but are likely to impact fMRI in the
near future include parallel transmission and the so-called

dynamic field camera.
In analogy with PI, which benefits signal reception, parallel
transmission uses multiple coil elements to improve signal
excitation. Specifically, it aims to mitigate inhomogeneities in
the RF transmit field typical of high-field MRI, through simultaneous control of the fields transmitted through multiple coil
elements (Katscher & Bornert, 2006). This control, as well as its
safe operation, requires specialized hardware and software that
only very recently has started to become available on scanners
operating at 3.0 T and above.
A dynamic field camera allows monitoring of the MRI
signal and correcting imperfections by using an array of MR
field probes, placed at strategic locations around the object
under study (Barmet, De Zanche, & Pruessmann, 2008).
Using this approach, the effects of gradient vibrations, eddy
currents, temperature fluctuations in MR hardware, and some
of the physiologically induced field changes that originate
from the subject can be corrected; this is expected to significantly improve temporal stability and quality of fMRI data.
Acknowledgments
We acknowledge the Intramural Research Program of the
National Institute of Neurological Disorders and Stroke for
support.
and Applications; Positron Emission Tomography and Neuroreceptor
Mapping In Vivo.
Bibliography
Ahn, C. B., Lee, S. Y., Nalcioglu, O., & Cho, Z. H. (1986). An improved nuclear
magnetic resonance diffusion coefficient imaging method using an optimized pulse
sequence. Medical Physics, 13, 789793.
Bandettini, P. A., Wong, E. C., Hinks, R. S., Tikofsky, R. S., & Hyde, J. S. (1992). Time
Medicine, 25, 390397.
Barmet, C., De Zanche, N., & Pruessmann, K. P. (2008). Spatiotemporal magnetic field
monitoring for MR. Magnetic Resonance in Medicine, 60, 187197.
Barry, R. L., Strother, S. C., Gatenby, J. C., & Gore, J. C. (2011). Data-driven
optimization and evaluation of 2D EPI and 3D PRESTO for BOLD fMRI at 7 Tesla: I.
Focal coverage. NeuroImage, 55, 10341043.
Birn, R. M., Diamond, J. B., Smith, M. A., & Bandettini, P. A. (2006). Separating
respiratory-variation-related fluctuations from neuronal-activity-related fluctuations
in fMRI. NeuroImage, 31, 15361548.
Bodurka, J., & Bandettini, P. A. (2002). Toward direct mapping of neuronal activity: MRI
detection of ultraweak, transient magnetic field changes. Magnetic Resonance in
Medicine, 47, 10521058.
Bowtell, R., & Mansfield, P. (1991). Gradient coil design using active magnetic
screening. Magnetic Resonance in Medicine, 17, 1519 discussion 1921.
Butts, K., Riederer, S. J., Ehman, R. L., Thompson, R. M., & Jack, C. R. (1994).
Interleaved echo planar imaging on a standard MRI system. Magnetic Resonance in
Medicine, 31, 6772.
Chapman, B. L. (1999). Shielded gradients. And the general solution to the near field
problem of electromagnet design. MAGMA, 9, 146151.
Chu, R., de Zwart, J. A., van Gelderen, P., et al. (2004). Hunting for neuronal currents:
Absence of rapid MRI signal changes during visual-evoked response. NeuroImage,
23, 10591067.
Cohen, M. S., & Schmitt, F. (2012). Echo planar imaging before and after fMRI: A
personal history. NeuroImage, 62, 652659.
Constable, R. T., & Spencer, D. D. (1999). Composite image formation in z-shimmed
functional MR imaging. Magnetic Resonance in Medicine, 42, 110117.
Cox, R. W., Jesmanowicz, A., & Hyde, J. S. (1995). Real-time functional magneticresonance-imaging. Magnetic Resonance in Medicine, 33, 230236.
de Zwart, J. A., Ledden, P. J., Kellman, P., van Gelderen, P., & Duyn, J. H. (2002).
Design of a SENSE-optimized high-sensitivity MRI receive coil for brain imaging.
de Zwart, J. A., Ledden, P. J., van Gelderen, P., et al. (2004). Signal-to-noise ratio and
parallel imaging performance of a 16-channel receive-only brain coil array at 3.0
Tesla. Magnetic Resonance in Medicine, 51, 2226.
de Zwart, J. A., van Gelderen, P., Kellman, P., & Duyn, J. H. (2002). Application of
sensitivity-encoded echo-planar imaging for blood oxygen level-dependent
functional brain imaging. Magnetic Resonance in Medicine, 48, 10111020.
Derbyshire, J. A., Wright, G. A., Henkelman, R. M., & Hinks, R. S. (1998). Dynamic
scan-plane tracking using MR position monitoring. Journal of Magnetic Resonance
Imaging, 8, 924932.
Donahue, M. J., Hoogduin, H., van Zijl, P. C., et al. (2011). Blood oxygenation leveldependent (BOLD) total and extravascular signal changes and DeltaR2* in human
visual cortex at 1.5, 3.0 and 7.0 T. NMR in Biomedicine, 24, 2534.
Duyn, J. H. (2012). The future of ultra-high field MRI and fMRI for study of the human
Ehman, R. L., & Felmlee, J. P. (1989). Adaptive technique for high-definition MR
imaging of moving structures. Radiology, 173, 255263.
Feldman, R. E., Hardy, C. J., Aksel, B., Schenck, J., & Chronik, B. A. (2009).
Experimental determination of human peripheral nerve stimulation thresholds in a
3-axis planar gradient system. Magnetic Resonance in Medicine, 62, 763770.
Frahm, J., Bruhn, H., Merboldt, K. D., & Hanicke, W. (1992). Dynamic MR imaging of
human brain oxygenation during rest and photic stimulation. Journal of Magnetic
Glover, G. H., Li, T. Q., & Ress, D. (2000). Image-based method for retrospective
correction of physiological motion effects in fMRI: RETROICOR. Magnetic
Goldman, R. I., Stern, J. M., Engel, J., Jr., & Cohen, M. S. (2000). Acquiring
simultaneous EEG and functional MRI. Clinical Neurophysiology, 111, 19741980.
Griswold, M. A., Jakob, P. M., Heidemann, R. M., et al. (2002). Generalized
autocalibrating partially parallel acquisitions (GRAPPA). Magnetic Resonance in
Medicine, 47, 12021210.
Heijtel, D. F. R., de Zwart, J. A., Van Gelderen, P., & Duyn, J. H. (2009). The feasibility of
a generalized passive shimming construct for human brain imaging. In: 17th
scientific meeting and exhibition, April 1824, 2009. Honolulu, HI 3077.
Hennig, J., & Speck, O. (2012). High-field MR imaging. Springer.
Jenkinson, M., Bannister, P., Brady, M., & Smith, S. (2002). Improved optimization for
the robust and accurate linear registration and motion correction of brain images.
Judenhofer, M. S., Wehrl, H. F., Newport, D. F., et al. (2008). Simultaneous PET-MRI:
A new approach for functional and morphological imaging. Nature Medicine, 14,
459465.
Katscher, U., & Bornert, P. (2006). Parallel RF transmission in MRI. NMR in
Koch, K. M., Brown, P. B., Rothman, D. L., & De Graaf, R. A. (2006). Sample-specific
diamagnetic and paramagnetic passive shimming. Journal of Magnetic Resonance,
182, 6674.
Kwong, K. K., Belliveau, J. W., Chesler, D. A., et al. (1992). Dynamic magnetic
resonance imaging of human brain activity during primary sensory stimulation.
89, 56755679.
Larkman, D. J., Hajnal, J. V., Herlihy, A. H., et al. (2001). Use of multicoil arrays for
separation of signal from multiple slices simultaneously excited. Journal of
Laufs, H., Daunizeau, J., Carmichael, D. W., & Kleinschmidt, A. (2008). Recent
advances in recording electrophysiological data simultaneously with magnetic
resonance imaging. NeuroImage, 40, 515528.
Laufs, H., & Duncan, J. S. (2007). Electroencephalography/functional MRI in human
epilepsy: What it currently can and cannot do. Current Opinion in Neurology, 20,
417423.
Lauterbur, P. C. (1973). Image formation by induced local interactions Examples
employing nuclear magnetic-resonance. Nature, 242, 190191.
Lee, C. C., Jack, C. R., Jr., Grimm, R. C., et al. (1996). Real-time adaptive motion
correction in functional MRI. Magnetic Resonance in Medicine, 36, 436444.
95
Liu, Z., de Zwart, J. A., Chang, C., et al. (2014). Neuroelectrical decomposition of
spontaneous brain activity measured with functional magnetic resonance imaging.
Mansfield, P. (1977). Multi-planar image-formation using NMR spin echoes. Journal of
Mcnab, J. A., Edlow, B. L., Witzel, T., et al. (2013). The human connectome project and
beyond: Initial applications of 300 mT/m gradients. NeuroImage, 80, 234245.
Moeller, S., Yacoub, E., Olman, C. A., et al. (2010). Multiband multislice GE-EPI at 7
Tesla, with 16-fold acceleration using partial parallel imaging with application to
high spatial and temporal whole-brain fMRI. Magnetic Resonance in Medicine, 63,
11441153.
Ogawa, S., Lee, T. M., Kay, A. R., & Tank, D. W. (1990). Brain magnetic resonance
Osterbauer, R. A., Wilson, J. L., Calvert, G. A., & Jezzard, P. (2006). Physical and
physiological consequences of passive intra-oral shimming. NeuroImage, 29,
245253.
Polimeni, J. R., Fischl, B., Greve, D. N., & Wald, L. L. (2010). Laminar analysis of 7T
BOLD using an imposed spatial activation pattern in human V1. NeuroImage, 52,
13341346.
Qin, L., van Gelderen, P., Derbyshire, J. A., et al. (2009). Prospective head-movement
correction for high-resolution MRI using an in-bore optical tracking system.
Ra, J. B., & Rim, C. Y. (1993). Fast imaging using subencoding data sets from multiple
detectors. Magnetic Resonance in Medicine, 30, 142145.
Raj, D., Paley, D. P., Anderson, A. W., Kennan, R. P., & Gore, J. C. (2000). A model for
susceptibility artefacts from respiration in functional echo-planar magnetic
resonance imaging. Physics in Medicine and Biology, 45, 38093820.
Reilly, J. P. (1989). Peripheral nerve stimulation by induced electric currents: Exposure
to time-varying magnetic fields. Medical & Biological Engineering & Computing,
27, 101110.
Roberts, D. C., Marcelli, V., Gillen, J. S., et al. (2011). MRI magnetic field stimulates
rotational sensors of the brain. Current Biology, 21, 16351640.
Roemer, P. B., Edelstein, W. A., Hayes, C. E., Souza, S. P., & Mueller, O. M. (1990). The
Rosenkranz, K., & Lemieux, L. (2010). Present and future of simultaneous EEG-fMRI.
MAGMA, 23, 309316.
Sander, C. Y., Hooker, J. M., Catana, C., et al. (2013). Neurovascular coupling to D2/D3
dopamine receptor occupancy using simultaneous PET/functional MRI.
110, 1116911174.
Schmitt, F., Stehling, M. K., & Turner, R. (1998). Echo-planar imaging: Theory,
technique and application. Springer.
Schroth, G., & Klose, U. (1992a). Cerebrospinal fluid flow. I. Physiology of cardiacrelated pulsation. Neuroradiology, 35, 19.
Schroth, G., & Klose, U. (1992b). Cerebrospinal fluid flow. II. Physiology of respirationrelated pulsations. Neuroradiology, 35, 1015.
Medicine, 67, 12101224.
Shmueli, K., van Gelderen, P., de Zwart, J. A., et al. (2007). Low-frequency fluctuations
in the cardiac rate as a source of variance in the resting-state fMRI BOLD signal.
Sodickson, D. K., & Manning, W. J. (1997). Simultaneous acquisition of spatial
harmonics (SMASH): Fast imaging with radiofrequency coil arrays. Magnetic
Speck, O., Stadler, J., & Zaitsev, M. (2008). High resolution single-shot EPI at 7T.
MAGMA, 21, 7386.
Triantafyllou, C., Hoge, R. D., Krueger, G., et al. (2005). Comparison of physiological
noise at 1.5 T, 3 T and 7 T and optimization of fMRI acquisition parameters.
Turner, R. (1992). Magnetic resonance imaging of brain function. American Journal of
Physiological Imaging, 7, 136145.
Ugurbil, K., Hu, X. P., Chen, W., et al. (1999). Functional mapping in the human brain
using high magnetic fields. Philosophical Transactions of the Royal Society of
London. Series B, Biological Sciences, 354, 11951213.
96
van der Zwaag, W., Francis, S., Head, K., et al. (2009). fMRI at 1.5, 3 and 7 T:
Characterising BOLD signal changes. NeuroImage, 47, 14251434.
van Gelderen, P., de Zwart, J. A., Starewicz, P., Hinks, R. S., & Duyn, J. H. (2007). Realtime shimming to compensate for respiration-induced B0 fluctuations. Magnetic
van Gelderen, P., Duyn, J. H., Ramsey, N. F., Liu, G., & Moonen, C. T. (2012). The
PRESTO technique for fMRI. NeuroImage, 62, 676681.
Vedrine, P., Aubert, G., Beaudet, F., et al. (2010). Iseult/INUMAC whole body 11.7 T
MRI magnet status. IEEE Transactions on Applied Superconductivity, 20,
696701.
Webb, P., & Macovski, A. (1991). Rapid, fully automatic, arbitrary-volume in vivo
shimming. Magnetic Resonance in Medicine, 20, 113122.
Weiskopf, N. (2012). Real-time fMRI and its application to neurofeedback. NeuroImage,
62, 682692.
Wiesinger, F., Boesiger, P., & Pruessmann, K. P. (2004). Electrodynamics and
ultimate SNR in parallel MR imaging. Magnetic Resonance in Medicine, 52,
376390.
Wiesinger, F., Van De Moortele, P. F., Adriany, G., et al. (2004). Parallel imaging
performance as a function of field strength An experimental investigation using
electrodynamic scaling. Magnetic Resonance in Medicine, 52, 953964.
Wiggins, G. C., Polimeni, J. R., Potthast, A., et al. (2009). 96-Channel receive-only head
coil for 3 Tesla: Design optimization and evaluation. Magnetic Resonance in
Medicine, 62, 754762.
Wiggins, G. C., Triantafyllou, C., Potthast, A., et al. (2006). 32-channel 3 Tesla receiveonly phased-array head coil with soccer-ball element geometry. Magnetic
Wilson, J. L., Jenkinson, M., & Jezzard, P. (2002). Optimization of static field
homogeneity in human brain using diamagnetic passive shims. Magnetic
Wright, S. M., & Wald, L. L. (1997). Theory and application of array coils in MR
spectroscopy. NMR in Biomedicine, 10, 394410.
Yacoub, E., Harel, N., & Ugurbil, K. (2008). High-field fMRI unveils orientation columns
in humans. Proceedings of the National Academy of Sciences of the United States of
America, 105, 1060710612.
Zaitsev, M., Dold, C., Sakas, G., Hennig, J., & Speck, O. (2006). Magnetic resonance
imaging of freely moving objects: Prospective real-time motion correction using an
external optical motion tracking system. NeuroImage, 31, 10381050.
High-Field Acquisition
RS Menon, The University of Western Ontario, London, ON, Canada
Glossary
B0 Refers to the main static magnetic field of the magnet

used for MRI.
Blood oxygenation level-dependent effect (BOLD) The
biophysical mechanism whereby the oxygenation state of
the hemoglobin in a red blood cell is altered in response to
neural activity changes. The change in magnetic state of the
hemoglobin molecule (to either more diamagnetic or more
Historical Roots
Overview
The explosion in human and animal brain mapping applications over the past 20 years has, in large part, been driven by
advances in high-field (HF) and ultrahigh-field (UHF) MRI
scanners, with each driving advances in the other (Figure 1).
This symbiotic growth represents a confluence of many unanticipated factors. As is so often the case in science, new
technologies motivated by a particular scientific question get
co-opted when the technology proves more adept for something else. For example, the first three human 4T instruments
were obtained by institutions wishing to study cardiac metabolism using MR spectroscopy. One of these became a workhorse for the early demonstration and mechanistic studies of
blood oxygenation level-dependent (BOLD) in humans, but
the pressure on the major manufacturers to provide higherfield MRI scanners to amplify the BOLD effect came only later
as fMRI and multimodality brain mapping laboratories came
into being.
In part, such an evolution has also been driven by the fact
that tremendous challenges have to be met between the first
installation of a higher field strength magnet and its adaptation
for routine use by the clinical and neuroscience communities.
The first installed UHF instruments were the 8T installed at the
Ohio State University in 1998 and the 7T instrument installed
in 1999 at the University of Minnesota, at a time when 3T was
still not in routine use for fMRI. But the routine use of 7T for
neuroscience has been slow, despite the installation of over 60
such systems. It has been very difficult to do whole-brain echo
planar imaging (EPI) for fMRI on UHF scanners, although
recent advances in radio frequency (RF) shimming, multiplexed acquisitions and B0 shimming have reawakened the
desire for doing fMRI at 7T and above. In the mean time,
using less technically demanding sequences, unanticipated
image contrasts in novel anatomical imaging sequences have
become another driving force for the adaptation of these
higher and higher magnetic fields (Lee et al., 2010). As with
BOLD, such contrasts had been predicted (Luo et al., 2010) but
required higher field strengths to be visualized well.
In this article, the rationale for performing fMRI with BOLD
at the highest available magnetic fields is discussed from a
paramagnetic) influences the MRI signal intensity for certain

types of MRI acquisitions.
Echo planar imaging (EPI) One of the first and still one of
the most rapid methods for acquiring images rapidly, with a
bonus of being sensitive to the magnetic state of the
hemoglobin molecules due to the length and placement of
the echo train used in the acquisition.
broad experimental and theoretical perspective. This argument

is based on sensitivity to the desired BOLD changes in the
smallest vessels in the brain (i.e., the capillaries). Some of the
concepts and challenges in performing fMRI at UHF are discussed. For discussion purposes, HF is defined as 3T, very high
field as 4T and 4.7T, while UHF is defined as any field strength
about that, generally meaning 7T or greater. This is an evolving
definition. Twenty-five years ago, manufacturers marketed
1.5T as HF MRI and UHF consisted of three scanners from
GE, Siemens/Varian (SISCO), and Philips operating at 4T.
Magnetic Field Dependence of BOLD

The first measurements of the relaxation times of oxygenated
and deoxygenated blood were made in 1982 (Thulborn et al.,
1982). In this fundamental experiment, the transverse relaxation time (T2) of whole blood was experimentally shown to
depend on the square of the magnetic field (i.e., B20) and to be
consistent with an exchange process of water protons between
sites of different magnetic fields. Interestingly, these authors
stated that the in vivo measurement would not be possible on
the more standard 0.39T MRI systems used at the time, but
should be feasible on experimental HF 1.9T systems being used
for spectroscopy. This was the first argument that higher
fields would be more sensitive for detecting changes in blood
oxygenation.
In the later part of the same decade, Seiji Ogawa and colleagues at Bell Laboratories did the seminal imaging experiments to detect blood oxygenation changes in the vessels and
tissue using a horizontal bore Varian 7T animal MRI system
(Ogawa & Lee, 1990; Ogawa et al., 1990a, 1990b). In order to
accentuate the contrast between oxygenated blood and deoxygenated blood, Ogawa used gradient-echo imaging rather than
the spin-echo approach used by Thulborn et al. The distinction
between the two acquisitions can be found elsewhere in this
encyclopedia. Ogawa manipulated blood flow, oxygenation,
and metabolism to demonstrate the BOLD and its relationship
to neural activity. He also suggested that one could use the
BOLD effect in such a manner as to detect neural activity in
humans, much as positron emission tomography (PET) was
used for at the time (Ogawa et al., 1990a). This work led to the
http://dx.doi.org/10.1016/B978-0-12-397025-1.00010-5
97
Magnetic Field strength
98
INTRODUCTION TO ACQUISITION METHODS | High-Field Acquisition
10T
5T
0T
1990
2000
2010
1980
Year of first human images
2020
Figure 1 Progression of magnetic fields used for human MRI since the
first human studies. Using media sources, publications, and press
releases, the dates most closely related to the first human images are
reported.
use of gradient echo in all three of the first contemporaneous

demonstrations of the BOLD effect in humans in 1992.
Oxygen is carried from the lungs by the hemoglobin molecule in red blood cells. Oxygen exchanges from the blood to
the tissue primarily at the capillary level, resulting in capillary
and venous oxygenation levels that are 3035% lower than the
fully saturated arterial side. In its simplest manifestation, the
BOLD effect as exploited for fMRI relies on the fact that as
neurons become more active, they increase their demand for
oxygen. For reasons still not fully understood, the regional
cerebral blood flow increases (25100%), far in excess of the
demand for oxygen (010%), resulting in a paradoxical situation where blood vessels in the region of the active neurons are
hyperoxygenated relative to the resting brain. There is still
controversy over these exact numbers (Barinaga, 1997).
Increased oxygenation in blood vessels decreases the susceptibility difference between the vessels and the brain tissue since
oxygenated hemoglobin has similar diamagnetic properties to
brain, while deoxygenated blood is more paramagnetic and
induces more dephasing of the transverse component of the
water protons near and in the vessels. Increased oxygenations
lead to longer T2 and apparent transverse relaxation time (T2*)
values and consequently increase MRI signal intensity in spinecho and gradient-echo images as signal dephasing decreases.
An early paper describing much of the theory behind the
BOLD effect modeled the T2* change in large and small vessels
in the brain (Ogawa et al., 1993). Notably, the Monte Carlo
simulations predicted that large vessels had a linear dependence
on field for gradient-echo imaging, while small vessels would
show a quadratic dependence on field. In order to produce a
quadratic dependence on field, the models require that water
diffuse in a magnetic field gradient over a distance scale that
does not allow the spin echo or gradient echo to be refocused.
Capillaries and very small venules with significant deoxyhemoglobin concentrations are the only such structures related to
brain activity that can provide a magnetic field gradient with
the appropriate length scale, that is, a magnetic field gradient
that decays significantly over a distance of about 10 mm. Some
of this early work comparing spin echo and gradient echo for
BOLD was performed as part of Peter Bandettinis doctoral
thesis at the Medical College of Wisconsin, inspiring more
sophisticated models as computational power increased (Fujita,
2001; Klassen & Menon, 2007).
The results from Thulborn and Ogawa should have immediately argued for the use of higher field strengths for fMRI, but
there was a great deal of controversy about the field dependence of the BOLD effect. Of the three initial demonstrations
of the BOLD effect in humans, two used EPI at 1.5T (Bandettini
et al., 1992; Kwong et al., 1992) and one used conventional
fast low angle shot MRI (FLASH) at 4T (Ogawa et al., 1992).
Comparable signal-to-noise ratio (SNR) and contrast-to-noise
ratio (CNR) were seen at both field strengths on average. The
superiority of EPI for dynamic acquisition and from an SNR/
CNR perspective was clear, as was evident from earlier results
in cats (Turner et al., 1991), but the 4T signals were two to ten
times higher than those at 1.5T, compensating for the reduced
stability of FLASH acquisitions. The first direct field strength
comparison between 1.5T and 4T came from in 1993 (Turner
et al., 1993). It was noted that the 4T result was five times
higher than the 1.5T result, adjusting for different echo times
certainly supralinear. The lower resolution of the EPI techniques of the time precluded the identification of tissue and
vessels in order to separate out the contributions of these two
signal sources. Using a higher-resolution FLASH sequence at
0.5T, 1.5T, and 4T finally demonstrated a power-law dependence for tissue regions where no obvious venous vessels were
located and a linear dependence for large vessels (Gati et al.,
1997). In addition to providing validation of the theory, this
article also demonstrated that the majority of the BOLD signal
at the lower fields was coming from large venous vessels, as the
tissue BOLD signal was simply too small to observe at those
fields. This had been predicted by careful simulation studies
done at the Massachusetts General Hospital (MGH)
(Boxerman et al., 1995). Similar results have been found comparing 4T to 7T, with the added contribution of demonstrating
the improved spatial localization provided by spin-echo (SE)
techniques at the highest fields (Duong et al., 2003).
There are many compelling reasons to perform fMRI acquisitions at higher field strengths. These factors are to a certain
extent interdependent as discussed in the following text.
Arguments for HF Acquisition of BOLD

Resolution
The convolutions of the human cortical surface confer no preferred orientation to which slices can be aligned. As such, the
general practice of having imaging slices whose through-plane
thickness is greater than the in-plane resolution is not warranted
and leads to unpredictable partial volume effects in both
anatomical imaging and functional imaging. This suggests that
resolution should be isotropic. At a minimum, the isotropic
resolution should be sufficient to resolve the cerebral cortex in
the subject. For the adult human cortex (maximally 3 mm thick),
this requires a minimum isotropic spatial resolution of 1.5 mm
based on Nyquist sampling. This resolution is of course insufficient to resolve the lamellar or columnar organization of the
cortex or even the pial vessels. For the thinnest cortices encountered in neonates, nonhuman primates, and some parts of the
adult brain, spatial resolution below 0.5 mm is desired. Many of
the deep brain nuclei one would like to study in anatomical and
functional imaging also require sub-millimeter resolution. Standard anatomical protocols at 3T fall short of this goal, with the
very best approaching 1 1 1 mm. State-of-the-art 3T fMRI

protocols typically achieve 2 2 2 mm resolution. Thus, for
many advanced neuroscience questions, higher-resolution
fMRI would be attractive.
Examining this in more detail, the increase in field strength
from 3T to 7T provides an approximately 2.33-fold increase in
the SNR of a single-echo planar image used for fMRI acquisitions. However, fMRI is a fundamentally signal-starved process,
and thus, the decision to sacrifice this additional SNR for
increased resolution should be considered carefully. If one does
choose to retain the same SNR as is available at 3T, the decrease
in voxel dimension supported by the increase in field scales as
the cube root of the ratio of the field strengths. Thus, at 7T, one
can image a voxel that is 33% smaller on a side while preserving
the same image SNR as at 3T. Practically speaking, an
8 mm3 voxel (2 mm on a side) at 3T can be reduced to
3.43 mm3 (1.51 mm on a side) at 7T based solely on SNR scaling
with magnetic field. This barely resolves the cortical ribbon if the
voxel placement was perfect. Thus, SNR gains on their own
cannot provide the desired resolution, but must rely on gains
in CNR and SNR discussed further below.
In fMRI, the apodization imposed by the T2* decay during
the echo train increases the width of the voxel point spread
function beyond the voxel size specified on the scanner. In
general, acquisitions done with an echo train that is shorter
than the T2* of the tissue do not suffer from significant blurring, but short echo trains are harder to achieve as one pushes
for higher resolution. In an attempt to shorten the echo train
length, other unanticipated degradations of the resolution can
occur. In particular, spatial resolution is further compromised
in partial Fourier acquisitions where the nether regions of
k-space are not sampled in an attempt to keep the echo train
short. Thus, one must critically examine the acquisition parameters to accurately draw conclusions about the true spatial
resolution of such experiments.
There are other compelling reasons to try to increase spatial
resolution in fMRI that are also very important, but not always
well appreciated. For example, the primarily through-plane
dephasing in thick slices can cause signal loss in a slice. As
another example, the spatial encoding for 2-D and 3-D EPI can
be compromised by the susceptibility gradients that derive
from inhomogeneous magnetic fields over the subjects brain.
The magnitude of the resulting distortions is proportional to
the rate of transversal of k-space. Since EPI covers the
phase-encode direction at a more relaxed rate (lower effective
bandwidth) than the readout direction, the distortion is considerably larger in this direction. This results in uncertainties in
the overlay of functional imaging data on top of anatomical
imaging data. These distortions also have to be accounted for if
the fMRI data are to be used for interventions, such as presurgical mapping. Small isotropic voxels can go a long way toward
mitigating these effects.
All these arguments for higher resolution are based on
practical concerns unrelated to detection of small regions of
activation. However, as will be discussed further in the succeeding text, there are also arguments to be made on the basis of
improved spatial localization.
SNR and Temporal SNR

As mentioned, the SNR of a single EPI image increases roughly
linearly with magnetic field. Various factors including longer
99
longitudinal relaxation times as well as increased receiver

bandwidths at higher fields (related to keeping the echo train
shorter than T2*) conspire to make the actual gain somewhat
less than linear (Gati et al., 1997). The SNR measurement for a
single image is often made as the signal in a region of interest
(ROI) in the brain divided by the standard deviation of the
noise in an ROI outside the brain. This measurement is somewhat more complex in the case of parallel imaging techniques
and phased array coil combinations, but these subtleties go
beyond the discussion here. However, this image SNR is not
the relevant measure for fMRI signal detection. If one were to
image an agar gel phantom repeatedly using an EPI time series,
the measurement of the signal in an ROI in the phantom
divided by the standard deviation of that signal over time
would yield essentially the same SNR as measured with the
approach mentioned earlier in the paragraph (for a stable
scanner and a large ROI). However, the same measurement
done in a human head would yield a lower apparent SNR,
because there are additional temporal fluctuations in the ROI
that derive from physiological noise sources in the brain. Thus,
the temporal SNR (tSNR) is the more relevant parameter, since
it describes the noise background against which dynamic
changes in the BOLD signal must be detected.
Contrast and CNR

The change in BOLD signal (DS) between a baseline (S) and a
task state (S DS), or more generally any two states, is usually
the relevant quantity to detect in an fMRI experiment. The
signal change DS is termed the contrast, and the quantity DS/S
is defined as the fractional signal change. The objective of the
fMRI experiment is to detect the signal change above the noise in
the time series. As shown many years ago, the CNR is given by
the product of the SNR (more rigorously tSNR) and DS/S. The
CNR is the single most important parameter for determining the
ability to detect a statistically significant activation in the brain
with fMRI. CNR increases with field because DS/S increases
with field (linearly for larger veins and quadratically with capillaries as noted) and tSNR also increases with field at very high
resolutions (because it becomes thermally noise-dominated).
Thus, at high resolution, the CNR gain is the product of two
quantities that increase with field strength. This multiplicative
bonus is what allows spatial resolution to exceed the modest
gains predicted from just the raw image SNR gain with field. At
conventional fMRI resolutions, where tSNR is essentially flat
beyond 2T, the CNR increase with field strength is limited
to the gains expected solely from DS/S increases. This is the
regime where much of cognitive neuroscience is currently
done, and those experiments can expect less dramatic improvements with field. However, these lower-resolution improvements can potentially be parlayed into shorter acquisitions or
fewer trials for such studies, so there is still a benefit at conventional voxel sizes.
Interaction of Resolution and CNR

The BOLD signal arises from cortical and subcortical gray
matter, where cell bodies and synapses lie in close proximity
to the microvasculature. When using an 8 mm3 voxel at 3T, the
voxel is virtually guaranteed to contain white matter and/or
100
cerebrospinal fluid, thus reducing the CNR of the BOLD effect.

The physiological fluctuations present in the cerebrospinal
fluid (CSF) dramatically increase the noise in a voxel. All 3T
fMRI experiments are dominated by physiological noise (i.e.,
image-to-image fluctuations caused by respiration and cardiac
sources resulting in lower tSNR). Physiological noise, being a
modulation of the signal in the voxel, is therefore proportional
to signal in the voxel. To avoid the dilution of the gray matter
BOLD signal with both inactive tissue (making DS/S smaller)
and noise-generating CSF (making tSNR lower), smaller voxels
must be used. Thus, somewhat counterintuitively, CNR can
improve even as raw image SNR decreases because the tSNR
is improved. This strategy works particularly well at UHF. At
the current time, using available 32 channel head coils, some
7T sites are reporting 500 mm isotropic resolution for both
fMRI and anatomical imaging. This would give 48 pixels
across the cortical ribbon in the adult human brain, sufficient
to address most of the issues discussed earlier.
Sensitivity
In fMRI, the concept of sensitivity is also important. Ideally,
one wishes to be sensitive to the BOLD signal only from the
capillaries. Sensitivity to capillary BOLD changes is desirable,
because the capillaries are in the closest proximity to the active
neurons and BOLD signal changes in those capillaries presumably best reflect what the neighboring neurons are doing. As
those capillary level changes flow downstream, they pool
together in large veins with changes from other regions and
become easier to detect but further (millimeter to centimeter)
from the neuronal source of activation. Capillary sensitivity is
to be preferred over sensitivity to draining veins, yielding
greater linearity between neural activity and BOLD than the
larger vessels do. This has implications in any kind of graded
paradigm, where BOLD signal is used to explain neural activity.
However, the fractional signal change from the capillaries is
small, as is their volume fraction, and so the BOLD signal in
downstream draining venules and veins dominates, regardless
of field strength. For many of the questions asked by cognitive
neuroscientists, this difference is somewhat moot due to the
blurring that occurs in the preconditioning of the data. Nonetheless, higher resolution has a role to play even when accurate
localization of the neural activity is not warranted. Higher
image resolution dramatically improves the effective point
spread function of fMRI by reducing or eliminating partial
volume effects with the penetrating intracortical and pial
veins (Figure 2). High spatial resolution allows one to spatially
resolve and mask out the pial surface BOLD signal from further
analysis. Intelligent smoothing that avoids the CSF, white
matter, and pial surfaces can be even more beneficial.
The temporal dynamics of the fMRI response to a task also
offer some intriguing opportunities for enhancing spatial resolution as well. As was known from optical imaging for many
years, there appears to be a small transient hypooxygenation of
the blood starting 200 ms after stimulus onset, which switches
within 2 s to the more familiar hyperoxygenation response.
The initial transient (or initial dip in fMRI parlance) is
thought to occur in the capillaries that are in the immediate
vicinity of the active neurons, before the compensatory blood
flow response becomes active. Once the flow increases, a larger
and less spatially precise BOLD increase sweeps into the
Pial surface
Artery
Vein
Grey matter
2 mm
White matter
Figure 2 Schematic relationship between the vasculature and the

cortical vessels. Oxygenated (red) surface arteries traverse the pial
surface and send penetrating arterioles into the cortex to supply the
capillaries. Penetrating venules bring the partially deoxygenated blood
back up to the surface where it is collected by pial veins (purple). The
green and yellow columns indicate the hypothetical arrangement of
ocular dominance columns in the human primary visual cortex, with
green corresponding to one eye and yellow to the other. There is not a
one-to-one relationship between the penetrating venules or the surface
veins, which implies that to resolve the BOLD signal from a set of left or
right eye columns, sensitivity to the capillaries that are in close
opposition to the neurons (black) in the appropriate column is necessary.
Furthermore, the nonspecific BOLD signal from the surface
vasculature needs to be suppressed to be able to distinguish between
the columns of each eye. Note that at the best working resolution of
2 2 2 mm at 3T, these columns cannot be resolved, and neither can
the pial vessels be separated from the cortex.
general area, literally watering the garden for the sake of a

single thirsty flower (Malonek & Grinvald, 1996). The initial
dip was first imaged at 4T and appears somewhat more robust
at UHF. It appears to be better confined to the site of neural
activity. It is however not commonly used in the neuroscience
community because the effect is small, but we may see greater
interest as fMRI at 7T becomes more mainstream.
The final benefit for UHF fMRI applications is in the localization of columnar or laminar neural activity (Figure 2). A few
experiments have been performed in humans at 4T and 7T,
showing ocular dominance columns and orientation pinwheels.
These are likely to be the next generation of neuroscience experiments, where researchers drill down to examine the fine cortical
organization of an areas specialization. To do so also requires
high spatial resolution and capillary sensitivity. Such experiments will clearly benefit from the ability to suppress the draining veins on the pial surface by spatially separating them from
the cortex proper. Without such suppression, the cortical veins
dominate the fMRI signal and prevent differentiation of columnar or laminar organization. While alternative approaches using
spin-echo sequences can also aid in large vessel suppression, due
to speed and power deposition issues, gradient-echo EPI continues to dominate human brain mapping applications a quarter
century after the first BOLD experiments.
Future Considerations
Currently, 7T is the next major stepping stone in field strength
for both fMRI and anatomical imaging, representing the cutting edge with over 60 instruments sited around the world.
Bleeding edge could well be considered the less than a handful of 9.4T and higher systems installed or contemplated. As
Figure 1 demonstrates, the development of higher and higher
magnetic fields for human MRI is tapering. With the
101
Movie 1 Time course of task-related activity in a BOLD fMRI experiment from a single voxel assumed to contain the arteries, veins, capillaries, and
neurons and glia. (a) Baseline BOLD signal from a single voxel. Artery provides oxygenated blood to the brain (visually red), and arterioles deliver
this oxygenated blood to the capillaries where oxygen exchange takes place with the neurons (shown as black in their quiescent state). Venules collect
this partially deoxygenated blood and deliver it to veins, both shown as purple, as they appear optically. (b) Continuation of baseline acquisition.
Oscillations in the BOLD signal come from physiological noise sources such as cardiac and respiratory movements, neuronal oscillations (responsible
for resting state fMRI) and thermal noise. (c) Continued baseline acquisition. (d) Task stimulates neurons and glia. (e) Transient deoxygenation occurs in
the capillaries before blood flow-increasing mechanisms step in. Capillaries become more purple and consequently more paramagnetic. (f) Blood flow
increases dramatically, washing in more oxygen than is required for the metabolism. This results in the capillaries becoming hyperoxygenated (redder)
and consequently more diamagnetic. (g) Capillary blood flow, flush with more oxygenated blood flows into venules and veins. (h) Stimulus shuts
off. (i) BOLD signal decreases in a poststimulus undershoot, due to either continuing oxygen consumption in the absence of flow or vasodilation effects,
which increase the volume fraction of paramagnetic perturber. (j) Capillary blood washes into venules and veins, continuing undershoot. (k) BOLD
signal recovers to baseline as capillary and venous oxygenation and volume returns to prestimulus conditions. (l) Homeostasis.
unpredictable availability of liquid helium and the lack of a

reliable source for UHF magnets, it is likely that new UHF MRI
installations may stagnate for the next few years until alternative
sources for both helium and magnets are established. Nonetheless, with an installed base that includes virtually all the worlds
major MRI centers, software, consoles, and RF hardware will
continue to evolve toward finding that killer app for 7T as well
as potential clinical utility. This repeats a cycle seen in the transition from 0.5T to 1.5T and then 1.5T to 3T. In the latter case, fMRI
was the driving force to higher fields, with clinical applications
coming later. At 7T, surprising benefits for anatomical imaging
are taking precedence over fMRI, which is an encouraging sign for
future clinical applications in diagnostic imaging. One cannot
expect fMRI applications to be far behind however.

Echo-Planar Imaging; Evolution of Instrumentation for Functional
Magnetic Resonance Imaging; fMRI at High Magnetic Field: Spatial
Resolution Limits and Applications; High-Speed, High-Resolution
Acquisitions; Pulse Sequence Dependence of the fMRI Signal;
Susceptibility-Weighted Imaging and Quantitative Susceptibility
Mapping.
References
Medicine, 25, 390397.
Barinaga, M. (1997). What makes brain neurons run? Science, 276, 196198.
Boxerman, J. L., et al. (1995). The intravascular contribution to fMRI signal change:
Monte Carlo modeling and diffusion-weighted studies in vivo. Magnetic Resonance
Duong, T. Q., Yacoub, E., Adriany, G., Hu, X., Ugurbil, K., & Kim, S. G. (2003).
Microvascular BOLD contribution at 4 and 7T in the human brain: Gradient-echo
and spin-echo fMRI with suppression of blood effects. Magnetic Resonance in
Medicine, 49, 10191027.
Fujita, N. (2001). Extravascular contribution of blood oxygenation level-dependent
signal changes: A numerical analysis based on a vascular network model. Magnetic
Gati, J. S., Menon, R. S., Ugurbil, K., & Rutt, B. K. (1997). Experimental determination
of the BOLD field strength dependence in vessels and tissue. Magnetic Resonance
Klassen, L. M., & Menon, R. S. (2007). NMR simulation analysis of statistical effects on
quantifying cerebrovascular parameters. Biophysical Journal, 92, 10141021.
Kwong, K. K., et al. (1992). Dynamic magnetic resonance imaging of human brain
Lee, J., et al. (2010). Sensitivity of MRI resonance frequency to the orientation of brain
tissue microstructure. Proceedings of the National Academy of Sciences of the
United States of America, 107, 51305135.
Luo, J., He, X., dAvignon, D. A., Ackerman, J. J., & Yablonskiy, D. A. (2010). Proteininduced water 1H MR frequency shifts: Contributions from magnetic susceptibility
and exchange effects. Journal of Magnetic Resonance, 202, 102108.
Ogawa, S., & Lee, T. M. (1990). Magnetic resonance imaging of blood vessels at high
fields: In vivo and in vitro measurements and image simulation. Magnetic
Ogawa, S., Lee, T. M., Kay, A. R., & Tank, D. W. (1990a). Brain magnetic
resonance imaging with contrast dependent on blood oxygenation.
America, 87, 98689872.
Ogawa, S., Lee, T. M., Nayak, A. S., & Glynn, P. (1990b). Oxygenation-sensitive
contrast in magnetic resonance image of rodent brain at high magnetic fields.
102
Ogawa, S., et al. (1992). Intrinsic signal changes accompanying sensory

stimulation: Functional brain mapping with magnetic resonance imaging.
89, 59515955.
Ogawa, S., et al. (1993). Functional brain mapping by blood oxygenation leveldependent contrast magnetic resonance imaging. A comparison of signal
characteristics with a biophysical model. Biophysical Journal, 64, 803812.
field. Biochimica et Biophysica Acta (BBA) - General Subjects, 714, 265270.
Turner, R., Bihan, D. L., Moonen, C. T. W., Despres, D., & Frank, J. (1991). Echo-planar
time course MRI of cat brain oxygenation changes. Magnetic Resonance in
Medicine, 22, 159166.
Turner, R., et al. (1993). Functional mapping of the human visual cortex at 4 and 1.5 tesla
using deoxygenation contrast EPI. Magnetic Resonance in Medicine, 29, 277279.
Relevant Websites
http://www.adni-info.org ADNI protocol.
http://www.cis.rit.edu/htbooks/mri/inside.htm Spin-echo and gradient-echo
animations.
http://www.diagnosticimaging.com Varian grows ultra high-field MRI market.
http://www.nasdaq.com/aspx/call-transcript.aspx?StoryId1266171&Titleagilenttechnologies-inc-presents-at-barclays-global-healthcare-conference-mar-122013-08-30-am Agilent bows out of magnet business.
http://en.wikipedia.org/wiki/Paramagnetism Paramagnetism.
http://en.wikipedia.org/wiki/Blood Red blood cells.
http://en.wikipedia.org/wiki/Monte_Carlo_method Monte Carlo method.
High-Speed, High-Resolution Acquisitions

LL Wald, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA; Harvard-MIT Division
of Health Sciences and Technology, Cambridge, MA, USA
JR Polimeni, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
Abbreviations
ADC
BOLD
CAIPI
CAIPIRINHA
CBV
CNR
CSF
EPI
EV
fCNR
FLASH
fMRI
FOV
GM
GRAPPA
GRE
HDR
Apparent diffusion coefficient

Blood-oxygen-level dependent
Controlled aliasing in parallel imaging
Controlled aliasing in parallel imaging
results in higher acceleration
Cerebral blood volume
Contrast-to-noise ratio
Cerebrospinal fluid
Echoplanar imaging
Extra-vascular
Functional contrast-to-noise ratio
Fast low-angle shot
Functional magnetic resonance imaging
Field of view
Gray matter
Generalized autocalibrating partially
parallel acquisitions
Gradient-recalled echo
Hemodynamic response
Symbols
B0
D
esp
espeff
M0
PSFbio
Main magnetic field

Diffusion constant
Echo spacing
Effective echo spacing
Equilibrium magnetization
Biological point-spread function
Introduction
For the past two decades, the functional imaging community has
measured the BOLD response at essentially the same spatiotemporal resolution. This stagnant situation is driven by difficult
instrumental barriers and the feeling that the community is
already operating near the biological limits, namely, that the
spatiotemporal resolution is limited by the spatial scale at which
blood flow is controlled and the temporal resolution is limited by
the speed of the hemodynamic response. Nonetheless, whenever
someone pushed either domain, additional information about
brain substructure seemed to appear, including columnar
(Cheng, 2012; Fukuda, Moon, Wang, & Kim, 2006; Goodyear,
Nicolle, & Menon, 2002; Kim, Duong, & Kim, 2000; Kim &
Fukuda, 2008; Yacoub, Harel, & Ugurbil, 2008) and laminar
functional architecture (Goense & Logothetis, 2006; Goense,
Merkle, & Logothetis, 2012; Harel, Lin, Moeller, Ugurbil, &
Yacoub, 2006; Lu et al., 2004; Polimeni, Fischl, Greve, & Wald,
HRF
InI
iSNR
MB
MC
MPRAGE
PSF
RBC
RF
SE
SENSE
SH
SMS
SNR
SPM
TE
TR
tSNR
WM
PSFinst
R
R*
2
T1
T2
T*
2
V1
Hemodynamic response function

Inverse imaging
Image signal-to-noise ratio
Multiband
Multi-coil
Magnetization prepared rapid gradient echo
Point-spread function
Red blood cell
Radio frequency
Spin echo
Sensitivity encoding
Spherical harmonic
Simultaneous multi-slice
Signal-to-noise ratio
Statistical parametric mapping
Echo time
Repetition time
Time-series signal-to-noise ratio
White matter
Instrumental point-spread function

Acceleration factor
Total transverse relaxation rate
Longitudinal relaxation time
Irreversible transverse relaxation time
Total transverse relaxation time
Primary visual cortex
2010; Ress, Glover, Liu, & Wandell, 2007; Silva & Koretsky, 2002;
Tian et al., 2010; Yu, Qian, Chen, Dodd, & Koretsky, 2014) as well
as timing information (Chang et al., 2013; Lin et al., 2013; Silva &
Koretsky, 2002; Yu et al., 2012). These recurring empirical observations have recently been backed up by non-MR-based measures
of hemodynamics suggesting that some degree of blood flow
regulation is present at every level of the vasculature. These findings have eroded the feeling that we are firmly held back by
biological limits and fueled a push to reduce the acquisition
barriers. As a result of advances on many fronts, we have succeeded in reducing spatial and temporal resolutions from the longstanding standard of 3 3 3 mm3 voxels and TR 3 s by a
factor of 10 in either time or space and nearly as impressive factors
in each if applied together. For example, the low-resolution
standard whole-brain protocol on our 7 T scanner is now
1.5 mm isotropic (8 smaller voxel volume) at a TR of 1.2 s
(2.5 faster). Both the spatial and the temporal resolution
improvements have shown benefit beyond what a simple
http://dx.doi.org/10.1016/B978-0-12-397025-1.00011-7
103
104
INTRODUCTION TO ACQUISITION METHODS | High-Speed, High-Resolution Acquisitions
sensitivity/resolution trade-off argument or a simplistic application of sampling theory would suggest.

Previously, forays into higher spatial or temporal resolution
came at a high cost, such as the loss of whole-brain coverage (to
gain speed) or the use of segmented or multishot sequences (to
gain encoding ability and thus resolution). Lack of whole-brain
coverage has obvious drawbacks for understanding distributed
function, and the use of multishot sequences both reduces temporal resolution and leads to considerably higher signal variance in
the time series. In multishot acquisitions, sections of k-space can be
phase-modulated by physiological processes (respiratory, cardiac,
etc.). These modulations within k-space lead to time-dependent
amplitude effects such as ringing and ghosting, whereas phase
modulations of a single-shot image affect all of k-space equally
and are rendered irrelevant by the magnitude operation. Thus, this
article will focus solely on single-shot acquisitions.
The increases in spatial resolution largely stem from
improvements in gradients coupled with highly parallel array
detection and accelerated imaging. These encoding improvements have reduced the encoding burden of single-shot imaging to the point where 1 mm isotropic imaging (27-fold
smaller voxels than conventional 3 mm acquisitions) has
become standard for ultrahigh-field fMRI studies, thus surpassing biological limitations. Although a 1 mm isotropic voxel has
27 less signal than we are used to, the functional imaging
sensitivity is not reduced by this factor. It likely benefits from
reduced partial volume averaging with nonactivated GM (and
WM) and, even more important, less partial volume averaging
with nonactivating and extremely noisy CSF.
In addition to high spatial resolution, the temporal resolution of fMRI has been revolutionized (increased by up to
tenfold). This recent development comes from a method called
simultaneous multislice (SMS), a.k.a. multiband (MB) imaging reviewed recently (Feinberg & Setsompop, 2013). Unlike
conventional parallel imaging that speeds up the traversal of
k-space in EPI (improving image quality) but does not substantially increase fMRI temporal resolution, SMS acceleration
directly increases the time-series temporal resolution.
The Minnesota group first recognized (Feinberg et al., 2010;
Moeller et al., 2010) that with the ubiquitous availability of
highly parallel brain arrays, the time was right for the parallel
imaging technique introduced by Larkman et al. in 2001,
which unaliases simultaneously acquired slices (Larkman
et al., 2001). Setsompop et al. solved the problem of how to
apply CAIPIRINHA shifts (Breuer et al., 2005, 2006) to EPI
(Setsompop et al., 2012). This greatly improved on a less
successful earlier attempt (Nunes, Hajnal, Golay, & Larkman,
2006) and cemented the techniques future by greatly reducing
the g-factor noise penalty. The penalty is essentially eliminated
for modest (two- to threefold) accelerations (Setsompop et al.,
2012; Setsompop, Gagoski, et al., 2012), and the blippedCAIPI method makes possible even higher accelerations, as
much as a factor of 10 or 12 (Feinberg & Setsompop, 2013).
Thus, we are now armed with a method that can speed up
the fMRI acquisition as much as an order of magnitude, capturing conventional 3 mm whole-brain time series with a temporal resolution of 0.3 s, well under the hemodynamic
response width of about 45 s. The question becomes, what
value is this? If no part of the BOLD response is changing on
these timescales, why bother resolving them? The answer
empirically emerging suggests there is great value (Griffanti
et al., 2014; Tong, Hocke, & Frederick, 2013; Ugurbil et al.,

2013; Xu et al., 2013). Some value likely stems from fully
Nyquist sampling physiological fluctuations (cardiac and
respiratory), preventing them from aliasing into the frequency
band of the BOLD signal (thus a reduction of the relevant
noise). But a larger contribution likely arises from a more
efficient sampling of the slow BOLD response, a hypothesized
effect discussed in more detail below.
Altogether, it seems the time is ripe to reexamine the barriers to high-spatiotemporal-resolution fMRI. In this article, we
examine the engineering and biological issues surrounding
high spatial and temporal resolution in fMRI. We review the
important parameters that go into determining BOLD sensitivity, such as temporal signal-to-noise ratio (tSNR) and physiological noise; recent acquisition advances; and some fMRI
examples exploiting them, and finally look toward future technologies for further advances.
Detecting BOLD Signal Changes

Sensitivity is one of the most serious limiting factors in the tradeoffs for increased spatiotemporal resolution in fMRI. Functional
activation is a pixels intensity change on activation. Thus, the
acquisitions tSNR, defined as a pixels mean signal intensity
divided by the standard deviation of its temporal fluctuations
(st) is a crucial metric since it tells us the smallest signal change
not masked by noise fluctuations. Measuring the BOLD signal
change as a percentage of the noise defines the BOLD functional
contrast-to-noise ratio (fCNR); fCNR DS/st where DS is the
signal change between two activation states (e.g., activation and
rest). A simple manipulation relates fCNR and tSNR:
fCNR tSNRDS=S
[1]
The BOLD signal changes stem from small blood oxygenationinduced changes in the transverse relaxation rate (R2* 1/T2*). For
small changes in R*,
2 between the activated and deactivated states,
the fractional signal change DS/S can be shown to be equal to
TE DR2*, where DR2* is the difference in relaxation rates of the
two states. Note that TE is a fixed user-selected parameter and DR*
2
is a biological response to the stimulus that the user has little
control over. Thus, DS/S is a bad metric for assessing most acquisition protocol parameters (except for TE).
Putting the expression for DS/S into the fCNR formula
provides
fCNR TEDR2 *tSNR DR2 *=R2 *tSNR
[2]
where the second equation utilizes the theoretically optimum

*).
value of TE; TE T*(1/R
2
2
Thus, only three factors contribute the BOLD measurement
sensitivity (fCNR): TE, DR2*, and tSNR. At a given B0 field
strength, the DR2* factor is determined mainly by the biology of
the blood supply and metabolic response and is considered
outside of the acquisition optimization, although it is modulated
by many aspects of the subjects condition, including caffeine use
(Laurienti et al., 2002; Mulderink, Gitelman, Mesulam, & Parrish, 2002), hematocrit levels (Levin et al., 2001), and subject
attention (OCraven, Rosen, Kwong, Treisman, & Savoy, 1997).
Thus, it is taken as a constant of nature for the purposes of this
discussion. Note that DR2* and even the ratio DR2*/R2* increase

with field strength (Bandettini et al., 1994; Gati, Menon, Ugurbil,
& Rutt, 1997; McKenzie, Drost, & Carr, 1994; Turner et al., 1993;
Yacoub et al., 2001a; Yacoub, Van De Moortele, Shmuel, &
Ugurbil, 2005), providing a motivation to perform functional
experiments on the highest-field-strength scanner available.
In contrast to DR2*, the acquisitions TE is set precisely by the
user to six or more significant digits. Thus, the only question is,
set to what? Fortunately, it is simple to show that the product
of TE and tSNR (and thus fCNR) is optimized when TE is set to
T2*. Here, DR2* and the time-series noise st are taken to be
independent of TE, which is not quite true for the noise,
since some components of the physiological fluctuations that
contribute to the time-series variance have a BOLD-like TE
dependence (Kruger & Glover, 2001). Nonetheless, it is fairly
easy to show that this is not a large effect on the optimal TE for
typical physiological noise fractions.
The local T2* changes with location across the brain and is
dependent on issues such as the quality of the local shim as well
as properties of the cortex. Figure 1 shows a 7 T cortical T*
2 map
calculated from a 0.33 mm in-plane resolution (1 mm slice
thickness) multiecho FLASH acquisition. Only voxels touching
the middle layer of the cortex (determined from automatically
generated laminar surfaces) were painted on the inflated cortex
representation (Cohen-Adad et al., 2012). Interestingly, both
variations due to local shims (near susceptibility regions of the
sinuses) and intrinsic cortical differences (such as the shortened
T*
2 in the primary motor and sensory cortex) are seen. Typically,
the TE is set to a slightly lower value than T2*, for example, to
30 ms when the average cortical T2* is closer to 40 ms at 3 T and
to 20 ms when T2* is about 30 ms at 7 T. This reflects the nature
of the optimization curve that has little penalty for setting TE to
a value under the true T2* but a larger penalty for setting it longer
than T2*. Thus, TE is typically set to the shortest T2* value
expected in the brain region studied.
When TE is set, the only remaining factor in the CNR expression of eqn [2] is tSNR. Thus, tSNR becomes the principle metric
by which acquisitions are assessed. Increasing it (subject to spatiotemporal resolution constraints) is the goal of any acquisition
refinement. tSNR is affected by nearly every instrumental effect,
such as the coils sensitivity, scanner stability, many sequence
parameters, and also physiological processes such as physiological modulations (physiological noise) and subject motion. It is
imperative that fMRI practitioners know the tSNR for every
acquisition and fMRI facilities monitor it in daily phantom
runs for signs of instrumental problems.
105
Instrumental Spatial Resolution in fMRI

The localization power of the imaging method is commonly
referred to as the instrumental resolution and is characterized
by the point-spread response function PSFinst of the camera.
This is the response of the instrument to a point source and
forms the effective pixel size of the image. A structure is considered resolved by the Nyquist criterion if it is at least 2 pixels
across, so PSFinst determines the smallest structure resolvable.
In rectangular sampled Fourier imaging, the nominal PSF is a
sinc function with a full width at half max given by the FOV
divided by the matrix size: the nominal image resolution. The
size and shape of the pixel are altered by any effect that
modulates the signal intensity across k-space, such as the T*
2
or T2 decay in GRE and SE EPI. Other degradations come from
patient movement, postprocessing or image reconstruction
operations that involve interpolations or resampling, and systematic pixel size and position alterations accompanying
image distortions from B0 susceptibility gradients.
Limitations on Spatial Resolution: Distortion in EPI

Image distortion (in EPI) and blurring (in spiral) single-shot
fMRI are major instrumental limitations on the spatial resolution of fMRI. They both arise from the same source, so we
concentrate on deriving the magnitude of distortion in EPI
knowing that a similar oscillating gradient and susceptibility
field produces a similar magnitude blurring in spiral imaging.
Single-shot echoplanar imaging suffers from local image distortions in the vicinity of susceptibility gradients. The effect is
proportional to the rate of traversal of k-space. The ky (phase
encode) direction is nearly 100-fold slower in traversal, due to
the asymmetry of EPI. Therefore, the vast majority of image
distortion occurs in the phase encode direction. In EPI, the
effect is characterized by the shift in the imaging pixel resulting
from an off-resonance field shift DB0 caused by a susceptibility
gradient. This shift is proportional to the velocity in k-space.
The ky velocity is often characterized by the effective echo
spacing espeff. The echo spacing (esp) is simply the time
between successive ky lines, or the half period of the readout
waveform. The espeff is simply the esp corrected for the parallel
imaging acceleration factor, Ry; espeff esp/Ry when a parallel
imaging method is used, since parallel imaging speeds up the
traversal of ky by a factor of Ry. The espeff is also a measure of
Figure 1 Left: Automatically generated intermediate cortical surfaces. Right: T2* of the voxels of the middle surface at 7 T. T2* is about 3035 ms
for the frontal and parietal cortex but lower in somatosensory cortex and in problem susceptibility regions. Reproduced from Cohen-Adad, J.,
Polimeni, J. R., Helmer, K. G., Benner, T., McNab, J. A., Wald, L. L., et al. (2012). T2* mapping and B0 orientation-dependence at 7 T reveal cyto- and
myeloarchitecture organization of the human cortex. NeuroImage, 60, 10061014.
106
the bandwidth across the final reconstructed image in the PE

direction, after the SENSE or GRAPPA reconstruction.
Note that other methods that decrease EPI readout length,
such as partial Fourier methods, do not increase the ky velocity
and do not improve the image distortion. Also, the common
notion that the length of the EPI readout solely determines
distortion is not quite correct. Typical echo spacings used on a
Siemens MAGNETOM Trio, A Tim System 3T whole-body scanner are 0.47, 0.69, 0.76, and 1.04 ms for 3, 2, 1.5, and 1 mm
isotropic resolutions, respectively. The esp is largely set by gradient performance, and thus, the factor of Ry in espeff becomes one
of our most important tools for reducing distortion and thus
improving the instrumental resolution of fMRI acquisitions.
Since the bandwidth across the final reconstructed image
FOVy is 1/espeff, a frequency shift of Dn 1/espeff would
shift a voxel by an entire FOVy. Perhaps, the most relevant
metric is the distortion in millimeters for a unit DB0 shift.
This metric is

distortion mm=DB0 G

gG1 s1
espeff sFOV y mm [3]
2p
Here, the units of each quantity are shown in square

brackets and g/2p 4258[G s1] for protons. Thus, we seek to
decrease distortions through either reducing esp (faster, stronger gradients), increasing Ry (larger parallel imaging acceleration factors), or reducing the phase encode FOV (zoomed
imaging). Although higher-field-strength scanning is expected
to have increased DB0 susceptibility field shifts, this is partially
mitigated by improved parallel imaging performance at higher
fields (Wiesinger et al., 2004).
The image blurring caused by longer EPI readouts is also an
important barrier to high-resolution fMRI. The nominal resolution
(i.e., FOV/matrix size) always underestimates the voxel size. In EPI,
the T*
2 decay causes a multiplicative filtering kernel in the phase
encode direction of k-space. For full k-space acquisitions, the effect
on the voxel size is modest if the EPI readout length is less than T*.
2
In this case, the exponential decay boosts high-k-space data points
in the first part of the readout and attenuates them in the latter half,
providing little net blurring (when the readout length is equal to T*
2
or less) (Buxton, 2009). In contrast, partial Fourier acquisitions do
not record the early high-k-space data points. In this case, the
exponential decay provides an exponential k-space filter that can
significantly increase the voxel size beyond the nominal resolution. A rule of thumb is to limit the EPI readout duration to no
more than twice T*,
2 or shorter if possible. Without significant
acceleration from parallel imaging, it would be impossible for
current gradient sets to meet this criterion for 1 mm EPI. Again,
highly parallel imaging from 32-channel brain arrays has proven
critical to the current generation of high-resolution acquisitions.
Underappreciated Benefits of Improved Spatial Resolution

The push for increased instrumental resolution is driven by both
the need for better localization of the activation within cortical
regions and improved sensitivity. The need for instrumental
spatial resolution to improve localization is easy to understand,
but its side benefit of improved fCNR compared to its effect on
image SNR (iSNR) is more subtle. iSNR is directly modulated by
the reduced number of protons in the voxel associated with the
higher-resolution images. Often, the decrease in fCNR is much
less than the decrease seen in iSNR when the spatial resolution is
increased. The improved BOLD contrast provided by higherspatial-resolution acquisitions can arise from multiple sources.
First, reduced partial volume averaging within the voxel with
WM and CSF increases BOLD contrast. Both WM and CSF dilute
the BOLD effect since they lack blood. The CSF also adds significant physiological noise to the time series, being the noisiest of
the three brain components (Bianciardi et al., 2009). Secondly,
improving the spatial resolution in the slice direction reduces
through-plane dephasing dropouts above susceptibility areas
such as the sinuses and ear canals. Third, smaller voxels reduce
overall time-series physiological noise, which scales with the
signal strength in the voxel (Triantafyllou et al., 2005). To impact
partial volume dilution problem, the isotropic resolution should
be high enough to resolve the folded cerebral cortex. For typical
cortex (23 mm thick), this requires an isotropic spatial resolution of 1.0 to 1.5 mm. Although well aligned with the goal of
overcoming biological PSF barriers in the BOLD effect, standard
protocols fall short of this goal.
Thus, improving spatial resolution actually mitigates some
problems, and it often surprises people that the resolution of the
fMRI experiment can be pushed beyond what is expected from
looking at the individual images. Finally, improved image resolution improves the localization of the neuronal activation by
allowing the analysis to focus on voxels distant from the pial
surface and its larger veins; thus, improved instrumental resolution can improve biological resolution (Polimeni et al., 2010).
Current Limits to Instrumental Resolution

Current instrumental resolution limits are set by a combination of
the image encoding limitations discussed earlier and sensitivity.
Even though some of the encoding limitations are worse at higher
field, the improved parallel imaging performance, increased
image sensitivity, and increased BOLD contrast appear to outweigh the negatives, and most high-spatial-resolution imaging is
performed at as high a field strength as possible. With current
gradient technology approaching 80 mT m1 gradient strength at
slew rates of 200 T m1 s1, and close-fitting 32-channel brain
arrays providing EPI accelerations of up to R 4, high-quality
single-shot EPI can be obtained at 1 mm isotropic resolution
and as high as 0.75 mm isotropic resolution as shown in Figure 2.
While the actual image resolution is always coarser than the
nominal resolution quoted (FOV/matrix size) due to the T*
2
effects discussed earlier, examination of the image, or better still
the average of a few images, will show whether the ability to
resolve anatomy has been degraded significantly by these effects.
Side-Stepping fMRI Distortion Effects

The lack of correspondence between activated anatomy
depicted in the fMRI data and the structures visible in
high-resolution conventional scans such as the MPRAGE
T1-weighted anatomical image constitutes one of the main
drawbacks to the presence of residual distortion in the echo
planar images. Yet now that the nominal resolution of the EPI
is comparable to (or even better than) standard volume anatomical scans (such as the 1 mm isotropic MPRAGE), a glance
at anatomical content of the EPI (such as in Figure 2) brings
into question the need to utilize conventional scans to depict
anatomy. This situation suggests two possibilities to ameliorate

the correspondence problem. The first is to utilize an alignment algorithm that utilizes the fine anatomical features of EPI
(specifically the GM/WM border) to drive the alignment procedure, possibly adding in some degree of nonrigidness (Greve
& Fischl, 2009). This strategy was used to align 1 mm 7 T fMRI
in the visual cortex to cortical surfaces derived from volume T1
scans acquired at 3 T (Polimeni et al., 2010).
The second strategy is to eliminate the conventional anatomical images entirely and derive all of the anatomical information from EPI scans acquired with the same readout
parameters as the functional study. In this case, identical distortion will be present on all the images, and although distorted, they will be identically distorted, and therefore,
functionally activated areas will be in correspondence to the
correct anatomical location. The EPI readout can be straightforwardly grafted onto (1) a T1-weighted inversion-prepared
scan; (2) a T2 spin echo sequence; (3) a diffusion-weighted
spin echo that yields fractional anisotropy, apparent diffusion
coefficient (ADC), and even fiber direction information; and,
of course, (4) T*
2 weighted images (the functional scans
themselves). Since EPI is extremely efficient, collecting all of
these contrasts can be accomplished in as little as 5 min.
One of the most challenging uses of the anatomical information is the generation of cortical surfaces such as the WM and
pial surface. This is usually done with high-quality T1 volumetric
data input into algorithms, such as FreeSurfer, which is tuned
for a particular T1 image contrast. To generate the FreeSurfer
surfaces and parcellations from EPI input data, Renvall et al.
acquired inversion recovery-prepared T1 EPI at 1 mm isotropic
with 26 prep times in just under 3 min (Renvall, Witzel, Wald, &
Polimeni, 2014). A T1 and M0 map was fit to the data and used
to generate the 3 T T1 contrast typically used as an input. The
results of this procedure performed at 7 T with a 32-channel
brain array are shown in Figure 3. In addition to the T1 information, the corresponding information from the distortionmatched EPI diffusion scans has proven valuable in identifying
activated brainstem nuclei (Beissner et al., 2014).
R=2
R=3
R=4
R=5
107
Prospects for Improved PSFinst

Even more highly parallel imaging
Although the improved sensitivity of ultrahigh-field fMRI and
the improved encoding ability of highly parallel array coils
have allowed 1 mm whole-brain fMRI to become feasible,
further improvements are possible. Although R 3 and R 4
accelerated imaging is obtainable with the current generation
of 32-channel brain arrays with reduced distortion and T*
2
blurring, even further improvements are likely possible with
64- and higher-channel coils. Keil et al. compared a 32-ch and
64-ch brain array built on nearly identical formers (Keil et al.,
2013). While the benefit of doubling the channels is marginal
for unaccelerated imaging, the sensitivity of R 4 accelerated
imaging (intrinsic SNR gain and g-factor gain) was about 60%
in the peripheral cortex and 20% in the center of the brain. The
brain-center gain comes almost exclusively from the g-factor
reduction. Figure 4 shows a simulation validating this finding
and extending it to a 128-channel brain array, which is found
to have 36% higher SNR in the center compared to the 32-ch
array for R 4 accelerated imaging. While it is unfortunate that
these central SNR boosts do not extend to an unaccelerated
image, the R 4 acceleration (or more!) is typical of what is
needed for high-spatial-resolution single-shot imaging.
Improved B0 shimming
As discussed earlier, the image distortions from susceptibility
gradients are a major barrier to high-spatial-resolution singleshot EPI. Another way to mitigate this problem is to approach
it at its source and improve brain shimming. This solution strikes
at the heart of the problem and impacts other areas where offresonance effects are problematic. Additionally, gains in shimming are synergistic to the methods outlined earlier aimed at
reducing fMRIs sensitivity to off-resonance; the best results will
be obtained when both strategies are deployed.
In the brain, these field excursions are created by susceptibility differences at tissue/air and tissue/bone interfaces around
Figure 2 Left; One millimeter resolution diffusion-weighted images showing improvement in frontal lobe susceptibility distortion as acceleration is
increased beyond R 2. 3 T 32-ch acquisition. Right: Five averages of a 7 T single-shot GRE-EPI acquired at 0.75 mm isotropic resolution with
R 3 GRAPPA and a 32-ch array.
108
1900
T1 (ms)
3800
Figure 3 Inversion-prepared 7T T1 EPI acquired at 1.1 mm isotropic resolution whole brain in <3 min. The readout parameters of the EPI were
matched to the fMRI data to ensure identical distortions. 26 prep times were used and T1 and M0 were fit to the recovery curve to generate the T1 map.
Then, a T1-weighted image was synthesized to match the graywhite/CSF intensity differences at 3 T, which FreeSurfer expects. Shown to the right
are the resulting surfaces and parcellation obtained on the all-EPI dataset. Courtesy of J. Polimeni and V. Renvall.
128-ch
R=4
R=4
R=4
SNR
64-ch
100
Simulated SNR; fourfold acceleration

32-ch
Figure 4 Simulation of the SNR for fourfold accelerated imaging for a 32-ch, 64-ch, and 128-ch brain array on a tight-fitting helmet. The gain over the
32-ch array is 23% and 36% higher in the center for the 64-ch and 128-ch array, respectively. This central SNR boost derives from the improved
g-factor and is not seen in unaccelerated imaging. Simulations courtesy of Boris Keil, MGH.
the sinus cavities and ear canals. The difficulty with improving
B0 shimming has been that the field perturbations are subjectdependent and localized in space (the deviation map DB0(x,y,z)
contains high spatial orders). Conventional shimming with
first-, second-, and perhaps some third-order spherical harmonics is effective at canceling the spatial patterns that resemble spherical harmonics but are unable to cancel the principle
features of DB0(x,y,z) (Spielman, Adalsteinsson, & Lim, 1998)
although some practitioners have advocated for fourth- and
some fifth-order spherical harmonics (Pan, Lo, & Hetherington, 2012). High-order spherical harmonic coils require large
inductances and are notoriously inefficient at producing fields
and difficult to switch rapidly due to the inductance and eddy
currents created. These issues have kept the traditional spherical harmonic shim coil approaches to third order or less.
Local shim methods, such as placing diamagnetic material in
the mouth and ear canals, have met with some success (Wilson,
Jenkinson, & Jezzard, 2002), but a more patient-friendly external
method that requires reasonable currents is to use a matrix of small
loop coils placed on a cylinder around the body. While it is computationally more work to compute the currents due to the nonorthogonality of the field patterns, this is no longer a barrier. It has
recently been shown that most of this higher-order inhomogeneity
can be canceled using such arrays with reasonable currents if the
shim cylinder is brought inside the gradient coil (and thus closer to
the head) (Juchem, Nixon, Diduch, et al., 2010; Juchem, Nixon,
McIntyre, Rothman, & de Graaf, 2010, Juchem et al., 2011). The
interference between shim coils and RF coils then becomes a major
limitation. Optimally, both arrays want to be immediately adjacent to the body to optimize their performance. In the impressive
demonstration at 7 T by Juchem et al., the shim coils needed to be
moved away from the body to suboptimal locations to make room
for the receive array (Juchem, Nixon, Diduch, et al., 2010; Juchem
et al., 2011). This required 100-turn coils (a large amount of copper
near the RF coils). In addition to being moved away to clear a path
for the RF coils, the shim elements were mounted on a cylinder.
It has recently been recognized that the shim loops could be
combined with the RF receive array loops, providing both

maximum shim efficacy and optimal RF reception (Han, Song, &
Truong, 2013; Stockman et al., 2013, 2014; Truong, Darnell, &
Song, 2014). The localized field patterns of the small loop coils play
double duty, being useful for parallel imaging acceleration and for
shimming small, localized regions where high-spatial-frequency
shim fields are needed. As the simulations in Figure 5 show, given a
sufficient number of elements, such as the 64-channel and 128channel arrays modeled, it is possible to essentially eliminate the
major susceptibility field perturbations in the brain at 7 T.
Biological Limits of BOLD Spatial Resolution

While it is clear that small (e.g., columnar or laminar sized)
point sources of activation require sufficient image resolution
to localize, it is also required that the biological control of
the BOLD effect be at least equally well localized. If the BOLD
effect is dominated by upstream control of, for example, flow in
the arterioles, then the entire watershed will activate, possibly
precluding the ability to isolate individual columns or laminae.
Additionally, as the deoxygenated blood pools and is diluted in
downstream veins (Turner, 2002), there is the potential that
the BOLD-activated blob is displaced well downstream from
the activation site. These biological effects on BOLD activation
mapping are collectively referred to as imposing a biological
point-spread function (PSFbio), the PSF being the shape an
imaging instrument converts a true point-source input into. MR
work to determine the PSFbio has placed values on it in the
12 mm range (Park, Ronen, Kim, & Ugurbil, 2005; Shmuel,
Yacoub, Chaimow, Logothetis, & Ugurbil, 2007) although
lower-field studies have shown larger values (34 mm) (Engel,
Glover, & Wandell, 1997; Parkes et al., 2005).
Fortunately, recent microscopy work is well positioned to
help determine the biological limitations. The BOLD signal
reflects a complex interplay between changes in the metabolic
rate of oxygen consumption, blood flow, and blood volume.
The arterioles are commonly considered to be the source of
blood flow regulation since they possess the smooth muscle
tissue needed to control vessel diameter and thus downstream
flow. Changes at the capillary level were conventionally
believed to be simply a consequence of upstream regulation
64-ch
MC
128-ch
MC
at the feeding arterioles with the capillaries themselves having

no ability to regulate blood flow on their own. Yet recent
studies have identified evidence for extremely fine-scale regulation within a capillary network (Chaigneau, Oheim, Audinat,
& Charpak, 2003) and mechanisms for rapid and precise blood
flow regulation at the capillary level, including the observed
direct neural control of vascular sphincters via interneurons or
coordinated regulation of capillary diameter by pericytes
(Hamilton, Attwell, & Hall, 2010; Murphy & Wagner, 1994;
Peppiatt, Howarth, Mobbs, & Attwell, 2006); the closer the
control structures are to the neurons, the shorter the delay in
blood flow response. In a more recent study combining direct
two-photon microscopy of capillary diameter with calcium
imaging, it was found that the vascular dilation actually preceded the astrocytic calcium signaling (Nizar et al., 2013),
which not only demonstrates a rapid vascular response but
also calls into question the role of astrocytes in neurovascular
coupling. Recent data from an animal model show that the
HDR is affected by anesthesia levels (Cohen, Ugurbil, & Kim,
2002) and may be faster in the absence of anesthesia (Pisauro,
Dhruv, Carandini, & Benucci, 2013), which could lead to
another revision on our estimates of the specificity of neurovascular coupling based on previous invasive animal studies.
This new understanding of blood flow regulation and neurovascular coupling will inevitably impact future fMRI studies.
PSFbio and B0: Compartmental Origin of BOLD

The changes in the water compartments that contribute to
BOLD signal at different B0 are one of the primary acquisition
effects determining our ability to localize the origin of the
activation. For example, the large vessel intravascular compartments are long suspected of producing a BOLD effect relatively
distant from the neuronal source of the activation (Menon,
Ogawa, Tank, & Ugurbil, 1993; Ogawa et al., 1993; Polimeni
et al., 2010; Turner, 2002), and the relative contribution of
different vessel sizes changes with B0. Thus, the switch from
intravascular dominance to extravascular dominance at high
B0 is thought to be one of the primary reasons the biological
PSF is thought to improve at ultrahigh field.
3rd SH
4th SH
5th SH
6th SH
Slice 1
Slice 2
Slice 3
2nd SH
(at acq.)
109
Figure 5 Simulated effect of higher-order shim sets on 7 T B0 maps for three representative slices. The B0 field maps are acquired in a healthy
subject after conventional second-order SH shimming. Then, higher-order simulation fields are applied to attempt to mitigate the standard susceptibility
issues. Each slice is separately optimized (dynamic shimming). Note that either high-order SH or high-order MC shimming can substantially mitigate
the B0 disturbances. Simulation courtesy of Jason Stockman, MGH.
110
In order to understand the relative contributions of the compartments and how they change with field strength, one must
model the induced field distortions around the complex vessel
architecture, as well as how the water moves randomly among
the different magnetic environments inside and outside the vessels and cells. This has been extensively pursued with Monte
Carlo modeling (Boxerman, Bandettini, et al., 1995; Boxerman,
Hamberg, Rosen, & Weisskoff, 1995; Martindale, Kennerley,
Johnston, Zheng, & Mayhew, 2008; Ogawa et al., 1993; Uludag,
Muller-Bierl, & Ugurbil, 2009). In this picture, the red blood cells
(RBC), making up 40% of the blood volume, are the source of
the paramagnetism modulated by activation and are delivered
fully oxygenated into the brains arteries. While water is seen to
effortlessly move in and out of the RBC, it is trapped either inside
or outside the vasculature for timescales longer than the experiThus, water is described as belonging to either
ment (T2 or T*).
2
an intravascular (IV) or an extravascular (EV) compartment. The
extravascular compartment contains about 20 more water than
the intravascular compartment. Given our interest in spatial
localization, it is also useful to keep track of the relative contributions from various vessel sizes; typically, a distribution of
vessel sizes and orientations are studied. Finally, the motion of
the water within these compartments is studied assuming a
diffusion constant, D, of about 1 mm2 ms1.
At low field strengths (B0 1.5 T), these models show the
gradient recalled echo (GRE) experiment is weighted toward
blood vessels with diameters above 20 mm, while the spin
echo (SE) effect peaks for vessel with 15 mm diameter and
is relatively small for vessels with diameters above 25 mm
(Boxerman, Bandettini, et al., 1995; Martindale et al., 2008).
At 1.5 T, the IV contribution accounts for about 2/3 of the
R2*-based BOLD signal (Boxerman, Bandettini, et al., 1995;
Martindale et al., 2008). In contrast, Martindale and colleagues
suggested that at 3 T, the EV compartment accounts for approximately 2/3 of the signal from small vessels (6 mm diameter)
and 3/4 of the signal from larger vessels (50 mm diameter)
(Martindale et al., 2008). For 7 T, the modeling shows that
nearly all of the GRE-BOLD signal is extravascular (Martindale
et al., 2008; Uludag et al., 2009). For SE, the intravascular
component can be significant for small vessels and like the
GRE experiment is higher at low B0 (Oja, Gillen, Kauppinen,
Kraut, & van Zijl, 1999; Uludag et al., 2009).
A recent Monte Carlo modeling study included relaxation
time information from higher-field-strength measurements and
explicitly studied the fraction of the BOLD signal originating
from the micro- and macrovasculature as a function of TE and
B0 (in addition to the EV and IV components) (Uludag et al.,
2009). In this study, macrovasculature was modeled as a worstcase vessel with 200 mm diameter orientated orthogonal to B0
comprising 5% of the voxel. The microvasculature was modeled
as randomly oriented vessels. The microvascular CBV was taken
to be 2.5% with the fractional contributions from arterioles,
capillaries, and venules of 20%, 40%, and 40%, respectively,
each with a single diameter (16, 6, and 16 mm, respectively).
The SE micro/macro ratio was found to exceed the GRE ratio
for all TEs and B0 values. Additionally, the relative SE microvascular contribution as a function of field strength peaks for
B0 7 T, and a greater microvascular fraction is achieved with
longer TE than the typical choice (TE T2). For GRE acquisitions, the micro/macro ratio can be increased by choosing a
lower field strength, a surprising finding that is likely due to
the worst-case choice for microvasculature in the model. It is

also important to keep in mind that most modeling studies
attempt to study an average voxel and determine what fraction
of the BOLD effect came from subcomponents of the voxel. This
is different from modeling the expected vascular fractions found
in different voxels. For example, a high-resolution voxel in the
center of the gray matter will likely have different vascular
constituents than a voxel centered on the pial vessels (which is
likely to have several times more blood volume and a size
distribution skewed toward the larger diameters).
Experimental Observations on PSFbio in the Visual Cortex

at 7 T
The various effects altering the spatial fidelity of an activation
pattern across macroscopic portions of the cortex can perhaps
be best appreciated by activating a known pattern in the cortex
and observing the resulting fMRI map on the flattened cortex.
This is most readily done in the primary visual cortex where a
fairly accurate mapping between the visual field and the V1
cortex is known (Hinds, Polimeni, Rajendran, et al., 2008;
Polimeni, Balasubramanian, & Schwartz, 2006). Although
most of the estimates of PSFbio originate from retinotopic
experiments (Engel et al., 1997; Park et al., 2005; Shmuel
et al., 2007), Polimeni et al. were the first to demonstrate that
it is possible to activate relatively recognizable shapes in the
visual cortex (Polimeni et al., 2010). This requires, of course,
not only good instrumental resolution (1 mm isotropic in this
case) but also faithful registration onto the cortical surface
(needed since the shape is only recognizable on the flattened
cortex). They also went on to analyze the activation maps as a
function of cortical depth and the average partial volume content of each depth (percent GM, WM, and CSF).
Figure 6 reproduces some of these results. These 1 mm
isotropic 7 T gradient echo EPI data were acquired in about
5 min. The first thing noticeable about the M activations is
that the deviations from the expected pattern sampled tangentially along the laminar surfaces are not consistent across
cortical depths. Thus, the biological effect is more complicated
than a simple convolution process with a zero-mean Gaussianshaped PSF. In some places, the representation is relatively
faithful; in other locations, it is both blobby and displaced.
Additionally, the PSFbio clearly varies with laminar depth with
the highest fidelity away from the pial surface. This is consistent with degradation of the pattern by draining veins, which
reside on the pial surface; the density of large draining veins
exhibits a step-function increase at the pial surface.
Therefore, it is probably beneficial to break PSFbio into two
directions defined by the local cortical geometry: a tangential PSF
that would be meaningful for assessing the response from a
single activated column and a radial PSF useful for assessing
the ability to isolate laminar activation. Furthermore, the distribution of draining surface veins is highly modulated as a function of tangential position. The crowns of the gyri are relatively
free of large vessels, but the banks and fundi of the sulci are
packed with veins. Thus, we would also expect the tangential
PSFbio of the superficial layers would be dependent on the local
cortical curvature. Other observations about PSFbio from this
experiment included the importance of the differential imaging
task for subtracting out common-mode activation errors; the

differential map is considerably higher fidelity than that of either
of the two stimulus conditions alone.
Prospects for Improved PSFbio

Although seemingly set by nature, there are multiple proposals for
improving the PSFbio of fMRI experiments. The most ubiquitous is
the move to ever-higher B0 to try to eliminate the IV component of
the BOLD signal. Switching to a spin echo experiment is also seen
to be advantageous since the spin echo refocuses the signal changes
around large vessels isolating the presumably better localized
smaller vessels (Boxerman, Bandettini, et al., 1995; Boxerman,
Hamberg, et al., 1995). Moving away from the BOLD effect and
using an iron oxide contrast agent-based CBV effect also improve
localization since this method fully eliminates IV signal (Kim &
Kim, 2010, 2011; Moon, Fukuda, & Kim, 2013; Park et al., 2005;
Zhao, Wang, Hendrich, Ugurbil, & Kim, 2006). Finally, gaining
improved spatial localization from examining either very early
parts of the activation (Chen, Bouchard, McCaslin, Burgess, &
Hillman, 2011; Shmuel et al., 2007), including the predip (Hu,
Le, & Ugurbil, 1997; Mitra, Ogawa, Hu, & Ugurbil, 1997; Yacoub
et al., 2001b), or the very last part of the stimulation, a.k.a. the
CBV-driven poststimulus undershoot (Zhao, Jin, Wang, & Kim,
2007). Improving PSFbio by using small voxels to localize a specific vascular environment (e.g., mid to deep lamina) was discussed earlier (Polimeni et al., 2010). Perhaps, the ultimate
breakthrough for improving the biological spatiotemporal limitations will be an MR contrast mechanism resulting from neuronal currents rather than hemodynamics (Bandettini, Petridou, &
Bodurka, 2005; Petridou et al., 2006).
Patient motion mitigation

Extending the biological considerations that effect PSFbio to
include cognitive effects, we must consider subject motion as
a major degrader of spatial resolution in fMRI. Although
postprocessing rigid body motion corrections can be applied,
motion effects are not entirely mitigated since the patient can
move on a timescale that is fast compared to TR, causing a
111
stack-of-cards tilting artifact, which is a nonrigid body effect.

Additional nonrigid effects include the changes in distortion
pattern as the susceptibility-producing tissues are altered in
configuration relative to B0, spin-history effects as the excitation dynamics of a given spin change as it is moved into the
slices excitation field before its time, and reception intensity
modulation as the spins move closer or farther from the stationary receive coils. The fact that using the motion parameters
as regressors after motion correction is an effective way of
removing unwanted variance from the time series suggests
that many of the motions effects on image intensity remain
after motion correction (Hutton et al., 2011). The effect on the
images of many of the motion phenomena listed earlier can be
straightforwardly modeled, suggesting that more could be
done to explicitly incorporate their effects into the image
processing.
Ideally, the scanner should independently track the rigid
body motion of the head in real time and continuously
update the acquisition coordinate system appropriately. Such
a scheme goes beyond eliminating the need for retrospective
motion correction by removing significant variance in the
fMRI time series (from movement-induced spin-history
effects). Prospective motion correction has been implemented
using the images in the time series themselves to detect motion
(Thesen, Heid, Mueller, & Schad, 2000), but the resulting
feedback time of several seconds is too slow to correct the
many effects. An independent system is needed to measure
the six motion parameters with high sensitivity and temporal
resolution. There are many candidate sensors available using
optical video tracking devices or magnetic field probes, which
can measure position using the scanners gradient fields
(Maclaren, Herbst, Speck, & Zaitsev, 2013). A common issue
to all external tracking devices is finding a subject-friendly way
to attach the fiducial marker to the skull. The most workable
method is attachment to the upper teeth. Attachment to the
skin is problematic in that movements of the facial muscles
might cause the system to adjust the image coordinate system
when no brain motion is present. Despite the problems, there is
a potentially large payoff to solving this engineering challenge.
stimulus 1
stimulus 2
Flattened cortex
Cortical surface
5.000
0.500
0.500
5.000
Figure 6 7 T resolution test pattern acquired with 1 mm isotropic voxels analyzed as a function of depth analyzed on the folded cortex. The two
stimuli in the block design consisted of a pattern logarithmically warped to create an M pattern on V1. PSFbio appears to improve for depths more
distant from the pial surface, suggesting that avoiding pial vessels improves BOLD localization and resolution.
112
Instrumental Temporal Resolution in fMRI

Similarly to defining an instrumental spatial resolution, we can
define the temporal resolution of fMRI as the fastest time
interval in which the fMRI volumes are acquired. This is typically the TR time for the acquisition. The Nyquist sampling
theorem states that the highest temporal signal frequency discernible with such sampling is nmax 1/(2 TR). The temporal
resolution is typically dependent on the spatial resolution,
with conventional whole-brain 3 mm isotropic resolution EPI
acquired with a TR just over 3 s. A conventional 1 mm isotropic whole-brain acquisition requires a TR of about 10 s.
The SMS-EPI technique accelerates the EPI acquisition
by acquiring multiple slices simultaneously, thereby covering
the region of interest in fewer steps, and utilizing a parallel
imaging reconstruction technique to separate the multiple
slices (Feinberg & Setsompop, 2013; Larkman et al., 2001).
The number of slices acquired simultaneously, and thus
the speedup factor, is referred to as the MB factor (Feinberg
& Setsompop, 2013). The blipped-CAIPI addition to SMS-EPI
shifts every other slice by a fraction of the FOV to provide
increased distance between aliased pixels (Setsompop,
Gagoski, et al., 2012). This provides a critical component that
reduces the g-factor noise penalty of the reconstruction
enabling higher MB acceleration factors. Note that in contrast
to conventional parallel imaging, the data are not undersampled and there is no noise penalty equivalent to the R
penalty in conventional acceleration.
Figure 7 shows images from a fast (TR 1.2 s) 7 T wholebrain fMRI study acquired at 1.5 mm isotropic resolution. An
in-plane GRAPPA acceleration of Ry 3 was used to reduce
spatial distortion and shorten the EPI readout. Typically, it
takes about 90 slices to cover the brain at a 1.5 mm resolution
(with no slice gap), and this requires a TR of 6 s. An MB factor
of 5 was used to reduce the TR to 1.2 s. Figure 8 shows a more
extreme use of SMS to improve temporal resolution. In this
case, the brain was covered with 56 2.5 mm axial slices, also
with 2.5 mm in-plane resolution. The 3 T acquisition used a
Figure 7 Axial, coronal, and sagittal reformats of an axial acquired

1.5 mm resolution single-shot whole-brain EPI at 7 T. This modest
spatial resolution of 1.5 T was acquired with a modest acceleration of
Ry 3 and an SMS sequence with a modest multiband factor of MB 5
allowing a temporal resolution of TR 1.2 s, a current state-of-the-art
compromise between spatial and temporal resolutions in whole-brain
fMRI.
64-channel commercial headneck array, no in-plane acceleration, a TE 30 ms (for optimal BOLD contrast), and MB 12
for a TR 391 ms. Thus, the scanner was acquiring slices at a
rate of 143 slices per second! At this rate, both cardiac and
respiratory modulations are Nyquist-sampled, which prevents
their nuisance fluctuations from accidentally aliasing into the
frequency band of the BOLD signal (which is typically much
lower for a block design experiment).
Biological Limits on BOLD Temporal Resolution

Figure 9 shows the canonical hemodynamic response function
(HRF) assumed for many fMRI studies. The HRF peaks about
6 s poststimulus onset, and its width is about 4 s. Together with
the poststimulus undershoot, it lasts a full 20 s. Figure 9 also
shows the power spectrum of this HRF on a logarithmic scale
showing that there is very little spectral energy at frequencies
above about 0.5 Hz. Superimposed on the figure is the approximate frequency bands of the cardiac and respiratory cycle, as
well as the maximum frequencies present in signals that can be
sampled with a TR 23 s. This suggests that the conventional
sampling rate of 23 s already captures the vast majority of the
energy in the BOLD signal spectrum. The TR 391 ms example
earlier would capture spectral components up to 1.3 Hz. At this
point in the spectrum, the power density is reduced by 10
orders of magnitude compared to its peak level. It seems that
capturing additional components of the BOLD spectrum is not
a good reason to push the temporal resolution.
For the previously mentioned reasons, it is commonly
believed that rapid sampling is unlikely to benefit fMRI and our
ability to measure brain dynamics is limited by the biology of
cerebrovascular physiology rather than by our imaging technology. This belief is now being overturned. The arterioles are commonly considered to be the source of blood flow regulation since
they possess the smooth muscle tissue needed to control vessel
diameter and thus downstream flow. Changes at the capillary
level were conventionally believed to be simply a consequence
of upstream regulation at the feeding arterioles with the capillaries
themselves having no ability to regulate blood flow on their own.
Yet the recent studies reviewed earlier have identified evidence for
extremely fine-scale regulation within a capillary network.
Faster temporal sampling allows one to resolve the transients of the HRF, and the detection of the initial onset of the
BOLD response can be exploited to achieve improved spatial
specificity. While the initial dip of the HRF has been exploited
in fMRI studies (Duong, Kim, Ugurbil, & Kim, 2000; Kim et al.,
2000; Yacoub et al., 2001b) and its existence (i.e., the existence
of a transient rapid increase in deoxyhemoglobin immediately
following neuronal activation) has been demonstrated in invasive optical imaging studies (Devor et al., 2003), its detection
remains elusive (Buxton, 2001). It is also conceivable that this
initial dip may only be reliably detected with both high spatial
sampling and temporal sampling (Tian et al., 2010). While
recent evidence suggests that this initial dip may not reflect a
transient increase in the cerebral metabolic rate of oxygen (a
metabolic signal) but may represent a rapid initial increase in
cerebral blood volume (a vascular signal) (Sirotin, Hillman,
Bordier, & Das, 2009; Uludag, 2010), it still appears to be
more spatially specific than the peak response that occurs up
to 6 s poststimulus. This indicates that fMRI signals that reflect
vascular changes precisely reflect neuronal activation: the
113
Figure 8 Subset of slices from a 12-fold accelerated SMS run acquired at 3 T with a 64-ch headneck array. Fifty-six 2.5 mm thick slices were acquired
with TR 391 ms and TE 30 ms (143 slices per second). Courtesy of Kawin Setsompop, MGH.
Power spectrum (a.u.)
HDF power (a.u.)
Canonical HRF
0.5
10
20
30
Time after stimulus onset (s)
Cardiac band
1.0
100
105
HRF power spectrum

2-3 s TR band
Respiration band
1010
0
2
3
Frequency (Hz)
Figure 9 Canonical hemodynamic response function (HRF) (from SPM) and its power spectrum with the respiratory, cardiac, and 23 s TR bands
marked. Note that the spectrum has very little power after 1.5 Hz, suggesting little BOLD signal will be captured by capturing BOLD frequencies above
1.5 Hz.
parsimonious model where metabolic signals are naturally

more specific to neural activity than vascular signals has been
replaced with a model where vascular signals themselves can
be highly specific to neuronal activity.
Whether or not a dip can be detected, the earliest regime of
the hemodynamic response appears to provide tighter spatial
specificity (Chen et al., 2011; Menon & Goodyear, 1999; Yu
et al., 2012), and thus, the ability to sample more rapidly is
likely to provide gains in spatial specificity. The propagation of

the vascular response from the locus of neural activity has been
observed in optical imaging studies (Chen et al., 2011) as well as
in an fMRI study where the earliest BOLD signal changes were
localized to the capillary bed within the parenchyma, while later
changes were tracked in the diving venules (Yu et al., 2012).
Using the inverse imaging (InI) method, which can sample
the fMRI signal across the entire brain at temporal sampling
114
intervals at or below 100 ms (albeit with coarse spatial resolution), Lin et al. had shown that the temporal precision of the
BOLD signal is high enough to detect difference in onset time
in cortical responses to visual stimuli presented 100 ms apart
(Chang et al., 2013; Lin et al., 2013). Silva and Koretsky had
shown that onset times in rodents show laminar differences
(Silva & Koretsky, 2002). These specialized studies have clearly
benefited from the high temporal resolutions they have used.
Additionally, ultrafast sampling has proved useful in restingstate connectivity studies (Griffanti et al., 2014; Tong et al.,
2013; Ugurbil et al., 2013).
Given the successes of ultrafast functional imaging, it is worth
revisiting the logic that dismissed it. The basic idea was that the
hemodynamic changes are slow enough that they are adequately
temporally resolved with 3 s temporal resolution. When we
sample a band-limited waveform with maximum frequency present of nmax (sometimes called the Nyquist frequency), we must
sample at the Nyquist rate of twice this bandwidth (2nmax), and
the time period between samples (called the dwell time) is the
inverse of this rate; tdwell 1/(2 nmax). It is possible to oversample
the signal; that is, sample at a rate much higher than the Nyquist
rate (say, a rate 20nmax) and then low-pass filter the resultant
signal back to nmax, but sampling theory tells us that this strategy
will not improve the final SNR. The higher sampling rate lets in
more of the white noise spectrum, but then, the low-pass filtering
simply removes this noise again. So, if the largest frequencies
present in the HRF are about 0.3 Hz (the spectral power is
reduced by a factor of 1000 at this frequency), the Nyquist
sampling rate is 0.6 Hz and the dwell time is 1.7 s. In good
agreement with common perceptions, sampling theory suggests
that sampling faster than this will have little benefit.
The solution to the apparent contradiction comes from asking for a physical interpretation of tdwell and its equivalence in
our imaging experiments. In a conventional voltage signal measurement, the signal recording system connects a sample-andhold device to the signal voltage during the dwell period. During
that time, charge is integrated on the capacitor of the sampleand-hold. This has two purposes. Firstly to hold the signal so
the ADC can go through its comparisons, which is how it
measures the voltage. The second purpose is to integrate noise
fluctuations over the dwell period. This has a filtering effect; the
longer tdwell, the lower the noise variance in a repeated measurement. This aspect of the signal sampling process is critical. In
this view, no matter how you sample, there are no time gaps
where the signal is not being integrated on the capacitor of the
sample-and-hold. You can sample at the minimum rate (the
Nyquist rate) with long dwell times, or you can sample at 10
this rate with 10 shorter dwell times. In both cases, the signal
will be connected to the sample-and-hold capacitor for all the
time available and thus samples at maximum 100% efficiency, a
critical criterion implicit in sampling theory.
How about for imaging sequences? How long does a single
EPI image sample the changing signal intensity? The answer is
it samples it for the duration of the EPI readout, which is about
30 ms for conventional 3 mm EPI. It does not matter whether
the TR is 0.3, 3, or 30 s; the given pixels BOLD signal is sampled
once for an effective integration time of 30 ms in that TR period
and then proceeds, unsampled, until the next TR. The efficiency
is thus 30 ms out of 3 s for conventional studies, about 1%. This
is horribly inefficient and far from the maximally efficient sampling rate demanded by the Nyquist sampling theory. What can
we do to improve the efficiency? Sample faster!
The earlier mentioned analysis assumes that the noise in the

signal is a conventional thermal white noise. In fMRI, it is possible
to be dominated by physiological fluctuations that have limited
spectral content. In this case, there are significant correlations
between time points, and faster sampling will help less and less.
If the time points are fully correlated, there is no reason to sampling faster. Thus, the autocorrelation function of the time series
becomes an important quantity for estimating the statistics of
signal and noise. This quantity is related to the number of statistically independent degrees of freedom present in the dataset.
Conclusions
The last decade has seen distinct improvements in the spatial and
temporal resolution of the fMRI acquisition. Acquisition engineering has left the field with considerable gains in sensitivity
from advanced RF array designs and higher field strengths to
considerably cleaner, faster, less distorted single-shot imaging
with improved gradients and parallel imaging acceleration. The
potential benefit of more routine use of the currently exotic
high-end acquisitions is just starting to propagate from specialized studies to more typical studies. Moreover, future needs in
image quality and spatial and temporal resolution are still considerable. Luckily, a long list of technologies at different stages of
development offers considerable promise for future improvements. They attack the problem at the acquisition hardware
level through the coils of MRI, gradient, shim, and transmitter
and receiver, and through improved sampling efficiencies in
volume coverage. The field has also made progress addressing
acquisition problems through postprocessing software such as
nonrigid alignment tools and distortion corrections. Similar
postprocessing steps have helped with variance removal of
motion-induced and biological effects (vein and CSF avoidance). While progress will appear slow, and developments initially only benefits a single laboratory, successful developments
ultimately impact all brain-mapping practitioners.
Acknowledgments
The author gratefully acknowledges the contribution of
Kawin Setsompop and Christina Triantafyllou for their help
in formulating this manuscript. He also acknowledges support
from the National Institutes of Health through grants
U01MH093765, R01EB224334, R01EB006847, K01EB001498,
and P41EB015896.
See also: INTRODUCTION TO ACQUISITION METHODS: EchoPlanar Imaging; Evolution of Instrumentation for Functional Magnetic
Resonance Imaging; fMRI at High Magnetic Field: Spatial Resolution Limits
and Applications; Functional MRI Dynamics; Pulse Sequence Dependence
of the fMRI Signal; Temporal Resolution and Spatial Resolution of fMRI.
References
Bandettini, P. A., Petridou, N., & Bodurka, J. (2005). Direct detection of neuronal activity
with MRI: Fantasy, possibility, or reality? Applied Magnetic Resonance, 29, 6588.
Bandettini, P. A., Wong, E. C., Jesmanowicz, A., Prost, R., Cox, R. W., Hinks, R. S., et al.
(1994). MRI of human brain activation at 0.5 T, 1.5 T and 3.0 T: Comparison of DR*2

and functional contrast to noise ratio. In: Proceedings of the second annual meeting
of the Society of Magnetic Resonance in Medicine, San Francisco.
Beissner, F., Polimeni, J. R., Bianciardi, M., Renvall, V., Eichner, C., Napadow, V., et al.
(2014). Imaging the human brainstem at 7 Tesla using multi-modal echo-planar
imaging. In: Proceedings of the ISMRM, Milan, Italy.
Bianciardi, M., Fukunaga, M., van Gelderen, P., Horovitz, S. G., de Zwart, J. A., Shmueli, K.,
et al. (2009). Sources of functional magnetic resonance imaging signal fluctuations in
the human brain at rest: A 7 T study. Magnetic Resonance Imaging, 27, 10191029.
Boxerman, J. L., Bandettini, P. A., Kwong, K. K., Baker, J. R., Davis, T. L., Rosen, B. R., et al.
(1995). The intravascular contribution to fMRI signal change: Monte Carlo modeling
and diffusion-weighted studies in vivo. Magnetic Resonance in Medicine, 34, 410.
Boxerman, J. L., Hamberg, L. M., Rosen, B. R., & Weisskoff, R. M. (1995). MR contrast
due to intravascular magnetic susceptibility perturbations. Magnetic Resonance in
Medicine, 34, 555566.
Breuer, F. A., Blaimer, M., Heidemann, R. M., Mueller, M. F., Griswold, M. A., &
Jakob, P. M. (2005). Controlled aliasing in parallel imaging results in higher
acceleration (CAIPIRINHA) for multi-slice imaging. Magnetic Resonance in
Medicine, 53, 684691.
Breuer, F. A., Blaimer, M., Mueller, M. F., Seiberlich, N., Heidemann, R. M.,
Griswold, M. A., et al. (2006). Controlled aliasing in volumetric parallel imaging (2D
CAIPIRINHA). Magnetic Resonance in Medicine, 55, 549556.
Buxton, R. B. (2001). The elusive initial dip. NeuroImage, 13, 953958.
Buxton, R. B. (2009). Introduction to functional magnetic resonance imaging: Principles
and techniques (2nd edn). Cambridge University Press. http://www.cambridge.org/
us/academic/subjects/medicine/neurology-and-clinical-neuroscience/introductionfunctional-magnetic-resonance-imaging-principles-and-techniques-2nd-edition.
Chaigneau, E., Oheim, M., Audinat, E., & Charpak, S. (2003). Two-photon imaging of
capillary blood flow in olfactory bulb glomeruli. Proceedings of the National
Chang, W.-T., Nummenmaa, A., Witzel, T., Ahveninen, J., Huang, S., Tsai, K. W.-K.,
et al. (2013). Whole-head rapid fMRI acquisition using echo-shifted magnetic
resonance inverse imaging. NeuroImage, 78C, 325338.
Chen, B. R., Bouchard, M. B., McCaslin, A. F.H, Burgess, S. A., & Hillman, E. M.C (2011). Highspeed vascular dynamics of the hemodynamic response. NeuroImage, 54, 10211030.
Cheng, K. (2012). Revealing human ocular dominance columns using high-resolution
functional magnetic resonance imaging. NeuroImage, 62, 10291034.
Cohen, E. R., Ugurbil, K., & Kim, S.-G. (2002). Effect of basal conditions on the
Journal of Cerebral Blood Flow and Metabolism, 22, 10421053.
Cohen-Adad, J., Polimeni, J. R., Helmer, K. G., Benner, T., McNab, J. A., Wald, L. L.,
et al. (2012). T2* mapping and B0 orientation-dependence at 7 T reveal cytoand myeloarchitecture organization of the human cortex. NeuroImage, 60,
10061014.
Devor, A., Dunn, A. K., Andermann, M. L., Ulbert, I., Boas, D. A., & Dale, A. M. (2003).
Coupling of total hemoglobin concentration, oxygenation, and neural activity in rat
somatosensory cortex. Neuron, 39, 353359.
Duong, T. Q., Kim, D. S., Ugurbil, K., & Kim, S. G. (2000). Spatiotemporal dynamics of
the BOLD fMRI signals: Toward mapping submillimeter cortical columns using the
early negative response. Magnetic Resonance in Medicine, 44, 231242.
Engel, S. A., Glover, G. H., & Wandell, B. A. (1997). Retinotopic organization in human
visual cortex and the spatial precision of functional MRI. Cerebral Cortex, 7, 181192.
Feinberg, D. A., Moeller, S., Smith, S. M., Auerbach, E., Ramanna, S., Gunther, M., et al.
(2010). Multiplexed echo planar imaging for sub-second whole brain FMRI and fast
diffusion imaging. PloS One, 5, e15710.
Feinberg, D. A., & Setsompop, K. (2013). Ultra-fast MRI of the human brain with
simultaneous multi-slice imaging. Journal of Magnetic Resonance, 229, 90100.
Fukuda, M., Moon, C. H., Wang, P., & Kim, S. G. (2006). Mapping iso-orientation
columns by contrast agent-enhanced functional magnetic resonance imaging:
Reproducibility, specificity, and evaluation by optical imaging of intrinsic signal.
Journal of Neuroscience, 26, 1182111832.
Goense, J. B., & Logothetis, N. K. (2006). Laminar specificity in monkey V1 using highresolution SE-fMRI. Magnetic Resonance Imaging, 24, 381392.
Goense, J., Merkle, H., & Logothetis, N. K. (2012). High-resolution fMRI reveals
laminar differences in neurovascular coupling between positive and negative BOLD
responses. Neuron, 76, 629639.
Goodyear, B. G., Nicolle, D. A., & Menon, R. S. (2002). High resolution fMRI of ocular
dominance columns within the visual cortex of human amblyopes. Strabismus, 10,
129136.
Greve, D. N., & Fischl, B. (2009). Accurate and robust brain image alignment using
boundary-based registration. NeuroImage, 48, 6372.
Griffanti, L., Salimi-Khorshidi, G., Beckmann, C. F., Auerbach, E. J., Douaud, G.,
Sexton, C. E., et al. (2014). ICA-based artefact removal and accelerated fMRI
acquisition for improved resting state network imaging. NeuroImage, 95, 232247.
115
Hamilton, N. B., Attwell, D., & Hall, C. N. (2010). Pericyte-mediated regulation of

capillary diameter: A component of neurovascular coupling in health and disease.
Frontiers in Neuroenergetics, 2, 114.
Han, H., Song, A. W., & Truong, T. K. (2013). Integrated parallel reception, excitation,
and shimming (iPRES). Magnetic Resonance in Medicine, 70, 241247.
Harel, N., Lin, J., Moeller, S., Ugurbil, K., & Yacoub, E. (2006). Combined imaginghistological study of cortical laminar specificity of fMRI signals. NeuroImage, 29,
879887.
Hinds, O., Polimeni, J. R., Rajendran, N., et al.Balasubramanian, M., Wald, L. L.,
Augustinack, J. C., (2008). The intrinsic shape of human and macaque primary
visual cortex. Cerebral Cortex, 18, 25862595.
Hu, X., Le, T. H., & Ugurbil, K. (1997). Evaluation of the early response in fMRI in
individual subjects using short stimulus duration. Magnetic Resonance in Medicine,
37, 877884.
Hutton, C., Josephs, O., Stadler, J., Featherstone, E., Reid, A., Speck, O., et al. (2011). The
impact of physiological noise correction on fMRI at 7 T. NeuroImage, 57, 101112.
Juchem, C., Brown, P. B., Nixon, T. W., McIntyre, S., Rothman, D. L., & de Graaf, R. A.
(2011). Multicoil shimming of the mouse brain. Magnetic Resonance in Medicine,
66, 893900.
Juchem, C., Nixon, T. W., Diduch, P., Rothman, D. L., Starewicz, P., & de Graaf, R. A.
(2010). Dynamic shimming of the human brain at 7 Tesla. Concepts in Magnetic
Resonance Part B: Magnetic Resonance Engineering, 37B, 116128.
Juchem, C., Nixon, T. W., McIntyre, S., Boer, V. O., Rothman, D. L., & de Graaf, R. A.
(2011). Dynamic multi-coil shimming of the human brain at 7 T. Journal of
Juchem, C., Nixon, T. W., McIntyre, S., Rothman, D. L., & de Graaf, R. A. (2010).
Magnetic field homogenization of the human prefrontal cortex with a set of localized
electrical coils. Magnetic Resonance in Medicine, 63, 171180.
Keil, B., Blau, J. N., Biber, S., Hoecht, P., Tountcheva, V., Setsompop, K., et al. (2013).
A 64-channel 3 T array coil for accelerated brain MRI. Magnetic Resonance in
Medicine, 70, 248258.
Kim, D. S., Duong, T. Q., & Kim, S. G. (2000). High-resolution mapping of isoorientation columns by fMRI. Nature Neuroscience, 3, 164169.
Kim, S. G., & Fukuda, M. (2008). Lessons from fMRI about mapping cortical columns.
The Neuroscientist: A Review Journal Bringing Neurobiology, Neurology and
Kim, T., & Kim, S. G. (2010). Cortical layer-dependent arterial blood volume
changes: Improved spatial specificity relative to BOLD fMRI. NeuroImage, 49,
13401349.
Kim, T., & Kim, S. G. (2011). Temporal dynamics and spatial specificity of arterial
and venous blood volume changes during visual stimulation: Implication for
BOLD quantification. Journal of Cerebral Blood Flow and Metabolism, 31,
12111222.
Kruger, G., & Glover, G. H. (2001). Physiological noise in oxygenation-sensitive
Larkman, D. J., Hajnal, J. V., Herlihy, A. H., Coutts, G. A., Young, I. R., & Ehnholm, G.
(2001). Use of multicoil arrays for separation of signal from multiple slices
simultaneously excited. Journal of Magnetic Resonance Imaging, 13, 313317.
Laurienti, P. J., Field, A. S., Burdette, J. H., Maldjian, J. A., Yen, Y. F., & Moody, D. M.
(2002). Dietary caffeine consumption modulates fMRI measures. NeuroImage, 17,
751757.
Levin, J. M., Frederick Bde, B., Ross, M. H., Fox, J. F., von Rosenberg, H. L.,
Kaufman, M. J., et al. (2001). Influence of baseline hematocrit and hemodilution on
BOLD fMRI activation. Magnetic Resonance Imaging, 19, 10551062.
Lin, F.-H., Witzel, T., Raij, T., Ahveninen, J., Wen-Kai Tsai, K., Chu, Y.-H., et al. (2013).
fMRI hemodynamics accurately reflects neuronal timing in the human brain
measured by MEG. NeuroImage, 78C, 372384.
Lu, H., Patel, S., Luo, F., Li, S. J., Hillard, C. J., Ward, B. D., et al. (2004). Spatial
correlations of laminar BOLD and CBV responses to rat whisker stimulation with
neuronal activity localized by FOS expression. Magnetic Resonance in Medicine,
52, 10601068.
Maclaren, J., Herbst, M., Speck, O., & Zaitsev, M. (2013). Prospective motion correction
in brain imaging: A review. Magnetic Resonance in Medicine, 69, 621636.
Martindale, J., Kennerley, A. J., Johnston, D., Zheng, Y., & Mayhew, J. E. (2008).
Theory and generalization of Monte Carlo models of the BOLD signal source.
McKenzie, C. A., Drost, D. J., & Carr, T. J. (1994). The effect of magnetic field strength
on signal change dS/S in functional MRI with BOLD contrast. In: Proceedings of the
second annual meeting of the Society of Magnetic Resonance in Medicine, San
Francisco.
Menon, R. S., & Goodyear, B. G. (1999). Submillimeter functional localization in human
striate cortex using BOLD contrast at 4 Tesla: Implications for the vascular pointspread function. Magnetic Resonance in Medicine, 41, 230235.
Menon, R. S., Ogawa, S., Tank, D. W., & Ugurbil, K. (1993). Tesla gradient recalled
echo characteristics of photic stimulation-induced signal changes in the human
primary visual cortex. Magnetic Resonance in Medicine, 30, 380386.
116
Mitra, P. P., Ogawa, S., Hu, X., & Ugurbil, K. (1997). The nature of spatiotemporal
changes in cerebral hemodynamics as manifested in functional magnetic resonance
Moon, C. H., Fukuda, M., & Kim, S. G. (2013). Spatiotemporal characteristics and
vascular sources of neural-specific and -nonspecific fMRI signals at submillimeter
columnar resolution. NeuroImage, 64, 91103.
Mulderink, T. A., Gitelman, D. R., Mesulam, M. M., & Parrish, T. B. (2002). On the use
of caffeine as a contrast booster for BOLD fMRI studies. NeuroImage, 15, 3744.
Murphy, D. D., & Wagner, R. C. (1994). Differential contractile response of cultured
microvascular pericytes to vasoactive agents. Microcirculation, 1, 121128.
Nizar, K., Uhlirova, H., Tian, P., Saisan, P. A., Cheng, Q., Reznichenko, L., et al. (2013).
In vivo stimulus-induced vasodilation occurs without IP3 receptor activation and
may precede astrocytic calcium increase. Journal of Neuroscience, 33, 84118422.
Nunes, R. G., Hajnal, J. V., Golay, X., & Larkman, D. J. (2006). Simultaneous slice
excitation and reconstruction for single-shot EPI. In: Proceedings of ISMRM.
OCraven, K. M., Rosen, B. R., Kwong, K. K., Treisman, A., & Savoy, R. L. (1997). Voluntary
attention modulates fMRI activity in human MT-MST. Neuron, 18, 591598.
Oja, J. M., Gillen, J., Kauppinen, R. A., Kraut, M., & van Zijl, P. C. (1999). Venous blood
effects in spin-echo fMRI of human brain. Magnetic Resonance in Medicine, 42,
617626.
Pan, J. W., Lo, K. M., & Hetherington, H. P. (2012). Role of very high order and degree
B0 shimming for spectroscopic imaging of the human brain at 7 tesla. Magnetic
Park, J., Ronen, J., Kim, D. S., & Ugurbil, K. (2005). Spatial specificity of high
resolution GE BOLD and Spin Echo (SE) BOLD fMRI in the cat visual cortex at 9.4
Tesla. In: Proceedings of the ISMRM, Miami Beach, FL.
Parkes, L. M., Schwarzbach, J. V., Bouts, A. A., Deckers, R. H., Pullens, P.,
Kerskens, C. M., et al. (2005). Quantifying the spatial resolution of the gradient echo
and spin echo BOLD response at 3 Tesla. Magnetic Resonance in Medicine, 54,
14651472.
Peppiatt, C. M., Howarth, C., Mobbs, P., & Attwell, D. (2006). Bidirectional control of
CNS capillary diameter by pericytes. Nature, 443, 700704.
Petridou, N., Plenz, D., Silva, A. C., Loew, M., Bodurka, J., & Bandettini, P. A. (2006).
Direct magnetic resonance detection of neuronal electrical activity. Proceedings of
the National Academy of Sciences of the United States of America, 103,
1601516020.
Pisauro, M. A., Dhruv, N. T., Carandini, M., & Benucci, A. (2013). Fast hemodynamic
responses in the visual cortex of the awake mouse. Journal of Neuroscience, 33,
1834318351.
Polimeni, J. R., Balasubramanian, M., & Schwartz, E. L. (2006). Multi-area visuotopic
map complexes in macaque striate and extra-striate cortex. Vision Research, 46,
33363359.
Polimeni, J. R., Fischl, B., Greve, D. N., & Wald, L. L. (2010). Laminar analysis of 7 T
13341346.
Renvall, V., Witzel, T., Wald, L. L., & Polimeni, J. R. (2014). Fast variable inversion
recovery time EPI for anatomical reference and quantitative T1 mapping.
In: Proceedings of the ISMRM, Milan, Italy.
Ress, D., Glover, G. H., Liu, J., & Wandell, B. (2007). Laminar profiles of functional
activity in the human brain. NeuroImage, 34, 7484.
Setsompop, K., Cohen-Adad, J., Gagoski, B. A., Raij, T., Yendiki, A., Keil, B., et al.
(2012). Improving diffusion MRI using simultaneous multi-slice echo planar
Medicine, 67, 12101224.
Shmuel, A., Yacoub, E., Chaimow, D., Logothetis, N. K., & Ugurbil, K. (2007). Spatiotemporal point-spread function of fMRI signal in human gray matter at 7 Tesla.
Silva, A. C., & Koretsky, A. P. (2002). Laminar specificity of functional MRI onset times
during somatosensory stimulation in rat. Proceedings of the National Academy of
Sirotin, Y. B., Hillman, E. M.C, Bordier, C., & Das, A. (2009). Spatiotemporal precision
and hemodynamic mechanism of optical point spreads in alert primates.
106, 1839018395.
Spielman, D. M., Adalsteinsson, E., & Lim, K. O. (1998). Quantitative assessment of

improved homogeneity using higher-order shims for spectroscopic imaging of the
brain. Magnetic Resonance in Medicine, 40, 376382.
Stockman, J. P., Witzel, T., Blau, J. N., Zhao, W., Polimeni, J. R., & Wald, L. L. (2013).
Combined shim-RF array for highly efficient shimming of the brain at 7 Tesla.
In: Proceedings of the international society for magnetic resonance in medicine 21st
annual meeting, Salt Lake City, UT.
Stockman, J. P., Witzel, T., Keil, B., Mareyam, A., Polimeni, J. R., LaPierre, C. D., et al.
(2014). A 32ch combined RF shim brain array for efficient B0 shimming and RF
reception at 3 T. In: Proceedings of the ISMRM, Milan, Italy.
Thesen, S., Heid, O., Mueller, E., & Schad, L. R. (2000). Prospective acquisition
correction for head motion with image-based tracking for real-time fMRI. Magnetic
Tian, P., Teng, I. C., May, L. D., Kurz, R., Lu, K., Scadeng, M., et al. (2010). Cortical
depth-specific microvascular dilation underlies laminar differences in blood
oxygenation level-dependent functional MRI signal. Proceedings of the National
Tong, Y., Hocke, L. M., & Frederick, B. D. (2013). Short repetition time multiband echoplanar imaging with simultaneous pulse recording allows dynamic imaging of the
cardiac pulsation signal. Magnetic Resonance in Medicine, 72, 12681276.
Triantafyllou, C., Hoge, R. D., Krueger, G., Wiggins, C. J., Potthast, A., Wiggins, G. C.,
et al. (2005). Comparison of physiological noise at 1.5 T, 3 T and 7 T and
optimization of fMRI acquisition parameters. NeuroImage, 26, 243250.
Truong, T. K., Darnell, D., & Song, A. W. (2014). Integrated RF/shim coil array for
parallel reception and localized B0 shimming in the human brain at 3 T.
In: Proceedings of the ISMRM, Milan, Italy.
Turner, R. (2002). How much cortex can a vein drain? Downstream dilution of
activation-related cerebral blood oxygenation changes. NeuroImage, 16,
10621067.
Turner, R., Jezzard, P., Wen, H., Kwong, K. K., Le Bihan, D., Zeffiro, T., et al. (1993).
Functional mapping of the human visual cortex at 4 and 1.5 Tesla using
deoxygenation contrast EPI. Magnetic Resonance in Medicine, 29, 277279.
Ugurbil, K., Xu, J., Auerbach, E. J., Moeller, S., Vu, A. T., Duarte-Carvajalino, J. M.,
et al. (2013). Pushing spatial and temporal resolution for functional and diffusion
MRI in the Human Connectome Project. NeuroImage, 80, 80104.
Uludag, K. (2010). To dip or not to dip: Reconciling optical imaging and fMRI data.
107, E23; author reply E24.
Wiesinger, F., Van de Moortele, P. F., Adriany, G., De Zanche, N., Ugurbil, K., &
Pruessmann, K. P. (2004). Parallel imaging performance as a function of field
strength An experimental investigation using electrodynamic scaling. Magnetic
Wilson, J. L., Jenkinson, M., & Jezzard, P. (2002). Optimization of static field
homogeneity in human brain using diamagnetic passive shims. Magnetic
Xu, J., Moeller, S., Auerbach, E. J., Strupp, J., Smith, S. M., Feinberg, D. A., et al.
(2013). Evaluation of slice accelerations using multiband echo planar imaging at
3 T. NeuroImage, 83, 9911001.
America, 105, 1060710612.
Yacoub, E., Shmuel, A., Pfeuffer, J., Van De Moortele, P. F., Adriany, G., Andersen, P.,
et al. (2001a). Imaging brain function in humans at 7 Tesla. Magnetic Resonance in
Medicine, 45, 588594.
Yacoub, E., Shmuel, A., Pfeuffer, J., Van De Moortele, P. F., Adriany, G., Ugurbil, K.,
et al. (2001b). Investigation of the initial dip in fMRI at 7 Tesla. NMR in
Yacoub, E., Van De Moortele, P. F., Shmuel, A., & Ugurbil, K. (2005). Signal and noise
738750.
Yu, X., Glen, D., Wang, S., Dodd, S., Hirano, Y., Saad, Z., et al. (2012). Direct imaging
of macrovascular and microvascular contributions to BOLD fMRI in layers IV-V of
the rat whisker-barrel cortex. NeuroImage, 59, 14511460.
Yu, X., Qian, C., Chen, D. Y., Dodd, S. J., & Koretsky, A. P. (2014). Deciphering
laminar-specific neural inputs with line-scanning fMRI. Nature Methods, 11,
5558.
Zhao, F., Jin, T., Wang, P., & Kim, S. G. (2007). Improved spatial localization of
post-stimulus BOLD undershoot relative to positive BOLD. NeuroImage, 34,
10841092.
Zhao, F., Wang, P., Hendrich, K., Ugurbil, K., & Kim, S. G. (2006). Cortical layerdependent BOLD and CBV responses measured by spin-echo and gradient-echo
fMRI: Insights into hemodynamic regulation. NeuroImage, 30, 11491160.
Basic Principles of Magnetoencephalography

R Hari and L Parkkonen, Aalto University, Espoo, Finland
M Hamalainen, Aalto University, Espoo, Finland; Massachusetts General Hospital, Charlestown, MA, USA
Introduction
Human brain function involves many intermingled timescales.
Sensory percepts, cognitive processes, motor activity, and
social interaction all rely on accurate neuronal timing ranging
from submilliseconds to seconds. Magnetoencephalography
(MEG) is currently routinely available to address brain functions at the required high temporal resolution.
Modern whole-scalp neuromagnetometers comprise
helmet-shaped arrays of more than 300 SQUIDs (superconducting quantum interference devices) and are able to capture
all spatial and temporal information present at the distance of
the sensors. Consequently, the most urgent methodological
challenges today are to interpret the MEG signals properly by
employing sophisticated data analysis methods.
The skull and scalp affect the brains electric potential distributions on the scalp (measured with electroencephalography, EEG) but do not smear the magnetic signals; MEG is thus
able to see cortical events through the skull. Importantly,
MEG and EEG reflect neuronal activity directly rather than
through the associated hemodynamic or metabolic effects.
Therefore, MEG/EEG and hemodynamic methods, e.g. BOLD
fMRI, are set apart not only by their different temporal and
spatial resolutions but also by the physiological origin of the
measured signals.
MEG excels in picking up activity in fissural cortex, poorly
accessible even with intracranial recordings. In contrast, EEG
receives an overwhelming contribution from the activity in the
gyri, and the activity of the fissural cortex is often difficult to
discern from the ongoing, unaveraged EEG signals.
Review articles and textbooks are available on the MEG
technique and its applications (e.g., Aine, 2010; Baillet,
Mosher, & Leahy, 2001; Del Gratta, Pizzella, Torquati, &
Romani, 1999; Hamalainen & Hari, 2002; Hansen, Kringelbach, & Salmelin, 2010; Hari, 2011; Hari, Parkkonen, &
Nangini, 2010; Hari & Salmelin, 2012; Salmelin, 2007).
From Neuronal Currents to MEG Signals

Neuronal currents produce weak magnetic fields that can be
detected outside the head with MEG when tens of thousands of
neurons act in concert. Most of the observed MEG signals are
assumed to arise from postsynaptic currents of pyramidal neurons in the neocortex. The passively propagating postsynaptic
currents in, for example, apical dendrites can be described by
unidirectional intracellular current flow that diminishes exponentially due to leakage through the cell membrane. The postsynaptic potentials last an order of magnitude longer than
action potentials do, and they are thus more likely to overlap
in time. For optimal summation, the contributing neural
structures need to be in parallel and close to each other,

which is true for apical dendrites of cortical pyramidal cells.
MEG Instrumentation and Noise Rejection

Modern MEG instruments employ helmet-shaped arrays of
more than 300 SQUID sensors. SQUIDs provide excellent
sensitivity, but they require cryogenic temperatures (achieved
with liquid helium; 4 K or 269 C) to operate, and thus,
other sensor solutions are searched for. Devices employing
high-critical temperature SQUIDs (operational in liquid nitrogen; 77 K) suffer from higher noise that still limits their usability in brain research. New magnetoresistive sensors can pick up
magnetic signals from the heart (Pannetier-Lecoeur et al.,
2011) but do not, with their present-day sensitivity, provide
feasible MEG recordings. Atomic magnetometers (Kominis,
Kornack, Allred, & Romalis, 2003) have already been used to
reliably pick up, for example, auditory-evoked brain responses.
In addition, recent introduction of SQUID-based ultralowfield (microtesla) MRI provides a new means of acquiring
MEG and MRI information in a single recording session
(Vesanen et al., 2013).
SQUID-based MEG systems employ superconducting flux
transformers that couple the brains magnetic field to the
SQUIDs. A simple pickup loop, a magnetometer, or an axial
gradiometer with an oppositely wound compensation coil
further away from the head is most sensitive to source currents
a few centimeters away from the center of the loop. It is to be
noted that this kind of sensors yield correlated measurements
even 10 cm apart and, therefore, it is not straightforward to
infer the locations of the sources from sensor-level data
directly. More near-sighted planar gradiometers, with two
oppositely wound in-plane loops, pick up the maximum signal
directly above the source current and thus markedly facilitate
estimating the active sites from sensor-level data.
MEG signal frequencies range from DC to about 1 kHz,
with most activity below 100 Hz. Interesting high-frequency
signals, with significant contributions from axonal activity,
include, for example, auditory brainstem responses and the
about 600-Hz oscillatory somatosensory evoked fields.
The tiny MEG signals are easily contaminated by magnetic
interference from the environment (power lines, moving vehicles, elevators, stimulators, and response devices) and from the
subject (cardiac cycle, respiration, eye movements and blinks,
muscular activity, movement, and articulation). Environmental interference can be attenuated with a passive magnetic
shield, sometimes augmented with an active compensation
system. In addition, information from reference channels further away from the head and gradiometric configurations of
the pickup coils can help dampen the interference. Moreover,
http://dx.doi.org/10.1016/B978-0-12-397025-1.00012-9
117
118
INTRODUCTION TO ACQUISITION METHODS | Basic Principles of Magnetoencephalography
several computational methods can be applied to further

improve the signal-to-noise ratio and to isolate the brain signals of interest. For example, signal space separation (Taulu &
Simola, 2006) allows reliable MEG recordings even in patients
wearing implanted stimulators. Sources of some artifacts, for
example, of eye movements and blinks, can be explicitly
included in the source model so that their contribution can
be diminished.
activity from elsewhere. Beamformers can be implemented in

either time or frequency domain.
Importantly, even a focal current appears spatially distributed when analyzed with a distributed model (e.g., MNE),
whereas dipole modeling of a spatially distributed source current necessarily yields a focal source estimate. Still, many
users confusingly consider the distributed models more physiological than the current dipoles just because of their
appearance.
Finding the Sources
Four Decades of MEG Research
To identify the source currents in the brain, one first has to

know the position of the subjects head with respect to MEG
sensor array to align the MEG data with anatomical MRI. For
this purpose, a set of small head-position indicator coils can be
placed on the scalp and their locations measured by means of
magnetic fields they generate when a current is fed through
them. Head position can be tracked during the recording
for continuous compensation of head movements. In contrast
to fMRI, head movements in MEG do not induce false signals,
but they rather blur or spatially offset the estimated source
activity.
To infer the underlying brain activity, we need a solution to
the MEG inverse problem. We thus first need to determine the
appropriate elementary current source model and then compare the predictions of the model with the actually measured
signals; for the latter task, we need a solution to the forward
problem, that is, an analytic or numerical solution to Maxwells
equations to compute the magnetic field for a given elementary
source. Finally, since the MEG inverse problem does not
possess a unique solution, anatomically and physiologically
motivated constraints are needed, which lead to different
source estimation methods depending on the constraints
employed; see the discussion below and the review by Baillet
et al. (2001).
An appropriate and widely used source model for MEG is a
current dipole, a representation of the net effect of concerted
postsynaptic currents in a limited cortical area. For a small
number (<10) of such elementary equivalent sources, the
locations, orientations, and strengths can be uniquely determined and followed as a function of time. Typical dipole
strengths are 2100 nAm. In some cases, a single current dipole
is sufficient to explain the data, while a more complex pattern
of brain activity can be accounted for by modeling it as a
constellation of several current dipoles.
Another way of estimating the sources is to assume a distribution of a large number of current dipoles and to constrain
them to the cortical mantle. Such a distributed estimate has a
unique solution if, in addition to explaining the recorded MEG
signals, it is further required that, for example, the total power
(L2 norm) or total amplitude (L1 norm) is minimized. The
resulting estimates are often called minimum-norm or
minimum-current estimates (MNE/MCE), respectively.
The third popular approach is beamforming, which also
employs the current dipole as the elementary source model,
but now, the brain volume is scanned by a sequential application of a spatial filter that is optimized to pass activity from the
target location with unit gain while maximally suppressing
MEG started in the early 1970s with measurements of the

magnetic counterparts of signals already known in EEG to
demonstrate the feasibility and characteristics of the new
method. The move toward more integrative brain functions
was facilitated by improved instrumentation, more sophisticated data analysis methods, and the complementary use of
other imaging modalities, especially anatomical and functional MRI. The principal milestones of MEG during these
first four decades have been recently reviewed (Aine, 2010;
Hari & Salmelin, 2012).
In the 1980s, MEG was used to pinpoint the cortical generators of various evoked and event-related potentials and to
explore the functional organization of sensory projection cortices. Further studies addressed the effects of interstimulus
interval (known in fMRI as repetition suppression), attention,
and stimulus changes.
Introduction of whole-scalp MEG systems in the 1990s
allowed studies of activation sequences and higher-level cognitive processes as data were acquired simultaneously from the
whole cortex. Now, it also became possible to study brain
rhythms, with a focus on frequencies from 5 to 40 Hz. The
vision- and attention-related parieto-occipital alpha-rhythm
and the movement- and touch-related Rolandic mu rhythm
continue to be applied in a multitude of MEG studies today.
Creative experimental setups help to broaden the applicability of MEG; for example, one can frequency-tag continuous
sensory stimuli and thereby follow them up to the cortex and
study their role in perception. Using this approach, we have
studied the brain correlates of the bistable percepts that subjects have when they view ambiguous figures (Parkkonen,
Andersson, Hamalainen, & Hari, 2008). When we superimposed dynamic noise on Rubins vase/faces image and updated
the noise at 12 Hz in the vase region and at 15 Hz in the face
region, these tags were clearly visible in the occipital MEG
signals and their relative strengths covaried with the alternating
vase/faces percepts. The modulation apparently reflected topdown effects to the early visual cortices.
The whole-scalp coverage of MEG devices also allows studies of functional connectivity, with strong emphasis on temporal aspects, for example, phase locking.
Several recent MEG applications involve simultaneous
peripheral measurements. Figure 1 shows an example where
cortexmuscle coherence (computed between MEG and surface electromyogram) has been used as a measure of cortical
outflow to muscles while the subject was maintaining isometric contraction and simultaneously observing the
experimenters transient finger pinches. These motor acts
Subject
119
Experimenter
Frequency (Hz)
40
1.3
Power
1.2
30
1.1
1
20
0.9
0.8
10
0.7
0.08
Frequency (Hz)
40
Coherence
0.06
30
0.04
20
0.02
10
Time
Time (s)
Figure 1 Experimental setup and results of an MEG study implying both activation and stabilization of the primary motor cortex when the subject
observes transient motor acts of another person. Left: Subject is keeping steady isomeric contraction against a force transducer while his brain activity is
recorded with whole-scalp MEG. He observes the experimenter (middle panel) to perform intermittently phasic pinches against a similar force
transducer; only the experimenters hand is visible. Right panels show examples of the results: Group-level (N 9) brain map (top) implicates activation
in the sensorimotor cortex; timefrequency map of relative MEG power (middle) implies activation of the primary motor cortex at frequencies of
up to 18 Hz, whereas the coherence map (bottom) implies a transient stabilization of the motor cortex around 20 Hz. Modified from Hari, R.,
Bourguignon, M., Piitulainen, H., Smeds, E., De Tie`ge, X., & Jousmaki, V. (2014). Human primary motor cortex is both activated and stabilized during
observation of other persons phasic motor actions. Philosophical Transactions of the Royal Society B, 369, 20130171, with permission.
activated the viewers primary motor cortex, evidenced by suppression of MEG power, as demonstrated earlier, but at the
same time as a novel finding cortexmuscle coherence
increased at slightly higher frequencies, around 20 Hz. Thus,
the seen actions both activate and suppress neurons in the
primary motor cortex, but at different frequency bands (Hari
et al., 2014). The stabilization of the motor cortex, as indicated by the transiently increased cortexmuscle coherence,
might reflect prevention of automatic imitation of the
observed movements.
One exciting novel direction is decoding, or multivariate
pattern classification, of brain activity using machine-learning
algorithms; such techniques have successfully been used on
static fMRI activation patterns. Due to its high temporal resolution, MEG readily allows time-resolved decoding, which
can be applied, for example, to estimate when a certain feature
of the stimulus has been analyzed in the brain (Cichy,
Pantazis, & Oliva, 2014; Ramkumar, Jas, Pannasch, Hari, &
Parkkonen, 2013). In addition, similar techniques can be useful in characterizing cortical processing of naturalistic stimuli
(Kauppi, Parkkonen, Hari, & Hyvarinen, 2013; Koskinen
et al., 2013).
Altogether, these new data-driven approaches are changing
the view of how brain imaging can be used to address neuroscientific questions. Decoding results also show that MEG
signals contain much more information than we currently
extract and interpret. In the future, decoding might be applied
to the very complex MEG data sets from two simultaneously

recorded, interacting subjects (Baess et al., 2012).
Future Prospects
With its good temporal resolution and clear advantages over
EEG, MEG is gaining a well-established role in human neuroscience, bringing the much-needed temporal aspect to brain
imaging: more than 150 centers globally are currently using
whole-scalp MEG. Extremely intensive research focuses on
brain rhythms, their modulations, and functional connectivity,
in both healthy and diseased individuals. Accordingly,
Buzsaki, Logothetis, and Singer (2013) considered the study
of brain rhythms to be among the largest growing fields in
systems neuroscience, mainly because of the crucial importance of accurate timing in brain function. The frequencies
and temporal characteristic of brain rhythms are surprisingly
similar in species with very different brain sizes (Buzsaki et al.,
2013), emphasizing their evolutionary importance.
The established clinical applications of MEG include preoperative localization of eloquent brain areas and epileptic
foci. Emerging clinical applications include follow-up during
stroke recovery. Importantly, the modified vasomotor control
in stroke does not as such affect MEG signals, whereas it alters
the hemodynamic fMRI responses (Forss et al., 2012; Rossini
et al., 2004). Clinical research of chronic pain may benefit
120
from the possibility to differentiate between cortical responses

to selective stimulation of the slow- and fast-conducting pain
afferents (for a review, see Kakigi, Inui, & Tamura, 2005). One
rapidly growing area of study is development: brain maturation is reflected in the frequency content and distribution of
the spontaneous MEG/EEG brain rhythms and in the time lags
and shapes of evoked responses.
Multimodal brain imaging is advancing, but it is still
unclear which of the multiple MEG/EEG features best correspond to BOLD fMRI. Both similarities and differences
between the methods are interesting from the neuroscience
point of view.
MEG has departed from physics laboratories and now has
an established role in human brain imaging: no other noninvasive technique allows monitoring cortical events at the
speed they occur and at a reasonably good spatial resolution.
These features, combined with the rapid development of
analysis approaches and experimental settings, have enabled
neuroscientists and clinicians to develop plausible neurophysiological models of perception, cognition, and action and to
understand how and when different neural systems interact in
both healthy and diseased individuals.
Acknowledgments
This work has been supported by the Academy of Finland
(Grant No. 131483 and No. 263800), European Research
Council (Advanced Grant No. 232946), the European Union
Seventh Framework Programme (FP7/20072013) under
grant agreement no. 604102 (Human Brain Project), and the
National Institutes of Health (Grant No. 5P41EB015896 and
No. 2R01EB009048).

Anatomical MRI for Human Brain Morphometry; Basic Principles of
Electroencephalography; fMRI at High Magnetic Field: Spatial
Resolution Limits and Applications; INTRODUCTION TO ANATOMY
AND PHYSIOLOGY: Anatomy and Physiology of the Mirror Neuron
System; Auditory Cortex; Brain Sex Differences; Cytoarchitecture and
Maps of the Human Cerebral Cortex; Development of Structural and
Functional Connectivity; Functional Connectivity; Functional
Organization of the Primary Visual Cortex; Genoarchitectonic Brain
Maps; Motor Cortex; Somatosensory Cortex; The Resting-State
Physiology of the Human Cerebral Cortex; Topographic Layout of
Monkey Extrastriate Visual Cortex; Vestibular Cortex; INTRODUCTION
TO CLINICAL BRAIN MAPPING: Developmental Brain Atlases;
Disorders of Audition; Disorders of Language; Hemodynamic and
Metabolic Disturbances in Acute Cerebral Infarction; Imaging Genetics
of Neuropsychiatric Disease; Language; Limbic to Motor Interactions
during Social Perception; Mapping Neurobiological Alterations in
Obsessive-Compulsive Disorder; Neuropsychiatry; Pain Syndromes;
Presurgical Assessment for Epilepsy Surgery; Recovery and
Rehabilitation Poststroke; Schizophrenia; Temporal Lobe Epilepsy;
INTRODUCTION TO COGNITIVE NEUROSCIENCE: Bilingualism;
Imaging Studies of Reading and Reading Disability; Memory Attribution
and Cognitive Control; Music; Naming; Reading; Salience/Bottom-Up
Attention; Semantic Processing; Speech Perception; Speech
Production; Substantia Nigra; INTRODUCTION TO METHODS AND

MODELING: Computing Brain Change over Time; Diffusion Tensor
Imaging; Distributed Bayesian Inversion of MEG/EEG Models; Dynamic
Causal Models for Human Electrophysiology: EEG, MEG, and LFPs;
Effective Connectivity; Forward Models for EEG/MEG; Granger
Causality; Image Reconstruction in MRI; Methodological Issues in fMRI
Functional Connectivity and Network Analysis; Modeling Brain Growth
and Development; Neural Mass Models; Probability Distribution
Functions in Diffusion MRI; Resting-State Functional Connectivity; The
General Linear Model; INTRODUCTION TO SOCIAL COGNITIVE
NEUROSCIENCE: Action Perception and the Decoding of Complex
Behavior; Biological Motion; Body Perception; Cultural Neuroscience;
Dual-Process Theories in Social Cognitive Neuroscience; Face
Perception: Extracting Social Information from Faces: The Role of Static
and Dynamic Face Information; Mindfulness: Mechanism and
Application; The Neural Correlates of Social Cognition and Social
Interaction; The Use of Brain Imaging to Investigate the Human Mirror
Neuron System; INTRODUCTION TO SYSTEMS: Action
Understanding; Cortical Action Representations; Early Auditory
Processing; Face Perception; Multisensory Integration and Audiovisual
Speech Perception; Naming; Neural Correlates of Motor Deficits in
Young Patients with Traumatic Brain Injury; Pain: Acute and Chronic;
Somatosensory Processing; Speech Sounds; Visuomotor Integration;
Visuospatial Attention.
References
Aine, C. J. (2010). Highlights of 40 years of SQUID-based brain research and clinical
applications. In: S. Supek & A. Susak (Eds.), Advances in Biomagnetism,
BIOMAG2010. IFMBE Proceedings. (vol. 28, pp. 934). Berlin: Springer. ISBN
978-3-642-12197-5.
Baillet, S., Mosher, J., & Leahy, R. (2001). Electromagnetic brain mapping. IEEE Signal
Processing Magazine, 18, 1430.
Baess, P., Zhdanov, A., Mandel, A., Parkkonen, L., Hirvenkari, L., Makela, J. P., et al.
(2012). MEG dual scanning: A procedure to study interacting humans. Frontiers in
Human Neuroscience, 6, Article 83.
Buzsaki, G., Logothetis, N., & Singer, W. (2013). Scaling brain size, keeping timing:
Evolutionary preservation of brain rhythms. Neuron, 80, 751764.
Cichy, R. M., Pantazis, D., & Oliva, A. (2014). Resolving human object recognition in
space and time. Nature Neuroscience, 17, 455462.
Del Gratta, C., Pizzella, V., Torquati, K., & Romani, G. L. (1999). New trends in
magnetoencephalography. Electroencephalography and Clinical Neurophysiology,
50, 5973.
Forss, N., Mustanoja, S., Roiha, K., Kirveskari, E., Makela, J. P., Salonen, O., et al.
(2012). Activation in parietal operculum parallels motor recovery in stroke. Human
Brain Mapping, 33, 534541.
Hamalainen, M., & Hari, R. (2002). Magnetoencephalographic characterization of
dynamic brain activation: Basic principles, and methods of data collection and
source analysis. In A. Toga, & J. Mazziotta (Eds.), Brain Mapping: The Methods.
(2nd ed.). Amsterdam: Academic Press.
Hansen, P. C., Kringelbach, M. L., & Salmelin, R. (Eds.). (2010). MEG. An Introduction
to Methods. New York: Oxford University Press.
Hari, R. (2011). Magnetoencephalography: Methods and applications. In D. L.
Schomer, & F. H. Lopes Da Silva (Eds.), Niedermeyers Electroencephalography:
Basic Principles, Clinical Applications, and Related Fields, (6th ed.). New York:
Lippincott Williams & Wilkins.
Hari, R., Bourguignon, M., Piitulainen, H., Smeds, E., De Tie`ge, X., & Jousmaki, V.
(2014). Human primary motor cortex is both activated and stabilized during
observation of other persons phasic motor actions. Philosophical Transactions of
the Royal Society B, 369, 20130171.
Hari, R., Parkkonen, L., & Nangini, C. (2010). The brain in time: Insights from
neuromagnetic recordings. Annals of the New York Academy of Science, 1191,
89109.
Hari, R., & Salmelin, R. (2012). Magnetoencephalography: From SQUIDs to
neuroscience. Neuroimage 20th anniversary special edition. NeuroImage, 61,
386396.

Kakigi, R., Inui, K., & Tamura, Y. (2005). Electrophysiological studies on human pain
perception. Clinical Neurophysiology, 116, 743763.
Kauppi, J. P., Parkkonen, L., Hari, R., & Hyvarinen, A. (2013). Decoding
magnetoencephalographic rhythmic activity using spectrospatial information.
Kominis, I. K., Kornack, T. W., Allred, J. C., & Romalis, M. V. (2003). A subfemtotesla
multichannel atomic magnetometer. Nature, 422, 569596.
Koskinen, M., Viinikanoja, J., Kurimo, M., Klami, A., Kaski, S., & Hari, R. (2013).
Identifying fragments of natural speech from the listeners MEG signals. Human
Pannetier-Lecoeur, M., Parkkonen, L., Sergeeva-Chollet, N., Polovy, H., Fermon, C., &
Fowley, C. (2011). Magnetocardiography with sensors based on giant
magnetoresistance. Applied Physics Letters, 98, 153705.
Parkkonen, L., Andersson, J., Hamalainen, M., & Hari, R. (2008). Early visual brain areas
reflect the percept of an ambiguous scene. Proceedings of the National Academy of
Sciences in the United States of America, 105, 2050020504.
121
Ramkumar, P., Jas, M., Pannasch, S., Hari, R., & Parkkonen, L. (2013). Feature-specific
information processing precedes concerted activation in human visual cortex.
Rossini, P. M., Altamura, C., Ferretti, A., Vernieri, F., Zappasodi, F., Caulo, M., et al.
(2004). Does cerebrovascular disease affect the coupling between neuronal activity
and local haemodynamics? Brain, 127, 99110.
Salmelin, R. (2007). Clinical neurophysiology of language: The MEG approach. Clinical
Neurophysiology, 118, 237254.
Taulu, S., & Simola, J. (2006). Spatiotemporal signal space separation method for
rejecting nearby interference in MEG measurements. Physics in Medicine and
Biology, 51, 17591768.
Vesanen, P. T., Nieminen, J. O., Zevenhoven, K. C., Dabek, J., Parkkonen, L. T.,
Zhdanov, A. V., et al. (2013). Hybrid ultra-low-field MRI and
magnetoencephalography system based on a commercial whole-head
neuromagnetometer. Magnetic Resonance in Medicine, 69, 17951804.
Molecular fMRI
A Hai and A Jasanoff, Massachusetts Institute of Technology, Cambridge, MA, USA
Glossary
Bloodbrain barrier (BBB) A system of tight junctions

between endothelial cells and adhering astrocytes that
prevents most blood-borne substances, including typical
MRI contrast agents, from entering the brain.
Chemical exchange saturation transfer (CEST) agent An
MRI contrast agent that acts via the CEST effect.
CEST effect A contrast mechanism that relies on the
exchange of a spectrally resolved labile proton pool with bulk
water protons. Saturating irradiation delivered at the nuclear
magnetic resonance (NMR) frequency of the labile protons
suppresses water proton signal at the bulk water frequency,
due to chemical exchange between the two proton
pools.
Introduction
The realization that the dynamics of cerebral blood flow can be
coupled to contrast in magnetic resonance imaging (MRI) scans
opened the door to using MRI for the noninvasive imaging
of neural activity-dependent blood flow changes in the brain
(Belliveau et al., 1990, 1991; Ogawa, Lee, Kay, & Tank, 1990;
Ogawa et al., 1992). This has transformed the fields of cognitive
neuroscience and clinical neurology and has given rise to what
are now the most prominent techniques to explore brain activation noninvasively, collectively known as functional magnetic resonance imaging (fMRI). Because conventional fMRI
signals arise from cerebral hemodynamic processes, however,
they provide only an indirect readout of neuronal activity
(Logothetis & Wandell, 2004). Hemodynamic changes arise
from a complex interplay of chemical signaling pathways that
originate in both neurons and glia (Iadecola, 2004; Iadecola &
Nedergaard, 2007). Hemodynamic signals therefore do not
permit the discrimination of neural activity components associated with different cell types, neurotransmitters, or intracellular pathways; they also display nonlinear and sometimes
sluggish dynamics with respect to neural signals.
In recent years, there have been growing attempts to combine MRI with molecular probes that allow monitoring of
neurophysiological processes at molecular and cellular levels.
Functional imaging with such probes (molecular fMRI) can
provide far greater specificity than hemodynamic imaging and
also potentially superior spatial and temporal resolution.
Molecular imaging with MRI is far less well developed as an
approach, compared with optical imaging techniques or positron emission tomography (PET). In particular, MRI probes are
less sensitively detected than either optical or PET probes
(Weissleder & Pittet, 2008). Compared with optical imaging,
however, molecular fMRI offers far greater spatial coverage and
depth penetration into the tissue. Compared with PET molecular imaging (reviewed in this volume), MRI offers far better
Heteronuclear agent An MRI molecular imaging probe that

incorporates NMR-detectable atoms other than protons and
can be imaged by dedicated MRI methods.
Hyperpolarization Any of several techniques for boosting
the polarization of a spin population beyond the level
normally achieved at thermal equilibrium in the field of an
NMR or MRI instrument. Hyperpolarized substances can
sometimes be detected with great sensitivity by MRI.
T1 contrast agent An MRI contrast agent that accelerates
longitudinal (T1) relaxation and is conventionally visualized
via signal enhancements in T1-weighted scans.
T2 contrast agent An MRI contrast agent that accelerates
transverse (T2) relaxation and is conventionally visualized
via signal decreases in T2-weighted scans.
spatial and temporal resolution, as well as the possibility of

dynamic sensing using MRI contrast agents that can be modulated by binding to target analytes in the brain. In the remainder of this article, we will introduce the basic mechanisms of
molecular MRI agents and discuss how they may be applied for
in vivo imaging of neurophysiological processes.
MRI Contrast Agents

The first MRI contrast agents were molecular compounds recognized for their ability to increase the nuclear magnetic relaxation rates of water molecules in the tissue. Because water
proton density and relaxation are the primary determinants
of conventional MRI signals, molecules that influence relaxation rates can modulate the MRI contrast by brightening or
darkening portions of the imaged tissue (Merbach, Helm, &
Toth, 2013). Such agents are now used in a wide variety of
applications, including as blood pool agents for enhancing
hemodynamic fMRI signals (Chen et al., 2001; Leite et al.,
2002; Mandeville et al., 2001). More generally, molecular
imaging agents for MRI can be divided into three main groups,
according to the mechanisms by which they operate: (1) agents
that increase the longitudinal (T1) or transverse (T2) spin relaxation rates, often termed T1 or T2 contrast agents; (2) agents
that employ the chemical exchange saturation transfer (CEST)
effect; and (3) heteronuclear imaging agents that contain
nuclei other than hydrogen (1H), such as carbon (13C) and
fluorine (19F), and can be detected using modified MRI equipment, but with a substantially lower signal due to their small
quantity in the tissue. Different contrast agents that bind to or
mimic compounds relevant to neurophysiology and brain
activity and that employ these mechanisms are being continually developed and tested. We will discuss each mechanism
and explore the main examples of its use for molecular
brain fMRI.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00013-0
123
124
INTRODUCTION TO ACQUISITION METHODS | Molecular fMRI
T1 and T2 fMRI Probes

Typical MRI contrast is determined by proton density and by
the so-called T1 and T2 relaxation times that reflect the dynamics of nuclear spin magnetization during an MRI scan. T1
describes the characteristic time required for return to equilibrium magnetization after an MRI pulse sequence; T1-weighted
scans are brighter in areas of shorter T1. T2 describes the duration of MRI signal persistence after a pulse sequence; T2weighted scans are darker in areas of shorter T2. Paramagnetic
species shorten T1 and T2 relaxation times and can therefore act
as contrast agents in T1- and T2-weighted scans (Figure 1).
Contrast agents usually linearly increase 1/T1 (R1) or 1/T2
(R2) with constants of proportionality r1 or r2, respectively.
Agents that exhibit r1 r2 are referred to as T1 agents and are
observed primarily through T1-weighted imaging; compounds
that have r1 r2 are referred to as T2 agents and are usually
observed using T2-weighted MRI. Given typical relaxivities,
most contrast agents must be applied at 10100 mM concentrations to produce detectable effects on MRI contrast in vivo.
T1 contrast agents usually contain paramagnetic metal ions

bound to a chelator that reduces the inherent toxicity of metal
ions in the tissue. Gadolinium (Gd3) ions are most frequently
incorporated into T1 contrast agents (Caravan, 2006), but
manganese and iron ions are also increasingly used. T2 contrast
agents usually contain crystalline metal compounds such as
particles of iron oxide ranging from several nanometers to
hundreds of nanometers in diameter (Vogl et al., 1996). Such
nanoparticles exhibit cooperative magnetic behavior and are
termed superparamagnetic; microscopic magnetic fields produced by superparamagnetic particles in an MRI scanner are
particularly potent sources of T2 relaxation.
For T1 or T2 agents to be used in functional imaging of the
brain, modulation of their contrast effects must be coupled to
neural activity in some way. One of the first successful attempts
at developing contrast agents that are coupled to neural activity
made use of the paramagnetic divalent ion manganese (Mn2)
as a tracer for monitoring neuronal calcium (Ca2) ions (Lin &
Koretsky, 1997). Calcium ions participate in neural signaling
events such as synaptic activity, neurotransmitter release, and
H O
H
H
O
%
25
N
N
O
O
N
O
Gd
O
O
O
25
H
H
O
H
(a)
% change
2
1
0
1
2
3
20
(b)
30
40
50
Time (min.)
60
70
(c)
Figure 1 T1 and T2 contrast agents for molecular (functional magnetic resonance imaging) fMRI. (a) T1 contrast agents most commonly consist of
paramagnetic atoms such as gadolinium, manganese, or iron, bound to a chelate. A canonical example, Gd3diethylenetriaminepentaacetic acid, is
shown at the left. Such contrast agents interact with water molecules (blue) either directly (dotted line) or through space to promote changes in
water proton T1 magnetic relaxation rate. A shortened T1 results in better recovery of the (magnetic resonance imaging) MRI signal (black traces at the
right) between repetitions of the pulse sequence (gray bars), thereby increasing the observed image intensity. (b) T2 agents, usually in the form of
polymer-coated superparamagnetic nanoparticles (green), induce magnetic field inhomogeneities (yellow) that promote relaxation of nearby diffusing
water protons (blue arrows) and a reduction of the MRI signal observed after each repetition of the pulse sequence (right panel). (c) A proteinbased contrast agent derived from the heme domain of the bacterial cytochrome P450-BM3 binds the neurotransmitter dopamine with an 80% change
in T1 relaxivity in vivo (Shapiro et al., 2010). Shown in the upper left panel is a coronal slice of a rat brain injected with the dopamine-sensing agent
with (orange circle) and without (blue circle) equimolar dopamine. The upper right panel shows color-coded signal change through the injection
of the agent; because the contrast agent turns off in the presence of dopamine, the coinjection region shows little signal change while the sensor-only
region shows a 25% signal increase. The bottom panel shows a molecular fMRI measurement made using the sensor during three pulses of
potassium stimulation (gray bars) in intracranially injected rat striatum. The snapshots above show signal variation in the injected region over one
stimulus cycle. The green trace shows the time course of significantly modulated voxels in the images. Reprinted from Jasanoff, A. (2007). MRI contrast
agents for functional molecular imaging of brain activity. Current Opinion in Neurobiology, 17, 593600, with permission from Elsevier,
Copyright (2007).

electric signaling in the form of dendritic spikes, and their
abundance in neural tissue poses an advantage for a mimetic
contrast agent. Manganese can enter the cell using the same
voltage-gated Ca2 channels through which calcium ions pass
(Meiri & Rahamimo, 1972; Narita, Kawasaki, & Kita, 1990).
These data show that manganese accumulates in active cells and
slowly washes out (on the order of days) and thus acts as a T1weighted MRI label for neural activity (Lin & Koretsky, 1997)
and an agent for enhancing contrast dependent on neural
architecture in the brain (Aoki, Wu, Silva, Lynch, & Koretsky,
2004; Pautler, Silva, & Koretsky, 1998; Silva et al., 2008).
Further efforts to create calcium-sensitive T1 contrast agents
made use of the calcium chelators 1,2-bis-(O-aminophenoxy)
ethane-N,N,N,N-tetraacetic acid (BAPTA) (Li, Fraser, &
Meade, 1999) and ethylene glycol tetraacetic acid (Angelovski
et al., 2008) covalently conjugated to derivatives of the paramagnetic gadolinium (Gd3)-1,4,7,10-tetraazacyclododecane1,4,7,10-tetraacetic acid (Gd-DOTA) complex. These agents
show changes in relaxivity in response to physiologically relevant Ca2 concentrations in vitro.
Other endogenous metal ions such as copper and zinc also
influence neural function and processes of neuropathology
(Que, Domaille, & Chang, 2008), albeit not as ubiquitously
as calcium. In particular, mobile zinc ions are coreleased
with glutamate in some brain regions and may play a part
in regulating synaptic plasticity. Zinc-binding contrast agents
have been formed by combining paramagnetic chelating
moieties with zinc-binding motifs such as N,N,N0 ,N0 -tetrakis(2pyridylmethyl)ethylenediamine (Hanaoka et al., 2002), dipicolylamine (DPA) (Esqueda et al., 2009; Zhang, Lovejoy, Jasanoff,
& Lippard, 2007), and 2,20 -azanediyldiacetate (Major, Parigi,
Luchinat, & Meade, 2007). Gadolinium-based zinc sensors
derived from these platforms have been shown to undergo
two- to threefold changes in r1 and to allow in vitro detection of
physiologically relevant Zn2 concentrations as low as 30 mM. A
manganese porphyrin-DPA conjugate displays more modest
zinc-dependent r1 changes (Zhang et al., 2007) but was shown
to undergo Zn2-dependent uptake by cells and to provide
preferential contrast enhancement of hippocampal neurons
in vivo (Lee et al., 2010), possibly reflecting enhanced zinc content of these cells. A Gd3 chelator fused to a copper recognition
motif has been demonstrated to respond to copper by modulating its T1 relaxivity in vitro (Que & Chang, 2006). Disrupted
copper homeostasis is associated with Alzheimers disease
and amyloid accumulation (Squitti & Polimanti, 2013), though
a role for copper in normal neural signaling processes has not
been established.
Combining superparamagnetic iron oxide (SPIO) nanoparticles with neurophysiologically relevant sensing domains can
actuate T2 relaxivity changes suitable for functional imaging. A
prominent application of this principle to calcium sensing
made use of two groups of SPIO nanoparticles conjugated to
the calcium-sensing protein calmodulin (CaM) and to a
Ca4CaM-binding peptide (RS20) (Atanasijevic, Shusteff, Fam,
& Jasanoff, 2006). In the presence of calcium, the CaM and
RS20-functionalized SPIO nanoparticles interact and cause
aggregation of the particles and a change in T2 relaxivity with
a calcium sensitivity of 1 mM in vitro. Another example of iron
oxide-based T2 contrast agent uses intraventricularly injected
microscale iron oxide particles, which are spontaneously taken
125
up by neural progenitor cells in the brain in vivo (Sumner,

Shapiro, Maric, Conroy, & Koretsky, 2009). Although this
technique does not allow monitoring of neural signaling per
se, it was shown to allow tracking of migrating cells that
participate in the maintenance and plasticity of neural circuitry
in the forebrain.
More recent efforts make use of protein-based contrast
agents, which can act as genetically encoded MRI sensors suitable for biosynthesis or expression in genetically modified subjects (Matsumoto & Jasanoff, 2013). One family of protein
molecular imaging agents was formed using directed in vitro
evolution of an iron-containing protein, derived from the heme
domain of the bacterial cytochrome P450-BM3, to bind the
neurotransmitters dopamine (Shapiro et al., 2010) and serotonin (Brustad et al., 2012). In the resulting probes, dopamine
binding to a site near the proteins paramagnetic heme iron
results in a drop in MRI signal due to reduced access of water
protons to the iron and reduced T1 relaxivity in the presence of
the dopamine at concentrations of several micromolar. This
dopamine sensor was shown to detect neural activity elicited
by potassium stimulation in live rat brains (Figure 1(c)).
Another series of studies demonstrated that a genetically
expressed nanoparticle contrast agent formed from the iron
storage protein ferritin could act as an endogenously expressed
contrast agent in virally transduced (Genove, DeMarco, Xu,
Goins, & Ahrens, 2005) or transgenic (Cohen, Dafni, Meir,
Harmelin, & Neeman, 2005) animals. A sensor for neuronal
kinase activity was constructed from genetically engineered
ferritins (Shapiro, Szablowski, Langer, & Jasanoff, 2009) and
characterized in vitro, suggesting long-term prospects for engineering functional imaging reporters from these species. Additional MRI gene reporting strategies have been proposed based
on paramagnetic metal transporters (Gruppi et al., 2012;
Zurkiya, Chan, & Hu, 2008) or by combining the expression
of a reporter enzyme with a synthetic MRI contrast agent substrate (Hsieh & Jasanoff, 2012). One of the earliest such
attempts combined the expression of the well-known bgalactosidase enzyme with a responsive T1 contrast agent that
enabled reporter detection in frog embryos (Louie et al., 2000).
CEST Agents
A different group of MRI contrast agents makes use of compounds that can exchange protons with surrounding water molecules in what is termed proton CEST (Ward, Aletras, & Balaban,
2000). In this modality, chemicals containing exchangeable protons with resonance frequencies that are well resolved from
protons in bulk water are imaged using a specialized MRI pulse
sequence (Figure 2). In the CEST pulse sequence, strong
saturating radiofrequency irradiation is delivered at the resonance frequency of the exchanging protons; this suppresses their
magnetization and detectability by MRI. Because the saturated
protons are in exchange with water protons that give rise to most
of the MRI contrast, the overall MRI signal in proximity to the
CEST agent is also reduced. The proton exchange rate, frequency
offset between bound and bulk water protons, intensity of
saturation irradiation, and relaxation rates all combine to determine the magnitude of resulting CEST contrast (Woessner,
Zhang, Merritt, & Sherry, 2005; Zhou, Wilson, Sun, Klaus, &
126
O H
H
O
H O
COOH
HO
NH2
(a)
24
14
4
(b)
Figure 2 Chemical exchange saturation transfer (CEST) agents are

chemicals that contain exchangeable protons with resonance frequencies
that are well resolved from protons in bulk water. (a) An example shown
is the indole nitrogen proton (indigo) of 5-hydroxytryptophan. The
nuclear magnetic resonance spectrum of this compound in solution is
schematized by the gray trace at the bottom left, where resonances of the
CEST agent protons and water protons are indicated by indigo and cyan
arrowheads, respectively. The right panel shows the CEST pulse
sequence, in which strong saturating radiofrequency irradiation (red) is
delivered at the resonance frequency of the exchanging protons. Because
the saturated protons are in exchange with water protons that give rise
to most of the MRI contrast, the overall MRI signal due to water protons
in proximity to the CEST agent is also reduced (cyan arrowheads).
(b) The CEST effect can be used to detect proton transfer between the
amine group of the ubiquitous neurotransmitter glutamate and nearby
water molecules (Cai et al., 2012). This work demonstrated that cerebral
artery occlusion stroke in rat brain generates a detectable increase of
the glutamate CEST signal. Shown are maps acquired 1 h (left) and 4.5 h
(right) after the induction of stroke. Areas ipsilateral and contralateral
to the stroke are indicated by white and black rectangles, respectively.
The color scale indicates the magnitude of contrast due to CEST probespecific radiofrequency saturation, with respect to control irradiation.
Reprinted from Cai, K. J., et al., (2012). Magnetic resonance imaging of
glutamate. Nature Medicine, 18, 302306, with permission from
Macmillan Publishers Ltd, Copyright 2012.
van Zijl, 2004). Because the selectivity with which CEST effects
can be experimentally manipulated using the MRI pulse
sequence, CEST contrast can be switched on and off. On the
other hand, CEST contrast is typically weaker than relaxationbased MRI contrast, and millimolar concentrations of exchangeable protons are typically required to produce observable effects.
CEST contrast and CEST agents have been applied to detect
a variety of phenomena relevant to functional brain imaging.
Subtle changes in brain pH are associated with neural activity
(Chesler, 2003), and because pH changes relate closely to
proton exchange, they are therefore particularly suitable for
detection by CEST agents. CEST contrast arising from saturation of intrinsic exchanging amide protons has been used to
measure pH in vivo, and pH changes of roughly 0.5 units
associated with ischemic stroke in rat brains could be imaged
(Zhou, Payen, Wilson, Traystman, & van Zijl, 2003). Sensitivity

of this method or of related T1 contrast-based molecular imaging approaches (Raghunand, Zhang, Sherry, & Gillies, 2002)
would need to be improved in order to detect normal brain
activity via pH.
An effort to detect gene expression by CEST made use of a
genetically expressed lysine-rich protein (LRP) reporter of
which the proton exchange between its amide protons and
water molecules is detected by CEST MRI in rat brains (Gilad
et al., 2007). Although the signal changes produced by the LRP
were small and required long imaging time (>30 min), they are
potentially less prone to artifacts than MRI changes reported by
relaxation-based agents such as ferritin, and they do not require
slow and potentially toxic accumulation of metal ions. Another
recent CEST approach enabled specific detection of proton
transfer between the amine group of the ubiquitous neurotransmitter glutamate and water molecules (Cai et al., 2012). This
work demonstrated that cerebral artery occlusion in rat brain
generates a 100% increase of the glutamate CEST signal in the
appropriate frequency shift (Figure 2(b)). In addition, the
authors showed increase in CEST signal upon intravenous
injection of glutamate in a tumor model with bloodbrain
barrier (BBB) disruption. Although these experiments demonstrated molecular MRI of glutamate in rat brain under extreme
physiological conditions, a follow-up study (Cai et al., 2013)
also showed the ability of the technique to generate a static map
of glutamate in healthy human brains similar to PET studies
(Ametamey et al., 2007), but without the need for exogenous
agents.
Molecular imaging using CEST MRI in the brain suffers from
signal reduction due to the magnetization transfer effect from
other endogenous molecules. A variation of CEST MRI termed
PARACEST uses paramagnetic lanthanides for significantly
higher concentration delectability, in the nanomolar range
(Zhang, Merritt, Woessner, Lenkinski, & Sherry, 2003). Initial
attempts to use a lanthanide-based agent in the form of a thulium (Tm3) chelate bound to the ligand DOTAM-glycine-lysine
for brain imaging show uptake of the agent in mouse brain
tumor assay (Li et al., 2011). Although this study has not
shown sensitivity in the nanomolar range, it nonetheless opens
the possibility for a more sensitive family of contrast agents for
brain MRI.
Heteronuclear Probes
Molecular imaging agents containing nuclei other than protons, such as carbon (13C) and fluorine (19F), may be imaged
using modified MRI hardware specifically tuned to the resonance frequencies of these nuclei. The MRI signal arising from
such heteronuclear probes is considerably weaker than that of
endogenous water protons because of the much lower abundance of heteronuclear species, compounded by the intrinsically lower sensitivity of MRI techniques to nuclei other than
hydrogen. A long history of magnetic resonance spectroscopy
and spectroscopic imaging has enabled the detection of
13
C-containing metabolites related to brain function. Using
these approaches, it has been possible to perform functional
studies that detect the effect of neural activity on glutamate
metabolism (Rothman et al., 1992; Sibson et al., 1997), albeit

with low temporal resolution due to the insensitivity of MRI to
endogenous 13C. A strategy for breaking past this sensitivity
limit makes use of a technique called dynamic nuclear polarization (DNP) to enhance the polarization, and hence the
detectability, of 13C species beyond what can be achieved
using conventional MRI (Ardenkjaer-Larsen et al., 2003;
Golman, int Zandt, & Thaning, 2006). DNP and related hyperpolarization techniques are implemented outside the MRI
scanner, and hyperpolarized substances are then injected and
imaged in the subject. Because polarization decays back to
thermal equilibrium levels by T1 relaxation processes, manipulation and imaging using hyperpolarized agents must be performed rapidly, within a few minutes for 13C. In the work of
Golman et al. (2006), 13C-labeled pyruvate was hyperpolarized and injected in vivo. Using spectroscopic MRI techniques,
the study demonstrates simultaneous maps of pyruvate, lactate, and alanine with millimeter spatial resolution, enabling
measurements of metabolic turnover rates over tens of
seconds. Similar approaches, perhaps in conjunction with
efforts to polarize substances more specifically related to neurochemistry (Allouche-Arnon, Lerche, Karlsson, Lenkinski, &
Katz-Brull, 2011; Allouche-Arnon et al., 2011), may eventually
prove useful for molecular fMRI in the nervous system. An
additional possible avenue involves the use of silicon nanoparticles as hyperpolarizable contrast agents; these nanoparticles display relaxation times on the order of minutes to hours
and at room temperature (Aptekar et al., 2009), allowing
imaging to take place over a much longer period of time than
with 13C-labeled agents. This advantage, together with the
ability to easily functionalize silicon with biologically relevant
molecules, allows for a myriad of potential applications.
Efforts to image 19F-labeled compounds benefit from the
low background of 19F in biological subjects and the relative
sensitivity with which fluorinated compounds can be detected
by MRI, 90% that of protons, even without hyperpolarization. Imaging of 19F-labeled amyloidophilic compounds
can be used for the in vivo detection of amyloid beta plaques
in mouse models of Alzheimers disease with submillimeter
resolution and imaging times of a couple of hours (Higuchi
et al., 2005). Another 19F imaging study makes use of a
Gdpeptide19F complex whereby the 19F MRI signal is attenuated by an intramolecular Gd3 chelate moiety and is modulated by the activity of proteases that cleave the probe
(Mizukami et al., 2008). Both of these studies open the door
for functional imaging of neuropathologic pathways using
fluorinated probes. An additional and recent study combining
heteronuclear imaging of 19F with CEST exploits the chemical
shift change of a 5,50 -difluoro derivative of BAPTA upon binding to Ca2 ions for the detection of Ca2 concentrations as
low as 0.5 mM (Bar-Shir et al., 2013). Combining 19F MRI
detection with high spatial and temporal resolution is challenging, but functional measurements may still be possible in
cases where appropriate trade-offs can be made.
Challenges for Molecular fMRI of the Brain

The delivery of contrast agents into the brain is problematic
due to the existence of the bloodbrain barrier. This system of
tight junctions between the vascular endothelial cells and
127
adhering astrocytes not only prevents potentially harmful substances in the bloodstream from entering the brain but also
blocks therapeutics and imaging agents. Strategies to transiently
disrupt the BBB include the administration of a hyperosmotic
shock by intravascular injection of a hypertonic substance such
as 25% mannitol (Neuwelt & Rapoport, 1984) and more
recently by the application of focused or unfocused ultrasound,
in which the BBB is disrupted by sonic pressure waves amplified
by intravascular gas-filled microbubbles (Vykhodtseva,
McDannold, & Hynynen, 2008). Both osmotic shock and ultrasound methods have been used to deliver T1 and T2 agents in
sufficient quantities for MRI observation. Other trans-BBB
delivery methods use endogenous transport mechanisms
involving transferrin and insulin receptors (Pardridge, 2012)
and cell-penetrating peptides (Santra et al., 2004) to deliver
agents across the BBB, but these may not be effective enough
for the delivery of MRI contrast agents at useful doses.
The requirement for exogenous delivery of contrast agents is
a substantial drawback of many molecular fMRI approaches,
compared with hemodynamic fMRI. A significant advantage of
molecular techniques is that they can in principle achieve
much higher spatial and temporal resolution, however,
because they are not limited by the spatiotemporal properties
of blood flow changes. The ultimate spatial resolution of MRI
is usually placed in the 110 mm range, limited by the diffusion
of water molecules in the tissue; in practice, this resolution is
rarely achieved, however, because of the long measuring times
required for the buildup of adequate signal-to-noise ratio,
particularly in vivo. Current molecular MRI techniques can
provide spatial resolution on the order of 100 mm and temporal resolution on the order of seconds, but with trade-offs
between the two. Substantial efforts are needed to move
toward millisecond timescales and micrometer spatial features
most relevant to neuronal activity and structure. Gains are
most likely to be made by improving the potency of MRI
contrast agents, going to higher MRI magnetic fields, and optimizing pulse sequences for molecular applications. Molecular
fMRI techniques are still in their infancy, but offer one of few
paths toward truly noninvasive whole-brain analysis of neural
activity at molecular and cellular levels, particularly if technological developments continue along their present course.

Contrast Agents in Functional Magnetic Resonance Imaging; Obtaining
Quantitative Information from fMRI; PET; Optical imaging.
References
Allouche-Arnon, H., Lerche, M. H., Karlsson, M., Lenkinski, R. E., & Katz-Brull, R.
(2011). Deuteration of a molecular probe for DNP hyperpolarization A new
approach and validation for choline chloride. Contrast Media & Molecular Imaging,
6, 499506.
Allouche-Arnon, H., et al. (2011). A hyperpolarized choline molecular probe for
monitoring acetylcholine synthesis. Contrast Media & Molecular Imaging, 6,
139147.
Ametamey, S. M., et al. (2007). Human PET studies of metabotropic glutamate receptor
subtype 5 with C-11-ABP688. Journal of Nuclear Medicine, 48, 247252.
Angelovski, G., Fouskova, P., Mamedov, I., Canals, S., Toth, E., & Logothetis, N. K.
(2008). Smart magnetic resonance imaging agents that sense extracellular calcium
fluctuations. Chembiochem, 9, 17291734.
128
Aoki, I., Wu, Y. J.L, Silva, A. C., Lynch, R. M., & Koretsky, A. P. (2004). In vivo detection
of neuroarchitecture in the rodent brain using manganese-enhanced MRI.
Aptekar, J. W., et al. (2009). Silicon nanoparticles as hyperpolarized magnetic
resonance imaging agents. ACS Nano, 3, 40034008.
Ardenkjaer-Larsen, J. H., et al. (2003). Increase in signal-to-noise ratio of >10,000
times in liquid-state NMR. Proceedings of the National Academy of Sciences of the
Atanasijevic, T., Shusteff, M., Fam, P., & Jasanoff, A. (2006). Calcium-sensitive MRI
contrast agents based on superparamagnetic iron oxide nanoparticles and
calmodulin. Proceedings of the National Academy of Sciences of the United States
of America, 103, 1470714712.
Bar-Shir, A., et al. (2013). Metal ion sensing using ion chemical exchange saturation
transfer (19)F magnetic resonance imaging. Journal of the American Chemical
Society, 135, 1216412167.
Belliveau, J. W., et al. (1990). Functional cerebral imaging by susceptibility-contrast
NMR. Magnetic Resonance in Medicine, 14, 538546.
Belliveau, J. W., et al. (1991). Functional mapping of the human visual-cortex by
magnetic-resonance-imaging. Science, 254, 716719.
Brustad, E. M., et al. (2012). Structure-guided directed evolution of highly selective
p450-based magnetic resonance imaging sensors for dopamine and serotonin.
Journal of Molecular Biology, 422, 245262.
Cai, K. J., et al. (2012). Magnetic resonance imaging of glutamate. Nature Medicine, 18,
302306.
Cai, K., et al. (2013). Mapping glutamate in subcortical brain structures using
high-resolution GluCEST MRI NMR in Biomedicine, .
Caravan, P. (2006). Strategies for increasing the sensitivity of gadolinium based MRI
contrast agents. Chemical Society Reviews, 35, 512523.
Chen, Y. C.I, Mandeville, J. B., Nguyen, T. V., Talele, A., Cavagna, F., & Jenkins, B. G.
(2001). Improved mapping of pharmacologically induced neuronal activation using
the IRON technique with superparamagnetic blood pool agents. Journal of Magnetic
Chesler, M. (2003). Regulation and modulation of pH in the brain. Physiological
Reviews, 83, 11831221.
Cohen, B., Dafni, H., Meir, G., Harmelin, A., & Neeman, M. (2005). Ferritin as an
endogenous MRI reporter for noninvasive imaging of gene expression in C6 glioma
tumors. Neoplasia, 7, 109117.
Esqueda, A. C., et al. (2009). A new gadolinium-based MRI zinc sensor. Journal of the
American Chemical Society, 131, 1138711391.
Genove, G., DeMarco, U., Xu, H. Y., Goins, W. F., & Ahrens, E. T. (2005). A new
transgene reporter for in vivo magnetic resonance imaging. Nature Medicine, 11,
450454.
Gilad, A. A., et al. (2007). Artificial reporter gene providing MRI contrast based on
proton exchange. Nature Biotechnology, 25, 217219.
Golman, K., int Zandt, R., & Thaning, M. (2006). Real-time metabolic imaging.
103, 1127011275.
Gruppi, F., Liang, J., Bartelle, B. B., Royzen, M., Turnbull, D. H., & Canary, J. W. (2012).
Supramolecular metal displacement allows on-fluorescence analysis of manganese
(II) in living cells. Chemical Communications, 48, 1077810780.
Hanaoka, K., et al. (2002). Design and synthesis of a novel magnetic resonance imaging
contrast agent for selective sensing of zinc ion. Chemistry & Biology, 9,
10271032.
Higuchi, M., Iwata, N., Matsuba, Y., Sato, K., Sasamoto, K., & Saido, T. C. (2005). F-19
and H-1 MRI detection of amyloid beta plaques in vivo. Nature Neuroscience, 8,
527533.
Hsieh, V., & Jasanoff, A. (2012). Bioengineered probes for molecular magnetic
resonance imaging in the nervous system. ACS Chemical Neuroscience, 3,
593602.
Iadecola, C. (2004). Neurovascular regulation in the normal brain and in Alzheimers
disease. Nature Reviews. Neuroscience, 5, 347360.
Iadecola, C., & Nedergaard, M. (2007). Glial regulation of the cerebral microvasculature.
Nature Neuroscience, 10, 13691376.
Lee, T., Zhang, X.-A., Dhar, S., Faas, H., Lippard, S. J., & Jasanoff, A. (2010). In vivo
imaging with a cell-permeable porphyrin-based MRI contrast agent. Chemistry &
Biology, 17, 665673.
Leite, F. P., et al. (2002). Repeated fMRI using iron oxide contrast agent in awake,
behaving macaques at 3 Tesla. NeuroImage, 16, 283294.
Li, W. H., Fraser, S. E., & Meade, T. J. (1999). A calcium-sensitive magnetic resonance
imaging contrast agent. Journal of the American Chemical Society, 121, 14131414.
Li, A. X., et al. (2011). In vivo detection of MRI-PARACEST agents in mouse brain
tumors at 9.4 T. Magnetic Resonance in Medicine, 66, 6772.
Lin, Y. J., & Koretsky, A. P. (1997). Manganese ion enhances T-1-weighted MRI during
brain activation: An approach to direct imaging of brain function. Magnetic
Logothetis, N. K., & Wandell, B. A. (2004). Interpreting the BOLD signal. Annual Review
of Physiology, 66, 735769.
Louie, A. Y., et al. (2000). In vivo visualization of gene expression using magnetic
resonance imaging. Nature Biotechnology, 18, 321325.
Major, J. L., Parigi, G., Luchinat, C., & Meade, T. J. (2007). The synthesis and in vitro
testing of a zinc-activated MRI contrast agent. Proceedings of the National Academy
Mandeville, J. B., Jenkins, B. G., Kosofsky, B. E., Moskowitz, M. A., Rosen, B. R., &
Marota, J. J.A (2001). Regional sensitivity and coupling of BOLD and CBV changes
during stimulation of rat brain. Magnetic Resonance in Medicine, 45, 443447.
Matsumoto, Y., & Jasanoff, A. (2013). Metalloprotein-based MRI probes. FEBS Letters,
587, 10211029.
Meiri, U., & Rahamimo, R. (1972). Neuromuscular transmission Inhibition by
manganese ions. Science, 176, 308309.
Merbach, A. S., Helm, L., & Toth, E. (2013). The chemistry of contrast agents in medical
magnetic resonance imaging. Chichester, UK: Wiley.
Mizukami, S., et al. (2008). Paramagnetic relaxation-based F-19 MRI probe to detect
protease activity. Journal of the American Chemical Society, 130, 794795.
Narita, K., Kawasaki, F., & Kita, H. (1990). Mn and Mg influxes through Ca channels of
motor-nerve terminals are prevented by verapamil in frogs. Brain Research, 510,
289295.
Neuwelt, E. A., & Rapoport, S. I. (1984). Modification of the bloodbrain-barrier in the
chemotherapy of malignant brain-tumors. Federation Proceedings, 43, 214219.
Ogawa, S., Lee, T. M., Kay, A. R., & Tank, D. W. (1990). Brain magnetic-resonanceimaging with contrast dependent on blood oxygenation. Proceedings of the National
Ogawa, S., et al. (1992). Intrinsic signal changes accompanying sensory stimulation
Functional brain mapping with magnetic-resonance-imaging. Proceedings of the
Pardridge, W. M. (2012). Drug transport across the bloodbrain barrier. Journal of
Pautler, R. G., Silva, A. C., & Koretsky, A. P. (1998). In vivo neuronal tract tracing using
manganese-enhanced magnetic resonance imaging. Magnetic Resonance in
Medicine, 40, 740748.
Que, E. L., & Chang, C. J. (2006). A smart magnetic resonance contrast agent for
selective copper sensing. Journal of the American Chemical Society, 128,
1594215943.
Que, E. L., Domaille, D. W., & Chang, C. J. (2008). Metals in neurobiology: Probing
their chemistry and biology with molecular imaging. Chemical Reviews, 108,
15171549.
Raghunand, N., Zhang, S. R., Sherry, A. D., & Gillies, R. J. (2002). In vivo magnetic
resonance imaging of tissue pH using a novel pH-sensitive contrast agent,
GdDOTA-4AmP. Academic Radiology, 9, S481S483.
Rothman, D. L., et al. (1992). H-1 C-13 NMR measurements of 4-C-13 glutamate
turnover in human brain. Proceedings of the National Academy of Sciences of the
Santra, S., et al. (2004). TAT conjugated, FITC doped silica nanoparticles for
bioimaging applications. Chemical Communications, 28102811.
Shapiro, M. G., Szablowski, J. O., Langer, R., & Jasanoff, A. (2009). Protein
nanoparticles engineered to sense kinase activity in MRI. Journal of the American
Chemical Society, 131, 24842486.
Shapiro, M. G., et al. (2010). Directed evolution of a magnetic resonance imaging
contrast agent for noninvasive imaging of dopamine. Nature Biotechnology, 28,
264270.
Sibson, N. R., Dhankhar, A., Mason, G. F., Behar, K. L., Rothman, D. L., &
Shulman, R. G. (1997). In vivo C-13 NMR measurements of cerebral glutamine
synthesis as evidence for glutamate-glutamine cycling. Proceedings of the National
Silva, A. C., et al. (2008). Detection of cortical laminar architecture using manganeseenhanced MRI. Journal of Neuroscience Methods, 167, 246257.
Squitti, R., & Polimanti, R. (2013). Copper phenotype in Alzheimers disease: Dissecting
the pathway. American Journal of Neurodegenerative Disease, 2, 4656.
Sumner, J. P., Shapiro, E. M., Maric, D., Conroy, R., & Koretsky, A. P. (2009).
In vivo labeling of adult neural progenitors for MRI with micron sized
particles of iron oxide: Quantification of labeled cell phenotype. NeuroImage, 44,
671678.
Vogl, T. J., et al. (1996). Superparamagnetic iron oxide-enhanced versus gadoliniumenhanced MR imaging for differential diagnosis of focal liver lesions. Radiology,
198, 881887.

Vykhodtseva, N., McDannold, N., & Hynynen, K. (2008). Progress and problems in the
application of focused ultrasound for bloodbrain barrier disruption. Ultrasonics,
48, 279296.
Ward, K. M., Aletras, A. H., & Balaban, R. S. (2000). A new class of contrast agents for
MRI based on proton chemical exchange dependent saturation transfer (CEST).
Weissleder, R., & Pittet, M. J. (2008). Imaging in the era of molecular oncology. Nature,
452, 580589.
Woessner, D. E., Zhang, S. R., Merritt, M. E., & Sherry, A. D. (2005). Numerical solution
of the Bloch equations provides insights into the optimum design of PARACEST
agents for MRI. Magnetic Resonance in Medicine, 53, 790799.
Zhang, X. A., Lovejoy, K. S., Jasanoff, A., & Lippard, S. J. (2007). Water-soluble
porphyrins imaging platform for MM zinc sensing. Proceedings of the National
129
Zhang, S. R., Merritt, M., Woessner, D. E., Lenkinski, R. E., & Sherry, A. D. (2003).
PARACEST agents: Modulating MRI contrast via water proton exchange. Accounts
of Chemical Research, 36, 783790.
Zhou, J. Y., Payen, J. F., Wilson, D. A., Traystman, R. J., & van Zijl, P. C. M. (2003).
Using the amide proton signals of intracellular proteins and peptides to detect pH
effects in MRI. Nature Medicine, 9, 10851090.
Zhou, J. Y., Wilson, D. A., Sun, P. Z., Klaus, J. A., & van Zijl, P. C. M. (2004).
Quantitative description of proton exchange processes between water and
endogenous and exogenous agents for WEX, CEST, and APT experiments. Magnetic
Zurkiya, O., Chan, A. W.S, & Hu, X. (2008). MagA is sufficient for producing magnetic
nanoparticles in mammalian cells, making it an MRI reporter. Magnetic Resonance
in Medicine, 59, 12251231.
Pulse Sequence Dependence of the fMRI Signal

P Jezzard and PJ Koopmans, University of Oxford, Oxford, UK
Abbreviation
ASL
BOLD
CBF
CBV
EPI
FLASH
GE
PRESTO
Arterial spin labeling (CBF-weighted pulse

sequence)
Blood oxygenation level-dependent
Cerebral blood flow
Cerebral blood volume
Echo-planar imaging (pulse sequence)
Fast low-angle shot (pulse sequence)
Gradient echo
Principles of echo shifting with a train of
observations (pulse sequence)
Introduction
By far, the vast majority of functional MRI (fMRI) studies in the
literature have used the blood oxygenation level-dependent
(BOLD) contrast mechanism as their source of fMRI signal
and, by far, the most commonly used MRI pulse sequence
has been the gradient-echo (GE) version of the echo-planar
imaging (EPI) technique. For this reason, a substantial portion
of this article is dedicated to the GE-EPI sequence and its signal
dependency. However, other types of pulse sequence can be
used, and so some of the other flavors of fMRI sequence will
also be discussed. One prominent alternative is to use a spinecho (SE) refocusing pulse within the sequence, which alters
the sensitivity of the fMRI signal to intravascular versus extravascular signal and which also alters the size regime of blood
vessels to which the fMRI signal is most sensitive. However,
radically different types of MRI pulse sequence also exist, such
as those that report more specifically on changes in cerebral
blood volume (CBV) or those that report more explicitly on
cerebral blood flow (CBF). Even more exotic are approaches
that aim to probe changes in the diffusion coefficient of tissue
water as cells swell in response to metabolic activity or
approaches that aim to report more directly on neuronal currents via their associated magnetic field fluctuations.
BOLD fMRI Sequences

As mentioned in the preceding text, the majority of published
fMRI studies have used the BOLD contrast mechanism as
their source of image contrast. Ultimately, the BOLD signal is
sensitive to the local concentration of deoxyhemoglobin,
since this is more paramagnetic than oxyhemoglobin or
tissue (Pauling & Coryell, 1936). Additionally, the T2 value of
deoxyhemoglobin is shorter than oxyhemoglobin (Thulborn,
Waterton, Matthews, & Radda, 1982). For these reasons, it is
possible to use either a GE MRI pulse sequence or a SE
MRI pulse sequence to detect changes in the concentration
of deoxyhemoglobin in the tissue during neuronal activation.
RF
SE
T1
T2
T2*
TE
TR
VASO
Radio frequency
Spin echo
Longitudinal relaxation time constant
Transverse relaxation time constant
Transverse relaxation time constant, including
the effects of field inhomogeneities
Pulse sequence echo time
Pulse sequence repeat time
Vascular space occupancy (CBV-weighted pulse
sequence)
As is now well known, the amount of local deoxyhemoglobin

actually decreases in the normal brain during neuronal activity,
since increases in local blood flow delivery overcompensate for
the additional oxygen demand of the tissue. This implies that
for a GE or SE sequence, the signal intensity should increase
slightly in regions of the brain engaged in a functional task that
elevate local metabolism.
SE Versus GE
There is, however, a significant difference in the specific sensitivity of GE and SE sequences. The theory to explain this
(Boxerman, Hamberg, Rosen, & Weisskoff, 1995; Boxerman
et al., 1995; Kennan, Zhong, & Gore, 1994) builds on work
done originally to describe the biophysics of injectable exogenous (gadolinium-based) contrast agents to measure blood volume using the method of dynamic susceptibility contrast
imaging. Deoxyhemoglobin represents an analogous endogenous contrast agent to gadolinium, albeit with a lower paramagnetic susceptibility. Figure 1 shows a schematic representation of
the predicted change in relaxivity for the GE and SE signals as a
function of vessel size. It can be seen that at small vessel dimensions (in the range of capillaries), both the GE and SE signals
show a similar increase in relaxivity with increasing vessel size.
However, beyond the size scale of capillaries, the GE relaxivity
change continues to increase and remains sensitive to a wide
range of vessel sizes, whereas the SE signal reaches a peak in
relaxivity sensitivity and then falls off with increasing vessel size.
The origin of this effect lies in the interplay between the
diffusion of tissue water and the extent of the microscopic field
gradients surrounding the blood vessels. In the case of small
vessels (of the size scale of capillaries), the SE sequence does
not refocus the effects of dephasing of the extravascular water
spins that surround the vessels, since the diffusion distance of
water during the echo time (TE) of the pulse sequence is of a
similar scale to the extent of the field gradients. However, for
larger veins, the extent of the field gradients is much larger than
the diffusion distance of water during the TE time. Therefore, a SE
sequence will tend to refocus the signal from magnetic field
http://dx.doi.org/10.1016/B978-0-12-397025-1.00014-2
131
132
INTRODUCTION TO ACQUISITION METHODS | Pulse Sequence Dependence of the fMRI Signal

GE Sequences
4.0
Fast low-angle shot

Gradient echo
DR2, DR2* (s-1)
3.0
2.0
1.0
Spin echo
10
Vessel radius (mm)
100
Figure 1 Expected relaxivity changes in R2 (1/T2, relevant to spin-echo

sequences) and R2* (1/T2*, relevant to gradient-echo sequences) at
1.5 T for water spins surrounding vessels of different sizes containing
venous levels of deoxyhemoglobin. Dephasing of signal in the
extravascular field gradients leads to signal loss (increases relaxivity)
that is vessel-size-dependent. Inspired by Boxerman J.L., Hamberg L.M.,
Rosen B.R., & Weisskoff R.M. (1995). MR contrast due to intravascular
magnetic susceptibility perturbations. Magnetic Resonance in
Medicine, 34, 555566.
inhomogeneities, meaning that there is little fMRI signal from

extravascular spins that surround large vessels. Conversely, GE
sequences are unable to refocus the effects of magnetic field
inhomogeneity and so remain sensitive to changes in the field
gradients surrounding both large and small vessels. This has the
advantage for GE sequences that they offer a larger signal change,
but it does mean that they tend to suffer more from draining
vein artifacts where fMRI signals can be observed some distance
from the true site of neuronal activity. An extensive modeling
paper comparing the two approaches, based on a decades worth
of T2 and T2* reports at various field strengths, can be found in
Uludag, Mueller-Bierl, and Ugurbil (2009).
Field Strength Dependence

Another important parameter in the observed fMRI signal
behavior is its dependence on the static magnetic field strength.
At low magnetic fields (around 1.5 T), the combination of
blood T2 and T2*, versus the T2 and T2* of the surrounding
tissue, means that a substantial fraction of the fMRI signal is
predicted to arise from intravascular water, especially for GE
sequences. However, as the magnetic field strength is increased
(many sites now have access to 7 T scanners or even higher),
there is a gradual shift towards an fMRI signal that is dominated by extravascular signal (Gati, Menon, Ugurbil, & Rutt,
1997; Van der Zwaag et al., 2009). In practice, this results in a
preference for higher field strength for studies in which high
resolution is sought. Indeed, because of the different behavior
of the physiological noise dependency with field strength versus the thermal noise dependency with field strength, there
may be no sensitivity benefit to using 7 T scanners unless a
high spatial resolution regime is used where the physiological
noise dominates the thermal noise (Bodurka, Ye, Petridou,
Murphy, & Bandettini, 2007; Olman & Yacoub, 2011).
Some of the earliest work done in human fMRI (Ogawa et al.,

1992) used the simple fast low-angle shot (FLASH) pulse
sequence (Frahm, Haase, & Matthaei, 1986). This GE-weighted
sequence uses low flip angle radio-frequency (RF) pulses to
excite the spins, which are then sampled using a GE readout.
The advantage of this sequence in the early days of fMRI was
that it did not require any (at the time) specialist gradient
hardware. However, it suffers from being time inefficient (at
least by the standards of what is desirable for the regular
sampling of the fMRI signal) and also can exhibit a variety of
image artifacts that make the statistics of fMRI a challenge. In
particular, scanner instabilities and breathing cycles can introduce ghosting phenomena into the images that mask the
desired fMRI signal changes. Another potential confound for
the FLASH sequence is that if the flip angle is too high relative
to the scan repeat time (TR), then the sequence can become
sensitive to changes in flow velocity in the arterial vessels,
yielding the so-called in-flow artifact, whereby erroneous
fMRI signal can be seen in the large vessels feeding the active
tissue bed (in essence, this is the converse of the downstream
draining vein effect referred to earlier in the text).
Echo-planar imaging
At the time of writing, the most commonly used pulse
sequence for fMRI is the EPI sequence (Mansfield, 1977).
This sequence reads out a number of lines of k-space following each RF excitation pulse and potentially can acquire all the
required lines of k-space to form an image following a single
RF excitation pulse (the so-called snapshot EPI). The benefit of
the EPI pulse sequence is its speed, since it is capable of
acquiring an entire multislice volume through the brain in
< 2 s. The trade-off with EPI is that it is generally restricted to
low spatial resolutions (typically 2 mm in-plane, although
higher resolutions are possible), and it suffers from geometric
distortion of the images that complicates the registration of EPI
data to high-resolution structural data. Notwithstanding this,
GE-EPI has become the workhorse sequence used in fMRI and
so deserves some further specific discussion.
An important parameter in any fMRI sequence is the TE. For
maximum sensitivity of the pulse sequence, the optimal TE
value will be the one that maximizes the contrast-to-noise
ratio of the phenomenon being studied, in this case the
BOLD fMRI signal. To first approximation, the maximum sensitivity to signal change occurs when the TE value matches the
underlying T2* value for the tissue. This is a field-dependent
and brain region-dependent value, but a useful rule of thumb
(Glover, 2001) is to use a value of 1/T2* 1/T2 c B0 (where
c 4.8 (sT )1 and T2 0.095 s). If the T2* varies locally, then
in some circumstances a shorter TE value than would be the
case normally might actually increase the BOLD sensitivity,
contrary to the expectation that a longer TE time might offer
more BOLD fMRI signal contrast. Poser, Versluis, Hoogduin,
and Norris (2006) proposed the PAID method to deal with
the TE dependency: Parallel imaging acceleration allows the
acquisition of multiple EPI readouts after a single excitation
with different TEs. These are subsequently combined using a
BOLD sensitivity (%)
200
160
120
80
40
-400
-300
-200
-100
100
Phase-encode direction shim gradient (mT m-1)

Figure 2 Effect of background shim gradients in the phase-encoding
direction on the resulting BOLD sensitivity in the case of a typical gradientecho EPI fMRI experiment (BOLD sensitivity is defined as the product of
the echo time, TE, and the T2*-induced signal loss). Note that the phaseencoding shim gradient causes a change in the effective echo time (TE)
and leads to a quadratic dependence in BOLD sensitivity. Inspired by
Deichmann R., Josephs O., Hutton C., Corfield D.R., & Turner R. (2002).
Compensation of susceptibility-induced BOLD sensitivity losses in echoplanar fMRI imaging. NeuroImage, 15, 120135; Deichmann R., Gottfried
J.A., Hutton C., & Turner R. (2003). Optimized EPI for fMRI studies of
the orbitofrontal cortex. NeuroImage, 19, 430441.
data-driven, weighted approach ensuring optimal BOLD sensitivity in each voxel individually.
Deichmann, Josephs, Hutton, Corfield, and Turner (2002)
had further shown that the presence of any background macroscopic field gradients (poor shim), particularly any that are
in the phase-encoding direction for an EPI sequence, can result
in a significant change to the fMRI experiments BOLD sensitivity from its optimal value. This can be understood by reference to Figure 2 that shows the effect of the presence of a
phase-encoding direction shim gradient on BOLD sensitivity.
Finally, background macroscopic fields in the slice direction
can reduce image SNR due to the top and bottom of a slice
having a different phase at the time of the echo. Many compensation strategies have been proposed including z-shim
gradient blips in the slice direction (Constable & Spencer,
1999; Deichmann, Gottfried, Hutton, & Turner, 2003; Glover,
1999; Yang, Williams, Demeure, Mosher, & Smith, 1998), the
use of thin slices (Merboldt, Finsterbusch, & Frahm, 2000),
and RF pulse manipulations that locally prephase the slice such
that all is in-phase at the time of the echo (Stenger, Boada, &
Noll, 2000).
A specific issue associated with the EPI sequence (mentioned in the preceding text) is its sensitivity to geometric
distortion. This is caused by the low effective bandwidth of
EPI in the phase-encoding direction, which means that any
background macroscopic (shim) field inhomogeneities can
cause misplacement of signal in the resulting image, and consequent distortions. It is possible to ameliorate this problem by
acquiring separate information on the magnetic field distribution (Jezzard & Balaban, 1995) and then using this to relocate
the signal to its correct position or by running two EPI
sequences, one with positive phase-encoding blips and one
with negative phase-encoding blips, and then by using the
133
opposing distortions to derive the correct positions

(Andersson, Skare, & Ashburner, 2003). Another means of
minimizing the problem is to employ parallel imaging techniques (now standard on modern scanners) to reduce the
effective time between readout echoes (and hence increase
the phase-encoding bandwidth). A final variant of EPI that is
worthy of mention and that offers the prospect of a further
time saving is the use of multiband techniques (Breuer et al.,
2005; Feinberg et al., 2010; Larkman et al., 2001; Setsompop
et al., 2012) that enable multiple slices to be excited and
spatially encoded simultaneously and subsequently separated
into their component slices. The signal-to-noise penalty for
this is minimal, but care does need to be taken to avoid cross
contamination of fMRI signal fluctuations between slices
(Cauley, Polimeni, Bhat, Wald, & Setsompop, 2013). A particular benefit of multiband fMRI is likely to be for resting-state
studies, where the increased temporal density of sampling
offers great statistical improvement (Smith et al., 2013).
Spiral
An alternative readout technique to EPI is the spiral imaging
pulse sequence (Ahn, Kim, & Cho, 1986). This sequence is very
similar to EPI, but with a different (spiral) trajectory through
k-space, again potentially allowing data for a full image to be
acquired following a single RF excitation pulse. Spiral imaging
was developed in part to address the gradient hardware
demands of EPI, where severe switching of the gradient amplifiers is necessary. Additionally, it can address the EPI problem
of dead time between the excitation and the readout as the
optimal TE is relatively long (3540 ms at 3 T) compared to
the readout duration. A spiral-in trajectory does not have the
echo at its center but at the end, making TR almost equal to TE
and allowing a speedup similar to the principles of echo shifting with a train of observations (PRESTO) (see succeeding
text). This benefit disappears at high resolution, however, as
the longer readout causes an excessive TE. A drawback of the
spiral sequence is that it requires the k-space trajectory to be
accurately produced in order to avoid missing the echo or to
avoid image reconstruction artifacts that are much harder to
correct than the ones encountered in EPI. Improvements in
hardware in recent years have led to the interesting situation
that artifacts in spiral imaging not only can now be better
controlled but also have allowed EPI to become standard on
modern scanners. Finally, the relatively smooth gradients
reduce sound levels, in turn improving patient comfort. Overall, the spiral imaging method is not widely used, despite its
excellent suitability for low-resolution, low TR scanning.
Principles of echo shifting with a train of observations

An early alternative pulse sequence to EPI that has found
sustained use is the PRESTO technique introduced by Liu,
Sobering, Duyn, and Moonen (1993). This method not only
combines the principles of EPI and FLASH but also includes a
trick to delay the refocusing of the readout signal to a subsequent TR period so that the 3-D PRESTO method can offer a TE
time that is longer than the TR time. In this way, a TE that is
long enough to encode BOLD signal can be used in conjunction with a TR time that is short enough to achieve a rapid
full-volume readout. When combined with the acquisition of
several echoes (k-space lines) per readout module, the PRESTO
134
method offers similar image readout times to EPI, but avoids

such severe in-plane geometric distortion. Used in conjunction
with parallel imaging acceleration, one can even acquire a full
echo-train readout in the time conventionally spent waiting for
the TE, effectively halving the volume TR, but similar to the
spirals in the preceding text, this only works for low-resolution
(i.e., short readout time) protocols. A caveat that must be
mentioned in regard to the PRESTO method is that it is susceptible to in-flow contamination from arterial vessels if it is
run with a TR time that is too short (Duyn, Moonen, van
Yperen, de Boer, & Luyten, 1994).
SE Sequences
The other main class of BOLD fMRI technique is the SE contrast, which has some advantages over GE contrast. These are
that (i) the macroscopic background field dephasing effects are
refocused (this does not avoid EPI distortion, but does counter
through-slice dephasing); (ii) throughout the brain, T2 varies
considerably <T2* so a single TE is optimal everywhere; and
(iii) at high field strengths, the BOLD signal is more localized
to the capillary bed due to the refocusing of extravascular
dephasing around large vessels (as shown in Figure 1). It
should be noted that SE sequences will still be sensitive to
true T2 changes from the intravascular water in the larger
vessels and so are not immune to large vessel effects, but their
sensitivity to draining veins is greatly reduced due to the short
T2 of venous blood at high field (Duong et al., 2003).
SE sequences have drawbacks, however, which have prevented their widespread use. First and foremost, their loss in
fMRI sensitivity is usually considered too great (Bandettini,
Wong, Jesmanowicz, Hinks, & Hyde, 1994; Thulborn, Chang,
Shen, & Voyvodic, 1997). Most fMRI studies seek to study subtle
effects, and therefore, sensitivity is of utmost importance. Furthermore, research is often focused on group differences where
intersubject anatomical variability is the most limiting factor on
spatial resolution, rather than the sequence resolution. The second main argument against T2-weighted BOLD experiments is
that they are too impractical to perform properly. A purely T2weighted sequence would require the readout to consist of a
string of refocusing pulses as found in turbo spin-echo
sequences, which can quickly lead to prohibitive RF power deposition levels. In practice, therefore, EPI readout modules have
been used instead to measure the SE, but these add a significant
amount of T2* weighting, thereby reintroducing large-vein
effects. Segmented EPI can be used to reduce this contribution,
but Goense and Logothetis (2006) have shown that very large
segmentation factors are needed for it to be effective. This can
increase the volume TR time by an order of magnitude; however,
SE-EPI is already a slow sequence compared with GE-EPI due to
the long TE (6080 ms). Overall, SE-EPI has its niche
applications, but for most fMRI work, the benefits do not generally outweigh the challenges (Norris, 2012).
CBV-Weighted fMRI Sequences

The earliest human fMRI studies did not in fact use BOLD
contrast but instead used injected exogenous contrast agents to
achieve their signal. The earliest study of Belliveau et al. (1991)
used a gadolinium-based T2-weighted contrast agent to measure

changes in CBV in response to a visual stimulation. Though
simple, this approach has not been widely used subsequently
due to its invasive nature and its poor suitability for longitudinal
studies. However, recently, there has been a renewed interest in
injectable contrast agents with the use of ferumoxytol (a compound used in the treatment of iron-deficiency anemia in
patients with chronic kidney disease) as a blood volume contrast
agent. Unlike gadolinium-based agents, it has a longer half-life in
the blood and so allows repeated studies to be performed within
a single-scan session (Qiu, Zaharchuk, Christen, Ni, & Moseley,
2012). These sequences rely on T2* contrast and so require a GE
pulse sequence.
An alternative approach to CBV-weighted fMRI that does not
require injection of a contrast agent is the vascular space occupancy (VASO) method (Lu, Golay, Pekar, & Van Zijl, 2003).
This technique uses the fact that tissue water is redistributed
between an intravascular environment and an extravascular
environment as the blood volume in the tissue increases during
functional activation. By nulling the blood signal using an
inversion-recovery preparation, theory would predict that the
extravascular tissue signal would decrease during periods of
functional activation, as some extravascular water will redistribute into the blood compartment. One subtlety to the
VASO method is that it is not strictly possible to simultaneously
null the signal in all blood compartments, since the T1 time is
different in arterial versus venous blood. Nevertheless, VASO
has been used in fMRI studies to assess qualitatively the changes
in blood volume during neuronal activation. In this sense, it is
not so much considered a workhorse for general fMRI (the use
of inversion makes it a rather slow sequence) but as a good tool
to investigate physiology. This includes the physiology of the
BOLD signal itself, which, despite BOLDs widespread use, is far
from well understood at present.
CBF-Weighted fMRI Sequences

Another fundamental physiological parameter of importance
in functional studies is the change in CBF that accompanies
neuronal activity. The BOLD signal is indirectly influenced by
CBF changes, since they in turn alter the delivery of oxygenated
hemoglobin to the tissue. However, it is possible to directly
measure CBF changes associated with neuronal activity using
the principles of arterial spin labeling (ASL). This technique
compares images acquired after the incoming arterial blood
has been inverted (various methods to achieve inversion can
be adopted) with those acquired without the arterial inversion.
The difference signal reports on the delivery of incoming arterial blood.
Figure 3 shows a schematic illustration of the acquisition of
ASL data in a time course fashion, such that it can report on
functional changes in CBF. An example of this use of ASL in an
fMRI context is the turbo ASL method introduced by Wong,
Luh, and Yu (2000) although other similar approaches have
been published subsequently. An important observation that
can be made from Figure 3 is that since the inverted (tag) and
uninverted (control) images are collected at different time
points, it is not trivial to correctly calculate the CBF time course
during transitions in the functional paradigm and is also
135
water to the brain can be measured in an analogous way to

O-15 positron emission tomography. A current obstacle to this
method, however, is the high cost of oxygen-17 that makes
human-scale use of this technique unfeasible until prices
decrease.
CBF
BOLD
T C T C T C T C T C T C T C T C T C
Figure 3 Interaction of perfusion signal and BOLD signal in the case
of a time course arterial spin labeling experiment that uses a gradientecho readout. The BOLD signal does not cancel during transitions in the
fMRI paradigm, and poor estimation of the CBF signal will also result
from the different acquisition times of the tag image and control image.
These effects require careful analysis to correctly separate the BOLD
and ASL time courses. Inspired by Woolrich et al. 2006.
difficult to separate the effects of BOLD from the effects of CBF

(Woolrich, Chiarelli, Gallichan, Perthen, & Liu, 2006).
Another point worthy of note for fMRI implementations of
ASL is that unlike the BOLD image contrast that instantaneously reports on changes in the deoxyhemoglobin content
via its associated magnetic field effects, the ASL signal reports
on the integrated arrival of arterial blood into the tissue voxel
over the time of the preceding inversion delay (often one or
more seconds). This has implications for interpreting the
detailed CBF time course of any rapidly changing fMRI paradigm. At the opposite end of the temporal resolution spectrum,
ASL offers particular advantages over BOLD in the regime of
slow changes in signal (over minutes or even hours) where the
BOLD signal is unable to achieve meaningful statistics,
whereas the ASL signal can still be robust (Wang et al., 2003).
More Exotic fMRI Methods

In closing, it is worth mentioning that other more exotic MRI
pulse sequences exist with which to study neuronal activity.
One is to use functional spectroscopy to assess changes in
lactate or even in the concentration of neurotransmitters such
as glutamate (Schaller, Mekle, Xin, Kunz, & Gruetter, 2013).
Another is to use a diffusion sensitization to try to measure
postulated changes in the size of the cells as they undergo
metabolic activity (LeBihan, Urayama, Aso, Hanakawa, &
Fukuyama, 2006), although it is challenging to confidently
separate this effect from other more vascular effects (Miller
et al., 2007). An even more challenging quest has been the
use of MRI to measure subtle phase or magnitude effects arising directly from the small neuronal currents associated with
dendritic electrical transmission (Bodurka & Bandettini, 2002;
Song & Takahashi, 2001; Xiong, Fox, & Gao, 2003). To date,
there has been no convincing evidence that MRI is able to
achieve this, although there have been tantalizing suggestions
that it can. Finally, it is possible to use an entirely different
approach using inspired or injected oxygen-17 (Zhu, Zhang,
Zhang, Ugurbil, & Chen, 2009) whereby the delivery of O-17
and Applications; High-Field Acquisition; MRI and fMRI Optimizations
and Applications; Perfusion Imaging with Arterial Spin Labeling MRI;
Susceptibility-Weighted Imaging and Quantitative Susceptibility
Mapping.
References
Ahn, C., Kim, J., & Cho, Z. (1986). High speed spiral scan echo planar NMR imaging.
IEEE Transactions on Medical Imaging, MI-5, 27.
Andersson, J. L., Skare, S., & Ashburner, J. (2003). How to correct susceptibility
distortions in spin-echo echo-planar images: Application to diffusion tensor
Bandettini, P. A., Wong, E. C., Jesmanowicz, A., Hinks, R. S., & Hyde, J. S. (1994).
Spin-echo EPI of human brain activation using BOLD contrast: A comparative study
at 1.5 T. NMR in Biomedicine, 7, 1220.
Belliveau, J. W., Kennedy, D. N., McKinstry, R. C., et al. (1991). Functional mapping of
the human brain visual cortex by magnetic resonance imaging. Science, 254,
716719.
Medicine, 47, 10521058.
Bodurka, J., Ye, F., Petridou, N., Murphy, K., & Bandettini, P. A. (2007). Mapping the
MRI voxel volume in which thermal noise matches physiological noise
Implications for fMRI. NeuroImage, 34, 542549.
Boxerman, J. L., Bandettini, P. A., Kwong, K. K., et al. (1995). The intravascular
contribution to fMRI signal change: Mote Carlo modeling and diffusion-weighted
studies in vivo. Magnetic Resonance in Medicine, 34, 410.
Medicine, 34, 555566.
Breuer, F. A., Blaimer, M., Heidermann, R. M., Mueller, M. F., Griswold, M. A., &
Jakob, P. M. (2005). Controlled aliasing in parallel imaging results in higher
acceleration (CAIPIRIHNA) for multi-slice imaging. Magnetic Resonance in
Medicine, 53, 684691.
Cauley, S. F., Polimeni, J. R., Bhat, H., Wald, L. L., & Setsompop, K. (2013). Interslice
leakage artifact reduction technique for simultaneous multislice acquisitions.
functional MR imaging. Magnetic Resonance in Medicine, 42, 110117.
Deichmann, R., Gottfried, J. A., Hutton, C., & Turner, R. (2003). Optimized EPI for fMRI
studies of the orbitofrontal cortex. NeuroImage, 19, 430441.
Deichmann, R., Josephs, O., Hutton, C., Corfield, D. R., & Turner, R. (2002).
Compensation of susceptibility-induced BOLD sensitivity losses in echo-planar
fMRI imaging. NeuroImage, 15, 120135.
Duong, T. Q., Yacoub, E., Adriany, G., Hu, X., Ugurbil, K., & Kim, S. G. (2003).
Microvascular BOLD contribution at 4 and 7 T in human brain: Gradient-echo and
spin-echo fMRI with suppression of blood effects. Magnetic Resonance in
Medicine, 49, 10191027.
Duyn, J. H., Moonen, C. T., van Yperen, G. H., de Boer, R. W., & Luyten, P. R. (1994).
Inflow versus deoxyhemoglobin effects in BOLD functional MRI using gradient
echoes at 1.5 T. NMR in Biomedicine, 7, 8388.
Feinberg, D. A., Moeller, S., Smith, S. M., et al. (2010). Multiplexed echo planar
imaging for sub-second whole brain fMRI and fast diffusion imaging. PLoS One, 5,
e15710.
Frahm, J., Haase, A., & Matthaei, D. (1986). Rapid NMR imaging of dynamic processes
using the FLASH technique. Magnetic Resonance in Medicine, 3, 321327.
Glover, G. H. (1999). 3D z-shim method for reduction of susceptibility effects in BOLD
fMRI. Magnetic Resonance in Medicine, 42, 290299.
136
Glover, G. H. (2001). Hardware for functional MRI. In P. Jezzard, P. M. Matthews &

S. M. Smith (Eds.), Functional MRI: An introduction to methods. Oxford: Oxford
University Press.
Goense, J. B., & Logothetis, N. K. (2006). Laminar specificity in monkey V1 using highresolution SE-fMRI. Magnetic Resonance in Medicine, 24, 381392.
Jezzard, P., & Balaban, R. S. (1995). Correction for geometric distortion in
echo planar images from B0 field variations. Magnetic Resonance in Medicine, 34,
6573.
Kennan, R. P., Zhong, J., & Gore, J. C. (1994). Intravascular susceptibility contrast
mechanisms in tissues. Magnetic Resonance in Medicine, 31, 921.
(2001). Use of multicoil arrays for separation of signal from multiple slices
simultaneously excited. Journal of Magnetic Resonance Imaging: JMRI, 13,
313317.
LeBihan, D., Urayama, S., Aso, T., Hanakawa, T., & Fukuyama, H. (2006). Direct and fast
detection of neuronal activation in the human brain with diffusion MRI. Proceedings
82638268.
Liu, G., Sobering, G., Duyn, J., & Moonen, C. T. (1993). A functional MRI technique
combining principles of echo-shifting with a train of observations (PRESTO).
Medicine, 50, 263274.
Physics C, 10, L55L58.
Merboldt, K. D., Finsterbusch, J., & Frahm, J. (2000). Reducing inhomogeneity artifacts
in functional MRI of human brain activation thin sections vs gradient
compensation. Journal of Magnetic Resonance, 145, 184191.
Miller, K. L., Bulte, D. P., Devlin, H., et al. (2007). Evidence for a vascular contribution
to diffusion FMRI at high b value. Proceedings of the National Academy of Sciences
of the United States of America, 104, 2096720972.
Norris, D. G. (2012). Spin-echo fMRI: The poor relation? NeuroImage, 62,
11091115.
Olman, C. A., & Yacoub, E. (2011). High-field fMRI for human applications: An
overview of spatial resolution and signal specificity. The Open Neuroimaging
Journal, 5, 7489.
Pauling, L., & Coryell, C. D. (1936). The magnetic properties and structure
of hemoglobin, oxyhemoglobin and carbonmonoxyhemoglobin.
America, 22, 210216.
Poser, B. A., Versluis, M. J., Hoogduin, J. M., & Norris, D. G. (2006). BOLD contrast
sensitivity enhancement and artifact reduction with multiecho EPI: Parallel-acquired
inhomogeneity-desensitized fMRI. Magnetic Resonance in Medicine, 55,
12271235.
Qiu, D., Zaharchuk, G., Christen, T., Ni, W. W., & Moseley, M. E. (2012). Contrastenhanced functional blood volume imaging (CE-CBV): Enhanced sensitivity for
brain activation in humans using the ultrasmall superparamagnetic iron oxide agent
ferumoxytol. NeuroImage, 62, 17261731.
Schaller, B., Mekle, R., Xin, L., Kunz, N., & Gruetter, R. (2013). Net increase of lactate
and glutamate concentration in activated human visual cortex detected with
magnetic resonance spectroscopy at 7 Tesla. Journal of Neuroscience Research, 91,
10761083.
Medicine, 67, 12101224.
Smith, S. M., Beckmann, C. F., Andersson, J., et al. (2013). Resting-state fMRI in the
human connectome project. NeuroImage, 80, 144168.
Song, A. W., & Takahashi, A. M. (2001). Lorentz effect imaging. Magnetic Resonance in
Medicine, 19, 763767.
Stenger, V. A., Boada, F. E., & Noll, D. C. (2000). Three-dimensional tailored RF pulses
for the reduction of susceptibility artifacts in T2*-weighted functional MRI. Magnetic
Thulborn, K. R., Chang, S. Y., Shen, G. X., & Voyvodic, J. T. (1997). High-resolution
echo-planar fMRI of human visual cortex at 3.0 Tesla. NMR in Biomedicine, 10,
183190.
Uludag, K., Mueller-Bierl, B., & Ugurbil, K. (2009). An integrative model for activityinduced signal changes for gradient and spin echo functional imaging. NeuroImage,
48, 150165.
Van der Zwaag, W., Francis, S., Head, K., et al. (2009). fMRI at 1.5, 3 and 7 T:
Characterizing BOLD signal changes. NeuroImage, 47, 14251434.
Wang, J., Aguirre, G. K., Kimberg, D. Y., Roc, A. C., Li, L., & Detre, J. A. (2003). Arterial
spin labeling perfusion fMRI with very low task frequency. Magnetic Resonance in
Medicine, 49, 796802.
Wong, E. C., Luh, W. M., & Yu, H. C. (2000). Turbo ASL: Arterial spin labeling with
higher SNR and temporal resolution. Magnetic Resonance in Medicine, 44,
511515.
Woolrich, M. W., Chiarelli, P., Gallichan, D., Perthen, J., & Liu, T. T. (2006). Bayesian
inference of hemodynamic changes in functional arterial spin labeling. Magnetic
Xiong, J., Fox, P. T., & Gao, J. H. (2003). Directly mapping magnetic field effects of
neuronal activity by magnetic resonance imaging. Human Brain Mapping, 20,
4149.
Yang, Q. X., Williams, G. D., Demeure, R. J., Mosher, T. J., & Smith, M. B. (1998).
Removal of local field gradient artifacts in T2*-weighted images at high field by
gradient-echo slice excitation profile imaging. Magnetic Resonance in Medicine, 39,
402409.
Zhu, X. H., Zhang, N., Zhang, Y., Ugurbil, K., & Chen, W. (2009). New insights into
central roles of cerebral oxygen metabolism in the resting and stimulus-evoked
brain. Journal of Cerebral Blood Flow and Metabolism, 29, 1018.
Myelin Imaging
R Turner, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
Glossary
BOLD The iron-containing compound that causes the

T2*-decay in the MRI signal is deoxygenated haemoglobin
found in the bloods red cells, the signal is said to be Blood
Oxygenation Level Dependent (BOLD), a term devised by its
discoverer Seiji Ogawa. Because neural activity in a given
region tends to increase the oxygenation of its blood supply,
which significantly increases the MRI signal, BOLD signal
has been the basis for the majority of functional MRI studies
in the years since its discovery in 1991.
Magnetic resonance imaging (MRI) A technique that uses
the fact that the magnetic moment of water protons within
an object can be aligned in a large magnetic field, with an
energy difference between orientations parallel with and
opposing to the applied magnetic field which corresponds
to a radiofrequency electromagnetic field.
T1 After excitation with a pulse of radiofrequency
electromagnetic energy, the proton spins relax with an
exponential decay of time constant T1, the longitudinal
relaxation time, to their original orientation parallel to the
applied magnetic field.
Introduction
In human brain, the combination of lipids and proteins known
collectively as myelin comprises about half of the dry weight of
white matter (Siegel, Agranoff, & Gavulic, 1999). The myelin
content of gray matter, which is always lower than in white
matter, varies strikingly between cortical areas, reaching a maximum in the primary motor cortex and a minimum in several
prefrontal regions.
Broadly speaking, the dry-weight composition of myelin is
about 30% protein (including myelin basic protein), about 20%
cholesterol, about 20% galactolipids containing sulfur in their
head groups, and about 30% phospholipids. The nonmyelin
components of white matter are similar, but the proportion of
galactolipids is strikingly lower than that of myelin. Gray matter
contains comparatively more protein and less lipid and has a
higher water content (80%) compared with white matter (70%).
Historically, most of the anatomical research on myelin has
been carried out using histological techniques: brain tissue is
fixed using formalin or other fixatives such as Bodian No. 2,
then sliced with a macrotome into sections about 40 mm thick,
and then finally stained to reveal the presence of myelin. Popular
stains for myelin include the Gallyas silver stain, Luxol fast blue,
and Weigerts method. In addition, immunohistochemical stains
can be used, such as MBP IHC antibody, which selectively stains
myelin basic protein.
It should be noted that some fixatives, such as those containing ethanol or acetic acid, are incompatible with MRI
scanning, because their proton spectra have two closely spaced
T2* Once excited, but before the spin magnetization has

returned to its original orientation, the signal that it
generates in a receiver coil loses its phase coherence due to
local random variations in magnetic field, often caused by
localized tissue components such as iron-containing
compounds. This incoherence, which attenuates the
received signal, increases with a decay time of T2*, the
transverse relaxation time.
Turbo spin-echo sequence To generate a magnetic
resonance image, the radiofrequency electromagnetic field
and three linear magnetic field gradients that pass through
the object to be imaged must be switched on and off, and
the resulting radiofrequency signal must be acquired, in a
highly detailed computer-controlled sequence of events.
One such imaging sequence is known as the turbo spinecho sequence. The image intensity provided by this
sequence is desirably unaffected by the local variations of
magnetic field that result in the decay of the signal with a
time constant T2*, but instead reflects other aspects of
tissue composition.
peaks, giving a blurred double image. Furthermore, the quality

of myelin staining depends on the appropriate combination of
fixative and stain some stains give very disappointing results
when the wrong fixative has been used. Formalin fixation
enables reasonably good-quality MR imaging of cadaver
brain, although the relaxation times are considerably reduced
due to the molecular cross-linking that accompanies fixation.
After the tissue has been sectioned, staining for myelin basic
protein then provides satisfactory micrographs.
What appears on such micrographs (see, e.g., Figure 1
showing a Gallyas-stained section of human brain) is a dense
stain in white matter and lighter staining in gray matter. The
pattern of staining in gray matter is strikingly well organized.
Everywhere in the cortex reveals fibers radial to the cortical
surface and, in addition, two tangential bands, known as the
bands of Baillarger, after their discoverer in 1840. Patches of
the cortex up to 20 mm across often have a consistent pattern
of myelin staining, with boundaries where an abrupt change
into another pattern marks a different cortical area. The cortical
myelin staining pattern has been described as myeloarchitectonics since Oscar Vogt so named it in 1903, and the history of
myeloarchitecture has been excellently reviewed by Nieuwenhuys (Geyer & Turner, 2013). Spatial differences in myeloarchitecture enable a detailed classification of the cortex into areas
that are likely to have common functional properties (see
Geyer & Turner, 2013).
It is a remarkable characteristic of magnetic resonance imaging of the brain, first pointed out by Young et al. (1981), that
excellent contrast between gray matter and white matter image
http://dx.doi.org/10.1016/B978-0-12-397025-1.00015-4
137
138
INTRODUCTION TO ACQUISITION METHODS | Myelin Imaging

scientific value of mapping myelin in human brain and spatially
tracking its changes over time in response to development,
maturation, and learning. This article will summarize research
on the development, roles, and importance of myelin in the
brain and discuss recent work that may lead to a quantitative
noninvasive evaluation of cortical and white matter myelination
using MRI techniques.
The Process of Myelination
Figure 1 Micrograph of human brain tissue stained for myelin using the
Gallyas silver stain technique.
3000
2500
2000
1500
1000
T1
(ms)
Figure 2 Map of T1 in the normal human brain, from the Max Planck
Institute for Human Cognitive and Brain Sciences, Leipzig. The data were
acquired using the MP2RAGE sequence at 7 T, with isotropic spatial
resolution of 0.5 mm. An axial slice is shown, from a whole-brain data set
acquired in 45 min.
intensities can be observed in images that are sensitive to differences in the longitudinal relaxation time T1 (Figure 2). But it has
taken many years to better understand the biophysical origins of
the T1 differences between white matter and gray matter. This
would be surprising if it were not for the fact that myeloarchitecture has itself been sadly neglected in neuroanatomy, neurology, cognitive science, and neuroradiology for close to a century,
since the initial pioneering work of Thudichum (1884), Vogt
and Vogt (1919), and Flechsig (1920). It is only recently that
imaging neuroscientists (Geyer, Weiss, Reimann, Lohmann, &
Turner, 2011; Glasser & Van Essen, 2011; Sereno, Lutti,
Weiskopf, & Dick, 2013) have begun to realize the enormous
Structurally, myelin exists in the central and peripheral nervous

system as a coating around many of the axonal processes of
neurons. This coating consists of a bilamellar membrane,
largely composed of lipids, wrapped in a tight spiral round
each axon. The spacing between each turn is about 12 nm
(Waxman, Kocsis, & Stys, 1995). At birth (Brody, Kinney,
Kloman, & Gilles, 1987), only a few axonal tracts in the
human brain and their corresponding cortical areas are already
myelinated. These include the optic nerve and the core of the
corticospinal tracts. In both white matter and the cortex, myelination takes place rapidly in the first year of life but continues
well into adulthood (Grydeland, Walhovd, Tamnes, Westlye, &
Fjell, 2013; Young et al., 2013). Myelination of previously
unmyelinated axons is performed by a specialized type of glial
cell, the oligodendrocyte. There is evidence (Sherman & Brophy,
2005; Simons & Lyons, 2013) that myelination is initiated
both by the diameter of the adjacent axon and also by the
transmission of action potentials along it (Wake, Lee, & Fields,
2011), a bootstrapping mechanism that enables myelination to
respond to experiential demands as the organism matures.
How do axons become sheathed with myelin? Snaidero
et al. (2014) describes what is known regarding the relevant
mechanisms. An oligodendrocyte extends a tongue of plasma
membrane that encounters the axon and starts to wrap it with
myelin by passing round and round the axon while remaining
in contact with the axonal membrane itself and broadening at
each turn. The extending membrane, as it forms sequential
further layers, is supplied with fresh lipids and proteins via
cytoplasmic channels in the developing sheath that remain
open until the process is completed. A single oligodendrocyte
can wrap several adjacent axons, but it appears that there is a
restricted time window when any given oligodendrocyte is
capable of performing this task, a duration of only about 5 h
(Czopka, Ffrench-Constant, & Lyons, 2013).
Effects of Myelination
What functional benefits and disadvantages does myelination
of axons confer? Exploring this question may lead to rapid
progress in understanding the functional roles of cortical
areas identifiable by their distinctive patterns of myelination
and better understanding of changes in brain structure related
to maturation and learning. There are five important effects,
which may be simply stated:
Myelination of axons
(a) accelerates the conduction speed of action potentials by an
order of magnitude (Waxman, 1980),
(b) greatly decreases energy cost of transmission (Harris &
Attwell, 2012),

(c) increases robustness of axons (Staal & Vickers, 2011),
(d) reduces electrical crosstalk between axons and other
nearby neurites,
(e) reduces synaptic plasticity by inhibiting neurite growth
(McGee, Yang, Fischer, Daw, & Strittmatter, 2005; Ng,
Cartel, Roder, Roach, & Lozano, 1996).
Myelin Mapping Using MRI

As mentioned in the preceding text, MRI sequences sensitive to
the longitudinal relaxation time T1 provide images with excellent gray/white matter contrast (Figure 2). The reasons for this
were little explored during the first 15 years of the development
of MRI. It was commonly hypothesized that the higher water
content of gray matter, as compared with white matter, was the
main cause of its longer T1 (see Dortch et al., 2013 for a
perpetuation of this myth). In discussion of contrast mechanisms, the already well-known biochemical makeup of brain
tissue was crudely categorized as metabolites and macromolecules. However, the pioneering work by Koenig, Brown, Spiller,
and Lundbom (1990), Koenig (1991), and Kucharczyk,
Macdonald, Stanisz, and Henkelman (1994) showed that the
large difference in T1 between gray matter and white matter
could be explained almost entirely by the greater concentration
of myelin in white matter. Further, this difference was shown
to arise very largely from specific components in myelin not
from proteins and phospholipids but instead from the abundant membrane lipids cholesterol and cerebroside.
To understand this result, it is necessary to appreciate that T1
relaxation is by definition the dissipation of energy that was
introduced into the spin system by the RF excitation pulse.
This energy is dispersed through the coupling of water spins to
the lattice, a large thermal reservoir consisting of comparatively
large static or slowly moving molecules with a broad NMR
spectrum. In the brain tissue, especially white matter, the lattice
consists largely of membranes, many of which are composed of
myelin. The rate at which spins are relaxed by this lattice
depends on the residence time of water molecules at the membrane surface during which they can lose spin magnetization
and hence energy to the lattice and on the coupling effectiveness of the molecular environment at the surface (Ceckler,
Wolff, Yip, Simon, & Balaban, 1992). It is argued that the ends
of cholesterol and cerebroside molecules to which water molecules have access, at the membrane surfaces, provide uniquely
effective sites for relaxation of water proton spins. Not coincidentally, such sites also provide excellent coupling for the
inverse process of magnetization transfer from membrane molecules to free water (see the succeeding text).
Not all longitudinal (T1) relaxation can easily be explained
in this way. Paramagnetic contrast agents, such as manganese
chloride and ferritin, relax spin magnetization through the
local rapidly varying magnetic fields with frequency components at the Larmor frequency that they provide due to thermal
vibrations. Where such materials occur naturally in brain
tissue, for instance, ferritin in the basal ganglia and in cortical
myelin (Fukunaga et al., 2010), they will also contribute to T1
relaxation.
Recent work by Stuber and coworkers (Stuber et al., 2014)
comparing quantitative MRI of T1 and T2* with proton beam
microscopy of the elemental composition of slices from the
139
same block of cadaver brain tissue has revealed that T1 depends

only weakly on iron content but strongly on myelin content.
These authors used a general linear model to identify the
contribution voxel-by-voxel of myelin and iron to the relaxation properties of the tissue. This is a strategy also used, without the help of ground-truth tissue composition data, by
Rooney et al. (2007) and more recently Callaghan, Helms,
Lutti, Mohammadi, and Weiskopf (2014). The conclusion
can be reached that measurements of the relaxation rate R1
(1/T1) provide a quite reliable guide to the amount of myelin
present in a voxel of healthy cortex or white matter, with rather
less confidence in iron-rich deep brain regions such as the
putamen, red nuclei, and substantia nigra.
It should be noted that, despite the confusing nomenclature,
the so-called T2-weighted images, acquired using a turbo spinecho sequence, are generally not T2-weighted at all (see Geyer &
Turner, 2013, MRI methods for in-vivo cortical parcellation, for
a fuller discussion). Instead, the excellent gray/white matter
contrast that they show demonstrates that they are weighted
by magnetization transfer rate (MTR), T1, and proton density.
The images used for cortical parcellation by Glasser and Van
Essen (2011), using the ratio between T1-weighted images and
T2-weighted images, are thus largely T1-weighted and indeed
indicate cortical myelin, as the authors claim.
In recent years, greater attention has been paid by
researchers to the possibility of assessing myelin density using
the techniques of MTR and imaging of myelin water fraction
(MWF). MTR uses the phenomenon, discovered by Wolff and
Balaban (1989), that excitation of protons attached to large
molecules within the tissue causes more rapid relaxation of
neighboring free water proton spins. Because this process also
depends on good coupling between the relevant macromolecules and free water molecules, one can expect a very similar
spatial dependence to that of T1. The highly relaxing molecules
of cholesterol and cerebroside are again likely to dominate
(Ceckler et al., 1992; Koenig, 1991). Maps of MTR (e.g.,
Dortch et al., 2013) appear to be almost identical to maps of
R1 (Weiskopf et al., 2013). One important difference might
arise from the insensitivity of MTR to the presence of paramagnetic contrast agents. Thus, one should expect the linear
relationship between values of R1 and MTR to break down in
iron-rich brain regions. Efficient MTR mapping has been developed extensively by Helms, Dathe, and Dechent (2010), but
the signal to noise available per unit time is inevitably lower
than that achievable with quantitative T1 mapping methods,
such as MP2RAGE (Marques et al., 2010).
But both of these methods may turn out to be less accurate
in estimation of myelin content than the third possibility,
MWF (MacKay et al., 1994; Zhang, Kolind, Laule, & Mackay,
2014). Myelin water fraction mapping uses T2 relaxometry, in
which spin-echo images are acquired over a wide range of echo
times. The data are analyzed to reveal a spectrum of T2 values,
which cluster into relatively narrow peaks that can readily be
identified as arising, respectively, from relatively free extracellular and cytoplasmic water and water trapped between the
layers in the myelin sheaths. The partial volumes of these
compartments can be estimated quite accurately, and one can
be confident that the myelin water fraction corresponds closely
to the total amount of myelin.
When the maps that are expected to correspond to myelin
density acquired by each of these methods are compared, a
140
problem appears. Maps of MWF show much greater inhomogeneity throughout the white matter than do T1 maps or MTR
maps. Histograms of T1 and MTR are very sharply peaked at
values corresponding to white matter, with a variance of perhaps
20%, but MWF values can vary systematically by a factor of up to
two from region to region (e.g., Zhang et al., 2014). Clearly,
these methods are measuring different aspects of myelin.
In order to resolve this discrepancy, it is tempting to suggest
that MWF measures all the myelin in a given voxel, while T1 and
MTR maps sample only the myelin that is in close proximity to
relatively free intracellular water, that is, myelin adjacent to the
axonal lumen or surrounding the outer layer of the myelin
sheath. There is already evidence that the exchange time of
water between compartments in white matter is more than
half a second (Kalantari, Laule, Bjarnason, Vavasour, &
MacKay, 2011). This is much longer than the presumed residence time of water molecules at the membranes optimal
relaxing sites (end groups of cholesterol and cerebroside). In
this model, then, the processes resulting in T1 relaxation and
magnetization transfer are localized only to the surface layers of
myelin, the inner layers having insufficiently rapid interchange,
either by spin transfer or chemical exchange, to interact with the
free water. If this model is correct, combining results from MWF
and T1/MTR mapping may offer a simple opportunity to infer
maps of other aspects of white matter myelin, such as the mean
number of wraps and perhaps the mean axonal diameter.
One drawback of MWF mapping is the duration required
for data collection. While this has recently been accelerated
using more efficient acquisition methods such as GRASE
(Prasloski et al., 2012), the time needed is still more than
double that required for an MP2RAGE map of T1 with equivalent spatial resolution. It needs to be mentioned that rapid
acquisition methods such as mcDESPOT that require multivariate fitting of data with prior estimation of several variables
have been shown to provide unrealistic values of MWF
(Lankford & Does, 2013; Zhang et al., 2014).
Applications of Myelin Mapping

In Vivo Cortical Parcellation Using Myeloarchitectural
Features
Since the discovery of BOLD contrast in 1990, which allowed
noninvasive mapping of human brain activity in response to
experimental tasks, research on human brain has dramatically
expanded. One weakness of the methods that have become
widely popular, however, is the issue of attributing location to
specific brain activity. Human brains are folded sufficiently
differently from each other, and evidently distinct cortical
areas lie so differently on the folded structure that localization
of brain activity often involves a fair amount of standardized
guesswork (see Turner, 2013). This prevents precise comparison of activation patterns across human subjects and rules out
attempts to relate functional activity to its neural substrate.
The observation that myelin plays a major role in several
types of MRI contrast (Barbier et al., 2002; Clark, Courchesne,
& Grafe, 1992) has led to a significant growth of interest in the
possibility of using MRI-observable myeloarchitecture as the
basis for localization of BOLD fMRI-detected neural activity.
Pioneering studies by Bridge et al. (2005), Sanchez-Panchuelo,
Francis, Schluppeck, and Bowtell (2012), and others have shown

that a good correspondence can be found between some areas
defined by myeloarchitecture and by functional activity. This
opens the possibility of systematic identification of cortical
areas in vivo using myelin maps (Geyer et al., 2011; Glasser &
Van Essen, 2011). Still further, the opportunity is presented of
normalizing the cortices of a group of experimental subjects by
performing surface normalization of the myelin maps themselves, thus precisely aligning corresponding regions with similar
functions across the group of brains (Tardif, Dinse, Schafer,
Turner, & Bazin, 2013).
Studies of Development and Plasticity

Despite the debate regarding the best MRI method for characterizing myelin in the human brain, it is quite clear that T1
maps, MTC maps, and MWF maps derive almost all of their
contrast from the presence of myelin. It is thus inviting (Brody
et al., 1987) to study the maturation of infant brains using such
techniques. Pyramidal neurons are generally not yet efficient
until their axons have been myelinated, and as mentioned
earlier, myelination is partly driven by experience. Thus, studies, such as those in progress by Dubois et al. (2013), are likely
to reveal the developmental trajectories of the entire brain
networks as new skills are learned, either explicitly or by processes of probabilistic learning.
MRI studies of adult brain plasticity generated by learning
have become increasingly popular, as researchers have realized
that the brains are designed to take continuously the imprint of
experience (see the critical review by Lovden et al., 2013). In
particular, changes in white matter structure have been detected
with diffusion-weighted MRI (dMRI), using the index of
fractional anisotropy as a measure of white matter reorganization
(Scholz, Klein, Behrens, & Johansen-Berg, 2009). However, it is
naive to base dMRI analyses on the assumption of a single fiber
direction in each voxel (Jones, Knosche, & Turner, 2013). It is
likely that mapping myelination more directly, using T1 or MTC
maps, which can be acquired with far greater SNR than FA maps,
will enable more realistic interpretation of such changes over
time.
Discussion and Summary

Myelin imaging has become an important tool in neuroscience
and neurodevelopmental studies. From a neuroimaging perspective, the following research questions need to be addressed,
probably with the help of animal model studies:
(a) Why do T1 and MTC maps differ from MWF maps?
(b) What MRI sequences offer the most rapid acquisition of
signal to noise per unit time for parameters allowing inference of myelin density?
(c) Can the progressive myelination of specific fascicles be
detected and followed during the process of neuronal
maturation?
(d) Why is cortical myelin associated with high iron content,
while white matter myelin has much lower iron
concentrations?

In summary, myelin imaging is now a very healthy application
of the rapidly growing practice of quantitative MRI, in which
the image intensity takes on a physical meaning, instead of
being labeled in arbitrary units. Myelination is vital for normal
brain function, and it is imperative to have a deeper scientific
understanding of its time course and its role in shaping neural
circuits.

Anatomical MRI for Human Brain Morphometry.
References
Barbier, E. L., Marrett, S., Danek, A., Vortmeyer, A., van Gelderen, P., Duyn, J., et al.
(2002). Imaging cortical anatomy by high-resolution MR at 3.0 T: Detection of the
stripe of Gennari in visual area 17. Magnetic Resonance in Medicine, 48,
735738.
Bridge, H., Clare, S., Jenkinson, M., Jezzard, P., Parker, A. J., & Matthews, P. M.
(2005). Independent anatomical and functional measures of the V1/V2 boundary in
human visual cortex. Journal of Vision, 5, 93102.
Brody, B. A., Kinney, H. C., Kloman, A. S., & Gilles, F. H. (1987). Sequence of central
nervous system myelination in human infancy. I. An autopsy study of myelination.
Journal of Neuropathology and Experimental Neurology, 46(3), 283301.
Callaghan, M. F., Helms, G., Lutti, A., Mohammadi, S., & Weiskopf, N. (2014). A
general linear relaxometry model of R1 using imaging data. Magnetic Resonance in
Medicine, http://dx.doi.org/10.1002/mrm.25210.
Ceckler, T. L., Wolff, S. D., Yip, V., Simon, S. A., & Balaban, R. S. (1992). Dynamic and
chemical factors affecting water proton relaxation by macromolecules. Journal of
Clark, V. P., Courchesne, E., & Grafe, M. (1992). In vivo myeloarchitectonic analysis of
human striate and extrastriate cortex using magnetic resonance imaging. Cerebral
Cortex, 2, 417424.
Czopka, T., Ffrench-Constant, C., & Lyons, D. A. (2013). Individual oligodendrocytes
have only a few hours in which to generate new myelin sheaths in vivo.
Developmental Cell, 25(6), 599609.
Dortch, R. D., Moore, J., Li, K., Jankiewicz, M., Gochberg, D. F., Hirtle, J. A., et al.
(2013). Quantitative magnetization transfer imaging of human brain at 7 T.
Dubois, J., Dehaene-Lambertz, G., Kulikova, S., Poupon, C., Huppi, P. S., &
Hertz-Pannier, L. (2013). The early development of brain white matter: A review of
imaging studies in fetuses, newborns and infants. Neuroscience, pii: S0306-4522
(13)01069-5.
Flechsig, P. (1920). Anatomie des menschlichen Gehirns und Ruckenmarks auf
myelogenetischer Grundlage. Leipzig: G. Thieme.
Fukunaga, M., Li, T. Q., van Gelderen, P., de Zwart, J. A., Shmueli, K., Yao, B., et al.
(2010). Layer-specific variation of iron content in cerebral cortex as a source of MRI
contrast. Proceedings of the National Academy of Sciences of the United States of
America, 107(8), 38343839.
Geyer, S., & Turner, R. (Eds.). (2013). Microstructural parcellation of the human
cerebral cortex from Brodmanns post-mortem map to in vivo mapping with highfield magnetic resonance imaging. Heidelberg: Springer.
Geyer, S., Weiss, M., Reimann, K., Lohmann, G., & Turner, R. (2011). Microstructural
parcellation of the human cerebral cortex From Brodmanns post-mortem map to
in vivo mapping with high-field magnetic resonance imaging. Frontiers in Human
Glasser, M. F., & Van Essen, D. C. (2011). Mapping human cortical areas in vivo based
on myelin content as revealed by T1- and T2-weighted MRI. Journal of
Neuroscience, 31(32), 1159711616.
Grydeland, H., Walhovd, K. B., Tamnes, C. K., Westlye, L. T., & Fjell, A. M. (2013).
Intracortical myelin links with performance variability across the human lifespan:
Results from T1- and T2-weighted MRI myelin mapping and diffusion tensor
imaging. Journal of Neuroscience, 33(47), 1861818630.
Harris, J. J., & Attwell, D. (2012). The energetics of CNS white matter. Journal of
Neuroscience, 32(1), 356371.
Helms, G., Dathe, H., & Dechent, P. (2010). Modeling the influence of TR and excitation
flip angle on the magnetization transfer ratio (MTR) in human brain obtained
from 3D spoiled gradient echo MRI. Magnetic Resonance in Medicine, 64(1),
177185.
141
Jones, D. K., Knosche, T. R., & Turner, R. (2013). White matter integrity, fiber count,
and other fallacies: the dos and donts of diffusion MRI. Neuroimage, 73,
239254.
Kalantari, S., Laule, C., Bjarnason, T. A., Vavasour, I. M., & MacKay, A. L. (2011).
Insight into in vivo magnetization exchange in human white matter regions.
Koenig, S. H. (1991). Cholesterol of myelin is the determinant of gray-white contrast in
MRI of brain. Magnetic Resonance in Medicine, 20(2), 285291.
Koenig, S. H., Brown, R. D., 3rd, Spiller, M., & Lundbom, N. (1990). Relaxometry of
brain: Why white matter appears bright in MRI. Magnetic Resonance in Medicine,
14(3), 482495.
Kucharczyk, W., Macdonald, P. M., Stanisz, G. J., & Henkelman, R. M. (1994).
Relaxivity and magnetization transfer of white matter lipids at MR imaging:
Importance of cerebrosides and pH. Radiology, 192(2), 521529.
Lankford, C. L., & Does, M. D. (2013). On the inherent precision of mcDESPOT.
Lovden, M., Wenger, E., Martensson, J., Lindenberger, U., & Backman, L. (2013).
Structural brain plasticity in adult learning and development. Neuroscience and
Biobehavioral Reviews, 37(9 Pt B), 22962310.
MacKay, A., Whittall, K., Adler, J., Li, D., Paty, D., & Graeb, D. (1994). In vivo
visualization of myelin water in brain by magnetic resonance. Magnetic Resonance
in Medicine, 31(6), 673677.
Marques, J. P., Kober, T., Krueger, G., van der Zwaag, W., Van de Moortele, P. F., &
Gruetter, R. (2010). MP2RAGE, a self bias-field corrected sequence for improved
segmentation and T1-mapping at high field. NeuroImage, 49(2), 12711281.
McGee, A. W., Yang, Y., Fischer, Q. S., Daw, N. W., & Strittmatter, S. M. (2005).
Experience-driven plasticity of visual cortex limited by myelin and Nogo receptor.
Science, 309(5744), 22222226.
Ng, W. P., Cartel, N., Roder, J., Roach, A., & Lozano, A. (1996). Human central nervous
system myelin inhibits neurite outgrowth. Brain Research, 720(12), 1724.
Prasloski, T., Rauscher, A., MacKay, A. L., Hodgson, M., Vavasour, I. M., Laule, C.,
et al. (2012). Rapid whole cerebrum myelin water imaging using a 3D GRASE
sequence. NeuroImage, 63(1), 533539.
Rooney, W. D., Johnson, G., Li, X., Cohen, E. R., Kim, S. G., Ugurbil, K., et al. (2007).
Magnetic field and tissue dependencies of human brain longitudinal 1H2O
relaxation in vivo. Magnetic Resonance in Medicine, 57(2), 308318.
Sanchez-Panchuelo, R. M., Francis, S. T., Schluppeck, D., & Bowtell, R. W. (2012).
Correspondence of human visual areas identified using functional and
anatomical MRI in vivo at 7 T. Journal of Magnetic Resonance Imaging, 35(2),
287299.
Scholz, J., Klein, M. C., Behrens, T. E., & Johansen-Berg, H. (2009). Training
induces changes in white-matter architecture. Nature Neuroscience, 12, 13701371.
Sereno, M. I., Lutti, A., Weiskopf, N., & Dick, F. (2013). Mapping the human cortical
surface by combining quantitative T(1) with retinotopy. Cerebral Cortex, 23(9),
22612268.
Sherman, D. L., & Brophy, P. J. (2005). Mechanisms of axon ensheathment and myelin
growth. Nature Reviews Neuroscience, 6(9), 683690.
Siegel, G. J., Agranoff, B. W., & Gavulic, L. M. (1999). Basic neurochemistry:
Molecular, cellular and medical aspects (6th ed.). Philadelphia: Lippincott-Raven.
Simons, M., & Lyons, D. A. (2013). Axonal selection and myelin sheath generation in
the central nervous system. Current Opinion in Cell Biology, 25(4), 512519.
Snaidero, N., Mobius, W., Czopka, T., Hekking, L. H., Mathisen, C., Verkleij, D., et al.
(2014). Myelin membrane wrapping of CNS axons by PI(3,4,5)P3-dependent
polarized growth at the inner tongue. Cell, 156(12), 277290.
Staal, J. A., & Vickers, J. C. (2011). Selective vulnerability of non-myelinated axons to
stretch injury in an in vitro co-culture system. Journal of Neurotrauma, 28(5),
841847.
Stuber, C., Morawski, M., Schafer, A., Labadie, C., Wahnert, M., Leuze, C., et al. (2014).
Myelin and iron concentration in the human brain: A quantitative study of MRI
contrast. NeuroImage, 93, 95106.
Tardif, C. L., Dinse, J., Schafer, A., Turner, R., & Bazin, P.-L. (2013). Multi-modal
surface-based alignment of cortical areas using intra-cortical T1 contrast. In
Multimodal brain image analysis (pp. 222232). Lecture notes in computer
science8159, (pp. 222232).
Thudichum, J. L.W (1884). A treatise on the chemical constitution of the brain. London:
Baillie`re, Tindall, and Cox.
Turner, R. (2013). Where matters: New approaches to brain analysis. In: S. Geyer & R.
Turner (Eds.), Microstructural parcellation of the human cerebral cortex. Heidelberg:
Springer.
Vogt, C., & Vogt, O. (1919). Allgemeinere Ergebnisse unserer Hirnforschung. Journal
fur Psychologie und Neurologie, 25, 279461.
Wake, H., Lee, P. R., & Fields, R. D. (2011). Control of local protein synthesis and initial
events in myelination by action potentials. Science, 333(6049), 16471651.
142
Waxman, S. G. (1980). Determinants of conduction velocity in myelinated nerve fibers.

Muscle and Nerve, 3(2), 141150.
Waxman, S. G., Kocsis, J. D., & Stys, P. K. (Eds.), (1995). The axon: Structure, function
and pathophysiology. New York: Oxford University Press.
Weiskopf, N., Suckling, J., Williams, G., Correia, M. M., Inkster, B., Tait, R., et al.
(2013). Quantitative multi-parameter mapping of R1, PD(*), MT, and R2(*) at 3 T: A
multi-center validation. Frontiers in Neuroscience, 7, 95.
Wolff, S. D., & Balaban, R. S. (1989). Magnetization transfer contrast (MTC) and tissue
water proton relaxation in vivo. Magnetic Resonance in Medicine, 10(1), 135144.
Young, I. R., Burl, M., Clarke, G. J., Hall, A. S., Pasmore, T., Collins, A. G., et al. (1981).
Magnetic resonance properties of hydrogen: Imaging the posterior fossa. AJR.
American Journal of Roentgenology, 137(5), 895901.
Young, K. M., Psachoulia, K., Tripathi, R. B., Dunn, S. J., Cossell, L., Attwell, D., et al.
(2013). Oligodendrocyte dynamics in the healthy adult CNS: Evidence for myelin
remodeling. Neuron, 77(5), 873885.
Zhang, J., Kolind, S. H., Laule, C., & Mackay, A. L. (2014). Comparison of myelin water
fraction from multiecho T2 decay curve and steady-state methods. Magnetic
Resonance in Medicine, http://dx.doi.org/10.1002/mrm.25125.
Functional Near-Infrared Spectroscopy

RJ Cooper, University College London, London, UK
DA Boas, Harvard Medical School, Charlestown, MA, USA
Introduction
Using light to noninvasively study the brain is made possible
by the fact that many biological tissues, including human skin
and bone, are relatively transparent to near-infrared light. The
exploitation of this near-infrared window in 1977 resulted in
the first spectroscopic measurements of the brain in vivo, proving that near-infrared light can traverse the human scalp and
skull and return to be measured at the surface (Jobsis, 1977).
The existence of this window is particularly advantageous
because there are a number of physiologically interesting
molecules that exhibit distinct absorption spectra in the
near-infrared range, most notably oxyhemoglobin and deoxyhemoglobin. Near-infrared spectroscopy (NIRS), in its simplest form, is the measurement of changes in the
concentration of these two molecules. Using a single source
location emitting at two wavelengths of near-infrared light and
a single detector (which constitutes one channel), NIRS systems can determine the changes in concentration of both
hemoglobin species in the tissue through which the detected
NIR light has traveled. The ability to measure changes in oxyhemoglobin concentration and deoxyhemoglobin concentration at high temporal resolution allows NIRS to be used to
study the functional response of the brain to external stimuli.
The overcompensation of the cerebral vasculature to the
increased oxygen demand of activated groups of neurons
gives rise to a hemodynamic response, the same physiological
phenomenon that produces the blood oxygen level-dependent
(BOLD) signal of functional magnetic resonance imaging
(fMRI; Logothetis, Pauls, Augath, Trinath, & Oeltermann,
2001). By measuring this hemodynamic response to external
stimuli, NIRS has been used extensively to study healthy brain
function and the impact of cerebral pathology on functional
hemodynamics. This specific use of near-infrared techniques is
now often referred to as functional NIRS, or fNIRS (Boas,
Elwell, Ferrari, & Taga, 2014).
While fNIRS is an effective method of investigating brain
function, the techniques spatial resolution is limited by the
separation between sources and detectors, which is typically
between 20 and 30 cm. However, by extrapolating fNIRS
approaches and applying dense arrays of sources and detectors
that include a range of sourcedetector separations, spatial
information can be obtained in all three dimensions (Boas,
Chen, Grebert, & Franceschini, 2004; Correia, Banga, Everdell,
Gibson, & Hebden, 2009). Although there is a range of nomenclature, this approach is now most commonly referred to as
diffuse optical tomography, or diffuse optical topography
(DOT). While the rarity of absorption interactions allows
near-infrared light to traverse several centimeters of tissue, the
predominance of scattering interactions renders the light field
diffuse, placing a fundamental limit on the resolution of DOT
methods. However, with careful hardware design and the
application of accurate photon transport models and image

reconstruction approaches, a spatial resolution as good as
5 mm has been demonstrated through the intact human
scalp and skull (Habermehl et al., 2012; Zeff, White, Dehghani,
Schlaggar, & Culver, 2007). NIRS and imaging technologies are
developing quickly, and a range of fNIRS and DOT systems are
now commercially available. Wireless, wearable systems are
also being developed that will, in the near future, allow highspatiotemporal resolution images of the superficial regions of
the brain to be obtained in real time, with few limitations
imposed on the location or movement of the subject. Such
systems will further extend the already wide range of applications of fNIRS technologies (Boas et al., 2014).
Theoretical Basis
NIRS relies on an understanding of how light of a given wavelength interacts with tissue. The intensity of light that will pass
through a purely absorbing medium is determined by a simple
exponential relationship, with the intensity decaying exponentially with optical path length. However, biological tissues are
not purely absorbing. At near-infrared wavelengths, scattering
is by far the dominant interaction. In such a medium, the path
traversed by each photon resembles a random walk, increasing
the average optical path length and thus increasing the likelihood of absorption. As a result, the simple exponential relationship must be modified to account for the effect of
scattering. The modified BeerLambert law states that for a
given wavelength of light,
I
exDma G
I0
[1]
where I0 and I are the input and detected intensities, respectively, x is the separation between source and detector, and ma is
the absorption coefficient of the medium. In a medium containing multiple absorbers, the total absorption coefficient is simply
a linear sum of the absorption coefficients of each absorber,
which is proportional to the concentration of that absorber in
the medium. The loss of intensity due to photons being scattered away from the detector are represented by G. The variable
D is the differential path length factor (or DPF). The DPF is
dependent upon the reduced scattering coefficient ms, the
absorption coefficient ma, and the geometry of the source and
detector. The product xD represents the average optical path
length of photons that reach the detector. For a nonzero scattering coefficient, the DPF will always be greater than 1.
Because of the complexities of optically coupling a NIR
source to biological tissue, I0 of eqn [1] is generally unknown.
Similarly, the loss factor G is difficult to calculate. These
unknowns can be eliminated by measuring the changes in
optical intensity between two distinct states, such that
http://dx.doi.org/10.1016/B978-0-12-397025-1.00016-6
143
144
INTRODUCTION TO ACQUISITION METHODS | Functional Near-Infrared Spectroscopy
ln

I2
I1
I2
ln
ln
xDDma
I0
I0
I1
[2]
where I1 is the detected intensity for state 1 and I2 is the

detected intensity for state 2. This assumes that the input
intensity I0 and loss factor G are the same for both states,
which is generally true for small physiological changes in tissue
optical properties over a short period. The sourcedetector
separation (x) is known, and D can be either assumed or
measured in more advanced diffuse optical imaging systems
(Gibson, Hebden, & Arridge, 2005). Equation [2] therefore
allows the change in absorption coefficient between two states
(Dma) to be calculated using only a measurement of the change
in detected intensity between those two states.
Human tissues are composed of a number of absorbers of
NIR light. The most dominant are water, oxyhemoglobin, deoxyhemoglobin, lipids, melanin, and a number of cytochrome
species that are important in cellular metabolism (Boas, Pitris,
& Ramanujam, 2012). A change in concentration of any of these
components will result in a change in optical absorption. The
total absorption coefficient of a medium is given by the sum of
the absorption coefficients of its constituent absorbers. Therefore, by obtaining measures of the change in detected intensity
at N wavelengths, the change in absorption coefficient (and
therefore the change in concentration) of N chromophores can
be calculated. Although multiwavelength versions are available,
the majority of diffuse optical systems employ 2 wavelengths of
NIR light. By assuming that any change in the concentrations
of water, lipids, and melanin will be negligible over the duration
of an experiment and given that the concentration of cytochrome species is approximately 12% that of hemoglobin
(Cooper & Springett, 1997), a 2-wavelength measurement is
sufficient to measure changes in oxyhemoglobin concentration
and deoxyhemoglobin concentration.
Image Reconstruction
Although the resolution of any diffuse optical system is limited
by the dominance of scattering interactions in biological tissues, all multichannel diffuse optical systems provide significant spatial information. To extract the maximum available
spatial information from diffuse optical data, a detailed modeling and image reconstruction paradigm must be applied. Linear image reconstruction for diffuse optical approaches
assumes that an image of changes in chromophore concentration (DX) can be computed via
DX J 1 DY
[3]
where DY is a vector of the measured changes in the optical

parameter (usually intensity). The matrix J, often referred to as
the sensitivity matrix, defines how the measured optical intensity at each channel will be affected by a change in chromophore concentration in a given location. To calculate J, it is
necessary to know the exact locations of each source and
detector and to have an accurate model of the structural anatomy of the head. This model can be produced using structural
images of the subject (usually a segmented MRI image) or
using a suitable generic atlas that can be registered to the
subjects cranial landmarks (Cooper et al., 2012; Ferradal,
Eggebrecht, Hassanpour, Snyder, & Culver, 2013). Once a
suitable head structure is defined, a model of how the photons
emitted at each source location travel through the head tissues

can be produced. This model will define how the intensity at a
given detector will change given a localized perturbation in
chromophore concentration and can be used to calculate J.
Image reconstruction constitutes the inversion of J in order to
obtain the image (DX). This process of image reconstruction
removes a number of the assumptions required for the
channel-wise calculation of changes in chromophore concentration, including the need to assume a value for the DPF.
The Hemodynamic Response Function

The basic fNIRS experimental paradigm is to induce a change
in cortical chromophore concentration by application of an
external stimulus. The increase in neuronal electrochemical
activity in the regions of the brain associated with the processing of that stimulus results in an increased demand for oxygen
and glucose. This increase in demand is met by a response from
the local vasculature, via what is known as neurometabolic
neurovascular coupling (Logothetis et al., 2001; Steinbrink
et al., 2006). Arteriole dilation results in a local increase in
cerebral blood flow, and the associated changes in hemoglobin
concentrations can be measured by fNIRS systems.
Naively, one would expect an increase in neuronal activity
to result in a localized decrease in oxyhemoglobin concentration and increase in deoxyhemoglobin concentration, as more
oxygen is extracted from the blood. In fact, the classic hemodynamic response function consists of an increase in oxyhemoglobin concentration and a decrease in deoxyhemoglobin
concentration. This is due to the fact that the increased rate of
oxygen consumption and the corresponding increase in localized cerebral blood flow are not balanced. The seminal
positron-emission tomography study of 1986 by Fox and
Raichle found that the local increase in cerebral blood flow
was approximately 6 times larger than the increase in oxygen
consumption (Fox & Raichle, 1986). Although this value of the
flowconsumption ratio is still the subject of debate with
values ranging from 2 to 10 (Mintun et al., 2001), the overcompensation of localized cerebral blood flow is the basis of
the hemodynamic signal observed by fNIRS and is also the
basis of the BOLD signal of fMRI.
The hemodynamic response function, as recorded by fNIRS,
is small relative to the changes in hemoglobin concentrations
caused by systemic physiology such as the cardiac cycle and
changes in blood pressure. As a result, functional activation
can rarely be observed in response to a single trial of a given
stimulus. Instead, the stimulus must be repeated in a block or
event-related experimental design. Simple block averaging or
sophisticated statistical parametric mapping approaches (Tak &
Ye, 2014) can then be applied to fNIRS data in much the same
way as is performed in fMRI. A classic fNIRS hemodynamic
response function is shown in Figure 1(b).
Instrumentation
There are three distinct categories of NIRS systems based on
the type of measurement they obtain. The simplest, least
expensive, and most common are known as continuous
Scalp
HbO
Source
Gray matter
(cortex)
Whiter
matter
Detector
D Concentration (mM)
Cerebrospinal Skull
fluid (CSF)
3 cm
(a)
145
Human brain
14
12
10
8
6
4
2
0
-2
-4
HbT
HbR
-5
(b)
-5
10
Time (s)
15
20
(mM-cm)
0.02
-0.02
(c)
(d)
2.7
0.3
-0.1
-0.8
DHbO
(0.1 mMol)
(e)
(f)
Figure 1 Panel (a) depicts a single sourcedetector pair (channel) at the scalp and illustrates the tissues to which the channel is sensitive (adapted with
permission from Hillman, E. M. C. (2007). Optical brain imaging in vivo: Techniques and applications from animal to man. Journal of Biomedical Optics,
12, 051402). Panel (b) shows a classic hemodynamic response function, as recorded by fNIRS over the primary motor cortex. Time zero marks the
onset of a 2 s duration motor task (adapted with permission from Huppert, T. J., Hoge, R. D., Diamond, S. G., Franceschini, M. A., Boas, D. A., (2006). A
temporal comparison of BOLD, ASL, and NIRS hemodynamic responses to motor stimuli in adult humans. NeuroImage 29, 368382. doi:16/j.
neuroimage.2005.08.065). Panel (c) depicts an imaging array that allows the production of 2-D images of functional activation that can be mapped on
to a model of the cerebral cortex, as shown in panel (d) (adapted with permission from Takeuchi, M., Hori, E., Takamoto, K., Tran, A., Satoru, K.,
Ishikawa, A., et al. (2009). Brain cortical mapping by simultaneous recording of functional near infrared spectroscopy and electroencephalograms
from the whole brain during right median nerve stimulation. Brain Topography, 22, 197214. doi:10.1007/s10548-009-0109-2). Panel (e) shows the
layout of a high-density array used for diffuse optical tomography (DOT), and panel (f) shows corresponding 3-D functional activation maps reconstructed
using a realistic head model (adapted with permission from Hassanpour, M. S., White, B. R., Eggebrecht, A. T., Ferradal, S. L., Snyder, A. Z., Culver, J. P.
(2014). Statistical analysis of high density diffuse optical tomography. NeuroImage, 85 (Part 1), 104116. doi:10.1016/j.neuroimage.2013.05.105).
wave (CW) systems, which employ sources that emit light at a

constant intensity (Scholkmann et al., 2014). CW systems
only obtain measures of the intensity of the NIR light arriving
at each detector. Frequency-domain systems use sources of
NIR light modulated at 100 MHz such that both the
intensity and the phase of the detected signal can be measured

for each channel. The addition of the phase measurement
allows the average optical path length of detected photons
to be calculated, which, in turn, allows absolute hemoglobin
concentrations to be determined (Franceschini et al., 2007;
146
OLeary, Boas, Chance, & Yodh, 1995). The third category is

time-domain systems. Time-domain systems use fast pulsed
laser sources and sensitive photon-counting detectors to
measure the actual flight time of individual photons
(Torricelli et al., 2014). By sampling over a high number of
laser pulses, time-domain systems produce histograms of
photon flight time for each sourcedetector pair. These histograms (referred to as temporal point spread functions) contain significantly more information than can be obtained by
CW or frequency-domain systems. Furthermore, the sensitivity of the detectors used in time-domain systems allows
measurements to be obtained across significantly longer
sourcedetector separations, which has enabled the production of 3-D, depth-resolved images of the whole uncompressed breast (Enfield et al., 2007, 2013) and of the whole
newborn infant head (Austin et al., 2006; Gibson et al., 2006;
Hebden et al., 2002).
Array Design
The vast majority of fNIRS systems employ an array of optical
fibers that carry light between the instrumentation and the
scalp. The arrangement of source and detector fibers on the
scalp has a significant impact on the utility and accuracy of
the resulting data. The longer the separation between a source
and a detector on the scalp, the deeper into the tissue the average
detected photon will travel. The deeper the average photon
travels, the deeper the regions of tissue to which that channel
will be sensitive (Arridge, 1995). In practice, a balance must be
obtained between the sourcedetector separation and the
amount of light available for detection, which drops by approximately 1 order of magnitude for every 10 mm of separation.
The majority of detectors will not be sensitive enough to detect
light that has traversed more than 4050 mm, which limits the
depths to which fNIRS is typically sensitive. A channel with a
separation of 30 mm will sample the superficial cortex in most
adults, while obtaining a sufficient number of photons to ensure
a high signal quality.
The array of optical fibers can consist of a single channel
(Figure 1(a)) or can be designed to be conducive to the production of images. The simplest form of imaging array consists
of a fixed grid pattern, (Figure 1(c)). Such approaches are
limited to providing two-dimensional information because
any location in the target tissue is only sampled by a single
channel. These approaches are often referred to as DOT.
To produce images that contain information in the third
(depth) dimension, that is, to perform DOT, the array must
provide overlapping measurements (Figure 1(e)). Ideally,
these measurements will include a range of sourcedetector
separations up to 45 mm to ensure cortical sensitivity and
short (<15 mm) separations to allow superficial tissues to be
independently sampled. This is important because for a channel to sample the brain, light must travel through the scalp and
skull to the brain and back again. As a result, diffuse optical
techniques are vulnerable to contamination from scalp hemodynamics. While this interference can often be averaged out,
by sampling it directly with short-separation channels, it can
be directly and efficiently removed (Gagnon, Yucel, Boas, &
Cooper, 2014).
Applications
An excellent survey of the broad range of applications of these
technologies can be found in a recent special issue of Neuroimage, which celebrates 20 years of fNIRS. The issue contains
58 papers, a summary of which is provided in the introductory
article (Boas et al., 2014). The applications described by these
papers can be categorized into five domains: neurodevelopment, perception and cognition, motor control, psychiatric
disorders, and neurology and anesthesia.
Neurodevelopment studies are the largest growth area for
fNIRS as the portability and noninvasive nature of the technique overcome many of the challenges associated with performing neuroimaging studies of infants and children.
Numerous studies are elucidating language development,
visual-working memory, behavioral development, and
resting-state functional connectivity (Cristia et al., 2013;
Homae et al., 2010; Lloyd-Fox, Blasi, & Elwell, 2010). Exciting
recent clinical applications have demonstrated that fNIRS can
help us to better understand the atypical neurodevelopment
associated with attention deficit hyperactivity and autism
spectrum disorders (Fox, Wagner, Shrock, Tager-Flusberg, &
Nelson, 2013; Monden et al., 2012).
The largest clinical application of fNIRS is currently in the
study of psychiatric disorders, including schizophrenia,
affective disorders, and pathological aging. A comprehensive
review by Ehlis et al. describes investigations of the phenomenological characteristics of these psychiatric disorders, treatment effects, and genetic influences (Ehlis, Schneider,
Dresler, & Fallgatter, 2014).
Multimodal Applications
A major advantage of fNIRS is the ease with which it can be
combined with other neuroimaging modalities. Because glass
and plastic optical fibers are used to deliver light to the head of
the subject, fNIRS can be used in combination with magnetoencephalography (MEG) and MRI without producing susceptibility artifacts and in combination with electroencephalography
(EEG) without producing electrical artifacts.
Simultaneous fNIRS and EEG or MEG is appealing because
of the ability to explore neurovascular coupling by obtaining
concurrent measures of the neuronal and hemodynamic
responses to stimuli. Simultaneous fNIRS and MEG has been
used to study neurovascular coupling and habituation effects
in humans using median-nerve stimulation (Ou et al., 2009).
Combining fNIRS with EEG has shown great promise in the
study of epileptic disorders. Epileptic seizures are unpredictably and often in association with excessive motion. Because
fNIRS is relatively insensitive to motion artifacts and can be
applied for long periods in combination with EEG, it has been
shown to have great potential in the study of the neurovascular
coupling of ictal and interictal events (Cooper et al., 2011;
Nguyen et al., 2013; Roche-Labarbe et al., 2008).
The combination of fNIRS with fMRI has been used to cross
validate the two modalities (Eggebrecht et al., 2012; Steinbrink
et al., 2006) and to develop a better understanding of the
physiological processes that underlie both techniques. Early

work established that the hemodynamic responses as measured by fNIRS and fMRI are spatially and temporally correlated (Strangman, Culver, Thompson, & Boas, 2002).
Subsequent work demonstrated that the fMRI BOLD signal is
better correlated with the deoxyhemoglobin than the oxyhemoglobin signal (Huppert et al., 2006) and revealed that
fNIRS can be used to evaluate the intravascular versus extravascular contributions to the BOLD signal (Huppert, Allen,
Diamond, & Boas, 2009).
The hemodynamic signal measured by fNIRS and BOLD
fMRI is an indirect measure of neuronal activity and is the
result of the competition between changes in oxygen consumption and cerebral blood flow. Efforts have therefore focused on
estimating functional changes in the relative cerebral metabolic rate of oxygen (rCMRO2), in order to obtain a measure
that better represents the neuronal response.
Functionally induced changes in rCMRO2 can be estimated
using BOLD and perfusion-sensitive MRI data if a hypercapnic
calibration technique is applied during each study and if blood
volume is assumed to be related to blood flow by a simple
power law (Davis, Kwong, Weisskoff, & Rosen, 1998). By
applying fNIRS in conjunction with fMRI, it is possible to
estimate rCMRO2 without assuming a flowvolume relationship and without exposing the subject to a hypercapnic challenge (Huppert et al., 2009; Tak, Jang, Lee, & Ye, 2010; Yucel
et al., 2012). These approaches present the exciting possibility
of achieving quantitative multimodal neuroimaging.

Optical Image Reconstruction.
References
Arridge, S. R. (1995). Photon-measurement density functions. Part I: Analytical forms.
Applied Optics, 34, 73957409. http://dx.doi.org/10.1364/AO.34.007395.
Austin, T., Gibson, A. P., Branco, G., Yusof, R. M., Arridge, S. R., Meek, J. H., et al.
(2006). Three dimensional optical imaging of blood volume and oxygenation in the
neonatal brain. NeuroImage, 31, 14261433. http://dx.doi.org/10.1016/j.
Boas, D. A., Chen, K., Grebert, D., & Franceschini, M. A. (2004). Improving the diffuse
optical imaging spatial resolution of the cerebral hemodynamic response to brain
activation in humans. Optics Letters, 29, 15061508.
Boas, D. A., Elwell, C. E., Ferrari, M., & Taga, G. (2014). Twenty years of functional
near-infrared spectroscopy: Introduction for the special issue. NeuroImage, 85(Part
1), 15. http://dx.doi.org/10.1016/j.neuroimage.2013.11.033.
Boas, D. A., Pitris, C., & Ramanujam, N. (2012). Handbook of biomedical optics. Boca
Raton: CRC Press.
Cooper, R. J., Caffini, M., Dubb, J., Custo, A., Tsuzuki, D., Fischl, B., et al. (2012).
Validating atlas-guided DOT: A comparison of diffuse optical tomography informed
by atlas and subject-specific anatomies. NeuroImage, http://dx.doi.org/10.1016/j.
Cooper, R. J., Hebden, J. C., OReilly, H., Mitra, S., Michell, A. W., Everdell, N. L., et al.
(2011). Transient haemodynamic events in neurologically compromised infants:
A simultaneous EEG and diffuse optical imaging study. NeuroImage, 55,
16101616, 16/j.neuroimage.2011.01.022.
Cooper, C. E., & Springett, R. (1997). Measurement of cytochrome oxidase and
mitochondrial energetics by nearinfrared spectroscopy. Philosophical
Transactions of the Royal Society of London. Series B: Biological Sciences, 352,
669676. http://dx.doi.org/10.1098/rstb.1997.0048.
Correia, T., Banga, A., Everdell, N. L., Gibson, A. P., & Hebden, J. C. (2009). A
quantitative assessment of the depth sensitivity of an optical topography system
using a solid dynamic tissue-phantom. Physics in Medicine and Biology, 54,
62776286. http://dx.doi.org/10.1088/0031-9155/54/20/016.
147
Cristia, A., Dupoux, E., Hakuno, Y., Lloyd-Fox, S., Schuetze, M., Kivits, J., et al. (2013).
An online database of infant functional near infrared spectroscopy studies: A
community-augmented systematic review. PLoS ONE, 8, e58906. http://dx.doi.org/
10.1371/journal.pone.0058906.
functional MRI: Mapping the dynamics of oxidative metabolism. Proceedings of the
National Academy of Sciences, 95, 18341839, http://dx.doi.org/doi: VL 95.
Eggebrecht, A. T., White, B. R., Ferradal, S. L., Chen, C., Zhan, Y., Snyder, A. Z., et al.
(2012). A quantitative spatial comparison of high-density diffuse optical
tomography and fMRI cortical mapping. NeuroImage, 61, 11201128. http://dx.doi.
org/10.1016/j.neuroimage.2012.01.124.
Ehlis, A.-C., Schneider, S., Dresler, T., & Fallgatter, A. J. (2014). Application of
functional near-infrared spectroscopy in psychiatry. NeuroImage, 85(Part 1),
478488. http://dx.doi.org/10.1016/j.neuroimage.2013.03.067.
Enfield, L., Cantanhede, G., Douek, M., Ramalingam, V., Purushotham, A., Hebden, J.,
et al. (2013). Monitoring the response to neoadjuvant hormone therapy for locally
advanced breast cancer using three-dimensional time-resolved optical
mammography. Journal of Biomedical Optics, 18, 56012. http://dx.doi.org/
10.1117/1.JBO.18.5.056012.
Enfield, L. C., Gibson, A. P., Everdell, N. L., Delpy, D. T., Schweiger, M., Arridge, S. R.,
et al. (2007). Three-dimensional time-resolved optical mammography of the
uncompressed breast. Applied Optics, 46, 36283638. http://dx.doi.org/10.1364/
AO.46.003628.
Ferradal, S. L., Eggebrecht, A. T., Hassanpour, M., Snyder, A. Z., & Culver, J. P. (2013).
Atlas-based head modeling and spatial normalization for high-density diffuse
optical tomography: In vivo validation against fMRI. NeuroImage, 10.1016/j.
Fox, P. T., & Raichle, M. E. (1986). Focal physiological uncoupling of cerebral
blood flow and oxidative metabolism during somatosensory stimulation in
human subjects. Proceedings of the National Academy of Sciences, 83,
11401144.
Fox, S. E., Wagner, J. B., Shrock, C. L., Tager-Flusberg, H., & Nelson, C. A. (2013).
Neural processing of facial identity and emotion in infants at high-risk for autism
spectrum disorders. Frontiers in Human Neuroscience, 7, http://dx.doi.org/
10.3389/fnhum.2013.00089.
Franceschini, M. A., Thaker, S., Themelis, G., Krishnamoorthy, K. K., Bortfeld, H.,
Diamond, S. G., et al. (2007). Assessment of infant brain development with
frequency-domain near-infrared spectroscopy. Pediatric Research, 61, 546551.
http://dx.doi.org/10.1203/pdr.0b013e318045be99.
Gagnon, L., Yucel, M. A., Boas, D. A., & Cooper, R. J. (2014). Further improvement in
reducing superficial contamination in NIRS using double short separation
measurements. NeuroImage, 85(Part 1), 127135. http://dx.doi.org/10.1016/j.
Gibson, A. P., Austin, T., Everdell, N. L., Schweiger, M., Arridge, S. R., Meek, J. H., et al.
(2006). Three-dimensional whole-head optical tomography of passive motor
evoked responses in the neonate. NeuroImage, 30, 521528.
Gibson, A. P., Hebden, J. C., & Arridge, S. R. (2005). Recent advances in diffuse optical
imaging. Physics in Medicine and Biology, 50, R1R43.
Habermehl, C., Holtze, S., Steinbrink, J., Koch, S. P., Obrig, H., Mehnert, J., et al.
(2012). Somatosensory activation of two fingers can be discriminated with
ultrahigh-density diffuse optical tomography. NeuroImage, 59, 32013211. http://
dx.doi.org/10.1016/j.neuroimage.2011.11.062.
Hebden, J. C., Gibson, A., Yusof, R. M., Everdell, N., Hillman, E. M.C, Delpy, D. T., et al.
(2002). Three-dimensional optical tomography of the premature infant brain.
Physics in Medicine and Biology, 47, 41554166. http://dx.doi.org/10.1088/00319155/47/23/303.
Homae, F., Watanabe, H., Otobe, T., Nakano, T., Go, T., Konishi, Y., et al. (2010).
Development of global cortical networks in early infancy. Journal of Neuroscience,
30, 48774882. http://dx.doi.org/10.1523/JNEUROSCI.5618-09.2010.
Huppert, T. J., Allen, M. S., Diamond, S. G., & Boas, D. A. (2009). Estimating cerebral
oxygen metabolism from fMRI with a dynamic multicompartment Windkessel
model. Human Brain Mapping, 30, 15481567. http://dx.doi.org/10.1002/
hbm.20628.
Huppert, T. J., Hoge, R. D., Diamond, S. G., Franceschini, M. A., & Boas, D. A. (2006).
A temporal comparison of BOLD, ASL, and NIRS hemodynamic responses to motor
stimuli in adult humans. NeuroImage, 29, 368382. doi:16/j.
Jobsis, F. F. (1977). Noninvasive, infrared monitoring of cerebral and myocardial
oxygen sufficiency and circulatory parameters. Science, 198, 12641267.
Lloyd-Fox, S., Blasi, A., & Elwell, C. E. (2010). Illuminating the developing brain: The
past, present and future of functional near infrared spectroscopy. Neuroscience and
Biobehavioral Reviews, 34, 269284. http://dx.doi.org/10.1016/j.
neubiorev.2009.07.008.
148
Neurophysiological investigation of the basis of the fMRI signal. Nature, 412,
150157. http://dx.doi.org/10.1038/35084005.
Mintun, M. A., Lundstrom, B. N., Snyder, A. Z., Vlassenko, A. G., Shulman, G. L., &
Raichle, M. E. (2001). Blood flow and oxygen delivery to human brain during
functional activity: Theoretical modeling and experimental data. Proceedings of the
National Academy of Sciences, 98, 68596864. http://dx.doi.org/10.1073/
pnas.111164398.
Monden, Y., Dan, H., Nagashima, M., Dan, I., Tsuzuki, D., Kyutoku, Y., et al. (2012).
Right prefrontal activation as a neuro-functional biomarker for monitoring acute
effects of methylphenidate in ADHD children: An fNIRS study. Neuroimaging
Clinics, 1, 131140. http://dx.doi.org/10.1016/j.nicl.2012.10.001.
Nguyen, D. K., Tremblay, J., Pouliot, P., Vannasing, P., Florea, O., Carmant, L., et al.
(2013). Noninvasive continuous functional near-infrared spectroscopy combined
with electroencephalography recording of frontal lobe seizures. Epilepsia, 54,
331340. http://dx.doi.org/10.1111/epi.12011.
OLeary, M. A., Boas, D. A., Chance, B., & Yodh, A. G. (1995). Experimental images of
heterogeneous turbid media by frequency-domain diffusing-photon tomography.
Optics Letters, 20, 426428. http://dx.doi.org/10.1364/OL.20.000426.
Ou, W., Nissila, I., Radhakrishnan, H., Boas, D. A., Hamalainen, M. S., &
Franceschini, M. A. (2009). Study of neurovascular coupling in humans
via simultaneous magnetoencephalography and diffuse optical imaging
acquisition. NeuroImage, 46, 624632. http://dx.doi.org/10.1016/j.
Roche-Labarbe, N., Zaaimi, B., Berquin, P., Nehlig, A., Grebe, R., & Wallois, F. (2008).
NIRS-measured oxy- and deoxyhemoglobin changes associated with EEG spikeand-wave discharges in children. Epilepsia, http://dx.doi.org/10.1111/j.15281167.2008.01711.x.
Scholkmann, F., Kleiser, S., Metz, A. J., Zimmermann, R., Mata Pavia, J., Wolf, U., et al.
(2014). A review on continuous wave functional near-infrared spectroscopy and
imaging instrumentation and methodology. NeuroImage, 85(Pt 1), 627. http://dx.
doi.org/10.1016/j.neuroimage.2013.05.004.
Steinbrink, J., Villringer, A., Kempf, F., Haux, D., Boden, S., & Obrig, H. (2006).
Illuminating the BOLD signal: Combined fMRI-fNIRS studies. Magnetic Resonance
Imaging, 24, 495505. doi:16/j.mri.2005.12.034.
Strangman, G., Culver, J. P., Thompson, J. H., & Boas, D. A. (2002). A quantitative
comparison of simultaneous BOLD fMRI and NIRS recordings during functional
brain activation. NeuroImage, 17, 719731. doi:06/nimg.2002.1227.
Tak, S., Jang, J., Lee, K., & Ye, J. C. (2010). Quantification of CMRO(2) without
hypercapnia using simultaneous near-infrared spectroscopy and fMRI
measurements. Physics in Medicine and Biology, 55, 32493269. http://dx.doi.org/
10.1088/0031-9155/55/11/017.
Tak, S., & Ye, J. C. (2014). Statistical analysis of fNIRS data: A comprehensive review.
NeuroImage, 85(Part 1), 7291. http://dx.doi.org/10.1016/j.
Torricelli, A., Contini, D., Pifferi, A., Caffini, M., Re, R., Zucchelli, L., et al. (2014). Time
domain functional NIRS imaging for human brain mapping. NeuroImage, 85(Part 1),
Yucel, M. A., Huppert, T. J., Boas, D. A., & Gagnon, L. (2012). Calibrating the BOLD
signal during a motor task using an extended fusion model incorporating DOT,
BOLD and ASL data. NeuroImage, 61, 12681276. http://dx.doi.org/10.1016/j.
Zeff, B. W., White, B. R., Dehghani, H., Schlaggar, B. L., & Culver, J. P. (2007).
Retinotopic mapping of adult human visual cortex with high-density diffuse optical
tomography. Proceedings of the National Academy of Sciences, 104, 1216912174.
http://dx.doi.org/10.1073/pnas.0611266104.
Perfusion Imaging with Arterial Spin Labeling MRI

TT Liu, University of California, San Diego, CA, USA
Introduction
Scientific inquiry into the relationship between brain activity
and blood flow can be traced back to a series of experiments
performed in the late nineteenth century by Angelo Mosso,
showing changes in cerebral blood pulsation during the performance of various mental activities by patients with skull
defects (James, 1890). Later, Roy and Sherrington demonstrated increases in brain blood volume (and presumably
blood flow) in response to nerve stimulation of anesthetized
animals (Roy & Sherrington, 1890). In the 1940s, the ability to
obtain quantitative measures of whole brain blood flow was
demonstrated with the nitrous oxide method of Kety and
Schmidt (Kety & Schmidt, 1948; Small, 2004). Although further advances were made in the 1960s, extending this basic
approach to obtain regional measures of brain perfusion, it
was not until the introduction in the early 1970s of tomographic imaging methods, such as computed tomography
(CT) and positron emission tomography (PET), that the modern era of mapping of brain perfusion would begin (Raichle,
1998). These were followed in the early 1990s by the introduction of regional brain perfusion imaging methods using magnetic resonance imaging (MRI; Rosen, Belliveau, Vevea, &
Brady, 1990; Williams, Detre, Leigh, & Koretsky, 1992).
At present, methods for measuring brain perfusion in
humans include single-photon emission computed tomography,
PET, xenon-enhanced CT, dynamic perfusion CT, dynamic susceptibility contrast (DSC) MRI, and arterial spin labeling (ASL)
MRI (Wintermark et al., 2005). Building upon the basic principles described in the seminal work of Kety and Schmidt (Kety &
Schmidt, 1948), these methods are all based on the measurement of the concentration of a tracer that is delivered to and
cleared from the tissue by blood flow, with additional clearance
due to the natural decay of the tracer. For quantitative measures
of cerebral blood flow (CBF), PET is generally considered
the gold standard, as its accuracy has been validated in nonhuman primate models (Raichle, Martin, Herscovitch, Mintun,
& Markham, 1983). However, its adoption for routine measures
of CBF has been limited by the need for an arterial catheter, the
use of radioactive tracers, and the need for a cyclotron (Carroll
et al., 2002). Both CT and DSC-MRI are widely used to measure
perfusion in clinical settings (Wintermark et al., 2005), but their
application for brain mapping research studies has been limited
by the need to inject contrast agents and, in the case of CT,
concerns about exposure to ionizing radiation. In contrast, ASL
MRI uses arterial water as an endogenous tracer, obviating the
need for the injection of tracers, and the associated MRI image
acquisition process does not involve ionizing radiation. As a
result, ASL can provide measures of regional perfusion with
moderately high spatial resolution in a completely noninvasive
manner, making it amenable to repeated scans and longitudinal
studies. In addition, ASL is well suited to characterizing functional changes in perfusion. Because of these properties, the
adoption of ASL for the measurement of brain perfusion in

both research studies and clinical applications is growing.
Cerebral Blood Flow

CBF or perfusion is a measure of the rate of delivery of arterial
blood to a capillary bed in the brain tissue. The standard unit
of measurement for CBF is milliliters of blood per 100 g of
tissue per minute, and a typical value in the human brain is
60 ml per 100 g per minute. Assuming an average brain tissue
density of 1 g ml1, the average CBF may also be written as
60 ml per 100 ml per minute 0.01 s1. Note that this last
expression for CBF means that within a 1 s period, approximately 1% of the total tissue volume consists of freshly delivered blood.
ASL Methods
Most ASL methods measure CBF by taking the difference DM of
two sets of images: tag images, in which the magnetization of
arterial blood is inverted or saturated, and control images, in
which the magnetization of arterial blood is fully relaxed. The
difference between the control and tag images yields an image
that is proportional to the blood that has been delivered. To
reduce noise in the CBF estimate, a number of tag and control
images (e.g., 50 tag and 50 control) are typically acquired in an
interleaved fashion, and the average difference is computed.
The time between the acquisition of the tag images and that of
control images is on the order of 24 s, so that an ASL scan
with 100 total images takes 200400 s.
There are a variety of ASL methods that have been developed, and these methods can be divided into three main
classes: (1) pulsed ASL (PASL) in which short radio frequency
(RF) pulses are used to tag the blood over an extended spatial
region that is proximal to the imaging region of interest, (2)
continuous ASL (CASL) in which a long (on the order of several
seconds) RF waveform or train of pulses is used in conjunction
with gradient fields to tag flowing blood spins as they traverse
an irradiated plane (this class also includes pseudocontinuous
ASL or pCASL), and (3) velocity-selective ASL (VS-ASL) in which
an RF pulse train is applied that selectively saturates flowing
spins with no spatial selectivity.
Perfusion Quantification
The ASL difference signal DM not only is proportional to CBF
but also exhibits a complex dependence on a number of physiological parameters. Variations in these physiological parameters can cause systematic errors in the CBF measurements, and
the goal of quantitative ASL methods is to minimize these
http://dx.doi.org/10.1016/B978-0-12-397025-1.00017-8
149
150
INTRODUCTION TO ACQUISITION METHODS | Perfusion Imaging with Arterial Spin Labeling MRI
errors (Buxton, 2005; Wong, 2005). Two major sources of error

are variations in (1) the transit delay, defined as the time
required for tagged spins to flow from the tagging region to
the imaging region, and (2) the temporal width of the arterial
bolus, defined as the time required for the set of all tagged
spins to cross a plane. Additional sources of error are reviewed
in Liu & Brown (2007).
Transit delays arise in spatial tagging methods because of
the need to place the tagging slab in PASL or the tagging plane
in CASL some distance (13 cm) from the imaging slice in
order to minimize the inadvertent perturbation of spins in
the imaging region by the tagging pulse. Transit delay errors
can be minimized by using prior knowledge of transit delay
values (Dai, Robson, Shankaranarayanan, & Alsop, 2012) in
conjunction with the appropriate choice of pulse sequence
timing parameters to ensure that the tagged blood has time
to travel from the tagging region to the imaging region. In
contrast to CASL and PASL, transit delays are typically negligible in VS-ASL because the velocity-selective tagging process
saturates arterial blood with velocities down to 12 cm s1,
corresponding to vessels (roughly 50100 m arterioles) that
are close to the capillary bed and within the imaging region.
This insensitivity to transit delay makes VS-ASL a particularly
attractive method for studies of subjects, such as stroke
patients, who may exhibit long transit delays.
The temporal width of the arterial bolus is inherently well
controlled with CASL methods, whereas robust and uniform
control of bolus width with PASL methods is more difficult due
to variations in the bolus width across brain regions and subjects. Saturation pulses (e.g., QUIPSS II and Q2TIPS) can be
applied at a specified time after the inversion process to define

the bolus width in PASL (Luh, Wong, Bandettini, & Hyde,
1999; Wong, Buxton, & Frank, 1998a).
With appropriate attention to quantitative issues, ASL can
provide CBF measures that show good agreement with the
gold standard PET measures of both baseline CBF (Chen,
Wieckowska, Meyer, & Pike, 2008; Donahue, Lu, Jones,
Pekar, & Van Zijl, 2006; Xu et al., 2010; Ye et al., 2000) and
functional changes in CBF (Feng et al., 2004). Example quantitative ASL CBF maps are shown in the top row of Figure 1.
ASL CBF measures exhibit moderately high reliability and
reproducibility for studies performed at a single site (Chen,
Wang, & Detre, 2011; Jahng et al., 2005; Jiang et al., 2010;
Wang et al., 2011) and across multiple sites (Gevers et al.,
2011; Petersen, Mouridsen, & Golay, 2010).
Signal-to-Noise Ratio
In a typical ASL experiment, about 1 s is allowed for the delivery of blood, corresponding to 1 ml of blood delivered to
100 ml of tissue for the typical CBF value of 60 ml per 100 g
per minute discussed previously. As a result, the overall magnetic resonance (MR) signal due to the delivered blood is only
about 1% of the total signal due to the tissue. This small
percentage contributes to the low intrinsic signal-to-noise
ratio (SNR) of ASL methods. Of the three major classes of
ASL methods, CASL has the highest SNR, followed by PASL,
and then VS-ASL (Chen et al., 2011; Wong, Buxton, & Frank,
1998b; Wong et al., 2006).
CBF in ml/100g-min using OptPCASL
20
40
60
80
100
120
Figure 1 Examples of baseline cerebral blood flow (CBF) maps (top row), vascular territory maps (middle row), and functional activation maps (bottom
row). The baseline CBF maps show the spatial distribution of perfusion (with physiological units of milliliter per 100 g per minute) in the brain of a
healthy young volunteer. The vascular territory maps show the territories supplied by the right carotid artery (red), the left carotid artery (green), and the
vertebral arteries (blue). The functional activation maps show those brain regions in which the functional CBF response was significantly correlated
(p < 0.001, corrected for multiple comparisons) with the timing pattern of a visual stimulus (Image Credit: David S. Shin).
Cardiac and respiratory fluctuations are a major source of
noise in ASL experiments, especially at higher field strengths.
These can be partially attenuated with physiological noise
reduction methods (Behzadi, Restom, Liau, & Liu, 2007;
Restom, Behzadi, & Liu, 2006) and background suppression
methods that attenuate the static tissue component. However,
background suppression methods can lead to an underestimation of CBF values (Garcia, Duhamel, & Alsop, 2005; Shin, Liu,
Wong, & Liu, 2011).
Image Acquisition
For ASL, the choice of the tagging method (PASL, CASL, and VSASL) is largely independent of the choice of imaging method. As
a result, ASL studies can take advantage of the wide array of 2-D
and 3-D MRI imaging pulse sequences that have been developed. For 2-D imaging, in which the imaging data are acquired
on a slice-by-slice basis, echo planar imaging and spiral
sequences are widely used (Wang et al., 2004). There is an
increasing use of 3-D acquisitions that can offer whole brain
coverage, simultaneous acquisition of all slices, and greater SNR
as compared with 2-D acquisitions (Duhamel & Alsop, 2004;
Fernandez-Seara et al., 2005; Gunther, Oshio, & Feinberg,
2005). With the simultaneous acquisition of slices in a 3-D
acquisition, the longitudinal relaxation of the tagged spins is
the same across slices, leading to a greater consistency in SNR as
compared with 2-D acquisitions, where the superior slices are
acquired at a longer inversion time (with greater relaxation of
the tagged spins) and can exhibit lower SNR as compared to the
inferior slices. There is typically a greater degree of throughplane blurring associated with 3-D acquisitions as compared
to 2-D methods, but these effects can be partly addressed
through the use of variable flip angles in the echo train or robust
multishot acquisitions (Nielsen & Hernandez-Garcia, 2012;
Tan, Hoge, Hamilton, Gunther, & Kraft, 2011).
Typical ASL image acquisition protocols provide CBF values
over the entire brain with a spatial resolution on the order of
35 mm. To improve SNR, the through-plane resolution is
often chosen to be slightly larger than the in-plane resolution
(e.g., 3 3 mm in-plane resolution with a 5 mm slice thickness). With the use of fast imaging sequences and higher
magnetic field strengths, ASL acquisitions with in-plane resolutions of 12 mm (and 58 mm slice thickness) have been
demonstrated (Grossman et al., 2009; Zuo et al., 2013).
Mapping of Vascular Territories

In conventional ASL acquisitions, the arterial blood from all of
the vessels is tagged, and the resulting perfusion maps reflect
the blood that is supplied by all of the feeding arteries. With
vessel-encoded ASL (VEASL), selective tagging of the arteries is
performed, such that certain vessels are tagged, while other
vessels remain in the control condition (Gunther, 2006;
Wong, 2007). As shown in the second row of Figure 1,
VEASL produces vascular territory maps, reflecting the extent
to which each territory is perfused by a feeding artery. This
process can be performed in an SNR-efficient manner such that
a VEASL scan provide both whole brain CBF maps and vascular
151
territory maps in the same time that a conventional ASL scan

requires to provide a whole brain CBF map (Helle, Rufer, van
Osch, Jansen, & Norris, 2012; Wong, 2007).
Use of ASL for Functional Imaging

Perfusion functional MRI (fMRI) based on ASL provides measures of functional changes in CBF and offers a useful complement to fMRI studies based upon blood oxygenation leveldependent (BOLD) contrast. Perfusion fMRI can be used to
measure dynamic changes in CBF that occur over time in
response either to external stimuli (e.g., a flashing checkerboard pattern) or as a reflection of intrinsic spontaneous
brain activity (e.g., resting-state neural fluctuations; Aguirre
& Detre, 2012; Aguirre, Detre, & Wang, 2005; Borogovac &
Asllani, 2012). From these dynamic measures, we can make a
map indicating where there are statistically significant changes
in CBF, characterize the amplitude of these changes and their
spatial distribution, examine the functional connectivity
between brain regions, and also examine features of the
dynamic response, such as rise and fall times. The third row
in Figure 1 shows functional activation maps of the functional
CBF response to a visual stimulus.
Aside from the use of different pulse sequence and acquisition parameters, the mechanics of an ASL fMRI experiment are
similar to that of a BOLD fMRI experiment, with data being
acquired as the subject is either performing a task (i.e., task
state) or lying quietly (i.e., control or rest state) in the scanner.
With real-time processing and analysis of the data (HernandezGarcia, Jahanian, Greenwald, Zubieta, & Peltier, 2011), there is
also the opportunity for fMRI-guided biofeedback in which the
subject attempts to modify their brain activity in response to an
fMRI indicator of their brain response.
Processing of Functional ASL Data

In most ASL fMRI experiments, control and tag images are
acquired in an interleaved fashion. A perfusion time series can
then be formed from the running subtraction of the control and
tag images. For example, given an interleaved acquisition of the
form (Tag[0], Control[0], Tag[1], Control[1],. . .), surround subtraction over the image acquisition time series produces the
perfusion weighted time series: (Control[0] (Tag[0] Tag
[1])/2], (Control[0] Control[1])/2 Tag[1], . . .). This type of
differencing is referred to as surround subtraction and represents
one specific approach to the filtered subtraction of control and
tag images (Liu & Wong, 2005). ASL data can also be processed
using general linear model (GLM) and Bayesian approaches that
can increase the sensitivity to estimate functional CBF responses
(Hernandez-Garcia, Jahanian, & Rowe, 2010; Mumford,
Hernandez-Garcia, Lee, & Nichols, 2006; Woolrich, Chiarelli,
Gallichan, Perthen, & Liu, 2006).
As discussed earlier, cardiac and respiratory fluctuations are
a major source of noise in ASL experiments, especially at higher
field strengths. Since the inherent SNR of ASL fMRI methods
can be roughly one to two orders of magnitude lower than that
of BOLD fMRI (Aguirre, Detre, Zarahn, & Alsop, 2002; Liau,
Perthen, & Liu, 2008; Perthen, Bydder, Restom, & Liu, 2008),
152
the need for methods to reduce physiological noise is especially pronounced. Retrospective image-based correction
methods have been shown to significantly reduce physiological noise for perfusion fMRI studies (Behzadi et al., 2007;
Restom et al., 2006).
Temporal Resolution and Insensitivity to LowFrequency Drifts

The temporal resolution of perfusion fMRI is inherently poorer
than BOLD fMRI because of the necessity to form tag and
control images and to allow time for blood to be delivered
from the tagging region to the imaging slice. In a typical PASL
experiment, a repetition time (TR) of 2 s or more is used, so that
one tag and control image pair is acquired every 4 s. For CASL,
the TR is typically longer (on the order of 4 s) than for PASL,
due to the longer time required for the CASL tagging process.
By comparison, the temporal resolution of BOLD fMRI is
typically 12 s and can be as low as 100 ms with more recently
developed methods (Feinberg et al., 2010; Zahneisen et al.,
2011). Methods for improving temporal resolution include
turbo-ASL (Wong, Luh, & Liu, 2000) and single-shot ASL
(Duyn, Tan, van Gelderen, & Yongbi, 2001). When quantitative measures of CBF are not needed, these methods can be
useful for mapping perfusion-related changes in the brain
(Hernandez-Garcia, Lee, Vazquez, Yip, & Noll, 2005).
The lower temporal resolution of ASL is often considered a
disadvantage because the reduced number of time points
reduces the potential statistical degrees of freedom as compared to BOLD. However, ASL can provide an advantage in
experiments where the signals of interest vary slowly with time.
Low-frequency drifts are present in most BOLD fMRI time
series data and tend to reduce the degrees of freedom and
hence the statistical power of BOLD experiments. ASL can
deal effectively with low-frequency confounds because the
running subtraction of the control and tag images (Liu &
Wong, 2005) greatly attenuates the low-frequency drifts that
are unrelated to functional activity. This can make ASL more
sensitive than BOLD for experimental paradigms with long
periods (i.e., long blocks) where a slow time course of functional activity is anticipated, such as the response to an administered drug (Aguirre et al., 2002).
Spatial Localization and Relation to Neural Activity

Because perfusion methods directly measure the amount of
arterial blood that has been delivered to the capillary bed and
exchanged with tissue, the functional CBF signal may be more
localized to the sites of neuronal activation than the BOLD
signal, which tends to be more localized to the venules and
veins (Kim & Duong, 2002; Luh, Wong, Bandettini, Ward, &
Hyde, 2000; Pimentel, Vilela, Sousa, & Figueiredo, 2013;
Tjandra et al., 2005). As compared to the BOLD signal
(which exhibits a complex dependence on changes in CBF,
the cerebral rate of oxygen metabolism (CMRO2), and cerebral
blood volume), perfusion fMRI provides a quantitative measure of changes in a single physiological quantity and therefore
has the potential to provide a better reflection of neural
activity. A number of studies suggest that the relationship

between CBF changes and neural activity may be more direct
than the relationship found between BOLD and neural activity
(Aguirre et al., 2002; Miller et al., 2001; Raoult et al., 2011;
Tjandra et al., 2005; Wang et al., 2003).
Simultaneous Estimates of CBF and BOLD

With the use of BOLD-sensitive image acquisitions, ASL
methods can be used to obtain simultaneous estimates of functional changes in CBF and BOLD. Although more complicated
to acquire than BOLD measures alone, the acquisition of
both CBF and BOLD responses can offer a richer and more
nuanced interpretation of brain function. For example, in a
study comparing the response to memory encoding in young
and older adults, Restom et al. (Restom, Bangen, Bondi,
Perthen, & Liu, 2007) found that while the BOLD responses
were similar between populations, the older subjects showed
significantly greater functional CBF responses and significantly
lower baseline CBF levels. The observations were found to be
consistent with a greater increase of the CMRO2 response in
the older subjects. The combination of CBF and BOLD measures
also provides the capability to obtain calibrated fMRI estimates of
functional changes in CMRO2, which has been shown in animal
studies to be correlated with functional changes in neuronal
activity (Davis, Kwong, Weisskoff, & Rosen, 1998; Hyder,
2004). The calibrated fMRI approach has been used to characterize the functional CMRO2 response in a wide range of studies,
including those of primary sensory areas (Chiarelli et al.,
2007; Hoge et al., 1999), epileptic discharges (Stefanovic et al.,
2005), HIV (Ances, Vaida, Ellis, & Buxton, 2011), aging
(Hutchison, Shokri-Kojori, Lu, & Rypma, 2013), and the effects
of pharmacological agents, such as caffeine (Chen & Parrish,
2009).
Conclusion
ASL MRI offers the ability to image brain perfusion in a
completely noninvasive fashion, without the need for ionizing
radiation or injected tracers. Its accuracy and precision are
comparable or superior to those of alternate methods, such
as PET and CT. ASL MRI can provide measures of both baseline
perfusion and functional changes in perfusion with moderately high temporal and spatial resolution. ASL MRI has been
widely used for research studies, and its adoption for clinical
studies is growing with the increasing availability of this
method on standard MRI systems.

Obtaining Quantitative Information from fMRI; Positron Emission
Tomography and Neuroreceptor Mapping In Vivo; Pulse Sequence
Dependence of the fMRI Signal; Temporal Resolution and Spatial
Resolution of fMRI.
References
Aguirre, G. K., & Detre, J. A. (2012). The development and future of perfusion fMRI for
dynamic imaging of human brain activity. NeuroImage, 62, 12791285.
Aguirre, G. K., Detre, J. A., & Wang, J. (2005). Perfusion fMRI for functional
neuroimaging. International Review of Neurobiology, 66, 213236.
Aguirre, G. K., Detre, J. A., Zarahn, E., & Alsop, D. C. (2002). Experimental design and
the relative sensitivity of BOLD and perfusion fMRI. NeuroImage, 15, 488500.
Ances, B., Vaida, F., Ellis, R., & Buxton, R. (2011). Testretest stability of calibrated
BOLD-fMRI in HIV and HIV subjects. NeuroImage, 54, 21562162.
Behzadi, Y., Restom, K., Liau, J., & Liu, T. T. (2007). A component based noise
correction method (CompCor) for BOLD and perfusion based fMRI. NeuroImage,
37, 90101.
Borogovac, A., & Asllani, I. (2012). Arterial Spin Labeling (ASL) fMRI: Advantages,
theoretical constrains, and experimental challenges in neurosciences. International
Journal of Biomedical Imaging, 2012, 818456.
Buxton, R. B. (2005). Quantifying CBF with arterial spin labeling. Journal of Magnetic
Carroll, T. J., Teneggi, V., Jobin, M., Squassante, L., Treyer, V., Hany, T. F., et al.
(2002). Absolute quantification of cerebral blood flow with magnetic resonance,
reproducibility of the method, and comparison with H2(15)O positron emission
tomography. Journal of Cerebral Blood Flow and Metabolism, 22, 11491156.
Chen, Y., & Parrish, T. B. (2009). Caffeines effects on cerebrovascular reactivity and
coupling between cerebral blood flow and oxygen metabolism. NeuroImage, 44,
647652.
Chen, Y., Wang, D. J.J, & Detre, J. A. (2011). Testretest reliability of arterial spin
labeling with common labeling strategies. Journal of Magnetic Resonance Imaging,
33, 940949.
Chen, J. J., Wieckowska, M., Meyer, E., & Pike, G. B. (2008). Cerebral blood flow
measurement using fMRI and PET: A cross-validation study. International Journal of
Biomedical Imaging, 2008, 516359.
Chiarelli, P. A., Bulte, D. P., Gallichan, D., Piechnik, S. K., Wise, R., & Jezzard, P.
(2007). Flow-metabolism coupling in human visual, motor, and supplementary
motor areas assessed by magnetic resonance imaging. Magnetic Resonance in
Medicine, 57, 538547.
Dai, W., Robson, P. M., Shankaranarayanan, A., & Alsop, D. C. (2012). Reduced
resolution transit delay prescan for quantitative continuous arterial spin labeling
perfusion imaging. Magnetic Resonance in Medicine, 67, 12521265.
Donahue, M. J., Lu, H., Jones, C. K., Pekar, J. J., & Van Zijl, P. C.M (2006). An account
of the discrepancy between MRI and PET cerebral blood flow measures. A high-field
MRI investigation. NMR in Biomedicine, 19, 10431054.
Duhamel, G., & Alsop, D. C. (2004). Single-shot susceptibility insensitive whole brain
3D fMRI with ASL. In: 12th ISMRM scientific meeting, Kyoto, p. 518.
Duyn, J. H., Tan, C. X., van Gelderen, P., & Yongbi, M. N. (2001). High-sensitivity
single-shot perfusion-weighted fMRI. Magnetic Resonance in Medicine, 46, 8894.
Feinberg, D. A., Moeller, S., Smith, S. M., Auerbach, E., Ramanna, S., Glasser, M. F.,
et al. (2010). Multiplexed echo planar imaging for sub-second whole brain FMRI
and fast diffusion imaging. PLoS One, 5, e15710.
Feng, C.-M., Narayana, S., Lancaster, J. L., Jerabek, P. A., Arnow, T. L., Zhu, F., et al.
(2004). CBF changes during brain activation: fMRI vs. PET. NeuroImage, 22,
443446.
Fernandez-Seara, M. A., Wang, J., Wang, Z., Rao, H., Guenther, M., Feinberg, D. A.,
et al. (2005). Continuous arterial spin labelling perfusion measurements using
single shot 3D GRASE at 3 T. In: 13th ISMRM scientific meeting, Miami Beach,
p. 1160.
Garcia, D. M., Duhamel, G., & Alsop, D. C. (2005). Efficiency of inversion pulses for
background suppressed arterial spin labeling. Magnetic Resonance in Medicine, 54,
366372.
Gevers, S., van Osch, M. J., Bokkers, R. P., Kies, D. A., Teeuwisse, W. M., Majoie, C. B.,
et al. (2011). Intra- and multicenter reproducibility of pulsed, continuous and
pseudo-continuous arterial spin labeling methods for measuring cerebral perfusion.
Journal of Cerebral Blood Flow and Metabolism, 31(8), 17061715.
Grossman, E. J., Zhang, K., An, J., Voorhees, A., Inglese, M., Ge, Y., et al. (2009).
Measurement of deep gray matter perfusion using a segmented true-fast imaging
with steady-state precession (True-FISP) arterial spin-labeling (ASL) method at 3 T.
Gunther, M. (2006). Efficient visualization of vascular territories in the human brain by
cycled arterial spin labeling MRI. Magnetic Resonance in Medicine, 56, 671675.
Gunther, M., Oshio, K., & Feinberg, D. A. (2005). Single-shot 3D imaging techniques
improve arterial spin labeling perfusion measurements. Magnetic Resonance in
Medicine, 54, 491498.
Helle, M., Rufer, S., van Osch, M. J.P, Jansen, O., & Norris, D. G. (2012). Selective
multivessel labeling approach for perfusion territory imaging in pseudo-continuous
arterial spin labeling. Magnetic Resonance in Medicine, 68, 214219.
153
Hernandez-Garcia, L., Jahanian, H., Greenwald, M. K., Zubieta, J.-K., & Peltier, S. J.
(2011). Real-time functional MRI using pseudo-continuous arterial spin labeling.
Hernandez-Garcia, L., Jahanian, H., & Rowe, D. B. (2010). Quantitative analysis of
arterial spin labeling FMRI data using a general linear model. Magnetic Resonance
Imaging, 28, 919927.
Hernandez-Garcia, L., Lee, G. R., Vazquez, A. L., Yip, C.-Y., & Noll, D. C. (2005).
Quantification of perfusion fMRI using a numerical model of arterial spin labeling
that accounts for dynamic transit time effects. Magnetic Resonance in Medicine, 54,
955964.
Hoge, R. D., Atkinson, J., Gill, B., Crelier, G. R., Marrett, S., & Pike, G. B. (1999). Linear
coupling between cerebral blood flow and oxygen consumption in activated human
cortex. Proceedings of the National Academy of Sciences of the United States of
America, 96, 94039408.
Hutchison, J. L., Shokri-Kojori, E., Lu, H., & Rypma, B. (2013). A BOLD perspective on
age-related neurometabolic-flow coupling and neural efficiency changes in human
visual cortex. Frontiers in Psychology, 4, 244.
Hyder, F. (2004). Neuroimaging with calibrated FMRI. Stroke, 35, 26352641.
Jahng, G. H., Song, E., Zhu, X. P., Matson, G. B., Weiner, M. W., & Schuff, N. (2005).
Human brain: Reliability and reproducibility of pulsed arterial spin-labeling
perfusion MR imaging. Radiology, 234, 909916.
James, W. (1890). The principles of psychology. Cambridge, MA: Harvard.
Jiang, L., Kim, M., Chodkowski, B., Donahue, M. J., Pekar, J. J., Van Zijl, P. C.M, et al.
(2010). Reliability and reproducibility of perfusion MRI in cognitively normal
subjects. Magnetic Resonance Imaging, 28, 12831289.
Kety, S. S., & Schmidt, C. F. (1948). The nitrous oxide method for the quantitative
determination of cerebral blood flow in man: Theory, procedure and normal values.
Journal of Clinical Investigation, 27, 476483.
Kim, S. G., & Duong, T. Q. (2002). Mapping cortical columnar structures using fMRI.
Physiology & Behavior, 77, 641644.
Liau, J., Perthen, J. E., & Liu, T. T. (2008). Caffeine reduces the activation extent and
contrast-to-noise ratio of the functional cerebral blood flow response but not the
BOLD response. NeuroImage, 42, 296305.
Liu, T. T., & Brown, G. G. (2007). Measurement of cerebral perfusion with arterial spin
labeling: Part 1. Methods. Journal of the International Neuropsychological Society,
13, 517525.
Liu, T. T., & Wong, E. C. (2005). A signal processing model for arterial spin labeling
functional MRI. NeuroImage, 24, 207215.
Luh, W. M., Wong, E. C., Bandettini, P. A., & Hyde, J. S. (1999). QUIPSS II with thinslice TI1 periodic saturation: A method for improving accuracy of quantitative
perfusion imaging using pulsed arterial spin labeling. Magnetic Resonance in
Medicine, 41, 12461254.
Luh, W. M., Wong, E. C., Bandettini, P. A., Ward, B. D., & Hyde, J. S. (2000).
Comparison of simultaneously measured perfusion and BOLD signal increases
during brain activation with T(1)-based tissue identification. Magnetic Resonance in
Medicine, 44, 137143.
Miller, K. L., Luh, W. M., Liu, T. T., Martinez, A., Obata, T., Wong, E. C., et al. (2001).
Nonlinear temporal dynamics of the cerebral blood flow response. Human Brain
Mapping, 13, 112.
Mumford, J. A., Hernandez-Garcia, L., Lee, G. R., & Nichols, T. E. (2006). Estimation
efficiency and statistical power in arterial spin labeling fMRI. NeuroImage, 33, 103114.
Nielsen, J.-F., & Hernandez-Garcia, L. (2012). Functional perfusion imaging using
pseudocontinuous arterial spin labeling with low-flip-angle segmented 3D spiral
readouts. Magnetic Resonance in Medicine, 69, 382390.
Perthen, J. E., Bydder, M., Restom, K., & Liu, T. T. (2008). SNR and functional
sensitivity of BOLD and perfusion-based fMRI using arterial spin labeling with spiral
SENSE at 3 T. Magnetic Resonance Imaging, 26, 513522.
Petersen, E. T., Mouridsen, K., & Golay, X. (2010). The QUASAR reproducibility study,
Part II: Results from a multi-center Arterial Spin Labeling testretest study.
Pimentel, M. A.F, Vilela, P., Sousa, I., & Figueiredo, P. (2013). Localization of the hand
motor area by arterial spin labeling and blood oxygen level-dependent functional
magnetic resonance imaging. Human Brain Mapping, 34, 96108.
Raichle, M. E. (1998). Behind the scenes of functional brain imaging: A historical and
physiological perspective. Proceedings of the National Academy of Sciences of the
Raichle, M. E., Martin, W. R., Herscovitch, P., Mintun, M. A., & Markham, J. (1983).
Brain blood flow measured with intravenous H2(15)O. II. Implementation and
validation. Journal of Nuclear Medicine, 24, 790798.
Raoult, H., Petr, J., Bannier, E., Stamm, A., Gauvrit, J.-Y., Barillot, C., et al. (2011).
Arterial spin labeling for motor activation mapping at 3 T with a 32-channel coil:
Reproducibility and spatial accuracy in comparison with BOLD fMRI. NeuroImage,
58, 157167.
154
Restom, K., Bangen, K. J., Bondi, M. W., Perthen, J. E., & Liu, T. T. (2007). Cerebral
blood flow and BOLD responses to a memory encoding task: A comparison between
healthy young and elderly adults. NeuroImage, 37, 430439.
Restom, K., Behzadi, Y., & Liu, T. T. (2006). Physiological noise reduction for arterial
spin labeling functional MRI. NeuroImage, 31, 11041115.
Rosen, B. R., Belliveau, J. W., Vevea, J. M., & Brady, T. J. (1990). Perfusion imaging
with NMR contrast agents. Magnetic Resonance in Medicine, 14, 249265.
Roy, C. S., & Sherrington, C. S. (1890). On the regulation of the blood-supply of the
brain. Journal of Physiology, 11, 85108.
Shin, D. D., Liu, H. L., Wong, E. C., & Liu, T. T. (2011). Effect of background
suppression on CBF quantitation in pseudo continuous arterial spin labeling.
In: 19th annual ISMRM scientific meeting, Montreal, p. 2101.
Small, S. A. (2004). Quantifying cerebral blood flow: Regional regulation with global
implications. Journal of Clinical Investigation, 114, 10461048.
Stefanovic, B., Warnking, J. M., Kobayashi, E., Bagshaw, A. P., Hawco, C., Dubeau, F.,
et al. (2005). Hemodynamic and metabolic responses to activation, deactivation and
epileptic discharges. NeuroImage, 28, 205215.
Tan, H., Hoge, W. S., Hamilton, C. A., Gunther, M., & Kraft, R. A. (2011). 3D GRASE
PROPELLER: Improved image acquisition technique for arterial spin labeling
perfusion imaging. Magnetic Resonance in Medicine, 66, 168173.
Tjandra, T., Brooks, J. C., Figueiredo, P., Wise, R., Matthews, P. M., & Tracey, I. (2005).
Quantitative assessment of the reproducibility of functional activation measured with
BOLD and MR perfusion imaging: Implications for clinical trial design. NeuroImage,
27, 393401.
Medicine, 49, 796802.
Wang, J., Li, L., Roc, A. C., Alsop, D. C., Tang, K., Butler, N. S., et al. (2004). Reduced
susceptibility effects in perfusion fMRI with single-shot spin-echo EPI acquisitions
at 1.5 Tesla. Magnetic Resonance Imaging, 22, 17.
Wang, Y., Saykin, A. J., Pfeuffer, J., Lin, C., Mosier, K. M., Shen, L., et al. (2011).
Regional reproducibility of pulsed arterial spin labeling perfusion imaging at 3 T.
Williams, D. S., Detre, J. A., Leigh, J. S., & Koretsky, A. P. (1992). Magnetic resonance
imaging of perfusion using spin inversion of arterial water. Proceedings of the
Wintermark, M., Sesay, M., Barbier, E., Borbely, K., Dillon, W. P., Eastwood, J. D., et al.
(2005). Comparative overview of brain perfusion imaging techniques. Stroke, 36,
e83e99.
Wong, E. C. (2005). Quantifying CBF with pulsed ASL: Technical and pulse sequence
factors. Journal of Magnetic Resonance Imaging, 22, 727731.
Wong, E. C. (2007). Vessel-encoded arterial spin-labeling using pseudocontinuous
tagging. Magnetic Resonance in Medicine, 58, 10861091.
Wong, E. C., Buxton, R. B., & Frank, L. R. (1998a). Quantitative imaging of perfusion
using a single subtraction (QUIPSS and QUIPSS II). Magnetic Resonance in
Medicine, 39, 702708.
Wong, E. C., Buxton, R. B., & Frank, L. R. (1998b). A theoretical and experimental
comparison of continuous and pulsed arterial spin labeling techniques for
quantitative perfusion imaging. Magnetic Resonance in Medicine, 40, 348355.
Wong, E. C., Cronin, M., Wu, W. C., Inglis, B., Frank, L. R., & Liu, T. T. (2006).
Velocity-selective arterial spin labeling. Magnetic Resonance in Medicine, 55,
13341341.
Wong, E. C., Luh, W. M., & Liu, T. T. (2000). Turbo ASL: Arterial spin labeling with
higher SNR and temporal resolution. Magnetic Resonance in Medicine, 44,
511515.
Woolrich, M. W., Chiarelli, P., Gallichan, D., Perthen, J., & Liu, T. T. (2006). Inferring
blood volume, blood flow, and blood oxygenation changes from functional ASL
data. In: 14th ISMRM scientific meeting, Seattle, in press.
Xu, G., Rowley, H. A., Wu, G., Alsop, D. C., Shankaranarayanan, A., Dowling, M., et al.
(2010). Reliability and precision of pseudo-continuous arterial spin labeling
perfusion MRI on 3.0 T and comparison with 15O-water PET in elderly subjects at
risk for Alzheimers disease. NMR in Biomedicine, 23, 286293.
Ye, F. Q., Berman, K. F., Ellmore, T., Esposito, G., van Horn, J. D., Yang, Y., et al.
(2000). H(2)(15)O PET validation of steady-state arterial spin tagging cerebral
blood flow measurements in humans. Magnetic Resonance in Medicine, 44,
450456.
Zahneisen, B., Grotz, T., Lee, K. J., Ohlendorf, S., Reisert, M., Zaitsev, M., et al. (2011).
Three-dimensional MR-encephalography: Fast volumetric brain imaging using
rosette trajectories. Magnetic Resonance in Medicine, 65, 12601268.
Zuo, Z., Wang, R., Zhuo, Y., Xue, R., St Lawrence, K. S., & Wang, D. J.J (2013).
Turbo-FLASH based arterial spin labeled perfusion MRI at 7 T. PLoS One, 8,
e66612.
Positron Emission Tomography and Neuroreceptor Mapping In Vivo

R Lanzenberger and A Hahn, Medical University of Vienna, Vienna, Austria
Glossary
5-HT1A Serotonin-1A receptor.

5-HTT Serotonin transporter.
BBB Blood-brain barrier.
FDG 2-deoxy-2-[18F]fluoro-D-glucose.
Introduction
Positron emission tomography (PET) is an imaging technique
from the field of nuclear medicine. Together with singlephoton emission computed tomography (SPECT), it provides
the unique opportunity to quantify various binding proteins in
the living human brain. This includes, but is not limited to, the
depiction of physiological processes such as perfusion and
metabolism as well as imaging of neurotransmitter systems
by quantitative description of receptors, transporters, and
enzymes. The current article provides a basic introduction
into acquisition principles of PET and different imaging possibilities. The overview of [18F]FDG imaging (2-deoxy-2-[18F]
fluoro-D-glucose), a major PET application, is then followed
by specific implementations regarding the depiction of neurotransmitter systems. This covers the specific characteristics of
reversible radioligands for receptor quantification as well as
advances and challenges in psychiatric and neurological
disorders.
Data Acquisition
The main advantage of PET is that specific functional information is obtained at a molecular level with nano- to picomolar
sensitivity (Wadsak & Mitterhauser, 2010). Hence, only a
minor amount of radioactively labeled substance provides sufficient signal (mostly) without interfering with the biological
system itself. However, the radiation exposure to the patient
also presents the major drawback of PET. For instance, a typical
[18F]FDG scan with an application dosage of 3.6 MBq kg1
already yields an effective dose of 7 mSv for a 70 kg person
(Deloar et al., 1998).
Radioligands
A key component of each PET scan is the radioligand (also
called radiotracer or radiopharmaceutical), which consists of
two parts: the radioactive isotope and the biological tracer
(Wadsak & Mitterhauser, 2010). The first gives a detectable
signal, which in PET is obviously a positron-emitting isotope.
The most common radioactive isotopes are 18F (with a half-life
of 109.8 min), 11C (20.4 min), 13N (10 min), and 15O
(2 min). For the production of these isotopes, a cyclotron
is required and, considering their short half-life, only
MDD Major depressive disorder.

PET Positron emission tomography.
SPECT Single photon emission computed tomography.
SUV Standard uptake value.
[18F]-labeled ligands may be available for transport. The second part of the radioligand is the biological tracer, whose
binding properties define which target molecule will be
imaged. The challenge for the radiochemist/radiopharmacist
is not only to combine the radioactive isotope and the biological tracer into a single molecule but also to develop and
produce a final radioligand that meets specific characteristics
(see succeeding text) in order to allow reliable quantification of
the process or protein of interest.
Measurement Principle
The radioligand is incorporated into the body, mostly by intravenous injection. After the positron is emitted from the radioligand, it travels a short distance until it reacts with a nearby
electron in a process called annihilation. From the annihilation site, two photons are emitted in opposite directions each
with 511 keV. The photons are then perceived simultaneously
by the detector ring within a typical timing window of 814 ns
(Cherry, 2006). This coincidence detection is one of the major
advantages of PET in comparison to SPECT as it provides a
100-fold increase in detection sensitivity, which directly
improves image quality (Rahmim & Zaidi, 2008). Arriving at
the detector ring, the photons then hit the scintillation crystal,
which converts them into visible light. Coupling the crystal to a
photomultiplier tube enables amplification and transformation of light into an electrical signal, which is further processed
by the reconstruction computer.
The main limitations in terms of image resolution are given
by the positron range, photon noncollinearity, and further
detector-related effects (Moses, 2011; Rahmim & Zaidi,
2008). As mentioned, positrons pass a short distance before
an energy level for annihilation is reached. This distance,
known as the positron range, varies for different isotopes
between 0.6 mm for 18F and 2.5 mm for 15O (or reaches values
beyond 6 mm for higher energetic isotopes such as 62Cu and
82
Rb) (Jodal, Le Loirec, & Champion, 2012). Noncollinearity
refers to the observation that the trajectories of the emitted
photons may deviate from 180 due to nonzero energies after
annihilation. The angle varies with a standard deviation of
0.25 , and its effect on image resolution is dependent on the
radius of the detector ring (Moses, 2011; Rahmim & Zaidi,
2008). Both of the earlier mentioned effects cause blurring
of the recorded images in mm range. The third limitation
includes the size of the scintillation crystals as well as
http://dx.doi.org/10.1016/B978-0-12-397025-1.00018-X
155
156
INTRODUCTION TO ACQUISITION METHODS | Positron Emission Tomography and Neuroreceptor Mapping In Vivo
intercrystal scattering and penetration, which continuously

improve with new technological advances (Rahmim & Zaidi,
2008). Additional developments in image reconstruction algorithms may yield a maximum image resolution of 1.52.4 mm
for high-resolution PET scanners (Varrone et al., 2009).
Imaging Applications
Imaging Neurotransmitter Systems

In contrast to the rather unspecific signal of [18F]FDG, PET
further enables quantitative description of specific single neuronal receptors and transporters. Following an overview of
specific radioligand characteristics, we will give a practical
overview of such applications in basic and clinical research
with exemplary descriptions of the serotonin and dopamine
neurotransmitter systems. For details on receptor quantification and modeling, the reader is referred elsewhere in this
encyclopedia.
[18F] FDG SUV
[18F]FDG presents the major clinical application of PET as

various disorders are accompanied by alterations in glucose
metabolism. In principle, FDG is trapped in the early pathway
of glucose metabolism (Wadsak & Mitterhauser, 2010). Following the uptake of the radioligand into the cell, it is metabolized in the mitochondria by the enzyme hexokinase.
Considering that the radioligand comprises an [18F] molecule
instead of a hydroxyl group at position 2, no further metabolic
reaction takes place. In addition, the inversion of the initial
step by dephosphorylation is energetically unfavorable in most
cells. This leads to an accumulation of [18F]FDG making it an
irreversible tracer, especially for measurement durations of
<1 h (Muller-Schauenburg, 2010). The disadvantage of this
radioligand concerns its unspecific signal, where, for instance,
most tumors cannot be distinguished from inflammatory processes. Still, the use of radiolabeled FDG has become one of the
major clinical imaging tools. In practice however, manual
interpretation of PET images by an experienced physician or

semiquantitative assessment using the standard uptake value
(SUV) represents the predominant manner of examination. It
is calculated as the radioactivity concentration in tissue (e.g.,
kBq ml1) divided by injected dose. The injected dose is further normalized to a patient-specific property such as body
weight, body surface area, or body mass index (Yeung et al.,
2002). Figure 1 shows an example of an [18F]FDG SUV image
of patients with unilateral temporal lobe epilepsy. Calculation
of SUVs represents a useful alternative to full quantification,
but potential bias from variations in uptake duration, plasma
glucose levels, and patient size or weight (Keyes, 1995), as well
as different population groups (Yeung et al., 2002), should be
kept in mind.
T-values
15
(a)
(b)
Figure 1 Patients with unilateral temporal lobe epilepsy undergoing [18F]FDG PET imaging. (a) The axial and coronal slices show a marked reduction in
standard uptake values (SUVs) in the left temporal lobe. (b) In the voxel-wise statistical evaluation, left vs right hemisphere SUV was compared
across an entire patient group with strongest differences in the hippocampus (corrected for multiple comparisons).
Radioligand properties
Although some of the following characteristics may also apply
for other radioligands, the following description highlights
specific properties for quantitative imaging of neuronal receptors. Besides being nontoxic and safe, most radioligands are
assumed to cross the bloodbrain barrier (BBB) via passive
diffusion (except, e.g., [18F]FDG, which uses active glucose
transport). Although practical approaches for BBB imaging
exist (Bauer et al., 2010), it is usually desired to avoid efflux
by transporter proteins such as P-glycoprotein (P-gp) to ensure
that the radioligand reaches its target molecule (Pike, 2009).
Crossing the BBB already implies that the radioligand exhibits
certain characteristics in terms of lipophilicity, size, and
weight. In general, passive brain entry can be obtained by
most radioligands with a log P value (n-octanol/water partition
coefficient as index for lipophilicity) of 23.5 at physiological
pH, low molecular weight (<450 Da), and small crosssectional area (<80 A2) (Laruelle, Slifstein, & Huang, 2003;
Pike, 2009). Although lipophilicity is a major factor for BBB
passage, highly lipophilic tracers will show increases in nonspecific binding in the brain, which, in turn, decreases the
signal-to-noise ratio (Pike, 2009). High lipophilicity also
implies high binding to plasma proteins, hence reducing the
fraction of radioligand that is available for brain uptake.
Another important characteristic of a radioligand is given
by its selectivity. Ideally, it binds to only one target receptor
with appropriate affinity (Pike, 2009). There are, however,
certain examples for radioligands that show high affinity
for several receptor subtypes. For instance, [18F]setoperone
binds to both dopamine D2 and serotonin-2A receptors.
Consideration of the different topological distributions of
these target molecules in the brain gives a striatal signal
corresponding to D2 binding, while radioligand signal in
cortical areas will represent serotonin-2A receptors (Laruelle
et al., 2003). To summarize, the level of selectivity depends
on the affinity for the different receptor subtypes as well as
the distribution of the target proteins within certain regions
of interest.
Though the required affinity of a radioligand is usually in
the range of 10.01 nM, it also depends on the concentration
of the target receptor (Laruelle et al., 2003). High affinity is,
however, often associated with high lipophilicity, which in
turn increases nonspecific binding. Hence, increasing the affinity of a radioligand will only result in better image quality (i.e.,
signal-to-noise ratio) if the nonspecific binding remains constant (Laruelle et al., 2003). Another issue associated with
affinity is the scan duration. Increases in affinity will also lead
to longer scan times since the binding equilibrium required for
quantification is reached later.
As mentioned previously, the radioligand should not interfere with the biological system for most imaging applications,
and it is therefore applied at low doses that lack pharmacological effects (tracer doses). Ideally, the radioligand application
leads to an occupancy of target proteins of < 1%. This also
satisfies the linearity requirements for the kinetic modeling
procedures (Laruelle et al., 2003). On the other hand, this
further implies that radioligands need to be synthesized at a
high specific activity.
Finally, it is desirable that radioligands exhibit limited
peripheral metabolism. This increases the amount of parent
radioligand available for specific receptor binding, which in
157
turn increases the signal-to-noise ratio. Despite high metabolism, most radioligands still represent excellent imaging properties because the radioactive metabolites are more polar
than the parent compound and hence do not cross the BBB.
An elegant example of avoiding radioactive metabolites in
the human brain is given by the serotonin-1A antagonist
WAY-100635 (Pike, 2009). Labeling of this compound at the
O-methyl site leads to high amounts of the radioactive metabolite WAY-100634, which shows high affinity to the same
target receptor. Shifting the labeling position to the carbonyl
site avoids this problem as the main radioactive metabolite
does not cross the BBB (Osman et al., 1998).
Serotonin imaging
The serotonin (5-HT) system is one of the phylogenetically
oldest neurotransmitter systems in the human brain (Saulin,
Savli, & Lanzenberger, 2011). Up to now, 16 receptor subtypes
and one transporter have been identified (Polter & Li, 2010).
These receptors are classified into seven different families by
their pharmacological properties. Except for the 5-HT3 receptor
family, which comprises ionotropic receptors, all other subtypes are G protein-coupled receptors (Bockaert, Claeysen,
Dumuis, & Marin, 2010). Considering that the serotonergic
neurotransmitter system is involved in a variety of psychiatric
disorders (Paterson, Kornum, Nutt, Pike, & Knudsen, 2013;
Savli et al., 2012), in vivo imaging of these receptors provides
novel insight into these pathophysiological mechanisms. The
broad interest in the serotonin system is also reflected by
thorough evaluations of available and upcoming radioligands
(Paterson et al., 2013; Saulin et al., 2011) as well as a recently
established comprehensive database (Savli et al., 2012). Figure 2 shows the different topological distributions of major
serotonin binding proteins.
Among this variety of 5-HT receptors, investigation of the
main inhibitory subtype (5-HT1A) has been of major interest in
several psychiatric disorders due to its high density in the
human brain, excellent pharmacological characterization
(Saulin et al., 2011), and radiotracer availability (Paterson
et al., 2013). For instance, the investigation of patients suffering from panic disorder with PET showed decreases in 5-HT1A
binding (Neumeister et al., 2004), which normalized in cortical areas (postsynaptic) but not in the raphe region (presynaptic) after treatment with selective serotonin reuptake inhibitors
(SSRI) (Nash et al., 2008). Similarly, patients with social anxiety disorder also exhibited reduced pre- and postsynaptic
5-HT1A binding (Lanzenberger et al., 2007). However, after
SSRI therapy, further decreases in receptor binding were
observed in cortical areas but not in the raphe region
(Spindelegger et al., 2009). In addition, SSRI administration
led to a stronger interregional association between the dorsal
raphe nucleus and the amygdalahippocampus complex in
these patients (Hahn et al., 2010). The distinct changes of preand postsynaptic receptor binding may relate, for example, to
differences in internalization processes or G protein coupling
since only postsynaptic but not 5-HT1A autoreceptors in the
raphe nuclei inhibit adenylyl cyclase via the Gia-subunit
(Polter & Li, 2010).
The etiology and treatment effects of major depressive disorder (MDD) have also been linked to the serotonergic system.
However, the results have been more controversial with
decreases (Drevets et al., 1999; Hirvonen et al., 2008; Sargent
158
5-HT1A binding
(a)
5-HT1B binding
1.5
(b)
0
(c)
5-HT2A binding
5-HTT binding
(d)
Figure 2 Topographical distribution of major binding proteins of the serotonin neurotransmitter system in healthy human subjects. These
include the major inhibitory ((a) 5-HT1A and (b) 5-HT1B) and excitatory receptor subtypes ((c) 5-HT2A) as well as the serotonin transporter ((d) 5-HTT
or SERT). The marked difference in binding distributions may relate to the variability of physiological processes and mental disorders where
the serotonergic neurotransmitter system is involved.
et al., 2000) and increases (Parsey et al., 2010) in 5-HT1A

binding depending on the quantification procedure. Treatment of these patients with SSRIs showed either no change
(Moses-Kolko et al., 2007; Sargent et al., 2000) or decreases in
raphe 5-HT1A binding (Gray et al., 2013), which is supported
by rodent studies (Richardson-Jones et al., 2010). Conversely,
electroconvulsive therapy led to decreases only within postsynaptic receptor binding in treatment-resistant depressive
patients (Lanzenberger et al., 2012).
Quantification of the serotonin transporter (5-HTT or
SERT) gave important insight into further differentiation of
MDD (Meyer, 2007). Patients with axis I comorbidities
(major clinical syndromes) exhibited decreased SERT binding
(Parsey et al., 2006), whereas subjects with severe pessimism
showed increases in SERT (Meyer et al., 2004).
Imaging of extracellular serotonin levels and endogenous
neurotransmitter release itself has been shown to be more
difficult than for dopamine (see succeeding text). This was
attributed to the ratio of high- and low-affinity states of receptors and availability of agonist or antagonist radioligands,
basal 5-HT concentration, and the challenge method used to
increase or decrease endogenous neurotransmitter levels
(Paterson, Tyacke, Nutt, & Knudsen, 2010).
Dopamine imaging
Similar to serotonin imaging, the dopaminergic neurotransmitter system has been subject to extensive investigation
using PET (Ito, Takahashi, Arakawa, Takano, & Suhara,
2008). This includes dementias and Parkinsons disease
(Walker & Rodda, 2011), schizophrenia (Howes & Kapur,
2009), and depression (Dunlop & Nemeroff, 2007). In addition to receptor and transporter imaging, a topic of particular
interest is the quantification of endogenous dopamine release

with PET. Physiological changes of dopamine levels can be
indirectly inferred from changes in radioligand binding such
as [11C]raclopride (D2 receptor antagonist) (Ginovart, 2005)
or [11C]-()-PHNO (D2/3 receptor agonist) (Willeit et al.,
2008). This has been of major interest for studies on psychiatric disorders such as schizophrenia, as these patients are
thought to exhibit increased dopamine levels (Howes &
Kapur, 2009). For instance, intravenous amphetamine challenge increases dopamine levels. This leads to competition
between the endogenous neurotransmitter and the radioligand
at the target receptor and hence yields a decrease in measured
radioligand binding. In addition to this direct competition
model (which relates to changes in affinity (Ginovart,
2005)), a second mechanism has been observed. That is,
decreases in D2 density have also been demonstrated to be
attributable to receptor internalization following amphetamine administration (Sun, Ginovart, Ko, Seeman, & Kapur,
2003). The internalized receptors may not be accessible for the
radioligand, for example, due to unfavorable endosomal pH
levels, and hence further decrease the observed receptor binding (Ginovart, 2005).
The usage of agonist radioligands such as [11C]-()-PHNO is
theoretically superior to that of antagonists during challenge
conditions (Paterson et al., 2010). More precisely, G proteincoupled receptors (including D2/3) exhibit high- and low-affinity
states. In contrast to antagonist radioligands that bind equally to
both, endogenous neurotransmitters and agonists will bind only
to high-affinity receptors. Hence, provoking direct competition
through increased dopamine levels will potentially affect the
entire pool of binding sites that are available for the agonist
radioligand. On the other hand, an antagonist radioligand is
still unchallenged in its binding of the low-affinity receptors,
which decreases signal-to-noise ratio for imaging of endogenous
neurotransmitter release. These theoretical considerations have
also proved useful in practice with higher signal-to-noise
ratio for agonist radioligands (Narendran et al., 2004; Willeit
et al., 2008).
Further Imaging Applications

Although not of lesser importance, additional applications can
only be mentioned superficially for completeness. This
includes imaging of amyloid plaques, which is of essential
interest in Alzheimers disease. The radioligand [11C]PIB,
which is selective for in vivo amyloid-b deposits (Ikonomovic
et al., 2008), has been successfully established (Klunk et al.,
2004; Price et al., 2005), and together with [18F]FDG imaging,
it provides improved assessment of these patients (Devanand
et al., 2010; Ossenkoppele et al., 2012). For a more detailed
description on amyloid tracers, refer elsewhere in this
encyclopedia.
Another interesting aspect of PET imaging is the radioactive
labeling of amino acid analogs. Exemplary applications are
a-[11C]methyl-L-tryptophan ([11C]AMT) for the serotonin synthesis rate (Diksic & Young, 2001), [18F]FDOPA as dopamine
precursor (Chen et al., 2006), and methionine imaging with
[18F]FET or [11C]methionine (Wadsak & Mitterhauser, 2010).
Finally, it is worth mentioning that the combination of PET
with other imaging modalities such as structural (Kraus et al.,
2012) or functional MRI (Hahn et al., 2012; Salimpoor,
Benovoy, Larcher, Dagher, & Zatorre, 2011) as well as genetic
information (Willeit & Praschak-Rieder, 2010) may provide
novel insights into essentials of basic human brain function
as well as pathological alterations.
See also: INTRODUCTION TO ANATOMY AND PHYSIOLOGY:

Transmitter Receptor Distribution in the Human Brain;
INTRODUCTION TO CLINICAL BRAIN MAPPING: Alzheimers
Disease; Amyloid Tracers; INTRODUCTION TO METHODS AND
MODELING: Computerized Tomography Reconstruction Methods;
Pharmacokinetic Modeling of Dynamic PET.
References
Bauer, M., Karch, R., Neumann, F., Wagner, C. C., Kletter, K., Muller, M., et al. (2010).
Assessment of regional differences in tariquidar-induced P-glycoprotein
modulation at the human bloodbrain barrier. Journal of Cerebral Blood Flow and
Bockaert, J., Claeysen, S., Dumuis, A., & Marin, P. (2010). Classification and signaling
characteristics of 5-HT receptors. In C. P. Muller & B. L. Jacobs (Eds.), Handbook
of the behavioral neurobiology of serotonin. London: Elsevier.
Chen, W., Silverman, D. H., Delaloye, S., Czernin, J., Kamdar, N., Pope, W., et al.
(2006). 18 F-FDOPA PET imaging of brain tumors: Comparison study with 18 F-FDG
PET and evaluation of diagnostic accuracy. Journal of Nuclear Medicine, 47,
904911.
Cherry, S. R. (2006). The 2006 Henry N. Wagner Lecture: Of mice and men (and
positrons) Advances in PET imaging technology. Journal of Nuclear Medicine, 47,
17351745.
Deloar, H. M., Fujiwara, T., Shidahara, M., Nakamura, T., Watabe, H., Narita, Y., et al.
(1998). Estimation of absorbed dose for 2-[F-18]fluoro-2-deoxy-D-glucose using
whole-body positron emission tomography and magnetic resonance imaging.
European Journal of Nuclear Medicine, 25, 565574.
Devanand, D. P., Mikhno, A., Pelton, G. H., Cuasay, K., Pradhaban, G.,
Dileep Kumar, J. S., et al. (2010). Pittsburgh compound B (11C-PIB) and
159
fluorodeoxyglucose (18 F-FDG) PET in patients with Alzheimer disease, mild

cognitive impairment, and healthy controls. Journal of Geriatric Psychiatry and
Neurology, 23, 185198.
Diksic, M., & Young, S. N. (2001). Study of the brain serotonergic system with labeled
alpha-methyl-L-tryptophan. Journal of Neurochemistry, 78, 11851200.
Drevets, W. C., Frank, E., Price, J. C., Kupfer, D. J., Holt, D., Greer, P. J., et al. (1999).
PET imaging of serotonin 1A receptor binding in depression. Biological Psychiatry,
46, 13751387.
Dunlop, B. W., & Nemeroff, C. B. (2007). The role of dopamine in the pathophysiology
of depression. Archives of General Psychiatry, 64, 327337.
Ginovart, N. (2005). Imaging the dopamine system with in vivo [11C]raclopride
displacement studies: Understanding the true mechanism. Molecular Imaging and
Biology, 7, 4552.
Gray, N. A., Milak, M. S., Delorenzo, C., Ogden, R. T., Huang, Y. Y., Mann, J. J., et al.
(2013). Antidepressant treatment reduces serotonin-1A autoreceptor binding in
major depressive disorder. Biol Psychiatry, 74, 2631.
Hahn, A., Lanzenberger, R., Wadsak, W., Spindelegger, C., Moser, U., Mien, L.-K., et al.
(2010). Escitalopram enhances the association of serotonin-1A autoreceptors to
heteroreceptors in anxiety disorders. Journal of Neuroscience, 30, 1448214489.
Hahn, A., Wadsak, W., Windischberger, C., Baldinger, P., Hoflich, A. S., Losak, J., et al.
(2012). Differential modulation of the default mode network via serotonin-1A
receptors. Proceedings of the National Academy of Sciences of the United States of
America, 109, 26192624.
Hirvonen, J., Karlsson, H., Kajander, J., Lepola, A., Markkula, J., Rasi-Hakala, H., et al.
(2008). Decreased brain serotonin 5-HT1A receptor availability in medication-naive
patients with major depressive disorder: An in-vivo imaging study using PET and
[carbonyl-11C]WAY-100635. International Journal of Neuropsychopharmacology,
11, 465476.
Howes, O. D., & Kapur, S. (2009). The dopamine hypothesis of schizophrenia: Version
IIIthe final common pathway. Schizophrenia Bulletin, 35, 549562.
Ikonomovic, M. D., Klunk, W. E., Abrahamson, E. E., Mathis, C. A., Price, J. C.,
Tsopelas, N. D., et al. (2008). Post-mortem correlates of in vivo PiB-PET amyloid
imaging in a typical case of Alzheimers disease. Brain, 131, 16301645.
Ito, H., Takahashi, H., Arakawa, R., Takano, H., & Suhara, T. (2008). Normal database of
dopaminergic neurotransmission system in human brain measured by positron
emission tomography. NeuroImage, 39, 555565.
Jodal, L., Le Loirec, C., & Champion, C. (2012). Positron range in PET imaging: An
alternative approach for assessing and correcting the blurring. Physics in Medicine
and Biology, 57, 39313943.
Keyes, J. W.Jr., (1995). SUV: standard uptake or silly useless value? Journal of Nuclear
Medicine, 36, 18361839.
Klunk, W. E., Engler, H., Nordberg, A., Wang, Y., Blomqvist, G., Holt, D. P., et al. (2004).
Imaging brain amyloid in Alzheimers disease with Pittsburgh compound-B. Annals
of Neurology, 55, 306319.
Kraus, C., Hahn, A., Savli, M., Kranz, G. S., Baldinger, P., Hoflich, A., et al. (2012).
Serotonin-1A receptor binding is positively associated with gray matter volume A
multimodal neuroimaging study combining PET and structural MRI. NeuroImage,
63, 10911098.
Lanzenberger, R., Baldinger, P., Hahn, A., Ungersboeck, J., Mitterhauser, M.,
Winkler, D., et al. (2012). Global decrease of serotonin-1A receptor binding after
electroconvulsive therapy in major depression measured by PET. Molecular
Lanzenberger, R. R., Mitterhauser, M., Spindelegger, C., Wadsak, W., Klein, N.,
Mien, L.-K., et al. (2007). Reduced serotonin-1A receptor binding in social anxiety
disorder. Biological Psychiatry, 61, 10811089.
Laruelle, M., Slifstein, M., & Huang, Y. (2003). Relationships between radiotracer
properties and image quality in molecular imaging of the brain with positron
emission tomography. Molecular Imaging and Biology, 5, 363375.
Meyer, J. H. (2007). Imaging the serotonin transporter during major depressive disorder
and antidepressant treatment. Journal of Psychiatry and Neuroscience, 32, 86102.
Meyer, J. H., Houle, S., Sagrati, S., Carella, A., Hussey, D. F., Ginovart, N., et al. (2004).
Brain serotonin transporter binding potential measured with carbon 11-labeled
DASB positron emission tomography: Effects of major depressive episodes and
severity of dysfunctional attitudes. Archives of General Psychiatry, 61, 12711279.
Moses, W. W. (2011). Fundamental limits of spatial resolution in PET. Nuclear Instruments
and Methods in Physics Research Section A, 648(Suppl. 1), S236S240.
Moses-Kolko, E. L., Price, J. C., Thase, M. E., Meltzer, C. C., Kupfer, D. J.,
Mathis, C. A., et al. (2007). Measurement of 5-HT1A receptor binding in depressed
adults before and after antidepressant drug treatment using positron emission
tomography and [11C]WAY-100635. Synapse, 61, 523530.
Muller-Schauenburg, W. (2010). Energy metabolism (FDG) and the general two tissue
compartment model. In S. Dittrich, J. Van den Hoff & R. P. Maguire (Eds.), PET
pharmacokinetics course manual. Scotland: Loch Lomond.
160
Narendran, R., Hwang, D. R., Slifstein, M., Talbot, P. S., Erritzoe, D., Huang, Y., et al.
(2004). In vivo vulnerability to competition by endogenous dopamine: Comparison
of the D2 receptor agonist radiotracer (-)-N-[11C]propyl-norapomorphine ([11C]
NPA) with the D2 receptor antagonist radiotracer [11C]-raclopride. Synapse, 52,
188208.
Nash, J. R., Sargent, P. A., Rabiner, E. A., Hood, S. D., Argyropoulos, S. V.,
Potokar, J. P., et al. (2008). Serotonin 5-HT1A receptor binding in people with panic
disorder: Positron emission tomography study. British Journal of Psychiatry, 193,
229234.
Neumeister, A., Bain, E., Nugent, A. C., Carson, R. E., Bonne, O., Luckenbaugh, D. A.,
et al. (2004). Reduced serotonin type 1A receptor binding in panic disorder. Journal
of Neuroscience, 24, 589591.
Osman, S., Lundkvist, C., Pike, V. W., Halldin, C., Mccarron, J. A., Swahn, C. G., et al.
(1998). Characterisation of the appearance of radioactive metabolites in monkey and
human plasma from the 5-HT1A receptor radioligand, [carbonyl-11C]WAY-100635
Explanation of high signal contrast in PET and an aid to biomathematical modelling.
Nuclear Medicine and Biology, 25, 215223.
Ossenkoppele, R., Tolboom, N., Foster-Dingley, J. C., Adriaanse, S. F., Boellaard, R.,
Yaqub, M., et al. (2012). Longitudinal imaging of Alzheimer pathology using [11C]
PIB, [18 F]FDDNP and [18 F]FDG PET. European Journal of Nuclear Medicine and
Molecular Imaging, 39, 9901000.
Parsey, R. V., Hastings, R. S., Oquendo, M. A., Huang, Y. Y., Simpson, N., Arcement, J.,
et al. (2006). Lower serotonin transporter binding potential in the human brain
during major depressive episodes. The American Journal of Psychiatry, 163, 5258.
Parsey, R. V., Ogden, R. T., Miller, J. M., Tin, A., Hesselgrave, N., Goldstein, E., et al.
(2010). Higher serotonin 1A binding in a second major depression cohort:
Modeling and reference region considerations. Biological Psychiatry, 68, 170178.
Paterson, L. M., Kornum, B. R., Nutt, D. J., Pike, V. W., & Knudsen, G. M. (2013). 5-HT
radioligands for human brain imaging with PET and SPECT. Medicinal Research
Reviews, 33, 54111.
Paterson, L. M., Tyacke, R. J., Nutt, D. J., & Knudsen, G. M. (2010). Measuring
endogenous 5-HT release by emission tomography: Promises and pitfalls. Journal
of Cerebral Blood Flow and Metabolism, 30, 16821706.
Pike, V. W. (2009). PET radiotracers: Crossing the bloodbrain barrier and surviving
metabolism. Trends in Pharmacological Sciences, 30, 431440.
Polter, A. M., & Li, X. (2010). 5-HT1A receptor-regulated signal transduction pathways
in brain. Cellular Signalling, 22, 14061412.
Price, J. C., Klunk, W. E., Lopresti, B. J., Lu, X., Hoge, J. A., Ziolko, S. K., et al. (2005).
Kinetic modeling of amyloid binding in humans using PET imaging and
Pittsburgh compound-B. Journal of Cerebral Blood Flow and Metabolism, 25,
15281547.
Rahmim, A., & Zaidi, H. (2008). PET versus SPECT: Strengths, limitations and
challenges. Nuclear Medicine Communications, 29, 193207.
Richardson-Jones, J. W., Craige, C. P., Guiard, B. P., Stephen, A., Metzger, K. L.,
Kung, H. F., et al. (2010). 5-HT1A autoreceptor levels determine vulnerability to
stress and response to antidepressants. Neuron, 65, 4052.
Salimpoor, V. N., Benovoy, M., Larcher, K., Dagher, A., & Zatorre, R. J. (2011).
Anatomically distinct dopamine release during anticipation and experience of peak
emotion to music. Nature Neuroscience, 14, 257262.
Sargent, P. A., Kjaer, K. H., Bench, C. J., Rabiner, E. A., Messa, C., Meyer, J., et al.
(2000). Brain serotonin1A receptor binding measured by positron emission
tomography with [11C]WAY-100635: Effects of depression and antidepressant
treatment. Archives of General Psychiatry, 57, 174180.
Saulin, A., Savli, M., & Lanzenberger, R. (2011). Serotonin and molecular imaging in
humans using PET. Amino Acids, 42, 20392057.
Savli, M., Bauer, A., Mitterhauser, M., Ding, Y. S., Hahn, A., Kroll, T., et al. (2012).
Normative database of the serotonergic system in healthy subjects using multitracer PET. NeuroImage, 63, 447459.
Spindelegger, C., Lanzenberger, R., Wadsak, W., Mien, L. K., Stein, P.,
Mitterhauser, M., et al. (2009). Influence of escitalopram treatment on 5-HT(1A)
receptor binding in limbic regions in patients with anxiety disorders. Molecular
Sun, W., Ginovart, N., Ko, F., Seeman, P., & Kapur, S. (2003). In vivo evidence for
dopamine-mediated internalization of D2-receptors after amphetamine: Differential
findings with [3H]raclopride versus [3H]spiperone. Molecular Pharmacology, 63,
456462.
Varrone, A., Sjoholm, N., Eriksson, L., Gulyas, B., Halldin, C., & Farde, L. (2009).
Advancement in PET quantification using 3D-OP-OSEM point spread function
reconstruction with the HRRT. European Journal of Nuclear Medicine and Molecular
Imaging, 36, 16391650.
Wadsak, W., & Mitterhauser, M. (2010). Basics and principles of radiopharmaceuticals
for PET/CT. European Journal of Radiology, 73, 461469.
Walker, Z., & Rodda, J. (2011). Dopaminergic imaging: Clinical utility now and in the
future. International Psychogeriatrics, 23(Suppl. 2), S32S40.
Willeit, M., Ginovart, N., Graff, A., Rusjan, P., Vitcu, I., Houle, S., et al. (2008). First
human evidence of d-amphetamine induced displacement of a D2/3 agonist
radioligand: A [11C]-()-PHNO positron emission tomography study.
Neuropsychopharmacology, 33, 279289.
Willeit, M., & Praschak-Rieder, N. (2010). Imaging the effects of genetic
polymorphisms on radioligand binding in the living human brain: A review on
genetic neuroreceptor imaging of monoaminergic systems in psychiatry.
Yeung, H. W., Sanches, A., Squire, O. D., Macapinlac, H. A., Larson, S. M., & Erdi, Y. E.
(2002). Standardized uptake value in pediatric patients: An investigation to
determine the optimum measurement parameter. European Journal of Nuclear
Medicine and Molecular Imaging, 29, 6166.
Susceptibility-Weighted Imaging and Quantitative Susceptibility Mapping

E Mark Haacke, Wayne State University, Detroit, MI, USA
JR Reichenbach, Friedrich-Schiller University, Jena, Germany
Y Wang, Cornell University, New York, NY, USA
Introduction
Conventional clinical magnetic resonance imaging is, to a large
degree, dominated by anatomical imaging based on spin
density, T1, T2, and T2* contrasts. Gradient echo imaging or
T2* imaging has always played a key role in detecting hemorrhages and the presence of iron because of its sensitivity to
local changes in magnetic field that induce signal loss (a reduction of T2*). About 20 years ago, E Mark Haacke (EMH) began
to focus on phase information as a source of contrast during a
sabbatical in 1993 in Erlangen, Germany, at Siemens Healthcare. This led to two early papers on the role of phase and
susceptibility to study oxygen saturation and validating the
blood oxygen level-dependent mechanism related to the role
of veins (Haacke et al., 1997; Haacke, Lai, Yablonskiy, & Lin,
1995). Already at this time, the concept of high-pass filtering
had been implemented to remove unwanted low spatial frequency information and reveal the interesting anatomical
information shown in phase imaging. Shortly after this, in
1995, Jurgen Reichenbach joined EMHs group in St. Louis
and spent 2 years adding his insight into the role of susceptibility in MR imaging. Later, this filtered phase was used as a
mask (Haacke, Xu, Cheng, & Reichenbach, 2004; Reichenbach
et al., 1998; Reichenbach, Venkatesan, Schillinger, Kido, &
Haacke, 1997) to create susceptibility-weighted images, a technique that is very sensitive to the presence of iron and therefore
small microbleeds as well (Haacke, Raza, Wu, & Kou, 2013;
Tong et al., 2003).
As presented in their 1995 work (Haacke et al., 1995),
phase imaging provides an imaging form of spectroscopy
since it is a frequency-sensitive imaging approach. In this
early paper, it was clearly shown that excellent susceptibility
contrast could be obtained even between the gray matter and
white matter. The problem in dealing with phase images is that
there are a variety of other sources of phase shifts that obscure
the phase from local susceptibility structures. These include
tissue conductivity effects, multiple radio-frequency coil contributions, linear phase shifts (from eddy currents), quadratic
phase shifts (from concomitant gradient fields), partial volume
effects, and insufficient or lack of flow compensation. To further complicate the issue, if the phase exceeds p, then it will
alias and this aliased phase needs to be unwrapped to be
properly processed. To remove most of these other sources of
phase, a high-pass filter was applied leaving effectively the local
fields. From this new phase image, a mask was made to apply
to the original magnitude data to create a susceptibilityweighted image.
However, these phase data, despite its being filtered, still
suffered from the inherent nonlocal characteristics associated
with all surrounding magnetic susceptibilities with the association dependent on orientation, distance, echo time, and field
strength. Ideally, one would like to see the magnetic field

source itself rather than this indirect biomarker of the presence
of an object with a susceptibility value different than its surroundings. Recently, an inverse reconstruction approach has
been proposed that maps the phase (or, equivalently, the
magnetic field) into a source image (Deville et al. 1979;
Salomir, de Senneville, & Moonen, 2003), which is today
referred to as quantitative susceptibility mapping (QSM). The
QSM data processing steps are illustrated in Figure 1. We will
review some of the key points needed to produce a robust
method for QSM including data acquisition and phase
reconstruction, phase unwrapping, removal of background
fields, image processing, solving the ill-posed inverse problem,
signal-to-noise ratio, visualization of the data, and interpretation of the results in terms of absolute measures of iron.
Predicting Magnetic Field from a Susceptibility Map

Using the approach presented in Salomir et al. (2003), assuming that the main field B0 is in the z-direction and noting tissue
object susceptibility (relative to water) distribution as Dw(r)
and its associated field in the z-direction as Dbz(r), we can write
Dbz r B0 Dwr *gr
[1]
where g(r) is the point-dipole response or Greens function

defined as
gr
1 3 cos 2 y 1
4p
r3
[2]
with y the azimuthal orientation of r and exclusion of r 0 in

eqn [1] and where * denotes the mathematical convolution
operation. Equation [2] is commonly referred as the dipole
kernel in QSM. The convolution in eqn [1] can be more efficiently computed in k-space using the convolution theorem.
We need the Fourier transform of g(r)

1=3 k2z =k2 , for k 6 0
G k
[3]
0, for k 0
where kx, ky, and kz are the coordinates in k-space and
k2 k2x k2y k2z . Let B(k) FT[Dbz(r)], w(k) FT[Dw(r)].
Then, the magnetic field for an object with susceptibility
Dw(r) is found in k-space as
Bk B0 Gkwk
[4]
As illustrated in Figure 2, using a 3-D numerical model of

the human brain and applying eqn [4] show the expected
nonlocal phase behavior originating from the different structures in the brain such as the globus pallidus (GP), midbrain,
and veins.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00019-1
161
162
INTRODUCTION TO ACQUISITION METHODS | Susceptibility-Weighted Imaging and Quantitative Susceptibility Mapping
Magnitude
Brain mask
Brain
extraction
Original phase
Unwrapped phase
Background
field
removal
Phase
unwrapping
Susceptibility map
Processed phase
Inverse
filtering
Figure 1 QSM data processing steps. *The phase unwrapping step may not be necessary.
CSF
0.7 rad
0.45 ppm
WM
GM
CN
PUT
Veins
TH
-0.06 ppm
Transverse view
Transverse view
-0.7 rad
GP
RN
SN
Coronal view
Coronal view
Saginal view
Sagittal view
Figure 2 Susceptibility model (left) and phase images (right) from a numerical 3-D model of the brain in three orthogonal views (CSF, cerebrospinal
fluid; WM, white matter; GM, gray matter; CN, caudate nucleus; PUT, putamen; TH, thalamus; GP, globus pallidus; SN, substantia nigra; RN, red
nucleus).
Phase as a Function of Local Field and Echo Time

In order to extract the local magnetic field, the phase from a
gradient echo sequence is required. With no other sources of
field inhomogeneity except those from objects with nonzero
susceptibility differences, the phase for a left-handed system
can be written as
fr gDbz r TE
[5]
where g is the gyromagnetic ratio and TE is the echo time. In a

left-handed system, veins parallel to the field and small veins
with partial volume perpendicular to the field (Xu & Haacke,

2006) will appear positive or bright on phase images. Equation
[5] is precise for a single proton or isochromat. When we deal
with a collection of spins in a voxel in MRI, things become
more complicated. If the field is uniform over a voxel, then eqn
[5] is precise. If the field varies over the voxel, eqn [5] is still
valid with Dbz interpreted as the field averaged over the voxel
weighted by the local spin densities and f is the phase of the
total signal in the voxel (Wang, 2012). Additional terms nonlinear in TE may be included for long TE and subvoxel structures (He & Yablonskiy, 2009; Wharton & Bowtell, 2012;

Yablonskiy, Sukstanskii, Luo, & Wang, 2013). In practice, we
find that the best aspect ratio to use at higher fields appears to
be between 1:1:2 and 1:1:4 for in-plane to through plane
resolution (Deistung et al., 2008; Xu & Haacke, 2006).
We now comment on the phase data acquisition with an
emphasis on its usage in SWI. To best image veins using SWI,
the echo time at 3 T is usually chosen to be 20 ms, which
makes the phase in a normally oxygenated vein parallel to the
field roughly p (Reichenbach et al., 2000). In general, phase
will be independent of field strength if the product of B0 TE is
kept constant. Of key importance is the fact that at higher
field strength, SWI (and hence QSM) will have better SNR and
will become faster and faster since as B0 increases, TE will be
reduced and, therefore, TR can also be accordingly reduced
(Deistung et al., 2008). If one wants to see smaller vessels,
then going to longer echo times not only generates more T*
2
effect but also brings to life more phase information.
Although this can be used to amplify the appearance of
microbleeds and small deoxygenated veins in stroke, for
example, it is counterproductive in estimating high susceptibility accurately for structures with large amounts of iron. The
reason for this is the substantial T2* dephasing at long TEs
resulting in very poor SNR in phase estimation and the nonlinearity issue alluded to earlier in the text. The product of the
volume and susceptibility (representing the magnetic
moment) will be conserved in that case (Liu et al., 2013,
2012; Schweser, Deistung, Lehr, & Reichenbach, 2010).
Hence, it would be advantageous to use multiple TEs from
short to long to be sensitive to a range of susceptibility values
(Wang, 2012). To avoid aliasing in veins, a better choice of
echo time would be around 1213 ms as then there would be
no aliasing even in the extravascular field terms for vessels
perpendicular to the main field and with normal levels of
deoxyhemoglobin. To avoid flow-induced phase, the 3-D
gradient echo sequence is flow-compensated for the read,
phase encoding, partition encoding, and slice select gradients
(Reichenbach et al., 1997; Xu, Liu, Spincemaille, Prince, &
Wang, 2013). This helps to remove one more source of phase
error. The high-pass filter removes most of the other errors
although still leaves behind a reduced susceptibility and edge
artifacts.
Creating a Susceptibility Map

The susceptibility distribution Dw(r) can be obtained by
reworking eqn [4] into

Dwr FT1 G1 k Bk=B0
[6]
Due to the zeros of G(k), this inverse is ill-posed: that
is, there can be multiple mathematical susceptibility distributions corresponding to the same measured field. To select
a solution that corresponds to the true physical imaging
situation, additional prior information is needed (Kressler
et al., 2010). This process is referred to as regularization.
The simplest regularization is to introduce a k-space truncation threshold t and construct a regularized inverse filter
G 1(k) such as (Haacke, Tang, Neelavalli, & Cheng, 2010;
Schweser, Deistung, Sommer, & Reichenbach, 2013; Shmueli
et al., 2009)
163
G01 k
8
>
>
>
<

1
1 k2
1 k2z
2
, when z2 > t
3 k
3 k

2
2 n
>
1
k
1
k
>
z
z
>
: sgn 2 2 tn1 , n 0 2, when
3 k 3 k

1 k2z
t
3 k2
[7]
With this approach, G 1(k) is gradually reduced to zero as

|G(k)| gets close to zero. This threshold approach is chosen to
smooth the signal to zero. Removing this region of k-space
produces erroneous susceptibility values (although often yielding a reasonably good estimate of the susceptibility) and results
that are often biased and shape-dependent. When the threshold is low, there will be streaking artifacts, and when the
threshold is high, there will be high levels of smoothing.
The task of picking the right solution to an ill-posed inverse
problem is challenging because of data noise and priorinformation uncertainty. For example, the probability distribution of data noise in a given imaging situation may be known. In
that case, there is a well-established mathematical approach to
obtain an optimal solution, the so-called maximum a posteriori
estimate in Bayesian statistics (Barber, 2012). To start with, one
can assume Gaussian noise in phase data, which is reasonable
when SNR is sufficiently high. The solution is penalized when it
deviates from the prior information. Prior information can
include structural information available through the set of edge
locations M in the image. Similar to Gaussian noise (with noise
amplitude n(r) and noise variance s2(r)) that can be characterized
2
2
by en =2s , any structural deviation penalty may be represented
X
R
as e with Rw l jMr rwr j summing all deviations
r
(binary mask Mr 1 8r=

2 M; 0 8r 2 M and l is a scaling
factor typically chosen such that R n2/2s2 for a given solution
(the discrepancy principle)). Then, the optimal solution would be
given by
wr argminwr wDbl r =B0 wr *gr 22 Rw
[8]
where the weighting factor w2 1/2s2 is determined from

phase noise (magnitude squared) and Dbl(r) is the field variation induced by local susceptibility sources. This is referred as
the morphology-enabled dipole inversion (De Rochefort et al.,
2010; Liu et al., 2012; Liu et al., 2013). Noise regions should be
masked out in eqn [8] (through a weighting factor), where the
Gaussian noise assumption is violated. Equation [8] can be
solved using the Newton method in optimization (Nocedal &
Wright, 1999) and various other optimization algorithms
(Bilgic, Pfefferbaum, Rohlfing, Sullivan, & Adalsteinsson,
2012; Liu, Liu, et al., 2012; Schweser, Sommer, Deistung, &
Reichenbach, 2012). The edge information can come from the
magnitude and phase images (Liu, Liu, et al., 2012; Schweser
et al., 2012). When R(w) 0, eqn [8] reduces to a least-squares
fit (Cheng, Neelavalli, & Haacke, 2009).
An alternate approach to improve the information in the
cone of singularity is to use an efficient k-space/image-domain
iterative algorithm (Tang et al., 2013). In each iteration, the
data points in the cone of singularities are updated with
geometry-dependent information. For example, to reduce the
streaking artifacts coming from the high susceptibility veins,
the geometry of the veins can be used to force the susceptibility
164
outside the veins to be zero. The smoothness constraint can

also be applied to the regions inside the veins (e.g., forcing the
veins to have a locally uniform susceptibility value) to further
reduce the streaking artifacts inside the veins.
Phase Reconstruction, Phase Unwrapping,

and Removal of Background Fields
Todays MR scanners use an array of radio-frequency coils.
Each coil sensitivity function has its own magnitude and
phase. All coil data can be combined using a complex coil
sensitivity function (Pruessmann, Weiger, Scheidegger, & Boesiger, 1999; Roemer, Edelstein, Hayes, Souza, & Mueller, 1990)
to obtain a pristine phase image. If this is not done properly,
then cusp artifacts will be generated (Hammond et al., 2008;
Robinson, Grabner, Witoszynskyj, & Trattnig, 2011).
As a complex number can only define phase in a 2p period,
artificial jumps occur in a phase map, and phase unwrapping is
necessary by imposing spatial smoothness. Because of noise and
digitization, phase unwrapping is a nontrivial problem. There
are a variety of approaches to deal with phase unwrapping such
as path finding and global error minimization (Ghiglia & Pritt,
1998). There are a number of different single-echo phase
unwrapping techniques including image quality-guided phase
unwrapping (Abdul-Rahman et al., 2007; Witoszynskyj,
Rauscher, Reichenbach, & Barth, 2009), Laplacian-based
methods (Schofield & Zhu, 2003), and 3-D optimizationbased unwrapping (prelude in FSL Jenkinson, 2003). The selection of the phase unwrapping algorithm is usually a trade-off
between robustness and time efficiency. There are also phase
unwrapping algorithms that are based on multiecho data such
as the CAMPUS approach (Feng, Neelavalli, & Haacke, 2013).
Using the short effective TEs derived with this approach, much of
the phase aliasing can be avoided. The major advantages of
CAMPUS are its speed and its ability to provide phase unwrapping on a pixel-by-pixel basis without the need for segmentation
algorithms.
The field variation Dbz(r) extracted from the unwrapped
phase f(r) in practice is a combination of the background
field Dbb(r) induced by the global geometry, airtissue interfaces, and magnetic sources outside the body and the field
variation Dbl(r) induced by the tissue susceptibility
distribution:
Dbz r Dbl r Dbb r
[9]
In QSM, only Dbl(r) is of interest. The background field may

be removed prior to solving eqn [8]. The original high-pass
filtering used in some manufacturers implementation of SWI
not only unwraps the phase but also removes the low spatial
frequency components of the tissue field. However, it also
causes erroneous input into eqn [8]. Fortunately, Maxwells
equations can be used to separate background and tissue fields
based upon their source separations including (1) solving the
Laplacian equation using a truncated spectral method and
assuming a periodic boundary value condition, which is
referred as the sophisticated harmonic artifact reduction for
phase data (SHARP) method (Schweser, Deistung, Lehr, &
Reichenbach, 2011); (2) projecting the Laplacian equation
solution onto the dipole field functions, which is referred as

the projection onto dipole field (PDF) method (Liu et al.,
2011a); and (3) solving the Laplacian equation precisely
assuming a boundary value, which is referred the Laplacian
boundary value method (Zhou, Liu, Spincemaille, & Wang,
2013). These methods work well but not perfectly. The accuracy of the SHARP-processed phase images is dependent on the
truncation parameter, the size of the spherical kernel, and its
specific boundary assumption (Schweser et al., 2011; Sun &
Wilman, 2013; Wu, Li, Guidon, & Liu, 2012). The PDF has
difficulty in separating sources near the boundary where the
orthogonality of dipole fields suffers.
Another alternative is the geometry-dependent artifact correction approach (Neelavalli, Cheng, Jiang, & Haacke, 2009),
in which the geometry of the airtissue interfaces is obtained
from the magnitude images and the background field induced
by these airtissue interfaces is predicted through a fastforward calculation. This method is found to be effective in
reducing the background field, but the accuracy depends on
the correctness of the extracted geometries.
Validation of QSM and Complexity of Tissue

Susceptibility
All quantitative techniques have to be validated with their
accuracies calibrated by reference standards, and this validation is particularly important for methods involving regularization. There are many possible regularization approaches and
consequently many QSM techniques. Before being used, each
technique should be tested on (a) simulation data where the
truth is known, (b) MRI data for a phantom with a range of
known susceptibility values, and (c) in vivo human data where
another reference standard is available (De Rochefort et al.,
2010; Liu, Liu, et al., 2012; Liu et al., 2011; Schweser et al.,
2012; Tang et al., 2013).
A useful in vivo reference standard (limited to the accuracy
of the dipole approximation) comes from MRI: the calculation
of susceptibility through multiple orientation sampling (COSMOS) allows for the determination of susceptibility without
assuming any regularization (Liu, Spincemaille, de Rochefort,
Kressler, & Wang, 2009). In each orientation of COSMOS data
acquisition, the cone of dipole kernel singularity is rotated
according to the field direction. Thus, the missing data in the
cone of singularity can be found by combining the data collected at the different orientations. Although this effectively
eliminates the singularity problem, it requires collecting at
least three datasets with different orientations. Both the prolonged scan time and the rotation of the head or body parts
make it impractical in clinical practice but make it a great
in vivo reference standard for validating any regularizationbased singular orientation QSM technique.
Equation [1] can be equivalently expressed in a differential
form similar to the Laplacian equation, which requires a
boundary value specification for a definite solution. Similarly,
the susceptibility solution uses the boundary value specified in
the background field removal, the imperfection of which may
be a source of error for potential global shifts in some QSM
algorithms (basically, the susceptibility distribution is inherently a spatial map of relative susceptibilities, Dw). For

example, in the brain, the cerebrospinal fluid (CSF) may be
used as a reference region.
There is now clear evidence that the susceptibility of myelin,
and thus the susceptibility of white matter, is anisotropic (Lee
et al., 2010; Li et al., 2012; Wharton & Bowtell, 2012; Wisnieff
et al., 2013). Consequently, the magnetic susceptibility values
depend on the orientation of the white matter fiber bundles
with respect to the main magnetic field. Therefore, care has to
be exercised in choosing the reference region, in particular
when comparing quantitative results from different studies.
Sources of Noise
The Bayesian approach is quite robust (Liu, Xu, Spincemaille,
Avestimehr, & Wang, 2012d), but noise does propagate into
QSM images. Noise sources include but are not limited to (i)
white noise as transformed from k-space (Fourier domain of
phase images) back to the susceptibility map, (ii) streaking
along the cone of singularity, (iii) streaking within the object
itself, and (iv) other false susceptibility information generated
from phase information that does not correspond to a conventional magnetic field such as linear (echo shifting) and quadratic (concomitant gradient paper) phase offsets, RF coil
phase shifts, chemical shift effects, or phase from flowing
spins that are not properly flow-compensated. This latter
group tends to add systematic noise in the form of artifacts in
the images. The white noise in QSM can be estimated using
simulations (Tang et al., 2013) and we find that
sw
R
ppm
gB0 TESNRmag
[10]
where sw is the standard deviation in the susceptibility map,

SNRmag is the SNR in the magnitude image, and R represents
the translation of the random noise from the original phase
images into the susceptibility maps. For example, for a single
orientation approach, a k-space truncation threshold of 0.1 for
the inverse filter, R, is found to be roughly 4. This implies that
the error in susceptibility in ppm is also equal to 1/SNRmag,
when B0 3 T, TE 5 ms. That is, a 10% error in the magnitude
image leads to a 10% error in ppm in the susceptibility map.
Besides these issues, noise effects also depend on the particular QSM algorithm used for reconstructing the susceptibility
map, as they treat noise amplification upon inversion differently
(see Creating a Susceptibility Map; Shuai et al., 2013).
Interpretation of the Results in Terms of Absolute Iron

Content
The practical question for QSM is: How accurately can the
susceptibility be mapped to total iron content? The relationship
between Dw in ppm and iron depends on whether one is imaging ferritin (Hopp et al., 2010; Zheng, Haacke, Webb, & Nichol,
2012; Zheng, Nichol, Liu, Cheng, & Haacke, 2013), ferritin in
cadaver brain (Langkammer et al., 2010, 2012a,2012b), or ferritin or other sources of iron in in vivo human studies. Only the
first two can actually be validated, although many groups use
the results of Hallgren and Sourander to estimate the accuracy of
165
any given iron measurement method (Haacke et al., 2005).

Estimates of the slope between Dw and iron concentration are
roughly 0.6 ppb per microgram iron per gram wet tissue
obtained from the in vivo data (Shmueli et al., 2009; Wharton
& Bowtell, 2010), which is smaller than the 0.8 ppb susceptibility per microgram iron per gram wet tissue obtained from
cadaveric brain data (Zheng et al., 2013).
Clinical Examples
Currently, the use of QSM is predominantly for measuring iron
in the form of ferritin, hemosiderin, and deoxyhemoglobin.
Quantifying iron offers different and more detailed information than only visualizing the presence of iron with SWI. For
example, measuring iron in the basal ganglia can be used as a
marker for abnormal levels of iron in diseases such as
Parkinsons disease, multiple sclerosis, Huntingtons disease,
and neuroferritinopathies (Haacke et al., 2005; Langkammer
et al., 2013). Iron can also be used to monitor microbleeds in
traumatic brain injury (Liu, Surapaneni, et al., 2012c). Measuring hemosiderin in microbleeds can be used to ascertain if the
bleed changes over time.
A comparison of SWI and QSM is shown in Figures 3 and 4.
Measuring deoxyhemoglobin can be used for monitoring oxygen saturation changes (Haacke et al., 2010) in stroke or intracranial hypertension when there is a perfusion deficit. An
example of the latter is shown in Figure 5 indicating an
increase in deoxyhemoglobin and therefore a region of
reduced perfusion. The ability of using SWI and QSM to visualize and quantify changes in venous oxygen saturation can
also be seen from Figure 6, which shows the changes of image
contrast in SWI and QSM between precaffeine administration
and postcaffeine administration. Note that the improved contrast of the veins in the postcaffeine SWI and QSM is due to the
decreased oxygen saturation (hence increased deoxyhemoglobin or susceptibility) of the veins, caused by caffeine-induced
vaso-constriction (Haacke et al., 2010; Sedlacik et al., 2008).
QSM can provide a reliable measurement of hematoma volume (Figure 7; Shuo et al., 2013). QSM at 3 T provides significantly better data than current standard MRI for depiction of
the deep brain stimulation targets (Figure 8; Liu et al., 2013c).
QSM may provide a new vision into inflammation in multiple
sclerosis by depicting iron in lesions replete with macrophage
activity (Figure 9; Chen et al., 2014). Finally, the geometry and
TE dependence of phase information usually hamper the effectiveness of SWI, especially for high isotropic resolution. These
problems can be overcome by the use of true SWI (tSWI)
generated from susceptibility maps (Figure 10) since the resulting susceptibilities from QSM no longer have either orientation or echo time dependence (at least theoretically) (Gho
et al., 2013; Liu, Neelavalli, Cheng, Tang, & Mark, 2013b).
Conclusions and Future Applications

Although we have focused in this article on QSM technology in
the brain, there are many other parts of the body where SWI
(and, hence, we expect QSM) can find clinical applications.
166
Figure 3 (a) Original magnitude image. (b) Original phase image. (c) Minimum intensity projection of SWI. (d) Maximum intensity projection of the
susceptibility maps.
167
Figure 4 Maximum intensity projection (MIP) of susceptibility maps (a) and minimum intensity projection (mIP) of SWI (b) for a TBI case. Note that
the inhomogeneities show clearly with the minimum intensity since any low intensity signal loss or artifact will show in the mIP even if it occurs
in only a single slice. This will not be a problem when the maximum intensity is used, a major advantage of susceptibility mapping (i.e., that it has
positive contrast).
Figure 5 An example MR angiogram (a), SWI (b), and thresholded susceptibility map (c) for a case of intracranial hypertension. The threshold
in the QSM was set to 200 ppb and those veins that show purple here represent abnormally high levels of deoxyhemoglobin (indicative of perfusion
deficit in the brain). Images courtesy of Jiangtao Liu and Shuang Xia.
168
300
250
200
150
100
50
(a)
(b)
0.2
ppm
0.15
0.1
0.05
(c)
(d)
Figure 6 Minimum intensity projections of SWI (a and b) and maximum intensity projections of susceptibility maps (c and d) for pre- and
postcaffeine administration. Here, (a) and (c) are the projections of SWI and QSM for precaffeine administration, while (b) and (d) are for postcaffeine
administration. The effective slice thickness is 16 mm for all the images.
Figure 7 An example of intracranial hemorrhage: (a) a T2*-weighted gradient echo magnitude image with contrast dependent on TE and other imaging
parameters and (b) QSM demonstrating very strong susceptibility (1 ppm) of blood degeneration products (mostly hemosiderin).
Figure 8 Depiction of deep brain stimulation targets (a) with standard T2-weighted image and (b) with QSM. The zoomed images in (c) and (d) show
the subthalamic nuclei (white arrows) and globus pallidus (black arrows).
Figure 9 Example images from a patient with multiple sclerosis: (a) standard T2-weighted FLAIR and (b) QSM. While T2-weighted FLAIR demonstrates
a relative increase in water in MS lesions, QSM shows the presence of iron in the MS lesions (arrows in b) possibly indicating macrophage activity.
Figure 10 A comparison between minimum intensity projections (mIPs) of conventional SWI and tSWI. (a) Transverse mIP of conventional SWI.
(b) Transverse mIP of tSWI. (c) Sagittal mIP of conventional SWI. (d) Sagittal mIP of tSWI. For transverse mIPs (a and b), the effective slice thickness
is 32 mm, while for the sagittal mIPs, the effective slice thickness is 8 mm. The voxel size of the original dataset is 0.5 0.5 2mm3.
For sagittal mIPs, interpolation was performed to get isotropic resolution, for visualization purposes. Note that the blooming artifact of some of
the major bleeds has been reduced using tSWI (arrows).

These include imaging the vessel wall (Yang et al., 2009), spine
(Fujima et al., 2011; Wang et al., 2011), liver (Tao et al., 2012),
and kidney (Mie et al., 2010), to mention just a few. Since the
early work of evaluating the effects of susceptibility on T2 of
blood as a function of oxygen saturation by Thulborn, Waterton, Matthews, and Radda (1982), current methods of QSM,
extensions to susceptibility tensor mapping of Liu et al. (Liu,
2010; Liu, Li, Wu, Jiang, & Johnson, 2012), and the potential
of imaging structures such as bone or calcium with little or no
signal by Buch, Ye, Cheng, Neelavalli, & Haacke (2013), the
use of susceptibility mapping promises to address important
clinical questions in the years to come.

Anatomical MRI for Human Brain Morphometry; High-Field
Acquisition; High-Speed, High-Resolution Acquisitions; MRI and fMRI
Optimizations and Applications; Myelin Imaging; Obtaining
Quantitative Information from fMRI; Perfusion Imaging with Arterial
Spin Labeling MRI; INTRODUCTION TO CLINICAL BRAIN
MAPPING: Alzheimers Disease; Brain Inflammation, Degeneration,
and Plasticity in Multiple Sclerosis; Brain Mapping Techniques Used to
Guide Deep Brain Stimulation Surgery; Demyelinating Diseases;
Huntingtons Disease for Brain Mapping: An Encyclopedic Reference;
Primary Progressive Aphasia; Recovery and Rehabilitation Poststroke;
The Anatomy of Parkinsonian Disorders; INTRODUCTION TO
COGNITIVE NEUROSCIENCE: Substantia Nigra; INTRODUCTION
TO METHODS AND MODELING: Bayesian Model Inversion; Image
Reconstruction in MRI; Tissue Properties from Quantitative MRI.
References
Abdul-Rahman, H. S., Gdeisat, M. A., Burton, D. R., Lalor, M. J., Lilley, F., &
Moore, C. J. (2007). Fast and robust three-dimensional best path phase
unwrapping algorithm. Applied Optics, 46, 66236635.
Barber, D. (2012). Bayesian reasoning and machine learning. Cambridge: Cambridge
University Press.
Bilgic, B., Pfefferbaum, A., Rohlfing, T., Sullivan, E. V., & Adalsteinsson, E. (2012). MRI
estimates of brain iron concentration in normal aging using quantitative
susceptibility mapping. NeuroImage, 59, 26252635.
Buch, S., Liu, S., Ye, Y., Cheng, Y., Neelavalli, J., & Haacke, E. M. (2014). Susceptibility
mapping of air, bone, and calcium in the head. Magnetic Resonance in Medicine,
http://dx.doi.org/10.1002/mrm.25350.
Chen, W., Gauthier, S., Gupta, A., Comunale, J., Liu, T., Wang, S., et al. (2014).
Quantitative susceptibility mapping of multiple sclerosis lesions at various ages.
Radiology, 271, 183192.
Cheng, Y. C. N., Neelavalli, J., & Haacke, E. M. (2009). Limitations of calculating field
distributions and magnetic susceptibilities in MRI using a Fourier based method.
Physics in Medicine and Biology, 54, 11691189.
De Rochefort, L., Liu, T., Kressler, B., Liu, J., Spincemaille, P., Lebon, V., et al. (2010).
Quantitative susceptibility map reconstruction from MR phase data using bayesian
regularization: Validation and application to brain imaging. Magnetic Resonance in
Medicine, 63, 194206.
Deistung, A., Rauscher, A., Sedlacik, J., Stadler, J., Witoszynskyj, S., &
Reichenbach, J. R. (2008). Susceptibility weighted imaging at ultra high magnetic
field strengths: Theoretical considerations and experimental results. Magnetic
Deville, G., Bernier, M., & Delrieux, J. M. (1979). NMR multiple echoes observed in
solid He3. Physical Review B, 19, 5666.
Feng, W., Neelavalli, J., & Haacke, E. M. (2013). Catalytic multiecho phase unwrapping
scheme (CAMPUS) in multiecho gradient echo imaging: Removing phase wraps on
a voxel-by-voxel basis. Magnetic Resonance in Medicine, 70, 117126.
Fujima, N., Kudo, K., Terae, S., Ishizaka, K., Yazu, R., Zaitsu, Y., et al. (2011). Noninvasive measurement of oxygen saturation in the spinal vein using SWI:
Quantitative evaluation under conditions of physiological and caffeine load.
171
Ghiglia, D. C., & Pritt, M. D. (1998). Two-dimensional phase unwrapping: Theory,

algorithms, and software. Wiley.
Gho, S.-M., Liu, C., Li, W., Jang, U., Kim, E. Y., Hwang, D., et al. (2013). Susceptibility
map-weighted imaging (SMWI) for neuroimaging. Magnetic Resonance in
Medicine, http://dx.doi.org/10.1002/mrm.24920.
Haacke, E. M., Cheng, Y. C. N., House, M. J., Liu, Q., Neelavalli, J., Ogg, R. J., et al.
(2005). Imaging iron stores in the brain using magnetic resonance imaging.
Haacke, E. M., Lai, S., Reichenbach, J. R., Kuppusamy, K., Hoogenraad, F. G., Takeichi, H.,
et al. (1997). In vivo measurement of blood oxygen saturation using magnetic
resonance imaging: A direct validation of the blood oxygen level-dependent concept in
functional brain imaging. Human Brain Mapping, 5, 341346.
Haacke, E. M., Lai, S., Yablonskiy, D. A., & Lin, W. (1995). In vivo validation of the bold
mechanism: A review of signal changes in gradient echo functional MRI in the
presence of flow. International Journal of Imaging Systems and Technology, 6,
153163.
Haacke, E. M., Raza, W., Wu, B., & Kou, Z. (2013). the presence of venous damage
and microbleeds in traumatic brain injury and the potential future role of
angiographic and perfusion magnetic resonance imaging. In C. W. Kreipke, & J. A.
Rafols (Eds.), Cerebral blood flow, metabolism, and head trauma (pp. 7594).
New York: Springer, Available from: http://link.springer.com/chapter/10.1007/9781-4614-4148-9_4.
Haacke, E. M., Tang, J., Neelavalli, J., & Cheng, Y. C. N. (2010). Susceptibility mapping
as a means to visualize veins and quantify oxygen saturation. Journal of Magnetic
Haacke, E. M., Xu, Y., Cheng, Y. C. N., & Reichenbach, J. R. (2004). Susceptibility
weighted imaging (SWI). Magnetic Resonance in Medicine, 52, 612618.
Hammond, K. E., Lupo, J. M., Xu, D., Metcalf, M., Kelley, D. A. C., Pelletier, D., et al.
(2008). Development of a robust method for generating 7.0 T multichannel phase
images of the brain with application to normal volunteers and patients with
neurological diseases. NeuroImage, 39, 16821692.
He, X., & Yablonskiy, D. A. (2009). Biophysical mechanisms of phase contrast in
gradient echo MRI. Proceedings of the National Academy of Sciences of the United
Hopp, K., Popescu, B. F.G, McCrea, R. P. E., Harder, S. L., Robinson, C. A.,
Haacke, E. M., et al. (2010). Brain iron detected by SWI high pass filtered phase
calibrated with synchrotron X-ray fluorescence. Journal of Magnetic Resonance
Imaging, 31, 13461354.
Jenkinson, M. (2003). Fast, automated, N-dimensional phase-unwrapping algorithm.
Kressler, B., de Rochefort, L., Liu, T., Spincemaille, P., Jiang, Q., & Wang, Y. (2010).
Nonlinear regularization for per voxel estimation of magnetic susceptibility
distributions from MRI field maps. IEEE Transactions on Medical Imaging, 29,
273281.
Langkammer, C., Krebs, N., Goessler, W., Scheurer, E., Ebner, F., Yen, K., et al. (2010).
Quantitative MR imaging of brain iron: A postmortem validation study. Radiology,
257, 455462.
Langkammer, C., Krebs, N., Goessler, W., Scheurer, E., Yen, K., Fazekas, F., et al.
(2012). Susceptibility induced gray-white matter MRI contrast in the human brain.
Langkammer, C., Liu, T., Khalil, M., Enzinger, C., Jehna, M., Fuchs, S., et al. (2013).
Quantitative susceptibility mapping in multiple sclerosis. Radiology, 267,
551559.
Langkammer, C., Schweser, F., Krebs, N., Deistung, A., Goessler, W., Scheurer, E., et al.
(2012). Quantitative susceptibility mapping (QSM) as a means to measure brain
iron? A post mortem validation study. NeuroImage, 62, 15931599.
Lee, J., Shmueli, K., Fukunaga, M., van Gelderen, P., Merkle, H., Silva, A. C., et al.
(2010). Sensitivity of MRI resonance frequency to the orientation of brain tissue
microstructure. Proceedings of the National Academy of Sciences of the United
Li, X., Vikram, D. S., Lim, I. A. L., Jones, C. K., Farrell, J. A. D., & van Zijl, P. C. M.
(2012). Mapping magnetic susceptibility anisotropies of white matter in vivo in the
human brain at 7 T. NeuroImage, 62, 314330.
Liu, C. (2010). Susceptibility tensor imaging. Magnetic Resonance in Medicine, 63,
14711477.
Liu, T., Eskreis-Winkler, S., Schweitzer, A. D., Chen, W., Kaplitt, M. G., Tsiouris, A. J.,
et al. (2013). Improved subthalamic nucleus depiction with quantitative
susceptibility mapping. Radiology, 269(1), 216223.
Liu, T., Khalidov, I., de Rochefort, L., Spincemaille, P., Liu, J., Tsiouris, A. J., et al.
(2011). A novel background field removal method for MRI using projection onto
dipole fields (PDF). NMR in Biomedicine, 24, 11291136.
Liu, C., Li, W., Wu, B., Jiang, Y., & Johnson, G. A. (2012). 3D fiber tractography with
susceptibility tensor imaging. NeuroImage, 59, 12901298.
172
Liu, J., Liu, T., de Rochefort, L., Ledoux, J., Khalidov, I., Chen, W., et al. (2012).
Morphology enabled dipole inversion for quantitative susceptibility mapping using
structural consistency between the magnitude image and the susceptibility map.
Liu, T., Liu, J., de Rochefort, L., Spincemaille, P., Khalidov, I., Ledoux, J. R., et al.
(2011). Morphology enabled dipole inversion (MEDI) from a single-angle
acquisition: Comparison with COSMOS in human brain imaging. Magnetic
Liu, S., Mok, K., Neelavalli, J., Cheng, Y. C. N., Tang, J., Ye, Y., et al. (2013). Improved
MR venography using quantitative susceptibility-weighted imaging. Journal of
Magnetic Resonance Imaging, http://dx.doi.org/10.1002/jmri.24413.
Liu, S., Neelavalli, J., Cheng, Y.-C. N., Tang, J., & Mark, Haacke E. (2013). Quantitative
susceptibility mapping of small objects using volume constraints. Magnetic
Liu, T., Spincemaille, P., de Rochefort, L., Kressler, B., & Wang, Y. (2009). Calculation
of susceptibility through multiple orientation sampling (COSMOS): A method for
conditioning the inverse problem from measured magnetic field map to
susceptibility source image in MRI. Magnetic Resonance in Medicine, 61, 196204.
Liu, T., Surapaneni, K., Lou, M., Cheng, L., Spincemaille, P., & Wang, Y. (2012).
Cerebral microbleeds: Burden assessment by using quantitative susceptibility
mapping. Radiology, 262, 269278.
Liu, T., Wisnieff, C., Lou, M., Chen, W., Spincemaille, P., & Wang, Y. (2013). Nonlinear
formulation of the magnetic field to source relationship for robust quantitative
susceptibility mapping. Magnetic Resonance in Medicine, 69, 467476.
Liu, T., Xu, W., Spincemaille, P., Avestimehr, A. S., & Wang, Y. (2012). Accuracy of the
morphology enabled dipole inversion (MEDI) algorithm for quantitative
susceptibility mapping in MRI. IEEE Transactions on Medical Imaging, 31, 816824.
Mie, M. B., Nissen, J. C., Zollner, F. G., Heilmann, M., Schoenberg, S. O.,
Michaely, H. J., et al. (2010). Susceptibility weighted imaging (SWI) of the kidney at
3 T Initial results. Zeitschrift fur Medizinische Physik, 20, 143150.
Neelavalli, J., Cheng, Y. N., Jiang, J., & Haacke, E. M. (2009). Removing background
phase variations in susceptibility-weighted imaging using a fast, forward-field
calculation. Journal of Magnetic Resonance Imaging, 29, 937948.
Nocedal, J., & Wright, S. J. (1999). Numerical optimization. Berlin: Springer.
Pruessmann, K. P., Weiger, M., Scheidegger, M. B., & Boesiger, P. (1999). SENSE: Sensitivity
encoding for fast MRI. Magnetic Resonance in Medicine, 42, 952962.
Reichenbach, J. R., Barth, M., Haacke, E. M., Klarhofer, M., Kaiser, W. A., & Moser, E.
(2000). High-resolution MR venography at 3.0 Tesla. Journal of Computer Assisted
Tomography, 24, 949957.
Reichenbach, J. R., Essig, M., Haacke, E. M., Lee, B. C., Przetak, C., Kaiser, W. A., et al.
(1998). High-resolution venography of the brain using magnetic resonance
imaging. Magma, 6, 6269.
Reichenbach, J. R., Venkatesan, R., Schillinger, D. J., Kido, D. K., & Haacke, E. M.
(1997). Small vessels in the human brain: MR venography with deoxyhemoglobin
as an intrinsic contrast agent. Radiology, 204, 272277.
Robinson, S., Grabner, G., Witoszynskyj, S., & Trattnig, S. (2011). Combining phase
images from multi-channel RF coils using 3D phase offset maps derived from a
dual-echo scan. Magnetic Resonance in Medicine, 65, 16381648.
Roemer, P. B., Edelstein, W. A., Hayes, C. E., Souza, S. P., & Mueller, O. M. (1990). The
Salomir, R., de Senneville, B. D., & Moonen, C. T. (2003). A fast calculation method for
magnetic field inhomogeneity due to an arbitrary distribution of bulk susceptibility.
Concepts in Magnetic Resonance Part B: Magnetic Resonance Engineering, 19B,
2634.
Schofield, M. A., & Zhu, Y. (2003). Fast phase unwrapping algorithm for interferometric
applications. Optics Letters, 28, 11941196.
Schweser, F., Deistung, A., Lehr, B. W., & Reichenbach, J. R. (2010). Differentiation
between diamagnetic and paramagnetic cerebral lesions based on magnetic
susceptibility mapping. Medical Physics, 37, 5165.
Schweser, F., Deistung, A., Lehr, B. W., & Reichenbach, J. R. (2011). Quantitative
imaging of intrinsic magnetic tissue properties using MRI signal phase: An
approach to in vivo brain iron metabolism? NeuroImage, 54, 27892807.
Schweser, F., Deistung, A., Sommer, K., & Reichenbach, J. R. (2013). Toward online
reconstruction of quantitative susceptibility maps: Superfast dipole inversion.
Schweser, F., Sommer, K., Deistung, A., & Reichenbach, J. R. (2012). Quantitative
susceptibility mapping for investigating subtle susceptibility variations in the human
Sedlacik, J., Helm, K., Rauscher, A., Stadler, J., Mentzel, H. J., & Reichenbach, J. R. (2008).
Investigations on the effect of caffeine on cerebral venous vessel contrast by using
susceptibility-weighted imaging (SWI) at 1.5, 3 and 7 T. NeuroImage, 40(1), 1118.
Shmueli, K., de Zwart, J. A., van Gelderen, P., Li, T., Dodd, S. J., & Duyn, J. H. (2009).
Magnetic susceptibility mapping of brain tissue in vivo using MRI phase data.
Shuai, Wang, Liu, T., Chen, W., Spincemaille, P., Wisnieff, C., Tsiouris, A. J., et al.
(2013). Noise effects in various quantitative susceptibility mapping methods. IEEE
Transactions on Biomedical Engineering, http://dx.doi.org/10.1109/
TBME.2013.2266795.
Shuo, Wang, Lou, M., Liu, T., Cui, D., Chen, X., & Wang, Y. (2013). Hematoma volume
measurement in gradient echo MRI using quantitative susceptibility mapping.
Stroke: A Journal of Cerebral Circulation, 44, 23152317.
Sun, H., & Wilman, A. H. (2013). Background field removal using spherical mean value
filtering and Tikhonov regularization. Magnetic Resonance in Medicine, http://dx.
doi.org/10.1002/mrm.24765.
Tang, J., Liu, S., Neelavalli, J., Cheng, Y. C. N., Buch, S., & Haacke, E. M. (2013).
Improving susceptibility mapping using a threshold-based K-space/image domain
iterative reconstruction approach. Magnetic Resonance in Medicine, 69,
13961407.
Tao, R., Zhang, J., Dai, Y., You, Z., Fan, Y., Cui, J., et al. (2012). Characterizing
hepatocellular carcinoma using multi-breath-hold two-dimensional susceptibilityweighted imaging: Comparison to conventional liver MRI. Clinical Radiology, 67,
e91e97.
Tong, K. A., Ashwal, S., Holshouser, B. A., Shutter, L. A., Herigault, G., Haacke, E. M.,
et al. (2003). Hemorrhagic shearing lesions in children and adolescents with
posttraumatic diffuse axonal injury: Improved detection and initial results.
Radiology, 227, 332339.
Wang, Y. (2012). Principles of magnetic resonance imaging: Physics concepts, pulse
sequences, & biomedical applications. Charleston, SC: CreateSpace Independent
Publishing Platform.
Wang, M., Dai, Y., Han, Y., Haacke, E. M., Dai, J., & Shi, D. (2011). Susceptibility
weighted imaging in detecting hemorrhage in acute cervical spinal cord injury.
Wharton, S., & Bowtell, R. (2010). Whole-brain susceptibility mapping at high field: A
comparison of multiple- and single-orientation methods. NeuroImage, 53,
515525.
Wharton, S., & Bowtell, R. (2012). Fiber orientation-dependent white matter contrast in
Wisnieff, C., Liu, T., Spincemaille, P., Wang, S., Zhou, D., & Wang, Y. (2013). Magnetic
susceptibility anisotropy: Cylindrical symmetry from macroscopically ordered
anisotropic molecules and accuracy of MRI measurements using few orientations.
Witoszynskyj, S., Rauscher, A., Reichenbach, J. R., & Barth, M. (2009). Phase
unwrapping of MR images using Phi UN A fast and robust region growing
algorithm. Medical Image Analysis, 13, 257268.
Wu, B., Li, W., Guidon, A., & Liu, C. (2012). Whole brain susceptibility mapping using
compressed sensing. Magnetic Resonance in Medicine, 67, 137147.
Xu, Y., & Haacke, E. M. (2006). The role of voxel aspect ratio in determining apparent
vascular phase behavior in susceptibility weighted imaging. Magnetic Resonance
Imaging, 24, 155160.
Xu, B., Liu, T., Spincemaille, P., Prince, M., & Wang, Y. (2013). Flow compensated
quantitative susceptibility mapping for venous oxygenation imaging. Magnetic
Resonance in Medicine, http://dx.doi.org/10.1002/mrm.24937.
Yablonskiy, D. A., Sukstanskii, A. L., Luo, J., & Wang, X. (2013). Voxel spread
function method for correction of magnetic field inhomogeneity effects in
quantitative gradient-echo-based MRI. Magnetic Resonance in Medicine, 70(5),
12831292.
Yang, Q., Liu, J., Barnes, S. R. S., Wu, Z., Li, K., Neelavalli, J., et al. (2009). Imaging the
vessel wall in major peripheral arteries using susceptibility-weighted imaging.
Zheng, W., Haacke, E. M., Webb, S. M., & Nichol, H. (2012). Imaging of stroke: A
comparison between X-ray fluorescence and magnetic resonance imaging methods.
Zheng, W., Nichol, H., Liu, S., Cheng, Y.-C. N., & Haacke, E. M. (2013). Measuring iron
in the brain using quantitative susceptibility mapping and X-ray fluorescence
Zhou, D., Liu, T., Spincemaille, P., & Wang, Y. (2013). Background field removal by
solving the laplacian boundary value problem. NMR in Biomedicine, 27(3),
312319.
Temporal Resolution and Spatial Resolution of fMRI

PA Bandettini, National Institute of Mental Health, Bethesda, MD, USA
Glossary
Gadolinium-DTPA A paramagnetic contrast agent used for

mapping perfusion and blood volume.
Gradient-echo imaging Imaging method that uses only
gradients to refocus spins to create an image. These are
acquired immediately following an excitation pulse and
need to be obtained before the signal decays based on its
T2* relaxation rate. The signal magnitude in these images is
dependent on the T2* decay.
Hemodynamic response function The brain activation
response as seen through its effects on the changes in blood
oxygenation.
RF coil Radio-frequency coil for either excitation or signal

detection.
Spin-echo imaging Imaging method that involves the
refocusing of spins with a 180 RF pulse and collection at the
peak of this refocusing period. The signal magnitude in these
images is dependent on the amount of T2 decay.
Susceptibility T2: The rate of transverse relaxation that is
measured by multiple 180 pulse excitation. Even with
repeated spin refocusing, the signal decays away due to the
tissue T2. T2*: The rate of transverse relaxation decays
immediately following an RF excitation pulse.
Nomenclature
GRAPPA
EPI
fMRI
MRI
RF
SENSE
SMASH
SNR
ASL
BOLD
CMRO2
Arterial spin labeling

Blood oxygen level-dependent
Cerebral metabolic rate of oxygen
consumption
Echo planar imaging
Functional MRI
Introduction
The discovery of functional magnetic resonance imaging
(fMRI) in the spring of 1991 started revolution in brain imaging. With fMRI, it was possible to noninvasively map human
brain activation at a temporal resolution on the order of seconds and a spatial resolution on the order of millimeters using
a slightly modified clinical MRI scanner. This was a breakthrough in functional imaging methodology and remains the
method of choice for mapping brain activation in humans.
While the technique has limitations, even after over 20 years,
it continues to improve steadily in sophistication. With these
improvements, applications continue to expand.
Within a very short time after the first fMRI experiments
were reported, researchers around the world were designing
experiments that tested the limits of fMRI. This article looks
closely at the hardware, pulse sequence, and physiological
determinants of the spatial and temporal limits of fMRI.
fMRI benefits from advances coming from a wide range of
areas, including physics, engineering, signal processing, and neuroscience. Figure 1 shows what I like to call the four pillars of
fMRI: hardware and pulse sequences, methodology, interpretation, and applications. Advancement of fMRI fundamentally
requires input and iteration among these four areas. As methods
improve, more sophisticated applications and more in-depth
interpretation are possible. As the technology advances with
higher fields, better coils, and more sophisticated pulse
Generalized autocalibrating partially parallel

acquisition
Magnetic resonance imaging
Radio frequency
Sensitivity encoding
Simultaneous acquisition of spatial harmonics
Signal to noise ratio
sequences, fMRI methodology grows taking advantage of the

improved resolution and signal to noise ratio (SNR). Interpretative advances, including a growing appreciation of neuronal
hemodynamic coupling and variability, also benefit from a
more detailed stable signal. All feed into clinical and
neuroscience applications, which continue to grow in breadth
and sophistication. Figure 1 graphically displays this fundamental concept.
This article includes the following sections: A short History
of Functional Contrast in fMRI, The Hemodynamic Response
Function, Spatial Limits, and Temporal Limits. In the first
two sections, the background and context of fMRI are set. All
limits in fMRI ultimately come down to hemodynamics and
acquisition. The goal of this article is that the reader comes
away with a working perspective of what the temporal and
spatial limits are and what determines them.
A Short History of Functional Contrast in fMRI

The front cover of the November 1991 issue of Science showed
something revolutionary a human brain with a detailed, highfidelity overlay of activation in the visual cortex. Here, with the
groundbreaking results of Belliveau et al. (1991), MRI as a
means to map brain activation in humans was introduced. The
approach involved two sequential bolus injections of the
susceptibility contrast agent, gadolinium-DTPA, to map blood
volume during rest and during activation. They used a new
http://dx.doi.org/10.1016/B978-0-12-397025-1.00020-8
173
174
INTRODUCTION TO ACQUISITION METHODS | Temporal Resolution and Spatial Resolution of fMRI
Technology
Methodology
Coil arrays
High field strength
High resolution
Novel sequences
Paradigm design
Univariate/multivariate
Multi-modal integration
Real-time feedback
Classification
Fluctuations
Dynamics
Functional resolution
Healthy brain organization

Clinical research
Clinical applications
Interpretation
Applications
Figure 1 The interacting components of functional MRI (fMRI)

essential to its development. fMRI has been evolving as hardware,
methods, and interpretation advance. All of these four pillars of fMRI
evolution have benefited from the others.
high-speed acquisition technique called echo planar imaging

(EPI; Ordidge et al., 1988, 1989) to capture the transient dynamics involved as the bolus rapidly washed through the brain.
During activation, a localized increase in blood volume was
color-coded and superimposed on the otherwise typical grayscale MRI scans. Shortly following these results, a completely
noninvasive MRI-based technique was introduced that utilized
endogenous functional contrast associated with localized
changes in blood oxygenation during activation. Between the
early spring and late fall of 1991, the first successful experiments
in endogenous functional contrast fMRI were carried out
(Bandettini, 2012; Kwong, 2012; Ugurbil, 2012). These first
experiments were published within 2 weeks of each other in
the early summer of 1992 (Bandettini, Wong, Hinks, Tikofsky, &
Hyde, 1992; Kwong et al., 1992; Ogawa et al., 1992).
The mechanism of endogenous contrast by which these
early results were based was pioneered in animal and phantom
studies by Ogawa et al., who coined the term blood oxygenation level-dependent (BOLD) contrast (Ogawa & Lee, 1990;
Ogawa, Lee, Nayak, & Glynn, 1990), and by Turner et al., who
further demonstrated this contrast in cat apnea models
(Turner, Lebihan, Moonen, Despres, & Frank, 1991).
The basics of BOLD contrast are the following: Hemoglobin
is more paramagnetic (lower magnetic susceptibility) than the
rest of tissue when deoxygenated and has the same susceptibility
as that of the tissue when fully oxygenated. When deoxygenated
and within a magnetic field, microscopic field inhomogeneities
are created around the deoxyhemoglobin and around blood
vessels containing deoxyhemoglobin as a result of the different
susceptibilities, leading to an attenuated MR signal. During rest,
the venous blood is slightly deoxygenated and therefore
relatively paramagnetic as some oxygen is delivered to the
brain tissue. With activation, blood flow locally increases
more than what is required by the brain activation-related
increase in oxidative metabolic rate, causing an increase in
blood oxygenation and a decrease in the amount of deoxygenated hemoglobin, therefore creating a small MRI signal
increase.
Another noninvasive fMRI technique that emerged almost
simultaneously with BOLD fMRI was arterial spin labeling
(ASL; Detre, Leigh, Williams, & Koretsky, 1992). ASL is sensitive to blood perfusion and to changes in perfusion with
activation. With ASL, blood is labeled with a radio frequency
(RF) pulse. This RF-labeled inflowing blood alters the signal in
the plane being imaged in proportion to the perfusion in each
voxel. ASL is unique in that maps of baseline and active-state
perfusion may be made, whereas with BOLD contrast, only
maps of changes can be obtained. ASL, while having lower SNR
than BOLD, has a very stable baseline and the potential for
quantification.
Other techniques for noninvasive assessment of brain physiology and physiological changes with activation include the
mapping of blood volume (Lu, Golay, Pekar, & Van zijl, 2003),
cerebral oxidative metabolic rate (Davis, Kwong, Weisskoff, &
Rosen, 1998; Hoge et al., 1999), temperature (Yablonskiy,
Ackerman, & Raichle, 2000), and diffusion coefficient (Le
bihan, Urayama, Aso, Hanakawa, & Fukuyama, 2006). In theory, MRI is sensitive to subtle changes in magnetic fields
induced by neuronal activity (Bandettini, Petridou, & Bodurka,
2005), yet efforts to image this effect in humans have been
largely unsuccessful. Increases in sensitivity and specificity may
allow neuronal current imaging to be feasible in the future.
BOLD fMRI is the brain activation mapping contrast of
choice for almost all neuroscientists because it is the easiest
to implement and is the most sensitive (temporal contrast to
noise ratio ranges from 1 to 10) by a factor of 24 relative to
other MRI-based methods. The need for sensitivity and ease of
use outweighs, most of the time, the advantages in specificity,
quantitation, or baseline information inherent to ASL.
Picking up in 1992, only a handful of laboratories could
perform fMRI because it required not only an MRI scanner but
also the capability of performing high-speed MRI and highly
stable EPI. EPI is a technique by which an entire image (or
plane) is collected with the use of a single RF pulse and a
single subsequent signal echo hence the name EPI. Collecting an entire image in 30 ms (as with EPI) freezes physiological processes that contribute in slower multishot methods to
nonrepeatable artifacts. EPI has significantly higher temporal
stability than multishot techniques, which is critical for fMRI.
Until about 1996, the hardware for performing EPI was not
available on clinical systems. Now, practically every standard
MRI scanner is equipped to perform EPI.
The pulse sequence typically used since about 1993 is
gradient-echo EPI. Typical (or slightly outdated) parameters
are echo time (TE), 40 ms; matrix size, 64 64; field of view,
24 cm; and slice thickness, 4 mm (voxel dimension of about
4 mm 4 mm 4 mm). Today, using accelerated techniques
with local RF coil arrays, voxel dimensions of
1.5 mm 1.5 mm 1.5 mm can be obtained routinely
(Feinberg et al., 2010; Pruessmann, Weiger, Scheidegger, &
Boesiger, 1999; Setsompop et al., 2012). Typically, wholebrain volume coverage using a TR of 2 s is performed. Time
series are collected, lasting on the order of 58 min. A typical
experiment involves the collection of multiple time series per
subject scanning session. The practical upper limit of time to
keep a subject in the scanner is about 2 h allowing for about
an hour of functional time series collection. Regarding hardware, in about the year 2002, the standard field strength
increased from 1.5 to 3 T, improving sensitivity as both MRI
signal and BOLD contrast (Ogawa et al., 1993) increase with
field strength. Up until about 1999, the standard practice was

to use a quadrature RF coil. Currently, the standard is to use a
multichannel receive coil having from 8 to 32 channels. The
use of this type of coil translates into either an increase in
sensitivity (smaller coils have greater sensitivity at the expense
of less coverage hence the need for more RF coils) or an
increase in resolution (and/or speed) that comes with a novel
strategy known as sensitivity encoding (SENSE; Pruessmann,
Weiger, Bornert, & Boesiger, 2001) or generalized autocalibrating partially parallel acquisition (GRAPPA; Griswold
et al., 2002). Furthermore, methods such as SENSE combined
with some latest advances of multiband excitation increasing
temporal efficiency by another factor of 3 (Feinberg et al., 2010;
Setsompop et al., 2012) allow single-shot EPI to be used for
imaging at submillimeter resolution in a manner that is about
two to eight times more time efficient, allowing up to 128-slice
whole-brain acquisition to be carried out in about a second.
Typical brain activation paradigms involve either steadystate activation (usually continued for at least 10 s at a time),
called box-car designs or multiple brief activations in a time
series, called event-related designs. Event-related designs have
a higher flexibility than box-car designs with only a small
decrement in sensitivity. For postprocessing, platforms such
as SPM, FSL, BrainVoyager, and AFNI are commonly used.
The fundamental approach in all of functional imaging creation from MRI time series is the statistical comparison of what
is expected to happen in the hemodynamic responses, as
defined by a reference function or a regressor, with the
what actually does happen the data, on a voxel-wise basis.
In recent years, more naturalistic stimuli and model functions
have evolved. Resting-state fMRI makes no assumption of the
temporal structure other than it is correlated with other regions
showing similar activity. Model functions of neuronal activity
are typically convolved with a hemodynamic response
function (HRF) that represents how neuronal activity is
manifested by the BOLD signal change shifting and smoothing the response. The next section describes this HRF.
175
blood volume relative to flow and metabolic rate, (2) a perseveration of metabolic rate relative to flow and volume, and (3) a
postundershoot in flow. Currently, there is no clear consensus
on which mechanism determines the postundershoot as papers
have demonstrated evidence for each of the three.
A transient (<500 ms) preundershoot (Hu, Le, & Ugurbil,
1997) is much more rarely seen in fMRI. In fact, its very
existence has been debated for at least 15 years. The leading
hypothesis for this transient is an increase in oxidative metabolic rate that slightly precedes an increase in flow, leading to a
negative deflection of the BOLD signal.
The BOLD signal change magnitude is sensitive to both
physical (i.e., MRI) and physiological variables. The magnitude
of the BOLD signal change is directly dependent on field
strength and TE. The physiological variables that influence
the BOLD signal can vary on a voxel-wise basis, providing a
challenge for the user who would like to draw neuronal inferences from the signal change. The primary physiological determinant of the magnitude of the BOLD signal is the resting
blood volume per voxel as this can range from 2% to 100%
(large draining vein).
The fMRI signal change latency can vary up to 4 s from
region to region. The latency variation across the brain roughly
follows the signal change magnitude, with the primary determining variable, again, being the baseline blood volume. The
working model is that large draining veins are typically downstream and therefore experience changes in oxygenation at a
later time than venules and capillaries adjacent to the region of
activation.
Methods for looking through the hemodynamics are continually developed. These include task timing modulation
(Menon, Luknowsky, & Gati, 1998), parametric manipulation
of the task intensity or neuronal activity, large vessel masking,
and calibration approaches.
In the following two sections, the spatial and temporal
limits of fMRI as well as the determining factors of these
limits are described in detail.
The Hemodynamic Response Function

Brain activation is associated with a localized increase in cerebral
blood flow and volume that outstrips the relatively small
increase in cerebral oxidative metabolic rate, leading to an overall increase in local blood oxygenation. BOLD contrast is the
most common of fMRI techniques; however, the BOLD signal is
not fully understood including characteristics that include the
preundershoot (Buxton, 2001), postundershoot (Jones, 1999),
transients (Birn, Saad, & Bandettini, 2001), and magnitude and
latency differences (Bellgowan, Saad, & Bandettini, 2003). All of
these characteristics are exquisitely sensitive to the interplay
between baseline and changes in vascular and metabolic variables that vary on a voxel, region, subject, and population-wide
scale (Buxton, Wong, & Frank, 1998).
The HRF has been modeled mathematically such that a
general canonical response can be used for analysis.
Physiological parameter-based models of the HRF have also
been constructed, lending insight into the relative significance
of underlying variables in determining the HRF characteristics
(Buxton et al., 1998).
Of the dynamics observed, the postundershoot in the signal
is perhaps the most common lasting up to 40 s. The leading
hypotheses for the postundershoot are (1) a perseveration of
Spatial Limits
The spatial limits of fMRI are determined by the available SNR,
scanning hardware, pulse sequence, neurovascular coupling
specificity, and brain activation paradigm design. With regard
to spatial limits, it is interesting that the current upper limit of
functional resolution just less than 0.5 mm approximately
matches the smallest functional unit of brain function delineation known that of cortical columns. Neuronal populations at more fine delineations are more homogeneous. If this
remains true, it would be a fortuitous match of fMRI limits to
the limits of cortical unit organization.
Spatial Limits: Scanning Hardware

It is considered optimal to have the fMRI time series image SNR
near 100 as this matches the maximum temporal SNR that one
can typically obtain with a time series of images (Bodurka, Ye,
Petridou, Murphy, & Bandettini, 2007). This temporal SNR
ceiling is determined by the predominance of physiological
noise in the brain. If one is working with a SNR above these
values, it is common to trade this sensitivity for higher spatial
176
resolution as MRI SNR is directly proportional to voxel

volume.
SNR is proportional to field strength, voxel volume, RF coil
size and proximity to tissue, and receiver bandwidth, among
other things. SNR increases linearly with field strength and
voxel volume; however, the relationship to coil arrays is more
complicated depending on the coil size, sensitivity profile,
and number of coils in the array.
Magnetic field gradients spatially encode the MRI signal. A
higher gradient strength allows more spatial detail to be
obtained. The more rapidly gradients can be switched (for
spatial encoding), the more quickly an image can be formed.
For EPI, rapid gradient switching is essential as the entire image
is formed in less than 30 ms. High gradient switching requires
the use of high-powered gradient amplifiers or a lowinductance gradient coil. After about the year 2000, highpowered amplifiers were the solution of choice allowing entire
bore of the magnet to remain open. Once rapid gradient
switching was in place, the limits on gradient switching rate
were no longer hardware-related but physiological. Above a
gradient switching rate threshold, peripheral nerves are
excited causing twitching. While this is uncomfortable to
the subject, it is not dangerous unless the stimulation occurred
in the heart which fortunately is far removed from the region
of most rapid change of magnetic field. Currently, gradient
switching rate is kept within strict limits, thus limiting the
spatial resolution using EPI. The use of a local head coil allows
slightly faster gradient switching (and either more speed or
higher resolution) as the gradients do not extend beyond the
head region and are thus smaller. Recently, the use of a head
gradient coil has resurfaced with an extremely highperformance scanner designed for high resolution and high
values of diffusion weighting (Setsompop et al., 2013).
& Ugurbil, 2002). Figure 2 shows maps from Yacoub et al.

(2008), demonstrating the mapping of ocular dominance
and smaller still orientation columns in humans. These
are the highest-resolution and most functionally detailed fMRI
maps yet obtained in humans.
As mentioned, biologic limits are imposed on the speed of
gradient switching. In recent years, pulse sequence and acquisition schemes have been developed to bypass these limits
somewhat. The first scheme is the use of multiple coil arrays
to help assist in spatial encoding. For typical acquisition, if raw
data are undersampled, image aliasing would occur. This aliasing can be unwrapped with the help of the spatially unique
information provided by individual RF elements in a coil
array in either raw data space or image space using GRAPPA
Spatial Limits: Pulse Sequence

Of the first few groups performing fMRI, only one group the
University of Minnesota collected data not using EPI. They
used multishot imaging. Multishot refers to the number of
excitation RF pulses required to form an image. While the
resolution possible with multishot imaging is much higher
than that with EPI, all the data do not have to be acquired
before the signal dies away. For multishot imaging, only a
few or one line per RF excitation is acquired. Because of
this, the technique takes longer, allowing more physiological
process such as breathing and heartbeat to occur. These processes make the time series of multishot images prohibitively
noisy significantly reducing BOLD signal detectability.
Recently, strategies for improving single-shot EPI resolution
have been implemented with success for fMRI.
The highest-resolution results with fMRI have been
obtained with voxel volumes of about 0.4 mm3 using either
multishot or single-shot EPI techniques. It should be noted
that these results could only be obtained at the SNR provided
by high field strengths. Ocular dominance columns were
imaged at 4 T (Cheng, Waggoner, & Tanaka, 2001; Menon,
Ogawa, Strupp, & Ugurbil, 1997), and orientation columns
were imaged at 7 T (Yacoub, Harel, & Ugurbil, 2008). Several
groups have reported layer-specific activation in cats and primates using a 7 T scanner (Logothetis, Merkle, Augath, Trinath,
Figure 2 The highest-resolution human functional imaging so far. This

demonstrates ocular dominance column and orientation column
activation in the human visual cortex. These units approximately match
the smallest known functional delineation scale of neurons. Adapted from
Yacoub, E., Harel, N., & Ugurbil, K. (2008). High-field fMRI unveils
orientation columns in humans. Proceedings of the National Academy of
Sciences of the United States of America, 105, 1060710612 with
permission. Copyright (2008) National Academy of Sciences, U.S.A.

and SENSE, respectively (Blaimer et al., 2004). These
approaches, introduced in about 2000, allowed EPI acquisition windows to be decreased by up to a factor of 4. Instead of a
30 ms readout window length for a 64 64 matrix sized image,
it may take less than 10 ms. However, to achieve higher resolution, window length could be kept constant at say 30 ms.
Now, it was possible to create a 256 256 matrix size singleshot echo-planar image using a readout window typical of
standard 64 64-resolution imaging. Typically, acceleration
factors of 23 are used. This was a breakthrough across all of
imaging, and with EPI, it allowed extremely high resolution to
be obtained with a single excitation.
Another limit to spatial resolution is the issue of maximum
number of slices per repetition time (TR). For EPI, the TR is the
amount of time between sequential volume acquisitions. With
most acquisition strategies, the limit for the number of slices
per TR is about 15 slices. The dimensions of the average brain
are width 140 mm/5.5 in., length 167 mm/6.5 in., and
height 93 mm/3.6 in. This problem becomes particularly
acute when extremely high resolution and thin slices are
desired. Reducing the slice thickness requires more slices and
therefore a longer TR, or else, alternatively, the study is limited
to a small slab of the brain which is generally undesirable. A
longer TR required to image the whole brain with thin slices
results in less data points per time series. The lower sampling
rate not only reduces statistical power but also less effectively
captures the hemodynamic response and the artifactual fluctuations, preventing clear separation of the two.
Until recently, the problem of the TR, brain coverage, and
slice thickness trade-off was significant and almost prohibitive
for whole-brain studies that required high resolution and short
TRs. In about 2010, a new acquisition strategy generally called
multiband acquisition conceived independently two groups
(Feinberg et al., 2010; Setsompop et al., 2012) and allowed
multiple slices to be obtained in the same time as one slice
was previously obtained, thus increasing through-plane acceleration by up to 900%. Recently, the combination of SENSE/
GRAPPA techniques along with the described multiband technique has allowed 128 slices of 1 1 1 mm3 voxel volume to
be obtained in about 2 s.
Currently, fMRI is performed using SENSE acceleration factor of 2 at 3 T, resulting in approximately 2 mm3 voxels and
only 16 slices obtained per second, allowing whole-brain coverage in about 2.5 s. Multiband is not standard on clinical
scanners and likely will not become standard before 2016.
Spatial Limits: Hemodynamic Limits

As described briefly in The Hemodynamic Response Function
section, arterioles and arteries dilate with brain activation, causing an increase in blood flow, volume, and oxygenation. This
increase occurs first in the region that is active but then moves
downstream from this area. A large issue in fMRI in the mid
1990s was the draining vein effect (Menon, 2012; Menon
et al., 1995). Strategies were developed to selectively image
capillary changes or to identify and eliminate downstream
draining veins and even upstream inflowing arteries.
Specifically, pulse sequence strategies for the removal of
upstream or downstream large vessel effects include the use
of spin-echo acquisition (Bandettini, Wong, Jesmanowicz,
177
Hinks, & Hyde, 1994), diffusion weighting (or velocity nulling

gradients; Boxerman et al., 1995; Song, Wong, Tan, & Hyde,
1996), ASL (Aguirre & Detre, 2012; Wang et al., 2003), blood
volume imaging (Lu & Van zijl, 2012), high-field acquisition,
and outer volume saturation. Large vessels and vascularized
regions are able to be identified, rather than removed, through
several approaches: observing the standard deviation of the
signal (i.e., higher pulsatility of large vessels; Menon, 2002),
dark lines in a T2*-weighted image (Menon et al., 1995),
transient dark regions following a bolus injection of gadolinium, and flow-weighted scans revealing rapid inflow effects.
Spin-echo acquisition involves the use of an excitation
pulse and then a 180 refocusing pulse followed by acquisition. After the initial excitation pulse, spins precessing at different frequencies (due to their experiencing slightly different
magnetic fields in tissue) begin to lose phase coherence with
each other within voxels, leading to signal reduction due to
destructive interference. The 180 refocusing pulse reverses the
precession direction and thus causes all spins to gain full
coherence again assuming that they continue to experience
the same magnetic field. If microscopic perturbations exist, a
diffusing spin may end up after 20 ms at a very different
location and in the presence of a different magnetic field
magnitude. If the fields are spatially larger, they vary more
slowly over space such that a diffusing spin would not
experience a significantly different field. Thus, the spin-echo
signal is selectively attenuated by small susceptibility perturbations associated with capillaries and red blood cells which
distort the field approximately on the same scale that a typical
water molecule diffuses in about 2050 ms.
While spin-echo sequences are sensitive to small compartments, one caveat, especially when imaging at magnetic fields
of 3 T or below (where intravascular signal is higher due to
relatively longer T2 of blood at low field), is that red blood cells
in large vessels otherwise known as the intravascular signal
can influence the spin-echo brain activation contrast. This
leads to the same draining vein effects even with spin echo.
Other caveats are that in EPI, the true spin echo is only at the
very center of the raw data space, thus causing most spin-echo
EPI signal to be gradient-echo EPI for the higher spatial frequencies (edges of raw data space). Another caveat is that the
functional contrast with spin-echo sequences is about a factor
of 24 less than gradient echo.
At high fields or with diffusion weighting, the intravascular
signal may be extremely low and therefore not a problem.
Diffusion weighting removes intravascular signal but does
not remove the extravascular signal; therefore, it is only effective in eliminating large vessel effects when used in combination with spin-echo sequences (Song et al., 1996) that are not
sensitive to large vessel extravascular gradients.
At 7 T, intravascular signal is naturally much lower, therefore
allowing the effective delineation with spin-echo sequences of
detailed orientation columns (Yacoub et al., 2008). At lower
fields, a small amount of diffusion weighting will also remove
intravascular signal. However, performing spin-echo EPI with
diffusion weighting at low field to null out intravascular signal
leaves one with almost no signal remaining at all. For most uses
of fMRI, the drawbacks of spin-echo imaging and the addition
of diffusion weighting greatly outweigh any small advantages.
However, imaging at high field does bring the significant
178
advantage of higher contrast and sensitivity and less intravascular signal. BOLD contrast is more selective to capillaries at higher
field for two reasons: First, because of the stronger effect of field
strength on T2* of blood than tissue, there is less intravascular
(and therefore large vessel) signal. Second, small compartment
dephasing effects show a slightly higher Bo dependence than
large compartment; therefore capillary effects, while still small,
will be somewhat greater relative to these effects at low field.
ASL, a method for imaging baseline and changes in perfusion, is known to be minimally sensitive to large vessel effects.
ASL is highly selective to imaging brain activation-related
changes in capillary perfusion. This technique has the added
advantages of high temporal stability, the option for quantitation, and the ability to obtain maps of baseline perfusion. The
disadvantages of this method include a lower functional contrast to noise than BOLD by a factor of about 24, a necessity
for a longer TR to allow for the tagging pulse, and a limit to the
spatial coverage per TR.
Outer volume spin saturation has also been used to eliminate inflow effects and therefore upstream flow changes. Typically, this is not a major problem for multislice acquisition as
most slices have adjacent slices that are naturally saturated.
The upper spatial resolution of fMRI appears to be ultimately determined by the hemodynamics. In humans, individual orientation column activations (<0.5 mm; Yacoub et al.,
2008) and specific cortical layer function have been successfully imaged.
Temporal Limits
Similar to the spatial limits of fMRI, the temporal limits are
also determined by SNR, scanning hardware, pulse sequence,
hemodynamic response, and brain activation paradigm timing. However, in contrast to spatial limits which appear to
fortuitously match the upper limit of the spatial organization
of neurons the sluggish and spatially variable hemodynamic
response is the most significant determinant of the upper limits
of temporal resolution and is much slower than what is known
about the rapidity with which neurons and cortical areas communicate. It is also possible to scan much faster than the limits
imposed by the hemodynamic sluggishness and uncertainty.
The limit imposed by hemodynamics is on the order of seconds, whereas the limit imposed by hardware could be as short
as 100 ms. Neuronal firing occurs on the order of milliseconds.
So, importantly, the upper temporal resolution of fMRI is three
orders of magnitude slower than the neuronal firing rate, yet
the spatial resolution of fMRI is on the same order of magnitude as the spatial distribution and size of functional units.
Before delving further into temporal resolution limits, it is
important to outline what is specifically meant by temporal
resolution limits. Temporal resolution can have the following
definitions: (1) fastest image acquisition rate or fastest volume
acquisition rate, (2) minimum time for the signal to deviate
significantly from baseline, (3) fastest rate at which the brain
can be repeatedly turned on and off and still elicit a signal
change, (4) minimum time that the brain can be turned on and
still elicit a signal change, (5) standard deviation of the baseline signal, (6) standard deviation over time of the hemodynamic response, and (7) standard deviation or simply
variability (since the distribution is not typically Gaussian) of

the hemodynamic response over space. This last measure is
what is typically meant by temporal resolution, as it is closest
to the measure of the ability to resolve the relative timings of
different regions of the brain.
Temporal Limits: Scanning Hardware and Rapid Pulse

Sequences
Scanning hardware that may lead to higher temporal resolution includes the primary magnet, RF coil arrays, and, to some
extent the gradient coils. The SNR can be improved with an
increase in field strength and number of receive coils. Smaller
gradient coils may allow faster gradient switching, thus allowing imaging at slightly faster rates. Any approach that increases
SNR will lead to at least a small increase in temporal resolution
in that subtle differences in signal change timing may be
obtained with less averaging. Of course, as will be discussed,
fast image acquisition and high SNR do not necessarily translate to increased functional temporal resolution in the presence
of a highly variable hemodynamic response across brain
regions and even voxels within a region.
As described earlier in this article, it is possible to collect
over 100 slices in less than a second using SENSE or GRAPPA
with multiband acquisition. However, TR reduction reduces
the available signal due to decreased time for longitudinal
magnetization recovery. For single-slice acquisition, a TR of
as low as 50 ms is possible, yet the SNR at this rate would
likely be very small. Because each time point does not represent
a new degree of freedom, statistical power would decrease at
these short TR values. Some methods exist that do not involve
the use of imaging gradients at all (Hennig, 2012; Lin et al.,
2012) allowing very rapid acquisition yet still facing the
limitation of incomplete longitudinal magnetization recovery
that reduces the overall SNR. Currently, the best practice of
those interested in connectivity assessment is the collection of
an entire brain volume using SENSE and multiband acquisition and a TR of 400 ms. The shorter TR is not intended to
increase temporal resolution of detection of the hemodynamic
response but rather to allow enhanced filtering of artifactual
signal changes that occur on a faster timescale than BOLD and
would otherwise be aliased into the BOLD frequencies.
One ongoing challenge has been to collect an entire imaging volume with a single excitation. This approach is known as
echo volume imaging (EVI; Mansfield, Coxon, & Hykin, 1995;
Song, Wong, & Hyde, 1994) and may be extremely useful for
post hoc motion correction methods since head motion here is
manifested as fully rigid body motion as opposed to a shearing
that is manifested by through-plane motion during multislice
acquisition.
Temporal Limits: Hemodynamics

Just as hemodynamics set the upper limits on spatial resolution, they impose an even more severe limit on temporal
resolution. Hemodynamic changes start to occur about 2 s
following activation and, after about 10 s, plateau in the on
state. With activation cessation, the signal takes slightly longer
to return to baseline. Typically, the latency differences across

the brain (across regions and also voxels within regions) are 2
4 s and are mostly due to nonneuronal hemodynamic factors
such as upstream or downstream blood flow changes. Figure 3
shows magnitude and latency maps from a repeated yet brief
(1 s) simple motor cortex task of finger tapping. This figure
demonstrates that the longest delays are correlated with the
largest fMRI signal which correlates to where the draining
veins are as shown in the venogram.
Specific sequences such as spin echo and ASL have been
shown to be more specific to capillary effects than to vein
effects. Spatial maps using spin echo and ASL appear more
precise than those obtained using gradient-echo BOLD;
however, it is inconclusive if the temporal resolution is
improved. First, with ASL, the temporal resolution is severely
limited by the necessity of an additional RF pulse to invert the
inflowing spins and a waiting period of about a second to
allow spins to flow into the plane. High-speed ASL approaches
exist (Liu et al., 2000; Wong, Luh, & Liu, 2000), but they have
generally not caught on due to the intrinsically low SNR of
ASL.
While work has pushed the precision to which we can use
hemodynamic changes to infer neuronal timings, the limits are
as follows: minimum neuronal activation time necessary to
elicit a response, <16 ms (essentially no limit); absolute
179
onset certainty, about / 2 s; relative onset timing accuracy

with calibration, 100 ms; and relative onset timing without
calibration, 4 s.
Calibration, in this context, involves a specific modulation
of the brain activation timing such that the onset time differences in the same regions or voxels with a task timing modulation are measured rather than the onset timing across
regions. Papers that have explored this approach are few
(Bellgowan et al., 2003; Henson, Price, Rugg, Turner, & Friston,
2002; Menon & Kim, 1999; Menon et al., 1998) as it is challenging to find paradigms that lend themselves to these types
of studies. Figure 4 shows one such example where the task
was twofold: word recognition and word rotation. These two
tasks were both used. The subject showed delayed response
time with angle of rotation and with nonwords. From Figure 4,
it is easy to see that with delays due to the recognizing of
nonwords, a widening in the fMRI response width is seen in
the left inferior prefrontal gyrus thought to be the word
generation region. This is explained simply by the fact that it
takes longer to process nonwords and this region is therefore
active longer than nonwords. However, for word rotation
also causing response delays the width of the hemodynamic
response in this region is not changed. Rather, the onset time is
delayed, suggesting that this word processing module is
+2 s
Latency
-2 s
Magnitude
Venogram
50
2100
40
2080
2060
30
2040
20
2020
10
2000
1980
8 10 12 14 16 18 20
Time (s)
-2
-1.5
-1
-0.5
0
0.5
Delay (s)
1.5
Figure 3 The primary limits on the temporal resolution unpublished data. A simple finger-tapping task was performed for 1 s. Multiple averages were
obtained. The hemodynamic response easily captures the 1 s stimulation; however, a spread in latencies of 2 s occurs within the motor cortex.
This spread is spatially correlated with the magnitude and the venogram shows where large vessels are. Large draining veins receive oxygenated
blood from active tissue. This represents the major obstacle for high-resolution fMRI the spatial heterogeneity of the hemodynamic response.
180
Word versus nonword
0, 60, 120 Rotation
Regions of interest
(a)
(b)
Inferior frontal gyrus
(a)
(b)
Precentral gyrus
(a)
(b)
Middle temporal gyrus

Figure 4 Depiction of the hemodynamic response for both the lexical (words vs. nonwords) and rotation effects (degree of rotation). The x-axis depicts
time in seconds, and the y-axis depicts percent signal change. This suggests that word processing is neuronally downstream from the word
rotation module. Looking at the left prefrontal gyrus response, with longer processing for nonwords, the width of the response varies, but with
upstream rotation required, the onset of the left prefrontal gyrus activation is delayed. Adapted from Bellgowan, P. S. F., Saad, Z. S., & Bandettini, P. A.
(2003). Understanding neural system dynamics through task modulation and measurement of functional MRI amplitude, latency, and width.
Proceedings of the National Academy of Sciences of the United States of America, 100, 14151419 with permission. Copyright (2003) National
Academy of Sciences, U.S.A.
neuronally downstream from the word rotation region. The

differences in these measurements are on the same order as the
reaction time differences.
The best temporal resolution obtained across regions without calibration or task modulation has been described in a
paper by Formisano and Goebel (2003) in which differences
on the order of seconds were resolved.
Lastly, aside from using pulse sequences to select capillary
effects or using paradigms to modulate brain activity timings in
a precise manner that might be calibrated, another novel
approach has been reported. Ogawa et al. have used the understanding that the inhibitory connections in the brain have a
specific temporal window with which they interact. Using a
paired pulse paradigm both in rat models and in human brain,
they observed the inhibitory effect of an initial stimulation on
the second stimulation. With the rat brain stimulation of
right forepaw and then the left forepaw the optimal delay was
in a window of 50 ms after the initial stimulation. With the
human brain visual cortex stimulation and then a second
identical stimulation the optimal inhibitory stimulation was
in the range of 200 ms (Ogawa et al., 2000). This approach,
using a sluggish, ill-behaved hemodynamic response, was able
to probe the rapid dynamics of inhibitory networks by relying
simply on the amplitude modulation for specifically timed
paired pulses.
Finally, with regard to temporal resolution limits, approximations can be summarized as follows: (1) Fastest image
acquisition rate (EPI can be obtained in about 10 ms) or fastest
volume acquisition rate (one volume every 400 ms for wholebrain coverage), (2) minimum time for the signal to deviate
significantly from baseline (about 2 s), (3) fastest rate at which

the brain can be repeatedly turned on and off and still elicit a
signal change (between frequencies of 0.5 and 1 Hz), (4) minimum time that the brain can be turned on and still elicit a
signal change (no lower limit here as we have gone down to
16 ms and still elicit a response with event-related fMRI), (5)
standard deviation of the baseline signal (0.2%), (6) standard
deviation over time of the hemodynamic response (about
400 ms), (7) standard deviation of the hemodynamic response
over space (about 2 s).
Conclusion
This article covered some of the history of fMRI and basics of
the hemodynamic response and then delineated the MRI
acquisition parameters and hemodynamic variables associated
with the current limits in the spatial resolution and temporal
resolution of fMRI. With regard to spatial resolution, fMRI is
doing quite well able to resolve down to the smallest known
unit of functional organization in the brain: orientation
columns. With regard to temporal resolution, fMRI can acquire
whole-brain data quite rapidly but cannot with certainty
differentiate relative onset times from different regions of
the brain that occur closer in time than about 2 s. However,
there are still opportunities for calibration and the potential
for increased hemodynamic specificity allowing, assuming
enough SNR, more precise delineation of shorter time differences in the future. Clever paradigms can differentiate onset
modulation down to less than 100 ms and can resolve

inhibitory interactions on the order of tens of milliseconds. In
addition, there seems to be no lower limit on the minimum
activation duration necessary to elicit a hemodynamic
response. The spatial resolution and temporal resolution
niche that fMRI currently occupies actually fills quite a large
domain where principles of human brain organization can be
characterized. The future will certainly hold improvements in
sensitivity and interpretability with further hardware, pulse
sequence, and activation paradigm development.
See also: INTRODUCTION TO ACQUISITION METHODS: EchoPlanar Imaging; Evolution of Instrumentation for Functional Magnetic
Resonance Imaging; fMRI at High Magnetic Field: Spatial Resolution
Limits and Applications; Functional Near-Infrared Spectroscopy; HighSpeed, High-Resolution Acquisitions; Obtaining Quantitative
Information from fMRI; Obtaining Quantitative Information from fMRI;
Perfusion Imaging with Arterial Spin Labeling MRI; Pulse Sequence
Dependence of the fMRI Signal; Susceptibility-Weighted Imaging and
Quantitative Susceptibility Mapping; INTRODUCTION TO
COGNITIVE NEUROSCIENCE: Reading; INTRODUCTION TO
METHODS AND MODELING: Artifacts in Functional MRI and How to
Mitigate Them; Computing Brain Change over Time; Convolution
Models for FMRI; Design Efficiency; Dynamic Causal Models for fMRI;
Effective Connectivity; Granger Causality; Resting-State Functional
Connectivity; INTRODUCTION TO SYSTEMS: Large-Scale
Functional Brain Organization.
Bibliography
Aguirre, G. K., & Detre, J. A. (2012). The development and future of perfusion fMRI for
dynamic imaging of human brain activity. Neuroimage, 62, 12791285.
Bandettini, P. A. (2012). Sewer pipe, wire, epoxy, and finger tapping: The start of fMRI at
the Medical College of Wisconsin. Neuroimage, 62, 620631.
Bandettini, P. A., Petridou, N., & Bodurka, J. (2005). Direct detection of neuronal
activity with MRI: Fantasy, possibility, or reality? Applied Magnetic Resonance, 29,
6588.
course EPI of human brain-function during task activation. Magnetic Resonance in
Medicine, 25, 390397.
Bandettini, P. A., Wong, E. C., Jesmanowicz, A., Hinks, R. S., & Hyde, J. S. (1994).
Spin-echo and gradient-echo EPI of human brain activation using bold contrast A
comparative-study at 1.5 T. NMR in Biomedicine, 7, 1220.
Bellgowan, P. S.F, Saad, Z. S., & Bandettini, P. A. (2003). Understanding neural system
dynamics through task modulation and measurement of functional MRI amplitude,
latency, and width. Proceedings of the National Academy of Sciences of the United
Belliveau, J. W., Kennedy, D. N., Mckinstry, R. C., Buchbinder, B. R., Weisskoff, R. M.,
Cohen, M. S., et al. (1991). Functional mapping of the human visual-cortex by
magnetic-resonance-imaging. Science, 254, 716719.
Birn, R. M., Saad, Z. S., & Bandettini, P. A. (2001). Spatial heterogeneity of the
nonlinear dynamics in the fMRI BOLD response. Neuroimage, 14, 817826.
Blaimer, M., Breuer, F., Mueller, M., Heidemann, R. M., Griswold, M. A., & Jakob, P. M.
(2004). SMASH, SENSE, PILS, GRAPPA: How to choose the optimal method.
Topics in Magnetic Resonance Imaging, 15, 223236.
Bodurka, J., Ye, F., Petridou, N., Murphy, K., & Bandettini, P. A. (2007). Mapping the
MRI voxel volume in which thermal noise matches physiological noise
Implications for fMRI. Neuroimage, 34, 542549.
Boxerman, J. L., Bandettini, P. A., Kwong, K. K., Baker, J. R., Davis, T. L., Rosen, B. R.,
et al. (1995). The intravascular contribution to fMRI signal change Monte-carlo
modeling and diffusion-weighted studies in-vivo. Magnetic Resonance in Medicine,
34, 410.
Buxton, R. B. (2001). The elusive initial dip. Neuroimage, 13, 953958.
181
Cheng, K., Waggoner, R. A., & Tanaka, K. (2001). Human ocular dominance columns as
revealed by high-field functional magnetic resonance imaging. Neuron, 32,
359374.
functional MRI: Mapping the dynamics of oxidative metabolism. Proceedings of
18341839.
diffusion imaging. PLoS One, 5, e15710.
Formisano, E., & Goebel, R. (2003). Tracking cognitive processes with functional MRI
mental chronometry. Current Opinion in Neurobiology, 13, 174181.
Hennig, J. (2012). Functional spectroscopy to no-gradient fMRI. Neuroimage, 62,
693698.
Henson, R. N., Price, C. J., Rugg, M. D., Turner, R., & Friston, K. J. (2002).
Detecting latency differences in event-related BOLD responses: Application to words
versus nonwords and initial versus repeated face presentations. Neuroimage, 15,
8397.
Hoge, R. D., Atkinson, J., Gill, B., Crelier, G. R., Marrett, S., & Pike, G. B. (1999).
Investigation of BOLD signal dependence on cerebral blood flow and oxygen
consumption: The deoxyhemoglobin dilution model. Magnetic Resonance in
Medicine, 42, 849863.
Hu, X. P., Le, T. H., & Ugurbil, K. (1997). Evaluation of the early response in fMRI in
individual subjects using short stimulus duration. Magnetic Resonance in Medicine,
37, 877884.
Jones, R. A. (1999). Origin of the signal undershoot in BOLD studies of the visual
cortex. NMR in Biomedicine, 12, 301308.
Kwong, K. K. (2012). Record of a single fMRI experiment in May of 1991. Neuroimage,
62, 610612.
Poncelet, B. P., et al. (1992). Dynamic magnetic-resonance-imaging of human brain
Le bihan, D., Urayama, S. I., Aso, T., Hanakawa, T., & Fukuyama, H. (2006). Direct and
fast detection of neuronal activation in the human brain with diffusion MRI.
103, 82638268.
Lin, F. H., Tsai, K. W., Chu, Y. H., Witzel, T., Nummenmaa, A., Raij, T., et al. (2012).
Ultrafast inverse imaging techniques for fMRI. Neuroimage, 62, 699705.
Liu, H. L., Pu, Y. L., Nickerson, L. D., Liu, Y. J., Fox, P. T., & Gao, J. H. (2000).
Comparison of the temporal response in perfusion and BOLD-based event-related
functional MRI. Magnetic Resonance in Medicine, 43, 768772.
Logothetis, N. K., Merkle, H., Augath, M., Trinath, T., & Ugurbil, K. (2002).
Ultra high-resolution fMRI in monkeys with implanted RF coils. Neuron, 35,
227242.
Lu, H., Golay, X., Pekar, J. J., & Van zijl, P. C.M (2003). Functional magnetic resonance
Medicine, 50, 263274.
Lu, H., & Van zijl, P. C. (2012). A review of the development of Vascular-SpaceOccupancy (VASO) fMRI. Neuroimage, 62, 736742.
Mansfield, P., Coxon, R., & Hykin, J. (1995). Echo-volumar imaging (EVI) of the brain
at 3.0 T First normal volunteer and functional imaging results. Journal of
Computer Assisted Tomography, 19, 847852.
Menon, R. S. (2002). Postacquisition suppression of large-vessel BOLD signals in
high-resolution fMRI. Magnetic Resonance in Medicine, 47, 19.
Menon, R. S. (2012). The great brain versus vein debate. Neuroimage, 62, 970974.
Menon, R. S., & Kim, S. G. (1999). Spatial and temporal limits in cognitive
neuroimaging with fMRI. Trends in Cognitive Sciences, 3, 207216.
Menon, R. S., Luknowsky, D. C., & Gati, J. S. (1998). Mental chronometry using
latency-resolved functional MRI. Proceedings of the National Academy of Sciences
Menon, R. S., Ogawa, S., Hu, X., Strupp, J. P., Anderson, P., & Ugurbil, K. (1995).
BOLD based functional MRI at 4 Tesla includes a capillary bed contribution: Echoplanar imaging correlates with previous optical imaging using intrinsic signals.
182
Menon, R. S., Ogawa, S., Strupp, J. P., & Ugurbil, K. (1997). Ocular dominance in
human V1 demonstrated by functional magnetic resonance imaging. Journal of
Ogawa, S., & Lee, T. M. (1990). Magnetic-resonance-imaging of blood-vessels at high
fields In vivo and in vitro measurements and image simulation. Magnetic
in magnetic-resonance image of rodent brain at high magnetic-fields. Magnetic
Ogawa, S., Lee, T. M., Stepnoski, R., Chen, W., Zhuo, X. H., & Ugurbil, K. (2000). An
approach to probe some neural systems interaction by functional MRI at neural time
scale down to milliseconds. Proceedings of the National Academy of Sciences of the
magnetic-resonance-imaging A comparison of signal characteristics with a
Ogawa, S., Tank, D. W., Menon, R., Ellermann, J. M., Kim, S. G., Merkle, H., et al.
(1992). Intrinsic signal changes accompanying sensory stimulation Functional
brain mapping with magnetic-resonance-imaging. Proceedings of the National
Ordidge, R. J., Coxon, R., Howseman, A., Chapman, B., Turner, R., Stehling, M., et al.
(1988). Snapshot head imaging at 0.5 T using the echo planar technique. Magnetic
Ordidge, R. J., Howseman, A., Coxon, R., Turner, R., Chapman, B., Glover, P., et al.
(1989). Snapshot imaging at 0.5 T using echo-planar techniques. Magnetic
Pruessmann, K. P., Weiger, M., Bornert, P., & Boesiger, P. (2001). Advances in
sensitivity encoding with arbitrary k-space trajectories. Magnetic Resonance in
Medicine, 46, 638651.
Medicine, 67, 12101224.
Setsompop, K., Kimmlingen, R., Eberlein, E., Witzel, T., Cohen-Adad, J., Mcnab, J. A.,
et al. (2013). Pushing the limits of in vivo diffusion MRI for the Human Connectome
Project. Neuroimage, 80, 220233.
Song, A. W., Wong, E. C., & Hyde, J. S. (1994). Echo-volume imaging. Magnetic
Song, A. W., Wong, E. C., Tan, S. G., & Hyde, J. S. (1996). Diffusion weighted fMRI at
1.5 T. Magnetic Resonance in Medicine, 35, 155158.
Turner, R., Lebihan, D., Moonen, C. T.W, Despres, D., & Frank, J. (1991). Echo-planar
time course MRI of cat brain oxygenation changes. Magnetic Resonance in
Medicine, 22, 159166.
Ugurbil, K. (2012). Development of functional imaging in the human brain (fMRI): The
University of Minnesota experience. Neuroimage, 62, 613619.
Medicine, 49, 796802.
Wong, E. C., Luh, W. M., & Liu, T. T. (2000). Turbo ASL: Arterial spin labeling with higher
SNR and temporal resolution. Magnetic Resonance in Medicine, 44, 511515.
Yablonskiy, D. A., Ackerman, J. J.H, & Raichle, M. E. (2000). Coupling between
changes in human brain temperature and oxidative metabolism during prolonged
visual stimulation. Proceedings of the National Academy of Sciences of the United
America, 105, 1060710612.
MRI and fMRI Optimizations and Applications

PA Ciris and R Todd Constable, Yale University School of Medicine, New Haven, CT, USA
Abbreviations
BOLD Blood oxygenation level dependent

CBF Cerebral blood flow
CBV Cerebral blood volume
DSI Diffusion spectrum imaging
DTI Diffusion tensor imaging
EPI Echo planar imaging
fMRI Functional magnetic resonance imaging
HARDI High angular resolution diffusion imaging
Introduction
Magnetic resonance imaging (MRI) has revolutionized brain
imaging since the first MR images were collected showing
excellent soft tissue contrast with high spatial resolution. The
contrast characteristics obtainable with MRI were unprecedented compared to existing modalities at the time, and basic
T1 and T2 contrast imaging approaches have since been
extended to depict iron and myelin content, diffusion, perfusion, functional activation, and functional connectivity.
Within each of these realms, there are numerous applications
to understanding the neurophysiology of the brain and the
normal and abnormal distribution of the parameters these
methods measure, as a function of age, gender, genotype, or
disease. In this article, we review some of the more recent
developments in acquisition strategies for different brain imaging applications with emphasis on the information such
methods can provide, and some of their strengths and weaknesses. The article is divided into three sections covering highresolution anatomical imaging (morphometry), microstructural imaging (based on diffusion imaging), and functional
imaging (chiefly blood oxygenation level-dependent (BOLD)
contrast but also considering measures of cerebral blood flow
(CBF) and blood volume (CBV)).
MRI Magnetic resonance imaging

ODF Orientation distribution function
PDF Probability density function
RF Radio frequency
SNR Signal-to-noise ratio
TR Repetition time
VASO Vascular space occupancy
VERVE Venous refocusing for volume estimation
performance, in addition to providing an accurate brain volume for registration of multiple subjects.
Submillimeter anatomical scans are now being obtained at
7 T or higher. At such high field strengths, additional steps are
often needed to account for radio frequency (RF) inhomogeneities on both transmit and receive sides of the equation
(Adriany et al., 2005; Lutti et al., 2012; Van de Moortele
et al., 2005), compensation for susceptibility effects, and the
resultant loss of signal or geometric distortion. High-resolution
acquisitions also benefit from prospective motion correction
(Schulz et al., 2012). T*
2 mapping (Cohen-Adad et al., 2012 at
7 T, Budde, Shajan, Hoffmann, Ugurbil, & Pohmann, 2011 at
9.4 T), susceptibility mapping (Deistung et al., 2013; Schafer
et al., 2012), and frequency difference mapping (Wharton &
Bowtell, 2012) methods have provided exquisite depictions of
neuroanatomy, as well as insights into iron and/or myelin
concentrations and orientations of underlying structures. The
measurement of myelin content in the cortex has recently
garnered great attention, and there is much interest in examining the relationship between functional activity as measured by
functional magnetic resonance imaging (fMRI) and myelin
content (Barazany & Assaf, 2012; Bock et al., 2013; Lutti
et al., 2012).
Advances in Morphometry (Structural Imaging)
Microstructural Imaging (Diffusion Imaging)
Most brain MR imagers now operate at 3 T, and at this field

strength, obtaining high-resolution structural volume acquisitions of the brain with outstanding gray-to-white matter contrast, with high signal-to-noise ratios (SNRs) and voxel
dimensions around 1 mm3, is considered routine. Parallel
imaging advances (Griswold et al., 2002; Pruessmann, Weiger,
Scheidegger, & Boesiger, 1999; Sodickson & Manning, 1997)
have allowed such acquisitions to be easily completed in 5
10 min, and advances such as the PROPELLER sequence (Pipe,
1999; Pipe & Zwart, 2006) have allowed such acquisitions to
become fairly robust to motion. Obtaining high-resolution
volume scans allows for measures of morphometric features
that can be associated with functional activity or behavioral
Water molecules inside tissues experience random motion due

to thermal energy, the distribution of which is strongly influenced by the local environment, such as cellular membranes,
myelin sheaths, and macromolecules (Le Bihan, 1995). Diffusion MRI uses strong bipolar gradients to magnetically label
water molecules: diffusion leads to signal attenuation, revealing the underlying displacement and microstructure. The distribution of such microscopic displacements within an MRI
voxel can be described by a diffusion probability density function (PDF) (Callaghan, 1991). The diffusion PDF, along an
orientation over a given diffusion time, can be recovered from
the Fourier transform of signal attenuation at multiple diffusion encoding gradient areas, that is, q-values (Callaghan,
http://dx.doi.org/10.1016/B978-0-12-397025-1.00021-X
183
184
INTRODUCTION TO ACQUISITION METHODS | MRI and fMRI Optimizations and Applications
1991; Cory & Garroway, 1990; Wedeen, Hagmann, Tseng,

Reese, & Weisskoff, 2005).
Diffusion tensor imaging (DTI) has extensively been used
to study white matter anisotropy (Basser, Mattiello, & LeBihan,
1994; Douek, Turner, Pekar, Patronas, & Le Bihan, 1991) and
neural fiber architecture (Conturo et al., 1999; Mori, Crain,
Chacko, & van Zijl, 1999; Wedeen, 1996). DTI provides gross
fiber orientation and quantitative indices such as fractional
anisotropy and diffusivity, but is unable to resolve multiple
fiber orientations within a voxel (Basser, Pajevic, Pierpaoli,
Duda, & Aldroubi, 2000; Lazar et al., 2003; Mori & van Zijl,
2002; Tournier, Calamante, Gadian, & Connelly, 2004), which
can lead to major tract reconstruction artifacts (Tuch et al.,
2002; Wiegell, Larsson, & Wedeen, 2000). Complex fiber
architectures, such as branching and crossing patterns within
a voxel, are ubiquitous in the brain (Schmahmann & Pandya,
2006), and their accurate identification requires finer sampling
of the diffusion PDF with strong gradients in many directions,
that is, high angular resolution diffusion imaging (HARDI).
Diffusion spectrum imaging (DSI) (Callaghan, Eccles, & Xia,
1988; Lin, Wedeen, Chen, Yao, & Tseng, 2003; Tuch et al.,
2002; Wedeen et al., 2000, 2005) acquires multiple q-values
and diffusion orientations on a lattice in q-space, such that a 3D Fourier transform yields the 3-D spin-displacement PDF.
The radial projection of the spin-displacement PDF along a
certain orientation gives the orientation distribution function
(ODF), and the maxima of the ODF identify fiber orientations.
Intermediate methods that improve identification of complex
fiber architecture include Q-ball imaging (Tuch, Reese, Wiegell,
& Wedeen, 2003) and related methods that balance assumptions and compromises between acquisition time and hardware requirements (Jansons & Alexander, 2003; Tournier et al.,
2004; Zhan, Stein, & Yang, 2004). Typical whole-brain acquisition durations can be as long as 10 min for Q-ball (i.e., 60
directions) and 45 min for DSI (i.e., 257 directions)
(Setsompop et al., 2012).
Although reconstruction errors are possible with every
method, there is a steady increase in performance from DTI
to HARDI methods through DSI (Gigandet, 2009; Wedeen
et al., 2008). DSI can accurately show anatomical fiber crossings in the optic chiasm, centrum semiovale, and brain stem;
fiber intersections in the gray matter, including cerebellar folia
and the caudate nucleus; and radial fiber architecture in cerebral cortex (Wedeen et al., 2008). DSI in ex vivo specimens (515
directions) has determined that fiber pathways of the forebrain
are organized as a highly curved 3-D grid derived from the
principal axes of development (Wedeen et al., 2012). Stronger
gradients are desirable for shorter diffusion gradient durations
and diffusion encoding times, leading to shorter echo times
and higher SNR, as well as higher b-values and angular resolution. Multichannel coils are desirable for improved SNR,
shorter acquisitions through parallel imaging, and multiple
slice encoding, as well as accompanying improvements in
spatial resolution and decreases in echo planar imaging (EPI)
susceptibility artifacts. A gradient strength of 300 mT m1
(200 mT m1 s1) has recently been achieved by the Human
Connectome Project; substantial gains in the sensitivity and
efficiency of HARDI or DSI acquisitions with accompanying
improvements in the accuracy and resolution of tractography
have been demonstrated using a combination of simultaneous
multislice acquisition and compressive sampling reconstruction with a custom 64-channel brain array at 3 T (Setsompop
et al., 2013). Such developments could enable new insights
into connectional neuroanatomy and the operation of neural
networks, as demonstrated by the ability to probe the distribution of axonal diameters in vivo, as a noninvasive index of
action potential conduction velocity (McNab et al., 2013).
Functional Imaging (fMRI)

Since the earliest work of Ogawa et al. demonstrating the
BOLD phenomena (Ogawa, Lee, Kay, & Tank, 1990),
gradient-echo imaging has been the standard imaging
approach for the vast majority of functional imaging studies.
Numerous works have shown that spin-echo imaging can offer
more specificity in terms of localizing activation to the capillary bed while avoiding oxygenation changes in larger draining
veins (Constable, Kennan, Puce, McCarthy, & Functional,
1994), but the sensitivity given up for this slight gain in spatial
specificity is typically too great for most studies, unless imaging
at very high field strengths (Budde, Shajan, Zaitsev, Scheffler, &
Functional, 2013; De Martino et al., 2012; Norris, 2012;
Olman et al., 2012). Introducing diffusion weighting in fMRI
can also improve localization of neuronal activity by removing
undesired vascular influences or introduce perfusion contrast
based on intravoxel incoherent motion (Song, 2012; Song,
Woldorff, Gangstead, Mangun, & McCarthy, 2002; Song,
Wong, Tan, & Hyde, 1996).
Spatial specificity in group studies is necessarily limited
by the correspondences across subjects in terms of both
anatomical features and functional features within those
anatomical structures. The typical BOLD imaging sequence is
a gradient-echo EPI sequence, used in the single shot mode,
where an entire data matrix for a slice of 64 64 points is
acquired following a single excitation pulse. EPI is used
because whole-brain coverage can easily be obtained with
repetition times (TRs) of 3 s or less. With standard EPI
acquisitions, there is a trade-off between the number of slices
required and the minimum TR available, and in the past, very
short TRs could only be used if a limited number of slices were
obtained (Constable & Spencer, 2001, among others).
Recently, however, using the concepts of parallel imaging
whereby the receiver coils allow one to separate otherwise
overlapping data, simultaneous multislice imaging (multiband
and multiplexed imaging) approaches have been introduced
that allow anywhere from three to six times, relative to standard EPI, the maximum number of slices to be obtained in a
fixed TR (Feinberg, Reese, & Wedeen, 2002; Feinberg & Setsompop, 2013; Feinberg et al., 2010; Larkman et al., 2001).
This allows much thinner slices to be acquired while maintaining whole-brain coverage with short TRs, now of 1 s or less. TRs
as short as around 600 ms have been shown to greatly benefit
fMRI statistical power (Constable & Spencer, 2001). The slight
loss of thermal SNR with this reduced TR is more than compensated for by the reduction in physiological noise achieved
by obtaining many more samples within a functional run or
resting-state period. Potentially, even faster sequences are on
the horizon with the advent of nonlinear magnetic field gradients for spatial encoding (Hennig et al., 2008; Stockmann,

Ciris, Galiana, Tam, & Constable, 2010; Stockmann et al.,
2012; Tam, Stockmann, Galiana, & Constable, 2012).
Other Measures of Brain Activity

Local neuronal electric currents produce transient weak local
magnetic fields. These magnetic field perturbations cause signal attenuation in MRI, providing a more direct measurement
of brain activity compared to BOLD. However, despite promising initial results in phantoms (Bodurka & Bandettini, 2002)
and in vitro (Petridou et al., 2006), sufficient sensitivity to
measure these changes has not yet been demonstrated in vivo
(Chu et al., 2004; Huang, 2013; Luo, Jiang, & Gao, 2011;
Mandelkow et al., 2007; Parkes, de Lange, Fries, Toni, & Norris,
2007; Tang, Avison, Gatenby, & Gore, 2008).
Functional imaging generally relies on a mismatch between
local changes in tissue oxygen supply and demand, and different
aspects of this relationship can be measured with MRI. Both
CBV and CBF changes with activation and MR pulse sequences
have been developed to measure these physiological parameters.
Intravascular injection of contrast agents can be used to measure
both CBF and CBV. CBF can be determined from the delivery of
a bolus of contrast to vasculature; however, similar to all bolus
tracking methods, this approach suffers from the difficulty of
accurate characterization of the arterial input function. CBV can
be determined by scaling the difference in signal intensities
before and after contrast injection, or from the time integral of
the signal time course during the first pass of contrast. Some
limitations of these approaches are the short blood half-life of
gadolinium-DTPA and the lack of approved iron-oxide agents
with longer half-lives for human studies. Furthermore, injections are typically not suitable for functional studies with complex stimulation paradigms. Some noninvasive measurement
approaches are reviewed in the succeeding text.
Cerebral Blood Flow

While BOLD signal changes are considered large if they are on
the order of 12%, the CBF changes associated with brain
activation can be as large as 40% (Feng et al., 2004; Li et al.,
2000; Mark & Pike, 2012), making this a potentially attractive
mechanism to target for activation mapping. However, all CBF
measurement sequences require the subtraction of two slightly
different acquisitions (an acquisition with spin labeling and a
second acquisition without labeling), followed by the typical
subtraction of activation and control conditions (Aguirre,
Detre, Zarahn, & Alsop, 2002; Wong, Buxton, & Frank,
1997). This double subtraction leads to very poor SNR in the
maps in addition to requiring doubling the effective TR in
order to obtain pairs of images to subtract. For these reasons,
CBF mapping is not routinely used, although it can be very
important for examining changes in baseline brain activity
levels as a function of drug or disease. CBF is also an essential
element of calibrated BOLD experiments relating changes in
BOLD, CBF, and CBV to changes in the cerebral metabolic rate
of oxygen consumption (Buxton, 2012; Buxton, Wong, &
Frank, 1998; Buxton, Frank, et al., 1998; Kim & Ogawa, 2012).
Approaches for measuring CBF include both pulsed arterial
spin labeling and continuous arterial spin labeling. While both
185
approaches use endogenous water as a freely diffusible tracer,

the latter somewhat more efficient, it requires a separate coil for
the labeling and is generally more difficult to implement. In
either of these sequences, if one uses a relatively long TE, then
both CBF and BOLD contrasts can be obtained simultaneously,
and some researchers have taken advantage of such an
approach. FAIR (Kwong, Chesler, Weisskoff, & Rosen, 1994),
EPISTAR (Edelman et al., 1994), and PICORE (Wong et al.,
1997) variants of arterial spin labeling (ASL) refer to differences
in the geometry of labeling, control, and imaging regions, which
give very similar perfusion results despite differences in static
tissue contrast (Wong et al., 1997), while QUIPSII (quantitative
imaging of perfusion using a single subtraction version II;
Wong et al., 1997) and Q2TIPS (QUIPSS II with thin-slice TI1
periodic saturation; Luh, Wong, Bandettini, & Hyde, 1999) refer
to the management of bolus transit durations between labeling
and imaging regions.
Cerebral Blood Volume

Upon brain activation, CBV increases from a baseline value of
57% of voxel volume by approximately 20%, leading to
changes in voxel volume comparable to changes in BOLD
signal (12%). Although these CBV changes appear to localize
well with changes in neural activity (Kim et al., 2012), CBV
measurement is typically invasive or difficult especially in
humans and rarely performed. Noninvasive MRI approaches
for CBV quantification in humans include the following: Vascular space occupancy (VASO) can determine relative changes
in total CBV by assuming a certain baseline CBV level (Lu,
Golay, Pekar, & Van Zijl, 2003; Scouten & Constable, 2007,
2008); inflow VASO (iVASO) and iVASO with dynamic
subtraction can determine the absolute arteriolar contribution
to CBV by acquiring data at multiple TI times that are approximately matched to arterial transit times and fitting to a biophysical model (Donahue et al., 2010; Hua, Qin, Pekar, & van
Zijl, 2011); venous refocusing for volume estimation (VERVE)
can determine relative predominantly venous contributions to
CBV based on the T2 dependence of partially deoxygenated
blood on refocusing rate and oxygen saturation (Chen &
Pike, 2009; Stefanovic & Pike, 2005); and finally, absolute
total CBV can be determined from VASO acquisitions at multiple TI values at rest and during activation and fitting to a
biophysical model (Ciris, Qiu, & Constable, 2013; Glielmi,
Schuchard, & Hu, 2009; Gu, Lu, Ye, Stein, & Yang, 2006).
CBVCBF Relationship and Compartmental Effects

CBV and oxygenation changes in arterial, capillary, and venous
compartments impact BOLD differently. Venous CBV has the
largest impact on BOLD due to large oxygenation changes on
the venous side (Griffeth & Buxton, 2011). Arterial CBV is
dominant during respiratory manipulations (Ito, Ibaraki,
Kanno, Fukuda, & Miura, 2005) and responds rapidly during
functional activation (Drew, Shih, & Kleinfeld, 2011; Hillman
et al., 2007; Kim, Hendrich, Masamoto, & Kim, 2007; Vazquez,
Fukuda, Tasker, Masamoto, & Kim, 2010). Venous CBV
increases slowly with extended stimulus durations (Drew
et al., 2011), reaching a magnitude similar to the arterial CBV
change (Kim & Kim, 2011). At steady state, the relative change
186
in venous CBV is about half that of total CBV (Lee, Duong,

Yang, Iadecola, & Kim, 2001). After stimulus offset, arterial
CBV rapidly decreases to baseline or exhibits a small prolonged
poststimulus undershoot (also observed in CBF (Jin & Kim,
2008) and in surface arteriolar vessel diameters (Drew et al.,
2011)), while venous CBV recovers slowly without undershoot. This complicated mechanism may further involve
changes in arterial/arteriolar deoxyhemoglobin (Hillman
et al., 2007), oxygen saturation, and CBV, potentially significant enough to impact the BOLD signal change (Vazquez et al.,
2010). Significant capillary CBV changes have also been suggested (Hillman et al., 2007; Krieger, Streicher, Trampel, &
Turner, 2012; Stefanovic et al., 2008; Tian et al., 2010), given
that capillaries are the major source of oxygen extraction and
closer to the activation site (Krieger et al., 2012). Many fMRI
calibration studies assume that CBV 0.8CBF0.38 based on
measurements of total CBV in macaques during respiratory
manipulation using PET (Grubb, Raichle, Eichling, & TerPogossian, 1974), with the underlying assumption that the
BOLD-induced fractional change in venous CBV is the same
as the fractional change in total CBV (Buxton, 2012; Buxton,
Frank, et al., 1998; Buxton, Wong, & Frank, 1998; Kim &
Ogawa, 2012). The exponent relates to the degree to which
rising perfusion is accommodated through blood flow velocity
versus volume increases (diameter change or recruitment),
which may differ across functional challenges, brain regions,
and species (Ito, Takahashi, Hatazawa, Kim, & Kanno, 2001;
Jones, Berwick, & Mayhew, 2002; Kida, Rothman, & Hyder,
2007; Mandeville et al., 1999; Wu, Luo, Li, Zhao, & Li, 2002),
with gender (Ciris, Qiu, & Constable, 2012) or age. Smaller
exponents (0.180.23) have been suggested based on measurements of the relative venous contribution to CBV using VERVE
in humans (Chen & Pike, 2009). The time- and compartmentdependent behavior may further depend on other parameters
such as stimulus strength and spatial extent (Kim & Kim, 2010)
and should be considered in the interpretation of BOLD
results.
Additional Considerations
Sinuses and other air-tissue interfaces cause large susceptibility
gradients especially near orbitofrontal and inferior temporal
regions of the brain. EPI acquisitions are associated with
extended readout durations (along the phase encoding direction), exacerbating erroneous phase accumulation in these
regions, leading to severe image artifacts such as geometric
distortions, signal intensity variations, and complete signal
loss. These artifacts can be partially corrected or compensated
for using additional acquisitions, that is, field mapping (Aksit,
Derbyshire, & Prince, 2007; Jezzard & Balaban, 1995), point
spread function mapping (Dragonu et al., 2013; Robson, Gore,
& Constable, 1997; Zaitsev, Hennig, & Speck, 2004; Zeng &
Constable, 2002), and z-shimming (Constable, 1995; Constable & Spencer, 1999) methods (in-plane or through-plane).
Shortening the readout duration (along the phase encoding
direction), by using parallel imaging methods or multishot
acquisitions, is very effective for reducing artifact severity.
Similarly high-bandwidth acquisitions reduce the length of
the readout window and hence geometric distortion, but at
the cost of decreased SNR. Spiral-in/spiral-out (Glover & Law,
2001) or more recent asymmetrical spin-echo spiral (Brewer,

Rioux, DArcy, Bowen, & Beyea, 2009) acquisitions have also
been shown to contain artifacts and recover BOLD activations
in severely affected regions. Asymmetrical spin-echo acquisitions are hybrid spin-echo/gradient-echo acquisitions, where
the tuning between these can range anywhere from pure spinecho to pure gradient-echo or a combination in between. The
spin-echo sequences retain sensitivity to microscopic BOLD
effects but refocus static field inhomogeneities including signals from larger veins. A combination of gradient and
asymmetrical echoes attempts to retain the high sensitivity of
gradient-echoes to the BOLD effect while reducing the static
field effects (Stables, Kennan, & Gore, 1998; Weisskoff, Zuo,
Boxerman, & Rosen, 1994), and such sequences have even
been combined with z-shimming (Heberlein & Hu, 2004).
Although EPI slices are acquired in milliseconds and wholebrain volumes are acquired in seconds, fMRI acquisitions
typically extend to several minutes for sufficient functional
contrast and statistical power, and subject motion remains an
important consideration. Postprocessing is typically used to
register images at slightly different head positions, and some
motion-compensated EPI sequences have been developed,
such as PROPELLER-EPI (Kramer, Jochimsen, & Reichenbach,
2012). In addition to simple displacements, susceptibility
effects from air-tissue interfaces and resulting distortions and
artifacts are different at each head position, such that even
prospective motion correction may not completely eliminate
effects of motion. Motion of air-tissue interfaces as far as the
lungs can cause significant susceptibility effects in the brain,
and real-time correction of respiratory motion-induced susceptibility effects may be necessary, especially at high fields (van
Gelderen, de Zwart, Starewicz, Hinks, & Duyn, 2007). Realtime monitoring of motion and updating of the scan prescription is slowly becoming a reality and may become widely
available in the near future (Maclaren, Herbst, Speck, &
Zaitsev, 2013; Maclaren et al., 2012).
We have not discussed acquisition strategies from the point
of view of a paradigm, but there are numerous subtleties that
should be considered in designing experiments that can accurately probe the cognitive function of interest (Savoy, 2005).
Block paradigms are designed to establish a steady state of
neuronal and hemodynamic change, and since transitions
between activation and control conditions are minimal, these
sequences are more efficient and effective at detecting very
small changes in brain activity. Event-related designs typically
require assumptions of linearity across multiple stimuli, more
complicated postprocessing, and higher temporal resolution
(Josephs, Turner, & Friston, 1997), however, can enable paradigms precluded by block designs. Advantages of event-related
designs include the ability to perform priming experiments and
the ability to examine the neurophysiological response to individual stimuli. Spatial and temporal patterns in the spontaneous activity of the brain can also be investigated without the
use of paradigms (functional connectivity, resting-state fMRI;
Biswal, Yetkin, Haughton, & Hyde, 1995; Constable et al.,
2013). Such data can be used to examine functional networks
within the brain and potentially even lead to atlases of minimal functional subunits (Shen, Papademetris, & Constable,
2010; Shen, Tokoglu, Papademetris, & Constable, 2013). The
extensive flexibility that fMRI provides, through trade-offs

between spatial resolution, temporal resolution, coverage,
SNR, and acquisition duration, can be fully exploited to
match requirements of each experimental design.
Summary
In summary, many advances continue to be made in the development of high spatial and temporal resolution MRI acquisition strategies. In anatomical scanning, the move to higher
field strength has provided unprecedented opportunities for
improving spatial resolution while producing images with very
high SNR. Advances in diffusion imaging have led to extensive
improvements in fiber tracking, and the integration of structural information with functional information is really just
beginning. In functional MRI, advances continue to be made
in the development of sequences that are maximally sensitive
to neuronal activity and minimally sensitive to motion and
other sources of artifacts. The field continues to expand rapidly
and new applications of MRI are constantly invented.

Anatomical MRI for Human Brain Morphometry; Diffusion MRI; EchoPlanar Imaging; fMRI at High Magnetic Field: Spatial Resolution Limits
and Applications; High-Speed, High-Resolution Acquisitions;
Obtaining Quantitative Information from fMRI; Perfusion Imaging with
Arterial Spin Labeling MRI; Pulse Sequence Dependence of the fMRI
Signal; Susceptibility-Weighted Imaging and Quantitative Susceptibility
Mapping; Temporal Resolution and Spatial Resolution of fMRI.
References
Adriany, G., Van de Moortele, P. F., Wiesinger, F., Moeller, S., Strupp, J. P.,
Andersen, P., et al. (2005). Transmit and receive transmission line arrays for 7 Tesla
parallel imaging. Magnetic Resonance in Medicine, 53(2), 434445.
Aguirre, G. K., Detre, J. A., Zarahn, E., & Alsop, D. C. (2002). Experimental design and
the relative sensitivity of BOLD and perfusion fMRI. NeuroImage, 15(3), 488500.
Aksit, P., Derbyshire, J. A., & Prince, J. L. (2007). Three-point method for fast and
robust field mapping for EPI geometric distortion correction. In: 4th IEEE ISBI:
International Symposium on Biomedical Imaging, Washington DC.
Barazany, D., & Assaf, Y. (2012). Visualization of cortical lamination patterns with
magnetic resonance imaging. Cerebral Cortex, 22(9), 8.
Basser, P. J., Mattiello, J., & LeBihan, D. (1994). MR diffusion tensor spectroscopy and
imaging. Biophysical Journal, 66(1), 259267.
Basser, P. J., Pajevic, S., Pierpaoli, C., Duda, J., & Aldroubi, A. (2000). In vivo fiber
tractography using DT-MRI data. Magnetic Resonance in Medicine, 44(4), 625632.
Biswal, B., Yetkin, F. Z., Haughton, V. M., & Hyde, J. S. (1995). Functional connectivity
in the motor cortex of resting human brain using echo-planar MRI. Magnetic
Bock, N. A., Hashim, E., Janik, R., Konyer, N. B., Weiss, M., Stanisz, G. J., et al. (2013).
Optimizing T1-weighted imaging of cortical myelin content at 3.0 T. NeuroImage,
65, 112.
Medicine, 47(6), 10521058.
Brewer, K. D., Rioux, J. A., DArcy, R. C., Bowen, C. V., & Beyea, S. D. (2009).
Asymmetric spin-echo (ASE) spiral improves BOLD fMRI in inhomogeneous
regions. NMR in Biomedicine, 22(6), 654662.
Budde, J., Shajan, G., Hoffmann, J., Ugurbil, K., & Pohmann, R. (2011). Human
imaging at 9.4 T using T(2) *-, phase-, and susceptibility-weighted contrast.
187
Budde, J., Shajan, G., Zaitsev, M., Scheffler, K., & Functional, Pohmann R. (2013). MRI
in human subjects with gradient-echo and spin-echo EPI at 9.4 T. Magnetic
Buxton, R. B. (2012). Dynamic models of BOLD contrast. NeuroImage, 62, 953961.
Buxton, R. B., Frank, L. R., Wong, E. C., Siewert, B., Warach, S., & Edelman, R. R.
(1998). A general kinetic model for quantitative perfusion imaging with arterial spin
labeling. Magnetic Resonance in Medicine, 40(3), 383396.
Callaghan, P. (1991). Principles of nuclear magnetic resonance microscopy. Oxford,
UK: Oxford Science Publications, Clarendon Press.
Callaghan, P. T., Eccles, C. D., & Xia, Y. (1988). NMR microscopy of dynamic
displacements k-space and q-space imaging. Journal of Physics E: Scientific
Instruments, 21, 820822.
Chen, J. J., & Pike, G. B. (2009). BOLD-specific cerebral blood volume and blood flow
changes during neuronal activation in humans. NMR in Biomedicine, 22(10),
10541062.
Chu, R., de Zwart, J. A., van Gelderen, P., Fukunaga, M., Kellman, P., Holroyd, T., et al.
(2004). Hunting for neuronal currents: Absence of rapid MRI signal changes during
visual-evoked response. NeuroImage, 23(3), 10591067.
Ciris, P. A., Qiu, M., & Constable, R. T. (2014). Noninvasive MRI measurement of
the absolute cerebral blood volume-cerebral blood flow relationship during
visual stimulation in healthy humans. Magnetic Resonance in Medicine, 72(3),
864875.
Ciris, P. A., Qiu, M., & Constable, R. T. (2014). Non-invasive quantification of absolute
cerebral blood volume during functional activation applicable to the whole
human brain. Magnetic Resonance in Medicine, 71, 580590.
et al. (2012). T(2)* mapping and B(0) orientation-dependence at 7 T reveal cytoand myeloarchitecture organization of the human cortex. NeuroImage, 60(2),
10061014.
Constable, R. T. (1995). Functional MR, imaging using gradient-echo echo-planar
imaging in the presence of large static field inhomogeneities. Journal of Magnetic
Resonance Imaging, 5(6), 746752.
Constable, R. T., Kennan, R. P., Puce, A., McCarthy, G., & Functional, Gore J. C.
(1994). NMR imaging using fast spin echo at 1.5 T. Magnetic Resonance in
Medicine, 31(6), 686690.
Constable, R. T., Scheinost, D., Finn, E. S., Shen, X., Hampson, M., Winstanley, F. S.,
et al. (2013). Potential use and challenges of functional connectivity mapping in
intractable epilepsy. Frontiers in Neurology, 4, 39.
functional MR imaging. Magnetic Resonance in Medicine, 42(1), 110117.
Constable, R. T., & Spencer, D. D. (2001). Repetition time in echo planar functional
MRI. Magnetic Resonance in Medicine, 46(4), 748755.
Conturo, T. E., Lori, N. F., Cull, T. S., Akbudak, E., Snyder, A. Z., Shimony, J. S., et al.
(1999). Tracking neuronal fiber pathways in the living human brain. Proceedings of
the National Academy of Sciences of the United States of America, 96(18),
1042210427.
Cory, D. G., & Garroway, A. N. (1990). Measurement of translational displacement
probabilities by NMR: An indicator of compartmentation. Magnetic Resonance in
Medicine, 14(3), 435444.
De Martino, F., Schmitter, S., Moerel, M., Tian, J., Ugurbil, K., Formisano, E., et al.
(2012). Spin echo functional MRI in bilateral auditory cortices at 7 T: An application
of. NeuroImage, 63(3), 13131320.
Deistung, A., Schafer, A., Schweser, F., Biedermann, U., Turner, R., &
Reichenbach, J. R. (2013). Toward in vivo histology: A comparison of quantitative
susceptibility mapping. NeuroImage, 65, 299314.
Donahue, M. J., Sideso, E., MacIntosh, B. J., Kennedy, J., Handa, A., & Jezzard, P.
(2010). Absolute arterial cerebral blood volume quantification using inflow
vascular-space-occupancy with dynamic subtraction magnetic resonance imaging.
Douek, P., Turner, R., Pekar, J., Patronas, N., & Le Bihan, D. (1991). MR color mapping
of myelin fiber orientation. Journal of Computer Assisted Tomography, 15(6),
923929.
Dragonu, I., Lange, T., Baxan, N., Snyder, J., Hennig, J., & Zaitsev, M. (2013).
Accelerated point spread function mapping using signal modeling for accurate
echo-planar imaging geometric distortion correction. Magnetic Resonance in
Medicine, 69(6), 16501656.
Drew, P. J., Shih, A. Y., & Kleinfeld, D. (2011). Fluctuating and sensory-induced
vasodynamics in rodent cortex extend arteriole capacity. Proceedings of the
National Academy of Sciences of the United States of America, 108(20),
84738478.
188
Edelman, R. R., Siewert, B., Adamis, M., Gaa, J., Laub, G., & Wielopolski, P. (1994).
Signal targeting with alternating radiofrequency (STAR) sequences: Application to
MR angiography. Magnetic Resonance in Medicine, 31(2), 233238.
diffusion imaging. PloS One, 5(12), e15710.
Feinberg, D. A., Reese, T. G., & Wedeen, V. J. (2002). Simultaneous echo refocusing in
EPI. Magnetic Resonance in Medicine, 48(1), 15.
Feinberg, D. A., & Setsompop, K. (2013). Ultra-fast MRI of the human brain with
simultaneous multi-slice imaging. Journal of Magnetic Resonance, 229, 90100.
Feng, C. M., Narayana, S., Lancaster, J. L., Jerabek, P. A., Arnow, T. L., Zhu, F., et al.
(2004). CBF changes during brain activation: fMRI vs. PET. NeuroImage, 22,
443446.
Gigandet, X. (2009). Global brain connectivity analysis by diffusion MR tractography:
Algorithms, validation and applications. Lausanne: Ecole Polytechnique Federale de
Lausanne.
Glielmi, C. B., Schuchard, R. A., & Hu, X. P. (2009). Estimating cerebral blood volume
with expanded vascular space occupancy slice coverage. Magnetic Resonance in
Medicine, 61(5), 11931200.
Glover, G. H., & Law, C. S. (2001). Spiral-in/out BOLD fMRI for increased SNR
and reduced susceptibility artifacts. Magnetic Resonance in Medicine, 46(3),
515522.
Griffeth, V. E., & Buxton, R. B. (2011). A theoretical framework for estimating cerebral
oxygen metabolism changes using the calibrated-BOLD method: Modeling the
effects of blood volume distribution, hematocrit, oxygen extraction fraction, and
tissue signal properties on the BOLD signal. NeuroImage, 58(1), 198212.
Grubb, R. L., Jr., Raichle, M. E., Eichling, J. O., & Ter-Pogossian, M. M. (1974). The
effects of changes in PaCO2 on cerebral blood volume, blood flow, and vascular
mean transit time. Stroke: A Journal of Cerebral Circulation, 5(5), 630639.
Gu, H., Lu, H., Ye, F. Q., Stein, E. A., & Yang, Y. (2006). Noninvasive quantification of
cerebral blood volume in humans during functional activation. NeuroImage, 30(2),
377387.
Heberlein, K. A., & Hu, X. (2004). Simultaneous acquisition of gradient-echo and
asymmetric spin-echo for single-shot z-shim: Z-SAGA. Magnetic Resonance in
Medicine, 51(1), 212216.
Hennig, J., Welz, A. M., Schultz, G., Korvink, J., Liu, Z., Speck, O., et al. (2008). Parallel
imaging in non-bijective, curvilinear magnetic field gradients: A concept study.
Magma, 21(12), 514.
Hillman, E. M., Devor, A., Bouchard, M. B., Dunn, A. K., Krauss, G. W., Skoch, J., et al.
(2007). Depth-resolved optical imaging and microscopy of vascular compartment
dynamics during somatosensory stimulation. NeuroImage, 35(1), 89104.
Hua, J., Qin, Q., Pekar, J. J., & van Zijl, P. C. (2011). Measurement of absolute arterial
cerebral blood volume in human brain without using a contrast agent. NMR in
Biomedicine, 24(10), 13131325.
Huang, J. (2013). Detecting neuronal currents with MRI: A human study. Magnetic
Ito, H., Ibaraki, M., Kanno, I., Fukuda, H., & Miura, S. (2005). Changes in cerebral blood
flow and cerebral oxygen metabolism during neural activation measured by positron
emission tomography: Comparison with blood oxygenation level-dependent
contrast measured by functional magnetic resonance imaging. Journal of Cerebral
Blood Flow and Metabolism, 25(3), 371377.
Ito, H., Takahashi, K., Hatazawa, J., Kim, S. G., & Kanno, I. (2001). Changes in human
regional cerebral blood flow and cerebral blood volume during visual stimulation
measured by positron emission tomography. Journal of Cerebral Blood Flow and
Metabolism, 21(5), 608612.
Jansons, K. M., & Alexander, D. C. (2003). Persistent angular structure: New insights
from diffusion MRI data. Dummy version. Information Processing in Medical
Imaging, 18, 672683.
Jezzard, P., & Balaban, R. S. (1995). Correction for geometric distortion in echo
planar images from B0 field variations. Magnetic Resonance in Medicine, 34(1), 6573.
Jin, T., & Kim, S. G. (2008). Cortical layer-dependent dynamic blood oxygenation,
cerebral blood flow and cerebral blood volume responses during visual stimulation.
NeuroImage, 43(1), 19.
Jones, M., Berwick, J., & Mayhew, J. (2002). Changes in blood flow, oxygenation, and
volume following extended stimulation of rodent barrel cortex. NeuroImage, 15(3),
474487.
Josephs, O., Turner, R., & Friston, K. (1997). Event-related f MRI. Human Brain
Mapping, 5(4), 243248.
Kida, I., Rothman, D. L., & Hyder, F. (2007). Dynamics of changes in blood flow,
volume, and oxygenation: Implications for dynamic functional magnetic resonance
imaging calibration. Journal of Cerebral Blood Flow and Metabolism, 27(4),

690696.
Kim, S. G., Harel, N., Jin, T., Kim, T., Lee, P., & Zhao, F. (2012). Cerebral blood volume
MRI with intravascular superparamagnetic iron oxide nanoparticles. NMR in
Kim, T., Hendrich, K. S., Masamoto, K., & Kim, S. G. (2007). Arterial versus total blood
volume changes during neural activity-induced cerebral blood flow change:
Implication for BOLD fMRI. Journal of Cerebral Blood Flow and Metabolism, 27(6),
12351247.
Kim, T., & Kim, S. G. (2010). Cortical layer-dependent arterial blood volume
changes: Improved spatial specificity relative to BOLD fMRI. NeuroImage, 49(2),
13401349.
Kim, T., & Kim, S. G. (2011). Temporal dynamics and spatial specificity of arterial
and venous blood volume changes during visual stimulation: Implication for
BOLD quantification. Journal of Cerebral Blood Flow and Metabolism, 31(5),
12111222.
Kim, S. G., & Ogawa, S. (2012). Biophysical and physiological origins of blood
oxygenation level-dependent fMRI signals. Journal of Cerebral Blood Flow and
Kramer, M., Jochimsen, T. H., & Reichenbach, J. R. (2012). Functional magnetic
resonance imaging using PROPELLER-EPI. Magnetic Resonance in Medicine,
68(1), 140151.
Krieger, S. N., Streicher, M. N., Trampel, R., & Turner, R. (2012). Cerebral blood
volume changes during brain activation. Journal of Cerebral Blood Flow and
Metabolism, 32(8), 16181631.
Kwong, K. K., Chesler, D. A., Weisskoff, R. M., & Rosen, B. R. (1994). Perfusion MR
imaging. In: Proceedings of the Society of Magnetic Resonance, San Francisco, CA
(p. 1005).
(2001). Use of multicoil arrays for separation of signal from multiple slices. Journal
of Magnetic Resonance Imaging, 13(2), 313317.
Lazar, M., Weinstein, D. M., Tsuruda, J. S., Hasan, K. M., Arfanakis, K.,
Meyerand, M. E., et al. (2003). White matter tractography using diffusion tensor
deflection. Human Brain Mapping, 18(4), 306321.
Le Bihan, D. (1995). Molecular diffusion, tissue microdynamics and microstructure.
NMR in Biomedicine, 8(78), 375386.
Lee, S. P., Duong, T. Q., Yang, G., Iadecola, C., & Kim, S. G. (2001). Relative changes
of cerebral arterial and venous blood volumes during increased cerebral blood
flow: Implications for BOLD fMRI. Magnetic Resonance in Medicine, 45(5),
791800.
Li, T. Q., Haefelin, T. N., Chan, B., Kastrup, A., Jonsson, T., Glover, G. H., et al. (2000).
Assessment of hemodynamic response during focal neural activity in human using
bolus tracking, arterial spin labeling and BOLD techniques. NeuroImage, 12(4),
442451.
Lin, C. P., Wedeen, V. J., Chen, J. H., Yao, C., & Tseng, W. Y. (2003). Validation of
diffusion spectrum magnetic resonance imaging with manganese-enhanced rat
optic tracts and ex vivo phantoms. NeuroImage, 19(3), 482495.
Medicine, 50(2), 263274.
Luh, W. M., Wong, E. C., Bandettini, P. A., & Hyde, J. S. (1999). QUIPSS II with thinslice TI1 periodic saturation: A method for improving accuracy of quantitative
perfusion imaging using pulsed arterial spin labeling. Magnetic Resonance in
Medicine, 41(6), 12461254.
Luo, Q., Jiang, X., & Gao, J. H. (2011). Detection of neuronal current MRI in
human without BOLD contamination. Magnetic Resonance in Medicine, 66(2),
492497.
Lutti, A., Stadler, J., Josephs, O., Windischberger, C., Speck, O., Bernarding, J., et al.
(2012). Robust and fast whole brain mapping of the RF transmit field B1 at 7 T. PloS
One, 7(3), e32379.
Maclaren, J., Armstrong, B. S., Barrows, R. T., Danishad, K. A., Ernst, T., Foster, C. L.,
et al. (2012). Measurement and correction of microscopic head motion during
magnetic resonance imaging of the brain. PloS One, 7(11), e48088.
Maclaren, J., Herbst, M., Speck, O., & Zaitsev, M. (2013). Prospective motion
correction in brain imaging: A review. Magnetic Resonance in Medicine, 69(3),
621636.
Mandelkow, H., Halder, P., Brandeis, D., Soellinger, M., de Zanche, N., Luechinger, R.,
et al. (2007). Heart beats brain: The problem of detecting alpha waves by neuronal
current imaging in joint EEG-MRI experiments. NeuroImage, 37(1), 149163.
Mandeville, J. B., Marota, J. J., Ayata, C., Moskowitz, M. A., Weisskoff, R. M., &
Rosen, B. R. (1999). MRI measurement of the temporal evolution of relative CMRO
(2) during rat forepaw stimulation. Magnetic Resonance in Medicine, 42(5),
944951.

Mark, C. I., & Pike, G. B. (2012). Indication of BOLD-specific venous flow-volume
changes from precisely controlled hyperoxic vs. hypercapnic calibration. Journal of
McNab, J. A., Edlow, B. L., Witzel, T., Huang, S. Y., Bhat, H., Heberlein, K., et al. (2013).
The Human Connectome Project and beyond: Initial applications of 300 mT/m
gradients. NeuroImage, 80, 235245.
Mori, S., Crain, B. J., Chacko, V. P., & van Zijl, P. C. (1999). Three-dimensional
tracking of axonal projections in the brain by magnetic resonance imaging. Annals
of Neurology, 45(2), 265269.
Mori, S., & van Zijl, P. C. (2002). Fiber tracking: principles and strategies A technical
review. NMR in Biomedicine, 15(78), 468480.
Norris, D. G. (2012). Spin-echo fMRI: The poor relation? NeuroImage, 62(2),
11091115.
Academy of Sciences of the United States of America, 87(24), 98689872.
Olman, C. A., Harel, N., Feinberg, D. A., He, S., Zhang, P., Ugurbil, K., et al. (2012).
Layer-specific fMRI reflects different neuronal computations at different depths in
human V1. PloS One, 7(3), e32536.
Parkes, L. M., de Lange, F. P., Fries, P., Toni, I., & Norris, D. G. (2007). Inability to
directly detect magnetic field changes associated with neuronal activity. Magnetic
Petridou, N., Plenz, D., Silva, A. C., Loew, M., Bodurka, J., & Bandettini, P. A. (2006).
Direct magnetic resonance detection of neuronal electrical activity. Proceedings of
1601516020.
Pipe, J. G. (1999). Motion correction with PROPELLER MRI: Application to head motion
and free-breathing cardiac imaging. Magnetic Resonance in Medicine, 42(5),
963969.
Pipe, J. G., & Zwart, N. (2006). Turboprop: Improved PROPELLER imaging. Magnetic
Sensitivity encoding for fast MRI. Magnetic Resonance in Medicine, 42(5),
952962.
Robson, M. D., Gore, J. C., & Constable, R. T. (1997). Measurement of the point spread
function in MRI using constant time imaging. Magnetic Resonance in Medicine,
38(5), 733740.
Savoy, R. L. (2005). Experimental design in brain activation MRI: Cautionary tales. Brain
Research Bulletin, 67(5), 361367.
Schafer, A., Forstmann, B. U., Neumann, J., Wharton, S., Mietke, A., Bowtell, R., et al.
(2012). Direct visualization of the subthalamic nucleus and its iron distribution
using high-resolution susceptibility mapping. Human Brain Mapping, 33(12),
28312842.
Schmahmann, J. D., & Pandya, D. N. (2006). Fiber pathways of the brain. New York:
Oxford University Press.
Schulz, J., Siegert, T., Reimer, E., Labadie, C., Maclaren, J., Herbst, M., et al. (2012). An
embedded optical tracking system for motion-corrected magnetic resonance
imaging at 7 T. Magma, 25(6), 443453.
Scouten, A., & Constable, R. T. (2007). Applications and limitations of whole-brain
MAGIC VASO functional imaging. Magnetic Resonance in Medicine, 58(2),
306315.
Scouten, A., & Constable, R. T. (2008). VASO-based calculations of CBV change:
Accounting for the dynamic CSF volume. Magnetic Resonance in Medicine, 59(2),
308315.
Setsompop, K., Cohen-Adad, J., Gagoski, B. A., Raij, T., Yendiki, A., Keil, B., et al.
(2012). Improving diffusion MRI using simultaneous multi-slice echo planar
imaging. NeuroImage, 63(1), 569580.
Setsompop, K., Kimmlingen, R., Eberlein, E., Witzel, T., Cohen-Adad, J., McNab, J. A.,
Project. NeuroImage, 80, 220233.
Shen, X., Papademetris, X., & Constable, R. T. (2010). Graph-theory based parcellation
of functional subunits in the brain from resting-state fMRI data. NeuroImage, 50(3),
10271035.
Shen, X., Tokoglu, F., Papademetris, X., & Constable, R. T. (2013). Groupwise wholebrain parcellation from resting-state fMRI data for network node identification.
Sodickson, D. K., & Manning, W. J. (1997). Simultaneous acquisition of spatial
harmonics (SMASH): Fast imaging with radiofrequency coil arrays. Magnetic
Song, A. W. (2012). Diffusion modulation of the fMRI signal: Early investigations on the
origin of the BOLD signal. NeuroImage, 62(2), 949952.
Song, A. W., Woldorff, M. G., Gangstead, S., Mangun, G. R., & McCarthy, G. (2002).
Enhanced spatial localization of neuronal activation using simultaneous apparent-
189
diffusion-coefficient and blood-oxygenation functional magnetic resonance

imaging. NeuroImage, 17(2), 742750.
1.5 T. Magnetic Resonance in Medicine, 35(2), 155158.
Stables, L. A., Kennan, R. P., & Gore, J. C. (1998). Asymmetric spin-echo imaging of
magnetically inhomogeneous systems: Theory, experiment, and numerical studies.
Stefanovic, B., Hutchinson, E., Yakovleva, V., Schram, V., Russell, J. T., Belluscio, L.,
et al. (2008). Functional reactivity of cerebral capillaries. Journal of Cerebral Blood
Flow and Metabolism, 28(5), 961972.
Stefanovic, B., & Pike, G. B. (2005). Venous refocusing for volume estimation: VERVE
functional magnetic resonance imaging. Magnetic Resonance in Medicine, 53(2),
339347.
Stockmann, J. P., Ciris, P. A., Galiana, G., Tam, L., & Constable, R. T. (2010). O-space
imaging: Highly efficient parallel imaging using second-order nonlinear. Magnetic
Stockmann, J., Galiana, G., Tam, L., Juchem, C., Nixon, T., & Constable, R. (2012). In vivo
O-space imaging with a dedicated 12 cm Z2 insert coil on a human 3 T scanner using
phase map calibration. Magnetic Resonance in Medicine, 69(2), 12.
Tam, L. K., Stockmann, J. P., Galiana, G., & Constable, R. T. (2012). Null space
imaging: Nonlinear magnetic encoding fields designed complementary to receiver
coil sensitivities for improved acceleration in parallel imaging. Magnetic Resonance
in Medicine, 68(4), 11661175.
Tang, L., Avison, M. J., Gatenby, J. C., & Gore, J. C. (2008). Failure to direct detect
magnetic field dephasing corresponding to ERP generation. Magnetic Resonance in
Medicine, 26(4), 484489.
Tian, P., Teng, I. C., May, L. D., Kurz, R., Lu, K., Scadeng, M., et al. (2010). Cortical
depth-specific microvascular dilation underlies laminar differences in. Proceedings
of the National Academy of Sciences of the United States of America, 107(34),
1524615251.
Tournier, J. D., Calamante, F., Gadian, D. G., & Connelly, A. (2004). Direct estimation of
the fiber orientation density function from diffusion-weighted MRI data using
spherical deconvolution. NeuroImage, 23(3), 11761185.
Tuch, D. S., Reese, T. G., Wiegell, M. R., Makris, N., Belliveau, J. W., & Wedeen, V. J.
(2002). High angular resolution diffusion imaging reveals intravoxel white matter
fiber heterogeneity. Magnetic Resonance in Medicine, 48(4), 577582.
Tuch, D. S., Reese, T. G., Wiegell, M. R., & Wedeen, V. J. (2003). Diffusion MRI of
complex neural architecture. Neuron, 40(5), 885895.
Van de Moortele, P. F., Akgun, C., Adriany, G., Moeller, S., Ritter, J., Collins, C. M.,
et al. (2005). B(1) destructive interferences and spatial phase patterns at 7 T
with a head transceiver array coil. Magnetic Resonance in Medicine, 54(6),
15031518.
van Gelderen, P., de Zwart, J. A., Starewicz, P., Hinks, R. S., & Duyn, J. H. (2007). Realtime shimming to compensate for respiration-induced B0 fluctuations. Magnetic
Vazquez, A. L., Fukuda, M., Tasker, M. L., Masamoto, K., & Kim, S. G. (2010). Changes
in cerebral arterial, tissue and venous oxygenation with evoked neural stimulation:
Implications for hemoglobin-based functional neuroimaging. Journal of Cerebral
Wedeen, V. J., Davis, T. L., Lautrup, B. E., Reese, T. G., & Rosen, B. R. (1996). Diffusion
anisotropy and white matter tracts. NeuroImage, 3(1), S146S146. http://dx.doi.
org/10.1016/S1053-8119(96)80148-0.
Wedeen, V. J., Hagmann, P., Tseng, W. Y., Reese, T. G., & Weisskoff, R. M. (2005).
Mapping complex tissue architecture with diffusion spectrum magnetic resonance
imaging. Magnetic Resonance in Medicine, 54(6), 13771386.
Wedeen, V. J., Reese, T. G., Tuch, D. S., Weigel, M. R., Dou, J. -G., Weiskoff, R. M.,
et al. (2000). Mapping fiber orientation spectra in cerebral white matter with
Fourier-transform diffusion MRI. In: Proceedings of the 8th Annual Meeting of the
ISMRM (p. 82).
Wedeen, V. J., Rosene, D. L., Wang, R., Dai, G., Mortazavi, F., Hagmann, P., et al.
(2012). The geometric structure of the brain fiber pathways. Science, 335(6076),
16281634.
Wedeen, V. J., Wang, R. P., Schmahmann, J. D., Benner, T., Tseng, W. Y., Dai, G., et al.
(2008). Diffusion spectrum magnetic resonance imaging (DSI) tractography of
crossing fibers. NeuroImage, 41(4), 12671277.
Weisskoff, R. M., Zuo, C. S., Boxerman, J. L., & Rosen, B. R. (1994). Microscopic
susceptibility variation and transverse relaxation: Theory and experiment. Magnetic
Wharton, S., & Bowtell, R. (2012). Fiber orientation-dependent white matter contrast in
States of America, 109(45), 1855918564.
Wiegell, M. R., Larsson, H. B., & Wedeen, V. J. (2000). Fiber crossing in human brain
depicted with diffusion tensor MR imaging. Radiology, 217(3), 897903.
190
Wong, E. C., Buxton, R. B., & Frank, L. R. (1997). Implementation of quantitative

perfusion imaging techniques for functional brain mapping using pulsed arterial
spin labeling. NMR in Biomedicine, 10(45), 237249.
Wu, G., Luo, F., Li, Z., Zhao, X., & Li, S. J. (2002). Transient relationships among
BOLD, CBV, and CBF changes in rat brain as detected by functional MRI. Magnetic
Zaitsev, M., Hennig, J., & Speck, O. (2004). Point spread function mapping with parallel
imaging techniques and high acceleration factors: Fast, robust, and flexible method
for echo-planar imaging distortion correction. Magnetic Resonance in Medicine,

52(5), 11561166.
Zeng, H., & Constable, R. T. (2002). Image distortion correction in EPI: Comparison of
field mapping with point spread function mapping. Magnetic Resonance in
Medicine, 48(1), 137146.
Zhan, W., Stein, E. A., & Yang, Y. (2004). Mapping the orientation of intravoxel crossing
fibers based on the phase information of diffusion circular spectrum. NeuroImage,
23(4), 13581369.
fMRI at High Magnetic Field: Spatial Resolution Limits and Applications

E Yacoub, K Ugurbil, and N Harel, University of Minnesota, Minneapolis, MN, USA
Glossary
Cortical column A group of neurons with similar

functional preferences spanning from the pial surface to the
white matter.
Gradient echo Refers to the use of dephasing and rephasing
magnetic field gradients to generate transverse
magnetization. The measured signal is reflective of T2 and
T2* decay.
Laminar/Laminae The structure of the neocortex is
relatively uniform and consists of six horizontal layers
segregated principally by cell type and neuronal
High-Field High-Resolution fMRI to Map

the Human Brain
A detailed understanding of how distributed large-scale systems
in the brain operate requires characterization of the organizations and interconnections of the most fundamental building
blocks of neural populations. Cortical columns are prominent
examples of such structurally and functionally specialized units
and have been studied extensively (Hubel & Wiesel, 1959;
Mountcastle, 1957). Such functional units (i.e., cortical columns) were shown to be about 1 mm in width and organized
in a periodic fashion. To map these structures would require
imaging with submillimeter spatial resolutions and specificities.
In humans, the development of noninvasive in vivo neuroimaging methods may be the only opportunity to characterize such
neuronal architectures as postmortem information about such
functional organizations is in general quite limited. Such a
development would be invaluable for both systems and cognitive neuroscience, as it would provide a mechanism for investigating the fundamentals of how the human brain works. The
neuroimaging method that promises sufficient spatial resolution, specificity, and volume coverage is functional magnetic
resonance imaging (fMRI) and, more specifically, high-field
fMRI. Since the introduction of fMRI (Kwong et al., 1992;
Ogawa et al., 1992), there has been a relentless push toward
higher and higher magnetic fields for both animal and human
studies. The primary driving force toward higher fields has been
increases in the functional sensitivity (contrast-to-noise ratio
(CNR) and signal-to-noise ratio (SNR)) along with the spatial
specificity of the blood oxygen level-dependent (BOLD) fMRI
signal (Yacoub et al., 2001, 2003), the most commonly
employed methodology for noninvasive brain mapping. While
there are other fMRI approaches, such as arterial spin labeling
(Edelman et al., 1994; Kim, 1995) and cerebral blood volume
measurements (Lu, Golay, Pekar, & Van Zijl, 2003; Mandeville
et al., 1998), to date, for human studies, BOLD fMRI has been
the only technique to demonstrate sufficient sensitivity for submillimeter spatial resolution applications. Further, high fields
are well suited for high-resolution studies as increases in the
temporal (or physiological) noise in BOLD fMRI signals (Hyde,
connections. The different layers are referred to as the

cortical laminae.
Segmented image acquisition When multiple acquisitions
(radio frequency excitations) are used to sample the entire
object, as opposed to a single shot acquisition, which
acquires all of the spatial frequency information of an
object following a single excitation and data readout
period.
Spin echo The refocusing of the transverse magnetization
(T2) via a 180 or series of 180 radio frequency pulses. The
measured signal is reflective of T2 decay.
Biswal, & Jesmanowicz, 2001; Kruger & Glover, 2001; Triantafyllou et al., 2005) result in limited advantages to running lowresolution fMRI studies at high fields. In general, applications
that would otherwise be SNR-starved at 3 T (i.e., higher spatial
and temporal resolution protocols) are ideally suited for higher
fields (i.e., 7 T). While recent work has demonstrated the neuroscience utility of higher temporal resolution fMRI (Feinberg
et al., 2010; Smith et al., 2012), despite the slow hemodynamic
response, historically, pushing the limits of spatial resolution,
while challenging, has proven to be extremely fruitful, opening
opportunities to understand how the living human brain functions at its most fundamental levels.
While high-field gains allow for higher spatial resolution
images, because BOLD fMRI relies on the hemodynamic
response to map brain function, the acquisition of highresolution images alone does not guarantee increases in the
resolution of the functional mapping (Olman & Yacoub,
2011). The spatial resolution and specificity limits of fMRI
depend on both the pulse sequence and parameter choices
and the magnetic field strength used (Uludag, Muller-Bierl, &
Ugurbil, 2009), which can all result in varying sensitivities to
the vascular response and the subsequent functional point
spread function. Conventional fMRI applications are not really
concerned with this because the functional organizations, or
information sought from fMRI signals, are typically segregated
on the order of several millimeters (i.e., hypercolumns and/or
cortical areas; Olman & Yacoub, 2011), conservatively within
the vascular point spread function of the BOLD response at any
field (Engel, Glover, & Wandell, 1997; Shmuel, Yacoub,
Chaimow, Logothetis, & Ugurbil, 2007b). Further, if one is
only interested in the information present in the functional
signals and not the source or spatial organization of the information, it has been shown that some of this information can
be decoded from lower-resolution images (Haynes & Rees,
2005; Kamitani & Tong, 2005). The source of these decoding
signals or how they relate to columnar-level organizations
is, however, controversial (Freeman, Brouwer, Heeger, &
Merriam, 2011; Shmuel et al., 2007a). In any case, even
today, because of the lack of access to higher-field magnets
and the technical challenges associated with higher-resolution
http://dx.doi.org/10.1016/B978-0-12-397025-1.00022-1
191
192
INTRODUCTION TO ACQUISITION METHODS | fMRI at High Magnetic Field: Spatial Resolution Limits and Applications
acquisitions, very high-resolution neuroscience applications

are generally not even attempted in human fMRI, despite the
rapidly increasing availability of 7 T MRI systems.
On the other hand, studies that aim to map high-resolution
columnar or laminar-specific information must be cognizant of
the limitations of the functional signals being used to interpret
the underlying neuronal activity. Irrespective of this, because of
its ease of implementation and its relatively high CNR and
acquisition efficiency, gradient-echo (GE)-fMRI techniques are
almost always used regardless of whether high-resolution functional information is desired. It has, however, been well established that a significant component of the GE-fMRI response
originates from large vessels (Duyn, Moonen, Yperen, Boer, &
Luyten, 1994; Frahm, Merboldt, Hanicke, Kleinschmidt, &
Boecker, 1994; Kim, Hendrich, Hu, Merkle, & Ugurbil, 1994;
Lai et al., 1993; Lee, Glover, & Meyer, 1995; Menon, Ogawa,
Tank, & Ugurbil, 1993; Segebarth et al., 1994), which can be
several millimeters away from the neural activity and can contaminate desirable tissue signals. This effect, which can result in
more subtle variations in lower-resolution functional organizations (Olman & Yacoub, 2011), can be much more problematic
when higher-resolution mapping is desired. The use of higher
magnetic fields alleviates this concern somewhat as intravascular
contributions to the BOLD signal are much less (Constable,
Kennan, Puce, Mccarthy, & Gore, 1994; Gao et al., 1995; Oja,
Gillen, Kauppinen, Kraut, & Van Zijl, 1999) pronounced.
Despite this inherent lack of high spatial specificity, many of
the published fMRI studies that aimed to map columnar organizations in humans (Cheng, Waggoner, & Tanaka, 2001; Dechent
& Frahm, 2000; Goodyear & Menon, 2001; Menon, Ogawa,
Strupp, & Ugurbil, 1997) have utilized GE-fMRI. To alleviate
the spatial specificity problem, these studies employed differential mapping (i.e., comparing two activated conditions instead of
an activated condition against a baseline condition), diffusion
weighting (Boxerman et al., 1995; Song, Wong, Tan, & Hyde,
1996), masking of voxels demonstrating high-amplitude
responses (Cheng et al., 2001; Kim et al., 1994; Shmuel, Yacoub,
Chaimow, Logothetis, & Ugurbil, 2007b), or phase-specific
information (Menon, 2002) or have simply chosen an imaging
volume that avoids areas known to be void of large vessels.
Avoiding contaminating vessels has been done effectively in
animal models (Moon, Fukuda, Park, & Kim, 2007), but is
much more difficult to do in humans (Gardner, Sun, Tanaka,
Heeger, & Cheng, 2006; Yacoub, Shmuel, Logothetis, & Ugurbil,
2007), especially because only small fields of view in specific
brain areas have been feasible, due to the inefficiencies of higherresolution acquisitions in humans. Alternatively, the use of spinecho (SE)-based BOLD fMRI at high fields (Goense & Logothetis,
2006; Harel, Lin, Moeller, Ugurbil, & Yacoub, 2006; Lee, Silva, &
Kim, 2002; Lee, Silva, Ugurbil, & Kim, 1999; Yacoub, Van De
Moortele, Shmuel, & Ugurbil, 2005; Yacoub et al., 2003; Zhao,
Wang, Hendrich, & Kim, 2005; Zhao, Wang, Hendrich, Ugurbil,
& Kim, 2006; Zhao, Wang, & Kim, 2004) has been shown to be
advantageous in reducing the macrovascular contributions, as
predicted (Ogawa, Lee, Kay, & Tank, 1990; Uludag et al., 2009).
This occurs because, compared with GE-fMRI, SE-based BOLD at
high (but not low) fields, in addition to the smaller intravascular
contribution, is much less sensitive to extravascular signals from
large vessels (Harel et al., 2006; Yacoub et al., 2005; Zhao et al.,
2004, 2006), and despite the much lower CNR compared with
GE-fMRI, its CNR at high fields, such as 7 and 9.4 T, is sufficient

to generate reliable responses at submillimeter spatial resolutions. Approaches to reduce inherent nonspecific fMRI signals
can be advantageous; however, since columnar-level organizations in humans are largely unknown, without a priori information about the functional organization, as was the case in the
mapping of human ocular dominance columns (ODCs)
(Horton & Hedley-Whyte, 1984), there is no way to validate
the integrity of the functional maps or ascertain whether they
are spatially distorted (and how much) by nonspecific larger
vessel signals. The use of fMRI to map ODCs, which had been
well characterized with postmortem anatomical data, allowed
for an intrinsic evaluation of the specificity of the BOLD response
(Yacoub et al., 2007). Having a ground truth allowed this work
to establish that BOLD fMRI signals (GE and SE) at submillimeter spatial resolutions are reliable enough to be reproducible (even) across different scanning days and that SE-based
BOLD maps depicted organizations more consistent with previous anatomical data in humans. GE maps were also able to
resolve these structures, however, only in portions of the field
of view (FOV) that were void of large veins (see Figure 1). The
validation of spatial specificity is invaluable for mapping columnar organizations with fMRI, as in the general case there is not
any obvious clinical symptom, outside of the case of ODCs, that
would render such functional organizations visible in postmortem anatomical data. The most one could hope for as a
ground truth, for human studies, would be to use invasive
Spin
echo
Gradient
echo
1 mm
Figure 1 ODC maps from a flat gray matter region along the calcarine
sulcus from the same subject on several different days. On the left is
the overlap of two different scan days using SE at 7 T, while on the right
is the overlap of two different scans using GE. Red or blue pixels
indicate a voxels preference to the right or left eye stimulation. The
expected spatial pattern is an alternating preference (1 mm width,
2 mm cycle) to the right or left eye running along the sulcus. The SE map
retains this pattern throughout the region, while the GE map is
interrupted by extravascular changes around large vessels somewhere
near the region of interest. Reproduced from Figure 5 in Yacoub, E.,
Shmuel, A., Logothetis, N., & Ugurbil, K. (2007). Robust detection of
ocular dominance columns in humans using Hahn Spin Echo BOLD
functional MRI at 7 Tesla. Neuroimage, 37, 116177.
animal models (i.e., optical imaging of intrinsic signals) as a
guide. However, these data are somewhat limited in the information they have provided about columnar organizations
(Blasdel & Salama, 1986; Bonhoeffer & Grinvald, 1991; Hubel
& Wiesel, 1959, 1962, 1963, 1968, 1977; Mountcastle, 1957;
Shmuel & Grinvald, 1996; Shoham, Hubener, Schulze, Grinvald,
& Bonhoeffer, 1997; Weliky, Bosking, & Fitzpatrick, 1996). Following the demonstrated reliability of high-field SE-based BOLD
signals to map ODCs in humans, the same cortical area was
mapped in the same subjects using an orientation-dependent
paradigm, demonstrating, prior to any other technique, invasive
or otherwise, orientation preference at the columnar level in the
human (Yacoub, Harel, & Ugurbil, 2008). These results did also
closely resemble what had been shown in animal models
(Figure 2). More importantly, this work showed that high-field
high-resolution fMRI could reliably conduct novel explorations
of previously unmapped and potentially unknown columnar
systems in the human brain, suggesting that high-field fMRI
itself could be the ground truth for human brain mapping.
In general, however, to build on this work and/or to
facilitate further mapping of high-resolution functional
architectures in the human requires technical improvements
due to the inefficiencies and limitations of high-resolution
fMRI acquisitions.
Technical Challenges of Higher-Resolution fMRI

Highly problematic to increasing the spatial resolution in fMRI
is the subsequent increase in acquisition time during any single
echo-planar imaging (EPI) (Mansfield, 1977) readout train and
the consequential longer volume repetition times (TRs) due to
Scalebar = 0.5 mm
(a)
193
the many more slices needed to cover the same volume. Longer
acquisition times result in increases in distortions, loss of spatial
resolution, loss of SNR, and increases in susceptibility or other
artifacts ubiquitous to EPI. Nearly all human fMRI studies,
irrespective of spatial resolution, use 2-D SE-based EPI because,
relatively speaking, the sampling time for a single slice, as well as
for an entire volume, is fast. 3-D imaging (i.e., echo-volume
imaging, EVI) (Mansfield, Harvey, & Stehling, 1994), while
having the advantage of higher SNR, can be hampered by physiological noise or motion, which is convolved over the volume
acquisition time. Segmented (2-D or 3-D) EPI can be used to
shorten the readout trains, with a similar caveat of physiological
noise and motion sensitivity. Choosing between 3-D and 2-D
(segmented or single-shot) acquisitions for high-resolution
fMRI might be determined by whether or not physiological
noise limits the functional sensitivity of 3-D acquisitions and
whether or not 2-D acquisitions have sufficient static SNR or
spatial resolution along any specific direction. Cases can be
made to utilize non-EPI-based acquisitions for applications
that require reduced distortions or susceptibility effects; however, the vast majority of fMRI studies cannot afford such a
penalty in efficiency, especially since there are numerous ways
to mitigate artifacts and improve overall image quality in EPI
(Glasser et al., 2013). Spiral sampling trajectories have been
shown to have advantages over EPI for fMRI (Yang et al.,
1998) with associated artifacts manifesting as blurring; however,
the technical requirements of spiral sampling have slowed its
progression into clinical scanners, and thus for the aforementioned reasons, fMRI studies today, be they high- or low-resolution, use 2-D SE-based EPI.
Apart from image segmentation, long acquisition times can
be mitigated using reduced FOV (or zoomed) imaging
0
(b)
Phase
Figure 2 fMRI orientation and ocular dominance maps in a human subject. Ocular dominance and orientation columns in human visual cortex. (a) Red
and blue represent voxels that demonstrated preference to right and left eye stimulation, respectively. (b) Depicts the orientation preference maps
from the same cortical areas as their corresponding ODC maps in (a). ODC borders are marked with solid black lines on both the ODC and
orientation maps. (Color bar for orientation map (b): calculated phase at the stimulus frequency; scale bar: 0.5 mm.) Variant of Figure 2 reproduced
from Yacoub, E., Harel, N., & Ugurbil, K. (2008). High-field fMRI unveils orientation columns in humans. Proceedings of the National Academy of
Sciences of the United States of America, 105, 10 60710 612.
194
(i.e., outer-volume suppression; Heidemann et al., 2012b;

Pfeuffer et al., 2002) or inner-volume excitation (Duong et al.,
2002; Feinberg et al., 1985; Yacoub et al., 2003, 2005, 2007,
2008), such that the amount of phase encoding that needs to be
done in a single shot is minimized. Parallel imaging can also be
used for this purpose, with the caveat that it can be highly costly
in terms of image SNR. For GE-EPI, there is sufficient functional
CNR to permit highly accelerated single-shot high-resolution
images without reducing the FOV imaging. In SE-based imaging, because a 180 refocusing (RF) pulse is needed, transmit
field inhomogeneities result in lower SNR, reducing the SNR
available for parallel imaging. To make matters worse, the echo
time needed for optimum BOLD contrast is around two times
longer than what is used for GE imaging, and power deposition
limits prevent scanning at the minimum TRs. Ultimately, this
results in extremely inefficient acquisitions, with fast TRs not
typically even practical. As such, efficient large-volume or full
FOV submillimeter-level resolution imaging with SE-based
BOLD contrast is extremely challenging. Further, when using
limited imaging volumes, slight motion of the subject results in
a loss of useful functional information that cannot be recovered
by retrospective motion correction, as the imaged slice moves
into the white matter or outside the cortical area that was
originally targeted. In terms of pulse sequences, there are
several alternatives that could be used to obtain or optimize
T2-weighted images, such as SSFP (Miller & Jezzard, 2008),
HASTE (Poser & Norris, 2007; Ye, Zhuo, Xue, & Zhou, 2010)
(or TSE/FSE), or PINS (Koopmans, Boyacioglu, Barth, & Norris,
2012; Norris, Koopmans, Boyacioglu, & Barth, 2011) pulses, to
improve transmit efficiencies at high fields. While all of these
have been proposed for T2-weighted fMRI, none of them,
besides zoomed 2-D SE-based EPI (Yacoub et al., 2007, 2008)
and more recently 3-D gradient and spin echo (GRASE)
(described in the succeeding text), have demonstrated the
required combination of efficiency, spatial resolution, functional contrast, and specificity to be viable for ultrahigh (submillimeter-level) resolution applications, the primary reason
for using high-field T2-weighted BOLD in the first place. Therefore, even if such high spatial specificity is required, the cost of
acquiring high-resolution SE-based BOLD images is unduly
expensive, making GE methods (where parallel imaging and
full FOV imaging are more tolerable), and dealing with the
lower spatial specificity, as or even more attractive.
The Extension of High-Specificity Submillimeter fMRI

to Larger FOVs and beyond V1
Since the work on ocular dominance (Yacoub et al., 2007) and
orientation columns (Yacoub et al., 2008) in humans at 7 T,
which were limited to a single slice prescribed over flat cortical
gray matter regions in primary visual areas, efforts have been
made to extend this high-resolution mapping to more general
use. Extending high-resolution functional mapping entails
mapping smaller areas, areas outside of V1, and areas where
the gray matter is generally more tortuous. In order to do this,
the high-specificity mapping and efficiency of the 2-D SE
inner-volume method (Yacoub et al., 2003, 2005, 2007,
2008), which used a single thick slice, would need to be
extended to multiple slices (or a volume) while simultaneously
achieving high isotropic resolution. Note that while it was

shown that the reduced FOV 2-D SE-based EPI method provided a neuroscience utility over conventional GE-EPI (Yacoub
et al., 2007), due to orthogonal RF pulses cross-irradiating
tissue slabs when doing inner-volume imaging, multislice 2D SE images with inner-volume excitation are not practical,
making the general applications of this approach extremely
limited. A promising alternative that has been proposed is 3D single-shot GRASE (Feinberg & Oshio, 1991; Gunther,
Oshio, & Feinberg, 2005; Oshio & Feinberg, 1991) with
inner-volume excitation (Feinberg, Harel, Ramanna, Ugurbil,
& Yacoub, 2008; Yacoub, Ugurbil, & Olman, 2009), a 3-D
extension of the 2-D inner-volume approach. The advantages
of the 3-D approach are its ability to extend coverage and
achieve higher SNR compared with 2-D, permitting, ultimately, higher (submillimeter) isotropic resolutions; reductions in the specific absorption rate; and enhanced functional
contrast due to stimulated echoes. It should be noted that
while being heavily T2-weighted in nature, 3-D GRASE does
have significant contributions from stimulated echoes
(Goerke, Van De Moortele, & Ugurbil, 2007). As such, the
functional specificity of 3-D GRASE-based BOLD signals cannot be presumed. Notwithstanding, the first application of this
approach to columnar-level fMRI in humans was the investigation of axis of motion preference in human area MT. Highresolution T2-weighted fMRI maps were generated across a 3-D
volume along the complex tortuosity of the superior temporal
sulcus and then segregated according to cortical depth. These
results provided the first direct evidence of the columnar
response properties in human area MT, showing axis of motion
selective feature organization, in the range of what might have
been predicted based on limited data from animal models
(Zimmermann et al., 2011) (Figure 3). The integrity of these
functional maps with respect to nonspecific effects commonly
observed in GE-fMRI was evaluated as part of a separate study
(De Martino et al., 2013).
Cortical Depth-Dependent Spatial Specificity

of fMRI Signals
While columnar studies average functional signals across the
cortical depth, to understand the different stages of neuronal
processes or interactions would require cortical depthdependent analyses. Such an analysis may even permit exclusion
of undesirable nonspecific surface-related effects, which oftentimes contaminate GE-fMRI signals (Harel et al., 2006). In a
recent study, fMRI signals from 3-D GRASE and 2-D GE were
acquired and analyzed according to cortical depth. fMRI
responses from 3-D GRASE, while having an overall lower sensitivity compared with GE, did not show a bias to responses from
the surface, as was present in GE signals. The bias was quantified
not only as a larger response near the surface but also by measuring the specificity of the functional response via axis of
motion tuning curves. The tuning curves were generally sharper
and not dependent on depth in 3-D GRASE, while the wider GE
tuning curves deteriorated toward the surface (Figure 4). Of note
is that the surface-related bias in the GE data was exclusive to the
surface as it was found that there were biases in voxel preference
to a single axis of motion direction across cortical depths, likely
195
Figure 3 Illustration representing axis of motion columnar mapping approach. (a) Results of MT localization are projected onto the cortical
reconstruction of the subjects left hemisphere (neurological convention). High-resolution cortical grid sampling is performed. Zoomed in view of the
subjects STS with overlaid streamlines at two relative cortical depths (0.5 and 0.8%). In order to not suffer from residual contribution from
superficial blood vessels, sampling was restricted to the midlevel and deeper layers. (b) Results of the high-resolution cortical grid sampling for the
motion direction experiment showing columnar organization of axis of motion features in two sampled layers (scale bar 1 mm, color frames
representing the streamlines in zoomed in view). (c) Representation of the high-resolution cortical grid sampling showing four three-dimensional
vertical slices through the sampled cortical layers depicting the consistency of cortical columns tangential to the surface. Reproduced from Figure 3
in Zimmermann, J., Goebel, R., De Martino, F., Van De Moortele, P. F., Feinberg, D., Adriany, G., Chaimow, D., Shmuel, A., Ugurbil, K., & Yacoub, E.
(2011). Mapping the organization of axis of motion selective features in human area MT using high-field fMRI. PLoS One, 6, E28716.
originating from the surface and spreading through the cortical

depth. As such, as with the mapping of columnar architectures
with fMRI, caution must be exercised when using GE-fMRI signals. On the contrary, it is expected that T2-weighted (in this case
3-D GRASE) layer-specific fMRI studies at high fields can be more
clearly sensitive to neuronal interactions, as was shown in fMRI
studies using the cat model (Harel et al., 2006). A recent study
(Olman et al., 2012) did investigate layer-specific fMRI responses
(using 3-D GRASE) during an object recognition task and found
that there was a larger response to scrambled objects in the
middle layers, reflective of differences in local feed-forward or
feed-backward mechanisms. While this study could not determine with certainty the source of the observed effect, it was the
first study to demonstrate the sensitivity of fMRI signals to layerspecific modulations originating from neuronal processes
(Figure 5). While the functional signal origins and spatial specificities of 3-D GRASE have not been fully characterized, it is clear
that it does not resemble typical GE-fMRI contrast and the associated nonspecific signals.
Future Avenues for High-Resolution fMRI

Accelerated imaging techniques in MRI have been instrumental
in improving the efficiency of high-resolution imaging,
specifically at high fields where high-resolution imaging is

feasible in terms of SNR but where shortening of the T2/T2*
relaxation times makes faster imaging imperative. Reduction in
the number of phase-encode lines needed to generate highresolution images without signal aliasing, as can be done with
conventional parallel imaging, obfuscates the need for reduced
FOV imaging. However, due to limitations in the coil sensitivity profile, which is used to unalias the signals, and the intrinsic
SNR loss due to undersampling of the data, the total SNR
penalty may sometimes be unmanageable. Despite this, it has
been shown that with GE-based BOLD imaging, very highresolution full FOV 2-D SE-based EPI images can be generated
at high fields with exquisite image quality (Olman & Yacoub,
2011; Polimeni, Fischl, Greve, & Wald, 2010). On top of this,
recently applied 2-D slice-accelerated techniques (Feinberg
et al., 2010; Moeller et al., 2010; Setsompop et al., 2012) (in
combination with in-plane phase-encode accelerations) have
made such high-resolution images across the entire brain feasible within conventional TRs, making whole-brain submillimeter fMRI applications in humans a real possibility
(Figure 6). 3-D GE techniques, on the other hand, can instead
utilize phase-encode accelerations along 2 dimensions (Poser,
Koopmans, Witzel, Wald, & Barth, 2010). While significantly
reducing the volume acquisition time, accelerations along 2
dimensions come with an additional undersampling-related
196
S1 2.4
S1
3D GRASE
GE
Tuning specificity
2.2
2
1.8
1.6
1.4
1
S2
10 %
90 %
Tuning specificity
1.9
1.8
1.7
1.6
1.5
1.4
1.3
10 %
S3
90 %
1.8
Tuning specificity
1.7
1.6
BOLD% change
1.2
Stimulus probability
1
1
Intact
0.5
Scrambled
0
0.5
1
Distance from WM
Figure 5 An example of a selected cluster of significantly modulated

voxels. Voxels most strongly modulated by stimulus presentation
(p < 0.001) are shown overlaid on the T1-weighted anatomical reference,
illustrating adherence of activation to GM. Map on lower right
indicates probability that part of an intact or scrambled object occurred in
each region of the visual field; image subtends 7.6 . Green arrows
indicate one region of interest and corresponding visual field location.
Laminar profiles are shown with shading indicating standard error; seven
scans. Reproduced from Figure 3 in Olman, C. A., Harel, N., Feinberg, D.
A., He, S., Zhang, P., Ugurbil, K., & Yacoub, E. (2012). Layer-specific
fMRI reflects different neuronal computations at different depths in
human V1. Plos One, 7, E32536.
1.5
1.4
1.3
1.2
1.1
10 %
WM -> CSF
90 %
Figure 4 Single subjects specificity of the responses to the preferred

axis of motion in human area MT for both 3-D GRASE (red) and GE-EPI
(blue). Error bars represent the variability (standard error) across the
different tuning directions. Specificity is computed as the ratio between
the preferred response and the average response to the nonpreferred
directions. Reproduced from Figure 7 in De Martino, F., Zimmermann, J.,
Muckli, L., Ugurbil, K., Yacoub, E., & Goebel, R. (2013). Cortical depth
dependent functional responses in humans at 7 T: Improved specificity
with 3D GRASE. Plos One, 8, E60514.
SNR penalty, not present in 2-D slice-accelerated techniques.

Reduced FOV GE approaches (Heidemann, Anwander, Feiweier, Knosche, & Turner, 2012a; Heidemann et al., 2012b; Pfeuffer et al., 2002), which typically use outer-volume suppressionbased methods versus inner-volume excitation, might still be
advantageous to boost SNR and efficiency or to circumvent the
limitations in the coil sensitivity profiles. Ongoing technological improvements are, however, continuing to make large FOV
and even whole-brain high-resolution GE-fMRI studies the way
to go.
There are also alternative avenues to more efficiently extend

the imaging FOVs of higher resolution spin echo or
T2-weighted imaging at high fields. Such as 3-D multislab
inner-volume imaging (Vu, Feinberg, Harel, Ugurbil, &
Yacoub, 2013), the use of accelerated imaging (Chen &
Feinberg, 2013), specialized RF pulses (Norris et al., 2011)
and coils, and the use of parallel transmit techniques (Wu
et al., 2013a). 2-D SE-based EPI could, in principle, be applied
using the methods employed for large FOV high-resolution GE
acquisitions as discussed in the preceding text. However, the
needed refocusing pulses significantly constrain the temporal
efficiency due to SAR limits. The use of multibanded PINS
(Koopmans et al., 2012; Norris et al., 2011) pulses or parallel
transmit-constrained multibanded RF pulses (Wu, Ugurbil, &
Van De Moortele, 2013b) could be used to significantly
increase the temporal efficiency, because they can reduce the
needed RF energy (and thus SAR) to excite multiple slices.
Parallel transmit techniques, however, may ultimately be the
most valuable option as an even more significant impediment
in T2-weighted imaging is the transmit profile inhomogeneity
that severely limits SNR, prohibiting significant amounts of inplane acceleration, which in the end limits the achievable
spatial resolution. If only portions of the brain are needed,
multichannel array coils designed for specific sensory areas
(Adriany et al., 2001, 2013) allow for locally uniform and
efficient transmit fields that are extremely robust across subjects, circumventing the need for subject-specific parallel transmit methods. In such cases, techniques such as 3-D GRASE or
197
Figure 6 Single-shot (single-volume) EPI at 7 T acquired with a 0.9 mm isotropic resolution. In-plane undersampling of 3 and a slice acceleration of 3
were used to acquire the volume (150 slices) in 3.7 s. Data were acquired axially.
2-D SE-based EPI, in combination with in-plane accelerations,

could efficiently achieve (with sufficient SNR) larger volume
coverage for higher-resolution T2-weighted images.
Ultimately, the development of high-field high-resolution
imaging techniques for human applications is opening the
door to noninvasive neuroscience investigations, in animals
or humans, which were previously never thought possible. As
outlined in this article, there are an array of strategies and
possibilities within the fMRI technique, making the most optimal approach unclear. Continued advances in hardware and
pulse sequences, as well as characterizations of the functional
imaging signals (Uludag et al., 2009), will all direct and contribute to the advancement of the study of the human brain at
its most fundamental levels.
Acknowledgments
This project was supported by the WM KECK Foundation under
the NIH grants P41 EB015894, P30 NS076408, R44-NS073417,
R21NS075525 U54MH091657, and S10RR026783. The authors
would like to thank Joseph Vu, Eddie Auerbach, and Steen
Moeller for their data in Figure 6.

Functional MRI Dynamics; High-Field Acquisition; High-Speed, HighResolution Acquisitions; MRI and fMRI Optimizations and Applications;
Pulse Sequence Dependence of the fMRI Signal; Temporal Resolution
and Spatial Resolution of fMRI; INTRODUCTION TO ANATOMY
AND PHYSIOLOGY: Functional Organization of the Primary Visual
Cortex; INTRODUCTION TO METHODS AND MODELING: Models
of fMRI Signal Changes; INTRODUCTION TO SYSTEMS:
Somatosensory Processing.
References
Adriany, G., Pfeuffer, J., Yacoub, E., Van De Moortele, P.-F., Shmuel, A., Andersen, P.,
et al. (2001). A half-volume transmit/receive coil combination for 7 Tesla
applications. In: Proceedings of the 9th scientific meeting and exhibition, ISMRM,
Glasgow, UK, 1097.
Adriany, G., Schillak, S., Waks, M., Tramm, B., Roebroeck, A., Formisano, E., et al.
(2013). A flexible 4 ch. Transmit/16 ch. Receive auditory cortex array for hires fMRI
at 7 Tesla. In: ISMRM 21st, Salt Lake City 0074.
Blasdel, G. G., & Salama, G. (1986). Voltage-sensitive dyes reveal a modular
organization in monkey striate cortex. Nature, 321, 579585.
Bonhoeffer, T., & Grinvald, A. (1991). Iso-orientation domains in cat visual cortex are
arranged in pinwheel-like patterns. Nature, 353, 429431.
Boxerman, J. L., Bandettini, P. A., Kwong, K. K., Baker, J. R., Davis, T. J., Rosen, B. R.,
et al. (1995). The intravascular contribution to fMRI signal changes: Monte Carlo
modeling and diffusion-weighted studies in vivo. Magnetic Resonance in Medicine,
34, 410.
Chen, L., & Feinberg, D. (2013). Simultaneous multi-volume GRASE imaging.
In: ISMRM 21st annual meeting, Salt Lake City, 2365.
revealed by high-field functional magnetic resonance imaging. Neuron, 32, 359374.
Constable, R., Kennan, R., Puce, A., Mccarthy, G., & Gore, J. (1994). Functional NMR
imaging using fast spin echo at 1.5 T. Magnetic Resonance in Medicine, 31, 686690.
De Martino, F., Zimmermann, J., Muckli, L., Ugurbil, K., Yacoub, E., & Goebel, R.
(2013). Cortical depth dependent functional responses in humans at 7 T: Improved
specificity with 3D GRASE. PLoS One, 8, E60514.
Dechent, P., & Frahm, J. (2000). Direct mapping of ocular dominance columns in
human primary visual cortex. Neuroreport, 11, 32473249.
Duong, T. Q., Yacoub, E., Adriany, G., Hu, X., Ugurbil, K., Vaughan, J. T., et al. (2002).
High-resolution, spin-echo BOLD, and CBF fMRI at 4 and 7 T. Magnetic Resonance
Duyn, J. H., Moonen, C. T. W., Yperen, G. H., Boer, R. W., & Luyten, P. R. (1994).
Inflow versus deoxyhemoglobin effects in BOLD functional MRI using gradient
echoes at 1.5 T. NMR in Biomedicine, 7, 8388.
Edelman, R. E., Siewer, B., Darby, D. G., Thangaraj, V., Nobre, A. C., Mesulam, M. M.,
et al. (1994). Quantitative mapping of cerebral blood flow and functional localization
with echo-planar MR imaging and signal targeting with alternating radio frequency.
Radiology, 192, 513520.
visual cortex and the spatial precision of functional MRI. Cerebral Cortex, 7,
181192.
198
Feinberg, D. A., Harel, N., Ramanna, S., Ugurbil, K., & Yacoub, E. (2008). Submillimeter single-shot 3D GRASE with inner volume selection for T2-weighted fMRI
applications at 7 Tesla. In: 16th annual meeting of the international society for
magnetic resonance in medicine, Toronto.
Feinberg, D., Hoenninger, J., Crooks, L., Kaufman, L., Watts, J., & Arakawa, M. (1985).
Inner volume MR imaging: Technical concepts and their application. Radiology,
156, 743747.
(2010). Multiplexed echo planar imaging for sub-second whole brain fMRI and fast
diffusion imaging. PLoS One, 5, E15710.
Feinberg, D. A., & Oshio, K. (1991). GRASE (gradient- and spin-echo) MR imaging: A
new fast clinical imaging technique. Radiology, 181, 597602.
Frahm, J., Merboldt, K. D., Hanicke, W., Kleinschmidt, A., & Boecker, H. (1994). Brain
or vein-oxygenation or flow? on signal physiology in functional MRI of human brain
activation. NMR in Biomedicine, 7, 4553.
Freeman, J., Brouwer, G. J., Heeger, D. J., & Merriam, E. P. (2011). Orientation
decoding depends on maps, not columns. Journal of Neuroscience: The Official
Journal of the Society for Neuroscience, 31, 47924804.
Gao, J., Xiong, J., Schiff, L. J., Roby, J., Lancaster, J., & Fox, P. (1995). Fast spin-echo
characteristics of visual stimulation-induced signal changes in the human brain.
Gardner, J. L., Sun, P., Tanaka, K., Heeger, D. J., & Cheng, K. (2006). Classification
analysis with high spatial resolution fMRI reveals large draining veins with
orientation specific responses. In: Society for neuroscience society for neuroscience
annual meeting 640.14/O7, Atlanta.
Glasser, M. F., Sotiropoulos, S. N., Wilson, J. A., Coalson, T. S., Fischl, B.,
Andersson, J. L., et al. (2013). The minimal preprocessing pipelines for the human
connectome project. NeuroImage, 80, 105124.
Goense, J. B., & Logothetis, N. K. (2006). Laminar specificity in monkey V1 using highresolution SE-fMRI. Magnetic Resonance Imaging, 24, 381392.
Goerke, U., Van De Moortele, P. F., & Ugurbil, K. (2007). Enhanced relative BOLD
signal changes in T(2)-weighted stimulated echoes. Magnetic Resonance in
Medicine, 58, 754762.
Goodyear, B. G., & Menon, R. S. (2001). Brief visual stimulation allows mapping of
ocular dominance in visual cortex using fMRI. Human Brain Mapping, 14, 210217.
Gunther, M., Oshio, K., & Feinberg, D. A. (2005). Single-shot 3D imaging techniques
improve arterial spin labeling perfusion measurements. Magnetic Resonance in
Medicine, 54, 491498.
Harel, N., Lin, J., Moeller, S., Ugurbil, K., & Yacoub, E. (2006). Combined imaginghistological study of cortical laminar specificity of fMRI signals. NeuroImage, 29,
879887.
Haynes, J. D., & Rees, G. (2005). Predicting the orientation of invisible stimuli from
activity in human primary visual cortex. Nature Neuroscience, 8, 686691.
Heidemann, R. M., Anwander, A., Feiweier, T., Knosche, T. R., & Turner, R. (2012). kspace and q-space: Combining ultra-high spatial and angular resolution in diffusion
imaging using ZOOPPA at 7 T. NeuroImage, 60, 967978.
Heidemann, R. M., Ivanov, D., Trampel, R., Fasano, F., Meyer, H., Pfeuffer, J., et al.
(2012). Isotropic submillimeter fMRI in the human brain at 7 T: Combining reduced
field-of-view imaging and partially parallel acquisitions. Magnetic Resonance in
Medicine, 68, 15061516.
Horton, J., & Hedley-Whyte, E. T. (1984). Mapping of cytochrome oxidase patches and
ocular dominance columns in human visual cortex. Philosophical Transactions of
the Royal Society of London. Series B: Biological Sciences, 304, 255272.
Hubel, D. H., & Wiesel, T. N. (1959). Receptive fields of single neurones in the cats
striate cortex. Journal of Physiology, 148, 574591.
Hubel, D. H., & Wiesel, T. N. (1962). Receptive fields, binocular interaction and
functional architecture in the cats visual cortex. Journal of Physiology, 160,
106154.
Hubel, D. H., & Wiesel, T. N. (1963). Shape and arrangement of columns in cats striate
cortex. Journal of Physiology, 165, 559568.
Hubel, D. H., & Wiesel, T. N. (1968). Receptive fields and functional architecture of
monkey striate cortex. Journal of Physiology, 195, 215243.
Hubel, D. H., & Wiesel, T. N. (1977). Functional architecture of macaque monkey visual
cortex. Proceedings of the Royal Society of London [Biological Sciences], 198,
159.
Hyde, J. S., Biswal, B., & Jesmanowicz, A. (2001). High-resolution fMRI using
multislice partial k-space GR-EPI with cubic voxels. Magnetic Resonance in
Medicine, 46, 114125.
Kamitani, Y., & Tong, F. (2005). Decoding the visual and subjective contents of the
human brain. Nature Neuroscience, 8, 679685.
Kim, S.-G. (1995). Quantification of relative cerebral blood flow change by flowsensitive alternating inversion recovery (FAIR) technique: Application to functional
mapping. Magnetic Resonance in Medicine, 34, 293301.
Kim, S.-G., Hendrich, K., Hu, X., Merkle, H., & Ugurbil, K. (1994). Potential pitfalls of
functional MRI using conventional gradient-recalled echo techniques. NMR in
Koopmans, P. J., Boyacioglu, R., Barth, M., & Norris, D. G. (2012). Whole brain, high
resolution spin-echo resting state fMRI using PINS multiplexing at 7 T.
Kruger, G., & Glover, G. H. (2001). Physiological noise in oxygenation-sensitive
Lai, S., Hopkins, A. L., Haacke, E. M., Li, D., Wasserman, B. A., Buckley, P., et al.
(1993). Identification of vascular structures as a major source of signal contrast in
high resolution 2D and 3D functional activation imaging of the motor cortex at
1.5 T: Preliminary results. Magnetic Resonance in Medicine, 30, 387392.
Lee, A. T., Glover, G. H., & Meyer, G. H. (1995). Discrimination of large venous vessels
in time-course spiral blood-oxygen-level-dependent magnetic resonance functional
neuroimaging. Magnetic Resonance in Medicine, 33, 745754.
Lee, S. P., Silva, A. C., & Kim, S. G. (2002). Comparison of diffusion-weighted highresolution CBF and spin-echo BOLD fMRI at 9.4 T. Magnetic Resonance in
Medicine, 47, 736741.
Lee, S.-P., Silva, A., Ugurbil, K., & Kim, S.-G. (1999). Diffusion-weighted spin-echo
fMRI at 9.4 T: Microvascular/tissue contribution to BOLD signal changes. Magnetic
Medicine, 50, 263274.
Mandeville, J. B., Marota, J. J., Kosofsky, B. E., Keltner, J. R., Weissleder, R., Rosen, B. R.,
et al. (1998). Dynamic functional imaging of relative cerebral blood volume during Rat
forepaw stimulation. Magnetic Resonance in Medicine, 39, 615624.
Mansfield, P., Harvey, P. R., & Stehling, M. K. (1994). Echo-volumar imaging. Magma,
2, 291294.
Menon, R. S. (2002). Postacquisition suppression of large-vessel BOLD signals in
high-resolution fMRI. Magnetic Resonance in Medicine, 47, 19.
Menon, R., Ogawa, S., Strupp, J. P., & Ugurbil, K. (1997). Ocular dominance in human
V1 demonstrated by functional magnetic resonance imaging. Journal of
Menon, R. S., Ogawa, S., Tank, D. W., & Ugurbil, K. (1993). 4 Tesla gradient recalled
echo characteristics of photic stimulation-induced signal changes in the human
primary visual cortex. Magnetic Resonance in Medicine, 30, 380386.
Miller, K. L., & Jezzard, P. (2008). Modeling SSFP functional MRI contrast in the brain.
Multiband multislice GE-EPI at 7 Tesla, with 16-fold acceleration using partial
Moon, C. H., Fukuda, M., Park, S. H., & Kim, S. G. (2007). Neural interpretation of
blood oxygenation level-dependent fMRI maps at submillimeter columnar
resolution. Journal of Neuroscience, 27, 68926902.
Mountcastle, V. B. (1957). Modality and topographic properties of single neurons of
cats somatic sensory cortex. Journal of Neurophysiology, 20, 408434.
Norris, D. G., Koopmans, P. J., Boyacioglu, R., & Barth, M. (2011). Power independent
of number of slices (PINS) radiofrequency pulses for low-power simultaneous
multislice excitation. Magnetic Resonance in Medicine, 66, 12341240.
Ogawa, S., Lee, T.-M., Kay, A. R., & Tank, D. W. (1990). Brain magnetic resonance
Oja, J. M. E., Gillen, J., Kauppinen, R. A., Kraut, M., & Van Zijl, P. C. M. (1999). Venous
blood effects in spin-echo fMRI of human brain. Magnetic Resonance in Medicine,
42, 617626.
Olman, C. A., Harel, N., Feinberg, D. A., He, S., Zhang, P., Ugurbil, K., et al. (2012).
Layer-specific fMRI reflects different neuronal computations at different depths in
human V1. PLoS One, 7, E32536.
Olman, C. A., & Yacoub, E. (2011). High-field fMRI for human applications: An
overview of spatial resolution and signal specificity. The Open Neuroimaging
Journal, 5, 7489.
Oshio, K., & Feinberg, D. A. (1991). GRASE (gradient- and spin-echo) imaging: A novel
fast MRI technique. Magnetic Resonance in Medicine, 20, 344349.
Pfeuffer, J., Van De Moortele, P. F., Yacoub, E., Adriany, G., Andersen, P., Merkle, H.,
et al. (2002). Zoomed functional imaging in the human brain at 7 Tesla with
simultaneously high spatial and temporal resolution. NeuroImage, 17, 272286.
Polimeni, J. R., Fischl, B., Greve, D. N., & Wald, L. L. (2010). Laminar analysis of 7 T
13341346.
Poser, B. A., Koopmans, P. J., Witzel, T., Wald, L. L., & Barth, M. (2010). Three
dimensional echo-planar imaging at 7 Tesla. NeuroImage, 51, 261266.
Poser, B. A., & Norris, D. G. (2007). Fast spin echo sequences for BOLD functional MRI.
Magma, 20, 1117.
Segebarth, C., Belle, V., Delon, C., Massarelli, R., Decety, J., Le Bas, J.-F., et al. (1994).
Functional MRI of the human brain: Predominance of signals from extracerebral
veins. Neuroreport, 5, 813816.
echo planar imaging with reduced G-factor penalty. Magnetic Resonance in
Medicine, 67, 12101224.
Shmuel, A., & Grinvald, A. (1996). Functional organization for direction of motion and
its relationship to orientation maps in cat area 18. Journal of Neuroscience: The
Official Journal of the Society for Neuroscience, 16, 69456964.
Shmuel, A., Raddatz, G., Chaimow, D., Logothetis, N., Ugurbil, K., & Yacoub, E. (2007).
Origin of decoding signals in the visual cortex: Gray matter or macroscopic blood
vessels?. Chicago: Human Brain Mapping.
Shmuel, A., Yacoub, E., Chaimow, D., Logothetis, N. K., & Ugurbil, K. (2007). Spatiotemporal point-spread function of fMRI signal in human gray matter at 7 Tesla.
Shoham, D., Hubener, M., Schulze, S., Grinvald, A., & Bonhoeffer, T. (1997). Spatiotemporal frequency domains and their relation to cytochrome oxidase staining in cat
visual cortex. Nature, 385, 529533.
Smith, S. M., Miller, K. L., Moeller, S., Xu, J., Auerbach, E. J., Woolrich, M. W., et al.
(2012). Temporally-independent functional modes of spontaneous brain activity.
109, 31313136.
1.5 T. Magnetic Resonance in Medicine, 35, 155158.
Triantafyllou, C., Hoge, R. D., Krueger, G., Wiggins, C. J., Potthast, A., Wiggins, G. C.,
et al. (2005). Comparison of physiological noise at 1.5 T, 3 T and 7 T and
optimization of fMRI acquisition parameters. NeuroImage, 26, 243250.
Vu, A., Feinberg, D., Harel, N., Ugurbil, K., & Yacoub, E. (2013). Diagonal multi-slab
inner volume 3D GRASE imaging for high resolution T2 weighted fMRI. In: ISMRM
21st annual meeting, Salt Lake City, 2364.
199
Weliky, M., Bosking, W. H., & Fitzpatrick, D. (1996). A systematic map of direction
preference in primary visual cortex. Nature, 379, 725728.
Wu, X., Schmitter, S., Auerbach, E. J., Moeller, S., Ugurbil, K., & Van De Moortele, P. F.
(2013). Simultaneous multislice multiband parallel radiofrequency excitation with
independent slice-specific transmit B1 homogenization. Magnetic Resonance in
Medicine, 70, 630638. http://dx.doi.org/10.1002/mrm.24828.
Wu, X., Ugurbil, K., & Van De Moortele, P. F. (2013). Peak RF power constrained pulse
design for multi-band parallel excitation. In: ISMRM 21st meeting, Salt Lake City,
4253.
Yacoub, E., Duong, T. Q., Van De Moortele, P. F., Lindquist, M., Adriany, G., Kim, S. G.,
et al. (2003). Spin-echo fMRI in humans using high spatial resolutions and high
magnetic fields. Magnetic Resonance in Medicine, 49, 655664.
America, 105, 1060710612.
Yacoub, E., Shmuel, A., Logothetis, N., & Ugurbil, K. (2007). Robust detection of ocular
dominance columns in humans using Hahn Spin Echo BOLD functional MRI at
7 Tesla. NeuroImage, 37, 11611177.
Yacoub, E., Shmuel, A., Pfeuffer, J., Van De Moortele, P. F., Adriany, G., Andersen, P.,
et al. (2001). Imaging brain function in humans at 7 Tesla. Magnetic Resonance in
Medicine, 45, 588594.
Yacoub, E., Ugurbil, K., & Olman, C. (2009). Feasibility of detecting differential layer
specific activations in humans using SE BOLD fMRI at 7 T. In: Proceedings of the
magnetic resonance in medicine, Honolulu.
Yacoub, E., Van De Moortele, P. F., Shmuel, A., & Ugurbil, K. (2005). Signal and noise
738750.
Yang, Y., Glover, G. H., Van Gelderen, P., Patel, A. C., Mattay, V. S., Frank, J. A., et al.
(1998). A comparison of fast MR scan techniques for cerebral activation studies at
1.5 Tesla. Magnetic Resonance in Medicine, 39, 6167.
Ye, Y., Zhuo, Y., Xue, R., & Zhou, X. J. (2010). BOLD fMRI using a modified HASTE
sequence. NeuroImage, 49, 457466.
Zhao, F., Wang, P., Hendrich, K., & Kim, S. G. (2005). Spatial specificity of cerebral
blood volume-weighted fMRI responses at columnar resolution. NeuroImage, 27,
416424.
Zhao, F., Wang, P., Hendrich, K., Ugurbil, K., & Kim, S. G. (2006). Cortical
layer-dependent BOLD and CBV responses measured by spin-echo and
gradient-echo fMRI: Insights into hemodynamic regulation. NeuroImage, 30,
11491160.
Zhao, F., Wang, P., & Kim, S. G. (2004). Cortical depth-dependent
gradient-echo and spin-echo BOLD fMRI at 9.4 T. Magnetic Resonance in
Medicine, 51, 518524.
Zimmermann, J., Goebel, R., De Martino, F., Van De Moortele, P. F., Feinberg, D.,
Adriany, G., et al. (2011). Mapping the organization of axis of motion
selective features in human area MT using high-field fMRI. PLoS One, 6,
E28716.
INTRODUCTION TO METHODS AND MODELING
The complexity and diversity of neuroimaging methods used today have made this one of the most promising
fields for innovation and discovery in all of science, with a host of algorithms and techniques that have had
truly global impact. Novel methods to collect, analyze, and model brain images have revolutionized the fields
of neurology and psychiatry. They continue to open up vast new frontiers for understanding of the brain how
it is organized structurally and functionally, how it develops, and how brain measures relate to cognition,
behavior, and even genetics.
For the last two decades, there has also been a revolution in how brain images are analyzed a deeper
understanding of the statistics of brain signals and images led to powerful new methods for detecting significant
changes in the brain, or features that emerge or change during cognitive tasks, or with a disease process.
To a large degree, these developments were accelerated by novel mathematics for representing and modeling
signals, detecting patterns, and understanding causal effects in time series of signals in the brain. Whole
branches of mathematics have been adapted and extended for studying brain data from the topology of
random fields to dynamic causal models, and a rapidly developing theory of graphs, networks, and topological
measures to study connectomes, patterns of connections inferred from functional synchrony or anatomical
circuitry. Even the mathematics of continuum mechanics fluid flow, differential geometry, and relativity has
been used to model anatomical surfaces in the brain, flatten them, match them, and register them, leading to
sophisticated methods now widely used to align and compare observations from people whose anatomy is
different.
This vast and rich field is surveyed here by experts in its many domains.
The analysis of anatomical MRI was accelerated by the field of computational anatomy, concerned with
modeling aspects of brain structure as statistical fields of static or dynamic signals. One such approach
surface-based modeling employs parametric mesh surfaces that can be graphically visualized, merged, and
combined. Several articles in this section deal with the basic processing and analysis of brain structural data,
from voxel-based and manual morphometry to the broad field of image registration, which enables the
alignment of brain data from different individuals, populations, and imaging methods.
Some of the foremost experts in surface-based analysis of brain data describe how anatomy can be modeled
using 3D meshes, giving rise to the processing of measures on surfaces as complex and variable as the human
cortex. Special attention is given to the modeling brain changes over time, using methods that detect and model
characteristic patterns of development and disease. Clearly, these methods have broad applications in clinical
neuroscience and the understanding of progressive degenerative diseases such as the dementias.
A further broad set of articles survey diffusion-based MRI methods used to collect and analyze the structural
connectivity of the brain, and assess white matter microstructure.
A major shift in the field of brain mapping, which has recently gathered momentum, is to model the
interactions and connectivity among brain regions. This effort has been eased by developments in computational fiber tracking (tractography), network theory, and new methods to model and test hypotheses about the
statistics of fiber pathways in the brain.
The handling of functional images of the brain has evolved rapidly and extensively for over two decades. A
set of articles cover experimental design in fMRI, and the modeling of the hemodynamic response, as well as
causal relationships in time series of functional data. Special considerations arise when modeling data from
MEG and EEG, and several articles cover the development of sophisticated methods for inverse problems and
signal reconstruction, including Bayesian approaches and efforts to fuse information across several complementary modalities. There are several articles covering the modeling and testing of complex hypotheses
regarding functional and effective connectivity, as well as practical considerations in measuring it and interpreting it.
201
202
Introduction to Methods and Modeling
Finally, a number of articles cover the informatics and databasing of brain data. Neuroinformatics is
evolving to encompass numerous national and global efforts for meta-analysis of results, detection of genetic
and disease-related influences on brain measures, and has led to unprecedented collaborative efforts in
population-based imaging.
Paul Thompson
Karl Friston
Computerized Tomography Reconstruction Methods

GT Herman, City University of New York, New York, NY, USA
Data Collection and Preprocessing

Even though modern computerized tomography (CT) devices
typically reconstruct a whole three-dimensional (3-D) distribution, for ease of understanding the principles underlying
reconstruction methods, we restrict our attention in this
article to the problem of reconstructing a 2-D object f (r, f)
from its 1-D projections.
x-Ray CT
A possible schematic for CT is shown in Figure 1. The data
collection takes place in M steps. A source and a detector strip
are rotated between two steps of the data collection by a small
angle but are assumed to be stationary while the measurement
is taken. The detector strip consists of 2N 1 detectors, spaced
equally on an arc whose center is the source position. The line
from the source to the center of rotation O goes through the
center of the central detector. As indicated in that figure, any
real-number pair (, y) defines a line and we use [Rf] (, y) to
denote the line integral of f along that line.
A CT scanner does not measure directly such line integrals.
Rather, the detector counts the number of photons that arrive
at it having gone through the head. Such a count by itself is not
sufficient to estimate the integral of f between the source and
the detector; we also need a calibration measurement that
provides an estimate of the number of photons that left the
source. Then, the logarithm of the ratio of the count during
calibration and during the actual measurement with the
patient in the scanner provides an estimate of the line integral
of the x-ray attenuation coefficient, distribution of which is the
f that we wish to reconstruct.
This simple description hides many problems that exist
with the actual data collection. One example is scatter that
arises due to the fact that on the way from the source to the
detector strip, a photon may scatter and get counted by a
detector that is not the one toward which it was heading
originally. Another, example is beam hardening, which is due
to the fact that the x-ray photons generated by the source in a
CT scanner have a range of possible energies and the same
tissue has different x-ray attenuation coefficients for photons
at different energies. Typically, we decide that our f is supposed
to represent the distribution of x-ray attenuation at a particular
energy, but the measurements are unavoidably made using
photons with a whole range of energies and that introduces
an error into our estimate of the line integrals of f. Such
problems necessitate that the raw data collected by the CT
scanner be preprocessed, the result of which is assumed to be
a sufficiently accurate estimate of the line integrals of f.
Emission CT (Positron Emission Tomography and

Single-Photon Emission Computerized Tomography)
Emission CT has as its major emphasis the quantitative determination of the moment-to-moment changes in the chemistry and
flow physiology of injected or inhaled compounds labeled with
radioactive atoms. In this case, the distribution to be reconstructed is the distribution of radioactivity in the body cross
section, and the measurements are used to estimate the total
activity along lines of known locations. Figure 2 illustrates a
device, a so-called positron emission tomography (PET) scanner,
for doing this and shows a clinical brain image produced by
this device. As explained in the caption of that figure, the device
allows us to image how the compound (in this case FDG)
distributes itself in the brain: if the compound uptake is increased
in lesions, then the images can be used for locating such lesions.
Reconstruction Algorithms
Basic Concepts of Reconstruction Algorithms
The input to a reconstruction algorithm is estimates, obtained
by a CT scanner (for details, see Herman, 2009), of the values
of [Rf](, y) for the pairs (1, y1),. . ., (I, yI). Let
Ri f Rf li , yi
[1]
Let yi denote the estimate of Rif and y the I-dimensional

vector whose ith component is yi. The reconstruction problem
is as follows: given the data y, estimate f.
In the mathematically idealized reconstruction problem,
we seek an expression for the operator R1 (the inverse of R).
A major class of algorithms, called transform methods, estimate f
based on such expressions for R1. A popular example is the
filtered backprojection (FBP) algorithm (see Chapters 8 and 10 of
Herman, 2009).
In this article, we concentrate on the other major category
of reconstruction algorithms: the series expansion methods. In a
transform method, the continuous operators in the expression
for R1 are implemented as discrete ones, operating on functions whose values are known only for finitely many values of
their arguments. The series expansion approach is basically
different. The problem itself is discretized at the beginning:
estimating f is translated into finding a finite set of numbers.
Series Expansion Methods

Based on a region that is assumed to contain the support of f,
we fix a set of J basis functions {b1,. . ., bJ}. These are chosen so
that, for any f whose support is contained in the assumed
region that we may wish to reconstruct, there exists a linear
http://dx.doi.org/10.1016/B978-0-12-397025-1.00286-4
203
204
INTRODUCTION TO METHODS AND MODELING | Computerized Tomography Reconstruction Methods
Source position
S0
S1
SM1
Angular scan
SM2
Sm
N
nl
m
l
O
Object to be
reconstructed
q
B
1
0 Reading
1
Detector
strip
N
Figure 1 A standard method of CT data collection. Reproduced from Herman, G. T. (2009). Fundamentals of computerized tomography: Image
reconstruction from projections (2nd ed.). New York: Springer.
combination of the basis functions that is an adequate approximation of f.

An example of such an approach is the n n digitization in
which we cover the region by an n n array of identical small
squares, called pixels. Here, J n2 and

1, if r, f is inside the jth pixel
bj r, f
[2]
0, otherwise
Then, the n n digitization of the picture f is the picture f^
defined by
f^r, f
J
X
xj bj r, f
[3]
j1
where xj isX
the average value of f inside the jth pixel. In shortJ
hand, f^
xb.
j1 j j
Another (and usually preferable) way of choosing the basis
functions is the following. Generalized KaiserBessel window
functions, which are also known by the simpler name blobs,
form a large family of functions that can be defined in a
Euclidean space of any dimension. Here, we restrict ourselves
to 2-D and define
ba, a, d r, f
8
<
:
q

2
2
I2 a 1 ar
Ca, a, d 1 ar
, if 0 r a
0,
otherwise
[4]
where Ik denotes the modified Bessel function of the first kind of

order k, a stands for the nonnegative radius of the blob, and a is
a nonnegative real number that controls the shape of the blob.
The multiplying constant Ca,a,d is defined in (6.52) of Herman
(2009). A blob is circularly symmetrical. It has the value zero for
all r a and its first derivatives are continuous everywhere. The
smoothness of blobs can be controlled by the choice of the

parameters a, a, and d; they can be made very smooth.
Any fixed function ba,a,d gives rise to basis functions {b1,. . .,
bJ} by selecting a set G {g1,. . .,gJ} of grid points and defining bj
as ba,a,d with its center shifted from the origin to gj. In practice,
it is advisable that G be chosen as the hexagonal grid with
sampling distance d, as defined in (6.51) of Herman (2009).
For blobs to achieve their full potential, the selection of the
parameters a, a, and d is important; see Herman (2009).
Irrespective how the basis functions have been chosen, any
picture f^that can be represented as a linear combination of the
basis function bj is uniquely determined by the choice of the
coefficients xj, 1 j J, in the formula [3]. We use x to denote
the vector whose jth component is xj and refer to x as the image
vector.
It is easy to see that, under some mild mathematical
assumptions,
Ri f Ri f^
J
X
xj Ri bj
[5]
j1
for 1 i I, Since bj are user-defined, usually Ribj can be easily

calculated by analytic means. For example, in the case when bj
are defined by eqn [2], Ribj is just the length of intersection
with the jth pixel of the line of the ith position of the sourcedetector pair. We use ri,j to denote our calculated value of Ribj.
Since yi is an estimate of Ri f, we get that, for 1 i I,
yi
J
X
ri , j x j
[6]
j1
Let R denote the matrix whose (i, j)th element is ri,j. We refer
to this matrix as the projection matrix. Let e be the I-dimensional
205
error vector e to be samples of random variables. For example

(for details, see Section 6.4 of Herman, 2009), if we assume that
the vector mX is such that every component of both x and mX and
every component of e are independent samples from zero-mean
Gaussian random variables with standard deviations s and n,
respectively, then the Bayesian estimate is the vector x that minimizes (with t s/n, the signal-to-noise ratio)
t 2 ky Rxk2 kx mX k2
[8]
Algebraic Reconstruction Techniques
Figure 2 Top: A Philips Allegro PET scanner that has 17 864

scintillation crystals to collect its data. Bottom: Brain scan produced by
this scanner of an epilepsy patient who has been injected with
fluorodeoxyglucose (FDG) tagged with a radioactive isotope whose decay
generates positrons that annihilate and produce pairs of gamma rays
to be detected by the crystals to identify a line that contains the location
of the annihilation. From the total activity along a large number of
such lines, the distribution of the annihilation frequency, and hence of the
FDG, can be reconstructed. See the increased FDG uptake (dark) at
about two oclock, indicating the seizure focus site. Images were
provided by J. Karp of the University of Pennsylvania.
In this section, we discuss in detail one typical category of series

expansion methods, namely, the algebraic reconstruction techniques (ART). All ART are iterative procedures: they produce a
sequence of vectors x(0), x(1),. . . that is supposed to converge to
x*. The process of producing x(k1) from x(k) is referred to as an
iterative step.
In ART, x(k1) is obtained from x(k) by considering a single
one of the I approximate equations; see eqn [6]. In fact, the
equations are used in a cyclic order. We use ik to denote k(mod
I) 1; that is, i0 1, i1 2,. . ., iI 1 I, iI 1, iI 1 2,. . ., and we
use ri to denote the J-dimensional column vector whose jth
component is ri,j. An important point here is that this specification is incomplete because it depends on how we index the
lines for which the integrals are estimated. Since the order in
which we do things in ART depends on the indexing i for the
set of lines for which data are collected, the specification of ART
as a reconstruction algorithm is complete only if it includes the
indexing method for the lines, which we refer to as the data
access ordering. We return to this point in the succeeding text.
A particularly simple variant of ART is the following:
x0 is arbitrary
xk1 xk ck rik
[9]
where, using a sequence of real-valued relaxation parameters

l(k),

bi ri xk
[10]
ck lk k k 2
ri
k
It is easy to check that, for k 0, if l(k) 1, then

column vector whose ith component, ei, is the difference
between the left- and right-hand sides of eqn [6]. We refer to
this as the error vector. Then, eqn [6] can be rewritten as
y Rx e
[7]
The series expansion approach leads us to the discrete reconstruction problem: based on eqn [7], given the data y, estimate the
image vector x. If the solution to this problem is x*, then the
P
estimate f* of f is given by f* Jj1xj*bj.
In eqn [7], the vector e is unknown. The simple approach of
trying to solve eqn [7] by assuming that e is the zero vector is
dangerous: y Rx may have no solutions, or it may have many
solutions with none of them any good for the practical problem at hand. Some criteria have to be developed, indicating
which x ought to be chosen as a solution of eqn [7]. One way of
doing this is by considering both the image vector x and the
yik
J
X
k1
rik , j xj
[11]
j1
This method has an interesting mathematical property. Let

L {x|Rx y}. A sequence x(0), x(1), x(2),. . . generated by eqns
[9] and [10] converges to a vector x* in L, provided that L is not
empty and that, for some e1 and e2 and for all k,
0 < e1 lk e2 < 2
0
[12]
Furthermore, if x is chosen to be the vector with zero

components, then ||x*|| < ||x||, for all x in L other than x*.
A proof of this can be found in Section 11.2 of Herman (2009).
This result is not useful by itself because the condition
that L is not empty is unlikely to be satisfied in a real tomographic situation. However, as it is shown in Section 11.3
of Herman (2009), it can be used to derive the following
206
ART algorithm that converges to the minimizer of eqn [8],

provided only that eqn [12] holds:
u0 is the I-dimensional zero vector
x0 mX
uk1 uk ck eik
xk1 xk tck rik
[13]
where
ck lk

k
t yik rik , xk uik
2
1 t 2 ri
[14]
Note that both in eqns [9] and [13], the updating of x(k) is
very simple: we just add to x(k) a multiple of the vector rik . This
updating of x(k) can be computationally very inexpensive. Consider, for example, the basis functions associated with a digitization into pixels [2]. Then, ri,j is just the length of intersection
of the ith line with the jth pixel. This has two consequences.
First, most of the components of the vector rik are zero. Second,
the location and size of the nonzero components of rik can be
rapidly calculated from the geometric location of the ikth line
relative to the n n grid using a digital difference analyzer methodology (see Section 4.6 of Herman, 2009).
the evaluation results were done within the software package

SNARK09 (Klukowska, Davidi, & Herman, 2013).
We studied actual cross sections of human heads (Figs. 4.2
and 4.5(a) in Herman, 2009). Based on them, we created a
head phantom and used SNARK09 to obtain the density in
each of 243 243. The resulting array of numbers is represented in Figure 3(a).
A reconstruction is a digitized picture. If it is a reconstruction from simulated projection data of a test phantom, we can
judge its quality by comparing it with the digitization of the
phantom. Visual evaluation is the most straightforward way.
One may display both the phantom and the reconstruction
and observe whether all features in which one is interested in
the phantom are reproduced in the reconstruction and
whether any spurious features have been introduced by the
reconstruction process. A difficulty with such a qualitative
evaluation is its subjectivity; people often disagree on which
of the two pictures resembles a third one more closely.
It appears desirable to use a picture distance measure that
indicates the closeness of the reconstruction to the phantom.
In the following example of such a measure (r), tu,v and ru,v
denote the densities of the vth pixel of the uth row of the
digitized test phantom and the reconstruction, respectively,
and t denotes the average of the densities in the digitized test
phantom. We assume that both pictures are n n.
Comparison of Reconstruction Methods

We are now going to illustrate and compare various reconstruction algorithms. The generation of images and their projection
data, the reconstructions from such data, the evaluation of the
results, and the graphical presentation of both the images and
n X
n
X
u1 v1
jtu, v ru, v j=
n X
n
X
jtu, v j
[15]
u1 v1
Such a global measure cannot possibly reflect all the ways in

which two pictures may differ from each other. Rank ordering
Figure 3 A head phantom (a) and its reconstructions from the same projection data using ART with blobs, l(k) 0.05, 5Ith iteration and efficient
ordering (b), ART with blobs, l(k) 0.05, 5Ith iteration and sequential ordering (c), ART with pixels, l(k) 0.05, 5Ith iteration and efficient ordering
(d), ART with blobs, l(k) 1.0 2Ith iteration and efficient ordering (e), and FBP (f). Reproduced from Herman, G. T. (2009). Fundamentals of
computerized tomography: Image reconstruction from projections (2nd ed.). New York: Springer.

reconstructions based on such measures of closeness to the
phantom can be misleading. We recommend instead a statistical hypothesis testing-based methodology that allows us to evaluate the relative efficacy of reconstruction methods for a given
task. In Section 5.2 of Herman (2009), there is a detailed
discussion of the use of this methodology for the task of
detecting small low-contrast tumors in the brain. In the succeeding text, we report on the performance of algorithms for
the same task. We do not repeat the details here, but note that
the methodology consists of (a) generation of random samples
from an ensemble of representative phantoms and simulation
of the data collection by a CT scanner; (b) reconstruction from
the data by the algorithms; (c) assignment of a figure of merit
(FOM) to each reconstruction (in our case, we used the imagewise region of interest (IROI) FOM that measures the usefulness
of the reconstruction for tumor detection); and (d) calculation
of a P-value, which is the probability of observing a difference
in the average values of the IROI not smaller than what we have
actually observed if the null hypothesis that the reconstructions are equally helpful tumor detection were true (the smallness of the P-value indicates the significance by which we can
reject the null hypothesis).
For all our experiments, the data collection geometry is the
one described in Figure 1 with M 720 and 2N 1 345 and
we used realistically simulated CT projection data. The exact
method of data collection is described in Section 5.8 of
Herman (2009).
We report only on the variant of ART described by eqns [9]
and [10]. (The performance of the ART algorithm specified in
eqns [13] and [14] is illustrated in Section 12.5 of Herman,
2009). In all cases, we choose x(0) to represent a uniform
picture, with an estimated average value of the phantom
assigned to every pixel (see Section 6.3 of Herman, 2009).
We first show that the data access ordering can have a significant effect on the practical performance of the algorithm. With
data collection such as depicted in Figure 1, it is tempting to use
the sequential ordering: access the data in the order g(Nl, 0), g
((N 1) l, 0),. . ., g(Nl, 0), g(Nl, D), g((N 1)l, D),. . .,
g(Nl, D),. . .,. . .,g(Nl, (M 1)D), g((N 1)l, (M 1)D),. . .,g
(Nl, (M 1)D), where g(nl, mD) denotes the approximation of
the line integral from the m the source position to the nth
detector. However, this sequential ordering is inferior to what
is referred to as the efficient ordering in which the order of
projection directions mD and, for each view, the order of lines
within the view are chosen so as to minimize the number of
commonly intersected pixels by a line and the lines selected
recently. This can be made precise by considering the decomposition into a product of prime numbers of M and of 2N 1
(Herman & Meyer, 1993). The efficient data access ordering
translates into faster initial convergence of ART (illustrated in
Fig. 11.2 of Herman (2009) by plotting r of eqn [15] against the
number of times the algorithm cycled through the data). The
reconstructions produced by the efficient and sequential orderings after five cycles through the data (i.e., x(5I)) are in Figure 3
(b) and 3(c), respectively. Visually, there is little difference
between them. This is confirmed by the values of the distance
measure r in Table 1, which is only slightly smaller for the
efficient ordering than for the sequential one. However, the statistical evaluation is unambiguous: The IROI is larger for the
efficient ordering and the associated P-value was found to be
207
Table 1
Picture distance measures r and average IROIs for the
various algorithms used in Figure 3
Reconstruction in
IROI
Figure 3(b)
Figure 3(c)
Figure 3(d)
Figure 3(e)
Figure 3(f)
0.0373
0.0391
0.0470
0.0488
0.0423
0.1794
0.1624
0.1592
0.1076
0.1677
Reproduced from Table 11.1 of Herman, G. T. (2009). Fundamentals of computerized

tomography: Image reconstruction from projections (2nd ed.). New York: Springer.
<109. Thus, the null hypothesis that the two data access orderings are equally good can be rejected in favor of the alternative
that the efficient ordering is better with extreme confidence.
Next, we emphasize the importance of the basis functions.
In Figure 4, we plot the picture distance measure r against the
number of times ART cycled through all the data. The two cases
that we compare are when the basis functions are based on
pixels [2] and when they are based on blobs [4]. The results are
quite impressive: as measured by r, blob basis functions are
much better. The result of the 5Ith iteration of the blob reconstruction is shown in Figure 3(b), while that of the 5Ith iteration of the pixel reconstruction is shown in Figure 3(d). The
blob reconstructions are clearly superior. By looking at Table 1,
we see a great improvement in the picture distance measure r.
From the point of view of IROI, ART with blobs is found
superior to ART with pixels with the P-value < 1010.
Underrelaxation is also a must when ART is applied to real
data. In the experiments reported so far, l(k) was set equal to
0.05 for all k. If we do not use underrelaxation (i.e., we set l(k)
to 1 for all k), we get from the standard projection data the
unacceptable reconstruction shown in Figure 3(e). Note that
in this case, we used the 2Ith iterate, further iterations gave
worse results. The reason for this is in the nature of ART: After
one iterative step with l(k) 1, the associated measurement is
satisfied exactly as shown in eqn [11], and so, the process
jumps around satisfying the noise in the measurements.
Underrelaxation reduces the influence of the noise. Note in
Table 1 that the figure of merit IROI produced by the taskoriented study for the case without underrelaxation is much
smaller than for the other cases.
Finally, we compare the best of our ART reconstruction
(Figure 3(b)) with one produced by a similarly carefully
selected variant of FBP (Figure 3(f)); for details of the FBP
choices, see Chapter 10 of Herman (2009). Visually, they are
very similar. According to r in Table 1, ART is superior to FBP,
and the same is true according to IROI with extreme significance (the P-value is <1013). This confirms the reports in the
literature that ART with blobs, underrelaxation, and efficient
ordering generally outperforms FBP in numerical evaluations
of the quality of the reconstructions.
Acknowledgments
Much of this article is based on various parts of the book Gabor
T. Herman: Fundamentals of Computerized Tomography: Image
Reconstruction from Projections, 2nd ed., Springer, 2009.
208
ART 0.05 pixel
ART 0.05 blob
ART with blobs :: Relative error

0.105
0.1
0.095
0.09
Relative error
0.085
0.08
0.075
0.07
0.065
0.06
0.055
0.05
0.045
0.04
0.035
0
10
12
Iteration
14
16
18
20
Figure 4 Values r for ART reconstructions with pixels (light) and blobs (dark), plotted at multiples of I iterations. Reproduced from Herman, G. T.
(2009). Fundamentals of computerized tomography: Image reconstruction from projections (2nd ed.). New York: Springer.
In particular, all the figures are based on figures that appeared

in that book and the same is true for the table. The reuse of
material from the book in this article is with kind permission
from Springer Science Business Media B.V.
The current research of the author is supported by the National
Science Foundation Award No. DMS-1114901.

Positron Emission Tomography and Neuroreceptor Mapping In Vivo;
INTRODUCTION TO METHODS AND MODELING: Bayesian
Multiple Atlas Deformable Templates; Bayesian Model Inversion;
Bayesian Model Inference; Lesion Segmentation; Modeling Brain
Growth and Development; Optical Image Reconstruction; Tissue
Classification; Voxel-Based Morphometry.
References
Herman, G. T. (2009). Fundamentals of computerized tomography: Image
reconstruction from projections (2nd ed.). New York: Springer.
Herman, G., & Meyer, L. (1993). Algebraic reconstruction techniques can be
made computationally efficient. IEEE Transactions on Medical Imaging, 12,
600609.
Klukowska, J., Davidi, R., & Herman, G. T. (2013). SNARK09 A software package for
the reconstruction of 2D images from ID projections. Computer Methods and
Programs in Biomedicine, 110, 424440.
Relevant Website
http://www.dig.cs.gc.cuny.edu/software/snark09 SNARK09: A Programming System
for the Reconstruction of 2D Images from ID Projections.
Pharmacokinetic Modeling of Dynamic PET

Q Guo, Imanova Ltd, London, UK; AbbVie Translational Sciences, North Chicago, IL, USA; Kings College London, London, UK;
Imperial College London, London, UK
RN Gunn, Imanova Ltd, London, UK; Imperial College London, London, UK; University of Oxford, Oxford, UK
Glossary
BPND Binding potential.

HPLC High-performance liquid chromatography.
IRF Impulse response function
KI Irreversible uptake rate constant.
MA Multilinear analysis.
Introduction
Tomographic detection of radiolabeled molecules in tissues of
interest with positron emission tomography (PET) facilitates the
study of normo-/pathophysiology and therapeutic interventions. Such radiolabeled molecules can be drug candidates or
probes that may bind to and produce readouts from the target
biology of interest. In either case, quantitative information on
specific biological parameters of interest can be derived by applying biomathematical models to the kinetic data that have been
measured with PET. For drugs, this allows estimation of parameters such as the free brain concentration (Gunn et al., 2012) and
target engagement at differing dosing levels (Abanades et al.,
2011; Cunningham, Rabiner, Slifstein, Laruelle, & Gunn, 2009;
Salinas et al., 2013). For specific imaging probes, this allows
measurement of a range of G protein-coupled receptors, transporters, enzymes, or basic physiology such as blood flow
and metabolism (cf. Kety, 1951; Mintun, Raichle, Kilbourn,
Wooten, & Welch, 1984; Sokoloff et al., 1977). In this article,
we will focus on PET pharmacokinetic modeling for receptor
systems, but the modeling and mathematics presented generalize to other target biology.
The purpose of introducing modeling to dynamic PET quantification is to accurately characterize the biological properties of
the system and estimate the intrinsic parameter values free from
confounds. For example, when the total uptake in tissue is taken
as the outcome measure, even if the same dose of radiotracer is
injected to each subject, the uptake value measured at certain time
points after the injection may still differ between subjects. This
could be simply due to the difference in subjects weights rather
than any variation in the target biology. Even when the uptake is
normalized to a standard uptake value (SUV, e.g., by dividing the
uptake by injected dose and multiplying by weight or body
surface area), this still does not account for the differences in
metabolism of radiotracers due to peripheral effects or blood
flow in the target tissue. In order to address these issues properly
in a quantitative manner, it is necessary to measure both the input
and the output data for the system and apply appropriate pharmacokinetic modeling techniques to the dynamic data so that the
biological parameters of interest can be determined independent
of confounds in the peripheral and target tissues.
This article first introduces the PET preprocessing step that
enables derivation of the system input and output data before
MRTM Multilinear reference tissue model.

PET Positron emission tomography.
ROI Region of interest.
SRTM Simplified reference tissue model.
SUV Standard uptake value.
VT Volume of distribution.
describing the general pharmacokinetic models with plasma

and reference tissue input. Then, parameter estimation
methods are presented followed by a discussion on studylevel analyses within or across populations. In the article, we
focus on systems where the radiolabeled compound was
injected at a tracer amount (i.e., its mass is very low so that it
does not perturb the biological system under study) and present examples in the context of radioligandreceptor binding.
Data Preprocessing
PET pharmacokinetic modeling is applied to concentration time
profiles in tissues of interest, and these data must first be accurately extracted from the measured emission data themselves.
First, the raw emission data are reconstructed using either analytic
or iterative tomographic reconstruction techniques with the
appropriate corrections for detector normalization, attenuation,
scatter, and detector dead time. Having reconstructed the
dynamic images, it is necessary to correct for any interframe
motion present in the time series this can be achieved using
image registration techniques that typically examine a spatial
similarity metric between image volumes prior to applying a
6-parameter rigid body transformation to correct for motion,
which can be implemented with SPM (Wellcome Trust Center
for Neuroimaging, http://www.fil.ion.ucl.ac.uk/spm) or FSL
(FMRIB Center, http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/).
The concentration time profiles in tissues of interest can
then be derived from individual voxel data to enable parametric image generation from anatomically (or functionally;
Tziortzi et al., 2013) defined regions of interest (ROIs) to
enable regional parameter estimation. While ROIs can be
delineated manually, this is time-consuming, and automated
methods based on the nonlinear deformation of stereotaxic
atlases in conjunction with adjunct structural MRI data are
usually preferred (Hammers et al., 2003; Tziortzi et al., 2011).
PET pharmacokinetic modeling methods also require an input
function that contains information on the concentration of radiotracer that is delivered to the target tissue of interest. This enables
tracer kinetic models to estimate biological parameters specific to
the target tissue of interest rather than being confounded by
peripheral effects. For example, this means that differences in
injected activity, body weight, physiology/metabolism, or other
http://dx.doi.org/10.1016/B978-0-12-397025-1.00287-6
209
210
INTRODUCTION TO METHODS AND MODELING | Pharmacokinetic Modeling of Dynamic PET
Reference
tissue
Specific
binding
Non-specific
binding
Free
radioligand
Blood
Target
tissue
Figure 1 Schematic drawing for delivery of a radiolabeled ligand to a tissue from the vasculature and subsequent binding to specific and nonspecific
sites in brain tissue. PET provides concentration time courses in tissue, and associated arterial cannulation and sampling provides a concentration
time course in blood. Adapted from an original drawing by Terry Jones.
peripheral effects do not impact on the biological parameters

estimated from the tomographic tissue data. Input data can be
the measured arterial plasma concentration that is derived via
arterial cannulation and concomitant blood sampling during
the scan. Alternatively, it may be derived from the image itself
either from a region of interest over a blood pool or via a reference
tissue that is devoid of the specific target of interest (see Figure 1).
The PET pharmacokinetic modeling process can then be
applied to the system input (plasma or reference tissue concentration time course) and output data (tissue concentration
time course) to derive parameter estimates of interest. This
involves the selection of appropriate PET pharmacokinetic
model and the estimation of the model parameters using a
suitable parameter estimation technique.
PET Pharmacokinetic Models

Plasma Input Models
If an arterial plasma radioactivity time course and associated
HPLC measures of the parent radioactivity fraction have also
been acquired to allow for an estimate of the plasma concentration time course, then these data need to be modeled to
derive an estimate of the parent plasma radioactivity and
whole blood radioactivity time courses the former as the
input function for brain tissue and the latter to correct for
blood volume contamination (the assumption here is that
any labeled metabolite species do not enter the brain if
they do, modeling approaches become more complicated
and are beyond the scope of this article).
As radiolabeled compounds are given at tracer levels (typically < 10 mg), their behavior in the body is well described by
tracer compartmental systems (Jacquez, 1998; Lassen & Perl,
1979). These models assume that the behavior of the tracer is

described by a set of compartments linked by rate constants
describing the transfer of the compound between compartments. Compartments may be spatially distinct or congruent
but with a different biological state of the tracer (e.g., native/
metabolized or free/bound). Each compartment assumes instantaneous mixing and the overall observation for the PET system is
the sum of all the compartments that describe the tracer behavior
in the tissue and any contribution from the blood. The equations
that govern these compartmental systems can be derived from
the principle of the conservation of mass and lead to a set of firstorder linear differential equations. It is the values of the rate
constants that can be derived from the kinetic data that impart
important information on the underlying biological system, for
instance, the receptor concentration. The individual rate constants are often referred to as microparameters, but frequently,
it is the combinations of these parameters (or macroparameters)
that are the focus for parameter estimation as they balance both
biological specificity and good numerical identifiability.
An analytic solution can be derived for all plasma input
compartmental models including both those that display
reversible and irreversible kinetics. Reversible systems assume
that there is bidirectional exchange of tracer between
compartments, whereas irreversible systems assume that there
is a unidirectional exchange between one of the compartments
(see Figure 2(a) and (b)).
The general equation for a plasma input compartmental
model is derived from the tissue impulse response function:
IRFt
n
X
fi eyi t
[1]
i1
where n is the total number of tissue compartments in the

target tissue. This equation can be derived from the theory of
Reversible
target system
Plasma input
CT1
Irreversible
target system
CT
CT1
CT
CP
CT
211
CT
CP
CTn
(a)
CT
CT
CTn
CT1
CT
(b)
CT1
CT
Reference tissue input
CT
CT
CT
CTn
CP
CT
CTn
CR1
CR
CP
CR1
CR
CR
CR
CR
CRm
CR
(c)
CRm
(d)
Figure 2 General plasma input (a, b) and reference tissue input (c, d) compartmental systems for an arbitrary number of compartments. (a) and (c) have
reversible kinetics in the target tissues. (b) and (d) have irreversible kinetics in the target tissue. The reference tissues in (c) and (d) have reversible kinetics.
linear systems (Gunn, Gunn, & Cunningham, 2001) and combined with knowledge of the plasma input function, CP(t),
provides an equation for the tissue time course, CT(t):
CT t
n
X
fi eyi t Cp t
[2]
the system. This parameter measures the net trapping rate of

tracer into tissue if a constant tracer concentration were to be
maintained in plasma and can be estimated from the impulse
response function:
KI lim IRFt
[5]
fn
[6]
t!1
i1
where is the convolution operator.

The
Xndelivery of the tracer to the tissue is given by
f.
K1
i1 i
Reversible kinetics yi > 0
For tracers that exhibit reversible kinetics, the volume of distribution (VT, or more strictly a partition coefficient that is
defined by the ratio of the total concentration in tissue to the
total concentration in plasma at equilibrium; Innis et al.,
2007) is equal to the integral of the impulse response function:
1
VT
IRFt
[3]
In practice, a PET regional time activity curve also includes a

contribution from whole blood within the region of interest,
and thus, the full operational equation for the PET measurement is
PETt VB CB t 1 VB
n
X
fi eyi t CP t
[7]
i1
where VB is the regional fractional blood volume and CB is the

concentration time course in whole blood.
n
X
f
i1
yi

Irreversible kinetics yi6n > 0, yn 0
[4]
For tracers that exhibit irreversible kinetics, the net irreversible

uptake rate constant from plasma, KI, is used to characterize
Reference Tissue Input Models

Reference tissue input models avoid the need for blood sampling and metabolite analysis by deriving an input function
from the dynamic image data itself. They are frequently
employed in the quantification of ligandreceptor binding,
and the reference tissue is chosen as a region (usually based
212
on anatomy) that is devoid of the target receptor system allowing for measurement of the tracer time course in the absence of
receptor binding. Mathematically, the equations can be again
derived along the principles of linear systems theory, but here,
one derives two sets of equations, one for the reference tissue
time course and one for the target tissue time course. Both of
these equations include the plasma time course, and it is the
substitution for this term that yields a functional equation
describing the target tissue time course as a function of
the reference tissue time course without any dependence
on the plasma concentration (see Figure 2(c) and (d))
(Cunningham et al., 1991; Gunn et al., 2001).
The general equation for a reference tissue input compartmental model is given by
CT t f0 CR t
mn1
X
fi eyi t CR t
Parameter Estimation Methods

The PET modeling approaches may be broadly divided
into model-driven methods and data-driven methods. The
model-driven methods use a particular compartmental structure to describe the behavior of the tracer and allow for an
estimation of either micro- or macrosystem parameters,
whereas the data-driven methods are based on the general
model equations that generalize to an arbitrary number of
compartments and allow for the estimation of macroparameters. Whether using model-driven or data-driven
methods, the optimum estimate of the model variables (b)
for a given data set is determined by minimizing the weighted
sum of the square differences (WSSQ) between the model
prediction (f(xi, b)) and the measured data (yi):
[8]
WSSQ
i1
where m is the total number of tissue compartments in the

reference tissue; n is the total number of tissue compartments
in the target tissue; CT and CR are the concentration time
courses in the target and reference tissues, respectively; and
RI f0 is the ratio of delivery (K1) of the tracer between the
target tissue and the reference tissue (Gunn et al., 2001).
n
X
wi yi f xi , b2
[13]
i1
where wi is the weight that accounts for the variance associated

with each data point i. This formulates a maximum likelihood
estimation problem (Beck & Arnold, 1977) that can be solved
using an appropriate optimization technique.
Model-Driven Methods
Reversible target tissue kinetics yi > 0
For reference tissue models that exhibit reversible kinetics in

both the target and the reference tissues, the partition coefficient between the target and the reference tissues at equilibrium is given by the integral of an equivalent impulse response
for the reference tissue system:
1
VT
IRFt
[9]
VR
0
f0
mn1
X
i1
fi
yi
[10]
For reversible radioligand studies, this parameter allows calculation of the binding potential, BPND VT =VR 1 (Innis
et al., 2007).

Irreversible target tissue kinetics yi6mn1 > 0, ymn1 0
For reference tissue models that exhibit irreversible kinetics in

the target tissue and reversible kinetics in the reference tissue,
the reference normalized irreversible uptake rate constant from
plasma is given by
KI
lim IRFt
VR t!1
[11]
fmn1
[12]
In practice, the PET regional time activity curves in both the

reference and the target tissues also include a contribution
from whole blood. For reference tissue approaches, this is
often ignored (as the purpose is to avoid blood sampling).
However, an explicit formulation including a blood volume
term has also been given previously, and the bias introduced
by ignoring this can be estimated (Gunn et al., 2001).
As described previously, the generic equation for the tissue

impulse response function for any compartmental model is
nonlinear (i.e., a sum of exponentials with an additional
delta function for reference tissue input models). Therefore,
for a specific model, such as a one-tissue compartment model
(1TC) or two-tissue compartment model (2TC) with arterial
plasma input (see Figure 3), the rate constants between compartments can be estimated using nonlinear optimizers,
such as LevenbergMarquardt algorithm (Levenberg, 1944;
Marquardt, 1963) and many others. The identifiability (%
COV) of each parameter, expressed as the standard error of
their estimated values, can be calculated from the diagonal of
the covariance matrix (Carson, 1986). Often, more than one
compartment model is fitted to the dynamic data in practice to
investigate different model configurations. As the sum of
squares is always smaller when more parameters are fitted,
the optimal model should be chosen based on the principle
of parsimony where the model complexity is balanced with
parameter identifiability. For this purpose, the criterion that
accounts for both the sum of squared residuals and the number
of parameters to fit, such as Akaike (Akaike, 1974) and Schwarz
(Schwarz, 1978) criteria and F-test (Cunningham, 1985;
Landaw & DiStefano, 1984), can be used to select the best
model (see Figure 4 for an example of model selection with
[11C]PBR28).
Pharmacokinetic modeling can be applied to the dynamic
data on both ROI level and voxel level with the voxel-based
analysis being able to produce functional images where the
value in each voxel represents a macroparameter such as the
binding potential or the volume of distribution. As the application of nonlinear fitting is computationally expensive on a
voxel basis, methods have been developed to transform the
nonlinear equation to establish a linear relationship between
the dependent and independent variables allowing simple
K1
K1
CF+NS+SP
CP
CT
CP
k2
K1
k3
CF+NS
k2
213
CSP
CT
CF+NS+SP
CT
CF+NS
CR
k2
k4
CP
K1
k2
(a)
(b)
(c)
Figure 3 A range of PET compartmental models commonly used to quantify PET radiotracers. These include models for tracers that exhibit reversible
kinetics and models that use either a plasma or a reference tissue input function: (a) A one-tissue compartment model (1TC), (b) a two-tissue
compartment model (2TC), and (c) a simplified reference tissue model (SRTM). Here, the compartments are depicted in terms of radioligand binding and
constitute either free (F) radioligand, nonspecifically bound (NS) radioligand, specifically bound (SP) radioligand, or some combination of them.
Parent plasma activity (kBq ml1)
102
1TC
VT
K1
AIC
VT
BRS 6.52
0.08
32.6
8.03
0.15 44.8
THA 5.79
0.10
48.5
7.01
0.19 16.8
STR
0.10
45.2
5.56
0.18 25.1
101
100
2TC
4.59
K1
AIC
101
0
20
(a)
40
60
Time (min)
80
(b)
20
20
15
10
0
(C)
Brain stem
Thalamus
Striatum
ROI activity (kBq/ml)
ROI activity (kBq ml1)
Brain stem
Thalamus
Striatum
20
40
60
Time (min)
15
10
80
(d)
20
40
60
Time (min)
80
Figure 4 Compartmental modeling of dynamic PET data acquired in human brain with translocator protein radiotracer [11C]PBR28 with arterial
sampling. (a) Parent plasma concentration; (b) quantification results including estimates for VT, K1, and the Akaike information criteria (AIC) in the brain
stem (BRS), thalamus (THA), and striatum (STR) for 1TC and 2TC model fitting; (c) nonlinear fitting with a 1TC model to the time activity curves
(TACs); and (d) nonlinear fitting with a 2TC model to the TACs. The 2TC is a better model to characterize this tracer than the 1TC as
determined by the AIC.
214
linear regression to be used. One such method involves establishing a set of kinetic basis functions, which can be used for
both specific compartmental models and data-driven
approaches (Gunn, Gunn, Turkheimer, Aston, & Cunningham,
2002). When applied to a simplified reference tissue model
(SRTM, where both the target and the reference regions are
represented by a single compartment (Lammertsma & Hume,
1996)), a spectrum of basis functions are formed, which is the
convolution of the reference curve with a series of single exponentials with different coefficients (Gunn, Lammertsma,
Hume, & Cunningham, 1997). This transforms the problem
into a linear equation and enables the coefficients to be estimated using standard linear least squares. In addition to the
high computational cost, parametric analysis can suffer from
higher levels of noise as compared to ROI-based analysis. To
address this issue, methods such as SRTM2 have been developed that incorporate additional constraints on the model
parameters (Wu & Carson, 2002), and alternative approaches
have also introduced spatial constraints based on the kinetic
information in the neighborhood of a voxel (Zhou, Huang,
Bergsneider, & Wong, 2002). As more constraints are introduced, additional care should be taken to assess bias.
Data-Driven Methods
Compared to model-driven methods, data-driven methods do
not require a priori selection of a specific compartmental
model to describe the data. These methods are often based
on the linearization of the data and thus allow for fast implementation and are particularly useful for parametric analysis to
generate functional images.
One group of these data-driven approaches is the graphical
methods, which employ a transformation of the data such that,
after a certain time, a standard linear regression of the transformed data yields the macrosystem parameter of interest. For
example, the Patlak plot enables the estimation of the irreversible uptake constant KI for an irreversible system (Patlak &
Blasberg, 1985; Patlak, Blasberg, & Fenstermacher, 1983),
and the Logan plot allows for a direct estimation of the volume
of distribution VT for a reversible system (Logan et al., 1990,
1996). As standard linear regression assumes noiseless data on
the x-axis, graphical analyses can lead to noise-induced bias in
parameter estimates when noise is present in both the x- and
the y-variables (Carson, 1993; Cunningham, 1985; Slifstein &
Laruelle, 2000). When bias becomes an issue, other estimation
methods, such as total least squares (Varga & Szabo, 2002)
and likelihood estimation (Ogden, 2003), can be applied.
Alternatively, by rearranging the x- and y-variables of the linear
equation, a multilinear relationship can be established with
reduced noise in the x-variables, and the macroparameters
such that the volume of distribution or the binding potential
can be estimated using multilinear regression with plasma
(MA1, Ichise, Toyama, Innis, & Carson, 2002) or reference
input (MRTM, Ichise et al., 2003), respectively.
In addition to the graphical and multilinear methods, spectral analysis and basis pursuit are basis function methods that
do not assume a particular model to describe the data. Instead,
they are able to return information on the number of tissue
compartments evident in the data and thus are considered as
transparent techniques. The methods characterize the system
as a sum of basis functions (convolution of single exponentials
with either plasma or reference input) with spectral analysis

using nonnegative least squares to fit the data (Cunningham &
Jones, 1993), whereas basis pursuit uses a regularization term
to solve the underdetermined system of equations without
positivity constraints on the coefficients (Gunn et al., 2002).
Apart from the kinetic analyses described earlier, equilibrium methods provide an alternative approach to estimate the
macroparameters such as the total volume of distribution. As
the total volume of distribution is defined as the ratio of the
tracer concentrations in the target tissue and the plasma at
equilibrium, equilibrium methods allow for the direct measurement of this ratio after the system reaches equilibrium,
rather than by estimating the equilibrium situation from
kinetic analysis (Carson et al., 1993). This method requires
the radiotracer to possess fast enough kinetics so that an equilibrium state can be reached within the time window of scanning with a bolus plus infusion injection design.
Study-Level Analyses
PET pharmacokinetic modeling yields quantitative outcome
parameters for individual scans. However, these scans are typically part of larger studies where either subjects are scanned
longitudinally over time or different populations of subjects
are scanned in a cross-sectional manner. Thus, there are further
modeling and statistical analysis techniques that are applied to
these outcome measures at the study level.
For intrasubject longitudinal studies, the reproducibility of
the analysis techniques is often assessed initially in a testretest
design in terms of the variability (%VAR) or the intraclass
correlation coefficient (Koch, 1982). Having demonstrated
good reproducibility, these outcome measures can be used to
determine changes in the target biology following a physiological/psychological or pharmacological intervention. For intersubject studies, standard statistical tests can be applied to
determine differences in the biological parameter of interest
across groups (e.g., in different disease states to identify if a
biological target is altered).
In addition to these statistical analyses at the study level,
there are other dynamic modeling techniques that can be
applied. For instance, in drug occupancy studies, the relationship between cold drug concentrations in plasma and the
target occupancy in the brain as measured with a radioligand
can be evaluated with pharmacokineticreceptor occupancy
models that describe the drugs binding behavior at the target
of interest across subjects over time (Abanades et al., 2011).
This is important for characterizing the target residence time of
the drug and identifying whether there is a simple direct relationship or a more complex indirect relationship between the
plasma concentration and target occupancy (Salinas et al.,
2013). Such techniques also allow the prediction of drug
target interactions under repeat dosing regimes based simply
on single-dose data sets.

Computerized Tomography Reconstruction Methods; Diffeomorphic
Image Registration; Nonlinear Registration Via Displacement Fields;
Rigid-Body Registration.
References
Abanades, S., van der Aart, J., Barletta, J. A., Marzano, C., Searle, G. E., Salinas, C. A.,
et al. (2011). Prediction of repeat-dose occupancy from single-dose data:
characterisation of the relationship between plasma pharmacokinetics and
brain target occupancy. Journal of Cerebral Blood Flow and Metabolism, 31(3),
944952.
Akaike, H. (1974). A new look at the statistical model identification. IEEE Transactions
on Automatic Control, 19(6), 716723.
Beck, J. V., & Arnold, K. J. (1977). Parameter estimation in engineering and science
(vol. 8). New York: Wiley.
Carson, R. (1986). Parameter estimation in positron emission tomography. Positron
emission tomography and autoradiography: Principles and applications for the
brain and heart. New York: Raven Press, pp. 347390.
Carson, R. (1993). PET parameter estimation using linear integration methods: Bias and
variability considerations. Annals of Nuclear Medicine, 7, S102.
Carson, R. E., Channing, M. A., Blasberg, R. G., Dunn, B. B., Cohen, R. M., Rice, K. C.,
et al. (1993). Comparison of bolus and infusion methods for receptor quantitation:
Application to [18F]cyclofoxy and positron emission tomography. Journal of
Cerebral Blood Flow and Metabolism, 13(1), 2442.
Cunningham, V. (1985). Non-linear regression techniques in data analysis. Informatics
for Health and Social Care, 10(2), 137142.
Cunningham, V. J., Hume, S. P., Price, G. R., Ahier, R. G., Cremer, J. E., & Jones, A. K.
(1991). Compartmental analysis of diprenorphine binding to opiate receptors in the
rat in vivo and its comparison with equilibrium data in vitro. Journal of Cerebral
Cunningham, V., & Jones, T. (1993). Spectral analysis of dynamic PET studies. Journal
of Cerebral Blood Flow and Metabolism, 13(1), 1523.
Cunningham, V., Rabiner, E., Slifstein, M., Laruelle, M., & Gunn, R. (2009). Measuring
drug occupancy in the absence of a reference region: The Lassen plot re-visited.
Gunn, R. N., Gunn, S. R., & Cunningham, V. J. (2001). Positron emission tomography
compartmental models. Journal of Cerebral Blood Flow and Metabolism, 21(6),
635652.
Gunn, R. N., Gunn, S. R., Turkheimer, F. E., Aston, J., & Cunningham, V. (2002).
Positron emission tomography compartmental models a basis pursuit strategy for
kinetic modeling. Journal of Cerebral Blood Flow and Metabolism, 22(12),
14251439.
Gunn, R. N., Lammertsma, A., Hume, S., & Cunningham, V. (1997). Parametric imaging
of ligandreceptor binding in PET using a simplified reference region model.
Gunn, R. N., Summerfield, S. G., Salinas, C. A., Read, K. D., Guo, Q., Searle, G. E., et al.
(2012). Combining PET biodistribution and equilibrium dialysis assays to assess
the free brain concentration and BBB transport of CNS drugs. Journal of Cerebral
Hammers, A., Allom, R., Koepp, M. J., Free, S. L., Myers, R., Lemieux, L., et al. (2003).
Three-dimensional maximum probability atlas of the human brain, with particular
reference to the temporal lobe. Human Brain Mapping, 19(4), 224247.
Ichise, M., Liow, J., Lu, J., Takano, A., Model, K., Toyama, H., et al. (2003). Linearized
reference tissue parametric imaging methods: Application to [11C]DASB positron
emission tomography studies of the serotonin transporter in human brain. Journal
of Cerebral Blood Flow and Metabolism, 23(9), 10961112.
Ichise, M., Toyama, H., Innis, R. B., & Carson, R. E. (2002). Strategies to improve
neuroreceptor parameter estimation by linear regression analysis. Journal of
Innis, R., Cunningham, V., Delforge, J., Fujita, M., Gjedde, A., Gunn, R., et al. (2007).
Consensus nomenclature for in vivo imaging of reversibly binding radioligands.
Jacquez, J. A. (1998). Compartmental analysis in biology and medicine (3rd ed.). Ann
Arbor, MI: Biomedware.
215
Kety, S. S. (1951). The theory and applications of the exchange of inert gas at the lungs
and tissues. Pharmacological Reviews, 3(1), 141.
Koch, G. G. (1982). Intraclass correlation coefficient. Encyclopedia of Statistical
Sciences, 4, 213217.
Lammertsma, A., & Hume, S. (1996). Simplified reference tissue model for PET receptor
studies. NeuroImage, 4(3), 153158.
Landaw, E., & DiStefano, J. (1984). Multiexponential, multicompartmental, and
noncompartmental modeling. II. data analysis and statistical considerations.
American Journal of Physiology, 246(5), R665R677.
Lassen, N., & Perl, W. (1979). Tracer kinetic methods in medical physiology. New York:
Raven Press.
Levenberg, K. (1944). A method for the solution of certain nonlinear problems in least
squares. Quarterly of Applied Mathematics, 2, 164168.
Logan, J., Fowler, J. S., Volkow, N. D., Wang, G. J., Ding, Y. S., & Alexoff, D. L. (1996).
Distribution volume ratios without blood sampling from graphical analysis of PET
data. Journal of Cerebral Blood Flow and Metabolism, 16(5), 834840.
Logan, J., Fowler, J. S., Volkow, N. D., Wolf, A. P., Dewey, S. L., Schlyer, D. J., et al.
(1990). Graphical analysis of reversible radioligand binding from time-activity
measurements applied to [N-11C-methyl]-()-cocaine PET studies in human
subjects. Journal of Cerebral Blood Flow and Metabolism, 10(5), 740747.
Marquardt, D. (1963). An algorithm for least-squares estimation of nonlinear parameters.
Journal of the Society for Industrial and Applied Mathematics, 11(2), 431441.
Mintun, M. A., Raichle, M. E., Kilbourn, M. R., Wooten, G. F., & Welch, M. J. (1984). A
quantitative model for the in vivo assessment of drug binding sites with positron
emission tomography. Annals of Neurology, 15(3), 217227.
Ogden, R. T. (2003). Estimation of kinetic parameters in graphical analysis of PET
imaging data. Statistics in Medicine, 22(22), 35573568.
Patlak, C. S., & Blasberg, R. G. (1985). Graphical evaluation of blood-to-brain transfer
constants from multiple-time uptake data. generalizations. Journal of Cerebral Blood
Flow and Metabolism, 5(4), 584590.
Patlak, C. S., Blasberg, R. G., & Fenstermacher, J. D. (1983). Graphical evaluation of
blood-to-brain transfer constants from multiple-time uptake data. Journal of
Salinas, C., Weinzimmer, D., Searle, G., Labaree, D., Ropchan, J., Huang, Y., et al.
(2013). Kinetic analysis of drugtarget interactions with PET for characterization of
pharmacological hysteresis. Journal of Cerebral Blood Flow and Metabolism, 33(5),
700707.
Schwarz, G. (1978). Estimating the dimension of a model. The Annals of Statistics, 6(2),
461464.
Slifstein, M., & Laruelle, M. (2000). Effects of statistical noise on graphic analysis of
PET neuroreceptor studies. Journal of Nuclear Medicine, 41(12), 20832088.
Sokoloff, L., Reivich, M., Kennedy, C., Des Rosiers, M., Patlak, C. S., Pettigrew, K. D.,
et al. (1977). The [14C] deoxyglucose method for the measurement of local cerebral
glucose utilisation: Theory, procedure, and normal values in the conscious and
anesthetized albino rat. Journal of Neurochemistry, 28(5), 897916.
Tziortzi, A. C., Haber, S. N., Searle, G. E., Tsoumpas, C., Long, C. J., Shotbolt, P., et al.
(2013). Connectivity-based functional analysis of dopamine release in the
striatum using diffusion-weighted MRI and positron emission tomography. Cereb
Cortex, 24(5), 11651177.
Tziortzi, A. C., Searle, G. E., Tzimopoulou, S., Salinas, C., Beaver, J. D., Jenkinson, M.,
et al. (2011). Imaging dopamine receptors in humans with [11C]-()-PHNO:
Dissection of D3 signal and anatomy. NeuroImage, 54(1), 264277.
Varga, J., & Szabo, Z. (2002). Modified regression model for the Logan plot. Journal of
Wu, Y., & Carson, R. (2002). Noise reduction in the simplified reference tissue model
for neuroreceptor functional imaging. Journal of Cerebral Blood Flow and
Metabolism, 22(12), 14401452.
Zhou, Y., Huang, S. C., Bergsneider, M., & Wong, D. F. (2002). Improved parametric
image generation using spatial-temporal analysis of dynamic PET studies.
NeuroImage, 15(3), 697707.
Optical Image Reconstruction

S Arridge and RJ Cooper, University College London, London, UK
Introduction
The use of light in the near infrared to investigate functional
activation is increasingly widely spread and is referred to as
functional near-infrared spectroscopy (fNIRS). The interaction
of light with biological tissue is dominated by scattering interactions. As a result, light traveling a distance of more than a few
millimeters into tissue will form a diffuse field. Despite this,
multichannel diffuse optical imaging systems can yield significant spatial information and allow the mapping of changes in
optical properties (and, by proxy, functional activation) in the
cortex with a resolution as good as 510 mm (Habermehl
et al., 2012).
The process of producing an image from multichannel
diffuse optical imaging data has three distinct phases. The
first is to produce a model of how light travels through the
object under investigation given the specific arrangement of
optical sources on the surface. The second is to use this photon
transport model to predict the change in optical measurement
(usually intensity) that would be measured by each channel for
a given change in tissue optical properties. This yields what is
known as a sensitivity matrix. The third and final phase is
image reconstruction, which requires the solution to the
inverse problem in which the sensitivity matrix is inverted.
The fundamental paradigm for mapping the cortex using
diffuse optical imaging involves invoking a hemodynamic
response to a particular cognitive task or external stimulus
and mapping the difference between the pre- and poststimulus
states. In general, the dependence of the optical signal on the
hemodynamic response is nonlinear, which is stated as a nonlinear forward problem
y Ax
[1]
Image reconstruction based on eqn [1] is a nonlinear inverse

problem and is mathematically and computationally difficult.
However, reconstructing an image of a change in optical properties lends itself to a linearized simplification of the forward
problem that can be defined as
Dy JDx
[2]
where Dy is a vector of the change in measured parameter, Dx is

the change in optical properties (i.e., the image), and J @A/@x
is the sensitivity matrix.
The Forward Problem: Approximating J

Modeling Light Transport in Tissue
All image reconstruction approaches require a model of light
propagation in the object under investigation. The radiative
transport equation provides a near-complete description of
light propagation in a medium of known optical properties
and constant refractive index (Arridge, 1999). However, solving the radiative transport equation to provide the photon
density at every point in a 3-D volume is computationally
demanding, and more efficient approaches are usually necessary. By assuming that, after a small number of scattering
events, the distribution of directions of propagation of individual photons is nearly isotropic, the radiative transport equation simplifies to what is commonly referred to as the diffusion
equation or diffusion approximation. This equation can be
solved at significantly less computational expense. While the
assumption of diffusivity is valid for most tissues, it can break
down in regions of low scatter (such as in the cerebrospinal
fluid), at boundaries between tissues, and near the locations of
the optical sources.
In simple geometries, it is possible to solve the diffusion
equation (and the radiative transport equation) analytically.
Greens functions can be used to solve the diffusion equation if
each source is modeled as a delta function in both space and
time. By convolving a number of such solutions, the light field
produced by extended sources can also be modeled. While
more sophisticated Greens function techniques have been
developed, such solutions are generally limited to cases where
the target object can be modeled as a slab or semi-infinite
space. Despite this, Greens function approaches have been
used successfully for simple diffuse optical imaging applications (Culver, Siegel, Stott, & Boas, 2003).
For the more complex geometries of multilayered models of
the head and brain, it is necessary to apply numerical techniques to solve the equations governing light propagation. The
most commonly applied to diffuse optical imaging is the finite
element method (FEM) (Arridge, Schweiger, Hiraoka, & Delpy,
1993). The FEM can be used to provide approximate solutions
to the diffusion equation in a 3-D finite element mesh. A
number of other numerical approaches have been devised,
including the finite difference method (Pogue & Patterson,
1994) and the finite volume method (Ren, Abdoulaev, Bal, &
Hielscher, 2004).
The boundary element method (BEM) produces a model of
light propagation by representing a 3-D volume as a set of
closed surfaces, where the tissue within each surface is assumed
to be homogeneous. Greens theorem is used to transform the
diffusion equation to a set of integral equations defined only
on these surfaces. This can significantly simplify the required
meshing procedure and reduce the dimensionality of the forward problem. As a result, BEM can provide a semi-analytic
solution to the forward problem in an efficient manner (Elisee,
Gibson, & Arridge, 2011).
Instead of seeking solutions to the diffusion equation to
calculate photon density in tissue, statistical techniques such as
the Monte Carlo method simulate the trajectories of individual
photons. The 3-D volume is subdivided into elements with
specific values of the absorption (ma) and reduced scattering
(ms0 ) coefficients. Each simulated photon is given a weight on
http://dx.doi.org/10.1016/B978-0-12-397025-1.00288-8
217
218
INTRODUCTION TO METHODS AND MODELING | Optical Image Reconstruction
entering the model. As it enters an element, the photon is also

assigned a random scattering length and scattering angle using
probability distributions that depend on the local value of ms0 .
If that scattering length is less than the length of that photons
path through the element, the photon is moved that scattering
length and its direction of travel is then altered by the random
scattering angle. This process is repeated until the photon
leaves the volume. The photons initial weight is attenuated
by the distance it travels using the BeerLambert law and the
local values of ma. As the photon travels, the weight it loses in
each element is assigned to that element. The time-varying or
steady-state photon density in the 3-D volume can therefore be
modeled by repeating this process for a high number of photons (Fang, 2010). Monte Carlo approaches have long since
been considered the gold standard for modeling light propagation because they are not dependent on the assumption of
diffusivity. As a result, Monte Carlo models tend to be more
accurate than FEM approaches close to the source positions, at
tissue boundaries, and in regions of low scatter. The biggest
obstacle to the use of Monte Carlo methods in diffuse optical
imaging has been their computational demand. However, the
efficiency of such simulations has improved significantly in
recent years, and it is now possible to calculate photon density
in a dense 3-D adult head model under a minute per source
position (Fang & Boas, 2009a).
Sensitivity Matrices
There are several ways that the linearized sensitivity matrix J
can be constructed from a model of photon transport. When
simple analytic models based on the diffusion equation are
employed, then explicit expressions for J can be derived, again
assuming simple geometries such as a semi-infinite space.
When Monte Carlo methods are used, it is possible to calculate
the derivatives of the photon weights at the same time as
calculating the data itself. In general, for complex arbitrary
geometries and inhomogeneous parameters, an explicit perturbation can be made: adding a small variation to the absorption in each voxel and calculating the resulting change in
measurement. This method can be applied to any model
but is computationally expensive, requiring a new forward
solution for each voxel and each source. Instead, most computational techniques exploit the reversibility of photon propagation to show that the sensitivity of a given sourcedetector
pair can be expressed as the product of the fluence resulting
from the source and an adjoint fluence resulting from a
fictitious source placed at the location of the detector. In
Figure 1 are shown several different forms of the sensitivity
function from one source and detector. The differences are to
some extent subtle but are significant in terms of the image
reconstruction because of the severe ill-posedness of the
problem.
Structural Geometries and Mesh Generation

All of the light propagation models described earlier require an
accurate model of the geometry of the object under investigation. The production of accurate structural models is a
significant and challenging component of optical image reconstruction. The FEM inherently demands a finite element mesh
model of the object. Monte Carlo simulations can be performed in voxelized or in 3-D mesh-based structural models,
while BEM solutions require a series of surface meshes
(Figure 2).
Studies of diffuse optical imaging and reconstruction
methods have employed a wide range of structural models.
Many image reconstruction simulations and phantom studies
have employed semi-infinite slab and cylindrical geometries.
Early studies of functional activation modeled the brain as a
homogeneous slab, discretized into a regular grid (Everdell
et al., 2005). Such approaches, while crude, are computationally efficient and can provide sufficient spatial information to
address hypotheses relating to the lateralization or gross localization of cognitive processes.
To improve the registration of diffuse optical images to the
brain, realistic head geometries were soon developed. The
simplest consisted of a generic, homogenous head model to
which the source and detector locations were registered
(Gibson et al., 2006).
The optical properties of the fundamental tissues of the
head (i.e., the scalp, skull, cerebrospinal fluid, and gray and
white matter) vary markedly. As a result, the use of multilayered head geometries greatly improves the accuracy of
models of light transport while also helping to constrain the
process of image reconstruction and allowing the resulting
images to be inherently registered to the cortical anatomy.
The production of a finite element mesh is relatively
straightforward for simple homogeneous volumes, but the
efficient production of multilayered meshes of the complex
structure of the brain is a significant challenge and has been
the subject of active research in recent years (Fang & Boas,
2009b; Gibson et al., 2003). A number of software packages
have emerged that allow users to take structural images of the
subjects head and brain (usually via MRI or CT) and produce
accurate, subject-specific, multilayered head meshes (Fang &
Boas, 2009b). The positions of the sources and detectors can be
registered to these multilayered models using 3-D digitization
or photogrammetric techniques.
The resulting multilayered finite element meshes can be
used to solve the forward problem. Using a head model based
on subject-specific structural images constitutes the current
best practice for diffuse optical image reconstruction. However, one of the advantages of optical imaging is that the
systems are portable and can therefore be applied in a wide
range of environments. Requiring a structural MRI for each
subject undermines this advantage. This issue can be overcome by using a generic head model as a substitute for the
subject-specific anatomy. Such generic models are usually produced using an MRI atlas, that is, a spatial average of the head
anatomy of the appropriate population (Custo et al., 2010).
The segmented atlas can be used to generate appropriate
meshes. To employ an atlas model requires careful measurement of the subjects cranial landmarks and scalp surface as
well as accurate measurement of the source and detector
positions relative to the scalp. This information allows the
atlas model to be spatially registered to the subjects external
anatomy. The use of atlas models has been shown to yield
images that, while less accurate than the subject-specific case,
are still accurate enough to localize functional activation to
within 12 cm (Cooper et al., 2012).
219
Figure 1 Examples of sensitivity functions generated by different models. First column: the direct light field produced by the source; second column:
the adjoint field produced by the detector; third column: the resultant sensitivity function. In the first row, the model is the infinite space solution to
the diffusion equation, which has a spherically symmetrical form. In the second row, the boundary conditions for a square domain are introduced.
The third row is the case for a head-shaped mesh, but with homogeneous optical parameters. The fourth row includes realistic optical properties in
each tissue layer. The sensitivity matrix J is formed by compositing all such functions for each sourcedetector pair.
Figure 2 Left: A three-layer BEM model of the scalp and skull and cortical surface. Right: Solution of fluence on the cortical surface for a point source.
220

estimated image D^
x . If l is increased, the contribution of the
term ||Dx||2 (referred to as the image norm) increases and the
estimated image becomes less sensitive to the residual norm
and therefore to variations in the data. A lower value of l
renders the solution more sensitive to noise in the data.
Regularization of the image reconstruction problem also
has a strong effect on the scale of the reconstructed image.
Careful and consistent selection of the regularization parameter is therefore essential to the production of meaningfully
scaled images that can be compared across experiments,
subjects, and populations. There are a number of different
methods for selecting the regularization parameter, though in
many cases it is still performed subjectively. One of the bestknown methods is the discrepancy principle that states that l
should be chosen such that the error in the data-fitting term
should be comparable to the measurement noise. Also common is the L-curve approach. The L-curve is the image norm
plotted against the residual norm for a range of values of
regularization parameter on a loglog scale. The value of l
that minimizes both the image and residual norms can then
be selected (Correia, Gibson, Schweiger, & Hebden, 2009).
Finally, the nonuniqueness of the solution is often constrained by restricting the image to the surface of the cortex.
This can be done as a postreconstruction step by projecting all
reconstructed voxels onto the surface or within a BEM framework
by directly posing the problem as a deconvolution of the data
from the scalp measurement surface onto the cortical surface.
Figure 3 shows an example reconstruction using this technique.
The Inverse Problem: Inverting J

To obtain our image (Dx of eqn [2]), we must invert the
sensitivity matrix J. Image reconstruction for diffuse optical
imaging is, however, a highly underdetermined problem.
That is to say, there are significantly more unknowns (i.e., the
number of pixels or voxels in the desired image and the number of rows of Dx) than there are measurements (the number of
rows of Dy). The sensitivity matrix J does not therefore have an
exact inverse. As well as being ill-posed due to the small number of measurements, the inverse problem is also ill-posed in
the sense that the errors in the reconstructed image are disproportionately sensitive to small changes in the data (e.g., photon counting noise) as well as systematic errors due to motion,
displacement of optical fibers, surface effects such as sweating,
and skin hemodynamics. Therefore, in common with many
other medical imaging problems, regularization is required.
This can be stated within a Bayesian framework as the employment of prior information. The best-known approach is the
output least squares method that looks for the solution to a
minimization problem such as
1
l
kJDx Dy k2 kLDx k2
2
2
[3]
such that the estimated image can be obtained via

D^
x JT J lLT L
1
JT Dy
where l is referred to as the regularization parameter and L is a

matrix encoding prior information. The most common form of
regularization is to employ a Markov random field that
enforces a constraint that neighboring voxels should be similar
unless they belong to different tissue types (e.g., gray matter
and cerebospinal fluid (CSF)). The value of the regularization
parameter affects how perturbations in the data Dy alter the
Dynamic Imaging
An important feature of fNIRS is its dynamic aspect. This is
implicit in eqn [2] because the measurements are typically
-40 -30 -20 -10
10
20
30
40
-40
-30
50
40
-20
30
-10
20
10
10
-10
-20
20
-30
40
30
40
20
20
40
-20
-40
-40
-20
50
Figure 3 Side and top views of a cortical map of a functional activation. An activation of the primary motor and somatosensory regions in response to
arm motion is clearly visible.

made between an activation and a resting state. A typical
experiment induces the activation as a repeated sequence of
activation and rest, and data are averaged over successive
periods to improve signal to noise ratio. The aim is to observe
a change in oxy- and deoxyhemoglobin signals that correlates
with the stimulus. The time course of these responses informs
an estimation of the hemodynamic response function (HRF).
A problem with simple measurements is that the signal is
confounded by changes occurring in the skin surface and with
temporal effects caused by heartbeat, breathing, and motion.
The idea of a spatiotemporal analysis is to treat the problem as
a combination of signals at different rates and with different
spatial dependencies. Thus, in dynamic imaging, we consider
both the data and image, and possibly the model, to be timevarying, so that eqn [1] becomes
y t At xt
[4]
Although increasing the dimensionality of the data could lead to

a more computationally expensive reconstruction process, the
possibility arises to impose temporal prior constraints through
appropriate models, which may make the inverse problem better
posed. In particular, we consider a model such as
xt Zt; f
[5]
which describes the time-varying image in terms of a timevarying model Z and a vector of explanatory variables f. A
well-known example is the general linear model that assumes
that eqn [5] is the convolution of a known response function
with a set of experimental designs; Z is then referred to as the
design matrix. However, nonlinear models including higherorder convolution processes and adaptive filters can also be
considered.
Time-series methods have been applied in fNIRS; for a
review, see Huppert, Diamond, Franceschini, and Boas
(2009). In previous work using statistical parametric mapping
(SPM) methodology on fNIRS data, the optical measurement
data have been converted into chromophore concentrations
using the modified BeerLambert law (Koh et al., 2007; Tachtsidis, Koh, Stubbs, & Elwell, 2010; Tachtsidis et al., 2009), and a
model based on homogeneous diffusion and nearest-neighbor
measurements (Ye, Tak, Jang, Jung, & Jang, 2009). Boas, Dale,
and Franceschini (2004) showed that brain activations can be
more accurately localized, and their spatial extent defined, by
performing an image reconstruction rather than merely analyzing individual measurement channels. In Heiskala, Hiltunen, and Nissila (2009), it was shown that accurate modeling
of the optical background can also significantly improve reconstructed images. This suggests that superior results can be
expected by combining the SPM analysis with accurate modeling of the head, using either individual anatomical data or
generic data from an atlas.
Rather than the general linear model, which assumes a
time-invariant HRF, time-series estimation approaches using
adaptive filters have been proposed. This idea was introduced
in Kolehmainen, Prince, Arridge, and Kaipio (2000) for
dynamic imaging without physiological parameter inputs and
extended in Prince et al. (2003), where a linear state-space
model was applied to time-varying image reconstruction. Signal sources such as the heartbeat were modeled by
221
superimposed quasi-sinusoidal signals with a priori known

frequency, where the model parameters were signal amplitude
and phase. A Kalman filter in combination with spatial
regularization was used to reconstruct spatially and temporally
resolved images from highly underdetermined time-series
data. This approach was the first to propose an explicit model
for the confounds due to breathing and heartbeat, but did not
use an explicit neurophysiological model. A combined SPM
and Kalman filter model was reported in Hu, Hong, Ge, and
Jeong (2010).

Functional Near-Infrared Spectroscopy.
References
Arridge, S. R. (1999). Optical tomography in medical imaging. Inverse Problems, 15(2),
R41.
Arridge, S. R., Schweiger, M., Hiraoka, M., & Delpy, D. T. (1993). A finite element
approach for modeling photon transport in tissue. Medical Physics, 20(2),
299309.
Boas, D. A., Dale, A. M., & Franceschini, M. A. (2004). Diffuse optical imaging of brain
activation: Approaches to optimizing image sensitivity, resolution, and accuracy.
NeuroImage, 23(Suppl. 1), S275S288.
Cooper, R. J., Caffini, M., Dubb, J., Custo, A., Tsuzuki, D., Fischl, B., et al. (2012).
Validating atlas-guided DOT: A comparison of diffuse optical tomography informed
by atlas and subject-specific anatomies. NeuroImage, 62, 19992006.
Correia, T., Gibson, A., Schweiger, M., & Hebden, J. (2009). Selection of
regularization parameter for optical topography. Journal of Biomedical Optics,
14(3), 034044.
Culver, J. P., Siegel, A. M., Stott, J. J., & Boas, D. A. (2003). Volumetric diffuse optical
tomography of brain activity. Optics Letters, 28(21), 20612063.
Custo, A., Boas, D. A., Tsuzuki, D., Dan, I., Mesquita, R., Fischl, B., et al. (2010).
Anatomical atlas-guided diffuse optical tomography of brain activation.
NeuroImage, 49(1), 561567.
Elisee, J., Gibson, A., & Arridge, S. (2011). Diffuse optical cortical mapping using the
boundary element method. Biomedical Optics Express, 2(3), 568578.
Everdell, N. L., Gibson, A. P., Tullis, I. D.C, Vaithianathan, T., Hebden, J. C., &
Delpy, D. T. (2005). A frequency multiplexed near-infrared topography system for
imaging functional activation in the brain. Review of Scientific Instruments, 76(9),
093705.
Fang, Q. (2010). Mesh-based monte carlo method using fast ray-tracing in plucker
coordinates. Biomedical Optics Express, 1(1), 165175.
Fang, Q., & Boas, D. A. (2009a). Monte carlo simulation of photon migration in 3D
turbid media accelerated by graphics processing units. Optics Express, 17(22),
2017820190.
Fang, Q., & Boas, D. A. (2009b). Tetrahedral mesh generation from volumetric binary
and grayscale images. In IEEE international symposium on biomedical imaging:
From nano to macro, 2009. ISBI 09 (pp. 11421145).
Gibson, A. P., Austin, T., Everdell, N. L., Schweiger, M., Arridge, S. R., Meek, J. H., et al.
(2006). Three-dimensional whole-head optical tomography of passive motor
evoked responses in the neonate. NeuroImage, 30(2), 521528.
Gibson, A. P., Riley, J., Schweiger, M., Hebden, J. C., Arridge, S. R., & Delpy, D. T.
(2003). A method for generating patient-specific finite element meshes for head
modelling. Physics in Medicine and Biology, 48(4), 481.
Habermehl, C., Holtze, S., Steinbrink, J., Koch, S. P., Obrig, H., Mehnert, J., et al.
(2012). Somatosensory activation of two fingers can be discriminated with
ultrahigh-density diffuse optical tomography. NeuroImage, 59(4), 32013211.
Heiskala, J., Hiltunen, P., & Nissila, I. (2009). Significance of background optical
properties and time-resolved information in diffuse optical imaging of term
neonates. Physics in Medicine and Biology, 54, 535554.
Hu, X. S., Hong, K. S., Ge, S. S., & Jeong, M. Y. (2010). Kalman estimator and general
linear model-based on-line brain activation mapping by near-infrared spectroscopy.
Biomedical Engineering Online, 9, 82.
Huppert, T. J., Diamond, S. G., Franceschini, M. A., & Boas, D. A. (2009). HomER: A
review of time-series analysis methods for near-infrared spectroscopy of the brain.
Applied Optics, 48(10), 280298.
222
Koh, P. H., Glaser, D. E., Flandin, G., Kiebel, S., Butterworth, B., Maki, A., et al. (2007).
Functional optical signal analysis: A software tool for near-infrared spectroscopy
data processing incorporating statistical parametric mapping. Journal of Biomedical
Optics, 12, 064010.
Kolehmainen, V., Prince, S., Arridge, S. R., & Kaipio, J. P. (2000). A state estimation
approach to non-stationary optical tomography problem. Journal of the Optical
Society of America A, 20, 876884.
Pogue, B. W., & Patterson, M. S. (1994). Forward and inverse calculations for nearinfrared imaging using a multigrid finite difference method. In: R.R. Alfano
(Ed.), Advances in optical imaging and photon migration. Vol. 21 (pp. 176180).
Proc. OSA.
Prince, S., Kolehmainen, V., Kaipio, J. P., Franceschini, M. A., Boas, D., & Arridge, S. R.
(2003). Time series estimation of biological factors in optical diffusion tomography.
Physics in Medicine and Biology, 48(11), 14911504.
Ren, K., Abdoulaev, G. S., Bal, G., & Hielscher, A. H. (2004). Algorithm for solving the
equation of radiative transfer in the frequency domain. Optics Letters, 29(6), 578580.
Tachtsidis, I., Koh, P. C., Stubbs, C., & Elwell, C. E. (2010). Functional optical
topography analysis using statistical parametric mapping (SPM) methodology with
and without physiological confounds. In E. Takahashi & D. F. Bruley (Eds.),
Advances in experimental medicine and biology. Vol. 662. Oxygen transport to
tissue XXXI (pp. 237243). USA: Springer.
Tachtsidis, I., Leung, T. S., Chopra, A., Koh, P. C., Reid, C. B., & Elwell, C. E.
(2009). False positives in functional near-infrared topography. In P. Liss, P.
Hansell, D. F. Bruley, & D. K. Harrison (Eds.), Advances in experimental
medicine and biology: Vol. 645. Oxygen transport to tissue XXX
(pp. 307314). USA: Springer.
Ye, J. C., Tak, S. H., Jang, K. E., Jung, J. W., & Jang, J. D. (2009). NIRSSPM: Statistical
parametric mapping for near-infrared spectroscopy. NeuroImage, 44, 428447.
Image Reconstruction in MRI

L Ying, State University of New York at Buffalo, Buffalo, NY, USA
Z-P Liang, University of Illinois at Urbana-Champaign, Urbana, IL, USA
Glossary
Aliasing Image artifact due to undersampling of k-space. In

Fourier reconstruction (from Cartesian data), aliasing
manifests itself as folding over (ghosting) of some parts of the
object. In filtered backprojection reconstruction (from polar
data), angular undersampling results in streaking artifacts.
Asymmetrical k-space sampling Collection of more data
points on one side of the k-space origin than on the other.
This data acquisition scheme is often used in partial-Fourier
imaging.
Backprojection Mathematical operation that maps a onedimensional function (projection profile) to a higherdimensional function by assigning (backprojecting) the
value of each point in the projection to a line, a plane, or a
hyperplane.
Compressed sampling (sensing) Signal processing
techniques for acquiring and reconstructing a signal from subNyquist samples by solving underdetermined linear systems.
Fast Fourier transform (FFT) Efficient algorithms to
compute discrete Fourier transforms.
Filtered backprojection Technique used for image

reconstruction from a set of projection profiles (or polar
k-space data). It involves filtering the projection profiles by a
suitable filter function and then backprojecting the filtered
projections into the image domain.
Frequency encoding Linear mapping of spatial location to
the resonance frequency of MR signals.
Gibbs ringing artifact Image artifact associated with the
approximation of a discontinuous function by a truncated
Fourier series. This artifact manifests itself as spurious
ringing near the area of discontinuities.
k-Space Spatial-frequency domain of the image.
Nyquist frequency (rate) Minimum sampling frequency
of a signal beyond which aliasing will occur in any
linear reconstruction from the sampled values. This
frequency is twice the maximum frequency of a bandlimited
signal.
Phase encoding Linear mapping of spatial location to the
phase of MR signals.
Sparse sampling Sampling below the Nyquist rate.
Nomenclature
d(k)
d(k, t)
L
R
s(r)
Measured k-space data

Measured (k, t)-space data
Total number of receiver coils in parallel imaging
Acceleration factor (undersampling factor) in
parallel MRI
Sensitivity function of a receiver coil
Imaging Equation
MRI experiments, especially fMRI experiments, often use an
array of receiver coils for data acquisition. The data collected by
an individual coil (after proper simplifications and processing
such as filtering and demodulation) can be expressed as
d k rrs rei2pkr dr
[1]
where r(r) is the desired image function, s(r) denotes the
sensitivity function of the th receiver coil for 1, 2, . . ., L,
and the modulating factor ei2pkr represents phase and frequency encoding effects introduced using magnetic field gradients. If the sensitivity weighting effects are ignored (e.g., for
coils with spatially uniform sensitivity), we have the standard
Fourier transform imaging scheme (known as Fourier encoding). Otherwise, the sensitivity functions of different coils can
r(r)
r(r, t)
r^r
Dk
F
Field of view or spatial support of an image

function
Desired image
Desired dynamic images
Reconstructed image
Nyquist sampling interval (i.e., Dk 1/W)
Sparsifying transform
be utilized for spatial encoding (known as sensitivity encoding)

as is done in parallel imaging.
In practice, d(k) is measured over a discrete set of k-space
points generated by a chosen sampling trajectory. A number of
k-space sampling trajectories are possible depending on how
the gradient field is applied during data acquisition. Figure 1
shows three examples used for 2-D imaging. Among them,
Cartesian sampling is commonly used in clinical scans. In 2-D
uniform Cartesian sampling,

k kx , ky nDkx , mDky ,
n N, N 1, . .. ,N 1; m M, M 1, . .., M 1 [2]
The sampling intervals are often chosen to satisfy the
Nyquist sampling requirement:
http://dx.doi.org/10.1016/B978-0-12-397025-1.00289-X
Dkx
1
1
, Dky
Wx
Wy
[3]
223
224
INTRODUCTION TO METHODS AND MODELING | Image Reconstruction in MRI
ky
ky
kx
(a)
ky
kx
(b)
kx
(c)
Figure 1 Examples of k-space sampling schemes used in MRI experiments: (a) cartesian sampling, (b) polar sampling, and (c) spiral sampling.
where Wx and Wy specify the field of view along the x and y

directions, respectively.
However, sub-Nyquist sampling (i.e., sampling intervals
larger than the Nyquist interval) has also found increasing
use in MRI experiments to reduce scan time. We will discuss
the reconstruction of the desired image function r(r) from
both Nyquist and sub-Nyquist data.
Basic Reconstruction Methods

Image reconstruction is an ill-posed mathematical problem.
Practical reconstruction methods provide only an approximation of the true image function. This section describes several
popular methods used in practice for image reconstruction
from Nyquist data without additional constraints. The subsequent section will discuss image reconstruction with constraints or with sub-Nyquist data.
Fourier Reconstruction
For Cartesian k-space data sampled uniformly above the
Nyquist rate, image reconstruction is usually done by applying
the FFT (fast Fourier transform) along each dimension. For
simplicity, consider the one-dimensional case (say, along x)
with a single receiver coil. The reconstruction method can be
summarized as
r^x Dkx
N1
X
dnDkx ei2pnDkx x , jxj <
nN
1
2Dkx
[4]
which is popularly known as the Fourier reconstruction formula.

The pixel values of r^x, say, r^mDx for m N, N 1, .. .,
N 1 and Dx 1/(2NDkx), can be evaluated efficiently using
an FFT algorithm.
The Fourier reconstruction r^x given by eqn [4] is related
to the true image function r(x) by the following convolution
equation:
1
r^x
rx^hx x^d^
x
[5]
1
where h(x), known as the point spread function, is given by
hx Dkx
sin 2pNDkx x ipDkx x

e
sin pDkx x
[6]
The convolution effects result in a loss of resolution in r^x

and Gibbs ringing artifact. The Gibbs ringing artifact is a common image distortion that exists in Fourier reconstructions,
which manifests itself as spurious ringing around sharp edges
(Figure 2). The maximum undershoot or overshoot of the
spurious ringing is about 9% of the intensity discontinuity
and is independent of the number of data points used in the
reconstruction. The frequency of oscillation, however,
increases as more data points are used. For this reason, when
a large number of data points are used in practice, the spurious
ringing does not cover an appreciable distance in the reconstructed image and thus becomes invisible.
A straightforward method to reduce the Gibbs ringing artifact is to apply a weighting function w(n) (e.g., the Hamming
window function) on the measured data d^nDk wndnDkx
to reduce or remove data discontinuities in d(nDkx) at the ends
before the Fourier reconstruction formula is applied. This operation, known as windowed Fourier reconstruction, reduces Gibbs
ringing artifact at the expense of spatial resolution.
Filtered Backprojection Reconstruction

For polar k-space data, a conventional approach to image
reconstruction is to use the well-known filtered backprojection
algorithm. For example, in the two-dimensional case, the
reconstruction formula is given by
p 1
r^x, y
Hkdp k, fei2pkxcos fysinf dkdf
[7]
0 1
where dp(k, f) d(k cos f, k cos f) represents the polar k-space

data and H(k) is a filter function applied in the radial direction.
In the noiseless case, H(k) |k|P(k/kmax), where P() is the
rectangular window function of unit width and kmax is
the maximum frequency that the data acquisition covers in
the radial direction. For noisy data, several more practical filter
functions are used, including the SheppLogan filter H(k) |k|
sinc(pk/kmax)P(k/kmax) and the generalized Hamming filter H
(k) |k|(0.54 0.46 cos(2pk/kmax)P(k/kmax). The reconstruction formula is, in essence, a discrete version of the 2-D inverse

Fourier transform in the polar form. It is often known as
filtered backprojection reconstruction because it can be interpreted as consisting of two steps. The first step is to apply
the 1-D inverse Fourier transform in the radial direction to
the polar k-space data filtered by H(k). This step yields a
filtered projection P^r, f of the desired image based on the
projection-slice theorem (connecting the Fourier transform to
the Radon transform). The second step is to backproject each
filtered projection P^r, f using the backprojection operator:
P^r, f ! P^xcos f ysin f, f for all the projection angles,
which will yield the final image r^x, y.
Reconstruction from Sensitivity-Encoded Data

Sensitivity encoding using multiple coils of different sensitivity
profiles has become an effective tool for fast imaging. Assume
that L coils are used for simultaneous data acquisition. To
achieve a factor of R acceleration, k-space is undersampled
along the phase encoding (say, x) direction by a factor of R as
compared with conventional Fourier imaging (Figure 3(a)).
Applying the standard Fourier reconstruction method in
225
eqn [4] to the sub-Nyquist data collected by the th coil

(ignoring the data truncation effects) yields
r^ x
R1
X

^ s x m W
^
r x mW
[8]
m0
^ < x < W=2, where W

^ 1=RDkx
for 1, 2,. . ., L and W=2 W
denotes the reduced field of view. Such a Fourier reconstruction
contains significant aliasing artifacts as illustrated in Figure 3(b).
These aliased images from multiple coils can be combined to
obtain an unaliased image as the final reconstruction. Several
methods have been proposed for doing so, one of which is
described here to illustrate the basic concept. Assuming that
R L, we can solve for r(x) pixel by pixel from eqn [8]. More
specifically, rewriting eqn [8] in matrix form
Sr r^
[9]
where

3
^ s1 x R 1W
^
s1 x s1 x W

6 s2 x s2 x W
^ s2 x R 1W
^ 7
7
S6
4
5

^ sL x R 1W
^
sL x sL x W
2
Figure 2 An example of Fourier reconstruction with truncation artifacts.
Rky
Coil 1
Coil 2
Coil 3
Coil 4
ky
(a)
kx
(b)
Figure 3 (a) Cartesian undersampling used in sensitivity encoding (solid lines are acquired and dashed lines are skipped); (b) Fourier reconstructions
from undersampled data acquired by different coils (R 2, L 4).
226

2
3
2
3
r^1 x
rx
^
6
7
6 r^2 x 7
r xW
7 and r
7
^ 6
r6
4
5
4 5

^
r x R 1W
r^L x
ky
Equation [9] is known as the SENSE reconstruction formula,

which can also be derived from Papoulis generalized sampling
theorem. Clearly, perfect reconstruction of r(x) requires (a)
that r^L x is noiseless and not corrupted by the data truncation
artifact, (b) that there is precise knowledge of s(x) to form S,
^ < x < W=2. These
and (c) that S is nonsingular for W=2 W
conditions are usually difficult to meet. To address the issue of
measurement noise, the best linear unbiased estimator (BLUE)
of the desired image is obtained as

1
r SH C1 S SH C1 r^
[10]
kx
n0
N1
Figure 4 k-Space samples in partial-Fourier imaging (solid dots

indicate locations of acquired data).
where C is the noise covariance matrix of all receiver coils.

When the covariance matrix is close to an identity matrix, the
BLUE is equivalent to the least-squares solution. The coil sensitivities are usually estimated from images obtained from a
separate calibration scan before or after the accelerated scans.
The sensitivity function of the th coil is derived from the
sensitivity-modulated image of the coil, normalized by the
image acquired by a body coil with uniform sensitivity.
Another approach is to acquire additional autocalibration
signals. The central k-space data after Fourier transformation
produce low-resolution reference images. To derive the sensitivities, these low-resolution reference images are divided by
their sum-of-squares combination. When S is close to singular,
SENSE reconstruction becomes ill-conditioned. To address
the issue, regularization is usually used. For example, the simplest approach is the Tikhonov regularization:
sometimes also used in the phase encoding direction when an

asymmetrical set of phase encoding measurements is acquired
to reduce data acquisition time. Usually, n0 is much smaller
than N, typically n0 16 16 or 32 with N being on the order
of 128. Such a data acquisition scheme is motivated by the
consideration that the central k-space data d(nDkx) for
n n0, n0 1 . . ., n0 1 can be used to obtain a lowresolution phase image ^x (a reasonable approximation of
the phase of the desired image), which can then be used as a
constraint to recover the missing data by data symmetrization/
extrapolation. Phase-constrained data symmetrization is often
done using an iterative algorithm known as projection onto
convex sets (POCS), which is summarized as

1
r SH C1 S lI SH C1 r^
The projection operators 1 and 2 in eqn [12] are defined as
[11]
rm1 x 1 2 frm xg
1 frxg jrxjei^x
where l is a scalar regularization parameter.
[12]
[13]
and
Constrained Reconstruction
Conventional methods for image reconstruction are based on a
key mathematical assumption that the desired image function
is support-limited. This assumption enables image reconstruction from discrete measurements. In practice, additional mathematical assumptions can be made about the image function,
such as low-frequency phase variation, sparsity, and lowrankness. These assumptions, formulated as mathematical
constraints, can help improve image reconstruction from limited data. This section describes three representative constrained reconstruction methods.
Reconstruction from Partial-Fourier Data with Phase

Constraints
In partial-Fourier imaging, k-space is sampled asymmetrically
to give, for example, d(nDkx) for n n0, n0 1, . . ., N 1,
where n0 < N (Figure 4). Such a sampling scheme arises in
the frequency encoding direction when a short echo time is
used to avoid spin dephasing due to short T2*, caused by local
susceptibility changes or uncompensated motion effects. It is
2 frxg
1
frxg
[14]
in which is the Fourier transform operator and is a data

replacement operator defined as
n
o dnDk n n N 1
x
0
[15]
d^nDkx ^
dnDkx otherwise
This algorithm has found useful practical applications.
Reconstruction from Sub-Nyquist Data with Sparsity

Constraints
Sparse models have found increasing use in image reconstruction because MR images are sparse in a number of bases (e.g.,
wavelets). Figure 5 shows an example of sparsity of an image
after a wavelet transform. Enforcing the sparsity constraint has
been studied in the context of compressed sensing (CS). It has
enabled high-quality image reconstruction from highly undersampled k-space data.
Assume that r(r) is sparse in basis {(r)}. Then,
P
r(r) c(r) will have a small number (say, L) of nonzero
coefficients c for 1, 2, . . ., L. If we know the locations (i.e.,

{1, 2, . . ., L}) of these coefficients, we in principle need only L
encodings to determine the values of the corresponding coefficients. In practice, we usually do not know the locations of
the nonzero coefficients. Determining both the locations and
values of these coefficients is a basis pursuit problem that is
addressed in the CS theory. Specifically, in order to reconstruct
the original desired image r from sub-Nyquist k-space data,
both data acquisition and image reconstruction should satisfy
certain requirements.
In data acquisition, sampling of k-space should be
incoherent (instead of being structured or uniform as in
conventional Fourier imaging) so that aliasing artifacts are
randomized (Figure 6). Although random sampling of kspace in all dimensions has a high degree of incoherence, it is
generally impractical as k-space trajectories have to be relatively
227
smooth due to practical constraints. Random variable-density

phase encodings with fully sampled frequency encodings offer
a practical option for incoherent sampling for Cartesian sampling trajectories. Radial and spiral trajectories give incoherent
aliasing. In those schemes, high-energy low-frequency image
components alias less than lower-energy higher-frequency
components, and aliasing appears incoherent in the image
domain.
In reconstruction, nonlinear algorithms are often used in
order to incorporate the sparsity constraint. Representing the
imaging equation in matrix-vector form as Er d, where E is
the Fourier encoding matrix with incoherent sub-Nyquist sampling, r is the desired image in vector form, and d is the
measured data vector, the sparsity-minimization reconstruction is given by
Figure 5 (a) A brain image and (b) its wavelet transform coefficient map.
ky
(b)
kx
ky
(a)
kx
ky
(c)
kx
Figure 6 (a) Fully acquired k-space; (b) 1-D variable-density undersampling along the phase encoding (ky) direction and the incoherent artifacts in the
reconstructed image; (c) 2-D variable-density Poisson-disk undersampling along both the phase encoding (ky) and frequency encoding (kx)
directions and the aliasing artifacts in the Fourier reconstruction.
228

r arg min kFrk0 s:t: kEr dk2 < s
[16]
where F represents a sparsifying transform (basis) for r and s

is a tolerance of data inconsistency. The previously mentioned
optimization problem is not practical because solving eqn [16]
is NP-hard and the solution is sensitive to noise. Instead, the
reconstruction is often obtained by solving the following convex optimization problem:
r arg
min jjEr djj22 ljjFrjj1
[17]
where l is a regularization parameter. This method (often

known as CS reconstruction) has emerged as an effective tool
for image reconstruction from undersampled k-space data
acquired using a single receiver coil or multiple receiver coils.
Reconstruction from Sub-Nyquist Data with Low-Rank

Constraints
In many dynamic imaging experiments (such as functional
imaging), the desired image is a function of both space and
time. These functions r(r, t) often have a high degree of spatiotemporal correlation, which admits the following expression:
rr, t
P
X
c r t
[18]
These functions are called Pth-order partially separable

(with P being the separation rank or order). Correspondingly,
the (k, t)-space signal d(k, t) is often Pth-order partially
separable (PS). It can be shown that the Casorati matrix

formed from d(km, tn) from any sampling points specified by
N
{km}M
m1 and {tn}n1,
2
3
dk1 , t1 dk1 , t2 dk1 , tN
6 dk2 , t1 dk2 , t2 dk2 , tN 7
6
7
Cd 6
[19]
7;
..
4
5
dkM , t1 dkM , t2 dkM , tN
has a rank no larger than P. Therefore, the row (or column)

vectors of C(d) reside in a P-dimensional subspace. This property can be exploited for recovery of C(d) when many of its
entries are missing or for image reconstruction from highly
undersampled data. More specifically, let A : NM ! Q be
a sampling operator used for data acquisition, with Q being
the number of data points measured and d 2 Q being the
measured data vector. The rank-minimization reconstruction
is given by
^ arg min rankC s:t: jjAC djj2 < s
C
CNM
C2
[20]
with s being a preselected noise tolerance. A more general

regularization-based formulation is
^ arg min jjAC djj2 C
C
2
C2CNM
[21]
where is a regularization functional that favors matrices with

low rank. Rank-minimization reconstruction has found useful
applications in both dynamic imaging (Figure 7) and spectroscopic imaging.
Figure 7 An fMRI image sequence reconstructed using conventional Fourier reconstruction method (top) and using the PS model with the same
number of encodings that sparsely sample (k, t)-space (bottom).
Acknowledgments
This work was supported by NSF grant CBET 1265612 and
NIH-R01-EB013695. The authors thank Yihang Zhou for preparing the figures in the article.
See also: INTRODUCTION TO ACQUISITION METHODS: EchoPlanar Imaging; High-Speed, High-Resolution Acquisitions; MRI and
fMRI Optimizations and Applications; Temporal Resolution and Spatial
Resolution of fMRI; INTRODUCTION TO METHODS AND
MODELING: Computerized Tomography Reconstruction Methods.
Further Reading
Bertero, M., & Boccacci, P. (1998). Introduction to inverse problems in imaging.
Bristol, Philadelphia: Institute of Physics Publishing.
229
Cande`s, E. J., Romberg, J. K., & Tao, T. (2006). Robust uncertainty principles: Exact
signal reconstruction from highly incomplete frequency information. IEEE
Transactions on Information Theory, 52, 489509.
Donoho, D. L. (2006). Compressed sensing. IEEE Transactions on Information Theory,
52, 12891306.
Kak, A. C., & Slaney, M. (1988). Principles of computerized tomographic imaging.
Piscataway, NJ: IEEE Press.
Liang, Z.-P. (2007). Spatiotemporal imaging with partially separable functions.
IEEE International Symposium on Biomedical Imaging, Arlington, TX, pp. 988991.
Liang, Z.-P., & Lauterbur, P. C. (1999). Principles of magnetic resonance imaging: A
signal processing perspective. Piscataway, NJ: IEEE Press.
Lustig, M., Donoho, D., & Pauly, J. M. (2007). Sparse MRI: The application of
compressed sensing for rapid MR imaging. Magnetic Resonance in Medicine, 58,
11821195.
Ying, L., & Liang, Z.-P. (2010). Parallel MRI using phased array coils. IEEE Signal
Processing Magazine, 27, 9098.
Artifacts in Functional MRI and How to Mitigate Them

L Hernandez-Garcia and M Muckley, University of Michigan, Ann Arbor, MI, USA
Glossary
Aliasing The immediate result of not collecting enough

samples in a given signal (or image). It generally manifests
itself as the appearance of the high-frequency components
of the signal as lower-frequency components. In MR images,
this often means wrapping of the edge of an image around to
the opposite edge.
Autocorrelation A measure of how one part of a signal (or
image) is correlated with other parts of the signal (or image).
If a signal is autocorrelated, it means that the samples are not
independent from each other.
BOLD effect The Blood Oxygenation Level Dependent
(BOLD) effect is the resulting change in image intensity due
to changes in oxygenation in brain tissue resulting from
neuronal activation. This signal change is the basis for most
modern FMRI experiments.
Cost function Measure of an undesirable property.
Generally, it quantifies mathematically a property that we
want to minimize in a given optimization problem. For
example, in order to reduce distortion, we might want to
search for a correction that minimizes the difference
between the observed data and a predictive model.
Introduction
This article is devoted to the things that can (and do) go wrong
during acquisition of functional MRI (fMRI) data, particularly
BOLD-weighted time series. For this article, the operational
definition of an artifact is any violation of the assumptions
about the image that results in degradation of the quality of the
data. As such, one has to be mindful of this fact when analyzing
any type of data, because interesting phenomena such as blood
flow effects, cardiac rate, and the BOLD itself could be considered artifacts by this definition. The topic of artifacts in fMRI is
quite broad because of the large number of things that can go
wrong in an image in MRI. There is a vast literature about these
aberrations as they pertain to clinical imaging (see, e.g., Bellon,
Haacke, et al., 1986; Henkelman, 1996; Hornak, 1997), but
providing a comprehensive classification of image artifacts is
not our goal here. Instead, we aim to provide the reader an
understanding of the implicit assumptions made in functional
imaging time series and the most common violations of those
assumptions. Sometimes, these can be prevented or at least
mitigated by careful experimental and pulse sequence design.
Other times, they cannot be prevented but instead must be
corrected or, at least, accounted for during the analysis of
the data.
In order to understand and categorize fMRI artifacts, let us
first take a look at what fMRI time series data consist of.
Although fMRI time series are essentially 3-D movies, in the
Field map An image whose pixel intensities are determined

by the magnitude of the magnetic field. They generally are
used to determine the distortion of the magnetic field.
Geometric distortion Any image artifact that causes the
objects in the image to be warped.
Ghosting Image artifact where part of the image is
replicated and superimposed on other parts of the image.
Inverse problem Any problem that can be framed with an
equation of the form y f(x), where y is an observed
quantity and x is the unknown parameter of interest.
Rigid body transformation A transformation performed on
an image that does not deform the objects in the image. This
is generally limited to translations (shifts), reflections, and
rotations.
Shimming In MRI this refers to the procedure of making the
main magnetic field (B0) as homogeneous as possible.
Originally this is done by the placement of small pieces of
iron, or shims, around the bore of the magnet (passive
shimming). However, it is refined for every scan by
activating a set of secondary electromagnets, referred to as
shim coils (active shimming).
bulk of the analysis techniques applied to the fMRI, the data

are arranged in the shape of a matrix (2-D). Each row of this
matrix represents a whole 3-D volume acquired at a particular
time, a 3-D movie frame, if you will. The image intensity of all
pixels from all the slices is concatenated to form a single row.
This procedure is repeated for each 3-D image acquired in the
time series, and the rows are stacked on top of each other to
form a matrix with as many columns as pixels in one of the 3-D
images and as many rows as images in the time series. By doing
this, each position along a row represents a location in space,
and each position along a column represents a position in
time. An example of an fMRI time series arranged in this way
is shown in Figure 1.
This arrangement makes it easy to perform linear regression
analyses, independent or principal component analysis, etc.
(of course, one could also use columns to encode time and
rows to encode space and still use the same framework).
However, there are a number of assumptions implicitly
made when analyzing this matrix, and most are violated to
some degree. These violations are what give rise to artifacts in
fMRI. Clearly, it is crucial to address these violations to the best
of our abilities lest the results from the analysis also be artifactual. Here are the main assumptions:
Assumption 1: Each time course (column in our case) comes
from a single voxel only. This assumption is primarily violated
by the movement of the subjects head during the scan, but also
geometric image distortions from off-resonance and
http://dx.doi.org/10.1016/B978-0-12-397025-1.00290-6
231
232
INTRODUCTION TO METHODS AND MODELING | Artifacts in Functional MRI and How to Mitigate Them
imperfections in the acquisition pulse sequences can cause

voxels to be misplaced, and spatially correlated noise can mix
the signals from different voxels.
Assumption 2: The data in each image (row) correspond to a
single time point. This assumption is violated quite severely in
most fMRI experiments because images are typically acquired
in sequential order, such that the time interval between
acquisitions of the first and the last slices for a given volume
can be almost the whole repetition time (TR) of the acquisition
(typically 23 s).
Assumption 3: Most analysis techniques assume that the
noise present in each voxel is independent or uncorrelated to
the rest of the voxels. However, noise in MRI is typically autocorrelated across the image. This happens mainly because of
the images that are reconstructed from raw k-space signals by
Fourier transforms, which are essentially a weighted sum of all
the data. Thus, if one data point in the raw signal (k-space) is
corrupted by correlated noise, this noise shows up in the all the
pixels of the reconstructed image.
Assumption 4: Similar to the previous assumption, we also
assume that the noise at each time point is independent from
other time points. However, fMRI noise is well known to have
an autoregressive nature in part because of physiological fluctuations (e.g., heartbeat, respiration, and low-frequency oscillations) and in part because of drifts in the scanners hardware.
Assumption 5: We assume that changes in signal intensity
over the time series are caused by the BOLD responses induced
by the experimental paradigm. Obviously, there are many
other potential sources of signal fluctuation. Some sources
are physiological noise, signal fluctuations due to movement
(partial volume effects), subject noncompliance, etc.
Clearly, there are many violations to the basic assumptions
made by most analysis techniques, but most of them can be
overcome to an acceptable degree through preprocessing techniques and by including the sources of the artifact in the
statistical models. The rest of the article is devoted to describing
the nature of most of these artifacts and the most popular
correction techniques to mitigate them. The level of technical
detail throughout the article is generally not very high, as it is
intended to serve as a general resource to the neuroscientist.
Having said that, some of the concepts are explained in greater
detail than may seem necessary because they are particularly
important and ubiquitous in image analysis, so we feel it is
important that all investigators have a firm grasp of them.
Subject Motion and Realignment

20
Time points
40
60
80
100
120
140
1
6
7
voxels
10 11
104
Figure 1 fMRI data consist of a movie of 3-D images. However, it is

much more convenient to rearrange the data into a 2-D matrix such that
each pixels signal intensity over time is a column of that matrix. In
addition to easier access to the data, this arrangement lends itself to
matrix algebra manipulations much more readily.
Subject motion is perhaps the most obvious and pervasive

artifact that one has to contend with in fMRI. Most analyses
of the time series data assume that every time course comes
from a single voxel, but as the subject moves his/her head, the
contents of that voxel (i.e., that location in space) will
change. There are several implications associated with this
phenomenon.
The first implication is the obvious misregistration of the
images to each other. In other words, the contents of the image
are shifted and rotated from image to image. The solution to this
problem is to move the contents of each image in the time series
to match a reference image. Typically, we choose the middle
image in the time series as a reference and realign the rest to
that one. The term realignment refers to rotating and shifting an
image to match another without any deformation of its content
(Friston, Ashburner, et al., 1995; Friston, Williams, et al., 1996).
In order to understand the details of how this is done, it is
important to realize that the realignment process can be
thought of as resampling each 3-D image in the time series
with a rotated and shifted sampling grid (see Figure 2).
Figure 2 As the subjects head moves in the scanner, the contents of the image grid change. Conversely, we can also think of this as moving the
imaging grid for the purpose of realignment. Our mission is to interpolate the contents of the new grid from the neighboring data.
The first step in this process is to determine the appropriate
coordinates of that new sampling grid, but before we discuss
that, let us review the concept of rigid body transformations
(i.e., shifting and rotating images without warping them).
Shifting a set of coordinates in space can be easily accomplished by adding the desired shift to each one of their
axes. For example, a point (x1, y1) can be shifted to the right
by adding some shift xs to the x coordinate. In three dimensions, this can be generalized to a simple equation in matrix
notation:
2
3 2 3 2 3
x1
xs
x2
4 y2 5 4 y1 5 4 ys 5
z2
z1
zs
[1]
Rotating objects is a bit more complicated, but it can also be

boiled down to a simple matrix operation. For example, if we
want to rotate a point on the xy-plane, say (x1, y1), about the
origin by an angle y, we would carry out the following
operations:
x2 x1 cos y y1 sin y
[2]
y2 x1 sin y y1 cos y
[3]
As before, we can write this xy-plane rotation as a single

equation in matrix form, generalized to three dimensions, as
32 3
2 3 2
x1
cos y sin y 0
x2
4 y2 5 4 sin y cos y 0 54 y1 5
[4]
0
0
1
z2
z1
The same procedure can be used to produce rotations on
each plane. The rationale for doing this with matrices is that we
can combine all the rotations and shifts into a single matrix
operation that rotates and shifts the coordinates of an object:
2 3
2 3
x2
x1
6 y2 7
6 7
6 7 A6 y1 7
[5]
4 z2 5
4 z1 5
1
1
Note that the 1 appended to the coordinate vectors is there
simply to make the dimensions of the matrix multiplication
work. Thus, multiplying the coordinates of the each voxel by
matrices like the one described earlier allows us to perform
rigid body transformations on the coordinates of each voxel in
the image. The next step in the process is simply to interpolate
the data at the new locations from the data at the old locations.
(Interpolation is discussed in more detail in the slice timing
section.)
But how do we determine what the transformation matrix
should be? This is generally done by searching for a combination of matrix entries that will produce the best match between
the reference image and the target image that we are trying to
realign. There are many ways to define what the best match
means. A measure of agreement between two images can be the
residual sum of squares of the voxels intensities at each location. (These measures are often referred to as cost functions.)
Another can be the correlation coefficient between the two
images. Other measures of agreement exist as well, such as
computing the mutual information between the two images,
which computes the agreement between the statistical distributions of the two images. The mutual information metric is
233
particularly useful when trying to coregister images acquired

with different imaging modalities, for example, a T2-weighted
image and a T1-weighted image, but is generally not used for
realigning fMRI time series because it is more computationally
expensive than other techniques. Generally, the most popular
cost function is the normalized correlation because of its accuracy and speed, as shown in Jenkinson, Bannister, et al. (2002).
As stated, the realignment process consists of a search for
the transformation matrix that will maximize the agreement
between the images. The search process is usually an iterative
procedure by which we systematically vary each entry of the
transformation matrix. After each variation, we test whether
that new matrix improved the fit or made it worse. If the fit
improves after the change, we continue incrementing (or
decrementing) that entry until the fit stops improving. This
class of algorithms is referred to as gradient methods. There
is a great deal of literature on search optimization methods,
but that is beyond the scope of this article. For more information on this topic, we refer the reader to texts such as Boyd and
Vandenberghe (2004).
The woes of movement in fMRI are unfortunately not limited to the realignment of the images. Consider the picture in
Figure 3. If the subject moves her head by some fraction of a
voxels length in one direction, the proportions of white matter, gray matter, and cerebrospinal fluid in that voxel will
change. While this is not an issue in homogeneous voxels
that contain only one type of tissue, it can cause a major source
of variation in signal intensity on the tissue boundaries. Unfortunately, there is no good way to correct for these partial
volume effects in each image. However, the variation in signal
intensity produced by partial volume effects in a time series of
images is a function of the amount of movement. While we do
not know what this function is at each voxel, we can make a
first-order approximation by assuming that the change in signal intensity is directly proportional to the weighted sum of the
movement parameters. In practical terms, this means that we
can use the motion parameters calculated by the realignment
algorithm as confounds and append them to the design matrix.
In fact, we can add higher-order terms to the approximation by
also appending the square, cube, etc. of the realignment
parameters. This approach can reduce the residual variance of
the data quite significantly. A word of caution: if the subjects
movement is correlated with the task, the movement parameters cannot be used as confounds, since they will essentially
Figure 3 Consider a voxel (in blue) that contains both gray matter and
white matter. When the subject moves, the fraction of gray matter and
white matter in that voxel changes, as depicted in the figure.
234
remove the effects of interest. In fact, it becomes extremely

difficult to separate the effects of interest (i.e., the task) from
the effect of the subjects movement. Hence, it is very important to ensure that the movement parameters are not correlated
with the design matrix, by orthogonalizing them (orthogonalization refers to the process of systematically regressing out the
columns of a matrix from each other see Strang, 2006). In
many cases, movement may simply not be separable from the
effects of interest.
BOLD-weighted fMRI time series are sensitive to magnetic
field inhomogeneity, which leads to image deformations and
signal loss, as we discuss in subsequent sections. For now, let us
recall that all materials have the ability to perturb a magnetic
field (magnetic susceptibility is a fundamental property of
materials that describes their ability to modify a magnetic
field). While these changes are subtle compared to the large
magnetic field of an MRI scanner, they have a noticeable effect
on the images. These artifacts become more complicated in the
presence of motion for two reasons: the shape and distribution
of the magnetic field are affected by the presence of the object
and its position in the main magnetic field. As a result, as the
object moves, the magnetic field distribution in the bore of the
magnet changes. This leads to ghosting artifacts and changes in
the off-resonance artifacts pattern (also discussed in the succeeding text). The net result is a time-varying deformation of
the images in the time series.
There has been considerable effort spent in the literature to
correct for these time-varying distortions. Generally speaking,
there are two approaches that people use to reduce the variance
in the time series introduce by geometric distortions. The first
one is to try to unwarp the images by modeling the physics of
the geometric distortions as a time-varying deformation field
that can be estimated. This approach can successfully correct
for the image deformations although it is fairly complex and
computationally intensive (Andersson, Hutton, et al., 2001;
Andersson & Skare, 2002). The second approach is the same
as the one taken to correct for partial volume effects (see the
previous section): to use the motion parameters obtained from
a rigid body realignment to model the deformations
(Johnstone, Ores Walsh, et al., 2006). While the partial volume
effects and the geometric distortions are not separable under
this model, they are typically just confounds in most fMRI
studies and of no interest to the investigator. In other words,
we do not care which is which.
As a final note for this section, the best motion correction is
not as good as preventing movement in the first place. It is
simply crucial that subjects avoid any movement while being
scanned. Careful packing of the head with pillows is a common and effective practice. Most importantly, making sure that
the subjects are comfortable, relaxed, and cooperative when
they go into the scanner will be tremendously helpful.
multiband excitation (Moeller, Auerbach, van de Moortele,

Adriany, & Ugurbil, 2008; Moeller, Yacoub, Olman, Auerbach,
Strupp, Harel, et al., 2010; Wu et al., 2013)). As a result, the
sampling time of the data at each voxel depends on which slice
that voxel belongs to. This has important consequences for the
analysis of fMRI time series data. For example, consider an
fMRI experiment in which the slices are collected sequentially
from bottom to top. In the case of a typical linear regression
analysis to detect activation, if we construct a general linear
model based on the onset times of the activation, the raw data
will have shifted in time relative to this model differently from
slice to slice. If the first slice is being used as a reference for
timing in the construction of the general linear model, the last
slice will be shifted by as much as (N 1) TR/N, where N is
the number of slices and TR is the repetition time (or time it
takes between acquisitions of the same slice. Typical TRs in
fMRI are in the order of 23 s). This temporal shift can have a
profound effect on the results of the analysis if it is not appropriately handled as shown in Figure 4.
The good news is that there are simple corrections for the
temporal shifts (Sladky, Friston, et al., 2011). The simplest
approach is to shift the data in time such that all the slices
are collected at the same time. This can be accomplished voxel
by voxel by interpolating the data at the desired time points
from data that were actually collected at the surrounding time
points. One can also construct a separate general linear model
that is appropriately shifted in time for each slice when analyzing the data using regression analysis.
Interpolation of data is an important and pervasive step in
signal and image processing, so we will give a brief overview of
what is involved. For more on the subject, please see
Oppenheim, Schafer, et al. (1999) or similar textbooks on the
subject. In its simplest form, one can interpolate a missing
datum by averaging its surrounding data points. One can
increase the number of points that are used in the average to
reduce the interpolation error, but the neighboring data must be
weighted such that the nearest points contribute the most to the
average. Provided that the data are smooth, continuous and
periodic (within reason), the more data are used in the interpolation process, the more accurate the result will be. It can be
shown that the interpolation that preserves the most amount of
information is a weighted average of the whole time series and
The data you think you have
Slice Timing Errors: Interpolation or Remodeling

The bulk of fMRI studies are done using multislice imaging
sequences, which collect the image slices sequentially by exciting one slice at a time (alternatively, one could use 3-D imaging sequences, which excite the whole volume at a time (van
der Zwaag, Francis, & Bowtell, 1996; Yang et al., 2006) or
The data you really have

Figure 4 A simulated BOLD response from a slice that is collected later
than the reference slice in the volume. If the lag between slices is
neglected, the model for the expected will be shifted in time relative to the
true response.
235
Raw
290
280
270
260
250
240
50
100
150
200
250
200
250
Slice time corrected

300
Global signal
290
280
270
260
250
240
50
100
150
Scan
Figure 5 Data interpolation can propagate noise through the neighboring data points as evidence by the figure. Here, the early settling of the signal due
to T1 relaxation and several instances of movement by the subject introduce spikes or discontinuities in the raw data. The slice timing interpolation
process can propagate those discontinuities as ripples through the neighboring data points. Note that this sort of artifact also occurs when interpolating
data in space.
Original signal
Modulated signal
Time
domain
Frequency
domain
Ghosting artifact from
movement in the
arteries
Figure 6 If a time series signal, like the sinusoid shown in the figure (blue), is modulated by another sinusoid, the frequency content of that
signal (red) becomes split and shifted in frequency. The same thing occurs in two dimensions. In this case, movement in the arteries modulates the
signal coming from the spins inside them. As a result, the reconstructed image shows multiple copies of the arterial spins scattered along the
phase encode direction.
the weights are determined by a sinc function. (The sinc() function is defined as sinc(t) sin(t)/t.)
In practical terms, most fMRI analysis software interpolate
data by a process that is mathematically equivalent to a sinc
interpolation, as follows. It can be shown that the Fourier
transform of a time-shifted function is equal to the Fourier
transform of the original function multiplied by a linear
phase term. In other words, if
F o F ff t g
[6]
then shifting the function in time by T means

Foei2poT F ff t T g
[7]
By taking advantage of the multiplication properties of the

Fourier transform, the left-hand side of this equation can be
expressed as a convolution in the time domain, as follows:
236
f t *sinct T F ff t T g
[8]
approach is to build the temporal shift into the analysis. In the

case of the usual linear regression analysis, the general linear
model can be shifted in time to match the timing of each slice.
The convolution in the left-hand side of the equation is

nothing but a weighted average of the data in function f(t),
where the weights are determined by the sinc() function. This
is very useful because Fourier transforms can be computed very
quickly using algorithms like the fast Fourier transform (FFT).
Hence, most fMRI analysis packages (e.g., FMRIB (functional
MRI of the brain) software library (FSL) and statistical parameter
mapping (SPM)) speed up the computation process by the
following three-step process:
Image Distortion
Ghosting
Ghosts in MRI are image artifacts where certain parts of the
object become copied and superimposed in the wrong part of
the image. In order to understand why ghosting occurs and
how to correct it, we must recall that MR images are formed by
computing the Fourier transform of raw data. When the raw
data are corrupted, or the assumptions about the raw data are
wrong, the resulting artifact will be a Fourier transform of that
error. In the case of ghosting, it occurs when some parts of the
raw data are modulated by a function of time, like movement
(Bellon et al., 1986; Henkelman, 1996; Stadler, Schima,
et al., 2007).
In order to understand what happens to the image as a
result of this modulation, consider the following. It can be
shown that modulation by a periodic function in the time
domain corresponds to splitting and shifting of the signal in
the frequency domain and vice versa. For example, Figure 6
shows what happens to the Fourier transform of simple sinusoid when it is modulated by another sinusoid. The same is
true in an MRI image. When the signal intensity from a brain
region is modulated by pulsatility during acquisition, as in the
case of an artery, it is Fourier transform (i.e., the reconstructed
image shows multiple copies smeared across the image).
But perhaps ghosting can be most easily understood as a
specific form that occurs in the case of echo-planar imaging
(EPI), the most common fMRI acquisition technique. EPI
1. Compute the FFT of the data.

2. Add linear phase to the result.
3. Compute the inverse FFT of the result of step 2.
Note that this interpolation procedure is the same also used for
interpolating missing data in 3-D images from their neighbors.
In fact, it is fairly ubiquitous in fMRI analysis as it is used at
multiple steps of data processing, such as the rigid body
realignment process described in the previous section, or in
spatial normalization.
Finally, one must be aware that interpolating data often
means that we are also interpolating noise. In other words, the
noise in one sample of the time series also gets averaged and
propagates throughout the whole series. As a result, the degree
of autocorrelation in a time series is affected by the amount of
temporal shift applied to the time series. Since ordinary least
squares (linear regression) analysis assumes temporal independence from sample to sample, this must be taken into account
during analysis. A second point is that any large discontinuities
in the data, say, a noise spike or a quick movement by the
subject, will also affect the surrounding time points, as evidenced by Figure 5. In those cases, it is better to remove such
data points before slice timing correction is applied. Another
10
8
6
4
Ky
2
0
2
4
6
8
10
10
10
Kx
Figure 7 In an echo-planar imaging sequence, the k-space data are collected rapidly line by line, as in the pattern shown in the left panel. If there is a
mismatch between the timing of the odd line and the timing of the even lines, we observe ghosts of the original object superimposed on the image
because of the modulation of the signal along the phase encode direction (ky in this case).
Field map
237
Reconstructed image
Figure 8 Sample field map used for inhomogeneity correction during reconstruction of spiral images.
works by switching the gradients rapidly in order to acquire

the raw, k-space data (Fourier domain) line by line in a
Cartesian raster pattern as depicted in Figure 7. EPI ghosting
occurs when timing errors in the system hardware cause the
samples to imperfectly line up at every other line. These phase
shifts can be the result of imperfections in the pulse sequence
timing or in the hardware. For example, the gradients may
have a faster response when they are positive than when they
are negative. In this case, every other line of the k-space data is
shifted, and this is the same as multiplying (modulating) data
along one dimension by a function that oscillates every other
sample. As the 1-D example would predict, this leads to
multiple copies of the object appearing in the image. This is
referred to as the N/2 ghost because the center of the ghost is
shifted by one-half of the number of pixels along the readout
dimension (N). N/2 ghost artifacts are typically corrected by
measuring the size of the timing error through a reference
scan and then simply shifting the k-space samples back to
their correct locations in k-space (Jezzard & Clare, 1999).
Sometimes, the modulation is more complex than a shift
between even and odd lines of k-space, and this cannot
completely account for the ghost. More sophisticated
methods are available, sometimes requiring additional calibration scans (Buonocore & Zhu, 2001; Chan, Chen, et al.,
2004; Grieve, Blamire, et al., 2002; Haacke & Lenz, 1987;
Kim, Nielsen, et al., 2008; Pfeuffer, Van de Moortele, et al.,
2002; Porter, Calamante, et al., 1999; Xiang & Ye, 2007).
Off-Resonance
You may recall that the resonant frequency of protons is determined by the magnetic field to which they are exposed. This
magnetic field is generated by the MRI scanner, but it is affected
by the chemical environment of the protons. Hence, if the
magnetic field is distorted or if the signal comes from protons
that are not part of a water molecule, but fat instead, which is
also rich in hydrogen atoms, one can expect the signal to be
affected in some way.
In Cartesian imaging (i.e., sequences that collect the k-space
data following a Cartesian grid, like spin warp sequences), the
fat signals frequency shift becomes a spatial shift in the reconstructed image. In other words, the fat components are shifted
Figure 9 In this experiment, the subject wore a metallic hairpin. The

metallic hairpin causes a large distortion of the magnetic field, which led
to a loss of signal in the posterior region of the brain.
a few pixels along the readout dimension. In faster, single-shot

imaging, the fat components of the image become smeared
across the image. The simplest solution to this problem is to
include a saturation pulse before the pulse sequence that is
applied at the resonant frequency of fat protons. These pulses
remove the contribution of the fat signal to the image, which is
of no interest in fMRI (Hornak, 1997; Sarlls, Pierpaoli, et al.,
2011; Totterman, Weiss, et al., 1989).
The presence of a body in a magnetic field typically affects
that magnetic field, depending on the physical properties of
the material, namely, its magnetic susceptibility. In the case of
a human head in an MRI scanner, the magnetic field is typically
most deformed at the edges between air and tissue. Regions
such as the orbitofrontal lobes and the ear canals are particularly problematic in this regard. See Figure 8 for an example of
a map of the magnetic field, as deformed by a human head.
238
While imaging techniques that use spin echoes can undo these
off-resonance effects, most functional imaging is carried out
using gradient echoes, precisely because the BOLD effect is
caused by distortion of the magnetic field at the microscopic
level (Hornak, Szumowski, et al., 1988). Unfortunately, by
being sensitive to the BOLD effect, the pulse sequences will
also be sensitive to other off-resonance effects. On the right
panel, one can see how a BOLD-weighted image has been
affected by the inhomogeneity around the orbitofrontal lobe
despite using advanced correction techniques during
reconstruction.
In order to mitigate the inhomogeneity effects on the
image, let us first consider the different ways in which it affects
the signal. If the magnetic field varies from top to bottom of the
slice (through-plane), this will cause the spins on the top part
of the slice to precess at a different rate than the ones near the
bottom of the slice. As a result, the magnetization vectors of the
spins will get out of phase with each other, and the net magnetization vector from voxels in that slice will be reduced
because of destructive interference (i.e., cancelation of the
vectors). This generally produces signal voids that cannot be
recovered. Figure 9 shows a very dramatic example of this
phenomenon, in which a subject inadvertently wore a metallic
hairpin in the scanner, which caused major magnetic field
distortion and destroyed the signal in a large part of the image.
The image acquisition parameters can be adjusted to reduce
these effects, though. The most obvious thing to do would be
to reduce the echo time, in order to reduce the time allowed for
the spins to lose phase coherence, but then, we would also lose
sensitivity to the BOLD effect. While one can try to correct for
the magnetic field distortions through careful shimming, even
through additional hardware inserted in the subjects mouth in
order to reshape the field (Constable & Spencer, 1999; Glover,
1999; Wilson & Jezzard, 2003), these approaches tend to be
impractical for most investigators. One can also speed up the
acquisition time, which requires higher performance from the
gradients or using parallel imaging techniques to undersample
the data (Blaimer, Breuer, et al., 2004; Blaimer et al., 2004;
Griswold, Jakob, et al., 2002; Pruessmann, Weiger, et al.,
1999). Finally, one can also reduce the thickness of the slices,
thus allowing a smaller range of precession rates within each
voxel. However, each of these approaches has an associated
cost with it (Glover, Li, et al., 2000; Irarrazabal, Meyer, et al.,
1996; Pandey, 2009). As we will discuss in the next section, the
less time is spent collecting data and the smaller the voxel size,
the lower the signal-to-noise ratio (SNR) of the image.
When the magnetic field is distorted along the slice (inplane distortion), then the effect is that the signal from the
voxels in that region becomes misregistered and the image is
distorted. When the magnetic field is distorted along the slice
(in-plane distortion), then the effect is that the signal from the
voxels in that region becomes misregistered and the image is
distorted, that is, different parts of the brain can appear in the
wrong locations. Fortunately, this type of artifact can be recovered, at least partially. One strategy is to simply undo the
distortions related to the inhomogeneities by processing the
images after reconstruction.
The MRI signal equation is a well-known model of the
observed signal under ideal imaging conditions (Nishimura,
1996). In the presence of field inhomogeneities, it becomes
h
i
st mr ei2pkt r eigBoff r t dr
[9]
Here, the brackets are used to indicate the extra term added
to the original equation in order to account for the magnetic
field inhomogeneity. The Boff(r) term is a spatial map of the
magnetic field deviations from the ideal homogeneous case. If
we want to estimate the distortions from the images themselves, this term needs to be estimated. If an EPI sequence is
used, the data samples in the frequency encode direction are
applied with very small time interval differences (on the order
of a few microseconds). This causes the influence of the field
map to be approximately constant in the frequency encode
direction, and so the only distortion effects occur in the
phase encode direction with an EPI sequence. One can take
advantage of this by modeling the field map itself as being a
sum of cosine functions (Andersson et al., 2001). Using this,
one can estimate the distortions in the phase encode direction
and undo them in a manner similar to motion registration.
However, this method also assumes a rigid body motion
model, and so it will not be able to undo geometric distortion
effects where one signal is on top of another one.
One strategy is to collect a field map, such as the one in
Figure 7, and use it to calculate the deformation field: a map of
the misregistration of each voxel as a result of the field map
distortion. Measuring the field map is a simple procedure that
only requires measuring the phase difference between two
gradient-echo images acquired with different echo times
(Hornak et al., 1988). If we know the field map, we know
that then a pixel will appear shifted as a function of the magnetic field distortion at that pixels true location (Duyn, Yang,
et al., 1998; Jezzard & Balaban, 1995; Jezzard & Clare, 1999).
In the case of an EPI sequence, the shift is predominantly in the
phase encode direction and determined by

Dr r gBoff r N 2tramp NDt
[10]
where r() is the extent of the pixel shift, tramp is the ramp
time of the EPI k-space trajectory, t is the time between
samples, and N is the number of lines in k-space. The correction can then be applied by simply undoing all the shifts in the
image, that is, shifting the pixels back by the calculated
amount. Due to this methods simplicity and the popularity
of EPI sequences for imaging in fMRI, this is the most popular
technique for field inhomogeneity compensation in fMRI.
If a non-EPI sequence is used (such as a spiral), more
sophisticated correction techniques are required. One popular
approach is to approximate the field map as being constant
over voxels and use this assumption to more or less
demodulate the field map effects. This method is also quite
effective and has been used for some time for non-Cartesian
field map distortion correction (Noll, Meyer, et al., 1991).
Both of these methods make approximations to deal with
the physics effects caused by field inhomogeneity. To
completely compensate for these effects in a more general
case, we would instead want to solve an optimization problem
of the following form:
1
x^ argmin ky Axk22
2
x
[11]
where A is a system matrix containing the effects of the
sampling trajectory and field map, x is the actual object
(the image), and y is the observed signal. By making more
conservative approximations than those previously discussed, practical algorithms have been developed for solving
this full problem. The strategy is then to solve the inverse
problem by iterating over different objects (i.e., images) and
search for the map that produces the best fit between the
calculated signal from the object and the observed signal.
This is again an optimization problem, where the goal is to
minimize a cost function that describes the discrepancy
between an observed signal and a predicted one. However,
in contrast to the realignment example that we discussed
earlier, the number of unknowns is not limited to a handful
of movement parameters, but it consists of the signal intensity at each voxel. There are a number of strategies that one
can take to facilitate the search, such as imposing smoothness conditions in the data. These iterative methods tend to
be more complex and computationally expensive but they
can be very powerful. These full solvers are generally the best
techniques for removing geometric distortions; however,
they require the most computation time and they are typically not included in standard software packages. The
approximations made by the other methods discussed in
this section generally work quite well and have been in use
in various areas of fMRI for a number of years, so their
properties and performance are well known.
One major aspect of using field inhomogeneity correction
techniques that rely on a field map is the estimation of the
field map itself. Field maps are calculated from the phase
information in the MRI data, which is very susceptible to
noise since it requires dividing one image by another. Since
fMRI is a low SNR regime of MRI to begin with, these noise
effects can be very problematic when implementing field
map-based methods. A number of methods for compensating
for noise effects have been developed over the years. In his
work on correcting field distortions in EPI images, Jezzard
proposed fitting polynomial functions to the field map data
to try to control these noise effects over time (Jezzard &
Balaban, 1995). Another way to control the noise in field
map estimation is to estimate the field map and then smooth
it. Over most of the brain, large changes do not occur in the
field map intensity, the only exception being brain interface
edges around the sinuses. More recently, a number of
methods motivated by statistical estimation techniques have
been proposed, such as the one in Funai, Fessler, et al. (2008).
These methods control the noise effects by assuming some
prior knowledge of what a field map should look like. Since
field maps are usually expected to be smooth, these techniques may penalize large differences between neighboring
voxels in the field map estimation process. Field map estimation techniques are still a topic of research, as it is still an open
problem to find the right balance of smoothing, computation
speed, and robustness.
Ultimately, the best correction technique for each study
will depend on the study. Studies examining the inferior
frontal regions of the brain may want to use more sophisticated field inhomogeneity correction techniques since these
areas of the brain are very susceptible to field distortions.
If the area of the brain being studied is far away from the air
239
10
20
30
40
50
60
10
20
30
40
50
60
Figure 10 An example of white pixel noise. A single spike in the

frequency domain (the raw data) produces a sinusoid across the image.
The frequency of the sinusoid depends on where the white pixel spike
occurs during the acquisition.
sinuses, then more conservative field inhomogeneity correction techniques could be used or possibly no correction
techniques at all.
Noise
Noise is a common term that is used to describe unwanted
signals that are recorded along with the desired signals in any
type of measurement. In general, noise either can be additive or
can modulate (multiplicative) the signal. Noise is generally
thought to be random, but it can also have a deterministic
structure to it. Noise and random processes constitute a field
of study onto itself, but we will only discuss a few practical
aspects that are most relevant to this article. Let us begin by
considering thermal noise in the image, that is, random, independent fluctuations in signal intensity due to the thermal
motion in the sample as well as the scanners electronics.
There is not much that can be done about it, but we can
think about some simple rules that will help minimize it. The
signal observed from a single voxel is directly proportional to
the amount of magnetization available in that voxel and hence
to its volume. The available magnetization of each spin (M0) is
determined by the relaxation constants of the tissue in combination with the choice of echo time and TR. Noise, on the
other hand, is a random process, and the more time one
spends collecting data, the more it cancels itself out. Specifically, we can measure the noise level as the standard deviation
of the signal. It can be shown that for an independent,
Gaussian noise source, the standard deviation decreases with
the square root of the number of averages collected. In MRI,
this boils down to the amount of time spent sampling and
averaging signals (TA/D). The SNR of a measurement is typically
calculated as the signal level divided by its standard deviation
(i.e., the noise level). Putting it all together, we see that
240
Figure 11 An example of a zipper artifact. This artifact is the opposite

of the white pixel artifact. Here, the noise source is a sinusoid at a
fixed frequency in the k-space data. This translates into an artifact that
appears as a line in the spatial location corresponding to the frequency of
that noise. This usually occurs because of there is a poorly insulated
device in the scanner room that radiates electromagnetic noise at the
frequency of the power lines (50 or 60 Hz).
SNR
p
signal
M0 V T A=D
sn
[12]
The implication of this is that higher spatial resolution

(smaller volume per voxel) comes at a heavy price. For example, in order to cut the voxel dimensions in half (and decrease
the volume by eightfold), we would have to spend 64 times
the amount of time collecting data in order to maintain the
same SNR.
While random noise can only be removed by collecting
more data, structured noise can often be characterized and
removed from the signals. However, it is often difficult to
identify and remove noise in MRI because it usually gets introduced into the raw MR signals (aka echoes or free induction
decays) before reconstruction. Often, the raw data are discarded and only the reconstructed images are preserved for
postprocessing. This means that (1) we typically end up
observing the Fourier transform of the noise and (2) the raw
data and the noise are processed together during the reconstruction process. As a result, noise sources that would otherwise be obvious become difficult to identify and remove from
the images.
The simplest example of this artifact occurs when a single
spike of electromagnetic noise is picked up by the scanner
during image acquisition. Since the Fourier transform of a
single spike is a sinusoid function, the resulting reconstructed
image shows a striped pattern across the image (see Figure 10).
These artifacts are fairly common and sometimes referred to as
white pixel. They typically arise from metal objects in the
scanner room rattling against other metal objects. The spikes

are not very intense and often go undetected. However, the
BOLD effect is also very subtle, so these artifacts can often
contribute a significant amount of variance to the signal and
hence make it harder to detect the activation. In our experience,
we find that spike detection and removal can play a significant
role in fMRI.
A related artifact is the presence of electromagnetic noise
emitted from an electronic device in the room that is not
properly shielded. Typically, this electromagnetic noise is an
oscillating field at the frequency of the AC input voltage into
the building (50 or 60 Hz, depending on the country). Unless
the raw data are being acquired in a non-Cartesian trajectory
(e.g., spiral imaging), this artifact will appear in the reconstructed image as a single line superimposed on the image.
The reason for this appearance is again determined by the
Fourier transform reconstruction. Since the artifact is present
in every echo at the same frequency, the Fourier transform of
every echo will contain a spike at the same location. The
second Fourier transform along the second dimension of the
data will depend on the time delay between each echo acquisition. In general, though, the image will appear as if a straight
line had been drawn on top of the image along the phaseencoding dimension. See Figure 11 for an example.
As a general rule, it is crucial to realize that the relationship
between raw MR data and reconstructed images is determined
by the Fourier transform (often, there are other signal processing steps involved as well). The same is true for most image
artifacts, so it is a very good practice to understand the properties of Fourier transforms and not discard the raw signals in
fMRI at least until the reconstructed data have undergone some
degree of quality control or visual inspection (Bellon et al.,
1986; Dietrich, Reiser, et al., 2008; Henkelman, 1996).
The largest source of noise in fMRI is also the most pervasive one: the sample itself. In addition to the bulk head
movements discussed earlier, the hearts pulsatility gets propagated down the arterial tree and affects the MRI images in
several ways. Pulsatile blood flow causes the tissue around the
arteries to move and deform slightly. These slight movements
translate into small misregistration of the voxels that cannot
be easily corrected by the methods described earlier. They also
change in the fraction (partial volumes) of each tissue type
and blood present inside each voxel and the oxygen content
of the blood present in that voxel. To further complicate
things, fresh inflowing blood water has not experienced
any of the RF excitation pulses of the MRI experiment, so it
is fully relaxed unlike the water that was stationary in the
tissue. As a result, inflow effects can lead to signal
enhancements.
Respiration introduces fluctuations into the MR images
mainly in three different ways. The most obvious one is related
to subtle movements of the head and the tissue as the patients
whole body is pushed by the movement of the lungs and the
intracranial pressure oscillates with respiration and alters the
volume of the cerebrospinal fluid. The second way is that as
the shape of the subjects body changes, so does its interaction
with the main magnetic field of the MRI scanner. The oscillations in magnetic field at the head due to respiratory movement are subtle, but they still manage to shift the resonant
frequency of the protons enough to be a significant source of
241
Original respiratory waveform

3000
2500
2000
200
400
600
800
1000
1200
1st sine basis

0.5
0
0.5
2
10
12
14
16
18
20
14
16
18
20
14
16
18
20
1st cosine basis

1
0.5
0
0.5
2
10
12
2nd sine basis

0.8
0.6
0.4
0.2
0
0.2
0.4
2
10
12
Figure 12 A sample set of basis functions constructed by inserting integer numbers of sinusoids between the start and the end of each respiratory
cycle. The original raw respiratory waveform is shown in the top panel sampled at the plethysmographs sampling rate. Note that the basis
functions, on the other hand, are downsampled to the sampling rate of the scanner.
300
225
150
75
0
Figure 13 This figure shows a sample map of the standard deviation at each voxel in a time series before (left) and after (right) removal of
physiological noise by the RETROICOR method. The reduction in variance is quite noticeable and it is usually observed most dramatically in heavily
vascularized regions.
noise in fMRI (recall that the BOLD signals of interest are only
in the order of less than 2% of the MR signal).
In general, these physiological fluctuations are handled by
filtering them out of MRI signals. While the simplest approach
would be to construct some sort of band-stop frequency filter,
we run into two obstacles. First, the sampling rate of most fMRI
experiments is too low to sample the heartbeat adequately, so
the heartbeats contribution is usually aliased and difficult to
identify without any external measurements in order to design

the filter. Secondly, often times, the respirations frequency is
in the range of the cognitive task that we are trying to identify,
so applying a simple filter is likely to remove the signal of
interest as well. Given these challenges, investigators try to
estimate the contribution of physiological fluctuations to the
net MR signal as accurately as possible and then subtract this
contribution from the signal. One strategy to achieve this is to
242
measure those fluctuations independently using a

plethysmography belt (essentially a strain sensor around the
subjects chest that records the respiration) and a pulse oximeter to record the cardiac waveform. The waveforms collected by the plethysmograph and oximeter are then regressed
out from the signal intensity waveform at every voxel. While we
usually just regress out the raw cardiac signals from the MRI
time series, we construct a discrete cosine basis model for the
respiratory signal and regress that model out of the MRI signal,
in order to capture the variance of the respiratory contributions
more effectively. This means that we create several regressors
(five or six) for the respiration. These regressors are constructed
by first identifying the peaks and using those to define each
respiratory cycle. Then, we construct the first regressor by placing a single cosine wave from one peak to the next. The second
regressor has two whole cosine waves for each cardiac cycle,
and so on. The result is a set of basis functions that should
capture the variance of the MR signal due to respiration without having an explicit biophysical model. Figure 12 shows a
raw respiration time course and the first few terms of the basis
set for the model note that the model is downsampled to the
same acquisition rate as our data, much coarser than the respiratory waveform! This strategy underlies the most popular class
of physiological correction methods in the literature, RETROspective Image CORrection (RETROICOR) (Glover et al.,
2000), as well as the k-space version of it, RETROspective
k-space CORrection (RETROKCOR) (Hu, Le, et al., 1995).
These methods are quite effective in removing unwanted
physiological fluctuations and can boost the sensitivity of fMRI
quite significantly. As an example, consider Figure 13 that
shows a variance map from an fMRI time series along with
the variance of the same data set after removing physiological
fluctuations through RETROICOR.
Very often, though, the cardiac and respiratory waveforms
are not available so it is desirable to identify physiological
noise from the fMRI data. There are several methods in the
literature available to do this. The general strategy is to decompose the fMRI time series into its eigenvectors (principal components) or into components that are maximally independent
(independent component analysis) (McKeown, Hansen, et al.,
2003; Perlbarg, Bellec, et al., 2007; Thomas, Harshman, et al.,
2002). We then try to identify which components correspond
to physiological noise by using prior knowledge. For example,
we can identify those components that are strongest in the
white matter and cerebrospinal fluid (CSF) and assume that
they are due to physiological noise, since we know that the sort
of BOLD effect signal fluctuations that happen occur in the
gray matter. Another approach is to identify highly vascularized regions, such as the circle of Willis, and use those as a
mask to identify the noise components. An example of this is
the CompCor method, which uses variance maps to identify
vasculature regions in arterial spin labeling data as well as
BOLD data (Behzadi, Restom, et al., 2007).
Finally, we should comment about the structure of the
noise in fMRI data. It is well known that fMRI time series
noise is not independent, but rather autocorrelated to some
degree. This autocorrelation structure arises in part from the
MRI scanner itself as its signal drifts due to hardware imperfections (Bullmore, Long, et al., 2001) and also from physiological fluctuations (Lund, Madsen, et al., 2006; Purdon &
Weisskoff, 1998). Some fMRI techniques, such as arterial spin

labeling (Detre, Leigh, et al., 1992), however, circumvent this
problem because they require pairwise subtractions of the time
series data, thus canceling out the drifting structure (Aguirre,
Detre, et al., 2002). However, the analysis of BOLD data
requires that this autocorrelation be dealt with appropriately.
A simple, albeit imperfect, approach is to include a high-pass
filter in the analysis, but it is more effective to explicitly whiten
the data and include the whitening process into the general
linear model during the analysis stage (Friston, Josephs, et al.,
2000; Lenoski, Baxter, et al., 2008; Woolrich, Ripley, et al.,
2001; Worsley, 2003). We should also note that the structure
of the fMRI noise is also not independent along the spatial
dimension. The nature of the Fourier reconstruction and postprocessing, such as motion correction methods and interpolation of missing locations, introduces spatial correlations across
the image that are unrelated to neural activations of interest.
Further autocorrelation arises when using parallel imaging
techniques, an increasingly popular method to accelerate
image acquisition (Fukunaga, Horovitz, et al., 2006; Worsley,
2005; Zarahn, Aguirre, et al., 1997). This latter correlation is
introduced by the mixing of spatial data from multiple coils
(Pruessmann et al., 1999). The topic of autocorrelation is
covered in greater detail elsewhere in this book, so we will
merely point it out in this article.
Acknowledgment
The authors would like to thank Keith Newnham, Ryan Smith,
and Krisanne Litinas for collecting the images used in this
article.

Anatomical MRI for Human Brain Morphometry; Echo-Planar Imaging;
and Spatial Resolution of fMRI.
References
Aguirre, G., Detre, J., et al. (2002). Experimental design and the relative sensitivity of
BOLD and perfusion fMRI. NeuroImage, 15(3), 488500.
Andersson, J., Hutton, C., et al. (2001). Modeling geometric deformations in EPI time
series. NeuroImage, 13(5), 903919.
Andersson, J., & Skare, S. (2002). A model-based method for retrospective correction
of geometric distortions in diffusion-weighted EPI. NeuroImage, 16(1), 177199.
Behzadi, Y., Restom, K., et al. (2007). A component based noise correction method
(CompCor) for BOLD and perfusion based fMRI. NeuroImage, 37(1), 90101.
Bellon, E., Haacke, E., et al. (1986). MR artifacts: A review. American Journal of
Roentgenology, 147(6), 12711281, 0361-1803X.
Blaimer, M., Breuer, F., et al. (2004). SMASH, SENSE, PILS, GRAPPA: How to choose
the optimal method. Topics in Magnetic Resonance Imaging, 15(4), 223236.
Boyd, S. P., & Vandenberghe, L. (2004). Convex optimization. Cambridge, UK:
Cambridge University Press.
Bullmore, E., Long, C., et al. (2001). Colored noise and computational inference in
neurophysiological (fMRI) time series analysis: Resampling methods in time and
wavelet domains. Human Brain Mapping, 12(2), 6178.
Buonocore, M. H., & Zhu, D. C. (2001). Image-based ghost correction for interleaved
EPI. Magnetic Resonance in Medicine, 45(1), 96108.
Chan, R. C., Chen, E. Y., et al. (2004). Executive dysfunctions in schizophrenia:
Relationships to clinical manifestation. European Archives of Psychiatry and Clinical
Constable, R., & Spencer, D. (1999). Composite image formation in z-shimmed
functional MR imaging. Magnetic Resonance in Medicine, 42(1), 110117.
Detre, J., Leigh, J., et al. (1992). Perfusion imaging. Magnetic Resonance in Medicine,
23(1), 3745.
Dietrich, O., Reiser, M. F., et al. (2008). Artifacts in 3-T MRI: Physical background and
reduction strategies. European Journal of Radiology, 65(1), 2935, 0720-0048X.
Duyn, J. H., Yang, Y., et al. (1998). Simple correction method for k-space trajectory
deviations in MRI. Journal of Magnetic Resonance, 132(1), 150153, 1090-7807.
Friston, K. J., Ashburner, J., et al. (1995). Spatial registration and normalization of
images. Human Brain Mapping, 3(3), 165189.
Friston, K. J., Josephs, O., et al. (2000). To smooth or not to smooth? Bias and
efficiency in fMRI time-series analysis. NeuroImage, 12(2), 196208.
Friston, K. J., Williams, S., et al. (1996). Movement-related effects in fMRI time-series.
Fukunaga, M., Horovitz, S. G., et al. (2006). Large-amplitude, spatially correlated
fluctuations in BOLD fMRI signals during extended rest and early sleep stages.
Funai, A. K., Fessler, J. A., et al. (2008). Regularized field map estimation in MRI. IEEE
Transactions on Medical Imaging, 27(10), 14841494.
Glover, G. H. (1999). 3D z-shim method for reduction of susceptibility effects in BOLD
fMRI. Magnetic Resonance in Medicine, 42(2), 290299, 0740-3194.
Glover, G. H., Li, T. Q., et al. (2000). Image-based method for retrospective correction of
physiological motion effects in fMRI: RETROICOR. Magnetic Resonance in
Medicine, 44(1), 162167.
Grieve, S. M., Blamire, A. M., et al. (2002). Elimination of Nyquist ghosting caused by
read-out to phase-encode gradient cross-terms in EPI. Magnetic Resonance in
Medicine, 47(2), 337343.
Griswold, M., Jakob, P., et al. (2002). Generalized autocalibrating partially parallel
acquisitions (GRAPPA). Magnetic Resonance in Medicine, 47(6), 12021210.
Haacke, E. M., & Lenz, G. W. (1987). Improving MR image quality in the presence of
motion by using rephasing gradients. AJR. American Journal of Roentgenology,
148(6), 12511258.
Henkelman, R. M. (1996). Whole Body Magnetic Resonance Artifacts. eMagRes, John
Wiley & Sons, Ltd.
Hornak, J. P. (1997). Basics of NMR. Rochester Institute of Technology 19962011
(Online book: http://www.cis.rit.edu/htbooks/nmr/nmr-main.htm).
Hornak, J. P., Szumowski, J., et al. (1988). Magnetic field mapping. Magnetic
Hu, X., Le, T., et al. (1995). Retrospective estimation and correction of physiological
fluctuation in functional MRI. Magnetic Resonance in Medicine, 34(2), 201212.
Irarrazabal, P., Meyer, C., et al. (1996). Inhomogeneity correction using an estimated
linear field map. Magnetic Resonance in Medicine, 35(2), 278282.
Jenkinson, M., Bannister, P., et al. (2002). Improved optimization for the robust and
accurate linear registration and motion correction of brain images. NeuroImage,
17(2), 825841.
Jezzard, P., & Balaban, R. (1995). Correction for geometric distortion in echo-planar
images from B0 field distortions. Magnetic Resonance in Medicine, 34(1), 6573.
Jezzard, P., & Clare, S. (1999). Sources of distortion in functional MRI data. Human
Brain Mapping, 8(23), 8085.
Johnstone, T., Ores Walsh, K. S., et al. (2006). Motion correction and the use of motion
covariates in multiple-subject fMRI analysis. Human Brain Mapping, 27(10), 779788.
Kim, Y. C., Nielsen, J. F., et al. (2008). Automatic correction of echo-planar imaging
(EPI) ghosting artifacts in real-time interactive cardiac MRI using sensitivity
encoding. Journal of Magnetic Resonance Imaging, 27(1), 239245.
Lenoski, B., Baxter, L. C., et al. (2008). On the performance of autocorrelation
estimation algorithms for fMRI analysis. IEEE Journal of Selected Topics in Signal
Processing, 2(6), 828838.
Lund, T., Madsen, K., et al. (2006). Non-white noise in fMRI: Does modelling have an
impact? NeuroImage, 29(1), 5466.
McKeown, M. J., Hansen, L. K., et al. (2003). Independent component analysis of
functional MRI: What is signal and what is noise? Current Opinion in Neurobiology,
13(5), 620629.
Moeller, S., Auerbach, E., van de Moortele, P.-F., Adriany, G., & Ugurbil, K. (2008).
fMRI with 16 fold reduction using multibanded multislice sampling. In Proceedings
of the 16th Annual Meeting of ISMRM, Toronto, Canada, p. 2366.
243
Nishimura, D. G. (1996). Principles of magnetic resonance imaging. Stanford, CA:
Stanford University Press.
Noll, D. C., Meyer, C. H., et al. (1991). A homogeneity correction method for magnetic
resonance imaging with time-varying gradients. IEEE Transactions on Medical
Imaging, 10(4), 629637.
Oppenheim, A. V., Schafer, R. W., et al. (1999). Discrete-time signal processing. Upper
Saddle River, NJ: Prentice Hall.
Pandey, K. K. (2009). Mitigation of motion artifacts in functional MRI: A combined
acquisition, reconstruction and post processing approach. (Doctoral dissertation).
Retrieved from ProQuest Dissertations and Theses.
Perlbarg, V., Bellec, P., et al. (2007). CORSICA: Correction of structured noise in fMRI
by automatic identification of ICA components. Magnetic Resonance Imaging,
25(1), 3546.
Pfeuffer, J., Van de Moortele, P., et al. (2002). Correction of physiologically induced
global off-resonance effects in dynamic echo-planar and spiral functional imaging.
Porter, D. A., Calamante, F., et al. (1999). The effect of residual Nyquist ghost in
quantitative echo-planar diffusion imaging. Magnetic Resonance in Medicine,
42(2), 385392.
Pruessmann, K., Weiger, M., et al. (1999). SENSE: Sensitivity encoding for fast MRI.
Purdon, P. L., & Weisskoff, R. M. (1998). Effect of temporal autocorrelation due to
physiological noise and stimulus paradigm on voxel-level false-positive rates in
fMRI. Human Brain Mapping, 6(4), 239249.
Sarlls, J. E., Pierpaoli, C., et al. (2011). Robust fat suppression at 3T in high-resolution
diffusion-weighted single-shot echo-planar imaging of human brain. Magnetic
Sladky, R., Friston, K. J., et al. (2011). Slice-timing effects and their correction in
functional MRI. NeuroImage, 58(2), 588594.
Stadler, A., Schima, W., et al. (2007). Artifacts in body MR imaging: Their
appearance and how to eliminate them. European Radiology, 17(5), 12421255,
09387994.
Strang, G. (2006). Linear algebra and its applications. Belmont, CA: Thomson-Brooks/
Cole.
Thomas, C. G., Harshman, R. A., et al. (2002). Noise reduction in BOLD-based fMRI
using component analysis. NeuroImage, 17(3), 15211537.
Totterman, S., Weiss, S. L., et al. (1989). MR fat suppression technique in the evaluation
of normal structures of the knee. Journal of Computer Assisted Tomography, 13(3),
473479, 03638715.
van der Zwaag, W., Francis, S., & Bowtell, R. (2006). Improved echo volumar imaging
(EVI) for functional MRI. Magnetic Resonance in Medicine, 56(6), 13201327.
Wilson, J., & Jezzard, P. (2003). Utilization of an intra-oral diamagnetic passive shim in
functional MRI of the inferior frontal cortex. Magnetic Resonance in Medicine,
50(5), 10891094.
Woolrich, M. W., Ripley, B. D., et al. (2001). Temporal autocorrelation in univariate
linear modeling of FMRI data. NeuroImage, 14(6), 13701386.
Worsley, K. J. (2003). Detecting activation in fMRI data. Statistical Methods in Medical
Research, 12(5), 401418.
Worsley, K. J. (2005). Spatial smoothing of autocorrelations to control the degrees of
freedom in fMRI analysis. NeuroImage, 26(2), 635641.
Wu, X., et al. (2013). Simultaneous multislice multiband parallel radiofrequency
excitation with independent slice-specific transmit B1 homogenization. Magnetic
Xiang, Q.A., & Ye, F. Q. (2007). Correction for geometric distortion and N/2 ghosting in
EPI by phase labeling for additional coordinate encoding (PLACE). Magnetic
Yang, Y., et al. (1996). Fast 3D functional magnetic resonance imaging at 1.5 T with
spiral acquisition. Magnetic Resonance in Medicine, 36(4), 620626.
Zarahn, E., Aguirre, G. K., et al. (1997). Empirical analyses of BOLD fMRI statistics. I.
Spatially unsmoothed data collected under null-hypothesis conditions. NeuroImage,
5(3), 179197.

C Lenglet, University of Minnesota Medical School, Minneapolis, MN, USA
Introduction
One of the most popular and widely used (Assaf & Pasternak,
2008; Jellison et al., 2004) mathematical models to describe
the primary orientation of white matter axonal pathways, in a
simple yet powerful way, is called the diffusion tensor (hence the
name diffusion tensor imaging (DTI)). This model was introduced in 1994 (Basser, Mattiello, & Lebihan, 1994a, 1994b),
shortly after the demonstration, in vivo, that tissue organization
affects diffusion-weighted signal obtained using magnetic resonance imaging (MRI) and can therefore be quantified noninvasively (Beaulieu, 2002). This discovery opened, in turn,
new avenues to investigate the integrity and connectivity patterns of the human brain and spinal cord (Dong et al., 2004;
Le Bihan et al., 2001; Mori & Zhang, 2006; White, Nelson, &
Lim, 2008).
Water molecules are under constant translational motion
and can therefore be used as microscopic probes for the
medium in which they diffuse. Free diffusion (i.e., unhindered
and unrestricted) can be characterized by the mean-squared
molecular displacement hrTriover a certain amount of time t
using Einsteins equation (Einstein, 1905) hrTri 6Dt, where
r 2 3 and D, respectively, denote the three-dimensional displacement vector and the self-diffusion coefficient.
In the brain, or any other structured tissue like the heart,
this idealistic situation does not hold in general, as various
intra- and extracellular compartments (e.g., axons and glial
cells) create physical barriers to free-diffusing water molecules,
effectively reducing (Finch, Harmon, & Muller, 1971; Hansen,
1971; Le Bihan et al., 1986) the diffusion coefficient, which is
called apparent diffusion coefficient (ADC) to take this phenomenon into account. In the gray matter, apparent diffusion
remains largely isotropic since, at current imaging spatial resolution (18 mm3), because of their complex microarchitecture, cortical and subcortical areas generally do not exhibit
preferred directions of diffusion. In any other white matter
areas, apparent diffusion is direction-dependent (i.e., anisotropic) due to the underlying organization of axonal fibers. A
single scalar value such as the ADC is therefore insufficient to
fully capture this information, and it was generalized to the
apparent diffusion tensor D, a 3 3 symmetrical and positivedefinite matrix capable of encoding the properties of diffusion
in three dimensions.
Anisotropic Diffusion and the Diffusion Tensor Model

The idea that tissue ADC anisotropy could be quantified using
diffusion-weighted imaging (DWI) was introduced in the early
1980s (Wesbey, Moseley, & Ehman, 1984) and initially attributed to the presence and orientation of myelinated axons
(Thomsen, Henriksen, & Ring, 1987): water diffuses preferentially along axons than across them. Subsequent studies
(Chenevert, Brunberg, & Pipe, 1990; Chien, Buxton, Kwong,
Brady, & Rosen, 1990; Doran et al., 1990) further refined this
concept in the human brain, after the demonstration by
Moseley et al. of anisotropic water diffusion in vivo in the cat
brain and spinal cord (Moseley et al., 1990).
To quantify the effect of diffusion on the MR signal in a
given direction q, the StejskalTanner pulsed-gradient spinecho (PGSE) sequence (Stejskal & Tanner, 1965) is widely
used. The general form of the MR signal equation is
Z
T
Sq, t S0
pr, teiq r dr
3
where S0 is a reference signal without diffusion gradient and p

(r, t) is the so-called ensemble average propagator (EAP). The
EAP characterizes the probability of displacement r due to
diffusion. If we make the assumption that diffusion is free
and isotropic, the EAP follows a Gaussian distribution and
the MR signal simplifies to S(q, t) S0ebD, where the scalar
quantity b |q|2t is the so-called b-value (Le Bihan, 1991) and
encodes the amount of diffusion weighting. If we now assume
that diffusion is free, but anisotropic, D can be generalized to a
diffusion tensor D (Stejskal, 1965) so that we have
Sq, t S0 ebg
Dg
[1]
where g [gx, gy, gz] is the unit vector defined as g q/|q|. D can
be interpreted as the covariance matrix of the displacement
vector r, such that hrTri 6Dt.
Estimation of the Diffusion Tensor

Because the diffusion tensor is symmetrical, it has six independent components that need to be estimated from the diffusionweighted data:
2 xx xy xz 3
D D D
D 4 Dxy Dyy Dyz 5
Dxz Dyz Dzz
Linear regression techniques (Basser & Le Bihan, 1992;
Basser et al., 1994a, 1994b) can be used to solve this problem
by recognizing that eqn [1] may be rewritten as follows for a
given diffusion gradient g:

Sq, t
ln
[2]
b:bT d
S0
with b [gxgx, 2gxgy, 2gxgz, gygy, 2gygz, gzgz]and d [Dxx, Dxy, Dxz,
Dyy, Dyz, Dzz].
This is where the choice of q becomes important. Since we
need to solve for six unknown variables, at least N 6, DWI
measurements are required and several practical questions
arise to minimize the uncertainty of the tensor estimation
procedure (Jones, Horsfield, & Simmons, 1999; Koay, Carew,
Alexander, Basser, & Meyerand, 2006; Koay, Chang, Pierpaoli,
& Basser, 2007; Maximov, Grinberg, & Shah, 2011). Assuming
t is constant (which is not always true as t relates to DWI
http://dx.doi.org/10.1016/B978-0-12-397025-1.00291-8
245
246
INTRODUCTION TO METHODS AND MODELING | Diffusion Tensor Imaging
sequence parameters that can be adjusted, but we will make

this hypothesis here), the only quantities that can be optimized
are the orientation and magnitude of q. How many diffusion
gradients g q/|q| are needed? How should they be distributed? What b-value(s) (i.e., amplitude |q|) should be used?
We will summarize the findings about these questions in
Strategies for Optimal DTI Acquisitions section and focus
here on the optimization techniques typically used to calculate
d, given a set of N data points with different q.
With a set of measurements at varying and noncollinear
qi1. . .N, eqn [2] becomes the following linear system (where t
has been omitted since it is assumed to be constant):

3
2
Sq1
ln
6
7
S0
6
7
6
7
6
7
6
7
4
SqN 5
ln
S0
2 xx 3
D
6 xy 7
6
3
2
D 7
y
y y
y
7
g1x g1x 2g1x g1 2g1x g1z g1 g1 2g1 g1z g1z g1z 6
6 Dxz 7
76
6
7
56 yy 7
b4
[3]
6D 7
y z z z
x x
x y
x z y y
6
gN gN 2gN gN 2gN gN gN gN 2gN gN gN gN 6 yz 7
7
4D 5
zz
D
Equation [3] is of the form Y Bd, with Y the vector of
log-transformed normalized DWI signals. The B-matrix B
(Mattiello, Basser, & Le Bihan, 1994, 1997) encodes the effects
of the imaging and diffusion gradients and describes the interaction between elements of the diffusion tensor to model the
diffusion signal Y.
The most straightforward way to estimate d is to obtain six
measurements, one baseline signal S0, and invert eqn [3], such
that d B1Y. However, this approach has several drawbacks,
as it is highly sensitive to artifacts (Gallichan et al., 2010; Le
Bihan, Poupon, Amadon, & Lethimonnier, 2006) and thermal
noise (Gudbjartsson & Patz, 1995; Henkelman, 1985), which
inevitably affect diffusion-weighted data (Andersson, 2008;
Jones & Basser, 2004). Artifacts arise from physiological
noise, such as subject motion or cardiac pulsation, and are
challenging to deal with since they are, by nature, difficult to
model. Conversely, models of signal variability due to thermal
noise can be used to mitigate its effects on the estimation of the
diffusion tensor. It is not the focus of this article to discuss in
detail the origins of physiological and thermal noise, and we
now summarize computational strategies that have been introduced to deal with them.
Least Squares Methods

Traditional approaches to solve eqn [3] in a more reliable
fashion rely on ordinary weighed least squares (OLS) or
weighed least squares (WLS) techniques. By acquiring N > 6
diffusion-weighted images, an overdetermined N 6 system is
constructed, which can be solved by using the pseudo-inverse
of B, such that d (BTB)1BTY (Anderson, 2001; Papadakis,
Xing, Huang, Hall, & Carpenter, 1999). Although simple and
fast, this OLS approach makes two important assumptions
about noise properties: normality and additivity. Unfortunately, these assumptions do not hold in general for two
reasons: (1) The appropriate noise model for S0 and S(qi) is

Rician, although it is true that for reasonable signal-to-noise
levels, it can be approximated by a normal distribution (Pajevic
& Basser, 2003); (2) S0 and S(qi) undergo a log transformation
to obtain the linear system in eqn [3], which renders the
normal assumption invalid. WLS approaches have been introduced to deal with this situation by weighting each logtransformed measurement appropriately to take into account
heteroscedasticity (i.e., different noise variance per measurement) (Jones, 2009; Salvador et al., 2005; Tristan-Vega,
Aja-Fernandez, & Westin, 2012).
In order to avoid the constraints imposed by the linearization of eqn [1] and therefore preserve homoscedasticity and
the Rician distribution of residuals, nonlinear least squares
(NLLS) techniques have been introduced to estimate d directly
from S(qi). They usually perform better than OLS and WLS
approaches (Jones, 2009; Koay, Chang, Carew, Pierpaoli, &
Basser, 2006) at the cost of higher computational demands
(due to the use of iterative nonlinear regression techniques
such as the LevenbergMarquardt algorithm or Newtons
method) and sensitivity to initialization.
Robust and Constrained Methods

Physiological noise, due mainly to breathing and cardiac pulsation, has been shown to consistently affect the accuracy of
DTI data (Walker et al., 2011) especially in brain regions such
as the cerebellum and genu of the corpus callosum. In addition
to appropriate thermal noise models, it is therefore important
to detect and reject outlier measurements (Landman, Bazin,
Smith, & Prince, 2009; Maximov et al., 2011). This can be
achieved by incorporating robust estimators into the linear or
NLLS techniques described in the preceding text. For example,
the well-known GemanMcClure M-estimator (Geman &
McClure, 1987) has been proposed (Chang, Jones, & Pierpaoli,
2005; Mangin, Poupon, Clark, Le Bihan, & Bloch, 2002) and
requires minimizing the following objective function:
w2
N
X
h
i
T
oi Sqi S0 eb:b d
i1
where oi (r2i C2)1 is the M-estimator weighting function, C

is a scale factor, and ri is the ith residual between the measured
T
and predicted signals, S(qi) and S0 eb:b d . By comparing the
deviation between these two quantities, oi enables the detection and rejection of outlier diffusion-weighted signals.
The diffusion tensor is a positive-definite matrix, which
means that its three eigenvalues must always be positive (we
will provide an interpretation of this mathematical property in
Properties of the Diffusion Tensor section). Under the effects
of thermal and/or physiological noise, this property may be
violated, especially in highly anisotropic areas such as the
corpus callosum. Constrained estimation methods (Koay,
Chang, et al., 2006) have therefore been proposed to enforce
this physical characteristic. Cholesky decomposition can be
used, by expressing the diffusion tensor as the square of an
upper triangular matrix U (Koay, Carew, et al., 2006; Maximov
et al., 2011). It is then sufficient to ensure positivity of the
diagonal elements of U to preserve the positive definiteness of
D UTU. Koay, Carew, Alexander, Basser, and Meyerand
(2006) showed that constrained NLLS methods were more

effective to deal with this issue than constrained OLS. Other
mathematical models have been proposed to ensure the positivity of the diffusion tensors: they include variational methods
(Tschumperle & Deriche, 2003; Wang, Vemuri, Chen, &
Mareci, 2004), which can also naturally incorporate spatial
regularity, and geometric methods (Arsigny, Fillard, Pennec,
& Ayache, 2006; Lenglet, Rousson, Deriche, & Faugeras, 2006),
which rely on the intrinsic properties of the space of
symmetrical positive-definite matrices to derive well-defined
metrics between tensors.
Properties of the Diffusion Tensor

We now introduce some important quantities that can be
extracted from the diffusion tensor to characterize tissue
microstructure. A tensor D can be diagonalized, since it is
symmetrical and positive-definite, which means that it can be
expressed as
D VLV T
where V is an orthogonal matrix whose columns define the
eigenvectors v1, v2, and v3 of D, and L is a diagonal matrix
composed of the associated eigenvalues l1 l2 l3. Geometrically, this means that the diffusion tensor can be thought of and
represented by an ellipsoid, as illustrated in Figure 1. The three
axes of the ellipsoid are defined by the eigenvectors, while its
scale along each axis is given by the corresponding eigenvalue.
Figure 1 shows two examples of diffusion tensors and their
graphical representations. An isotropic tensor is represented by
a spherical ellipsoid, while an anisotropic tensor results in an
elongated ellipsoid. In the brain, spherical ellipsoids are typically found in the cerebrospinal fluid and in cortical/subcortical
areas. Anisotropic ellipsoids appear in white matter fiber
pathways such as the corpus callosum, corticospinal tract, and
superior longitudinal fasciculus, where the principal eigenvector
is used to approximate the local orientation of fibers and for
further analysis such as tractography (Conturo et al., 1999;
Jones, Simmons, Williams, & Horsfield, 1999; Mori, Crain,
Chacko, & Van Zijl, 1999). v1 can be represented using an
RGB (red, green, and blue) color code by, respectively, mapping
247
its three coordinates (x, y, z) to each color channel (Makris et al.,

1997; Pajevic & Pierpaoli, 1999), thereby providing a convenient visual depiction of the white matter orientation in a single
image (see Figure 2). It is important to note here that the main
limitation of the diffusion tensor model is its inability to
describe fiber configurations with more than one pathway.
Secondary and tertiary eigenvectors are, by nature, orthogonal
to v1 and can be used to characterize diffusion in the plane
orthogonal to the fiber pathway (Song et al., 2002; WheelerKingshott & Cercignani, 2009).
From the eigenvalues, it is possible to derive several rotationally invariant quantities (Alexander, Hasan, Kindlmann,
Parker, & Tsuruda, 2000; Basser & Pierpaoli, 1996; Conturo,
Mckinstry, Akbudak, & Robinson, 1996; Hasan, Basser, Parker,
& Alexander, 2001; Westin et al., 2002) like the mean diffusivity (MD), fractional anisotropy (FA), relative anisotropy (RA),
linear anisotropy (LA), planar anisotropy (PA), and spherical
anisotropy (SA). MD is independent of the orientation of
diffusion and is an overall evaluation of the displacement of
water molecules, while anisotropy indices quantify the degree
of directionality of diffusion. They are defined as follows:
l1 l2 l3
3
q
2
l1 l2 l2 l3 2 l3 l1 2
q
FA

2 l21 l22 l23
q
l1 l2 2 l2 l3 2 l3 l1 2
p
RA
2l1 l2 l3
MD
LA
l1 l2
l1 l2 l3
PA
2l2 l3
l1 l2 l3
SA
3l3
l1 l2 l3
MD and FA have been widely used in a variety of clinical

and neuroscience studies (Horsfield & Jones, 2002; Le Bihan
et al., 2001), as will be summarized in Applications of DTI
u3
l3
l1
l2
u2
3
0
0
0
3
0
0
0
3
u1
6
0
0
0
2
0
0
0
2
Figure 1 Graphical representation of the diffusion tensor as a three-dimensional ellipsoid: (Left) Isotropic diffusion tensor characterized by a spherical
ellipsoid. All three eigenvalues are equal and there is no preferred direction of diffusion. (Right) Anisotropic diffusion tensor characterized by an
elongated ellipsoid. The principal eigenvalue is twice that of the left example, while the secondary and tertiary eigenvalues are smaller.
248
MD
FA
Fiber orientation
Figure 2 Diffusion tensor parameters: (Left) Mean diffusivity, (center) fractional anisotropy, (right) color-coded principal direction of diffusion. Fiber
pathways oriented leftright are in red, anteriorposterior are in green, and inferiorsuperior are in blue. Data from the Human Connectome Project
(http://www.humanconnectome.org/) with spatial resolution 1.25 1.25 1.25 mm3.
section. Figure 2 shows an example of MD and FA for an

axial slice of data from the Human Connectome Project
(Sotiropoulos et al., 2013; Van Essen et al., 2013).
Strategies for Optimal DTI Acquisitions

As mentioned in Estimation of the Diffusion Tensor section,
the choice of diffusion gradients g and b-value(s) defines (partially) the acquisition protocol for DTI data and, through
eqn [3], directly influences the accuracy and precision with
which diffusion tensors can be estimated. The main limiting
factors always remain acquisition time and signal-to-noise
ratio (SNR). The general consensus is that the optimal b-value
lies within 700 and 1500 s mm2, with 1000 s mm2 being
the most commonly used value (Alexander, Lee, Lazar, & Field,
2007; Jones, 2009; Kingsley & Monahan, 2004). Moreover,
because higher b-values come at the cost of lower SNR, it was
demonstrated that this value can be reduced to the range
7001000 s mm2 for optimal estimation of v1, and
9501100 s mm2 for optimal estimation of FA (Alexander &
Barker, 2005). It is also recommended to acquire one measurement without diffusion weighting (S_0) for every 510
diffusion-weighted measurements (Alexander & Barker, 2005;
Jones, Horsfield, et al., 1999).
Although the theoretical minimum number of diffusionweighted measurements is 6, the choice of overall number and
spatial distribution of diffusion gradients has been extensively
studied (Hasan, Parker, & Alexander, 2001; Hope, Westlye, &
Bjornerud, 2012; Jones, 2004; Jones, Horsfield, et al., 1999;
Papadakis, Xing, Huang, et al., 1999). For DTI, 2030 uniformly distributed directions have been shown (Jones, 2004;
Papadakis, Xing, Houston, et al., 1999; Skare, Hedehus,
Moseley, & Li, 2000) to provide a good trade-off between
acquisition time and robust parameter estimation. More specifically, at least 20 directions are required for reliable estimation of FA, while at least 30 directions must be used to estimate
the tensor orientation and MD (Jones, 2004).
The three-dimensional distribution of the set of diffusion
gradients can also play a significant role in the reliability of
tensor estimates, especially at low SNR (Landman et al., 2007).
It is therefore important to make sure that sampling gradients
are organized as uniformly as possible in order to minimize the
rotational dependence of noise propagation (Batchelor,

Atkinson, Hill, Calamante, & Connelly, 2003). The electrostatic repulsion scheme (Jones, Horsfield, et al., 1999) is widely
used. More recently, incrementally optimal schemes have
been introduced in order to guarantee that any subset of the
diffusion gradient orientations remains optimal (Cook,
Symms, Boulby, & Alexander, 2007; Deriche, Calder, &
Descoteaux, 2009; Dubois, Poupon, Lethimonnier, & Le
Bihan, 2006). Such approaches ensure that, if the scan is
stopped before completion, existing data are still uniformly
distributed.
Applications of DTI
The diffusion tensor and derived quantities such as FA and MD
are sensitive markers of microstructural changes occurring in
the brain (Alexander et al., 2007; Dong et al., 2004; Horsfield &
Jones, 2002; Le Bihan et al., 2001), in the context of
developmental, neurodegenerative, or neuropsychiatric disorders (Sajjadi et al., 2013; White et al., 2008; Yoshida, Oishi,
Faria, & Mori, 2013). Although one must remain cautious
about findings in fiber crossing areas, where the diffusion
tensor model is incomplete (see Properties of the Diffusion
Tensor section) and unable to fully characterize complex white
matter configurations (Lenglet et al., 2009; ODonnell &
Westin, 2011), DTI has demonstrated tremendous potential,
over the past 1520 years, of providing critical insights into
pathological processes affecting the central nervous system.
In multiple sclerosis (Bozzali, Cercignani, Sormani, Comi,
& Filippi, 2002; Werring, Clark, Barker, Thompson, & Miller,
1999), increased MD and decreased FA have been observed,
which may reflect demyelination and axonal loss. In epilepsy,
DTI provides additional information to better identify epileptogenic regions (Arfanakis et al., 2002). In traumatic brain
injury (TBI), DTI seems to help uncover specific white matter
pathways of the frontal and temporal areas, with alterations
shown to correlate with cognitive and behavioral data (Niogi &
Mukherjee, 2010). For brain tumors, which is the second largest clinical application of DTI, tractography has shown to
provide important information about fiber pathways (Lazar,
Alexander, Thottakara, Badie, & Field, 2006; Mori et al., 2002)
near tumors, which can be used for surgical planning purposes.

DTI has also been used to differentiate tumor types and edema
(Lu et al., 2004). In stroke, the largest clinical application of
DTI, MD, and FA provides unique information about the
course of ischemia as well as possible outcome (Mukherjee
et al., 2000; Schlaug, Siewert, Benfield, Edelman, & Warach,
1997). DTI has also been shown to provide unique information for other white matter-altering pathologies such as
Alzheimers disease, Friedreichs and spinocerebellar ataxias,
amyotrophic lateral sclerosis, and CreutzfeldtJakob disease
(Dong et al., 2004; Horsfield & Jones, 2002).
Acknowledgments
The author is partly supported by NIH grant P41 EB015894.
Data were provided in part by the Human Connectome Project, WU-Minn Consortium (Principal Investigators: David Van
Essen and Kamil Ugurbil; 1U54MH091657), funded by 16
NIH Institutes and Centers that support the NIH Blueprint
for Neuroscience Research, and by the McDonnell Center for
Systems Neuroscience at Washington University.

Diffusion MRI; Echo-Planar Imaging; High-Field Acquisition; MRI and
fMRI Optimizations and Applications; Myelin Imaging;
INTRODUCTION TO ANATOMY AND PHYSIOLOGY: Basal
Ganglia; Cerebellum: Anatomy and Physiology; Cytoarchitectonics,
Receptorarchitectonics, and Network Topology of Language; Thalamus:
Anatomy; The Brain Stem; INTRODUCTION TO CLINICAL BRAIN
MAPPING: Alzheimers Disease; Brain Mapping Techniques Used to
Guide Deep Brain Stimulation Surgery; Functional Surgery: From
Lesioning to Deep Brain Stimulation and Beyond; Huntingtons Disease
for Brain Mapping: An Encyclopedic Reference; The Anatomy of
Parkinsonian Disorders; The Role of Neuroimaging in Amyotrophic
Lateral Sclerosis; INTRODUCTION TO METHODS AND
MODELING: Fiber Tracking with DWI; Probability Distribution
Functions in Diffusion MRI; Q-Space Modeling in Diffusion-Weighted
MRI; Tissue Microstructure Imaging with Diffusion MRI; Tract
Clustering, Labeling, and Quantitative Analysis; Tract-Based Spatial
Statistics and Other Approaches for Cross-Subject Comparison of
Local Diffusion MRI Parameters.
References
Alexander, D. C., & Barker, G. J. (2005). Optimal imaging parameters for fiberorientation estimation in diffusion MRI. NeuroImage, 27, 357367.
Alexander, A. L., Hasan, K., Kindlmann, G., Parker, D. L., & Tsuruda, J. S. (2000). A
geometric analysis of diffusion tensor measurements of the human brain. Magnetic
Alexander, A. L., Lee, J. E., Lazar, M., & Field, A. S. (2007). Diffusion tensor imaging of
the brain. Neurotherapeutics, 4, 316329.
Anderson, A. W. (2001). Theoretical analysis of the effects of noise on diffusion tensor
Andersson, J. L. (2008). Maximum a posteriori estimation of diffusion tensor
parameters using a Rician noise model: Why, how and but. NeuroImage, 42,
13401356.
Arfanakis, K., Hermann, B. P., Rogers, B. P., Carew, J. D., Seidenberg, M., &
Meyerand, M. E. (2002). Diffusion tensor MRI in temporal lobe epilepsy. Magnetic
Arsigny, V., Fillard, P., Pennec, X., & Ayache, N. (2006). Log-Euclidean metrics for fast
and simple calculus on diffusion tensors. Magnetic Resonance in Medicine, 56,
411421.
249
Assaf, Y., & Pasternak, O. (2008). Diffusion tensor imaging (DTI)-based white matter
mapping in brain research: A review. Journal of Molecular Neuroscience, 34,
5161.
Basser, P. J., & Le Bihan, D. (1992). Fiber orientation mapping in an anisotropic
medium with NMR diffusion spectroscopy. In: Eleventh annual meeting of the
society for magnetic resonance in medicine (ISMRM), 1992 Berkeley, CA, Berkeley,
CA: ISMRM (International Society for Magnetic Resonance in Medicine).
Basser, P. J., Mattiello, J., & Lebihan, D. (1994a). Estimation of the effective selfdiffusion tensor from the NMR spin echo. Journal of Magnetic Resonance. Series B,
103, 247254.
Basser, P. J., Mattiello, J., & Lebihan, D. (1994b). MR diffusion tensor spectroscopy
and imaging. Biophysical Journal, 66, 259267.
Basser, P. J., & Pierpaoli, C. (1996). Microstructural and physiological features of
tissues elucidated by quantitative-diffusion-tensor MRI. Journal of Magnetic
Resonance. Series B, 111, 209219.
Batchelor, P. G., Atkinson, D., Hill, D. L., Calamante, F., & Connelly, A. (2003).
Anisotropic noise propagation in diffusion tensor MRI sampling schemes. Magnetic
Beaulieu, C. (2002). The basis of anisotropic water diffusion in the nervous system A
technical review. NMR in Biomedicine, 15, 435455.
Bozzali, M., Cercignani, M., Sormani, M. P., Comi, G., & Filippi, M. (2002).
Quantification of brain gray matter damage in different MS phenotypes by use of
diffusion tensor MR imaging. AJNR - American Journal of Neuroradiology, 23,
985988.
Chang, L. C., Jones, D. K., & Pierpaoli, C. (2005). RESTORE: Robust estimation of
tensors by outlier rejection. Magnetic Resonance in Medicine, 53, 10881095.
Chenevert, T. L., Brunberg, J. A., & Pipe, J. G. (1990). Anisotropic diffusion in
human white matter: Demonstration with MR techniques in vivo. Radiology, 177,
401405.
Chien, D., Buxton, R. B., Kwong, K. K., Brady, T. J., & Rosen, B. R. (1990). MR diffusion
imaging of the human brain. Journal of Computer Assisted Tomography, 14,
514520.
1042210427.
Conturo, T. E., Mckinstry, R. C., Akbudak, E., & Robinson, B. H. (1996). Encoding of
anisotropic diffusion with tetrahedral gradients: A general mathematical diffusion
formalism and experimental results. Magnetic Resonance in Medicine, 35, 399412.
Cook, P. A., Symms, M., Boulby, P. A., & Alexander, D. C. (2007). Optimal acquisition
orders of diffusion-weighted MRI measurements. Journal of Magnetic Resonance
Imaging, 25, 10511058.
Deriche, R., Calder, J., & Descoteaux, M. (2009). Optimal real-time Q-ball imaging
using regularized Kalman filtering with incremental orientation sets. Medical Image
Analysis, 13, 564579.
Dong, Q., Welsh, R. C., Chenevert, T. L., Carlos, R. C., Maly-Sundgren, P.,
Gomez-Hassan, D. M., et al. (2004). Clinical applications of diffusion tensor
imaging. Journal of Magnetic Resonance Imaging, 19, 618.
Doran, M., Hajnal, J. V., Van Bruggen, N., King, M. D., Young, I. R., & Bydder, G. M.
(1990). Normal and abnormal white matter tracts shown by MR imaging using
directional diffusion weighted sequences. Journal of Computer Assisted
Dubois, J., Poupon, C., Lethimonnier, F., & Le Bihan, D. (2006). Optimized diffusion
gradient orientation schemes for corrupted clinical DTI data sets. Magnetic
Resonance Materials in Physics, Biology and Medicine, 19, 134143.
Einstein, A. (1905). Uber die von der molekularkinetischen Theorie der Warme
geforderte Bewegung von in ruhenden Flussigkeiten suspendierten Teilchen.
Annalen der Physik, 322, 549560.
Finch, E. D., Harmon, J. F., & Muller, B. H. (1971). Pulsed NMR measurements of the
diffusion constant of water in muscle. Archives of Biochemistry and Biophysics,
147, 299310.
Gallichan, D., Scholz, J., Bartsch, A., Behrens, T. E., Robson, M. D., & Miller, K. L.
(2010). Addressing a systematic vibration artifact in diffusion-weighted MRI. Human
Geman, S., & McClure, D. E. (1987). Statistical methods for tomographic image
reconstruction. Bulletin of the International Statistical Institute, 52, 521.
Gudbjartsson, H., & Patz, S. (1995). The Rician distribution of noisy MRI data. Magnetic
Hansen, J. R. (1971). Pulsed NMR study of water mobility in muscle and brain tissue.
Biochimica et Biophysica Acta, 230, 482486.
Hasan, K. M., Basser, P. J., Parker, D. L., & Alexander, A. L. (2001). Analytical
computation of the eigenvalues and eigenvectors in DT-MRI. Journal of Magnetic
250
Hasan, K. M., Parker, D. L., & Alexander, A. L. (2001). Comparison of gradient

encoding schemes for diffusion-tensor MRI. Journal of Magnetic Resonance
Imaging, 13, 769780.
Henkelman, R. M. (1985). Measurement of signal intensities in the presence of noise in
MR images. Medical Physics, 12, 232233.
Hope, T., Westlye, L. T., & Bjornerud, A. (2012). The effect of gradient sampling
schemes on diffusion metrics derived from probabilistic analysis and tract-based
spatial statistics. Magnetic Resonance Imaging, 30, 402412.
Horsfield, M. A., & Jones, D. K. (2002). Applications of diffusion-weighted and
diffusion tensor MRI to white matter diseases A review. NMR in Biomedicine, 15,
570577.
Jellison, B. J., Field, A. S., Medow, J., Lazar, M., Salamat, M. S., & Alexander, A. L.
(2004). Diffusion tensor imaging of cerebral white matter: A pictorial review of
physics, fiber tract anatomy, and tumor imaging patterns. AJNR - American Journal
of Neuroradiology, 25, 356369.
Jones, D. K. (2004). The effect of gradient sampling schemes on measures derived from
diffusion tensor MRI: A Monte Carlo study. Magnetic Resonance in Medicine, 51,
807815.
Jones, D. K. (2009). Gaussian modeling of the diffusion signal. In H. Johansen-Berg, &
T. E.J Behrens (Eds.), Diffusion MRI: From quantitative measurement to in vivo
neuroanatomy. Amsterdam: Elsevier.
Jones, D. K., & Basser, P. J. (2004). Squashing peanuts and smashing pumpkins:
How noise distorts diffusion-weighted MR data. Magnetic Resonance in Medicine,
52, 979993.
Jones, D. K., Horsfield, M. A., & Simmons, A. (1999). Optimal strategies for measuring
diffusion in anisotropic systems by magnetic resonance imaging. Magnetic
Jones, D. K., Simmons, A., Williams, S. C., & Horsfield, M. A. (1999). Non-invasive
assessment of axonal fiber connectivity in the human brain via diffusion tensor MRI.
Kingsley, P. B., & Monahan, W. G. (2004). Selection of the optimum b factor for
diffusion-weighted magnetic resonance imaging assessment of ischemic stroke.
Koay, C. G., Carew, J. D., Alexander, A. L., Basser, P. J., & Meyerand, M. E. (2006).
Investigation of anomalous estimates of tensor-derived quantities in diffusion tensor
Koay, C. G., Chang, L. C., Carew, J. D., Pierpaoli, C., & Basser, P. J. (2006). A unifying
theoretical and algorithmic framework for least squares methods of estimation in
diffusion tensor imaging. Journal of Magnetic Resonance, 182, 115125.
Koay, C. G., Chang, L. C., Pierpaoli, C., & Basser, P. J. (2007). Error propagation
framework for diffusion tensor imaging via diffusion tensor representations. IEEE
Landman, B. A., Bazin, P. L., Smith, S. A., & Prince, J. L. (2009). Robust estimation of
spatially variable noise fields. Magnetic Resonance in Medicine, 62, 500509.
Landman, B. A., Farrell, J. A., Jones, C. K., Smith, S. A., Prince, J. L., & Mori, S. (2007).
Effects of diffusion weighting schemes on the reproducibility of DTI-derived
fractional anisotropy, mean diffusivity, and principal eigenvector measurements at
1.5 T. NeuroImage, 36, 11231138.
Lazar, M., Alexander, A. L., Thottakara, P. J., Badie, B., & Field, A. S. (2006). White
matter reorganization after surgical resection of brain tumors and vascular
malformations. AJNR - American Journal of Neuroradiology, 27, 12581271.
Le Bihan, D. (1991). Molecular diffusion nuclear magnetic resonance imaging.
Magnetic Resonance Quarterly, 7, 130.
Le Bihan, D., Breton, E., Lallemand, D., Grenier, P., Cabanis, E., & Laval-Jeantet, M.
(1986). MR imaging of intravoxel incoherent motions: Application to diffusion and
perfusion in neurologic disorders. Radiology, 161, 401407.
Le Bihan, D., Mangin, J. F., Poupon, C., Clark, C. A., Pappata, S., Molko, N., et al.
(2001). Diffusion tensor imaging: Concepts and applications. Journal of Magnetic
Le Bihan, D., Poupon, C., Amadon, A., & Lethimonnier, F. (2006). Artifacts and pitfalls
in diffusion MRI. Journal of Magnetic Resonance Imaging, 24, 478488.
Lenglet, C., Campbell, J. S., Descoteaux, M., Haro, G., Savadjiev, P., Wassermann, D.,
et al. (2009). Mathematical methods for diffusion MRI processing. NeuroImage, 45,
S111S122.
Lenglet, C., Rousson, M., Deriche, R., & Faugeras, O. (2006). Statistics on the manifold
of multivariate normal distributions: Theory and application to diffusion tensor MRI
processing. Journal of Mathematical Imaging and Vision, 25, 423444.
Lu, S., Ahn, D., Johnson, G., Law, M., Zagzag, D., & Grossman, R. I. (2004). Diffusiontensor MR imaging of intracranial neoplasia and associated peritumoral edema:
Introduction of the tumor infiltration index. Radiology, 232, 221228.
Makris, N., Worth, A. J., Sorensen, A. G., Papadimitriou, G. M., Wu, O., Reese, T. G., et al.
(1997). Morphometry of in vivo human white matter association pathways with
diffusion-weighted magnetic resonance imaging. Annals of Neurology, 42, 951962.
Mangin, J. F., Poupon, C., Clark, C., Le Bihan, D., & Bloch, I. (2002). Distortion
correction and robust tensor estimation for MR diffusion imaging. Medical Image
Analysis, 6, 191198.
Mattiello, J., Basser, P. J., & Le Bihan, D. (1994). Analytical expressions for the b matrix
in NMR diffusion imaging and spectroscopy. Journal of Magnetic Resonance,
Series A, 108, 131141.
Mattiello, J., Basser, P. J., & Le Bihan, D. (1997). The b matrix in diffusion tensor
echo-planar imaging. Magnetic Resonance in Medicine, 37, 292300.
Maximov, I. I., Grinberg, F., & Shah, N. J. (2011). Robust tensor estimation in diffusion
tensor imaging. Journal of Magnetic Resonance, 213, 136144.
Mori, S., Crain, B. J., Chacko, V. P., & Van Zijl, P. C. (1999). Three-dimensional
tracking of axonal projections in the brain by magnetic resonance imaging. Annals
of Neurology, 45, 265269.
Mori, S., Frederiksen, K., Van Zijl, P. C., Stieltjes, B., Kraut, M. A., Solaiyappan, M.,
et al. (2002). Brain white matter anatomy of tumor patients evaluated with diffusion
tensor imaging. Annals of Neurology, 51, 377380.
Mori, S., & Zhang, J. (2006). Principles of diffusion tensor imaging and its applications
to basic neuroscience research. Neuron, 51, 527539.
Moseley, M. E., Cohen, Y., Kucharczyk, J., Mintorovitch, J., Asgari, H. S.,
Wendland, M. F., et al. (1990). Diffusion-weighted MR imaging of anisotropic water
diffusion in cat central nervous system. Radiology, 176, 439445.
Mukherjee, P., Bahn, M. M., Mckinstry, R. C., Shimony, J. S., Cull, T. S., Akbudak, E.,
et al. (2000). Differences between gray matter and white matter water diffusion
in stroke: Diffusion-tensor MR imaging in 12 patients. Radiology, 215, 211220.
Niogi, S. N., & Mukherjee, P. (2010). Diffusion tensor imaging of mild traumatic brain
injury. The Journal of Head Trauma Rehabilitation, 25, 241255.
ODdonnell, L. J., & Westin, C. F. (2011). An introduction to diffusion tensor image
analysis. Neurosurgery Clinics of North America, 22, 185196, viii.
Pajevic, S., & Basser, P. J. (2003). Parametric and non-parametric statistical analysis of
DT-MRI data. Journal of Magnetic Resonance, 161, 114.
Pajevic, S., & Pierpaoli, C. (1999). Color schemes to represent the orientation
of anisotropic tissues from diffusion tensor data: Application to white matter
fiber tract mapping in the human brain. Magnetic Resonance in Medicine, 42,
526540.
Papadakis, N. G., Xing, D., Houston, G. C., Smith, J. M., Smith, M. I., James, M. F.,
et al. (1999). A study of rotationally invariant and symmetric indices of diffusion
anisotropy. Magnetic Resonance Imaging, 17, 881892.
Papadakis, N. G., Xing, D., Huang, C. L., Hall, L. D., & Carpenter, T. A. (1999). A
comparative study of acquisition schemes for diffusion tensor imaging using MRI.
Sajjadi, S. A., Acosta-Cabronero, J., Patterson, K., Diaz-De-Grenu, L. Z.,
Williams, G. B., & Nestor, P. J. (2013). Diffusion tensor magnetic resonance imaging
for single subject diagnosis in neurodegenerative diseases. Brain, 136, 22532261.
Salvador, R., Pena, A., Menon, D. K., Carpenter, T. A., Pickard, J. D., & Bullmore, E. T.
(2005). Formal characterization and extension of the linearized diffusion tensor
model. Human Brain Mapping, 24, 144155.
Schlaug, G., Siewert, B., Benfield, A., Edelman, R. R., & Warach, S. (1997). Time course
of the apparent diffusion coefficient (ADC) abnormality in human stroke. Neurology,
49, 113119.
Skare, S., Hedehus, M., Moseley, M. E., & Li, T. Q. (2000). Condition number as
a measure of noise performance of diffusion tensor data acquisition schemes with
MRI. Journal of Magnetic Resonance, 147, 340352.
Song, S. K., Sun, S. W., Ramsbottom, M. J., Chang, C., Russell, J., & Cross, A. H.
(2002). Dysmyelination revealed through MRI as increased radial (but unchanged
axial) diffusion of water. NeuroImage, 17, 14291436.
Sotiropoulos, S. N., Jbabdi, S., Xu, J., Andersson, J. L., Moeller, S., Auerbach, E. J.,
et al. (2013). Advances in diffusion MRI acquisition and processing in the Human
Connectome Project. NeuroImage, 80, 125143.
Stejskal, E. O. (1965). Use of spin echoes in a pulsed magnetic-field gradient to study
anisotropic, restricted diffusion and flow. The Journal of Chemical Physics, 43,
35973603.
presence of a time-dependent field gradient. The Journal of Chemical Physics, 42,
288292.
Thomsen, C., Henriksen, O., & Ring, P. (1987). In vivo measurement of water self diffusion
in the human brain by magnetic resonance imaging. Acta Radiologica, 28, 353361.
Tristan-Vega, A., Aja-Fernandez, S., & Westin, C. F. (2012). Least squares for diffusion
tensor estimation revisited: Propagation of uncertainty with Rician and non-Rician
signals. NeuroImage, 59, 40324043.
Tschumperle, D., & Deriche, R. (2003). Variational frameworks for DT-MRI estimation,
regularization and visualization. In: Proceedings of the ninth IEEE international
conference on computer vision Volume 2. Washington, DC: IEEE Computer
Society. http://www.computer.org/portal/web/guest/contact.

Van Essen, D. C., Smith, S. M., Barch, D. M., Behrens, T. E., Yacoub, E., Ugurbil, K.,
et al. (2013). The WU-minn human connectome project: An overview. NeuroImage,
80, 6279.
Walker, L., Chang, L. C., Koay, C. G., Sharma, N., Cohen, L., Verma, R., et al. (2011).
Effects of physiological noise in population analysis of diffusion tensor MRI data.
Wang, Z., Vemuri, B. C., Chen, Y., & Mareci, T. H. (2004). A constrained variational
principle for direct estimation and smoothing of the diffusion tensor field from
complex DWI. IEEE Transactions on Medical Imaging, 23, 930939.
Werring, D. J., Clark, C. A., Barker, G. J., Thompson, A. J., & Miller, D. H. (1999).
Diffusion tensor imaging of lesions and normal-appearing white matter in multiple
sclerosis. Neurology, 52, 16261632.
251
Wesbey, G. E., Moseley, M. E., & Ehman, R. L. (1984). Translational molecular selfdiffusion in magnetic resonance imaging. II. Measurement of the self-diffusion
coefficient. Investigative Radiology, 19, 491498.
Westin, C. F., Maier, S. E., Mamata, H., Nabavi, A., Jolesz, F. A., & Kikinis, R. (2002).
Processing and visualization for diffusion tensor MRI. Medical Image Analysis, 6,
93108.
Wheeler-Kingshott, C. A., & Cercignani, M. (2009). About axial and radial
diffusivities. Magnetic Resonance in Medicine, 61, 12551260.
White, T., Nelson, M., & Lim, K. O. (2008). Diffusion tensor imaging in psychiatric
disorders. Topics in Magnetic Resonance Imaging, 19, 97109.
Yoshida, S., Oishi, K., Faria, A. V., & Mori, S. (2013). Diffusion tensor imaging of
normal brain development. Pediatric Radiology, 43, 1527.
Probability Distribution Functions in Diffusion MRI

Y Rathi and C-F Westin, Harvard Medical School, Boston, MA, USA
ODF Orientation distribution function.

RATP Return to axis probability.
RTOP Return to origin probability.
Glossary
EAP Ensemble average diffusion propagator.

fODF Fiber orientation distribution function.
The Diffusion Propagator

Diffusion MRI (dMRI) allows for non-invasive investigation
of the neural architecture of the brain. Consequently, it is
increasingly being used in clinical settings for investigating several brain disorders such as, Alzheimers disease, stroke, schizophrenia, mild traumatic brain injury, etc. (Shenton et al., 2012;
Thomason & Thompson, 2011). dMRI reveals the tissue structure by probing the motion of water molecules. This motion of
water molecules can be represented in terms of a probability
distribution function, often termed as the ensemble average
diffusion propagator (EAP), given by Callaghan (1991):
Eqei2pqr dq;
[1]
P r
3
where E(q) S(q)/S(0) is the normalized diffusion signal measured at the location q in q-space. Note that, the actual signal
with diffusion sensitization in the gradient direction q is represented by S(q), whereas S(0) is the signal without any diffusion
weighting. The average diffusion propagator P(r) gives the
probability (likelihood) of water molecules to undergo a net
displacement r during the diffusion weighting time D of the
diffusion experiment. In other words, the diffusion propagator
P(r) is the Fourier transform of the normalized signal E(q).
Several methods have been proposed to estimate the diffusion propagator P(r) from measurements made in q-space. One
of the first approaches was proposed by Basser, Mattiello, and
LeBihan (1994), which assumed a Gaussian distribution of
water molecules. Under this assumption, the propagator is
completely defined by a diffusion tensor D, and this type of
imaging protocol was aptly named as diffusion tensor imaging
(DTI). Thus, the probability of displacement r in DTI is given by
1

Pr p3=2 jDj 2 exp p2 r T D1 r :
[2]
This method, however, makes several strong assumptions

about the underlying tissue structure, namely, that only one
principal fiber direction exists (coinciding with the principal
eigenvector of the diffusion tensor) at each voxel and that the
diffusion can be characterized by a Gaussian distribution function. Later works, showed that these assumptions are too simplistic and that several crossings fibers exist at each voxel, and
that the diffusion is primarily non-Gaussian in the higher
q-value regime (Cohen & Assaf, 2002; Tuch, Reese, Wiegell, &
Wedeen, 2003).
Apart from the more traditional DTI, it is nowadays standard to use High Angular Resolution Diffusion Imaging
(HARDI) which involves acquiring diffusion signals at a single

b-value (single q-shell) in several gradient directions spread
over the unit sphere in a quasi-uniform manner (Assemlal,
Tschumperle, Brun, & Siddiqi, 2011; Tuch et al., 2003). This
protocol allows for resolving the complex angular structure of
the neural fibers, by computing an orientation distribution
function (ODF). The diffusion ODF is the marginal distribution of the EAP and is given by:
ODFu
Prur k dr;
[3]
where u is a unit vector and k is an arbitrary integer, which

determines the sharpness of the ODF peaks. Figure 1 shows the
estimated ODFs computed using the above expression with
k 2 and using the radial basis function approach given in
Rathi et al. (2014). Two different radial basis functions (Gaussian and inverse multi-quadric) were used to estimate the ODFs
in the small rectangular region shown in the color coded FA
image. In Aganj et al. (2010) and Tristan-Vega, Westin, and
Aja-Fernandez (2009), the authors derived this expression for
the ODF (with k 2), which ensures that it is a true probability
distribution function (sum is 1). This is in contrast to the
Q-ball-based ODF expression used in Tuch (2004), where an
artificial normalization factor had to be used to make the ODF
a true probability distribution function. Finally, the expression
in Tuch (2004) for the ODF also had the effect of blurring the
zarslan
peaks of the ODF, making it susceptible to noise. In O
et al. (2013), the authors generalized the expression for the
ODF to arbitrary k to obtain sharper ODF peaks. While the
ODF allows to estimate multiple diffusion directions at various
crossing angles, yet, it does not provide information about the
radial signal decay (with increasing b-value), which is known
to be sensitive to various anomalies of white matter (Cohen &
Assaf, 2002).
To obtain accurate information about the neural architecture, diffusion spectrum imaging (DSI) was proposed in
Wedeen, Hagmann, Tseng, Reese, and Weisskoff (2005).
This dMRI technique involves acquiring multiple measurements over a Cartesian grid of points in the q-space, followed
by the application of discrete Fourier transform to obtain an
estimate of the EAP. Unfortunately, a large number of measurements required by DSI make it impractical to use in
clinical settings. Accordingly, to speed-up the acquisition of
dMRI (and DSI) data, two complementary approaches have
been proposed, namely: (i) the use of compressed sensing
(CS) to reduce the number of measurements (Cande`s,
http://dx.doi.org/10.1016/B978-0-12-397025-1.00292-X
253
254
INTRODUCTION TO METHODS AND MODELING | Probability Distribution Functions in Diffusion MRI
Figure 1 Orientation distribution function (ODF) estimated using (a) Gaussian and (b) generalized inverse multiquadric for the rectangular region
shown on a coronal color-coded FA slice.
Romberg, & Tao, 2006; Michailovich, Rathi, & Dolui, 2011;

Rathi et al., 2011), and (ii) the use of multi-slice acquisition
sequences for faster data acquisition (Feinberg et al., 2010;
Setsompop et al., 2011).
Several imaging and analysis schemes, which use fewer
measurements than traditional DSI, have also been proposed
in the literature (Assemlal et al., 2011; Barmpoutis, Vemuri, &
Forde, 2008; Descoteaux, Deriche, Bihan, Mangin, & Poupon,
2010; Hosseinbor, Chung, Wu, & Alexander, 2012; Jensen,
Helpern, Ramani, Lu, & Kaczynski, 2005; Merlet, Caruyer, &
Deriche, 2012; Wu & Alexander, 2007; Ye, Portnoy, Entezari,
Blackband, & Vemuri, 2012, Ye, Portnoy, Entezari, Vemuri, &
Blackband, 2011; Zhang, Schneider, Wheeler-Kingshott, &
Alexander, 2012). Each of these techniques captures a different aspect of the underlying tissue organization, which is
missed by HARDI. Traditional methods of EAP estimation
that account for the non-monoexponential (radial) decay of
diffusion signals require a relatively large number of measurements at high b-values (greater than 3000 s mm2) (Assaf,
Freidlin, Rohde, & Basser, 2004; Mulkern et al., 2001). Consequently, their associated scan times are deemed to be too
long for non-cooperative patients, which has led to the development of CS based techniques for reducing the number of
measurements in dMRI scans (Merlet & Deriche, 2013; Rathi
et al., 2011).
An alternative set of methods based on spherical deconvolution have also been proposed in the literature (Jian &
Vemuri, 2007; Tournier, Calamante, Gadian, & Connelly,
2004). These methods assume a particular model for a single
fiber response function and deconvolve the signal to obtain a
fiber orientation distribution function (fODF). This approach
is different than the one in eqn [3], where the ODF is computed from the marginal of the diffusion propagator.
Several structural features of the tissue can be obtained from
zarslan et al., 2013). For example,
the diffusion propagator (O
the return-to-origin probability (RTOP), given by P(0), is proportional to the inverse of the average pore volume. Similarly,
the return-to-axis probability (RTAP)
RTAP
E? d?
1
hAi
[4]
is inversely proportional to the average pore cross-sectional

area. This measure can be used to estimate the average axon
diameter for a given fiber bundle. Similarly, the return-to-plane
probability (RTPP) can be used to estimate the mean length of
the cylinders (axons) at each voxel:
RTPP
Ejj djj :
[5]
In addition, several other statistical features, such as multivariate kurtosis, mean-squared displacement and higher order
moments can be computed from the diffusion propagator.
These features can provide additional insights on the amount
of restricted diffusion (due to smaller pore sizes) at each voxel.
Thus, measures derived from the diffusion propagator can
provide important structural details regarding the tissue microstructure. Finally, brain connectivity analysis can also be done
using the information obtained from the diffusion propagator.
For example, in Rathi et al. (2013), the authors propose a
unified framework for model estimation (diffusion propagator
estimation) and tractography for tracing neural fiber bundles
in the brain. Subsequently, brain network analysis can be
used to understand network level differences in two populations (e.g. healthy controls and sczhiophrenia) (Hagmann
et al., 2008).
Thus, knowing the diffusion propagator (the probability
distribution function of the diffusion of water molecules)
allows for estimating several biological and statistical properties of the white matter in the brain.
INTRODUCTION TO METHODS AND MODELING | Probability Distribution Functions in Diffusion MRI
References
Aganj, I., Lenglet, C., Sapiro, G., Yacoub, E., Ugurbil, K., & Harel, N. (2010). Reconstruction
of the orientation distribution function in single-and multiple-shell q-ball imaging within
constant solid angle. Magnetic Resonance in Medicine, 64, 554566.
Assemlal, H.-E., Tschumperle, D., Brun, L., & Siddiqi, K. (2011). Recent advances in
diffusion MRI modeling: Angular and radial reconstruction. Medical Image Analysis,
15, 369396.
Barmpoutis, A., Vemuri, B. C., & Forde, J. R. (2008). Fast displacement probability
profile approximation from hardi using 4th-order tensors. In ISBI (pp. 911914). .
Callaghan, P. T. (1991). Principles of NMR microscopy. Houston: Tecmag Inc.
Cande`s, E. J., Romberg, J., & Tao, T. (2006). Robust uncertainty principles: Exact signal
reconstruction from highly incomplete frequency information. IEEE Transactions on
Information Theory, 52, 489509.
Cohen, Y., & Assaf, Y. (2002). High b-value q-space analyzed diffusion-weighted MRS
and MRI in neuronal tissuesA technical review. NMR in Biomedicine, 15, 516542.
Descoteaux, M., Deriche, R., Bihan, D. L., Mangin, J. F., & Poupon, C. (2010). Multiple
q-shell diffusion propagator imaging. Medical Image Analysis, 15(4), 603621.
Feinberg, D. A., Moeller, S., Smith, S. M., Auerbach, E., Ramanna, S., Glasser, M. F.,
et al. (2010). Multiplexed echo planar imaging for sub-second whole brain fMRI and
fast diffusion imaging. PLoS One, 5(12), e15710.
Hagmann, P., Cammoun, L., Gigandet, X., Meuli, R., Honey, C. J., Wedeen, V. J., et al.
(2008). Mapping the structural core of human cerebral cortex. PLoS Biology, 6,
159170.
Hosseinbor, A. P., Chung, M. K., Wu, Y. C., & Alexander, A. L. (2012). Bessel Fourier
orientation reconstruction (BFOR): An analytical diffusion propagator reconstruction
for hybrid diffusion imaging and computation of q-space indices. NeuroImage, 64,
650670.
kurtosis imaging: The quantification of non-gaussian water diffusion by means of
Jian, B., & Vemuri, B. (2007). A unified computational framework for deconvolution to
reconstruct multiple fibers from diffusion weighted MRI. IEEE Transaction on
Medical Imaging, 26, 14641471.
Merlet, S., Caruyer, E., & Deriche, R. (2012). Parametric dictionary learning for
modeling EAP and ODF in diffusion MRI. In MICCAI.
Merlet, S. L., & Deriche, R. (2013). Continuous diffusion signal, EAP and ODF estimation
via compressive sensing in diffusion MRI. Medical Image Analysis, 17, 556572.
Michailovich, O., Rathi, Y., & Dolui, S. (2011). Spatially regularized compressed
sensing for high angular resolution diffusion imaging. TMI, 30, 11001115.
Mulkern, R. V., Vajapeyam, S., Robertson, R. L., Caruso, P. A., Rivkin, M. J., &
Maier, S. E. (2001). Biexponential apparent diffusion coefficient parametrization in
adult vs newborn brain. Magnetic Resonance Imaging, 19, 659668.
255
Ozarslan, E., Koay, C. G., Shepherd, T. M., Komlosh, M. E., Irfanoglu, M. O.,
Pierpaoli, C., et al. (2013). Mean apparent propagator (map) MRI: A novel
diffusion imaging method for mapping tissue microstructure. NeuroImage, 78,
1632.
Rathi, Y., Gagoski, B., Setsompop, K., Michailovich, O., Ellen Grant, P., & Westin, C.-F.
(2013). Diffusion propagator estimation from sparse measurements in a
tractography framework. In Medical image computing and computer-assisted
interventionMICCAI 2013 (pp. 510517). Berlin Heidelberg: Springer.
Rathi, Y., Michailovich, O., Setsompop, K., Bouix, S., Shenton, M., & Westin, C.-F.
(2011). Sparse multi-shell diffusion imaging. MICCAI, 14, 5865.
Rathi, Y., Niethammer, M., Laun, F., Setsompop, K., Michailovich, O., Ellen Grant, P.,
et al. (2014). Diffusion propagator estimation using radial basis functions. In
Computational diffusion MRI and brain connectivity (pp. 5766). Berlin Heidelberg:
Springer.
Setsompop, K., Borjan, A., Gagoski, J. R., Polimeni, T. W., Wedeen, V. J., & Wald, L. L.
Medicine, 67, 12101224.
Shenton, M. E., Hamoda, H. M., Schneiderman, J. S., Bouix, S., Pasternak, O., Rathi, Y.,
et al. (2012). A review of magnetic resonance imaging and diffusion tensor
imaging findings in mild traumatic brain injury. Brain Imaging and Behavior, 6,
137192.
Thomason, M. E., & Thompson, P. M. (2011). Diffusion imaging, white matter, and
psychopathology. Annual Review of Clinical Psychology, 7, 6385.
Tournier, J.-D., Calamante, F., Gadian, D., & Connelly, A. (2004). Direct estimation of
spherical deconvolution. NeuroImage, 23, 11761185.
Tristan-Vega, A., Westin, C.-F., & Aja-Fernandez, S. (2009). Estimation of fiber
orientation probability density functions in high angular resolution diffusion
Tuch, D. S. (2004). Q-ball imaging. Magnetic Resonance in Medicine, 52, 13581372.
Tuch, D., Reese, T., Wiegell, M., & Wedeen, V. (2003). Diffusion MRI of complex neural
architecture. Neuron, 40, 885895.
Wedeen, V. J., Hagmann, P., Tseng, W. Y. I, Reese, T. G., & Weisskoff, R. M. (2005).
Wu, Y. C., & Alexander, A. L. (2007). Hybrid diffusion imaging. NeuroImage, 36,
617629.
Ye, W., Portnoy, S., Entezari, A., Blackband, S. J., & Vemuri, B. C. (2012). An efficient
interlaced multi-shell sampling scheme for reconstruction of diffusion propagators.
IEEE Transactions on Medical Imaging, 31, 10431050.
Ye, W., Portnoy, S., Entezari, A., Vemuri, B. C., & Blackband, S. J. (2011). Box spline
based 3d tomographic reconstruction of diffusion propagators from MRI data.
Biomedical imaging: From nano to macro, 2011 IEEE international symposium on,
397400, IEEE.
Zhang, H., Schneider, T., Wheeler-Kingshott, C. A., & Alexander, D. C. (2012). NODDI:
Practical in vivo neurite orientation dispersion and density imaging of the human
brain NeuroImage, 61(4), 10001016.
Q-Space Modeling in Diffusion-Weighted MRI

I Aganj, Massachusetts General Hospital, Harvard Medical School, MA, USA
G Sapiro, Duke University, NC, USA
N Harel, University of Minnesota Medical School, MN, USA
Glossary
FunkRadon transform A transform from the unit sphere

to itself, which takes the integral on each great circle
to the two points farthest from it.
Gyromagnetic ratio Ratio of the magnetic dipole moment
to the angular momentum. For the proton,
g 2. 68 108 rad s1 T1.

2pn
Hann window wn 0:5 1 cos N1
:
Myelin The material in a sheath around the axon of a
neuron.
Introduction
Diffusion-weighted imaging (DWI) is a noninvasive imaging
technology that provides valuable information about the
microarchitecture of biological tissue, by measuring the microscopic diffusion of water in three-dimensional (3-D) space.
Through fiber tracking, DWI provides a unique in vivo quantitative measurement of the brains anatomical connectivity. In
this article, we review several DWI signal acquisition strategies.
During the scanning process, diffusion-sensitizing gradient
!
pulses G with the duration d attenuate the image intensity
values. More precisely, parameterizing
the diffusion acquisi!
!
tion with the q-vector q gd G =2p (with g the gyromagnetic
ratio), each volume element
(voxel) of the DW image will have
!
an intensity value S q that is less than S(0), depending on
the amount of local water diffusion at the voxel. Assuming d is
sufficiently small, the 3-D probability density function (PDF)
of the displacement of water molecules after a certain amount
of time t (which depends on the acquisition sequence) has the
following
relationship with the signal attenuation
! !Fourier

E q S q =S0 (Callaghan, 1991):
Z !
!!
!
!
P x
E q e2pix q d3 q
[1]
3

!
where P x , which is also called the ensemble average propagator, carries important structural properties of the underlying
tissue, with applications such as the indication of white matter
anomalies (Assaf et al., 2002). The popularity of DWI in general, however, is largely thanks to its ability to quantify fiber
orientations in vivo. To that end, the diffusion orientation
distribution function (ODF) marginal PDF of diffusion of
water in a given direction u^ is defined as (Tuch, 2002;
Wedeen, Hagmann, Tseng, Reese, & Weisskoff, 2005)
Z 1
ODFu^
P r u^r 2 dr
[2]
0
Orientation distribution function (ODF) Marginal

probability density function of diffusion of water in a given
direction.
q-Space The reciprocal space parameterized by the q-vector.
q-Vector The frequency vector, pointing to a specific
frequency of the PDF of diffusion.
Tractography Fiber tracking, for example, by following the
principal direction of diffusion.
Voxel Volume element in a 3-D image.
Wavelet transform A representation of a function by a
certain orthonormal series.
Since the diffusion of water is hindered in the direction perpendicular to axons, the peaks of the diffusion ODF are often
aligned with the fiber orientations. The diffusion PDF and
subsequently ODF are considered real, positive, and antipodally symmetrical, thereby making real and symmetric spherical
harmonics basis suitable for representation of the orientational
diffusion information (Anderson, 2005; Descoteaux, Angelino,
Fitzgibbons, & Deriche, 2007; Hess, Mukherjee, Han, Xu, &
Vigneron, 2006).

!
!
The frequency spectrum of P x , measured as E q , is
required everywhere in the reciprocal q-space to allow for the

!
!
computation of P x at any point. However, E q is only
available on a finite set of q-vectors corresponding to the
acquired DW images. Therefore, depending on the acquisition
scheme, an interpolation model is needed to estimate the
!
values of E q in the entire q-space from the set of available
discrete data points.
The radial monoexponential model (Stejskal & Tanner,
1965),
Equ^ et2pq
ADCu^
[3]

! !
^ assumes that the diffusion signal decays
where q q , q qu,
2
^ with a rate propormonoexponentially in each direction u,

tional to the apparent diffusion coefficient ADCu^. When
!
E q is measured on a sphere (i.e., with a fixed q qs), eqn
[3] can be rewritten as Eqs u^ ebADCu^ , where the acquisition
b-value is defined as b t(2pqs)2. A popular example of the
monoexponential model is the diffusion tensor imaging (DTI)
(Basser, Mattiello, & LeBihan, 1994), which is used extensively
in clinical research. DTI assumes the quadratic formulation
^ which models the diffusion signal based on
ADCu^ u^T Du,
the free (anisotropic) diffusion of water molecules, as
http://dx.doi.org/10.1016/B978-0-12-397025-1.00293-1
257
258
INTRODUCTION TO METHODS AND MODELING | Q-Space Modeling in Diffusion-Weighted MRI

!
T !
2 !
E q e4p tq Dq
[4]
where D is the symmetric and positive-definite second-order

diffusion tensor. The principal direction of the diffusion tensor, that is, the eigenvector corresponding to the largest eigenvalue of D, strongly aligns with the direction of the myelinated
axons when a single fiber bundle passes through the voxel.
Given that the diffusion tensor has only six unknowns to be
estimated, only six DW images along with one baseline
image S(0) must be acquired, thereby maintaining a low
acquisition time (although more images are usually needed
to reduce the sensitivity to noise). Nonetheless, this comes at
the price of oversimplification of the diffusion profile, particularly resulting in the inability of DTI to reconstruct multiple
fiber orientations. To remedy this, the signal may be measured
with a much higher angular resolution on a sphere, as
described in the Multishell Sampling section. However, the
inexact radial interpolations (such as eqn [3]) would introduce
error in signal modeling when the q-space is sampled only on a
sphere.
In the rest of this article, we review a number of q-space
sampling schemes that attempt to minimize the errors arising
from diffusion modeling by covering the entire q-space. We
discuss the sampling of the q-space on a Cartesian grid, on
multiple spheres, and through compressed sensing (CS).
Diffusion Spectrum Imaging

The Fourier relationship in eqn [1] has been used to compute
characteristics of the PDF of diffusion from the diffusion signal
in q-space imaging (Assaf et al., 2002; Assaf, Mayk, & Cohen,
2000). Diffusion spectrum imaging (DSI) further provides
structural information from tissue architecture through Cartesian discretization and sampling of the q-space (Tuch, 2002;
Wedeen et al., 2000, 2005).
DSI acquires the diffusion signal on a regular 3-D lattice

within a sphere in the q-space, that is, !q an!j !n 23 , k!n k2 nmax ,
where a > 0 is the q-space sampling interval and nmax is the
radius of the sphere in lattice units. At each location, DW signal
is acquired for N 43 pn3max points on the q-space (Figure 1,
left). The PDF of diffusion is then reconstructed in a 3-D lattice
via discrete Fourier transform of the diffusion signal (the discrete version of eqn [1]), after being multiplied by a Hann
window to avoid ringing artifacts.
DSI
Among the acquisition schemes that have been proposed

for DWI so far, DSI is the least model-dependent. Basically,
DSI only assumes the PDF of diffusion to have a bounded

!
!
1
, and to be bandlimited,
domain, P x 0, x 2a
1

!
!

E q 0, q > anmax (deconvolution methods may be
2
used when these conditions are not satisfied; Canales-Rodrguez, Iturria-Medina, Aleman-Gomez, & Melie-Garca, 2010).
Thus, contrary to DTI and spherical acquisitions, no strong
assumption on the form of the signal is made. In particular,
errors arising from assuming exponential decay for the diffusion signal are not present in this method.
ODFs can be computed from DSI at each voxel by interpo
!
lating the discrete P x and computing eqn [2] numerically
inside a sphere with the radius nmax. Orientational information
obtained from DSI may be used in tractography to track brain
white matter pathways (Schmahmann et al., 2007), identify
crossing fibers (Wedeen et al., 2008), and map the structural
network of the human brain (Hagmann et al., 2008).
A DSI dataset is represented in a 6-D space, which is the
Cartesian product of two 3-D spaces, one representing the
voxel location and the other representing the pattern of diffusion within voxel. As a result, DSI provides us with ample
information about the tissue microstructure, but at the price
of a high acquisition time. The number of DW images to be
acquired in a scan is typically significantly higher for DSI
than for spherical acquisitions, increasing the possibility of
motion artifacts. This, however, may be alleviated through CS
(Bilgic et al., 2012, 2013; Lee, Wilkins, & Singh, 2012; Menzel
et al., 2011; Saint-Amant & Descoteaux, 2011; Setsompop
et al., 2013), as described in the Compressed Sensing section,
and information theoretical approaches (Knutsson & Westin,
2014). Typical parameter values for brain DSI were suggested
by Wedeen et al. (2005) as nmax 5, N 515, with a sampling
interval of a 20 mm1 resulting in a maximum b-value of
17 000 s mm2. A lower practical maximum b-value of
6500 s mm2, however, was later advised by Kuo, Chen,
Wedeen, and Tseng (2008) for the same number of q-space
measurement samples.
Multishell Sampling
DWI is the only available tool that allows to noninvasively
quantify the neural fiber orientation in vivo, primarily through
Single-shell HARDI
Three-shell HARDI
Figure 1 Q-space acquisition schemes of DSI (left), single-shell HARDI (middle), and three-shell HARDI (right), each with a total of 515 sample points.

tractography. High-angular-resolution diffusion imaging
(HARDI) (Tuch et al., 2002) is the acquisition scheme
designed to increase the angular resolution of the rich orientational information obtained from DWI. With HARDI, more
complex models than the diffusion tensor can be exploited,
enabling the resolution of multiple fiber bundles passing
through the voxel.
HARDI maximizes the angular information primarily by
ensuring that the q-space is uniformly sampled in as
many orientations as possible and that (in single-shell
HARDI) the sample points have a fixed magnitude so their
orientations are their only discrepancy. Accordingly, a set of
N sample points are acquired on a sphere of radius qs, as

n!
o
!
q i qs uî j qs q i , i 1, ... ,N , in such a way that the sur2
face of the sphere is sampled uniformly (Figure 1, middle).

Given that the b-value of all the sample points is the constant
b t(2pqs)2, this q-shell can be identified by this single b-value.
Since the diffusion data are only available on the q-shell, as
!
Eqs uî (in addition to the origin, E 0 1), a model is needed
in order to interpolate and extrapolate the inside and outside
of the shell, respectively, so the PDF and ODF of diffusion can
be computed. Tuch (2004) proposed the q-ball imaging recon!
struction that assumes the diffusion data (E q ) to be nonzero
only on the q-shell and computes the diffusion ODF (a blurred
version of eqn [2], without the factor r2), using the Funk
Radon transform of the diffusion signal. Conversely, Jansons
and Alexander (2003) proposed the persistent angular structure
model, which computes the diffusion PDF assuming that

!
P x can have nonzero values only on the surface of a sphere.
2
Later, the monoexponential model, Equî Eqs uî q =qs , initially discussed by Stejskal and Tanner (1965), was used to
zarslan, Shepherd, Vemuri,
compute the diffusion PDF (O
Blackband, & Mareci, 2006) and ODF (Aganj et al., 2010;
Canales-Rodrguez, Melie-Garca, & Iturria-Medina, 2009;
Tristan-Vega, Westin, & Aja-Fernandez, 2010). The exponential
model is particularly consistent with E(0) 1, and is compatible with the free diffusion that is modeled with the diffusion
tensor. Other approaches to reconstruct HARDI data include
spherical deconvolution that computes the fiber ODF
(Anderson & Ding, 2002; Tournier, Calamante, Gadian, &
Connelly, 2004), multitensor models that use a mixture of
Gaussians to represent the diffusion (Alexander, Barker, &
b=1
b=2
b=3
b=4
259
Arridge, 2002; Assaf, Freidlin, Rohde, & Basser, 2004; Behrens

et al., 2003; Chen et al., 2005), and higher-order tensors that
generalize the second-order diffusion tensor (Jensen, Helpern,
Ramani, Lu, & Kaczynski, 2005; Liu, Mang, & Moseley, 2010;
zarslan & Mareci, 2003). For more details on HARDI
O
reconstruction techniques, see the review by Seunarine and
Alexander (2014).
Keeping all the sample points on the sphere provides an
excellent uniform angular resolution by eliminating the confounding factor of the magnitude of the q-vector. However, the
interpolation/extrapolation models in HARDI reconstruction
are often not exact, resulting in angular distributions that vary
with the choice of the b-value. For instance, in the presence of a
single fiber bundle, the slow- and fast-diffusing components
make the signal estimation with the monoexponential model
inexact (Niendorf, Dijkhuizen, Norris, van Lookeren, &
Nicolay, 1996), producing spurious orientations affecting tractography (Jbabdi, Sotiropoulos, Savio, Grana, & Behrens,
2012). Even assuming that the single-compartment diffusion
tensor model, eqn [4], is exact for a single fiber bundle, a
region with two-way fiber crossing would still produce a bi!
T
T
!
!
2 !
2 !
exponential signal E q le4p tq D1 q 1 le4p tq D2 q
(with Di being the diffusion tensor of the ith fiber and l the
fraction of the first bundle). The estimation of these two diffusion tensors from a single q-shell is ill-posed, even when the
data are available with infinite angular resolution (Scherrer &
Warfield, 2012). Figure 2 illustrates an example where assuming the monoexponential model, sampling a signal with a
radially biexponential profile on a single q-shell produces
ODFs with peak directions that strongly depend on the acquisition b-value (Aganj et al., 2010).
To reduce the errors arising from HARDI signal modeling
while still maintaining the high angular resolution, the diffusion signal may be acquired on multiple q-shells (Figure 1,
right), which increases the radial resolution and allows to take
advantage of richer models. In particular, the multiexponential
P
2
âi u^q ,
decay model (Niendorf et al., 1996), Equ^ M
i1 li u
PM
with 0 < ai u^, li u^ 1 and i1 li u^ 1, requires acquisition
of at least 2M 1 q-shells to parameterize the signal with M
exponentials. The multiexponential model has been used to
compute properties such as the diffusion tensor (Ronen, Kim,
Garwood, Ugurbil, & Kim, 2003), mean and zero displacement
zarslan et al., 2006; Wu &
(Assaf et al., 2000), diffusion PDF (O
Alexander, 2007), and ODF (Aganj et al., 2010; Kamath et al.,
b=5
b=6
b=7
b = 1,2,3
(mono-exp.)
b = 1,2,3
(bi-exp.)
Figure
from a diffusion signal with a cross ()-shaped diffusion profile and radially biexponential decay:
! 2 ODF reconstruction
2
2
E q jsinfjq =2 jcos fjq =2 , where f is the azimuthal angle. From left to right, reconstructions use a single q-shell (b-values of 1, ..., 7 with
monoexponential model) and three q-shells (combined b-values of 1, 2, 3 with mono- and biexponential models). The fiber directions of the ODFs
computed with the monoexponential model depend on the acquisition b-value, and only the biexponential model correctly resolves them from low bvalues. Dark red represents negative values. Reproduced from Aganj, I., Lenglet, C., Sapiro, G., Yacoub, E., Ugurbil, K., & Harel, N. (2010).
Reconstruction of the orientation distribution function in single- and multiple-shell q-ball imaging within constant solid angle. Magnetic Resonance in
Medicine, 64, 554566.
260
2012). The example in Figure 2 shows how a biexponential fit

can correctly resolve fiber orientations from the same b-values
using which the monoexponential model fails.
Other methods for fusion of multiple q-shells compute the
PDF of diffusion and subsequently DWI features by modeling
the diffusion signal using GaussianLaguerre and spherical
harmonics functions (Assemlal, Tschumperle, & Brun, 2009;
Caruyer & Deriche, 2012; Cheng, Ghosh, Deriche, & Jiang,
2010; Cheng, Ghosh, Jiang, & Deriche, 2010; Ozarslan, Koay,
zarslan et al., 2013),
Shepherd, Blackband, & Basser, 2009; O
the solution of the Laplace equation (Descoteaux, Deriche, Le
Bihan, Mangin, & Poupon, 2011; Hosseinbor, Chung, Wu, &
Alexander, 2013), and radial basis functions (Rathi, Niethammer,
Laun, Setsompop, Michailovich, et al., 2014). Furthermore, multiple q-shells have been exploited to measure the non-Gaussianity
of the diffusion by diffusional kurtosis imaging (Jensen et al.,
2005) and Gaussian modeling of the diffusivity (Rathi, Michailovich, Setsompop & Westin, 2014; Yablonskiy, Bretthorst, &
Ackerman, 2003), compute the diffusion ODF by spherical wavelet decomposition (Khachaturian, Wisco, & Tuch, 2007), estimate diffusion spectrum measures in hybrid diffusion imaging
(Wu, Field, & Alexander, 2008), and reconstruct the fiber ODF via
the gamma distribution model of diffusivity (Jbabdi et al., 2012;
Sotiropoulos et al., 2013) and nonnegative spherical deconvolution (Cheng, Deriche, Jiang, Shen, & Yap, 2014). CS acquisition
has also been proposed for multiple shells (Duarte-Carvajalino
zarslan, Johnson, & Meyerand, 2012; Merlet,
et al., 2013; Koay, O
Caruyer, Ghosh, & Deriche, 2013; Merlet & Deriche, 2013; Rathi,
Michailovich, Laun, Setsompop, Grant, et al., 2014), which is
covered in the Compressed Sensing section.
As in single-shell HARDI, sample points in multishell
HARDI are uniformly distributed on each q-shell. However,
this raises the question of the sampling scheme in each shell
relative to the other shells. The diffusion signal may be
acquired on the same set of directions for all the shells, allowing
for straightforward fitting of the multiexponential model independently at each direction (Aganj et al., 2010). Nevertheless,
to increase the total number of sampled orientations, a staggered multishell scheme may be used where the sampling
directions are not aligned among shells (Caruyer, Lenglet,
Sapiro, & Deriche, 2013; Cheng, Shen, & Yap P-T, 2014; DeSantis, Assaf, Evans, & Jones, 2011; Kamath et al., 2012; Koay et al.,
2012; Ye, Portnoy, Entezari, Blackband, & Vemuri, 2012; Zhan
et al., 2011). In addition, using a Bayesian model, one can
reduce the number of necessary excitations for multishell
HARDI (Freiman, Afacan, Mulkern, & Warfield, 2013).
Compressed Sensing
Long acquisition time is a major hindrance to the clinical use
of DWI. Acquiring fewer sample points in the k-space and/or qspace reduces the acquisition time, albeit at considerable cost
to the image quality. CS (Candes, Romberg, & Tao, 2006;
Donoho, 2006), aka compressive sampling, improves the
trade-off between the resolution of the reconstructed image
and the acquisition time, through a specific acquisition scheme
that allows the reconstruction artifacts due to the limited sample size to be removed more effectively. Specifically, CS
requires that random undersampling produce incoherent
artifacts in a sparse representation of the image, so the artifacts

can be reduced by enforcing sparsity, thereby reconstructing
the image with a higher resolution than predicted by the
Nyquist Shannon sampling theorem. In this section, we
review CS approaches to DTI, DSI, and HARDI.
To improve DTI through CS, the wavelet-domain sparsity of
the direction-dependent component of the DW image has
been exploited to reconstruct the diffusion tensors from undersampled k-space (Pu et al., 2011). Along the same lines, diffusion images have been used in other approaches to interpolate
undersampled k-spaces (Ma, Limin, Rong, & Shaohua, 2013;
Welsh, DiBella, Adluru, & Hsu, 2013), some incorporating the
joint sparsity of DW images (Wu et al., 2014; Zhu et al., 2012),
correcting for the phase (Gao, Li, Zhang, Zhou, & Hu, 2013),
or using parallel imaging (Shi et al., in press). In addition, in a
mixture-of-Gaussians model, the vector of compartment mixture fractions has been considered sparse leading to CS
(Landman et al., 2012).
CS has been proposed to accelerate DSI acquisition to overcome its long scan time. Menzel et al. (2011) and Lee et al.
(2012) constructed the PDF of diffusion while considering it to
be sparse in the wavelet domain and to have small total variation. To that end, non-Cartesian q-space sampling has also
been proposed (Aboussouan, Marinelli, & Tan, 2011). In addition, adaptive dictionaries (Bilgic et al., 2012, 2013) with symmetry and positivity considerations (Gramfort, Poupon, &
Descoteaux, 2014) have also been chosen as the sparse domain,
significantly reducing the DSI acquisition time. Sampling strategies and sparsifying transforms in the literature have been
extensively compared (Paquette, Merlet, Gilbert, Deriche, &
Descoteaux, in press; Saint-Amant & Descoteaux, 2011).
In HARDI, directional quantities are often represented in the
spherical harmonics basis, which, however, is not necessarily a
sparse basis for the diffusion signal. Accordingly, overcomplete
spherical ridgelets basis (Dolui, Kuurstra, & Michailovich, 2012;
Michailovich & Rathi, 2010; Michailovich, Rathi, & Dolui, 2011;
Rathi, Michailovich, Laun, et al., 2014), spherical wavelet basis
(Tristan-Vega & Westin, 2011), Bayesian framework and spatial
redundancy (Duarte-Carvajalino et al., 2013), and sparse reproducing kernels (Ahrens, Nealy, Perez, & van der Walt, 2013)
have been proposed for sparse representation of the ODF. In
multishell acquisitions, a q-space acquisition scheme has been
designed to maximize the incoherence among the sample points
(Koay et al., 2012). CS acquisition with continuous parameterization of the diffusion signal from HARDI has been proposed
using fixed sparse spaces (Merlet & Deriche, 2013) and dictionary learning (Cheng, Jiang, Deriche, Shen, & Yap, 2013; Merlet
et al., 2013; Ye, Vemuri, & Entezari, 2012). Additionally, balanced undersampling of k-space over all diffusion directions has
been suggested (Awate & DiBella, 2013; Mani, Jacob, Guidon,
Magnotta, & Zhong, 2014). Sparse fiber ODF computation has
also been investigated by limiting the number of fiber directions
in spherical deconvolution (Daducci, Van De Ville, Thiran, &
Wiaux, 2014).
Lastly, in contrast to multishell acquisition where the qspace sampling is tangentially dense on the spheres and radially sparse, in a tomography-inspired acquisition scheme
zarslan, & Basser, 2009; Pickalov & Basser, 2006),
(Jarisch, O
the sampling has been chosen radially dense on lines and
tangentially sparse. This approach takes advantage of its

resemblance to the computed tomography (CT) and reconstructs the PDF of diffusion using high-efficiency CT methods
and also by applying physical constraints.
Acknowledgments
This research was in part supported by a grant from the Massachusetts Alzheimers Disease Research Center (5 P50
AG005134), the MGH Neurology Clinical Trials Unit, and the
Harvard NeuroDiscovery Center, in addition to the NIH 1 R01
NS083534, R01 NS085188, P41 EB015894, P30 NS076408,
and the Human Connectome Project (U54 MH091657) grants.

Diffusion MRI; INTRODUCTION TO ANATOMY AND
PHYSIOLOGY: Cytoarchitectonics, Receptorarchitectonics, and
Network Topology of Language; INTRODUCTION TO METHODS
AND MODELING: Diffusion Tensor Imaging; Fiber Tracking with DWI;
Probability Distribution Functions in Diffusion MRI; Tissue
Microstructure Imaging with Diffusion MRI.
References
Aboussouan, E., Marinelli, L., & Tan, E. (2011). Non-cartesian compressed sensing for
diffusion spectrum imaging. Proceedings of the International Society for Magnetic
Aganj, I., Lenglet, C., Sapiro, G., Yacoub, E., Ugurbil, K., & Harel, N. (2010).
Reconstruction of the orientation distribution function in single- and multiple-shell
q-ball imaging within constant solid angle. Magnetic Resonance in Medicine, 64,
554566.
Ahrens, C., Nealy, J., Perez, F., & van der Walt, S. (2013). Sparse reproducing
kernels for modeling fiber crossings in diffusion weighted imaging. In IEEE
proceedings of the tenth International Symposium on Biomedical Imaging (ISBI)
(pp. 688691).
Alexander, D. C., Barker, G. J., & Arridge, S. R. (2002). Detection and modeling of nonGaussian apparent diffusion coefficient profiles in human brain data. Magnetic
Anderson, A. W. (2005). Measurement of fiber orientation distributions using high
angular resolution diffusion imaging. Magnetic Resonance in Medicine, 54,
11941206.
Anderson, A., & Ding, Z. (2002). Sub-voxel measurement of fiber orientation using high
angular resolution diffusion tensor imaging. Honolulu, HI: ISMRM.
Assaf, Y., Ben-Bashat, D., Chapman, J., Peled, S., Biton, I. E., Kafri, M., et al. (2002).
High b-value q-space analyzed diffusion-weighted MRI: Application to multiple
sclerosis. Magnetic Resonance in Medicine, 47, 115126.
Assaf, Y., Mayk, A., & Cohen, Y. (2000). Displacement imaging of spinal cord using qspace diffusion-weighted MRI. Magnetic Resonance in Medicine, 44, 713722.
Assemlal, H.-E., Tschumperle, D., & Brun, L. (2009). Efficient and robust computation
of PDF features from diffusion MR signal. Medical Image Analysis, 13, 715729.
Awate, S. P., & DiBella, E. V. R. (2013). Compressed sensing HARDI via rotationinvariant concise dictionaries, flexible K-space undersampling, and multiscale
spatial regularity. In IEEE proceedings of the tenth International Symposium on
Biomedical Imaging (ISBI) (pp. 912).
Behrens, T. E. J., Woolrich, M. W., Jenkinson, M., Johansen-Berg, H., Nunes, R. G.,
Clare, S., et al. (2003). Characterization and propagation of uncertainty in diffusionweighted MR imaging. Magnetic Resonance in Medicine, 50, 10771088.
Bilgic, B., Chatnuntawech, I., Setsompop, K., Cauley, S. F., Yendiki, A., Wald, L. L.,
et al. (2013). Fast dictionary-based reconstruction for diffusion spectrum imaging.
261
Bilgic, B., Setsompop, K., Cohen-Adad, J., Yendiki, A., Wald, L. L., & Adalsteinsson, E.
(2012). Accelerated diffusion spectrum imaging with compressed sensing using
adaptive dictionaries. Magnetic Resonance in Medicine, 68, 17471754.
Callaghan, P. T. (1991). Principles of nuclear magnetic resonance microscopy. Oxford:
Clarendon Press.
Canales-Rodrguez, E. J., Iturria-Medina, Y., Aleman-Gomez, Y., & Melie-Garca, L.
(2010). Deconvolution in diffusion spectrum imaging. NeuroImage, 50, 136149.
Canales-Rodrguez, E. J., Melie-Garca, L., & Iturria-Medina, Y. (2009). Mathematical
description of q-space in spherical coordinates: Exact q-ball imaging. Magnetic
Candes, E. J., Romberg, J., & Tao, T. (2006). Robust uncertainty principles: Exact signal
reconstruction from highly incomplete frequency information. IEEE Transactions on
Information Theory, 52, 489509.
Caruyer, E., & Deriche, R. (2012). Optimal regularization for MR diffusion signal
reconstruction. In IEEE proceedings of the ninth International Symposium on
Biomedical Imaging (ISBI) (pp. 5053).
Caruyer, E., Lenglet, C., Sapiro, G., & Deriche, R. (2013). Design of multishell sampling
schemes with uniform coverage in diffusion MRI. Magnetic Resonance in Medicine,
69, 15341540.
Chen, Y., Guo, W., Zeng, Q., Yan, X., Rao, M., & Liu, Y. (2005). Apparent diffusion
coefficient approximation and diffusion anisotropy characterization in DWI. In G.
Christensen & M. Sonka (Eds.), Information Processing in Medical Imaging
(Vol. 3565, pp. 246257). Berlin/Heidelberg: Springer.
Cheng J, Shen D, & Yap P-T (2014). Designing Single- and Multiple-Shell Sampling
Schemes for Diffusion MRI Using Spherical Code. In: Golland, P. et al., (Eds.),
Medical Image Computing and Computer-Assisted Intervention MICCAI 2014,
Vol. 8675, (pp. 281288). Boston, MA: Springer International Publishing.
Cheng, J., Deriche, R., Jiang, T., Shen, D., & Yap, P.-T. (2014). Non-negative spherical
deconvolution (NNSD) for estimation of fiber orientation distribution function in
single-/multi-shell diffusion MRI. NeuroImage, 101, 750764.
Cheng, J., Ghosh, A., Deriche, R., & Jiang, T. (2010). Model-free, regularized, fast, and
robust analytical orientation distribution function estimation. In T. Jiang, et al.
(Eds.), Medical Image Computing and Computer-Assisted Intervention MICCAI
2010 Vol. 6361, (pp. 648656). Berlin/Heidelberg: Springer.
Cheng, J., Ghosh, A., Jiang, T., & Deriche, R. (2010). Model-free and analytical EAP
reconstruction via spherical polar fourier diffusion MRI. In T. Jiang, et al. (Eds.),
Medical image computing and computer-assisted intervention MICCAI 2010
Vol. 6361, (pp. 590597). Berlin/Heidelberg: Springer.
Cheng, J., Jiang, T., Deriche, R., Shen, D., & Yap, P.-T. (2013). Regularized spherical
polar fourier diffusion MRI with optimal dictionary learning. In K. Mori, et al. (Eds.),
Medical Image Computing and Computer-Assisted Intervention MICCAI 2013
Vol. 8149, (pp. 639646). Berlin/Heidelberg: Springer.
Daducci, A., Van De Ville, D., Thiran, J.-P., & Wiaux, Y. (2014). Sparse regularization
for fiber ODF reconstruction: From the suboptimality of and priors to. Medical
Image Analysis, 18, 820833.
DeSantis, S., Assaf, Y., Evans, C. J., & Jones, D. K. (2011). Improved precision in the
charmed model of white matter through sampling scheme optimization and model
parsimony testing. Magnetic Resonance in Medicine, 71(2), 661671.
Descoteaux, M., Angelino, E., Fitzgibbons, S., & Deriche, R. (2007). Regularized, fast, and
robust analytical Q-ball imaging. Magnetic Resonance in Medicine, 58, 497510.
Descoteaux, M., Deriche, R., Le Bihan, D., Mangin, J.-F., & Poupon, C. (2011). Multiple
q-shell diffusion propagator imaging. Medical Image Analysis, 15, 603621.
Dolui, S., Kuurstra, A., & Michailovich, O. V. (2012). Rician compressed sensing for
fast and stable signal reconstruction in diffusion MRI. SPIE 8314 Proceedings on
medical imaging 2012: Image processing, Vol. 8314, 83144Q.
Donoho, D. L. (2006). Compressed sensing. IEEE Transactions on Information Theory,
52, 12891306.
Duarte-Carvajalino, J. M., Lenglet, C., Xu, J., Yacoub, E., Ugurbil, K., Moeller, S., et al.
(2013). Estimation of the CSA-ODF using Bayesian compressed sensing of multishell HARDI. Magnetic Resonance in Medicine, 72(5), 14711485.
Freiman, M., Afacan, O., Mulkern, R., & Warfield, S. (2013). Improved multi B-value
diffusion-weighted MRI of the body by simultaneous model estimation and image
reconstruction (SMEIR). In K. Mori, et al. (Eds.), Medical Image Computing and
Computer-Assisted Intervention MICCAI 2013 vol. 8151, (pp. 18). Berlin/
Heidelberg: Springer.
Gao, H., Li, L., Zhang, K., Zhou, W., & Hu, X. (2013). PCLR: Phase-constrained lowrank model for compressive diffusion-weighted MRI. Magnetic Resonance in
Medicine, 72(5), 13301341.
Gramfort, A., Poupon, C., & Descoteaux, M. (2014). Denoising and fast diffusion
imaging with physically constrained sparse dictionary learning. Medical Image
Analysis, 18, 3649.
Hagmann, P., Cammoun, L., Gigandet, X., Meuli, R., Honey, C. J., Wedeen, V. J., et al.
(2008). Mapping the structural core of human cerebral cortex. PLoS Biology, 6, e159.
262
Hess, C. P., Mukherjee, P., Han, E. T., Xu, D., & Vigneron, D. B. (2006). Q-ball
reconstruction of multimodal fiber orientations using the spherical harmonic basis.
Hosseinbor, A. P., Chung, M. K., Wu, Y.-C., & Alexander, A. L. (2013). Bessel Fourier
orientation reconstruction (BFOR): An analytical diffusion propagator
reconstruction for hybrid diffusion imaging and computation of q-space indices.
Jansons, K. M., & Alexander, D. C. (2003). Persistent angular structure: New insights from
diffusion magnetic resonance imaging data. Inverse Problems, 19, 1031.
Jarisch, W. R., Ozarslan, E., & Basser, P. J. (2009). Computed tomographic (CT)
reconstruction of the average propagator from diffusion weighted MR data.
Honolulu, HI: ISMRM.
Jbabdi, S., Sotiropoulos, S. N., Savio, A. M., Grana, M., & Behrens, T. E.J (2012).
Model-based analysis of multishell diffusion MR data for tractography: How to get
over fitting problems. Magnetic Resonance in Medicine, 68, 18461855.
Jensen, J. H., Helpern, J. A., Ramani, A., Lu, H., & Kaczynski, K. (2005).
Diffusional kurtosis imaging: The quantification of non-Gaussian water diffusion by
means of magnetic resonance imaging. Magnetic Resonance in Medicine, 53,
14321440.
Kamath, A., Aganj, I., Xu, J., Yacoub, E., Ugurbil, K., Sapiro, G., et al. (2012).
Generalized constant solid angle ODF and optimal acquisition protocol for fiber
orientation mapping. In MICCAI workshop on Computational Diffusion MRI, Nice,
France.
Knutsson, H., & Westin, C-F. (2014). From Expected Propagator Distribution to Optimal
Q-space Sample Metric. In: Golland, P. et al., (Eds.) Medical image computing and
computer-assisted intervention MICCAI 2014, Vol. 8675, (pp. 217224). Boston,
MA: Springer International Publishing.
Khachaturian, M. H., Wisco, J. J., & Tuch, D. S. (2007). Boosting the sampling
efficiency of q-ball imaging using multiple wavevector fusion. Magnetic Resonance
Koay, C. G., Ozarslan, E., Johnson, K. M., & Meyerand, M. E. (2012). Sparse and
optimal acquisition design for diffusion MRI and beyond. Medical Physics, 39,
24992511.
Kuo, L.-W., Chen, J.-H., Wedeen, V. J., & Tseng, W.-Y. I. (2008). Optimization of
diffusion spectrum imaging and q-ball imaging on clinical MRI system.
Landman, B. A., Bogovic, J. A., Wan, H., ElShahaby, F. E.Z, Bazin, P.-L., & Prince, J. L.
(2012). Resolution of crossing fibers with constrained compressed sensing using
diffusion tensor MRI. NeuroImage, 59, 21752186.
Lee, N., Wilkins, B., & Singh, M. (2012). Accelerated diffusion spectrum imaging via
compressed sensing for the human connectome project. In SPIE 8314 Proceedings
on medical imaging 2012: Image processing (vol. 8314, , p. 83144G). .
Liu, C., Mang, S. C., & Moseley, M. E. (2010). In vivo generalized diffusion tensor
imaging (GDTI) using higher-order tensors (HOT). Magnetic Resonance in
Medicine, 63, 243252.
Ma, H. T., Limin, Z., Rong, R., & Shaohua, W. (2013). Compressed sensing on DTI via
rotating interpolation. In TENCON 20132013 IEEE Region 10 Conference (31194)
(pp. 14).
Mani, M., Jacob, M., Guidon, A., Magnotta, V., & Zhong, J. (2014). Acceleration of high
angular and spatial resolution diffusion imaging using compressed sensing with
multichannel spiral data. Magnetic Resonance in Medicine.
Menzel, M. I., Tan, E. T., Khare, K., Sperl, J. I., King, K. F., Tao, X., et al. (2011).
Accelerated diffusion spectrum imaging in the human brain using compressed
sensing. Magnetic Resonance in Medicine, 66, 12261233.
Merlet, S., Caruyer, E., Ghosh, A., & Deriche, R. (2013). A computational diffusion MRI
and parametric dictionary learning framework for modeling the diffusion signal and
its features. Medical Image Analysis, 17, 830843.
Merlet, S. L., & Deriche, R. (2013). Continuous diffusion signal, EAP and ODF
estimation via compressive sensing in diffusion MRI. Medical Image Analysis, 17,
556572.
Michailovich, O., & Rathi, Y. (2010). On approximation of orientation distributions
by means of spherical ridgelets. IEEE Transactions on Image Processing, 19,
461477.
Michailovich, O., Rathi, Y., & Dolui, S. (2011). Spatially regularized compressed
sensing for high angular resolution diffusion imaging. IEEE Transactions on
Niendorf, T., Dijkhuizen, R. M., Norris, D. G., van Lookeren, C. M., & Nicolay, K. (1996).
Biexponential diffusion attenuation in various states of brain tissue: Implications for
diffusion-weighted imaging. Magnetic Resonance in Medicine, 36, 847857.
Ozarslan, E., Koay, C., Shepherd, T. M., Blackband, S. J., & Basser, P. J. (2009). Simple
harmonic oscillator based reconstruction and estimation for three-dimensional qspace MRI. Honolulu, HI: ISMRM.
Ozarslan, E., Koay, C. G., Shepherd, T. M., Komlosh, M. E., Irfanoglu, M. O.,
Pierpaoli, C., et al. (2013). Mean apparent propagator (MAP) MRI: A novel diffusion
imaging method for mapping tissue microstructure. NeuroImage, 78, 1632.
Ozarslan, E., & Mareci, T. H. (2003). Generalized diffusion tensor imaging and analytical
relationships between diffusion tensor imaging and high angular resolution
diffusion imaging. Magnetic Resonance in Medicine, 50, 955965.
Ozarslan, E., Shepherd, T. M., Vemuri, B. C., Blackband, S. J., & Mareci, T. H. (2006).
Resolution of complex tissue microarchitecture using the diffusion orientation
transform (DOT). NeuroImage, 31, 10861103.
Paquette, M., Merlet, S., Gilbert, G., Deriche, R., & Descoteaux, M. (in press).
Comparison of sampling strategies and sparsifying transforms to improve
compressed sensing diffusion spectrum imaging. Magnetic Resonance in Medicine.
Pickalov, V., & Basser, P. J. (2006). 3-D tomographic reconstruction of the average
propagator from MRI data. In IEEE proceedings of third International Symposium on
Biomedical Imaging: Nano to macro (pp. 710713).
Pu, L., Trouard, T. P., Ryan, L., Chuan, H., Altbach, M. I., & Bilgin, A. (2011). Modelbased compressive diffusion tensor imaging. In IEEE International Symposium on
Biomedical Imaging: From nano to macro (pp. 254257).
Rathi, Y., Michailovich, O., Laun, F., Setsompop, K., Grant, P. E., & Westin, C. F.
(2014). Multi-shell diffusion signal recovery from sparse measurements. Medical
Rathi, Y., Michailovich, O., Setsompop, K., & Westin, C. F. (2014). A dual spherical
model for multi-shell diffusion imaging. Vol. 90340Q. http://dx.doi.org/10.1117/
12.2043493.
Rathi, Y., Niethammer, M., Laun, F., Setsompop, K., Michailovich, O., Grant, P. E., et al.
(2014). Diffusion propagator estimation using radial basis functions. In T. Schultz,
et al. (Eds.), Computational Diffusion MRI and Brain Connectivity (pp. 5766):
Nagoya, Japan: Springer International Publishing.
Ronen, I., Kim, K.-H., Garwood, M., Ugurbil, K., & Kim, D.-S. (2003). Conventional DTI
vs. slow and fast diffusion tensors in cat visual cortex. Magnetic Resonance in
Medicine, 49, 785790.
Saint-Amant, E., & Descoteaux, M. (2011). Sparsity characterisation of the diffusion
propagator. Montreal, Canada: ISMRM.
Scherrer, B., & Warfield, S. K. (2012). Parametric representation of multiple white matter
fascicles from cube and sphere diffusion MRI. PLoS One, 7, e48232.
Schmahmann, J. D., Pandya, D. N., Wang, R., Dai, G., DArceuil, H. E.,
de Crespigny, A. J., et al. (2007). Association fibre pathways of the brain: Parallel
observations from diffusion spectrum imaging and autoradiography. Brain, 130,
630653.
Setsompop, K., Kimmlingen, R., Eberlein, E., Witzel, T., Cohen-Adad, J., McNab, J. A.,
Project. NeuroImage, 80, 220233.
Seunarine, K. K., & Alexander, D. C. (2014). Chapter 6 Multiple fibers: Beyond the
diffusion tensor. In H. Johansen-Berg & T. E. J. Behrens (Eds.), Diffusion MRI.
San Diego, CA: Academic Press. (2nd ed., pp. 105123).
Shi, X., Ma, X., Wu, W., Huang, F., Yuan, C., & Guo, H. (in press). Parallel imaging
and compressed sensing combined framework for accelerating high-resolution
diffusion tensor imaging using inter-image correlation. Magnetic Resonance in
Medicine.
Sotiropoulos, S. N., Jbabdi, S., Xu, J., Andersson, J. L., Moeller, S., Auerbach, E. J.,
et al. (2013). Advances in diffusion MRI acquisition and processing in the Human
Connectome Project. NeuroImage, 80, 125143.
presence of a time-dependent field gradient. The Journal of Chemical Physics, 42,
288292.
Tournier, J. D., Calamante, F., Gadian, D. G., & Connelly, A. (2004). Direct estimation of
Tristan-Vega, A., & Westin, C.-F. (2011). Probabilistic ODF estimation from reduced
HARDI data with sparse regularization. In G. Fichtinger, et al. (Eds.), Medical Image
Computing and Computer-Assisted Intervention MICCAI 2011 Vol. 6892,
(pp. 182190). Berlin/Heidelberg: Springer.
Tristan-Vega, A., Westin, C.-F., & Aja-Fernandez, S. (2010). A new methodology for the
estimation of fiber populations in the white matter of the brain with the FunkRadon
transform. NeuroImage, 49, 13011315.
Tuch, D. S. (2002). Diffusion MRI of complex tissue structure. In Division of Health
Science and Technology, Ph.D. Massachusetts Institute of Technology.
Tuch, D. S. (2004). Q-ball imaging. Magnetic Resonance in Medicine, 52,
13581372.
Tuch, D. S., Reese, T. G., Wiegell, M. R., Makris, N., Belliveau, J. W., & Wedeen, V. J.
(2002). High angular resolution diffusion imaging reveals intravoxel white matter
fiber heterogeneity. Magnetic Resonance in Medicine, 48, 577582.

Wedeen, V. J., Hagmann, P., Tseng, W.-Y. I., Reese, T. G., & Weisskoff, R. M. (2005).
Wedeen, V. J., Reese, T. G., Tuch, D. S., Dou, J.-G., Weiskoff, R. M., & Chessler, D.
(2000). Mapping fiber orientation spectra in cerebral white matter with Fouriertransform diffusion MRI. In Proceedings of the eighth annual meeting of the ISMRM
(pp. 82).
Wedeen, V. J., Wang, R. P., Schmahmann, J. D., Benner, T., Tseng, W. Y.I, Dai, G., et al.
crossing fibers. NeuroImage, 41, 12671277.
Welsh, C. L., DiBella, E. V.R, Adluru, G., & Hsu, E. W. (2013). Model-based
reconstruction of undersampled diffusion tensor k-space data. Magnetic Resonance
Wu, Y.-C., & Alexander, A. L. (2007). Hybrid diffusion imaging. NeuroImage, 36,
617629.
Wu, Y.-C., Field, A. S., & Alexander, A. L. (2008). Computation of diffusion function
measures in q-space using magnetic resonance hybrid diffusion imaging. IEEE
263
Wu, Y., Zhu, Y.-J., Tang, Q.-Y., Zou, C., Liu, W., Dai, R.-B., et al. (2014). Accelerated
MR diffusion tensor imaging using distributed compressed sensing. Magnetic
Yablonskiy, D. A., Bretthorst, G. L., & Ackerman, J. J.H (2003). Statistical model for
diffusion attenuated MR signal. Magnetic Resonance in Medicine, 50, 664669.
Ye, W., Portnoy, S., Entezari, A., Blackband, S. J., & Vemuri, B. C. (2012). An efficient
interlaced multi-shell sampling scheme for reconstruction of diffusion propagators.
Ye, W., Vemuri, B. C., & Entezari, A. (2012). An over-complete dictionary based regularized
reconstruction of a field of ensemble average propagators. In IEEE proceedings of ninth
International Symposium on Biomedical Imaging (ISBI) (pp. 940943).
Zhan, L., Leow, A. D., Aganj, I., Lenglet, C., Sapiro, G., Yacoub, E., et al. (2011).
Differential information content in staggered multiple shell hardi measured by the
tensor distribution function. In IEEE International Symposium on Biomedical
Imaging: From nano to macro (pp. 305309).
Zhu, Y., Wu, Y., Zheng, Y., Wu, E. X., Ying, L., & Liang, D. (2012). A model-based method
with joint sparsity constraint for direct diffusion tensor estimation. In IEEE proceedings
of ninth International Symposium on Biomedical Imaging (ISBI) (pp. 510513).
Fiber Tracking with DWI

J-D Tournier, Florey Neuroscience Institutes, Heidelberg West, VIC, Australia
S Mori, Johns Hopkins University School of Medicine, Baltimore, MD, USA
DWI Diffusion-weighted image

FACT Fiber assignment by continuous tracking
HARDI High angular resolution diffusion imaging
ODF Orientation density function
Abbreviations
DEC Directionally encoded color

DTI Diffusion tensor imaging
DW Diffusion weighting
Diffusion MRI can provide information about the orientation

of white matter pathways within each image voxel. While this
information can be displayed as 2-D directionally encoded
color (DEC) maps, this can only reveal a cross section of
white matter tracts; it is difficult to appreciate their often convoluted 3-D trajectories from a slice-by-slice inspection.
Computer-aided 3-D tract-tracing techniques (a.k.a. fiber
tracking or tractography) can be very useful to delineate and
visualize tract trajectories and appreciate their relationships
with other white matter tracts and/or gray matter structures.
Fiber-tracking techniques essentially work by using fiber orientation estimates (whether provided using diffusion tensor
imaging (DTI) or more advanced higher-order models) to
establish how one particular point in 3-D space might connect
with other regions.
How Does Fiber Tracking Work?

The Streamline Approach
The simplest and most common approach to fiber tracking is
the so-called streamline approach, also known as fiber assignment by continuous tracking (FACT) (Mori, Crain, Chacko, &
van Zijl, 1999). The idea in this case is to consider 3-D space as
continuous and simply to follow the local fiber orientation
estimate in small incremental steps. Starting from a userspecified seed point, this process gradually delineates the
path of the white matter fibers through the seed point, resulting in a 3-D curve or streamline that should in the ideal case
correspond to the path of the white matter pathway of interest,
as illustrated in Figure 1.
In practice, streamline tractography is typically performed
using a large number of seed points densely packed within a
seed ROI. This provides a much richer representation of the
tract, including any potential branching and fanning of the
tract. It also provides some resilience to errors introduced by
inaccuracies in the location of the seed point, which might
otherwise lead to the delineation of tracts of no interest that
happen to run adjacent to the tract of interest at that point.
Other Approaches
Voxel linking
This approach is the earliest form of fiber tracking and is
based on the concept of simply linking one of the adjacent
voxels (e.g., Jones, Simmons, Williams, & Horsfield, 1999;

Koch, Norris, & Hund-Georgiadis, 2002; Parker, WheelerKingshott, & Barker, 2002): if the fiber orientation estimate in
one voxel points toward the center of an adjacent voxel and this
voxels orientation estimate likewise points toward the center of
the first voxel, then it is likely that a white matter pathway
connects through these two voxels (Figure 2). By starting from
a user-specified seed voxel, adjacent voxels can be identified
that likely belong to the same structure. These new voxels can
then be considered in turn, and voxels adjacent to them can be
investigated. By using this type of region-growing approach, the
region in space that is likely to be connected with the seed point
can be identified. This approach can be extended to provide a
more fine-grained description of that connectivity, by assigning to each voxel an index of its probability of connection,
providing results that better reflect the uncertainty inherent in
these approaches (Anwander, Tittgemeyer, von Cramon, Friederici, & Knosche, 2007; Descoteaux, Deriche, Knosche, &
Anwander, 2009; Koch et al., 2002; Parker et al., 2002). An
issue with these voxel-linking approaches is the poor angular
resolution inherent in limiting propagation to directions joining voxel centers. Even if all 3 3 3 nearest neighbors are
included, this only provides a total of 26 directions that can
be followed, with an angular resolution of 45 . This inherently means that the results will be blurred to some extent in
the orientation domain and introduce more spread (and
potentially bias) in the results than might have been obtained
using other methods.
Global approaches
More recently, advanced algorithms have been proposed to
perform global tractography (e.g., Fillard, Poupon, & Mangin,
2009; Kreher, Mader, & Kiselev, 2008). These methods attempt
to simultaneously estimate the set of all pathways in the brain,
using a process of optimization. The reason this might be
advantageous is that this allows the algorithm to consider
nonlocal effects, for example, the fact that a voxel has a fixed
volume, and therefore, the reconstruction should not allow
more tract volume to exist within each voxel than is physically
possible. These approaches have the potential to provide more
biologically plausible reconstructions but are currently limited
by the typically enormous amount of computation involved in
solving this type of problem.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00294-3
265
266
INTRODUCTION TO METHODS AND MODELING | Fiber Tracking with DWI
Figure 1 Fiber assignment by continuous tracking (FACT). Starting

from the user-defined seed point (arrow), the algorithm traces out a path
following the local estimate of the fiber orientation (black lines). The
resulting streamline provides an estimate of the path of the white matter
pathway.
knowledge about the trajectory of the tract of interest. In its

simplest form, tract editing is done simply by supplying
another, distinct region that the tract of interest is expected to
run through; such an ROI is commonly referred to as a waypoint, inclusion, or AND ROI. The idea is that if the fibertracking algorithm deviates from the real path, it is very
unlikely to come back to it by chance and enter this second
ROI. Streamlines that do not run through both ROIs are therefore discarded.
It is also possible to reject streamlines when they enter
regions that they are not expected to run through; such an ROI
is commonly referred to as an exclusion or NOT ROI. Similarly,
though less commonly used, streamlines can be included based
on their entering one of a set of regions, using an OR operation.
In this way, users can combine multiple ROIs to impose as
much anatomical prior information as is deemed reasonable.
What constitutes reasonable in this context is a subjective
judgment; it is possible, for instance, to outline the entire pathway of interest as an inclusion ROI and the rest of the brain as an
exclusion ROI, in which case fiber tracking would be somewhat
redundant. In general, fiber tracking is most informative when
the results match the expectation with minimal use of prior
information. When imposing too much prior information, the
algorithm can only provide what is essentially already known.
When imposing little prior information and the results do not
match the expectation, there is a good chance the results might
be due to an artifact of the fiber-tracking method, rather than
genuine biology; it can however be very difficult to distinguish
between the two, making the results ambiguous.
Challenges in Fiber Tracking

Crossing Fibers and Partial Volume Averaging
Figure 2 Illustration of fiber tracking by voxel linking. The idea is

essentially to establish whether two adjacent voxels are connected,
based on simple rules. In this case, the rule is that the center of one
voxel must be within a certain angle of the direction of the other voxel,
and vice versa. Starting from the seed voxel (colored red), adjacent
voxels that satisfy the criterion are included (colored gray). In the next
iteration, the neighbors of these newly included voxels are considered,
until no further voxels can be found.
Adding Prior Anatomical Information: Tract Editing

Fiber tracking is subject to a number or problems (described in
the succeeding text) that will introduce errors. The fibertracking algorithm however has no way of assessing which
results are real and which are artifact (i.e., false-positives).
One of the most effective ways of dealing with such errors is
the so-called tract-editing or multi-ROI approach, illustrated in
Figure 3. This technique can be considered as a way of removing false-positives based on the users prior anatomical
Fiber tracking relies on accurate estimates of fiber orientations.

Most implementations simply use the direction of the major
eigenvector of the diffusion tensor as the fiber orientation
estimate. Unfortunately, the diffusion tensor model can only
characterize one fiber orientation per voxel; when multiple
fiber bundles with distinct orientations are colocated within
an individual voxel, the orientation estimated will in general
not correspond to either fiber orientations present. While this
problem was initially thought to affect only a few areas of brain
white matter, it is now clear that the problem is endemic to
diffusion imaging, with serious implications for DTI-based
fiber tracking (Jeurissen, Leemans, Tournier, Jones, & Sijbers,
2013). Thankfully, there are now many approaches that can
estimate multiple fiber orientations per voxel, typically based
on high angular resolution diffusion imaging (HARDI) data
(Tournier, Mori, & Leemans, 2011).
While there are many potential ways that this multifiber
information could be used for fiber tracking, in practice, the
simplest and most widely used consists of simply extending the
original streamline algorithm to use one of the orientations
identified at each spatial location. When multiple orientations
are present, most algorithms will simply pick the orientation
closest to the incoming direction of tracking (Behrens, Berg,
Jbabdi, Rushworth, & Woolrich, 2007; Berman et al., 2008;
Haroon, Morris, Embleton, Alexander, & Parker, 2009;
Jeurissen, Leemans, Jones, Tournier, & Sijbers, 2011; Parker &
Alexander, 2005; Wedeen et al., 2008), as illustrated in
(a)
Exclusion
(NOT)
region
Inclusion
(AND)
region
Seed
region
(b)
267
(c)
Figure 3 Illustration of tract editing using regions of interest. (a) Using a large seed region leads to the delineation of a number of different
branches. (b) The tract of interest is known to run through the green region; placing an inclusion ROI there removes the most obvious false-positives.
(c) If the tract of interest is known not to project to the red region, an exclusion ROI can be used to remove any spurious trajectories through it.
Figure 4 The FACT algorithm can easily be extended to handle crossing

fiber information. The algorithm starts from the user-defined seed point
(arrow) and proceeds in small steps, as for the standard FACT approach.
However, at each step, the algorithm may be faced with a number of
possible orientations to follow. The simplest approach is to select the
orientation that is most closely aligned with the current direction of the
streamline; this is equivalent to choosing the path of least curvature. In the
absence of any other information, this is the most sensible approach since
the path of least curvature must be the most likely path.
Figure 4. Alternatively, a number of methods also explicitly

track along all possible orientations, assigning an index of
probability to each branch based on the turning angle, to
produce a more distributed model of connectivity (Chao
et al., 2008). In some probabilistic approaches, any fiber
orientation within a certain turning angle of the incoming
direction is considered suitable candidates for sampling (see
later text for a description of probabilistic approaches); these
will therefore preferentially track through crossing fiber regions
while still allowing for changes in direction that would not be
permitted using most methods mentioned previously
(Tournier, Calamante, & Connelly, 2012).
Uncertainty: Noise and Limited Angular Resolution

Diffusion imaging is inherently a noisy technique, and this
introduces uncertainty into the results. Imaging noise will
translate into noisy orientation estimates, and this will cause
streamlines to deviate from their true trajectory. In general, any

measurement will be contaminated by noise to some extent,
and diffusion imaging is no exception. However, the effect of
noise on fiber-tracking results is altogether different, and its
impact can be profound. This is due to the way streamlines
propagate through the data, visiting many different voxels and
therefore accumulating errors from each noisy orientation estimate as tracking proceeds. This accumulation effect is compounded by the fact that streamlines that deviate into adjacent
structures may then delineate a completely different path;
given the size of most white matter structures, even a relatively
small deviation of a few millimeters could therefore have a
dramatic effect on the results.
Another source of uncertainty is the intrinsic angular resolution of the DW signal, as illustrated in Figure 5. The signal
varies smoothly as a function of orientation, and this means
that we can only obtain blurred estimates of fiber orientations. This is particularly relevant for higher-order models that
aim to characterize the fiber orientation distribution. Most
implementations simply extract the peak(s) of this blurred
distribution, which not only provides much tighter estimates
but also imposes the assumption that fibers from the same
bundle are completely straight and parallel within a voxel.
This may be a good approximation in many regions of the
white matter, but there will undoubtedly be regions where this
assumption does not hold.
A number of methods have been proposed to deal with
uncertainty in fiber tracking. In general, the idea is to provide
an estimate of all the paths originating from the seed point(s)
that are plausible given the data and its uncertainty, rather than
a single best-guess path. This is akin to providing the confidence interval of a measurement, in addition to its actual estimate. In general, a measurement is not informative without an
idea of its confidence interval, since we cannot otherwise assess
whether an observed difference in the measurement is significant or relevant. This is also true of tractography, with the
additional problem that a confidence interval on a trajectory is
quite difficult to envisage: there is no simple scalar estimate of
the standard deviation or confidence interval of a path.
The way this uncertainty is typically represented in fiber
tracking is by generating an estimate of the distribution of
possible paths, approximated by a set of representative trajectories. This is akin to approximating a normal distribution as a
set of representative samples drawn from the distribution, as
illustrated in Figure 6. This nonparametric approach is in fact
much more general than using parametric measures such as the
268
Fiber configuration
DW signal
Fiber ODF
Figure 5 The intrinsic angular resolution of the DW signal itself introduces uncertainty as to the exact fiber configuration. The three configurations on
the left are all predominantly aligned leftright, and consequently, the DW signal intensity is smallest along that axis (middle). The DW signal is
inherently broad, and this essentially blurs the signal. This means that the DW signal for the three configurations shown will be essentially identical, and
consequently, the estimated diffusion or fiber orientation density function (ODF) will be the same in all three cases. The practice of using the peak
orientation of the fiber or diffusion ODF as the best fiber orientation estimate is appealing as it provides much tighter results, but this is only valid
for one of the three configurations shown. It is clear that some ambiguity remains as to what the true fiber orientations are, and this source of uncertainty
should be included in probabilistic algorithms.
Figure 6 Any distribution can be approximated using a set of

representative samples. A Gaussian distribution (left) can be represented
by a set of values drawn at random from its probability density function
(PDF); any property of the distribution can then be computed in a
straightforward manner from these samples (mean, standard deviation,
etc.). While this is needlessly complex for a Gaussian distribution, this
approach can be used to represent much more complex, multimodal
distributions for which no simple model exists, such as the distribution
of streamline trajectories from a given seed point, as shown on the right.
The most likely path (blue), as might be obtained using deterministic
approaches, can be viewed as being the mean of the distribution. As
shown in this illustration, this most likely path may be very different from
some of the other possible paths. This information is not available using
deterministic approaches, yet knowledge of these other likely paths may
significantly influence interpretation and/or the decision-making process.
standard deviation, since it can be applied to any type of data,

regardless of whether or not they can be approximated by a
normal distribution. This approach is therefore much more
suitable for fiber tracking, since streamlines clearly cannot be
assumed to originate from a Gaussian distribution.
The most common approach to estimating uncertainty in
fiber tracking is the concept of probabilistic streamlines. These
extend the simple deterministic streamline approach by following a random orientation sample from within the range of
possible orientations, rather than a single peak orientation, as
illustrated in Figure 7. This means that each successive streamline will take a slightly different path through the data that
nonetheless remain consistent with the estimated orientations
and their associated uncertainty. These methods therefore rely
on the availability of an estimate of the uncertainty around each
fiber orientation. Various methods exist for this step, including
bootstrap approaches (Berman et al., 2008; Haroon et al., 2009;
Figure 7 The streamline algorithm can also be extended to take the

various sources of uncertainty into account. As before, tracking is
initiated from the user-defined seed point (arrow) and proceeds by taking
small steps along the local fiber orientation estimate. In this case,
however, the fiber orientation estimate used is taken from the range of
likely possible orientations at this location, by drawing a random sample
from the probability density function (PDF) of the fiber orientation. This
generally incorporates a curvature constraint by ensuring that the fiber
orientation sample is taken from within a cone of uncertainty (Jones,
2003) about the current direction of tracking. By generating a large
number of such streamlines, an approximation to the distribution of
possible paths is produced.
Jeurissen et al., 2011; Jones, 2008; Whitcher, Tuch, Wisco,

Sorensen, & Wang, 2008) and various modeling approaches
including Markov chain Monte Carlo (MCMC) (Behrens,
Johansen-Berg, et al., 2003; Behrens, Woolrich, et al., 2003;
Behrens et al., 2007; Hosey, Harding, Carpenter, Ansorge, &
Williams, 2008; Hosey, Williams, & Ansorge, 2005).
Conclusion
Diffusion MRI fiber tracking is clearly a very exciting technology, being the only method that can be used to delineate white

matter pathways in the human brain in vivo. It is also a very
efficient method, since the same dataset can be used to delineate any white matter pathway (within the limitations of the
data quality and reconstruction approach used), in contrast to
tracer studies that can typically only be used to trace one
pathway at a time. For this reason, it has very rapidly been
adopted by neuroscientists and clinicians. However, it is also
clear that fiber tracking is not without its limitations and
idiosyncrasies, and this unfortunately makes it very easy for
inexperienced users to come to the wrong conclusions. It is
therefore essential that scientists and clinicians become well
acquainted with the methods and particularly with their limitations before applying them in practice.

Diffusion MRI; INTRODUCTION TO METHODS AND
MODELING: Diffusion Tensor Imaging; Probability Distribution
Functions in Diffusion MRI; Q-Space Modeling in DiffusionWeighted MRI.
References
Anwander, A., Tittgemeyer, M., von Cramon, D. Y., Friederici, A. D., & Knosche, T. R.
(2007). Connectivity-based parcellation of Brocas area. Cerebral Cortex, 17, 816825.
Behrens, T. E.J, Berg, H. J., Jbabdi, S., Rushworth, M. F. S., & Woolrich, M. W. (2007).
Probabilistic diffusion tractography with multiple fibre orientations: What can we
gain? NeuroImage, 34, 144155.
Behrens, T. E. J., Johansen-Berg, H., Woolrich, M. W., Smith, S. M.,
Wheeler-Kingshott, C. A.M, Boulby, P. A., et al. (2003). Non-invasive mapping of
connections between human thalamus and cortex using diffusion imaging. Nature
Behrens, T. E. J., Woolrich, M. W., Jenkinson, M., Johansen-Berg, H., Nunes, R. G.,
Clare, S., et al. (2003). Characterization and propagation of uncertainty in diffusionweighted MR imaging. Magnetic Resonance in Medicine, 50, 10771088.
Berman, J. I., Chung, S., Mukherjee, P., Hess, C. P., Han, E. T., & Henry, R. G. (2008).
Probabilistic streamline q-ball tractography using the residual bootstrap.
Chao, Y.-P., Chen, J.-H., Cho, K.-H., Yeh, C.-H., Chou, K.-H., & Lin, C.-P. (2008). A
multiple streamline approach to high angular resolution diffusion tractography.
Medical Engineering & Physics, 30, 989996.
Descoteaux, M., Deriche, R., Knosche, T. R., & Anwander, A. (2009). Deterministic and
probabilistic tractography based on complex fibre orientation distributions. IEEE
Fillard, P., Poupon, C., & Mangin, J.-F. (2009). A novel global tractography algorithm
based on an adaptive spin glass model. Medical Image Computing and ComputerAssisted Intervention, 12, 927934.
269
Haroon, H. A., Morris, D. M., Embleton, K. V., Alexander, D. C., & Parker, G. J. M. (2009).
Using the model-based residual bootstrap to quantify uncertainty in fiber orientations
from Q-ball analysis. IEEE Transactions on Medical Imaging, 28, 535550.
Hosey, T. P., Harding, S. G., Carpenter, T. A., Ansorge, R. E., & Williams, G. B. (2008).
Application of a probabilistic double-fibre structure model to diffusion-weighted MR
images of the human brain. Magnetic Resonance Imaging, 26, 236245.
Hosey, T., Williams, G., & Ansorge, R. (2005). Inference of multiple fiber orientations in
high angular resolution diffusion imaging. Magnetic Resonance in Medicine, 54,
14801489.
Jeurissen, B., Leemans, A., Jones, D. K., Tournier, J.-D., & Sijbers, J. (2011).
Probabilistic fiber tracking using the residual bootstrap with constrained spherical
deconvolution. Human Brain Mapping, 32, 461479.
Jeurissen, B., Leemans, A., Tournier, J.-D., Jones, D. K., & Sijbers, J. (2013).
Investigating the prevalence of complex fiber configurations in white matter tissue
with diffusion magnetic resonance imaging. Human Brain Mapping, 34,
27472766.
Jones, D. K. (2003). Determining and visualizing uncertainty in estimates of
fiber orientation from diffusion tensor MRI. Magnetic Resonance in Medicine, 49,
712.
Jones, D. K. (2008). Tractography gone wild: Probabilistic fibre tracking using the wild
bootstrap with diffusion tensor MRI. IEEE Transactions on Medical Imaging, 27,
12681274.
Jones, D. K., Simmons, A., Williams, S. C., & Horsfield, M. A. (1999). Non-invasive
assessment of axonal fiber connectivity in the human brain via diffusion tensor MRI.
Koch, M. A., Norris, D. G., & Hund-Georgiadis, M. (2002). An investigation of
functional and anatomical connectivity using magnetic resonance imaging.
Kreher, B. W., Mader, I., & Kiselev, V. G. (2008). Gibbs tracking: A novel approach for
the reconstruction of neuronal pathways. Magnetic Resonance in Medicine, 60,
953963.
Mori, S., Crain, B., Chacko, V., & van Zijl, P. (1999). Three-dimensional tracking of
axonal projections in the brain by magnetic resonance imaging. Annals of
Parker, G., & Alexander, D. (2005). Probabilistic anatomical connectivity derived from
the microscopic persistent angular structure of cerebral tissue. Philosophical
Transactions of the Royal Society of London, Series B: Biological Sciences, 360,
893902.
Parker, G. J. M., Wheeler-Kingshott, C. A. M., & Barker, G. J. (2002). Estimating
distributed anatomical connectivity using fast marching methods and diffusion
tensor imaging. IEEE Transactions on Medical Imaging, 21, 505512.
Tournier, J., Calamante, F., & Connelly, A. (2012). MRtrix: Diffusion tractography in
crossing fiber regions. International Journal of Imaging Systems and Technology,
22, 5366.
Tournier, J.-D., Mori, S., & Leemans, A. (2011). Diffusion tensor imaging and beyond.
Wedeen, V. J., Wang, R. P., Schmahmann, J. D., Benner, T., Tseng, W. Y.I, Dai, G., et al.
crossing fibers. NeuroImage, 41, 12671277.
Whitcher, B., Tuch, D. S., Wisco, J. J., Sorensen, A. G., & Wang, L. (2008). Using the
wild bootstrap to quantify uncertainty in diffusion tensor imaging. Human Brain
Mapping, 29, 346362.
Tract Clustering, Labeling, and Quantitative Analysis

M Maddah, Cellogy Inc., Menlo Park, CA, USA; SRI International, Menlo Park, CA, USA
Abbreviations
MRI
ROI
Region of interest
Introduction
A healthy brain white matter contains millions of myelinated
axons that connect different regions of the gray matter. Bundles
of these axons, often called fiber tracts, ensure proper signal
transfer in the brain and enable its function. Many neuropsychiatric diseases are hypothesized to be associated with disruption and damage to the white matter fiber tracts.
Understanding the pattern of connectivity of fiber tracts, their
properties in healthy subjects, and how they are affected in
each diseased population is of fundamental interest to neuroscientists, neurosurgeons, and the medical community in general. With the advent of diffusion tensor imaging, in vivo study
of the fiber tracts, which was out of reach of other imaging
modalities, became a reality (Basser, Mattiello, & LeBihan,
1994). The presence of a fiber tract that consists of thousands
of microscopic axons running parallel to each other in a given
neighborhood can be detected as reduction in the diffusivity
signal normal to the fiber pathway. A tensor describing the
directional dependence (anisotropy) of the water diffusivity is
most commonly extracted. Trajectories of the fiber bundles are
then reconstructed using a tractography procedure (Mori,
Crain, Chacko, & van Zijl, 1999) usually by following the
major eigenvector of the tensor or similar alternatives (see
Figure 1(a) for an example of tractography output).
Three-dimensional (3-D) visualization of the fiber trajectories is sometimes used to explore the anatomical connectivity
network of the brain, in order to complement functional connectivity maps and to understand how it is affected by aging,
diseases of the brain, or brain lesions. It is also a valuable tool
in surgical planning, risk assessment, and intraoperative
mapping of the tracts (Duncan, 2010). The information conveyed by such visualizations can be greatly improved if the
trajectories are grouped into bundles based on some similarity
measures and labeled based on their correspondence to anatomical fiber tracts (see Figure 1(b) for an example of clustered
trajectories).
Another important application of diffusion tensor magnetic
resonance imaging (MRI) (and other variants of diffusion MRI)
is to quantify differences in the tract connectivity, shape, or
diffusion properties and correlate these differences to the underlying microscopic changes. Clustering and labeling of the trajectories are prerequisites to tract-based quantitative analysis,
where statistics of a parameter of interest are measured over or
along a tract. In multisubject studies, in particular, clustering
and anatomical labeling of trajectories play an important role in
ensuring that the comparison is performed over the same anatomical bundle across all cases.
This article focuses on the clustering and labeling of the fiber

trajectories as well as quantitative analysis of the diffusion tensor
MRI data. We will explore the challenges of clustering and labeling of the trajectories and review different clustering methods,
how the similarity between trajectories is defined, and how
anatomical information can be used to guide the clustering.
Challenges in Clustering and Labeling of Fiber

Trajectories
Despite continued efforts to devise a robust trajectory clustering and labeling algorithm, development of a reliable
approach has been elusive. Several factors make clustering
and labeling of fiber trajectories challenging. First, the presence
of noise in the diffusion data, fiber crossings, and imperfection
of tractography techniques result in trajectory fragments,
missing data, and outliers that do not resemble any anatomical
fiber tract. Most tractography algorithms use some empirical
criteria to terminate tracing the trajectories, such as arriving at a
point with small diffusion anisotropy or experiencing a deflection larger than a given angle. Such criteria do not necessarily
relate to the actual boundaries of the anatomical tracts and lead
to broken trajectories, which in turn complicates the clustering.
Second, the definition of a fiber bundle is applicationdependent. For example, some fiber tracts such as the cingulum include trajectories that do not run from one end of the
tract to the other but instead fan out in the middle of the tract.
In some other instances, such as in clustering of the corpus
callosum, one might be interested either in segmenting the
entire extent of the tract or in subdividing it into smaller
regions such as rostrum, genu, truncus, isthmus, and splenium.
This procedure not only complicates labeling of the trajectories
but also impedes the ability to construct a mathematical
definition for the tract so that the proper similarity measure
can be used to cluster the trajectories.
Depending on the application, fiber trajectories may be
clustered based on their spatial proximity or shape similarity at
least over a major segment along their length or, alternatively,
segmented based on the gray matter regions they connect. In the
first case, which is the main focus of this article, a similarity
measure is needed to define groups of trajectories that represent
anatomical tracts. However, as will be discussed in the next
section, no consensus on the definition of a similarity measure
has been achieved. In the second approach, often a parcellation
of the gray matter, defined by an anatomical atlas or produced
based on functional data, is used to seed the tractography. This
approach is based solely on the trajectory end points, and often
http://dx.doi.org/10.1016/B978-0-12-397025-1.00295-5
271
272
INTRODUCTION TO METHODS AND MODELING | Tract Clustering, Labeling, and Quantitative Analysis
Figure 1 Sagittal view showing (a) fiber trajectories produced by tractography seeded from the entire white matter and (b) output of a clustering
algorithm that groups these trajectories based on their similarity to each other and to a set of prototype trajectories that represent anatomical bundles.
Reproduced from Maddah, M., Grimson, W. E. L., Warfield, S. K., & Wells, W. M. (2008). A unified framework for clustering and quantitative
analysis of white matter fiber tracts. Medical Image Analysis, 12, 191202.
no further clustering of the trajectories and the associated

similarity definition is required. These methods rely on an accurate gray matter parcellation of the brain and deal with the
problem of defining regions or nodes that the tracts of interest
are connecting. Hybrid approaches in which information from
both gray matter parcellation and entire trajectory pathways in
the white matter is used are gaining more popularity. See
ODonnell, Golby, and Westin (2013) for a discussion and
review of the recent methods.
Third, in order to produce consistent bundles across multiple subjects that represent anatomically meaningful tracts, it is
important to incorporate anatomical information, such as an
atlas of white matter tracts (clustering approach), an atlas of
gray matter regions (parcellation approach), or both. Otherwise, manual selection of extracted bundles or tuning of the
parameters that control the clustering algorithm to avoid
under- and overclustering is necessary. The questions are how
to construct atlases for diffusion MRI data, what information
should be encoded in such atlases, and how to incorporate
them in the clustering algorithm.
Finally, clustering of fiber trajectories often deals with a
large dataset as the input, especially if whole-brain tractography and multiple-subject studies are involved. This necessitates
computationally efficient methods for calculating the similarity between trajectories.
Clustering Methods for Fiber Trajectories

In clustering of fiber trajectories, the input is a set of fiber
trajectories, generated by a tractography algorithm and represented as an ordered set of points in the 3-D space, and the
output is the assignment of labels to trajectories. The label
assignment can be either deterministic or probabilistic. A probabilistic clustering has the potential to deal with the inherent
uncertainty in assigning the trajectories to clusters and can
allow weighted statistics over the clustered tract, generating
more robust results, less sensitive to the presence of outliers.
In discriminative or similarity-based methods, pairwise
comparison of the fiber trajectories based on a similarity metric
is performed, and then, those fiber trajectories are grouped
Table 1
A summary of model-based tract clustering approaches
Reference
Model
Clayden, Storkey, and

Bastin (2007)
Maddah, Grimson,
et al. (2008)
Maddah, Zollei, et al.
(2008)
Wassermann, Bloy,
Kanterakis, Verma,
and Deriche (2010)
Wang et al. (2011)
Maddah et al. (2011)
Beta-mixture model of similarity cosines
Ratnarajah, Simmons,
and Hojjatoleslami
(2011)
Liu, Vemuri, and
Deriche (2012)
Gamma-mixture model of the distance from

each trajectory to cluster centerline
Same as in the preceding reference with the
Dirichlet distribution of model parameters
Gaussian process of tract probability map
Hierarchical Dirichlet process mixture model
Gamma-mixture model of the distance from
each trajectory to cluster center line or plane
Gaussian mixture model of regression
representation of trajectories
Gaussian mixture model of tract
based on the calculated similarity. Examples of discriminative

algorithms are spectral clustering methods (Brun, Knutsson,
Park, Shenton, & Westin, 2004; ODennell & Westin, 2005).
Generative or model-based clustering methods have also
been proposed, which represent each tract by a parametric
model and then learn model parameters from the data. Table 1
summarizes some of these approaches.
Any clustering process requires a well-defined similarity
measure in order to produce consistent results. A variety of
similarity measures that are based on the distance between
trajectories, their shape similarity, start and end points, or a
combination of these have been proposed. To circumvent the
problem of high and variable dimension of the input trajectories, several groups have used the Hausdorff distance between
the trajectories (Corouge, Gerig, & Gouttard, 2004; ODonnell
& Westin, 2005) or similar metrics such as the closest point
distance and the mean of closest distance (Corouge et al.,
2004). Shimony, Snyder, Lori, and Conturo (2002) used a
combination of the dot product of the tangent between
trajectories and average point distance. Ding, Gore, and
Anderson (2003) used the length ratio and the Euclidean
distance between corresponding segments. However, corresponding segments are calculated with the assumption that
seed points correspond to each other. Brun et al. (2004) used a
9-D shape descriptor including the mean and square root of the
covariance matrix of the points on the trajectories. Leemans,
Sijbers, De Backer, Vandervliet, and Parizel (2006) found the
closest subcurves in the curvature-torsion space and varied the
length of the subcurves to deal with the curve matching problem.
Maddah, Mewes, Haker, Grimson, and Warfield (2005) used the
B-spline representation of 3-D curves to calculate the distance.
Clayden, Bastin, and Storkey (2006) used a combination of
shape and length of the trajectories. Tsai, Westin, Hero, and
Willsky (2007) used dual-rooted graphs to capture both local
and global differences. Maddah, Grimson, Warfield, and Wells
(2008) proposed a distance transform map to efficiently compute
the similarity between the trajectories and cluster centers.
Berkiten and Acar (2010) used pivot points defined as points
on a trajectory that are themselves the closest neighbors of their
closest point on the other trajectory. Mani, Kurtek, Barillot, and
Srivsastana (2010) used a combination of distance, shape,
orientation, and the scale of the trajectories. Other methods
include dynamic time wrapping (Shao et al., 2010) and finding
the longest common subsequences (Bohm et al., 2011).
The choice of clustering has some implications for the
computational efficiency of the algorithm. Similarity-based
methods are often based on pairwise comparisons of the
fiber trajectories, which scale quadratically with the number
of trajectories and thus are computationally demanding,
especially when the distance metric depends on the cluster
assignment. Some approximations to the problem have been
proposed. For example, ODonnell and Westin (2007) used
the Nystrom method to sample and cluster a small subset of
the trajectories and then used these as a reference to cluster the
rest of the trajectories. El Kouby, Cointepas, Poupon, Rivie`re, &
Golestani (2005) divided the space into 3-D cells, clustered
these cells based on their connectivity, and then used these
cells to cluster the trajectories. A similar approach was taken by
Klein et al. (2007). Finally, Bohm et al. (2011) used a lowerbounding distance to reduce the computation time. Alternatively, generative methods are based on comparison of trajectories to parameters of the estimated model (e.g., cluster
centers), which grows linearly with the number of trajectories.
However, they often require iterative processes in parameter
learning to converge (Maddah, Grimson, et al., 2008).
Tract Labeling and Integration of Anatomical

Knowledge
Regardless of the clustering algorithm and the similarity measure used, an unsupervised algorithm is not guaranteed to
produce the clusters of interest for a given application. The
user only has control over the number of clusters and some
ad hoc adjustment of the clustering parameters, and the
algorithm could easily overcluster or undercluster the input
data. A supervised clustering algorithm that benefits from
anatomical information is thus desirable in most applications.
Once anatomical data are used in the clustering step, the
273
correspondence between clusters across different subjects,

needed for population studies, is also automatically known.
The common way to represent anatomical information is to
use an atlas, for which labels are known within a reference
coordinate. The atlas can be used to label the trajectory bundles
to anatomical tract or to guide the clustering algorithm in order
to guarantee that it produces anatomically meaningful bundles. In diffusion MRI studies, similar to structural atlases, an
atlas can be defined as a set of 3-D regions, each labeled in
correspondence to an anatomical tract or a set of 3-D maps that
encode the probability of the presence of a given tract at each
voxel (Mori et al., 2007; Wakana, Jiang, Nagae-Poetscher, van
Zijl, & Mori, 2004). An atlas of fiber tracts can further encode
information that represents the local orientation of the tracts
(Robinson, Rueckert, Hammers, & Edwards, 2010). One
approach is to represent each tract by a set of trajectories
mapped into a reference space, which are labeled by an expert
(Catani & Thiebaut de Schotten, 2008; Maddah et al., 2005) or
by a clustering algorithm (ODonnell & Westin, 2006; Ziyan,
Sabuncu, Grimson, & Westin, 2009). An alternative approach
is to build a parametric model that encodes the spatial and
shape information of the tracts, mainly by a set of prototype
medial representations (Maddah, Miller, Sullivan, Pfefferbaum, & Rohlfing, 2011). Building an atlas involves multisubject data processing and coregistration into a common
space. Registration can be performed based on scalar fields
such as T2 images or maps of fractional anisotropy, mapping
of diffusion tensor fields, or direct registration of the trajectories (Ziyan, Sabuncu, ODonnell, & Westin, 2007; Zvitia,
Mayer, Shadmi, & Greenspan, 2009).
The information encoded in the atlas can be used to guide
the clustering algorithm in several fashions depending on the
type of the atlas. Region of interest (ROI)-based methods are the
most common approach. The atlas can be used to seed
the tractography, exclude the outlier trajectories, or delineate
the desired trajectories (Prasad et al., 2011; Suarez, Commowick,
Prabhu, & Warfield, 2012; Wakana et al., 2007). Fiber trajectories
can be also segmented by mapping ROIs onto the subject space
and grouping the trajectories based on the gray matter ROIs they
are connecting (Xia, Turken, Whitfield-Gabrieli, & Gabrieli,
2005) or their overlap with the white matter ROIs (Jiang, van
Zijl, Kim, Pearlson, & Mori, 2006). Extensions of this approach
to multiple ROI selection (Merhof, Greiner, Buchfelder, &
Nimsky, 2010) or employing it as a preprocessing step for subsequent clustering (Guevara et al., 2010) has been also proposed.
Alternatively, with the atlas defined as a set of labeled trajectories,
they can be mapped into each subject space to group the subject
trajectories based on their similarity to atlas trajectories (Jin et al.,
2012; Maddah et al., 2005; ODonnell & Westin, 2007; Ziyan
et al., 2009). Finally, if the atlas is constructed as a set of tract
models, they can be used as a prior in model-based probabilistic
clustering methods (Maddah, Zollei, Grimson, Westin, & Wells,
2008; Maddah et al., 2011; Wang, Grimson, & Westin, 2011;
Wassermann & Deriche, 2008).
Quantitative Analysis
The ultimate goal of processing diffusion MRI data is the
quantitative assessment of spatial and temporal differences in
274
Figure 2 An example of tract-based quantitative analysis. (a) Unclustered trajectories from uncinate fasciculus (UF), inferior fronto-occipital
fasciculus (IFO), and inferior fronto-occipital fasciculus (ILF). (b) Trajectories grouped into anatomically meaningful bundles. (c) Trajectories colored
based on the local variation on fractional anisotropy (FA). The goal of tract-based quantitative analysis is to measure these spatial variations for
each tract. Note that in (b) and (c), clusters are spatially shifted for better visualization.
the white matter fiber tracts, either in a single subject or in a

population. Single-subject studies may target normal brain
development and aging or progress of a neurodisease and
therapy. Population studies, on the other hand, may reveal
differences between healthy and diseased subjects. In either
case, it is important that the parameters are measured and
compared at the same location for the entire dataset.
Quantitative analysis of diffusion MRI data has been conducted with three main approaches: ROI-based methods,
voxel-based methods, and tract-oriented methods. Earlier
clinical studies used ROI-based methods, where parameters,
such as fractional anisotropy, are averaged over manually or
semiautomatically defined regions of interest. The main advantage of ROI-based methods is that they provide an easy route to
examine hypotheses related to the role of a particular tract in a
specific brain disorder. However, such ROI-based methods
require user interaction to specify the ROIs, and their accuracy
is limited by the reliability of that specification. It has been
shown that ROI size, shape, number, and location not only
affect the measured quantities but also influence the significance of the group analysis (Kanaan et al., 2006). A possible
remedy is to use a tractography algorithm and define the ROI
as the volume spanned by the trajectories specific to a given
tract. Grouping and labeling of the trajectories thus become a
prerequisite to such tract-based ROI definition.
In voxel-based methods (Abe et al., 2010; Van Hecke, Sijbers, De Backer, Poot, Parizel, & Leemans, 2009; Smith et al.,
2006), the datasets are registered onto a common coordinate
system and then averaged and compared voxel by voxel. This is
algorithmically simple, but it is critical to obtain a good image
alignment (Kanaan et al., 2006). The main advantage of voxelbased methods over ROI-based approaches is that they are
user-independent, preserve spatial variations, and are suited
for whole-brain analysis. The latter is particularly advantageous
when no hypothesis regarding the location of brain changes is
available a priori. However, apart from the registration errors
and partial volume effects, associating the observed differences
to specific tracts is difficult (Colby et al., 2012).
In tract-oriented methods (Colby et al., 2012; Corouge,
Fletcher, Joshi, Gouttard, & Greig, 2006; Goodlett, Fletcher,
Gilmore, & Gerig, 2009; Maddah, Grimson, et al., 2008;
ODonnell, Westin, & Golby, 2009; Schulte et al., 2013;
Yeatman, Dougherty, Myall, Wandell, & Feldman, 2012),
quantitative parameters are computed along fiber trajectories,
generating a profile for each tract that summarizes statistics of a
scalar diffusion measure of interest. Such tract-orientated analysis reveals spatial information that is otherwise lost in commonly used ROI-based methods, yet unlike in voxel-wise
methods, correspondence to anatomical tracts is maintained

(see Figure 2). To output such profiles, two main processing
steps are needed. First, trajectories need to be grouped to
represent a single anatomical fiber tract of interest. This can
be done manually (e.g., Colby et al., 2012) or more efficiently
in population studies using a clustering algorithm (e.g.,
Schulte et al., 2013). Second, point correspondence between
the trajectories should be calculated so that the averaging is
performed over points that represent the same landmark on
the fiber tract profile. Different approaches have been taken to
determine the point correspondence between the trajectories.
A common approach is to specify reference points manually
and define points at equal arc lengths to be corresponding to
each other (Colby et al., 2012; Corouge et al., 2006; Yeatman
et al., 2012). Smoothing and resampling of the trajectories, for
example, with a B-spline, are sometimes used to improve
results. In another approach, Maddah, Grimson, et al. (2008)
represented each tract with a centerline and calculated a
distance map and Voronoi diagram for each centerline. The
Voronoi diagram is used to determine the correspondence
between the points on the centerline and the points on the
trajectories. Finally, ODonnell et al. (2009) used a prototype
trajectory and found the optimal trajectory points for each
point on the prototype by minimizing a cost function.
Acknowledgment
This work is supported by NIAAA Grant AA012388.

Diffusion MRI; INTRODUCTION TO METHODS AND MODELING:
Diffusion Tensor Imaging; Surface-Based Morphometry; Tensor-Based
Morphometry; Tract-Based Spatial Statistics and Other Approaches for
Cross-Subject Comparison of Local Diffusion MRI Parameters.
References
Abe, O., Takao, H., Gonoi, W., Sasaki, H., Murakami, M., Kabasawa, H., et al. (2010).
Voxel-based analysis of the diffusion tensor. Neuroradiology, 52, 699710.
Berkiten, S., & Acar, B. (2010). A pointwise correspondence based DT-MRI fiber
similarity measure. IEEE Engineering in Medicine and Biology Society, 2010,
26942697.
Bohm, C., Mai, S. T., Feng, J., Plant, C., He, X., & Shao, J. (2011). A novel similarity
measure for fiber clustering using longest common subsequence. In: Proceedings
of the data mining for medicine and healthcare workshop, pp. 19.
Brun, A., Knutsson, H., Park, H. J., Shenton, M. E., & Westin, C.-F. (2004). Clustering
fiber tracts using normalized cuts. Medical Image Computing and ComputerAssisted Intervention, 3216, 368375.
Catani, M., & Thiebaut de Schotten, M. (2008). A diffusion tensor imaging tractography
atlas for virtual in vivo dissections. Cortex, 44, 11051132.
Clayden, J. D., Bastin, M. E., & Storkey, A. J. (2006). Improved segmentation
reproducibility in group tractography using a quantitative tract similarity measure.
Clayden, J. D., Storkey, A. J., & Bastin, M. E. (2007). A probabilistic model-based
approach to consistent white matter tract segmentation. IEEE Transactions on
Colby, J. B., Soderberg, L., Lebel, C., Dinov, I. D., Thompson, P. M., & Sowell, E. R.
(2012). Along-tract statistics allow for enhanced tractography analysis. NeuroImage,
59, 32273242.
Corouge, I., Fletcher, P. T., Joshi, S., Gouttard, S., & Greig, G. (2006). Fiber tractoriented statistics for quantitative diffusion tensor MRI analysis. Medical Image
Analysis, 10, 786798.
Corouge, I., Gerig, G., & Gouttard, S. (2004). Towards a shape model of white matter
fiber bundles using diffusion tensor MRI. ISBI, 1, 344347.
Ding, Z., Gore, J. C., & Anderson, A. W. (2003). Classification and quantification of
neuronal fiber pathways using diffusion tensor MRI. Magnetic Resonance in
Medicine, 49, 716721.
Duncan, J. S. (2010). Imaging in the surgical treatment of epilepsy. Nature Reviews
El Kouby, V., Cointepas, Y., Poupon, C., Rivie`re, D., Golestani, N., Poline, J. B., et al.
(2005). MR diffusion-based inference of a fiber bundle model from a population of
subjects. Medical Image Computing and Computer-Assisted Intervention, 8,
196204.
Goodlett, C. B., Fletcher, P. T., Gilmore, J. H., & Gerig, G. (2009). Group analysis of DTI fiber
tract statistics with application to neurodevelopment. NeuroImage, 45, S133S142.
Guevara, P., Poupon, C., Rivie`re, D., Cointepas, Y., Descoteaux, M., Thirion, B., et al. (2010).
Robust clustering of massive tractography datasets. NeuroImage, 54, 19751993.
Jiang, H., van Zijl, P. C. M., Kim, J., Pearlson, G. D., & Mori, S. (2006). DtiStudio:
Resource program for diffusion tensor computation and fiber bundle tracking.
Computer Methods and Programs in Biomedicine, 81, 106116.
Jin, Y., Shi, Y., Zhan, L., Li, J., de Zubiacaray, G. I., McMahon, K. L., et al. (2012).
Automatic population HARDI white matter tract clustering by label fusion of multiple
tract atlases. Multimodal Brain Image Analysis, 7509, 147156.
Kanaan, R. A., Shergill, S. S., Barker, G. J., Catani, M., Ng, V. W., Howard, R., et al.
(2006). Tract-specific anisotropy measurement in diffusion tensor imaging.
Psychiatry Research, 146, 7382.
Klein, J., Bittihn, P., Ledochowitsch, P., Hahn, H. K., Konard, O., Rexilius, J., et al.
(2007). Grid-based spectral fiber clustering. Medical imaging: Visualization and
image-guided procedures, 65091E.
Leemans, A., Sijbers, J., De Backer, S., Vandervliet, E., & Parizel, P. (2006). Multiscale
white matter fiber tract coregistration: A new feature-based approach to align
diffusion tensor data. Magnetic Resonance in Medicine, 55, 14141423.
Liu, M., Vemuri, B. C., & Deriche, R. (2012). Unsupervised automatic white matter fiber
clustering using a Gaussian mixture model. Proceedings of the IEEE International
Symposium on Biomedical Imaging, 2012, 522525.
Maddah, M., Grimson, W. E.L, Warfield, S. K., & Wells, W. M. (2008). A unified
framework for clustering and quantitative analysis of white matter fiber tracts.
Medical Image Analysis, 12, 191202.
Maddah, M., Mewes, A. U.J, Haker, S., Grimson, W. E.L, & Warfield, S. K. (2005).
Automated atlas-based clustering of white matter fiber tracts from DTMRI. Medical
Image Computing and Computer-Assisted Intervention, 8, 188195.
Maddah, M., Miller, J. V., Sullivan, E. V., Pfefferbaum, A., & Rohlfing, T. (2011). Sheetlike white matter fiber tracts: Representation, clustering, and quantitative analysis.
Medical Image Computing and Computer-Assisted Intervention, 14, 191199.
Maddah, M., Zollei, L., Grimson, W. E.L, Westin, C.-F., & Wells, W. M. (2008). A
mathematical framework for incorporating anatomical knowledge in DT-MRI analysis.
IEEE International Symposium on Biomedical Imaging, 4543943, 105108.
Mani, M., Kurtek, S., Barillot, C., & Srivsastana, A. (2010). A comprehensive
Riemannian framework for the analysis of white matter fiber tracks. IEEE
International Symposium on Biomedical Imaging.
Merhof, D., Greiner, G., Buchfelder, M., & Nimsky, C. (2010). Fiber selection from
diffusion tensor data based on Boolean operators. Bildverarbeitung fur die Medizin,
147151.
Mori, S., Crain, B., Chacko, V., & van Zijl, P. (1999). Three dimensional tracking of
axonal projections in the brain by magnetic resonance imaging. Annals of
Mori, S., Oishi, K., Jiang, H., Jiang, L., Li, X., Akhter, K., et al. (2007). Stereotaxic white
matter atlas based on diffusion tensor imaging in an ICBM template. NeuroImage,
40, 570582.
275
ODonnell, L., Golby, A. J., & Westin, C.-F. (2013). Fiber clustering versus the
parcellation-based connectome. NeuroImage, 80, 283289.
ODonnell, L., & Westin, C. F. (2005). White matter tract clustering and correspondence
in populations. Medical Image Computing and Computer-Assisted Intervention, 8,
140147.
ODonnell, L., & Westin, C.-F. (2006). High-dimensional white matter atlas generation
and group analysis. Medical Image Computing and Computer-Assisted
Intervention, 9, 243251.
ODonnell, L., & Westin, C.-F. (2007). Automatic tractography segmentation using a
high-dimensional white matter atlas. IEEE Transactions on Medical Imaging, 26,
15621575.
ODonnell, L., Westin, C.-F., & Golby, A. J. (2009). Tract-based morphometry for white
matter group analysis. NeuroImage, 45, 832844.
Prasad, G., Jahanshad, N., Aganj, I., Lenglet, C., Sapiro, G., Toga, A. W., et al. (2011).
Atlas-based fiber clustering for multi-subject analysis of high angular resolution
diffusion imaging tractography. ISBI, 276280.
Ratnarajah, N., Simmons, A., & Hojjatoleslami, A. (2011). Probabilistic clustering and
shape modelling of white matter fibre bundles using regression mixtures. Medical
Image Computing and Computer-Assisted Intervention, 14, 2532.
Robinson, E. C., Rueckert, D., Hammers, A., & Edwards, A. D. (2010). Probabilistic
white matter and fiber tract atlas construction. ISBI, 11531156.
Schulte, T., Maddah, M., Muller-Oehring, E. M., Rohlfing, T., Pfefferbaum, A., &
Sullivan, E. V. (2013). Fiber tract-driven topographical mapping (FTTM) reveals
microstructural relevance for interhemispheric visuomotor function in the aging
Shao, J., Hahn, K., Yang, Q., Bohm, C., Wohlschlager, A. M., Myers, N., et al. (2010).
Combining time series similarity with density-based clustering to identify fiber
bundles in the human brain. In: IEEE International Conference on Data Mining
Workshops, pp. 747754.
Shimony, J. S., Snyder, A. Z., Lori, N., & Conturo, T. E. (2002). Automated fuzzy
clustering of neuronal pathways in diffusion tensor tracking. ISMRM, p. 10.
Smith, S. M., Jenkinson, M., Johansen-Berg, H., Rueckert, D., Nichols, T. E.,
Mackay, C. E., et al. (2006). Tract-based spatial statistics: Voxelwise analysis of
multi-subject diffusion data. NeuroImage, 31, 14871505.
Suarez, R. O., Commowick, O., Prabhu, S. P., & Warfield, S. K. (2012). Automated
delineation of white matter fiber tracts with a multiple region-of-interest.
Tsai, A., Westin, C.-F., Hero, A. O., & Willsky, A. S. (2007). Fiber tract clustering on
manifolds with dual rooted-graphs. IEEE Conference on Computer Vision and
Pattern Recognition, pp. 16.
Van Hecke, W., Sijbers, J., De Backer, S., Poot, D., Parizel, P. M., & Leemans, A.
(2009). On the construction of a ground truth framework for evaluating voxel-based
diffusion tensor MRI analysis methods. NeuroImage, 46, 692707.
Wakana, S., Caprihan, A., Panzenboeck, M. M., Fallon, J. H., Perry, M., Gollub, R. L.,
et al. (2007). Reproducibility of quantitative tractography methods applied to
cerebral white matter. NeuroImage, 36, 630644.
Wakana, S., Jiang, H., Nagae-Poetscher, L. M., van Zijl, P. C.M, & Mori, S. (2004).
Fiber tract-based atlas of human white matter anatomy. Radiology, 230, 7787.
Wang, X., Grimson, W. E.L, & Westin, C.-F. (2011). Tractography segmentation using a
hierarchical Dirichlet processes mixture model. NeuroImage, 54, 290302.
Wassermann, D., & Deriche, R. (2008). Simultaneous manifold learning and
clustering: Grouping white matter fiber tracts using a volumetric white matter
atlas. MICCAI workshop Manifolds in medical imaging: Metrics, learning and
beyond.
Wassermann, D., Bloy, L., Kanterakis, E., Verma, R., & Deriche, R. (2010).
Unsupervised white matter fiber clustering and tract probability map generation:
Applications of a Gaussian process framework for white matter fibers. NeuroImage,
51, 228241.
Xia, Y., Turken, A., Whitfield-Gabrieli, S., & Gabrieli, J. (2005). Knowledge-based
classification of neuronal fibers in entire brain. Medical Image Computing and
Computer-Assisted Intervention, 8, 205212.
Yeatman, J. D., Dougherty, R. F., Myall, N. J., Wandell, B. A., & Feldman, H. M. (2012).
Tract profiles of white matter properties: Automating fiber-tract quantification. PLoS
One, 7, e49790.
Ziyan, U., Sabuncu, M. R., Grimson, W. E.L, & Westin, C.-F. (2009). Consistency
clustering: A robust algorithm for group-wise registration, segmentation, and
automatic atlas construction in diffusion MRI. International Journal of Computer
Vision, 85, 279290.
Ziyan, U., Sabuncu, M. R., ODonnell, L., & Westin, C.-F. (2007). Nonlinear registration
of diffusion MR images based on fiber bundles. Medical Image Computing and
Computer-Assisted Intervention, 10, 351358.
Zvitia, O., Mayer, A., Shadmi, R., & Greenspan, H. (2009). Co-registration of white
matter tractographies by adaptive-mean-shift of Gaussian mixture modeling. IEEE
Tissue Microstructure Imaging with Diffusion MRI

G Nedjati-Gilani and DC Alexander, University College London, London, UK
Introduction
Diffusion magnetic resonance imaging (MRI) provides a unique
noninvasive window into the microstructure of biological tissue.
The technique sensitizes the MR signal to the dispersion of water
molecules in tissue from diffusion over timescales from about
1 ms to 1 s. During that time, water molecules at body temperature move average distances of on the order of ones to tens of
micrometers. At this length scale, the cellular architecture of the
tissue restricts and impedes the mobility of the water and so
determines the pattern of dispersion. Diffusion MR measurements are thus sensitive to various histological features of the
tissue, such as size, density, orientation, permeability, and shape
of cells and membranes. Diffusion MR microstructure imaging
aims to provide virtual histology, by estimating these features
from combinations of diffusion MR measurements and mapping them over the brain, as well as other organs or samples.
Standard diffusion MRI techniques, such as apparent diffusion coefficient mapping, diffusion tensor imaging, and diffusion spectrum imaging, provide indices, such as mean diffusivity
(MD) and fractional anisotropy (FA), that are sensitive to various
histological features. However, these indices lack specificity. All
the histological features listed in the preceding text can affect
both MD and FA. While changes in either index arise from
differences in the tissue microstructure, the indices themselves
say little about which specific properties are different.
The general strategy in microstructure imaging is to use a
mathematical model that relates specific properties of the cellular architecture of tissue to the dispersion pattern of water molecules and its evolution over time and thus to diffusion MR
signals. We solve an inverse problem to estimate the tissue
properties by fitting the model to MR measurements. In imaging,
this means acquiring various different diffusion MR images with
different settings on the scanner (diffusion times, b-values, etc.);
this provides a set of measurements in each voxel of the image to
which we fit our model and estimate its parameters. Thus, we can
map the parameters over the image. Figure 1 gives an illustration
of the process for one particular technique.
A general feature of microstructure imaging techniques is that
the parameters they map relate to tissue features much smaller
than the resolution of the image. The example in Figure 1 maps
indices of axon density and diameter; the image voxels represent
blocks of tissue with size of order 1 mm3, whereas the axons
themselves have diameter of order 1 mm. The values in the parameter maps are not measurements of single cells or structures, but
are statistical in nature: a mean axon diameter or average density
over the thousands or millions the voxel contains.
Brain Tissue Microstructure

This section provides some background information on neurons, axons, and glia (see Figure 2), which are the tissue
structures in the brain that microstructure imaging generally

aims to measure. This section focuses on the pertinent properties that microstructure imaging is potentially sensitive to, such
as cell size and permeability. More detailed information on the
function and structure of these cells can be found in earlier
articles.
Neurons are the processing centers of the central nervous
system (CNS) and are responsible for transmitting and receiving
electrical signals to and from different functional areas in the
brain. The diameter of the neuronal cell body is approximately
1025 mm (Bear, Connor, & Paradiso, 2007) and is surrounded
by a plasma membrane that is selectively permeable to ions and
molecules. Experiments on Aplysia neurons estimate the water
permeability coefficient to be 1.9 10 6 ms 1 (Stein, 1967).
Given the typical neuronal size, this corresponds to an intracellular water residence time of 12 s, indicating that neurons are
effectively impermeable on the timescale of diffusion MRI measurements. The neuronal cell body has a branching extension
consisting of thousands of individual dendrites, which take in
electrical signals from neighboring neurons. The dendrites are
approximately 1 mm in diameter and can extend over 100 mm
from the cell body (Jacobs, Schall, & Scheibel, 1993).
Axons are approximately cylindrical projections from neuronal cell bodies that are designed to transport electrical signals
over larger-scale distances in the brain. Groups of axons that
connect the same functional areas form tightly packed, typically
parallel bundles of fibers known as tracts. The length of axons in
the CNS ranges from 1 mm to over 1 m. Their diameters range
from 0.1 to 20 mm (Waxman, 1995); however, histology studies
indicate that axons with diameters greater than 5 mm are rare in
the human brain (Aboitiz, Schiebel, Fisher, & Zaidel, 1992). All
axons are surrounded by a plasma membrane, along which the
electrical signals from the neurons travel; the majority of axons
with a diameter of greater than 0.2 mm are also surrounded by
layers of myelin, a phospholipid bilayer produced by the oligodendrocyte glial cells (Bauman & Pham-Dinh, 2001), which
increases their resistance, thus increasing the speed of signal
propagation. As a large number of axons are surrounded by
myelin sheaths, the permeability of axons is dependent upon
the permeability of the myelin lipid layers. Data regarding the
water permeability of myelin are scarce; however, experiments
using synthetic bilipid layers suggest permeabilities of approximately 1 10 5 ms 1 (Stein, 1967). This corresponds to intracellular water residence times on the order of 100 ms. Diffusion
MRI is sensitive to water exchange on this timescale, particularly
when using stimulated echo sequences (Merboldt, Hanicke, &
Frahm, 1985), which can accommodate diffusion times up to
approximately 250 ms for in vivo clinical scans (Latt et al., 2009).
Glial cells such as astrocytes, oligodendrocytes, and microglia are present in both the gray matter and white matter in the
brain in order to support and repair the axons and neurons.
Astrocytes are large, star-shaped cells with numerous processes
extending out from the cell body. Within the gray matter, the
http://dx.doi.org/10.1016/B978-0-12-397025-1.00296-7
277
278
INTRODUCTION TO METHODS AND MODELING | Tissue Microstructure Imaging with Diffusion MRI
Figure 1 An exemplar microstructure imaging technique. The true diffusion MRI signal due to white matter tissue structure (bottom left) is
approximated by a simplified mathematical model using infinitely long parallel cylinders (top left). The model is fit to diffusion-weighted MR images
(center) in order to generate maps of axon diameter and density within the corpus callosum (right).
Figure 2 An electron microscopy image of the white matter, showing

both axons and glial cells. The dark myelin sheaths surrounding the
axons are indicated by the clear arrow. N shows the nucleus of an
oligodendrocyte glial cell, with C showing the surrounding cytoplasm
within its cell body. M indicates a microglial cell. The solid arrow and
arrowhead indicate mitochondria and other organelles inside the axons
and glia, which are too small to be measured with current microstructure
imaging techniques. Image courtesy of Simon Richardson.
processes extend radially up to 50 mm from the cell body,

whereas in the white matter, the astrocytic processes are longer
and finer, extending up to 300 mm from the cell body along the
axon orientation (Reichenbach & Wolburg, 2005). As one of
the functions of astrocytes is to regulate the amount of water
within the brain, the cells are relatively permeable to water.
Fluorescence imaging techniques, such as in Solenov, Watanabe, Manley, and Verkman (2004), estimate the permeability
of the astrocyte membrane to be approximately 5 10 4 ms 1,
an order of magnitude greater than that of axons. Oligodendrocytes are generally smaller than astrocytes and are primarily
found in the brain white matter where they are responsible for
myelinating axons. Oligodendrocyte cells can be divided into
subclasses dependent on their size and the number of axons
they myelinate. The smallest type I oligodendrocytes, with cell
diameters of approximately 1520 mm, can myelinate 2030
axons, whereas the largest type IV oligodendrocytes, with
diameters of >40 mm, only myelinate 13 large axons

(Bunge, 1968). Microglia are macrophages that provide the
first immune response within the CNS and are more commonly found in the gray matter rather than in the white matter.
They are the smallest of the glial cells with cell body diameters
of approximately 10 mm, although their processes can extend
out up to around 50 mm (Perry, 2001). For typical diffusion
MRI timescales, the mean squared displacement for a water
molecule at body temperature is smaller than the diameter of
the larger glial cells; therefore, microstructure imaging techniques may not have the sensitivity to measure the size of
some oligodendrocytes and astrocytes.
Smaller structures such as neurofilaments, microtubules,
mitochondria, and other organelles exist within the axons,
neurons, and glia. The diameter of these structures is on the
scale of 0.1 mm for mitochondria and nm for microtubules
and neurofilaments (Waxman, 1995). Therefore, they are
most likely too small to be measured using diffusion MRI,
although their presence may still influence the motion of
water molecules within brain tissue.
Microstructure Imaging Techniques

This section reviews several standard microstructure imaging
techniques divided into classes by the histological features they
estimate.
Fiber Orientation
One class of microstructure imaging technique uses models
designed primarily to estimate fiber orientations for
tractography. Some simple compartment models are useful for
this purpose. The ball-and-stick model (Behrens et al., 2003)
assumes that the white matter MR signal comes from two separate populations of water: one trapped inside axons, which can
move only in the direction of the fiber, and the other outside but
around the axons, which diffuses freely and isotropically. The
parameters of the model are the diffusivity, the orientation of
the stick component, and the ratio of the signals coming from
the two compartments. The signal ratio, or volume fraction,
relates to the density of fibers. Thus, fitting the model provides
estimates of two histological parameters: the fiber density and
the fiber orientation. The composite hindered and restricted
model of diffusion (CHARMED) proposed by Assaf, Freidlin,
Rohde, and Basser (2004) similarly separates intra-axonal and
extra-axonal compartments but uses more complex models for
each compartment. Specifically, it models the axons as a collection of straight parallel impermeable cylinders with a distribution of radii typical of the human white matter. The model for
the intra-axonal signal then uses a model of diffusion restricted
within a cylinder; the extra-axonal signal assumes anisotropic
free diffusion with greater hindrance in the directions perpendicular to the fibers than parallel.
A limitation of the basic ball-and-stick model or CHARMED
is the assumption of a single orientation common to all fibers
within each voxel. However, these kinds of model extend easily
to cope with multiple distinct fiber populations, for example, at
fiber crossings, by simply including multiple stick (or more
generally intra-axonal) compartments, as in Hosey, Williams,
and Ansorge (2005), Assaf and Basser (2005), and Behrens,
Johansen-Berg, Jbabdi, Rushworth, and Woolrich (2007). For
more general configurations of fibers, we can consider the signal
as a convolution of signals from a single fiber with an orientation
distribution of fibers (Tournier, Calamante, Gadian, & Connelly,
2004) and deconvolve the signal with a model of the single fiber
signal to estimate the fiber orientation distribution as in Tournier
et al. (2004), Alexander (2005b), Tournier, Calamante, and
Connelly (2007), Sakaie and Lowe (2007), DellAcqua et al.
(2007), and Anderson (2005). Other techniques (Kaden,
Knosche, & Anwander, 2007; Sotiropoulos, Behrens, & Jbabdi,
2012; Zhang, Schneider, Wheeler-Kingshott, & Alexander, 2012)
use simple parametric models for the fiber orientation distribution, such as the Watson and Bingham distributions (Mardia &
Jupp, 1990). Various review articles, for example, Alexander
(2005a), Seunarine and Alexander (2009), and Tournier, Mori,
and Leemans (2011), cover the range of techniques for mapping
fiber orientations in more detail.
Fiber Composition
Other techniques focus on estimating parameters describing
the composition of fiber bundles, such as axon density and
diameter distribution. Stanisz, Wright, Henkelman, and Szafer
(1997) proposed a three-compartment model of nervous tissue: one population of water inside elongated ellipsoidal
axons, another inside spherical glial cells, and a third in the
extracellular space. Each compartment has its own dimensions,
volume fraction, membrane permeability, and internal diffusivity and relaxation constants. Fitting the full model provides
estimates of all these parameters but requires a very rich data
set containing low noise measurements with a wide range of
diffusion times and b-values. The only demonstration of the
technique is on an excised bovine optic nerve using a high-field
small-bore scanner with very high magnetic field gradients.
The AxCaliber technique introduced by Assaf, BlumenfeldKatzir, Yovel, and Basser (2008) uses the CHARMED model but
fits for the axon diameter distribution, modeled as a twoparameter gamma distribution, rather than assuming a fixed
typical distribution. The model is similar to that of Stanisz et al.
(1997), but simpler, because it assumes impermeable membranes and has no glial cell compartment. Experiments on excised
279
tissue samples show good agreement between the estimated axon

diameter distribution in various nerve samples and axon diameter histograms measured on histology images. Later work by
Barazany, Basser, and Assaf (2009) adapted the technique to
map the axon diameter distribution over the corpus callosum of
a live rat. The recovered distributions match axon diameter histograms from histology of different regions of the corpus callosum
and reflect the known trend in the mammalian brain of lowdiameter axons at the two ends of the corpus callosum (genu
towards the front of the brain and splenium at the back) and high
diameters in the midbody (Aboitiz, Rodriguez, Olivares, & Zaidel,
1996; Aboitiz et al., 1992; Lamantia & Rakic, 1990).
The ActiveAx technique (Alexander et al., 2010; Dyrby,
Sogaard, Hall, Ptito, & Alexander, 2013; Zhang, Hubbard,
Parker, & Alexander, 2011) addresses some key limitations of
the techniques in Stanisz et al. (1997) and Assaf et al. (2008),
which prevent widespread usage in brain mapping. First, the
acquisition requires high gradient strengths and long acquisition
times that are not feasible on human imaging systems or live
volunteers. Second, they assume a particular and known fiber
orientation and cannot map fiber properties over the whole
brain where the fiber orientation varies. The original version of
ActiveAx in Alexander et al. (2010) addresses these limitations by
combining optimized high-angular resolution diffusion imaging
(HARDI) (Alexander, 2008) with a simplified model designed to
minimize complexity while capturing the dependence of the
data on acquisition parameters (diffusion time, b-value, etc.).
The model assumes a single axon diameter in each voxel rather
than the gamma distribution model in AxCaliber and includes
both a free water contribution, as in Barazany et al. (2009),
and an isotropically restricted compartment similar to the glial
cell component of Stanisz et al. (1997). Experiments show
compelling results from fixed monkey brains, recovering the
lowhighlow trend in axon diameter in the corpus callosum
with high reproducibility, and preliminary results from human
volunteers show similar trends, albeit more weakly. Examples of
parameter maps estimated with CHARMED, AxCaliber, and
ActiveAx are presented in Figure 3.
Later generations of ActiveAx include a fiber dispersion
parameter (Zhang et al., 2011). Although the assumption of
straight parallel fibers may be reasonable in major pathways
such as the corpus callosum and corticospinal tracts, many
more peripheral pathways have less directional coherence. In
such regions, an assumption of straight parallel fibers tends to
cause overestimates of the axon diameter, because we effectively
view some of them obliquely, so they appear to have larger cross
sections. Zhang et al. (2011) used a Watson distribution of fiber
orientations and demonstrated good separation of the effects of
axon diameter and dispersion through parameter estimation
using similar data to the original ActiveAx paper of Alexander
et al. (2010). The addition of the fiber dispersion parameter not
only extends the portion of white matter over which the technique gives sensible results but also provides a useful new parameter, the orientation dispersion index. Fiber crossings still pose
some difficulties for the model (Zhang & Alexander, 2010).
Gray Matter Properties

While most diffusion MRI techniques for the brain have
focused on the white matter, as discussed in the preceding
280
Figure 3 This figure, taken from Assaf et al. (2013), demonstrates several of the techniques discussed in Section Fiber Composition. (a) shows an axon
density map estimated using CHARMED. (b) shows estimates of axon diameter distributions in the rat corpus callosum estimated using AxCaliber (Barazany
et al., 2009), whereas (c) shows estimates of the single axon diameter index using ActiveAx (Dyrby et al., 2013). (d) shows an eccentricity map estimated
using a double-PFG sequence (Shemesh et al., 2012a), which is discussed further in Section Perspectives. Reprinted from Assaf, Y., Alexander, D. C.,
Jones, D. K., Bizzi, A., Behrens, T. E. J., Clark, C. A., Cohen, Y., Dyrby, T. B., Huppi, P. S., Knoesche, T. R., LeBihan, D., Parker, G. J. M., & Poupon, C. (2013).
The CONNECT project: Combining macro- and microstructure. NeuroImage, 80, 273282, Copyright (2013), with permission from Elsevier.
text, recently promising techniques for probing histological

properties of the gray matter have begun to emerge.
Jespersen, Kroenke, Ostergaard, Ackerman, and Yablonskiy
(2007) used a model similar to the spherical convolution
technique discussed in the preceding text to estimate the distribution of orientations of neurites (axons or dendrites) in
either the white matter or gray matter. Subsequent experimental work in Jespersen et al. (2010) shows that neurite density
estimates from fitting the model correlate well with optical
myelin staining intensity and stereological estimation of neurite density using electron microscopy. Later work by Jespersen,
Leigland, Cornea, and Kroenke (2012) further demonstrates
that the estimated neurite orientation distributions show excellent agreement to those quantified from histology using Golgi
staining.
The neurite orientation dispersion and density imaging
(NODDI) technique introduced by Zhang et al. (2012) aims
to estimate a similar set of histological properties through a
practical imaging protocol. The protocol in Jespersen et al.
(2007) uses a large number of measurements with different
b-values and gradient orientations making it impractical for
large-scale studies. NODDI uses the experiment design optimization in Alexander (2008) to construct a more economical
protocol, which consists of two HARDI shells with b-values
around 700 and 2500 smm 2. Acquisition can take as little as
10 min on current standard clinical MRI scanners, making
NODDI feasible for clinical studies. Complexity of the model
is reduced in various ways, in particular by using a Watson
distribution to represent fiber dispersion in a similar way to

Zhang et al. (2011). NODDI thus separates and maps individually three histological properties of the tissue, neurite density,
orientation dispersion, and CSF contribution, that the
traditional FA index from DTI confounds. The technique is
now being adopted in clinical studies such as Winston,
Symms, Alexander, Duncan, and Zhang (2013), which show
that indices from NODDI are better able to distinguish pathologies such as focal cortical dysplasia more readily than those
from DTI.
Exchange Imaging
Exchange rate, or membrane permeability, is another important histological property of tissue that affects water mobility
and thus the diffusion MR signal. Permeability is an important
property, because it can highlight tissue damage or disease;
damaged axonal myelin sheaths, for example, can permit
more water to pass through the wall of the axon than healthy
myelin sheaths. Precise mathematical models relating membrane permeability to the signal are not straightforward to
construct, but various approximations are available.
Karger, Pfeifer, and Heink (1988) provided a simple framework for incorporating the effects of exchange on the diffusion
MR measurements by modeling the signals due to intra- and
extra-axonal water as a weakly coupled system. Originally formulated to model exchange between two freely diffusing pools
of protons, the Karger equations have also been modified to
model exchange between free and restricted sites (Price, 2009),
and in this formulation, it is one of the most commonly used
methods for modeling axonal exchange (Fieremans, Novikov,
Jensen, & Helpern, 2010; Meier, Dreher, & Leibfritz, 2003;
Nilsson et al., 2009; Stanisz et al., 1997). However, simulation
studies by Nilsson et al. (2010) show that the approximations
used to derive the Karger equations lead to bias in the estimated microstructure parameters.
Lasic, Nilsson, Latt, Stahlberg, and Topgaard (2011)
introduced the apparent exchange rate (AXR) mapping technique, which uses various approximations to find a potentially
practical way to estimate and map an index of exchange rate.
The work uses a specialist pulse sequence that is not widely
available on clinical scanners, although later work by Nilsson
et al. (2013) demonstrates feasibility of the technique on live
human subjects. An example of an in vivo AXR map is shown in
Figure 4.
Perspectives
Microstructure imaging remains an emerging technology.
Although the first clinically feasible techniques are starting to
appear and gain widespread attention from the imaging user
community, considerable refinement of those techniques is
still possible, and a wide range of new possibilities are on the
horizon.
The mathematical models that underpin current microstructure imaging techniques remain a gross simplification of reality,
and refinements are needed to improve the fit to the data and
281
thus the accuracy of parameter estimates. Various studies, for

example, Panagiotaki et al. (2012) and Ferizi, Tariq, Zhang, and
Alexander (2013), compare a wide range of different combinations of compartments for their ability to explain data acquired
from white matter tissue. These studies justify the choices of
model in current microstructure imaging techniques, such as
Alexander et al. (2010), Zhang et al. (2011), and Zhang et al.
(2012), from the list of currently available models. However,
these models ignore various potentially important effects, such
as axonal undulation (Nilsson, Latt, Stahlberg, van Westen, &
Hagslatt, 2012) and beading (Budde & Frank, 2010), permeability (Lasic et al., 2011), and multiple subcompartments with
different intrinsic diffusivities (Jbabdi, Sotiropoulos, Savio,
Grana, & Behrens, 2012; Scherrer et al., 2013). Parameter estimates from current models are imperfect; for example, axon
diameter indices from ActiveAx consistently overestimate
expected values (Alexander et al., 2010; Dyrby et al., 2013;
Zhang et al., 2011); incorporating these other effects in the
underlying model may help to align the estimates with expected
values. Such models also provide estimates of interesting new
parameters.
Other improvements are likely through improved measurement techniques. A key limiting factor in measuring axon
diameter (or pore sizes in general) with diffusion MR is the
gradient strength available in the imaging device (Dyrby et al.,
2013). Dyrby et al. (2013) demonstrated the effect of increasing maximum gradient strength on maps of axon diameter and
density in both simulation and using fixed tissue and an experimental imaging system. They show clear benefits of increasing
gradient strength from around 60 mT m 1, which is typical of
Figure 4 Nilsson et al. (2013) showed maps of the apparent exchange rate (AXR) compared to standard DTI metrics such as fractional anisotropy (FA),
mean diffusivity (MD), and the apparent diffusion coefficient (ADC). Reprinted from Nilsson, M., Latt, J., Wirestam, R., Stahlberg, F., Karlsson, N.,
Johansson, M., Sundgren, P. C., & van Westen, D. (2013). Noninvasive mapping of water diffusional exchange in the human brain using filter-exchange
imaging. Magnetic Resonance in Medicine, 69, 15721580, Copyright (2012), with permission from John Wiley & Sons Ltd.
282
90
180
PGSE
Readout(RO)
(a)
90
180
180
dPFG
(b)
90
180
OGSE
(c)
90
180
L-N
(d)
Figure 5 The PGSE sequence (Stejskal & Tanner, 1965) shown in (a) is the standard diffusion MR sequence. However, (c) OGSE (Callaghan &
Komlosh, 2002) improves sensitivity to axon diameter, whereas (b) dPFG (Lawrenz & Finsterbusch, 2011; Shemesh et al., 2012a) and (d) longnarrow
(LN) (Laun et al., 2011) sequences provide sensitivity to pore shape.
current human scanners and provides sensitivity to axons with

diameters of approximately 4 mm and above, to 300 mT m 1,
which is sensitive to axons with diameters of approximately
2 mm and above. Recent experiments on the one-off highgradient human MRI system (McNab et al., 2013), which can
reach up to 300 mT m 1, show promising results from the
AxCaliber technique on live humans for the first time.
Further benefits can come from moving away from the
standard diffusion MR pulse sequence, which is still the
pulsed-gradient spin-echo (PGSE) sequence proposed by
Stejskal and Tanner (1965). A range of these emerging pulse
sequences is presented in Figure 5, along with the standard
PGSE sequence. Oscillating gradient spin-echo (OGSE)
sequences (Callaghan & Komlosh, 2002; Does, Parsons, &
Gore, 2003) probe shorter diffusion times and so are sensitive
to structures with shorter length scales. Phenomenological
results from OGSE, for example, Portnoy, Flint, Blackband,
and Stanisz (2013) and Van, Holdsworth, and Bammer
(2013), show that different timescales produce different contrasts in brain imaging, which reveals opportunities for new
models to identify and map the features that cause these differences. The technique potentially provides a specific advantage for measuring axon diameters, because the majority of
axons have diameters less than the lower limit of diameters
we can measure with PGSE and currently achievable gradient
strengths. Other pulse sequences, such as double-pulsed field
gradient (dPFG) sequences (Cory, Garroway, & Miller, 1990),
also offer advantages over PGSE for estimating pore sizes
(Ozarslan & Basser, 2008; Shemesh, Ozarslan, Komlosh,
Basser, & Cohen, 2010). Such sequences are not generally
available on standard MR systems, but can be implemented,
and early demonstrations of their usage for estimating axon
diameters are beginning to appear (Koch & Finsterbusch, 2011;
Komlosh et al., 2013). However, as shown in Drobnjak, Siow,
and Alexander (2010) and Drobnjak and Alexander (2011),
numerical results suggest that OGSE, rather than dPFG, provides the greatest sensitivity to the axon diameter, at least for a
simple system with straight parallel fibers; subsequent work
provides the mathematical models to support an adaptation of
ActiveAx for OGSE (Ianus, Siow, Drobnjak, & Alexander,
2012) and an early demonstration in the rat corpus callosum
(Siow, Drobnjak, Ianus, Christie, & Alexander, 2013).
Double-PFG sequences do however offer access to a range of
other interesting features that PGSE lacks sensitivity to. Various
authors, for example, Shemesh et al. (2012a), Lawrenz and
Finsterbusch (2011), and Jespersen (2012), construct dPFG protocols enabling estimation of apparent eccentricity, which
reflects the shape of restricting pores, independent of their
orientation distribution, and separates this microscopic anisotropy from the macroscopic anisotropy of pores with coherent
orientation. More general efforts to estimate pore shape offer
future possibilities. Laun, Kuder, Semmler, and Stieltjes (2011)
showed that the shape of any pore is recoverable using combinations of longnarrow pulses, as shown in Figure 6, and later
work by Kuder, Bachert, Windschuh, and Laun (2013) demonstrates the technique experimentally using a physical phantom
and hyperpolarized gas to provide the required signal. Shemesh,
Westin, and Cohen (2012b) proposed a combination of PGSE
and dPFG measurements to recover pore shape and
demonstrated experimentally recovery of a circular pore. As
Kuder and Laun (2013) later pointed out, that technique works
only for shapes with simple symmetries, but they go on to show
how to generalize it for arbitrary pore shapes. Precise pore shape
recovery requires gradient strengths and acquisition time well in
excess of what is available on current human imaging systems,
and these techniques will not become available for brain mapping in the near future. However, apparent eccentricity measurements do translate to human imaging, as shown by Lawrenz and
Finsterbusch (2013), and are the practical face of pore shape
imaging.
A further key area for improvement of microstructure imaging techniques is to extend beyond diffusion MRI and combine
with measurements from other MR or other imaging modalities. Techniques such as T2-spectroscopy potentially provide
information on pore size and shape at much smaller length
scales see, for example, the discussion in Kaden and Alexander (2013) and can also help measurements of exchange
(Dortch, Harkins, Juttukonda, Gore, & Does, 2013). Various
optical techniques are also sensitive to pore shape and may
combine with diffusion MRI to provide better estimates of pore
density and size distribution (Proverbio, Siow, Alexander, &
Gibson, 2013).
Current and future applications of microstructure imaging
offer exciting possibilities in brain mapping. The combination
with tractography is natural and compelling. The idea of tractometry (Bells et al., 2011) is to map microstructural parameters along fiber pathways extracted using tractography. The
technique treats the two steps independently, but combining
estimates of histological parameters and reconstruction of
brain connectivity offers deeper benefits. For example,
Sherbondy, Rowe, and Alexander (2010) showed how knowledge of the composition of individual fiber pathways resolves
long-standing ambiguities for tractography such as kissing versus crossing fibers.
Much of the development work for microstructure imaging
to date concentrates on normal healthy tissue. Recent work
283
Figure 6 Laun et al. (2011) showed how the combination of a long and narrow pulse, instead of two equal length pulses, can provide information about
pore shape. With infinitely thin pulses, the pore shape can be recovered almost exactly. Reprinted figure with permission from Laun, F. B., Kuder, T. A.,
Semmler, W., & Stieltjes, B. (2011). Determination of the defining boundary in nuclear magnetic resonance diffusion experiments. Physical Review
Letters, 107, 048102. Copyright (2011), by the American Physical Society.
begins to construct models for tissue affected by specific diseases. Wang et al. (2011) described a model for the diffusion
MR signal from the white matter that aims to separate the
axonal signal from partial volume with CSF, gray matter, and
other cellular compartments, particularly those that arise during inflammation, which is typical of diseases like multiple
sclerosis. The model for the axonal compartment is similar to
the spherical deconvolution model but discretized as originally
proposed by Ramirez-Mananares, Rivera, Vemuri, Carney, and
Mareci (2007), from which Wangs name of diffusion basis
spectrum imaging comes. The model includes an additional
spectrum of isotropically diffusing components. Various
results on animal tissue are promising for future translation
to humans. Figini et al. (2012) tested various mathematical
models to explain diffusion MR signal changes that occur in
prion diseases. These ideas potentially lead to disease-specific
imaging techniques tailored specifically for sensitivity to
particular pathologies. Similar work has been underway
outside the brain, for example, in cancer imaging (Colvin
et al., 2011; Panagiotaki et al., 2013; Xu, Does, & Gore,
2008), for some time.
A final note of caution: As with all model-based techniques,
microstructure imaging relies on the integrity of the underlying
model linking the measured data to tissue features of interest. It
will provide answers whether the model is correct or not, and
the models these techniques use are a gross simplification of
reality.

Diffusion MRI; INTRODUCTION TO ANATOMY AND
PHYSIOLOGY: Astrocytes, Oligodendrocytes, and NG2 Glia: Structure
and Function; Cell Types in the Cerebral Cortex: An Overview from the
Rat Vibrissal Cortex; Cytoarchitectonics, Receptorarchitectonics, and
Network Topology of Language; INTRODUCTION TO METHODS
AND MODELING: Diffusion Tensor Imaging; Fiber Tracking with DWI;
Q-Space Modeling in Diffusion-Weighted MRI.
References
Aboitiz, F., Rodriguez, E., Olivares, R., & Zaidel, E. (1996). Age-related changes in fibre
composition of the human corpus callosum: Sex differences. NeuroReport, 7,
17611764.
Aboitiz, F., Schiebel, A. B., Fisher, R. S., & Zaidel, E. (1992). Fiber composition of the
human corpus callosum. Brain Research, 598, 143153.
Alexander, D. C. (2005a). Multiple-fiber reconstruction algorithms for diffusion MRI.
Annals of the New York Academy of Sciences, 1064, 113133.
Alexander, D. C. (2005b). Maximum entropy spherical deconvolution for diffusion MRI.
Proceedings of Information Processing in Medical Imaging, 19, 7687.
Alexander, D. C. (2008). A general framework for experiment design in diffusion MRI
and its application in measuring direct tissue-microstructure features. Magnetic
Alexander, D. C., Hubbard, P. L., Hall, M. G., Moore, E. A., Ptito, M., Parker, G. J. M.,
et al. (2010). Orientationally invariant indices of axon diameter and density from
diffusion MRI. NeuroImage, 52, 13741389.
Anderson, A. W. (2005). Measurement of fiber orientation distributions using high
angular resolution diffusion imaging. Magnetic Resonance in Medicine, 54,
11941206.
284
Assaf, Y., Alexander, D. C., Jones, D. K., Bizzi, A., Behrens, T. E. J., Clark, C. A., et al.
(2013). The CONNECT project: Combining macro- and microstructure.
Assaf, Y., & Basser, P. J. (2005). Composite hindered and restricted model of diffusion
(CHARMED) MR imaging of the human brain. NeuroImage, 27, 4858.
Assaf, Y., Blumenfeld-Katzir, T., Yovel, Y., & Basser, P. J. (2008). AxCaliber: A method
for measuring axon diameter distribution from diffusion MRI. Magnetic Resonance
in Medicine, 59, 13471354.
Barazany, D., Basser, P. J., & Assaf, Y. (2009). In vivo measurement of axon diameter
distribution in the corpus callosum of rat brain. Brain, 132, 12101220.
Bauman, N., & Pham-Dinh, D. (2001). Biology of oligodendrocyte and myelin in the
mammalian central nervous system. Physiological Reviews, 81, 872927.
Bear, M. F., Connor, B. W., & Paradiso, M. A. (2007). Neuroscience: Exploring the brain
(3rd ed.). Baltimore: Lippincott, Williams and Wilkins.
Behrens, T. E.J, Johansen-Berg, H., Jbabdi, S., Rushworth, M. F. S., & Woolrich, M. W.
(2007). Probabilistic tractography with multiple fiber orientations: What can we
gain? NeuroImage, 34, 144155.
Behrens, T. E.J, Johansen-Berg, H., Woolrich, M. W., Smith, S. M.,
Bells, S., Cercignani, M., Deoni, S. L., Assaf, Y., Pasternak, O., Evans, J., et al. (2011).
Tractometry Comprehensive multi-modal quantitative assessment of white matter
along specific tracts In: Proceedings of the international society for magnetic
resonance in medicine, 678.
Budde, M. D., & Frank, J. A. (2010). Neurite beading is sufficient to decrease the
apparent diffusion coefficient after ischemic stroke. Proceedings of the National
Bunge, R. P. (1968). Glial cells and the central myelin sheath. Physiological Reviews,
48, 197210.
Callaghan, P. T., & Komlosh, M. E. (2002). Locally anisotropic motion in a
macroscopically isotropic system: Displacement correlations measured using
double pulsed gradient spin-echo NMR. Magnetic Resonance in Chemistry, 40,
S15S19.
Colvin, D. C., Loveless, M. E., Does, M. D., Yue, Z., Yankeelov, T. E., & Gore, J. C.
(2011). Earlier detection of tumor treatment response using magnetic resonance
diffusion imaging with oscillating gradients. Magnetic Resonance Imaging, 29,
315323.
Cory, D. G., Garroway, A. N., & Miller, J. B. (1990). Applications of spin transport as a
probe of local geometry. Polymer Preprints, 31, 149.
DellAcqua, F., Rizzo, G., Scifo, P., Clarke, R. A., Scotti, G., & Fazio, F. (2007). A modelbased deconvolution approach to solve fiber crossing in diffusion-weighted MR
imaging. IEEE Transactions on Medical Imaging, 54, 462472.
Does, M. D., Parsons, E. C., & Gore, J. C. (2003). Oscillating gradient measurements of
water diffusion in normal and globally ischemic rat brain. Magnetic Resonance in
Medicine, 49, 206215.
Dortch, R. D., Harkins, K. D., Juttukonda, M. R., Gore, J. C., & Does, M. D. (2013).
Characterizing inter-compartmental water exchange in myelinated tissue using
relaxation exchange spectroscopy. Magnetic Resonance in Medicine, 70,
14501459.
Drobnjak, I., & Alexander, D. C. (2011). Optimising time-varying gradient orientation for
microstructure sensitivity in diffusion-weighted MRI. Journal of Magnetic
Resonance, 212, 344354.
Drobnjak, I., Siow, B. M., & Alexander, D. C. (2010). Optimizing gradient waveforms for
microstructure sensitivity in diffusion-weighted MR. Journal of Magnetic
Dyrby, T. B., Sogaard, L. V., Hall, M. G., Ptito, M., & Alexander, D. C. (2013). Contrast
and stability of the axon diameter index from microstructure imaging with diffusion
MRI. Magnetic Resonance in Medicine, 70, 711721.
Ferizi, U., Schneider, T., Tariq, M., Wheeler-Kingshott, C. A. M., Zhang, H., &
Alexander, D. C. (2013). The importance of being dispersed: A ranking of
diffusion MRI models for fibre dispersion using in vivo human brain data.
Proceedings of Medical Image Computing and Computer Assisted Intervention,
16(Part I), 7481.
Fieremans, E., Novikov, D. S., Jensen, J. H., & Helpern, J. A. (2010). Monte Carlo study
of a two-compartment exchange model of diffusion. NMR in Biomedicine, 23,
711724.
Figini, M., Alexander, D. C., Fasano, F., Farina, L., Baselli, G., Tagliavini, F., et al.
(2012). Mathematical models of diffusion in prion disease. In: Proceedings of the
Italian chapter of the international society for magnetic resonance in medicine.
Hosey, T., Williams, G., & Ansorge, R. (2005). Inference of multiple fiber orientations in
high angular resolution diffusion imaging. Magnetic Resonance in Medicine, 54,
14801489.
Ianus, A., Siow, B. M., Drobnjak, I., & Alexander, D. C. (2012). Gaussian phase
distribution approximations for oscillating gradient spin echo diffusion MRI.
Jacobs, B., Schall, M., & Scheibel, A. B. (1993). A quantitative dendritic analysis of
Wernickes area in humans. II. Gender, hemispheric, and environmental factors.
Journal of Comparative Neurology, 327, 97111.
Jbabdi, S., Sotiropoulos, S. N., Savio, A. M., Grana, M., & Behrens, T. E.J (2012).
over fitting problems. Magnetic Resonance in Medicine, 68, 18461855.
Jespersen, S. N. (2012). Equivalence of double and single wave vector diffusion
contrast at low diffusion weighting. NMR in Biomedicine, 25, 813818.
Jespersen, S. N., Bjarkam, C. R., Nyengaard, J. R., Chakravarty, M. M., Hansen, B.,
Vosegaard, T., et al. (2010). Neurite density from magnetic resonance diffusion
measurements at ultrahigh field: Comparison with light microscopy and electron
microscopy. NeuroImage, 49, 205216.
Jespersen, S. N., Kroenke, C. D., Ostergaard, L., Ackerman, J. J.H, & Yablonskiy, D. A.
(2007). Modeling dendrite density from magnetic resonance diffusion
measurements. NeuroImage, 34, 14731486.
Jespersen, S. N., Leigland, L. A., Cornea, A., & Kroenke, C. D. (2012). Determination of
axonal and dendritic orientation distributions within the developing cerebral cortex
by diffusion tensor imaging. IEEE Transactions on Medical Imaging, 31, 1632.
Kaden, E., & Alexander, D. C. (2013). Can T2-spectroscopy resolve submicrometer
axon diameters? Proceedings of Information Processing in Medical Imaging, 23,
607618.
Kaden, E., Knosche, T. R., & Anwander, A. (2007). Parametric spherical deconvolution:
Inferring anatomical connectivity using diffusion MR imaging. NeuroImage, 37,
474488.
Karger, J., Pfeifer, H., & Heink, W. (1988). Principles and applications of self-diffusion
measurements by nuclear magnetic resonance. Advances in Magnetic Resonance,
12, 189.
Koch, M. A., & Finsterbusch, J. (2011). Towards compartment size estimation in vivo
based on double wave vector diffusion weighting. NMR in Biomedicine, 24,
14221432.
Komlosh, M. E., Ozarslan, E., Lizak, M. J., Horkayne-Szakaly, I., Friedlin, R. Z.,
Horkay, F., et al. (2013). Mapping average axon diameters in porcine spinal cord
white matter and rat corpus callosum using d-PFG MRI. NeuroImage, 78, 210216.
Kuder, T. A., Bachert, P., Windschuh, J. and Laun, F. B. (2013). Diffusion pore imaging
by hyperpolarized Xenon-129 Nuclear Magnetic Resonance. Physical Review
Letters, 111, 028101.
Kuder, T. A., & Laun, F. B. (2013). NMR-based diffusion pore imaging by double wave
vector measurements. Magnetic Resonance in Medicine, 70, 836841.
Lamantia, A.-S., & Rakic, P. (1990). Cytological and quantitative characteristics of four
cerebral commissures in the rhesus monkey. Journal of Comparative Neurology,
291, 520537.
Lasic, S., Nilsson, M., Latt, J., Stahlberg, F., & Topgaard, D. (2011). Apparent
exchange rate mapping with diffusion MRI. Magnetic Resonance in Medicine, 66,
356365.
Latt, J., Nilsson, M., van Westen, D., Wirestam, R., Stahlberg, F., & Brockstedt, S.
(2009). Diffusion-weighted MRI measurements on stroke patients reveal waterexchange mechanisms in sub-acute ischaemic lesions. NMR in Biomedicine, 22,
619628.
Laun, F. B., Kuder, T. A., Semmler, W., & Stieltjes, B. (2011). Determination of the
defining boundary in nuclear magnetic resonance diffusion experiments. Physical
Review Letters, 107, 048102.
Lawrenz, M., & Finsterbusch, J. (2011). Detection of microscopic diffusion anisotropy
on a whole-body MR system with double wave vector imaging. Magnetic Resonance
in Medicine, 66, 14051415.
Lawrenz, M., & Finsterbusch, J. (2013). Double-wave-vector diffusion-weighted
imaging reveals microscopic diffusion anisotropy in the living human brain.
Mardia, K. V., & Jupp, P. E. (1990). Directional statistics: Wiley series in probability and
statistics. Chichester: Wiley.
McNab, J. A., Edlow, B. L., Witel, T., Huang, S. Y., Bhat, H., Heberlein, K., et al. (2013).
The human connectome project and beyond: Initial applications of 300 mT m 1
gradients. NeuroImage, 80, 234245.
Meier, C., Dreher, W., & Leibfritz, D. (2003). Diffusion in compartmental systems. I. A
comparison and an analytical model with simulations. Magnetic Resonance in
Medicine, 50, 500509.
Merboldt, K.-D., Hanicke, W., & Frahm, J. (1985). Self-diffusion NMR imaging using
stimulated echoes. Journal of Magnetic Resonance, 64, 479486.
Nilsson, M., Alerstam, E., Wirestam, R., Stahlberg, F., Brockstedt, S., & Latt, J. (2010).
Evaluating the accuracy and precision of a two-compartment Karger model using
Monte Carlo simulations. Journal of Magnetic Resonance, 206, 5967.
Nilsson, M., Latt, J., Nordh, E., Wirestam, R., Stahlberg, F., & Brockstedt, S. (2009). On
the effects of a varied diffusion time in vivo: Is the diffusion in white matter
restricted? Magnetic Resonance Imaging, 27, 176187.
Nilsson, M., Latt, J., Stahlberg, F., van Westen, D., & Hagslatt, H. (2012). The
importance of axonal undulation in diffusion MR measurements: A Monte Carlo
simulation study. NMR in Biomedicine, 25, 795805.
Nilsson, M., Latt, J., Wirestam, R., Stahlberg, F., Karlsson, N., Johansson, M., et al.
(2013). Noninvasive mapping of water diffusional exchange in the human brain
using filter-exchange imaging. Magnetic Resonance in Medicine, 69, 15721580.
Ozarslan, E., & Basser, P. J. (2008). Microscopic anisotropy revealed by NMR double
pulsed field gradient experiments with arbitrary timing parameters. Journal of
Chemical Physics, 128, 154511.
Panagiotaki, E., Schneider, T., Siow, B. M., Hall, M. G., Lythgoe, M. F., &
Alexander, D. C. (2012). Compartment models of the diffusion signal in brain white
matter: A taxonomy and comparison. NeuroImage, 59, 22412254.
Panagiotaki, E., Walker-Samuel, S., Siow, B. M., Johnson, P., Pedley, R. B.,
Lythgoe, M. F., et al. (2013). In vivo characterisation of colorectal tumour
microstructure with DW-MRI. In: Proceedings of the international society for
magnetic resonance in medicine, 2105.
Perry, V. H. (2001). Microglia in the developing and mature central nervous system. In
K. R. Jessen & W. D. Richardson (Eds.), Glial cell development: Oxford: Oxford
University Press.
Portnoy, S., Flint, J. J., Blackband, S. J., & Stanisz, G. J. (2013). Oscillating and pulsed
gradient diffusion magnetic resonance microscopy over an extended b-value range:
Implications for the characterization of tissue microstructure. Magnetic Resonance
in Medicine, 69, 11311145.
Price, W. S. (2009). NMR studies of translational motion: Principles and applications.
Cambridge: Cambridge University Press.
Proverbio, A., Siow, B. M., Alexander, D. C., & Gibson, A. (2013). Multimodality
investigation of microstructures by the combination of diffusion NMR and diffuse
optical spectroscopy. In: Proceedings of the international society for magnetic
resonance in medicine, 3129.
Ramirez-Mananares, A., Rivera, M., Vemuri, B. C., Carney, P., & Mareci, T. (2007).
Diffusion basis functions decomposition for estimating white matter intravoxel fiber
geometry. IEEE Transactions on Medical Imaging, 26, 10911102.
Reichenbach, A., & Wolburg, H. (2005). Astrocytes and ependymal glia. In H.
Kettenmann, & B. R. Ransom (Eds.), Neuroglia: Oxford University Press.
Sakaie, K. E., & Lowe, M. J. (2007). An objective method for regularization of fiber
orientation distributions derived from diffusion-weighted MRI. NeuroImage, 34,
169176.
Scherrer, B., Schwartzman, A., Taquet, M., Prabhu, S. P., Sahin, M., Akhondi-Asl, A.,
et al. (2013). Characterizing the DIstribution of Anisotropic MicrO-structural
eNvironments with Diffusion-weighted imaging (DIAMOND). Proceedings of
Seunarine, K. K., & Alexander, D. C. (2009). Multiple fibers: Beyond the diffusion
tensor. In H. Johansen-Berg & T. E. J. Behrens (Eds.), Diffusion MRI: From
quantitative measurement to in vivo neuroanatomy: London: Academic Press.
Shemesh, N., Barazany, D., Sadan, O., Bar, L., Zur, Y., Barhum, Y., et al. (2012).
Mapping apparent eccentricity and residual ensemble anisotropy in the gray matter
using angular double-pulsed-field-gradient MRI. Magnetic Resonance in Medicine,
68, 794806.
Shemesh, N., Ozarslan, E., Komlosh, M. E., Basser, P. J., & Cohen, Y. (2010). From
single-pulsed field gradient to double-pulsed field gradient MR: Gleaning new
285
microstructural information and developing new forms of contrast in MRI. NMR in

Shemesh, N., Westin, C.-F., & Cohen, Y. (2012). Magnetic resonance imaging
by synergistic diffusion-diffraction patterns. Physical Review Letters, 108, 058103.
Sherbondy, A. J., Rowe, M. C., & Alexander, D. C. (2010). MicroTrack: An algorithm for
concurrent projectome and microstructure estimation. Proceedings of Medical
Image Computer and Computer Assisted Intervention, 13, 183190.
Siow, B. M., Drobnjak, I., Ianus, A., Christie, I., & Alexander, D. C. (2013). Pore size
estimation with oscillating gradient spin echo (OGSE) diffusion NMR.
In Proceedings of magnetic resonance in porous media.
Solenov, E., Watanabe, H., Manley, G. T., & Verkman, A. S. (2004). Sevenfold-reduced
osmotic water permeability in primary astrocyte cultures from AQP-4-deficient mice,
measured by a fluorescence quenching method. American Journal of Physiology Cell Physiology, 286, C426C432.
Sotiropoulos, S. N., Behrens, T. E.J, & Jbabdi, S. (2012). Ball and rackets: Inferring
fiber fanning from diffusion-weighted MRI. NeuroImage, 60, 14121425.
Stanisz, G. J., Wright, G. A., Henkelman, R. M., & Szafer, A. (1997). An analytical model
of restricted diffusion in bovine optic nerve. Magnetic Resonance in Medicine, 37,
103111.
Stein, W. D. (1967). The movement of molecules across cell membranes. London:
Academic Press.
presence of a time-dependent field gradient. Journal of Chemical Physics, 42,
288292.
Tournier, J.-D., Calamante, F., & Connelly, A. (2007). Robust determination of the fibre
orientation distribution in diffusion MRI: Non-negativity constrained super-resolved
Tournier, J.-D., Calamante, F., Gadian, D. G., & Connelly, A. (2004). Direct estimation
of the fiber orientation density function from diffusion-weighted MRI data using
Tournier, J.-D., Mori, S., & Leemans, A. (2011). Diffusion tensor imaging and beyond.
Van, A. T., Holdsworth, S. J., & Bammer, R. (2013). In vivo investigation of restricted
diffusion in the human brain with optimized oscillating diffusion gradient encoding.
Wang, Y., Wang, Q., Haldar, J. P., Yeh, F. C., Xie, M., Sun, P., et al. (2011).
Quantification of increased cellularity during inflammatory demyelination. Brain,
134, 35903601.
Waxman, S. G. (Ed.), (1995). The axon: Structure, function and pathophysiology.
Oxford: Oxford University Press.
Winston, G. P., Symms, M. R., Alexander, D. C., Duncan, J. S., & Zhang, H. (2013).
Clinical utility of NODDI in assessing patients with epilepsy due to focal cortical
dysplasia. In: Proceedings of the International Society of Magnetic Resonance in
Medicine, 784.
Xu, J., Does, M. D., & Gore, J. C. (2008). Sensitivity of MR diffusion measurements to
variations in intracellular structure: Effects of nuclear size. Magnetic Resonance in
Medicine, 61, 828833.
Zhang, H., & Alexander, D. C. (2010). Axon diameter mapping in the presence of
orientation dispersion with diffusion MRI. Proceedings of Medical Image
Computing and Computer Assisted Intervention, 13, 640647.
Zhang, H., Hubbard, P. L., Parker, G. J.M, & Alexander, D. C. (2011). Axon diameter
mapping in the presence of orientation dispersion with diffusion MRI. NeuroImage,
61, 13011315.
Zhang, H., Schneider, T., Wheeler-Kingshott, C. A.M, & Alexander, D. C. (2012).
NODDI: Practical in vivo neurite orientation dispersion and density imaging of the
human brain. NeuroImage, 61, 10001016.
Tissue Properties from Quantitative MRI

G Helms, Medical Radiation Physics, Lund University, Lund, Sweden
Glossary
Amide group Functional NHCO group in proteins and

peptides.
Cross relaxation Simultaneous flip of two opposing spins
at close range.
Ferritin Globular protein shell for intracellular storage of
iron (ferrihydrite).
Image Magnitude image of mixed contrast in integers with
arbitrary scaling.
Larmor frequency Precession frequency of transverse
magnetization, proportional to local B0 field experienced by
the protons.
Map Image(s) encoding the value of a physical parameter
(scalar, vector, or tensor) estimated from multiple images
acquired with a varying parameter.
Nomenclature
APT
B0
CA
Dapp
DT
EES
f0
FA
GE
kA!B and kB!A
MD
MDD
Microscopic Features of a size accessible by a light

microscope (as in histology) below the theoretical
resolution of MRI.
Phase image Image of p to p phase interval with arbitrary
zero.
Relaxation Processes restoring equilibrium longitudinal
magnetization (T1) and dephasing coherent transverse
magnetization (T2 and T2*).
Relaxivity Constant describing the proportionality between
concentration of contrast agent and induced change in
relaxation rate.
Self-diffusion Random translation motion in the absence
of a concentration gradient.
Tortuosity Restriction of self-diffusion in a porous space.
MT
Amide proton transfer
Static magnetic field in tesla (usually 1.5 T
or 3 T)
Contrast agent
Apparent diffusion coefficient/diffusivity
observed in tissue in ml/100 g min1
Diffusion tensor
Extracellular extravascular space
Larmor frequency offset in Hz difference
of local Larmor precession to RF carrier
frequency
Fractional anisotropy, derived from the
diffusion tensor
Gradient echo, without refocusing
radiofrequency pulse
Exchange rates proportionality (firstorder) constants describing an
equilibrium between the numbers in
states A and B (nA/B): kA!BnA kB!AnB
Mean diffusivity, derived from the
diffusion tensor
Main diffusion direction, derived from the
diffusion tensor
Principle of qMRI
In quantitative MRI (qMRI), biophysical properties that govern
the MRI signal are calculated from multiple colocalized MR
images, which have been acquired by varying the corresponding parameter in the pulse sequence. For example, spin echo
(SE) images obtained at different echo times (TE) yield the
PD
R1, R2, and R2*
rCBF
rCBV
rMTT
T1, T2, and T2*
TE
xm
Magnetization transfer interaction of

mobile water and protons associated with
macromolecules
Proton density relative concentration of
mobile, MR-visible water in tissue
Rate constants of longitudinal,
transverse, and effective transverse
relaxation
Regional cerebral blood flow in ml/
100 g min1
Regional cerebral blood volume in ml/
100 g
Mean transit time of blood
Time constants of longitudinal,
transverse, and effective transverse
relaxation
Echo time time between excitation pulse
and detection of signal
Magnetic susceptibility proportionality
constant between external magnetic
field and induced change in
magnetic field in matter (diamagnetic
wm < 0 and paramagnetic wm > 0)
transverse relaxation time, T2; gradient echo (GE) images

yield the effective transverse relaxation time, T2*. These parameter maps (of T2 or T*)
2 depict the average property of the tissue
captured in the underlying voxels. Since this cancels the arbitrary scaling of the images and the inhomogeneity of the
receive coils, maps are reproducible within errors and can
thus be compared longitudinally and between cohorts using
http://dx.doi.org/10.1016/B978-0-12-397025-1.00297-9
287
288
INTRODUCTION TO METHODS AND MODELING | Tissue Properties from Quantitative MRI
region-of-interest or voxel-based statistical analysis (Draganski

et al., 2011). Maps of physiological parameters (e.g., of vascular perfusion) are derived from dynamic models. Experiments
and models differ in resolution and level of sophistication,
with the aim to reduce bias and improve reproducibility.
The credo of qMRI is that these biophysical parameter maps
are more specific for the microscopic structure of tissue than
the mixed contrast of images. Development in infancy and
childhood (myelination and iron accumulation) imposes distinct changes on the biophysical parameters, while changes in
the aging adult brain are more subtle (Draganski et al., 2011).
Disease-related changes can be localized and dynamic (in
lesions) or widespread and sublime.
This article explains the mechanisms through which microscopic properties of brain tissue influence the observed biophysical parameters. Methods and models of qMRI are detailed
in textbooks (e.g., Johansen-Berg & Behrens, 2009; Tofts,
2003) and numerous reviews.
Dynamic Field Effects: Relaxation

The biophysical parameters related to SE and GE sequences
employed for conventional MRI are the proton density (PD)
and the relaxation times T1 and T2 (SE) and T2* (GE). In the
context of qMRI, however, the corresponding rate constants,
that is, the inverse of relaxation times (Rx 1/Tx), are often
reported since these are more directly linked to concentrations
and compartment sizes.
Mobile Water and Immobile Macromolecules

Relaxation is induced by the nuclear magnetic moments
experiencing a randomly varying magnetic field due to molecular thermal motion at 37 C. The main processes at the intraor intermolecular scale are dipoledipole interaction and/or
exchange of protons. Protons of rotationally restricted macromolecules or tightly associated water (sometimes referred to as
structural material) are MRI-invisible because their transverse magnetization decays rapidly with a T2 of about 10 ms
(Edzes and Samulski, 1978). The observed MR signal originates from mobile (free) water molecules, which have a sufficiently long T2. Estimates of PD are extrapolated from short
TE in multiecho SE (Whittall et al., 1997) or GE sequences
(Neeb, Zilles, & Shah, 2006) and usually reported as percentage of the protons in pure water (111 mol l1). Since the
mobile water molecules probe their environment, the observed
biophysical properties depend on brain microstructure. This
term is used in analogy to histology comprising neuronal
bodies, unmyelinated and myelinated axons, glial cells, vessels,
and extracellularextravascular space (EES). Water diffuses
over distances exceeding the typical cell size, the mean displacement by diffusion within TE being roughly 525 mm.
Thus, local relaxation properties are averaged, which constitutes a theoretical boundary of image resolution (Callaghan,
1991). Typical scales are given in Table 1.
Since the observed relaxation parameters depend on thermal molecular motion, these will change with temperature.
Most notable at lower temperature is a reduction of T1 and of
diffusion. On the other hand, these parameters may be used for
Table 1
Regimes of spatial scales in qMRI
Intra- and
intermolecular
Microscopic
Mesoscopic
Macroscopic
Dipoledipole interactions
<1 nm
< Diffusion, microcompartmental

exchange
Partial volume mean diffusion
length
MRI voxel
<10 mm
100 mm
1 mm
thermometry, if the dependence is sufficiently strong and can

be calibrated.
Microenvironments and Exchange

The microenvironments of water that are relevant for qMRI are
capillary, vascular, intracellular, extracellularextravascular,
and myelin subspaces. Practically all MR parameters are
explained in terms of these. They feature distinct physical
properties but are subject to exchange of water. To measure
the individual relaxation properties (e.g., R2A and R2B) of two
environments (or pools A and B), the exchange rates kA!B and
kB!A must be much smaller than the difference of the relaxation rates. The condition
kA!B kB!A absR2A R2B
[1]
indicates slow exchange with respect to T2 relaxation, so the

environments form compartments. In the case of fast
exchange
kA!B kB!A absR1A R1B
[2]
(here for T1 relaxation), a single component is observed at an

average rate
R1 nA R1A nB R1B
[3]
where the local rates (R1A and R1B) are weighted by the relative
number of protons (nA and nB). It has been established that the
water permeability of a single phospholipid bilayer (or cell
wall) is too high to allow for compartmentalization of extraand intracellular spaces (Koenig & Brown, 1985). Intermediate
exchange or weakly coupled conditions also lead to biexponential behavior, but other than for compartments
the observed rates and amplitudes deviate from the individual
values. Note that multiple exponential components are rather
difficult to fit reliably.
Diffusion and fast exchange conditions are the reasons why
the observed relaxation is mainly monoexponential. This is
well obeyed by R1, since R1 is smallest and subject to less
variation than R2. Equation [3] can be transformed into a
correlation between R1 and the inverse water content, which
has been confirmed experimentally (Kamman, Go, Brouwer, &
Berendsen, 1988), and in vivo at 3 T (Gelman et al., 2001)
albeit neglecting major ferritin stores.
Magnetization transfer (MT) imaging specifically targets
cross relaxation and exchange between macromolecules and
water. These processes are described by the same mathematics
and cannot be distinguished. MT contrast is evoked by implementing additional off-resonance radiofrequency (RF) pulses
into SE or GE MRI sequences. Such an MT pulse reduces the
which so far has not been fully determined in vivo. The

exchange of the visible pools of myelin water and intra-/
extracellular water has recently been fitted to variable flip
angle experiments, albeit neglecting MT effects (Deoni, Rutt,
Arun, Pierpaoli, & Jones, 2008).
longitudinal magnetization of the macromolecules but has

little effect on the free water. This saturation is then transferred
to the water (transfer time 25 ms parallel to T1 relaxation)
(Helms & Piringer, 2005) and observed as an attenuated signal
compared to the absence of pulses. In vivo MT measurements
are quantified by a two-pool model of free water (A) and
bound macromolecules (B), also called binary spin bath
(Sled & Pike, 2001), at various degrees of sophistication.
Most relevant parameters are the macromolecular fraction, nB,
and the forward transfer rate kA!B. The bound pool is two to
three times larger in the white matter (WM, 11%) than in
the gray matter (GM, 4%), much smaller in blood, and practically absent in the cerebrospinal fluid (CSF; Graham &
Henkelman, 1999).
Iron in the Brain

Iron is the most abundant paramagnetic trace element (30 times
than all others combined) but nonuniformly distributed in the
body and brain. Nonheme iron increases during maturation
with highest concentrations being observed in the nuclei of the
extrapyramidal motor system, especially the globus pallidus and
the reticular substantia nigra (Hallgren and Sourander, 1958).
Via the magnetic moment of its unpaired electrons, iron acts as
intrinsic contrast agent (CA). The magnetic moment of iron
depends on the molecular compound. Best known from fMRI
is the difference between oxyhemoglobin and deoxyhemoglobin in red blood cells. Cellular nonheme iron is covalently linked to or a cofactor of many enzymes. Excess iron is
stored within the protein ferritin or removed by macrophages in
the form of hemosiderin. Ferritin is a globular protein containing up to 4500 atoms of ferric iron (Fe(III), revealed by Perls
staining). Its magnetic moment increases with B0 (paramagnetic) because the ferritin core is largely antiferromagnetic
(Brooks, Vymazal, Goldfarb, Bulte, & Aisen, 1998). Since other
forms of iron are not aggregated or less abundant (Morris,
Candy, Oakley, Bloxham, & Edwardson, 1992), ferritin dominates the influence on relaxation.
Transverse magnetization is dephased by diffusion of water
through the inhomogeneous field (outer sphere relaxation), so
R2* and (less so) R2 are increased. Iron-rich structures thus
appear hypointense on T2- and T2*-weighted MRI (Drayer
et al., 1986). The relaxivities increase linearly with B0, so at
Myelin
Bundles of myelinated axons feature a highly ordered microstructure, which is the main source of contrast between GM
and WM. The myelin sheath consists of tightly wrapped multiple phospholipid membranes with embedded proteins. Myelin shortens T1 and decreases PD, because the invisible lipid
protons do strongly interact with water protons (Koenig,
Brown, Spiller, & Lundbom, 1990). Because exchange across
multiple membranes efficiently lowers the permeability, myelin water is trapped inside the sheath and forms a separate
compartment. Cross relaxation shortens T2 to about 15 ms
(MacKay et al., 1994). The myelin water fraction (Figure 1)
can be estimated by constrained inversion of multiple SEs onto
a grid of T2 values (Whittall et al., 1997). Intra- and extraaxonal water cannot be not discerned by T2. Myelin water
strongly contributes to MT, as derived from a four-pool
model (Stanisz, Kecojevic, Bronskill, & Henkelman, 1999),
60
80
100
120
mono-T2 (ms)
140
289
5
10
15
Myelin water fraction, MWF (%)
20
Figure 1 T2 relaxation time and myelin water fraction in a healthy adult. Pseudocolor maps of single exponential T2 (left) and an overlay of myelin water
fraction (MWF, right). The MWF was obtained at 3 T from a constrained inversion of 32 spin echoes; TE being multiples of 10 ms. The mono T2
values in WM are inversely correlated to MWF. The dots are external phantoms. Data courtesy of B. Madler, Bonn, Germany.
290
3 T and 7 T, a good correlation of R2* and nonheme iron

content has been established (Gelman et al., 1999; Yao et al.,
2009). Ferritin has a smaller effect on R1, which is yet enough
to make the globus pallidus appear similar to WM.
In summary, the major sources of structural MRI contrast
in the brain are the amount of macromolecules, the density of
myelinated axons, and the storage of nonheme iron. Table 2
gives a synopsis over the varying degrees of sensitivity of contrast parameters to macromolecules and iron. Multiparametric
information (R1, R2*, MT, and PD; Figure 2) can be obtained at
high resolution by multiecho FLASH approach (Draganski
et al., 2011). R1 and MT seem particularly suitable to depict
the axonal content of cortical areas (Figure 2; Dick et al., 2012)
or in the thalamus (Gringel et al., 2009). Yet,
Table 2
monoexponential relaxation parameters are far from being

specific for a certain source. For instance, it is difficult to
discern reduced myelin from extracellular edema in WM
lesions by relaxation alone.
Static Field Effects: Magnetic Susceptibility

Tissue reacts to the external static magnetic field of the scanner
(B0) by a small proportional change (DB0) that is characterized
by the magnetic susceptibility, wm:
DB0 wm B0
Water and fat are diamagnetic, meaning that small currents

slightly reduce the internal field according to Lenzs law by
about 106 (1 ppm). At 37 C, fat (wm 8.44 ppm) is less
diamagnetic than water (9.05 ppm). The presence of molecular magnetic dipoles that align to B0 (e.g., deoxyhemoglobin or
ferritin core) increases the local field at the microscopic level
(wm > 0), depending on dipole strength and concentration.
Brain tissue susceptibility varies within a range of 0.3 ppm
(Figure 3). Because differences in wm are detected via the Larmor
frequency offset (f0), high B0 fields increase the sensitivity.
Main sources of contrast and MR relaxation parameters
R2*
R2
R1
MT
Iron
Structural
Myelin discernible?
Strong
Medium
Small
None
Small
Medium
Strong
Strong
Anisotropy at high B0
Biexponential in WM
Monoexponential
Monoexponential
Magnitude (a.u)
WM
R2 (sec1)
R1 (sec1)
MT saturation (%)
GM
GM
GM
WM
WM
WM
CSF
[4]
GM
Blood
CSF
High
iron
CSF
Veins
CSF
4000 5000 6000 7000 8000 9000 1e+04 -0.5
(a)
(b)
0.5
1.5
2.5
(c)
0.2
0.4
0.6
0.8
1.2
1.4
10
20
30
40
50
60
(d)
Figure 2 GE-based relaxation parameter maps. Top: Parameter maps of signal magnitude (a), MT saturation (b), R1 (c), and R*2 (d) in a healthy
adult as acquired with 1 mm isotropic resolution at 3 T as in Draganski et al. (2011). Bottom: Histograms show the distribution of values in the
brain and show typical values for CSF, GM, and WM. MT is a structural contrast and insensitive to iron. Low MT reveals the high water content in
large vessels. The offset of WM compared to GM is due to the presence of myelin. R1 is mainly structural and thus similar to MT. The globus pallidus
appears similar to WM (arrow) indicating the influence of tissue iron. R*2 shows little structural contrast between GM and WM. Highly ordered fiber
bundles perpendicular to B0 (optic radiation and callosal fibers) display slightly higher values. The high sensitivity to iron enhances R2* in the
striatum and most prominently in the globus pallidus (arrow). Very high values (R2* > 50 s1) are observed in veins and meninges, enhancing
even smaller vessels, as seen in the genu of the corpus callosum.
Average R1 vs cortical depth in

probabilistic ROI of auditory core
291
Cross-subject-average R1 values sampled at 50% of

cortical depth onto inflated cortical surface
nt
lc
su
Ce
R1 (sec1)
0.8
Left hemisphere
TE 1.0 (core)
TE 1.1 (lateral)
TE 1.2 (medial)
0.7
ula
Ins
hls
sc
rus
gy
He
0.6
ral
or
ri
pe
0.5
Su
Wallace et
al. (2002)
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1

Deep
Superficial
(a)
Right hemisphere
Cortical depth fraction
rus
gy
o
mp
te
erio
Sup
0.70
ulcu
ral s
po
r tem
1 cm
R1
(sec1)
0.675
0.65
(b)
Figure 3 Mapping axonal content of cortical areas by R1. (a) Relaxation rate R1 (in sec1) as function of cortical depth, averaged within
probabilistically defined subdivisions of Brodmanns area 41. (b) Auditory core of Herschels gyrus depicted by a thresholded overlay of R1 at 50%
cortical depth. R1 mapping was performed at 3 T at 0.8 mm isotropic resolution with pertinent processing. Reproduced from Figure 2 of Dick, F.,
Tierney, A.T., Lutti, A., Josephs, O., Sereno, M.I., Weiskopf, N. (2012). In vivo functional and myeloarchitectonic mapping of human primary auditory
areas. Journal of Neuroscience, 32, 1609516105, with permission.
Highly myelinated WM of the internal capsule exhibits the

lowest susceptibilities in the brain, about 0.1 ppm lower than
in the cortex. The highest values are found in ferritin-rich deep
brain nuclei (Deistung et al., 2013). Venous blood has a particularly high susceptibility (>0.15 ppm higher than cortex). The
field inhomogeneities caused by regions of differing local susceptibility (like capillaries and veins) extend beyond the size of
these structures. They also depend on geometry and orientation
with respect to the B0 direction. The distribution of f0 in a
macroscopic voxel affects the GE signal phase (evolving during
TE with mean f0) and magnitude (by dephasing of transverse
relaxation). Since a GE is more rapidly dephased than an SE, it is
more sensitive to detect such microscopic inhomogeneities and
also increasingly sensitive to larger veins (! 100 mm)
(Boxerman, Hamberg, Rosen, & Weisskoff, 1995). This effect
of vasculature is also exploited in T2- or T2*-based dynamic
contrast enhancement (DCE: see succeeding text).
Phase images have a higher signal-to-noise ratio than magnitude images allowing for higher resolution. For venography,
changes in mean susceptibility can be highlighted by a spatial
high-pass filter of the phase image to impose a susceptibility
weighting onto the magnitude GE image (Reichenbach et al.,
1997). Phase-based susceptibility techniques can distinguish
between paramagnetic hemorrhage and diamagnetic calcification (Gupta et al., 2001).
In tissues with anisotropic microstructure (e.g., axonal
fibers), the relative orientation to the magnetic field affects
the observed f0 and R2*. The susceptibility can be estimated
from multiple phase images at tilted head positions
(Deistung et al., 2013). Such maps overcome the orientation
dependence of f0 and R2*, showing excellent delineation of
deep brain structures and subcortical U-fibers (Figure 4).
As static effects increase with B0, the corresponding parameters R*
2 and susceptibility become more sensitive. Both are
highly correlated in iron-rich GM at ultrahigh field strengths
(Figure 4) and provide a suitable measure for tissue iron
content (Yao et al., 2009). The presence of myelin can be

confounding since it increases R2* and decreases wm.
Diffusion-Weighted Imaging
The MRI signal is sensitized to self-diffusion, that is, the random translational motion of water, by an SE preparation with
pulsed field gradients for dephasing and refocusing of transversal magnetization (Johansen-Berg & Behrens, 2009). The
motion component along the direction of the gradient results
in incomplete refocusing and, thus, an attenuation of the
signal S0:

Sb S0 exp Dapp g2 G2 d2 D d=3 S0 exp Dapp b [5]
One commonly speaks of an apparent diffusion coefficient
(Dapp, approx. 0.7 mm2 ms1), because the observed attenuation is influenced by direction, amplitude (G), duration (d) of
the gradient pulses, and the diffusion time lag (D) between the
gradient pulses. The influence of these parameters are combined into the diffusion-weighting parameter b, which typically takes values around 1000 s mm2 1 ms mm2 in a
clinical setting. Equation [5] implicitly assumes consistent
Gaussian distributions of displacements over the experimental
range of D, which implies that the root-mean-square displacement of water molecules increases linearly in time:
2
Ds 2Dapp D
[6]
In an isotropic environment, where Dapp does not depend
on direction, the three-dimensional displacement is obtained
by replacing 2 with 6. In tissue, diffusion is hindered by the
semipermeable cell membranes, which couple the diffusivity
in extra- and intracellular subspaces. Changed tortuosity in EES
and volume shifts between subspaces (vasogenic and cytotoxic
edema) are likely the dominant factors to explain alterations of
292
100
R*2 (s-1)
80
Cortical GM
Deep GM
WM
Internal capsule
60
40
20
-100
100
200
0
Susceptibility difference (ppb)
Figure 4 Gradient echo-derived maps of the deep brain region at 7 T. In deep GM nuclei, R2* and susceptibility are highly correlated, indicating the
dominant influence of ferritin on both parameters (right, red dots). Iron-containing nuclei and WM tracts are sharply depicted on the susceptibility
map (lower left), which is independent on the direction of B0. Outlines in susceptibility appear blurred on frequency and R*2 maps. Mapping was performed
at 7 T at 0.4 mm isotropic resolution. Reproduced from graphical abstract of Deistung, A., Schafer, A, Schweser, F., Biedermann, U., Turner, R., &
Reichenbach, J.R. (2013). Toward in vivo histology: A comparison of quantitative susceptibility mapping (QSM) with magnitude-, phase-, and R2-imaging at
ultra-high magnetic field strength. NeuroImage, 65, 299314, with permission.
Dapp (Norris, 2001) in acute ischemia, tumors, and myelin

disorders. Since a decrease of Dapp is correlated to myelination
during development (Mukherjee et al., 2001), the slowly
exchanging intra-axonal component is an additional factor in
WM to explain Dapp and the anisotropy along the WM tracts,
which is lower but discernible at preterm (Huppi et al., 1998).
In the axon bundles of WM, diffusion is anisotropic. The
simplest model to describe the directional dependence of Dapp
is an ellipsoid, the diffusion tensor (DT). The main diffusion
direction (MDD) is that along the parallel axons. The mean
Dapp over all directions is mean diffusivity (MD). The degree of
anisotropy most widely used is the fractional anisotropy
(FA) is a scalar measure for axonal coherence. Increased
MD and reduced FA are the hallmarks of demyelination
(Figure 5).
The DT is a rather simplified model to describe diffusion in
brain tissue. First, it is not suited to describe the partial volume
effects arising from crossing axonal fibers. Second, DT imaging
measurements are often performed at just one value of b; D,
and d. Since tissue microstructure hinders diffusion at a wide
range of spatial and temporal scales, deviations from the monoexponential behavior of eqn [5] (or Gaussian distribution of
displacement) can be detected in the brain. Advanced concepts
comprise measurements at high angular resolution, at high b
values, q-space sampling (Callaghan, 1991), and advanced
models, for example, to assess axonal diameter (Alexander
et al., 2010). Thus, in a narrow sense, the term microstructure
has become connotated with diffusion imaging.
electrons and short-range intramolecular exchange; the latter

increase R*
2 (less so R2 and R1) by diffusion through the inhomogeneous B0 field. The change in R1, R2, and R*2 is proportional to the concentration of the CA (expressed by the
corresponding relaxivity). In particular, iron oxide CAs
increase the susceptibility in the vessels.
Vascular perfusion of tissue can be estimated from the DCE
after an intravascular bolus of gadolinium CA (Tofts, 2003). The
three physiological parameters of perfusion are regional cerebral
blood volume (rCBV, the partial volume of blood in the voxel),
regional cerebral blood flow (rCBF, the flow of blood through
the voxel), and the mean transit time (rMTT), where
rMTT rCBV/rCBF. As the bolus passes through the brain, the
relaxation times are shortened reflecting the rCBV and the vascular CA concentration. The temporal resolution has to be
sufficiently high to determine the arterial input function, that
is, the time course in a supplying artery, which is then deconvoluted from the slower time course in the tissue of the
first bolus. The T2*-weighted GE yields a larger signal change,
but a poorer representation of perfusion. T1 mapping is usually
too slow for bolus tracking but can be used to measure the slow
extravasation of CA into the EES (1020 min).
Arterial spin labeling techniques do not require CA
because the magnetization in an upstream slab is tagged by
RF (Williams, Detre, Leigh, & Koretsky, 1992). The inflowing
arterial blood then reduces the signal in the slice of interest,
when compared to a control experiment. Multiple repetitions
are required since the difference is about 1%.
Perfusion Imaging with Contrast Agents
Mobile Proteins and pH
This qualitative reasoning also holds when the relaxation in the

vascular subspace is altered by MR CAs. These are based on
either chelated gadolinium (low-molecular-weight, paramagnetic) or coated nanoparticles of iron oxide (high-molecularweight, superparamagnetic). The former increases R1 (less so
R2 and R2*) by dipoledipole interaction with unpaired
Similar to MT is amide proton transfer (APT) (Zhou, Lal,

Wilson, Tryastman, & van Zijl, 2003), which detects endogenous mobile proteins and peptides by specifically saturating the
exchangeable proton of the amide groups at 3.5 ppm from the
Larmor frequency of water. A control experiment with irradiation at 3.5 ppm and kinetic modeling yields the concentration
CSF
GM
GM
WM
FA
Control
293
MD (mm2 ms1)
Control
WM
CSF
0
0.2
0.4
0.6
0.8
CSF
FA
GM
Lesion X-ALD
0.5
GM
WM
0.2
0.4
2.5
MD (mm2 ms1)
X-ALD
Lesion CSF
WM
1.5
0.6
0.8
0.5
1.5
2.5
Figure 5 Mean diffusivity (MD) and fractional anisotropy (FA) in healthy brain and demyelination. Top: Healthy teenager. Bottom: Boy with bilateral
lesions (arrow) due to X-linked adrenoleukodystrophy, a rapidly progressing inflammatory demyelinating disease. The CSF-like appearance probably
indicates axonal loss following demyelination. Left: Pseudocolor overlays on T1-weighted MRI and whole-brain histograms of FA. Even in isotropic
CSF and GM, nonzero FA is observed due to image noise. The threshold at 0.3 indicates that higher FA is confined to WM. Right: Pseudocolor
overlays and whole-brain histograms of MD. A single peak of WM and GM is observed 0.7 mm2 ms1. MD is strongly increased to 1.6 mm2 ms1 in the
lesion but smaller than in CSF. Diffusion measured at 3 T at 2.2 mm resolution as in Dreha-Kulaczewski et al. (2012).
of amide groups and the exchange rates. From the latter, the
intracellular pH can be derived. APT is a chemically selective
technique and chiefly used to study brain tumors.
Summary and Outlook

The essence of MRI is averaging as protons of mobile water
probe different environments in tissue from a molecular to
microscopic scale by rapid and slow exchange, respectively.
By choice of suitable MRI parameters, the sensitivity for certain
tissue properties (myelin, iron, axonal fibers, and vascular
spaces) is improved though specificity is often compromised.
Increasingly complex experiments and models are being developed to exploit nonexponential and anisotropic behavior or
account for sources of bias. Further progress is expected by the
use of ultrahigh fields enhancing resolution and static field
effects and multiparametric approaches.

Contrast Agents in Functional Magnetic Resonance Imaging; Diffusion
MRI; High-Field Acquisition; Myelin Imaging; Obtaining Quantitative
Information from fMRI; Perfusion Imaging with Arterial Spin Labeling
MRI; Susceptibility-Weighted Imaging and Quantitative Susceptibility
Mapping; INTRODUCTION TO CLINICAL BRAIN MAPPING: Brain
Inflammation, Degeneration, and Plasticity in Multiple Sclerosis;
Demyelinating Diseases; Functional Characteristics of Brain Tumor
Vascularization; Inflammatory Disorders in the Brain and CNS;
INTRODUCTION TO METHODS AND MODELING: Diffusion
Tensor Imaging; Probability Distribution Functions in Diffusion MRI;
Q-Space Modeling in Diffusion-Weighted MRI; Tissue Microstructure
Imaging with Diffusion MRI.
References
Alexander, D. C., Hubbard, P. L., Hall, M. G., Moore, E. A., Ptito, M., Parker, G. J., et al.
(2010). Orientationally invariant indices of axon diameter and density from diffusion
MRI. NeuroImage, 52, 13741389.
Medicine, 34, 555566.
Brooks, R. A., Vymazal, J., Goldfarb, R. B., Bulte, J. W., & Aisen, P. (1998). Relaxometry
and magnetometry of ferritin. Magnetic Resonance in Medicine, 40, 227235.
Callaghan, P. T. (1991). Principles of NMR microscopy. Oxford: Oxford University
Press.
susceptibility mapping (QSM) with magnitude-, phase-, and R2-imaging at ultrahigh magnetic field strength. NeuroImage, 65, 299314.
Deoni, S. C., Rutt, B. K., Arun, T., Pierpaoli, C., & Jones, D. K. (2008). Gleaning multicomponent T1 and T2 information from steady-state imaging data. Magnetic
Dick, F., Tierney, A. T., Lutti, A., Josephs, O., Sereno, M. I., & Weiskopf, N. (2012).
In vivo functional and myeloarchitectonic mapping of human primary auditory areas.
Draganski, B., Ashburner, J., Hutton, C., Kherif, F., Frackowiak, R. S. J., Helms, G., et al.
(2011). Regional specificity of MR contrast parameters in normal ageing revealed by
voxel-based quantification (VBQ). NeuroImage, 55, 14231434.
Drayer, B., Burger, P., Darwin, R., Riederer, S., Herfkens, R., & Johnson, G. A. (1986).
MRI of brain iron. AJR. American Journal of Roentgenology, 147, 103110.
Dreha-Kulaczewski, S. F., Brockmann, K., Henneke, M., Dechent, P., Gartner, J., &
Helms, G. (2012). Assessment of myelination in hypomyelinating disorders by
quantitative MRI. Journal of Magnetic Resonance Imaging, 36, 13291338.
Edzes, H., & Samulski, E. (1978). The measurement of cross-relaxation effects in the
proton NMR spinlattice relaxation of water in biological systems: Hydrated
collagen and muscle. Journal of Magnetic Resonance, 31, 207229.
Gelman, N., Ewing, J. R., Gorell, J. M., Spickler, E. M., & Solomon, E. G. (2001).
Interregional variation of longitudinal relaxation rates in human brain at 3.0 T:
Relation to estimated iron and water contents. Magnetic Resonance in Medicine, 45,
7179.
294
Gelman, N., Gorell, J. M., Barker, P. B., Savage, R. M., Spickler, E. M., Windham, J. P.,
et al. (1999). MR imaging of human brain at 3.0 T: Preliminary report on transverse
relaxation rates and relation to estimated iron content. Radiology, 210, 759767.
Graham, S. J., & Henkelman, R. M. (1999). Pulsed magnetization transfer imaging:
Evaluation of technique. Radiology, 212, 903910.
Gringel, T., Schulz-Schaeffer, W., Elolf, E., Frolich, A., Dechent, P., & Helms, G. (2009).
Optimized high-resolution mapping of magnetization transfer (MT) at 3 Tesla for
direct visualization of substructures of the human thalamus in clinically feasible
measurement time. Journal of Magnetic Resonance Imaging, 29, 12851292.
Gupta, R. K., Rao, S. B., Jain, R., Pal, L., Kumar, R., Venkatesh, S. K., et al. (2001).
Differentiation of calcification from chronic hemorrhage with corrected gradient
echo phase imaging. Journal of Computer Assisted Tomography, 25, 698704.
Hallgren, B., & Sourander, P. (1958). The effect of age on the non-haemin iron in the
human brain. Journal of Neurochemistry, 3, 4151.
Helms, G., & Piringer, A. (2005). Simultaneous measurement of saturation and
relaxation in human brain by repetitive magnetisation transfer pulses. NMR in
Huppi, P. S., Maier, S. E., Peled, S., Zientara, P. G., Barnes, P. D., Jolesz, F. A., et al.
(1998). Microstructural development of human newborn cerebral white matter
assessed in vivo by diffusion tensor magnetic resonance imaging. Pediatric
Research, 44, 584590.
Johansen-Berg, H., & Behrens, T. E. J. (Eds.). (2009). Diffusion MRI From
quantitative measurement to in-vivo neuroanatomy. London: Academic Press.
Kamman, R. L., Go, K. G., Brouwer, W., & Berendsen, H. J. C. (1988). Nuclear magnetic
relaxation in experimental brain edema: Effects of water concentration, protein
concentration, and temperature. Magnetic Resonance in Medicine, 6, 265274.
Koenig, S. H., & Brown, R. D.III, (1985). The importance of the motion of water for
magnetic resonance imaging. Investigative Radiology, 20, 297305.
Koenig, S. H., Brown, R. D., III, Spiller, M., & Lundbom, N. (1990). Relaxometry of
brain: Why white matter appears bright in MRI. Magnetic Resonance in Medicine,
14, 482495.
MacKay, A., Whittall, K., Adler, J., Li, D., Paty, D., & Graeb, D. (1994). In vivo
visualization of myelin water by magnetic resonance. Magnetic Resonance in
Medicine, 31, 673677.
Morris, C. M., Candy, J. M., Oakley, A. E., Bloxham, C. A., & Edwardson, J. A. (1992).
Histo-chemical distribution of non-haem iron in the human brain. Acta Anatomica,
144, 235257.
Mukherjee, P., Miller, J. H., Shimony, J. S., Conturo, T. E., Lee, B. C. P., Almli, C. R.,
et al. (2001). Normal brain maturation during childhood: Developmental
trends characterized with diffusion-tensor MR imaging. Radiology, 221,
349358.
Neeb, H., Zilles, K., & Shah, N. J. (2006). A new method for fast quantitative mapping of
absolute water content in vivo. NeuroImage, 31, 11561168.
Norris, D. G. (2001). The effects of microscopic tissue parameters on the diffusion
weighted magnetic resonance imaging experiment. NMR in Biomedicine, 14,
7793.
Reichenbach, J. R., Venkatesan, R., Schillinger, D. J., Kido, D. K., & Haacke, E. M.
(1997). Small vessels in the human brain: MR venography with deoxyhemoglobin
as an intrinsic contrast agent. Radiology, 204, 272277.
Sled, J., & Pike, G. B. (2001). Quantitative imaging of magnetization transfer properties
in vivo using MRI. Magnetic Resonance in Medicine, 46, 923931.
Stanisz, G. J., Kecojevic, A., Bronskill, M. J., & Henkelman, R. M. (1999).
Characterizing white matter with magnetization transfer and T2. Magnetic Resonance
in Medicine, 42, 11281136.
Tofts, P. (Ed.). (2003). Quantitative MRI of the brain. Chichester: Wiley.
Whittall, K., MacKay, A., Graeb, D., Nugent, R., Li, D., & Paty, D. (1997). In vivo
measurement of T2 distributions and water contents in normal human brain.
Proceedings of the National Academy of Science of the United States of America, 89,
212216.
Yao, B., Li, T.-Q., van Gelderen, P., Shmueli, K., de Zwaart, J. A., & Duyn, J. H. (2009).
Susceptibility contrast in high field MRI of human brain as a function of tissue iron
content. NeuroImage, 44, 12591266.
Zhou, J., Lal, B., Wilson, D. A., Tryastman, R. J., & van Zijl, P. C. M. (2003). Using the
amide proton signals of intracellular proteins to detect pH effects in MRI. Nature
Medicine, 9, 10851090.
Intensity Nonuniformity Correction

JG Sled, Hospital for Sick Children, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
Introduction
Intensity nonuniformity is an image artifact commonly
observed on MRI scans that results in smooth gradations in
signal intensity across the image. Variously referred to as intensity nonuniformity, shading artifact, or bias field, these signal
variations degrade the numerical analysis of neuroimaging
data and in severe cases also interfere with the visual interpretation of images. The artifact arises from a number of scannerrelated sources and, due to the physical interaction between
magnetic fields and tissue, can never be fully eliminated from
the acquired MR signal. It is therefore an essential step in
almost any computational analysis of brain morphology to
first correct for intensity nonuniformity. As an illustration of
this process, Figure 1 shows a typical 3-D T1-weighted MRI
scan corrupted by intensity nonuniformity, an estimate of the
bias field, and the 3-D image after correction. Subtle levels bias,
on the order of 1030%, are typical for clinical images (Sled &
Pike, 1998a) and have little effect on visual assessment; however, at field strengths of 3 T and above (Boyes et al., 2008) or
in combination with multielement coils optimized for superficial sensitivity, the artifact is often plainly visible on the scan.
In this article, we review the causes of intensity nonuniformity, physical models for the artifact, and methods for
correcting the artifact in experimental data.
Sources of Intensity Nonuniformity

The primary cause of intensity nonuniformity in MRI is spatial
variation in the sensitivity of the radiofrequency coil. This
manifests itself in two ways: spatial variation in the strength
of the field B
1 that is used to excite the hydrogen nuclei and
spatial variation in the sensitivity R of the coil to detect these
precessing nuclei. The in this notation is the component of
these fields that rotates in the same direction as the precessing
magnetization of the nuclei. Typical MRI pulse sequences used
for high-resolution T1-weighted anatomical imaging such as
spoiled gradient echo or magnetization-prepared rapid
gradient echo are susceptible to B

1 and R variation in approximately equal proportion, whereas pulse sequences relying on
flip angles of 90 or 180 such as spin-echo sequences are less
sensitive to B
1 variation as signal intensity depends on the sine
of the flip angle. R variation is a spatially varying multiplicative factor that affects pulse sequences of all types.
Surface coils or multielement coils have sensitivity profiles
for B
1 and R that drop rapidly with distance from the coil
element. This leads to severe nonuniformity. However, even
volume coils such as birdcages that are designed for uniform
sensitivity when unloaded will show significant sensitivity variation when a human head is present. This patient-dependent
aspect of intensity nonuniformity defies simple calibrationtype corrections and has led to a significant research effort to
find effective correction techniques. Two physical effects

contribute to patient-dependent sensitivity variation, dielectric
standing waves and induced currents (Glover et al., 1985). At
intermediate field strengths of 1.5 and 3 T, dielectric standing
waves, which are dependent on the permittivity of tissue and
the wave length, tend to cause signal enhancement at the center
of the head. Tissue conductivity arising from ions in solution
leads to induced currents that partially attenuate the standing
waves. A surprising aspect of these induced currents is the
interaction with the shape of the head. In particular, an eccentric head shape that is otherwise symmetrical can lead to an
asymmetrical pattern of shading running diagonally across the
brain (Sled & Pike, 1998b). Left uncorrected, this asymmetry,
which differs between B

1 and R , has the potential to confound sensitive neuroanatomical analyses.
The advent of multichannel coils and scanners means that
the image reconstruction algorithms supplied with the scanner
include some correction for coil sensitivity. The SENSE reconstruction algorithm (Pruessmann, Weiger, Scheidegger, & Boesiger, 1999), for instance, requires explicit estimates of R for
each channel. In this context, the nonuniformity that one seeks
to remove for neuroanatomical analysis is the residual variation not accounted for by this initial vendor-supplied
correction, and that would typically be ignored for standard
radiological assessment.
Other factors besides coil sensitivity contribute to intensity
nonuniformity. Geometric distortion caused by nonlinearity in
the applied gradient fields leads to signal enhancement or
attenuation in proportion to the local expansion or contraction of the image. In pulse sequences that have long readouts
such as echo planar imaging, magnetic susceptibility variations
can also cause geometric distortion and signal loss due to R*
2
weighting. This effect is most apparent in the frontal lobe near
the sinuses in fast diffusion-weighted or functional scans. A
variety of other instrumental factors such as static magnetic
field variations and eddy currents also contribute to shading
through their effect on contrast generation.
Intensity Nonuniformity Correction Methods

A wide variety of techniques have been proposed for correcting
intensity nonuniformity. See Vovk, Pernus, and Likar (2007)
for a recent review. That such a diversity of techniques should
be proposed reflects both the importance of correcting this
artifact and the inherent difficulty in doing so. These methods
can be subdivided into prospective and retrospective techniques, the latter being suitable for analysis of existing data.
Prospective Correction Methods

Intensity nonuniformity correction methods that rely on additional measurements or physical models offer advantages with
http://dx.doi.org/10.1016/B978-0-12-397025-1.00298-0
295
296
INTRODUCTION TO METHODS AND MODELING | Intensity Nonuniformity Correction
1.25
1.00
(a)
(b)
(c)
0.75
Figure 1 Example of intensity nonuniformity correction. (a) A transverse slice from a T1-weighted 3-D scan acquired at 3 T. (b) An estimate of the
nonuniformity field. (c) A corrected image obtained by dividing the original image by the field estimate.
respect to accuracy over retrospective method. This is because

these methods are not constrained by assumptions about the
appearance of the image. Early work in this area applied either
a numerical simulation of the magnetic field pattern (McVeigh,
Bronskill, & Henkelman, 1986; Moyher, Vigneron, & Nelson,
1995), an electrostatic approximation, or empirical calibration
data obtained using phantoms. These approaches are suitable
for correcting the strong signal variations associated with
surface coils but lack the accuracy needed to correct the more
subtle variations typical for volume coils. Extending the simulation approach to account for the electrodynamic properties
of tissue is feasible (Alecci, Collins, Smith, & Jezzard, 2001) but
challenging, as the magnetic field patterns depend on anatomy
both inside and outside the field of view of the scan. A more
practical approach is the use of so-called sequence-based
methods that allow estimation of nonuniformity with a
modified acquisition protocol that includes additional
measurements (Milles et al., 2006; Noterdaeme, Anderson,
Gleeson, & Brady, 2009).
One strategy for sequence-based estimation of R is to
acquire an image that minimizes relaxation contrast such that
the residual variations in contrast can be attributed to coil
sensitivity (Wang, Qiu, Yang, Smith, & Constable, 2005). Any
image acquired in the same scan session can then be divided by
the estimate of R to correct for sensitivity variation. A difficulty with this approach, however, is that MR signal intensity is
proportional to both R and proton density, such that in the
absence of additional information, the two factors are indistinguishable. Therefore, one needs to make assumptions about
proton density variations being small or distributed in a predictable way to dissociate the effect of R. An alternate strategy
that avoids this difficulty is the use of sequence-based methods
based on signal ratios.
The ratio of two MRI scans acquired in the same session
produces an image whose contrast is independent of both R
and proton density. Signal ratios have been used extensively for
quantitative MRI techniques including diffusion tensor imaging, magnetization transfer ratio, and quantitative T1 and T2
methods. These methods also have the benefit that these ratios
are reproducible from scan to scan and can be compared
between groups. Further improvements in the precision of

these ratio methods can be gained by measuring B1 and
employing an image reconstruction method that takes into
account the spatial variations in this excitation field. Unlike
coil sensitivity, excitation field strength B1 is easily measured
using stock imaging sequences (Chavez & Stanisz, 2012;
Yarnykh, 2007) and can be done so rapidly because the needed
spatial resolution for the field map is low. The main disadvantage of ratio-based techniques is the need for additional scan
time, typically double that of a conventional contrast-weighted
scan. Also, proton density, a potentially informative source of
image contrast, is eliminated by this approach. These disadvantages are offset in many cases by the advantages for assessing tissue structure offered by quantitative methods.
Retrospective Correction Methods

Correction methods that can be applied to existing data provide a great practical advantage and are now a routine step in
processing MRI data for brain mapping studies. These methods
dissociate the nonuniformity artifact from the anatomy on the
basis of image appearance. A great variety of such methods
have been proposed, and the present discussion is by no
means an exhaustive review of this subject. An early example
of a retrospective correction method is homodyne filtering
(Haselgrove & Prammer, 1986; Lee & Vannier, 1996). In this
approach, the intensity nonuniformity is distinguished from
anatomy on the basis of spatial frequency. A low-pass filtered
version of the image is taken as an estimate of the nonuniformity artifact. Recognizing that the main sources of
nonuniformity, and R in particular, have a multiplicative
effect on the image, the corrected image is obtained by dividing
the original image by the estimate of the nonuniformity field.
This model for intensity nonuniformity can be written as
follows:
vx uxf x nx
[1]
where v is the measured image as a function of spatial location

x, u is the uncorrupted image, f is the multiplicative artifact,

and n is the image noise, independent of u and either
Gaussian- or Rician-distributed. When n is neglected, dividing
the image v by an estimate of f yields an estimate of u.
Homodyne filtering has two limitations. One is that the
spatial frequencies corresponding to brain anatomy and typical
nonuniformity patterns overlap such that anatomical contrast
is removed by this approach. The second is that the very low
spatial frequencies associated with nonuniformity are difficult
to estimate when the head is comparable in size to the spatial
wavelengths of interest. These insights led to a number of
improvements in the modeling of u and f. With respect to f,
subsequent work has made use of adaptive filters suitable for
smoothing a bounded domain or fitting of smooth basis functions such as polynomials (Dawant, Zijdenbos, & Margolin,
1993) or splines (Sled, Zijdenbos, & Evans, 1998). With
respect to u, the spectral overlap problem has often been
addressed by formulating u as a piecewise constant function
(Milchenko, Pianykh, & Tyler, 2006). An example of this
approach is the work of Meyer, Bland, and Pipe (1995)
where the image is first decomposed into patches of similar
image intensity. The field pattern is then estimated by solving
for a smooth field that is consistent with uniform intensity and
an unknown offset for each patch. This approach is closely
related to a broad class of methods that formulate tissue
classification and intensity nonuniformity correction as a single problem (Ahmed, Yamany, Mohamed, Farag, & Moriarty,
2002; Chen, Zhang, & Yang, 2012; Styner, Brechbuhler,
Szekely, & Gerig, 2000; Szilagyi, Szilagyi, & Benyo, 2012; Van
Leemput, Maes, Vandermeulen, & Suetens, 1999; Wells,
Grimson, Kikinis, & Jolesz, 1996).
In tissue classification, the resulting map of labeled tissue
regions is piecewise constant or a probabilistic generalization
of this idea. The problem of intensity nonuniformity estimation becomes that of finding an appropriately smooth correction field f that leads to a narrow distribution of tissue
intensities for each labeled region. The advantage of combining tissue classification and nonuniformity correction is that
one can leverage the extensive computational machinery developed for tissue classification, including brain atlases of the
prior probability for specific labels and models of intensity
statistics that include prior information on label adjacency
(Tohka, Dinov, Shattuck, & Toga, 2010; Wels, Zheng, Huber,
Hornegger, & Comaniciu, 2011). Two examples of combined
classification/nonuniformity correction methods are the FAST
algorithm (Zhang, Brady, & Smith, 2001) included with the
FMRIB software library and the unified segmentation algorithm (Ashburner & Friston, 2005) that is part of the spatial
parametric mapping software. These approaches are powerful
in the context of an extensive processing pipeline, particularly
when one of the goals is tissue classification. However, the
linking of the two problems restricts one to applications
where the supporting model data are available and valid. Concern about these limitations has motivated another class of
intensity nonuniformity correction methods, those based on
image intensity statistics.
An example of a method based on image intensity statistics
is the nonparametric nonuniform intensity normalization or
N3 (Sled et al., 1998) developed at the Montreal Neurological
Institute and Hospital. In this method, intensity nonuniformity is proposed to broaden the probability density
297
function of the image u such that peaks in this distribution

associated with specific tissue types lose definition. The problem then becomes that of estimating a smooth field f that can
be used to restore the original definition or sharpness to the
image histogram. The N3 algorithm iterates between estimating the probability density of u and the field f that corresponds
to this sharpened histogram. A number of related methods
have been proposed that are sometimes called uphill methods
for their effort to move signal intensity from the valleys to the
peaks of the histogram (Tustison et al., 2010; Vovk, Pernu, &
Likar, 2004). A related formulation of the problem is with
respect to entropy minimization (Ji, Glass, & Reddick, 2007;
Likar, Viergever, & Pernus, 2001; Mangin, 2000; Manjon et al.,
2007; Vovk, Pernus, & Likar, 2006). Histograms with narrow
peaks have lower entropy than corresponding dispersed distributions and therefore provide a basis for optimization. The
generality of these intensity statistic approaches has led to their
broad adoption, typically as the initial step in a processing
pipeline.
Validation and Accuracy

The difficulty of directly measuring the experimental variables
that cause intensity nonuniformity presents a challenge for
evaluating the accuracy of available correction methods
(Arnold et al., 2001; Belaroussi, Milles, Carme, Zhu, &
Benoit-Cattin, 2006). An often used approach to validation is
to compare and manually identify image regions that should
have equivalent signal intensity. Another approach is to assess
reproducibility across multiple scans (Goto et al., 2012). Simulated MRI data such as that from the BrainWeb database
(Collins et al., 1998) have also been widely used to evaluate
accuracy (Chua, Zheng, Chee, & Zagorodnov, 2009). However,
this approach is limited by the accuracy of the model used to
create the simulation, which may or may not include all of the
low spatial frequency variation present in real anatomy. It is
clear from quantitative MRI studies that contrast parameters
vary smoothly across the hemispheric white matter and
between different gray matter structures (Sled et al., 2004).
Even within the cerebral cortex, variations in myelination
lead to gradations in signal contrast. These subtle anatomical
variations will be either retained or removed depending on the
correction approach and the goals of the investigator.
An important consideration in applying retrospective
correction methods is specifying the smoothness of the
field estimate. Allowing for higher spatial frequencies in
the field estimate leads to corrected images that appear
progressively more like the piecewise constant image
model that was proposed. Mapping of B1 suggests that
spatial features on the order of 50200 mm are plausible
for the adult brain at 1.5 and 3 T. Smaller feature lengths of
3050 mm can lead to improved visual appearance and
better performance for tasks such as tissue classification
(Zheng, Chee, & Zagorodnov, 2009).
Conclusions and Future Directions

Intensity nonuniformity is a pervasive image artifact affecting
the accuracy of MRI scans of the human brain. Although
298
prospective correction techniques based on additional measurements are available, most brain mapping studies rely on
retrospective correction. These retrospective techniques are
easily applied and provide practical benefits by reducing scan
variability and improving the sensitivity of morphological
analyses. However, these methods struggle with a low level of
residual variation that is likely indistinguishable from true
spatial variations in the properties of the tissue. Prospective
correction methods have the potential to remove this residual
variation, but the associated increase in scan time, a factor of
two in the case of ratio methods, has limited their uptake. With
continuing improvements in data acquisition techniques,
signal-to-noise ratio (SNR) has superseded gradient hardware
performance as the limiting factor in high-resolution anatomical scanning. In this regime, an 11% reduction to the three
voxel dimensions corresponds to a doubling of scan time to
maintain equivalent SNR. The future therefore may see a shift
from retrospective to prospective correction methods as more
investigators opt for the advantages of quantitative MRI
acquisition techniques.

Anatomical MRI for Human Brain Morphometry; High-Speed, HighResolution Acquisitions; Obtaining Quantitative Information from fMRI;
INTRODUCTION TO ANATOMY AND PHYSIOLOGY: Cortical
Surface Morphometry; Motor Cortex; Myeloarchitecture and Maps of
the Cerebral Cortex; INTRODUCTION TO METHODS AND
MODELING: Artifacts in Functional MRI and How to Mitigate Them;
Cortical Thickness Mapping; Diffusion Tensor Imaging; Image
Reconstruction in MRI; Lesion Segmentation; Surface-Based
Morphometry; Tensor-Based Morphometry; Tissue Classification;
Tissue Microstructure Imaging with Diffusion MRI; Tissue Properties
from Quantitative MRI; Voxel-Based Morphometry.
References
Ahmed, M. N., Yamany, S. M., Mohamed, N., Farag, A. A., & Moriarty, T. (2002). A
modified fuzzy c-means algorithm for bias field estimation and segmentation of MRI
data. IEEE Transactions on Medical Imaging, 21, 193199. http://dx.doi.org/
10.1109/42.996338.
Alecci, M., Collins, C. M., Smith, M. B., & Jezzard, P. (2001). Radio frequency magnetic
field mapping of a 3 Tesla birdcage coil: Experimental and theoretical dependence
on sample properties. Magnetic Resonance in Medicine, 46, 379385. http://dx.doi.
org/10.1002/mrm.1201.
Arnold, J. B., Liow, J. S., Schaper, K. A., Stern, J. J., Sled, J. G., Shattuck, D. W., et al.
(2001). Qualitative and quantitative evaluation of six algorithms for correcting
intensity nonuniformity effects. NeuroImage, 13, 931943. http://dx.doi.org/
10.1006/nimg.2001.0756.
Ashburner, J., & Friston, K. J. (2005). Unified segmentation. NeuroImage, 26,
Belaroussi, B., Milles, J., Carme, S., Zhu, Y. M., & Benoit-Cattin, H. (2006). Intensity
non-uniformity correction in MRI: Existing methods and their validation. Medical
Image Analysis, 10, 234246. http://dx.doi.org/10.1016/j.media.2005.09.004.
Boyes, R. G., Gunter, J. L., Frost, C., Janke, J. L., Yeatman, T., Hill, D. L., et al. (2008).
Intensity non-uniformity correction using N3 on 3-T scanners with multichannel
phased array coils. NeuroImage, 39, 17521762. http://dx.doi.org/10.1016/j.
Chavez, S., & Stanisz, G. J. (2012). A novel method for simultaneous 3D B(1) and T(1)
mapping: The method of slopes (MoS). NMR in Biomedicine, 25, 10431055.
http://dx.doi.org/10.1002/nbm.2769.
Chen, Y., Zhang, J., & Yang, J. (2012). An anisotropic images segmentation and bias
correction method. Magnetic Resonance Imaging, 30, 8595. http://dx.doi.org/
10.1016/j.mri.2011.09.003.
Chua, Z. Y., Zheng, W., Chee, M. W., & Zagorodnov, V. (2009). Evaluation of
performance metrics for bias field correction in MR brain images. Journal of
Magnetic Resonance Imaging, 29, 12711279. http://dx.doi.org/10.1002/
jmri.21768.
Collins, D. L., Zijdenbos, A. P., Kollokian, V., Sled, J. G., Kabani, N. J., Holmes, C. J.,
et al. (1998). Design and construction of a realistic digital brain phantom. IEEE
Transactions on Medical Imaging, 17, 463468. http://dx.doi.org/10.1109/
42.712135.
Dawant, B. M., Zijdenbos, A. P., & Margolin, R. A. (1993). Correction of intensity
variations in MR images for computer-aided tissue classification. IEEE Transactions
on Medical Imaging, 12, 770781. http://dx.doi.org/10.1109/42.251128.
Glover, G. H., Hayes, C. E., Pelc, N. J., Edelstein, W. A., Mueller, O. M., Hart, H. R., et al.
(1985). Comparison of linear and circular polarization for magnetic resonance
imaging. Journal of Magnetic Resonance, 64, 255270. http://dx.doi.org/10.1016/
0022-2364(85)90349-X.
Goto, M., Abe, O., Miyati, T., Kabasawa, H., Takao, H., Hayashi, N., et al. (2012).
Influence of signal intensity non-uniformity on brain volumetry using an ATLASbased method. Korean Journal of Radiology, 13, 391402. http://dx.doi.org/
10.3348/kjr.2012.13.4.391.
Haselgrove, J., & Prammer, M. (1986). An algorithm for compensation of surface-coil
images for sensitivity of the surface coil. Magnetic Resonance Imaging, 4, 469472.
Ji, Q., Glass, J. O., & Reddick, W. E. (2007). A novel, fast entropy-minimization
algorithm for bias field correction in MR images. Magnetic Resonance Imaging, 25,
259264. http://dx.doi.org/10.1016/j.mri.2006.09.012.
Lee, S. K., & Vannier, M. W. (1996). Post-acquisition correction of MR
inhomogeneities. Magnetic Resonance in Medicine, 36, 275286.
Likar, B., Viergever, M. A., & Pernus, F. (2001). Retrospective correction of MR intensity
inhomogeneity by information minimization. IEEE Transactions on Medical Imaging,
20, 13981410. http://dx.doi.org/10.1109/42.974934.
Mangin, J. F. (2000). Entropy minimization for automatic correction of intensity
nonuniformity. In IEEE workshop on mathematical methods in biomedical image
analysis, proceedings (pp.162169).
Manjon, J. V., Lull, J. J., Carbonell-Caballero, J., Garcia-Marti, G., Marti-Bonmati, L., &
Robles, M. (2007). A nonparametric MRI inhomogeneity correction method.
Medical Image Analysis, 11, 336345. http://dx.doi.org/10.1016/j.
media.2007.03.001.
McVeigh, E. R., Bronskill, M. J., & Henkelman, R. M. (1986). Phase and sensitivity of
receiver coils in magnetic resonance imaging. Medical Physics, 13, 806.
http://dx.doi.org/10.1118/1.595967.
Meyer, C. R., Bland, P. H., & Pipe, J. (1995). Retrospective correction of intensity
inhomogeneities in MRI. IEEE Transactions on Medical Imaging, 14, 3641.
http://dx.doi.org/10.1109/42.370400.
Milchenko, M. V., Pianykh, O. S., & Tyler, J. M. (2006). The fast automatic algorithm for
correction of MR bias field. Journal of Magnetic Resonance Imaging, 24, 891900.
http://dx.doi.org/10.1002/jmri.20695.
Milles, J., Zhu, Y. M., Chen, N. K., Panych, L. P., Gimenez, G., & Guttmann, C. R.
(2006). Computation of transmitted and received B1 fields in magnetic resonance
imaging. IEEE Transactions on Biomedical Engineering, 53, 885895. http://dx.doi.
org/10.1109/TBME.2005.863955.
Moyher, S. E., Vigneron, D. B., & Nelson, S. J. (1995). Surface coil MR imaging of the
human brain with an analytic reception profile correction. Journal of Magnetic
Resonance Imaging, 5, 139144. http://dx.doi.org/10.1002/(ISSN)1522-2586.
Noterdaeme, O., Anderson, M., Gleeson, F., & Brady, S. M. (2009). Intensity correction
with a pair of spoiled gradient recalled echo images. Physics in Medicine and
Biology, 54, 34733489. http://dx.doi.org/10.1088/0031-9155/54/11/013.
http://dx.doi.org/10.1002/(ISSN)1522-2594.
Sled, J. G., Levesque, I., Santos, A. C., Francis, S. J., Narayanan, S., Brass, S. D., et al.
(2004). Regional variations in normal brain shown by quantitative magnetization
transfer imaging. Magnetic Resonance in Medicine, 51, 299303. http://dx.doi.org/
10.1002/mrm.10701.
Sled, J. G., & Pike, G. B. (1998a). Understanding intensity non-uniformity in MRI.
Sled, J. G., & Pike, G. B. (1998b). Standing-wave and RF penetration artifacts caused by
elliptic geometry: An electrodynamic analysis of MRI. IEEE Transactions on Medical
Imaging, 17, 653662. http://dx.doi.org/10.1109/42.730409.
Sled, J. G., Zijdenbos, A. P., & Evans, A. C. (1998). A nonparametric method for
automatic correction of intensity nonuniformity in MRI data. IEEE Transactions on
Medical Imaging, 17, 8797. http://dx.doi.org/10.1109/42.668698.
Styner, M., Brechbuhler, C., Szekely, G., & Gerig, G. (2000). Parametric estimate of
intensity inhomogeneities applied to MRI. IEEE Transactions on Medical Imaging,
19, 153165. http://dx.doi.org/10.1109/42.845174.

Szilagyi, L., Szilagyi, S. M., & Benyo, B. (2012). Efficient inhomogeneity compensation
using fuzzy c-means clustering models. Computer Methods and Programs in
Biomedicine, 108, 8089. http://dx.doi.org/10.1016/j.cmpb.2012.01.005.
Tohka, J., Dinov, I. D., Shattuck, D. W., & Toga, A. W. (2010). Brain MRI tissue
classification based on local Markov random fields. Magnetic Resonance Imaging,
28, 557573. http://dx.doi.org/10.1016/j.mri.2009.12.012.
Tustison, N. J., Avants, B. B., Cook, P. A., Zheng, Y., Egan, A., Yushkevich, P. A., et al.
(2010). N4ITK: Improved N3 bias correction. IEEE Transactions on Medical
Imaging, 29, 13101320. http://dx.doi.org/10.1109/TMI.2010.2046908.
Van Leemput, K., Maes, F., Vandermeulen, D., & Suetens, P. (1999). Automated modelbased bias field correction of MR images of the brain. IEEE Transactions on Medical
Vovk, U., Pernu, F., & Likar, B. (2004). MRI intensity inhomogeneity correction by
combining intensity and spatial information. Physics in Medicine and Biology, 49,
41194133. http://dx.doi.org/10.1088/0031-9155/49/17/020.
Vovk, U., Pernus, F., & Likar, B. (2006). Intensity inhomogeneity correction of
multispectral MR images. NeuroImage, 32, 5461. http://dx.doi.org/10.1016/j.
Vovk, U., Pernus, F., & Likar, B. (2007). A review of methods for correction of intensity
inhomogeneity in MRI. IEEE Transactions on Medical Imaging, 26, 405421.
http://dx.doi.org/10.1109/TMI.2006.891486.
299
Wang, J., Qiu, M., Yang, Q. X., Smith, M. B., & Constable, R. T. (2005). Measurement
and correction of transmitter and receiver induced nonuniformities in vivo. Magnetic
Resonance in Medicine, 53, 408417. http://dx.doi.org/10.1002/mrm.20354.
Wells, W. M., Grimson, W. L., Kikinis, R., & Jolesz, F. A. (1996). Adaptive segmentation
of MRI data. IEEE Transactions on Medical Imaging, 15, 429442. http://dx.doi.org/
10.1109/42.511747.
Wels, M., Zheng, Y., Huber, M., Hornegger, J., & Comaniciu, D. (2011). A
discriminative model-constrained EM approach to 3D MRI brain tissue
classification and intensity non-uniformity correction. Physics in Medicine and
Biology, 56, 32693300. http://dx.doi.org/10.1088/0031-9155/56/11/007.
Yarnykh, V. L. (2007). Actual flip-angle imaging in the pulsed steady state: A method
for rapid three-dimensional mapping of the transmitted radiofrequency field.
Magnetic Resonance in Medicine, 57, 192200. http://dx.doi.org/10.1002/
mrm.21120.
Zhang, Y., Brady, M., & Smith, S. (2001). Segmentation of brain MR images through a
hidden Markov random field model and the expectation-maximization algorithm.
IEEE Transactions on Medical Imaging, 20, 4557. http://dx.doi.org/10.1109/
42.906424.
Zheng, W., Chee, M. W., & Zagorodnov, V. (2009). Improvement of brain segmentation
accuracy by optimizing non-uniformity correction using N3. NeuroImage, 48,
Rigid-Body Registration
J Tohka, Tampere University of Technology, Tampere, Finland
Glossary
Affine transformation A transformation composed of

translations, rotations, shears, and scalings. In three
dimensions parameterized by 12 parameters.
Cost function A function which describes the goodness of a
certain transformation for image registration. The image
registration methods try to find a minimum value of such
cost functions.
Histogram For each intensity value, image histogram
provides the number of voxels with that intensity value. For
each pair (i,j) of intensity values, the joint histogram
provides the number of voxels having the intensity i in the
first image and the intensity j in the second image.
Introduction
Image registration aims to geometrically align one image with
another and is a prerequisite for all brain imaging applications
that compare images across subjects, across imaging modalities, or across time (Toga & Thompson, 2001). After the image
registration, the voxels in the two registered images are
assumed to have the same meaning so that the comparison
of the voxel value in one image with the value of the corresponding voxel (with the same coordinates) in the other image
makes sense. In addition to images, registration can analogously be applied to surfaces, contours, or point sets extracted
from the image.
The key issue in the image registration is to find the best
geometric transformation to bring the images into alignment,
that is, to determine a mapping from each voxel position in
one image (called source or floating image) to a corresponding
position in the other image (called target or reference image).
The application of this transformation to actually bring the
images into alignment is an easier process albeit there are
important aspects to consider too such as the choice of the
interpolation method. As Crum et al. (2004), we divide an
image registration method to three components.
First, it is necessary to restrict the set of possible geometric
transformations to find a useful transformation between the
two images that ameliorates irrelevant differences but preserves the important ones. The focus of this article is on
rigid-body and related affine transformations that are the
simplest class of the transformations with the fewest number
of parameters (from 6 to 12). Particularly, a rigid-body transformation is composed of rotations and translations. It does
not alter the shapes or sizes of the objects present in the
image and is therefore used to model different head positions
of the same subject. Thus, rigid-body registrations are used for
within-subject registrations required for the motion correction in functional magnetic resonance imaging (fMRI),
Image registration A process of geometrically aligning two

images.
Interpolation Approximation of a function value at a given
point by using its values at a discrete set of nearby points.
Mutual information A measure of mutual dependence of
two random variables. In image registration, mutual
information of two images is computed based on a joint
histogram.
Rigid body transformation A transformation composed of
rotations and translations of the space. In three dimensions
parameterized by 6 parameters.
registering the functional and structural image of the same

subject (this is often termed as intermodality registration) or
registering two images acquired at different times in a longitudinal study. Affine transformations, which, in addition to
translations and rotations, allow for scalings and shears, can
be used for the between-subject registration, that is, registering the images of two or more subjects into the same reference space, and serve as initializations for more flexible
nonlinear registration techniques. The section Rigid-Body
and Other Affine Transformations provides overview of
the rigid-body and affine transformations. Nonlinear transformations and registration, which allow for greater freedom
in geometric variation between the images, are dealt in the
subsequent articles.
The second component, dealt in the section How to Find
the Best Transformation? of an image registration method is
the criterion based on which the two images are registered. This
criterion can be based on geometric (anatomical) properties of
the images or image intensities. Traditionally, the distinction
between intra- and intermodality registration has been
stressed. The reason for this is that, in the intramodality case,
when the two images to be registered have been acquired using
the same modality, one can expect the two images to look
much more alike than in the intermodality case, where images
have been acquired using different modalities. However, this
distinction has been somewhat blurred since informationtheoretic registration criteria, explained in the section How
to Find the Best Transformation?, can be effectively used for
both intra- and intermodality registrations. However, automatic software tools often recommend the use of different
criteria for intra and intermodality registrations.
The third component of an image registration method is the
actual numerical algorithm used to perform the registration.
This is an important consideration because often, the registration criterion is expressed as a cost function that has to be
optimized using a numerical algorithm.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00299-2
301
302
INTRODUCTION TO METHODS AND MODELING | Rigid-Body Registration
Figure 1 Examples of rigid-body transformations. Clockwise from top left: Original MR image slice, translated image slice with dx,dy 20 voxels,
rotated image with qz 0.2618 radians (15 ), sheared image with kxy 0.3, scaled image with lx,ly 1.3, and rigid-body transformation combining the
aforementioned translation and rotation.
Rigid-Body and Other Affine Transformations

A rigid transformation in 3-D consists of a rotation of the
object along each coordinate axis and a translation of the
object. Utilizing a matrix notation, a rigid-body transformation
of a [ax, ay, az]T to b [bx, by, bz]T (a superscript T denotes the
matrix transpose) is written as

b T a Ux qx Uy qy Uz qz a d U qx , qy , qz a d
where d [dx,dy,dz]T is the translation vector; the 3 3 matrices
Ux(qx), Uy(qy), and Uz(qz) describe the rotation around x-,y-,
and z-axes, often termed roll, pitch, and yaw, by qx,qy, and qz
radians, respectively ; and U(qx,qy,qz) describes the composite
rotation. The matrices Ux, Uy, and Uz are

3
3
2
1
0
0
cos qy 0 sin qy
0 5, Uz
Ux 4 0 cos qx sin qx 5, Uy 4 0 1
sin
q
0
sin
q
cos
0
cos
qy
x
x 3
y
2
cos qz sin qz 0
4 sin qz cos qz 0 5
0
0
1
2
A general rigid-body transformation is parameterized by six

parameters that can be dx,dy,dz,qx,qy,qz, but several other parameterizations exist. The inverse of the rigid-body transformation
b Ua d is a UT(b d), since the inverse U1 of a rotation
matrix U is UT. Figure 1 demonstrates how rigid-body and
other affine transformations change the image.
An affine transformation can be composed, in addition to
rotation and translation, of scalings and shears, represented by
the following matrices:
3
2
3
1 kxy kxz
lx 0 0
L 4 0 ly 0 5, K 4 0 1 kyz 5
0 0 lz
0 0 1
A general affine transformation from a to b is represented as
b Va d, where V is a 3 3 (invertible) matrix and d is a
translation vector. This transformation has 12 parameters. In
addition, affine transform ations with 9 parameters (excluding
shears) and 7 parameters (excluding shears and assuming uniform scalings) can be considered. An affine transformation is

V
d
often represented by 44 matrix T
. This allows
000 1
writing an affine transformation of a vector as a single matrix
multiplication T[ax,ay,az,1]T.
An inverse mapping approach is generally used for applying
an affine transformation to an image. In the inverse mapping,
one takes a voxel of the target image, say, at the coordinates b
[bx,by,bz]T; tracks the corresponding voxel coordinates in the
source image, say a; and chooses the intensity value in the
target image R[b] according to the intensity value S[a] at a in
the source image. Point a is not usually located at the voxel
center, and therefore, an interpolation method has to be used
to find R[b]. There are a variety of interpolation techniques
available, and these have a large practical relevance to the
success of image registration.
How to Find the Best Transformation?

The approaches for finding the best transformation can be
divided into geometric approaches trying to match anatomical
features between the images and intensity-based approaches
trying to transform the images so that they are maximally
similar. The latter category is presently much more widely

used. An evaluation study showed that intensity-based
approaches, in general, outperformed the geometric ones
called surface-based approaches (West et al., 1999). The intensity-based and geometric registration approaches can be also
combined into a single, hybrid method such as in (Greve &
Fischl, 2009) aim to combine the distinct advantages of the
intensity and geometric approaches.
Most approaches in both categories are based on the minimization of a cost function. The value of the cost function at a
specific transformation T describes the quality of the transformation T; the smaller the value, the better the quality. The
resulting minimization problems typically do not have a
closed form solution, and they have to be minimized using
numerical algorithms.
Geometric Approaches
The geometric approaches try to match points, contours, or
surfaces, that is, geometric features, found in the images. The
geometric features should have an anatomical interpretation to
be useful for the brain image registration. The easiest case is
when n (noncoplanar) landmarks, each carrying specific anatomical meaning, have been identified in both images. Denote
these landmark sets, extracted from the two images being
registered, as {ai :i 1,. . .,n} and {bi :i 1,. . .,n}. Then, a cost
function for the registration can be written as
CL T 1=n
n
X
jjT ai bi jj2
i1
When T is a rigid-body transformation, the minimization of

CL(T ) has a closed form solution originally derived by Green
(1952). Numerical methods for solving this problem are reviewed
and compared by Eggert, Lorusso, and Fisher (1997), and an
example of the application within brain imaging is Evans, Marrett,
Torrescorzo, Ku, and Collins (1991). For more general classes of
affine transformations, no closed form solution exists, and
Fitzpatrick, Hill, and Maurer (2000) provided an overview of
algorithms for these cases. The cost function CL assumes that the
points with the same index j, aj and bj, mark the same anatomical
location; this is called point correspondence. More complex strategies based on geometric features, such as the hat-and-head algorithm by Pelizzari, Chen, Spelbring, Weichselbaum, and Chen
(1989), try to match surfaces found in the images. These methods
often cannot assume the point correspondence, and they use, for
example, the iterative closest points (ICP) algorithm for joint
estimation of point correspondence and transformation (Besl &
McKay, 1992). For registering point clouds {aj} and {bj} of na
and nb points, respectively,
the cost function is

Pa
CICP T ni1
minj T ai bj 2 . The iterative ICP algorithm
minimizing CICP alternates between two stages: (1) Given a transformation T, for each point ai, find the closest point in {bj} to
establish an approximate point correspondence; (2) update the
transformation given the point correspondence using the
methods for minimizing CL. This ICP algorithm is sensitive to
its initialization.
Intensity-Based Approaches
The intensity-based approaches try to match the intensity patterns over a predefined image region or the entire image
303
domain O (Hill, Batchelor, Holden, & Hawkes, (2001)

includes a detailed discussion on defining O) (Hill, Batchelor,
Holden, & Hawkes, 2001) includes a detailed discussion on
defining O. For this, a similarity criterion has to be defined and
turned into a cost function to drive the registration process.
Denote the source (floating) image by S and the target (reference) image by R. The simplest cost function is the sum of
squares difference (SSD):
CSSD T
X
a2O
T Sa Ra2
where T(S) denotes the image S after transforming it by the

transformation T. This cost function cannot be used to register
images that contain different information. It is also sensitive to
a small number of voxels that have large intensity differences
arising naturally, for example, in fMRI experiments (Freire &
Mangin, 2001). The cross correlation cost function
P
.
p
P
P
CNC T a2O T SaRa p
2
2
a2O
T Sa
a2O
Ra
may provide a more robust alternative for the motion correction within fMRI (Jenkinson, Bannister, Brady, & Smith,
2002).
The most widely used similarity measures for betweenmodality image registration are based on informationtheoretic concepts of mutual information and joint entropy
(Maes, Collignon, Vandermeulen, Marchal, & Suetens, 1997;
Pluim, Maintz, & Viergever, 2003; Wells et al., 1996). The
mutual information of two random variables is a measure of
their mutual dependence that is usually derived via the concept
of entropy. Maximizing the mutual information between the
images leads to an attractive alternative to SSD or correlationbased cost functions, because the assumption is that the images
to be registered show dependent information. This is a more
relaxed assumption than that the images would show the same
(CSSD) or correlated information (CNC). The mutual information is computed based on the joint probability density of
intensity values of images S and R, denoted as PS,R(i,j) and
the related marginal probability densities PS(i) and PR(j),
where i and j run over all possible voxel intensities. In practice,
these probability densities must be approximated by histograms. The joint entropy of the images S and R is then H(S,
P
R) i,jPS,R(i, j)log[PS,R(i, j)] and the marginal entropies as
P
P
H(S) iPS(i)log[PS(i)] and H(R) jPR(j)log[PR(j)].
Now, the negative of mutual information between the
images is
CMI T HS, T R HS HT R
Figure 2 demonstrates the intermodality registration using
CMI as the cost function.
For this and related widely used cost functions, such as
normalized mutual information, (Studholme, Hill, & Hawkes,
1999), it is fundamentally important how the probability densities are estimated and which interpolation method is chosen
(Maes, Vandermeulen, & Suetens, 1999; Tsao, 2003).
Alternative cost functions for between-modality registration
include partitioned image uniformity and ration image uniformity (Woods, Mazziotta, & Cherry, 1993), correlation ratio
(Roche, Malandain, Pennec, & Ayache, 1998), and various
application-specific cost functions, for example, Saad et al.
304
Mutual information
0.2
0.4
0.5
0.6
0.7
20
10
0
Rotation (degrees)
10
20
Final
0.02
0.02
0.015
0.015
Probability
Probability
Initial
0.3
0.01
0.005
0
PET intensity
0.01
0.005
0
MR intensity
PET intensity
MR intensity
Figure 2 MR-PET registration based on minimization of the mutual information cost function CMI. Initially, the fluorodeoxyglucose-PET (FDG-PET)
image is displaced by a rotation around z-axis of 20 . The initial joint histogram of the MR and PET images is shown in the bottom left. After the
minimization of the negative mutual information (CMI; shown here as a function of a single rotation parameter), the PET image is well aligned with the
MR image. The final joint histogram is shown in the bottom right, and it is more sharply peaked than the initial histogram indicating the
improvement in the alignment of the two images. The PET image here is Monte Carlo-simulated based on the MR image (Reilhac et al., 2005), and
therefore, the correct transformation between the images is known.
(2009). Instead of transforming one of the images as done

here, one can perform symmetric registration, where both
source and target images are transformed to ensure inverse
consistency (Reuter, Rosas, & Fischl, 2010).
Jenkinson & Smith, 2001), thus aiming at determining not

only a local minimum but also the smallest local minimum
(in practice a small local minimum) of the cost function.
Algorithms to Minimize Intensity-Based Cost Functions
Software and Evaluations
The cost functions of previous subsection have to be minimized by a numerical algorithm. The choice of the minimization algorithm is important because it can have a substantial
effect on the accuracy of the transformation found by the
algorithm. It is important here to make a difference between
local and global minima. A local minimum of a cost function is
a transformation that has a cost that is lower than the cost of
nearby transformations, and a global minimum is the transformation that has the lowest cost possible. Minimization
algorithms applied in brain image registration are usually
general-purpose numerical optimization algorithms such as
Powells, simplex, or Newtons method. These search for any
local minimum of the cost function, which makes them sensitive to initial conditions of the algorithm. The adverse effects of
this can be greatly reduced by using multiresolution techniques
(Collins, Neelin, Peters, & Evans, 1994; Maes et al., 1999) and
a good interpolation method; the latter is especially important
for the optimization information-theoretic cost functions such
as CMI (Tsao, 2003). Only few works have explicitly adopted
a global optimization approach (Jenkinson et al., 2002;
There is a plethora of freely available software implementations for rigid-body and affine registration of brain images.
Major software packages, such as SPM, FSL, and FreeSurfer,
all implement methods for affine registrations. Widely used
registration-specific software include AIR (Woods et al., 1993,
for the original version of the software) and MNI AutoReg
(Collins et al., 1994). Typically, the methods implemented in
the software tools follow the main lines presented in this
article, but implementation details of these tools differ considerably, and they each can require different preprocessing and
probably provide different results for an individual registration
task, even if using exactly the same cost function to drive the
registration process.
The retrospective evaluations of the affine brain image registration are rare but not nonexistent. West et al. (1997, 1999)
reached the conclusion that the intensity-based based methods
have the upper hand of the surface-based ones. Holden et al.
(2000) concluded that the use of mutual information based cost
functions has advantages over other cost functions when quantifying longitudinal anatomical change. Oakes et al. (2005)

concluded that the choice of motion correction software has
little effect on the outcome of statistical analysis of fMRI data.

Anatomical MRI for Human Brain Morphometry; Obtaining Quantitative
Information from fMRI; INTRODUCTION TO METHODS AND
Computing Brain Change over Time; Diffeomorphic Image Registration;
Nonlinear Registration Via Displacement Fields; Voxel-Based
Morphometry.
References
Besl, P. J., & McKay, Neil D. (1992). A method for registration of 3-D shapes. IEEE
Transactions on Pattern Analysis and Machine Intelligence, 14(2), 239256.
Collins, D., Neelin, P., Peters, T., & Evans, A. (1994). Automatic 3D intersubject
registration of MR volumetric data in standardized Talairach space. Journal of
Crum, W. R., Hartkens, T., & Hill, D. L. (2004). Non-rigid image registration: Theory
and practice. British Institute of Radiology, 77(2), S140153.
Eggert, D. W., Lorusso, A., & Fisher, R. B. (1997). Estimating 3-D rigid body
transformations: A comparison of four major algorithms. Machine Vision and
Applications, 9, 272290.
Evans, A. C., Marrett, S., Torrescorzo, J., Ku, S., & Collins, D. L. (1991). MRI-PET
correlation in three dimensions using a volume-of-interest (VOI) atlas. Journal of
Cerebral Blood Flow and Metabolism, 11, A69A78.
Fitzpatrick, M., Hill, D. L. G., & Maurer, C. R. (2000). Image registration. In M. Sonka &
J. M. Fitzpatrick (Eds.), Medical image processing. Handbook of medical imaging
(vol. 2. Bellingham, WA: SPIE Press.
Freire, L., & Mangin, J.-F. (2001). Motion correction algorithms may create spurious
brain activations in the absence of subject motion. NeuroImage, 14, 709722.
Green, B. F. (1952). The orthogonal approximation of an oblique structure in factor
analysis. Psychometrika, 17, 429440.
Greve, D. N., & Fischl, B. (2009). Accurate and robust brain image alignment using
boundary-based registration. NeuroImage, 48, 6372.
Hill, D. L. G., Batchelor, P. G., Holden, M., & Hawkes, D. J. (2001). Medical image
registration. Physics in Medicine and Biology, 46, R1R45.
Holden, M., Hill, D. L., Denton, E. R., Jarosz, J. M., Cox, T. C., Rohlfing, T., et al.
(2000). Voxel similarity measures for 3-D serial MR brain image registration. IEEE
Jenkinson, M., Bannister, P., Brady, M., & Smith, S. (2002). Improved optimization for
the robust and accurate linear registration and motion correction of brain images.
Jenkinson, M., & Smith, S. (2001). A global optimisation method for robust affine
registration of brain images. Medical Image Analysis, 5, 143156.
305
Maes, F., Collignon, A., Vandermeulen, D., Marchal, G., & Suetens, P. (1997).
Multimodality image registration by maximization of mutual information. IEEE
Maes, F., Vandermeulen, D., & Suetens, P. (1999). Comparative evaluation
of multiresolution optimization strategies for multimodality image
registration by maximization of mutual information. Medical Image Analysis, 3,
373386.
Oakes, T. R., Johnstone, T., Ores Walsh, K. S., Greischar, L. L., Alexander, A. L.,
Fox, A. S., et al. (2005). Comparison of fMRI motion correction software tools.
Pelizzari, C. A., Chen, G. T. Y., Spelbring, D. R., Weichselbaum, R. R., &
Chen, C.-T. (1989). Accurate three-dimensional registration of CT, PET,
and/or MR images of the brain. Journal of Computer Assisted Tomography, 13,
2026.
Pluim, J. P.W, Maintz, J. B.A, & Viergever, M. A. (2003). Mutual-information-based
registration of medical images: A survey. IEEE Transactions on Medical Imaging,
22, 9861004.
Reilhac, A., Batan, G., Michel, C., Grova, C., Tohka, J., Collins, D. L., et al. (2005). PETSORTEO: Validation and development of database of simulated PET volumes. IEEE
Transactions on Nuclear Science, 52, 13211328.
Reuter, M., Rosas, H. D., & Fischl, B. (2010). Highly accurate inverse consistent
registration: A robust approach. NeuroImage, 53, 11811196.
Roche, A., Malandain, G., Pennec, X., & Ayache, N. (1998). The correlation ratio as a
new similarity measure for multimodal image registration. In Medical image
computing and computer-assisted intervention MICCAI98 (pp. 11151124).
Berlin Heidelberg: Springer.
Saad, Z. S., Glen, D. R., Chen, G., Beauchamp, M. S., Desai, R., & Cox, R. W. (2009). A
new method for improving functional-to-structural MRI alignment using local
Pearson correlation. NeuroImage, 44, 839848.
Studholme, C., Hill, D. L. G., & Hawkes, D. J. (1999). An overlap invariant entropy
measure of 3D medical image alignment. Pattern Recognition, 32, 7186.
Toga, A. W., & Thompson, P. M. (2001). The role of image registration in brain
mapping. Image and Vision Computing, 19, 324.
Tsao, J. (2003). Interpolation artifacts in multimodality image registration based on
maximization of mutual information. IEEE Transactions on Medical Imaging, 22,
854864.
Wells, W. M., III, Viola, P., Atsumi, H., Nakajima, S., & Kikinis, R. (1996). Multi-modal
volume registration by maximization of mutual information. Medical Image Analysis,
1, 3551.
West, J., Fitzpatrick, J. M., Wang, M. Y., Dawant, B. M., Maurer, C. R., Jr.,
Kessler, R. M., et al. (1999). Retrospective intermodality registration techniques for
images of the head: Surface-based versus volume-based. IEEE Transactions on
West, J., Fitzpatrick, J. M., Wang, M. Y., Dawant, B. M., Maurer, C. R., Jr.,
Kessler, R. M., et al. (1997). Comparison and evaluation of retrospective
intermodality brain image registration techniques. Journal of Computer Assisted
Woods, R. P., Mazziotta, J. C., & Cherry, S. R. (1993). MRI-PET registration
with automated algorithm. Journal of Computer Assisted Tomography, 17,
536546.
Nonlinear Registration Via Displacement Fields

J Modersitzki, University of Lubeck, Lubeck, Germany; Fraunhofer MEVIS, Lubeck, Germany
S Heldmann and N Papenberg, Fraunhofer MEVIS, Lubeck, Germany
Introduction
Image registration, aka warping, fusion, or coregistration, is one
of the key technologies in imaging and an exciting task particularly in medical imaging. As such, it has attracted enormous
attention (see Brown, 1992; Haber, & Modersitzki, 2008; Fischer
& Modersitzki, 2008; Fitzpatrick, Hill, & Maurer, 2000; Glasbey,
1998; Goshtasby, 2005, 2012; Hajnal, Hawkes, & Hill, 2001;
Hill, Batchelor, Holden, & Hawkes, 2001; Holden, 2008; Lester
& Arridge, 1999; Maintz & Viergever, 1998; Modersitzki, 2004,
2009; Scherzer, 2006; Szeliski, 2006; Toga & Mazziotta, 2002;
van den Elsen, Pol, & Viergever, 1993; Yoo, 2004; Zitova &
Flusser, 2003, and references therein). Roughly speaking, the
goal of image registration is to automatically establish correspondences between different images displaying views of objects
or organs. These images may be acquired at different times, from
different devices or perspectives, or reveal even different types of
information. Many applications require nonlinear (i.e., not necessarily linear) alignment strategies and hence nonlinear registration enters into play.
There is a large number of application areas demanding for
image registration, and image registration has impact on basically every imaging technique (see also Modersitzki, 2009).
Specific examples include motion correction (Weickert &
Schnorr, 2001; see also Figure 1), data fusion (Maes,
Collignon, Vandermeulen, Marchal, & Suetens, 1997; see also
Figure 2), spatial normalization of data (Friston et al., 1995),
stitching (Szeliski, 2006) (generating a global picture from
partial views), template matching and identification (Altman
& Bland, 1983) (comparing current images with a data base),
tracking (Acton & Ray, 2006), and optical flow (Horn &
Schunck, 1981). Moreover, particular imaging modalities
such as diffusion tensor imaging rely on image registration
(Stejskal & Tanner, 1965). Therefore, image registration is an
important tool for computational anatomy, computer-aided
diagnosis, fusion of different modalities, intervention and
treatment planning, monitoring of diseases, motion correction, radiation therapy, or treatment verification, to name a
few (see also Alvarez, Weickert, & Sanchez, 1999; Ashburner &
Friston, 1999, 2003); Barron, Fleet, & Beauchemin, 1994;
Christensen, Rabbitt, & Miller, 1996; Craene, Camara, Bijnens,
& Frangi, 2009; Horn & Schunck, 1981; Peshko et al., 2014 and
particularly Modersitzki, 2009 for more examples).
Unfortunately, no unified treatment or general theory for
image registration has yet been established. It appears that each
application area has developed its own approaches and implementations. Depending on the application, the focus can be on
computing time (real-time applications like tracking), image
features, memory requirements (high-resolution histological
or 3-D images), accuracy of results, or others.
This article does not aim for a comprehensive overview on
image registration. The idea here is to provide a framework that
enables a discussion and comparison of a large subclass of

methods and techniques and to provide a basic understanding
of the conceptual difficulties of registration tasks. More precisely, a general, variational approach to nonlinear registration
is outlined (see also Amit, 1994; Fischer & Modersitzki, 2004b,
2006; Hermosillo, Chef dHotel, & Faugeras, 2002, and particularly Modersitzki, 2009 for details and precise formulas). The
underlying concepts are to divide the registration problem into
modular blocks and to address and discuss each block separately. Important blocks are data representation and scale, image
similarity (equivalently, image distance), ill-posedness and regularization, and the integration of additional constraints.
Although the configuration of a specific approach may
differ significantly for different applications, the underlying
concepts are identical. The images to be registered are typically
denoted by fixed image or reference R and moving image or
template T and are considered as maps, assigning points x in
the d-dimensional real space intensity values R(x) and T(x). It is
assumed that points x of the template image may have been
repositioned to a location x . This can be described by a map
y : d ! d with x y(x). The goal is to compute a nice y,
such that ideally T(y(x)) R(x) for all x.
Data Model
The structure of acquired medical data is typically an array of
intensity values associated with a discrete pixel structure, which
makes geometric transformation of images nontrivial. In general, it is not possible to exactly represent transformed versions
of an image on the original pixel structure. Figure 4 illustrates
this difficulty for the example of a 4-by-4 image. The first image
shows the original and the second one a rotated copy. The
problem is that the pixel structure (visualized by the red grid)
is intrinsically present. Already a simple rotation (second
image) changes the image structure, which results in a massive
complication for a comparison of objects (see also section
Distance Measures and the third image). A remedy is to
project the rotated image to the original pixel structure (fourth
image). Note that intensity values have to be invented (e.g.,
top-left pixel), and at the same time, intensity information has
been lost (e.g., top-left corner of the object). Moreover, intensity information that is associated with one pixel (e.g., top-left
white pixel in the original image) has been distributed over
several pixels in the projected image (see also partial volume
effects) and careful considerations are required in order to
resolve these issues. A standard approach is offered by interpolation techniques (Aldroubi & Grochening, 2001; Boor, 1978;
Camion & Younes, 2001; Duchon, 1976; Lehmann, Gonner, &
Spitzer, 1999; Light, 1996; Thevenaz, Blu, & Unser, 2000;
Wahba, 1990). Here, the idea is to generate a continuous
function I that can then be assessed at arbitrary points x:
http://dx.doi.org/10.1016/B978-0-12-397025-1.00300-6
307
308
INTRODUCTION TO METHODS AND MODELING | Nonlinear Registration Via Displacement Fields
Figure 1 High-speed echo-planar images with blip-up (left) and blip-down (right) gradients displaying the same tissue with severe distortions due to
inhomogeneous gradient fields: obvious spatial distortions along gradient directions and intensity distortion due to perturbed tissue density. Image
restoration in terms of both spatial position and intensity can be achieved via registration (see also Mohammadi, Nagy, Hutton, Josephs, & Weiskopf,
2011 and Ruthotto et al., 2012).
T1
CT
DBS electrode
CT
T2
T1
DBS electrode
Figure 2 Multimodal image fusion (right) of preoperative T1-weighted (left) and T2-weighted MRI and postoperative CT (middle) after surgical
implantation of an electrode for deep brain stimulation (DBS). DBS has become a well-established therapy for Parkinsons disease, dystonia, and
essential tremor. Accurate intrapatient registration of pre- and postoperative MRI and CT data for surgical planning and therapy control is needed.
High-quality imaging and registration are important for optimal therapy since the target region is small in the range of 23 mm. In addition to intrapatient
registration, registration across patients and to an atlas is used for optimal tuning of stimulation fields based on statistical information in order to
reduce side effects such as speech problems (cf. DHaese et al., 2012; Guo, Parrent, & Peters, 2007; Martens et al., 2011) (see also the IMPACT project,
http://www.impact-fp7.eu, supported by the EU, grant no. 305814 in HEALTH.2012.1.2-1).
Ix interpolatedata, parameters, x
[1]
where additional parameters are used to control the type of

interpolation, smoothness, and/or approximation properties
of the interpolant (see Figure 3 for an example and
Modersitzki (2009) for details). The transformed image can
be formulated in an Eulerian setting, where simply
T yx T yx for all x
[2]
or (x, T(x)) is mapped to (y(x), T(x)) when using a Lagrangian

framework.
Interpolation or, more precisely, approximation also
offers a concept of scale (see Figure 3 for an example).
Scale spaces are an example for such a setting (Aldroubi &
Grochening, 2001; Florack, Romeny, Koenderink, & Viergever,
1992; Haber & Modersitzki, 2005, 2006c; Haber et al., 2009b;
Lindeberg, 1994; Salden, Ter Haar Romeny, & Viergever, 1998).
They provide a great potential for a process that starts with the
important coarse features, adds more and more fine details and
structure, and ends with the original representation (see
Modersitzki, 2009 for details). Practically, this is an additional
regularization that precludes local minima, improves initial

guesses, and reduces computation time. Figure 3 shows an
example. Starting with the rightmost, an approximate solution
can be computed quickly and accurately, as the images are
simplified and very smooth. Note that since the images are
smooth by construction, a coarse representation can also be
used to reduce computation times. This intermediate solution
then serves as a starting guess for the next scale, where an
improved solution can be computed quickly due to a good
starting guess. This procedure can be repeated until the original
data is processed. However, it is important that the different
representations are linked together by a unified model. This is
the essential reason for the variational formulation used in this
article.
Distance Measures
Image similarity or, equivalently, distances provide a way of
emulating the eye of a trained expert. Another important
309
Figure 3 Multiscale representations of an MRI slice: from original and fine-scale (left) to very smooth and coarse-scale (right).
modeling aspect besides run-time and stability is the identification of important features from data. Volumetric image distances are most intuitive and can be formulated in terms of
energies. A simple example is the energy of the difference image
T(y) R:
DT y, R jjT yx Rxjj2L2 T yx Rx2 dx [3]

Image features can be based on points (often called landmarks) (Boesecke, Bruckner, & Ende, 1990; Bookstein, 1989;
Bookstein & Green, 1992; Glauns, Vaillant, & Miller, 2004;
Joshi & Miller, 2000; Rohr, 2001), surfaces (Audette, Ferrie, &
Peters, 2000; Barequet & Sharir, 1997; Fornefett, Rohr, &
Stiehl, 2000; Johnson & Hebert, 1997; Vaillant & Glauns,
2005; Yeo et al., 2008), volumetric data (Christensen, Joshi,
& Miller, 1997), shapes (Besl & McKay, 1992; Bookstein,
1984), or others (Durrleman, Pennec, Trouv, Thompson, &
Ayache, 2008; Glauns, Qiu, Miller, & Younes, 2008; Glauns,
Trouve, & Younes, 2004; Leow et al., 2005). Mathematically,
features fT and fR are computed from the images T and R,
respectively. Thus, feature-based image differences can also be
formulated in the previously mentioned setting:

[4]
d f R , f T dF T , F R DT; R
where d denotes a feature-based distance andF describes the
feature generating process formally.
Various distance measures are discussed in the literature
(see, e.g., Heldmann, 2006; Hermosillo, 2002; Modersitzki,
2004, 2009; Roche, 2001, and references therein). Among the
various choices for image distances are the energy or L2- norm
(3) (aka sum of squared differences or SSD), (normalized)
cross-correlation (Avants, Epstein, Grossman, & Gee, 2008),
normalized gradient fields (Haber & Modersitzki, 2006b,
2007; Pluim, Maintz, & Viergever, 2000), normalized Hessian
fields (Hodneland, Lundervold, Andersen, & Munthe-Kaas,
2013), and (normalized) mutual information (MI) (Boes &
Meyer, 1999; Collignon, Vandermeulen, Suetens, & Marchal,
1995; Modat et al., 2010; Pluim, Maintz, & Viergever, 1999;
Viola & Wells, 1995). For each application, a trade-off between
simple (typically more convex, robust, fast but limited in use,
and unimodal) and sophisticated (typically more general,
multimodal but less convex, more local minima, and unstable)
measures has to be found.
Additional important options include choices of the norm
in (3), certainties, weighting, focusing on structures, or windowing. The L2 norm is ideal for Gaussian noise, but not
robust in terms of outliers. The so-called L1 (or even L0)

norms, which are very popular in the image denoising community (Candes, Romberg, & Tao, 2006), can be used with
great success for certain applications. The Huber norm (Huber,
1973) provides a differentiable alternative to the L1 norm. The
KullbackLeibler divergence is an option for images that can be
interpreted as densities (Kullback & Leibler, 1951). This provides additional structure for application such as PET imaging,
where mass preservation and mass transport are issues (see,
e.g., Burger, Modersitzki, & Ruthotto, 2013; Ruthotto et al.,
2012). According to the transformation rule, T has to be modulated by the determinant of the Jacobian to T(y)det ry.
The integral in eqn [3] can also be restricted to a certain area
of interest such as to ignore parts of the data (background,
prominent structures not relevant to the correspondence task).
This can be seen as a special case of incorporating a weighting
function k inside the integral. Typical choices for k are characteristic functions, their approximations, and fuzzy weighting.
Another interpretation of this concept is related to certainty,
where weight and certainty become synonymous. To bypass an
averaging tendency of an integral measure, localized
approaches such as localized cross-correlation have been considered (Hermosillo, 2002; Hermosillo et al., 2002).
The earlier-mentioned strategies provide flexibility in terms
of geometry. However, intensity modulation can also be used to
advantage. Intensity mappings like windowing can be used to
focus on structures represented by certain intensity ranges. The
mass-preserving approach mentioned earlier in the text modifies
image intensities automatically according to mass transport.
More general approaches aim to establish a functional correspondence between image intensities, such that ideallyT(y(x))
s(R(x)) where y and s are to be found simultaneously (see
Heldmann, 2010; Keeling, 2007; Modersitzki & Wirtz, 2006;
Roche, Malandain, Pennec, & Ayache, 1998). Note that MI
aims for a relation of intensity values in T and R and thus is
even more general. However, MI decouples intensity from space
and a reshuffling of voxels does not effect MI. Therefore, these
approaches are quite different to MI.
Regularization
Image registration is an ill-posed problem in the sense of Hadamard (Hadamard, 1902; Modersitzki, 2009). This implies that
the information provided (one intensity value) is insufficient to
determine a solution (a displacement vector). Roughly speaking,
310
Figure 4 Rotated 4-by-4 pixel image, from left to right: original image, rotated image, rotated image with pixel grid, rotated image on pixel grid.
all points sharing the same intensity can be repositioned arbitrarily without changing the image distance. Figure 4 also illustrates a trivial example. Looking only in the one-parametric class
of rotations around the image center, four equivalent solutions
can be found (rotations about 0 , 90 , 180 , and 270 ). Without
further information, it is impossible to determine a particular
solution. In a nonlinear setting, the situation gets considerably
worse, as points with the same intensity can be shuffled around
arbitrarily. However, the problem is deeper and even the existence of solutions is nontrivial.
Regularization is a conceptual way to bypass these difficulties and to remove ambiguity. Tikhonov proposed a general
idea (Tikhonov, 1943) to add an additional term S to the illposed problem and to minimize a modified objective function
J(y),
Jy DT y, R aSy,
[5]
where the key role of S is to ensure the existence of solution for

the optimization problem (Burger et al., 2013; Droske &
Rumpf, 2004; Weickert & Schnorr, 2001).
Currently, most choices for regularization are based on
quadratic functionals. One example is the so-called thin-plate
spline energy, which has been used for landmark-based distance measures, where the image distance can be formulated as
a point measure (Bookstein, 1989; Rohr, 2001). Other quadratic choices are the mathematically motivated diffusion
(Fischer & Modersitzki, 2002b) and curvature (Fischer & Modersitzki, 2003b, 2004c; Henn, 2006b) regularizers and the very
popular elastic regularizer (Bajcsy & Kovai, 1989; Broit, 1981;
Fischler & Elschlager, 1973):
[6]
Sy l mjjryjj2Fro mjdiv yj2 dx
The basic idea in using this linear elasticity model is to decompose the transformation and to penalize rotation and expansion
and contraction by scalars l and m; (see, e.g., Modersitzki, 2004,
2009 for details). This linear elastic model has been a generator
and inspiration for a variety of approaches (Christensen, 1994;
Davatzikos, 1997; Fischer & Modersitzki, 2002a; Freeborough,
1998; Gee & Bajcsy, 1999; Kybic & Unser, 2000; Rueckert et al.,
1999). Note that the same remarks concerning weights as for the
distance measure apply (e.g., spatially dependent l and m (Kabus,
Franz, & Fischer, 2006)).
Particularly in a constrained setting, higher-order regularization is an issue (Burger et al., 2013; Fischer & Modersitzki,
2002a, 2003b, 2004c; Henn, 2006a; Yanovsky, Guyader, Toga,
Thompson, & Vese, 2008). Curvature regularization has been

introduced to ensure nonsingular solutions for landmark integration (Fischer & Modersitzki, 2003a, 2004a; Modersitzki &
Fischer, 2003), and more general hyperelastic regularizers are
used in combination with local rigidity constraints (Yanovsky
et al., 2008) or intensity modulation (Ruthotto, Hodneland, &
Modersitzki, 2012; Ruthotto et al., 2012). An important feature
of the nonlinear elasticity model in Burger et al. (2013) is an
explicit control of the deformation tensor det ry. This ensures
not only a one-to-one mapping y but also a computational
access to volume changes in the tissue.
Other regularization options have been discussed in the
literature (Arndt et al., 1996; Banerjee & Toga, 1994; Beuthien,
Kamen, & Fischer, 2010; Yang, Xue, Liu, & Xiong, 2011). Of
particular interest are demons (a sorting-type idea based on
Maxwells demons for electrodynamics) (Cahill, Noble, &
Hawkes, 2009; Guimond, Roche, Ayache, & Meunier, 2001;
Thirion, 1995, 1996, 1998; Vercauteren, Pennec, Perchant, &
Ayache, 2008; Yeo et al., 2010), the construction of geodesic
paths (exploiting Riemannian manifold structure) (Pennec,
Stefanescu, Arsigny, Fillard, & Ayache, 2005), the blending of
transformations (polyaffine transformations) (Arsigny,
Pennec, & Ayache, 2003, 2005), and the use of well-chosen
basis function (Ashburner & Friston, 1999, 2003; Rueckert
et al., 1998). Symmetrical (i.e., interchangeable in T and R)
or consistent methods (Christensen, 1999; Christensen &
Johnson, 2001; He & Christensen, 2003; Johnson & Christensen, 2002; Leow et al., 2005) provide additional options and
can also be used to enforce a one-to-one mapping.
For many applications, only one-to-one mappings are
plausible. One way to enforce this condition is to follow
geodesics on energy manifolds, which leads to diffeomorphic
image registration and is currently a very active area of
research (see, e.g., Ashburner, 2007; Ashburner & Friston,
2011; Auzias et al., 2011; Beg, Miller, Trouve & Younes,
2005; Cao, Miller, Mori, Winslow, & Younes, 2006; Chef
dHotel et al., 2002; Haber & Modersitzki, 2006a; Miller &
Younes, 2001; Ruthotto et al., 2012; Trouve, 1998; Twining &
Marsland, 2004; Vercauteren, Pennec, Perchant, & Ayache,
2007, 2009, to name a few). The idea is to generate a regularized and time-dependent velocity field. It can be shown
that the integrated displacement field is a diffeomorphism,
that is, an invertible function that maps one differentiable
manifold to another, such that both the function and its
inverse are smooth. Other options are to regularize on the
determinant of the Jacobian (Burger et al., 2013).
311
Constrained Image Registration
Conclusions
It seems to be natural to remove some of the ambiguity in the

registration problem by adding additional knowledge. The
variational approach outlined in this article provides a framework for this. Mathematically, eqn [5] is simply to be augmented by an additional penalty:
Despite tremendous improvements over the last years, image

registration is still an open problem and an active field of
research. In this article, focus is given to various modeling
aspects, for numerical implementations (see, e.g., Modersitzki,
2009 and references therein).
Jy DT y, R aSy bPy
(7)
Here, P can be an indicator function for plausible transformations (hard-constrained, e.g., rigidity: P 0 if y is rigid; P 1
otherwise) or a penalty for unwanted solutions (softconstrained). In the latter case, the penaltyR is typically
formulated in terms of an integral, that is, P(y) p(y)dx (e.g.,
volume changes: p log(det ry)2). Note that in the softconstrained setting, the constraint is in general not satisfied, for
example, P
6 0. Due to the averaging nature of the integral, this is
an issue if the target region is relatively small (measurement of
tumor growth (Haber & Modersitzki, 2004)). Soft constraints
can be advantageous if the information is fuzzy.
Regularization has to be added carefully to ensure the existence of solutions (e.g., for the volume change, hyperelasticity
has to be used as a regularizer to ensure the existence of a
transformation, such that ry exists and det ry is measurable
(Burger et al., 2013)), whereas constraints can be formulated
much more generally.
Though theoretically quite similar, the computational differences between hard and soft constraints are tremendous. Soft
constraints require an additional parameter b, which is not always
easy to be determined and has a negative impact on the condition
of the optimization problem and may lead to numerical instability. Another computational difference relates to the type of constraints: equality (p 0) or inequality (p 0). Constraints can be
formulated globally or locally. For example, volume preservation
can be formulated on the whole image domain or just a subset
such as bones. Depending on the constraints, a Lagrangian framework keeping the spatial setting fixed during transformation can
be computationally advantageous to the more common Eulerian
framework (see also Avants, Schoenemann, & Gee, 2006).
Important constraints in medical imaging include the correspondence of anatomical landmarks (Bookstein, 1989;
Bookstein & Green, 1992; Fischer & Modersitzki, 2003a,2003b,
2004a; Haber et al., 2009b; Hellier & Barillot, 2003; Johnson &
P
Christensen, 2002) (P y l jjy r l t l jj, where t l and r l are
landmarks in reference image and template image, respectively;
possible user interaction via landmark positioning, possible
automatic landmark detection, and good starting guess),
local rigidity of structures Aix bi y(x) 0 for x in Si; superior
results for images containing bones) (Haber, Heldmann, &
Modersitzki, 2009; Keeling & Ring, 2005; Little, Hill, & Hawkes,
1997; Loeckx, Maes, Vandermeulen, & Suetens, 2004; Modersitzki, 2008; Ruthotto, Hodneland, & Modersitzki, 2012; Staring,
Klein, & Pluim, 2006, 2007), and volume change-based constraints (p det ry 1 0 for x 2 S; monitoring tumor growth
and enforcing diffeomorphisms) (Fischer & Modersitzki, 2004a;
Haber, Horesh, & Modersitzki, 2010; Haber & Modersitzki,
2004, 2005, 2006a; Leow et al., 2007; Poschl et al., 2010;
Rohlfing, Maurer, Bluemke, & Jacobs, 2003; Zhu, Haker, & Tannenbaum, 2003).
References
Acton, S. T., & Ray, N. (2006). Biomedical image analysis: Tracking. San Rafael, CA:
Claypool Publisher.
Aldroubi, A., & Grochening, K. (2001). Nonuniform sampling and reconstruction in
shift-invariant spaces. SIAM Review, 43(3), 585620.
Altman, D., & Bland, J. (1983). Measurement in medicine: The analysis of method
comparison studies. The Statistician, 32, 307317.
Alvarez, L., Weickert, J., & Sanchez, J. (1999). A scale-space approach to nonlocal
optical flow calculations. Scale-space theories in computer vision. Berlin: Springer,
235246.
Amit, Y. (1994). A nonlinear variational problem for image matching. SIAM Journal on
Scientific Computing, 15(1), 207224.
Arndt, S., Rajarethinam, R., Cizadlo, T., OLeary, D., Downhill, J., & Andreasen, N. C.
(1996). Landmark-based registration and measurement of magnetic resonance
images: A reliability study. Neuroimaging, 67, 145154.
Arsigny, V., Pennec, X., & Ayache, N. (2003). A novel family of geometrical
transformations: Polyrigid transformations. Application to the registration of
histological slices, Research report 4837, INRIA. http://www.inria.fr/rrrt/rr-4837.
html.
Arsigny, V., Pennec, X., & Ayache, N. (2005). Polyrigid and polyaffine transformations:
A novel geometrical tool to deal with non-rigid deformations Application to the
registration of histological slices. Medical Image Analysis, 9(6), 507523. http://
authors.elsevier.com/sd/article/S1361841505000289, PMID: 15948656.
Ashburner, J. (2007). A fast diffeomorphic image registration algorithm. NeuroImage,
38(1), 95113.
Ashburner, J., & Friston, K. J. (1999). Nonlinear spatial normalization using basis
functions. Human Brain Mapping, 7, 254266.
Ashburner, J., & Friston, K. (2003). Spatial normalization using basis functions. In R.
Frackowiak, K. Friston, C. Frith, R. Dolan, K. Friston, C. Price, S. Zeki, J. Ashburner
& W. Penny (Eds.), Human brain function (2nd ed.). Waltham, MA: Academic Press.
Ashburner, J., & Friston, K. J. (2011). Diffeomorphic registration using geodesic
shooting and gaussnewton optimisation. NeuroImage, 55(3), 954967.
Audette, M. A., Ferrie, F. P., & Peters, T. M. (2000). An algorithmic overview of surface
registration techniques for medical imaging. Medical Image Analysis, 4(3),
201217.
Auzias, G., Colliot, O., Glauns, J. A., et al. (2011). Diffeomorphic brain registration
under exhaustive sulcal constraints. IEEE Transactions on Medical Imaging, 30(6),
12141227.
Avants, B. B., Epstein, C. L., Grossman, M., & Gee, J. C. (2008). Symmetric
diffeomorphic image registration with cross-correlation: Evaluating automated
labeling of elderly and neurodegenerative brain. Medical Image Analysis, 12(1),
2641.
Avants, B. B., Schoenemann, P. T., & Gee, J. C. (2006). Lagrangian frame diffeomorphic
image registration: Morphometric comparison of human and chimpanzee cortex.
Medical Image Analysis, 10(3), 397412.
Bajcsy, R., & Kovacic, S. (1989). Multiresolution elastic matching. Computer Vision,
Graphics, and Image Processing, 46(1), 121.
Banerjee, P. K., & Toga, A. W. (1994). Image alignment by integrated rotational
translational transformation matrix. Physics in Medicine and Biology, 39,
19691988.
Barequet, G., & Sharir, M. (1997). Partial surface and volume matching in three
dimensions. IEEE on Pattern Analysis and Machine Intelligence, 19, 929948.
Barron, J. L., Fleet, D. J., & Beauchemin, S. S. (1994). Performance of optical flow
techniques. International Journal of Computer Vision, 12(1), 4377.
Beg, M. F., Miller, M. I., Trouve, A., & Younes, L. (2005). Computing large deformation
metric mappings via geodesic flows of diffeomorphisms. International Journal of
Computer Vision, 61(2), 139157.
Besl, P. J., & McKay, N. D. (1992). A method for registration of 3-d shapes. IEEE
Transactions on Pattern Analysis and Machine Intelligence, 14(2), 239256.
312
Beuthien B., Kamen A., & Fischer B. (2010). Recursive greens function registration. In:
International conference on medical image computing and computer-assisted
intervention, pp. 546553.
Boes, J. L., & Meyer, C. R. (1999). Multivariate mutual information for registration. In C.
Taylor & A. Colchester (Eds.), Medical image computing and computer assisted
intervention (pp. 606612). Heidelberg: Springer-Verlag.
Boesecke, R., Bruckner, T., & Ende, G. (1990). Landmark based correlation of medical
images. Physics in Medicine and Biology, 35(1), 121126.
Bookstein, F. L. (1984). A statistical method for biological shape comparisons. Journal
of Theoretical Biology, 107, 475520.
Bookstein, F. L. (1989). Principal warps: Thin-plate splines and the decomposition
of deformations. IEEE on Pattern Analysis and Machine Intelligence, 11(6),
567585.
Bookstein, F. L., & Green, D. K. (1992). Edge information at landmarks in medical
images. Visualization in Biomedical Computing, 1808, 242258.
Boor, C. D. (1978). A practical guide to splines. New York: Springer.
Broit, C. (1981). Optimal registration of deformed images, PhD thesis, Computer and
information science, University of Pennsylvania, USA.
Brown, L. G. (1992). A survey of image registration techniques. ACM Computing
Surveys, 24(4), 325376.
Burger, M., Modersitzki, J., & Ruthotto, L. (2013). A hyperelastic regularization energy
for image registration. SIAM Journal on Scientific Computing, 35(1), B132B148.
Cahill, N. D., Noble, J. A., & Hawkes, D. J. (2009). Demons algorithms for fluid and curvature
registration. In: International symposium on biomedical imaging, pp. 730733.
Camion, V., & Younes, L. (2001). Geodesic interpolating splines. In M. Figueiredo, J.
Zerubia & A. K. Jain (Eds.), Proceedings of EMMCVPR 01. LNCS (Vol. 2134,
pp. 513527). Berlin Heidelberg: Springer.
Candes, E. J., Romberg, J. K., & Tao, T. (2006). Stable signal recovery from incomplete
and inaccurate measurements. Communications on Pure and Applied Mathematics,
59(8), 12071223.
Cao Y., Miller M. I., Mori S., Winslow R. L., & Younes L. (2006). Diffeomorphic
matching of diffusion tensor images. In: Computer vision and pattern recognition
workshop, p. 67.
Chef dHotel C., Hermosillo G., & Faugeras O. D. (2002). Flows of diffeomorphisms for
multi-modal image registration. ISBI, IEEE, pp. 753756.
Christensen, G. E. (1994). Deformable shape models for anatomy, PhD thesis, Sever
Institute of Technology, Washington University, USA.
Christensen, G. E. (1999). Consistent linear-elastic transformations for image matching.
Information processing in medical imaging. LCNS (Vol. 1613, pp. 224237).
Heidelberg: Springer-Verlag.
Christensen, G. E., & Johnson, H. J. (2001). Consistent image registration. IEEE
Christensen, G. E., Joshi, S. C., & Miller, M. I. (1997). Volumetric transformation of
brain anatomy. IEEE Transactions on Medical Imaging, 16(6), 864877.
Christensen, G. E., Rabbitt, R. D., & Miller, M. I. (1996). Deformable templates using
large deformation kinematics. IEEE Transactions on Image Processing, 5(10),
14351447.
Collignon, A., Vandermeulen, A., Suetens, P., & Marchal, G. (1995). 3d multi-modality
medical image registration based on information theory. Computational Imaging
and Vision, 3, 263274.
Craene, M. D., Camara, O., Bijnens, B. H., & Frangi, A. F. (2009). Large diffeomorphic
FFD registration for motion and strain quantification from 3D-US sequences. In:
International conference on functional imaging and modeling of the heart,
pp. 437446.
Davatzikos, C. (1997). Spatial transformation and registration of brain images using
elastically deformable models. Computer Vision and Image Understanding, 66(2),
207222.
DHaese, P.-F., Pallavaram, S., Li, R., et al. (2012). Cranialvault and its crave tools: A
clinical computer assistance system for deep brain stimulation (dbs) therapy.
Droske, M., & Rumpf, M. (2004). A variational approach to non-rigid morphological
registration. SIAM Applied Mathematics, 64(2), 668687.
Duchon, J. (1976). Interpolation des fonctions de deux variables suivant le principle de
la flexion des plaques minces. RAIRO Analyse Numerique, 10, 512.
Durrleman, S., Pennec, X., Trouv, A., Thompson, P., & Ayache, N. (2008). Inferring
brain variability from diffeomorphic deformations of currents: An integrative
approach. Medical Image Analysis, 12(5), 626637.
Fischer, B., & Modersitzki, J. (2002a). Curvature based registration with applications to
MR-mammography. In P. Sloot, C. Tan, J. Dongarra & A. Hoekstra (Eds.),
Computational Science ICCS 2002. LNCS (Vol. 2331, pp. 203206). Heidelberg:
Springer.
Fischer, B., & Modersitzki, J. (2008). Mathematics meets medicine An optimal
alignment. SIAG/OPT Views and News, 19(2), 17.
Fischer, B., & Modersitzki, J. (2002b). Fast diffusion registration. AMS Contemporary
Mathematics, Inverse Problems, Image Analysis, and Medical Imaging, 313,
117129.
Fischer, B., & Modersitzki, J. (2003a). Combining landmark and intensity driven
registrations. PAMM, 3, 3235.
Fischer, B., & Modersitzki, J. (2003b). Curvature based image registration. Journal of
Mathematical Imaging and Vision, 18(1), 8185.
Fischer, B., & Modersitzki, J. (2004a). Intensity based image registration with a
guaranteed one-to-one point match. Methods of Information in Medicine, 43,
327330.
Fischer, B., & Modersitzki, J. (2004b). A unified approach to fast image registration and
a new curvature based registration technique. Linear Algebra and its Applications,
380, 107124.
Fischer, B., & Modersitzki, J. (2006). Image fusion and registration A variational
approach. In E. Krause, Y. Shokin, M. Resch & N. Shokina (Eds.), Computational
science and high performance computing II. Notes on Numerical Fluid Mechanics
and Multidisciplinary Design (Vol. 91, pp. 193205). Heidelberg: Springer.
Fischer, B., & Modersitzki, J. (2008). Ill-posed medicine An introduction to image
registration. Inverse Problems, 24, 119.
Fischler, M. A., & Elschlager, R. A. (1973). The representation and matching of pictorial
structures. IEEE Transactions on Computers, 22(1), 6792.
Fitzpatrick, J. M., Hill, D. L.G, & Maurer, C. R.J (2000). Image registration. In M. Sonka
& J. M. Fitzpatrick (Eds.), Handbook of medical imaging. Medical Image Processing
and Analysis (Vol. 2, pp. 447513). Bellingham, WA: SPIE.
Florack, L., Romeny, B., Koenderink, J., & Viergever, M. (1992). Scale and the
differential structure of images. Image and Vision Computing, 10, 376388.
Fornefett, M., Rohr, K., & Stiehl, H. (2000). Elastic medical image registration using
surface landmarks with automatic finding of correspondences. In T. M. L. Alexander
Horsch (Ed.), Bildverarbeitung fur die Medizin 2000, Algorithmen, Systeme,
Anwendungen (pp. 4852). Informatik Heidelberg: Springer.
Freeborough, P. A. (1998). Modeling brain deformations in alzheimer disease by fluid
registration of serial 3D MR images. Journal of Computer Assisted Tomography,
22(5), 838843.
Friston, K. J., Ashburner, J., Frith, C. D., Poline, J.-B., Heather, J. D., &
Frackowiak, R. S.J (1995). Spatial registration and normalization of images. Human
Gee, J. C., & Bajcsy, R. (1999). Elastic matching: Continuum mechanical and
probabilistic analysis. Brain Warping, 183197.
Glasbey, C. (1998). A review of image warping methods. Journal of Applied Statistics,
25, 155171.
Glauns, J., Qiu, A., Miller, M. I., & Younes, L. (2008). Large deformation diffeomorphic
metric curve mapping. International Journal of Computer Vision, 80(3), 317336.
Glauns J., Trouve A., & Younes L. (2004). Diffeomorphic matching of distributions: A
new approach for unlabelled point-sets and submanifolds matching. In:
International conference on computer vision and pattern recognition, pp. 712718.
Glauns, J., Vaillant, M., & Miller, M. I. (2004). Landmark matching via large
deformation diffeomorphisms on the sphere. Journal of Mathematical Imaging and
Vision, 20(12), 179200.
Goshtasby, A. A. (2005). 2-D and 3-D image registration. New York: Wiley Press.
Goshtasby, A. A. (2012). Image registration: Principles, tools and methods. New York:
Springer.
Guimond, A., Roche, A., Ayache, N., & Meunier, J. (2001). Three-dimensional
multimodal brain warping using the demons algorithm and adaptive intensity
corrections. IEEE Transactions on Medical Imaging, 20(1), 5869.
Guo, T., Parrent, A. G., & Peters, T. M. (2007). Surgical targeting accuracy analysis of
six methods for subthalamic nucleus deep brain stimulation. Computer Aided
Surgery, 12(6), 325334.
Haber, E., Heldmann, S., & Modersitzki, J. (2009). A framework for image-based
constrained registration with an application to local rigidity. Linear Algebra and its
Haber, E., Horesh, R., & Modersitzki, J. (2010). Numerical methods for
constrained image registration. Numerical Linear Algebra with Applications,
17(23), 343359.
Haber, E., & Modersitzki, J. (2004). Numerical methods for volume preserving image
registration. Inverse Problems, Institute of Physics Publishing, 20(5), 16211638.
Haber E., & Modersitzki J. (2005). A scale space method for volume preserving
image registration. In: Proceedings of the 5th international conference on scale
space and PDE methods in computer vision, pp. 18.
Haber, E., & Modersitzki, J. (2006a). A multilevel method for image registration. SIAM
Journal on Scientific Computing, 27(5), 15941607.
Haber, E., & Modersitzki, J. (2006b). Image registration with a guaranteed displacement
regularity. International Journal of Computer Vision, 1. http://dx.doi.org/10.1007/
s11263-006-8984-4.

Haber, E., & Modersitzki, J. (2006c). Intensity gradient based registration and fusion of
multi-modal images. In C. Barillot, D. Haynor & P. Hellier (Eds.), Medical image
computing and computer-assisted intervention MICCAI 2006. LNCS (Vol. 3216,
pp. 591598). Springer.
Haber, E., & Modersitzki, J. (2007). Intensity gradient based registration and fusion of
multi-modal images. Methods of Information in Medicine, 46(3), 292299.
Haber E., Heldmann S., & Modersitzki J. (2009b) A scale-space approach to landmark
constrained image registration. In: Proceedings of the second international
conference on scale space methods and variational methods in computer vision
(SSVM), LNCS (pp. 112). Springer.
Hadamard, J. (1902). Sur les problemes aux derivees partielles et leur signification
physique. Princeton University Bulletin, Princeton, NY, pp. 4952.
Hajnal, J., Hawkes, D., & Hill, D. (2001). Medical image registration. Boca Raton, FL:
CRC Press.
He J., & Christensen G. E. (2003). Large deformation inverse consistent elastic image
registration. In: International conference on information processing in medical
imaging, pp. 438449.
Heldmann, S. (2006). Non-linear registration based on mutual information, PhD thesis,
University of Lubeck, Germany.
Heldmann S. (2010). Multi-modal registration of MR images with a novel least-squares
distance measure. In: Proceedings of the SPIE medical imaging: Image processing.
Hellier, P., & Barillot, C. (2003). Coupling dense and landmark-based approaches for
non rigid registration. IEEE Transactions on Medical Imaging, 22, 217227.
Henn, S. (2006a). A full curvature based algorithm for image registration. Journal of
Mathematical Imaging and Vision, 24(2), 195208.
Henn, S. (2006b). A multigrid method for a fourth-order diffusion equation with
application to image processing. SIAM Journal on Scientific Computing, 27(3),
831849.
Hermosillo, G. (2002). Variational methods for multimodal image matching, PhD thesis,
Universite de Nice, France.
Hermosillo, G. V., Chef dHotel, C., & Faugeras, O. (2002). Variational methods for
multimodal image matching. International Journal of Computer Vision, 50(3),
329343.
Hill, D. L.G, Batchelor, P. G., Holden, M., & Hawkes, D. J. (2001). Medical image
registration. Physics in Medicine and Biology, 46, R1R45.
Hodneland, E., Lundervold, A., Andersen, E., & Munthe-Kaas, A. A. (2013). A
normalized hessian method for image registration with application to DCE-MRI
medical images. Magnetic Resonance Imaging. Submitted and under revision.
Holden, M. (2008). A review of geometric transformations for nonrigid body
registration. Transactions on Medical Imaging, 27(1), 111128.
Horn, B. K.P, & Schunck, B. G. (1981). Determining optical flow. Artificial Intelligence,
17, 185204.
Huber, P. J. (1973). Robust regression: Asymptotics, conjectures, and monte carlo.
Annals of Statistics, 1, 799821.
Johnson, H. J., & Christensen, G. E. (2002). Consistent landmark and intensity-based
image registration. IEEE Transactions on Medical Imaging, 21(5), 450461.
Johnson A., & Hebert M. (1997). Surface registration by matching oriented points. In:
International conference on recent advances in 3-D digital imaging and modeling,
pp. 121128.
Joshi, S. C., & Miller, M. I. (2000). Landmark matching via large deformation
diffeomorphisms. IEEE Transactions on Image Processing, 9(8), 13571370.
Kabus, S., Franz, A., & Fischer, B. (2006). Variational image registration with local
properties. In J. P. W. Pluim, & Bostjan Likar, F. A. G. (Eds.), Biomedical image
registration: Third international workshop, WBIR 2006. LNCS (pp. 92100). Springer.
Keeling, S. L. (2007). Image similarity based on intensity scaling. Journal of
Mathematical Imaging and Vision, 29, 2134.
Keeling, S. L., & Ring, W. (2005). Medical image registration and interpolation by
optical flow with maximal rigidity. Journal of Mathematical Imaging and Vision,
23(1), 4765.
Kullback, S., & Leibler, R. A. (1951). On information and sufficiency. Annals of
Mathematical Statistics, 22, 7986.
Kybic, J., & Unser, M. (2000). Multidimensional elastic registration of images using
splines. In: ICIP in Vancouver, 1013 September 2000, Vol. II, pp. 455458.
Lehmann, T., Gonner, C., & Spitzer, K. (1999). Survey: Interpolation methods in
medical image processing. IEEE Transactions on Medical Imaging, 18(11),
10491075.
Leow, A., Huang, S.-C., Geng, A., Becker, J., Davis, S., Toga, A., & Thompson, P.
(2005). Inverse consistent mapping in 3d deformable image registration: Its
construction and statistical properties. International conference on information
processing in medical imaging, pp. 493503.
Leow, A. D., Yanovsky, I., Chiang, M.-C., et al. (2007). Statistical properties of jacobian
maps and the realization of unbiased large-deformation nonlinear image
registration. IEEE Transactions on Medical Imaging, 26(6), 822832.
313
Lester, H., & Arridge, S. R. (1999). A survey of hierarchical non-linear medical image
registration. Pattern Recognition, 32, 129149.
Light, W. A. (1996). Variational methods for interpolation, particularly by radial basis
functions. In D. Griffiths & G. Watson (Eds.), Numerical analysis 1995
(pp. 94106). London: Longmans.
Lindeberg, T. (1994). Scale-space theory in computer vision. Dordrecht: Kluwer
Academic Publishers.
Little, J., Hill, D., & Hawkes, D. (1997). Deformations incorporating rigid structures.
Computer Vision and Image Understanding, 66(2), 223232.
Loeckx, D., Maes, F., Vandermeulen, D., & Suetens, P. (2004). Nonrigid image
registration using free-form deformations with a local rigidity constraint, MICCAI.
LNCS (Vol. 3216, pp. 639646).
Maes, F., Collignon, A., Vandermeulen, D., Marchal, G., & Suetens, P. (1997).
Multimodality image registration by maximization of mutual information. IEEE
Maintz, J. B.A, & Viergever, M. A. (1998). A survey of medical image registration.
Martens, H. C.F, Toader, E., Decre, M. M.J, et al. (2011). Spatial steering of deep brain
stimulation volumes using a novel lead design. Clinical Neurophysiology, 122(3),
558566.
Miller, M., & Younes, L. (2001). Group actions, homeomorphisms, and matching: A
general framework. International Journal of Computer Vision, 41, 6184.
Modat, M., Vercauteren, T., Ridgway, G. R., Hawkes, D. J., Fox, N. C., & Ourselin, S.
(2010). Diffeomorphic demons using normalized mutual information, evaluation on
multimodal brain MR images. In: Proceedings of the SPIE medical imaging: Image
processing, 76 232K0176 232K8.
Modersitzki, J. (2004). Numerical methods for image registration. New York: Oxford
University Press.
Modersitzki, J. (2008). FLIRT with rigidity Image registration with a local non-rigidity
penalty. International Journal of Computer Vision, 76, 153163. http://dx.doi.org/
10.1007/s11263-007-0079-3.
Modersitzki, J. (2009). FAIR: Flexible algorithms for image registration. Philadelphia:
SIAM.
Modersitzki, J., & Fischer, B. (2003). Optimal image registration with a guaranteed oneto-one point match. In T. Wittenberg et al. (Eds.), Bildverarbeitung fur die Medizin
2003 (pp. 15): Heidelberg: Springer.
Modersitzki, J., & Wirtz, S. (2006). Combining homogenization and registration, In
J. P. Pluim et al. (Eds.), Biomedical image registration: Third international
workshop, WBIR 2006. LNCS (pp. 257263). Springer.
Mohammadi, S., Nagy, Z., Hutton, C., Josephs, O., & Weiskopf, N. (2011). Correction
of vibration artifacts in DTI using phase-encoding reversal (COVIPER). Magnetic
Poschl, C., Modersitzki, J., & Scherzer, O. (2010). A variational setting for volume
constrained image registration. Inverse Problems and Imaging, 4(3), 500522.
Pennec X., Stefanescu R., Arsigny V., Fillard P., & Ayache N. (2005). Riemannian
elasticity: A statistical regularization framework for nonlinear registration. In:
intervention, pp. 943950.
Peshko, O., Modersitzki, J., Terlaky, T., Menard, C., Craig, T., & Moseley, D. (2010).
Automatic localization and tracking of fiducial markers for organ motion analysis in
image-guided radiation therapy. In: Proceedings of the SPIE 2010, Medical
Imaging, pp. 14.
Pluim, J., Maintz, J., & Viergever, M. (1999). Mutual-information-based registration of
medical images: A survey. IEEE Transactions on Medical Imaging, 22, 9861004.
Pluim, J. P., Maintz, J. B.A, & Viergever, M. A. (2000). Image registration by
maximization of combined mutual information and gradient information. IEEE
Roche, A. (2001). Recalage dimages medicales par inference statistique, PhD thesis,
Universite de Nice, Sophia-Antipolis, France.
Roche, A., Malandain, G., Pennec, X., & Ayache, N. (1998). The correlation ratio as a
new similarity measure for multimodal image registration, MICCAI 1998. Lecture
Notes in Computer Science (Vol. 1496, pp. 11151124). Cambridge, MA: Springer
Verlag.
Rohlfing, T., Maurer, C. R., Jr., Bluemke, D. A., & Jacobs, M. A. (2003). Volumepreserving non-rigid registration of MR breast images using free-form deformation
with an incompressibility constraint. IEEE Transactions on Medical Imaging, 22(6),
730741.
Rohr, K. (2001). Landmark-based image analysis. Computational imaging and vision.
Dordrecht: Kluwer Academic Publishers.
Rueckert, D., Hayes, C., Studholme, C., Summers, P., Leach, M., & Hawkes, D. J.
(1998). Non-rigid registration of breast MR images using mutual information. In
A. C. F. Colchester, S. L. Delp & W. M. Wells (Eds.), MICCAI 98: Medical image
computing and computer-assisted intervention (pp. 11441152). Berlin: Springer.
314
Rueckert, D., Sonoda, L., Hayes, C., Hill, D., Leach, M., & Hawkes, D. (1999). Non-rigid
registration using free-form deformations. IEEE Transactions on Medical Imaging,
18(1), 712721.
Ruthotto, L., Gigengack, F., Burger, M., et al. (2012). A simplified pipeline for motion
correction in dual gated cardiac PET. In T. Tolxdorff, T. Deserno, H. Handels, &
H.-P. Meinzer (Eds.), Bildverarbeitung fur die Medizin 2012 (pp. 5156).
Ruthotto, L., Hodneland, E., & Modersitzki, J. (2012). Registration of dynamic contrast
enhanced MRI with local rigidity constraint, In B. Dawant, J. Fitzpatrick, D. Rueckert
& G. Christensen (Eds.), Biomedical image registration, 5th international workshop
WBIR 2012. Heidelberg: Springer, pp. 190198.
Ruthotto, L., Kugel, H., Olesch, J., et al. (2012). Diffeomorphic susceptibility artefact
correction of diffusion-weighted magnetic resonance images. Physics in Medicine
and Biology, 57, 57155731.http://stacks.iop.org/0031-9155/57/5715.
Salden, A. H., Ter Haar Romeny, B. M., & Viergever, M. A. (1998). Linear scale-space theory
from physical principles. Journal of Mathematical Imaging and Vision, 9(2), 103139.
Scherzer, O. (2006). Mathematical models for registration and applications to medical
imaging. New York: Springer.
Staring, M., Klein, S., & Pluim, J. (2006). Nonrigid registration using a rigidity
constraint. In J. Reihnardt, & J. Pluim (Eds.), Proceedings of the SPIE 2006,
medical imaging, 2006, SPIE-6144, 110
Staring, M., Klein, S., & Pluim, J. P.W (2007). A rigidity penalty term for nonrigid
registration. Medical Physics, 34(11), 40984108.
Stejskal, E., & Tanner, J. E. (1965). Spin diffusion measurements: Spin echoes in the
presence of a time-dependent field gradient. Journal of Chemical Physics, 42(1),
288292.
Szeliski, R. (2006). Image alignment and stitching: A tutorial. Foundations and Trends
in Computer Graphics and Vision, 2(1), 1104.http://dx.doi.org/10.1561/
0600000009.
Thevenaz, P., Blu, T., & Unser, M. (2000). Image interpolation and resampling. In I.
Bankman (Ed.), Handbook of medical imaging, processing and analysis
(pp. 393420). San Diego, CA: Academic Press.
Thirion, J.-P. (1995). Fast non-rigid matching of 3D medical images, Technical
report 2547, Institut National de Recherche en Informatique et en Automatique,
France.
Thirion, J.-P. (1996). Non-rigid matching using demons. In IEEE, Conference on
computer vision and pattern recognition, pp. 245251.
Thirion, J.-P. (1998). Image matching as a diffusion process: An analogy with Maxwells
demons. Medical Image Analysis, 2(3), 243260.
Tikhonov, A. N. (1943). On the stability of inverse problems. Doklady Akademii Nauk
SSSR, 39(5), 195198, in Russian.
Toga, A. W., & Mazziotta, J. C. (2002). Brain mapping: The methods (2nd ed.).
Waltham, MA: Academic Press.
Trouve, A. (1998). Diffeomorphisms groups and pattern matching in image analysis.

International Journal of Computer Vision, 28(3), 213221.
Twining, C. J., & Marsland, S. (2004). Constructing diffeomorphic representations for
the group-wise analysis of non-rigid registrations of medical images. IEEE
Vaillant M., & Glauns J. (2005). Surface matching via currents. In: International
conference on information processing in medical imaging, pp. 381392.
van den Elsen, P. A., Pol, E.-J. D., & Viergever, M. A. (1993). Medical image matching
A review with classification. IEEE Engineering in Medicine and Biology, 12, 2638.
Vercauteren, T., Pennec, X., Perchant, A., & Ayache, N. (2007). Non-parametric
diffeomorphic image registration with the demons algorithm, MICCAI 2007,
Brisbane, pp. 319326.
Vercauteren T., Pennec X., Perchant A., & Ayache N. (2008). Symmetric log-domain
diffeomorphic registration: A demons-based approach. In: International conference
on medical image computing and computer-assisted intervention, pp. 754761.
Vercauteren, T., Pennec, X., Perchant, A., & Ayache, N. (2009). Diffeomorphic demons:
Efficient non-parametric image registration. NeuroImage, 45(1), S61S72.
Viola, P., & Wells III, W. M. (1995). Alignment by maximization of mutual information
(pp. 1623). IEEE 1995.
Wahba, G. (1990). Spline models for observational data. Philadelphia: SIAM.
Weickert, J., & Schnorr, C. (2001). A theoretical framework for convex regularizers in
PDE-based computation of image motion. International Journal of Computer Vision,
45(3), 245264.
Yang, X., Xue, Z., Liu, X., & Xiong, D. (2011). Topology preservation evaluation of
compact support radial basis functions for image registration. Pattern Recognition
Letters, 32(8), 1621177.
Yanovsky, I., Guyader, C. L., Toga, A. L. A. W., Thompson, P. M., & Vese, L. (2008).
Unbiased volumetric registration via nonlinear elastic regularization. In: Workshop
on mathematical foundations of computational anatomy: Medical image computing
and computer-assisted intervention.
Yeo, B., Sabuncu, M., Vercauteren, T., Ayache, N., Fischl, B., & Golland, P. (2008).
Spherical demons: Fast surface registration. Medical Image Computing and
Computer Assisted Intervention, 11, 745753.
Yeo, B. T.T, Sabuncu, M. R., Vercauteren, T., Ayache, N., Fischl, B., & Golland, P.
(2010). Spherical demons: Fast diffeomorphic landmark-free surface registration.
Yoo, T. S. (2004). Insight into images: Principles and practice for segmentation,
registration, and image analysis. Wellesley, MA: AK Peters Ltd.
Zhu, L., Haker, S., & Tannenbaum, A. (2003). Area preserving mappings for the
visualization of medical structures. Medical Image Computing and Computer
Assisted Intervention, 2879, 277284.
Zitova, B., & Flusser, J. (2003). Image registration methods: A survey. Image and Vision
Computing, 21(11), 9771000.
Diffeomorphic Image Registration

J Ashburner, UCL Institute of Neurology, London, UK
MI Miller, Johns Hopkins University, Baltimore, MD, USA
Glossary
Action An attribute of the dynamics of a physical system,

which is fundamental to all of classical physics.
Adjoint The generalization of matrix transposes to
(possibly) infinite-dimensional situations.
Change of variables An important tool for integrating
functions, which is the counterpart to the chain rule of
differentiation.
Composition An operation that combines two functions
and gives a single function as the result.
Convolution A mathematical operation on two functions
that produces a third function that is typically viewed as a
modified version of one of the originals.
Deformation The transformation of an object from one
configuration to another.
Derivative A measurement of how a function changes when
the values of its inputs change.
Diffeomorphic Satisfies the requirements of a
diffeomorphism.
Diffeomorphism A differentiable mapping that has a
differentiable inverse.
Differentiable Something that can be differentiated.
Differential operator An operator defined as a function of
differentiation.
Discretization The process of transferring continuous
models and equations into discrete counterparts.
Displacement The difference between final and initial
positions, where the actual path is irrelevant.
Domain The set of input values over which a function is
defined.
Dynamical system A concept in mathematics where a rule
describes the time dependence of points in a geometric
space.
EPDiff An equation that arose in the EulerPoincare theory
applied to optimal motion on diffeomorphisms.
Euclidean An intuitively obvious system of geometry where
parallel lines never meet.
Euler integration A first-order numerical procedure for
solving ordinary differential equations with a given initial
value.
Gaussian A very commonly occurring continuous bellshaped probability distribution.
Generative model A model encoding a probability
distribution from which observable data are treated as a
sample.
Geodesic Pertains to the geometry of curved surfaces, where
geodesics take the place of the straight lines of plane
geometry.
Gradient descent A first-order (i.e., using only first
derivatives) optimization algorithm.
Greens function The impulse response of an
inhomogeneous differential equation.
Group A set of elements, together with an operation that

combines any two of its elements to form a third element
also in the set. The elements (and operation) satisfy four
conditions called the group axioms, namely, closure,
associativity, identity, and invertibility.
Hamiltonian A scalar function of canonical coordinates
(position and momentum), which corresponds to the total
energy of a system.
Hamiltonian mechanics A reformulation of classical
mechanics that provides a more abstract understanding of
the theory.
Identity A special type of element of a set, which leaves
other elements unchanged when composed with them.
Independent and identically distributed When each
random variable has the same probability distribution as the
others and all are mutually independent.
Inverse Generalizes concepts of a negation in relation to
addition and a reciprocal in relation to multiplication.
Iteration The repetition of a block of statements within a
computer program.
Jacobian Usually refers to the matrix of all first-order partial
derivatives of a vector-valued function.
Jacobian determinant The determinant of a Jacobian
matrix, which encodes the factor by which a function
expands or shrinks volumes.
Lagrangian mechanics A reformulation of classical
mechanics using the principle of stationary (least) action.
LDDMM Stands for large deformation diffeomorphic
mapping, which is an image registration approach using the
principle of stationary action.
Manifold A topological space or surface.
Mapping A synonym for function or denotes a particular
kind of function.
Metric An abstraction of the notion of distance.
Model A description of a system using mathematical
concepts and language.
Momentum (generalized, canonical, or conjugate
momentum) A generalization of the concepts of both linear
momentum and angular momentum.
Morphometric A quantitative analysis of form, a concept
that encompasses size and shape.
Noise Signal that is not explained by a model.
Norm A function assigning a positive length or size to a
vector.
Objective function A function that maps values of one or
more variables onto a real number, which intuitively
represents some cost.
Operator A mapping from one vector space to another.
Optimization Involves systematically estimating parameter
values that maximize or minimize an objective function.
Registration The process of transforming different sets of
data into one coordinate system.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00301-8
315
316
INTRODUCTION TO METHODS AND MODELING | Diffeomorphic Image Registration
Regularization A process of introducing additional

information in order to solve ill-posed problems or prevent
overfitting.
Riemannian geometry The branch of differential geometry
that studies smooth manifolds with a metric defined by an
inner product on the tangent space at each point, which
varies smoothly.
Shooting A method for solving a boundary value problem
by reducing it to the solution of an initial value problem.
Spatial normalization A term used by neuroimagers that
refers to warping images of different individuals to a
common coordinate system.
Template Some form of reference image, or set of images,
that serves as a model or standard for alignment with scans
of individual subjects.
Introduction
Tensor field Has a tensor at each point in space.

Translationally invariant Remains unchanged when every
point is shifted by the same amount.
Variance A measure of the dispersion of a set of numbers.
Variational Analysis deals with maximizing or minimizing
functionals, which are mappings from functions to real
numbers.
Velocity field A vector field used to mathematically describe
the motion of a fluid.
Viscous fluid Registration approaches that estimate
diffeomorphic mappings, although the estimated
trajectories do not follow geodesics.
E2 m, f , f
Deformations (warpings) are an important component of

most models of biological images. For example, most neuroimagers currently do some form of spatial normalization to
align data from different subjects to a common coordinate
system, thus enabling signal from brain images of different
subjects to be averaged or compared. Similarly, longitudinal
tracking of growth or atrophy within a single subject also
involves deformations, as do any other analyses of biological
shapes. Estimating the optimal deformations between images
is achieved by image registration. Medical image registration is
a large research area, with many practical applications. For
recent surveys of the field, see Mani and Arivazhagan (2013)
and Sotiras, Davatazikos, and Paragios (2012).
Technically, a diffeomorphism is a map between
manifolds, which is differentiable and has a differentiable
inverse. This article introduces some of the methods that can
be used for estimating invertible and differentiable deformations that map between images, although a number of important approaches have been omitted. Space prohibits a detailed
description of the symmetric image normalization method
(SyN) (Avants, Epstein, Grossman, & Gee, 2008; Avants &
Gee, 2004), as well as the various diffeomorphic approaches
based on constructing deformations via a scaling and squaring
procedure (Arsigny, Commowick, Pennec, & Ayache, 2006;
Ashburner, 2007; Vercauteren, Pennec, Perchant, & Ayache,
2009).
The following sections will sketch out some simple gradient
descent algorithms for image registration, where the aim is to
warp a template (m: O ! , where O d ) to match an image
(f: O ! ). Usually, a deformation field (f: O ! O) is estimated by locally minimizing some form of objective function:
f^ arg min E1 f E2 m, f , f
f
This article only considers an image matching term based

on the L2 norm, which essentially assumes that the image may
be modeled as a warped version of the template, with added
independent and identically distributed Gaussian noise of
known variance s2:

1
mf1 f 2
2s2
The notation mf1 denotes function composition and is

occasionally written simply as m(f1). This article also uses id
to denote the identity transform, such that mid m.
An additional term (E1) is included to penalize unlikely
deformations. The registration procedures sketched out here
differ mostly in how this penalty is imposed.
Small Displacement Approximation

Prior to introducing diffeomorphic registration algorithms, we
begin by presenting a gradient descent registration based on a
small displacement approximation. The aim is to estimate the
displacement field (u: O ! d) that minimizes the following
objective function:
1
2
E kLvk2
1
km id v f k2
2s2
Here, the penalty term involves minimizing Lv2, where L is

some form of differential operator. There are a wide variety of
operators to choose from, and the particular form will influence the properties of the estimated deformations. The Greens
function of the operator (K, such that KL{Lv v or L{LKu u) is
involved within the optimization procedure, which is summarized in Algorithm 1. Here, the { symbol denotes the adjoint of
the L operator which is a generalization of the transpose
operation on square matrices. The Greens function is usually
translationally invariant, so it can be conceptualized as a convolution operator (see Figure 1).
Gradient descent schemes require a suitable step size (e), by
which changes to the estimates should be scaled at each iteration. Convergence is very slow if e is too small, whereas algorithms can become unstable if it is too large. The value of e is
often fixed, although it is possible to combine the approach
with a line search that estimates the best value for each iteration. Faster convergence can often be achieved using both first
and second derivatives. Modersitzki (2009) described a number of alternative optimization approaches suitable for image
registration.
(a)
Greens function (K)
(b)
Figure 1 Discrete representations of an example differential operator

and Greens function in 2-D. Applying the operators involves convolution,
which may be done using discrete Fourier transforms.
We note that the estimated deformation (id v) may not be

diffeomorphic. The next few sections describe approaches for
estimating diffeomorphic mappings.
Algorithm 1 Small Displacement Approximation.
v
0
repeat
0
mid v
m
g rm
0 id
v
b s12 m f g
v v Ev Kb
until convergence
Viscous Fluid Methods

The set of possible diffeomorphisms over a particular domain
forms a mathematical group, where the natural operation on
two diffeomorphisms is the composition.
317
The small displacement framework treats displacement

fields as if they are additive yf y id f id id.
This is reasonable for very small displacements, but less accurate for larger ones. As an analogy, multiplication by numbers
close to 1 (the identity element of the multiplicative group of
positive real numbers) can be approximated by a small displacement model. For example, while 1.002 1.002
(1.002 1) (1.002 1) 1 1.004 may be reasonable, this
approximation is less satisfactory for numbers deviating further
(2 2 3).
Christensen, Rabbitt, and Miller (1993, 1996) introduced
the concept of viscous fluid registration, which allowed very
large deformations to be achieved while preserving (diffeomorphic) one-to-one mappings. Updates to the deformations
essentially involved composing a series of small deformations
together. Providing these are small enough to be one-to-one,
their compositions should also be one-to-one.
Algorithm 2 summarizes the viscous fluid registration
approach, which has been formulated to estimate both forward f f m and inverse mc f deformations. The
repeated compositions of a series of small deformations may
be conceptualized as a form of Euler integration. In practice,
integrations often make use of the fact that
id evf f evf and that when e is sufficiently small,
cid ev c eDcv. We use Dc to denote the Jacobian
tensor field of c and (Dc)v to denote multiplying matrices and
vectors at each point in O.
One obvious disadvantage of the viscous fluid approach is
that it does not minimize any clearly defined objective function, and the restoring force to the template is not related to the
magnitude of the deformation (Dupuis, Grenander, & Miller,
1998). Essentially, the solution is unregularized, so finding a
good solution depends on terminating the algorithm after a
suitable number of iterations.
Algorithm 2 Viscous Fluid.
C
id
f
id
repeat
0
mc
m
0
0
b s12 m f rm
v Kb
c cid Ev
f id Evf
until close enough
Large Deformation Diffeomorphic Metric Mapping

The large deformation diffeomorphic metric mapping
(LDDMM) algorithm (Beg, Miller, Trouve, & Younes, 2005)
is more principled than the viscous fluid approach. It
minimizes
1
2
1
1
E
kLvt k2 dt 2 mf1 f
2 0
2s
where f0 id and dtd ft vt ft . The aim is to optimize the timedependent velocity field, v, where the subscripts denote the
fields at time t (time is a slightly artificial construct for crosssectional registration but makes more intuitive sense for longitudinal growth modeling). The previously mentioned
318
formulation is for the continuous limit. In practice, some form

of discretization is required. An intuitive interpretation of the
approach is that it computes deformations from the composition of a series of N small deformations:

.. . id N1 vN1
f1 id N1 v1 id N1 vN1
N

1
1
1
f1
1 id NvN1 id NvN2 ... id Nv1
Given an initial (f0 id) and final (f1) diffeomorphism,
the regularization component of the objective function essentially finds the trajectory between them that minimizes the
integral of an energy term. This may be conceptualized in
terms of Lagrangian mechanics with only a kinetic energy
term (which links the approach to Riemannian geometry),
where the aim is to determine the trajectory of the evolving
diffeomorphism that satisfies the principle of least (stationary)
action (see, e.g., Marsden & Ratiu, 1999). For this model, the
action is defined as
1
kLvt k2 dt
2 0
In addition to minimizing the energy, the path found is also

a geodesic. In Riemannian geometry, this is the shortest path
connecting two points on a nonlinear manifold. A simple illustration of this concept would be the shortest distance between
two cities on the globe, where we measure distances tangentially along the surface. A piecewise
XN linear
approximation to the
Lv n , whereas it is given by
length would be given by N1
N
n1
1
kLvt kdt in a continuous setting. The distance satisfies the
0
conditions required of a metric, making it useful for assessing

similarities between anatomies (Miller, Trouve, & Younes, 2002).
Algorithm 3 shows a simplified version of the one developed by Beg et al. (2005), with a 2-D illustration of simple
image matching shown in Figure 2. In particular, integration
involves a simple Euler approach, which is not especially
v0
f 0,0
f 0,1
f f 0,1
|Df 0,1|
v0.2
f 0.2,0
mf 0.2,0
f 0.2,1
f f 0.2,1
|Df 0,2,1|
v0.4
f 0.4,0
mf 0.4,0
f 0.4,1
f f 0.4,1
|Df 0,4,1|
v0.6
f 0.6,0
mf 0.6,0
f 0.6,1
f f 0.6,1
|Df 0,6,1|
v0.8
f 0.8,0
mf 0.8,0
f 0.8,1
f f 0.8,1
|Df 0,8,1|
v1
f 1,0
mf 1,0
f 1,1
|Df 1,1|
Figure 2 Schematic illustration of velocity fields, diffeomorphisms, and warped images involved in LDDMM.

accurate unless N is large. A new notation is introduced, where
we define s, t ft f1
s . The notation |Dt,1| means to compute the Jacobian determinant of t,1, which is used when
introducing a change of variables.
Algorithm 3 Large Deformation Diffeomorphic Metric
Mapping.
for n 0 . . . N do
vNn 0
Nn , 0 id
Nn , 1 id
end for
repeat
for n 0 . . . N do
mNn mNn, 0
fNn f Nn , 1

bNn s12 DNn , 1 mNn fNn rmNn

vNn vNn e vNn KbNn
end for
for n N 1 . . . 0 do
Nn , 1 n1
id N1 vn1
N
N ,1
end for
for n 1 . . . N do

Nn , 0 n1
id N1 vNn
N ,0
end for
until convergence
Rather than warping a noiseless template to an image, it is
sometimes desirable to register two images (f0 and f1) together
in an inverse-consistent way (f 0 1, 0 f 1 and f 1 0, 1 f 0 ).
One strategy to achieve this within the LDDMM framework
(with a few adjustments to the integration procedure) is to
formulate the problem with an intermediate template computed from the two images (Ashburner & Ridgway, 2013;
Hart, Zach, & Niethammer, 2009; Niethammer, Hart, & Zach,
2009). This leads to the following definition of the force driving the registration:

1 Dt , 1 Dt , 0 ft0 ft1

bt
s2 Dt, 1 Dt , 0

D rf 0 D rf 1
t, 1
t, 0
t
t

D D
t, 1
t, 0
A disadvantage of LDDMM is that it requires a lot of memory to store a number of intermediate diffeomorphisms and
velocity fields. Rather than to determine the trajectory of the
evolving diffeomorphisms from the initial and final configurations (solving a boundary value problem), an alternative
approach would be to compute the trajectory from the initial
(or final) configuration and velocity (Miller, Trouve, & Younes,
2006). This strategy, called geodesic shooting, does not
require so much intermediate information to be stored.
Geodesic Shooting
Closer examination of Algorithm 3 shows that at any time
from
point, bt may
be determined
T
b1 via because mt m1 t, 1
and rmt Dt , 1 rm1 t , 1

bt s12 Dt , 1 mt ft rmt

T

Dt , 1 Dt , 1 b1 t, 1
319
When Algorithm 3 has converged, changes to the velocities

fall to zero, which implies that vt Kbt along the geodesic
solution. This allows registration to be formulated so that
only the final velocity (v1) is updated via the same gradient
descent approach as for LDDMM. (This may just be an approximation to the correct derivatives for registration via geodesic
shooting, as they differ from the more involved formulation in
Younes (2007). In practice however, the approach works well.)
The remainder of the velocity fields are computed from the
final one via geodesic shooting. Each gradient descent iteration
should bring v1 closer to its optimal solution, which in turn
should bring the remaining velocity fields closer to theirs.
Obtaining the geodesic trajectory from the final velocity can
be achieved by computing u1 L{Lv1 (known as the
momentum) and integrating the diffeomorphisms (t,1 and
1,t) backward in time using

T

vt K Dt, 1 Dt , 1 u1 t, 1
See Algorithm 4 for further details. Note that faster convergence of the optimization can be achieved by using both first
and second derivatives (Ashburner & Friston, 2011).
Algorithm 4 Geodesic Shooting, estimating final velocity.
v1
0
1,0
id
repeat
m1 m1, 0
b1 s12 m1 f rm1
v1 v1 Ev1 Kb1
u1 L{ Lv1
1, 1 id
for n N 1. .. 0 do
id N1 vn1
Nn , 1 n1
N
N ,1
1, Nn
uNn

id N1 vn1
1, n1
N
N

T

D
D
u1 Nn , 1
Nn , 1
n
N, 1
vNn KuNn
end for
until convergence
It is relatively straightforward to reformulate the algorithm
to estimate the initial velocity (v0) instead of the final one. In
this case, we obtain the following at the solution:

v0 K s12 D0, 1 m f 0, 1 rm
K s12 a0 rm

where a0 D0, 1 m f 0, 1 . From this, we see that the
diffeomorphic mappings can be reconstructed from a0, m, K,
and s2 (see Figure 3). For a morphometric study, where a
series of images are all registered with the same m, using the
same K and s2, a (sometimes known as the scalar momentum)
provides a useful representation of the deviation of each image
from the template (Singh et al., 2010). Algorithm 5 illustrates
an approach to registration, based on directly optimizing the
initial scalar momentum. A related scheme was used in Vialard,
Risser, Rueckert, and Cotter (2012).
Algorithms 4 and 5 use simple Euler integration approaches
to compute diffeomorphisms from a velocity field. It is possible to use more accurate integrators, but many of these require
320

m
1 m
2 m
a0 = | Df 0,1 | (m f f 0,1)
u0 horizontal
u0 vertical
v0
v0 horizontal
v0 vertical
Figure 3 Constructing the

Top row:
and horizontal
components of its gradients rm. Middle row:
velocity.

initial
template (m) and the vertical
initial scalar momentum a0 D0, 1 m f0, 1 and initial momentum u0 s1 a0 rm . Bottom row: initial velocity (v0 Ku0), shown as a quiver
plot, as well as in terms of its components.
2
du/dt, in addition to df/dt. Thesemay be

T derived from the
directional derivative of ut Dt, 1 Dt , 1 u1 t, 1 .
Algorithm 5 Geodesic Shooting, estimating initial scalar
momentum.
v0
0
1, 0 id
a0
0
repeat
f0 f 1, 0

a0 a0 E a0 D1, 0 m f0
0, 0 id
for n 1. . . N do
mn1
m0, n1
N
N
1 n1
un1
s2 a N rmn1
N
N
vn1
Kun1
N
N

Nn , 0 n1
id N1 vn1
N
N ,0

0, Nn
id N1 vn1
0, n1

N
N

n
aN D0, Nn a0 0, Nn
end for
until convergence

u_ dtd jDid tvj Did tvT uid tv t0
udivv DvT u Duv
This equation is sometimes known as the EPDiff equation

(as it arose in the EulerPoincare theory applied to optimal
motion on diffeomorphisms) and is an important component
of fluid dynamics.
Hamiltonian Mechanics
Another framework for diffeomorphic registration involves
parameterizing the dynamical system via particles. Typically,
qi(t) is used to denote the position vector of the ith particle,
and pi(t) is its associated momentum vector at time t. From
these, evolving momentums and velocity fields can be constructed from
X
dx qi t pi t
ut x
i
X
vt x
Kx qi t pi t
i
Early work on geodesic interpolating splines (Camion &

Younes, 2001; Joshi & Miller, 2000) involved minimizing the
action within a variational setting, but it was soon realized that
a geodesic shooting approach could also be used (Miller et al.,
2006; Mills, Shardlow, & Marsland, 2006). This framework
involves Hamiltonian mechanics, which is a generalization of
classical mechanics (see, e.g., Marsden & Ratiu, 1999). The

Hamiltonian represents the total energy in a system, consisting of the sum of kinetic and potential energy terms. For
geodesic interpolating splines, the Hamiltonian is simply a
kinetic energy term, defined as
XX

1
pi t T K qi t qj t pj t
q, p, t
2
The time evolution of the system is then given by

Hamiltons equations:
p_i
q_i
X

@

pTi rK qi qj pj
@qi
j

@ X
K qi qj pj
@pi
j
Marsland and McLachlan (2007) formulated volumetric

registration as a geodesic shooting problem involving particles.
A limitation of the approach is that the convolutions become
slow with large numbers of particles. More recent approaches
overcome this by inserting the particles into a regular mesh,
which is easier to convolve (Cotter, 2008).
Outlook
For many years, most people thought the Earth was flat. While
this was a reasonable working assumption for those who did
not travel far, it fails badly for exploring further afield. Similarly, small deformation approximations to image registration
which assume that displacements can be added and subtracted as if their geometry was Euclidean may be almost
close enough for many current neuroimaging applications.
However, to make real advances in modeling and understanding brain growth, development, aging and pathologies, we may
need to discard Euclids axioms and work within a Riemannian
geometry setting.
This article has focused on simple approaches to pairwise
diffeomorphic image registration. Although progress has been
made, there is much to be done in terms of fully integrating
diffeomorphic deformations into our generative models of brain
image data. Pairwise registration is only the Riemannian geometry equivalent of connecting two points with a straight line.

Bayesian Multiple Atlas Deformable Templates; Computing Brain
Change over Time; Modeling Brain Growth and Development;
Nonlinear Registration Via Displacement Fields; Tensor-Based
Morphometry.
References
Arsigny, V., Commowick, O., Pennec, X., & Ayache, N. (2006). A log-Euclidean
framework for statistics on diffeomorphisms. Medical image computing and
computer-assisted intervention MICCAI, 924931.
321

38(1), 95113.
Ashburner, J., & Friston, K. (2011). Diffeomorphic registration using geodesic shooting
and Gauss-Newton optimisation. NeuroImage, 55, 954967.
Ashburner, J., & Ridgway, G. R. (2013). Symmetric diffeomorphic modeling of
longitudinal structural MRI. Frontiers in Neuroscience, 6.
Avants, B., Epstein, C., Grossman, M., & Gee, J. (2008). Symmetric diffeomorphic
image registration with cross-correlation: Evaluating automated labeling of elderly
and neurodegenerative brain. Medical Image Analysis, 12(1), 2641.
Avants, B., & Gee, J. (2004). Geodesic estimation for large deformation anatomical
shape averaging and interpolation. NeuroImage, 23, 139150.
Beg, M., Miller, M., Trouve, A., & Younes, L. (2005). Computing large deformation
Camion, V., & Younes, L. (2001). Geodesic interpolating splines. In Energy
minimization methods in computer vision and pattern recognition (pp. 513527).
Berlin Heidelberg: Springer.
Christensen, G. E., Rabbitt, R. D., & Miller, M. I. (1993). A deformable neuroanatomy
textbook based on viscous fluid mechanics. In J. Prince & T. Runolfsson (Eds.),
Proceedings of the 27th annual conference on information sciences and systems
Citeseer.
Christensen, G., Rabbitt, R., & Miller, M. (1996). Deformable templates using large
deformation kinematics. IEEE Transactions on Image Processing, 5(10),
14351447.
Cotter, C. J. (2008). The variational particle-mesh method for matching curves. Journal
of Physics A: Mathematical and Theoretical, 41(34), 344003.
Dupuis, P., Grenander, U., & Miller, M. I. (1998). Variational problems on flows of
diffeomorphisms for image matching. Quarterly of Applied Mathematics, 56(3),
587.
Hart, G., Zach, C., & Niethammer, M. (2009). An optimal control approach for
deformable registration. In: IEEE computer society conference on computer vision
and pattern recognition workshops, 2009. CVPR Workshops 2009 (pp. 916),
IEEE.
Joshi, S. C., & Miller, M. I. (2000). Landmark matching via large deformation
diffeomorphisms. IEEE Transactions on Image Processing, 9(8), 13571370.
Mani, V., & Arivazhagan, S. (2013). Survey of medical image registration. Journal of
Biomedical Engineering, 1(2), 825.
Marsden, J. E., & Ratiu, T. S. (1999). Introduction to mechanics and symmetry: A basic
exposition of classical mechanical systems (Vol. 17). Springer Verlag.
Marsland, S., & McLachlan, R. (2007). A Hamiltonian particle method for diffeomorphic
image registration. Lecture Notes in Computer Science, 4584, 396.
Miller, M. I., Trouve, A., & Younes, L. (2002). On the metrics and Euler-Lagrange
equations of computational anatomy. Annual Review of Biomedical Engineering,
4(1), 375405.
Miller, M., Trouve, A., & Younes, L. (2006). Geodesic shooting for computational
anatomy. Journal of Mathematical Imaging and Vision, 24(2), 209228.
Mills, A., Shardlow, T., & Marsland, S. (2006). Computing the geodesic interpolating
spline. In Biomedical image registration (pp. 169177). Berlin Heidelberg:
Springer.
Modersitzki, J. (2009). FAIR: Flexible algorithms for image registration, Vol. 6
Philadelphia, USA: Society for Industrial and Applied Mathematics (SIAM).
Niethammer, M., Hart, G., & Zach, C. (2009). An optimal control approach for the
registration of image time-series. In: Proceedings of the 48th IEEE conference on
decision and control, 2009 held jointly with the 2009 28th chinese control
conference. CDC/CCC 2009 (pp. 24272434), IEEE.
Singh, N., Fletcher, P. T., Preston, J. S., Ha, L., King, R., Marron, J. S., et al. (2010).
Multivariate statistical analysis of deformation momenta relating anatomical shape
to neuropsychological measures. Medical image computing and computer-assisted
intervention MICCAI, 529537.
Sotiras, A., Davatazikos, C., & Paragios, N. (2012). Deformable medical image
registration: A survey. RR-7919, INRIA.
Vercauteren, T., Pennec, X., Perchant, A., & Ayache, N. (2009). Diffeomorphic demons:
Efficient non-parametric image registration. NeuroImage, 45(1), S61S72.
Vialard, F.-X., Risser, L., Rueckert, D., & Cotter, C. J. (2012). Diffeomorphic 3D image
registration via geodesic shooting using an efficient adjoint calculation.
Younes, L. (2007). Jacobi fields in groups of diffeomorphisms and applications.
Quarterly of Applied Mathematics, 65(1), 113134.
Lesion Segmentation
SK Warfield and X Tomas-Fernandez, Harvard Medical School, Boston MA, USA
Glossary
Lesion A lesion is any kind of abnormality in the brain.

Magnetic resonance imaging (MRI) MRI is a type of
imaging that uses nonionizing radio frequency energy to
Introduction
The development of imaging strategies for the optimal detection and characterization of lesions continues at a rapid pace.
Several modalities are in common use, including magnetic
resonance imaging (MRI), ultrasound, computed technology,
and positron emission tomography (PET). Each modality is
appropriate for certain types of lesions, but MRI is particularly
attractive due to its lack of ionizing radiation and the flexibility
of contrast mechanisms that it provides.
Expert and Interactive Segmentation

In routine clinical practice, the detection of lesions is important for diagnosis, directing intervention, and assessing
response to therapy. In clinical trials, it is often important to
have effective measures of the number of lesions, the size of
lesions, and how they change over time. Volumetric assessment of lesions is best carried out by segmentation of the
lesion, in which every voxel that is part of the lesion is delineated. This allows characterization of the entire volume of the
lesion and further measures such as lesion heterogeneity and
lesion shape. Furthermore, it allows the assessment of potential imaging biomarkers of response to therapy in the lesion,
such as diffusion weighted imaging (DWI) measures of cellularity or perfusion, or PET measures of metabolic activity.
Segmentation is usually carried out by an expert who is
trained to recognize normal anatomy and lesions in a particular modality or modalities under study. Most commonly, the
expert will delineate the lesion or lesions that they see in the
images interactively. A number of excellent software tools are
available to facilitate the delineation of user-observed regions
of interest.
However, the task of segmentation is challenging for experts
to carry out and leads to segmentations with errors in which
some voxels are incorrectly labeled. Expert segmentations may
have errors due to loss of attention or fatigue, due to changes in
perception over short or long periods of time, or due to subjective differences in judgment in regions in which the correct
decision is unclear. These errors may be well characterized as
locally random mislabeling and by structurally correlated
errors, such as consistent mislocalization of a segment of a
boundary.
Careful management of perception of the boundary can be
a challenge and depends on characteristics of the image such as
spatially encode the distribution of tissues in the brain and

body.
Segmentation The delineation of the location and extent of
structures visible in images.
display of contrast and the workspace environment. For example, a laterality bias in visual perception was identified as the
source of leftright asymmetry in some manual segmentations
and was found to be especially prominent in the hippocampus
(Maltbie et al., 2012). If present, this can be managed by
mirroring the images across the leftright plane of symmetry
and segmenting each structure twice, once appearing on the
left hand side and once on the right hand side, and then
averaging (Thompson et al., 2009). This is time-consuming
and therefore expensive and may be avoided by careful management of the experts perception.
The testretest reproducibility of interactive segmentation
has been characterized. In general, it has been found that an
expert rater will be more successful when the boundary of the
structure being delineated is readily observed and with a simple shape. Long and complicated boundaries are more difficult
to segment and lead to a reduction in interrater reliability
(Kikinis et al., 1992). Cortical gray matter, for example, can
be challenging to delineate (Warfield et al., 1995).
Variability in Lesion Segmentation

The interactive detection and delineation of the complete
extent of lesions by experts is very challenging to achieve.
As for normal anatomical structures with long and complex
boundaries, or with heterogeneous tissue contrast, the
testretest reproducibility of lesion detection and lesion segmentation has been low.
Quantitative assessment in multiple sclerosis (MS) is critical
both in understanding the natural history of disease and in
monitoring the effects of available therapies. Conventional
MRI-based measures include central nervous system atrophy
(Bermel & Bakshi, 2006), contrast-enhanced lesion count
(Barkhof et al., 2012), and T2w hyperintense lesion count
(Guttmann, Ahn, Hsu, Kikinis, & Jolesz, 1995). Such measures
have served as primary outcome in phase I and II trials and as
secondary outcome in phase III trials (Miller et al., 2004).
However, the quantitative analysis of lesion load is not without
difficulties. Because the natural change in lesion load year to
year is generally small, measurement error or variation in
lesion load assessment must be reduced as far as possible to
maximize the ability to detect progression. Ideally, measurement errors should be significantly less than the natural variability that occurs in individual patients over time (Wei,
Guttmann, Warfield, Eliasziw, & Mitchell, 2004). Although
http://dx.doi.org/10.1016/B978-0-12-397025-1.00302-X
323
324
INTRODUCTION TO METHODS AND MODELING | Lesion Segmentation
several factors influence lesion load measurements in MS, only

the variability introduced by the human operator who performs the measurements has been studied in detail.
Standard image analysis methods currently utilized in clinical trials are largely manual. Manual segmentation is difficult,
time-consuming, and costly. Errors occur due to low lesion
contrast and unclear boundaries caused by changing tissue
properties and partial volume effects. Segmentation inconsistencies are common even among qualified experts. Many studies have investigated the wide variability inherent to manual
MS lesion segmentation, finding an interrater volume variability of 14% and an intrarater volume variability of 6.5%
(Filippi, Horsfield, Bressi, et al., 1995). Further, other studies
have reported interrater lesion volume differences ranging
from 10% to 68% (Grimaud, Lai, Thorpe, & Adeleine, 1996;
Styne et al., 2008; Zijdenbos, Forghani, & Evans, 2002). Furthermore, during a longitudinal interferon beta-1b study (Paty
& Li, 1993), the authors attributed a significant decrease in MS
lesion volume during the third year of the study due to a
methodological change applied by the single observer who
performed the measurements. Because the same change was
applied consistently to all scans, it did not affect the found
intergroup differences, but it stressed the need for rigorous
quality control checks during long-term studies.
To reduce the intra- and interrater variability inherent in
manual lesion segmentation, many semiautomatic methods
have been proposed. These algorithms require the human
rater to identify the location of each lesion by clicking on the
center of the lesion and then automatically delineate the extent
of the lesion. In this way, the detection of the lesion relies on
the expert judgment, but the extent of the lesion is determined
by an automatic rule. A variety of rules to estimate the boundaries of each identified lesion have been investigated, including
the use of a local intensity threshold (Filippi, Horsfield, Tofts,
et al., 1995), region growing (Ashton et al., 2003), fuzzy connectedness (Udupa et al., 1997), intensity gradient (Grimaud
et al., 1996), or statistical shape priors (Shepherd, Prince, &
Alexander, 2012).
Semiautomatic lesion segmentation has demonstrated
reduced intrarater variability, but interrater variability is still
an issue due to the initialization by manual lesion identification. Given this, a substantial effort has been devoted to the
development of fully automatic segmentation algorithms capable of detecting and delineating lesions, especially in MS.
Lesion Segmentation Validation

Validation of segmentation in medical imaging is a challenging
task due to the scarcity of an appropriate reference standard to
which results of any segmentation approach can be compared.
Comparison to histology is helpful, but rarely available for
clinical data, and directly relating histology to MRI can be
difficult (Clarke et al., 1995). Consequently, validation studies
typically rely on expert evaluation of the imaging data. The
intra- and interexpert variability of manual segmentation
makes it challenging to distinguish the dissimilarities between
manual and automatic segmentation methods caused by errors
in the segmentation algorithm from those caused by variability
in the manual segmentation.
An excellent approach that overcomes the inter- and intraexpert reference variability consists in evaluation using synthetic image data (Kwan, Evans, & Pike, 1999). Since the
correct segmentation is known, this allows for direct comparison to the results of automatic segmentation algorithms.
Unfortunately, simulated images may not exhibit the wide
range of anatomy and acquisition artifacts found in clinical
data, and therefore, the conclusions may not generalize to the
broader range found in images of patients.
Given that expert measurements are highly variable, any
validation should always evaluate automatic segmentation
accuracy against a series of repeated measurements by multiple
experts. These multiple expert segmentations can be combined
using STAPLE (Akhondi-Asl & Warfield, 2013; Commowick,
Akhondi-Asl, & Warfield, 2012; Commowick & Warfield,
2010; Warfield, Zou, & Wells, 2004), which provides an optimal weighting of each expert segmentation, based on the comparison of each segmentation to a hidden reference standard
segmentation. The confidence of the expert performance estimates can also be estimated, indicating whether or not sufficient data are available to have high confidence in the reference
standard and the expert performance assessments. Ultimately,
the best automated segmentation algorithms should have an
accuracy similar to that of the best expert segmentations, but
with higher reproducibility.
Validation Metrics
Two main aspects characterize the validation of a segmentation
algorithm: accuracy and reproducibility.
Accuracy
The accuracy of segmentation can be evaluated in many different ways. A sensible evaluation criterion depends on the purpose of the segmentation procedure. If the goal is to estimate
the lesion volume, a measure often referred to as total lesion
load (TLL), the volumetric error would be the criteria of choice
(Garca-Lorenzo, Prima, Arnold, Collins, & Barillot, 2011;
Shiee et al., 2010; Van Leemput, Maes, Vandermeulen,
Colchester, & Suetens, 2001). The main limitation of such
approach is that it does not provide information regarding
the overlap with the reference segmentation. Thus, segmentation with exactly the same volume as the reference can be
completely wrong if a voxel by voxel comparison is made. It
has been demonstrated that high TLL correlation can be
achieved while still achieving a poor degree of precise spatial
correspondence. For example, Van Leemput et al. (2001)
reported a high TLL correlation but considerable disagreement
in spatial overlap between expert segmentations and between
expert and automatic measurements.
Commonly, brain segmentation literature describes the
spatial overlap of segmentations by means of the dice similarity coefficient (DSC) (Dice, 1945). The DSC between the automatic and reference segmentation is defined as the ratio of
twice the overlapping area to the sum of the individual areas.
The value of the index varies between 0 (no overlap) and 1
(complete overlap with the reference). This is an excellent
measure if the detection of every voxel of every lesion is critical.
In practice, evaluation of DSC of MS lesion segmentations is
dependent on the TLL of the patients (Zijdenbos, Dawant,

Margolin, & Palmer, 1994). This is in part because scans depicting high lesion burden will typically have some lesions with
unambiguous boundaries. Thus, DSC heavily reflects the presence of lesions with easy to detect boundaries, which are more
likely to be present in patients with an increased lesion burden
and less likely to occur in patients with a lower lesion burden.
The variation in the contrast of the boundaries of different
lesions has led to efforts to find alternative measures of
accuracy.
Given the disagreement in lesion boundaries among manual raters, some authors have proposed to validate lesion segmentation algorithms by reporting the number of correctly
detected lesions (Styne et al., 2008), where a lesion is defined
as detected if it overlaps at all with any lesion present in the
reference. Such a metric has the advantage of being insensitive
to error in the boundary of the lesion localization in the
manual reference standard segmentations. However, such
lesion counting measures cannot give information about the
accuracy of the boundary localization of the lesion. A commonly accepted recommendation is that validation measures
should assess both lesion detection and lesion delineation
accuracy (Wack et al., 2012).
Reproducibility
High reproducibility, of accurate segmentation, is crucial for
longitudinal trials to ensure that differences in segmentations
obtained over time result from changes in the pathology and
not from the variability of the segmentation approach.
To test interscan variability, MS patients may undergo a
scanrepositionscan experiment. As scans are obtained
within the same imaging session, it is assumed that the disease
has not evolved during this period. Such an approach was used
in Kikinis et al. (1999) and Wei et al. (2002) where reproducibility was measured using the coefficient of variation on
the TLL.
Reproducibility is a necessary but not sufficient part of
validation. One still needs to show that the method is accurate
and sensitive to changes in input data. Measuring accuracy
requires an independent estimate of the ground truth, an
often difficult task when using clinical data.
Validation Datasets
In order to provide objective assessments of segmentation
performance, there is a need for an objective reference standard
with associated MRI scans that exhibit the same major segmentation challenges as that of scans of patients. A database of
clinical MR images, along with their segmentations, may provide the means to measure the performance of an algorithm
by comparing the results against the variability of the expert
segmentations. However, an objective evaluation to systematically compare different segmentation algorithms also needs
an accurate reference standard.
An example of such a reference standard is the synthetic
brain MRI database provided by the Montreal Neurological
Institute that is a common standard for evaluating the segmentations of MS patients. The synthetic MS brain phantom available from the McConnell Brain Imaging Centre consists of
T1w, T2w, and proton density MRI sequences with different
acquisition parameters as well as noise and intensity
325
inhomogeneity levels (Kwan et al., 1999). The MS brain phantom was based on the original BrainWeb healthy phantom,
which had been expanded to capture three different MS lesion
loads: mild (0.4 cm3), moderate (3.5 cm3), and severe
(10.1 cm3). Each MS phantom was provided with its own MS
lesion ground truth.
Although the BrainWeb synthetic dataset provides a reference standard, it presents several limitations. First, the BrainWeb dataset just provides one brain model, which results in a
poor characterization of the anatomical variability present in
the MS population. Also, although the BrainWeb dataset is
based on real MRI data, the final model is not equivalent to
clinical scans in its contrast, and it produces an easier dataset to
segment than real clinical scans.
To overcome these limitations, most of the lesion segmentation algorithms also evaluate their results in a dataset consisting in clinical scans. Such an approach allows for a better
understanding of the performance of the evaluated algorithms
when faced with real data. Unfortunately, because each segmentation algorithm is validated with different datasets, comparison between different methodologies is more difficult.
A recent effort in providing publicly available datasets for
validation of MS lesion segmentation was released at the MS
Segmentation Grand Challenge held during the Medical Imaging Computing and Computer Assisted Intervention (MICCAI
2008) conference (Styne et al., 2008). For this event, the University of North Carolina at Chapel Hill (UNC) and Boston
Childrens Hospital (BCH) released a database of MS MRI
scans that contains anatomical MRI scans from 51 subjects
with MS.
Images were placed into two groups: a 20-subject training
group and a 31-subject testing group, the balance of the original 51 subject cohort. MS lesion manual reference data were
only available for those subjects in the training group. Organizers retained and continue to hold secret the interactively
delineated reference standard lesion segmentations of the testing group. To evaluate the performance of any segmentation
algorithms, researchers may upload their automatic segmentations of the testing data into the challenge website, where a
number of performance metrics are computed and an overall
performance ranking is provided. Since the competitors do not
have access to the reference standard segmentation, this evaluation of publicly available scans allows for a truly objective
comparison.
Intensity Artifact Compensation, Normalization, and

Matching
The MRI intensity scale in conventional structural imaging has
no absolute, physical meaning. Instead, images are formed
with a contrast that is related to spin density, T1 relaxation,
and T2 relaxation, without quantifying the precise value of
these parameters. As a consequence, the image intensities and
contrast are dependent on the particular pulse sequence, static
magnetic field strength, and imaging parameter settings such as
flip angle.
In addition, several phenomena of the physics of acquisition lead to a spatially varying intensity inhomogeneity,
which may be severe enough in some cases to perturb image
326
segmentation. These intensity nonuniformities arise from

radio frequency coil nonuniformity and coupling with the
patient (de Zwart et al., 2004). They can be compensated for
by measuring the RF receive profiles from a homogeneous
transmit field (Kaza, Klose, & Lotze, 2011). Filtering based on
the concept of separating low-frequency artifact from signal
through homomorphic filtering has also been widely used
(Brinkmann, Manduca, & Robb, 1998; Sled, Zijdenbos, &
Evans, 1998).
For accurate and reproducible segmentation, it is important
that the location of boundaries between structures in the
images be able to be detected despite these potential variations
in signal intensity. This can be facilitated by the creation of new
images in which the intensities are more similar between
subjects.
Nyul and Udupa (1999) proposed a piecewise linear mapping that adjusts the intensity histogram of an input image so
it that matches a reference histogram based on a set of predefined landmarks. Similar approaches based on intensity rescaling have been extensively used in MS lesion segmentation
(Anbeek, Vincken, van Osch, Bisschops, & van der Grond,
2004; Datta & Narayana, 2013; Shah et al., 2011).
An adaptive segmentation algorithm was developed that
achieved tissue segmentation and intensity inhomogeneity
compensation with an expectationmaximization (EM) algorithm (Wells, Grimson, Kikinis, & Jolesz, 1996). The intensity
model was learned through supervised classification, requiring
an interactive training for each imaging protocol. Since the
intensity adaptation utilizes the same intensity model for all
subjects, the final intensity-compensated images have the same
range of intensity distributions. This enables compensation for
intersubject and intrasubject intensity inhomogeneities.
In order to avoid interactive training of the intensity distributions, while still achieving intersubject MRI intensity matching, Weisenfeld and Warfield (2004) developed an algorithm
based on finding a smoothly varying intensity modulation
field that minimized the KullbackLeibler divergence between
pairs of acquisitions. This algorithm was able to simultaneously use T1w and T2w images, from pairs of scans of subjects, in order to identify an intensity transformation field that
drove the intensity distribution of the scan of one subject to
closely match the intensity distribution of the scan of the
second subject. This achieved intensity matching across scans.
Automated Lesion Segmentation Algorithms

The challenges of interactive and semiautomated lesion
segmentation have led to the development of fully automated
lesion segmentation algorithms. This work has grown out of early
efforts to develop segmentation algorithms for normal brain
tissue (Clarke et al., 1995; Vannier, Butterfield, & Jordan, 1985;
Vannier, Butterfield, Jordan, Murphy, Levitt, & Gado, 1985).
Segmentation in healthy brain MRI has been the topic of a
great deal of study, with most successful algorithms employing
voxelwise, intensity feature space-based classification. The
basic strategy is usually based on statistical classification theory. Given a multispectral grayscale MRI (i.e., T1w, T2w, and
fluid attenuated inversion recovery (FLAIR)) formed by a finite
set of N voxels, and the multispectral vector of observed
intensities Y (y1, . . ., yN) with yi 2 m , a statistical classifier

algorithm seeks to estimate Zi, a categorical random variable
referring to tissue class label by maximizing p(Zi|Yi), the probability of the class from the observed intensity at the given
voxel. A Bayesian formulation of voxelwise, intensity-based
classification can be posed as follows:

p Y i Zi pZ
pZi j Y i PK

p Y i Zi j pZ j
j0
The term p(Yi|Z j) is the likelihood of the observed feature

vector Yi and p(Z) is the tissue prior probability. The usefulness
of such a classification scheme was demonstrated in Vannier,
Butterfield, and Jordan (1985) with both a supervised
classification and an unsupervised classification on brain
MRI data.
Tissue segmentation algorithms differ in the estimation of
the likelihood p(Yi|Z j) and the tissue prior models p(Z). In
Wells et al. (1996), an algorithm suitable for images corrupted
by a spatially varying intensity artifact was proposed and
devised as an EM algorithm for simultaneously estimating the
posterior probabilities p(Zi|Yi) and the parameters of a model
of the intensity artifact. They modeled the likelihoods both
parametrically as Gaussians and nonparametrically using Parzen windowing. Van Leemput, Maes, Vandermeulen, and
Suetens (1999) extended Wells EM scheme to also update
the means and variances of tissue class Gaussians and also to
include both a spatially varying prior and a Markov random
field (MRF) spatial homogeneity constraint, replacing the
global tissue prior with the product of a spatially varying
prior p(Zi) and a prior based on the MRF neighborhood
p@ (Zi). Updating the model to include a spatially varying
prior and an MRF prior model results in the following Bayesian
formulation of voxelwise, intensity-based classification:
pZi j Y i PK
pY i j Zi pZi p@ Zi
j0 pY i j Zi
jpZi jp@ Zi j
Considering the success of such approach for healthy brain

MRI tissue segmentation, first attempts in MS lesion segmentation automation modified these voxelwise, intensity-based
classifiers to model white matter (WM) lesions on MRI as an
additional tissue class. This first attempts described MS lesion
segmentations burdened with false-positive misclassification
mainly happening in the sulcal GM (Kapouleas, 1989).
Any classification algorithm estimates an optimal boundary
between tissue types on a given feature space. Thus, tissue
classification relies on contrast between tissue types (i.e., WM
and MS lesions) on a particular feature space. However, the MS
lesion intensity distribution overlaps with that from healthy
tissues (Kamber, Louis Collins, Shinghal, Francis, & Evans,
1992; Zijdenbos et al., 1994); thus, an MRI intensity feature
space alone has limited ability to discriminate between MS
lesions and healthy brain tissues. This limitation, in turn,
generally results in lesion segmentation that is inaccurate and
hampered with false-positives.
Attempts to deal with the overlapping intensity range of
healthy tissues and MS lesions led to increased development of
model-based systems, which encoded knowledge of brain
anatomy by means of a digital brain atlas with a priori tissue
probability maps. For instance, Kamber, Shinghal, Collins,

Francis, and Evans (1995) proposed a model that compensated
for the tissue class intensity overlap by using a probabilistic
model of the location of MS lesions. Many MS lesions appear
in the WM but have an intensity profile that includes an
unambiguously bright region and a surrounding region more
similar in intensity to gray matter. By confining the search for
MS lesions to those regions with at least a 50% prior probability of being WM, the incorrect classification of gray matter as
MS lesion was greatly reduced. More recently, Shiee et al.
(2010) used a topologically consistent atlas to constrain the
search of MS lesions.
Warfield et al. (1995) used a different approach where the
gray matter was segmented for each patient under analysis,
rather than using a probabilistic model of the average location
of the WM for all patients. By first successfully identifying all of
the gray matter, the segmentation of lesions was then made
possible through an optimal two-class classifier that identified
normal WM and lesions using an optimal minimum distance
classifier. This approach was able to correct for both gray
matter as MS lesion and MS lesion as gray matter classification
errors. Later work by Warfield, Kaus, Jolesz, and Kikinis (2000)
extended the classifier intensity feature space by using a distance map generated from an aligned template segmentation
and demonstrated the efficacy of iterated segmentation and
nonrigid registration. The algorithm iterated between tissue
classification and elastic registration of the anatomical template to the segmentation of the subject generated by the
classifier, which led to an increasingly refined and improved
segmentation of normal anatomical structures and lesions.
An alternative approach attempting to improve lesion segmentation specificity proposed to extend the MRI intensity
feature space by including spatial features. Zijdenbos et al.
(2002) used an MRI intensity feature space that was extended
by the tissue probability of the given voxel based in a probabilistic tissue atlas. Instead of using the tissue prior probability,
Anbeek et al. (2004) and Hadjiprocopis and Tofts (2003)
proposed to extend the MRI intensity feature space by means
of the Cartesian and polar voxel coordinates. An alternative
way to encode spatial information was proposed by Younis,
Soliman, Kabuka, and John (2007), where local neighboring
information was included by extending the voxel intensity
feature by including the MRI intensity of the six neighboring
voxels. To account for the MRI intensity variability observed
at different parts of the brain, Harmouche, Collins, Arnold,
Francis, and Arbel (2006) proposed a Bayesian classification
approach that incorporates voxel spatial location in a standardized anatomical coordinate system and neighborhood information using MRF.
More recently, some authors instead of relying in a specific
set of features proposed to select the most discriminant features
from large sets including voxel intensities, spatial coordinates,
tissue prior probabilities, shape filters, curvature filters, and
intensity derivatives. For instance, Morra, Tu, Toga, and
Thompson (2008) and Wels, Huber, and Hornegger (2008)
introduced tens of thousands of features in a classification
process using an AdaBoost algorithm with a probabilistic
boosting tree to improve the training process. Another method
(Kroon et al., 2008) employed principal component analysis
to select those features explaining the greatest variability of the
training data, and then a threshold was computed in the new
327
coordinate system to perform the lesion segmentation. An

alternative approach was proposed by Geremia et al. (2011)
who used a feature space composed by local and context-rich
features. Context-rich features compare the intensities of the
voxel of interest with distant regions either in an extended
neighborhood or in the symmetrical counterpart with respect
to the midsagittal plane. This set of features was employed with
a random decision forest classifier to segment MS lesions.
Furthermore, after analysis of the decision forest fitting process, the authors reported that the most discriminative features
towards MS lesion segmentation were FLAIR intensities and
the spatial tissue prior probability.
The role of FLAIR was demonstrated by de Boer et al.
(2009), where a model of MS lesions surrounded mostly by
WM voxels was used again. Gray matter, WM, and CSF were
segmented but with false-positives possible due to the intensity
overlap of lesions with normal tissues. An optimal FLAIR
intensity threshold based on the region of gray matter segmentation was then computed, and lesion false-positives were
removed by a heuristic rule of eliminating lesion candidates
outside a region of likely WM. Similarly, Datta and Narayana
(2013) rejected segmented lesions located in the cortical gray
matter or in the choroid plexus by means of the ICBM tissue
atlas. Furthermore, it has been proposed to enhance the
contrast between MS lesions and healthy tissues in FLAIR
scans prior to generate the lesion segmentation by intensity
thresholding (Bijar, Khayati, & Penalver Benavent, 2013;
Souple et al., 2008).
Approaches to reduce the extent of lesion false-positives are
usually based on postprocessing steps, specifically experimentally tuned morphological operators, connectivity rules, and
minimum size thresholds, among others. However, these postprocessing steps may have to be retuned based on individual
features of each case or tailored to different subjects for different degrees of lesion burden.
Considering that MS lesions are exhibit by a highly heterogeneous appearance, the selection of an appropriately sensitive
and specific classifier feature space has proved to be a daunting
task. Some authors proposed not to model the lesions, but to
consider them as intensity outliers to the normal appearing
brain tissues model. The advantage of such approach is that it
avoids the need to model the heterogeneous intensity,
location, and shape of the lesions.
This approach was examined by Van Leemput et al. (2001),
where lesions were modeled as intensity outliers with respect
of a global Gaussian mixture model (GMM) initialized by an
aligned probabilistic tissue atlas. Similarly, Souple et al. (2008)
used a trimmed likelihood estimator (TLE) to estimate a tencomponent GMM and modeled MS lesions as GM intensity
outliers on an enhanced FLAIR image. Additional methods
further combine a TLE with a mean shift algorithm (GarcaLorenzo et al., 2011) or a hidden Markov chain (Bricq, Collet,
& Armspach, 2008).
Given the presence of structural abnormalities (i.e., WM
lesions, brain atrophy, and blood vessels) in MS patients,
there is the need of estimation algorithms that are robust in
the presence of outliers. For instance, Prastawa, Bullitt, and Ho
(2004) proposed to edit the training data by means of a
minimum covariance determinant. In Cocosco, Zijdenbos,
and Evans (2003), a clustering solution was proposed based
328
in the geometry of tissue class distributions to reject training

data. Weisenfeld and Warfield (2009) demonstrated a registration and fusion algorithm that was able to automatically learn
training data of normal tissues for an optimal classifier with an
accuracy indistinguishable from that of the best manual raters,
which provided high accuracy rates.
State-of-the-art lesion segmentation algorithms are primarily based on a patient global MRI intensity feature space, which
have limited sensitivity and specificity for MS lesions and
which require extensive postprocessing to achieve increased
accuracy. This limitation, in turn, results in MS lesion segmentation that is generally inaccurate and burdened with falsepositives. For instance, during the MS Grand Challenge
(Styne et al., 2008), the winning algorithm (Bricq et al.,
2008) reported a lesion false-positive rate (LFPR) of 55% and
a lesion true-positive rate (LTPR) of 42%. That is, of all the
detections of lesions generated by the automatic algorithm,
about half of them are segmentation errors. Furthermore, the
best lesion segmentation algorithm at the Grand Challenge
was able to detect, on average, less than half of the existing
lesions. These results are not as good as the performance of an
average human rater reported by the challenge organizers
(LTPR 68% and LFPR 32%).
Model of Population and Subject Intensities

To address these limitations, we have experimented with augmenting the imaging data used to identify lesions to include
both an intensity model of the patient under consideration and
a collection of intensity and segmentation templates that provide a model of normal tissue. We call this combination a
model of population and subject (MOPS) intensities.
Unlike the classical approach where lesions are characterized
by their intensity distribution compared to all brain tissues,
MOPS aims to distinguish locations in the brain with an abnormal intensity level when compared to the expected value in the
same location in a healthy reference population. This is achieved
by a tissue mixture model, which combines the MS patient
global tissue intensity model with a population local tissue
intensity model derived from a reference database of MRI
scans of healthy subjects (Tomas-Fernandez & Warfield, 2012).
Global GMM MRI Brain Tissue Segmentation

Consider a multispectral grayscale MRI (i.e., T1w, T2w, and
FLAIR) formed by a finite set of voxels. Our aim is to assign
each voxel to one of classes (i.e., GM, WM, and CSF) considering the observed intensities Y (Y1, . . ., YN) with yi e m . Both
observed intensities and hidden labels are considered to be
random variables denoted, respectively, as Y (Y1, .. ., YN) and
Z (Z1, .. ., ZN). Each random variable Zi ek (zi1, .. ., ziK) is a
K-dimensional vector with each component zik being 1 or
0 according whether Yi did or did not arise from the kth class.
It is assumed that the observed data Y are described by the
conditional probability density function f(Y|Z, fY)that incorporates the image formation model and the noise model and
depends on some parametersfY. Also, the hidden labels are
assumed to be drawn according to some parametric probability
distribution f(Z|fZ), which depends on parameters fZ.
Segmenting the observed image Yis to propose an estimate Z^ of Z on the basis ofY, to this purpose, the parameter c (fZ1, . . ., fZK; fY1, . . ., fYK) needs to be estimated
somehow. If the underlying tissue segmentation Z was
known, estimation of the model parameters would be
straightforward. However, only the image Y is directly
observed, making it natural to tackle this problem as one
involving missing data making the EM algorithm the candidate for model fitting. The EM algorithm finds the
parameter c that maximizes the complete data loglikelihood by iteratively maximizing the expected value of
the log-likelihood log(f(Y, Z|c)) of the complete data (Y,
Z), where the expectation is based on the observed data Y
and the estimated parameters c m obtained in the previous
iteration m:
log LC c log f Y, Zj c
YN X K
log
f Z i ek j fZk f Y i j Z i ek , fYk
i1
k1
XN XK
i1
z log f Z i
k1 ik
ek j fZk

log f Y i Z i ek , fYk
E-step: The E-step requires the computation of the conditional expectation of log(Lc(c)) given Y, using c m for c, which
can be written as

Qc; c m Ecm log LC c Y
As the complete data log-likelihood log LC(c), is linear in
the hidden labels zij, the E-step simply requires the calculation
of the current conditional expectation of Zi given the observed
data Y. Then,

m

f Z i ej j fm

Zj f Y i Z i ej , fYj
Ecm Zi ej j Y PK

f Z i ek j fm f Y i Z i ek , fm
Zk
k1
Yk
that corresponds to the posterior probability that the ith member of the sample belongs to the jth class.
M-step: The M-step on the mth iteration requires the maximization of Q(c; c m) with respect to c over the parameter
space to give the updated estimate c m1. The mixing proportions pk are calculated as follows:

1 XN
m

f
Z
e
,
c
pk f Z i ek j fm1
Y
i
k i
Zk
i1
N
The update of fY on the M-step of the (m 1)th iteration, it
is estimated by maximizing log LC(c) with respect to fY:

XN XK
m @ log f Y i Z i ek , fYk
f
e
j
Y
,c
0
i
i
k
i1
k1
@fY
Consider that f(Yi|Zi ek, fYk) is described by a Gaussian
distribution parameterized by fYk (mk, Sk)
f Y i j Zi ek , fYk
1
m=2
2p
jSk j
1=2
T 1
1
e 2 Y i mk Sk Y i mk
with mk and Sk being, respectively, the intensity mean vector

and covariance matrix for tissue k. Thus, the update equations
may be written as

PN
mm1
k
m

i1 Y i f Z i ek Y i , c

PN
m

i1 f Z i ek Y i ,c

m
m T
Y i mm
i1 f Z i ek j Y i , c Y i mk
k

PN
f Zi ek Y i ,c m
PN
Sm1
k
329

log LC c log f Y, P,Z c
XN XK
i1
z log pk f Y i j Z ik ,c k f P ik j Y i ,Z ik , c k
k1 ik

m , S N Y m ,S
z
log
p
p
N
Y
i
i Pik Pik
k Pik
k k
k1 ik
XN XK
i1
i1
Local Reference Population GMM Intensity Tissue Model

Consider a reference population P formed by R healthy subjects aligned to the MS patient. Each reference subject is composed of a multispectral grayscale MRI V(i.e., T1w, T2w, and
FLAIR scans) and the corresponding tissue segmentation (i.e.,
GM, WM, and CSF); thus, P (V, L) (V1, . . ., VR; L1, . . ., LR).
Each reference grayscale MRI Vr (Vr1, . . ., VrN) is formed by a
finite set of N voxels with V ri em . Also, each reference tissue
segmentation Lr (Lr1, .. ., LrN) is formed by a finite set of N
voxels where Lri ek (lri1, .. ., lriK) is a K-dimensional vector
with each component lrik being 1 or 0 according whether Vri
did or did not arise from the kth class.
At each voxel i, the reference population P intensity distribution will be modeled as a GMM parameterized by
ji (pPi, mPi, SPi) with pPi, mPi, and SPi, respectively, the population tissue mixture vector, the population mean intensity
vector, and the population intensity covariance matrix at
voxel i.
Because (V, L) are observed variables, j i can be derived
using the following expressions:

1X
p Lij ek
jeNR
R

P
jeNR V ij p Lij ek

mPik P
jeNR p Lij ek
pPik
P
SPik
jeNR

V ij mPik p Lij ek

jeNR p Lij ek
V ij mPik
P
T
where p(Lij ek) is the probability of voxel i of the jth reference

subject belonging to tissue k given by Lj and NR is the neighborhood centered in voxel i of radius R voxels.
Once the local tissue model is estimated from P, the intensity likelihood of Y can be derived as
YN XK
f Y,Zj j i1 k1

T 1
1
f Zi ek j ik
e 2 Y i mPik SPik Y i mPik
m=2
m=2
2p
jSPik j
with f(Zi ek| j ik) pPik.
Combining Global and Local Models

Consider that in addition to the patient scan Y, we observe an
aligned template library of R healthy subjects P (V, L)
(V1, . . ., VR; L1, . . ., LR).
Since the observed population data P is conditionally independent of the observed patient scan Y, the formation model
parametrized by c can be expressed as
Given that the underlying tissue segmentation Z is

unknown, the EM algorithm will be used to find the parameters that maximize the complete log-likelihood.
E-step: The E-step requires the computation of the conditional expectation of log(LC(c)) given (Y, P), using the current
parameter estimate c m:

Qc; c m Ecm log LC c Y, P
Since the complete log-likelihood is linear in the hidden
labels zij, the E-step requires the calculation of the current
conditional expectation of Zi given the observed data (Y, P):
Ecm Z i ek j Y, P PK

pk pPik N Yi mk , Sk N Yi mPik , SPik

p 0 p 0 N Yi m 0 , S 0 N Yi m 0 , S
k0 1 k
Pik
Pik
Pik0
M-step: Because the local reference population model

parameter j is constant, the Maximization step will consist of
the maximization of Q(c; c m) with respect to c, which results
in the same update equations derived in Wells et al. (1996).
In order to be robust to the presence of outliers, we used a TLE
to estimate c. The TLE was proposed as a modification of the
maximum likelihood estimator in the presence of outliers in the
observed data (Neykov, Filzmoser, Dimova, & Neytchev, 2007).
Using the TLE, the complete log-likelihood can be expressed as
log LC c log

f
Y
,
P
,Z
vi vi
vi c
i1
Y
h
where for a fixed c, f(Yv(1), Pv(1), Zv(1)|c, j 1) . . . f(Yv(N), Pv

for i 1, . . ., N with v (v(1), . . ., v(N)) being
the corresponding permutation of indices sorted by their probabilityf(Yv(i), Pv(i), Zv(i)|c) and h is the trimming parameter
corresponding to the percentage of values included in the
parameter estimation. In other words, now, the likelihood is
only computed using the voxels that are more likely to belong
to the proposed model.
The TLE was computed using the fast-TLE algorithm, in
which iteratively, the N h voxels with the highest estimated
likelihood are selected to estimate c m1 using the update
equations. These two steps are iterated until convergence.
It follows intuitively that the local intensity model downweighs
the likelihood of those voxels that have an abnormal intensity
given the reference population. Since MRI structural abnormalities
will show an abnormal intensity level compared to similarly
located brain tissues in healthy subjects, we seek to identify MS
lesions by searching for areas with low likelihood LC(c).
(N), Zv(N)|c, j N)
Illustrative Applications of Segmentation with the

MOPS Intensities
We evaluated MOPS using the MS Grand Challenge dataset
(Styne et al., 2008). The MS Grand Challenge website accepts
330
new segmentations and rates them with a score that summarizes

the performance of the segmentation algorithm. A score of 90
was considered to equal the accuracy of a human rater. MOPS
achieved a score of 84.5, which ranks as the best performing
algorithm over all the 17 lesion segmentation algorithms for
which results have been submitted (Figure 1).
The lesion detection rates of MOPS were consistently more
specific, and at least equally sensitive, to previously reported
algorithms (Figure 2). This demonstrates that a model of
lesions as global intensity outliers within each subjects MRI

is less able to discriminate true lesions than the joint MOPS
intensities. MOPS is able to successfully identify lesions in
patients with pediatric-onset multiple sclerosis as will be illustrated later (Figure 3). Furthermore, MOPS is able to detect
atypical local intensities through comparison to images of a
healthy reference population, so MOPS can detect many types
of brain abnormalities. Figure 4 illustrates the successful detection of a pediatric brain tumor.
MS Grand Challenge scores

85
84.46
84
83
82.12
82.07
82
Score
81
80
80
79.9
79.1
79
78.19
78
77
76
75
ek
be
11
08
tio
20
20
la
zo
04
n
re
20
Lo
a-
10
.,
al
11
20
et
20
le
up
ie
ci
ar
An
Sh
So
ia
08
20
em
er
ic
Br
pu
po
of ct
el bje
od su
M nd
a
Participant team
Figure 1 Comparison of lesion segmentation performance of different algorithms from the MS Lesion Segmentation Grand Challenge (Styne et al.,
2008). The highest score is best.
1 f(Yi, Zi|)
T1w MRI
1.00
0.75
0.50
0.25
0.00
(a)
(c)
1 f(Yi, Pi, Zi|)
T2w MRI
1.00
0.75
0.50
0.25
0.00
(b)
(d)
Figure 2 Comparison of detection of a brain tumor from (a) T1w MRI

and (b) T2w MRI, using a (c) global intensity model and (d) model of
population and subject (MOPS). The figure demonstrates the improved
lesion sensitivity of the voxel lesion probability derived by MOPS enabling
accurate localization of the brain tumor.
Figure 3 Illustration of lesion segmentation with MOPS from an MRI

scan of a patient with pediatric onset multiple sclerosis.
Figure 4 Illustration of tractography of the corticospinal tract in the

region of the brain tumor detected automatically by MOPS. Careful
assessment of the path of the corticospinal tract allows for optimization
of the surgical approach to minimize the risk of loss of function following
surgery.
Conclusion
Lesion segmentation is an important task, regularly carried out
by experts using interactive and semiautomatic segmentation
tools. Automated algorithms for segmentation of lesions have
explored a wide range of techniques and are increasingly effective for a range of types of pathology. Advances in MS lesion
segmentation enable quantitative and accurate detection of
lesions from high-quality MRI.

Anatomical MRI for Human Brain Morphometry; Myelin Imaging;
INTRODUCTION TO CLINICAL BRAIN MAPPING: Demyelinating
Diseases; MRI in Clinical Management of Multiple Sclerosis;
INTRODUCTION TO METHODS AND MODELING: Diffeomorphic
Image Registration; Intensity Nonuniformity Correction; Nonlinear
Registration Via Displacement Fields; Posterior Probability Maps.
References
Akhondi-Asl, A., & Warfield, S. K. (2013). Simultaneous truth and performance level
estimation through fusion of probabilistic segmentations. IEEE Transactions on
Medical Imaging, http://dx.doi.org/10.1109/TMI.2013.2266258.
Anbeek, P., Vincken, K. L., van Osch, M. J., Bisschops, R. H. C., & van der Grond, J.
(2004). Automatic segmentation of different-sized white matter lesions by voxel
probability estimation. Medical Image Analysis, 8, 205215. http://dx.doi.org/
10.1016/j.media.2004.06.019.
Ashton, E. A., Takahashi, C., Berg, M. J., Goodman, A., Totterman, S., & Ekholm, S.
(2003). Accuracy and reproducibility of manual and semiautomated quantification of
MS lesions by MRI. Journal of Magnetic Resonance Imaging, 17, 300308. http://
dx.doi.org/10.1002/jmri.10258.
Barkhof, F., Simon, J. H., Fazekas, F., Rovaris, M., Kappos, L., de Stefano, N., et al.
(2012). MRI monitoring of immunomodulation in relapse-onset multiple sclerosis
331
trials. Nature Reviews. Neurology, 8, 1321. http://dx.doi.org/10.1038/

nrneurol.2011.190.
Bermel, R. A., & Bakshi, R. (2006). The measurement and clinical relevance of brain
atrophy in multiple sclerosis. Lancet Neurology, 5, 158170. http://dx.doi.org/
10.1016/S1474-4422(06)70349-0.
Bijar, A., Khayati, R., & Penalver Benavent, A. (2013). Increasing the contrast of the
brain MR FLAIR images using fuzzy membership functions and structural similarity
indices in order to segment MS lesions. PloS One, 8, e65469. http://dx.doi.org/
10.1371/journal.pone.0065469.
Bricq, S., Collet, C., & Armspach, J. P. (2008). Markovian segmentation of 3D brain
MRI to detect multiple sclerosis lesions. In 15th IEEE International Conference on
Image Processing (pp. 733736).
Brinkmann, B. H., Manduca, A., & Robb, R. A. (1998). Optimized homomorphic
unsharp masking for MR grayscale inhomogeneity correction. IEEE Transactions on
Medical Imaging, 17(2), 161171. http://dx.doi.org/10.1109/42.700729.
Clarke, L. P., Velthuizen, R. P., Camacho, M. A., Heine, J. J., Vaidyanathan, M.,
Hall, L. O., et al. (1995). MRI segmentation: Methods and applications. Magnetic
Cocosco, C. A., Zijdenbos, A. P., & Evans, A. C. (2003). A fully automatic and robust
brain MRI tissue classification method. Medical Image Analysis, 7, 513527. http://
dx.doi.org/10.1016/S1361-8415(03)00037-9.
Commowick, O., Akhondi-Asl, A., & Warfield, S. K. (2012). Estimating a reference
standard segmentation with spatially varying performance parameters: Local MAP
STAPLE. IEEE Transactions on Medical Imaging, 31(8), 15931606. http://dx.doi.
org/10.1109/TMI.2012.2197406.
Commowick, O., & Warfield, S. K. (2010). Estimation of inferential uncertainty in
assessing expert segmentation performance from STAPLE. IEEE Transactions on
Medical Imaging, 29(3), 771780. http://dx.doi.org/10.1109/TMI.2009.2036011.
Datta, S., & Narayana, P. A. (2013). A comprehensive approach to the segmentation of
multichannel three-dimensional MR brain images in multiple sclerosis.
NeuroImage. Clinical, 2, 184196. http://dx.doi.org/10.1016/j.nicl.2012.12.007.
de Boer, R., Vrooman, H. A., van der Lijn, F., Vernooij, M. W., Ikram, M. A.,
van der Lugt, A., et al. (2009). White matter lesion extension to automatic brain
tissue segmentation on MRI. NeuroImage, 45, 11511161.
de Zwart, J. A., Ledden, P. J., van Gelderen, P., Bodurka, J., Chu, R., & Duyn, J. H.
(2004). Signal-to-noise ratio and parallel imaging performance of a 16-channel
receive-only brain coil array at 3.0 Tesla. Magnetic Resonance in Medicine, 51(1),
2226. http://dx.doi.org/10.1002/mrm.10678.
Dice, L. R. (1945). Measures of the amount of ecologic association between species.
Ecology, 26, 297. http://dx.doi.org/10.2307/1932409.
Filippi, M., Horsfield, M. A., Bressi, S., Martinelli, V., Baratti, C., Reganati, P., et al.
(1995). Intra- and inter-observer agreement of brain MRI lesion volume
measurements in multiple sclerosis. A comparison of techniques. Brain, 118(Pt 6),
15931600.
Filippi, M., Horsfield, M. A., Tofts, P. S., Barkhof, F., Thompson, A. J., & Miller, D. H.
(1995). Quantitative assessment of MRI lesion load in monitoring the evolution of
multiple sclerosis. Brain, 118(Pt 6), 16011612.
Garca-Lorenzo, D., Prima, S., Arnold, D. L., Collins, D. L., & Barillot, C. (2011).
Trimmed-likelihood estimation for focal lesions and tissue segmentation in multisequence MRI for multiple sclerosis. IEEE Transactions on Medical Imaging, 113.
http://dx.doi.org/10.1109/TMI.2011.2114671.
Geremia, E., Clatz, O., Menze, B. H., Konukoglu, E., Criminisi, A., & Ayache, N. (2011).
Spatial decision forests for MS lesion segmentation in multi-channel magnetic
resonance images. NeuroImage, 57, 378390.
Grimaud, J., Lai, M., Thorpe, J., & Adeleine, P. (1996). Quantification of MRI lesion
load in multiple sclerosis: A comparison of three computer-assisted techniques.
Guttmann, C. R., Ahn, S. S., Hsu, L., Kikinis, R., & Jolesz, F. A. (1995). The evolution of
multiple sclerosis lesions on serial MR. AJNR. American Journal of Neuroradiology,
16, 14811491.
Hadjiprocopis, A., & Tofts, P. (2003). An automatic lesion segmentation method for fast
spin echo magnetic resonance images using an ensemble of neural networks.
In IEEE XIII workshop on neural networks for signal processing (IEEE Cat.
No.03TH8718) (pp. 709718).
Harmouche, R., Collins, L., Arnold, D., Francis, S., & Arbel, T. (2006). Bayesian MS
lesion classification modeling regional and local spatial information. In: Eighteenth
international conference on pattern recognition (ICPR06) (pp. 984987).
Kamber, M., Shinghal, R., Collins, D. L., Francis, G. S., & Evans, A. C. (1995). Modelbased 3-D segmentation of multiple sclerosis lesions in magnetic resonance brain
images. IEEE Transactions on Medical Imaging, 14, 442453. http://dx.doi.org/
10.1109/42.414608.
Kamber, M., Louis Collins, D., Shinghal, R., Francis, G. S., & Evans, A. C. (1992).
Model-based 3D segmentation of multiple sclerosis lesions in dual-echo MRI data.
332
In: Proceedings of the SPIE: Visualization in biomedical computing 1992, Chapel

Hill, NJ. vol. 1808 (pp. 590600).
Kapouleas, I. (1989). Automatic detection of multiple sclerosis lesions in MR brain
images. In: Proceedings of the annual symposium on computer application in
medical care (pp. 739745).
Kaza, E., Klose, U., & Lotze, M. (2011). Comparison of a 32-channel with a 12-channel
head coil: are there relevant improvements for functional imaging? Journal of
Magnetic Resonance Imaging, 34(1), 173183. http://dx.doi.org/10.1002/
jmri.22614.
Kikinis, R., Guttmann, C. R., Metcalf, D., Wells, W. M., Ettinger, G. J., Weiner, H. L.,
et al. (1999). Quantitative follow-up of patients with multiple sclerosis using MRI:
Technical aspects. Journal of Magnetic Resonance Imaging, 9, 519530.
Kikinis, R., Shenton, M. E., Gerig, G., Martin, J., Anderson, M., Metcalf, D., et al. (1992).
Routine quantitative analysis of brain and cerebrospinal fluid spaces with MR
imaging. Journal of Magnetic Resonance Imaging, 2(6), 619629.
Kroon, D., Oort, E.V., & Slump, K. (2008). Multiple sclerosis detection in multispectral
magnetic resonance images with principal components analysis. MS Lesion
Segmentation (MICCAI 2008 Workshop).
Kwan, R. K., Evans, A. C., & Pike, G. B. (1999). MRI simulation-based evaluation of
image-processing and classification methods. IEEE Transactions on Medical
Maltbie, E., Bhatt, K., Paniagua, B., Smith, R. G., Graves, M. M., Mosconi, M. W., et al.
(2012). Asymmetric bias in user guided segmentations of brain structures.
NeuroImage, 59(2), 13151323. http://dx.doi.org/10.1016/j.
Miller, D. H., Filippi, M., Fazekas, F., Frederiksen, J. L., Matthews, P. M., Montalban, X.,
et al. (2004). Role of magnetic resonance imaging within diagnostic criteria for
multiple sclerosis. Annals of Neurology, 56, 273278.
Morra, J., Tu, Z., Toga, A., & Thompson, P. (2008). Automatic segmentation of MS
lesions using a contextual model for the MICCAI grand challenge. MS Lesion
Segmentation, (MICCAI 2008 Workshop).
Neykov, N., Filzmoser, P., Dimova, R., & Neytchev, P. (2007). Robust fitting of mixtures
using the trimmed likelihood estimator. Computational Statistics & Data Analysis,
52, 299308. http://dx.doi.org/10.1016/j.csda.2006.12.024.
Nyul, L. G., & Udupa, J. K. (1999). On standardizing the MR image intensity scale.
Paty, D. W., & Li, D. K. (1993). Interferon beta-1b is effective in relapsing-remitting
multiple sclerosis. II. MRI analysis results of a multicenter, randomized, doubleblind, placebo-controlled trial. UBC MS/MRI Study Group and the IFNB Multiple
Sclerosis Study Group. Neurology, 43(4), 662667.
Prastawa, M., Bullitt, E., & Ho, S. (2004). A brain tumor segmentation framework based
on outlier detection. Medical Image Analysis, 8, 275283.
Shah, M., Xiao, Y., Subbanna, N., Francis, S., Arnold, D. L., Collins, D. L., et al. (2011).
Evaluating intensity normalization on MRIs of human brain with multiple sclerosis.
Medical Image Analysis, 15(2), 267282. http://dx.doi.org/10.1016/j.
media.2010.12.003, pii: S1361-8415(10)00133-7.
Shepherd, T., Prince, S. J., & Alexander, D. C. (2012). Interactive lesion segmentation
with shape priors from offline and online learning. IEEE Transactions on Medical
Imaging, 31, 16981712. http://dx.doi.org/10.1109/TMI.2012.2196285.
Shiee, N., Bazin, P. L., Ozturk, A., Reich, D. S., Calabresi, P. A., & Pham, D. L. (2010). A
topology-preserving approach to the segmentation of brain images with multiple
sclerosis lesions. NeuroImage, 49, 15241535.
Sled, J. G., Zijdenbos, A. P., & Evans, A. C. (1998). A nonparametric method for
automatic correction of intensity nonuniformity in MRI data. IEEE Transactions on
Souple, J., Lebrun, C., Ayache, N., & Malandain, G. (2008) An Automatic Segmentation
of T2-FLAIR Multiple Sclerosis Lesions. MS Lesion Segmentation (MICCAI 2008
workshop).
Styne, M., Lee, J., Chin, B., Chin, M.S., Commowick, O., Tran, H., et al. (2008). 3D
Segmentation in the Clinic: A Grand Challenge II, MS Lesion Segmentation
(MICCAI 2008 Workshop).
Thompson, D. K., Wood, S. J., Doyle, L. W., Warfield, S. K., Egan, G. F., & Inder, T. E.
(2009). MR-determined hippocampal asymmetry in full-term and preterm neonates.
Hippocampus, 19(2), 118123. http://dx.doi.org/10.1002/hipo.20492.
Tomas-Fernandez, X., & Warfield, S. K. (2012). Population intensity outliers or a new
model for brain WM abnormalities. In: Ninth IEEE international symposium on
biomedical imaging (ISBI) (pp. 15431546), IEEE.
Udupa, J. K., Wei, L., Samarasekera, S., Miki, Y., van Buchem, M. A., & Grossman, R. I.
(1997). Multiple sclerosis lesion quantification using fuzzy-connectedness
principles. IEEE Transactions on Medical Imaging, 16, 598609. http://dx.doi.org/
10.1109/42.640750.
Van Leemput, K., Maes, F., Vandermeulen, D., Colchester, A., & Suetens, P. (2001).
Automated segmentation of multiple sclerosis lesions by model outlier detection.
Van Leemput, K., Maes, F., Vandermeulen, D., & Suetens, P. (1999). Automated
model-based tissue classification of MR images of the brain. IEEE Transactions on
Vannier, M. W., Butterfield, R. L., Jordan, D., Murphy, W. A., Levitt, R. G., & Gado, M.
(1985). Multispectral analysis of magnetic resonance images. Radiology, 154(1),
221224. http://dx.doi.org/10.1148/radiology.154.1.3964938.
Vannier, M. W., Butterfield, R. L., & Jordan, D. (1985). Multispectral analysis of
magnetic, resonance images. Radiology, 154, 221224.
Wack, D. S., Dwyer, M. G., Bergsland, N., Di Perri, C., Ranza, L., Hussein, S., et al.
(2012). Improved assessment of multiple sclerosis lesion segmentation agreement
via detection and outline error estimates. BMC Medical Imaging, 12, 17. http://dx.
doi.org/10.1186/1471-2342-12-17.
Warfield, S. K., Kaus, M., Jolesz, F. A., & Kikinis, R. (2000). Adaptive, template
moderated, spatially varying statistical classification. Medical Image Analysis, 4,
4355.
Warfield, S., Dengler, J., Zaers, J., Guttmann, C. R., Wells, W. M., 3rd., Ettinger, G. J.,
et al. (1995). Automatic identification of gray matter structures from MRI to improve
the segmentation of white matter lesions. Journal of Image Guided Surgery, 1(6),
326338. http://dx.doi.org/10.1002/(SICI)1522-712X.
Warfield, S. K., Zou, K. H., & Wells, W. M. (2004). Simultaneous truth and performance
level estimation (STAPLE): An algorithm for the validation of image segmentation.
IEEE Transactions on Medical Imaging, 23, 903921. http://dx.doi.org/10.1109/
TMI.2004.828354.
Wei, X., Guttmann, C. R., Warfield, S. K., Eliasziw, M., & Mitchell, J. R. (2004). Has your
patients multiple sclerosis lesion burden or brain atrophy actually changed?
Multiple Sclerosis, 10, 402406.
Wei, X., Warfield, S. K., Zou, K. H., Wu, Y., Li, X., Guimond, A., et al. (2002).
Quantitative analysis of MRI signal abnormalities of brain white matter with high
reproducibility and accuracy. Journal of Magnetic Resonance Imaging, 209,
203209. http://dx.doi.org/10.1002/jmri.10053.
Weisenfeld, N. I., & Warfield, S. K. (2009). Automatic segmentation of newborn brain
MRI. NeuroImage, 47, 564572. http://dx.doi.org/10.1016/j.
Weisenfeld, N. I., & Warfield, S. K. (2004). Normalization of joint image-intensity
statistics in MRI using the KullbackLeibler divergence. In Proceedings of the 2004
IEEE international symposium on biomedical imaging: From nano to macro,
Arlington, VA, April 1518, 2004.
Wells, W. M., Grimson, W. L., Kikinis, R., & Jolesz, F. A. (1996).
Adaptive segmentation of MRI data. IEEE Transactions on Medical Imaging, 15,
429442.
Wels, M., Huber, M., & Hornegger, J. (2008). Fully automated segmentation of multiple
sclerosis lesions in multispectral MRI. Pattern Recognition and Image Analysis, 18,
347350. http://dx.doi.org/10.1134/S1054661808020235.
Younis, A. A., Soliman, A. T., Kabuka, M. R., & John, N. M. (2007). MS lesions
detection in MRI using grouping artificial immune networks. In IEEE 7th
international symposium on bioinformatics and bioengineering (pp. 11391146).
Zijdenbos, A. P., Dawant, B. M., Margolin, R. A., & Palmer, A. C. (1994). Morphometric
analysis of white matter lesions in MR images: Method and validation. IEEE
Transactions on Medical Imaging, 13, 716724. http://dx.doi.org/10.1109/
42.363096.
Zijdenbos, A. P., Forghani, R., & Evans, A. C. (2002). Automatic pipeline analysis of
3-D MRI data for clinical trials: Application to multiple sclerosis. IEEE Transactions
on Medical Imaging, 21, 12801291.
Relevant Websites
http://brainweb.bic.mni.mcgill.ca/brainweb/selection_ms.html BrainWeb Lesion
Simulator.
http://www.spl.harvard.edu/publications/item/view/1180 Warfield/Kaus database.
http://crl.med.harvard.edu/software STAPLE validation software.
http://martinos.org/qtim/miccai2013/ Multimodal Brain Tumor Segmentation.
http://www.sci.utah.edu/prastawa/software.html Brain Tumor Simulator.
http://www.ia.unc.edu/MSseg/ Multiple Sclerosis Lesion Segmentation Grand
Challenge.
Manual Morphometry
N Roberts, University of Edinburgh, Edinburgh, UK
Glossary
Cavalieri method A stereological probe for estimating

volume.
Cycloid The curve traced by a point on the rim of a
circular wheel as the wheel rolls along a straight
line. Provides appropriate orientation (i.e., sine-weighted
directions) for test lines on stereological test systems
used for estimating surface by the Vertical Sections
method.
Grey-white matter boundary The boundary
between cerebral cortex and underlying white
matter.
Introduction
The aim of this article is to provide a concise description of the
correct methods to be applied for obtaining reliable measurements of the volume and surface area of the living brain and of
its internal compartments and individual brain structures using
medical imaging techniques such as magnetic resonance
imaging (MRI) and X-ray computed tomography (CT) by manual means. The methods in question have been developed
within the discipline of stereology (see Cruz-Orive, 1997;
Howard & Reed, 1998; Mouton, 2011; Roberts, Puddephat, &
McNulty, 2000; West, 2012) and are very convenient to use
when applied in combination with appropriate computer software. Stereology is defined as the statistical inference of geometric parameters from sampled information. The fact that
sampling is involved means that the measurements are estimates rather than exact values. Crucially sampling is performed
according to mathematically rigorous designs that ensure that
the results are unbiased. Furthermore, the use of systematic
sampling strategies means that the methods are highly efficient
and formulae have been developed for predicting the precision
of the estimate from the sampled information.
The ability to obtain a detailed 3D image of the anatomy of
the brain in a living individual is clearly an amazing scientific
achievement with many potential applications including the
prospect of obtaining detailed measurements of brain size.
This is acknowledged in the award of Nobel Prizes to Wilhelm
C. Rontgen (1901) for the discovery of x-rays and to Godfrey
N. Hounsfield and Allan MacLeod Cormack (1979) just under
80 years later for developing the CT technique in which x-rays
are used to produce 3D images of anatomy and pathology to
support clinical diagnosis. Likewise, Nobel Prizes were
awarded to Otto Stern (1943), Isidor I. Rabi (1944), and to
Felix Bloch and Edward M. Purcell (1952) relating to the
discovery of the magnetic moment of the proton and development and refinement of the resonance method for manipulating this magnetization and which paved the way for Paul C.
Lauterbur, USA and Peter Mansfield (2003) to develop the
Magnetic Resonance Imaging (MRI) A medical imaging

technique used to investigate the anatomy and physiology of
the body in health and disease without the use of ionizing
radiation. Images are formed using strong magnetic fields
and radio waves.
Pial surface The boundary between grey matter and
cerebrospinal fluid.
Stereology Statistical inference of geometric quantities
(e.g., volume and surface area) from sampled information
(i.e., point and intersection counts).
Vertical Sections method A stereological probe for
estimating surface area.
diagnostic imaging technique of MRI. The purpose in

highlighting these developments and the respect that exists
for the scientists who made them is to provide a perspective
from which to propose to the reader that the ability to make
proper measurements of the brain by analysis of 3D MRI and
CT images is potentially just as significant a human achievement. In this case, however, it is not so straightforward to
identify the individuals who made singular crucial developments. Rather, over centuries mathematicians and scientists
have learnt to think in 3D and have developed the relevant
theory for making measurements in 3D that forms the cornerstones of the subject of modern design-based stereology.
Stereology, is just as important an advance and as interesting
a subject as the discovery of x-rays or magnetic moments and
the ability to use these phenomena to produce accurate 3D
images. Stereology teaches the investigator how to think in
3D so as to perform a proper 3D sampling to obtain a robust
3D measurement.
Stereology was initially applied primarily in pathology laboratories for analysis of physical specimens via cutting and
staining techniques (e.g., to obtain an unbiased estimate of
the total number of neurons in the human brain) and is only
more recently being frequently used in combination with virtual cutting of 3D MRI and CT images for the study of living
subjects. The fact that medical images are stored in the virtual
world of the computer opens up exciting opportunities
whereby a computer interface may one day be developed
which allows stereological sampling to be performed via manual measurement in a virtual 3D world. For example, the
volume of an object may be estimated by directly counting
the number of points of a 3D lattice of test points (with known
number of test points per unit volume) which lie within the
structure of interest. Similarly, surface area may be estimated
by counting the number of intersections between an isotropic
distribution of test lines (with known test line length per unit
volume) and the boundary of the structure. Presently, however, in Medical Imaging applications stereological measurements are usually made in two stages. In particular, firstly 2D
http://dx.doi.org/10.1016/B978-0-12-397025-1.00303-1
333
334
INTRODUCTION TO METHODS AND MODELING | Manual Morphometry
sections (i.e., images) are obtained through the structure of

interest according to an appropriate unbiased sampling design
and secondly these images are overlain with corresponding test
systems comprising test points or test lines and appropriate
point and intersections counts are recorded via a mouse click.
This splitting of the sampling procedure underlying the
stereological methods of volume and surface area estimation
into an initial sectioning stage and subsequent point, or intersection, counting stage, has important implications with regard
to the software packages that are available to support the
application of stereological methods. Most important to note
is that, if the relevant sectioning is not performed on the
medical imaging system at the time of data acquisition, the
virtual sectioning of a 3D MRI or CT image presents significant
challenges in terms of how to manually or automatically prescribe and keep track of the absolute orientation in 3D space of
sections reformatted through a 3D array of voxels and also how
to interpolate the values of the signal intensity in the voxels
corresponding to the reformatted image. The development of a
convenient and practical computer interface for subsequently
manually performing point and intersection counting on the
resulting 2D images is of course also a significant design
challenge.
The definition of a section is an infinitely thin plane
through the object of interest such as may correspond to the
cut face produced by a knife. In the case, when virtual cuts are
reformatted through a 3D MR image the corresponding sections must have finite thickness otherwise there would be no
signal available to produce an image. MR images therefore do
not have the extremely high resolution provided by the silver
halide grains of a photograph. Rather each image pixel refers to
a small volume of tissue known as a voxel. This means that
whereas in the case of point counting on physical sections
where, when a more detailed appraisal is required one can
pick up a magnifying glass, zooming in on an MR image
will only reveal the blocky discrete nature of the image can
make it more difficult rather than easier to discern whether a
point lies inside or outside the transect of an object. Furthermore, blurring of structure boundaries produced via projection
effects within the slice of tissue represented in the section
image (i.e., so-called partial voluming) potentially introduces
a bias. In fact, the results of all image analysis studies made
using MRI will potentially be affected by bias due to partial
voluming and best advice is to reduce slice thickness as much
as possible whilst maintaining reasonable signal to noise ratio
to afford interpretation of the features of interest in the image.
Nowadays, the image that is typically analyzed in brain imaging studies performed using MRI, especially in healthy subjects,
is a so-called T1-weighted 3D image comprising cubic voxels
with side 1 mm and in which partial voluming artifact is likely
to be relatively insignificant compared to early studies where
series of 2D MR images were obtained with a slice thickness
that could be as high as 10 mm.
Details of the stereological methods that have been developed for volume and surface area estimation are described in
Volume Estimation by the Cavalieri Method and Surface
Area Estimation by the Exhaustive Vertical Sections Method
sections, respectively. The procedures that may be used to
predict the precision of the estimate are presented and in
both cases the application of the method in combination
with MRI is illustrated. In the Discussion section, software

packages that are available for applying the methods are
described and recent developments are discussed.
Volume Estimation by the Cavalieri Method

In this laboratory the Cavalieri method has been applied to
estimate the volume of whole brain (Calmon & Roberts, 2000;
Subsol, Roberts, Doran, Thirion, & Whitehouse, 1997), brain
stem (Edwards et al., 1999) prefrontal cortex (Cowell et al.,
2007; Gong et al., 2005; Powell, Lewis, Dunbar, Garca-Finana,
& Roberts, 2010; Powell et al., 2014), Brocas area (Keller et al.,
2007; Sluming, Barrick, Howard, Mayes, & Roberts, 2002),
hippocampus (Aggleton et al., 2005; Brooks, Whitehouse,
Majeed, & Roberts, 2000; Foster et al., 1999; Garca-Finana,
Denby, Keller, Wieshmann, & Roberts, 2006; Mackay et al.,
1998; Mackay et al., 2001), amygdala (Boucher et al., 2005;
Broks et al., 1998; Howard et al., 2000), mammillary bodies
(Denby et al., 2009; Tsivilis et al., 2008), spinal cord (Liu,
Edwards, Gong, Roberts, & Blumhardt, 1999), lateral ventricles
(Redmond, Barbosa, Blumhardt, & Roberts, 2000), and the
fetus (Roberts et al., 1994) and fetal brain (Garden & Roberts,
1996; Gong, Roberts, Garden, & Whitehouse, 1998).
Many investigators see the pre-requisite for accurate manual
measurement of the volume of a structure of interest using MRI
as being to obtain access to a software package that allows the
operator to trace out the boundary of the structure of interest
on as many successive images obtained through the object as
possible. The volume measurement is generally thought to
become more accurate the more time is spent drawing round
transects (i.e., performing so-called planimetry). However, a
much better approach is available and this is to employ the
Cavalieri method of modern design-based stereology in combination with point counting (see Figure 1). There are two
stages of sampling. Firstly, at the image acquisition stage, or
via reformatting of an already acquired 3D MR image, a series
of section images are obtained at a constant sampling interval
covering the entire object. As alarming as it may sound, one
can let go of the idea of obtaining a measurement on every
possible section. Instead one must learn how to sample and the
first rule is that on no account should sampling always begin at
the first MR image on which the object appears. As an alternative, to ensure the estimate is unbiased, the first section must be
obtained at a random position within the fixed sampling interval, T. The second sampling is to overlay each of the images
with a square grid of test points, with a new random position
(i.e., the first point will be random within the area represented
by a grid square) and new random orientation (i.e., the grid
should be spun and come to rest at random), and to manually
record the number of points which overlie all of the transects
through the structure of interest on all the sections.
Use of the Cavalieri method described above ensures that
the estimates obtained are unbiased but as mentioned many
investigators will be very concerned that information has been
lost by neglecting to measure on every MR image section and
by recording the number of test points hitting the object as
opposed to painstakingly tracing out the boundaries of each
object transect. As will be described below, sampling with
systematic sections and a systematic grid of test points is an
335
Figure 1 Example of Cavalieri sectioning (a) and area function A(x) which represents the area of the intersection between the object of interest
and a plane at the point of abscissa (continuous curve) (b). The volume is the area under the area function and the volume estimate is the area under
the histogram. Performing Cavalieri sectioning and point counting on every 45th section of the MR image obtained for the cerebral hemisphere
specimen shown in later Figure 2(b) produced a volume estimate of 450 cm3 with a CE of 2.6%. Reproduced with permission from Garcia-Finana, M.,
Cruz-Orive, L. M., Mackay, C. E., Pakkenberg, B., & Roberts, N. (2003). Comparison of MR imaging against physical sectioning to estimate the volume of
human cerebral compartments. NeuroImage, 18, 505516.
extremely efficient procedure. Also, fortunately mathematicians have developed formulae that can be used for predicting
the precision of the estimate from the sampled information. In
particular, the coefficient of error (CE) of the Cavalieri volume
estimate can be simply predicted from a knowledge of the
points recorded on successive sections through the structure
of interest.
The first authors to propose a formula for predicting the CE
of a Cavalieri volume estimate were Gundersen and Jensen
(1987) based on the theory developed by Matheron (1965,
1971). The prediction which is based on modeling the correlation structure of the data via analysis of the covariogram is
model based and therefore is indirect and may potentially be
biased. Gundersen and Jensen (1987) also showed that the
precision of point counting estimates of transect area could
be predicted using theory developed by Matern (1985). The
latter prediction formula required that a so-called dimensionless shape coefficient be computed for the structure of interest.
Fortunately, the value of this shape coefficient can be estimated
at the outset of a study by recording the number of intersections between the boundary of the object transects and a
square grid of test lines overlain on the 2D section images
with random orientation. This value can be used in all future
studies of the same structure.
Cruz-Orive developed an error prediction formula for the
Cavalieri method, which integrated both the sectioning and
point counting contributions described above and again
requiring the input of a value for the dimensionless shape
coefficient. This was tested in studies by Roberts et al. (1993,
1997) which revealed that this so-called general prediction
formula over-estimated the CE in the case of very regular
shaped objects leading to the development of an alternative
formula for so-called quasi-ellipsoidal objects (Roberts et al.,
2000). Subsequent work by Garca-Finana and Cruz-Orive

(2000a, 2000b), Garca-Finana and Cruz-Orive (2004) led to
the development of a new formula which improved matters in
that it is no longer necessary to decide between whether to use
the general or quasi-ellipsoidal formula, and which provides a
better fit to all datasets. Garca-Finana, Keller, and Roberts
(2009) have also developed a method for predicting confidence intervals on Cavalieri volume estimates.
Precision will, of course, potentially increase if more sections are analyzed and more points counted but as will be
demonstrated below the returns on this investment quickly
become highly diminishing. For all practical purposes obtaining of the order 510 sections through an object and counting
a total of the order 100200 test points on these sections will
produce CEs of between 3% and 5%. Furthermore, when an
investigator believes that performing planimetry on more and
more images will potentially provide a result with greater
accuracy they are probably always misguided as it is likely
that beyond a certain level (a level that typically coincides
with the precision afforded by using stereological methods
with moderate workloads), the reliability of the measurement
is always confounded by the fact that the operator will frequently waver slightly in tracing out the boundary. Point
counting does not introduce such errors.
An important question raised by many new observers as
they embark on performing point counting measurements is to
ask what it is that constitutes the point on the stereological test
system. Actually, the point is dimensionless and defined as the
vanishingly small place where the, say, upper segment of the
vertical line, and the rightward segment of the horizontal line,
representing each cross on the test system intersect. The
observer should consistently assess for each cross whether
this point lies inside or outside the transect of the structure of
336
interest on the MR image section. Point counting presents no

particular challenges with regard to manual coordination and
the zero dimensionality of the point means that there is no
equivalent to the wavering that occurs as one draws round the
structure transect in performing planimetry.
Figures 2 and 3 are taken from a study by Garca-Finana
et al. (2003) to investigate the accuracy of MRI for estimating
the volume of six postmortem cerebral hemisphere specimens
and the internal compartments of cortex and sub-cortex
(defined as white matter plus deep grey matter and excluding
cerebral ventricles) using the Cavalieri method. The cerebral
hemispheres were embedded in blocks of agarose gel as shown
in Figure 2(a) and a model produced by volume rendering of a
3D MRI dataset obtained for one of the specimens
(bequeathed by a 77-year-old male) is shown in Figure 2(b).
After MR imaging, each specimen was physically cut into a
series of systematic sections using the apparatus shown in
Figure 2(c) and volume estimates obtained by application of
the Cavalieri method in combination with point counting
directly on sub-sampled series of physical and MR image
sections were compared.
Firstly, however, an investigation was performed using the
3D MR image obtained for one of the specimens to investigate
the effect of sectioning intensity and grid size (i.e., separation
between test points) on the precision of a Cavalieri volume
Figure 2 A postmortem cerebral hemisphere specimen is embedded in

agarose gel (a) and a 3D MR image is obtained from which a 3D
rendering of the specimen may be produced (b). Afterwards physical
Cavalieri sections were obtained for the specimen using the apparatus
shown in (c) and volume estimates obtained from the physical
sections via point counting were compared with corresponding volume
estimates obtained from virtual Cavalieri sections obtained by
sampling the 3D MR image. Garcia-Finana, M., Cruz-Orive, L. M.,
Mackay, C. E., Pakkenberg, B., & Roberts, N. (2003). Comparison of MR
imaging against physical sectioning to estimate the volume of human
cerebral compartments. NeuroImage, 18, 505516.
estimate for the above-mentioned brain compartments. In

particular, in the upper row of Figure 3(a), the section area
of cortex, sub-cortex, and total hemisphere, measured exactly
by application of the image analysis technique, illustrated in
Figure 1(b), is plotted for successive MR sections along the
anterior to posterior axis. In the middle row of Figure 3(a), the
volume estimates obtained from sub-samples obtained with
increasing sampling intensity from the original dataset are
plotted against average number of sections in the sub-sample,
and in the lower row, the empirical CE among the volume
estimates obtained from the sub-samples is plotted against
average number of sections in the sub-sample. The smooth
continuous line in the panels of the lower row corresponds
to the CE predicted from the transect areas measured for one of
the sub-samples drawn at random. Inspection of the panels
reveals that for the two internal compartments no more than
seven systematic sections are needed in order to obtain a CE of
less than 3% and only three sections in the case of total
hemisphere volume (note the very smooth profile for total in
the upper right panel of Figure 3(a)). Furthermore, the excellent agreement between the main curve and the smooth continuous line in each panel confirms that the model-based
formula that is proposed for predicting the CE of the volume
estimate is very reliable.
The upper row of Figure 3(b) represents a similar plot to
that in the lower row of Figure 3(a) except that now the
additional contribution to the CE related to performing point
counting with a square grid of side 9.375 mm (i.e., 1 cm) on
the sections is included via a model formula (i.e., eqn [6.3] in
Garca-Finana et al., 2003) and with the square of the total CE
equivalent to the sum of the squares of the separate sectioning
and point counting CEs (eqn [3.4] in the same paper). In the
middle row of Figure 3(b), the ratio of the point counting and
sectioning contributions to the CE is plotted against the number of sections in the sub-sample, and it can be seen that when
between 5 and 10 sections are analyzed the contributions are
similar but as the number of sections increases the point
counting contribution becomes greater, and when the number
of sections reaches of the order 30 (which is close to the
average number of 36 physical sections cut from the cerebral
hemisphere specimens with a thickness of 4.54 mm) the point
counting contribution is about 5, 3, and 7 times larger than the
contribution due to sectioning for cortex, sub-cortex, and total,
respectively. In other words only relatively few sections need to
be appropriately sampled after which the emphasis should be
on counting a reasonable number of test points, but not too
many! Finally, in the bottom row of Figure 3(b), for the case
where 38 systematic MR sections are analyzed for one of the
specimens, the effect on the total CE of increasing the separation between points is plotted for grid sizes of 1 mm to 5 cm.
For the case of cortex and sub-cortex, using a grid size of 2 cm
still ensures an overall CE of less than 3% and in the case of
total even a grid size of 4 cm ensures an overall CE of less than
3%. The reader is referred to Garca-Finana et al. (2003) for
further details of this experiment.
With regard to the experimental aim of assessing the accuracy of MRI for estimating the volume of postmortem cerebral
hemisphere specimens, the weights of 5 of the specimens were
known and assuming a tissue density of 1.04 g cm3 corresponding volumes could be computed to compare with those
337
Figure 3 (a) Area function obtained with negligible measurement error from a complete set of 274 MR images for the specimen shown in Figure 2(b).
(b) Replicated volume estimates obtained from the complete dataset versus the number of Cavalieri sections (n) and (c) CE versus n. The smooth
line represents the predicted CE and the dashed lines relate to previous so-called general and quasi-ellipsoidal versions. (d) CE of the volume
estimator from the Cavalieri sections analyzed with a square grid of side 9.375 mm for each of the compartments of interest versus number of sections.
(e) Ratio of point counting to section error contributions versus n when grid size is 9.375 mm. (f) Behavior of total CE for n 38 Cavalieri sections
as grid size increases. Reproduced with permission from Garcia-Finana, M., Cruz-Orive, L. M., Mackay, C. E., Pakkenberg, B., & Roberts, N. (2003).
Comparison of MR imaging against physical sectioning to estimate the volume of human cerebral compartments. NeuroImage, 18, 505516.
obtained by point counting on the physical sections and MR

images. In particular for each approach the values of two
regression coefficients for the linear relationship between
brain volume and brain weight were determined (i.e., b1
intercept of 479.0 g and b2 1/r 0.96 cm3 g1). The 95%
confidence regions for these regression coefficients as computed from the volume estimates obtained by point counting
on the physical sections and MR sections are shown in the right
and left hand panels of Figure 4, respectively.
The model point is captured by the confidence intervals
from the point counting analysis of the physical sections but
not by the confidence intervals from the point counting analysis of the MR sections, thus casting doubt on the unbiasedness
of the MRI technique, and perhaps anticipated on account of
partial voluming artefact. The 3D MR images obtained for this
study using a 1.5 T MR system each refer to a slice thickness of
1.6 mm. The bias may become negligible if the 3D MR images
were to be obtained using a 3 T MR system which provides
higher signal in the same imaging time and produces 3D MR
images typically comprising isotropic voxels of side 1 mm (i.e.,
image resolution of 10 pixels cm1).
In this case, when the contents of the slice are well known
such as in brain imaging studies of healthy subjects (i.e., every
voxel comprises grey matter and/or white matter and/or CSF),
software is increasingly becoming available that can be used to
compute the slice contents and when this is the case the socalled Cavalieri slices method (McNulty, Cruz-Orive, Roberts,
Holmes, & Gual-Arnau, 2000) should be used instead of the
Cavalieri sections method. In the Cavalieri slices method volume is estimated as the sum of the amount of tissue in each
slice multiplied by T/t, where t is the slice thickness. In
McNulty et al. (2000), the reliability of formulae developed

for predicting the precision of volume estimates obtained using
the Cavalieri slices method is demonstrated using empirical
sub-sampling simulations performed on a paradigm highcontrast 3D MR image of the brain obtained by averaging
together 27 individual 3D MRI scans that were all obtained
for the same subject, and which enabled the grey and white
matter and CSF content of every voxel to be determined with
high reliability.
Surface Area Estimation by the Exhaustive Vertical

Sections Method
We now turn to consider the estimation of the surface area of
an object of interest. Here the test probes that will be used are
lines, rather than points. Crucially, whereas the test points are
zero-dimensional, the test lines are one-dimensional. In particular, they possess direction and in order for the surface area
estimate to be unbiased the test lines must have an isotropic
uniform random (IUR) distribution in space. In other words,
there must be an equal chance of the lines pointing in all
directions. This impacts very substantially on the design of
the sampling scheme by which the relevant sections are
obtained as will be discussed below. Furthermore, the work
to be performed by the operator on the 2D sections is now
intersection rather than point counting and, as will be
explained, the test lines may take the form of straight lines or
circles and even, in the case of the so-called Vertical Sections
design, cycloids.
338
Figure 4 Confidence regions for the regression coefficients (B0, B1) for each technique. The point (B0, B1) (479, 0.96) corresponds to the
postulated model. Reproduced with permission from Garcia-Finana, M., Cruz-Orive, L. M., Mackay, C. E., Pakkenberg, B., & Roberts, N. (2003).
Comparison of MR imaging against physical sectioning to estimate the volume of human cerebral compartments. NeuroImage, 18, 505516.
Obtaining surface area estimates using MRI is potentially

more straightforward than from physical sections. This is
because if one orients an object in a particular direction and
then takes an exhaustive series of physical sections through it,
test lines can only be placed in that object in the orientations
allowed by those specific cut planes. One is not able to readily
reassemble the object and cut it with a series of physical sections along a new cutting direction. Either at the acquisition
stage or in reformatting an acquired 3D dataset there are no
such constraints using MRI and new series of sections can be
readily obtained through the object in any prescribed
direction.
The direct prescription of isotropic sections is not standard
on MR systems and neither has this facility been incorporated
for convenient use in software available for reformatting 3D
MR images. The most popular method that is in general use
derives from the so-called Vertical Sections method (Baddeley
et al., 1987) in which physical sections are obtained perpendicular to the bench top on which the object may be placed. In
their paper, Baddeley et al. (1987) illustrate the Vertical Sections method for the case of estimating the surface area of a
Paddington Bear figurine. Firstly, in order to try to maximize
the angle over which the Vertical Sections sample the figurine,
horizontal cuts are made to divide the object into three pieces
one above the other. These pieces are then moved so that the
lower surface of each rests on the bench top and after being
rotated in systematic random directions relative to a reference
direction, a series of Vertical Sections is obtained through each
of the three pieces along the same sectioning direction. In the
case of MRI, the Vertical Sections method has been applied by
Ronan, Doherty, Delanty, Thornton, and Fitzsimons (2006)
and Ronan et al. (2007) to study the changes in brain surface
area in patients with temporal lobe epilepsy. Alternatively, the
so-called Exhaustive Vertical Sections method (Furlong et al.,
2013; Cruz-Orive et al., 2013; Roberts et al., 2000), which is
illustrated in Figure 5, may be applied.
The axial image plane is taken as the horizontal plane and
all the Vertical Sections are obtained perpendicular to this
plane. In particular, in Figure 5(c) and 5(d) two systematic
random scanning directions 90 apart are defined and the 3D
MRI brain dataset is virtually cut with systematic series of

Exhaustive Vertical Sections along both these directions, producing the two series of Vertical Cavalieri sections, shown in
Figure 5(b), which is reproduced from Cruz-Orive et al.
(2013). If an isotropic grid of lines is overlain on each Vertical
Sections the overall distribution of test lines in 3D will contain
many more lines which are oriented towards the direction of
the poles as opposed to the direction of the equator in a sphere
with polar axis aligned along the vertical direction. Thus the
test lines will not have the required isotropic distribution in
3D. Baddeley et al. (1987), however, describe how this bias can
be conveniently removed if an array of cycloids (Figure 5(e)
and 5(f)) replaces the isotropic test lines. The cycloid test
system is inherently weighted such that a greater length of the
test line is oriented in the horizontal rather than the vertical,
and this weighting exactly balances the Vertical Sectioning bias,
so that counting intersections with cycloids on Vertical Sections is identical to counting intersections with isotropic test
lines (or circles) on IUR sections. This ingenious development
has made the Vertical Sections method very convenient to
apply in the study of physical specimens, which may be conveniently cut perpendicular to the bench top. The Vertical
Sections method has also obtained some popularity for use
with MRI in that whereas isotropic sectioning designs produce
images in which the observer is continually having to view and
interpret anatomical relationships from a wide range of different and unfamiliar (e.g., upside down) directions, the Exhaustive Vertical Sections method can be set up so as to produce MR
images of the brain which range from being true sagittal to true
coronal in orientation and which therefore display brain
anatomy in a manner which is familiar to an investigator
such as a radiologist or anatomist. This makes intersection
counting much more convenient to perform.
There are two contributions to the variance associated with
the Cavalieri method, namely that due to sectioning and that
due to point counting, and there are three associated with the
Exhaustive Vertical Sections method, namely that due to systematic angular sampling about the vertical axis, a sectioning
contribution very similar to that which exists for the Cavalieri
method but now applied to each series of Exhaustive Vertical
339
z + 2T
f + 90
z +T
z
O
f
(a)
(b)
1
23
56
6
5
4
3
2
1
(d)
x3
Vertical
2d
Length = 8d
(e)
1
x1
(c)
Series 2, 127
Series 1, 37
x2
2d
5 cm
5 cm
(f)
Figure 5 Sampling of two mutually perpendicular UR directions normal to the corresponding vertical Cavalieri series of sections advocated to use to
estimate brain surface area (a, b). The vertical axis is perpendicular to the paper. Mutually perpendicular UR Cavalieri series normal to the axes
previously sampled at the angles 37 and 127 , respectively, hitting a brain to estimate its surface area. (e) Fundamental tile of the cycloid test grid (f)
containing a fundamental curve consisting of a double cycloid arc. To superimpose the test grid uniformly at random on a vertical section the
associated point of a fundamental curve is brought to coincide with a UR point sampled in the interior of the fundamental tile. The grid must be kept
fixed with the smaller cycloid axes parallel to the vertical direction. Also shown in the upper portions of the center and right sided panels of the figure are
the positions within the brain of the vertical sections corresponding to Series 1 and 2. The actual vertical sections, prepared with the aid of 3DSlicer
software, are shown in the respective lower portions of these panels. The pial and subcortical trace curves shown in red and blue, respectively, were
obtained using FreeSurfer software. The arrow in the first vertical section of Series 1 indicates the vertical direction. Reproduced with permission from
Cruz-Orive, L. M., Gelsvartas, J., & Roberts, N. (2013). Sampling theory and automated simulations, applied to human brain. Journal of Microscopy,
253, 119150.
Sections, and finally a contribution due to intersection counting with a cycloid grid. Up until recently, theory was only
sufficiently developed so as to provide formulae for modeling
the size of the angular sampling (Cruz-Orive & Gual-Arnau,
2002) and systematic sectioning contributions (Garca-Finana
& Cruz-Orive, 2000a, 2000b). In Cruz-Orive et al. (2013),
however, a new error prediction formula relating to the counting of intersections with a cycloid test system is presented and
computer simulations are performed to empirically investigate
its reliability. The relative contribution of all three terms in
estimating the surface area of the brain on Exhaustive Vertical
Sections is also described.
In order to be able to perform the above-mentioned simulations FreeSurfer software was first used to segment the pial
surface and boundary between cortical grey matter and white
matter in a 3D MR image obtained for a living 20-year-old
female subject. The tessellated surface that is produced has a
sub-voxel resolution in that the values that are obtained for
the, for example, percentage of grey matter in each voxel during
the segmentation step is used as the basis for performing an
interpolation to determine where the surface resides within
each voxel. Subsequently, two series of Extended Vertical Sections were reformatted through the tessellated surface, as
shown in Figure 5, and an example of the grey matter boundary for the fifth vertical section in the first series is shown in
Figure 6(a). A software package was written in this laboratory
to enable cycloid tests systems of varying areal density to be
overlain on the vertical sections and the number of intersections between the test system and the cortical boundary to be
automatically recorded, as shown in Figure 6(b).
The left and right columns of Figure 6(b) refer to the first
and second series of Vertical Sections, shown in Figure 5,
respectively, and in each panel the CE due to intersection
counting as predicted using the new formula is plotted against
corresponding empirical values obtained using Monte Carlo
simulations, for three different grid sizes increasing down the
column. Overall there is good agreement between the predicted and empirically determined CE. Thus a reasonably precise and unbiased estimate of the surface area of the cerebral
cortex may be obtained by counting intersections between the
boundary of the surface as it appears on two orthogonal series
of systematic vertical sections obtained with a random starting
angle and random starting position. Furthermore, as described
by Cruz-Orive et al. (2013), all the relevant theory exists to be
able to predict the CE of the surface area estimate. Just as
Garca-Finana and Cruz-Orive (2000a, 2000b) performed simulations to demonstrate the relative efficiency or sectioning
and point counting in estimating volume using the Cavalieri
method, Cruz-Orive et al. (2013) provide a launch point for
designing simulations to investigate the relative efficiency of
angular sampling, sectioning and intersection counting for
estimating surface area using the Extended Vertical Sections
method.
The study by Cruz-Orive et al. (2013) is of a living brain. No
ground truth exists and the main aim of the study is to present
relevant theory and to perform relevant simulations to investigate the reliability of formulae for predicting the precision of
surface area estimates obtained by the Extended Vertical Sections method. However, just as Garca-Finana and Cruz-Orive
(2000a, 2000b) investigated the accuracy of the Cavalieri
340
Figure 6 A vertical section from the vertical Cavalieri series 1 with the pial trace approximated by polygonal curves (in red) with a UR cycloid test
system superimposed and covering it entirely. The relevant intersections with the pial trace curves are marked by white dots. To predict the error
variance component due to intersection counting with the so-called fakir formula, intersection counts have to be scored separately for each fundamental
cycloid curve. To distinguish them, the fundamental curves have been colored alternatively in red and black. The centers of the hit links of the
polygonal chain are represented as red and black circles, respectively. The corresponding counts were collected automatically with the aid of the
StereoTool software. Model predictors of the coefficient of error due to intersection counting (on the pial traces with cycloid test grids), plotted against
the corresponding empirical values obtained by Monte Carlo replications. The checks were performed with grids of three different sizes on each of
the six sections from each of the two vertical Cavalieri series available. Reproduced with permission from Cruz-Orive, L. M., Gelsvartas, J., & Roberts, N.
(2013). Sampling theory and automated simulations, applied to human brain. Journal of Microscopy, 253, 119150.
method for estimating cortical volume using MRI, so Furlong

et al. (2013) performed a study of 16 cerebral hemisphere
postmortem specimens to investigate the accuracy of the
Extended Vertical Sections method for estimating cortical surface area using MRI. The left panel of the upper row of Figure 7
shows a color photograph of an axial cut section through one
of the specimens and in the right panel a magnified view of the
region corresponding to the white rectangle in the left panel is
displayed.
The image in the second row of Figure 7 is a black and
white version of the image in the upper row and in the lower
row an MR image corresponding to the same position in the
brain is shown. The black lines labeled 1, 2, and 3 in the
middle and lower panel of the right hand column of Figure 7
point to identical positions in the brain on the photograph and
MR image, respectively. The red dot at the end of line 1 in both
panels indicates that a cycloid in the same position in the
photograph and the MR image is adjudged to intersect the
pial surface in both. Likewise the two red dots at the end of
line 2 in both panels indicate that a cycloid in the same
position in the photograph and the MR image is adjudged to
cross a sulcus in both. However in the case of line 3, two red
dots are present at the end of the line in the photograph but are
absent in the MR image. This is because partial voluming artifact that is present in the MR image prevents a sulcus being
seen on MRI that is clearly visible in the photograph. On
average, pial surface area was estimated to be almost half the
extent using MRI compared to physical sectioning (i.e., 45%,
p < 0.05). No such problems exist in applying the Extended
Vertical Sections method to estimate the surface area of the
boundary between grey and white matter. Accurate application
of manual stereological methods for measuring the cortical
surface area, but not the surface area of the boundary between
grey and white matter, thus requires higher resolution MR
imaging than is typically performed at 3 T. Interestingly,
semi-automatic software such as FreeSurfer can provide an
accurate measurement of both pial surface area and the surface
area of the boundary between grey and white matter by first
extracting the latter and then growing a cerebral cortex on top
of this according to appropriate constraints to produce the
latter. Furthermore, 7 T MR imaging systems provide 3D MR
images with isotropic voxels of side 0.5 mm (i.e., resolution of
20 pixels cm1), in which the pial surface can be readily seen in
its entirety, in reasonable imaging times.
Figure 7 A digital color photograph of the upper face of the fourth slice
cut through a postmortem cerebral hemisphere specimen is shown
in (A1), and in (A2) the photograph of (A1) has been converted to a black
and white image, input to EasyMeasure software and overlain by a
cycloid test system with random position and oriented such that the
short axis of the cycloids lies parallel to the vertical direction. In (A3) the
MR image corresponding to the same position in the specimen as the
physical section shown in (A1) and (A2) has also been input to
EasyMeasure software and overlain with a cycloid test system with
random position (in this case, it is the same random position as the one
obtained for the physical section for illustrative purposes) and again
oriented such that the short axis of the cycloids lies parallel to the vertical
direction. Panels (B1), (B2), and (B3) refer to the same images as (A1),
(A2), and (A3), respectively, and in particular show a magnified view
of the region contained within the box outlined in white in (A1).
For further details see text. Reproduced with permission from
Furlong, C., Garca-Finana, M., Sahin, B., Anderson, A., Fabricius, K.,
Eriksen, N., et al. (2013). Application of stereological methods
to estimate postmortem brain surface area using 3 T MRI. Magnetic
Discussion
A further interesting advance is the development of the Isotropic Cavalieri method as reported by Cruz-Orive, RamosHerrera, and Artacho-Perula (2010). The advantage of using
the Isotropic Cavalieri method is firstly that explicit, as
opposed to model-based, formula exist for predicting the precision of the estimate, and secondly that an unbiased estimate
of surface area may conveniently also be obtained from the
acquired sections. Whereas in the traditional application of the
Cavalieri method sections may be obtained along an axis at
any arbitrary orientation through an object, in the case of the
Isotropic Cavalieri method the sectioning direction must be
isotropic in 3D. In the case, where for example total brain
volume and surface area is to be compared between two groups
for whom physical specimens have been obtained postmortem
a convenient way of generating Isotropic Cavalieri sections is to
embed each specimen in a sphere of agarose gel and then to
roll the sphere along the bench top until it comes to rest at
which point sectioning each sphere from, say, left to right will
produce Isotropic Cavalieri sections through each specimen
ready for analysis. In the case, where total brain volume and
surface area is to be compared between two groups for whom
341
3D MR images of the brain are available, an equivalent virtual

sectioning procedure is required. The basic procedure comprises (see Section 7.2 part (iii) of Cruz-Orive et al. (2010)),
firstly generating an isotropic axis through the object at the
centre point of the image volume via random choice of latitude
and longitude angles. Secondly rotating the object randomly
about this axis and thirdly cutting the object in a predetermined arbitrary way. The precision of the estimate can be
increased by taking a second series of sections orthogonal to
the first. The corresponding volume and surface area estimates
can then be averaged across the two or three series. Surprisingly, perhaps, very few software packages are available to
perform this simple sampling scheme conveniently, and especially to at the same time track and reliably record the position
and orientation of the reformatted image at each step.
Thus the ideal approach for estimating object volume
would be to combine the Isotropic Cavalieri and Cavalieri
slices methods. In particular, this will provide an unbiased
sampling design, correction for partial voluming artifact and
explicit formulae for predicting the precision of the estimate.
This will require further developments both in terms of the
availability of appropriate software packages to enable convenient isotropic sampling and developments in robust image
analysis approaches for correcting for partial volume artifact.
Meanwhile, provided that the slices to which the MR image
sections refer are relatively thin, the Cavalieri sections method
offers a practical, convenient, efficient, and unbiased sampling
design for estimating object volume with predictable precision.
An additional method of surface area estimation is the socalled Spatial Grid (Howard & Cruz-Orive, 1995). The main
sampling scheme is to obtain a series of sections in an identical
manner to the Isotropic Cavalieri method. However, rather
than superimposing a grid of test lines with new isotropic
orientation on each section, a square grid of test lines is superimposed with the same IUR position and orientation on each
section and a special counting scheme performed to identify
both the intersections that occur between the grid lines and the
object boundary in the plane and to also follow the corresponding grid lines as one scrolls down through the stack of
images and count the number of occasions which these pass in
and out of the object. This way a table may be produced of the
number of intersections between the object boundary and an
orthogonal grid of test lines and from which object surface area
may be readily computed. The spatial grid may potentially be
applied in combination with MRI, although software has yet to
be developed to afford a truly convenient interface for recording the intersection counts. Furthermore, by virtue of conveniently providing both volume and surface area estimates, and
because formulae are available for explicitly predicting the
precision of these estimates, the Isotropic Cavalieri method
may be considered to have superseded the Spatial Grid
method.
The software package that comes closest to providing a
convenient resource for reformatting sections in a 3D MR
dataset and performing point counting is Analyze software
(http://www.analyzedirect.com) developed at the MAYO
Foundation, Minnesota, USA, and Measure software developed
at Johns Hopkins University School of Medicine (Barta et al.,
1995). On occasions it may be more convenient to implement
the sectioning design with one software package such as
342
Analyze or 3DSlicer (http://www.slicer.org) and to perform the

point and intersection counting with a different software package such as EasyMeasure (Roberts et al., 2000).
Series of MR images reformatted at a chosen angle through
a 3D MR image will likely look very good, but there will of
course exist some degradation relative to the appearance of the
acquired images. In particular, the reformatted section will not
exactly coincide with the original voxels in the 3D array and
image signal intensities will need to be calculated via an interpolation algorithm and the resulting image potentially
smoothed. These effects will not only potentially confound
measurements made on reformatted images but also measurements made on images which may have been normalized to
so-called standard space (i.e., to the so-called Talairarch or
MNI-152 atlas).
Semi-automatic approaches are increasingly becoming
available for measuring brain volume using software such as
FSL, SPM, and FreeSurfer. The segmentations obtained using
these software will typically reflect the percentage of grey matter, white matter and CSF in each voxel, and total brain volume
is computed by integration of the relevant individual voxel
contents (i.e., grey and white matter) within an appropriately
drawn region of interest.
Interestingly, a Nobel Prize has not been awarded in respect
of the development of Ultrasound, at least not yet. The award
would, however, surely be richly deserved in view of the highly
significant impact ultrasound scanning has in medicine. The
fact that the sound waves do not pass through the skull to
enable brain imaging is obviously a major limitation of the
technique. Furthermore, whilst 3D ultrasound is now readily
available there has unfortunately not been a complementary
development in the capabilities for convenient 3D measurement using these systems. Fetal growth is unfortunately still
routinely assessed using potentially biased measures such as biparietal diameter and head circumference.
Finally, since this article is entitled manual morphometry it
is appropriate to make some remarks about work (i.e., physical
effort) and performance (i.e., manual coordination). There
have been several studies performed to suggest that sonographers performing ultrasound studies, and which include not
only the handling of the ultrasound probe but also image
analysis work that they may undertake, may develop fatigue
and possibly also musculoskeletal injuries (Baker & Coffin,
2013; Goyal et al., 2009). On the other hand, when performed
with good use (Alexander, 1932) making manual measurements can be a pleasurable activity. Furthermore, physical
engagement can interact positively with mental activity so as
to provide an enriched theoretical understanding. Hopefully,
the simulations that have been presented have provided convincing demonstration that in addition to being unbiased
stereological methods based on systematic sampling strategies
are highly efficient. This should lead to investigators performing manual measurement using what may be best described as
a deft touch, a light touch and with absolutely no danger of
developing repetitive strain injury.

Information from fMRI; INTRODUCTION TO ANATOMY AND

PHYSIOLOGY: Brain Sex Differences; Cortical Surface Morphometry;
Cytoarchitectonics, Receptorarchitectonics, and Network Topology of
Language; Embryonic and Fetal Development of the Human Cerebral
Cortex; Evolution of the Cerebral Cortex; Fetal and Postnatal
Development of the Cortex: MRI and Genetics; Gyrification in the
Human Brain; Quantitative Data and Scaling Rules of the Cerebral
Cortex; Sulci as Landmarks; INTRODUCTION TO METHODS AND
MODELING: Automatic Labeling of the Human Cerebral Cortex;
Bayesian Multiple Atlas Deformable Templates; Computing Brain
Change over Time; Cortical Thickness Mapping; Intensity
Nonuniformity Correction; Lesion Segmentation; Modeling Brain
Growth and Development; Sulcus Identification and Labeling; SurfaceBased Morphometry; Tensor-Based Morphometry; Tissue
Classification; Voxel-Based Morphometry.
References
Aggleton, J. P., Vann, S. D., Denby, C., Dix, S., Mayes, A. R., Roberts, N., et al. (2005).
Sparing of the familiarity component of recognition memory in a patient with
hippocampal pathology. Neuropsychologia, 43, 18101823.
Alexander, F. M. (1932). The use of the self. New York: E.P. Dutton.
Baddeley, A. J., Gundersen, G. H., & Cruz-Orive, L. M. (1986). Estimation of surface
area from vertical sections. Journal of Microscopy, 142, 259276.
Baker, J. P., & Coffin, C. T. (2013). The importance of an ergonomic workstation to
practicing sonographers. Journal of Ultrasound in Medicine, 32, 13631375.
Barta, P. E., Petty, R. G., McGilchrist, I., Lewis, R. W., Jerram, M., Casanova, M. F., et al.
(1995). Asymmetry of the planum temporale: Methodological considerations and
clinical associations. Psychiatry Research, 61, 137150.
Boucher, J., Cowell, P., Howard, M., Broks, P., Farrant, A., Roberts, N., et al. (2005). A
combined clinical neuropsychological and neuroanatomical study of adults with
high functioning autism. Cognitive Neuropsychiatry, 10, 165213.
Broks, P., Young, A. W., Maratos, E. J., Coffey, P. J., Calder, A. J., Isaac, C., et al.
(1998). Face processing impairments after encephalitis: Amygdala damage and
recognition of fear. Neuropsychologia, 36, 5970.
Brooks, J. C. W., Whitehouse, G. H., Majeed, T., & Roberts, N. (2000). Reduced
neuronal metabolism in hippocampus in chronic fatigue syndrome. The British
Journal of Radiology, 73, 12061208.
Calmon, G., & Roberts, N. (2000). Automatic measurement of changes in brain volume
on consecutive 3D MR images by segmentation propagation. Magnetic Resonance
Imaging, 18, 439453.
Cowell, P. E., Sluming, V. A., Wilkinson, I. D., Cezayirli, E., Romanowski, C. A.,
Webb, J. A., et al. (2007). Effects of sex and age on regional prefrontal brain volume
in two human cohorts. European Journal of Neuroscience, 1, 307318.
Cruz-Orive, L. M. (1997). Stereology of single objects. Journal of Microscopy, 186,
93107.
Cruz-Orive, L. M., Gelsvartas, J., & Roberts, N. (2013). Sampling theory and automated
simulations for vertical sections, applied to human brain. Journal of Microscopy,
253, 119150.
Cruz-Orive, L. M., & Gual-Arnau, X. (2002). Precision of circular systematic sampling.
Journal of Microscopy, 207, 225242.
Cruz-Orive, L. M., Ramos-Herrera, M. L., & Artacho-Perula, E. (2010). Stereology of
isolated objects with the invariator. Journal of Microscopy, 240, 94110.
Denby, C. E., Vann, S. D., Tsivilis, D., Aggleton, J. P., Montaldi, D., Roberts, N., et al.
(2009). The frequency and extent of mammillary body atrophy associated with
surgical removal of a colloid cyst. American Journal of Neuroradiology, 30,
736743.
Edwards, S. G.M, Gong, Q. Y., Liu, C., Zavartau, M. E., Jaspan, T., Roberts, N., et al.
(1999). Infratentorial atrophy on magnetic resonance imaging and disability in
multiple sclerosis. Brain, 122, 291301.
Foster, J. K., Meikle, A., Goodson, G., Mayes, A. R., Howard, M., Suenram, S. I., et al.
(1999). The hippocampus and delayed recall: Bigger is not necessarily better.
Memory, 7, 715732.
Furlong, C., Garca-Finana, M., Sahin, B., Anderson, A., Fabricius, K., Eriksen, N., et al.
(2013). Application of stereological methods to estimate post-mortem brain surface
area using 3 T MRI. Magnetic Resonance Imaging, 31, 456465.

Garca-Finana, M., & Cruz-Orive, L. M. (2000a). New approximations for the efficiency
of Cavalieri sampling. Journal of Microscopy, 199, 224238.
Garca-Finana, M., & Cruz-Orive, L. M. (2000b). Fractional trend of the variance in
Cavalieri sampling. Image Analysis & Stereology, 19, 7179.
Garca-Finana, M., & Cruz-Orive, L. M. (2004). Improved variance prediction for
systematic sampling on R. Statistics, 38, 243272.
Garca-Finana, M., Cruz-Orive, L. M., Mackay, C. E., Pakkenberg, B., & Roberts, N.
(2003). Comparison of MR imaging against physical sectioning to estimate the
volume of human cerebral compartments. NeuroImage, 18, 505516.
Garca-Finana, M., Denby, C. E., Keller, S. S., Wieshmann, U. C., & Roberts, N. (2006).
Degree of hippocampal atrophy is related to side of siezure onset in temporal lobe
epilepsy. American Journal of Neuroradiology, 27, 10461052.
Garca-Finana, M., Keller, S. S., & Roberts, N. (2009). Confidence intervals for the
volume of brain structures in Cavalieri sampling with local errors. Journal of
Neuroscience Methods, 179, 7177.
Garden, A. S., & Roberts, N. (1996). Fetal and fetal organ volume estimations using
MRI. American Journal of Obstetrics & Gynecology, 175, 442448.
Gong, Q. Y., Roberts, N., Garden, A. S., & Whitehouse, G. H. (1998). Fetal and fetal
brain volume estimation in the third trimester of human pregnancy using gradient
echo MR imaging. Magnetic Resonance Imaging, 16, 235240.
Gong, Q., Sluming, V., Mayes, A., Keller, S., Barrick, T., Cezayirli, E., et al. (2005).
Voxel-based morphometry and stereology provide convergent evidence of the
importance of medial prefrontal cortex for fluid intelligence in healthy adults.
Goyal, N., Jain, N., & Rachapalli, (2009). Ergonomics in radiology. Clinical Radiology,
64, 119126.
Gundersen, H. J., & Jensen, E. B. (1987). The efficiency of systematic sampling in
stereology and its prediction. Journal of Microscopy, 147, 229263.
Howard, M. A., Cowell, P. E., Boucher, J., Broks, P., Mayes, A., Farrant, A., et al. (2000).
Convergent neuroanatomical and behavioural evidence of an amygdala hypothesis
of autism. NeuroReport, 11, 29312935.
Howard, C. V., & Cruz-Orive, L. M. (1995). Estimation of individual feature surface area
with the vertical spatial grid. Journal of Microscopy, 178, 146151.
Howard, C. V., & Reed, M. G. (1998). Unbiased stereology: Three-dimensional
measurement in microscopy. Bios Scientific Publishers, Abingdon, Oxfordshire, UK.
Keller, S. S., Highley, J. R., Garcia-Finana, M., Sluming, V., Rezaie, R., & Roberts, N.
(2007). Sulcal variability, stereological measurement and asymmetry of Brocas area
on MR images. Journal of Anatomy, 211, 534555.
Liu, C., Edwards, S., Gong, Q., Roberts, N., & Blumhardt, L. D. (1999). 3D MRI
estimates of brain and spinal cord atrophy in multiple sclerosis. Journal of
Neurology, Neurosurgery, and Psychiatry, 66, 323330.
Mackay, C. E., Roberts, N., Mayes, A. R., Downes, J. J., Foster, J. K., & Mann, D.
(1998). An exploratory study of the relationship between face recognition memory
and the volume of medial temporal lobe structures in healthy young males.
Behavioural Neurology, 11, 320.
Mackay, C. E., Webb, J. A., Eldridge, P. R., Chadwick, D. W., Whitehouse, G. H., &
Roberts, N. (2001). Quantitative magnetic resonance imaging in consecutive
patients evaluated for surgical treatment of temporal lobe epilepsy. Magnetic
343
Matern, B. (1985). Estimating area of dot counts. In J. Lanke & G. Lindgren (Eds.),
Sampling contributions to probability and statistics in honour of gunnar bloom
(pp. 243257). Lund: University of Lund.
Matheron, G. (1965). Les variables regionalisees et leur estimation (thesis). Paris:
Masson et Cie.
Matheron, G. (1971). The theory of regionalized variables and its applications. In Les
Cahiers du Centre morphologie mathematique de Fontainebleau5. Ecole National
Superieure des Mines de Paris.
McNulty, V., Cruz-Orive, L. M., Roberts, N., Holmes, C. J., & Gual-Arnau, X. (2000).
Estimation of brain compartment volume from MR Cavalieri slices. Journal of
Mouton, P. R. (2011). Unbiased stereology: A concise guide. The Johns Hopkins
University Press, Baltimore, MD, USA.
Powell, J. L., Kemp, G. J., Dunbar, R. I.M, Roberts, N., Sluming, V., & Garca-Finana, M.
(2014). Different association between intentionality competence and prefrontal
volume in left and right handers. Cortex, 54, 6376.
Powell, J., Lewis, P., Dunbar, R. I.M, Garca-Finana, M., & Roberts, N. (2010). Orbital
prefrontal cortex volume correlates with social cognitive competence.
Neuropsychologia, 48, 35543562.
Redmond, L. T., Barbosa, S., Blumhardt, L. D., & Roberts, N. (2000). Short-term
ventricular volume changes on serial MRI in multiple sclerosis. Acta Neurologica
Scandinavica, 102, 99105.
Roberts, N., Cruz-Orive, L. M., Reid, N. M., Brodie, D. A., Bourne, M., & Edwards, R. H. T.
(1993). Unbiased estimation of human body composition by the Cavalieri method
using magnetic resonance imaging. Journal of Microscopy, 171, 239253.
Roberts, N., Cruz-Orive, L. M., Bourne, M., Herfkens, R. J., Karowski, R. A., &
Whitehouse, G. H. (1997). Analysis of cardiac function by MRI and stereology.
Journal of Microscopy, 187, 3142.
Roberts, N., Garden, A. S., Cruz-Orive, L. M., Whitehouse, G. H., & Edwards, R. H. T.
(1994). Estimation of fetal volume by magnetic resonance imaging and stereology.
British Journal of Radiology, 67, 10671077.
Roberts, N., Puddephat, M. J., & McNulty, V. (2000). The benefit of stereology for
quantitative radiology. The British Journal of Radiology, 73, 679697.
Ronan, L., Doherty, C. P., Delanty, N., Thornton, J., & Fitzsimons, M. (2006).
Quantitative MRI: A reliable protocol for measurement of cerebral gyrification using
stereology. Magnetic Resonance Imaging, 24, 265272.
Ronan, L., Murphy, K., Delanty, N., Doherty, C., Maguire, S., Scanlon, C., et al. (2007).
Cerebral cortical gyrification: A preliminary investigation in temporal lobe epilepsy.
Epilepsia, 48, 211219.
Sluming, V., Barrick, T. R., Howard, M. A., Mayes, A. R., & Roberts, N. (2002). Voxelbased morphometry reveals increased grey matter density in Brocas area in male
symphony orchestra musicians. NeuroImage, 17, 16131622.
Subsol, G., Roberts, N., Doran, M., Thirion, J.-P., & Whitehouse, G. H. (1997).
Automatic analysis of cerebral atrophy. Magnetic Resonance Imaging, 15, 917927.
Tsivilis, D., Vann, S. D., Denby, C., Roberts, N., Mayes, A. R., Montaldi, D., et al. (2008).
A disproportionate role for the fornix and mammillary bodies in recall versus
recognition memory. Nature Neuroscience, 11, 834842.
West, M. J. (2012). Basic stereology for biologists and neuroscientists. New York: Cold
Spring Harbor Laboratory Press.
Voxel-Based Morphometry
F Kurth and E Luders, UCLA School of Medicine, Los Angeles, CA, USA
C Gaser, Jena University Hospital, Jena, Germany
Introduction
The human brain is in a state of constant change and adaptation. This may be driven either by normal developmental or
aging processes or by the effects of learning, training, and new
occurrences in daily life. In addition to these aforementioned
changes, more systematic influences such as gender, disease,
and genes affect the brains structure. Using magnetic resonance imaging, brain changes and differences can be measured
noninvasively and in vivo, making them particularly interesting
for both basic research and clinical research. The easiest way to
assess brain changes (or group differences) is to measure
whole-brain volume. However, assessing the volume of the
entire brain is rather unspecific. So-called region-of-interest
(ROI) analyses are more sensitive to local changes than are
whole-brain assessments but are also subject to several limitations. For example, if one specific region is measured, other
brain structures are ignored, and possible effects remain undetected elsewhere in the brain. Moreover, ROIs are usually
created based on individual protocols and depend on raterspecific judgment calls, thus requiring a clearly definable and
unambiguous structure. For large parts of the brain, however, it
may be difficult to precisely define (or identify) unambiguous
boundaries. Finally, if an ROI is only partially different, this
will lower the sensitivity to detect any effects in this region.
This is where voxel-based morphometry (VBM) comes into
play, as VBM allows for the examination of brain changes
and/or group differences across the entire brain with a high
regional specificity (i.e., voxel by voxel), without requiring the
a priori definition of particular ROIs (Ashburner & Friston,
2000, 2001, 2007).
VBM: An Overview
VBM is an objective approach that enables a voxel-wise estimation of the local amount of a specific tissue. Most
commonly, VBM is directed at examining gray matter but it
can also be used to examine white matter. In the latter case,
however, the sensitivity is limited, for white matter areas are
characterized by large homogeneous regions with only subtle
changes in intensity. The concept of VBM comprises three basic
preprocessing steps: (1) tissue classification, (2) spatial
normalization, and (3) spatial smoothing, which are followed
by the actual statistical analysis. That is, if we know exactly
what tissue can be found at a specific voxel, we can quantify
and analyze it. This can be achieved by tissue classification.
Furthermore, if we know that a specific voxel is at exactly the
same anatomical location across all subjects (e.g., at the tip of
the Sylvian fissure), we can compare voxel values across subjects. This is achieved by spatial normalization. Each brain,
however, is unique; sulcal or gyral patterns, for example, vary
greatly across subjects (some sulci are even missing in some

brains). Thus, the success of spatial normalization is limited
and depends on the accuracy of the applied registration
method. In addition, parametric tests assume a Gaussian
distribution of the residuals, which is not necessarily true for
normalized tissue segments. Fortunately, these limitations can
be addressed by applying a Gaussian blurring to the normalized tissue segment. This is achieved by convolving with a
Gaussian function, which is commonly referred to as spatial
smoothing. The smoothed normalized tissue segments are
then entered into a statistical model to map changes within
brains over time and/or differences between brains. The
subsequent sections will further discuss these steps in detail;
an overview of the basic workflow is illustrated in Figure 1.
Tissue classification is based on intensity values and basically
serves to segment the brain into gray matter, white matter,
and cerebrospinal fluid after removing any nonbrain parts
(Ashburner & Friston, 1997, 2005; Rajapakse, Giedd, & Rapoport, 1997). However, intensity values in structural brain
scans are not exclusively attributable to different tissue
types, as an intensity-based tissue classification would
assume. Rather, inhomogeneities of the magnetic field will
lead to inhomogeneities in image intensity as well. This effect
is even more pronounced with high-field scanners, since it is
more difficult to keep the magnetic field homogeneous for
higher field strengths. As shown in Figure 1 (T1-weighted
image), the intensity inhomogeneity looks like a field of
smoothly varying brightness, which results in different intensities for the same tissue at different locations. Thus, image
intensity inhomogeneities need to be corrected before applying the actual tissue classification. This correction process is
usually referred to as bias correction. The bias-corrected
T1-weighted image can then be classified into any set of tissue
types (usually three different tissue types for the brain plus
one or more background types).
As shown in Figure 2 (left panel), the distributions of
intensities for each tissue class overlap, even after a bias
correction is applied. One reason for this overlap is that at a
common voxel size of 1 1 1 mm3, any given voxel can
contain more than one tissue. This is generally the case at the
border between the brain parenchyma and cerebrospinal fluid,
at boundaries between gray matter and white matter, and in
structures where white matter fibers cross the gray matter.
Thus, even in a bias field-corrected image, signal intensities
for different tissues will vary and result in a considerable
overlap and so-called partial volumes. Partial volumes can be
modeled explicitly in order to more accurately classify the
tissues and calculate local volumes (Tohka, Zijdenbos, &
http://dx.doi.org/10.1016/B978-0-12-397025-1.00304-3
345
346
INTRODUCTION TO METHODS AND MODELING | Voxel-Based Morphometry
Original image
(T1-weighted)
Inhomogeneity
correction
Tissue
classification
Gray matter segment

in native space
Linear
normalization
Nonlinear
normalization
Gray matter segment

in template space
Spatial
smoothing
Smoothed gray matter segment

in template space
Voxel-wise statistical testing

Figure 1 Workflow of a voxel-based morphometry (VBM) analysis. The analysis is based on high-resolution structural brain images. First, the T1weighted images are corrected for inhomogeneities and classified into different tissue types, such as gray matter, white matter, and cerebrospinal
fluid. The gray matter segment (i.e., the tissue of interest) is then spatially normalized to match a common template. Subsequently, the normalized gray
matter segment is smoothed with an isotropic Gaussian kernel. Finally, the smoothed normalized gray matter segments are entered into a statistical
model to conduct voxel-wise statistical tests and map significant effects.
Evans, 2004). To guide tissue classification, additional tissue

probability maps can be used to apply prior knowledge of
where in the brain different tissues can be expected
(Ashburner & Friston, 2005). This means that for each tissue,
a map of how probable it is to be represented by a certain voxel
in the image is used to drive and restrict the tissue classification
algorithm. While this may be valuable as long as the tissue
probability maps match the subjects tissue distribution, it can
lead to misclassifications in all populations that deviate from
these maps (e.g., child data) (Wilke, Holland, Altaye, & Gaser,
2008). Figure 2 (right panel) depicts the results of tissue
classification. Since an algorithm that accounts for partial volumes was used, the given segments encode a local volume
estimate of tissue content for every voxel.
Spatial Normalization
In addition to tissue classification, the individual brains or
the native gray matter segments (Figure 3(a)) must be spatially normalized in order to ensure a voxel-wise comparability. Spatial normalization can be divided in linear and
GM
WM
347
CSF
WM
Background
GM
CSF
Figure 2 Tissue classification. Left panel: Whole-brain images can be segmented into background and different tissue classes, such as gray matter
(GM), white matter (WM), and cerebrospinal fluid (CSF) based on their intensity. Note that these tissue-specific intensity distributions overlap, which can
be due to partial volume effects. Right panel: The GM, WM, and CSF segments (top) were obtained using a partial volume estimation, which allows
for more than one tissue per voxel. The partial volume estimation label (bottom) depicts the voxel values as transitions between tissue contents. GM is
shown in yellow, WM in red, and CSF in blue. Voxels containing both GM and WM are shown in varying shades of orange, depending on the mixture
of both tissues at this location. Voxels containing both GM and CSF are shown in varying shades of green, depending on the mixture of both tissues
at this location. As both voxel size and tissue content per voxel are known, proper estimations of local tissue volumes can be made.
Native
gray matter
Normalized
gray matter
Deformation
field
Modulated
gray matter
Subject 1
Subject 2
Figure 3 Spatial normalization. For visualization, two very different examples are depicted. Subject 1 is a 23-year-old male, while subject 2 is a 64year-old female. (a) While local gray matter volumes can be measured in native space in both brains, a voxel-wise comparison is not easily possible.
(b) After spatial normalization, both brains have the same size, shape, and overall pattern of major sulci and gyri. The local amount of gray matter can be
directly compared in voxel-wise statistical tests. (c) The Jacobian determinants derived from the deformation fields that were applied for spatial
normalization indicate different patterns of volume change for both subjects. The deformation forces needed to transform each subjects brain image
to the template and highlight regions that were expanded (blue/cyan) or compressed (red/yellow) to match the respective areas in the template.
Analyzing these deformation fields or the Jacobian determinants constitutes what is known as tensor-based or deformation-based morphometry.
(d) Multiplying these deformation fields (or more precisely, the Jacobian determinants) with the original normalized gray matter segments corrects for
the volume changes that occurred during the spatial normalization and is known as modulation. Voxel-wise statistical testing applied to these
segments will analyze the local gray matter volume as estimated in native space. Note that although both brains are very similar, the second subjects
smaller and probably slightly atrophic brain shows less local volume (evident as darker shades of orange).
nonlinear components. Linear normalization alters every part

of the image in exactly the same way and includes translation,
rotation, scaling, and shearing for each dimension (Ashburner
& Friston, 1997). Translation and rotation (each in the x-axis,
y-axis, and z-axis, yielding a total of six parameters) change the
position in space but do not alter shape or size of the brain.

This six-parameter transformation (also known as rigid body
transformation) is frequently used to realign images of the
same brain to each other and can be used, for example, to
detect changes over time in the same subject. The addition of
348
scaling and shearing (each again in the x-axis, y-axis, and z-axis,
yielding a total of 12 parameters) will alter the size and global
shape of the brain. A 12-parameter transformation (also
known as affine transformation) is frequently used to register
brains to a template space.
While linear transformations can correct for interindividual
differences in brain size, they cannot model local differences in
size and shape as the same transformation is applied to every
voxel. In contrast, nonlinear transformations allow the application of different changes in position, size, and shape locally
and thus correct for interindividual differences on a local scale
(Ashburner, 2007; Ashburner & Friston, 1999, 2005). Still, a
perfect match between any two brains is very unlikely because
brains are highly individual in their local anatomy (e.g., some
sulci and gyri cannot be found in all brains). Nevertheless, in
spite of minor remaining interindividual differences within the
normalized gray matter segments (Figure 3(b)), modern normalization techniques result in brains with a reasonable local
comparability (Ashburner, 2007).
All spatial transformations result in a deformation field
(Figure 3(c)) that describes how local structures were adjusted
to match two brains to each other (i.e., indicating if a part of
the brain had to be enlarged or compressed). The exact voxelwise volume changes can be easily derived from these
deformation fields as Jacobian determinants. Analyzing these
Jacobian determinants or the deformation fields themselves
constitutes what is known as tensor-based morphometry or
deformation-based morphometry. The Jacobian determinant
may also be used to correct resulting gray matter segments for
volume changes that occurred due to the spatial normalization. More specifically, suppose a structure of the brain with a
certain amount of gray matter becomes bigger during normalization. Consequently, this structure will seem to have larger
local gray matter values than are truly present. If the difference
between true gray matter and apparent gray matter can be
quantified which is exactly what the Jacobian determinants
do the measured gray matter can simply be corrected
(i.e., basically undoing the unwanted effects of the normalization). This way, the amount of original gray matter is preserved in the new space and reflected as so-called modulated
gray matter (Figure 3(d)).
Spatial Smoothing
The reason to smooth the images before statistical analysis is
threefold: First of all, parametric tests assume that the residuals
follow a Gaussian distribution. Simple smoothing of the images
satisfies this assumption by the central limit theorem (after
smoothing, the data are more normally distributed) and thus
makes a parametric test a valid choice (Ashburner & Friston,
2000; Nichols & Hayasaka, 2003). Second, as outlined earlier,
the spatial normalization is not perfect and small interindividual
differences remain. Smoothing accounts for these residual small
interindividual differences in local anatomy (Ashburner & Friston, 2000). Finally, according to the matched filter theorem,
smoothing renders the analysis sensitive to effects that approximately match the size of the smoothing kernel (Ashburner &
Friston, 2000). As smoothing kernels usually have a full width at
half maximum of 416 mm, this means that very small differences, which are possibly due to noise, are not picked up by the
analysis. Consequently, after smoothing, each voxel represents a
sphere similar to the smoothing kernel or, in other words, a
weighted mean of its own and its neighbors values.
Statistical Analysis
The smoothed normalized tissue segments can be analyzed in
statistical models using parametric tests, although nonparametric tests are also common. Usually, these tests will be
applied in a mass-univariate approach, which means that the
same test is applied for each voxel simultaneously. As in most
other neuroimaging analyses, this entails a severe multiple
comparison problem and an appropriate correction has to be
applied. In neuroimaging, two major levels of correction are
frequently used that are both based on Gaussian random field
theory (Worsley et al., 1996): a correction on a voxel level and
a correction on a cluster level (though a set-level correction is
also possible) (Friston, Holmes, Poline, Price, & Frith, 1996).
Assume the results are to be corrected controlling the familywise error (FWE) at p 0.05. At the voxel level, an FWE correction will assure that only in 1 out of 20 images a finding will
have reached significance by chance. This is a perfectly legitimate way of correcting the results. To apply an FWE correction
at cluster level, an arbitrary cluster-forming threshold must be
applied, say at p 0.001 uncorrected (Friston et al., 1996).
Given the smoothness of the data, smaller clusters are likely
to occur by chance thus constituting false positives. Larger
clusters, however, are less likely to occur and cluster-forming
thresholds will produce clusters that constitute real effects.
Controlling the FWE at the cluster level therefore means that
only in 1 out of 20 images a cluster of this extent will occur by
chance. This correction will consequently result in a spatial
extent threshold expressed as the minimum number of voxels
comprising the significance cluster.
Unfortunately, statistical parametric maps from structural
analyses vary considerably in local smoothness, meaning that
the appropriate extent threshold varies locally as well. In other
words, within the same image, there might be very smooth
regions where large clusters may occur by chance and relatively
rough regions where true effects may manifest as very small
clusters. Applying one single extent threshold for the whole
image is therefore inappropriate (Ashburner & Friston, 2000;
Hayasaka, Phan, Liberzon, Worsley, & Nichols, 2004). A possible solution is to correct each voxel individually based on the
local smoothness by rendering smoothness isotropic, which
results in locally varying extent thresholds. Another possibility
is to use a correction based on threshold-free cluster enhancement (TFCE) (Smith & Nichols, 2009). This method estimates a
voxel value that represents the accumulative cluster-like local
spatial support at a range of cluster-forming thresholds. TFCE
has a variety of advantages that make it an elegant solution to
correct for multiple comparisons in structural analyses. First of
all, it does not need an arbitrary cluster-forming threshold, making it more objective. Second, it combines statistics based on the
local significance as well as the spatial extent of this effect.
However, because the distribution of the TFCE values is not
known, permutation tests must be used to assess thresholds.

Diffeomorphic Image Registration; Nonlinear Registration Via
Displacement Fields; Rigid-Body Registration; Tensor-Based
Morphometry; Tissue Classification.
References
38, 95113.
Ashburner, J., & Friston, K. (1997). Multimodal image coregistration and
partitioningA unified framework. NeuroImage, 6, 209217.
Ashburner, J., & Friston, K. J. (1999). Nonlinear spatial normalization using basis
functions. Human Brain Mapping, 7, 254266.
Ashburner, J., & Friston, K. J. (2000). Voxel-based morphometryThe methods.
Ashburner, J., & Friston, K. J. (2001). Why voxel-based morphometry should be used.
839851.
349
Ashburner, J., & Friston, K. (2007). Voxel-based morphometry. In K. Friston, J.

Ashburner, S. Kiebel, T. E. Nichols & W. D. Penny (Eds.), Statistical parametric
mapping: The analysis of functional brain images. London: Elsevier.
Friston, K. J., Holmes, A., Poline, J. B., Price, C. J., & Frith, C. D. (1996). Detecting
activations in PET and fMRI: Levels of inference and power. NeuroImage, 4,
223235.
Hayasaka, S., Phan, K. L., Liberzon, I., Worsley, K. J., & Nichols, T. E. (2004).
Nonstationary cluster-size inference with random field and permutation methods.
Nichols, T., & Hayasaka, S. (2003). Controlling the familywise error rate in functional
neuroimaging: A comparative review. Statistical Methods in Medical Research, 12,
419446.
Rajapakse, J. C., Giedd, J. N., & Rapoport, J. L. (1997). Statistical approach to
segmentation of single-channel cerebral MR images. IEEE Transactions on Medical
Imaging, 16, 176186.
Smith, S. M., & Nichols, T. E. (2009). Threshold-free cluster enhancement: Addressing
problems of smoothing, threshold dependence and localisation in cluster inference.
Tohka, J., Zijdenbos, A., & Evans, A. (2004). Fast and robust parameter estimation for
statistical partial volume models in brain MRI. NeuroImage, 23, 8497.
Wilke, M., Holland, S. K., Altaye, M., & Gaser, C. (2008). Template-O-Matic: A toolbox
for creating customized pediatric templates. NeuroImage, 41, 903913.
Worsley, K. J., Marrett, S., Neelin, P., Vandal, A. C., Friston, K. J., & Evans, A. C.
(1996). A unified statistical approach for determining significant signals in images
of cerebral activation. Human Brain Mapping, 4, 5873.

JP Lerch, The Hospital for Sick Children, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
Glossary
Coordinate system A way to ensure that homologous

points are compared across subjects.
Cortical layer The horizontal unit of organization of the
cerebral cortex, composed of similar cells sharing input and
output characteristics.
Laminar organization The pattern of how the cortical layers
are organized in the cortex.
Introduction
The advent of high-resolution magnetic resonance imaging
(MRI) combined with advanced image processing algorithms
has given new life to the older neuroanatomical tradition of
mapping the thickness of the cortex. With the now common
availability of acquisitions and algorithms, a multitude of
papers have begun to explore cortical thickness mapping
across development, in health and disease, and in multiple
species.
The Anatomy of the Cerebral Cortex

All mammals have a cortex, and reptiles only have a threelayered neocortical primordium (Nieuwenhuys et al., 2008).
The mammalian cortex is composed of six layers: from outside
to inside, these are (1) the cell-sparse molecular layer; (2) the
external granular cell layer, consisting of small, densely packed
cells; (3) the external pyramidal cell layer containing large
pyramidal neurons; (4) the internal granular cell layer; (5)
the internal pyramidal cell layer; and (6) the multiform layer.
Not all areas of the mature cortex have six easily identified
layers, yet they will all have passed through a six-layered stage
at some point during development (Brodmann, 1908;
Economo, 1925; Nieuwenhuys et al., 2008).
Along with the obvious laminar organization, there is a
radial patterning of the cortex. Pyramidal neurons, the most
common cells in the cortex, send their apical dendritic shaft
toward the molecular layer (Figure 1). Their axons also emerge
from the cell body and descend toward the white matter. In
addition to this radial arrangement of the processes of individual neurons, parts of the cortex have columnar arrangement
wherein all cells contained within a cylinder spanning the
depth of the cortex will be part of a computational unit. In
the somatosensory cortex of the cat, for example, all neurons
along one radially penetrating microelectrode will respond to
the same cutaneous receptors at a particular site (Mountcastle,
1998). Parallel penetrations, however, found cortical regions
approximately 300 mm in size responding to the same receptors with sharp transitions between these blocks (Mountcastle,
Myelination The ensheathment of axons with myelin;

provides faster electrical communication and changes MRI
contrast.
Pyramidal neuron The main neuron type providing the key
outputs of the cortex.
Vertex The surface equivalent of a voxel; a point in the
surface based coordinate system.
1998). Multiple cortical regions follow a similar columnar

organization, most famously the orientation and ocular dominance columns of the visual cortex, though the question of
whether the entire cortex has columnar patterning remains
controversial (Nieuwenhuys et al., 2008).
The structure of the cortex is not homogenous across the
cortical sheet. Transitions in cortical architecture (layering, cell
types, myelination, etc.) define functionally separate regions,
as codified by Brodmann (1908) and Economo (1925), among
others (Zilles & Amunts, 2010). Functional imaging studies,
assessments of connectivity, and dense electrophysiological
recordings have further refined our understanding of the functional architecture of the cortex (Nieuwenhuys et al., 2008).
The human cortex is also massively and idiosyncratically
folded, with limited correspondence between folding patterns
and functional architecture (Amunts et al., 1999; Zilles &
Amunts, 2010).
Moving to the macro- or mesoscopic resolution enabled by
modern brain imaging, one can study the anatomy of the
cerebral cortex along with the three key dimensions: (1) surface
area, (2) thickness, and (3) folding pattern. The detailed architectonic patterning of the cortex is not yet accessible to imaging, though advances in field strength, acquisition strategies,
and image processing hold promise for changing that for at
least a subset of cortical regions (Bock et al., 2013; Geyer et al.,
2011; Leuze et al., 2012). The folding pattern of the cortex is
the most stochastic (Mangin, Jouvent, & Cachia, 2010). Key for
cortical thickness mapping is dividing the cortical sheet into its
thickness and area. One can superficially identify thickness
with a measure of the length of the cortical column and surface
area with the number of cortical columns. The genetic determination of surface area versus cortical thickness is different
(Winkler et al., 2010), and across evolution, one finds that
surface area differs by orders of magnitude across mammals,
whereas cortical thickness only changes 23-fold between
small rodents and simians (Mountcastle, 1998). Importantly,
surface area and cortical thickness correspond to incongruent
developmental pathways, and determining which of these two
components of cortical anatomy is affected in disease thus
provides insight into when an insult took place (Clowry,
Molnar, & Rakic, 2010).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00305-5
351
352
INTRODUCTION TO METHODS AND MODELING | Cortical Thickness Mapping
Molecular layer
(a)
corpus callosum
(b)
(c)
Figure 1 The organization of the cortex. (a, b) The laminal structure of the cortex using immunohistochemical staining of neuronal nuclei (NeuN).
The cell-sparse molecular layer is immediately obvious, and changes in neuronal density and size are visible to the trained eye as one descends toward
the corpus callosum. (c) The radial patterning of the cortex. This slice was obtained by imaging a Thy1YFP fluorescent mouse, featuring Golgi-like
fluorescence in a sparse population of neurons, with a two-photon microscope. The path taken by the apical dendrites toward the molecular layer is
immediately discernible.

Among the first in-depth studies of the thickness of the cortex
were Konstantin von Economos and Georg Koskinas in the
1920s. They found that cortical thickness varies between 1.5
and 4.5 mm and differs in respect to both location in the cortex
and position along the folding of the cortex, with the cortex
being thickest in the gyral crowns and thinnest in sulcal fundi
(Economo, 1925). The authors alluded to the methodological
pitfalls of their approach; sections have to be cut perpendicular
to the folding pattern of the cortex, making it impossible to
measure the thickness across the entire cortex from a single
brain. Comparing across subjects, moreover, has to be carefully
controlled so as to compare gyri to gyri and sulci to sulci.
Lastly, even trained experts will differ by up to 0.5 mm or
more regarding where they draw the boundary between the
white matter and the gray matter on the same slice (Economo,
1925). The advent of high-resolution MRI images has since
revolutionized the study of neuroanatomy, yet many of the
same methodological uncertainties remain and are compounded by the different contrast mechanisms produced by
MRI. The ease by which in vivo images of the brain could be
taken is also accompanied by the challenge of how to
efficiently map the thickness of the cortex across a large number of subjects (Figure 2).
The Methods
Algorithms to compute cortical thickness from MRIs follow
one of four strategies. The simplest, and therefore longest
extant, is manual measurements. Here, brain images are
assessed in a viewer and a digital caliper is employed to measure the distance between the white/gray matter boundary and
the pial surface boundary. These types of manual measures are
a direct analogue of cortical thickness measures performed on a
histology slice. The principal drawbacks are their laborious
nature, making them only suitable for a few restricted regions
of interest, and the difficulty associated with accurately estimating the thickness of the complex folded cortex on a 2-D
slice.
The second strategy for estimating cortical thickness determines the boundaries of the cortex through some combination
of tissue classification and automatic parcellation followed
by a boundary value problem approach to estimate the distance between the white matter and the cortical cerebro-spinal
353
Nonuniformity field
Native MRI
Final MRI
Classified MRI
Skull and dura mask
Masked classified MRI Structure segmentation
Registration target
White matter surface
Grey matter surface

Intersects of surfaces
Figure 2 Methods for extracting cortical thickness. An illustrative processing flow for extracting cortical thickness metrics, including registration,
nonuniformity correction, tissue classification, and surface fitting.
fluid (CSF). The use of Laplaces equation by Jones, Buchbinder, and Aharon (2000) popularized this approach to mapping
cortical thickness, and it has since been adapted to other species (Leigland et al., 2013; Lerch et al., 2008) by adding additional boundary constraints. The pathlines or streamlines
created between the inside and outside cortical surfaces
through these boundary value equations appear to mimic the
direction taken by cortical columns. This is especially the case
in more recent algorithms explicitly designed to approximate
the cortical column (Waehnert et al., 2013). One downside to
these voxel-based cortical thickness methods is that they lack a
coordinate system for the analysis of thickness across populations. The idiosyncratically folded nature of the cortex makes it
difficult to precisely align 3-D volumes of different subjects;
most voxel-based thickness methods thus rely on the parcellation of the cortex into ROIs and the computation of mean
cortical thickness in those ROIs.
The third, and most common, method of mapping cortical
thickness creates two polyhedral surfaces along the inside and
outside cortical boundaries and then defines cortical thickness
as the distance between these two surfaces. Both FreeSurfer
(Dale, Fischl, & Sereno, 1999; Fischl & Dale, 2000) and
CIVET (Kim et al., 2005; Lerch & Evans, 2005; Lyttelton et al.,
2007) use surface-based cortical thickness techniques. Briefly,
the preprocessing steps include linear alignment to Montreal
Neurological Institute (MNI) space, correction for nonuniformity, and tissue classification. The inside (gray/white)
boundary is then fit, and once complete, that surface is used as
a starting point to expand to the outside (gray/pial) boundary.
Cortical thickness is then defined as the distance between the
inside and outside surfaces. Using surface-based methods to
map cortical thickness has the great advantage of providing a
surface-based coordinate system, allowing for easy vertex-wise
(i.e., point by point) comparison of cortical thickness across
populations. Further postprocessing, including nonlinear

surface-based alignment, parcellation of the cortex, and
smoothing of the thickness maps along the surface, cements
the power of surface-based methods. The main downside is the
computational complexity.
The fourth commonly employed strategy for mapping cortical thickness is a hybrid of the voxel- and surface-based
methods. Cortical thickness is estimated using voxel-based
methods and a single surface is fit in order to provide a coordinate system and allow for surface-based smoothing (Gogtay
et al., 2004).
A Brief Survey of Applications

The combination of high-resolution in vivo MRI and automated methods to map the thickness of the cortex has produced a plethora of papers applying these techniques to studies
of normal development, aging, and disease. A few key studies
are touched upon in the succeeding text.
Development and Aging

The vast majority of cortical thickness studies of the developing
brain have started at age four or later, primarily due to the
changing contrast during early development when the brain is
mostly unmyelinated as well as the difficulty in keeping very
young children from moving while in the scanner. These studies have revealed a dynamic pattern of early cortical thickening
followed by a much longer and more extensive period of
cortical thinning (Shaw et al., 2008). The primary cause attributed to the thinning is synaptic pruning, though this remains
controversial and unproven and other mechanisms, such as
354
changes in myelination in the lower cortical layers, have also

been proposed (Paus, 2005, 2013). The patterns of thickening
and thinning are not uniform across the cortex. The primary
sensory and motor areas reach peak cortical thickness earliest
and association cortices, especially in the frontal lobes, last
(Shaw et al., 2008). There are subtle differences in cortical
development patterns between boys and girls (Lenroot et al.,
2007), between children of different IQs (Karama et al., 2013;
Shaw et al., 2006), and depending on environmental factors
such as musical training (Hyde et al., 2009). A significant
proportion of cortical thickness during development is
accounted for by genetics, though again this is a dynamic
process with the genetic versus environmental contributions
to variance in thickness changing with age (Lenroot et al.,
2009). Cortical thickness enters a period of very slow but
steady decreases throughout the remainder of ones life span.
The pattern is again regionally variant and is accompanied by
widening of the sulcal CSF space and subtle atrophy throughout the rest of the brain (Salat, 2004).
Disease
Among the earliest papers to map differences in cortical thickness in a population of subjects were those that dealt with
neurodegenerative diseases, in particular Huntingtons (Rosas
et al., 2002) and Alzheimers disease (Lerch et al., 2005), in each
case finding focal cortical atrophy that spread with disease progression or severity. Since then, most, if not all, mental health
conditions have been examined by studying populations of
affected subjects compared to matched controls. In addition to
detecting atrophy, some conditions, such as congenital amusia,
show focal cortical thickening (Hyde et al., 2007), and others
show altered developmental patterns (Shaw et al., 2007).
Networks
The brain is organized into networks, and the cortical thickness
mapping reflects network properties. For example, as Brocas
area increases or decreases in thickness, Wernickes area changes
in a correlated fashion (Lerch et al., 2006). These correlations in
the language network tighten with age (Lerch et al., 2006) and
can be detected within individual subjects (Raznahan et al.,
2011). The analysis of cortical thickness networks has furthermore been very fruitfully extended into graph theoretical frameworks, showing alterations in the covariance of the anatomy of
the cortex across development, aging, and disease (AlexanderBloch, Giedd, & Bullmore, 2013; Evans, 2013).
Validation and Conclusions

Cortical thickness mapping has been validated through three
strategies: (1) by comparison to postmortem samples, (2) by
comparing manual to automated measures on MR images, and
(3) through simulation approaches. Comparing MR measures

to histology found that measurements were within 0.25 mm of
each other and statistically indistinguishable (Rosas et al.,
2002). Comparisons of manual to automated MR measures
found similar levels of reliability (Kabani et al., 2001). Simulating altered cortices showed that different geometric definitions of cortical thickness had different sensitivities for
detecting the altered cortex and provided insights into the
effects of smoothing along the cortex (Lerch & Evans, 2005).
There has also been substantial ongoing work in determining
the effects of MR sequences or field strength on measures of
cortical thickness (Dickerson et al., 2008).
Ultimately, cortical thickness mapping has proved to be a
powerful technique for assessing changes in the cerebral cortex with development, aging, or disease, yet there is still room
for improvement in assuring that what we map from MR
images corresponds to the classic cortical thickness measurements from Nissl-stained sections. Going forward, advances
in field strength and image processing techniques tantalizingly suggest that we will be able to estimate profiles and
thicknesses of at least some cortical layers (Waehnert et al.,
2013), which could revolutionize how we map the anatomy
of the cortex. Studying alterations in cortical thickness using
MR imaging in animal models can, moreover, bring mechanistic insights into the cellular bases of how the cortex
changes (GrandMaison et al., 2013; Hebert et al., 2013;
Lerch et al., 2011).

Anatomical MRI for Human Brain Morphometry; INTRODUCTION TO
ANATOMY AND PHYSIOLOGY: Brain Sex Differences; Cell Types in
the Cerebral Cortex: An Overview from the Rat Vibrissal Cortex;
Columns of the Mammalian Cortex; Cortical Surface Morphometry;
Language; Cytoarchitecture and Maps of the Human Cerebral Cortex;
Embryonic and Fetal Development of the Human Cerebral Cortex;
Evolution of the Cerebral Cortex; Fetal and Postnatal Development of
the Cortex: MRI and Genetics; Gyrification in the Human Brain;
Quantitative Data and Scaling Rules of the Cerebral Cortex; Sulci as
Landmarks; Synaptic Organization of the Cerebral Cortex;
INTRODUCTION TO CLINICAL BRAIN MAPPING: Basic Concepts
of Image Classification Algorithms Applied to Study Neurodegenerative
Diseases; Developmental Brain Atlases; Differential Patterns of
Dysfunction in Neurodegenerative Dementias; Imaging Genetics of
Neuropsychiatric Disease; Imaging Genetics; INTRODUCTION TO
Cerebral Cortex; Bayesian Multiple Atlas Deformable Templates;
Computing Brain Change over Time; Intensity Nonuniformity
Correction; Manual Morphometry; Modeling Brain Growth and
Development; Nonlinear Registration Via Displacement Fields; SurfaceBased Morphometry; Tissue Classification; Voxel-Based Morphometry;
INTRODUCTION TO SYSTEMS: Hubs and Pathways; Large-Scale
Functional Brain Organization.
References
Alexander-Bloch, A., Giedd, J. N., & Bullmore, E. (2013). Imaging structural co-variance
between human brain regions. Nature Reviews. Neuroscience, 14, 322336.
Amunts, K., et al. (1999). Brocas region revisited: Cytoarchitecture and intersubject
variability. The Journal of Comparative Neurology, 412(2), 319341.
Bock, N. A., et al. (2013). Optimizing T1-weighted imaging of cortical myelin content at
3.0 T. NeuroImage, 65, 112.
Brodmann, K. (1908). Beitrage zur histologischen Lokalisation der Grosshirnrinde.
Clowry, G., Molnar, Z., & Rakic, P. (2010). Renewed focus on the developing human
neocortex. Journal of Anatomy, 217(4), 276288.
Dale, A. M., Fischl, B., & Sereno, M. I. (1999). Cortical surface-based analysis. I.
Segmentation and surface reconstruction. NeuroImage, 9(2), 179194.
Dickerson, B. C., et al. (2008). Detection of cortical thickness correlates of cognitive
performance: Reliability across MRI scan sessions, scanners, and field strengths.
Evans, A. C. (2013). Networks of anatomical covariance. NeuroImage, 80, 489504.
Fischl, B., & Dale, A. M. (2000). Measuring the thickness of the human cerebral cortex
from magnetic resonance images. Proceedings of the National Academy of Sciences
of the United States of America, 97(20), 1105011055.
parcellation of the human cerebral cortex From Brodmanns post-mortem Map to
Gogtay, N., et al. (2004). Dynamic mapping of human cortical development during
childhood through early adulthood. Proceedings of the National Academy of
Sciences of the United States of America, 101(21), 81748179.
GrandMaison, M., et al. (2013). Early cortical thickness changes predict b-amyloid
deposition in a mouse model of Alzheimers disease. Neurobiology of Disease, 54,
5967.
Hebert, F., GrandMaison, M., Ho, M., Lerch, J. P., Hamel, E., & Bedell, B. J. (2013).
Cortical atrophy and hypoperfusion in a transgenic mouse model of Alzheimers
disease. Neurobiology of Aging, 34(6), 16441652.
Hyde, K. L., et al. (2007). Cortical thickness in congenital amusia: When less is better
than more. Journal of Neuroscience, 27(47), 1302813032.
Hyde, K. L., Lerch, J., Norton, A. C., Forgeard, M., Winner, E., Evans, A. C., et al.
(2009). Musical training shapes structural brain development. Journal of
Neuroscience, 29(10), 30193025.
Jones, S. E., Buchbinder, B. R., & Aharon, I. (2000). Three-dimensional mapping of
cortical thickness using Laplaces equation. Human Brain Mapping, 11(1), 1232.
Kabani, N., Legoualher, G., Macdonald, D., & Evans, A. C. (2001). Measurement of
cortical thickness using an automated 3-D algorithm: A validation study.
NeuroImage, 13(2), 375380.
Karama, S., et al. (2013). Childhood cognitive ability accounts for associations between
cognitive ability and brain cortical thickness in old age. Molecular Psychiatry, 19(5),
555559.
Kim, J. S., et al. (2005). Automated 3-D extraction and evaluation of the inner and outer
cortical surfaces using a Laplacian map and partial volume effect classification.
NeuroImage, 27(1), 210221.
Leigland, L. A., Ford, M. M., Lerch, J. P., & Kroenke, C. D. (2013). The influence of fetal
ethanol exposure on subsequent development of the cerebral cortex as revealed by
magnetic resonance imaging. Alcoholism: Clinical and Experimental Research,
37(6), 924932.
355
Lenroot, R. K., et al. (2007). Sexual dimorphism of brain developmental trajectories

during childhood and adolescence. NeuroImage, 36(4), 10651073.
Lenroot, R. K., et al. (2009). Differences in genetic and environmental influences on the
human cerebral cortex associated with development during childhood and
adolescence. Human Brain Mapping, 30(1), 163174.
Lerch, J. P., & Evans, A. C. (2005). Cortical thickness analysis examined through power
analysis and a population simulation. NeuroImage, 24(1), 163173.
Lerch, J. P., et al. (2005). Focal decline of cortical thickness in Alzheimers disease
identified by computational neuroanatomy. Cerebral Cortex (New York, NY: 1991),
15(7), 9951001.
Lerch, J. P., et al. (2006). Mapping anatomical correlations across cerebral cortex
(MACACC) using cortical thickness from MRI. NeuroImage, 31(3), 9931003.
Lerch, J. P., et al. (2008). Cortical thickness measured from MRI in the YAC128 mouse
model of Huntingtons disease. NeuroImage, 41(2), 243251.
Lerch, J. P., et al. (2011). Maze training in mice induces MRI-detectable brain shape
changes specific to the type of learning. NeuroImage, 54(3), 20862095.
Leuze, C. W.U, et al. (2012). Layer-specific intracortical connectivity revealed with
diffusion MRI. Cerebral Cortex, 24(2), 328339.
Lyttelton, O., et al. (2007). An unbiased iterative group registration template for cortical
surface analysis. NeuroImage, 34(4), 15351544.
Mangin, J., Jouvent, E., & Cachia, A. (2010). In-vivo measurement of cortical
morphology: Means and meanings. Current Opinion in Neurology, 23(4), 359367.
http://dx.doi.org/10.1097/WCO.0b013e32833a0afc.
Mountcastle, V. B. (1998). Perceptual neuroscience. Cambridge, MA: Harvard
University Press.
Nieuwenhuys, R., Voogd, J., Voogd, J., & van Huijzen, C. (2008). The human central
nervous system. New York: Springer.
Paus, T. (2005). Mapping brain maturation and cognitive development during
adolescence. Trends in Cognitive Sciences, 9(2), 6068.
Paus, T. (2013). How environment and genes shape the adolescent brain. Hormones
and Behavior, 64(2), 195202.
Raznahan, A., et al. (2011). Patterns of coordinated anatomical change in human cortical
development: A longitudinal neuroimaging study of maturational coupling.
Neuron, 72, 113.
Rosas, H. D., et al. (2002). Regional and progressive thinning of the cortical ribbon in
Huntingtons disease. Neurology, 58(5), 695701.
Salat, D. H. (2004). Thinning of the cerebral cortex in aging. Cerebral Cortex, 14(7),
721730.
Shaw, P., et al. (2006). Intellectual ability and cortical development in children and
adolescents. Nature, 440(7084), 676679.
Shaw, P., et al. (2007). Attention-deficit/hyperactivity disorder is characterized by a
delay in cortical maturation. Proceedings of the National Academy of Sciences,
104(49), 1964919654.
Shaw, P., et al. (2008). Neurodevelopmental trajectories of the human cerebral cortex.
Journal of Neuroscience, 28(14), 35863594.
von Economo, C. (1925). Die Cytoarchitektonik der Hirnrinde des erwachsenen
Menschen. Berlin: Verlag von Julius Springer.
Waehnert, M. D., et al. (2013). Anatomically motivated modeling of cortical laminae.
NeuroImage, Pt 2, 210220.
Winkler, A. M., et al. (2010). Cortical thickness or grey matter volume? The importance of
selecting the phenotype for imaging genetics studies. NeuroImage, 53(3), 11351146.
Zilles, K., & Amunts, K. (2010). Centenary of Brodmanns mapconception and fate.
Nature Review Neuroscience, 11(2), 139145.
Automatic Labeling of the Human Cerebral Cortex

BT Thomas Yeo, National University of Singapore, Singapore, Singapore; Duke-NUS Graduate Medical School, Singapore,
Singapore; Massachusetts General Hospital, Charlestown, MA, USA
Glossary
fsaverage Subject FreeSurfer subject (Figure 1b and 1c)

obtained by averaging 40 subjects. This average subject
forms the basis of the FreeSurfer surface coordinate system
(Fischl, 2012).
Graphical Models The different algorithms in this article
can be summarized using graphical models. Graphical
models provide a general framework for representing
complex probabilistic models with explicit (conditional)
independence assumptions. See Figure 2 and Summary
section for more details.
Markov Random Field Markov Random Fields (MRFs)
provides a principal approach to impose a prior on the
spatial configuration of labels. One common prior is to
favor adjacent spatial locations to have the same labels. See
Spatially Dependent Priors: Markov Random Fields
section for more details.
Mixture Models Registration-based labeling assumes the

availability of pre-existing labels. By contrast, mixture
modeling only requires that each label generate its own
unique image features. Given observed image features, there
are algorithms (e.g., Expectation-Maximization) that
simultaneously estimate the labels and the probabilistic
distribution of image features for each label. See Mixture
Models section for more details.
MNI152 Template The International Consortium on Brain
Mapping (ICBM) average brain obtained by aligning and
averaging 152 subjects (Fonov et al., 2011).
Registration-based Labeling Registration is the process of
establishing spatial correspondences between images. The
resulting deformation can be used to transfer pre-existing
labels from an (single-subject or probabilistic) atlas to the
target brain. See Registration-based Labeling section for
more details.
Organization of the Cerebral Cortex
Registration-Based Labeling
The human cerebral cortex is a highly folded 2D sheet of neural

tissue that possesses a mosaic of functionally distinct areas
oriented parallel to its surface (Figure 1). Information processing proceeds via the transformation of neural signals across
these areas (Felleman & Van Essen, 1991; Ungerleider &
Desimone, 1986). Accurate labeling of areal locations is therefore an important problem in systems neuroscience. There are
four main criteria for distinguishing cortical areas (Felleman &
Van Essen, 1991; Kaas, 1987): function, architectonics,
connectivity, and topography. Each of these criteria can be
interrogated in the human cerebral cortex using a broad
range of techniques (Figure 1).
Because (1) cortical folds are visible to the naked eye and in
anatomical Magnetic Resonance Imaging (MRI) and (2) some
cortical folds are indicative of certain underlying cortical areas
(Fischl et al., 2008; Van Essen, Glasser, Dierker, Harwell, &
Coalson, 2012; Yeo, Sabuncu, Vercauteren, Holt, et al.,
2010b), cortical folds are often used as macroanatomical
landmarks for comparison of results across brain imaging
studies. Consequently, methods that can accurately label cortical folds across different subjects are important for studying
the human brain (Figure 1). The many types of cortical labeling criteria and data modalities are matched by the myriad of
published algorithms for estimating the labels. A comprehensive survey is outside the scope of this article. Instead, we will
focus on a few popular approaches that have been effective
across multiple types of cortical labeling criteria and imaging
modalities.
Suppose we want to label the cerebral cortex in a given brain

image (henceforth, referred to as target). The target brain could
be an image acquired from an individual subject or a model
that represents the population, for example, a template
obtained by averaging the brain images of multiple subjects.
The MNI152 template and FreeSurfer fsaverage subject are
examples of the latter case. Assuming the existence of a brain
atlas containing the labels of interests, one simple strategy is to
employ an image registration algorithm to spatially align the
target image and the atlas and then use the registration result to
transfer the labels from the atlas coordinates to the target image
coordinates (Christensen, Joshi, & Miller, 1997; Collins,
Holmes, Peters, & Evans, 1995; Miller, Christensen, Amit, &
Grenander, 1993; Thompson & Toga, 1996).
Single-Subject Atlas
In the simplest case, the atlas can be the labeled brain of a single
subject. This strategy has been used to transfer labels of cortical
folds or other macroanatomical brain structures from one
labeled subject to another (Lancaster et al., 2000; Sandor &
Leahy, 1997; Shen & Davatzikos, 2002; Tzourio-Mazoyer et al.,
2002). Cortical areas defined using architectonics can be transferred between histological slices and the MRI anatomical scan
of the same subject (Schormann & Zilles, 1998). Van Essen and
colleagues (Van Essen, 2004; Van Essen et al., 2012) had utilized
this strategy to transfer cortical areas derived from visuotopic
functional Magnetic Resonance Imaging (fMRI), task-based
http://dx.doi.org/10.1016/B978-0-12-397025-1.00306-7
357
358
INTRODUCTION TO METHODS AND MODELING | Automatic Labeling of the Human Cerebral Cortex
(a)
(b)
Area 6
7.6
12.5
Area 2
(e)
hOc5
Area 45
(c)
0.2
1.0
(d)
Figure 1 Different types of cortical labels. (a) Cortical labels based on macroanatomy. Gyral-based regions of interest were labeled in a training set of 40
subjects (Desikan et al., 2006), which were then used to train a Markov random field (MRF) classifier for labeling a new subject (Fischl et al., 2004)
from the OASIS (Marcus et al., 2007) dataset. Section Fusion of Registration-Based Labeling and Mixture Models discusses this general approach.
(b) Cortical label based on cortical function. The cortical label was estimated from an automated forward inference meta-analysis of the term MT in MNI
space (Yarkoni, Poldrack, Nichols, Van Essen, & Wager, 2011) and projected to FreeSurfer (Fischl, 2012) fsaverage surface space using
a nonlinear transformation estimated from 1000 subjects (Buckner, Krienen, Castellanos, Diaz, & Yeo, 2011). A high value indicates high likelihood that
studies associated with the motion-sensitive area MT report activations at that spatial location. (c) Cortical labels based on architectonics. Areas 2 (Grefkes,
Geyer, Schormann, Roland, & Zilles, 2001), 6 (Geyer, 2004), 45 (Amunts et al., 1999), and hOc5 (Malikovic et al., 2007) were delineated in ten postmortem
brains based on observer-independent cytoarchitectonic analysis. These areas were mapped onto the FreeSurfer fsaverage space to create prior probability
maps of different cytoarchitectonic areas (Fischl et al., 2008; Yeo et al., 2010b). Area hOc5 may correspond to the region in (b). Section Registration-Based
Labeling discusses this registration-based labeling approach. (d) Cortical labels based on resting-state functional connectivity MRI. Connectivity profiles of
every vertex across both cerebral hemispheres of 1000 subjects were computed and averaged in FreeSurfer fsaverage surface space. The averaged profiles
were modeled with a mixture of von MisesFisher distributions and clustered into networks of regions with similar patterns of connectivity (Yeo et al.,
2011). The resulting parcelation was projected to Caret (Van Essen & Dierker, 2007) PALS-B12 surface space for visualization. Section Mixture Models
discusses this general approach. (e) Cortical labels based on functional topography. Topography of visual areas in a single subject was interrogated using
phase-encoded retinotopic mapping with a rotating angular wedge visual stimuli and spectral analysis (Adapted from Swisher, J.D., Halko, M.A., Merabet,
L.B., McMains, S.A., & Somers, D.C. (2007). Visual topography of human intraparietal sulcus. The Journal of Neuroscience 27, 53265337). Red represents
the upper visual meridian, blue represents the contralateral horizontal meridian, and green represents the lower meridian.
fMRI, or histology of individual subjects to the cortical mantle of

an average subject. This strategy can even be used to warp the
cortical areas of the macaque monkey to an average human
subject for comparative neuroanatomy (Orban, Van Essen, &
Vanduffel, 2004; Van Essen & Dierker, 2007).
Multisubject or Population Atlas

Using a brain atlas comprising a single subject is problematic
because macroanatomical registration cannot perfectly align
the cortical labels of the atlas and those of the target brain.
One reason is the high intersubject variability in cortical folding (Ono, Kubik, Abernathey, et al., 1990; Zilles, Armstrong,
Schleicher, & Kretschmann, 1988), so that the correct correspondence is sometimes unclear even to a neuroanatomist.
Furthermore, macroanatomical features cannot fully predict
many cortical areas of interest (Amunts et al., 1999; Rajkowska
& Goldman-Rakic, 1995). This is especially problematic for
higher-order cortical areas (e.g., MT and Brocas areas) compared with lower-order areas, such as V1, whose alignment
accuracy can be as good as 23 mm using surface-based
registration (Fischl et al., 2008; Hinds et al., 2008; Yeo,

Sabuncu, Vercauteren, Ayache, et al., 2010a).
Consequently, a more accurate approach should reflect this
residual spatial variability in cortical areas after image registration. Given a training set of subjects with ground-truth labels,
we can register the subjects to the atlas and estimate the prior
probability of a cortical label at every spatial location. A target
subject that has been registered into atlas space inherits this
prior probability (Evans, Kamber, Collins, & MacDonald,
1994; Mazziotta et al., 1995).
This strategy has been used to compute a probabilistic
labeling of cortical folds (Collins, Zijdenbos, Baare, & Evans,
1999; Shattuck et al., 2008; Smith et al., 2004) and cortical
areas based on architectonics (Amunts et al., 1999; Eickhoff
et al., 2005; Fischl et al., 2008; Van Essen et al., 2012).
Mixture Models
The registration-based approach (Section Registration-Based
Labeling) assumes the availability of other labeled subjects.
However, in many situations, an atlas with prior information
might not be available. Therefore, an orthogonal approach is
to directly model the relationship between image features and
cortical labels in the absence of previously labeled training
subjects.
More formally, suppose there are N cortical locations. Let
x {xn} denote the set of cortical locations: n 2 {1, . . ., N}. Let
y {yn} and L {Ln} denote the image features and cortical
labels, respectively, at locations {xn}. We assume there are K
cortical labels of interest, so Ln 2 {1, . . ., K}. Our goal is to
estimate L.
One common approach is to assume the observed features
{yn} are generated from a mixture model. In particular, the
model assumes each cortical label Ln is independently drawn
from a probability distribution, that is, p(L) Pnp(Ln). This is a
key difference with Section Multisubject or Population Atlas,
where the prior came from the training data. Assuming identical distributions across spatial locations, p(Ln) is parameterized
P
by the vector m m1 ; . . . ; mK ; k mk 1.
Conditioned on the cortical label Ln at spatial location xn,
the observed features yn are assumed to be generated from the
distribution p(yn|Ln). We assume that p(yn|Ln) is parameterized
by y {y1, . . ., yK}. For example, if p(yn|Ln) is a Gaussian distribution, then yk might correspond to the mean and variance of
the k-th Gaussian distribution and the entire model is known
as a Gaussian mixture model.
A common way to solve for L is to maximize the likelihood
or posterior probability of the parameters m and y assuming the
observation of the image features y. This can be achieved via
numerical optimization schemes, such as the expectation
maximization (EM) algorithm (Dempster, Laird, & Rubin,
1977). These types of methods essentially perform a datadriven clustering and thus identify clusters of voxels or vertices
that are assigned a label. The well-known k-means clustering
algorithm (MacQueen et al., 1967) can be interpreted as a
special case of this mixture modeling approach.
This clustering (mixture model or k-means) strategy was
used for the segmentation of different tissue types in anatomical MRI data (Kapur, Grimson, Wells, & Kikinis, 1996; Teo,
Sapiro, & Wandell, 1997; Wells, Grimson, Kikinis, & Jolesz,
1996). The same approach has been applied to cortical labels
based on task-based fMRI (Flandin, Kherif, Pennec,
Malandain, et al., 2002; Flandin, Kherif, Pennec, Rivie`re,
et al., 2002; Goutte, Toft, Rostrup, Nielsen, & Hansen, 1999;
Penny & Friston, 2003), connectivity measured by diffusion
MRI (Anwander, Tittgemeyer, von Cramon, Friederici, &
Knosche, 2007; Beckmann, Johansen-Berg, & Rushworth,
2009; Klein et al., 2007; Mars et al., 2011; Nanetti, Cerliani,
Gazzola, Renken, & Keysers, 2009; Tomassini et al., 2007),
connectivity measured by resting-state fMRI (Bellec, RosaNeto, Lyttelton, Benali, & Evans, 2010; Cauda et al., 2011;
Chang, Yarkoni, Khaw, & Sanfey, 2013; Deen, Pitskel, &
Pelphrey, 2011; Golland, Golland, Bentin, & Malach, 2008;
Kahnt, Chang, Park, Heinzle, & Haynes, 2012; Kelly et al.,
2012; Kim et al., 2010; Yeo et al., 2011), and activation coordinates from meta-analysis of functional studies (Cauda et al.,
2012; Kelly et al., 2012).
In the context of cortical labeling, other popular clustering
approaches in the neuroimaging literature include hierarchical
clustering (Bellec et al., 2010; Cauda et al., 2011; Cieslik et al.,
359
2012; Eickhoff et al., 2011; Kelly et al., 2012), spectral clustering (Craddock, James, Holtzheimer, Hu, & Mayberg, 2012;
Thirion et al., 2006; van den Heuvel, Mandl, & Pol, 2008),
and fuzzy clustering (Cauda et al., 2011; Lee et al., 2012).
Unlike mixture modeling, these approaches do not enjoy a
simple generative modeling interpretation.
Fusion of Registration-Based Labeling and Mixture

Models
In Section Mixture Models, we assumed simple forms of the
prior p(L|m) and likelihood p(yn|Ln, y), which we estimated
from the subjects we are labeling, using the EM algorithm. In
this section, we consider more complex priors p(L|m) and
likelihood p(yn|Ln, y).
Spatially Varying, Spatially Independent Priors

In Section Mixture Models, we assumed p(L|m) to be paramP
eterized by the vector m [m1, . . ., mK], where
kmk 1. Therefore, such a model assumes that the prior probability of
observing different label classes is the same throughout the
cortex. However, we can reasonably expect this prior probability to vary across the brain (e.g., Figure 1(c)). Therefore, a
spatially varying prior probability of observing different cortical labels can constrain and improve the cortical labeling.
As discussed in Section Multisubject or Population Atlas,
we can obtain a prior for our target brain by registering to an
atlas constructed from other subjects that have been labeled. In
this case, m becomes a function of spatial location xn, so that if
we also assume spatial independence, we get
Y
Y
pLn jmxn
m x
[1]
pLjm
n
n Ln n
where mLn xn is the prior probability of observing label Ln at
P
spatial location xn; kmk(xn) 1 for all locations {xn}.
Spatially Dependent Priors: Markov Random Fields

In Section Spatially Varying, Spatially Independent Priors,
we assumed the prior probability of cortical labels to be independent across spatial locations. However, for many cortical
labels, the number of spatial locations along their boundaries
is significantly less than the number of spatial locations within
the labels. In other words, adjacent spatial locations are more
likely to have the same label than different labels. As another
example, we might expect adjacent vertices along the fundus of
a sulcus are more likely to have the same sulcal labels (Fischl
et al., 2004).
We can impose this kind of neighborhood spatial prior
using Markov random field (MRF) theory (Dobruschin,
1968; Spitzer, 1971). In an MRF, the labels L {Ln} are related
to
each
other
within
a
neighborhood
system
N fN xn , xn 2 xg where N xn are the neighboring locations
of xn , xn2
= N xn and xn 2 N xm , xm 2 N xn :
In the brain imaging context, the neighborhood N of a
location xn is often the surrounding voxels (Fischl et al.,
2002; Held et al., 1997; Van Leemput, Maes, Vandermeulen,
& Suetens, 1999; Zhang, Brady, & Smith, 2001) or vertices
360
(Fischl et al., 2004; Yeo, Sabuncu, Desikan, Fischl, & Golland,

2008). Furthermore, the following simple MRF model is commonly used:
pL
1
exp U L
ZU
may be advantageous to learn a spatially varying likelihood

(yn|Ln, y) (Fischl et al., 2002) because T1 relaxation is not
uniform over the gray matter. For example, T1 -relaxation in
the central sulcus is less than the rest of the cortex (Steen,
Reddick, & Ogg, 2000).
As another example, labeling cortical folds using a spatially
constant likelihood of mean curvature feature is ineffective
because the intrasulcal variation in mean curvature is much
larger than between sulci. Consequently, Fischl et al. (2004)
and Yeo et al. (2008) utilized a spatially varying likelihood for
labeling cortical folds.
[2]
where Z(U) ensures p(L) is a valid probability distribution and

U(L) is an energy function of the form
X
X X
U L
W Ln
V Ln ; Lm
[3]
n
x
x 2N
n
xn
and so we can write

pL
pL
X

1
exp n W Ln
ZW
X X

1
exp x
V Ln ; Lm

xm 2N xn
n
Z V
Y 1
exp W Ln
nZ
n
X X

1
exp x
V
L
;
L

n
m
xm 2N xn
n
Z V
Inference and Applications to Cortical Labeling

Depending on the applications, the MRF priors (Section
Spatially Dependent Priors: Markov Random Fields) can
be mixed and matched with different priors (Section
Spatially Varying, Spatially Independent Priors) and likelihoods (Section Learning the Likelihood). Exact inference of
a model that includes an MRF is generally computationally
infeasible. However, approximate inference can be accomplished via general classes of approximation algorithms,
including Markov chain Monte Carlo (Robert & Casella,
2004), variational inference (Wainwright & Jordan, 2008),
and graph cuts (Kolmogorov & Zabin, 2004).
The MRF strategy has been applied to labeling cortical folds
(Desikan et al., 2006; Destrieux, Fischl, Anders, & Halgren,
2010; Fischl et al., 2002; Klein & Tourville, 2012; Yeo et al.,
2008) and obtaining cortical labels based on resting-state
fMRI (Ryali, Chen, Supekar, & Menon, 2012) or task-based
fMRI (Rajapakse & Piyaratna, 2001; Svensen, Kruggel, & von
Cramon, 2000; Woolrich & Behrens, 2006).
[4]
[5]
The local clique potential W is commonly set by equating

1/Zn exp(W(Ln)) with the prior probability mLn xn from Section Spatially Varying, Spatially Independent Priors (Fischl
et al., 2002, 2004; Yeo et al., 2008). The clique potentials V can
be estimated from data, such as by iterative proportional fitting
(Jirousek & Preucil, 1995). However, they are often set manually. For example, setting V(Ln, Lm) bd(Ln Lm) (b > 0)
encourages neighboring labels to be the same (Zhang et al.,
2001). Fischl et al. (2004) learned an anisotropic neighborhood potential to reflect the observation that changes in sulcal
or gyral labels are more likely to occur in the direction of
highest surface curvature.
Learning the Likelihood
Summary
In Section Mixture Models, the parameters y of the likelihood

p(yn|Ln, y) were estimated from the target subjects. When previously labeled subjects are available, it may be advantageous
to estimate y from these subjects. If p(yn|Ln, y) is a Gaussian
distribution and yk is the mean and variance of the k-th Gaussian distribution, we can estimate yk by the sample mean and
variance of the training subjects.
One major advantage of estimating the likelihood from
training subjects is the possible increase in power to learn a
more complex likelihood p(yn|Ln, y). For example, suppose the
feature yn is the T1-relaxation parameter at the voxel n, then it
The different approaches in this article can be summarized

using graphical models (Figure 2). The conventions follow
that of Wainwright and Jordan (2008). The registration-based
approach (Section Registration-Based Labeling) has the simplest model (Figure 2(a)), where the labels L only depend on
the prior probabilities m specified by the atlas. Registration is
assumed to be already accomplished so the (implicit) dependency on image features used for registration is not shown. The
mixture modeling approach (Section Mixture Models) has a
more complex model (Figure 2(b)). The labels L are generated
from the prior m. The features y are then generated conditioned
L
m
(a)
(b)
L
Y
V
(c)
Figure 2 Graphical models summarizing approaches in this article. (a) Model corresponding to the registration-based approach (Section
Registration-Based Labeling). (b) Model corresponding to the mixture modeling approach (Section Mixture Models). (c) Model corresponding
to the MRF approach (Section Fusion of Registration-Based Labeling and Mixture Models). The shaded circles indicate that the features Y are
observed. The arrows indicate conditional dependencies. For example, in (b) and (c), y is conditionally dependent on y and L. L and y are independent.
However, L and y are no longer independent when conditioned on y.
on the labels L and the likelihood parameters y. Finally, the
MRF approach (Section Fusion of Registration-Based Labeling and Mixture Models) can be represented by the model in
Figure 2(c). Here, the local potentials W replace m and the
labels L also depend on the clique potentials V.
The approaches mentioned earlier have been especially
successful for cortical labeling based on macroanatomy, connectivity (diffusion and resting state), architectonics, and function (meta-analysis of activation coordinates). They are less
popular in task-based fMRI, which generally employs general
linear modeling of the hemodynamic response, and in visuotopic mapping, which generally employs spectral or Fourier
techniques.
Other approaches not covered in this article include independent component analysis; morphological approaches, such
as edge detection (Cohen et al., 2008; Nelson et al., 2010) and
watershed (Lohmann & von Cramon, 2000; Rettmann, Han,
Xu, & Prince, 2002); and machine learning techniques, such
as discriminative models (Tu et al., 2008), neural networks
(Mangin et al., 2004; Riviere et al., 2002), and label fusion
(Heckemann et al., 2006; Sabuncu, Yeo, Van Leemput, Fischl,
& Golland, 2010).

Functional Connectivity; Functional Organization of the Primary Visual
Cortex; Gyrification in the Human Brain; Sulci as Landmarks;
Transmitter Receptor Distribution in the Human Brain;
INTRODUCTION TO METHODS AND MODELING: Analysis of
Variance (ANOVA); Bayesian Multiple Atlas Deformable Templates;
Computational Modeling of Responses in Human Visual Cortex;
Contrasts and Inferences; Convolution Models for FMRI; Diffeomorphic
Image Registration; Diffusion Tensor Imaging; Effective Connectivity;
Fiber Tracking with DWI; Nonlinear Registration Via Displacement
Fields; Probability Distribution Functions in Diffusion MRI; Q-Space
Modeling in Diffusion-Weighted MRI; Resting-State Functional
Connectivity; Reverse Inference; Rigid-Body Registration; Sulcus
Identification and Labeling; Surface-Based Morphometry; The General
Linear Model; Tissue Classification; Tract Clustering, Labeling, and
Quantitative Analysis; INTRODUCTION TO SYSTEMS: Face
Perception; Hubs and Pathways; Large-Scale Functional Brain
Organization; Motion Perception; Neural Codes for Shape Perception;
Primate Color Vision.
References
Amunts, K., Schleicher, A., Burgel, U., Mohlberg, H., Uylings, H., & Zilles, K. (1999).
Brocas region revisited: Cytoarchitecture and intersubject variability. Journal of
Comparative Neurology, 412, 319341.
Anwander, A., Tittgemeyer, M., von Cramon, D. Y., Friederici, A. D., & Knosche, T. R.
(2007). Connectivity-based parcellation of Brocas area. Cerebral Cortex, 17,
816825.
Beckmann, M., Johansen-Berg, H., & Rushworth, M. F. (2009). Connectivity-based
parcellation of human cingulate cortex and its relation to functional specialization.
The Journal of Neuroscience, 29, 11751190.
Bellec, P., Rosa-Neto, P., Lyttelton, O. C., Benali, H., & Evans, A. C. (2010).
Multi-level bootstrap analysis of stable clusters in resting-state fMRI. NeuroImage,
51, 1126.
361
Buckner, R. L., Krienen, F. M., Castellanos, A., Diaz, J. C., & Yeo, B. T. (2011). The
organization of the human cerebellum estimated by intrinsic functional connectivity.
Cauda, F., Costa, T., Torta, D. M., Sacco, K., DAgata, F., Duca, S., et al. (2012). Metaanalytic clustering of the insular cortex characterizing the meta-analytic connectivity
of the insula when involved in active tasks. NeuroImage, 62(1), 343355.
Cauda, F., DAgata, F., Sacco, K., Duca, S., Geminiani, G., & Vercelli, A. (2011).
Functional connectivity of the insula in the resting brain. NeuroImage, 55, 823.
Chang, L. J., Yarkoni, T., Khaw, M. W., & Sanfey, A. G. (2013). Decoding the role of the
insula in human cognition: Functional parcellation and large-scale reverse
inference. Cerebral Cortex, 23, 739749.
Christensen, G. E., Joshi, S. C., & Miller, M. I. (1997). Volumetric transformation of
brain anatomy. IEEE Transactions on Medical Imaging, 16, 864877.
Cieslik, E. C., Zilles, K., Caspers, S., Roski, C., Kellermann, T. S., Jakobs, O., et al.
(2013). Is there one DLPFC in cognitive action control? Evidence for heterogeneity
from co-activation-based parcellation. Cerebral Cortex, 23(11), 26772689.
Cohen, A. L., Fair, D. A., Dosenbach, N. U., Miezin, F. M., Dierker, D., Van Essen, D. C.,
et al. (2008). Defining functional areas in individual human brains using resting
functional connectivity MRI. NeuroImage, 41, 45.
Collins, D. L., Holmes, C. J., Peters, T. M., & Evans, A. C. (1995). Automatic 3-D
model-based neuroanatomical segmentation. Human Brain Mapping, 3, 190208.
Collins, D. L., Zijdenbos, A. P., Baare, W. F., & Evans, A. C. (1999). Animal Insect:
Improved cortical structure segmentation. In Information processing in medical
imaging (pp. 210223). Berlin: Springer.
Craddock, R. C., James, G. A., Holtzheimer, P. E., Hu, X. P., & Mayberg, H. S. (2012). A
whole brain fMRI atlas generated via spatially constrained spectral clustering.
Human Brain Mapping, 33, 19141928.
Deen, B., Pitskel, N. B., & Pelphrey, K. A. (2011). Three systems of insular functional
connectivity identified with cluster analysis. Cerebral Cortex, 21, 14981506.
Dempster, A. P., Laird, N. M., & Rubin, D. B. (1977). Maximum likelihood from
incomplete data via the EM algorithm. Journal of the Royal Statistical Society: Series
B: Methodological, 39, 138.
Desikan, R. S., Segonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C., Blacker, D., et al.
(2006). An automated labeling system for subdividing the human cerebral cortex on
MRI scans into gyral based regions of interest. NeuroImage, 31, 968980.
Destrieux, C., Fischl, B., Anders, D., & Halgren, E. (2010). Automatic parcellation of
human cortical gyri and sulci using standard anatomical nomenclature.
NeuroImage, 53, 1.
Dobruschin, P. (1968). The description of a random field by means of conditional
probabilities and conditions of its regularity. Theory of Probability and Its
Eickhoff, S. B., Bzdok, D., Laird, A. R., Roski, C., Caspers, S., Zilles, K., et al. (2011).
Co-activation patterns distinguish cortical modules, their connectivity and
functional differentiation. NeuroImage, 57, 938949.
Eickhoff, S. B., Stephan, K. E., Mohlberg, H., Grefkes, C., Fink, G. R., Amunts, K., et al.
(2005). A new SPM toolbox for combining probabilistic cytoarchitectonic maps and
functional imaging data. NeuroImage, 25, 13251335.
Evans, A., Kamber, M., Collins, D., & MacDonald, D. (1994). An MRI-based
probabilistic atlas of neuroanatomy. In Magnetic resonance scanning and epilepsy
(pp. 263274). USA: Springer.
Felleman, D. J., & Van Essen, D. C. (1991). Distributed hierarchical processing in the
primate cerebral cortex. Cerebral Cortex, 1, 147.
Fischl, B. (2012). Freesurfer. NeuroImage, 62, 774781.
Fischl, B., Rajendran, N., Busa, E., Augustinack, J., Hinds, O., Yeo, B. T., et al. (2008).
Cortical folding patterns and predicting cytoarchitecture. Cerebral Cortex, 18,
19731980.
Fischl, B., Salat, D. H., Busa, E., Albert, M., Dieterich, M., Haselgrove, C., et al. (2002).
Whole brain segmentation: Automated labeling of neuroanatomical structures in the
human brain. Neuron, 33, 341355.
Fischl, B., Van Der Kouwe, A., Destrieux, C., Halgren, E., Segonne, F., Salat, D. H., et al.
(2004). Automatically parcellating the human cerebral cortex. Cerebral Cortex, 14,
1122.
Flandin, G., Kherif, F., Pennec, X., Malandain, G., Ayache, N., & Poline, J. B. (2002).
Improved detection sensitivity in functional MRI data using a brain parcelling
technique. In Medical image computing and computer- assisted intervention
(pp. 467474). London: Springer-Verlag.
Flandin, G., Kherif, F., Pennec, X., Rivie`re, D., Ayache, N., & Poline, J. B. (2002).
Parcellation of brain images with anatomical and functional constraints for fMRI data
analysis. In IEEE International Symposium on Biomedical Imaging (pp. 907910).
IEEE.
Fonov, V., Evans, A. C., Botteron, K., Almli, C. R., McKinstry, R. C., & Collins, D. L.
(2011). Unbiased average age-appropriate atlases for pediatric studies.
NeuroImage, 54(1), 313327.
362
Geyer, S. (2004). The microstructural border between the motor and the cognitive
domain in the human cerebral cortex. Advances in Anatomy, Embryology, and Cell
Biology, 174, 189.
Golland, Y., Golland, P., Bentin, S., & Malach, R. (2008). Data-driven clustering reveals
a fundamental subdivision of the human cortex into two global systems.
Neuropsychologia, 46, 540553.
Goutte, C., Toft, P., Rostrup, E., Nielsen, F.A., & Hansen, L. K. (1999). On clustering
fMRI time series. NeuroImage, 9, 298310.
Grefkes, C., Geyer, S., Schormann, T., Roland, P., & Zilles, K. (2001). Human
somatosensory area 2: Observer-independent cytoarchitectonic mapping,
interindividual variability, and population map. NeuroImage, 14, 617631.
Heckemann, R. A., Hajnal, J. V., Aljabar, P., Rueckert, D., Hammers, A., et al. (2006).
Automatic anatomical brain MRI segmentation combining label propagation and
decision fusion. NeuroImage, 33, 115126.
Held, K., Kops, E. R., Krause, B. J., Wells, W. M., III, Kikinis, R., & Muller-Gartner, H. W.
(1997). Markov random field segmentation of brain MR images. IEEE Transactions
van den Heuvel, M., Mandl, R., & Pol, H. H. (2008). Normalized cut group clustering of
resting-state fMRI data. PloS One, 3, e2001.
Hinds, O. P., Rajendran, N., Polimeni, J. R., Augustinack, J. C., Wiggins, G., Wald, L. L.,
et al. (2008). Accurate prediction of V1 location from cortical folds in a surface
coordinate system. NeuroImage, 39, 1585.
Jirousek, R., & Preucil, S. (1995). On the effective implementation of the iterative
proportional fitting procedure. Computational Statistics and Data Analysis, 19,
177189.
Kaas, J. H. (1987). The organization of neocortex in mammals: Implications for theories
of brain function. Annual Review of Psychology, 38, 129151.
Kahnt, T., Chang, L. J., Park, S. Q., Heinzle, J., & Haynes, J. D. (2012). Connectivitybased parcellation of the human orbitofrontal cortex. The Journal of Neuroscience,
32, 62406250.
Kapur, T., Grimson, W. E.L, Wells, W. M., III, & Kikinis, R. (1996). Segmentation of brain
tissue from magnetic resonance images. Medical Image Analysis, 1, 109127.
Kelly, C., Toro, R., Di Martino, A., Cox, C. L., Bellec, P., Castellanos, F. X., et al. (2012).
A convergent functional architecture of the insula emerges across imaging
modalities. NeuroImage, 61, 11291142.
Kim, J. H., Lee, J. M., Jo, H. J., Kim, S. H., Lee, J. H., Kim, S. T., et al. (2010).
Defining functional SMA and pre-SMA subregions in human MFC using resting
state fMRI: Functional connectivity-based parcellation method. NeuroImage, 49,
23752386.
Klein, A., & Tourville, J. (2012). 101 labeled brain images and a consistent human
cortical labeling protocol. Frontiers in Neuroscience, 6, 171. http://dx.doi.org/
10.3389/fnins.2012.00171.
Klein, J. C., Behrens, T. E., Robson, M. D., Mackay, C. E., Higham, D. J., &
Johansen-Berg, H. (2007). Connectivity-based parcellation of human cortex using
diffusion MRI: Establishing reproducibility, validity and observer independence in
BA 44/45 and SMA/pre-SMA. NeuroImage, 34, 204211.
Kolmogorov, V., & Zabin, R. (2004). What energy functions can be minimized via graph
cuts? IEEE Transactions on Pattern Analysis and Machine Intelligence, 26,
147159.
Lancaster, J. L., Woldorff, M. G., Parsons, L. M., Liotti, M., Freitas, C. S., Rainey, L.,
et al. (2000). Automated Talairach atlas labels for functional brain mapping. Human
Lee, M. H., Hacker, C. D., Snyder, A. Z., Corbetta, M., Zhang, D., Leuthardt, E. C., et al.
(2012). Clustering of resting state networks. PloS One, 7, e40370.
Lohmann, G., & von Cramon, D. Y. (2000). Automatic labelling of the human cortical
surface using sulcal basins. Medical Image Analysis, 4, 179188.
MacQueen, J., et al. (1967). Some methods for classification and analysis of
multivariate observations. In: Proceedings of the Fifth Berkeley Symposium on
Mathematical Statistics and Probability, CA, USA.
Malikovic, A., Amunts, K., Schleicher, A., Mohlberg, H., Eickhoff, S. B., Wilms, M., et al.
(2007). Cytoarchitectonic analysis of the human extrastriate cortex in the region of V5/
MT: A probabilistic, stereotaxic map of area hoc5. Cerebral Cortex, 17, 562574.
Mangin, J. F., Riviere, D., Cachia, A., Duchesnay, E., Cointepas, Y.,
Papadopoulos-Orfanos, D., et al. (2004). Object-based morphometry of the cerebral
cortex. IEEE Transactions on Medical Imaging, 23, 968982.
Marcus, D. S., Wang, T. H., Parker, J., Csernansky, J. G., Morris, J. C., & Buckner, R. L.
(2007). Open access series of imaging studies (oasis): Cross-sectional MRI data in
young, middle aged, nondemented, and demented older adults. Journal of Cognitive
Mars, R. B., Jbabdi, S., Sallet, J., OReilly, J. X., Croxson, P. L., Olivier, E., et al. (2011).
Diffusion-weighted imaging tractography-based parcellation of the human parietal
cortex and comparison with human and macaque resting-state functional
connectivity. The Journal of Neuroscience, 31, 40874100.
Mazziotta, J. C., Toga, A. W., Evans, A., Fox, P., Lancaster, J., et al. (1995).
A probabilistic atlas of the human brain: theory and rationale for its development.
The international consortium for brain mapping (ICBM). NeuroImage, 2, 89101.
Miller, M. I., Christensen, G. E., Amit, Y., & Grenander, U. (1993). Mathematical
textbook of deformable neuroanatomies. Proceedings of the National Academy of
Sciences, 90, 1194411948.
Nanetti, L., Cerliani, L., Gazzola, V., Renken, R., & Keysers, C. (2009). Group analyses
of connectivity-based cortical parcellation using repeated k-means clustering.
Nelson, S. M., Cohen, A. L., Power, J. D., Wig, G. S., Miezin, F. M., Wheeler, M. E., et al.
(2010). A parcellation scheme for human left lateral parietal cortex. Neuron, 67, 156.
Ono, M., Kubik, S., Abernathey, C. D., et al. (1990). Atlas of the Cerebral Sulci.
New York: Thieme.
Orban, G. A., Van Essen, D., & Vanduffel, W. (2004). Comparative mapping of higher
visual areas in monkeys and humans. Trends in Cognitive Sciences, 8, 315324.
Penny, W., & Friston, K. (2003). Mixtures of general linear models for functional
neuroimaging. IEEE Transactions on Medical Imaging, 22, 504514.
Rajapakse, J. C., & Piyaratna, J. (2001). Bayesian approach to segmentation of statistical
parametric maps. IEEE Transactions on Biomedical Engineering, 48, 11861194.
Rajkowska, G., & Goldman-Rakic, P. S. (1995). Cytoarchitectonic definition of prefrontal
areas in the normal human cortex: II. Variability in locations of areas 9 and 46 and
relationship to the Talairach coordinate system. Cerebral Cortex, 5, 323337.
Rettmann, M. E., Han, X., Xu, C., & Prince, J. L. (2002). Automated sulcal segmentation
using watersheds on the cortical surface. NeuroImage, 15, 329344.
Riviere, D., Mangin, J. F., Papadopoulos-Orfanos, D., Martinez, J. M., Frouin, V., &
Regis, J. (2002). Automatic recognition of cortical sulci of the human brain using a
congregation of neural networks. Medical Image Analysis, 6, 7792.
Robert, C. P., & Casella, G. (2004). In Monte Carlo Statistical Methods: (vol. 319).
New York: Springer-Verlag.
Ryali, S., Chen, T., Supekar, K., & Menon, V. (2012). A parcellation scheme based on
von MisesFisher distributions and Markov random fields for segmenting brain
regions using resting-state fMRI. NeuroImage, 65, 8396.
Sabuncu, M. R., Yeo, B. T., Van Leemput, K., Fischl, B., & Golland, P. (2010). A
generative model for image segmentation based on label fusion. IEEE Transactions
Sandor, S., & Leahy, R. (1997). Surface-based labeling of cortical anatomy using a
deformable atlas. IEEE Transactions on Medical Imaging, 16, 4154.
Schormann, T., & Zilles, K. (1998). Three-dimensional linear and nonlinear
transformations: An integration of light microscopical and MRI data. Human Brain
Mapping, 6, 339347.
Shattuck, D. W., Mirza, M., Adisetiyo, V., Hojatkashani, C., Salamon, G., Narr, K. L.,
et al. (2008). Construction of a 3D probabilistic atlas of human cortical structures.
Shen, D., & Davatzikos, C. (2002). Hammer: Hierarchical attribute matching mechanism
for elastic registration. IEEE Transactions on Medical Imaging, 21, 14211439.
Smith, S. M., Jenkinson, M., Woolrich, M. W., Beckmann, C. F., Behrens, T.,
Johansen-Berg, H., et al. (2004). Advances in functional and structural MR image
analysis and implementation as FSL. NeuroImage, 23, S208S219.
Spitzer, F. (1971). Markov random fields and Gibbs ensembles. The American
Mathematical Monthly, 78, 142154.
Steen, R. G., Reddick, W. E., & Ogg, R. J. (2000). More than meets the eye: Significant
regional heterogeneity in human cortical T1. Magnetic Resonance Imaging, 18,
361368.
Svensen, M., Kruggel, F., & von Cramon, D. Y. (2000). Probabilistic modeling of
single-trial fMRI data. IEEE Transactions on Medical Imaging, 19, 2535.
Swisher, J. D., Halko, M. A., Merabet, L. B., McMains, S. A., & Somers, D. C. (2007).
Visual topography of human intraparietal sulcus. The Journal of Neuroscience, 27,
53265337.
Teo, P. C., Sapiro, G., & Wandell, B. A. (1997). Creating connected representations of
cortical gray matter for functional MRI visualization. IEEE Transactions on Medical
Imaging, 16, 852863.
Thirion, B., Flandin, G., Pinel, P., Roche, A., Ciuciu, P., & Poline, J. B. (2006). Dealing
with the shortcomings of spatial normalization: Multi-subject parcellation of fMRI
datasets. Human Brain Mapping, 27, 678693.
Thompson, P., & Toga, A. W. (1996). A surface-based technique for warping threedimensional images of the brain. IEEE Transactions on Medical Imaging, 15, 402417.
Tomassini, V., Jbabdi, S., Klein, J. C., Behrens, T. E., Pozzilli, C., Matthews, P. M., et al.
(2007). Diffusion-weighted imaging tractography-based parcellation of the human
lateral premotor cortex identifies dorsal and ventral subregions with anatomical and
functional specializations. The Journal of Neuroscience, 27, 1025910269.
Tu, Z., Narr, K. L., Dollar, P., Dinov, I., Thompson, P. M., & Toga, A. W. (2008). Brain
anatomical structure segmentation by hybrid discriminative/generative models. IEEE
Tzourio-Mazoyer, N., Landeau, B., Papathanassiou, D., Crivello, F., Etard, O.,
Delcroix, N., et al. (2002). Automated anatomical labeling of activations in SPM
using a macroscopic anatomical parcellation of the MNI MRI single-subject brain.
Ungerleider, L. G., & Desimone, R. (1986). Cortical connections of visual area MT in the
macaque. Journal of Comparative Neurology, 248, 190222.
Van Essen, D. C. (2004). Organization of visual areas in macaque and human cerebral
cortex. In L. Chalupa, & J. Werner (Eds.), The visual neurosciences (pp. 507521).
Cambridge, MA: MIT Press.
Van Essen, D. C., & Dierker, D. L. (2007). Surface-based and probabilistic atlases of
primate cerebral cortex. Neuron, 56, 209225.
Van Essen, D. C., Glasser, M. F., Dierker, D. L., Harwell, J., & Coalson, T. (2012).
Parcellations and hemispheric asymmetries of human cerebral cortex analyzed on
surface-based atlases. Cerebral Cortex, 22, 22412262.
Van Leemput, K., Maes, F., Vandermeulen, D., & Suetens, P. (1999). Automated
Wainwright, M. J., & Jordan, M. I. (2008). Graphical models, exponential families,
and variational inference. Foundations and Trends in Machine Learning, 1, 1305.
Wells, W. M., III, Grimson, W. E. L., Kikinis, R., & Jolesz, F. A. (1996). Adaptive
segmentation of MRI data. IEEE Transactions on Medical Imaging, 15, 429442.
Woolrich, M. W., & Behrens, T. E. (2006). Variational Bayes inference of spatial
mixture models for segmentation. IEEE Transactions on Medical Imaging, 25,
13801391.
363
Yarkoni, T., Poldrack, R.A., Nichols, T.E., Van Essen, D.C., & Wager, T.D. (2011).
NeuroSynth. http://neurosynth.org. Accessed 21.05.13.
Yarkoni, T., Poldrack, R. A., Nichols, T. E., Van Essen, D. C., & Wager, T. D. (2011).
Large-scale automated synthesis of human functional neuroimaging data. Nature
Methods, 8, 665670.
Yeo, B. T., Krienen, F. M., Sepulcre, J., Sabuncu, M. R., Lashkari, D., Hollinshead, M.,
et al. (2011). The organization of the human cerebral cortex estimated by intrinsic
functional connectivity. Journal of Neurophysiology, 106, 11251165.
Yeo, B. T., Sabuncu, M. R., Desikan, R., Fischl, B., & Golland, P. (2008). Effects of
registration regularization and atlas sharpness on segmentation accuracy. Medical
Yeo, B. T., Sabuncu, M. R., Vercauteren, T., Ayache, N., Fischl, B., & Golland, P. (2010).
Spherical demons: Fast diffeomorphic landmark-free surface registration. IEEE
Yeo, B. T., Sabuncu, M. R., Vercauteren, T., Holt, D. J., Amunts, K., Zilles, K., et al.
(2010). Learning task-optimal registration cost functions for localizing
cytoarchitecture and function in the cerebral cortex. IEEE Transactions on Medical
Imaging, 29, 14241441.
hidden Markov random field model and the expectation-maximization algorithm.
Zilles, K., Armstrong, E., Schleicher, A., & Kretschmann, H. J. (1988). The human
pattern of gyrification in the cerebral cortex. Anatomy and Embryology, 179,
173179.
Sulcus Identification and Labeling

J-F Mangin, M Perrot, and G Operto, CEA, Gif-sur-Yvette, France; CATI Multicenter Neuroimaging Platform, Paris, France
A Cachia, Universite Paris Descartes, Paris, France
C Fischer, CEA, Gif-sur-Yvette, France; CATI Multicenter Neuroimaging Platform, Paris, France
J Lefe`vre, Aix-Marseille Universite, Marseille, France
D Rivie`re, CEA, Gif-sur-Yvette, France; CATI Multicenter Neuroimaging Platform, Paris, France
Before the advent of MRI, the cortical folding pattern of patients

was out of sight, out of mind. The sulcus nomenclature, which
was taught in the anatomy classes, had no real use except for
neuroanatomists and to some extent neurosurgeons. Few people
were aware of the considerable interindividual variability of the
folding pattern and of the complete lack of understanding of
the origin of this variability. The fantastic development of MRI
could have triggered a renewal of interest, but the actual scientific drive was functional imaging, which requires morphological variability to be removed to simplify statistical group
analysis. Hence, for the brain mapping community, the variability of the folding pattern is mainly an impediment to perfect
spatial normalization. Today, spatial normalization technologies have reached a very efficient stage where primary sulci,
which are good landmarks of primary architectural areas, are
reasonably aligned across subjects (Ashburner, 2007; Fischl
et al., 2008). It is tempting to consider that the variability of
the folding pattern is an epiphenomenon of low interest that
can be forgotten.
However, the normalization paradigm has provided the
opportunity to quantify the morphological variability, which
has raised awareness that this variability can be a very valuable
source of information. For instance, techniques like voxelbased morphometry or cortical thickness analysis have provided a myriad of insights about the impact of development,
pathologies, or cognitive skills on brain structures (Toga &
Thompson, 2003). Hence, the variability of the folding pattern
has received more and more attention. A wave of research
programs aiming at explaining the origin and the dynamics
of the folding process was triggered (Lefe`vre & Mangin, 2010;
Regis et al., 2005; Reillo, de Juan Romero, Garca-Cabezas, &
Borrell, 2011; Sun & Hevner, 2014; Taber, 2014; Toro &
Burnod, 2005; Van Essen, 1997). These research programs
propose various hypotheses leading to consider the folding
pattern as a proxy of the underlying architecture of the cerebral
cortex. Then, the sulci geometry could provide biomarkers of
abnormal development or the signature of specific architectures (Cachia et al., 2014; Dubois et al., 2008; Plaze et al.,
2011; Sun et al., 2012; Weiner et al., 2014).
The Need for Computational Anatomy

The quantification of the folding pattern is a difficult issue. The
simplest strategies rely on global or local gyrification indexes
measuring the amount of cortex buried into the folds (Schaer
et al., 2008; Toro et al., 2008; Zilles, Palomero-Gallagher, &
Amunts, 2013). A spectral approach can provide a richer insight
of the folding global features (Germanaud et al., 2012). Following the footsteps of the neuroanatomists is more ambitious
because it requires the identification of the sulci described in
the literature. Very few experts can perform this difficult and
tedious task for the complete cerebral cortex. With the usual
radiological point of view, namely, a series of slices, even the
largest sulci can be difficult to recognize, which explains the
scarcity of relevant knowledge to overcome the interindividual
variability (see Figure 1). 3-D rendering of the cortical surface is
of great help, but it is often insufficient to deal with unusual
folding patterns that require inspecting the shape of the fold
depths (Regis et al., 2005). Hence, combining 3-D and 2-D
views is often mandatory. Cortical inflation is an attractive
alternative to exhibit the buried cortex (Van Essen, Drury,
Joshi, & Miller, 1998), but the deformations from the actual
folding geometry can be disturbing for sulcus identification.
Whatever the visualization strategy, our ignorance with respect
to the origin of the variability prevents us to decode safely
configurations where the main sulci are split into pieces and
reorganized into unusual patterns. A dedicated atlas describing
the most usual patterns is probably the best guideline for sulcus
identification, but this atlas is not comprehensive because
it stems from the study of only 25 brains (Ono, Kubik, &
Abarnathey, 1990). The reliable identification of secondary
and tertiary folds (Petrides, 2012) is beyond reach with the
current state of knowledge.
The complexity of the cortical folding pattern is overwhelming for human experts. Hence, computational anatomy is now
a key player to help the field to harness the folding variability.
Alignment with a single-subject cortical surface atlas has the
merit to provide the rough localization of primary sulci
(Destrieux, Fischl, Dale, & Halgren, 2010), but is not sufficient
to obtain accurate definition of the sulci for shape analysis. The
idiosyncrasies of the template brain are not a good model for
any other brain. The solution could lie into multisubject atlases
(Heckemann, Hajnal, Aljabar, Rueckert, & Hammers, 2006),
but this approach may not be flexible enough to overcome the
ambiguities hampering a reliable pairwise alignment between
cortical patterns. Hence, the community developed alternatives
with a stronger computer vision flavor. First, bottom-up processing pipelines convert standard MR images into synthetic
representations of individual folding geometries; and second,
pattern recognition techniques match such representations
with a model of the sulci (see Figure 2). Automatic recognition
of the sulci provides a range of opportunities for morphometry
(see Figure 3; Mangin, Jouvent, & Cachia, 2010) or sulcusdriven spatial normalization (Auzias et al., 2011, 2013; Joshi
et al., 2010; Thompson & Toga, 1996).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00307-9
365
Figure 1 Sulci are very difficult to recognize in a stack of brain slices.
S.Pe.C.median.
F.C.L.r.diag.
F.C.L.r.asc.
F.C.L.r.ant.
An artificial neuroanatomis
S.Pe.C.marginal.
S.Pe.C.sup.
S.Pe.C.inter.
S.Pe.C.inf.
S.C.
F.C.L.r.retroC.tr.
F.I.P.Po.C.inf.
S.Po.C.sup.
S.Pa.sup.
S.GSM.
S.F.sup.
F.I.P.r.int.1
S.T.s.ter.asc.ant
F.I.P.r.int.2
S.F.inter.
3-D Retina
Elementary folds
S.F.inf.
F.I.P.
S.T.s.ter.asc.post.
S.F.inf.ant.
S.F.marginal.
Occipital
S.F.orbitaire.
S.Or.
F.C.L.a.
F.C.L.p.
Insula
S.T.pol.
S.T.i.post.
S.O.T.lat.post.
S.O.T.lat.med.
F.C.L.r.sc.post.
S.T.i.ant.
S.C.sylvian.
S.T.s.
F.C.L.r.sc.ant.
Sulcus model
(a)
(d)
(e)
(b)
Bottom-up
processing
Pattern recognition
Sulcus
recognition
(c)
(f)
Figure 2 A computer vision pipeline mimicking a human anatomist. Its 3-D retina is the standard space of the brain mapping community. After
detection of the building blocks of the folding pattern from a negative mold of the brain, the sulci of the standard nomenclature are reassembled
according to a model inferred from a learning database. Reproduced from Perrot, M., Rivie`re, D., and Mangin, J. F. (2011). Cortical sulci recognition and
spatial normalization. Medical Image Analysis, 15(4), 529550.
INTRODUCTION TO METHODS AND MODELING | Sulcus Identification and Labeling
367
Figure 3 Once identified, a sulcus provides various morphometric features like length (red), depth (yellow), surface area (blue), or average span
between its walls (right).
Bottom-Up Representations of the Folding Pattern

This section describes examples of bottom-up strategies. Each
approach aims at converting the implicit encoding of the cortical folding pattern embedded in the geometry of the cortical
surface into a synthetic graphical representation. Hence, the
pattern recognition system dedicated to sulcus recognition can
deal with more abstract representations than images. Abstract
representations open the door to machine learning strategies
beyond reach for image registration.
The first generation of techniques relied on voxel-based
representations of the cortex. After a pipeline leading to a
classification of gray matter and white matter, each elementary
fold is detected and represented by its median surface (see
Figure 2(d)). These pieces of surface stem, for instance, from
the 3-D skeletonization of a negative mold of white matter (see
Figure 2(c); Mangin et al., 1995; Mangin, Frouin, Bloch, Regis,
& Lopez-Krahe, 1995). This skeleton is a set of connected
surfaces generated from iterative homotopic erosions scalping
the mold while preserving its initial topology. This process can
be combined with a watershed algorithm using MR intensities
as altitude in order to impose the localization of the skeleton in
the crevasse corresponding to the cerebrospinal fluid filling
up the folds (Mangin et al., 2004). The skeleton is finally split
into elementary pieces at the level of the junctions between
folds or in case of local depth minima along the fold bottom
indicating the fusion between several primal folding entities.
A sibling approach restricts the skeletonization to the bounding hull of the cortex (Le Goualher et al., 1999). The resulting
2-D skeleton is split at junction points in order to define the
superior trace of each fold. Note that the few folds that do not
reach the bounding hull are missed by this process. Then, the
initial curve grows until the bottom of the fold in order to yield
a 2-D parameterized surface, which is the strength of the
approach (Vaillant & Davatzikos, 1997). Finally, these different methods represent the topography of the folding pattern as
a graph: The nodes are the elementary folds and the links
represent junctions or the fact that two parallel folds build up
a gyrus.
Some approaches put the focus on the deepest part of the
3-D folding geometry. For this purpose, the representation can
rely on the bottom lines of the folds defined from the 3-D
skeleton using simple topological considerations (Lohmann,
1998; Mangin, Regis, et al., 1995; Mangin, Frouin, Bloch,
Regis, & Lopez-Krahe, 1995). When the key focus is not even
the bottom lines but the deepest points of the folding, an
alternative to the skeleton-based strategy lies in depth-based
processing. For instance, a watershed-based algorithm using
depth as altitude can be used to split the negative mold of
whiter matter in the so-called sulcal basins associated with
depth local maxima (Lohmann & von Cramon, 2000). The
main difficulty is the pruning of the basins in order to keep
only the morphologically meaningful ones.
The end of the nineties coincided with a shift from volumetric processing to surface-based processing, thanks to the
maturity of the pipelines generating spherical cortical surfaces
(Dale, Fischl, & Sereno, 1999). This transition has increased
the trend to focus on the depth of the folding, because the
embedding of the cortical surface into the 3-D space is less
accessible once the cortex is represented as a 2-D mesh. When
dealing with cortical surface meshes, the bottom lines of the
sulci are detected using variants of surface-based skeletonization algorithms acting on buried regions defined from depth or
curvature (Kao et al., 2007; Li, Guo, Nie, & Liu, 2010; Seong
et al., 2010; Shi, Thompson, Dinov, & Toga, 2008). These
methods differ mainly not only in the way they combine
depth and curvature to achieve reliable localization of the
bottom lines but also in their pruning strategy to get rid of
spurious detections. Semiautomatic approaches have been
proposed to delineate the optimal sulcus bottom line from
manually selected extremities (Le Troter, Auzias, & Coulon,
2012; Shattuck et al., 2009). A strong advantage of the
368
surface-based strategies is their sensitivity to dimples, namely,

primal sketches of the folding visible in depth or curvature
maps. The dimples cannot be detected by 3-D skeletonization
algorithms because they are not completely folded (see
Figure 4(b)), which is problematic for studying the developing
brain (Dubois, Benders, Borradori-Tolsa, et al., 2008; Dubois,
Benders, Cachia, et al., 2008) or tertiary sulci.
While most of the bottom-up strategies aim at designing
methods performing automatic recognition of the sulci of the
standard nomenclature, a few approaches are dedicated to
research programs questioning the current models of the sulcal
anatomy. These approaches aim at inferring a new model of
the folding pattern overcoming the ambiguities raised by the
interindividual variability (see Figure 4). They mainly target
local maxima of cortical depth, which are supposed to result
from gyri buried into the folds (see Figure 5). The variable
depth of these buried gyri partly explains interindividual variability (Regis et al., 2005). Thanks to the spherical topology of
the cortical surface, the analogy with geology leads to simple
adaptations of the watershed notion to segregate the surface
into depth-based patches, the sulcal basins, which mimic
catchment basins, namely, geographic areas with a common
outlet for the surface runoff (Rettmann, Han, Xu, & Prince,
2002; Yang & Kruggel, 2008). The most recent approaches do
not even pay attention to the spatial extent of the catchment
basins but deal with simplistic representations based on the
deepest points called sulcal pits (Im et al., 2010; Lohmann, von
Cramon, & Colchester, 2008; Meng, Li, Lin, Gilmore, & Shen,
2014; Operto et al., 2012).
In order to enrich the representations and to postpone the
pruning to the sulcus recognition or model inference stage, a
hierarchical strategy inspired by the field of scale space has
(a)
been proposed (Cachia et al., 2001). In the same spirit,

graph-based approaches merging surface-based, line-based,
and point-based representations are in gestation (Bao, Giard,
Tourville, & Klein, 2012). Finally, in the context of developmental studies, an original approach dedicated to longitudinal
data has been designed to focus on the seeds of the folding
process, namely, the points of the cortical surface corresponding to local maxima of the folding rate (Lefe`vre et al., 2009).
Sulcus Recognition
Most of the graphic representations yielded by the pipelines of
the previous section include oversegmentation of the sulci of
the nomenclature. Indeed, the geometry of a sulcus often
includes subdivisions related to branches or interruptions.
Then, the sulcus recognition requires a reconstruction process
from the set of building blocks listed in the representation,
which amounts to a labeling with the sulcus names of the
nomenclature (see Figures 2 and 4). The number of names
involved in the labeling ranges from 10 to 65 in each hemisphere, according to the richness of the sulcus model. The
labeling can be viewed as a many-to-one matching between
the representation built for a given subject and the model of
the sulci. The model of the sulci can be simply a learning data
set of individual representations labeled by a human expert
(Lyu et al., 2010) or a probabilistic representation of the sulcus
variability inferred from this learning data set: maps of the
spatial variability of each sulcus after optimal alignment across
the data set (Perrot, Rivie`re, & Mangin, 2011) or different kinds
of random graph modeling the joint variability of pairs of sulci
(Mangin, Regis, et al., 1995; Mangin, Frouin, Bloch, Regis, &
(b)
(c)
Figure 4 Standard sulcus nomenclature. (a) Three frontal lobes; (b) the skeleton of the negative brain mold used to detect folds; (1) undetected
dimples; (c) labeling of the folds with the standard sulcus nomenclature (red, central; yellow, precentral; green, superior frontal; cyan, intermediate
frontal; violet, inferior frontal; blue, sylvian valley, etc.).
369
(a)
(b)
(c)
Figure 5 Toward an alphabet of the folding pattern. (a) White matter of the Figure 4 frontal lobes; (2) buried gyri also called plis de passage;
(b, c) labeling of the folds with the sulcal roots nomenclature corresponding to putative indivisible entities. Reproduced from Regis, J., Mangin, J.,
Ochiai, T., Frouin, V., Riviere, D., Cachia, A., Tamura, M., & Samson, Y. (2005). "Sulcal root" generic model: A hypothesis to overcome the
variability of the human cortex folding patterns. Neurologia Medico-Chirurgica, 45(1), 117.
Lopez-Krahe, 1995; Riviere et al., 2002; Shi et al., 2009; Yang &
Kruggel, 2009).
The labeling of the building blocks is driven by an optimization process often casted into a Bayesian framework aiming
at maximizing the similarity between the sulci defined by the
labeling and their model. With this regard, the multiatlas
strategy of Lyu et al. has a specific status since the model is
the set of bottom lines of several instances of each sulcus
efficiently matched with the candidate sulci using a spectral
method. For the other approaches, the global similarity measure to be optimized is a sum of local similarity measures.
These local measures can stem from local registrations between
a fold and probabilistic maps of the sulci (Perrot et al., 2011),
the output of a multilayer perceptron fed with features describing the shape of sulci or pairs of sulci and trained on the
learning database (Riviere et al., 2002), and more standard
potential functions acting on shape features like localization,
orientation, length, moments, or wavelet coefficients (Mangin,
Regis, et al., 1995; Mangin, Frouin, Bloch, Regis, & LopezKrahe, 1995; Shi, Tu, et al., 2009; Yang & Kruggel, 2009). For
all these methods, dealing with graphic representations rather
than images allows the optimization process to rely on sophisticated schemes like simulated annealing (Riviere et al., 2002),
genetic algorithms (Yang & Kruggel, 2009), or belief propagation (Shi, Tu, et al., 2009b).
The lack of gold standard and the fact that only two of these
methods using the same bottom-up pipeline are distributed to
the community prevent simple comparisons (http://brainvisa.
info) (Perrot et al., 2011; Riviere et al., 2002). The leave-oneout validation versus manual labeling of the method of Perrot
et al. has shown an 86% mean recognition rate across the 65
sulci provided in each hemisphere. The performance varies

from 95% for the largest primary sulci to 70% for the most
variable secondary sulci. Users of this method interested in
morphometry studies report the processing of more than
10 000 subjects.
Note that the main risk of the bottom-up strategies is undersegmentation, namely, situations where a building block includes
the frontier between two sulci. Overcoming this situation probably requires a top-down complementary strategy that is not explicitly embedded in current methods, except in the multiatlas
strategy that allows refinement of the individual representations
by analogy with the closest atlas (Lyu et al., 2010). Note also that
the strategy of Shi et al. aims at defining sulci as continuous curves,
to mimic manual tracing, which leads the method to fill up the
gaps existing in bottom-up representations (Shi, Tu, et al., 2009b).
The methods dealing with point-based representations shall be
protected from oversegmentation. In reality, they are prone to a
sibling issue: the sulcal pits or sulcal basin centroids of the model
are not detected in all brains. Nevertheless, dealing with points is
more comfortable than dealing with sulci because the many-toone matching problem becomes a one-to-one matching problem,
resulting in simpler formulations (Im et al., 2011; Lohmann &
von Cramon, 2000).
Inference of New Models of the Folding Pattern?

The success of the multiatlas strategy in neuroimaging
(Heckemann et al., 2006) could lead to consider that the future
of sulcus recognition is in pattern matching methods informed
by a very large data set of manually labeled sulci, in the spirit of
370
the approach of Lyu et al. (2010). This data set would play the
same role as the huge pools of translated documents of institutions like the European Union for automatic language translation. Indeed, todays most advanced translation services rely
on statistical pattern matching rather than on teaching the
rules of human language to the computer. To deal with the
lack of gold standard, the learning dataset could stem from a
consensus-based labeling effort of the community of neuroanatomists in order to generate the body of information
required for the machine to do the job correctly whatever the
brain idiosyncrasies. But with our current understanding of the
variability, would the consensual labeling of unusual patterns
be really reliable? Unlike the field of language translation,
mimicking human behavior is not necessarily the best strategy
for the computer.
It should be noted that the sulcal pits model used to label
individual sulcal pits does not stem from the anatomical literature but from the field of computational anatomy. The pits in
the model are clusters of individual pits detected after nonlinear alignment of a large set of cortical surfaces (Im et al.,
2010). The sulcal pits model is in good agreement with the
sulcal roots model proposed by a human anatomist as an
alphabet of putative indivisible atomic entities supposed to
be stable across individuals because of a developmental origin
(see Figure 5; Regis et al., 2005). The sulcal pits model provides
a good foretaste of the potential of computational anatomy for
paving the way toward new more objective models of the
folding patterns. Advances in the understanding of
the folding dynamics could also largely contribute to this
research program. For instance, the intrinsic geometry of the
cortical surface provided by the first eigenvectors of the
LaplaceBeltrami operator may be intimately associated with
the folding process. The associated coordinate system could be
the ideal alignment between subjects before model inference
or sulcus recognition (Shi, Dinov, & Toga, 2009; Shi, Sun, Lai,
Dinov, & Toga, 2010; Shi, Tu, et al., 2009).
The convoluted shape of the cerebral cortex is a challenge
for human binocular vision. In return, computer vision systems can be endowed with a dedicated architecture including
3-D retina and 3-D higher-level vision areas. Furthermore, this
vision architecture dedicated to the cortical surface can be
duplicated without limit, which overcomes the working memory overload disturbing human experts trying to model the
folding pattern variability. Manifold learning technology
applied on massive databases in the spirit of Ono et al. could
help us to segregate the different folding patterns existing in the
population, in order to trigger a research program aiming at
matching these patterns according to architectural clues provided by other imaging modalities (Ono et al., 1990; Sun,
Perrot, Tucholka, Riviere, & Mangin, 2009). Therefore, computational anatomy should be the perfect assistant to support the
neuroanatomists in their quest for a better model of the
variability.
Acknowledgments
This work was supported by the European FET Flagship project
Human Brain Project (SP2), the French Agence Nationale de
la Recherche (ANR-09-BLAN-0038-01 BrainMorph, ANR-14
APEX, and ANR-12JS03-001-01 MoDeGy), and the French

Plan Alzheimer Foundation (CATI multicenter imaging
platform).

Development of the Basal Ganglia and the Basal Forebrain; Embryonic
and Fetal Development of the Human Cerebral Cortex; Fetal and
Postnatal Development of the Cortex: MRI and Genetics; Gyrification in
the Human Brain; Sulci as Landmarks; INTRODUCTION TO
Cerebral Cortex.
References
38(1), 95113.
Auzias, G., Colliot, O., Glaune`s, J. A., Perrot, M., Mangin, J. F., Trouve, A., et al. (2011).
Diffeomorphic brain registration under exhaustive sulcal constraints. IEEE
Auzias, G., Lefe`vre, J., Le Troter, A., Fischer, C., Perrot, M., Regis, J., et al. (2013).
Model-driven harmonic parameterization of the cortical surface: HIP-HOP. IEEE
Bao, F., Giard, J., Tourville, J., & Klein, A. (2012). Automated extraction of nested
sulcus features from human brain MRI data. In IEEE Engineering in Medicine and
Biology Society (pp. 44294433).
Cachia, A., Borst, G., Vidal, J., Fischer, C., Pineau, A., Mangin, J. F., et al. (2014). The
shape of the ACC contributes to cognitive control efficiency in preschoolers. Journal
of Cognitive Neuroscience, 26(1), 96106.
Cachia, A., Mangin, J., Rivie`re, D., Boddaert, N., Andrade, A., Kherif, F., et al. (2001).
A mean curvature based primal sketch to study the cortical folding process from
antenatal to adult brain. In Medical image computing and computer-assisted
interventionMICCAI 2001 (pp. 897904).
Segmentation and surface reconstruction. NeuroImage, 9(2), 179194.
Destrieux, C., Fischl, B., Dale, A., & Halgren, E. (2010). Automatic parcellation of
Dubois, J., Benders, M., Borradori-Tolsa, C., Cachia, A., Lazeyras, F.,
Leuchter, R. H.-V., et al. (2008). Primary cortical folding in the human newborn: An
early marker of later functional development. Brain, 131(8), 20282041.
Dubois, J., Benders, M., Cachia, A., Lazeyras, F., Leuchter, R. H.-V., Sizonenko, S. V.,
et al. (2008). Mapping the early cortical folding process in the preterm newborn
brain. Cerebral Cortex, 18(6), 14441454.
Cortical folding patterns and predicting cytoarchitecture. Cerebral Cortex, 18(8),
19731980.
Germanaud, D., Lefe`vre, J., Toro, R., Fischer, C., Dubois, J., Hertz-Pannier, L., et al.
(2012). Larger is twistier: Spectral analysis of gyrification (SPANGY) applied to
adult brain size polymorphism. NeuroImage, 63(3), 12571272.
Heckemann, R. A., Hajnal, J. V., Aljabar, P., Rueckert, D., & Hammers, A. (2006).
Automatic anatomical brain MRI segmentation combining label propagation and
decision fusion. NeuroImage, 33(1), 115126.
Im, K., Choi, Y. Y., Yang, J. J., Lee, K. H., Kim, S. I., Grant, P. E., et al. (2011). The
relationship between the presence of sulcal pits and intelligence in human brains.
NeuroImage, 55(4), 14901496.
Im, K., Jo, H. J., Mangin, J.-F., Evans, A. C., Kim, S. I., & Lee, J.-M. (2010). Spatial
distribution of deep sulcal landmarks and hemispherical asymmetry on the cortical
surface. Cerebral Cortex, 20(3), 602611.
Joshi, A. A., Pantazis, D., Li, Q., Damasio, H., Shattuck, D. W., Toga, A. W., et al. (2010).
Sulcal set optimization for cortical surface registration. NeuroImage, 50(3), 950959.
Kao, C. Y., Hofer, M., Sapiro, G., Stem, J., Rehm, K., & Rottenberg, D. A. (2007). A
geometric method for automatic extraction of sulcal fundi. IEEE Transactions on
Medical Imaging, 26(4), 530540.
Le Goualher, G., Procyk, E., Collins, D., Venugopal, R., Barillot, C., & Evans, A. (1999).
Automated extraction and variability analysis of sulcal neuroanatomy. IEEE
Le Troter, A., Auzias, G., & Coulon, O. (2012). Automatic sulcal line extraction on
cortical surfaces using geodesic path density maps. NeuroImage, 61(4), 941949.

Lefe`vre, J., Leroy, F., Khan, S., Dubois, J., Huppi, P., Baillet, S., et al. (2009).
Identification of growth seeds in the neonate brain through surfacic Helmholtz
decomposition. Information Processing in Medical Imaging, 21, 252263.
Lefe`vre, J., & Mangin, J.-F. (2010). A reactiondiffusion model of human brain
development. PLoS Computational Biology, 6(4), e1000749.
Li, G., Guo, L., Nie, J., & Liu, T. (2010). An automated pipeline for cortical sulcal fundi
extraction. Medical Image Analysis, 14(3), 343359.
Lohmann, G. (1998). Extracting line representations of sulcal and gyral patterns in MR
images of the human brain. IEEE Transactions on Medical Imaging, 17(6),
10401048.
Lohmann, G., & von Cramon, D. Y. (2000). Automatic labelling of the human cortical
surface using sulcal basins. Medical Image Analysis, 4(3), 179188.
Lohmann, G., von Cramon, D. Y., & Colchester, A. C. (2008). Deep sulcal landmarks
provide an organizing framework for human cortical folding. Cerebral Cortex, 18(6),
14151420.
Lyu, I., Seong, J. K., Shin, S. Y., Im, K., Roh, J. H., Kim, M. J., et al. (2010). Spectralbased automatic labeling and refining of human cortical sulcal curves using expertprovided examples. NeuroImage, 52(1), 142157.
Mangin, J.-F., Frouin, V., Bloch, I., Regis, J., & Lopez-Krahe, J. (1995). From 3D
magnetic resonance images to structural representations of the cortex topography
using topology preserving deformations. Journal of Mathematical Imaging and
Vision, 5(4), 297318.
Mangin, J. F., Jouvent, E., & Cachia, A. (2010). In-vivo measurement of cortical
morphology: Means and meanings. Current Opinion in Neurology, 23(4),
359367.
Mangin, J., Regis, J., Bloch, I., Frouin, V., Samson, Y., & Lopez-Krahe, J. (1995). A
MRF based random graph modelling the human cortical topography. In Computer
vision, virtual reality and robotics in medicine (pp. 177183).
Mangin, J. F., Riviere, D., Cachia, A., Duchesnay, E., Cointepas, Y.,
Papadopoulos-Orfanos, D., et al. (2004). Object-based morphometry of the cerebral
cortex. IEEE Transactions on Medical Imaging, 23(8), 968982.
Meng, Y., Li, G., Lin, W., Gilmore, J. H., & Shen, D. (2014). Spatial distribution and
longitudinal development of deep cortical sulcal landmarks in infants. NeuroImage,
100, 206218.
Ono, M., Kubik, S., & Abarnathey, C. D. (1990). Atlas of the cerebral sulci. New York:
Georg Thieme.
Operto, G., Auzias, G., Le Troter, A., Perrot, M., Riviere, D., Dubois, J., et al. (2012).
Structural group analysis of cortical curvature and depth patterns in the developing
brain. In IEEE ISBI (pp. 422425).
Perrot, M., Rivie`re, D., & Mangin, J. F. (2011). Cortical sulci recognition and spatial
normalization. Medical Image Analysis, 15(4), 529550.
Petrides, M. (2012). The human cerebral cortex: An MRI atlas of the sulci and gyri in
MNI stereotaxic space. Amsterdam: Academic Press.
Plaze, M., Paille`re-Martinot, M. L., Penttila, J., Januel, D., de Beaurepaire, R.,
Bellivier, F., et al. (2011). "Where do auditory hallucinations come from?" A brain
morphometry study of schizophrenia patients with inner or outer space
hallucinations. Schizophrenia Bulletin, 37(1), 212221.
Regis, J., Mangin, J., Ochiai, T., Frouin, V., Riviere, D., Cachia, A., et al. (2005). "Sulcal
root" generic model: A hypothesis to overcome the variability of the human cortex
folding patterns. Neurologia Medico-Chirurgica, 45(1), 117.
Reillo, I., de Juan Romero, C., Garca-Cabezas, M., & Borrell, V. (2011). A role for
intermediate radial glia in the tangential expansion of the mammalian cerebral
cortex. Cerebral Cortex, 21(7), 16741694.
Rettmann, M. E., Han, X., Xu, C., & Prince, J. L. (2002). Automated sulcal segmentation
using watersheds on the cortical surface. NeuroImage, 15(2), 329344.
Riviere, D., Mangin, J., Papadopoulos-Orfanos, D., Martinez, J., Frouin, V., & Regis, J.
(2002). Automatic recognition of cortical sulci of the human brain using a
congregation of neural networks. Medical Image Analysis, 6(2), 7792.
371
Schaer, M., Cuadra, M. B., Tamarit, L., Lazeyras, F., Eliez, S., & Thiran, J. P. (2008). A
surface-based approach to quantify local cortical gyrification. IEEE Transactions on
Seong, J. K., Im, K., Yoo, S. W., Seo, S. W., Na, D. L., & Lee, J. M. (2010). Automatic
extraction of sulcal lines on cortical surfaces based on anisotropic geodesic
distance. NeuroImage, 49(1), 293302.
Shattuck, D. W., Joshi, A. A., Pantazis, D., Kan, E., Dutton, R. A., Sowell, E. R., et al.
(2009). Semi-automated method for delineation of landmarks on models of the
cerebral cortex. Journal of Neuroscience Methods, 178(2), 385392.
Shi, Y., Dinov, I., & Toga, A. W. (2009). Cortical shape analysis in the Laplace-Beltrami
feature space. Medical Image Computing and Computer-Assisted Intervention,
12(Pt 2), 208215.
Shi, Y., Sun, B., Lai, R., Dinov, I., & Toga, A. W. (2010). Automated sulci identification
via intrinsic modeling of cortical anatomy. Medical Image Computing and
Computer-Assisted Intervention, 13(Pt 3), 4956.
Shi, Y., Thompson, P. M., Dinov, I., & Toga, A. W. (2008). Hamilton-Jacobi skeleton on
cortical surfaces. IEEE Transactions on Medical Imaging, 27(5), 664673.
Shi, Y., Tu, Z., Reiss, A. L., Dutton, R. A., Lee, A. D., Galaburda, A. M., et al. (2009).
Joint sulcal detection on cortical surfaces with graphical models and boosted priors.
Sun, T., & Hevner, R. F. (2014). Growth and folding of the mammalian cerebral cortex:
From molecules to malformations. Nature Reviews Neuroscience, 15(4), 217232.
Sun, Z. Y., Kloppel, S., Rivie`re, D., Perrot, M., Frackowiak, R., Siebner, H., et al. (2012).
The effect of handedness on the shape of the central sulcus. NeuroImage, 60(1),
332339.
Sun, Z., Perrot, M., Tucholka, A., Riviere, D., & Mangin, J. (2009). Constructing a
dictionary of human brain folding patterns. In: MICCAI Proceedings, Berlin,
Hiedelberg: Springer Verlag, LNCS-5762.
Taber, L. A. (2014). Morphomechanics: Transforming tubes into organs. Current
Opinion in Genetics and Development, 27C, 713.
Thompson, P., & Toga, A. W. (1996). A surface-based technique for warping threedimensional images of the brain. IEEE Transactions on Medical Imaging, 15(4),
402417.
Toga, A. W., & Thompson, P. M. (2003). Temporal dynamics of brain anatomy. Annual
Review of Biomedical Engineering, 5, 119145.
Toro, R., & Burnod, Y. (2005). A morphogenetic model for the development of cortical
convolutions. Cerebral Cortex, 15(12), 19001913.
Toro, R., Perron, M., Pike, B., Richer, L., Veillette, S., Pausova, Z., et al. (2008).
Brain size and folding of the human cerebral cortex. Cerebral Cortex, 18(10),
23522357.
Vaillant, M., & Davatzikos, C. (1997). Finding parametric representations of the
cortical sulci using an active contour model. Medical Image Analysis, 1(4),
295315.
Van Essen, D. C. (1997). A tension-based theory of morphogenesis and compact wiring
in the central nervous system. Nature, 385(6614), 313318.
Van Essen, D. C., Drury, H. A., Joshi, S., & Miller, M. I. (1998). Functional and
structural mapping of human cerebral cortex: Solutions are in the surfaces.
95(3), 788795.
Weiner, K. S., Golarai, G., Caspers, J., Chuapoco, M. R., Mohlberg, H., Zilles, K., et al.
(2014). The mid-fusiform sulcus: A landmark identifying both cytoarchitectonic
and functional divisions of human ventral temporal cortex. NeuroImage, 84, 453465.
Yang, F., & Kruggel, F. (2008). Automatic segmentation of human brain sulci. Medical
Image Analysis, 12(4), 442451.
Yang, F., & Kruggel, F. (2009). A graph matching approach for labeling brain sulci
using location, orientation, and shape. Neurocomputing, 73, 179190.
Zilles, K., Palomero-Gallagher, N., & Amunts, K. (2013). Development of cortical
folding during evolution and ontogeny. Trends in Neurosciences, 36(5), 275284.
K Van Leemput, Harvard Medical School, Boston, MA, USA
O Puonti, Technical University of Denmark, Lyngby, Denmark
Abbreviations
EM
MAP
ML
Expectation-maximization
Computational methods for automatically segmenting magnetic resonance (MR) images of the brain have seen tremendous advances in recent years. So-called tissue classification
techniques, aimed at extracting the three main brain tissue
classes (white matter, gray matter, and cerebrospinal fluid),
are now well established. In their simplest form, these methods
classify voxels independently based on their intensity alone,
although much more sophisticated models are typically used
in practice (Anbeek, Vincken, van Bochove, van Osch, & van der
Grond, 2005; Ashburner & Friston, 1997, 2005; Awate, Tasdizen,
Foster, & Whitaker, 2006; Greenspan, Ruf, & Goldberger, 2006;
Marroquin, Vemuri, Botello, Calderon, & Fernandez-Bouzas,
2002; Pham & Prince, 1999; Rajapakse, Giedd, & Rapoport,
1997; Van Leemput, Maes, Vandermeulen, & Suetens,
1999a,1999b; Warfield, Kaus, Jolesz, & Kikinis, 2000; Wells,
Grimson, Kikinis, & Jolesz, 1996; Zeng, Staib, Schultz, &
Duncan, 1999; Zhang, Brady, & Smith, 2001).
This article aims to give an overview of often-used computational techniques for brain tissue classification. Although
other methods exist, we will concentrate on Bayesian modeling approaches, in which generative image models are constructed and subsequently inverted to obtain automated
segmentations. This general framework encompasses a large
number of segmentation methods, including those implemented in widely used software packages such as SPM, FSL,
and FreeSurfer, as well as techniques for automatically segmenting many more brain structures than merely the three
main brain tissue types only (Ashburner & Friston, 2005;
Fischl et al., 2002; Fischl, Salat et al., 2004; Fischl, van der
Kouwe et al., 2004; Guillemaud & Brady, 1997; Held et al.,
1997; Lorenzo-Valdes, Sanchez-Ortiz, Mohiaddin, & Rueckert,
2004; Marroquin et al., 2002; Menze et al., 2010; Pohl,
Fisher, Grimson, Kikinis, & Wells, 2006; Pohl et al., 2007;
Prastawa, Bullitt, Ho, & Gerig, 2004; Sabuncu, Yeo, Van
Leemput, Fischl, & Golland, 2010; Van Leemput, Maes, Vandermeulen, Colchester, & Suetens, 2001; Van Leemput et al.,
1999b; Wells et al., 1996; Xue et al., 2007; Zhang et al.,
2001).
We first introduce the general modeling framework and the
specific case of the Gaussian mixture model. We then discuss
maximum likelihood (ML) parameter estimation and the
expectationmaximization (EM) algorithm and conclude the
article with further model extensions such as MR bias field
models and probabilistic atlases.
Maximum a posteriori
Maximum likelihood
Generative Modeling Framework

Brain MR segmentation methods are often based on so-called
generative models, that is, probabilistic models that describe
how images can be generated synthetically. Such models generally consist of two parts:
A segmentation prior that makes predictions about where

neuroanatomical structures typically occur throughout the
image. Let l (l1, . . ., lI)T be a (vectorized) label image with a
total of I voxels, with li 2 {1, . . ., K} denoting the one of K
possible labels assigned to voxel i, indicating which of the K
anatomical structures the voxel belongs to. For the purpose
of tissue classification, there are typically K 3 labels,
namely, white matter, gray matter, and cerebrospinal
fluid. The segmentation prior then consists of a probability
distribution p(l|ul) that typically depends on a set of parameters ul.
A likelihood function that predicts how any given label
image, where each voxel is assigned a unique anatomical
label, translates into an image where each voxel has an
intensity. This is essentially a (often very simplistic) model
of how an MR scanner generates images from known anatomy: given a label image l, a corresponding intensity image
d (d1, . . ., dI)T is obtained by random sampling from some
probability distribution p(d| l, ud) with parameters ud,
where di denotes the MR intensity in voxel i.
In summary, the generative model is fully specified by two

distributions p(l|ul) and p(d|l, ud), which often depend on
parameters u (uTl , uTd )T that are either assumed to be known
in advance or, more frequently, need to be estimated from the
image data itself. The exact form of the used distributions
depends on the segmentation problem at hand. In general,
the more realistic the models, the better the segmentations
that can be obtained with them.
Once the exact generative model has been chosen and
appropriate values u^ for its parameters are known, properties
of the underlying segmentation of an image can be inferred
by

inspecting the posterior probability distribution p ljd, u^ .
Using Bayes rule, this distribution is given by
http://dx.doi.org/10.1016/B978-0-12-397025-1.00308-0

p djl, u^d p lju^l

p ljd, u^
p dju^
[1]
373
374
INTRODUCTION TO METHODS AND MODELING | Tissue Classification

P
with p dju^ l p djl, u^d p lju^l . For instance, one might
look for the segmentation ^l that has the maximum a posteriori
(MAP) probability

^l arg max p ljd, u^
[2]
l
or estimate the volume of the anatomical structure corresponding to label k by assessing its expected value

X
Vk lp ljd, u^
[3]
pdjl, ud

pdi jli , ud N di jmli , s2li
pljul
pli
[5]
where the parameters ul (p1, . . ., pK)T consist of a set of probP

abilities pk satisfying pk 0, 8 k and kpk 1. In other words,
this model assumes that the labels are assigned to the voxels
independently from one another, that is, the probability that a
certain label occurs in a particular voxel is unaffected by the
labels assigned to other voxels (eqn [4]) and each label occurs,
on average, with a relative frequency of pk (eqn [5]).
For the likelihood function, it is assumed that the intensity
in each voxel only depends on the label in that voxel and not
on that in other voxels
[7]
where
2
N djm, s
where Vk(l) counts the number of voxels that have label k in l.
[6]
and that the intensity distribution associated with each label k

is Gaussian with mean mk and variance s2k :
A very simple generative model that is nevertheless quite useful

in practice is the so-called Gaussian mixture model. In this
model, the segmentation prior is of the form
Y
pli jul
[4]
pljul
pdi jli ,ud
Gaussian Mixture Model
"
#
1
d m2
p exp
2s2
2ps2
[8]
and ud (m1, . . ., mK, s21, . . . s2K)T.

It is instructive to write down the probability with which
this model generates a given image d:
X
pdj l, ud plj ul
pdj u
l "
#
Y
X Y
Y
2
N di jmli , sli
pli
pdi ju
[9]
l
with
pdju

N djmk ,s2k pk
[10]
Equation [10] explains why this model is called the Gaussian mixture model: the intensity distribution in any voxel,
independent of its spatial location, is given by the same linear
superposition of Gaussians. Since no spatial information is
encoded in the model, it can directly be visualized as a way
to approximate the histogram, as shown in Figure 1.
Because of the assumption of statistical independence
between voxels, the segmentation posterior (eqn [1]) reduces
to a simple form that is factorized (i.e., appears as a product)
over the voxels:
Figure 1 In the Gaussian mixture model, the histogram is described as a linear superposition of Gaussian distributions: (a) MR scan of the head, after
removing all non-brain tissue and other pre-processing steps; and (b) corresponding histogram and its representation as a sum of Gaussians.
375
Figure 2 Visualization of the segmentation posterior corresponding to the data and model of figure 1. High and low intensities correspond to
high and low probabilities, respectively.

Q
Q

p djl, u^d p lju^l
^li , s^2li
^li
i N di jm
ip

p ljd, u^
QP
2
^k , s^k p^k
p dju^
i
k N di jm

Y
p li jdi , u^
where
[11]

N di jm^li , s^2li p^li

p li jdi , u^ P
^k , s^2k p^k
k N di jm
[12]
Therefore, the segmentation posterior is fully specified by

each voxels k posterior probabilities of belonging to each
structure; such segmentation posteriors can be visualized as
images where high and low intensities correspond to high
and low probabilities, respectively. The segmentation corresponding to the image and Gaussian mixture model of
Figure 1 is visualized in Figure 2 this way. It is worth noting
that the sum of all the structures
posterior probabilities adds to
P
one in each voxel: k p kjdi , u^ 1, 8i.
Because of the factorized form of the segmentation posterior, the MAP segmentation (eqn [2]) is simply given by

^l arg max p ljd, u^ arg max p li jdi , u^
[13]
l
l1 , ..., lI
that is, each voxel is assigned exclusively to the label with the
highest posterior probability. Similarly, the expected volume of
the anatomical structure corresponding to label k is given by
(eqn [3])

X

X
Vk lp ljd, u^
p kjdi , u^
[14]
l
that is, a soft count of voxels belonging to the structure, where

voxels contribute according to their posterior probability of
belonging to that structure.
Parameter Optimization Using the EM Algorithm

So far, we have assumed that appropriate values u^ of the model
parameters are known in advance. One possible strategy to
estimate these parameters is to manually click on some representative points in the image to be segmented or in similar
images obtained from other subjects and then collect statistics on the intensity of the selected voxels. In general, however,
such a strategy is cumbersome for such a versatile imaging
modality as MR, where intensities do not directly correspond
to physical properties of the tissue being scanned. By merely
altering the imaging protocol, upgrading the scanner, or collecting images from different scanner models or manufacturers, the values of u^ become inappropriate and need to be
constructed again using manual interaction.
This difficulty can be avoided by estimating appropriate
values for the model parameters automatically from each individual scan. This can be accomplished by estimating the
parameters that maximize the so-called likelihood function
p(d|u), which expresses how probable the observed image d
is for different settings of the parameter vector u:
u^ arg max pdju arg max log pdju
u
[15]
The last step is true because the logarithm is a monotonically

increasing function of its argument; it is used here because it
simplifies the subsequent mathematical analysis and also avoids
numerical underflow problems in practical computer implementations. The parameter vector u^ resulting from eqn [15] is commonly called the maximum likelihood (ML) parameter estimate.
Maximizing the (log) likelihood function in image segmentation problems is a nontrivial optimization problem for which
iterative numerical algorithms are needed. Although a variety of
standard optimization methods could potentially be used, for
the Gaussian mixture model, a dedicated and highly effective
optimizer is available in the form of the so-called expectation
maximization algorithm (EM). The EM algorithm belongs to a
family of optimization methods that work by repeatedly constructing a lower bound to the objective function, maximizing
that lower bound, and repeating the process until convergence
(Hunter & Lange, 2004). This process is illustrated in Figure 3.
~
For a given starting estimate of the model
parameters u, a
~ is constructed that
function of the model parameters Q uju
~
equals the log likelihood function at u
376
log p(d|q )
log p(d|q )
q
~
q
(Current
(a) estimate)
q
(b)
log p(d|q )
~
q
(Current
estimate)
log p(d|q )
(c)
~
q
(Current
estimate)
~
q
(Current
estimate)
q
(d)
log p(d|q )
log p(d|q )
(e)
~
q
(Current
estimate)
q
(f)
~
q q
(Current
estimate)
Figure 3 In the EM algorithm the maximum likelihood parameters are sought by repeatedly constructing a lower bound to the log likelihood function,
in such a way that the lower bound touches the log likelihood function exactly at the current parameter estimate (a). Subsequently the parameter
estimate is updated to the parameter vector that maximizes the lower bound (b). A new lower bound is then constructed at this new location (c) and
maximized again (d), and so forth ((e) and (f)), until convergence. In these plots, the log likelihood function is represented by a full line, and the
successive lower bounds with a broken line.

~u
~ log p dju
~
Q uj
[16]
but that otherwise never exceeds it

~ log pdju, 8u
Q uju
[17]

~ is then computed
The parameter vector maximizing Q uju
~ after which the
and used as the new parameter estimate u,
whole process is repeated. Critically, because of eqns [16]
~ to the parameter vector that
and [17], updating the estimate u
maximizes the lower bound automatically guarantees that the
log likelihood function increases, by at least the same amount
~
as the lower bound has increased. The consecutive estimates u
obtained this way are therefore increasingly better estimates of
the ML parameters one is guaranteed to never move in the
wrong direction in parameter space. This is a highly desirable
property for a numerical optimization algorithm.
While it is of course always possible to construct a lower
bound to an objective function, nothing is gained if optimizing
the lower bound is not significantly easier and/or faster to
perform than optimizing the objective function directly. However, in the case of the Gaussian mixture model, it is possible to
construct a lower bound for which the parameter vector maximizing it is given directly by analytic expressions. Therefore,
the resulting algorithm effectively breaks up a difficult maximization problem (of the log likelihood function) into many
smaller ones (of the lower bound) that are trivial to solve.
The trick exploited by the EM algorithm to construct its
lower bound is based on the property of the logarithm that it
is a concave function, that is, every chord connecting two
points on its curve lies on or below that curve. Mathematically,
this means that
log wx1 1 wx2 wlog x1 1 wlog x2
[18]
for any two points x1 and x2 and 0 w 1. It is trivial to show

that this also generalizes to more than two variables (the socalled Jensens inequality):
!
X
X
log
w k xk
wk log xk
[19]
k
where wk 0 and kwk 1, for any set of points {xk}. This can
now be used to construct a lower bound to the likelihood

function of the Gaussian
mixture
as follows. Recalling
model

Q P
2
that pdju i
k N di jmk , sk pk (eqns [9] and [10]), we
have that
"
#!
Y X

2
log pdju log
N di jmk , sk pk
[20]
i
log
X
i
log
"
X
di jmk ,s2k
#
pk
"

X N di jmk , s2 pk
"
X X
[21]
wik
#
wik

#

N di jmk , s2k pk

wik
i
k
|{z}
~
Quju
wik log
[22]
[23]
P i
for any set of weights {wik} that satisfy wik 0 and
kwk 1
(the last step
relies
on eqn [19]). We now have a lower bound
~ that satisfies eqn [17], but not eqn [16], so we
function Q uju
are not done yet. Instead of randomly assigning any valid K
weights wik to each voxel i (one weight for each label k), we can
satisfy eqn [16] by choosing the weights so that
wik P

~k
N di j~
m ,s
~2 p
k k
2
0
0N
~
~ k0
d
j~
m
,
s
p
i k
k
k0
[24]
By filling these weights into the definition of our lower

bound (eqn [23]), it is easy to check that eqn [16] is indeed
fulfilled with this choice.
~ to the paramSetting the new model parameter estimate u
eter vector that maximizes the lower bound requires finding
the location where

~
@Q uju
0,
@u
which yields the following parameter update equations:
~2k
s
P i
w di
Pi k i
~k
m
w
P i i k
~ 2
i wk di m
P i k
w
P i ik
i wk
~k
p
N
377
[25]
It is worth spending some time thinking about these

equations. The EM algorithm searches for the ML parameters
of the Gaussian mixture model simply by repeatedly applying
the update rules of eqn [25], where the weights wik are defined
in eqn [24]. These weights depend themselves on the current
estimate of the model parameters, which explains why the
algorithm involves iterating. By comparing eqn [24] to eqn
[12], we see that the weights represent nothing but the posterior probability of the segmentation, given the current
model parameter estimate. Thus, the EM algorithm repeatedly
computes the type of probabilistic segmentation shown in
Figure 2 based on its current parameter estimate and then
updates the parameter estimate accordingly. The update rules
of eqn [25] are intuitive: The mean and variance of the
Gaussian distribution associated with the kth label are simply
set to the weighted mean and variance of the intensities of
those voxels currently attributed to that label; similarly the
prior for each class is set to the fraction of voxels currently
attributed to that class.
Figure 4 shows a few iterations of the EM algorithm searching for the ML parameters of the brain MR data shown in
Figure 1(a).
Modeling MR Bias Fields

Although the Gaussian mixture model is a very useful tool for
tissue classification, it can often not be applied directly to MR
images. This is because MR suffers from an imaging artifact that
makes some image areas darker and other areas brighter than
they should be. This spatially smooth variation of intensities is
Figure 4 Iterative improvement of the Gaussian mixture model parameters for the MR image of figure 1(a), using the EM algorithm: initialization (a)
and parameter estimate after one (b), 10 (c) and 30 (d) iterations.
378
often referred to as MR intensity inhomogeneity or bias field

and is caused by imaging equipment limitations and electrodynamic interactions with the object being scanned. The bias
field artifact is dependent on the anatomy being imaged and its
position in the scanner and is much more pronounced in the
newest generation of scanners.
Since the Gaussian mixture model does not account for
smoothly varying overall intensity levels within one and the
same anatomical structure, it is very susceptible to segmentation errors when applied to typical MR data. However, this
problem can be avoided by explicitly taking a model for the
bias field artifact into account in the generative model. In
particular, we can model the artifact as a linear combination
of M spatially smooth basis functions:
M
X
cm fim
~2k
s
pdj l, ud
Y
i
N di
!
cm fim jmli , s2li
[27]
with parameters ud (m1, . . ., mK, s21, . . ., s2K, c1, . . ., cM)T, which

consist not only of the parameters associated with the Gaussian
distributions but also additionally of the M coefficients of the
bias field basis functions, cm.
As was the case with the original Gaussian mixture model,
model parameter estimation can be performed conveniently by
iteratively constructing a lower bound to the log likelihood
function. Following the exact same procedure as in the previous section, it can be shown (Van Leemput et al., 1999a; Wells
et al., 1996) that constructing the lower bound involves computing the following weights (note the dependency on the bias
field parameters in this case):

P
~k
~2k p
N di m ~cm fim j~
mk , s

P
i
2
~ k0 p
~ k0
mk0 , s
cm fm j~
k0 N d i
m~
wik P
di
P
cm fim
m~
i
i wk
[29]
Similarly, keeping the Gaussian mixture model parameters

fixed at their current values, the bias field parameters maximizing the lower bound are given by
T 1 T
~c
F SF F Sr
[30]
where
f11
B f2
1
FB
@
N
f1
m1
is shorthand for fm(xi), the value of the mth basis

where
function evaluated at voxel i, which has spatial location xi.
Suitable basis functions can be cosine functions, uniform
B-spline basis functions, or something similar. We can then
extend the Gaussian mixture model by still assigning each
voxel an intensity drawn from a Gaussian distribution associated with its label, but further adding the bias model to the
resulting intensity image to obtain the final bias field corrupted image d (because of the physics of MR, the bias field is
better modeled as a multiplicative rather than an additive
artifact. This can be taken into account by working with
logarithmically transformed intensities in the models, instead
of using directly the original MR intensities). With this model,
we have
wi
2
Pi k i
~k
di m ~cm fm m
P i
w
P i ik
i wk
~k
p
N
[26]
fim
i
i wk
~k
m
and
sik
1
f12 ... f1M
2
2 C
f2 ... fM C
A
N
fN
2 ... fM
X
X
~k
sik m
wik
i
~
2 , si
sk , S diag si , di Xk i ,
~k
s
s
k
k k
0
1
~
d1 d1
r@ A
dN d~N
[31]
[32]
Since eqns [29] and [30] depend on one another, one could
in principle try to maximize the lower bound by cycling
through these two equations, one at a time, until some convergence criterion is met. However, the desirable property of
the EM algorithm to never decrease the value of the likelihood
function with each new iteration still holds even when the
lower bound is not maximized but merely improved. Therefore, a more efficient strategy is to construct the lower bound
by computing the weights wik (eqn [28]) and then updating the
Gaussian mixture model parameters (eqn [29]) and subsequently the bias field parameters (eqn [30]) only once to
merely improve it. After that, a new lower bound is constructed
by recomputing the weights, which is again improved by
updating the model parameters, etc., until convergence. Such
an optimization strategy of only partially optimizing the EM
lower bound is known as so-called generalized EM.
The interpretation of the update equations is again very
intuitive (Van Leemput et al., 1999a; Wells et al., 1996), but
outside the scope of this article. Suffice it to say that by extending the Gaussian mixture model with an explicit model for the
bias field artifact this way, it is possible to obtain high-quality
segmentations of MR scans without errors caused by intensity
inhomogeneities, as illustrated in Figure 5.
[28]
Subsequently maximizing the lower bound is more complicated than in the Gaussian mixture model, however,
because setting the derivative with respect to the parameter
vector u to zero no longer yields analytic expressions for the
parameter update rules. If we keep the bias field parameters
fixed at their current values ~cm , and only maximize the lower
bound with respect to the Gaussian mixture model parameters, we obtain
Further Model Extensions

Although we have only described tissue classification techniques for unicontrast data so far (i.e., a single scalar intensity
value for each voxel), the generative models can easily be
extended to also handle multicontrast MR scans. In that scenario, the univariate Gaussian distributions are simply replaced
with their multivariate equivalents. Furthermore, rather than
using a single Gaussian to represent the intensity distribution of
379
Figure 5 Explicit modeling and estimating the bias field artifact in MR scans often improves segmentation results considerably. Shown are a few
sagittal slices from a brain MR scan (a); the posterior probability for white matter using the standard Gaussian mixture model (b); the same when a bias
field model is explicitly taken into account (c); and the automatically estimated bias field model (d). Note the marked improvement in segmentation
accuracy in the upper parts of the brain.
any given label, a mixture of two or three Gaussians can provide

more realistic intensity distribution models and yield more
accurate segmentation results (Ashburner & Friston, 2005;
Puonti, Iglesias, & Van Leemput, 2013).
Another class of extensions to the generative models covered in this article concentrates on the employed spatial model,
that is, the segmentation prior p(l|ul). As a result of the rather
simplistic modeling assumptions of the prior used so far (eqn
[5]), a voxels posterior probability of belonging to each of the
K structures is computed using only the local intensity of the
voxel itself (eqn [12]). Although this works quite well in some
applications, there is often an intensity overlap between the tobe-segmented structures, causing segmentation errors in such a
purely intensity-driven strategy.
One possible improvement to p(l|ul) is the so-called
Markov random field prior, which in typical usage encourages
the different labels to occur in spatial clusters, rather than
being scattered randomly throughout the image area (Held
et al., 1997; Marroquin et al., 2002; Van Leemput et al.,
1999b; Zhang et al., 2001). Although these priors have some
attractive computational properties, they do not encode any
information about the shape, organization, and spatial relationships of real neuroanatomical structures.
More powerful models can be obtained through so-called
probabilistic atlases either as stand-alone models or in
combination with Markov random field priors which encode

prior anatomical knowledge of where to expect each of the
tissue types in a typical human brain. Such atlases are constructed by spatially coregistering a large number of manually
annotated brain scans and counting the frequencies of occurrence of the different tissue types. The resulting atlas is then
brought into spatial correspondence with an image to be segmented, either as a preprocessing step (Van Leemput et al.,
1999a) or as part of the model parameter estimation process
within the generative modeling framework (Ashburner &
Friston, 2005; Fischl, Salat et al., 2004; Pohl et al., 2006; Puonti
et al., 2013). Either way, the frequencies are reformatted to
obtain spatially varying prior probabilities pik for every class k
in every voxel i, as shown in Figure 6. These prior probabilities
pik are then used in place of the generic pk in every equation of
the segmentation models of this article, yielding voxel classifications that no longer depend solely on the voxels local intensity alone but also on their spatial location. Furthermore, the
priors pik unambiguously associate segmentation classes to predefined anatomical structures and can be used to automatically
initialize the iterative update equations of the EM optimizers,
even in multicontrast data where initialization is otherwise
difficult. Finally, the spatial priors are also typically used to
discard voxels that are of no interest, such as the muscle, skin,
or fat in brain MR scans. As a result, the use of the spatial priors
380
Figure 6 Illustration of a probabilistic atlas aligned with an image-to-be-segmented. Top: anatomical scan to be segmented. Bottom: spatially varying
prior probability maps of white matter, gray matter, and cerebrospinal fluid, overlaid on the anatomical scan for illustration purposes. Bright and dark
intensities correspond to high and low probabilities, respectively.
pik contributes greatly to the overall robustness and practical

value of the tissue classification models discussed in this
article.

Intensity Nonuniformity Correction.
References
Anbeek, P., Vincken, K. L., van Bochove, G. S., van Osch, M. J. P., & van der Grond, J.
(2005). Probabilistic segmentation of brain tissue in MR imaging. NeuroImage,
27(4), 795804.
Ashburner, J., & Friston, K. J. (1997). Multimodal image coregistration and partitioning
A unified framework. NeuroImage, 6(3), 209217.
839885.
Awate, S. P., Tasdizen, T., Foster, N., & Whitaker, R. T. (2006). Adaptive Markov
modeling for mutual-information-based, unsupervised MRI brain-tissue
classification. Medical Image Analysis, 100(5), 726739.
human brain. Neuron, 33, 341355.
Fischl, B., Salat, D. H., van der Kouwe, A. J. W., Makris, N., Segonne, F., Quinn, B. T.,
et al. (2004). Sequence-independent segmentation of magnetic resonance images.
NeuroImage, 23, S69S84.
Fischl, B., van der Kouwe, A., Destrieux, C., Halgren, E., Segonne, F., Salat, D. H., et al.
(2004). Automatically parcellating the human cerebral cortex. Cerebral Cortex,
140(1), 1122.
Greenspan, H., Ruf, A., & Goldberger, J. (2006). Constrained gaussian mixture model
framework for automatic segmentation of MR brain images. IEEE Transactions on
Guillemaud, R., & Brady, M. (1997). Estimating the bias field of MR images. IEEE
Held, K., Kops, E. R., Krause, B. J., Wells, W. M., III, Kikinis, R., & Muller-Gartner, H. W.
(1997). Markov random field segmentation of brain MR images. IEEE Transactions
on Medical Imaging, 160(6), 878886.
Hunter, D. R., & Lange, K. (2004). A tutorial on MM algorithms. The American
Statistician, 580(1), 3037.
Lorenzo-Valdes, M., Sanchez-Ortiz, G. I., Elkington, A. G., Mohiaddin, R. H., &
Rueckert, D. (2004). Segmentation of 4D cardiac MR images using a probabilistic
atlas and the EM algorithm. Medical Image Analysis, 8(3), 255265.
Marroquin, J. L., Vemuri, B. C., Botello, S., Calderon, F., & Fernandez-Bouzas, A.
(2002). An accurate and efficient Bayesian method for automatic segmentation of
brain MRI. IEEE Transactions on Medical Imaging, 210(8), 934945.
Menze, B., Van Leemput, K., Lashkari, D., Weber, M. A., Ayache, N., & Golland, P.
(2010). A generative model for brain tumor segmentation in multi-modal images.
Medical Image Computing and Computer-Assisted Intervention-MICCAI,
2010(6362), 151159.
Pham, D. L., & Prince, J. L. (1999). Adaptive fuzzy segmentation of magnetic resonance
images. IEEE Transactions on Medical Imaging, 18, 737752.
Pohl, K. M., Bouix, S., Nakamura, M., Rohlfing, T., McCarley, R. W., Kikinis, R., et al.
(2007). A hierarchical algorithm for MR brain image parcellation. IEEE Transactions
Pohl, K. M., Fisher, J., Grimson, E. L., Kikinis, R., & Wells, W. M. (2006). A Bayesian
model for joint segmentation and registration. NeuroImage, 31, 228239.
Prastawa, M., Bullitt, E., Ho, S., & Gerig, G. (2004). A brain tumor segmentation
framework based on outlier detection. Medical Image Analysis, 8, 275283.
Puonti, O., Iglesias, J. E., & Van Leemput, K. (2013). Fast, Sequence Adaptive
Parcellation of Brain MR Using Parametric Models. In Medical Image Computing
and Computer-Assisted InterventionMICCAI 2013 (pp. 727734). Berlin/

Rajapakse, J. C., Giedd, J. N., & Rapoport, J. L. (1997). Statistical approach to
segmentation of single-channel cerebral MR images. IEEE Transactions on Medical
Imaging, 16, 176186.
Sabuncu, M. R., Yeo, B. T. T., Van Leemput, K., Fischl, B., & Golland, P. (2010). A
generative model for image segmentation based on label fusion. IEEE Transactions
Van Leemput, K., Maes, F., Vandermeulen, D., Colchester, A., & Suetens, P. (2001).
Automated segmentation of multiple sclerosis lesions by model outlier detection.
Van Leemput, K., Maes, F., Vandermeulen, D., & Suetens, P. (1999a). Automated
model-based bias field correction of MR images of the brain. IEEE Transactions on
Van Leemput, K., Maes, F., Vandermeulen, D., & Suetens, P. (1999b). Automated
381
Warfield, S. K., Kaus, M., Jolesz, F. A., & Kikinis, R. (2000). Adaptive, template
moderated, spatially varying statistical classification. Medical Image Analysis, 4,
4355.
Wells, W. M., III, Grimson, W. E.L, Kikinis, R., & Jolesz, F. A. (1996). Adaptive
segmentation of MRI data. IEEE Transactions on Medical Imaging, 150(4),
429442.
Xue, H., Srinivasan, L., Jiang, S., Rutherford, M., Edwards, A. D., Rueckert, D., et al.
(2007). Automatic segmentation and reconstruction of the cortex from neonatal
MRI. NeuroImage, 380(3), 461477.
Zeng, X., Staib, L. H., Schultz, R. T., & Duncan, J. S. (1999). Segmentation and
measurement of the cortex from 3D MR images using coupled surfaces propagation.
hidden Markov random field model and the expectationmaximization algorithm.
Tensor-Based Morphometry
J Ashburner and GR Ridgway, UCL Institute of Neurology, London, UK
Glossary
Adjoint transport Involves transporting geometric

information via its tangent vector (velocity fields) (http://en.
wikipedia.org/wiki/Adjoint_representation).
Allometry Is the study of the relationship between organism
size and its shape, anatomy, physiology, etc. (http://en.
wikipedia.org/wiki/Allometry).
Artifact Is an error in the representation of information
introduced by the measuring equipment or techniques
(http://en.wikipedia.org/wiki/Artifact_(error)).
Coadjoint transport Involves transporting geometric
information via its cotangent vector (momentum), such that
its structure is conserved (http://en.wikipedia.org/wiki/
Coadjoint_representation).
Deformation Is the transformation of an object from one
configuration to another (http://en.wikipedia.org/wiki/
Deformation_(mechanics)).
Diffeomorphic Satisfies the requirements of a
diffeomorphism (http://en.wikipedia.org/wiki/
Diffeomorphic).
Displacement Is the difference between final and initial
positions, where the actual path is irrelevant (http://en.
wikipedia.org/wiki/Displacement_field_(mechanics)).
Divergence Is an operation on a vector field that measures
the magnitude of the fields source or sink (http://en.
wikipedia.org/wiki/Divergence).
Exploratory analysis Is an approach to analyzing datasets to
summarize their main characteristics (http://en.wikipedia.
org/wiki/Exploratory_analysis).
Feature Is an individual measurable property of an observed
phenomenon (http://en.wikipedia.org/wiki/Features_
(pattern_recognition)).
General linear model Is a statistical linear model, which
may be either univariate or multivariate (http://en.
wikipedia.org/wiki/General_linear_model).
Generalized linear model Is a generalization of multiple
regression that allows response variables to be drawn from
distributions other than Gaussians (http://en.wikipedia.org/
wiki/Generalized_linear_model).
Generative model Is a model encoding a probability
distribution from which observable data are treated as a
sample (http://en.wikipedia.org/wiki/Generative_model).
Gradient of a scalar field Is a vector field pointing in the
direction of greatest rate of increase and whose magnitude is
that rate of increase (http://en.wikipedia.org/wiki/
Gradient).
Jacobian Usually refers to the matrix of all first-order partial
derivatives of a vector-valued function (http://en.wikipedia.
org/wiki/Jacobian).
Jacobian determinant Is the determinant of a Jacobian
matrix, which encodes the factor by which a function
expands or shrinks volumes (http://en.wikipedia.org/wiki/
Jacobian).
Landmark Is usually a biologically meaningful point, which

defines homologous parts of an organism across some
population (http://en.wikipedia.org/wiki/
Landmark_point).
Mapping Is a synonym for function or denotes a particular
kind of function (http://en.wikipedia.org/wiki/Map_
(mathematics)).
Mass-univariate statistics Concerns the analysis of
multivariate datasets, but with an assumption that
dependent variables are independent from each other.
Matrix logarithm Is a generalization of a scalar logarithm,
which is (in a sense) the inverse of a matrix exponential
(http://en.wikipedia.org/wiki/Matrix_logarithm).
Measure Is a generalization of the concepts of length, area,
and volume (http://en.wikipedia.org/wiki/Measure_
(mathematics)).
Model Is a description of a system using mathematical
concepts and language (http://en.wikipedia.org/wiki/
Mathematical_model).
Morphometric Is a quantitative analysis of form, a concept
that encompasses size and shape (http://en.wikipedia.org/
wiki/Morphometrics).
Multivariate statistics Concerns the analysis of datasets
where simultaneous observations of multiple dependent
variables (e.g., voxels in an image) are made (http://en.
wikipedia.org/wiki/Multivariate_statistics).
Nonparametric statistics Assumes that the observations are
not drawn from a probability distribution with a
characteristic structure or parameters (http://en.wikipedia.
org/wiki/Non-parametric_statistics).
Null hypothesis Is the general or default position (used by
frequentist statisticians) that there is no relationship
between two phenomena (http://en.wikipedia.org/wiki/
Null_hypothesis).
Objective function Is a function that maps values of one or
more variables onto a real number, which intuitively
represents some cost (http://en.wikipedia.org/wiki/
Objective_function).
Parallel transport Is a way of transporting geometric
information along smooth curves in a manifold (http://en.
wikipedia.org/wiki/Parallel_transport).
Parametric statistics Assumes that observations are drawn
from a type of probability distribution, such that inferences
may be made about the parameters of the distribution
(http://en.wikipedia.org/wiki/Parametric_statistics).
Pose Is an objects position and orientation relative to some
coordinate system (http://en.wikipedia.org/wiki/Pose_
(computer_vision)).
Principal component analysis Is a procedure that uses
orthogonal transformation to convert a set of possibly
correlated variables into a set of linearly uncorrelated
variables (http://en.wikipedia.org/wiki/
Principal_component_analysis).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00309-2
383
384
INTRODUCTION TO METHODS AND MODELING | Tensor-Based Morphometry
Principal geodesic analysis Is a generalization of principal

component analysis to non-Euclidean settings (http://en.
wikipedia.org/wiki/Principal_geodesic_analysis).
Random field Is a generalization of a stochastic process to
multiple dimensions, such that the underlying parameters
can be vectors or points on a manifold http://en.wikipedia.
org/wiki/Random_field).
Registration Is the process of transforming different sets of
data into one coordinate system (http://en.wikipedia.org/
wiki/Image_registration).
Regularization Is a process of introducing additional
information in order to solve ill-posed problems or prevent
overfitting (http://en.wikipedia.org/wiki/Regularization_
(mathematics)).
Shear Is displacement of points in a fixed direction by an
amount proportional to their signed distances from a line
parallel to that direction (http://en.wikipedia.org/wiki/
Shear_mapping).
Spatial normalization Is a term used by neuroimagers that
refers to warping images of different individuals to a
common coordinate system (http://en.wikipedia.org/wiki/
Spatial_normalization).
Statistical hypothesis testing Is a method for
making decisions using data from a scientific study (http://
en.wikipedia.org/wiki/Statistical_hypothesis_testing).
Statistical parametric map Is a statistical technique,
created by Karl Friston, for localizing statistically
significant differences among populations of images (http://
en.wikipedia.org/wiki/Statistical_parametric_mapping).
Introduction
Morphometrics refers to the quantitative analysis of form, which
is a concept that encompasses both the size and shape of an
organism or organ. In neuroimaging, morphometric approaches
are typically used to characterize differences among populations
of subjects or to identify features that correlate with some measurement of interest. These measurements may be clinical scores,
test score results, genetic measurements, or anything else of
interest to the investigator. The usual approaches involve extracting anatomical features or descriptors from MRI data of the
subjects and performing some form of statistical analysis on
them. This article concerns tensor-based morphometric techniques, which involve analyzing features that principally relate
to the relative volumes of structures, as estimated by image
registration. The mathematics involved in morphometrics can
be quite complicated, but we try to keep it relatively simple in
this article.
Morphometrics has a long history throughout many areas
of biology. Most applications do not have the benefit of imaging devices that enable 3-D volumetric scans to be collected,
so generally focus on working with things that can easily be
measured from the organ or organism itself. Traditional
approaches were limited to measures such as lengths, widths,
angles, and distances, which were subjected to statistical analysis. When technological advances made it easier to record
Strain tensor Is a description of stretching and shearing due

to shape changes, ignoring changes due to pose differences
(http://en.wikipedia.org/wiki/Deformation_(mechanics)).
Template Is some form of reference image, or set of images,
that serves as a model or standard for alignment with scans
of individual subjects.
Tensor field Has a tensor at each point in space (http://en.
wikipedia.org/wiki/Tensor_field).
Tensor-based morphometry Is a term used in
neuroimaging to refer to characterizing anatomical
differences among populations of subjects via Jacobians of
deformations (or similar).
Thin-plate spline Is a form of radial basis-function
representation of displacement fields that gives a smooth
representation (http://en.wikipedia.org/wiki/
Thin_plate_spline).
Univariate statistics Concerns the analysis of datasets
where a single dependent variable is measured (http://en.
wikipedia.org/wiki/Univariate).
Velocity field Is a vector field used to mathematically
describe the motion of a fluid (http://en.wikipedia.org/wiki/
Velocity_field).
Voxel Is a volume element in 3-D images, analogous to a
pixel (picture element) in 2-D images (http://en.wikipedia.
org/wiki/Voxel).
Voxel-based morphometry Is a term used in neuroimaging
to refer to characterizing anatomical differences among
populations of subjects via spatially blurred tissue maps (or
similar) (http://en.wikipedia.org/wiki/Voxelbased_morphometry).
the locations of landmarks, a number of new morphometric

approaches appeared, which were largely inspired by the
work of Thompson (1917, 1942). Instead of analyzing lengths,
widths, etc., the new geometric morphometrics (Adams,
Rohlf, & Slice, 2004; Rohlf & Marcus, 1993) involved analyzing landmark coordinates in space, after first correcting for
pose (and possibly size). Instead of treating data in a feature
by feature way, multivariate analyses of landmark positions, or
of thin-plate spline coefficients, preserved geometric relationships among all the points.
Most areas of biology are limited to making measurements
on the outside surface of whatever organ or organism they
chose to study, whereas neuroimagers have the advantage of
being able to measure a much wider variety of things inside the
brain. Some brain morphometric studies involve volumes
obtained by manually tracing regions in scans, although these
are mostly limited to a handful of structures with clear boundaries. While there may be a wealth of findings pertaining to
these particular structures (e.g., ventricles and hippocampi),
other brain regions can easily be neglected. It would be a
mistake to assume that neurological disorders only affect
those structures we can manually outline. Manual tracing of a
structure also ignores the potential variability within that structure, for example, one hippocampal subfield could be relatively
smaller and another relatively larger with no detectable change
in the overall volume.

Neuroimagers tend not to use much landmark data. In part,
this is because there are few discrete and readily identifiable
points within the brain. Instead, the field relies on correspondences estimated by automatic or semiautomatic image registration approaches. Providing the same software and settings
are used, such approaches should lead to fully reproducible
results, irrespective of who runs it.
The following section briefly describes some of the statistical testing procedures that may be applied to morphometric
features. This is followed by a section about the types of features that are typically extracted for tensor-based morphometric (TBM) studies.
Statistical Analysis
TBM usually involves the framework of statistical parametric
mapping (SPM) (Friston et al., 1995), which localizes statistically significant regional differences. Extensive details of the
procedures involved are described in other articles of this book,
so only a brief summary will be outlined here. Essentially,
image data from a number of subjects are preprocessed by
aligning them to a common anatomical frame of reference,
which gives a feature representation that is more amenable to
voxel-wise statistical testing.
SPMs of voxel-wise univariate measures allow simple questions to be addressed, such as where does the chosen morphometric feature correlate with a particular regressor of interest?
Typically, parametric statistical procedures (t-tests and F-tests)
are used within the frequentist framework. Hypotheses can be
formulated within the framework of a univariate general linear
model (GLM), whereby a vector of observations is modeled by
a linear combination of user-specified regressors (Friston et al.,
1995). The GLM is a flexible framework that allows many
different tests to be applied, ranging from group comparisons
and identification of differences that are related to specified
covariates such as disease severity or age to complex interactions between different effects of interest.
Because the pattern of difference to be determined is not
specified a priori, SPM analyses are a hybrid between statistical
hypothesis testing and exploratory analyses. Rather than test a
single hypothesis, the approach involves testing hypotheses at
each voxel of the preprocessed data. A Bonferroni correction
could be used to correct for the multiple comparisons if
the tests were independent, but this is not normally the case
because of the inherent spatial smoothness of the data. In
practice, a correction for the multitude of tests is usually
obtained via random field theory (Friston, Holmes, Poline,
Price, & Frith, 1996; Worsley et al., 1996), thus allowing a
correction for multiple dependent comparisons that controls
the rate of false-positive results. Alternatively, SPMs may be
corrected for the rate of false discoveries (Chumbley, Worsley,
Flandin, & Friston, 2010; Genovese, Lazar, & Nichols, 2002).
There are also a variety of other statistical analytic methods
that may be applied to the feature data. For example, nonparametric approaches (Nichols & Holmes, 2002) may be
applied in situations where parametric modeling assumptions
do not hold. In recent years, there has been a rediscovery of
Bayesian approaches by the neuroimaging community, leading
385
to various Bayesian inference procedures for localizing differences (Friston & Penny, 2003; Penny & Ridgway, 2013).
Voxel-wise Multivariate Analyses

Univariate GLMs are a special case of the more general multivariate GLM. In principle, SPMs can also be obtained from the
results of voxel-wise multivariate tests. Instead of one variable
per voxel of a subject, tests within a multivariate GLM could
effectively involve two or more variables. Following voxel-wise
multivariate tests, similar corrections based on random field
theory can be applied as in the univariate case (Cao & Worsley,
1999; Carbonell, Worsley, & Galan, 2011; Worsley, Taylor,
Tomaiuolo, & Lerch, 2004).
Readers without a mathematical background can safely skip
the remainder of this subsection. In a univariate GLM,
y Xb e, t- and F-contrasts can be seen as special cases of a
likelihood ratio test comparing a restricted model (X0, under
the null hypothesis) to the unrestricted full model (X)
F
y T XX X 0 X 0 y rankX rankX0
=
yT I XX y
rankX
SSH DFH
=
SSE DFE
where X denotes the pseudo-inverse of X (which can be

computed with, e.g., MATLABsppinv
command). The t-contrast
^ see
is just the signed version of F (with the sign of CT b;
succeeding text).
The multivariate equivalent is based on Wilks lambda (or
related test statistics, such as Roys greatest root), which has a
closely related form as it is also derived from the likelihood
ratio:
T

Y I XX Y
jSSEj

L T
Y I X 0 X 0 Y jSSH SSEj
In both univariate and multivariate cases, the sums of
squares (or sums of squares and cross products matrix) for
the hypothesis, SSH, can be expressed in terms of a contrast
C in the parameters b^ as follows:
SSH Y T XX X 0 X 0 Y

^T C CT X T X C CT b^
b
which allows one to test a general linear null hypothesis
CT b^ 0 without explicitly determining the implied reduced
model X0.
Whole-Brain Multivariate Analyses

An alternative to the SPM framework involves whole-brain
multivariate modeling. Within the frequentist setting, this
may be achieved by reducing the dimensionality of the data,
using a method such as principal component analysis, followed
by performing statistical tests using the multivariate linear
model (e.g., based on Wilks lambda, described in the preceding
text) (Ashburner et al., 1998). This type of approach is similar to
that used by conventional geometric morphometrics (Adams
et al., 2004; Klingenberg, 2011; Mitteroecker & Gunz, 2009;
Rohlf & Marcus, 1993; Slice, 2007), but with features derived
386
from deformations instead of just a few landmark coordinates

(as in Bookstein, 1997, 1999; Dryden & Mardia, 1998). When
applied on a global scale, this approach simply identifies
whether there are significant differences between overall shapes
among the brains of different populations.
More recently, Bayesian multivariate approaches (Bishop,
2006; Friston et al., 2008; Rasmussen & Williams, 2006) are
being applied, allowing more elegant approaches to be used to
circumvent the curse of dimensionality (see Ashburner and
Kloppel (2011) for more on this subject). Measures of statistical significance could be assessed using the principles underlying Bayesian model selection, although currently, it is more
common to see cross validation used.
Template
Image
Warped template
Warped image
Feature Representations
There are many ways of characterizing anatomical differences
among populations or finding correlations between anatomy
and, for example, disease severity. Over the years, there has
been a proliferation in the types of features that can be tested,
although most neuroimaging comparisons are made using the
voxel-based morphometric approach. However, a number of
other data representations may also be subjected to statistical
analysis.
One of the challenges for morphometry is to identify shape
modeling features that best differentiate among populations.
Where there are differences between the cortical thickness in
one population and that of another, then cortical thickness
would be the most discriminative shape feature to use. An
analysis of regional gray matter volumes may partially reveal
those differences, but it would not be as accurate as looking at
thickness itself. Similarly, if the difference between groups is
best characterized by cortical surface areas, then an analysis of
cortical thickness is unlikely to show much of interest. In
general, determining the most accurate representations of differences among populations of subjects is something to be
done empirically.
Deformation Fields
Currently, most morphometric studies in neuroimaging are
based on T1-weighted scans. MRI scans contain a variety of
artifacts, many of which will impact on any kind of morphometric analysis. These are especially important for studies that
combine scans from multiple scanners (Jovicich et al., 2009).
Spatial distortions arising from gradient nonlinearities impact
any kind of morphometric analysis, although there are a variety
of correction methods for these (Janke, Zhao, Cowin,
Galloway, & Doddrell, 2004; Jovicich et al., 2006). Further
information about optimizing image acquisition parameters,
artifact correction, etc., for large morphometric studies may be
found in Jack et al. (2008).
TBM requires that the images of all subjects in the study to
be aligned together by some form of spatial normalization.
In neuroimaging, the primary result of spatially normalizing a
series of images is that they all conform to the same space,
enabling region-by-region comparisons to be performed.
However, for TBM, the main objective is to obtain a set of
parameterizations of the spatial transformations required to
Figure 1 Illustration of warping some synthetic images. Note that it

shows an inexact matching between them, which is typically what would
be expected when aligning real MRI across subjects.
match the different shaped brains to the same template (see

Figures 1 and 2). For morphometric studies, these deformations
must be mappings from the template to each of the individuals
in the study, so these need to be inverted if the registration
algorithm generates mappings from each individual to the template. Encoded within each deformation is information about
the individual image shapes, which may be further characterized
using a variety of statistical procedures.
In theory, the choice of reference template used for spatial
normalization will influence the findings of a study. Basic
common sense tells us that intensity properties of the template
should match those of the study data. For example, less accurate findings would be obtained from a study where a meansquares difference matching term was used to align a set of
T2-weighted images to a template based on T1-weighted data.
In addition, registration errors can be reduced by having the
shape of the template brain as similar as possible to those of
the subjects in the study. Providing certain objective functions
are used to drive the alignment, this is often best achieved by
groupwise registration approaches, whereby the template is
computed as some form of shape and intensity average from
the brains in the study (Ashburner, Andersson, & Friston,
2000; Ashburner & Friston, 2009; Joshi, Davis, Jomier, &
Gerig, 2004).
An alternative approach involves aligning the images in a
study with multiple templates, which are single-subject images
of different subjects (Koikkalainen et al., 2011; Lepore et al.,
2008), that is followed by some form of feature averaging
procedure. Groupwise registration is often suboptimal when
it is driven by certain informationtheoretic objective functions, so these multitemplate (also known as multiatlas)
Deformation
Horizontal component
387
Vertical component
Identity
Displacements
Figure 2 The components of a 2-D deformation. Top row: The deformation (from Figure 1), with its horizontal and vertical components.
Middle row: An identity transform, with its horizontal and vertical components. Bottom row: Displacements obtained by subtracting the identity
transform from the deformation.
procedures are intended to reduce the bias incurred by selecting a particular individuals image as a template.
In general, one should not expect to obtain exactly the same
findings from morphometric studies using different image registration software. Different algorithms use different models and
assumptions, and in the absence of clear theoretical preferences,
the optimal ones can only be determined empirically. Image
registration algorithms have a number of settings, and changes
to these will generally lead to changes in the findings of a study.
For example, Figure 3 shows a simulated image aligned using a
variety of regularization settings (but the same algorithm), each
giving different maps of relative volumes. The more accurately the
registration model is specified, the more accurately the findings
from a study will reflect real underlying biological differences.
The Jacobian Tensors

A simple morphometric approach would be to examine the
deformations themselves by treating them as vector fields
representing displacements. These may be analyzed within a
multivariate framework (Ashburner et al., 1998) after appropriate corrections to factor out pose.
Some previous works have applied voxel-wise Hotellings
T2 tests on the displacements at each and every voxel (Gaser,
Volz, Kiebel, Riehemann, & Sauer, 1999; Thompson & Toga,
1999), with statistical significance assessed by random field
corrections (Cao & Worsley, 1999). However, this approach
does not directly localize differences that are intrinsic to the
brains themselves. Rather, it identifies those brain structures
that are in different locations in space, which depends upon
how the poses and possibly sizes of the brains are factored out
of the estimated deformations (Klingenberg, 2013).
The objective of TBM is usually to localize regions of shape
differences among groups of brains, based on deformations
that map points in a template (x1,x2,x3) to equivalent points in
individual source images (y1,y2,y3). In principle, the Jacobian
matrices of the deformations (a second-order tensor field given
by the spatial derivatives of the transformation; see Figure 4)
should be more reliable indicators of local brain shape than
displacements.
388
Figure 3 Effects of different regularization settings on estimates of Jacobian determinants. Left column: Image aligned with different regularization.
Middle column: Estimated deformations. Right column: Estimated Jacobian determinants (all shown on the same color scale).
A Jacobian matrix contains information about the local

stretching, shearing, and rotation involved in the deformation
and is defined at each point by
2
3
@y1 =@x1 @y1 =@x2 @y1 =@x3
J 4 @y2 =@x1 @y2 =@x2 @y2 =@x3 5
@y3 =@x1 @y3 =@x2 @y3 =@x3
determinants at each point (Davatzikos et al., 1996; Freeborough & Fox, 1998; Machado, Gee, & Campos, 1998;
Studholme et al., 2004). This type of morphometry is useful
for studies that have specific questions about whether growth
or volume loss has occurred. The field obtained by taking the
determinants at each point gives a map of structural volumes
relative to those of a reference image.
The Jacobian Determinants
Logarithms and Exponentials
Determinants of square matrices play an important role in

computational anatomy. The most straightforward form of
TBM involves comparing relative volumes of different brain
structures, where the volumes are derived from the Jacobian
There are a number of nonlinearities to consider when analyzing the shapes and sizes of structures. If a structure stays the
same shape but is doubled in length or width, its surface area
will be scaled by a factor of 4 and its volume by a factor of 8.
389
Figure 4 For 2-D deformations, a Jacobian tensor field encodes a 2 2 matrix at each point. Top: Horizontal and vertical gradients of the horizontal
component of the deformation in Figure 2. Bottom: Horizontal and vertical gradients of the vertical component.
Similarly, if the length is scaled by a factor of 3, its surface will

be scaled by nine and its volume by 27. A linear relationship
between the score and length (1, 2, 3) will mean that there
is some nonlinear relationship with area (1, 4, 9) and volume
(1, 8, 27). When relating size measurements with, for example,
a clinical score, should the analysis be set up so as to identify
correlations in length, area, or volume? A reasonable solution
is to work with the logarithms of the measures.
Growth is a process of self-multiplication. One cell divides
into two, then four, eight, etc. This means that for an organ
growing at a constant rate, the rate at which more tissue is
generated will be proportional to the amount of tissue in
existence. This leads to an exponential increase in size. Similarly, atrophy at a constant rate will lead to an exponential
decrease in size.
Log-transforming Jacobian determinants are only possible
if they are >0. This means that the deformations must be oneto-one mappings, such that there is no folding present (see
Figure 5). Many nonlinear image registration algorithms
parameterize deformations in terms of displacement fields,
which do not necessarily enforce well-behaved Jacobian determinants. In contrast, diffeomorphic registration algorithms use
a different way of encoding deformations, which involves
building up deformations by composing a number of much
smaller displacement fields together. Providing that the constituent deformations are sufficiently small to be one-to-one,
the result from composing them should also be a one-to-one
mapping (Christensen et al., 1995). Even so, the discrete
nature of the actual implementations means that care needs
to be taken when computing Jacobians to ensure that they have
positive determinants.
Some diffeomorphic approaches (Ashburner & Friston,
2011; Beg, Miller, Trouve, & Younes, 2005; Vialard, Risser,
Rueckert, & Cotter, 2012) generate a vector field referred to as
the initial velocity. Rather than analyze the features of the
deformations, it is possible to work instead with features
extracted from this initial velocity field. In particular, the divergence of the initial velocity provides a feature that is numerically similar to the logarithm of the Jacobian determinants.
These divergences encode the volumetric growth rates required
to achieve alignment of the images, according to the diffeomorphic registration model. If they are integrated over some
brain region, this gives the rate at which tissue flows into the
region (this is known as the divergence theorem, or Gausss
theorem). The divergence is computed by summing the diagonal elements of the Jacobian matrices of the velocity field.
One advantage of working with divergences, rather than the
logs of the Jacobian determinants, is that they are linear
390
Folded deformation
Jacobian determinants
Detail of folding
Figure 5 A deformation with folding. Left: Full deformation, generated by doubling the displacement in Figure 2. Center: Jacobian determinants,
containing two regions of negative values. Right: Detail of the folded region.
functions of the velocity fields and can often be better behaved

numerically. This brings TBM approaches a step closer to procedures such as principal geodesic analysis (Fletcher, Joshi,
Lu, & Pizer, 2003; Fletcher, Lu, Pizer, & Joshi, 2004). Divergences of displacement fields may also be used for morphometry (Chung et al., 2001; Thirion & Calmon, 1999).
(Huxley, 1932), whereby there is a logarithmic relationship

between the sizes of the various structures or organs and the
size of the entire organism. Although aware of some of the
limitations of the assumptions, Huxley conceptualized growth
as a process of self-multiplication of living substance, in which
TBM on Tensors
where x is the magnitude (weight, volume, length, etc.) of the

animal, y is the magnitude of the differentially growing organ,
and b and k are constants. This gives a relation between magnitudes, which can be modeled as y bxk. He considered the
meaning of the value k to be the rate of growth per unit weight,
which is the growth rate at any instant, divided by the size.
In neuroimaging, we generally do not consider the weight of
the subjects, although corrections for measurements such as
whole-brain volume or total intracranial volume are usually incorporated during statistical analyses. In general, findings are heavily
dependent upon the way that this global correction is made
(Barnes et al., 2010; Hu et al., 2011; Peelle, Cusack, & Henson,
2012), which can lead to widely divergent findings particularly
when comparing genders. These corrections account for some of
the multivariate nature of anatomical form.
If, instead of volumes, their logarithms are used, a GLM
may be fit such that log(y) log(b) k log(x). This GLM formulation can easily be extended so that population-specific log
(b) and k may be estimated. Of course, if volume estimates are
not constrained to be positive, there will be problems computing their logarithms. A preferable approach, not discussed in
any detail here, involves fitting a generalized linear model
(GLZ not to be confused with a GLM) or generalized additive
model to the untransformed data (Schuff et al., 2012).
Some shape information is lost if only the determinants of the

Jacobians are considered. With many subjects in a study, a potentially more powerful form of TBM can be attained using multivariate statistics on other measures derived from the Jacobian
matrices. This use of multivariate statistics not only tests for volumetric differences but also indicates whether there are any differences among lengths, areas, and the amount of shear.
Because the Jacobian matrices encode both local shape
(zooms and shears) and orientation, it is useful to remove
the latter prior to statistical analysis. A nonsingular Jacobian
matrix can be decomposed into a rotation matrix (R) and a
symmetrical positive definite matrix (U), such that J RU.
Matrix U (called the right stretch tensor) is derived by U
(JTJ)1/2 (using matrix square roots). For a purely rigid body
transformation, U I (the identity matrix). Deviations of U
away from I indicate a shape change, which can be represented
by a strain tensor E.
For any deformation, there is a whole continuum of ways of
defining strain tensors, based on a parameter m. When m is
nonzero, the family of strain tensors E is given by E(m) m1
(UmI). For the special case when m is zero, the Hencky strain
tensor is given by E(0) ln (U), where ln refers to a matrix
logarithm. Lepore et al. (2006, 2008) showed that a voxelwise multivariate analysis of Hencky strain tensors can exhibit
much greater sensitivity than a voxel-wise univariate analysis of
logarithms of Jacobian determinants. Many of the concepts
required for analysis of strain tensors are also found in the
literature on diffusion tensor imaging (Arsigny, Fillard,
Pennec, & Ayache, 2006; Pennec, 2009; Whitcher, Wisco,
Hadjikhani, & Tuch, 2007).
Allometry
Outside neuroimaging, biologists often consider allometry when
making comparisons. The ideas behind allometry were first
formulated in Sir Julian Huxleys Problems of Relative Growth
d
d
log y k log x
dt
dt
Longitudinal Data
Often, longitudinal data are used for morphometric analyses,
whereby anatomical scans of multiple subjects are collected
at multiple time points. Time differences between scans vary
from a few hours (Tost et al., 2010) to a few decades (Fisniku
et al., 2008) with intervals of a few months being common
for structural plasticity and intervals around a year being
common for neurodegenerative disease. Current applications
include characterizing patterns of atrophy in dementia
(Freeborough & Fox, 1998) or studying brain development
(see Figure 6). Other examples include studies into structural
391
Figure 6 Example of atrophy measured in a single individual via longitudinal registration. Three orthogonal sections of the subjects average image are
shown above the same sections through a map of volume change. Darker regions indicate shrinkage, whereas brighter regions indicate expansion.
392
plasticity, whereby anatomical changes may be attributed to

some type of intervention (Draganski et al., 2004). (This is a
situation where the direction of causality may be deduced from
computational anatomical studies of the human brain.)
These studies usually involve within-subject longitudinal
registration, followed by intersubject registration to project
shape changes from each subject into a common space (spatial
normalization). Physical changes over relatively short time
intervals are usually small, and longitudinal registration algorithms are very sensitive to biasing effects arising from not
treating all data equivalently. Subtle things, such as image
interpolation or the form of the regularization, have been
demonstrated to have especially troubling effects (Thompson,
Holland, & Alzheimers Disease Neuroimaging Initiative,
2011; Yushkevich et al., 2010). Previously, these concerns
were only theoretical. However, investigators pay more rather
attention to them (Fox, Ridgway, & Schott, 2011) now that
convincing evidence has been identified. Various solutions
have been proposed, which generally involve formulating longitudinal registration in a way that involves pairwise or groupwise consistency (Ashburner & Ridgway, 2013; Hua et al.,
2011; Modat et al., 2012; Reuter & Fischl, 2011; Reuter,
Schmansky, Rosas, & Fischl, 2012).
After intrasubject longitudinal registration has been done
and the deformations that align all subjects to a common
template space have been estimated, the next question concerns how best to transport the longitudinal information into
the common space. Currently, there are two approaches commonly used to transport this information. One approach
involves just warping the features, whereas the other involves
scaling the warped features by the Jacobian determinant of the
deformation with which they are warped. If the longitudinal
features are Jacobian determinants themselves, then the latter
option will result in spatially normalized features that encode
volumes in the original scans relative to those of the template
that defines the common space. In an analysis of logarithms of
Jacobian determinants, whether or not Jacobians obtained
from longitudinal registration (e.g., y0 and y1) are scaled by
the Jacobians of the spatially normalizing transformations
(e.g., j) should make no difference (because log(jy1) log
(jy0) log(y1) log(y0)). If logarithms are not used, it is unclear
whether or not it is generally better to rescale by the Jacobians
from the spatial normalization. It may be preferable for analyses that relate longitudinally estimated changes to those estimated cross-sectionally but is perhaps less appropriate for
other types of analyses.
Sometimes, it is desirable to do some form of analysis of
the Jacobian tensors themselves or to analyze some other
form of geometric information derived from within-subject
longitudinal registration. The most correct way to transport
these sorts of information to a common space is probably to
use a mathematical procedure known as parallel transport or
parallel translation. Physicists, from Einstein onwards, make
use of parallel transport, although more recently, it has
emerged in the field of computational anatomy (Qiu, Younes,
Miller, & Csernansky, 2008; Younes, Qiu, Winslow, & Miller,
2008). Simpler (but reasonably well-justified) approaches
for transporting intrasubject geometric information also
exist. These include adjoint transport and coadjoint transport
(Younes et al., 2008).
Outlook
Morphometric approaches used by neuroimagers tend to be
substantially different from those applied in other areas of
biology. Within neuroimaging, there tends to be much more
focus on localizing differences via mass-univariate approaches,
whereas multivariate approaches tend to be favored in other
fields. This difference in viewpoint has drawn criticism in the
past (Bookstein, 2001), although the neuroimaging field has
now begun to embrace multivariate methods rather more.
Currently, most morphometric analyses involve a purely
bottom-up procedure, whereby a pipeline of processing steps is
applied to the data. Although still at the early stages, we are
beginning to see hierarchical generative models emerge, which
combine statistical modeling with registration (Allassonnie`re,
Amit, & Trouve, 2007; Fishbaugh, Durrleman, & Gerig, 2011;
Niethammer, Huang, & Vialard, 2011; Prastawa, Awate, & Gerig,
2012). Instead of statistical analyses that attempt to explain how
the features were generated (ignoring the fact that they came from
nonlinear registration), these developments involve generative
models of the original image data. Such approaches may eventually enable top-down knowledge about disease status, age, etc., to
inform the registration and other image processing components.
As all neuroscientists know, top-down processing is essential for
making sense of the world (Mumford, 1991).
Acknowledgments
Image data used in Figure 6 were part of the OASIS:
longitudinal MRI data in nondemented and demented older
adults dataset (Marcus, Fotenos, Csernansky, Morris, &
Buckner, 2010), funded by grant numbers P50 AG05681,
P01 AG03991, R01 AG021910, P20 MH071616, and U24
RR021382.

Cortical Surface Morphometry; INTRODUCTION TO METHODS
AND MODELING: Analysis of Variance (ANOVA); Bayesian Model
Inference; Bayesian Model Inversion; Bayesian Multiple Atlas
Deformable Templates; Computing Brain Change over Time; Contrasts
and Inferences; Cortical Thickness Mapping; Crossvalidation;
Diffeomorphic Image Registration; False Discovery Rate Control;
Modeling Brain Growth and Development; Multi-voxel Pattern
Analysis; Nonlinear Registration Via Displacement Fields; Posterior
Probability Maps; Surface-Based Morphometry; The General Linear
Model; Topological Inference; Variational Bayes; Voxel-Based
Morphometry.
References
Adams, D., Rohlf, F., & Slice, D. (2004). Geometric morphometrics: Ten years of
progress following the revolution. Italian Journal of Zoology, 71(1), 516.
Allassonnie`re, S., Amit, Y., & Trouve, A. (2007). Towards a coherent statistical
framework for dense deformable template estimation. Journal of the Royal Statistical
Society, Series B: Statistical Methodology, 69(1), 329.
Arsigny, V., Fillard, P., Pennec, X., & Ayache, N. (2006). Log-Euclidean metrics for fast
and simple calculus on diffusion tensors. Magnetic Resonance in Medicine, 56(2),
411421.

Ashburner, J., Andersson, J. L., & Friston, K. J. (2000). Image registration using a
symmetric prior In three dimensions. Human Brain Mapping, 9(4), 212225.
Ashburner, J., & Friston, K. (2009). Computing average shaped tissue probability
templates. NeuroImage, 45(2), 333341.
Ashburner, J., & Friston, K. (2011). Diffeomorphic registration using geodesic shooting
and Gauss-Newton optimisation. NeuroImage, 55, 954967.
Ashburner, J., Hutton, C., Frackowiak, R., Johnsrude, I., Price, C., & Friston, K. (1998).
Identifying global anatomical differences: Deformation-based morphometry. Human
Ashburner, J., & Kloppel, S. (2011). Multivariate models of inter-subject anatomical
variability. NeuroImage, 56(2), 422439.
longitudinal structural MRI. Frontiers in Neuroscience, 6.
Barnes, J., Ridgway, G. R., Bartlett, J., Henley, S., Lehmann, M., Hobbs, N., et al.
(2010). Head size, age and gender adjustment in MRI studies: A necessary
nuisance? NeuroImage, 53(4), 12441255.
Beg, M., Miller, M., Trouve, A., & Younes, L. (2005). Computing large deformation
Bishop, C. (2006). Pattern recognition and machine learning. New York: Springer.
Bookstein, F. L. (1997). Landmark methods for forms without landmarks:
Morphometrics of group differences in outline shape. Medical Image Analysis, 1(3),
225243.
Bookstein, F. L. (1999). Brain warping. San Diego, CA: Academic Press, Chapter 10,
pp. 157182.
Bookstein, F. (2001). voxel-based morphometry should not be used with imperfectly
registered images. NeuroImage, 14(6), 14541462.
Cao, J., & Worsley, K. J. (1999). The geometry of the Hotellings T2 random field
with applications to the detection of shape changes. Annals of Statistics, 27(3),
925942.
Carbonell, F., Worsley, K., & Galan, L. (2011). The geometry of the Wilkss l random
field. Annals of the Institute of Statistical Mathematics, 63(1), 127.
Christensen, G., Rabbitt, R., Miller, M., Joshi, S., Grenander, U., Coogan, T., et al.
(1995). Topological properties of smooth anatomic maps. In Information
processing in medical imaging (pp. 101112). .
Chumbley, J., Worsley, K., Flandin, G., & Friston, K. (2010). Topological FDR for
neuroimaging. NeuroImage, 49(4), 30573064.
Chung, M. K., Worsley, K. J., Paus, T., Cherif, C., Collins, D. L., Giedd, J. N., et al.
(2001). A unified statistical approach to deformation-based morphometry.
NeuroImage, 14(3), 595606.
Davatzikos, C., Vaillant, M., Resnick, S. M., Prince, J. L., Letovsky, S., & Bryan, R. N.
(1996). A computerized approach for morphological analysis of the corpus
callosum. Journal of Computer Assisted Tomography, 20(1), 8897.
Draganski, B., Gaser, C., Busch, V., Schuierer, G., Bogdahn, U., & May, A. (2004).
Neuroplasticity: Changes in grey matter induced by training. Nature, 427(6972),
311312.
Dryden, I., & Mardia, K. (1998). Statistical shape analysis. New York: Wiley.
Fishbaugh, J., Durrleman, S., & Gerig, G. (2011). Estimation of smooth growth
trajectories with controlled acceleration from time series shape data. In Medical
image computing and computer-assisted intervention-MICCAI 2011 (pp. 401408):
Springer.
Fisniku, L., Brex, P., Altmann, D., Miszkiel, K., Benton, C., Lanyon, R., et al. (2008).
Disability and T2 MRI lesions: A 20-year follow-up of patients with relapse onset of
multiple sclerosis. Brain, 131(3), 808817.
Fletcher, P. T., Joshi, S., Lu, C., & Pizer, S. M. (2003). Gaussian distributions on Lie
groups and their application to statistical shape analysis. In Information processing
in medical imaging (pp. 450462): Springer.
Fletcher, P., Lu, C., Pizer, S., & Joshi, S. (2004). Principal geodesic analysis for the
study of nonlinear statistics of shape. IEEE Transactions on Medical Imaging, 23(8),
9951005.
Fox, N., Ridgway, G., & Schott, J. (2011). Algorithms, atrophy and Alzheimers disease:
Cautionary tales for clinical trials. NeuroImage, 57(1), 1518.
Freeborough, P. A., & Fox, N. C. (1998). Modelling brain deformations in Alzheimer
disease by fluid registration of serial MR images. Journal of Computer Assisted
Tomography, 22(5), 838843.
Friston, K., Chu, C., Mourao-Miranda, J., Hulme, O., Rees, G., Penny, W., et al. (2008).
Bayesian decoding of brain images. NeuroImage, 39(1), 181205.
Friston, K. J., Holmes, A. P., Poline, J.-B., Price, C. J., & Frith, C. D. (1996). Detecting
activations in PET and fMRI: Levels of inference and power. NeuroImage, 4,
223235.
Friston, K. J., Holmes, A. P., Worsley, K. J., Poline, J.-B., Frith, C. D., &
Frackowiak, R. S.J (1995). Statistical parametric maps in functional imaging: A
general linear approach. Human Brain Mapping, 2, 189210.
393
Friston, K., & Penny, W. (2003). Posterior probability maps and SPMs. NeuroImage,
19(3), 12401249.
Gaser, C., Volz, H.-P., Kiebel, S., Riehemann, S., & Sauer, H. (1999). Detecting
structural changes in whole brain based on nonlinear deformations Application to
schizophrenia research. NeuroImage, 10, 107113.
Genovese, C. R., Lazar, N. A., & Nichols, T. (2002). Thresholding of statistical maps in
functional neuroimaging using the false discovery rate. NeuroImage, 15(4), 870878.
Hu, X., Erb, M., Ackermann, H., Martin, J. A., Grodd, W., & Reiterer, S. M. (2011).
Voxel-based morphometry studies of personality: Issue of statistical model
specification-effect of nuisance covariates. NeuroImage, 54(3), 19942005.
Hua, X., Gutman, B., Boyle, C., Rajagopalan, P., Leow, A., Yanovsky, I., et al. (2011).
Accurate measurement of brain changes in longitudinal MRI scans using tensorbased morphometry. NeuroImage, 57(1), 514.
Huxley, J. (1932). Problems of relative growth. London: Methuen.
Jack, C. R., Bernstein, M. A., Fox, N. C., Thompson, P., Alexander, G., Harvey, D., et al.
(2008). The Alzheimers disease neuroimaging initiative (ADNI): MRI methods.
Journal of Magnetic Resonance Imaging, 27(4), 685691.
Janke, A., Zhao, H., Cowin, G. J., Galloway, G. J., & Doddrell, D. M. (2004). Use of
spherical harmonic deconvolution methods to compensate for nonlinear
gradient effects on MRI images. Magnetic Resonance in Medicine, 52(1),
115122.
Joshi, S., Davis, B., Jomier, M., & Gerig, G. (2004). Unbiased diffeomorphic atlas
construction for computational anatomy. NeuroImage, 23, 151160.
Jovicich, J., Czanner, S., Greve, D., Haley, E., van der Kouwe, A., Gollub, R., et al.
(2006). Reliability in multi-site structural MRI studies: Effects of gradient nonlinearity correction on phantom and human data. NeuroImage, 30(2), 436443.
Jovicich, J., Czanner, S., Han, X., Salat, D., van der Kouwe, A., Quinn, B., et al. (2009).
MRI-derived measurements of human subcortical, ventricular and intracranial brain
volumes: Reliability effects of scan sessions, acquisition sequences, data analyses,
scanner upgrade, scanner vendors and field strengths. NeuroImage, 46(1),
177192.
Klingenberg, C. P. (2011). MorphoJ: An integrated software package for geometric
morphometrics. Molecular Ecology Resources, 11(2), 353357.
Klingenberg, C. P. (2013). Visualizations in geometric morphometrics: How to read and
how to make graphs showing shape changes. Hystrix, Italian Journal of
Mammalogy, 24(1), 10.
Koikkalainen, J., Lotjonen, J., Thurfjell, L., Rueckert, D., Waldemar, G., & Soininen, H.
(2011). Multi-template tensor-based morphometry: Application to analysis of
Alzheimers disease. NeuroImage, 56(3), 11341144.
Lepore, N., Brun, C. A., Chiang, M.-C., Chou, Y.-Y., Dutton, R. A., Hayashi, K. M., et al.
(2006). Multivariate statistics of the Jacobian matrices in tensor based morphometry
and their application to HIV/AIDS. In Medical image computing and computerassisted interventionMICCAI 2006 (pp. 191198): Springer.
Lepore, N., Brun, C., Chou, Y.-Y., Chiang, M.-C., Dutton, R. A., Hayashi, K. M., et al.
(2008). Generalized tensor-based morphometry of HIV/AIDS using multivariate
statistics on deformation tensors. IEEE Transactions on Medical Imaging, 27(1),
129141.
Lepore, N., Brun, C., Chou, Y.-Y., Lee, A., Barysheva, M., De Zubicaray, G. I., et al.
(2008). Multi-atlas tensor-based morphometry and its application to a genetic study
of 92 twins. In 2nd MICCAI Workshop on Mathematical Foundations of
Computational Anatomy (pp. 4855).
Machado, A. M., Gee, J. C., & Campos, M. (1998). Atlas warping for brain
morphometry. In: SPIE Medical Imaging, Image Processing (pp. 642651),
Citeseer.
Marcus, D., Fotenos, A., Csernansky, J., Morris, J., & Buckner, R. (2010). Open access
series of imaging studies: Longitudinal MRI data in nondemented and demented
older adults. Journal of Cognitive Neuroscience, 22(12), 26772684.
Mitteroecker, P., & Gunz, P. (2009). Advances in geometric morphometrics.
Evolutionary Biology, 36(2), 235247.
Modat, M., Cardoso, M., Daga, P., Cash, D., Fox, N., & Ourselin, S. (2012). Inverseconsistent symmetric free form deformation. In Biomedical image registration
(pp. 7988): Springer.
Mumford, D. (1991). Mathematical theories of shape: Do they model perception?
In: San Diego 91, San Diego, CA: International Society for Optics and Photonics.
Nichols, T. E., & Holmes, A. P. (2002). Nonparametric permutation tests for functional
neuroimaging: A primer with examples. Human Brain Mapping, 15(1), 125.
Niethammer, M., Huang, Y., & Vialard, F. (2011). Geodesic regression for image timeseries. In Medical image computing and computer-assisted interventionMICCAI
2011 (pp. 655662): Berlin, Germany: Springer.
Peelle, J. E., Cusack, R., & Henson, R. N. (2012). Adjusting for global effects in voxelbased morphometry: Gray matter decline in normal aging. NeuroImage, 60(2),
15031516.
394
Pennec, X. (2009). Statistical computing on manifolds: From Riemannian geometry to

computational anatomy. In Emerging trends in visual computing (pp. 347386):
Springer.
Penny, W. D., & Ridgway, G. R. (2013). Efficient posterior probability mapping using
Savage-Dickey ratios. PLoS One, 8(3), e59655.
Prastawa, M., Awate, S. P., & Gerig, G. (2012). Building spatiotemporal anatomical
models using joint 4-d segmentation, registration, and subject-specific atlas
estimation. In Mathematical Methods in Biomedical Image Analysis (MMBIA), 2012
IEEE Workshop on, (pp. 4956), IEEE.
Qiu, A., Younes, L., Miller, M. I., & Csernansky, J. G. (2008). Parallel transport in
diffeomorphisms distinguishes the time-dependent pattern of hippocampal surface
deformation due to healthy aging and the dementia of the Alzheimers type.
Rasmussen, C., & Williams, C. (2006). Gaussian processes for machine learning.
Cambridge, MA: Springer.
Reuter, M., & Fischl, B. (2011). Avoiding asymmetry-induced bias in longitudinal
image processing. NeuroImage, 57(1), 19.
Reuter, M., Schmansky, N., Rosas, H., & Fischl, B. (2012). Within-subject template
estimation for unbiased longitudinal image analysis. NeuroImage, 61(4),
14021418.
Rohlf, F. J., & Marcus, L. F. (1993). A revolution morphometrics. Trends in Ecology &
Evolution, 8(4), 129132.
Schuff, N., Tosun, D., Insel, P. S., Chiang, G. C., Truran, D., Aisen, P. S., et al. (2012).
Nonlinear time course of brain volume loss in cognitively normal and impaired
elders. Neurobiology of Aging, 33(5), 845855.
Slice, D. E. (2007). Geometric morphometrics. Annual Review of Anthropology, 36,
261281.
Studholme, C., Cardenas, V., Blumenfeld, R., Schuff, N., Rosen, H., Miller, B., et al.
(2004). Deformation tensor morphometry of semantic dementia with quantitative
validation. NeuroImage, 21(4), 13871398.
Thirion, J.-P., & Calmon, G. (1999). Deformation analysis to detect and quantify active
lesions in three-dimensional medical image sequences. IEEE Transactions on
Thompson, D. W. (1917). On growth and form (1st ed.). Cambridge, UK: Cambridge
University Press.
Thompson, D. W. (1942). On growth and form (2nd ed.). Cambridge, UK: Cambridge
University Press.
Thompson, W., & Holland, D., & Alzheimers Disease Neuroimaging Initiative (2011).
Bias in tensor based morphometry Stat-ROI measures may result in unrealistic
power estimates. NeuroImage, 57(1), 14.
Thompson, P. M., & Toga, A. W. (1999). Brain warping. San Diego, CA: Academic
Press, Chapter 18, pp. 311336.
Tost, H., Braus, D. F., Hakimi, S., Ruf, M., Vollmert, C., Hohn, F., et al. (2010). Acute D2
receptor blockade induces rapid, reversible remodeling in human cortical-striatal
circuits. Nature Neuroscience, 13(8), 920922.
Vialard, F.-X., Risser, L., Rueckert, D., & Cotter, C. J. (2012). Diffeomorphic 3D image
registration via geodesic shooting using an efficient adjoint calculation.
Whitcher, B., Wisco, J. J., Hadjikhani, N., & Tuch, D. S. (2007). Statistical group
comparison of diffusion tensors via multivariate hypothesis testing. Magnetic
(1996). A unified statistical approach for determining significant voxels in images of
cerebral activation. Human Brain Mapping, 4, 5873.
Worsley, K. J., Taylor, J. E., Tomaiuolo, F., & Lerch, J. (2004). Unified univariate and
multivariate random field theory. NeuroImage, 23(Suppl 1), S189S195.
Younes, L., Qiu, A., Winslow, R., & Miller, M. (2008). Transport of relational structures
in groups of diffeomorphisms. Journal of Mathematical Imaging and Vision, 32(1),
4156.
Yushkevich, P., Avants, B., Das, S., Pluta, J., Altinay, M., Craige, C., et al. (2010). Bias
in estimation of hippocampal atrophy using deformation-based morphometry arises
from asymmetric global normalization: An illustration in ADNI 3 T MRI data.
NeuroImage, 50(2), 434445.
Surface-Based Morphometry
J Shi and Y Wang, Arizona State University, Tempe, AZ, USA
Glossary
Surface conformal parameterization A method to flatten

surfaces with the property that the flattened surfaces have
minimal angle distortions from the original surfaces.
Surface conformal representation Surface conformal factor
and mean curvature, which represent the intrinsic and
Introduction
extrinsic features of a surface, respectively. They uniquely

determine a surface in R^3, up to a rigid motion.
Surface fluid registration An algorithm extending the
image fluid registration method to surfaces, with correction
for distortions introduced by surface parameterization.
In a typical surface-based morphometry pipeline, after MRI

intensity is corrected with nonparametric nonuniform intensity normalization method, the images are usually spatially
normalized into the stereotaxic space using a global affine
transformation. Afterward, an automatic tissue-segmentation
algorithm is used to classify each voxel as the cerebrospinal
fluid (CSF), gray matter (GM), white matter (WM), or different
subcortical structures such as the hippocampus and lateral
ventricle. Usually, marching cube algorithm (Lorensen and
Cline, 1987) is used to generate the cortical or subcortical
surface meshes. Because the human cerebral cortex has a 3-D
highly convoluted topology structure, additional algorithms,
such as LaplaceBeltrami operator-based method (Shi et al.,
2013b), are applied to remove the geometric and topological
outliers and generate robust and accurate meshes for the following surface-based morphometry analyses.
registration and morphometry analysis. Brain surface parameterization has been studied extensively. A good surface parameterization preserves the geometric features and facilitates the
following surface signal processing. Some research proposed
quasi-isometric mappings (Schwartz et al., 1989) or areapreserving mappings (Brechbuhler et al., 1995). Another
branch of research used concepts from conformal geometry
to compute brain surface conformal parameterization
(Angenent et al., 1999; Hurdal and Stephenson, 2004). In
addition to angle-preserving property, conformal parameterization provides a rigorous framework for representing, splitting, matching, and measuring brain surface deformations.
According to differential geometry theory, a general surface
can be conformally mapped to one of three canonical spaces,
the unit sphere, the Euclidean plane, and the hyperbolic space.
For a closed genus-zero surface, the spherical conformal mapping method (Gu et al., 2004) can conformally map it to a
sphere by minimizing its harmonic energy (Figure 1(a)). For
brain surface analysis, sometimes, we introduce landmark
curves to annotate important anatomical regions. After surfaces
are cut open along these given landmark curves, one may get a
surface with multiple holes. Euclidean Ricci flow method
(Wang et al., 2012) or holomorphic 1-form method (Wang
et al., 2010) can conformally map them to the Euclidean plane
(Figure 1(b) and 1(c)). To model a topologically complicated
lateral ventricular surface, hyperbolic conformal geometry
emerges naturally as a candidate method because it can induce
hyperbolic conformal parameterizations without any singularities (Shi et al., 2012; Figure 1(d)). Such a set of global brain
surface conformal parameterization methods are technically
sound and numerically stable. They may increase computational accuracy and efficiency when solving partial differential
equations using grid-based or metric-based computations.
Brain Surface Conformal Parameterization
Brain Surface Registration
Parameterization of brain cortical and subcortical surfaces is a

fundamental problem for surface-based morphometry.
Sometimes, it is also called brain surface flattening. The goal
of surface parameterization is to find some mappings between
brain surfaces and some common flattening surfaces, that is,
some surfaces with constant Gaussian curvature. After that,
these common spaces serve as canonical spaces for surface
Brain surface registration or warping can be achieved by first

mapping each of the 3-D surfaces to a canonical parameter
space such as a sphere (Bakircioglu et al., 1999; Fischl et al.,
1999; Styner et al., 2006) or a planar domain (Pantazis et al.,
2010; Thompson and Toga, 2002). A flow, computed in the
parameter space of the two surfaces, induces a correspondence
field in 3-D. The flow can be computed by aligning curvature,
When registering structural MR images, the volume-based

methods (e.g., Christensen et al., 1996) have much difficulty
with the highly convoluted cortical surfaces due to the complexity and variability of the sulci and gyri. Early research
(Fischl et al., 1999; Thompson et al., 2000; Van Essen et al.,
2001) has demonstrated that surface-based brain mapping
may offer advantages over volume-based brain mapping as a
method to study the structural features of the brain, such as
surface deformation, as well as the complexity and change
patterns in the brain due to disease or developmental
processes.
Preprocessing for Surface-Based Morphometry
http://dx.doi.org/10.1016/B978-0-12-397025-1.00310-9
395
396
INTRODUCTION TO METHODS AND MODELING | Surface-Based Morphometry
Spherical harmonic
mapping
Euclidean
Ricci flow
Conformal slit
mapping
Hyperbolic
Ricci flow
g1
t1
t2
g3
g2
g1
g2
t1
2
t11
t2
g1
t21
(a)
(b)
(c)
(d)
g3
Figure 1 Illustration of different brain surface conformal parameterization methods.
sulcal depth, or other geometric maps of the surfaces, as

applied in FreeSurfer (Dale et al., 1999; Fischl et al., 1999),
or by aligning the surface parameterizations, as applied in
spherical harmonics (Styner et al., 2006), or by aligning meaningful landmark curves, as applied in the cortical pattern
matching algorithm (Thompson and Toga, 2002). Another
set of brain surface warping methods (e.g., Vaillant and
Glaunes, 2005) is based on the large deformation diffeomorphic metric mapping framework (Miller et al., 2002).
They compute diffeomorphic registrations between individual
and template surfaces by generating time-dependent diffeomorphisms in a metric space.
Next, we use a recently developed surface fluid registration
algorithm (Shi et al., 2013a) as an example to highlight some
key steps involved in a typical brain surface registration pipeline (as shown in Figure 2).
A brain surface is first conformally mapped onto a planar
rectangle space with holomorphic 1-form method (Wang et al.,
2011). Figure 2(b), 2(c), 2(f), and 2(g) shows the conformal
parameterizations of the study and template surfaces,
respectively; Figure 2(b) and 2(f) uses texture mapping to
show the angle-preserving property. Figure 2(c) and 2(g) is
the visualization of parameter space, from which we can see
that the geometric features of original surfaces are well preserved. The local conformal factor (Shi et al., 2013a), computed from surface conformal parameterization, encodes a lot
of geometric information about the surface. It can also be used
to compute surface mean curvatures. With differential geometry theories, one can prove that the conformal factor and mean
curve uniquely determine a closed surface in 3 , up to a rigid
motion. We call them the conformal representation of a surface. In
the system, the conformal factor and mean curvature are
summed up, and the dynamic range of the summation is
linearly scaled to form the feature image of a surface, as show
in Figure 2(d) and 2(h). Surface conformal parameterization
is capable of introducing fine-grained grid on surfaces and

converting a 3-D surface registration problem to a 2-D image
registration problem in the parameter domain. So surfaces in
the parameter domain are aligned with the fluid registration
method to maintain a smooth, one-to-one mapping
(Christensen et al., 1996). For a manifold fluid registration,
the traditional NavierStokes equation is extended to a general
form with a compensation term to correct for the area distortion introduced by surface parameterization. With conformal
parameterization, the compensation term is simplified to the
conformal factor. The inverse consistent image registration
algorithm (Christensen and Johnson, 2001) is incorporated
in the system to jointly estimate the forward and inverse transformations between a pair of feature images and to ensure the
symmetry of the registration, as shown in Figure 2(i). Since
conformal mapping and fluid registration generate diffeomorphic mappings, a diffeomorphic surface-to-surface mapping is then recovered that matches surfaces in 3-D.
Surface-Based Morphology Statistics

Since image intensities vary among scans, surface-based morphology may provide robust and biologically sound shape
statistics to characterize variations of brain shapes. Generally
speaking, surface-based morphology statistics can be classified
into two classes: One is the class of transformation-invariant
global shape descriptors that requires no surface registration;
the second class of features is some local measurements
defined on particular locations after the brain surface registration among the population. The first class of features is usually
concise and intrinsic to surface structure, and the second class
of features may lend themselves to immediate visualization.
The choice between different types of features usually depends
on specific applications.
(a)
(e)
Study
surface
(b)
Template
surface
(f)
Feature image
of study surface
Texture
mapping
Texture
mapping
Feature image
of study surface
(c)
Parameter space
visualization
(d)
(g)
Feature image
Parameter space
visualization
(h) of template surface
Forward mapping
Inverse mapping
397
Feature image
of template surface
(i) Inverse consistent fluid registration
Figure 2 Hippocampal surface registration with inverse consistent surface fluid registration algorithm. Adapted from Shi, J., Thompson, P. M.,
Gutman, B., et al. (2013). Surface fluid registration of conformal representation: Application to detect disease effect and genetic influence on
hippocampus. NeuroImage, 78, 111134, with permission.
Global Transformation-Invariant Shape Descriptors

The spherical harmonic representation uses a set of coefficients
that are associated with a specific set of spherical harmonics.
A spherical harmonic is an eigenfunction of the Laplace
Beltrami operator defined on the sphere. There is a countable
set of spherical harmonics that form an orthonormal basis for
the Hilbert space of square integrable functions. Similar to
Fourier series defined on planar domain, the spherical harmonics together with their coefficients can be used to represent
general functions defined on a unit sphere. These coefficients
are also called frequency coefficients and they induce rotationinvariant shape descriptors. A brain surface can be represented
as a vector-valued function defined on the sphere via conformal or area-preserving mapping of its surface to the sphere. The
brain surface (or functions defined on brain surfaces) can then
be decomposed in terms of linear combination of spherical
harmonics. The vector-valued spectrum, that is, the harmonic
coefficients expressed as components of a vector, can be used

to analyze the shape. The main geometric features are encoded
in the low-frequency part. By filtering out the high-frequency
coefficients, one can smooth the surface and compress the
geometry. By comparing the low-frequency coefficients, one
can match surfaces and compute the similarity of surfaces
(Chung et al., 2007; Gutman et al., 2009).
Surfaces can also be classified by conformal geometry. Two
surfaces are conformally equivalent if they can be conformally
mapped to each other. The conformal equivalence classes form
a finite dimensional shape space, which is called the modular
space. The universal covering space of the modular space is the
Teichmuller space. The Teichmuller shape representations are
intrinsic and invariant under conformal transformations and
rigid motions. Wang et al. (2009) computed the Teichmuller
space coordinates with hyperbolic Yamabe flow method and
applied them for lateral ventricular surface classification.
398
Kurtek et al. (2011) proposed the q-map representation of

surfaces and used it to study subcortical structure shapes. The
L2 distances between the q-maps are invariant to surface reparameterizations; thus, this method removes the parameterization variability. There is also certain interest to study
isometry-invariant features in computer vision field. Such features may be useful for longitudinal brain surface-based morphometry study and they deserve some further exploration.
Point-to-Point Local Surface Measurements

Thickness measurements
A popular local measurement is the brain structure thickness.
Brain GM is a 2-D highly convoluted shell of the human
cerebral cortex. The interface between the GM and the CSF is
the outer cortical surface, while the interface between the GM
and WM is the inner cortical surface. The thickness of the GM
shell is usually referred as the cortical thickness. A variety of
methods to estimate cortical thickness have been proposed.
For some subcortical structures, such as the hippocampus
and lateral ventricle, their long tube shape makes it natural to
define a distance between each surface point to the middle axis
of its shape contour, that is, the radial distance (Pizer et al.,
1999; Thompson et al., 2004). The thickness measures are
biologically intuitive and are defined on every surface point
and may be compared across subjects based on the one-to-one
surface registration results. Since different clinical populations
are expected to show different patterns of cortical thickness or
radial distance variations, such thickness measurements have
been frequently used as a quantitative index for characterizing
clinical populations.
deformation tensor is a 2 2 symmetrical matrix and has two

duplicate off-diagonal terms. The mTBM extracts the three
distinct components of the log(S) and forms a 3 1 vector.
The mTBM computes statistics from the Riemannian metric
tensors that retain the full information in the deformation
tensor fields and thus may be more powerful in detecting
surface difference than many other statistics.
Recent researches indicate that the cortical thickness and
cortical surface area are genetically independent (Panizzon
et al., 2009). We proposed to combine the thickness and
mTBM feature to form a new multivariate statistics (Wang
et al., 2011). Since thickness and mTBM measure complementary surface morphometry information, the new multivariate
morphology features may offer a more complete set of surface
statistics and boost statistical power.
Cortical surface asymmetry analysis

with Ricci flow and mTBM
(a)
Lateral ventricular surface morphometry in HIV/AIDS

with holomorphic 1-forms and mTBM
Tensor-based morphometry and multivariate tensor-based

morphometry
After establishing a one-to-one correspondence map between a
pair of surfaces, the Jacobian matrix J of the map is computed
as its derivative map between the tangent spaces of the surfaces.
Surface tensor-based morphometry (TBM) and its variant, multivariate tensor-based morphometry (mTBM), are defined to
measure local surface deformation based on the local surface
metric tensor changes. Practically, in the triangle mesh surface,
the derivative map is approximated by the linear map from one
face [v1, v2, v3] to another [w1, w2, w3]. First, we isometrically
embed the triangles [v1, v2, v3] and [w1, w2, w3] onto the plane;
the planar coordinates of the vertices of vi, wj are denoted using
the same symbols vi, wj. We can explicitly compute the Jacobian
matrix for the derivative map:
J w3 w1 , w2 w1 v3 v1 , v2 v1 1
Then, we use multivariate statistics on deformation tensors
and adapt the concept to surface tensors. We define the deformation tensors as S (JTJ)1/2. The TBM intends to study statistics of Jacobian determinant det(J) or log(det(J)).
For mTBM, we consider a new family of metrics, the logEuclidean metrics (Arsigny et al., 2006). These metrics make
computations on tensors easier to perform, as the transformed
values form a vector space, and statistical parameters can then
be computed easily using standard formulas for Euclidean
spaces. In practice, the matrix logarithm of the surface
(b)
ApoE4 effects on hippocampal surface morphometry with

inverse consistent surface fluid registration and mTBM
p<0.001
p<0.005
p<0.010
p<0.015
p<0.020
p<0.025
p<0.030
p<0.035
p<0.040
p<0.045
p<0.050
p>0.050
(c)
Figure 3 Applications of mTBM in group difference analyses. (a) The

brain asymmetry study results in 14 healthy control subjects; (b)
statistical p-map from ventricular surfaces between 11 HIV/AIDS patients
and 8 matched control subjects; (c) statistical p-map from all
nondemented subjects in Alzheimers Disease Neuroimaging Initiative
(ADNI) baseline subjects between ApoE e4 carriers and noncarriers
(N 558). Adapted from Wang, Y., Zhang, J., Gutman, B., et al. (2010).
Multivariate tensor-based morphometry on surfaces: Application to
mapping ventricular abnormalities in HIV/AIDS. NeuroImage, 49(3),
21412157, with permission; Wang, Y., Shi, J., Yin, X., et al. (2012).
Brain surface conformal parameterization with the Ricci flow. IEEE
Transactions on Medical Imaging, 31(2), 251264, with permission;
Shi, J., Thompson, P. M., Gutman, B., et al. (2013). Surface fluid
registration of conformal representation: Application to detect disease
effect and genetic influence on hippocampus. NeuroImage, 78, 111134,
with permission.
Statistical Inference and Applications of Surface-Based

Morphometry
The surface-based morphology statistics can be directly used to
assess group difference between a clinical population and normal controls, study the simultaneous effects of multiple factors
or covariates of interest, and evaluate disease burden,
progression, and response to interventions. Specifically,
Students t-test (for univariate statistics) and Hotellings T2
test together with Mahalanobis distance may be used for
group difference study and Pearson correlation for correlation
study. A rich set of machine learning algorithms, such as support vector machine, may use the obtained morphology statistics for disease diagnosis and prognosis research.
Given maps of surface-based morphology statistics, multiple comparisons methods, such as false discovery rate methods
and permutation methods, may be employed to assign overall
(corrected) p-values of the map (or the features in the map),
corrected for multiple comparisons. As a result, the generated
surface p-maps (usually by permutation tests) can help visualize the most statistically significant areas, and the corrected
p-values quantify the global statistical significance over the
whole brain cortical or subcortical surfaces.
Surface-based morphometry has been widely used to in
human brain mapping research (Fischl et al., 1999; Thompson
et al., 2000; Van Essen et al., 2001). Figure 3 illustrates several
p-maps from our prior work that show the group differences
detected by mTBM in different applications.

Bayesian Multiple Atlas Deformable Templates; Cortical Thickness
Mapping; False Discovery Rate Control; Rigid-Body Registration;
Tissue Classification.
References
Angenent, S., Haker, S., Tannenbaum, A., et al. (1999). On the LaplaceBeltrami
operator and brain surface flattening. IEEE Transactions on Medical Imaging, 18(8),
700711.
Arsigny, V., Fillard, P., Pennec, X., et al. (2006). Log-Euclidean metrics for fast and
simple calculus on diffusion tensors. Magnetic Resonance in Medicine, 56(2),
411421.
Bakircioglu, M., Joshi, S., & Miller, M. I. (1999). Landmark matching on brain surfaces
via large deformation diffeomorphisms on the sphere. In: Proceedings of the SPIE
medical imaging, pp. 710715.
Brechbuhler, C., Gerig, G., & Kubler, O. (1995). Parametrization of closed surfaces for
3-D shape description. Computer Vision and Image Understanding, 61(2),
154170.
Christensen, G. E., & Johnson, H. J. (2001). Consistent image registration. IEEE
Christensen, G. E., Rabbitt, R. D., & Miller, M. I. (1996). Deformable templates using
large deformation kinematics. IEEE Transactions on Image Processing, 5(10),
14351447.
Chung, M. K., Dalton, K. M., Shen, L., et al. (2007). Weighted fourier series
representation and its application to quantifying the amount of gray matter. IEEE
Dale, A. M., Fischl, B., & Sereno, M. I. (1999). Cortical surface-based analysis I:
Segmentation and surface reconstruction. NeuroImage, 9, 179194.
Fischl, B., Sereno, M. I., & Dale, A. M. (1999). Cortical surface-based analysis II:
Inflation, flattening, and a surface-based coordinate system. NeuroImage, 9(2),
195207.
399
Gu, X., Wang, Y., Chan, T. F., et al. (2004). Genus zero surface conformal mapping and
its application to brain surface mapping. IEEE Transactions on Medical Imaging,
23(8), 949958.
Gutman, B., Wang, Y., Morra, J., et al. (2009). Disease classification with hippocampal
shape invariants. Hippocampus, 19(6), 572578.
Hurdal, M. K., & Stephenson, K. (2004). Cortical cartography using the discrete
conformal approach of circle packings. NeuroImage, 23(Suppl. 1), S119S128.
Kurtek, S., Klassen, E., Ding, Z., et al. (2011). Parameterization-invariant shape
comparisons of anatomical surfaces. IEEE Transactions on Medical Imaging, 30(3),
849858.
Lorensen, W. E., & Cline, H. E. (1987). Marching cubes: A high resolution 3D surface
construction algorithm. SIGGRAPH Computer Graphics, 21(4), 163169.
Miller, M. I., Trouve, A., & Younes, L. (2002). On the metrics and Euler-Lagrange
equations of computational anatomy. Annual Review of Biomedical Engineering, 4,
375405.
Panizzon, M. S., Fennema-Notestine, C., Eyler, L. T., et al. (2009). Distinct genetic
influences on cortical surface area and cortical thickness. Cerebral Cortex, 19(11),
27282735.
Pantazis, D., Joshi, A., Jiang, J., et al. (2010). Comparison of landmark-based
and automatic methods for cortical surface registration. NeuroImage, 49(3),
24792493.
Pizer, S., Fritsch, D., Yushkevich, P., et al. (1999). Segmentation, registration, and
measurement of shape variation via image object shape. IEEE Transactions on
Schwartz, E. L., Shaw, A., & Wolfson, E. (1989). A numerical solution to the generalized
mapmakers problem: Flattening nonconvex polyhedral surfaces. IEEE Transactions
on Pattern Analysis and Machine Intelligence, 11(9), 10051008.
Shi, Y., Lai, R., & Toga, A. W. (2013b). Cortical surface reconstruction via unified Reeb
analysis of geometric and topological outliers in magnetic resonance images. IEEE
Shi, J., Thompson, P. M., & Wang, Y. (2012). Hyperbolic Ricci flow and its application
in studying lateral ventricle morphometry. In Multimodal brain image analysis
(pp. 6176). Berlin/Heidelberg: Springer.
Shi, J., Thompson, P. M., Gutman, B., et al. (2013a). Surface fluid registration of
conformal representation: Application to detect disease effect and genetic influence
on hippocampus. NeuroImage, 78, 111134.
Styner, M., Oguz, I., Xu, S., et al. (2006). Framework for the statistical shape
analysis of brain structures using SPHARM-PDM. The Insight Journal, (1071),
242250.
Thompson, P. M., Giedd, J. N., Woods, R. P., et al. (2000). Growth patterns in the
developing human brain detected using continuum-mechanical tensor mapping.
Nature, 404(6774), 190193.
Thompson, P. M., Hayashi, K. M., de Zubicaray, G. I., et al. (2004). Mapping
hippocampal and ventricular change in Alzheimers disease. NeuroImage, 22(4),
17541766.
Thompson, P. M., & Toga, A. W. (2002). A framework for computational anatomy.
Computing and Visualization in Science, 5, 112.
Vaillant, M., & Glaunes, J. (2005). Surface matching via currents. Information
Processing in Medical Imaging, 19, 381392.
Van Essen, D. C., Drury, H. A., Dickson, J., et al. (2001). An integrated software suite for
surface-based analyses of cerebral cortex. Journal of the American Medical
Informatics Association, 8(5), 443459.
Wang, Y., Dai, W., Gu, X., et al. (2009). Teichmuller shape space theory and its
application to brain morphometry. Medical Image Computing and ComputerAssisted Intervention, 12(Pt 2), 133140.
Wang, Y., Shi, J., Yin, X., et al. (2012). Brain surface conformal parameterization with
the Ricci flow. IEEE Transactions on Medical Imaging, 31(2), 251264.
Wang, Y., Song, Y., Rajagopalan, P., et al. (2011). Surface-based TBM boosts power to
detect disease effects on the brain: An N 804 ADNI study. NeuroImage, 56(4),
19932010.
Wang, Y., Zhang, J., Gutman, B., et al. (2010). Multivariate tensor-based morphometry
on surfaces: Application to mapping ventricular abnormalities in HIV/AIDS.
NeuroImage, 49(3), 21412157.
Relevant Websites
http://brainvis.wustl.edu/wiki/index.php/Caret:About CARET.
http://gsl.lab.asu.edu/conformal.htm Subcortical Morphometry System.
http://loni.usc.edu/ BrainSuite.
https://surfer.nmr.mgh.harvard.edu/ FreeSurfer.
Bayesian Multiple Atlas Deformable Templates

MI Miller, S Mori, X Tang, D Tward, and Y Zhang, Johns Hopkins University, Baltimore, MD, USA
Glossary
Atlas/template A reference image or manifold (e.g., surface,

curve, or point set) typically representing anatomy, to be
used for interpreting data of the same type.
Diffeomorphism A smooth invertible transformation with
a smooth inverse.
EM algorithm The abbreviation of
expectationmaximization algorithm, an iterative method
for finding maximum likelihood or maximum a posteriori
(MAP) estimates of parameters in statistical models.
Eulerian velocity A time dependent vector field, vt(x),
interpreted as the velocity of particles at each spatial
coordinate x, at time t. This is a natural way to express
velocity with respect to a stationary observer.
Gaussian random field A collection of random variables,
indexed by time or space or both, with the property that
when acted upon by any linear functional, the result is a
Gaussian random variable.
Geodesic The shortest path connecting two points. These
paths are stationary, that is, any small perturbation of the
geodesic will not change its length.
Geodesic flow A flow that generates the shortest path
between two points.
Group A set of objects (e.g., transformations) together with
a binary operation (e.g., composition) satisfying the
properties of closure, associativity, and existence of identity
and inverse elements.
Hypertemplate A template that constrains the infinite
dimensional template estimation problem within a Bayesian
strategy.
Lagrangian velocity A vector field, vlt(x) interpreted as the
velocity of the particle with the label x (typically its spatial
coordinate at time 0), at time t. This is a natural way to
express velocity with respect to an observer moving with the
flow.
Large deformation diffeomorphic metric mapping
(LDDMM) A computational algorithm for
calculating geodesic flows on the diffeomorphism
group, which minimizes a data attachment and
regularization cost.
Lie group A group whose elements form a smooth
manifold.
Introduction
The low-dimensional matrix Lie groups form the core dogma
for the now classic study of the kinematics of rigid bodies in
the field of rigid body mechanics. Their infinite dimensional
analog, the diffeomorphism group, one-to-one smooth transformations (Christensen, Miller, & Rabbit, 1995; Dupuis,
Likelihood fusion An integration of the log-likelihoods

obtained based on the information from each atlas. The loglikelihood is computed in the E-step of the EM algorithm.
Linear discriminant analysis (LDA) The optimal procedure
for classification between two Gaussians with different mean
and equal variance.
Manifold A set which can be locally parameterized by
smooth mappings to Euclidean space.
Maximum a-posteriori estimation (MAP) A method
similar to MLE in a Bayesian setting, wherein parameters to
be estimated have a prior distribution. The posterior
(likelihood of the parameters given the data), as a function
of the parameters, attains its maximum value at the MAP
estimate.
Maximum-likelihood estimation (MLE) A method of
estimating the parameters of a statistical model based on a
given sample. The likelihood, as a function of the
parameters, attains its maximum value at the MLEs.
Metric/metrizable space A set together with a function for
calculating distance between pairs of elements.
Mode approximation The approximation of the integral of
a function with respect to a probability measure, taking the
value of integral to be the integrand function evaluated at
the maximum of the probability measure. If the measure is
concentrated at its peak this will be a good approximation.
Momentum A linear form, acting on smooth velocity fields
to produce a real number. The term is to be understood by
analogy with mechanics, where the action of momentum on
velocity (e.g., mv v) is proportional to kinetic energy. Here
the action of momentum on velocity (i.e., (Lv| v)) is equal to
the energy of the velocity field (i.e., its norm squared).
MRI Magnetic resonance imagery, a medical imaging
technique used in radiology to visualize internal structures
of the brain and body in detail.
Orbit The orbit of a template, under the action of
transformations in a group, is the set of all possible
transformed templates.
Random generative model A stochastic model from which
the data is viewed as a random observation.
Subcortical The portion of the brain interior to the cerebral
cortex, including white matter tracts and gray matter nuclei.
Submanifold A subset of a manifold which is a manifold
itself.
Grenander, & Miller, 1998; Grenander & Miller, 2007; Miller

& Younes, 2001; Trouve, 1995; Younes, 2010), plays the central role in studying deformable structures in the field of
computational anatomy (CA) (Ashburner, 2007, 2009;
Grenander & Miller, 1998; Miller, 2004; Miller, Trouve, &
Younes, 2002; Pennec, 2011; Thompson & Toga, 2002). At
the heart of CA is the comparison of shape and form,
http://dx.doi.org/10.1016/B978-0-12-397025-1.00312-2
401
402
INTRODUCTION TO METHODS AND MODELING | Bayesian Multiple Atlas Deformable Templates
morphology, as pioneered by DArcy Thompson (Thompson,

1942). We are focusing on shapes formed by the submanifolds
of the human body in 3 . Comparison of their coordinates is
described via flows of diffeomorphic correspondences connecting them. The morphological space is made into a metrizable space via a metric induced via the geodesic lengths of the
flows. We call this diffeomorphometry; the diffeomorphic correspondences are a positioning system providing our biological systems with coordinates. Since the information is
transported along the geodesics defining the metric we call it
geodesic positioning, and the positions of information in coordinatized space geodesic coordinates (Miller et al., 2014).
This paper focuses on random generative models for the
orbits of human anatomy. Our model of anatomical objects is
that the set of anatomies I 2 I are carried by random transformations of the coordinate system represented by 2 G, a
group of one-to-one, smooth, transformations on the background space 3 . The random generative models allow us to
focus on derivation of several maximum-likelihood and MAP
estimation problems within this setup.
In this deformation setting, in which large deformation
diffeomorphic metric mapping (LDDMM) arises but is associated to multiple atlases, it is our most significant attempt to
bring together the multiple extensions over the past decade on
MAP estimation of atlases, segmentations, and disease scoring
with the random orbit models of CA. This multi-orbit generative model was in the earlier work of Allasioneire et al.
(Allassonnie`re & Kuhn, 2010; Allassonnie`re, Kuhn, & Trouve`,
2010) on multimodal models and random sampling. It is also
reminiscent of the jump-diffusion program (Grenander &
Miller, 1994) we began in the early 1990s in which deformations were much simpler, but the notion of having explanations
of an image based on multiple models of different parametric
dimension was certainly pursued there in much gorier detail.
Our foray here into explanations shared by multiple atlases has
much in common, as jumping from one atlas to another is
really the multimodal model explanation problem, although
we have chosen to focus on mode approximations in this
setting for computational reasons, rather than random sampling approaches as pursued in the former two examples.
The Algebraic Orbit Model of Deformable Templates

CA examines the interplay between imaged anatomical structures indexed implicitly or explicitly with a coordinate system,
and their group of transformations. A transformation 2 G is
applied to an anatomical structure or form I 2 I lying in some
set I called here the anatomical orbit; the deformable template
model of computational anatomy views these transformations
as group actions.
The Algebraic Orbit Model as Group Action

The two principal objects that we study in CA are substructures
in the human body (collections of 0, 1, 2, and 3 dimensional
submanifolds), and dense scalar and tensor imagery. The transformations are diffeomorphisms 2 G, a group of one-to-one,
smooth, transformations on the background space 3 , with
law of composition () ((()) and smooth inverse
1. In functional anatomy (Miller & Qiu, 2009) we associate

the reparameterizations 2 G of the manifold, the structural
phenotype, to the imagery the functional phenotypes. The
separation between structure and function is not always
distinct.
Statement 1: The algebraic orbit model I is that the elements
I 2 I and transformations 2 G interact as a pair via group
action (, I), denoted algebraically according to
, II
[1]
The orbit I is a homogeneous space under the action of G

so that for all , 2 G, ( ) I ( I), and for all I, I0 2 I
there exist 2 G such that I I.
This algebraic notion of models as a homogeneous space
under the action of diffeomorphisms is important as it extends
to morphological spaces the usual setting of rigid objects moving in a Euclidean space, which form a homogeneous
space under the action of the rotation and translation group.
We call this action of transferring functional and structural
information according to eqn [1] geodesic positioning (Miller
et al., 2014).
Dense Imagery: For images acting as a dense function

I : 3 ! , such as MRI imagery, then the transformation
acts on the right via its inverse
:
, III1
1
with I x I x, x 2 3
[2]
Vector Fields: For images representing vector fields,

I : 3 ! 3 a three-dimensional vector, several actions are
useful:

I dI1 ,whereIx dj1 x I 1 x
[3]
When I is a vector field of frames, that is, orthonormal basis of

3 , we have

dI1
d* I3 dI1
d* I3
,
,
1
I
[4]
k dI1 k k d* I3 dI1 k k d* I3 k
Tensor Images: For tensor images which are 3 3 nonnegative symmetric matrices, an action originally defined
by Alexander and Gee (Alexander, Gee, & Bajcsy, 1999)
rotates the eigenfunctions using the previous action on
frames and leaving the eigenvalues unchanged. Another
standard action is
:
IDID*1
[5]
The Random Observation Model

The random generative models (Grenander & Miller, 1998,
2007) have now been used extensively for deriving algorithms
for template estimation (Allassonnie`re, Amit, & Trouve, 2007;
Ma, Miller, Trouve, & Younes, 2008; Ma, Miller, & Younes,
2010), multi-atlas segmentation (Tang et al., 2013) and for
principal component analysis (PCA) based reconstruction of
shape (Qiu, Younes, & Miller, 2012; Tward, Ma, Miller, &
Younes, 2013). There are two forms of randomness, the

selection of the random element I 2 I which plays the role of
the source, and the random observation denoted ID the
output available to the observer, the MRI image, for example,
given the element in the orbit. We have to work towards
writing down the scoring model (ID, y), a function of jointly
measured imagery and the unknown parameters in the parameter space y 2 Y.

D
Ij mj
Kij E ID
i mi
403
Z
Dxi Dxj
K x, ydxdy:
[8]
For surfaces we have used other models associated to the

manifolds, introducing randomness associated to their vertex
representation (Ma et al., 2010).
Integrating over the Orbit Deformation Model

The Conditionally Gaussian Random Field Model
In the random orbit model, we model the observed image ID as
a random vector field resulting from some distortion or noise
process D 2 D operating on the element in the orbit I 2 I ; we
write the conditional density of observing ID 2 I D in the observation space, conditioned on I 2 I as p(ID|I). The generative
model matters because we will perform MAP estimation on
parameters y which are jointly measured with the image ID,
with the parameters taking several forms the disease type
associated to the image, the volume of a structure in the
image, the labeling of the image into a segmentation field of
subcortical structures, or the common template generated from
a population of measured anatomies.
Now we make explicit the conditional density p(ID|I); of
course while this may be simple given the underlying orbit
element I 2 I , we will have to deal with the complexity of not
knowing I, which makes the density high dimensional as it is a
hidden random field model (Kunsch, Geman, & Kehagias,
1995). For this reason, we emphasize the conditional dependence in the modeling. In the next section, we will address the
infinite dimensionality of not knowing the a priori of the
element in the orbit I 2 I .
One of the continuum models that makes sense with neighborhood structure (besides Poisson) are Gaussian random fields
in which the noise is Gaussian, implying that conditioned on I
then ID is a Gaussian random field with mean field m(x), x 2 X
determined by I and covariance operator K(x, y), x, y 2 X X. In
positron emission tomography this would only be a second
order representation as the Poisson model (Snyder & Miller,
1991) is more appropriate; modeling it as additive noise implies
that the noise multiplies with the mean making it more nonlinear. For the Gaussian case in which the image is a scalar
density, ID is a conditional Gaussian function with mean function EID(x) m(x), and covariance operator given by

K x, y E ID x mx ID y my :
[6]
Of course, removing the conditioning even the simple Gaussian model loses its natural second-order structure.
For images, we think of ID as associated to the lattice, with
discrete locations xi 2 X, i 1, . . ., n and associated voxel Dxi
with \ iDxi X. The simplest continuum model models the
observation as being generated from the integral within each
voxel, with the associated noise or distortion modeled as additive given the conditioned element in the orbit I 2 I :
Z
Ixdx noise
[7]
ID
i
Dxi
resulting in density jointly measured with the unknown

parameters.R Then the Gaussian mean becomes a vector
EID
i mi Dxi Ixdx, and the covariance a matrix:
Of course we have equipped our orbit with deformations,

coordinate transformations to accommodate the infinite variation of human structure. To generate our scoring model
p(ID, y) of the observable we are going to have to integrate
over all possible images in the orbit. This implies that even if
we have an explicit form for the conditional density on images,
which may even be Markov when viewed as a conditional
random field with local neighborhood structures, integrating
over all coordinate changes gives us a highly interconnected
hidden random field model (Kunsch et al., 1995).
For this, we exploit the dependence on the randomness
within the deformation orbit of the observed images ID by
conditioning on the atlas and deformation pair (Ia, ), with
the homogeneous orbit ensuring I Ia. These become the
conditioning arguments in the random field with conditional
density p(ID, y| Ia, a), conditioned on the pair , Ia. Taking the
atlas as given and fixed implies the scoring function with prior
density a()d becomes
Z

[9]
p ID , yjIa , a p ID , yjIa , a ad:
G
Here we use a() as the generic notation representing the prior

density on the mixing parameters, the mixing occurring over
diffeomorphisms. In the subsequent cases we will use p when
we mix over atlases, and then it will be a discrete probability.
We have to be careful as to what we mean by eqn [9]. The
group of diffeomorphisms is very big! In this case the prior
density is not well defined, and we will have to revisit this again
in the subsequent section. We solve our integration over the
nuisance variables of unknown deformation using the mode
approximation within the space of deformations.
Probabilistic Transformation via Diffeomorphic Flows

The diffeomorphic transformations 2 G are generated as
flows. If vt is a time-dependent vector field on 3 , the flow
associated to the differential equation y_ vt y is given,
together with its inverse, for t 2 [0, 1], by
dt
d1
t
vt t ,
d1
t vt ,
dt
dt
[10]
where df denotes the 3 3 Jacobian matrix of f : 3 ! 3 , and

both equations are solved with initial condition 0 1
0 id.
Here _ 2 3 is the Lagrangian velocity indexed to the initial
body configuration, with v 2 3 the Eulerian vector field
indexed to the flow coordinates as a function of time t. We
require the flows eqn [10] to generate smooth flows of diffeomorphisms (with inverse and well defined Jacobian) by constraining the spatial derivatives of vt to belong to a Hilbert
space V of C1 continuously differentiable vector fields. The
404
resulting group GV is given by (Dupuis et al., 1998;

Trouve, 1995)

Z 1
:
GV v1 :
[11]
kvt kV dt < 1 :
0
For purposes of computing the flows corresponding to

eqn [11], we rewrite the norm and inner product in V to
enforce this continuous differentiability condition by explicitly
introducing L , a matrix differential operator which is used to
define the inner-product <v, w > V in the Hilbert space by
defining the linear form m Lv dual to the vector field. Then
the inner-product between v, w 2 V becomes
:
:
< v, w>V Lv j w
Z X
3
3 i1
wi xmi dx
[12]
:
with norm k v k 2V (Lv|v).
When
Lv(dx) m(x)dx has vector
P
R
density m, then Lv
w i 3 mi xwi xdx. We call m Lv
the Eulerian momentum and we choose L to have sufficient
number of derivatives so that the norm being finite implies the
continuous embedding in differentiable functions with at least
1 spatial derivative.
We exploit the parameterization of the diffeomorphism
group by exploiting the geodesic flows from the identity.
We parameterize our group of flows via their initial vector
field vt0 2 V, _ t vt t , for the subset of flows
gtv0 , g_vt 0 vt gtv0 , t 2 0, 1 corresponding to geodesic connections
satisfying conservation (Miller, Trouve, & Younes, 2006)
between coordinate systems so that for all smooth w 2 V, with
g_v00 v0 ;

v v 1
Lvt
dgt 0 w gt 0
Lv0 j w:
[13]
This allows us to induce our distribution on robust deformations by expanding in the tangent space at the identity of the
group and shooting outwards. This initial tangent representation we call geodesic coordinates (Miller et al., 2014).
Our random model is induced by building the distribution
on the initial condition on the vector field at the identity
v0 vt0 determining the geodesic solutions, modeling it as a
zero-mean Gaussian random field with
X
Vi ci , Vi is Gaussian, with variance EVi 2 li : [14]
v0
i
P
We assume the Gaussian process is of trace class
li < 1.
Thus in our prior density we have reparameterized eqn [10]
in v0, and a(n) will correspond to a Gaussian random field
model on the initial tangent vector field which shoots the
geodesics. This is as we did in using the generative model
interpretation for template estimation originally formulated
in Ma et al., 2008. We shall see below that we will solve our
atlas interpretation via integration over the nuisance variables
of unknown deformation using the mode approximation
within this subset of geodesic deformations.
Multimodal Multi-Atlas Interpretation

Now we add the randomness of the atlas which generates the
unknown element in the orbit I 2 I to our random orbit
deformable template model, so that the pair a, Ia enters into

the random model. The orbit model is the union over individual atlas orbits:
:
[15]
I Ua fI : I 2 Ia , 2 GV g:
The Multimodal Multi-Atlas model

We make the estimation robust by limiting the complexity of
the family of models over all atlas classes via some known fixed
prior distribution p(A a), a 1, 2, . . .. We examine the MAP
problem in which the parameters y 2 Y are jointly distributed
with respect to the observed MRI imagery ID in the context of
a family of atlases {Ia}.
We use our atlases in two ways, which we call
interpretation. First, given the atlas Ia, we want to be able to
score the observed image ID according to our scoring function
p(ID, y|Ia), the conditional density. Second, given the family of
atlases, we would like to associate a score or probability to how
much each atlas is used in interpreting the observable denoted
as p(A a|ID, y).
We make the importance of these two interpretation functions explicit by examining the estimation of unknown, random parameters y 2 Y such as disease category and
segmentation labels. These are defined as some scalar or vector
random variables, which are jointly measurable with the
observed image and are scored based on their joint density.
MAP estimation delivers them by maximizing with respect to y.
Statement 2: Define our MAP estimator of y 2 Y in the multimodal mixture model as

y^ arg max p ID , y
y2Y
[16]
with the likelihood model for inference being the joint density

X
[17]
pA ap ID , yjIa :
p ID , y
a
We notice that since p(ID) is constant with respect to y, the

MAP estimator defined based on the joint-density is equivalent
to that based on the conditional density p(y|ID). With multiple
atlases generating the observed image, the fusion of the likelihood functions yields the multimodal mixture model with the
prior averaging over models. This is the generative model with
which we score each atlas image and perform inference on the
parameters. The image shares probability with many different
atlases.
We now show that at the heart of our MAP estimation is the
conditional probability of an atlas interpreting the observable

:

p A ajID Pr A ajID :
[18]
Of course, having observed the measured ID, the conditional probability p(A|ID) changes greatly from the prior
probability p(A). We demonstrate that the solution of the
MAP problem is this conditional probability. Essentially this
is an expectationmaximization (EM) algorithm iteration
(Dempster, Laird, & Rubin, 1977).
Statement 3: For real-valued interior points y 2 Y, the iteration y1, y2, . . . given by

X

:
ynew arg max
p A ajID , yold log p ID , yjIa
y
are monotonic in likelihood p(ID, ynew) p(ID, yold) of

eqn [17], with fixed points satisfying the same necessary maximizer conditions as the MAP estimator of eqns [16] and [17]
given by max y log pID , y.
To see this, calculate the maximizer
@y

X
p A ajID , yold log pID , yjIa
a
@ pID , y
I
X
y
a

p A ajID , yold
p ID , y
Ia
a
[20]
at fixed points ynew yold y* which gives the necessary interior point maximizer conditions:

old
X p ID , y j Ia
@ pID , yj Ia

pA a y D
pI ,yj Ia
ynew y*
p ID , yold
a

pÎD , yj Ia pa
0 :
p^ A aj ID , y P D
^
0
a0 p I , yj Ia pa
[19]
pID , y*
Large Deformation Diffeomorphic Metric Mapping

At the heart of these mode approximations is a basic computation called LDDMM (Ashburner, 2007; Beg, Miller, Trouve, &
Younes, 2005). If we take the most generic conditional Gaussian random field model, conditioned on I 2 I the observable
density is p(ID|I); given the diffeomorphism and template or
atlas generating I gv0 Ia , then log pID j I k ID Ia g1v0 1 k2 .
Then exploiting
R the fact that for geodesics gv0 to have constant
norm so that 10 k vt k 2Vdt k v0 k 2V, then the problem of finding
the mode reduces to computing Begs LDDMM solving for vt,
t 2 [0, 1] and taking v0. This is useful enough to make it a
statement.
v:_ v vv
This is the necessary maximizer conditions of eqn [17].

The MAP estimation is handled within the class of generative
models by representing the observable imagery ID as a conditionally Gaussian random field, conditioned on the atlas-charts
and the diffeomorphic change of coordinates of each chart. The
atlas-charts and their diffeomorphic correspondences are
unknown and viewed as latent variables. The iteration of
eqn [19] is an instance of the EM algorithm (Dempster et al.,
1977) yielding the likelihood-fusion equation which the a posteriori estimation maximizes. In the single-atlas case, one atlas is
used to interpret the image globally; in the multi-atlas orbit
model, multiple atlas-charts are used to interpret the image
locally. The conditional density we use is the random orbit
model p(ID, y|Ia) conditioned to each atlas, which will require
the mode approximation. We denote the diffeomorphisms
_ v which are also geodesics using the notation gv0 .
Statement 4: Mode Approximation to our Interpretation
Functions
Given the observable ID associated to unknown diffeomorphic
change of coordinates , define the optimizing geodesic shoots
g_v0 vgv0 , g_v00 v0 , according to,
[21]
with optimizing geodesic gva connecting atlas to data given by

va argmax k v0 k2V log p ID jg1v0 Ia :
v0
v0 , g_0 v0
[24]
Statement 5: Given ID which is conditionally Gaussian with

mean field Ia, then LDDMM solves for _ v, with v0 _ 0
according to
Z 1

2
k

k vt k2V dt:
[25]
v^ argmax k ID Ia v1
1

pA a@y p ID , y*jIa 0

d
Lvt j dgtv0 w gtv0 1 0 8 w 2 V
dt
405
[22]
Define the mode approximation to the nuisance integral of

eqn [9] as

:

[23]
p^ ID , yjIa p ID ,y, g1va jIa p ID , yjg1va Ia aa va :
Define the mode approximation to the atlas selector
function
Disease Estimation from Multiple Groups

Now we examine the problem of estimating the disease label
y 2 Y given the image data ID, with collections of subpopulations of atlases each with different diseases. For each disease
category, y 2 Y, the atlas anatomy is denoted as Iay for
ay 2 {1, . .., Ny}.
Given the incomplete data, the measured image ID with loglikelihood log p(ID, y), and the many atlases, calculate the MAP
estimator of the disease y 2 Y associated to the measurement:

[26]
y^ arg max log p ID , y :
y
The observable I is assumed to have conditional density

p(ID|I), with unobserved underlying anatomy I 2 I unknown.
The anatomy I is assumed to be a deformation of one of the
templates Iay , inheriting its parameter value y.
The approach here will be to calculate p(ID|y) by integrating
out the nuisance variables, then apply Bayes formula to obtain
p(y|ID). We used the conditional structure and the mode
approximation of eqn [23] to give our approximation:
pID j y
_
Ny
X
ay 1
Ny
X
Z
pay j y
GV
ay 1

p ID j Iay , ay , y aj ay ,yd
Ny
X

pay j yp ID , y, g1va j Iay
pay j yp^ ID , yj Iay :
a1
Using Bayes formula gives

D

PNy
D
ay 1 pyp ay y p I , y Iay
:
p yjI P
0
0
PNy0
0
^ ID , y
Ia 0
0
0
y p
p
a
p
y
a
1
0
y 2Y
y
y
y

We choose the atlas prior uniformly p ay
y N1y .
[28]
406
Disease Classification Algorithm: This gives us the disease

classification algorithm.
1. For each disease type y 2 Y, choose a set of atlases
Iay , ay 1, .. ., Ny and assign them prior probabilities p(ay),
and assign group priors related to disease p(y), and assign
deformation prior aay vay .
2. Compute the mode approximation of eqns [23], [24], and
[25] using LDDMM algorithm.

:
va
va
p^ ID , yjIay p ID , y, g1 y jIay p ID , yjg1 y Iay aay vay
3. Choose disease type from eqn [28] maximizing over
diseases:
PNy

^ D
ay 1 pyp ay y pI , yj Iay

0
PNy0
^ D 0
0
a1 pyp a y p I , y j Iay0
y 2Y

y^ arg max p^ yj ID P
Vk as in eqn [14], with the variance given by PCA. This gives the
finite dimensional prior in the dimensionality reduced
coordinates.
Two methods for estimating a deformation prior are illustrated in Figure 1, depicted by (e) and (f)(g). Shown in (e) are
given atlases Iay depicted as pointsfor each disease class (blue/
green), along with estimates of separate priors for each disease
type, aay , ay 1, ... , Ny , depicted as the Gaussian ellipsoids.
Shown in (f)(g) is the alternative where we represent the
entire disease via one prior for each disease type with (f)
showing the prior estimated from the group ay(), measured
with respect to a population template Iy (cyan) and (g) showing the preassigned prior to the groups taken from the
population.
This is illustrated in Figure 1 for a set of left hippocampal

surfaces. The crucial question becomes the calculation of the
deformation prior aay vay which we have examined in some
detail. The most obvious prior is based on the distance as
measured by the metric in deformation space V, the
probability depending on the norm of the initial vector field
in the tangent
space independent
of disease according to

avay exp 1=2 k vay k2V . However, this space is not
informed by the notion of supervised training of discriminating
dimensions. Essentially it is agnostic to the disease. Instead we
prefer to learn the prior aay vay based on training data so that
the discriminating components of the vector field are emphasized as has been done elsewhere (Tang et al., 2014).
Given enough training data, we may be able to estimate a
prior distribution for each atlas in each group. However, in
many situations we may only have limited training data, and
measuring one prior per disease group can still offer an
improvement over the agnostic case. Both of these approaches
are depicted in Figure 1. We now describe the approach to
measure variability with respect to a group template Iy,
denoted as ay(), which we then translate to each atlas to give
us aay . In these cases we use the finite-dimensional version of
the vector fields obtained via complete orthonormal bases
constructed via PCA or other equivalent methods. For this we
generate Iy for each group using the template estimation procedure in the section Template Generation, and calculate
mappings to the training data. We estimate the finitedimensional Gaussian group prior ay() centered at Iy with a
mean and covariance describing the variability in initial velocity for these mappings onto each of the disease subpopulations
y 2 Y according to

T X1

1
ay vy exp vy V y
v

V
[29]
y
y
y
2
with V y group means or population center for each group,
with Sy a common covariance. We make the atlas-specific
prior aay in Step 2 of the algorithm as a translated
version of the group prior, so that if gway is the geodesic
map of the template Iy to the element Iay , then
aay vay _ay vay way .
Dimensionality reduction is performed by PCA and then
modeling the initial vector field v0 using the Gaussian variates
Alzheimers Disease Classification

We perform a classification experiment using the shape
space metric, and the group specific priors described above
using data from the Alzheimers Disease Neuroimaging
Initiative. We consider surface representations for the left
hippocampus of male subjects, with a diagnosis of either
Alzheimers disease (AD) or normal aging (N), and use a
vertex based noise model for the conditional probability of
the observed image given the underlying atlas in the orbit p
(ID|I).
For the two groups, we chose ten atlases from each group
y {AD, N}, and for the disease-specific prior experiment we
train on all available data in a leave-one-out fashion
aay , ay 1,2 .. ., 10. To understand the variability involved in
this task, the top row of Figure 2 shows the selected atlases
(surfaces) and other training data (points) laid out in a 2D
coordinate system. The left/right axis shows the linear discriminate analysis (LDA) direction, while the up/down axis shows
the first principal component. Our test subjects were equally
divided between controls and ADs. We obtained an 80% accuracy, with 80% for both specificity and sensitivity; 80% of the
ADs were classified as AD, and 80% of the controls were
classified as control.
Shown in the bottom row of Figure 2 are results of performing a much more extensive experiment on the shape
phenotype of the amygdala-hippocampus-ventricle circuitry
for disease discrimination, performing classification analysis
on 385 subjects (210 normal aging and 175 of Alzheimers
disease) using one atlas for each group ay() y {AD, N}.
The atlas for each group is generated as the population center
via template estimation described in the section Template
Generation. In each case we assign uniform atlas priors with
equal disease prevalence; details of the mapping procedure
for generating the momentum diffeomorphometry feature
can be found in (Tang et al., 2014). PCA was first performed
on the initial momentum vectors on the shape of amygdala,
hippocampus, as well as ventricle to reduce the dimension of
the feature space, from which linear LDA was then used for
the two-group classification. Shown in the bottom row of
Figure 2 is the histogram of the LDA coefficients for each
subject. The final classification decision was made with a
threshold value of the LDA coefficient zero; the overall performance for sensitive and specificity averaged was in the
range of 86%.
407
(a)
Deformation cost a (ni1)
Group 1 atlas i
Measurement noise p(ID l f i1 . Ii1)
(b)
(c)
(d)
(e)
(f)
(g)
Figure 1 In (a), a set of left hippocampal atlases belonging to two categories (green, blue) are shown along with a target (red). A close up of a given
atlas is shown in (b), which is deformed to match the target as shown in (c). The influence of the deformation prior can be seen by comparing the
atlas to its deformation in (c), and the influence of measurement noise can be seen by comparing the deformed atlas to the target in (d). Two possible
methods for estimating a deformation prior are illustrated in (e) and (f)(g). (e) Shows atlas (points) for each disease class (blue/green), with an
estimated prior via each Gaussian ellipsoid. (f) Shows a set of group specific priors, measured with respect to a population template (cyan). (g) Shows
the same prior assigned to each atlas.
Multiple Atlas Segmentation

Now we examine the multi-atlas segmentation problem. Given
many atlases a1 , Ia1 , a2 , Ia2 , ... ;, the problem corresponds to
segmenting the single observed image ID into y denoting the
field of segmentation labels for the n voxels in the image,
y (W1, . .. Wn). Given the incomplete-data the measured
image ID with log-likelhood log p(ID, y) and the many atlases

calculate the MAP estimator of the segmentation

^ 2 , ... arg
^ 1, W
y^ W

max
log p ID , y :
yW1 , ..., Wn
[31]
Shown in Figure 3 is a depiction of the multi-atlas segmentation model.
Alzheimers disease
Normal
40
Normal
35
AD
30
25
20
15
10
0
15
10
10
15
Figure 2 Top row: Atlases (surfaces) and training data (points) for the Alzheimers disease classification experiment are shown in a 2D coordinate
system. The left/right axis corresponds to the LDA direction, while the up/down axis shows the first principal component. Bottom row: Demonstration of
the disease classification model via eqn [29] approximating the disease cohort distribution ay vay . This model approximates the disease cohort
distribution via LDA coefficients obtained from the PCA LDA classification procedure under the common covariance model. Here it is used in
differentiating 210 normal aging subjects from 175 subjects with AD. The feature space in the classification procedure was obtained from the initial
momentum vectors indexed at each vertex of the bilateral amygdala, hippocampus, as well as ventricle. Sensitivity plus specificity averaged at 86%, as
published in Tang et al. (2014), based on the diffeomorphometry deformation biomarkers.
(Ia5 , W a5)
(Ia6 , Wa6)
(Ia4 , Wa4)
(Ia7 , W a7)
Va ~ GRF (m, K)
7
p(ID | Ia, W)
(Ia1 , Wa1)
(Ia3 , Wa3)
(Ia2 , Wa2)
Figure 3 Figure shows the population of atlases and the target at the center to be segmented. The atlases consist of the idealized image values in the
Gaussian model and the segmentation labels represented via the pairs (Ia, Wa); the target to be segmented is modeled as a random field with
graph structure such that I, , are conditionally independent given W so that p(ID| W, , Ia) p(ID| W, Ia).

The stochastic model that we use for segmentation satisfies
a very natural conditional independence. Essentially, taking
y (W1, . . ., Wn) the random field as given, then the measured
image ID and diffeomorphic change in coordinates are conditionally independent, that is, as directed acyclic graphs y
splits ID and . Therefore the joint-probability on observable,
segmentation field and diffeomorphic change in coordinates
factors. As well we model the random observable as a conditionally independent, voxel by voxel field, conditioned on the
segmentation field. This gives us the following:

p ID jy W1 , .. ., Wn , , Ia p ID jy,Ia
which implies splitting

p ID , y W1 , ... , Wn , jIa p ID jy, Ia py, jIa
n
Y

p ID
i jWi , a py, jIa : [32]

i1
This greatly simplifies the mode-approximation of eqn [23] for

g v0 .
Given the segmentation labels and the atlas type, the density on the target is determined. The connection between the
coordinate transformation and the image comes through the
joint probability of the segmentation parameters and the coordinate transformation given by p(y, |Ia). Knowledge of the
segmentation field in the target links to the diffeomorphic
change in coordinates of the atlas. The Q-function in the EM
algorithm from eqn [19] computes the log-likelihood of the
complete data taken as the measured MRI and the atlas labeling X (ID, A) with complete-data log-likelihood log p(ID, A, y)
giving

n
o

Q y; yold E log p ID , y
A
ID , yold

P
a p A aj ID , yold log pID , yj Ia :
Segmentation Classification Algorithm: This gives us the following iterative algorithm based on the mode approximation.
1. For each atlas, initialize the optimal diffeomorphism as
old
a , where a is computed as the optimal diffeomorphism
connecting the global atlas imagery Ia and the observed
old
imagery ID. Initialize yold (Wold
1 , . . ., Wn ).
2. Compute the mode approximation of eqn [23] using
LDDMM algorithm to compute gva matching onto the segmentation labels yold:
pÎD , y W1 , ... , Wn j Ia pID ,y, gva j Ia
pID j y W1 , . .. , Wn ,gva , Ia py, gva j Ia
n
Y

va
p ID
i j Wi , a pW1 , .. ., Wn j g , Ia aa va
ynew arg
max
max
yW1 , ..., Wn gva , a1, 2, ...

Qgva y; yold
409
[35]
where

X

D old
^
log p ID ,y, gva jIa :
,
y
Qgva y; yold
p
A
ajI
a
5. Update the segmentation yold ynew, go to step 2.
2
kynew yold k
< 1e4 or the number
Stop the iteration if either
old 2
y
k k
of total iterations is > 30.
In the multi-atlas random orbit model, we introduce locality into the global representations of the deformable templates by allowing different atlases to be used to interpret
different voxels or different structures, thereby associate to
the segmentation field the field of atlas labels being used to
interpret it with A (A1, A2, . . .) the field of atlas labels Ai.
To maximize eqn [35], we iterate between fixing the diffeomorphism and maximizing the segmentation, and then
locally maximizing the diffeomorphisms for the fixed segmentation labeling.
The multi-atlas random orbit model of the observable ID
assumes that its mean fields are random deformations of atlascharts arising from perhaps different atlases, each locally indexing different parts in the human brain. The observed image ID
and segmentation field parameters y (W1, . . ., Wn) are linked
to the atlas via the diffeomorphism which transfers the atlas
labeling of the brain into anatomical regions-of-interest of the
target image. This is the explicit term pW1 , ... , Wn j gva , Ia in
eqn [33]. The image ID is modeled as conditionally Gaussian,
conditioned on thesegmentation
labels giving the product law

Q
pID j W, a ni1 p ID
i j Wi , a : We take the mean and variance
of ID
i to be determined by the atlas Aa interpreting the target
image and determined by the segmentation label
ma(Wi), sa(Wi). The different atlases have different mean and
variances for cortical gray, white, and cerebrospinal fluid (CSF)
representing the different substructures of the brain determining the means and standard deviations. For the second term
pW1 , ... , Wn j gva , Ia we use a simple counting probability
given by indicator functions. Given the mapping gva , then
the probability of label Wi is calculated by transferring the label
field Wa from the atlas and using the indicator function
dWa 1 xi Wi ) which for interior voxels is zero when the atlas
label does not agree with the target label, and is 1 otherwise.
On the boundary of structures in which there is fractional
overlap of voxels we use the fraction given by the overlap of
agreement based on nearest neighbor interpolation. For computational efficiency, we use the overlap via set distance calculations to calculate these.
[33]
i1
where we have used conditional independence of ID, gv

given y (W1, . . ., Wn) from eqn [32] and pgva j Ia aa va .
3. Compute the approximated atlas selector as:

p^ ID , yold j Ia pa
D old

[34]
P
p^ A aj I , y
^ D old j Ia pa
ap I , y
new
4. Obtain a new label image ynew (Wnew
1 , . . ., Wn ) by
jointly maximizing the approximate Q-function
Whole Brain Segmentation of Cortical and Subcortical

Structures
Shown in Figure 4 are whole brain segmentations of T1weighted images into 136 anatomical regions, including subcortical structures (e.g., the thalamus, the caudate, and the
hippocampus), white matter (e.g., the cerebellum white matter
and the cerebral white matter), cortex regions (e.g., the anterior
cingulate gyrus, the middle frontal gyrus, and the precentral
gyrus), as well as ventricles (the lateral ventricles, the third
ventricle, the fourth ventricle), in four representative cases.
410

Subcortical and Ventricular Structure Segmentation in
T1-weighted Images
(a)
(b)
(c)
(d)
Figure 4 Panels (a)(d) show the whole brain segmentations of T1weighted images into 136 anatomical regions, including subcortical
structures (e.g., the thalamus, the caudate, and the hippocampus), white
matter (e.g., the cerebellum white matter, the cerebral white matter),
cortex regions (e.g., the anterior cingulated gyrus, the middle frontal
gyrus, and the precentral gyrus), and as well as ventricles (the lateral
ventrical, the third ventricle, and the fourth ventricle), in four
representative cases.
(a)
After skull stripping and extraction of the lateral ventricles, it

arises naturally to apply the multi-atlas orbit model to the
segmentation of subcortical structures in a T1-weighted
image. Shown in Figure 6 are results from the experiment of
extracting 16 subcortical and ventricular structures, including
left and right hippocampus, amygdala, caudate, putamen, globus pallidus, thalamus, lateral ventricles, the third ventricle,
and the fourth ventricle, in 35 T1 images from three different
clinical groups. Among the 35 subjects, 15 are diagnosed as
Alzheimers disease, 14 are age-matched control subjects while
the other 6 are diagnosed as primary progressive aphasia.
In this experiment, to quantitatively evaluate the accuracy
of our algorithm, we employed a leave-one-out crossvalidation method on the datasets of Group 1 and Group 2.
For Group 3, we used datasets from Group 1 and Group 2 as
the atlases for segmentation. Manual segmentations were
regarded as the gold standard. The segmentation accuracy was
measured through the use of the Dice overlap coefficients. The
of overlap
Dice overlap is computed as: D Volume
Average volume .
The mean Dice values and the standard deviations computed from the automated segmentations from single-atlas
LDDMM and multi-atlas are shown in the top row of Figure 6.
Shown in the bottom row of Figure 6 are results from one
representative case, comparing Dice values of the multi-atlas
approach to approaches based on selection of any of the single
atlases. This figure clearly shows that the multi-atlas LDDMM
form an empirical upper bound in performance even for the
best combinations of the single-atlas approach for all structures. Regardless of the anatomical variability among these
three populations, the multi-atlas approach consistently outperformed the single-atlas approach. For all structures in all
three groups, statistical testing was performed determining the
improvements in Dice values as significant with p < 0.0005.
Whole Brain Segmentation in Diffusion Tensor Images
(b)
Figure 5 Panels (a) and (b) show the segmentation results of two
subjects with Alzheimers disease. For each panel, left to right: input
image, segmentation consisted of air, skull, gray matter, white matter,
CSF, and lateral ventricles, and the input image superimposed by the six
segmentation labels.
Skull stripping and Brain Tissue Segmentation in T1-weighted

Images
Shown in Figure 5 are results from the experiment of segmenting T1-weighted images into a six-label segmentation image
consisting of the air, the skull, the gray matter, the white
matter, the CSF, and as well as the lateral ventricles. In this
experiment, 28 atlases with given label images have been used
to segment the testing subjects.
The multi-atlas random orbit model can be easily extended to

D
D D
segment diffusion tensor images (DTIs) ID [ID
FA, IMD, Ix , Iy ,
D
D
Iz ], where IFA denotes the gray-scale fractional anisotropy
(FA) image obtained in the DTI, ID
MD denotes the gray-scale
D D
mean diffusivity (MD) image, and ID
x , Iy , Iz denote the absolute
value of the three elements of the primary eigenvector, respectively. In this experiment, 16 DTI atlases were presegmented
into 159 structures based on the anatomical criteria defined in
JHU-MNI-DTI single-subject atlas (Eve atlas (Mori & Crain,
2005)). Figure 7 demonstrates whole brain segmentation
results of three patients with different degrees of abnormalities.
A high level of segmentation accuracy is visually appreciable
for the wide variety of anatomical states.
Template Generation
Now we examine the atlas generation problem given many
observable ID1 , ID2 , . .. 2 I D the conditionally random field
space, the problem is to estimate the unknown template Ia 2 I .
The unknown template is modeled as an element in the orbit
Single-atlas LDDMM
411
Multi-atlas LDDMM
1
0.9
0.8
0.7
0.6
(a)
1.2
Multi-atlas LDDMM
1
0.8
0.6
le
th
ur
Fo
Th
ird
ve
ve
nt
nt
ric
ric
le
le
ric
nt
ve
L.
ve
nt
ric
pu
oc
pp
R.
am
am
hi
L.
le
s
pu
la
oc
pp
hi
L.
yg
yg
da
da
la
us
am
R.
th
L.
al
al
am
am
us
um
th
R.
pa
llid
um
llid
pa
ca
ud
R.
L.
e
at
e
at
L.
ud
ca
R.
ta
pu
am
R.
(b)
L.
R.
pu
ta
en
en
0.4
Figure 6 Panel (a): A comparison of the segmentation accuracy between single-atlas LDDMM (red) and multi-atlas LDDMM (green), in terms of mean
Dice overlaps. Statistics are computed from 16 subcortical and ventricular structures, including left and right hippocampus, amygdala, caudate,
putamen, globus pallidus, thalamus, lateral ventricles, the third ventricle, and the fourth ventricle, in 35 T1 images from three different clinical groups, 15
diagnosed as Alzheimers disease, 14 age-matched control subjects, and 6 diagnosed as primary progressive aphasia. Panel (b): Boxplots of
the Dice overlaps of 16 different structures for one representative subject, the Dice overlap of which were computed between the manual segmentation
and the automated segmentations obtained from single-atlas LDDMMs using 28 different atlases as well as the one from multi-atlas LDDMM
(blue dotted line).
Figure 7 Results of the whole brain segmentation into 159 structures in three representative cases with large anatomical variability. The segmentation
results are superimposed on color (upper row) and MD (bottom row) images. DTI colormap encoded the fiber orientation by red (left-right),
green (anterior-posterior), and blue (head-foot) colors.
412
of the group, whereas the observables are in the random

observable space. We follow Jun Mas work (Ma et al., 2008,
2010) on volume based template estimation which was derivative of (Allassonnie`re et al., 2007), and formulate the problem
as the unknown template is in the orbit of some given hypertemplate, denoted I0 2 I ,
Ia gva I0 2 I :
[36]
The unknown diffeomorphic change of coordinates determined by the initial vector field and geodesic flow gva , leading
the parameters to be estimated as y va. The observables IDi are
conditional random fields, conditioned on Ii, with density
p(ID|Ii). The Ii are in the orbit and are therefore some unknown
deformation of the unknown template, Ii gvi Ia 2 I , with gvi
the geodesic solution of eqn [21] with ni the initial tangent
vector g_v00i n0i . Of course the gv are not known and form the
latent variables for the EM algorithm. The unknown parameters are y va which determine the template Ia gva I0 .
Statement 6: The MAP estimation of the unknown template
Ia na I0 with ID ID1 , .. ., IDn is given by

[37]
nâ argmax p ID , y va
log pID j Ii vi Ia k IDi Ia vi 1 k2 const

k IDi I0 va 1 vi 1 k2 const
where k f k 2 is the square integral.

The observables form the incomplete data ID ID1 , ..., IDn
with the given hyper-template I0, and the unknown to be estimated is the initial tangent vector field y na of the geodesic
from the hyper-template generating the template Ia gva I0 . The
complete data becomes the set of vector fields generating the
orbit elements and the observables (v1, v2, ... vn, ID).
Statement 7: With y va andID ID1 , . .. , IDn , iterates given
:
by ynew argmax yva Q y; yold with

n
o

Q y; yold E log p ID , y va jv1 , v2 , .. ., I0 jID , yold
The algorithm and setup for template estimation is shown

in Figure 8.
One of the challenges here is that for each observable we
dont know the element in the orbit which gave rise to it, that
is, observable
IDi a conditional random field with density

p IDi
Ii with Ii 2 I . Since Ii is in the orbit, we model it as a
known diffeomorphic change of coordinates of the template
Ii vi Ia with the template a deformation of the hypertemplate Ia va I0 . The conditional Gaussian random field takes
the form (including only terms as a function of the data and
the parameters)
a ~ GRF (m, K)
I D3
I D2
I a = jna I0
I0
I = jn Ia
1
I D1~ GRF (jn Ia, )
1
Figure 8 Template estimation procedure: Showing a population of

observables IDi , i 1,2, ...,n, the observable space with the associated
hypertemplate in the orbit I0 2 I . Template estimation involves
estimating the diffeomorphism fva I0 which carries the hypertemplate to
the center. The observable is modeled as a conditionally Gaussian
vi
random
field with
D
mean field f Ia with conditional density
vi
i
p I j I Ia .
[40]
are monotonic in likelihood p(ID, ynew) p(ID, yold) of

eqn [38], with fixed points satisfying the same necessary maximizer conditions as the MAP estimator of eqn [37].
The Q function computes the conditional mean of the loglikelihood function. Defining the Jacobian weights and conditional mean
(
na
with the likelihood model for inference the joint density

Z

p ID , y va av1 , .. ., vn p ID , y va jv1 , . .., vn dv: [38]
[39]
bold y E
n
X
jdgvi yj
IDi , vold
a
i1
with
old
Pn
y
i1 E

IDi gvi y
dgvi y

IDi , vold
a
bold y
[41]
The Q-function becomes for y na

(
)
n

X
Q y va ;yold E
k IDi I0 gva 1 gvi 1 k2 j ID ,yold k va k2V
i1

q
old
k I I0 gva 1
bold k2 k va k2V :
[42]
As Ma (Ma et al., 2008) points out, given in eqns [41] and

[42] the algorithm is straightforward since this takes the form
of a weighted-LDDMM problem given by eqn [25] as originally
solved in Beg (Beg et al., 2005), but corresponds to the case
that the L2 squared error norm is adjusted by the Jacobian local
scale as the weight. For this we exploit the fact that in LDDMM
the minimization is over the entire flow of the vector field vt, t 2
[0,
just v0 encoding the geodesics) but at the minimizer
R 1 1] (not
2
2
0 k vt k v dt k v0 k V.
Template Generation Algorithm: The algorithm for template
generation involves the Mode Approximation for calculating
the conditional mean required for I to avoid integrating over
all possible deformations of the population to the iterative
template.
1. Let va 0 and take template as hypertemplate, Iold
a I 0.
2. To generate the mode-approximation, for each target, compute the optimal diffeomorphism as old
using LDDMM
i
connecting the target imagery IDi and the observed currently
estimated template new
Iold
a . Generate optimized mappings for
new
vi
vnew
i
_ vi vnew

,
id, for each i 1 . .., n, where

0
i
vnew
i
Z
argmax
v:_ v vv

kvt k2V dt k IDi
v1
Iold
a 1
vnew
k :
3. Compute the mode approximation based on these locally

optimized mappings, with
bnew y
n
X
new
jdvi yj, with
[43]
i1
new
Pn
y
i1 I
Di
new
new
vi y
dvi y
bold y

4. Update parameters ynew argmax yna Q^ y; yold and resulting template given by weighted LDDMM:
Single subject
argmax
d va
va :
va va
dt
new
p
k I I0 va 1 aold k2
new
I0 va
Inew
a
1
1
0
413
k vat k2V dt
[44]
5. Stop the iteration if the number of total iterations is
bigger than N, otherwise update the template
old
ynew vnew
Inew
yold vold
a
a ,Ia
a , go to step 2.
Shown in Figure 9 are atlases generated from T1-weighted MR
images of a normal elderly dataset with the age of 75 /5.9
years old. In this implementation, a set of normal elderly
human brain T1-weighted MR images were used. The template
estimation was applied to estimate the unknown atlas in the
orbit (the image in Figure 9 right column). For comparing
Nonlinear
average
Template
generation
Figure 9 Comparison of brain atlases for normal elderly dataset. The single subject was randomly selected from the elderly human brains and
served as a baseline image of the comparison. The template estimation atlas had preserved the image contrast of the single subject image, and was
sharper than the NGA image.
200%
180%
160%
140%
Dataset (Ref)
SS/Dataset
VTE/Dataset
120%
100%
80%
60%
40%
20%
0%
_R _L _R _L _R _L _R _L _R _L _R _L l_R l_L _R _L _R _L _R r_L _R r_L cle cle
en men ate date GP GP us mus ala dala pus pus nta nta ody ody ium rium rior rio rior rio ntri ntri
d
m a
m
r
d
e
e
e
o
b
t
fe e
te
ta uta au au
yg yg am cam _fro _fr V_b LV_ _at _a ost os _inf _in IV v al V
ala al
C
C
L
Pu P
Th Th Am Am poc po LV LV
LV LV V_p V_p LV LV III- ter
p
p
L
L
La
Hi
Hi
Figure 10 The normalized volumes of 24 subcortical brain structures for normal elderly dataset (blue), the single subject atlas (red) and the
atlas from template generation (purple). The template estimation atlas (purple) approximated the mean volumes of the dataset within 10% range, while
the single subject atlas (red) has severely biased structural volumes from the mean volumes.
414
atlas image quality, the nonlinear group average (NGA) atlas

was also generated by an iterative averaging procedure with
minimal deformation template algorithm (Evans et al., 1993;
Fonov et al., 2011). In Figure 9, the template estimation
yielded an atlas image (right column) which preserves the
image contrast as the single subject image in the dataset,
which is sharper than the nonlinear averaged image (Zhang
et al., 2011, 2014).
The template estimation ensures the estimated atlas as a
good representation of the observations. To evaluate this property, the volumes of 24 subcortical brain structures were measured in the subject images, the single subject atlas and the
template estimation atlas via manual segmentation. The brain
volume measurements were normalized by the mean value
from the dataset for easy comparison. Results in Figure 10
show that the template estimation atlas (purple) closely
approximated the mean structural volumes of the dataset,
while the single subject atlas (red) has severely biased structural volumes from the means (Zhang et al., 2014; Zhang,
Zhang, Miller, & Mori, 2012).
Acknowledgements
This work was supported by grants R01 MH056584, R24
HL085343, R01 EB000975, P50 MH071616, R01 EB001838,
P41 EB015909, R01 EB008171, R01 MH084803, U01
AG033655, RR025053-01, U01 NS082085-01.

Anatomical MRI for Human Brain Morphometry; Diffusion MRI; MRI
and fMRI Optimizations and Applications; Obtaining Quantitative
Information from fMRI; INTRODUCTION TO ANATOMY AND
PHYSIOLOGY: Amygdala; Basal Ganglia; Genoarchitectonic Brain
Maps; Thalamus: Anatomy; INTRODUCTION TO CLINICAL BRAIN
MAPPING: Alzheimers Disease; Brain Mapping Techniques Used to
Guide Deep Brain Stimulation Surgery; Developmental Brain Atlases;
Structural Abnormalities in Autism Spectrum Disorder;
INTRODUCTION TO METHODS AND MODELING: Diffeomorphic
Image Registration; Diffusion Tensor Imaging; Lesion Segmentation;
Nonlinear Registration Via Displacement Fields; Rigid-Body
Registration; Surface-Based Morphometry; Tensor-Based
Morphometry; Tissue Classification; Voxel-Based Morphometry;
INTRODUCTION TO SYSTEMS: Neural Codes for Shape
Perception.
References
Alexander, D. C., Gee, J. C., & Bajcsy, R. (1999). Strategies for data reorientation during
non-rigid warps of diffusion tensor images. Proceedings of Miccai99, 1999,
463472.
Allassonnie`re, S., Amit, Y., & Trouve, A. (2007). Towards a coherent statistical
framework for dense deformable template estimation. Journal of the Royal Statistical
Society: Series B (Statistical Methodology), 69, 329.
Allassonnie`re, S., & Kuhn, E. (2010). Stochastic algorithm for parameter estimation for
dense deformable template mixture model. ESAIM: Probability and Statistics, 14,
382408.
Allassonnie`re, S., Kuhn, E., & Trouve`, A. (2010). Bayesian consistent estimation in
deformable models using stochastic algorithms: Applications to medical images.
Journal De La Societe Francaise De Statistique, 151, 116.
38, 95113.
Ashburner, J. (2009). Computational anatomy with the SPM software. Magnetic
Beg, M. F., Miller, M. I., Trouve, A., & Younes, L. (2005). Computing large deformation
Computer Vision, 61, 139157.
Christensen, G., Miller, M. I., & Rabbit, R. D. (1995). Deformable templates using large
deformation kinematics. IEEE Transactions of Medical Imaging, 5, 14351447.
Dempster, A. P., Laird, N. M., & Rubin, D. B. (1977). Maximum likelihood from
incomplete data via the EM algorithm. Journal of the Royal Statistical Society: Series
B (Methodological), 39, 138.
Dupuis, P., Grenander, U., & Miller, M. I. (1998). Variation problems on flows of
diffeomorphisms for image matching. Quarterly of Applied Mathematics, 56,
617694.
Evans, A. C., Collins, D. L., Mills, S. R., Brown, E. D., Kelly, R. L., & Peters, T. M.
(1993). 3D statistical neuroanatomical models from 305 MRI volumes. Nuclear
Science Symposium and Medical Imaging Conference, 3, 18131817.
Fonov, V., Evans, A. C., Botteron, K., Almli, C. R., Mckinstry, R. C., & Collins, D. L.
Grenander, U., & Miller, M. I. (1994). Representations of knowledge in complexsystems. Journal of the Royal Statistical Society: Series B (Methodological), 56,
549603.
Grenander, U., & Miller, M. I. (1998). Computational anatomy: An emerging discipline.
Quarterly of Applied Mathematics, 56, 617694.
Grenander, U., & Miller, M. I. (2007). Pattern theory: From representation to inference.
Kunsch, H., Geman, S., & Kehagias, A. (1995). Hidden Markov random fields. The
Annals of Applied Probability, 5, 577602.
Ma, J., Miller, M. I., Trouve, A., & Younes, L. (2008). Bayesian template estimation in
computational anatomy. NeuroImage, 42, 252261.
Ma, J., Miller, M. I., & Younes, L. (2010). A Bayesian generative model for surface
template estimation. International Journal of Biomedical Imaging, 2010.
Miller, M. I. (2004). Computational anatomy: Shape, growth, and atrophy comparison
via diffeomorphisms. NeuroImage, 29, 1933.
Miller, M. I., & Qiu, A. (2009). The emerging discipline of computational functional
anatomy. NeuroImage, 45, S16S39.
Miller, M. I., Trouve, A., & Younes, L. (2002). On the metrics and EulerLagrange
equations of computational anatomy. Annual Review of Biomedical Engineering, 4,
375405.
Miller, M. I., Trouve, A., & Younes, L. (2006). Geodesic shooting for computational
anatomy. Journal of Mathematical Imaging and Vision, 24, 209228.
Miller, M. I., & Younes, L. (2001). Group actions, homeomorphisms, and matching: A
general framework. International Journal of Computer Vision, 41, 617694.
Miller, M. I., Younes, L., & Trouve, A. (2014). Diffeomorphometry and geodesic
positioning systems for human anatomy. Technology, 2, 36.
Mori, S., & Crain, B. J. (2005). MRI Atlas of Human White Matter. Amsterdam, Boston:
Elsevier.
Pennec, X. (2011). From Riemannian geometry to computational anatomy. Elements.
Qiu, A., Younes, L., & Miller, M. I. (2012). Principal component based diffeomorphic
surface mapping. IEEE Transactions on Medical Imaging, 31, 302311.
Snyder, D. L., & Miller, M. I. (1991). Random point processes in time and space.
Springer Texts in Electrical Engineering. New York: Springer-Verlag.
Tang, X., Holland, D., Dale, A. M., Younes, L., Miller, M. I., & The Alzheimers Disease
Neuroimaging Initiative. (2014). Shape abnormalities of subcortical and ventricular
structures in mild cognitive impairment and Alzheimers disease: Detecting,
quantifying, and predicting. Human Brain Mapping, 35, 37013725.
Tang, X., Oishi, K., Faria, A. V., Hillis, A. E., Ms, A., & Mori, S. (2013). Bayesian
parameter estimation and segmentation in the multi-atlas random orbit model. PLoS
One, 8.
Thompson, D. A. W. (1942). On growth and form. Cambridge: Cambridge University
Press.
Thompson, P. M., & Toga, A. W. (2002). A framework for computational anatomy.
Computing and Visualization in Science, 5, 1334.
Trouve, A. (1995). An approach of pattern recognition through infinite dimensional
group action. Research Report LMENS, 9599.

Tward, D. J., Ma, J., Miller, M. I., & Younes, L. (2013). Robust diffeomorphic mapping
via geodesically controlled active shapes. International Journal of Biomedical
Imaging, 2013, 205494.
Younes, L. (2010). Shapes and diffeomorphisms. Heidelberg: Springer.
Zhang, Y., Zhang, J., Hsu, J., Oishi, K., Faria, A. V., Albert, M., et al. (2014). Evaluation
of group-specific, whole-brain atlas generation using volume-based template
estimation (VTE): Application to normal and Alzheimers populations. NeuroImage,
84, 406419.
415
Zhang, Y., Zhang, J., Ma, J., Oishi, K., Faria, A. V., Miller, M. I., et al. (2011). Creation
of a population-representative brain atlas with clear anatomical definition.
Proceedings of the International Society for Magnetic Resonance in Medicine,
19, 135.
Zhang, Y., Zhang, J., Miller, M. I., & Mori, S. (2012). Population-based human brain
MRI atlas with sharp contrast and its application in image registration. Proceedings
of the International Society for Magnetic Resonance in Medicine, 20, 2570.
Computing Brain Change over Time

GR Ridgway, University of Oxford, Headington, UK; UCL Institute of Neurology, London, UK
KK Leung and J Ashburner, UCL Institute of Neurology, London, UK
Glossary
Diffeomorphism A smooth (technically differentiable)

mapping, such as a spatial transformation, that has a
smooth inverse.
Jacobian (tensor/matrix and determinant) The matrix of
all first-order partial derivatives of a mapping, or the
determinant thereof, at a given point. The Jacobian
determinant encodes the factor by which the mapping
expands or shrinks space. Considering every point in space,
the Jacobians form a tensor field.
Probabilistic segmentation An image in which each voxels
value indicates the probability that it belongs to a particular
region or tissue type.
Clinical and Neuroscientific Applications

Using serial imaging to compute changes in the brain over
time has important applications whenever an inherently longitudinal process is of interest. Such processes encompass growth
and development during childhood (Giedd et al., 1999; Gilmore et al., 2012; Sowell et al., 2004) and even in utero (Habas
et al., 2012; Studholme, 2011), healthy aging (Fjell et al., 2013;
Raz et al., 2005), structural plasticity (Draganski et al., 2004;
Zatorre, Fields, & Johansen-Berg, 2012), and neurodegeneration
or other disease-related change. Examples of neurological applications include Alzheimers disease (AD) (Fox, Freeborough,
& Rossor, 1996; Jack et al., 2009), frontotemporal dementia
(Avants, Anderson, Grossman, & Gee, 2007; Mahoney et al.,
2012), Huntingtons disease (Hobbs et al., 2010; Tabrizi et al.,
2011), multiple sclerosis (Eshaghi et al., 2014; Horakova
et al., 2008), and prion disease (Ishida et al., 1995). Examples
for psychiatric and affective disorders include schizophrenia
(Mathalon, Sullivan, Lim, & Pfefferbaum, 2001), bipolar disorder (Lyoo et al., 2010), and obsessivecompulsive disorder
(Lazaro et al., 2009).
Longitudinal imaging is particularly powerful for the evaluation of response to treatment (Douaud et al., 2013; Fox et al.,
2005; Jack et al., 2008); for example, Ridha et al. (2008) reported a fivefold reduction in the number of subjects required to
power an AD treatment trial using a measure of brain volume
change (the boundary shift integral, discussed in the succeeding
text) compared to the change in minimental state examination.
Serial MRI has proven capable of measuring preclinical brain
change in AD and other dementias and has the potential to
power a secondary prevention trial (Andrews et al., 2013).
Advantages of Longitudinal Imaging

Serial data have major advantages for measuring changes over
time compared to multiple cross-sectional samples at different
SPM Depending on context, either a statistical parametric

map or the Statistical Parametric Mapping software http://
www.fil.ion.ucl.ac.uk/spm/.
Statistical parametric map An image in which each voxel is
the result of a statistical test on a set of spatially aligned
images.
Tensor-based morphometry (TBM) Typically refers to
SPM-like analysis of Jacobian tensor fields, for example, the
Jacobian determinants following spatial normalization,
such that the value of each voxel in the reference space
equals the equivalent volume of the corresponding voxel in
the original (unnormalized) images.
Voxel-based morphometry (VBM) Can be seen as a form of
tissue-specific TBM.
stages, related to both increasing statistical power and reducing

confounds (Cook & Ware, 1983).
Longitudinal brain imaging data can dramatically improve
sensitivity because the interindividual variability is typically
much greater than the change over time. To give an example,
based on Leung, Barnes, et al. (2010), the coefficient of variation (i.e., the standard deviation as a percentage of the mean)
for the total hippocampal volume in healthy elderly is 12.5%
(100 659/5251), while the average annualized atrophy rate
in AD (in which hippocampal atrophy is pronounced) is only
4.63%; changes due to aging are 1.05%, and changes due to
even more subtle effects such as learning/plasticity are likely
to be far smaller. Complementary to this, the measurement
variability for longitudinal techniques is often much lower
than for repeated application of cross-sectional methods,
as will be noted several times in this article (see also Jovicich
et al., 2013).
Cross-sectional studies of aging and of disease are prone to
several confounds. The potential for birth-year cohort effects
(e.g., due to changes in nutrition or environmental factors) is
well known, but there is also the potential for other more
subtle cohort effects such as in disease-onset time; for example,
early-onset AD has been reported to progress more rapidly
than late-onset AD (Jacobs et al., 1994), which can lead to an
apparent deceleration across age even in the presence of
within-subject acceleration (Leung et al., 2013); though see
also Holland et al. (2012). A related confound is the healthy
survivor effect a form of selection bias whereby subjects
who are willing and able to participate in (or remain in) a
study are more likely to have milder symptoms (Thompson,
Hallmayer, OHara, & Alzheimers Disease Neuroimaging
Initiative, 2011).
Longitudinal data are perhaps most powerful in combination with an intervention (such as treatment or training),
where they allow causal interpretation of change rather than
simply difference. For example, cross-sectional group
http://dx.doi.org/10.1016/B978-0-12-397025-1.00313-4
417
418
INTRODUCTION TO METHODS AND MODELING | Computing Brain Change over Time
differences between people skilled or unskilled at juggling

could reflect structural correlates of propensity to learn to
juggle, or both brain differences and juggling ability could be
shared effects of a common cause related to parental or educational environment; longitudinal data provide compelling evidence of structural plasticity in response to learning (Draganski
et al., 2004; Scholz, Klein, Behrens, & Johansen-Berg, 2009).
(Though, see also Thomas and Baker (2013) and responses in
the same issue.)
subtle effects, motivating recent efforts towards standardization (Jack et al., 2011).
Finally, manual (or semiautomated) tracing often provides
an important foundation to evaluate fully automatic methods
(Good et al., 2002) and even to construct new automatic
approaches, such as segmentation propagation, discussed
shortly.
Image Registration
Overview of Methods
Manual Volumetry
Conceptually, the simplest method to compute brain change
over time is to manually trace a region of interest (ROI) in the
images for every time point. The volumes for the ROI can then
be analyzed, and the ROI can also be used to quantify nonvolumetric properties of each image (such as fMRI activity or
diffusion MRI anisotropy). Several software tools enable manual tracing (often including semiautomatic approaches, such
as manual initialization of computational procedures and/or
manual refinement of automated results); a popular free and
open-source package is ITK-SNAP (Yushkevich et al., 2006).
The disadvantages of manual tracing are clear: it requires
expert knowledge, is often very time-consuming, exhibits intraand interrater variability, can be prone to subjective biases, and
often relies on arbitrary conventions to define borders that are
unclear on typical MRI (such as boundaries between cortical
areas). Furthermore, constraints on time and/or expertise limit
the number of regions that can feasibly be considered. While
the regions most affected in a particular disease are often
known a priori, it is typically much less clear which regions
have the greatest differences among clinical or genetic subgroups (Ridgway et al., 2012; Scahill et al., 2013) or which
regions will be most informative for evaluating a candidate
treatment (cf. Fox et al., 2005). The lack of clear boundaries
and multitude of regions of interest are motivations for voxelor vertex-wise analysis (Section Voxel and Tensor-Based
Morphometry). Subjectivity warrants blinding the tracer to
aspects that could bias the study, such as the diagnostic status
of the scans in a clinical study or the hemisphere under consideration in a study of brain asymmetry; however, such blinding is often incomplete, for example, if the expert can easily
distinguish controls and patients from the scans themselves.
However, in relation to more complex methods discussed
next, it is important to recognize that manual tracing sometimes has advantages, such as unambiguous and straightforward interpretation, easily characterized sources of error
(interscan, intrarater, interrater, interscanner, etc.), and
reduced susceptibility to overt failure or bias in the presence
of pathology (see, e.g., Hobbs et al., 2011).
Differences in segmentation protocol can clearly lead to
differences in mean volumes, but they may also lead to differential sensitivity and specificity for example, a subregion
included in some protocols but excluded in others could be
the most affected part of the structure. Protocol differences
complicate the pooling of data from multiple studies, which
is particularly important for the study of rare diseases and/or
In general terms, image registration refers to geometrically

transforming one image to align with another (Hajnal, Hill,
& Hawkes, 2001). Its key components are therefore a way of
quantifying alignment, such as a voxel-based similarity measure (Holden et al., 2000); a geometric transformation model,
which can range from rigid body (rotation and translation,
having six degrees of freedom in three dimensions), through
parametric nonrigid models with tens to thousands of parameters, to nonparametric or voxel-wise deformation or flow
fields with millions of degrees of freedom (Crum, Hartkens,
& Hill, 2004; Holden, 2008); a way of resampling or interpolating the transformed image (Thevenaz, Blu, & Unser, 2000);
and an algorithm for optimizing the alignment as a function of
the transformation (see, e.g., Modersitzki, 2009).
Patterns of brain change are typically nonlinear, requiring
flexible high-dimensional models to parameterize them accurately. However, several techniques employ rigid, lowdimensional, or highly constrained transformations, before
visualizing or quantifying the residual differences after such
registration (Fox et al., 1996). (This idea also relates to the use
of voxel-based morphometry (VBM; Section Voxel and
Tensor-Based Morphometry) without modulation (Radua,
Canales-Rodrguez, Pomarol-Clotet, & Salvador, 2014) and
even to the use of scalar momentum maps in sophisticated
mathematical models of shape (Ashburner & Kloppel, 2011;
Qiu & Miller, 2008).) See, for example, Figures 1(a), 3(a),
and 3(b).
Segmentation
Many automatic methods have been developed for segmentation of brain (Leung et al., 2011), tissues (Ashburner & Friston,
2005), and regions (Fischl et al., 2002). Examples of CSF tissue
segments appear in Figure 1(b).
There are also several semiautomated procedures that refine
a rough initial segmentation (from rapid manual initialization
or from automatic approaches) using techniques such as intensity thresholding, region growing, and morphological operations (Freeborough, Fox, & Kitney, 1997) or through the
evolution of deformable surface, active contour, or level-set
models (e.g., Yushkevich et al., 2006).
Image registration allows a region segmented in one image
to be transferred to another image, known as segmentation
propagation (Collins, Holmes, Peters, & Evans, 1995). However, intersubject registration is a challenging problem, due to
the high degree of anatomical variability, which motivates
considering the propagation of segmentations from several
different subjects to the image being segmented, combining
Baseline
12-month repeat
419
24-month repeat
(a)
(b)
(c)
(d)
Figure 1 Example of change over time in Alzheimers disease, using subject 205 from MIRIAD (Malone et al., 2013). Columns correspond to axial
views (and zoomed versions) for three of the available time points. (a) Rigidly aligned images. (b) CSF segments (black denotes 0% tissue probability
and white 100%). (c) Jacobian determinants for transformations of each time point to a within-subject average image (dark colors denote relative
contraction and bright expansion). (d) Voxel-wise products of Jacobian determinants and the tissue segment for the average (white now denotes a value
of 1.4); the voxel-wise sum (integral) of these for each image estimates the same tissue volumes as integrating the individual time-point segments
in row (b). (Related video in Multi-media Annex.)
or fusing these to give a single more accurate segmentation

(Warfield, Zou, & Wells, 2004). This technique, sometimes
known as template library-based segmentation or multiatlas
fusion, has proven to be one of the most successful methods
for automatic regional segmentation (Cardoso et al., 2013;
Leung, Barnes, et al., 2010).
A collection of segmentations from different subjects in a
standard reference space can also be summed together to give a
spatial prior probability map, which can then be combined
with an intensity-based likelihood model via the Bayesian
theorem to segment another image registered to the same
space. Variations on this theme underpin some of the most
popular segmentation approaches, including those in the software packages SPM (Ashburner & Friston, 2005) and FreeSurfer (Fischl et al., 2002).
Volume Change and the Jacobian

For a transformation aligning two images, its spatial gradient (a
3 3 matrix for three-dimensional (3-D) transformations)
known as the Jacobian matrix or Jacobian tensor encodes the
(locally linear) shape change, and its determinant encodes the
local relative volume change (a Jacobian determinant of 1
means no change, values above 1 indicate expansion, and
values below 1 indicate contraction). (An illustration of the
determinant for a 2-D transformation can be found at http://
tinyurl.com/JacobianTutorial.) See Figure 1(c).
The sum of voxel-wise Jacobian determinants (multiplied
with the voxel-wise region/tissue probabilities for a
probabilistic segmentation) over a region in an image therefore

approximates the regions volume in the transformed image,
consistent with the appearance of the Jacobian determinant in
the formula for a change of variables in an integral. This
Jacobian integration technique can be used to determine the
volume of a segmented region (Boyes et al., 2006; Hua et al.,
2009) or tissue type (Anderson et al., 2012; Hobbs et al., 2010)
in multiple registered images based on the segmentation of
only a single template (Figure 1(d)). Used as a direct measure
(see Section Indirect and Direct Measurement of Change) of
volume change from one time points segmentation, it has
proven more precise (i.e., less variable) than the difference
in volume of separate segmentations for both time points
(Anderson et al., 2012; Boyes et al., 2006).
There are also other approaches to determining volume
change from registration without computing Jacobians, such as
direct deformation of tetrahedral (Ashburner, Andersson, &
Friston, 2000) or triangulated meshes (Das et al., 2012) or
transformation of cubes into nonplanar-faceted hexahedra
(Holland, Dale, & Alzheimers Disease Neuroimaging Initiative,
2011) (Modeled as planar-faceted irregular dodecahedra or tetrakis hexahedra (Grandy, 1997).) It is also possible to consider
volume-preserving push-forward transformations (Davatzikos,
Genc, Xu, & Resnick, 2001). However, there seem to be no
comparisons of these alternatives in the literature. Hypothetical
advantages of avoiding the Jacobian include concerns about the
use of finite differencing procedures including information from
neighboring voxels in different tissue types (Das et al., 2012) or
about the sensitivity of gradients to discretization errors,
420
amplified by the fact that the determinant is a cubic polynomial

(Lorenzi, Ayache, Frisoni, Pennec, & Alzheimers Disease Neuroimaging Initiative, 2013). Advantages of Jacobians include the
potential to accumulate the Jacobian tensor over a largedeformation diffeomorphic flow (Ashburner & Friston, 2011)
rather than only considering the integrated deformation (the
end point of the flow) and the potential to consider more
general shape changes than pure volume change.
Voxel and Tensor-Based Morphometry

Voxel-based morphometry (VBM) and tensor-based morphometry (TBM) are explained elsewhere in this encyclopedia.
However, it is informative in the current context to consider a
somewhat unusual perspective on them. The Jacobian integration naturally encompasses probabilistic and binary segmentations (e.g., allowing for partial volume and/or segmentation
uncertainty) and puts no constraint on the size or number of
regions considered.
Considering each voxel in a probabilistic tissue segmentation as a probabilistic ROI, then for each image, every voxel in
template space can be assigned with the (Jacobian-integrated)
corresponding value of probabilistic volume (as in Figure 1
(d)). This is exactly equivalent to the Jacobian-modulated
A1
spatially normalized tissue segments that form the basis of

VBM (Mechelli, Price, Friston, & Ashburner, 2005; Radua
et al., 2014). TBM at its simplest is just the analysis of the
Jacobian determinants themselves, without the tissue segmentation (i.e., the regions of interest are just the original voxels,
not their tissue probabilities).
The key questions for longitudinal VBM or TBM are how to
combine intra- and intersubject registration and how to
smooth the data in a way that reduces the cancellation of
neighboring expansion and contraction. Different approaches
for spatial normalization of within-subject transformations are
illustrated in Figure 2.
Concerns about tissue atrophy being partially canceled out
by expansion of neighboring cerebrospinal fluid motivated
Scahill, Schott, Stevens, Rossor, and Fox (2002) to separate
expansion and contraction. A theoretical issue with this is
that a group difference in variance alone could lead to a falsepositive difference in the separated means (for both expansion
and contraction potentially allowing this artifact to be identified). Alternatives include TBM without smoothing (though
this could hinder the use of random field theory for multiple
comparison correction); hybrids of TBM and VBM, such as
smoothing after multiplication with binarized tissue segments
(Hobbs et al., 2010) or tissue-weighted smoothing (e.g.,
A2
A
f2m
A
f1m
A1
Am
A2
f1T
fmT
f2T
Template
f1T
B
f2T =
A
B
fmT
f2T
B
B1
f2mfmT
Template
B2
(a)
f1m
B1
f2m
Bm
B2
(b)
f2m
fmT
f2m
n2m
f22 = f1
mT
fmT
nmT
n2m
1
f2T = fmT
f2mfmT
(c)
Template
(d)
Template
f2m
Figure 2 (a) Each time point (1, 2, . . .) of each subject (A, B, . . .) can be mapped to a template (T) with direct transformations f. (b) Within-subject
registration is more precise, motivating alignment via within-subject averages, composing between- and within-subject transformations. This enables
analysis of volumes for individual images in the template space; if interested purely in within-subject volume change, one could transform the within-subject
Jacobians (JA2m) without accounting for the between-subject volume changes (JAmT), but this is not mathematically rigorous. (c) Rao et al. (2004)
proposed to determine equivalent longitudinal transformations in template space; this conjugate map can be computed by considering the composition of
transformations around a loop, but only if one assumes there is a single transformation (fmT) mapping from template to subject that holds for all the
time points (and m) so this transformation can be inverted to get from a particular subject-space time point (2) to its template-space equivalent (20 ). (d) The
large-deformation diffeomorphic metric mapping framework characterizes transformations (f) by initial velocity fields (v). The mathematically rigorous
procedure of parallel translation (Younes, Qiu, Winslow, & Miller, 2008) then allows one to transport the within-subject velocity field along the path of the
between-subject transformation, preserving important properties in the process. If needed, equivalent images (e.g., 20 ) can be generated from the
template using the transported velocitys transformation, without any assumption about the direct transformation between 2 and 20 .

Hutton, Draganski, Ashburner, & Weiskopf, 2009), which
could use either binarized or raw tissue probabilities; and
also consideration of volume or cortical thickness change on
the cortex (Chung et al., 2003) where surface-based smoothing
avoids contamination with sulcal expansion.
Indirect and Direct Measurement of Change

A key methodological distinction in approaches for quantifying change is whether the technique involves separate measurement in each time point, from which the change is
quantified indirectly by the differences between the measurements, or whether it directly measures the difference between a
pair of time points. The intuitive appeal of direct approaches is
that the single measurement has only one source of measurement error, whereas the difference of two measures includes
errors from both. A simple analogy (due to Professor Nick Fox)
is that if one uses a tape to measure the heights of two individuals separately, the difference in these measures is likely to
be less precise than if the individuals stand back-to-back and
the (smaller) difference in heights is measured directly. Two of
the most well-known direct techniques for measurement of
brain change are the boundary shift integral, discussed next,
and SIENA (Camara et al., 2008, Horakova et al., 2008; Smith,
Stefano, Jenkinson, & Matthews, 2001; Smith et al., 2002),
which is based on directly measuring the shifts of brain edges.
Example: boundary shift integral

The boundary shift integral (BSI Freeborough & Fox, 1997;
Leung, Clarkson, et al., 2010) estimates the volume change
between a pair of rigidly aligned images based on the intensity
differences between them. The BSI requires manual
(Freeborough et al., 1997) or automatic (Leung et al., 2011)
masks, to standardize the intensities and to define a rough
boundary region to which the computations are restricted,
but as a direct measure of change, the BSI manages to be
more precise than difference in volumes of the masks on
which it is based. The BSI can be applied to brain, ventricular,
and hippocampal regions. Figure 3 illustrates the key
concept.
Groupwise or Series-Wise Methods

Direct measurement of a difference is fundamentally a pairwise
operation, but it is also helpful to distinguish a related class of
techniques that treat a within-subject time series of images as a
set (often known as groupwise methods, but perhaps more
helpfully called series-wise when used in the context of time series
data for each subject within a group of subjects). Such approaches
include registration of multiple time points to a particular reference image (Avants et al., 2007; Skrinjar, Bistoquet, & Tagare,
2008), often defined as an evolving within-subject average
(Ashburner & Ridgway, 2013; Reuter, Schmansky, Rosas, &
Fischl, 2012; Rohrer et al., 2013); spatiotemporal registration,
with temporal regularization of transformations (Guizard et al.,
2012); spatiotemporal or 4-D segmentation and/or surface
modeling of the registered time series (Cardoso, Clarkson,
Modat, & Ourselin, 2011; Nakamura, Fox, & Fisher, 2011; Reuter
et al., 2012; Wolz et al., 2010); concatenation of longitudinal
registration and longitudinal segmentation steps (Aubert-Broche
et al., 2012); and simultaneous combined registration and
421
segmentation of the set of images, often constraining or regularizing the temporal changes (Gilmore et al., 2012; Prastawa,
Awate, & Gerig, 2012; Xue, Shen, & Davatzikos, 2006).
Durrleman et al. (2013) also employed within-subject registration (to the baseline image) but in addition to a relatively
standard combination of within- and between-subject registration applied a novel 1-D time warp to allow for nonlinear (but
monotonic) timing differences between subjects (e.g., developmental delays).
Example: longitudinal modeling in SPM12

Groupwise or series-wise registration can be formulated as a
simple example of a generative model, whereby the individual
images are considered to be generated as deformed versions of
a within-subject template which could itself be a deformed
version of a between-subject template (Durrleman et al.,
2013). An example of this is the longitudinal modeling framework in the free and open-source software SPM12 (Ashburner
& Ridgway, 2013); each time point is considered as a rigidly
reoriented, nonrigidly warped, intensity inhomogeneitycorrupted version of an average shape and intensity
within-subject template. This generative model unifies image
registration and differential inhomogeneity correction (see
also Modat, Ridgway, Hawkes, Fox, & Ourselin, 2010). The
registration model is a diffeomorphic one (allowing large
highly convoluted deformations while preventing nonphysical
negative Jacobian determinants or folding) formulated such
that the registration of two time points to their average leads to
a transformation consistent with that directly relating the pair
(see also Tagare, Groisser, & Skrinjar, 2009).
A novel feature of the SPM framework is that the regularization of the transformation is scaled according to the interval
(between the median time and the time of the image under
consideration), based on the idea that larger deformations are
a priori more likely over longer intervals. Figure 1 was produced using SPM12s tissue segmentation and longitudinal
registration.
Nonvolumetric Change over Time

Although the focus of this article is volumetric brain change,
many of the techniques have direct application to the quantification of nonvolumetric changes over time. An example is
functional activity, measured with fMRI or PET, for which
between-session changes in conventional session-specific summaries (contrast images) can be straightforwardly studied
over tissue types, over regions, or at the voxel or vertex level
using essentially the same techniques (without having to worry
about preserving volume with Jacobian determinants). Returning to structural MRI, changes in intensity and contrast are
sometimes of interest (Salat et al., 2009; Vardhan, Prastawa,
Sharma, Piven, & Gerig, 2013), though these are typically nonquantitative. Various parameters such as relaxation time constants and magnetization transfer can be quantified and then
studied using similar techniques (Draganski et al., 2011), with
reduced susceptibility to some of the pitfalls mentioned in
Section Incidental and Artifactual Brain Changes.
Simple measures from diffusion-weighted MRI such as apparent diffusion coefficients or fractional anisotropy can also be
straightforwardly studied with related techniques (Keihaninejad
et al., 2013; Scholz et al., 2009); however, other measures require
422
(a)
(b)
w
B
(c)
Intensity
Intensity
IWM B
IWM
ICSF
(d)
IWM
ICSF
(e)
ICSF
IWM B
Intensity
Intensity
ICSF
x
Intensity
IWM
ICSF
x
Figure 3 Brain boundary shift integral illustration. (a) Original images for two time points, with brain masks overlaid in blue, and their voxel-wise
difference image. (b) Registered images and difference image. (c) Example of a 1-D transect through the ventricles between points A and B, shown on
each image and the difference; the BSI estimates the 1-D geometric change Dw from the corresponding intensity change. (d) Intensity profiles
along the transect and the shaded area (integral) between them. (e) The area estimated from voxel-wise intensity differences (vertical rectangles)
corresponds to the same area swept out by the horizontal shifts of parts of the intensity profiles; dividing this area by the intensity range gives
the average shift (a length change; a volume change would result from integrating over 3-D space). The final panel is a color-coded difference image
(for brain regions) overlaid on the original illustrating volume change in BSI (red: tissue loss, green: tissue gain).
more careful adjustment for spatial transformations (within- and

between-subject), such as reorientation of principal direction vectors (Schwartzman, Dougherty, & Taylor, 2005) and/or full diffusion tensors (Alexander, Pierpaoli, Basser, & Gee, 2001) or
modulation of fiber orientation distributions (Raffelt et al.,
2012). It must also be acknowledged that several applications
have more complex challenges, such as the evolution of lesions
in multiple sclerosis (Horakova et al., 2008); the occurrence of
edema, hematoma, hemorrhage, or contusions following traumatic brain injury (Kim, Avants, Whyte, & Gee, 2013); the growth
of brain tumors (Mang, Toma, Schuetz, Becker, & Buzug, 2012);

and changes following neurosurgery (Daga et al., 2012).
Statistical Modeling
While cross-sectional image processing of longitudinal data is
typically valid, though suboptimal, statistical analysis must
account for the dependence within-subject; false-positive rates
could be severely inflated if images from multiple time points are

treated as though they were from multiple independent subjects.
The simplest longitudinal statistical models are the repeated
measures or mixed analysis of variance (ANOVA) models and
special cases such as the familiar paired t-test. These models have
a within-subject time factor and often additional betweensubject factors such as group. Dependence of scans within the
time factor can be modeled by introducing a subject factor and/
or covariance components. Care is required when there are
multiple factors, since inclusion of a subject factor means the
residual variance relates only to the within-subject variability;
this is valid for testing the significance of time effects and of timeby-group interactions, but is not valid for testing the main effect
of group, as this must be judged against the between-subject
variability (see also http://nmr.mgh.harvard.edu/harvardagingbrain/People/AaronSchultz/GLM_Flex.html).
In mixed ANOVA models, it is often the interaction
between group and time that is of primary interest for example, testing whether controls and patients have different temporal trajectories. However, it is unfortunately very common to
see examples of the imagers fallacy (Poldrack et al., 2008) in
relation to this. For example, finding a significant effect of
time in patients but not in controls is insufficient; likewise, a
significant group difference at follow-up but not at baseline is
insufficient. This should be clear when one considers that in
each case, the significant effect could be p 0.04 and the nonsignificant one p 0.06, with virtually no group difference
between the temporal trajectories. The reason this is common
enough in the imaging literature to warrant the name imagers
fallacy is that while few researchers would wrongly interpret
two p-values in text or a table that were narrowly either side of
the critical level, it is far easier and far more common to
misinterpret the visually more striking difference of presence
versus absence of blobs in an SPM analysis (see also Jernigan,
Gamst, Fennema-Notestine, & Ostergaard, 2003).
Mixed ANOVA designs are powerful and widely applicable
to controlled (balanced) experiments, such as in the study of
structural plasticity; however, they are often inappropriate for
less well-controlled (unbalanced) observational studies, such
as those of aging or disease. This is because the time factor is
required to have consistent levels across subjects (e.g., all subjects scanned pretreatment and then 6 months later). Studies of
aging typically span too long an interval for purely longitudinal designs, requiring (unstructured or, ideally, structured)
multicohort longitudinal designs (Thompson, Hallmayer,
OHara, & Alzheimers Disease Neuroimaging Initiative,
2011) where different subjects have different sets of times at
different ages. Studies of disease often scan some subjects more
frequently or at different times than others, for example, more
subtly affected subjects might be scanned at shorter intervals
and/or followed up for longer.
A simple approach to longitudinal data analysis that avoids
the previously mentioned complexities of modeling withinsubject dependence and partially relaxes the requirement
for balanced data is a two-stage summary-statistic procedure
(sometimes known as the NIH method Fitzmaurice,
Davidian, Verbeke, & Molenberghs, 2008, p.7). At the first
level, within-subject change is fitted with simple regression
models, for example, low-order polynomials in time (which
do not require evenly spaced times or consistent timing across
subjects), and then, a second-level between-subject model
423
compares first-level summaries such as linear slopes or quadratic (acceleration) terms between subjects. This is formally
identical to the standard summary-statistic procedure for hierarchical models used in between-subject fMRI analysis (where
it is commonly known as the random-effects approach). It is
also worth noting that the common practice of comparing
annualized change in studies with just two time points for all
subjects is a special case.
Mixed-Effects Models and Other Advanced Approaches

The problem with the summary-statistic approach described
earlier is that it treats all subjects summaries the same, despite,
for example, one subjects slope being estimated from several
well-spaced time points, while another subject had only two
time points separated by a short interval, or one subjects data
were much noisier than anothers. These effects mean that
summaries for different subjects can have very different precisions, and optimal second-level modeling should take these
precisions into account. This is the essential idea underlying
mixed-effects or multilevel models (Bernal-Rusiel et al., 2012;
Chen, Saad, Britton, Pine, & Cox, 2013; Fitzmaurice et al.,
2008), which can also benefit from incomplete data (e.g.,
individuals with only a single time point, who cannot provide
slope summaries). Special forms of mixed-effects model have
been developed for pairwise direct measures of change (Frost,
Kenward, & Fox, 2004). Efficient implementation of spatiotemporal mixed-effects models for voxel or vertex-wise data is a
topic of ongoing research (Bernal-Rusiel et al., 2013).
Other advanced modeling approaches for longitudinal data
include generalized estimating equations (Fitzmaurice et al.,
2008; Li et al., 2013) and latent difference score modeling
(Raz et al., 2005). Finally, although outside the scope of this
article, two interesting avenues of research into sophisticated
statistical modeling are the estimation of disease-progression
models based on determining the optimal ordering of a set of
events in the disease process (Fonteijn et al., 2012; Huang &
Alexander, 2012) and the use of dynamic Bayesian networks to
characterize interregional interactions in longitudinal morphological change (Chen, Resnick, Davatzikos, & Herskovits, 2012).
Pattern Analysis
Whenever more than one measure of volume change is available per subject (whether a few regions or millions of voxels),
there is the potential to form a single univariate biomarker
from the multivariate features using machine learning or pattern analysis. Examples of this include the use of a binary
statistical ROI (stat-ROI) defined using univariate significance
testing (Hua et al., 2009) and linear weighted averages, where
the weights can be determined from various techniques, such
as support vector machines (Hobbs et al., 2010) and linear
discriminant analysis (Gutman et al., 2013). It is important to
define the stat-ROI or weight image from independent training
data or to properly cross validate. These references show considerable improvements in power from these novel biomarkers
compared to simpler unweighted averages of volume change
over tissues or anatomically defined regions.
424
Confounds and Pitfalls

Incidental and Artifactual Brain Changes
In addition to brain changes due to development, plasticity, or
disease, there are several other potential causes of change, real
or artifactual. Real but incidental brain change can be caused
by changes in hydration (Kempton et al., 2009; Walters, Fox,
Crum, Taube, & Thomas, 2001) or stage of the menstrual cycle
(Protopopescu et al., 2008). Such changes are likely to increase
unmodeled variability and hence reduce power, but it is also
possible to imagine scenarios where they could be more problematic, for example, if patients were typically scanned in the
morning and their matched controls (often spouses) in the
afternoon, systematic hydration differences could occur. Interpretation of treatment-associated volume changes can also be
complicated (e.g., Fox et al., 2005).
Artifactual changes can arise from various acquisitionrelated imperfections, perhaps most notably geometric distortions (Littmann, Guehring, Buechel, & Stiehl, 2006). Such
distortions can be corrected using detailed knowledge of the
scanner hardware (Jovicich et al., 2006). Without such knowledge, it is still possible to partially account for the relative
(within-subject) distortion using affine registration (Clarkson
et al., 2009) if one assumes that the distortions are approximately affine but true brain change is largely nonlinear; however, in atrophic diseases, there can of course be true affine
components that will be lost. Other problems are the intensity
inhomogeneity and the fact that it can vary within-subject due
to differences in positioning or hardware instability over time
(Lewis & Fox, 2004). Such issues are compounded in large
multicenter and/or multiscanner studies (Focke et al., 2011).
Some authors have concluded that the presence of a significant
effect for site, scanner, or field strength precludes the combination of such data; this overlooks the fact that studies frequently combine males and females or young and old, despite
their significant differences. The crucial point is to ensure that
age, gender, scanner, etc., are balanced across aspects of interest
such as diagnostic groups and to adjust statistically for them
(Barnes et al., 2010).
Algorithmic Asymmetries and Biases

While substantially reducing variance, sophisticated techniques for direct or series-wise measurement of change also
have the potential to add various forms of bias (an example of
the so-called bias-variance trade-off; Ashburner & Ridgway,
2013; Hua et al., 2013). Indeed, any technique that regularizes
change over time is, purposefully, biasing the measurement of
change towards zero, though this fact is overlooked surprisingly frequently.
More problematically, any technique that includes systematic asymmetries, such as treating one time point differently to
the others, has the potential to introduce biases away from zero
and hence can lead to false-positives or underestimation of
sample size (Holland, McEvoy, Dale, & Alzheimers Disease
Neuroimaging Initiative, 2012; Thompson, Holland, &
Alzheimers Disease Neuroimaging Initiative, 2011). Image
registration is often still asymmetrical (despite substantial
early work on this issue (Ashburner et al., 2000; Christensen,
1999; Cachier & Rey, 2000; Smith et al., 2001; Thirion, 1998)),
so registering all time points to a single arbitrarily chosen time
point (typically the first or last) is an important source of
potential bias, shown to be of practical importance for both
global (e.g., affine) transformations (Thomas et al., 2009;
Yushkevich et al., 2010) and local (nonlinear) deformations
(Hua et al., 2011). While one source of such bias is the differential interpolation of images that are resampled compared to
the static reference image, it is important to note that even
when affine transformations are used to initialize the search
for nonlinear deformations, such that no explicit interpolation
occurs, the estimation of the nonlinear transformation
includes an internal interpolation process that can still be
biased (Yushkevich et al., 2010).
Related examples of bias from asymmetry include cases
where the registration is symmetrical (or symmetrized), but a
particular time point is segmented, or an average image (used
for segmentation and/or between-subject registration) is created in the space of a particular time point rather than in an
average position and shape. More subtly, initialization and/or
regularization of nonlinear optimization processes that favor a
particular time point can introduce bias, for example, even
symmetrical registration of all time points to baseline could
introduce bias by virtue of the fact that greater changes over
greater time intervals are further from initial values and/or
more heavily affected by regularization terms. This has led
authors to consider registration of each image to every other
image (Leung, Ridgway, Ourselin, Fox, & Alzheimers Disease
Neuroimaging Initiative, 2012) or to a within-subject average
(Ashburner & Ridgway, 2013; Reuter & Fischl, 2011; Reuter
et al., 2012).
While much work has focused on theoretical symmetries in
image registration, it is important to note that more basic
approaches can also be of help. For example, running procedures
with images reordered and averaging results (Holland et al.,
2011; Smith et al., 2001), or even just randomizing the choice
of reference image, can mitigate minor biases. Related to this,
computing effect size (and hence power or sample-size) in relation to a control group will tend to cancel simple additive biases
that are equal in the two groups (Fox, Ridgway, & Schott, 2011).
The presence and magnitude of an additive bias are often
estimated by assuming linearity of brain volume change over
three time points (Thompson, Holland, & Alzheimers Disease
Neuroimaging Initiative, 2011; Yushkevich et al., 2010), with the
assumption that a deceleration is implausible in mildly affected
patients; however, it is important to note that simply fitting a
regression model to all available time points can give a misleading answer in the presence of dropout, since loss of the most
rapidly progressive subjects could lead to an apparent deceleration (Hua et al., 2013). Other means of evaluation, such as
simulations (Camara et al., 2008) scan-re-scan tests, or comparison to less biased but more variable cross-sectionally measured
changes, are therefore complementary (Fox et al., 2011).
Acknowledgments
This work was supported by the Medical Research Council
(grant number MR/J014257/1) and the Wellcome Trust
(grant number 091593/Z/10/Z). The Wellcome Trust Centre
for Neuroimaging is supported by core funding from the

Wellcome Trust (grant number 091593/Z/10/Z). The Dementia Research Centre is an Alzheimers Research UK Coordinating Centre and has also received equipment funded
by Alzheimers Research UK and Brain Research Trust. Data
used in the preparation of this article were obtained from the
MIRIAD database (http://miriad.drc.ion.ucl.ac.uk). The MIRIAD investigators did not participate in the analysis or writing
of this report. The MIRIAD dataset is made available through
the support of the UK Alzheimers Society (grant RF116). The
original data collection was funded through an unrestricted
educational grant from GlaxoSmithKline (grant 6GKC).

Automatic Labeling of the Human Cerebral Cortex; Bayesian Multiple
Atlas Deformable Templates; Cortical Thickness Mapping;
Crossvalidation; Diffeomorphic Image Registration; Intensity
Nonuniformity Correction; Manual Morphometry; Modeling Brain
Growth and Development; Multi-voxel Pattern Analysis; Nonlinear
Registration Via Displacement Fields; Rigid-Body Registration;
Surface-Based Morphometry; Tensor-Based Morphometry; The
General Linear Model; Tissue Classification; Tissue Properties from
Quantitative MRI; Tract-Based Spatial Statistics and Other Approaches
for Cross-Subject Comparison of Local Diffusion MRI Parameters;
Voxel-Based Morphometry.
References
Alexander, D., Pierpaoli, C., Basser, P., & Gee, J. (2001). Spatial transformations of
diffusion tensor magnetic resonance images. IEEE Transactions on Medical
Imaging, 20(11), 11311139.
Anderson, V. M., Schott, J. M., Bartlett, J. W., Leung, K. K., Miller, D. H., & Fox, N. C.
(2012). Gray matter atrophy rate as a marker of disease progression in AD.
Neurobiology of Aging, 33(7), 11941202.
Andrews, K. A., Modat, M., Macdonald, K. E., Yeatman, T., Cardoso, M. J., Leung, K. K.,
et al. (2013). Atrophy rates in asymptomatic amyloidosis: Implications for Alzheimer
prevention trials. PLoS One, 8(3), e58816.
Ashburner, J., Andersson, J. L., & Friston, K. J. (2000). Image registration using a
symmetric priorin three dimensions. Human Brain Mapping, 9(4), 212225.
Ashburner, J., & Friston, K. J. (2005). Unified segmentation. NeuroImage, 26(3),
839851.
Ashburner, J., & Friston, K. J. (2011). Diffeomorphic registration using geodesic
shooting and Gauss-Newton optimisation. NeuroImage, 55(3), 954967.
Ashburner, J., & Kloppel, S. (2011). Multivariate models of inter-subject anatomical
longitudinal structural MRI. Frontiers in Neuroscience, 6, 197.
Aubert-Broche, B., Fonov, V. S., Garca-Lorenzo, D., Mouiha, A., Guizard, N., Coupe, P.,
et al. (2012). A new framework for analyzing structural volume changes of
longitudinal brain MRI data. In STIA: Spatio-temporal image analysis for
longitudinal and time-series image data. Lecture Notes in Computer Science
(vol. 7570, pp. 5062). Verlag: Springer.
Avants, B., Anderson, C., Grossman, M., & Gee, J. C. (2007). Spatiotemporal
normalization for longitudinal analysis of gray matter atrophy in frontotemporal
dementia. International Conference on Medical Image Computing and ComputerAssisted Intervention Brisbane, 10, 303310.
Barnes, J., Ridgway, G. R., Bartlett, J., Henley, S. M.D, Lehmann, M., Hobbs, N., et al.
(2010). Head size, age and gender adjustment in MRI studies: A necessary
nuisance? NeuroImage, 53(4), 12441255.
Bernal-Rusiel, J. L., Greve, D. N., Reuter, M., Fischl, B., & Sabuncu, M. R.Alzheimers
Disease Neuroimaging Initiative. (2012). Statistical analysis of longitudinal
neuroimage data with linear mixed effects models. NeuroImage, 66C, 249260.
Bernal-Rusiel, J. L., Reuter, M., Greve, D. N., Fischl, B., & Sabuncu, M. R.Alzheimers
Disease Neuroimaging Initiative. (2013). Spatiotemporal linear mixed effects
modeling for the mass-univariate analysis of longitudinal neuroimage data.
425
Boyes, R. G., Rueckert, D., Aljabar, P., Whitwell, J., Schott, J. M., Hill, D. L.G, et al.
(2006). Cerebral atrophy measurements using Jacobian integration: Comparison
with the boundary shift integral. NeuroImage, 32(1), 159169.
Cachier, P., & Rey, D. (2000). Symmetrization of the non-rigid registration problem
using inversion-invariant energies: Application to multiple sclerosis. In
intervention. Lecture Notes in Computer Science (vol. 1935, pp. 472481).
Visegrad: Springer.
Camara, O., Schnabel, J. A., Ridgway, G. R., Crum, W. R., Douiri, A., Scahill, R. I., et al.
(2008). Accuracy assessment of global and local atrophy measurement techniques
with realistic simulated longitudinal Alzheimers disease images. NeuroImage,
42(2), 696709.
Cardoso, M. J., Clarkson, M. J., Modat, M., & Ourselin, S. (2011). Longitudinal cortical
thickness estimation using Khalimskys cubic complex. In International conference
on medical image computing and computer-assisted intervention. Lecture Notes in
Computer Science (vol. 6892, pp. 467475). Berlin: Springer.
Cardoso, M. J., Leung, K., Modat, M., Keihaninejad, S., Cash, D., Barnes, J., et al.
(2013). STEPS: Similarity and truth estimation for propagated segmentations and its
application to hippocampal segmentation and brain parcelation. Medical Image
Analysis, 17(6), 671684.
Chen, R., Resnick, S. M., Davatzikos, C., & Herskovits, E. H. (2012). Dynamic Bayesian
network modeling for longitudinal brain morphometry. NeuroImage, 59(3), 23302338.
Chen, G., Saad, Z. S., Britton, J. C., Pine, D. S., & Cox, R. W. (2013). Linear mixedeffects modeling approach to FMRI group analysis. NeuroImage, 73, 176190.
Christensen, G. E. (1999). Consistent linear-elastic transformations for image matching.
In Information processing in medical imaging. Lecture Notes in Computer Science
(vol. 1613, pp. 224237). Berlin: Springer.
Chung, M. K., Worsley, K. J., Robbins, S., Paus, T., Taylor, J., Giedd, J. N., et al.
(2003). Deformation-based surface morphometry applied to gray matter
deformation. NeuroImage, 18(2), 198213.
Clarkson, M. J., Ourselin, S., Nielsen, C., Leung, K. K., Barnes, J., Whitwell, J. L., et al.
(2009). Comparison of phantom and registration scaling corrections using the ADNI
cohort. NeuroImage, 47(4), 15061513.
Collins, D. L., Holmes, C. J., Peters, T. M., & Evans, A. C. (1995). Automatic 3-D
model-based neuroanatomical segmentation. Human Brain Mapping, 3, 190208.
Cook, N. R., & Ware, J. H. (1983). Design and analysis methods for longitudinal
research. Annual Review of Public Health, 4, 123.http://dx.doi.org/10.1146/
annurev.pu.04.050183.000245.
Crum, W. R., Hartkens, T., & Hill, D. L. G. (2004). Non-rigid image registration: Theory
and practice. British Journal of Radiology, 77, S140S153, Spec No 2.
Daga, P., Winston, G., Modat, M., White, M., Mancini, L., Cardoso, M. J., et al. (2012).
Accurate localization of optic radiation during neurosurgery in an interventional MRI
suite. IEEE Transactions on Medical Imaging, 31(4), 882891.
Das, S. R., Avants, B. B., Pluta, J., Wang, H., Suh, J. W., Weiner, M. W., et al. (2012).
Measuring longitudinal change in the hippocampal formation from in vivo highresolution T2-weighted MRI. NeuroImage, 60(2), 12661279.
Davatzikos, C., Genc, A., Xu, D., & Resnick, S. M. (2001). Voxel-based morphometry
using the RAVENS maps: Methods and validation using simulated longitudinal
atrophy. NeuroImage, 14(6), 13611369.
Douaud, G., Refsum, H., de Jager, C. A., Jacoby, R., Nichols, T. E., Smith, S. M., et al.
(2013). Preventing Alzheimers disease-related gray matter atrophy by B-vitamin
treatment. Proceedings of the National Academy of Sciences of the United States of
America, 110(23), 95239528.
Draganski, B., Ashburner, J., Hutton, C., Kherif, F., Frackowiak, R. S.J, Helms, G.,
et al. (2011). Regional specificity of MRI contrast parameter changes in normal
ageing revealed by voxel-based quantification (VBQ). NeuroImage, 55(4),
14231434.
Draganski, B., Gaser, C., Busch, V., Schuierer, G., Bogdahn, U., & May, A. (2004).
Neuroplasticity: Changes in grey matter induced by training. Nature, 427(6972),
311312.
Durrleman, S., Pennec, X., Trouve, A., Braga, J., Gerig, G., & Ayache, N. (2013).
Toward a comprehensive framework for the spatiotemporal statistical analysis
of longitudinal shape data. International Journal of Computer Vision, 103(1),
2259.
Eshaghi, A., Bodini, B., Ridgway, G. R., Garca-Lorenzo, D., Tozer, D., Sahraian, M. A.,
et al. (2014). Temporal and spatial evolution of grey matter atrophy in primary
progressive multiple sclerosis. Neuroimage, 86, 257264.
human brain. Neuron, 33(3), 341355.
Fitzmaurice, G., Davidian, M., Verbeke, G., & Molenberghs, G. (Eds.), (2008).
Longitudinal data analysis: A handbook of modern statistical methods. Chapman &
Hall.
426
Fjell, A. M., McEvoy, L., Holland, D., Dale, A. M., & Walhovd, K. B., Alzheimers Disease
Neuroimaging Initiative. (2013). Brain changes in older adults at very low risk for
Alzheimers disease. Journal of Neuroscience, 33(19), 82378242.
Focke, N. K., Helms, G., Kaspar, S., Diederich, C., Toth, V., Dechent, P., et al. (2011).
Multi-site voxel-based morphometrynot quite there yet. NeuroImage, 56(3),
11641170.
Fonteijn, H. M., Modat, M., Clarkson, M. J., Barnes, J., Lehmann, M., Hobbs, N. Z.,
et al. (2012). An event-based model for disease progression and its application in
familial Alzheimers disease and Huntingtons disease. NeuroImage, 60(3),
18801889.
Fox, N. C., Black, R. S., Gilman, S., Rossor, M. N., Griffith, S. G., Jenkins, L., et al. (May
2005). Effects of A-beta immunization (AN1792) on MRI measures of cerebral
volume in Alzheimer disease. Neurology, 64(9), 15631572, for the AN1792(QS21)-201 Study Team.
Fox, N. C., Freeborough, P. A., & Rossor, M. N. (1996). Visualisation and quantification
of rates of atrophy in Alzheimers disease. Lancet, 348(9020), 9497.
Fox, N. C., Ridgway, G. R., & Schott, J. M. (2011). Algorithms, atrophy and Alzheimers
disease: Cautionary tales for clinical trials. NeuroImage, 57(1), 1518.
Freeborough, P. A., & Fox, N. C. (1997). The boundary shift integral: An accurate and
robust measure of cerebral volume changes from registered repeat MRI. IEEE
Freeborough, P. A., Fox, N. C., & Kitney, R. I. (1997). Interactive algorithms for the
segmentation and quantitation of 3-D MRI brain scans. Computer Methods and
Programs in Biomedicine, 53(1), 1525.
Frost, C., Kenward, M. G., & Fox, N. C. (2004). The analysis of repeated direct
measures of change illustrated with an application in longitudinal imaging.
Statistics in Medicine, 23(21), 32753286.
Giedd, J. N., Blumenthal, J., Jeffries, N. O., Castellanos, F. X., Liu, H., Zijdenbos, A.,
et al. (1999). Brain development during childhood and adolescence: A longitudinal
MRI study. Nature Neuroscience, 2(10), 861863.
Gilmore, J. H., Shi, F., Woolson, S. L., Knickmeyer, R. C., Short, S. J., Lin, W., et al.
(2012). Longitudinal development of cortical and subcortical gray matter from birth
to 2 years. Cerebral Cortex, 22(11), 24782485.
Good, C. D., Scahill, R. I., Fox, N. C., Ashburner, J., Friston, K. J., Chan, D., et al. (2002).
Automatic differentiation of anatomical patterns in the human brain: Validation with
studies of degenerative dementias. NeuroImage, 17(1), 2946.
Grandy, J., (1997). Efficient computation of volume of hexahedral cells. Technical report,
Lawrence Livermore National Laboratory. URL http://doi.org/10.2172/632793.
Guizard, N., Fonov, V. S., Garca-Lorenzo, D., Aubert-Broche, B., Eskildsen, S. F., &
Collins, D. L. (2012). Spatio- temporal regularization for longitudinal registration to
an unbiased 3D individual template. In STIA: Spatio- temporal image analysis for
longitudinal and time-series image data. Nice, Lecture Notes in Computer Science
(vol. 7570, pp. 112). Springer.
Gutman, B. A., Hua, X., Rajagopalan, P., Chou, Y.-Y., Wang, Y., Yanovsky, I., et al.
(2013). Maximizing power to track Alzheimers disease and MCI progression by
LDA-based weighting of longitudinal ventricular surface features. NeuroImage, 70,
386401.
Habas, P. A., Scott, J. A., Roosta, A., Rajagopalan, V., Kim, K., Rousseau, F., et al.
(2012). Early folding patterns and asymmetries of the normal human brain detected
from in utero MRI. Cerebral Cortex, 22(1), 1325.
Hajnal, J. V., Hill, D. L., & Hawkes, D. J. (2001). Medical Image Registration. Boca
Raton, FL: CRC press.
Hobbs, N. Z., Henley, S. M.D, Ridgway, G. R., Wild, E. J., Barker, R. A., Scahill, R. I.,
et al. (2010). The progression of regional atrophy in premanifest and early
Huntingtons disease: A longitudinal voxel-based morphometry study. Journal of
Neurology, Neurosurgery and Psychiatry, 81(7), 756763.
Hobbs, N. Z., Pedrick, A. V., Say, M. J., Frost, C., Dar Santos, R., Coleman, A., et al.
(2011). The structural involvement of the cingulate cortex in premanifest and early
Huntingtons disease. Movement Disorders, 26(9), 16841690.
Holden, M. (2008). A review of geometric transformations for nonrigid body
Holden, M., Hill, D., Denton, E., Jarosz, J., Cox, T., Rohlfing, T., et al. (2000). Voxel
similarity measures for 3-D serial MR brain image registration. IEEE Transactions
Holland, D., & Dale, A. M.Alzheimers Disease Neuroimaging Initiative. (2011).
Nonlinear registration of longitudinal images and measurement of change in
regions of interest. Medical Image Analysis, 15(4), 489497.
Holland, D., Desikan, R. S., Dale, A. M., & McEvoy, L. K., Alzheimers Disease
Neuroimaging Initiative. (2012). Rates of decline in Alzheimer disease decrease with
age. PLoS One, 7(8), e42325.
Holland, D., McEvoy, L. K., & Dale, A. M., Alzheimers Disease Neuroimaging Initiative.
(2012). Unbiased comparison of sample size estimates from longitudinal structural
measures in ADNI. Human Brain Mapping, 33(11), 25862602.
Horakova, D., Cox, J. L., Havrdova, E., Hussein, S., Dolezal, O., Cookfair, D., et al.
(2008). Evolution of different MRI measures in patients with active relapsingremitting multiple sclerosis over 2 and 5 years: A casecontrol study. Journal of
Neurology, Neurosurgery and Psychiatry, 79(4), 407414.
Hua, X., Gutman, B., Boyle, C. P., Rajagopalan, P., Leow, A. D., Yanovsky, I., et al.
(2011). Accurate measurement of brain changes in longitudinal MRI scans using
tensor-based morphometry. NeuroImage, 57(1), 514.
Hua, X., Hibar, D. P., Ching, C. R.K, Boyle, C. P., Rajagopalan, P., Gutman, B. A., et al.
(2013). Unbiased tensor-based morphometry: Improved robustness and
sample size estimates for Alzheimers disease clinical trials. NeuroImage, 66,
648661.
Hua, X., Lee, S., Yanovsky, I., Leow, A. D., Chou, Y.-Y., Ho, A. J., et al. (2009).
Optimizing power to track brain degeneration in Alzheimers disease and mild
cognitive impairment with tensor-based morphometry: An ADNI study of 515
subjects. NeuroImage, 48(4), 668681.
Huang, J., & Alexander, D. C. (2012). Probabilistic event cascades for Alzheimers
disease. In Advances in neural information processing systems (pp. 31043112). .
http://books.nips.cc/papers/files/nips25/NIPS2012_1428.pdf.
Hutton, C., Draganski, B., Ashburner, J., & Weiskopf, N. (2009). A comparison between
voxel-based cortical thickness and voxel-based morphometry in normal aging.
NeuroImage, 48(2), 371380.
Ishida, S., Sugino, M., Koizumi, N., Shinoda, K., Ohsawa, N., Ohta, T., et al. (1995).
Serial MRI in early Creutzfeldt-Jacob disease with a point mutation of prion protein
at codon 180. Neuroradiology, 37(7), 531534.
Jack, C. R., Jr., Barkhof, F., Bernstein, M. A., Cantillon, M., Cole, P. E., Decarli, C., et al.
(2011). Steps to standardization and validation of hippocampal volumetry as a
biomarker in clinical trials and diagnostic criterion for Alzheimers disease.
Alzheimers Dement, 7(4), 474485, e4.
Jack, C. R., Jr., Lowe, V. J., Weigand, S. D., Wiste, H. J., Senjem, M. L.,
Knopman, D. S., et al. (2009). Serial PIB and MRI in normal, mild cognitive
impairment and Alzheimers disease: Implications for sequence of pathological
events in Alzheimers disease. Brain, 132(Pt 5), 13551365.
Jack, C. R., Jr., Petersen, R. C., Grundman, M., Jin, S., Gamst, A., Ward, C. P., et al.
(2008). Longitudinal MRI findings from the vitamin E and donepezil treatment study
for MCI. Neurobiol Aging, 29(9), 12851295.
Jacobs, D., Sano, M., Marder, K., Bell, K., Bylsma, F., Lafleche, G., et al. (1994). Age at
onset of Alzheimers disease: Relation to pattern of cognitive dysfunction and rate of
decline. Neurology, 44(7), 12151220.
Jernigan, T. L., Gamst, A. C., Fennema-Notestine, C., & Ostergaard, A. L. (2003). More
mapping in brain mapping: statistical comparison of effects. Human Brain
Mapping, 19(2), 9095.
Jovicich, J., Czanner, S., Greve, D., Haley, E., van der Kouwe, A., Gollub, R., et al.
(2006). Reliability in multi-site structural MRI studies: Effects of gradient
non-linearity correction on phantom and human data. NeuroImage, 30(2),
436443.
Jovicich, J., Marizzoni, M., Sala-Llonch, R., Bosch, B., Bartres-Faz, D., Arnold, J., et al.
(2013). Brain morphometry reproducibility in multi-center 3 T MRI studies: A
comparison of cross-sectional and longitudinal segmentations. NeuroImage, 83C,
472484.
Keihaninejad, S., Zhang, H., Ryan, N. S., Malone, I. B., Modat, M., Cardoso, M. J., et al.
(2013). An unbiased longitudinal analysis framework for tracking white matter
changes using diffusion tensor imaging with application to Alzheimers disease.
Kempton, M. J., Ettinger, U., Schmechtig, A., Winter, E. M., Smith, L., McMorris, T.,
et al. (2009). Effects of acute dehydration on brain morphology in healthy humans.
Human Brain Mapping, 30(1), 291298.
Kim, J., Avants, B., Whyte, J., & Gee, J. C. (2013). Methodological considerations in
longitudinal morphometry of traumatic brain injury. Frontiers in Human
Lazaro, L., Bargallo, N., Castro-Fornieles, J., Falcon, C., Andres, S., Calvo, R., et al.
(2009). Brain changes in children and adolescents with obsessive-compulsive
disorder before and after treatment: A voxel-based morphometric MRI study.
Psychiatry Research, 172(2), 140146.
Leung, K. K., Barnes, J., Modat, M., Ridgway, G. R., Bartlett, J. W., Fox, N. C., et al.
(2011). Brain MAPS: An automated, accurate and robust brain extraction technique
using a template library. NeuroImage, 55(3), 10911108.
Leung, K. K., Barnes, J., Ridgway, G. R., Bartlett, J. W., Clarkson, M. J., Macdonald, K.,
et al. (2010). Automated cross-sectional and longitudinal hippocampal volume
measurement in mild cognitive impairment and Alzheimers disease. NeuroImage,
51(4), 13451359.
Leung, K. K., Bartlett, J. W., Barnes, J., Manning, E. N., Ourselin, S., Fox, N. C., et al.
(2013). Cerebral atrophy in mild cognitive impairment and Alzheimer disease: Rates
and acceleration. Neurology, 80(7), 648654.

Leung, K. K., Clarkson, M. J., Bartlett, J. W., Clegg, S., Jack, C. R., Jr., Weiner, M. W.,
et al. (2010). Robust atrophy rate measurement in Alzheimers disease using multisite serial MRI: Tissue-specific intensity normalization and parameter selection.
NeuroImage, 50(2), 516523.
Leung, K. K., Ridgway, G. R., Ourselin, S., & Fox, N. C.Alzheimers Disease
Neuroimaging Initiative. (2012). Consistent multi-time-point brain atrophy
estimation from the boundary shift integral. NeuroImage, 59(4), 39954005.
Lewis, E. B., & Fox, N. C. (2004). Correction of differential intensity inhomogeneity in
longitudinal MR images. NeuroImage, 23(1), 7583.
Li, Y., Gilmore, J. H., Shen, D., Styner, M., Lin, W., & Zhu, H. (2013). Multiscale
adaptive generalized estimating equations for longitudinal neuroimaging data.
Littmann, A., Guehring, J., Buechel, C., & Stiehl, H.-S. (2006). Acquisition-related
morphological variability in structural MRI. Academic Radiology, 13(9),
10551061.
Lorenzi, M., Ayache, N., Frisoni, G. B., & Pennec, X.Alzheimers Disease Neuroimaging
Initiative. (2013). LCC- Demons: A robust and accurate symmetric diffeomorphic
registration algorithm. NeuroImage, 81, 470483.
Lyoo, I. K., Dager, S. R., Kim, J. E., Yoon, S. J., Friedman, S. D., Dunner, D. L., et al.
(2010). Lithium-induced gray matter volume increase as a neural correlate of
treatment response in bipolar disorder: A longitudinal brain imaging study.
Neuropsychopharmacology, 35(8), 17431750.
Mahoney, C. J., Downey, L. E., Ridgway, G. R., Beck, J., Clegg, S., Blair, M., et al.
(2012). Longitudinal neuroimaging and neuropsychological profiles of
frontotemporal dementia with C9ORF72 expansions. Alzheimers Research &
Therapy, 4(5), 41.
Malone, I. B., Cash, D., Ridgway, G. R., Macmanus, D. G., Ourselin, S., Fox, N. C., et al.
(2013). MIRIAD-public release of a multiple time point Alzheimers MR imaging
dataset. NeuroImage, 70, 3336.
Mang, A., Toma, A., Schuetz, T. A., Becker, S., & Buzug, T. M. (2012). A generic
framework for modeling brain deformation as a constrained parametric optimization
problem to aid non-diffeomorphic image registration in brain tumor imaging.
Methods of Information in Medicine, 51(5), 429440.
Mathalon, D. H., Sullivan, E. V., Lim, K. O., & Pfefferbaum, A. (2001). Progressive brain
volume changes and the clinical course of schizophrenia in men: A longitudinal
magnetic resonance imaging study. Archives of General Psychiatry, 58(2), 148157.
Mechelli, A., Price, C. J., Friston, K. J., & Ashburner, J. (2005). Voxel-based
morphometry of the human brain: Methods and applications. Current Medical
Imaging Reviews, 1(1), 19.
Modat, M., Ridgway, G. R., Hawkes, D. J., Fox, N. C., & Ourselin, S. (2010). Nonrigid
registration with differential bias correction using normalised mutual information.
In: IEEE International Symposium on Biomedical Imaging (ISBI) (pp. 356359).
Modersitzki, J. (2009). FAIR: Flexible algorithms for image registration Vol. 6.
Philadelphia, PA: SIAM.
Nakamura, K., Fox, R., & Fisher, E. (2011). CLADA: Cortical longitudinal atrophy
detection algorithm. NeuroImage, 54(1), 278289.
Poldrack, R. A., Fletcher, P. C., Henson, R. N., Worsley, K. J., Brett, M., & Nichols, T. E.
(2008). Guidelines for reporting an fMRI study. NeuroImage, 40(2), 409414.
Prastawa, M., Awate, S., & Gerig, G. (2012). Building spatiotemporal anatomical models
using joint 4-D segmentation, registration, and subject-specific atlas estimation. In
IEEE Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA)
(pp. 4956).
Protopopescu, X., Butler, T., Pan, H., Root, J., Altemus, M., Polanecsky, M., et al.
(2008). Hippocampal structural changes across the menstrual cycle. Hippocampus,
18(10), 985988.
Qiu, A., & Miller, M. I. (2008). Multi-structure network shape analysis via normal
surface momentum maps. NeuroImage, 42(4), 14301438.
Radua, J., Canales-Rodrguez, E. J., Pomarol-Clotet, E., & Salvador, R. (2014). Validity
of modulation and optimal settings for advanced voxel-based morphometry.
Raffelt, D., Tournier, J.-D., Rose, S., Ridgway, G. R., Henderson, R., Crozier, S., et al.
(2012). Apparent fibre density: A novel measure for the analysis of diffusionweighted magnetic resonance images. NeuroImage, 59(4), 39763994.
Rao, A., Chandrashekara, R., Sanchez-Ortiz, G., Mohiaddin, R., Aljabar, P., Hajnal, J.,
et al. (2004). Spatial transformation of motion and deformation fields using nonrigid
Raz, N., Lindenberger, U., Rodrigue, K. M., Kennedy, K. M., Head, D., Williamson, A.,
et al. (2005). Regional brain changes in aging healthy adults: general trends,
individual differences and modifiers. Cerebral Cortex, 15(11), 16761689.
Reuter, M., & Fischl, B. (2011). Avoiding asymmetry-induced bias in longitudinal
image processing. NeuroImage, 57(1), 1921.
Reuter, M., Schmansky, N. J., Rosas, H. D., & Fischl, B. (2012). Within-subject template
estimation for unbiased longitudinal image analysis. NeuroImage, 61(4), 14021418.
427
Ridgway, G. R., Lehmann, M., Barnes, J., Rohrer, J. D., Warren, J. D., Crutch, S. J., et al.
(2012). Early-onset Alzheimer disease clinical variants: multivariate analyses of
cortical thickness. Neurology, 79(1), 8084.
Ridha, B. H., Anderson, V. M., Barnes, J., Boyes, R. G., Price, S. L., Rossor, M. N., et al.
(2008). Volumetric MRI and cognitive measures in Alzheimer disease: Comparison
of markers of progression. Journal of Neurology, 255(4), 567574.
Rohrer, J. D., Caso, F., Mahoney, C., Henry, M., Rosen, H. J., Rabinovici, G., et al.
(2013). Patterns of longitudinal brain atrophy in the logopenic variant of primary
progressive aphasia. Brain and Language, 127, 121126.
Salat, D. H., Lee, S. Y., van der Kouwe, A. J., Greve, D. N., Fischl, B., & Rosas, H. D.
(2009). Age-associated alterations in cortical gray and white matter signal intensity
and gray to white matter contrast. NeuroImage, 48(1), 2128.
Scahill, R. I., Ridgway, G. R., Bartlett, J. W., Barnes, J., Ryan, N. S., Mead, S., et al.
(2013). Genetic influences on atrophy patterns in familial Alzheimers disease: A
comparison of APP and PSEN1 mutations. Journal of Alzheimers Disease, 35(1),
199212.
Scahill, R. I., Schott, J. M., Stevens, J. M., Rossor, M. N., & Fox, N. C. (2002). Mapping
the evolution of regional atrophy in Alzheimers disease: Unbiased analysis of fluidregistered serial MRI. Proceedings of the National Academy of Sciences of the
United States of America, 99(7), 47034707.
Scholz, J., Klein, M. C., Behrens, T. E.J, & Johansen-Berg, H. (2009). Training induces
changes in white-matter architecture. Nature Neuroscience, 12(11), 13701371.
Schwartzman, A., Dougherty, R. F., & Taylor, J. E. (2005). Cross-subject comparison of
principal diffusion direction maps. Magnetic Resonance in Medicine, 53(6),
14231431.
Skrinjar, O., Bistoquet, A., & Tagare, H. (2008). Symmetric and transitive registration of
image sequences. International Journal of Biomedical Imaging, 2008(686875), 19.
Smith, S. M., Stefano, N. D., Jenkinson, M., & Matthews, P. M. (2001). Normalized
accurate measurement of longitudinal brain change. Journal of Computer Assisted
Tomography, 25(3), 466475.
Smith, S. M., Zhang, Y., Jenkinson, M., Chen, J., Matthews, P. M., Federico, A., et al.
(2002). Accurate, robust, and automated longitudinal and cross-sectional brain
change analysis. NeuroImage, 17(1), 479489.
Sowell, E. R., Thompson, P. M., Leonard, C. M., Welcome, S. E., Kan, E., & Toga, A. W.
(2004). Longitudinal mapping of cortical thickness and brain growth in normal
children. Journal of Neuroscience, 24(38), 82238231.
Studholme, C. (2011). Mapping fetal brain development in utero using magnetic
resonance imaging: The big bang of brain mapping. Annual Review of Biomedical
Engineering, 13, 345368.
Tabrizi, S. J., Scahill, R. I., Durr, A., Roos, R. A., Leavitt, B. R., Jones, R., et al. (2011).
Biological and clinical changes in premanifest and early stage Huntingtons disease
in the TRACK-HD study: The 12-month longitudinal analysis. Lancet Neurology,
10(1), 3142.
Tagare, H., Groisser, D., & Skrinjar, O. (2009). Symmetric non-rigid registration: A
geometric theory and some numerical techniques. Journal of Mathematical Imaging
and Vision, 34(1), 6188.
Thevenaz, P., Blu, T., & Unser, M. (2000). Interpolation revisited. IEEE Transactions on
Thirion, J. P. (1998). Image matching as a diffusion process: An analogy with Maxwells
demons. Medical Image Analysis, 2(3), 243260.
Thomas, C., & Baker, C. I. (2013). Teaching an adult brain new tricks: A critical review
of evidence for training- dependent structural plasticity in humans. NeuroImage, 73,
225236.
Thomas, A. G., Marrett, S., Saad, Z. S., Ruff, D. A., Martin, A., & Bandettini, P. A.
(2009). Functional but not structural changes associated with learning: An
exploration of longitudinal voxel-based morphometry (VBM). NeuroImage, 48(1),
117125.
Thompson, W. K., Hallmayer, J., & OHara, R.Alzheimers Disease Neuroimaging Initiative.
(2011). Design considerations for characterizing psychiatric trajectories across the
lifespan: Application to effects of APOE-e4 on cerebral cortical thickness in Alzheimers
disease. The American Journal of Psychiatry, 168(9), 894903.
Thompson, W. K., & Holland, D.Alzheimers Disease Neuroimaging Initiative. (2011).
Bias in tensor based morphometry Stat-ROI measures may result in unrealistic
power estimates. NeuroImage, 57(1), 14.
Vardhan, A., Prastawa, M., Sharma, A., Piven, J., & Gerig, G. (2013). Modeling
longitudinal MRI changes in populations using a localized, information-theoretic
measure of contrast. In: IEEE International Symposium on Biomedical Imaging
(ISBI) (pp. 13961399).
Walters, R. J., Fox, N. C., Crum, W. R., Taube, D., & Thomas, D. J. (2001).
Haemodialysis and cerebral oedema. Nephron, 87(2), 143147.
Warfield, S. K., Zou, K. H., & Wells, W. M. (2004). Simultaneous truth and performance
level estimation (STAPLE): An algorithm for the validation of image segmentation.
428
Wolz, R., Heckemann, R. A., Aljabar, P., Hajnal, J. V., Hammers, A., Lotjonen, J., et al.
(2010). Measurement of hippocampal atrophy using 4D graph-cut segmentation:
Application to ADNI. NeuroImage, 52(1), 109118.
Xue, Z., Shen, D., & Davatzikos, C. (2006). CLASSIC: Consistent longitudinal
alignment and segmentation for serial image computing. NeuroImage, 30(2),
388399.
Younes, L., Qiu, A., Winslow, R. L., & Miller, M. I. (2008). Transport of relational
structures in groups of diffeomorphisms. Journal of Mathematical Imaging and
Vision, 32(1), 4156.
Yushkevich, P. A., Avants, B. B., Das, S. R., Pluta, J., Altinay, M., Craige, C., et al.
(2010). Bias in estimation of hippocampal atrophy using deformation-based
morphometry arises from asymmetric global normalization: An illustration in ADNI
3 T MRI data. NeuroImage, 50(2), 434445.
Yushkevich, P. A., Piven, J., Hazlett, H. C., Smith, R. G., Ho, S., Gee, J. C., et al. (2006).
User-guided 3D active contour segmentation of anatomical structures: Significantly
improved efficiency and reliability. NeuroImage, 31(3), 11161128.
Zatorre, R. J., Fields, R. D., & Johansen-Berg, H. (2012). Plasticity in gray and white:
Neuroimaging changes in brain structure during learning. Nature Neuroscience,
15(4), 528536.
Relevant Websites
http://www.fil.ion.ucl.ac.uk/spm/ SPM software.
http://fsl.fmrib.ox.ac.uk/ FSL (see SIENA, fsl_anat and FSLVBM, in particular).
http://www.itksnap.org ITK-SNAP software.
http://www.nitrc.org/forum/forum.php?thread_id3881&forum_id2 Longitudinal
MRI data-sets NITRC discussion post.
http://surfer.nmr.mgh.harvard.edu/ FreeSurfer software.
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalData Longitudinal MRI datasets FreeSurfer wiki page.
Modeling Brain Growth and Development

N Sadeghi, National Institutes of Health, Bethesda, MD, USA
G Gerig, University of Utah, Salt Lake City, UT, USA
JH Gilmore, University of North Carolina, Chapel Hill, NC, USA
Glossary
AD, RD Axial diffusivity (AD) and radial diffusivity (RD) are

derived from diffusion tensor images (DTIs). AD indicates
diffusivity along axonal fiber bundles, whereas RD represents
transversal diffusivity orthogonal to the axonal direction.
Axon Axons are nerve fibers that transmit information
between different neurons across different brain regions.
Bonferroni correction The Bonferroni correction is a
technique that corrects for multiple comparison when doing
multiple statistical tests; it is named after the mathematician
C. E. Bonferroni (18921960).
Corona radiata The corona radiata is a sheet of ascending
and descending axonal bundles, which radiate from the
brain stem towards major cortical regions including the
motor and sensory cortices.
Corpus callosum The corpus callosum is a bundle of the
brain white matter fibers that connects the right and the left
hemispheres and is responsible for interhemispheric
communication.
DTI Diffusion tensor imaging is an MRI method that
measures diffusion properties of molecules in human body
tissue. The local diffusion patterns are being used to map
axonal bundles representing brain white matter fiber structures
and applied to study connectivity of brain structures and
alterations of tissue diffusion in disease and injury.
FA Fractional anisotropy (FA) is a measure derived from
DTI. FA measures the directionality of local diffusivity in
brain white matter and is often associated with the amount
of structuring of axonal bundles.
Genu The anterior (front) portion of the corpus callosum is
called the genu, connecting the left and right frontal parts of
the brain cortex.
Gompertz function The Gompertz function is named after
Benjamin Gompertz (17791865) and represents a
mathematical model that shows a rapid increase followed by
slower growth.
Hypointense, hyperintense Hypo- and hyperintense are
terms used by radiologist to describe regions in image scans
that are of lower intensity (hypo) and are of higher intensity
(hyper) than the surrounding tissue.
Lateralization The term lateralization refers to the study of
brain function associated with the left and right
Early brain development is characterized by rapid organization

and structuring. Magnetic resonance diffusion tensor imaging
(MR-DTI) provides the possibility of capturing these changes
noninvasively by following individuals longitudinally in order
to better understand departures from normal brain development in subjects at risk for mental illness. This article illustrates
the modeling of neurodevelopmental trajectories from serial
hemispheres, respectively. The term refers to laterality,

which are asymmetrical preferences that humans show for
one side of the body over the other.
Logistic function A logistic function is a mathematical
model that resembles an S-curve. With initial slow growth,
the function accelerates but then slows down until growth
stops.
Monomolecular function A monomolecular function is a
mathematical growth modeling particularly used for disease
forecasting used in the prediction of plant diseases, for
example.
MRI Magnetic resonance imaging (MRI) is a medical
imaging technique to visualize internal structures of the
human body. The technique does use nuclear magnetic
resonance (NMR) properties of human body tissue in a
strong magnetic field. MRI yields high-contrast two- and
three-dimensional images without using x-rays.
Myelination Myelination is a brain maturation process
where axonal bundles are wrapped by myelin sheaths, a
process that is essential for proper functioning of the
nervous system. Little myelination exists at the time of birth,
but there is very rapid myelination of the whole brain during
the first 2 years of life.
MZ, DZ The term monozygotic (MZ) stands for identical
twins, whereas the term dizygotic (DZ) is used for fraternal
twins.
Singleton The term singleton is used here to differentiate
between one offspring that develops alone in the womb and
multiple offspring such as twins.
Spatiotemporal Spatiotemporal is a term used by scientists
to describe processes that show spatial (geometric) and
temporal (time) changes. In the context of early brain
development, one observes rapid changes of brain size and
shape with developmental age.
Splenium The posterior (back) portion of the corpus
callosum is called the splenium, connecting the left and right
parts of the back of the brain cortex.
T1W, T2W T1W and T2W stand for MRI protocols to
produce different contrasts of human body tissue, fat, and
water. The terms T1 and T2 stand for time constants for
proton relaxation, with weights to be used to generate
optimal contrast for radiological readings.
image data using a recently developed framework. Descriptions include the generation of normative models for healthy
singletons and twins and a statistical framework to predict
development at 2 years of age from neonatal data a capability
with excellent potential for preclinical diagnosis and eventual
early therapeutic intervention. As the brain develops, the water
content in the brain tissue decreases while protein content and
http://dx.doi.org/10.1016/B978-0-12-397025-1.00314-6
429
430
INTRODUCTION TO METHODS AND MODELING | Modeling Brain Growth and Development
fat content increase due to processes such as myelination and

axonal organization. Changes of signal intensity in structural
magnetic resonance imaging (MRI) and diffusion parameters
of diffusion tensor imaging (DTI) reflect these underlying biological changes.
Longitudinal neuroimaging studies provide a unique opportunity for understanding early brain maturation by taking
repeated scans of individuals over the first 2 years. Despite the
availability of anatomical images of the brain with unprecedented details, there has been little progress in accurate modeling
of brain development or in creating predictive models of structures that could help identify early signs of illness. We have
developed methodologies for the nonlinear parametric modeling
of longitudinal structural MRI and DTI changes over the neurodevelopmental period to address this gap. This research provides
a normative model of early brain growth trajectory as is represented in structural MRI and DTI data, which will be crucial for
improved understanding of the timing and potential mechanisms of atypical development. Growth trajectories are described
via intuitive parameters related to delay, rate of growth, and
expected asymptotic values, all descriptive measures that can
answer clinical questions related to quantitative analysis of
growth patterns. We demonstrate the potential of the framework
with application to a study of early brain development of healthy
controls (singletons and twins). Our framework is designed not
only to provide qualitative comparisons but also to give
researchers and clinicians quantitative parameters and a statistical testing scheme. Moreover, the method includes modeling of
growth trajectories of individuals, resulting in personalized brain
maturation profiles. The statistical framework also allows for the
prediction of subject-specific growth trajectories and confidence
intervals, a new scheme that will be crucial for efforts to improve
diagnosis for individuals and personalized treatment.
Brain Growth as Observed in Anatomical MRI

MRI is appropriate for longitudinal pediatric studies since it
does not use ionizing radiation and enables safe noninvasive
scanning of young children. The brain undergoes significant
changes during the first 2 years of life, with continued growth
into adulthood. Previous cross-sectional neuroimaging studies
have indicated an overall brain size increase during this period,
reaching 8090% of adult volume by age 2 (Pfefferbaum et al.,
1994). More recently, Knickmeyer et al. (2008) reported that
the total brain volume increases by 101% in the first year,
followed by 15% in the second year. In addition to morphometric measures such as volume and shape, including cortical
folding (Huppi, 2008; Knickmeyer et al., 2008; Murgasova,
2007; Xue et al., 2007), signal characteristics of brain tissue
also change, reflecting the maturation of the underlying tissue.
During the first 6 months after birth, the signal intensities of
the gray matter and white matter in T1-weighted (T1W) and
T2-weighted (T2W) MR images are the reverse of those seen in
adults. This is mainly due to the process of tissue myelination
since the white matter is mostly unmyelinated at birth. As the
white matter myelinates, signal intensity changes from hypointense to hyperintense relative to the gray matter in T1W MR
images. The reverse pattern is seen in T2W MR images (from
hyperintense to hypointense) as shown in Figure 1.
Neo
Year 1
Year 2
T1W
T2W
Figure 1 T1W and T2W images of an individual scanned at about 2

weeks, 1 year, and 2 years. The pattern of brain gray and white matter
contrast at birth is the reverse of what is seen at 2 years.
Myelination follows a spatiotemporal sequence as described

by histological studies (Yakovlev & Lecours, 1967) and qualitatively by neuroradiologists (Rutherford, 2002). However, quantitative assessment of the maturation pattern of white matter is
still lacking. The development of cognitive functions is associated with white matter maturation, and hence, abnormalities in
observed diffusivity of the white matter can be associated with
cognitive deficits diagnosed in later life.
Early White Matter Maturation

DTI provides additional information about the microstructure
of the brain. This method measures the average displacement
of water molecules within the tissue during a fixed time period.
There is more diffusion where molecules can travel freely, and
less diffusion where movement is impeded by obstacles such as
cell membranes, myelin, and macromolecules. Because the
diffusion of water molecules is shaped by the underlying tissue
structure, it is possible to gain an understanding of the underlying tissue structure by measuring diffusion. Fiber bundle
organization can be depicted in DTI since water diffuses preferentially parallel to the fiber direction and to a lesser extent in
cross sections. This anisotropic diffusion provides detailed
information about brain axonal organization. As the white
matter matures, diffusion of water molecules becomes more
restricted as brain tissue undergoes structuring and myelination. Monitoring changes of diffusion parameters therefore
provides information about the maturation pattern of the
white matter.
In DTI, 3-D motion of water molecules is modeled via a
second-order tensor at each voxel (Basser, Mattiello, & LeBihan, 1994). A tensor is represented as a diffusion matrix and
can be visualized as an ellipsoid where the length of each
primary axis represents an average diffusion in each spatial
direction (Mori & Zhang, 2006). The tensor information can
be summarized by simpler invariant quantitative measures
(independent of the orientation of the reference frame) related
to the size or shape of the tensor. For example, one of the most
common measurements is fractional anisotropy (FA), an index

from 0 (isotropic) to 1 (anisotropic) indicating the shape of
the tensor ranging from a sphere to a thin stick (Pierpaoli &
Basser, 1996). Another measurement is mean diffusivity that
can be explained by the average length of the axes of the
ellipsoid indicating the size of the tensor. This measure has
been proved useful for assessing the diffusion drop in brain
ischemia (van Gelderen et al., 1994), for example. More
recently, axial diffusivity (AD) and radial diffusivity (RD)
have been proposed to help better understand the changes of
the diffusion tensor (Alexander et al., 2007; Sadeghi, Prastawa,
Gilmore, Lin, & Gerig, 2010). AD is the length of the longest
axes of ellipsoid, indicating the fiber orientation, and RD is the
average of the two shorter axes. Analysis of DTI data of pediatric subjects has illustrated changes of these indices due to
development (Dubois, Hertz-Pannier, Dehaene-Lambertz,
Cointepas, & Le Bihan, 2006; Gilmore et al., 2007). Cascio
et al. found overall increases in FA during development and
reduced overall diffusion due to development (Cascio, Gerig, &
Piven, 2007). Geng et al. (Geng et al., 2012) illustrated the
rapid white matter diffusivity changes from birth to 2 years by
analysis of FA mapped along the length of fiber tracts, demonstrating that changes during the first year are much larger than
over the second year.
FA values can also be color-coded by using the direction of
the main axis of the local tensor ellipsoid. Red is used to
indicate the leftright direction, blue is used for superior
inferior, and green is used for anteriorposterior directions
(Pajevic & Pierpaoli, 1999). Figure 2 shows color-coded FA
images of one subject at 2 weeks, 1 year, and 2 years. The
brightness is weighted by the FA (Pajevic & Pierpaoli, 1999).
Objectives of Longitudinal Neuroimaging Studies

The defining feature of longitudinal studies is that subjects are
measured repeatedly over the course of the study. This is in
contrast to cross-sectional studies in which an individual is
measured at only one single time point. Longitudinal studies
enable assessment of within-individual changes in the
response variable and thereby have the capacity to separate
between cohort and age effects. The main aims of a longitudinal study are to characterize within-individual changes over
time and to determine whether within-individual changes in
the response are associated with specific covariates such as
treatment plan, clinical group, or biological factors.
The main characteristic of longitudinal data is the correlation among repeated measurements. As these measurements
Neo
Year 1
Year 2
Figure 2 Color-coded FA images of an individual subject. Left to right:

scans at 2 weeks, 1 year, and 2 years.
431
are obtained on the same individual, there is a correlation

among the measurements, with measurements obtained closer
in time being more correlated than the ones further apart. This
correlation among repeated measurements violates the fundamental independence assumption of most statistical regression
techniques (Fitzmaurice, Laird, & Ware, 2011) and requires
different analysis schemes.
Most longitudinal studies plan to obtain the same number
of measurements for each individual at the same time points;
however, this is difficult to achieve in clinical practice. With
studies that span over a longer period of time, it is inevitable
that some individuals will drop out of the studies and some
might miss their appointments and are rescheduled for different time points. The statistical analysis method as described in
the following can appropriately handle uneven spacing of time
points and also cope with missing data, which can also be
caused by exclusion of image data due to subject motion.
Longitudinal Pediatric Neuroimaging Studies

Understanding early brain development has great scientific
and clinical importance. The human brain undergoes rapid
organization and structuring early in life, and also, there is
great heterogeneity among different individuals. Longitudinal
modeling of longitudinal data yields a more accurate average
trajectory over time without the confounding cohort effects
(Diggle, Heagerty, Liang, & Zeger, 2002; Fitzmaurice et al.,
2011). This is of great importance when the development itself
is in question. Recently, longitudinal image data have become
available for the critical period of development just after birth.
However, normative models are still not available to describe
the normal pattern of development as evidenced by structural
and diffusion MRI.
By designing appropriate longitudinal statistical analysis,
we can model the average trajectory via a parametric function
that can summarize growth with a few parameters. This also
enables comparison of a normative population model to other
groups or to individuals. For example, we can model population changes of subjects who have been diagnosed with a
specific disease and compare this growth curve to the normative model to gain a better understanding of the pathology and
when deviation occurs. We can also gain a better understanding of the spatiotemporal sequence of maturation of the white
matter in the developing brain.
Once average trajectories for different groups are obtained,
we can make inferences about parameters of the regression. In
this work, we consider studying longitudinal changes of diffusion parameters of DTI for a group of infant subjects (N 26)
from 2 weeks to 2 years old to establish a normative pattern of
development along with its variability. The parametric Gompertz function (see succeeding text and figures for an illustration of the Gompertz function) is used to characterize these
changes over time as it uses intuitive parameters describing
growth: asymptote, delay, and speed. As a proof of concept,
the white matter regions that are known to mature at different
rates are analyzed and compared. We also applied the methodology to estimate developmental trajectories for twins and
singletons and compare these trajectories between the two
groups. We hypothesized that there may be group differences
432
between developmental trajectories of twins and singletons

due to differences in pre- and postnatal environments.
Growth Models
Brain growth functions clearly show the nonlinear nature of
changes, starting with rapid changes that flatten off with
increasing age. These characteristics can be observed in measurements of brain volumes, of head circumference, tissue
contrast not only in T1- or T2-weighted anatomical MRI but
also in white matter diffusion obtained from diffusion
weighted MRI (DW-MRI). Linear modeling therefore cannot
capture this structure and has to be replaced by nonlinear
growth modeling. Nonlinear models of growth are generally
based on a differential equation relating growth rate dy/dt to
response variable y (i.e., size and diffusion parameter; Karkach,
2006). This formulation has led to a variety of growth models,
such as exponential, monomolecular, logistic, and Gompertz
functions. We have demonstrated in Sadeghi et al. (2013) that
the parametric Gompertz function best suits the purpose of
modeling early brain development. Moreover, the parameters
of the Gompertz function also provide intuitive parameterization of growth in terms of asymptotic value, delay, and growth
rate: y asymptote exp ( delay exp ( speed t)).
Regional Characterization
Normative Models for White Matter Diffusivities
The nonlinear mixed effects are used to model the longitudinal
changes of diffusion parameters within anatomical regions of
interest. A white matter label map developed and disseminated
by Mori et al. (2008) was used to define regions of interest in
our infant image data set. We select 13 anatomical regions in
the atlas space as shown in Figure 4. In this study, the left and
right regions of anatomical locations are combined, giving a
total of eight regions. The labeling of regions in the atlas space
allows automatic partitioning of each subjects scan into the
different anatomical regions as all the subjects have been
mapped to the atlas space (for details on the image processing
pipeline, please see Sadeghi et al. (2012)). We then estimate
growth trajectories for these regions using the nonlinear mixed
effects (NLME) model of Lindstrom and Bates (1990). Figure 4
illustrates the average FA for each region. In all the regions, FA
increases with age; however, each region has its own distinct
temporal pattern. Most of the regions show a rapid growth in
the first year with continued growth but at a slower rate in the
second year; however, the genu of the corpus callosum shows a
steady growth during the first 2 years. The genu is one of the
regions that develops later and its maturation seems to continue into developmental stages later than the 2-year observation period.
Nonlinear Mixed Effects Model
Hypothesis Testing
Mixed effects models provide a powerful and flexible environment for analyzing longitudinal data, properly accounting for
the intercorrelation among observations on each subject
(Diggle et al., 2002). In the mixed effects model, the observed
data are assumed to be a combination of both fixed effects, b,
parameters associated with the entire population (or at least
within a subpopulation), and random effects, b, parameters that
are specific to an individual drawn at random from the population. A mixed effects model distinguishes between a withinsubject source of variability and a between-subject source of
variability. Correlation among repeated scans of an individual
is accounted for by incorporating random effects in the model.
Mixed effects model also results in a group trend (fixed effects)
that better reflects how individuals progress on average compared to a least-square fit as is shown in the Figure 3.
Parametric estimation of NLME is based upon the maximum of

the marginal likelihood or model evidence. The distribution of
fixed effects is approximated by the normal distribution (aka
the Laplace assumption). Knowing fixed effects and its sampling distribution, approximate confidence intervals of fixed
effects can be calculated and hypothesis testing can be performed between regions of interest.
We conduct hypothesis testing between pairs of regions to
determine the modes of longitudinal changes in terms of the
Gompertz growth parameters. With N number of regions, we
perform (N(N 1))/2 pairwise fitting of a nonlinear mixed
effects model. The significant parameters are determined through
t-tests, corrected for multiple comparisons by the Bonferroni
correction. The parameters that are found to be significant
between two pairs of regions can be interpreted as the
RD
0.007
0.006
0.005
0.004
0
200
400
600
Age (days)
800
200
400
Age (days)
600
800
200
400
Age (days)
600
800
Figure 3 Population growth models, represented as dashed black curves, obtained using nonlinear least-squares (NLS) fit on the left and with
nonlinear mixed effects (NLME) modeling in the middle. Colored points represent data observations, and colored curves represent the
individual growth trajectories. NLME (solid black) better models how individuals progress on average if compared with NLS (dashed black),
with overlay of both shown on the right.

distinguishing feature between the longitudinal trajectories of
these regions. Figure 5 shows population and individual growth
trajectories for FA and RD of the genu (shown in blue) compared
with the splenium (shown in red). The anterior region of the
corpus callosum is the genu with tracts ending in the prefrontal
cortex, whereas the splenium is the posterior region with tracts
ending in the occipital lobe. Both of these regions are unmyelinated at birth and develop quickly during the first 2 years of life.
Overall, the genu shows higher MD, RD, and AD during the first
2 years while FA shows higher values mostly for the second year.
This suggests that the genu is less mature at birth but develops
rapidly reaching the same level of MD and RD as the splenium by
the second year. Both the genu and splenium have relatively
higher AD compared with other regions of the brain, indicating
higher axonal organization for these regions.
Inference and Predictions

In addition to modeling the mean trajectory of diffusion properties over time and hypothesis testing among different
regions, another important aspect of longitudinal analysis is
the direct estimation of intraindividual changes over time.
Even if not all observations for all time points are available
for a subject, by pooling the data from other subjects in the
study along with the available observations for the individual,
prediction of an individual trajectory is possible. The estimation of personalized growth profiles is of significant clinical
interest as individuals respond differently to treatment and
show different growth trajectories. Figure 6 shows the approximate subject growth trajectory along with the subject-specific
prediction interval for RD values of an individual based on the
ALIC
PLIC
Genu
0.8
433
BCC
Sp
ExCap
RLIC
PTR
FA
0.6
0.4
0.2
200
400
600
800
Age (days)
Figure 4 Average growth trajectories of the anterior limb of internal capsule (ALIC) and posterior limb of internal capsule (PLIC); the genu, body, and
splenium of the corpus callosum (Genu, BCC, and Sp); external capsule (ExCap) and retrolenticular part of the internal capsule (RLIC); and posterior
thalamic radiation are shown. FA values increase for all these regions during early brain development, but different structures depict a distinct
spatiotemporal pattern.
0.8
FA
0.6
0.4
0.2
0.0
0.5
200
400
600
800
600
800
0.0015
0.0005
0
FA
RD (mm2 s-1)
Age (days)
200
400
Age (days)
Figure 5 Left: Color-coded FA of the corpus callosum at 6, 12, and 24 months (the left side of the image is the posterior region (splenium), whereas the
right side is the anterior region (genu) of cc). Right: Population and individual growth trajectories for the genu (blue) and splenium (red). Thick
curves are the average growth trajectories, whereas dashed curves are the individual trajectories. The following Gompertz parameters were
significantly different (p < 0.05) between these two regions: FA, asymptote and speed; RD, speed.
434
Neo
year 1
RD (mm2 s1)
0.0004
0.0008
0.0012
Population 95% prediction interval

Subject 95% prediction interval
Subject trajectory
Subject included time point(s)
Subject test time point(s)
200
400
Age (days)
600
800
Figure 6 Top: Posterior thalamic radiation is shown as red label on the neonate and year 1 FA scans of one subject. Bottom: Subject 95% prediction
interval compared with the overall prediction for RD of posterior thalamic radiation. Subject-specific interval calculated based on the subjects
scans at neonate and 1 year in addition to population parameters. Subjects year 2 RD value (red square) falls within the predicted range (blue region).
available scans at neonate and 1 year using NLME. The gray

shaded region in the figure shows the prediction interval based
on the population parameters and variability among individuals, whereas the blue region indicates the subject-specific
prediction interval based on the available population parameters and the new individuals available data. Also, in cases
when only a single scan is available, the intensity or diffusion
parameters of the subject can be compared with the normative
model to indicate whether an individual is within the normative range of variability. Using such an estimation scheme,
subject-specific growth trajectory and predictive intervals can
be predicted based on only one scan. Such predictions might
improve early detection and outcome as the subject-specific
prediction interval not only accounts for the populationestimated parameters but also considers the new individuals
available data.
Brain Maturation Differences: Singletons Versus Twins

Twin studies have provided a valuable insight into the heritability of disease; however, it might be difficult to generalize these
findings to a singleton population due to differences between
twins and singletons in pre- and postnatal environments
(Hulshoff Pol et al., 2002; Knickmeyer et al., 2011). The intrauterine environment might be suboptimal as twins share the
womb and compete for nutrition. Also, the family environment
can be suboptimal due to limited resources and competition

between the twins (Hay & OBrien, 1983). A recent study by
Knickmeyer et al. (Knickmeyer et al., 2011) found significant
differences in gray matter development in monozygotic (MZ)
twins compared with dizygotic (DZ) twins and singletons, but
no differences were found in intracranial volume, total white
matter volume, and lateral ventricle volume.
When we examined the compatibility of white matter developmental trajectories between twins and singletons, comparison of mean trajectories among MZ, DZ, and singletons
indicates that growth trajectories of MZ and dizygotic twins
are very similar. No significant differences were found between
the growth curves of MZ and DZ in terms of Gompertz parameters of asymptote, delay, and speed for any of the diffusion
measurements. To further investigate whether twins and singletons show any developmental differences, DZ and MZ individuals were combined as there were no differences in their
growth trajectories. Gestational age was controlled in the analysis as twin subjects are generally born earlier than singletons,
in our study by 3 weeks. When comparing the combined twin
group to singletons, the following regions showed significant
differences in the delay parameter of the AD measures: the right
and left anterior limb of the internal capsule (ALIC) and right
and left anterior corona radiata (Figure 7). There were no
significant differences in asymptote and speed parameters
between these two groups for any of the regions analyzed.
There were also no significant differences between FA and RD
200
400
600
0.0022
800
Singleton
200
Age (days)
600
800
600
800
0.0022
Anterior corona radiata L

Twin
0.0018
Singleton
0.0014
AD (mm2 s-1)
400
Age (days)
0.0010
0.0022
0.0018
Twin
0.0014
0.0010
AD (mm2 s-1)
Singleton
200
400
Age (days)
Anterior corona radiata R
Twin
0.0018
0.0010
AD (mm2 s-1)
0
Anterior limb of internal capsule L
0.0014
Twin
0.0018
Singleton
0.0014
0.0010
AD (mm2 s-1)
0.0022
Anterior limb of internal capsule R
435
200
400
600
800
Age (days)
Figure 7 Comparison of AD growth trajectories of twins and singletons for the ALIC and the anterior corona radiata. The delay parameter (p < 0.05)
was significantly different between twins and singletons in these two regions.
5
4.5
4
3.5
3
2.5
2
1.5
1
0.5
0
0
-0.5
-1
-1.5
-2
-2.5
-3
-3.5
-4
-4.5
-5
Figure 8 Differences in axial diffusion (AD) of twins versus singletons ((Twin Singleton)/Singleton)*100. Top: Differences in AD between twins and
singletons at birth. Bottom: Differences at 3 months. The changes from dark blue at birth to light blue at 3 months indicate that differences
between twins and singletons quickly become much smaller and reach the same white matter maturation values.
436
measures between these two groups. These preliminary findings suggest that twins and singletons follow similar growth
trajectories for most white matter regions. This study compared
21 anatomical regions, including projection fibers such as
internal capsule and corona radiata, association fibers including superior longitudinal fasciculus and external capsule, and
commissural fibers such as the genu, body, and splenium of
the corpus callosum. FA and RD did not differ between twins
and singletons in all the regions that were analyzed after correction for multiple comparisons. However, twins and singletons did exhibit differences in AD measures in the ALIC and the
anterior region of the corona radiata. There were significant
differences in the delay parameter of the Gompertz function
for these regions, indicating that twins were delayed compared
with singletons. However, twins appear to have caught up to
singletons by 34 months postterm as though they experience
a period of catch-up growth postbirth (Figures 7 and 8). There
were no significant differences in the asymptote parameter of
the Gompertz function, suggesting that the twinsingleton
differences observed early on in these regions disappear by
early childhood (Figure 7).
Acknowledgments
This research was supported by NIH grants R01 MH070890
(JHG, GG), Conte Center MH064065 (JHG,GG), and National
Alliance for Medical Image Computing (NA-MIC) U54
EB005149 (GG).

Anatomical MRI for Human Brain Morphometry; Diffusion MRI;
INTRODUCTION TO ANATOMY AND PHYSIOLOGY:
Language; INTRODUCTION TO CLINICAL BRAIN MAPPING:
Basic Concepts of Image Classification Algorithms Applied to Study
Neurodegenerative Diseases; Developmental Brain Atlases;
INTRODUCTION TO METHODS AND MODELING: Computing
Brain Change over Time; Diffeomorphic Image Registration; Diffusion
Tensor Imaging; Fiber Tracking with DWI; The General Linear Model.
References
Alexander, A. L., Lee, J. E., Lazar, M., Boudos, R., DuBray, M. B., Oakes, T. R., et al.
(2007). Diffusion tensor imaging of the corpus callosum in autism. Neuroimage,
34(1), 6173.
imaging. Biophysical Journal, 66(1), 259267.
Cascio, C. J., Gerig, G., & Piven, J. (2007). Diffusion tensor imaging: Application to the
study of the developing brain. Journal of the American Academy of Child &
Adolescent Psychiatry, 46(2), 213223.
Diggle, P., Heagerty, P., Liang, K., & Zeger, S. (2002). Analysis of longitudinal data
(2nd ed.). New York: Oxford University Press.
Dubois, J., Hertz-Pannier, L., Dehaene-Lambertz, G., Cointepas, Y., & Le Bihan, D.
(2006). Assessment of the early organization and maturation of infants cerebral
white matter fiber bundles: A feasibility study using quantitative diffusion tensor
imaging and tractography. NeuroImage, 30, 11211132.
Fitzmaurice, G. M., Laird, N. M., & Ware, J. H. (2011). Applied longitudinal analysis
(2nd ed.). New Jersey: Wiley.
Geng, X., Gouttard, S., Sharma, A., Gu, H., Styner, M., Lin, W., et al. (2012). Quantitative
tract-based white matter development from birth to age 2 years. NeuroImage, 61(3),
542557.
Gilmore, J., Lin, W., Corouge, I., Vetsa, Y., Smith, J. K., Kang, C., et al. (2007). Early
postnatal development of corpus callosum and corticospinal white matter assessed
with quantitative tractography. American Journal of Neuroradiology, 28(9),
17891795.
Hay, D. A., & OBrien, P. J. (1983). The La Trobe Twin Study: A genetic approach to the
structure and development of cognition in twin children. Child Development, 54(2),
317330.
Hulshoff Pol, H. E., Posthuma, D., Baare, W. F., De Geus, E. J., Schnack, H. G.,
van Haren, N. E., et al. (2002). Twinsingleton differences in brain structure using
structural equation modelling. Brain, 125(Pt 2), 384390.
Huppi, P. (2008). Neuroimaging of brain development - discovering the origins of
neuropsychiatric disorders? Pediatric Research, 64, 325.
Karkach, A. (2006). Trajectories and models of individual growth. Demographic
Research, 15(12), 347400, (URL http://www.demographic-research.org/volumes/
vol15/)12/).
Knickmeyer, R., Gouttard, S., Kang, C., Evans, D., Wilber, K., Smith, J., et al. (Nov
2008). A structural MRI study of human brain development from birth to 2 years.
Knickmeyer, R. C., Kang, C., Woolson, S., Smith, J. K., Hamer, R. M., Lin, W., et al.
(2011). Twinsingleton differences in neonatal brain structure. Twin Research and
Human Genetics, 14(3), 268276.
Lindstrom, M., & Bates, D. (1990). Nonlinear mixed effects models for repeated
measures data. Biometrics, 46, 673687.
Mori, S., Oishi, K., Jiang, H., Jiang, L., Li, X., Akhter, K., et al. (2008). Stereotaxic white
matter atlas based on diffusion tensor imaging in an ICBM template. NeuroImage,
40, 570582.
Mori, S., & Zhang, J. (2006). Principles of diffusion tensor imaging and its applications
to basic neuroscience research. Neuron, 51(5), 527539.
Murgasova, M., Dyet, L., Edwards, D., Rutherford, M., Hajnal, J., & Rueckert, D. (2007).
Segmentation of brain MRI in young children. Academic Radiology, 14.
Pajevic, S., & Pierpaoli, C. (1999). Color schemes to represent the orientation of
anisotropic tissues from diffusion tensor data: Application to white matter fiber
tract mapping in the human brain. Magnetic Resonance in Medicine, 42(3),
526540.
Pfefferbaum, A., Mathalon, D., Sullivan, E., Rawles, J., Zipursky, R., & Lim, K. (1994). A
quantitative magnetic resonance imaging study of changes in brain morphology
from infancy to late adulthood. Archives of Neurology, 51(9), 874887.
Pierpaoli, C., & Basser, P. J. (1996). Toward a quantitative assessment of diffusion
anisotropy. Magnetic resonance in Medicine, 36(6), 893906.
Rutherford, M. (Ed.), (2002). MRI of the neonatal brain: WB Saunders.
Sadeghi, N., Prastawa, M., Gilmore, J., Lin, W., & Gerig, G. (2010). Spatio-temporal
analysis of early brain development. In: Proceedings IEEE asilomar conference on
signals, systems and computers, (pp. 777781).
Sadeghi, N., Prastawa, M., Fletcher, P., Gilmore, J., Lin, W., & Gerig, G. (2012).
Statistical growth modeling of longitudinal DTI-MRI for regional characterization of
early brain development. In: Proceedings of the 2012 IEEE international symposium
on biomedical imaging: From nano to macro, (pp. 15071510).
Sadeghi, N., Prastawa, M., Fletcher, P. T., Wolff, J., Gilmore, J. H., & Gerig, G. (2013).
Regional characterization of longitudinal DT-MRI to study white matter maturation of
the early developing brain. In Neuroimage68, (pp. 236247).
van Gelderen, P., de Vleeschouwer, M. H., DesPres, D., Pekar, J., van Zijl, P., &
Moonen, C. T. (1994). Water diffusion and acute stroke. Magnetic Resonance in
Medicine, 31(2), 154163.
Xue, H., Srinivasan, L., Jiang, S., Rutherford, M., Edwards, A., Rueckert, D., et al.
(2007). Automatic cortical segmentation in the developing brain. IPMI, 257269.
Yakovlev, P., & Lecours, A. (1967). The myelogenetic cycles of regional maturation of
the brain. In A. Minkowski (Ed.), Regional development of the brain in early life
(pp. 370). Oxford: Blackwell Scientific.
Relevant Websites
http://www.ibisnetwork.org/ Brain Development in Autism.
http://www.cidd.unc.edu/piven/ Carolina Institute for Developmental Disabilities.
https://www.cidd.unc.edu/research/default.aspx?id45 Conte Center for
Schizophrenia.
http://www.child-encyclopedia.com/en-ca/child-brain/according-to-experts.html
Encyclopedia on early childhood development: Brain Development.
www.ucnia.org Utah Center for Neuroimage Analysis.
Tract-Based Spatial Statistics and Other Approaches for Cross-Subject

Comparison of Local Diffusion MRI Parameters
SM Smith, Oxford University Centre for Functional MRI of the Brain (FMRIB), Oxford, UK
G Kindlmann, University of Chicago, Chicago, IL, USA
S Jbabdi, Oxford University Centre for Functional MRI of the Brain (FMRIB), Oxford, UK
Introduction
As discussed in detail in previous articles, the diffusion of water
in brain tissue is affected by the local tissue microstructure; for
example, water diffuses more easily along the major axis of a
white matter fiber bundle than perpendicular to it. Magnetic
resonance diffusion imaging (sometimes referred to as Diffusion Tensor Imaging (DTI)) is sensitive to these effects, and, in
addition to tractography-based studies of long-range connectivity information (covered in other articles), there has been a
great deal of interest in using voxelwise measures derived from
diffusion data as local markers of the tissue microstructure. The
commonest example is the use of diffusion anisotropy as a
marker for white matter tract integrity, for example, for disease
diagnosis, tracking disease progression, finding disease subcategories, studying normal development/aging, and as complementary information to investigating normal brain function
(Horsfield & Jones, 2002; Lim & Helpern, 2002; Moseley, 2002;
Neil, Miller, Mukherjee, & Huppi, 2002; Pagani, Filippi, Rocca,
& Horsfield, 2005).
Diffusion anisotropy describes how variable the diffusion is
in different directions and is most commonly quantified via a
measure known as fractional anisotropy (FA) (Pierpaoli &
Basser, 1996). It is highest in major white matter tracts (maximum theoretical value 1) and lower in gray matter (GM),
while approaching 0 in cerebro-spinal fluid. As a marker for
tract integrity, FA is a useful quantity to compare across subjects as it is computable voxelwise, and is a scalar value that is
independent of the local fiber orientation (and therefore a
relatively objective and straightforward measure to compare
across subjects). A second common diffusion-derived parameter is the mean diffusivity (MD); this is the apparent diffusion
coefficient averaged over all directions, and therefore provides
complementary information to FA.
Some researchers have simply summarized diffusion characteristics globally (for example, histogram-based summary measures of FA (Cercignani, Inglese, Pagani, Comi, & Filippi, 2001;
Cercignani, Bammer, Sormani, Fazekas, & Filippi, 2003)), in
order to compare different subjects. However, most recent
work has been interested in spatially localizing interesting
diffusion-related changes. In order to achieve comparison of
diffusion parameters across subjects, it is first necessary to solve
the correspondence problem across subjects, for example, by aligning them all into some common space. This is by no means a
trivial problem to solve robustly and accurately, and the majority
of this article is devoted to the variety of methods that have been
proposed to achieve this. Many studies have, to this end, followed similar approaches to voxel-based morphometry (VBM,
originally developed for finding changes in GM density in T1weighted structural brain images; Ashburner & Friston, 2000;
Good et al., 2001). In VBM-style FA analysis, each subjects FA

image is warped into a standard brain space and then voxelwise
statistics are carried out to find areas which correlate with the
covariate of interest (e.g., patients vs. controls, disability score,
and age). However, there has been much debate about the
strengths and limitations of VBM, the most relevant question
being whether such an approach can guarantee that a given voxel
in common space contains data from the same part of the same
white matter tract from every subject.
In response to such concerns, various alternative methodologies for localized cross-subject investigation of diffusion
data have been suggested, including the use of hand-placed
regions-of-interest (ROI) and tractography-based and tractskeleton-based cross-subject correspondence; this article
describes such methods in detail. We also describe the variety
of diffusion-derived measures that one might compare across
subjects, and present example results that illustrate several of
the methodologies described.
Cross-Subject Registration (Image Alignment)

Before describing various specific approaches to cross-subject
comparison of local diffusion MRI parameters, we first give a
brief overview of image registration (alignment), as generic
alignment procedures form an important part of most of the
approaches covered in this article. We note, however, that this
section only covers image alignment. Other approaches have
been proposed, such as tractography-based methods that
attempt to match fiber bundles between subjects. These will
be covered in the Region-of-Interest and Tractography-Based
Strategies for Localizing Change section.
Registration is the spatial adjustment of one image to match
another. The contents of the input image are moved around
within the image matrix until they are well aligned with the
contents of the reference image. The input image is normally
of a single subjects brain, and the reference image might be a
different image of the same subject, a different subject entirely,
or a template image typically formed by averaging lots of
subjects images in some common space such as the MNI152.
Linear registration limits the motions applied to the input
image to: global translations, rotations, scalings, and shears
(squares become parallelograms). Such low degrees-offreedom (DoF) transformations (i.e., not many parameters
need adjusting) tend to be robust and accurate for aligning
images within subject (e.g., from a given subjects FA image to
the same subjects T1-weighted structural image), but are not
generally very accurate for registering between subjects, as local
image warping is required in such cases, due to detailed differences in brain shapes in different subjects.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00316-X
437
438
INTRODUCTION TO METHODS AND MODELING | Tract-Based Spatial Statistics and Other Approaches
Nonlinear registration is therefore typically used to align

between different subjects, or from a single subject to a standard template image. Such registration can apply local warps,
as opposed to the simple, global transformations applied by
linear registration. Nonlinear registration may be constrained
to only allow simple, coarse warps (low DoF), or may be
allowed to apply very finely-detailed, complex warps (high
DoF), in order to attempt to match the input image to the
reference image as perfectly as possible. Nonlinear registration
is normally initialized by linear registration, to get the general
orientation and size matched globally.
Nonlinear registration is implemented in many freely available software packages such as SPM, FSL, AFNI, AIR, and IRTK.
For example, the nonlinear registration approach known as
Image Registration Toolkit (IRTK, available from www.doc.
ic.ac.uk/dr; Rueckert et al., 1999) is based on free-form
deformations. The aim is to deform an image by moving the
control points of an underlying mesh. The warp field applied is
found for image positions between the mesh control points
using B-spline interpolation. The optimal warp is found by
moving the control point locations until the input image best
matches the reference image. This therefore attempts to both
optimize a voxel-based similarity measure at the same time as
imposing regularization (smoothness) on the warp field.
In diffusion MRI studies, a common first step in aligning
multiple subjects images to each other is linear nonlinear
registration, driven by the FA images. One definitely does not
want to change the topology of the images during this alignment it is necessary to keep the general tract structure intact
but it is still desirable to achieve the best registration possible,
given this limitation. It is therefore often necessary to use nonlinear alignment having intermediate DoF. At the low-DoF
extreme (e.g., linear-only registration with no nonlinear component), there is insufficient accuracy of alignment of even the
most major tracts. At the high-DoF extreme (very highdimensional warping), it is possible to align two images almost
perfectly, so that they look almost exactly like each other; the
problem here is that in order to achieve this, the original
images have been warped so much that one may not have
achieved overall structural homology, that is, preserved how
the different features (in this case, different white matter tracts)
relate to each other. A given tract (e.g., cingulum bundle) may

be warped so far that it becomes aligned to a totally different
tract in the target image (e.g., corpus callosum, CC).
It is common to align all subjects FA images to a standard
template, such as the MNI152 T1-weighted average image, or the
FMRIB58_FA, an average of FA images from 58 adults in
MNI152 standard space. Working in a commonly used standard
space is very convenient for reporting of results in a coordinate
system that is immediately understood by other researchers.
However, there are imaging studies where it is advisable to
identify a more study-specific target image, for example, studies
of very young infants, studies including subjects with severe
pathology or studies with nonhuman animals. In such cases a
recommended approach is to develop a study-specific template
(e.g., by iteratively aligning all subjects together and averaging).
In Figure 1, we show example registrations of three controls
and three Amyotrophic lateral sclerosis (ALS) patients, with
ROIs showing the CC. In each, the images on the left show
linear-only registration, and on the right the nonlinear registration results. In these examples, it is clear that linear-only
registration is insufficient to give good alignment. The overlaid
red edges are intensity edges from the target image.
VBM Overview and Application to Diffusion Data

VBM (Ashburner & Friston, 2000; Good et al., 2001) has been
used in many structural imaging studies, looking for localized
differences in GM density, typically between two groups of
subjects. The common approach can be simply summarized:
(Optional) Create a study-specific registration template by

aligning all subjects structural images to an existing standard space template image (such as the MNI152). Average
all aligned images to create the new template, and optionally smooth.
Align all subjects structural images to the chosen template,
normally first using linear and then nonlinear registration.
Segment each subjects structural image into different tissue
types. Generally use only the GM segmentation output.
Figure 1 Example registrations of three ALS patients (a, c) and three controls (b, d) (Ciccarelli et al., 2009). ROI through the anterior part of the corpus
callosum, in axial view. (a, b) Linear-only registration. (c, d) Linear nonlinear registration. The overlaid red edges are intensity edges from the
target image. Data kindly provided by Olga Ciccarreli.
Smooth the segmentation output data. This is done for

several reasons. First, smoothing of GM segmentation output produces an image which is intended to represent local
GM density that is, producing a measure of the local
balance between the count of GM and non-GM voxels.
Second, the smoothing helps ameliorate the effects of misalignment of structures when the registration is imperfect.
Third, it can increase sensitivity if the extent of smoothing
matches the size of an effect of interest. Fourth, smoothing
renders the data more Gaussian distributed, improving the
validity of the commonly used Gaussian random field
(GRF) theory thresholding approach. Typically between 4
and 16 mm full-width half maximum (FWHM) smoothing
(with a Gaussian linear filter) is applied.
Carry out voxelwise statistics, using any relevant covariates
for the cross-subject design matrix. A simple example would
model group membership (patient vs. control), with appropriate contrasts comparing the group means. The standard
approach is to use simple univariate statistics, meaning that
each voxel is processed separately the data for each voxel
constitutes a 1D (one-dimensional) vector of values, where
that one dimension is subject number, and the model is fit
separately to each voxels 1D data vector.
Threshold the resulting T-statistic (or F or Z) image, while
correcting for multiple comparisons across voxels. This is
typically done using GRF theory (Worsley, Evans, Marrett,
& Neelin, 1992), using either a voxel-based or cluster-based
approach (though extent-based thresholding can lead to
false positives in VBM due to smoothness nonstationarity;
Ashburner & Friston, 2000).
There are also various optimizations (Good et al., 2001) that

have been suggested to the above analysis protocol, such as
using the GM segmentation to drive the registration (instead
of the raw structural images), to make the registration better
conditioned, and modulating the segmentation output after
nonlinear registration, in order to compensate for local changes
in volume caused by the alignment process. VBM is most commonly carried out using the SPM software package, though
several other freely available packages (such as FSL and AFNI)
have also been used for VBM-style analyses. One of the reasons
VBM has become popular is that it allows the researcher,
subject to interpretation caveats, to find changes anywhere in
the brain it is not necessary to prespecify regions or features of
interest.
Recently, researchers have applied VBM-style analysis to test
for localized changes in diffusion-related images. Most commonly, this has involved testing FA images for voxelwise differences between two groups of subjects. The registration is
typically performed using the FA images directly. No segmentation step is necessary. Smoothing is usually carried out (with
no general agreement on how much is appropriate) before
running standard voxelwise statistics and thresholding. Typical
examples of this kind of approach can be found in Simon et al.
(2005), studying chromosome 22q11.2 deletion syndrome,
using 12 mm FWHM smoothing (Eriksson, Rugg-Gunn,
Symms, Barker, & Duncan, 2001; Rugg-Gunn, Eriksson,
Symms, Barker, & Duncan, 2001), studying epilepsy, using
8 mm FWHM smoothing (Barnea-Goraly et al., 2003), studying fragile X syndrome, using 4 mm FWHM smoothing and
439
(Buchel et al., 2004), testing for L-R asymmetry and handedness, using both 4 and 12 mm FWHM smoothing.
Problems of Interpretability in VBM-Style Analyses

Various papers (Ashburner & Friston, 2001, 2004; Bookstein,
2001; Davatzikos, 2004) have discussed the limitations and
strengths of VBM-style approaches when applied to structural
MRI data. It has been observed in particular that one must be
very careful not to misinterpret residual misalignments. How
can one guarantee that any given voxel (in the final space in
which voxelwise statistics will be carried out) contains data
from anatomically corresponding regions that is, the same
part of the same white matter tract from each and every subject? In the context of VBM-style analysis of FA data, consider
the following scenario: a patient group includes individuals
with greater ventricular sizes than a control group. The two
groups, however, have the same basic white-matter integrity.
Because of the differences in ventricular size/position, conventional (low to medium DoF) registration approaches will shift
the anterior section of the CC anteriorly in the patient group
relative to the controls; registration of the data (and subsequent smoothing) may not fully remove this group difference
in alignment. When voxelwise statistics are carried out, this
residual misalignment shows up as a group difference in FA;
at the front of the CC, it appears that FA (patients) > FA (controls), while at the back, the reverse is implied.
This problem is discussed in Simon et al. (2005), where the
authors are careful to interpret apparent FA changes as being in
fact due to changes in ventricle size. A further example of the
danger of misinterpretation can be seen in Bengtsson et al.
(2005), where FA is correlated against hours of piano practice.
The reported areas of change are mostly on the very edge of the
white matter tracts, and therefore possibly represent development of tract thickness rather than of FA within the tracts. In
our example results below, we show an even more striking
problem of interpretation in a VBM-style analysis of a
schizophrenic-control comparison.
Some researchers, aware of this problem, use careful post
hoc analyses to help disambiguate the interpretation of apparent differences. For example, Sommer, Koch, Paulus, Weiller,
and Buchel (2002) used a standard VBM-style approach (using
6 mm FWHM smoothing) and then checked afterwards that
the alignment was reasonable, looking at the WM-masked ROI
in the unsmoothed FA images, near the reported difference.
However, the reported FA difference is very close to cortical
GM, and it is difficult to be sure that differences in GM/WM
partial volume effects have not contributed to the result.
Indeed, some researchers even report apparent changes in FA
or MD in regions which seem to be primarily GM, and yet
discuss the findings as if they relate to changes in WM tract
integrity.
There have been various papers presenting investigations
of alignment issues specific to diffusion tensor data. Jones
et al. (2002) use FA to drive linear alignment across subjects.
Park et al. (2003) investigates alignment when driven by a
variety of diffusion-derived measures; high DoF nonlinear
registration is used, and alignment success is quantified via
similarity of final tractography maps. It is shown that using
440
all six tensor components to drive the registration gives better

overall alignment than other combinations of DTI-derived
information, including FA (although the differences were
not large).
In Park et al. (2004), this approach was then used to compare white matter structure in schizophrenics relative to controls, and does appear to help with the alignment issues
discussed above; however, even with this relatively sophisticated registration approach, the authors state that there were
still be some registration errors in the boundary of narrow
fiber bundles and for this reason, did not directly compare
their VBM-based tests between schizophrenics and controls.
It would appear that, in general, it is not safe to assume that
standard nonlinear registration can align FA data sufficiently
well across subjects to allow simple unambiguous interpretation of voxelwise statistics. Also, if one cannot guarantee that
alignment is correct, then it must be assumed that sensitivity
to true differences is suboptimal. One might possibly argue
that, despite problems of interpretability, these alignment
problems actually represent an advantage, because the range
of changes that the VBM approach is sensitive to is greater than
approaches where alignment issues have been resolved. However, the range of interpretations also gets larger. The key
point is that diffusion MRI is sensitive to microscopic features
of brain tissue. Ideally, we want to perform cross-subject comparisons of those same microscopic features. Misalignments
can introduce sensitivity to macrostructure, and can therefore
severely undermine interpretability.
As discussed earlier, the registration (or correspondence)
problem is not easily resolved by taking the DoF to the extreme,
forcing all images to look extremely similar (this is a possibility
with some nonlinear registration approaches); although it may
be possible to distort one image to look very much like another,
one does not necessarily have confidence that any given structure
has in fact been aligned to that same structure in the other
subject. Some nonlinear registration methods are able to go so
far in making one image look like another that they can even
break the topology of the image being distorted for example, a
single fiber bundle may be split into two disconnected bundles,
or two distinct tracts could be merged into one.
A second problem with VBM-style analyses lies in the arbitrary choice of smoothing extent. Smoothing can help ameliorate residual misalignments, though not in a well-controlled
way. It can also help improve sensitivity in the detection of
changes, if the extent of smoothing is matched to the spatial
extent of the structure of interest. However, it is not generally
known in advance what this will be, so there is no principled way
to choose the smoothing extent. If one were to try a range of
smoothing extents, the final interpretation can become more
confused, and multiple-comparison correction needs to be
made more aggressive. These issues are investigated in detail in
Jones, Symms, Cercignani, and Howard (2005), where it is
shown that the final results (of VBM-style FA analysis of schizophrenia data) depend very strongly on the amount of smoothing. Different smoothing extents (from 0 to 16 mm FWHM) are
applied, and apparent group differences appear and disappear
across the different tests. Likewise, Park et al. (2004) also investigated asymmetry in schizophrenia, using 3, 6, and 9 mm
FWHM smoothing; several of the apparent asymmetries were
quite different in the different cases.
As well as the problem of the arbitrariness of choice of

smoothing extent, smoothing increases the partial voluming
problem; one would like to know whether any estimated
change in FA is due to a change in FA in white matter rather
than a change in the relative amounts of different tissue types,
but smoothing exacerbates this ambiguity. If possible, it would
be good to obviate the need for simple 3D spatial smoothing of
diffusion data in such applications.
ROI and Tractography-Based Strategies for Localizing

Change
A simple alternative to VBM-style FA analysis is to specify an
ROI, usually by hand, separately for each subject (Ellis et al.,
1999; Kubicki et al., 2003). FA values are taken from the ROIs
and then compared across subjects. In the centers of the largest
tracts this can be a reliable approach; however, it can be hard to
objectively place ROIs for smaller/thinner tracts, particularly
given partial volume issues. Furthermore, this kind of
approach limits a study to only being sensitive to change in
those few parts of the brain where ROIs are placed. See references in Park et al. (2003) for more examples of this kind of
approach.
More sophisticated approaches use tractography (fiber bundle tracking, see Behrens et al. (2003) and Conturo et al.
(1999)) and later articles) to identify voxels from which to
take FA values for cross-subject comparison. In such
approaches, the relevant tracts are usually identified by initializing/constraining tractography using hand-drawn ROIs. For
example, in Pagani et al. (2005), DTI-related changes in the
pyramidal tracts were observed in patients with early MS-like
symptoms. ROIs were hand-drawn in a standard space to
identify the pyramidal tracts. These were then used to seed
streamlining-based tractography in each subjects original DTI
data, to define in each the pyramidal tract. The results were
then averaged to provide a mean pyramidal tract mask. Tests
were then carried out on various DTI-related metrics by linearly
aligning patient data into MNI152 space and taking summary
statistics using all voxels within this mask.
In the above approach, tractography is used to determine a
standard space ROI, but the final analysis still depends critically on the accuracy of alignment of each subject to the
standard space. In Jones et al. (2006), this problem is avoided
by using each subjects tractography results to estimate mean
FA in several major tracts, summarizing each tract with a single
mean FA value before comparing normals and schizophrenics.
Hence tractography is used to overcome the correspondence
problem because summary statistics can be computed from
anatomically corresponding regions in each subjects native
image space. However, one problem with such approaches is
that FA values are averaged across a large number of voxels that
form the tract trajectories, which may decrease sensitivity to
localized effects.
A still more sophisticated approach is to compare the variation of FA values along the tractography-derived fiber-bundles
directly across subjects, by representing the diffusion data simply as a function of distance along a bundle (Gong et al., 2005;
Lin et al., 2006; ODonnell, Westin, & Golby, 2009). Such arclength based approaches achieve correspondence between
is created in standard space. This is then fed into tractography,

which is applied to identify several major sheet-like fiber
structures whose curved 3D extent is summarized (using
sophisticated mesh modeling of the bounding tract surfaces)
with a curved 2D medial (central) surface. A variety of diffusion information is then projected/averaged down onto that
medial surface; see Figure 3. This surface representation of
white matter also allows one to incorporate shape and thickness measurements, and thus combine macroscopic and
microscopic (from tensor) cross-subject analyses (Zhang
et al., 2010). Similarly, in Yue et al. (2013), a related approach
is taken; tracts are modeled as principal surfaces using a
combination of principal component analysis and thin-plate
splines, and FA is then parameterized within the locally 2D
tract-center representation.
In general, the above combinations of registration and tractography solve the correspondence problem across subjects in a
way that is robust and rich (many different brain regions are
investigated), and have much in common with the tract-based
spatial statistics (TBSS) method described in the following section. While the above methods rely on a tractography step that
requires careful delineation of specific pathways (e.g.,
S0
subjects by assuming that the relative position along the tract is

comparable across subjects. For example, in Gong et al. (2005)
and Lin et al. (2006), tractography is used to find the cingulum
bundles and pyramidal tracts, respectively, and FA is parameterized according to the position within a tract. This allows crosssubject comparison of FA values along the given tract without
requiring accurate cross-subject registration (see, e.g., Figure 2).
In a similar approach (Corouge, Fletcher, Joshi, Gouttard, &
Gerig, 2006), the within-subject parameterization of the diffusion data along tracts is dealt with in an even more detailed way;
multiple tractography streamlines within a given fiber bundle are
identified and brought into as close alignment to each other as
possible. The diffusion tensors are then parameterized along the
different streamlines, and averaged across corresponding longitudinal positions to create mean tensor values along a single
median streamline (in a manner somewhat similar to the tract
skeleton approach described later). High reproducibility of
tensor-derived parameters (FA, MD, eigenvalues), parameterized
as a function of distance along the tract, is shown.
Yushkevich, Zhang, Simon, and Gee (2008) takes this kind
of approach further by parameterizing white matter as 2D
surfaces. A cross-subject average of all subjects tensor images
441
Sn
Anterior
Posterior
AC Point
Bilateral FA distribution of single subject
0.65
0.6
Bilateral FA distribution of males
0.65
Left Side
Right Side
PC Point
SD of left
Mean of left
SD of right
Mean of right
0.6
0.55
0.55
0.5
FA-value
FA value
0.5
0.45
0.4
0.4
0.35
0.35
0.3
Anterior
0.25
0.2
-50
0.45
-40
-30
-20
0.3
Posterior
-10
0
10
Arc-angle
20
30
40
50
0.25
-50
Anterior
-40
-30
-20
Posterior
-10
0
10
Arc-angle
20
30
40
50
Figure 2 An example approach of tractography-based FA parameterization, as presented in Gong et al. (2005). Top-left: reconstruction of the upper
cingulum tracts for one subject; red and white denote anterior and posterior parts, respectively. Top-right: illustration of the parameterization
procedure; position along the cingulum is parameterized as a function of angle in the defined coordinate system. Bottom-left: single-subject sampling of
FA along cingulum as a function of angle. Bottom-right: multi-subject combined data, showing cross-subject mean and standard deviation of FA
along cingulum, separately for left and right. Figure material kindly provided by Gaolong Gong and Tianzi Jiang.
442
Left cc
Right cc
Left ilf
Right ilf
Left cst
Right cst
Left slf
Left ifo
Right slf
Left unc
Right unc
Right ifo
Figure 3 An example approach of tractography-based medial (skeletonized) representation of tract structure, as presented in Yushkevich et al. (2008).
Top-left: fiber tracking results for the six selected fasciculi. Top-right: skeletons of the models fitted to the six fasciculi. Bottom: the result of
projecting tract-center MD values onto the medial surfaces, and then testing statistically across subjects. T-statistic maps on the medial surfaces show
where MD is significantly different in patients with pediatric chromosome 22q11.2 deletion syndrome, compared with controls. Figure material
kindly provided by Paul Yushkevich and James Gee.
cingulum, arcuate), various methods for automated identification and clustering of white matter bundles are emerging
(Durrleman, Fillard, Pennec, Trouv, & Ayache, 2011; Guevara
et al., 2012, 2011; Li et al., 2010; Yendiki et al., 2011). These
have the potential to aid inter-subject registration, feature
extraction (i.e., bundles) and feature matching across subjects.
Although not yet applied to cross-subject comparisons of diffusion measures, these clustering techniques provide a promising alternative to the skeleton-based methods presented below.
Tract-Based Spatial Statistics

As discussed earlier, strengths of VBM-style voxelwise analyses
are that they are fully automated, simple to apply, investigate the
whole brain, and do not require prespecifying and prelocalizing

regions or features of interest. The main limitation relates to
problems caused by alignment inaccuracies, including the danger of misinterpreting apparent results in voxels that do not in
fact correspond to white matter in all subjects. Tractographybased approaches have fairly complementary advantages and
disadvantages. They can overcome alignment problems by working in the space of individual subjects tractography results.
However, such approaches do not allow the whole brain to be
investigated, and generally require user intervention in order
to define the tracts to be tested (although ongoing research
into tractography, cross-subject alignment, averaging, atlasformation, and tract-matching/clustering, is ever-increasing the
possibility of robust, automated whole-brain multiple-tract tractography seeding with correspondence across subjects).
An alternative method, termed tract-based spatial statistics
(Smith et al., 2006, 2007), attempts to combine the different
strengths of each of these general approaches. TBSS aims to
solve the alignment and smoothing issues, while being fully
automated and investigating the whole brain not requiring
prespecification of tracts of interest. This is achieved by estimating a group mean FA skeleton, which represents the centers of all fiber bundles (fiber bundle is usually taken to mean a
collection of white matter axons all following a similar anatomical path (at least locally). Tract is sometimes used to
mean individual axons, but more commonly to fiber bundles;
furthermore, tract often implies that the collection of axons
have similar start and end locations. However, in general, and
in this article, the terms tract and fiber bundle are used
interchangeably) that are common across the subjects involved
in a study. Each subjects FA data is then projected onto the
mean FA skeleton in such a way that each skeleton voxel takes
the FA value from the local center of the nearest relevant tract,
thus hopefully resolving issues of alignment and correspondence. To briefly summarize the TBSS approach:
Align all subjects FA images to a common target using

nonlinear registration. At this stage, perfect alignment is
not expected or required.
Create the mean of all aligned FA images and apply
thinning, to create a skeletonized mean FA image. Threshold this to suppress areas of low cross-subject mean FA or
high cross-subject variability.
Project each subjects (aligned) FA image onto the skeleton,
by filling the skeleton with FA values from the nearest
relevant tract center. This is achieved, for each skeleton
voxel, by searching perpendicular to the local skeleton
structure for the maximum value in a given subjects FA
image.
Carry out voxelwise statistics across subjects on the
skeleton-space FA data.
The rest of this section describes TBSS in more detail.
443
Nonlinear Alignment
TBSS starts by registering all subjects FA images into a common space, using linear nonlinear registration (using FLIRT
(Jenkinson & Smith, 2001) and then FNIRT (Andersson,
Jenkinson, & Smith, 2007; Andersson, Smith, & Jenkinson,
2007)). The normal choice of registration target image is the
FMRIB58_FA. However, when a study-specific target is required
(see the registration discussion earlier), the recommended
approach is to identify the most typical subject of the entire
group, that is, to be the target image which minimizes the
amount of warping required for all other subjects to align to it.
To find this most typical subject, one can register every subject to
every other subject and choose the target subject as being the
one with the minimum mean deformation to all other subjects.
Creating the Mean FA Image and its Skeleton

Once all subjects FA images have been aligned to the chosen
target, the transformed images are then averaged to create a
mean FA image. This shows the white matter tracts that are
common across subjects on average. The mean FA is now fed
into the tract skeleton generation, which aims to represent all
tracts which are common to all subjects. The skeleton will
represent each such tract as a single line (or surface) running
down the center of the tract. Most contiguous sets of tracts
appear topologically to be curved sheets of a certain thickness
(e.g., CC), or, less frequently, curved tubes (e.g., the cingulum
bundle); see Figure 4. In the former case, one wants the skeleton to be a thin curved surface running down the center of the
sheet, and in the latter, to be a curved line running down the
center of the tube. Away from the center surface or line, the FA
values fall off gradually, becoming very low as one moves out
of white matter.
To achieve skeletonization, the local surface perpendicular
direction is estimated, and then a search is carried out in this
direction to identify the voxel with the highest FA; this is
Figure 4 Examples of fiber bundles; a thick sheet with a thin surface as its skeleton, and a tube, with a line as its skeleton.
444
Figure 5 Example mean FA image (grayscale) underneath the unthresholded (left) and thresholded (right) skeleton. Thresholding was applied at
FA 0.2.
deemed to be the center of the tract. One now has an FA

skeleton which should represent the different tract structures
in the mean FA image. This is thresholded in order to restrict
further analysis to points which are within white matter which
has been successfully aligned across subjects. Thresholding the
mean FA value between 0.2 and 0.3 generally is successful in
excluding voxels which are primarily GM or cortico-spinal
fluid (CSF) in the majority of subjects, and also means that
the skeleton does not run right up to the outermost edges of the
cortex, where the constraints on the nonlinear alignment mean
that the most variable (across subjects) tracts are not well
aligned. In other words, one is excluding from further analysis
those parts of the brain where it is unsafe to assume good tract
correspondence across subjects. See Figure 5 for examples of
unthresholded and thresholded mean FA skeletons, superimposed on top of the mean FA image.
Figure 6 shows the variation in aligned FA images relative
to the mean FA skeleton, from several subjects taken from a
study of stuttering. It can clearly be seen that the skeleton lies
within or near WM tracts in the majority of subjects, but that
the nonlinear alignment is not perfect (with voxelwise
accuracy).
Projecting Individual Subjects FA onto the Skeleton

Each subjects aligned FA image is now projected onto the
mean FA skeleton. The aim here is to account for residual
misalignments between subjects after the initial nonlinear registrations. At each point in the skeleton, a given subjects FA
image is searched in the (already-computed) perpendicular
tract direction to find the maximum FA value, and assign this
value to the skeleton voxel. This effectively achieves alignment
between the skeleton and this subjects FA image without
needing perfect nonlinear registration. Any systematic difference in exact tract location between groups of subjects should
therefore hopefully not bias the comparison of FA values
between the groups. An example ROI is shown in Figure 7.
Figure 6 Six individual subject FA maps (nonlinearly aligned into

standard space) underneath the mean FA skeleton. Data kindly provided
by Kate Watkins.
445
Other Skeleton-Based Work
Figure 7 Example region-of-interest showing skeleton and final search

vectors for a single subject.
Note that this approach is effectively achieving fine alignment across subjects in the direction perpendicular to the tract,
not in the direction parallel to the tract. This is what is required;
FA changes very quickly as one moves perpendicular to the
local fiber bundle, so even the smallest misalignments in this
direction have great effect on the final statistics. Parallel to the
tract, FA generally changes relatively slowly, so that the alignment provided by the initial nonlinear registration is sufficient
to align like with like across subjects.
Therefore the skeleton has been filled, for each subject, with
FA values from the centers of the nearest relevant tracts. Note
that the idea of taking a pure FA value from the center of a
tract in a way that claims to be unaffected by partial volume
effects is only strictly true for tracts wider than the relevant
voxel dimension. When this is not the case, that is, for the
thinnest tracts, the center peak FA value will reflect both the
tract width and the true peak FA value, due to partial voluming.
More recently (de Groot et al., 2013), there has been extensive work evaluating whether a more finely detailed nonlinear
warping could replace both stages of the TBSS registration (i.e.,
the initial nonlinear registration and the skeleton projections).
Validation was carried out using the relatively independent
information from tractography, showing that carefully tuned
nonlinear registration can indeed hope to improve on the
alignment accuracy onto the skeleton, as well as providing
better regularization (i.e., consistency of the projection along
the skeleton). Future versions of TBSS will aim to switch to this
approach.
TBSS is by no means the only approach that suggests working

in a skeleton-based summary space; for example, as described
above, both Corouge et al. (2006) and Yushkevich et al. (2008)
use medial surfaces to represent the results of tractography
analyses. Further related work can be found in the
anisotropy crease approach of Eberly (1996), Eberly, Gardner,
Morse, and Pizer (1994), and Kindlmann, Tricoche, and
Westin (2007); this is closer to the TBSS approach, as it analyses the entire brain rather than being initialized via tractography. Anisotropy creases leverage from computer vision a
mathematical definition of ridge and valley features (collectively termed creases, calculated using differential geometry
applied to the tensor data). While the FA ridge surfaces computed this way are conceptually the same as the FA skeleton
computed in TBSS, the mathematical definition and specifics
of implementation lead to a more continuous and potentially
more accurate modeling of FA structure. A recent approach
(Kindlmann, San Jose Estepar, Smith, & Westin, 2009) to crease
modeling uses a scale-space representation (different levels
of blurring) of tensor data. This method is able to detect both
planar and linear (tube-like) crease structures, and offers the
possibility to accurately model individual subjects continuous
skeletons even with relatively coarse resolution data.
Figure 8 shows an example (from Kindlmann et al., 2007)
of anisotropy crease surface extraction in a coronal slab of an
individual subjects data (acquired at 2.5 2.5 2.5 mm). For
anatomical context, (a) shows tractography results and labels
several major pathways. The FA ridge surfaces, shown in (b),
represent the major pathways as smooth surfaces. The FA valley
surfaces in (c) are shown with a semitransparent cutting plane
colored with the standard RGB colormap of the principal
eigenvector of the diffusion tensor (Pajevic & Pierpaoli,
1999), to illustrate how the valley surfaces generally separate
major tracts that are adjacent but distinctly oriented. This is
also visible in (d), which shows the valley surfaces in the
context of the tractography results. The creases and tractography are geometrically aligned and coherent, but arise from
completely different algorithms. It can be seen in (b) that the
cingulum bundles are not cleanly represented as surfaces; as
discussed in Creating the Mean FA Image and its Skeleton
section, they would be better represented as lines (tubes).
Ongoing work focuses on automatically detecting whether
local features are better modeled as surfaces and lines, and
extracting them accordingly.
Although anisotropy creases have to date not been applied
to clinical studies comparable to those with TBSS, initial experience has suggested that creases may offer improvements to
TBSS, as well as to other diffusion-related analyses. FA ridge
surfaces tend to include more small-scale structures than are
found by TBSS skeletonization; by operating in the continuous
tensor domain instead of the discrete voxel domain, anisotropy creases can still be found when the feature resolution is at
the scale of individual voxels. Complementing the ridge surfaces, the FA valley surfaces (seen in Figure 8) may play a role
in the search phase of TBSS, wherein maximal FA values in the
registered individual scan are located by searching from a point
on the FA skeleton. The valleys could add further robustness to
limiting the search correctly; they could be used to terminate
446
Figure 8 Anisotropy creases near the corpus callosum: CC; corpus callosum; IC; internal capsule; CR; corona radiata; FX; fornix; CB; cingulum
bundles; EC; external capsule; SLF; superior longitudinal fasciculus.
the search path, since they tend to delimit nearby but distinctly
oriented white matter tracts. Finally, to the extent that the
combination of ridges and valleys delineates the major white
matter pathways, the crease structures extracted from individual scans could guide and constrain nonrigid registration, to
help ensure that distinct tracts (of comparable anisotropy
levels) do not mistakenly overlap.
Statistical Modeling, Thresholding, and Multivariate

Approaches
Univariate Voxelwise Modeling
After data preprocessing such as in the VBM-style, tractparameterization or TBSS approaches, the data is ready to
feed into voxelwise (or pointwise) cross-subject statistical analysis. Each subjects FA image has been prealigned to a common
space or sampled onto a common representation, and the data
can be considered to be in the form of a 4D image (in the case
of TBSS this is sparse, i.e., skeletonized), with the fourth
dimension being subject number. In the case of the tractlength-parameterization approach, the data is a 2D image,
with position-along-tract and subject being the dimensions of
the preprocessed data. It is now possible to carry out voxelwise
statistics across subjects, for each point in space.
The simplest approach is to use univariate linear modeling, that is, process each voxel independently, applying the
general linear model (GLM, i.e., multiple regression) across

subjects. For example, one can easily use a two-regressor analysis to test for significant local FA differences between a group
of patients and a group of controls. Below we explain a few
simple models in a little more detail, and then go on to
describe how one might threshold the resulting statistic images
to find areas of significance.
Every voxel is processed separately from every other; hence
the data for any given standard space voxel can be considered
as a single 1D vector, with one entry per subject. The GLM
approach creates a model, or design matrix, that contains a
separate column (also referred to as covariate or regressor)
for each separate aspect of the data that needs modeling. For
example, the first regressor might model the group mean of the
control group, the second might model the group mean of the
patient group, and the third might model subject age. Each row
corresponds to a different subject. Model parameters (one for
each column in the model) are adjusted so as to give the best
model fit, thus minimizing the residual errors (noise) in the
model fitting. See Figure 9.
Questions are asked about aspects of the model fitting
through the specification of contrasts. Each contrast specifies
which model regressor is currently of interest, or possibly
which combination of regressors. In the example above, Contrast 1 [1 1 0] is asking where the fitted model parameter for
column 1 is greater than that for column 2, and hence is asking
whether the control group mean FA value is higher than the
Data
Model (design matrix)
Data vector for one standard space voxel

(each row = one subjects FA value)
Group 1
(controls)
Group 2
(patients)
Contrasts
447
Regressor 2
(patient group mean)
Regressor 3
Regressor 1
(subject ages, demeaned)
(control group mean)
Subject 1
0.55
-2
Subject 2
0.52
-7
Subject 3
0.48
Subject 4
0.59
Subject 5
0.47
Subject 6
0.51
Subject 7
0.42
-5
Subject 8
0.46
Contrast 1 (controls > patients)
-1
Contrast 2 (controls < patients)
-1
Contrast 3 (correlation with age)
Fitted
model
parameters
noise
Figure 9 Overview of general linear modeling (GLM), also known as multiple regression: data, model and contrasts.
patient group mean. The zero tells this contrast to ignore the
model parameter for the third regressor (age). Independently
of this, Contrast 2 is asking the reverse question: does the
patient group have the higher mean? Finally, Contrast 3
[0 0 1] is asking whether FA correlates with age across all
subjects. The third regressor might either have been included
in the model because the regression with age was of interest, or
simply in order to model out (or remove the effect of) age; in
the latter case, it would be referred to as a confound covariate,
and would not appear in any of the contrasts of interest.
Figure 10 shows several further examples of common
models, along with common contrasts used in conjunction
with such models.
Thresholding and Multiple Comparison Correction

The initial result of fitting a cross-subject model to the diffusion data is a raw statistic image such as a z-statistic, which
encodes how good the model fit is compared to the error in the
model fitting. There will be one z-statistic image generated
separately for each contrast. The final stage in the statistical
analysis requires the statistic image to be thresholded, in order
for the experimenter to be able to make a statement about the
significance of the results. This usually means generating a pvalue, allowing a statement such as if there were in reality no
underlying effect present the data is just noise there would
only be a 5% chance of seeing a result as strong as we found
(this is the definition of a p-value).
The thresholding is not, however, necessarily applied

directly to the raw z-statistic image. Before thresholding, the
statistic image may be further processed (e.g., to find clusters of
interesting signal), and the resulting processed image (or resulting image features) then tested for significance. The simplest
option here is to use the raw z-statistic image as it is; this is often
referred to as voxel-based thresholding, as the image features
to be tested for significance are just each voxels raw statistic
value. Each voxels value only represents that exact point in
space, unless the data has been smoothed during the preprocessing stages of the analysis. Another common choice is
to use cluster-based thresholding, which can have greater sensitivity than voxel-based, because clusters of extended area of
signal are identified, which are likely to have greater statistical
significance than the individual voxels considered in isolation
(because of the fact that pure noise would not tend to produce
clusters very often). In order to define such clusters, the raw
statistic image is first thresholded at some arbitrary level (e.g.,
Z > 2.3), and clusters of contiguous suprathreshold voxels are
found. The size of each cluster is then tested for significance by
estimating the p-value corresponding to the size.
However, although cluster-based thresholding is often
more sensitive than voxel-based, it has the drawback that
the results depend very strongly on the level of the initial
thresholding, and there is no principled and objective way of
choosing that level. In order to avoid such problems, the
recently-proposed threshold-free cluster enhancement (TFCE;
Smith & Nichols, 2009) can be used. This enhances cluster-like
areas in the raw z-statistic in a more continuous way, without the
448
1 2
1 7
1
4
1
0
1
3
1
4
1 5
1
3
1
1
1
1
1
0
0
0
0
0
0
0
0
1
1
1
0 2
0
0 7
0
0
4
0
0
5
0
1
0
3
1
0
2
1
0
0
1
0 5
1
1
1
1
0
0
0
0
1
1
1
1
1
1
1
1
1
1
0
0
0
0
0
0
0
0
1
1
0
0
0
0
0
0
0
0
1
1
0
0
c1 [ 0 1 ]
c1 [ 1 1 ]
c1 [ 1 1 0 0 ]
c1 [ 1 0 0 0 0 ]
c2 [ 0 1 ]
c2 [ 1 1 ]
c2 [ 1 1 0 0 ]
c2 [ 1 0 0 0 0 ]
0
0
1
1
c3 [ 0 0 1 0 ]
c4 [ 0 0 0 1 ]
c5 [ 0 0 1 1 ]
c6 [ 0 0 1 1 ]
(a)
(b)
(c)
(d)
Figure 10 Several common cross-subject models: (a) group mean and an effect of interest such as age or behavioral score. Note that the latter has
been demeaned (its mean has been subtracted) in order to make the fitting of the two regressors independent of each other. Contrast c1 where
does the data correlate with the effect of interest?; c2 where does the data correlate negatively with the effect of interest? (b) Two group
mean comparison, equivalent to an unpaired t-test. The first five subjects form group 1 and the next three form group 2. c1 where is the first groups
mean greater than the seconds?; c2 where is the second groups mean higher? (c) Two group mean comparison, with an additional separate
age regressor for each group. The age values have been split into the two separate regressors to allow an interaction test, that is, a test of whether the
correlation between the diffusion data and age is different in the two groups. Each set of age values was separately demeaned before being padded
by zeros in the regressors. c1 where is the mean of group 1 higher than that of group 2?; c2 where is the mean of group 2 higher?; c3 where
does the data in group 1 correlate with age?; c4 where does the data in group 2 correlate with age?; c5 where is the correlation with age
higher in group 1 than in group 2?; c6 where is the age correlation higher in group 2? (Note though that the interpretations given for c5 and c6
depend on the correlations being positive; if one or both is negative, the interpretation needs more careful thought, taking into account the results of c3
and c4.) (d) Paired two-group comparison, for example, to test before versus after treatment in subjects. Each pair of rows corresponds to a given
subjects before and after data. The first regressor models the beforeafter comparison; the other regressors model out each subjects mean
separately. This is equivalent to a paired t-test. c1 where is the data higher before than after treatment?; c2 where is the data higher after
treatment?
need for an initial hard thresholding. In this case, the features

tested for significance are voxel values, but now each voxels
value includes information not just about the strength of the
raw test statistic, but also the spatial extent of the local signal.
Once the statistical features of interest have been identified
(e.g., a list of clusters sizes), these are then tested for significance, generating a p-value for each feature; typically, features
with p > 0.05 are then discarded. A complication here is that pvalues can only be accurately generated for statistical images or
features if the null distribution of the features is known; in
other words, only if we know what the expected distribution
(or range) of the feature values would be in a hypothetical case
where no signal is present, can we determine how impressive
the values are that we actually have. In simple statistical modeling, a true z-statistic image has a known null distribution; it is
Gaussian, and knowing this, it is trivial to turn a z-statistic into
a p-value. However, for a variety of reasons (relating to both the
data and the preprocessing), almost all analyses of diffusion
data result in the statistic images/features not conforming to
simple, known distributions (see evidence for this later in the
article). As a result, methods of thresholding such as GRF
theory (Worsley et al., 1992; which is very popular for use in
thresholding functional MRI statistical images) are not generally accurate for use with diffusion analyses.
Of more accuracy and robustness are methods that estimate
the null distribution empirically (i.e., from the data). One
such example is mixture modeling (Everitt & Bullmore, 1999;
Woolrich, Behrens, Beckmann, & Smith, 2005), which fits
separate curves for the null and for the signal parts of the
statistic histogram. For a number of practical reasons (such as
the possibility of very large areas of signal), a second approach
is generally more suitable for diffusion data analyses: permutation testing (Nichols & Holmes, 2002). This generates the null
distribution by repeatedly randomizing the order of the subjects in the data (relative to the model). Each of these randomizations produces a resulting statistic image that looks as if the
data contained no signal of interest, and so over thousands of
random permutations, the histogram of the null distribution
can be built up. The statistic image (or set of statistical features)
that was originally estimated can then be compared against
this null distribution, in order to estimate accurate p-values.
The final issue that needs addressing is the problem of
multiple thresholdings across the many voxels or clusters
found in the brain; if one thresholds 10 000 standard-space
voxels for significance at the p < 0.05 level, then purely by
chance about 500 voxels will be (wrongly) reported as containing a significant effect of interest. This is clearly problematic, as
it means that one would find at least 500 false positives in
every study, regardless of whether or not there actually was
something interesting in the data. Researchers typically want to
control the rate of false positives not separately at every voxel
or cluster, but for the image as a whole. This is known as
controlling the family-wise error (FWE) rate, and if done
correctly, the researcher can then make a claim such as the
chance of finding a signal of interest this strong anywhere in
pure noise data is <5%.
A simple approach to achieving this multiple comparison
correction is to simply multiply the estimated p-values by the
number of comparisons made before applying the 0.05 threshold. This is known as Bonferroni correction, and is generally
over-conservative, partly because it does not take into account
any spatial smoothness in the data. However, again via the
application of permutation testing, it is straightforward to
carry out accurate multiple comparison correction.
Instead of building up (over random permutations of the
data) the null distribution separately at each point in the brain,
we can, at each permutation, find the maximum test statistic
value across the brain, and build up a null distribution of that.
We therefore know the null of the maximum (across space) test
statistic, and it we test our actual statistic values against that, we
have achieved control of the FWE. Although permutation testing can be slow (as it needs typically several thousand permutations of the data, model refitting and statistic feature
extraction), it is a very sensible approach to inference on diffusion analyses, being accurate and robust.
Dealing with Nonstationarity

The methods described earlier that deal with multiple comparisons across space all assume that various measures, such as
noise variance and data smoothness, do not vary across space.
When this is not true, the data is said to be (spatially) nonstationary. This assumption can be violated in real data for
several reasons; it could be truly a factor in the data (e.g.,
subjects may be less variable in the largest tracts), it may be due
to aspects of the MRI physics of the measurements (e.g., when
using parallel imaging), or could result from the preprocessing
analysis steps. In the case of voxel-wise skeleton-based methods,
for example, the skeleton itself can have nonstationarity in
terms of the number of voxels locally connected to any given
skeleton voxel of interest.
The cluster-size test depends on the local smoothness of the
image. Therefore, sensitivity and specificity of this type of test
can be affected by nonstationarity. To overcome this problem,
cluster sizes can be adjusted for nonstationarities using local
smoothness estimates based on random field theory
(Hayasaka, Luan Phan, Liberzon, Worsley, & Nichols, 2004).
An alternative fully nonparametric approach has been recently
proposed in Salimi-Khorshidi, Smith, and Nichols (2011). The
method uses the local empirical distribution of the clusterbased statistics, and estimates two permutation-based nulldistributions: a first-pass estimation of an empirical clustersize per voxel (i.e., in effect, an estimate of local smoothness),
and a second pass estimation of the cluster-size statistic
adjusted for local cluster size. Similarly, TFCE-based inference
can be corrected for the local null distribution; however,
although such correction does improve robustness against
nonstationarity, it was found that the (noncorrected) TFCE
measure is already significantly less vulnerable to nonstationarities in the data than cluster-based thresholding.
Multivariate Spatial Modeling

It is possible to extend univariate testing (i.e., testing each
voxel in isolation from each other) to multivariate testing
modeling all voxels simultaneously. A 4D (3D space x subjects)
FA dataset could be fed into an unsupervised clustering
449
approach (examples of unsupervised clustering/classification

are spectral clustering, principal component analysis and
independent component analysis (ICA); Beckmann & Smith,
2004; Hyvarinen, Karhunen, & Oja, 2001), in order to find
spatial patterns which characterize different cross-subject variability. For example, a single 4D multi-subject dataset might be
decomposed into one spatial map which describes the mean
difference in FA between patients and controls, a separate
spatial map which describes the difference between males
and females, a third map which describes the variation in FA
as a function of age, and a fourth map of an acquisition artifact
which affected just a few of the subjects. Such an approach uses
the richness present in a simultaneous analysis of the entire set
of voxels to find interesting patterns in the data, some of which
hopefully might be interpretable. For example, in Li et al.
(2012), a fully exploratory approach of multi-subject FA datasets revealed several white matter tracts that covary in their FA
values across subjects. These covariations in microstructure
may be the result of genetic variation or experience-dependent
plasticity, although other less interesting factors such as misregistration or partial volume effects may contribute.
In addition to the increase in sensitivity afforded by multivariate techniques, these methods can naturally be used for
multimodal data analyses (i.e., data with more than one type
of information). As all voxels are used simultaneously to find
interesting patterns of variations across subjects, these voxels
can be chosen to come from more than a single modality (e.g.,
FA and MD from diffusion data, and cortical thickness from
structural data). An example of such methods has been recently
proposed in Groves, Beckmann, Smith, and Woolrich (2011)
and Groves et al. (2012). In this work, data are modeled using
an ICA-type analysis that links the different types of data by
forcing the subject-weight-vector to be the same across modalities, for any given component. This method is extremely flexible, in that it allows for simultaneous modeling of very
different data regardless of their noise properties (which are
modeled separately for each type of data), or number of data
points (voxels). It is also capable of finding patterns that are
unique to each data set (e.g., artifacts), as well as patterns that
are shared across types of data. For instance, one component
might include regions where cortical thickness varies with age,
and white matter locations where FA follows the same crosssubject pattern of variation.
Alternatively, supervised methods for multivariate discriminant or regression (examples of supervised learning/classification are linear discriminant analysis, support vector machines
and Gaussian process models) are likely to become powerful
methods for interpreting the entire set of voxels simultaneously. For example, such methods can be trained to find
patterns in the data in order to optimize the classification of
subjects into different groups (such as patients who respond to
drug treatment and those who do not). The trained system can
then be applied to new data (e.g., a new subjects FA image
transformed into the common space of the other subjects) and
a prediction made about that subject. Many such methods are
in development in the field of machine learning, and the next
few years should see exciting and powerful advances.
Finally, multivariate techniques can also be applied in arclength based methods. In Zhu et al. (2010, 2011), two related
multivariate regression methods are presented. These methods
aim to find and model associations between DTI measures
450
along tracts. These approaches are flexible and sensitive. Covariates of interest (age and disease) can be used in the regression, and the methods can capture cross-subject variability in
the location of white matter changes.
Alternative Diffusion Measures to Test

There is no reason why only FA should be used to compare
diffusion characteristics across subjects. Other summary parameters such as MD, the individual tensor eigenvalues and the
principal tract direction, all contain different information
about local white matter tract structure, and could clearly be
combined to give richer investigations of localized microstructure and connectivity-related changes across subjects. One easy
way to achieve this is to simply apply the alignment processing
that was derived from the FA data to these other measures, for
example, in the case of TBSS, application of the warp fields
driven by the FA nonlinear registration, followed by the tractcenter skeleton projection. For example, in the multiple sclerosis
(MS) study presented below, after the initial FA-based analysis,
the principal diffusion eigenvalue and the average of the second
and third eigenvalues were tested for correlation with pathology
measures, to learn more about the biophysical processes
involved in the pathology; the first tensor eigenvalue describes
diffusion parallel to principal fiber direction, while the second
and third eigenvalues describe diffusion perpendicular to the
principal fiber direction, thus possibly informing about biological processes such as demyelination.
Theoretical considerations of the different possible tensorderived scalar quantities (FA, etc.) can lead to new combinations
of such parameters, in order to encapsulate different
information about the local tract structure. For example, Ennis

and Kindlmann (2006) propose a set of orthogonal tensor
invariants: in addition to the common measures of overall tensor
size (MD) and anisotropy (FA), a third measure, termed mode,
is proposed. The mode specifies the type of anisotropy; it varies
from 1 to 1 as the type of anisotropy ranges from planar (disklike; the second eigenvalue is close to the first, e.g., in areas of two
roughly equal fibers crossing) to linear (cigar-like; the second
eigenvalue is close to the third, e.g., where there is primarily one
dominant fiber present). Mode is exactly orthogonal (mathematically independent) to FA, thus it naturally complements
the ubiquitous use of FA for quantitative diffusion analysis.
The range of tensor shapes, and their parameterization by FA
and mode, is demonstrated in Figure 11. The diagram illustrates
how FA measures anisotropy (the distance to the isotropic
sphere), while mode measures the type of anisotropy. Individual tensor examples are depicted with superquadric glyphs
(Ennis, Kindlman, Rodriguez, Helm, & McVeigh, 2005).
Figure 12(a) depicts one coronal slice of a 2.5 mm diffusion
dataset with the standard RGB coloring of the principal eigenvector, and provides the anatomical context for interpreting (b),
which is the result of applying the colormap of Figure 11. While
much of the white matter is linearly anisotropic (positive mode,
shown in green and cyan), there are significant areas of planar
anisotropy as well. Figure 12(c) shows the principal eigenvector
in the upsampled slice, using the same cubic spline data interpolation used in the anisotropy crease method (Kindlmann
et al., 2007), and (d) shows the FA/mode colormap applied to
the same upsampled slice. Especially striking is the band of
planar anisotropy between the cingulum bundles and corpus
callosum, created by interpolating between linear anisotropy
along different directions. This planar anisotropy, however, is
Figure 11 Relationship between various tensor glyph shapes and tensor FA/mode.
451
Figure 12 Examples of color-coded principal tensor eigenvalue (red left-right, green front-back, blue up-down) and mode (colors as
shown in Figure 11), both in native data resolution and in the continuous-space upsampled approximation.
also present in the original discrete data, due to the partial

voluming inherent in MRI.
It is also possible to use nonscalar noninvariant features
derived from the diffusion data to look for changes across
subjects. For example, the principal diffusion eigenvector V1
(in general assumed to correspond to the principal tract direction) can be compared across subjects (as long as any rotations
carried out when registering different subjects together have
correctly been applied to the tract direction vector; Alexander,
Pierpaoli, Basser, & Gee, 2001). One might then test for a mean
change in tract direction between two subject groups, or look
for a change in cross-subject variability in the direction; either
measure would provide interesting information about differences in white matter connectivity.
Further interesting information can be obtained by looking
at how the tensor parameters estimated in a given voxel compare with those in neighboring voxels. One example of doing
this is found in an alternative measure to FA, known as lattice
anisotropy index (LI; Pierpaoli & Basser, 1996). LI quantitates
how much the directions of the tensor eigenvectors differ

between a given voxel and its neighbors; this is quite different
from FA, which just looks within voxel to see how different the
three eigenvalues are from each other. The main idea behind LI
is that in isotropic GM, the diffusion tensors in adjacent voxels
should be uncorrelated, whereas within well-ordered tracts, the
tensors in neighboring voxels should exhibit orientational
coherence. Additionally, LI may be less sensitive (than FA) to
variations in noise and diffusion contrast caused by changes in
the diffusion MRI acquisition parameters (such as b-value and
resolution), and hence may possibly be a more objective
measure of anisotropy than FA.
Relationships between neighboring voxels are utilized even
more fully in Kindlmann, Ennis, Whitaker, and Westin (2007).
Here, the fourth-order covariance tensor (which describes how
the diffusion tensor covaries across space within a local
neighborhood) may be decomposed into a meaningful 6 6
matrix of variances and covariances. The tensor covariance
potentially contains useful and rich information about tract
452
boundaries, junctions, crossing fibers, and partial volume

effects. Later we show an example of using the tensor covariance to attempt to disambiguate between partial volume effects
and FA changes.
Returning to simpler neighborhood information in the context of TBSS; even in skeleton-summarizing approaches, one
does not necessarily need to take just the maximum FA value
when projecting local tract information onto the skeleton; for
example, some integration measure of FA within the search
space could either give an average FA across the tract, or alternatively a measure of tract thickness, though interpretation
would need to be made carefully in the light of partial voluming
considerations. For example, in the skeleton-based approach
applied in Yushkevich et al. (2008), MD at a given point in a
tract is summarized in two different ways; the first samples MD
at the tract center, as defined by the voxel having maximum FA
(similar to TBSS), and the second averages the diffusion tensor
across the tract width, and calculates the MD from the resulting
average. The two measures are found to be largely in agreement,
but there are some areas of the brain where one is more sensitive
to cross-group changes than the other.
The tensor model, used to derive FA and MD, is by no means
the only way of modeling diffusion MRI data. Alternatives are
now favored for estimating fiber orientations and trajectories
(tractography, see other articles). Typically, high angular resolution diffusion imaging (HARDI) data are acquired and analyzed using models that, unlike DTI, do not imply a Gaussian
diffusion profile, and are therefore able to detect fiber orientation with greater precision. In addition to fiber orientation,
these models can be used to derive rotationally invariant scalar
measures, such as kurtosis (kurtosis is a measure of nonGaussianity, which requires data at multiple b-values (more
than 3), and therefore it is not strictly speaking a HARDI technique; Jensen, Helpern, Ramani, Lu, & Kaczynski, 2005) or
generalized FA (Tuch, 2004), that reflect tissue properties complementary to FA. For example, highly non-Gaussian diffusion
(nonzero Kurtosis) can imply the presence of restricted diffusion and/or multiple different materials/tissues being present
within a voxel. Another set of emerging models try to fit explicit
biophysical properties of tissues (e.g., axon diameter). These
models require nonconventional acquisitions at multiple diffusion times and b-values, and are at the moment mostly suitable only in high gradient-performance animal scanners.
Finally, if multiple diffusion parameters are to be tested
across subjects, the different tests do not need to be carried
out in isolation from each other; a vector of the different
parameters could be formed at each voxel (with each measure
appropriately normalized), and this vector tested across subjects using an appropriate multivariate statistic, such as
Hotellings trace, Wilks lambda or Pillais trace, or even a
trained/untrained discriminant function across the different
parameters. Such an approach could maximize sensitivity to
diffusion-related changes across subjects in a single test, without having to prespecify in advance which of the diffusion
parameters was likely to be of most value. Apart from problems
of large data size and dimensionality, there is of course no
reason why multivariate approaches should not be applied to
simultaneously investigate multiple diffusion parameters and
all voxels (Groves et al., 2011), taking us back to the discussion
above of multivariate, multimodal methods.
Interpretation Issues: Partial Volume Effects and

Complex Tract Structure
Great care is needed in the interpretation of voxelwise crosssubject results in areas of white matter where the local tract
structure is not simple. For example, at tract junctions, or areas
of crossing tracts, an apparent reduction in FA can in fact be
due to an increase in one of the tracts, if it is not the strongest
tract present (Jones et al., 2005; Tuch et al., 2005). Conversely,
selective degeneration of one fiber population in a region
where these fibers cross other healthy fibers, can lead to an
increase in FA in patients relative to controls. Clearly, interpreting FA as an indication of fiber integrity is not appropriate
in locations of white matter bundle crossings. A partial volume
model for crossing fibers was recently proposed to alleviate this
problem (Behrens, Johansen-Berg, Jbabdi, Rushworth, &
Woolrich, 2007; Jbabdi, Behrens, & Smith, 2010). The
model, originally designed to detect fiber orientations for tractography, also provides a measure of the relative contributions
from each fiber population to the overall signal in each voxel.
These partial volume fractions can be used as proxies for fiber
integrity that are specific to each of the crossing fiber populations. One complication with this approach is that the labeling
of the fiber populations need to be matched across subjects. In
Jbabdi et al. (2010), a two-stage fiber reassignment algorithm
is proposed to solve this matching problem.
A closely related problem lies in the interpretation of crosssubject differences in FA (etc.), when a voxel contains both
white matter and GM (or CSF) in this case, any estimated
change in FA is just as likely to be due to a change in the relative
amounts of different tissue types than to a change of FA within
the white matter. See the two foci of detected change in Jones
et al. (2005) for an example of this; at least one of these
appears to be localized well away from a predominantly
white-matter area. (This problem is greatly exacerbated when
applying 3D spatial smoothing, as this increases the number of
voxels containing a mix of different tissue types.) As one moves
away from the larger tracts, this effect will still occur within
even the tract-center voxels, if tract width is smaller than original voxel size (e.g., the Fornix). In this case, it is very difficult
to determine whether a reduction in FA is really due to withintract FA change or a change in tract thickness, and it is important to note that in such cases even approaches such as TBSS do
not easily resolve this problem. It is partly for that reason that
in TBSS the mean FA skeleton is thresholded, typically at 0.2,
rather than being allowed to fall all the way to zero.
In Lee et al. (2009), a method called T-SPOON was proposed, to reduce the problems associated with spatial smoothing in the interpretation of VBM-style analyses. The method
corrects for the blurring introduced in the registration/smoothing process by dividing the resulting registered FA maps by the
estimated local blurring of white matter (calculated by taking a
white-matter mask and applying the same registration/
smoothing to it). This amelioration of the blurring problems
of course cannot undo any original partial volume effects.
We have already discussed issues relating to interpolation of
diffusion data; for example, Figure 12 shows the extra fine
detail that can be seen if the full tensor data is upsampled,
compared to upsampling of the native-resolution summary
parameters such as FA. In general, if diffusion data is to be
resampled, more detail is preserved by resampling the raw data
or the full set of tensor parameters, rather than summary scalar
images such as FA. In Figure 13, we illustrate a further important point relating to partial-volume effects and interpolation
in diffusion data. We use very high resolution data in order to
be able to view what we consider the underlying ground-truth
structures, while also downsampling the raw data in order to
simulate how these structures would appear in more normal
resolution data. The data is a complete ex vivo human brain,
acquired at 0.7 0.7 0.7 mm resolution, using a 3D segmented spin-echo sequence on a 3 T Siemens Tim Trio over
99 h (Miller et al., 2011). In Figure 13(a), we see a cortical ROI
of the FA image derived from the original data. We consider
this the ground truth, in the sense that it shows clearly the
delineation of different tissue types. We can see high-FA white
matter, medium-FA cortical GM, and a thin low-FA band
which lies just inside the GM, immediately next to the
white-gray boundary. These delineations were verified by
superimposing and comparing the FA, MD and even higher-
453
resolution (0.33 0.33 0.33 mm) proton-density-weighted

anatomical images. In (d), we see the same image, overlaid
with the direction of the principal tensor eigenvector; note the
very clear anisotropy in the GM, perpendicular to the
white-gray boundary, caused by the predominance of fibers
within the GM running perpendicular to the boundary. In
(b), we see FA estimated via a downsampling (strictly speaking,
proper downsampling involves blurring followed by sampling
on a sparser grid of (larger) voxels than the original, with the
blurring extent and sampling grid size correctly matched to
each other. Here we have only carried out the first stage (blurring of the original raw data), and did not decimate the data
onto a sparser voxel grid, in order to allow us to maximize the
qualitative information in the data; note that at any given new
voxel the intensity (in raw data and derived FA, etc.) is correctly
representative of what we would expect to see had the original
images actually been acquired at the lower resolution, with a
large voxel centered on that position in space) of the original
raw data, achieved through convolving the original data by a
Figure 13 Various issues relating to partial volume effects at different image resolutions, as illustrated using high-resolution (0.7 mm) ex vivo
diffusion data (Miller et al., 2011). (a) FA of original ground truth data. (b) FA obtained by blurring the raw data to effectively give 2 mm voxels, and
then recomputing FA. (c) As for (b), but simulating 3.5 mm data. This shows what we expect to see from normal resolution diffusion data; the
tract appears thinner than it actually is, because of partial-volume effects at the white-gray boundary. (d) Principal eigenvectors in the original data,
showing clear anisotropy in the gray matter, oriented perpendicular to the white-gray boundary. Data kindly provided by Jennifer McNab and Karla Miller.
454
Gaussian kernel that results in an effective resolution of 2 mm;

we then re-estimate the FA. This shows the structure that we
would expect to see at a more normal diffusion data resolution. The tract appears thinner than it actually is (as judged,
e.g., by (a)), because of a partial-volume effect in voxels on the
white-gray boundary. These voxels include a mixture of white
matter fibers and GM containing anisotropy perpendicular to
that in the white matter, thus strongly reducing the FA. In (c),
we see the same thing but for 3.5 mm resolution data.
The most important message to take from these illustrations
is that tracts appear thinner, when judged by FA images derived
from normal resolution diffusion data, than in fact they are;
this has an impact on considerations of partial volume effects,
and other attempts to derive quantitative information such as
tract thickness, true underlying FA, etc. As mentioned above,
even in TBSS, when the tracts are thinner than voxel dimensions, it is not straightforward to tell whether apparent changes
in FA are caused by changes in tract thickness or true underlying FA; prompted by this, researchers have begun to develop
models that attempt to achieve this disambiguation by utilizing more of the information present in the diffusion data than
just the FA. We now present some initial progress in this
direction.
One might expect that the apparent FA in a given voxel is a
function of the true partial voluming (fractional content of
white and GM) and the true underlying FA in the white matter.
The previous results showing the reduction in FA caused by the
orthogonality of anisotropy in GM and neighboring white
matter means that this will most likely be a nonlinear function,
but possibly one that we can learn and verify from high resolution diffusion data. Once such a relation is learnt, one could
then hope to recover true underlying FA (in new, normal
resolution diffusion data), given the apparent FA and the partial volume estimation (PVE). In Figure 14, we show initial
results with such an approach. (a) The original (high) resolution MD image, which in this ex vivo data shows excellent graywhite contrast. We fed this into tissue-type segmentation using
FAST (Zhang, Brady, & Smith, 2001) from FSL, to give a white
matter PVE; this quantifies the fraction of a voxel believed to be
white matter. We then blurred this to obtain the equivalent
PVE that we would obtain in normal resolution data; this is
shown in blue in (b). In voxels where the white matter PVE is
zero the underlying MD image can be seen; in blue voxels, dark
blue represent low fractional white-matter content (i.e., high
levels of partial voluming) and bright blue shows voxels which
only contain white matter. We assume that the high resolution
FA image (c) represents the true underlying FA. We then
blurred the raw diffusion data and recomputed the FA, simulating FA that would be achieved at normal resolution acquisition, and applied skeletonization in order to only consider
tract-center voxels, to simplify interpretation of the modeling.
This is shown in red-yellow in (d), where it is clear, when
comparing colors with (c), that the nonlinear partial volume
effects (including the tract thinning discussed earlier) have
considerably reduced the FA in all of the thinner tracts. We
then modeled the apparent FA as a nonlinear (second-order
polynomial) function of true FA and PVE, and upon inverting
this model were able to reconstruct our best estimation of the
true FA derived from the apparent (low resolution) FA and the
PVE. (e) This recovery of the true FA, with clearly less bias in
estimated FA in the thinner tracts. Interestingly, when we
attempted to make this correction using nonlinear models
(up to fourth-order polynomials) of just apparent FA or PVE,
we were unable to achieve a reasonable recovery of the true FA.
However, such an approach assumes an accurate estimation
of white matter PVE, and this is not as accessible in reality as it
was here with this ex vivo data. In normal in vivo diffusion data,
the MD does not contain the same high contrast between tissue
types, and the use of structural data (which could provide
accurate PVE) is problematic because the slightest misalignment
between structural and diffusion voxels would probably invalidate the above approach. Furthermore, the assumption of a
correction based on within-voxel PVE and apparent FA does
not take into account the neighboring voxels, and so is likely
missing potentially useful information about variations across
voxels in tensor orientation, related again to the tract thinning
that we have seen. Hence, we proposed that the tensor covariance might be a useful way of indirectly telling us about partial
volume effects and the results of variations across neighboring
voxels of tensor orientation; we hypothesize that both effects
would be encoded in the cross-voxels tensor covariance. An
examples of the (symmetric) covariance is shown in (h), with
the six maps shown being the rotationally invariant tensor
covariance components (corresponding to spatial covariance
of MD, FA and mode). We repeated the above modeling,
attempting to recover true FA via a nonlinear combination of
the six relevant tensor covariance components and the apparent FA. This approach was even more successful in accurately
recovering the true underlying FA. The scatterplots shown in (f)
and (g) show the improvement in correspondence between the
estimated true FA versus the true FA, compared with the greater
spread seen in the apparent FA versus the true FA.
A separate approach has been proposed to deal with partial
volume effects with CSF (Metzler-Baddeley, OSullivan, Bells,
Pasternak, & Jones, 2012; Pasternak, Sochen, Gur, Intrator, &
Assaf, 2009). This is somewhat easier than gray/white PVE, as
the diffusion coefficient of CSF is about three times higher than
that of tissue. Therefore, a partial volume model that includes a
tensor compartment and a free water compartment can be
fitted to diffusion data, providing that CSF diffusivity is
assumed to be known, and constraints are imposed on the
tissue volume fractions (Pasternak et al., 2009). These constraints can be relaxed if one further acquires low b-value data
(e.g., b 300 s mm2), as these will have significant contribution from CSF signal and help fit the PVE model (Jbabdi,
Sotiropoulos, Savio, Grana, & Behrens, 2012).
Such modeling, although reducing bias in estimation of
underlying FA, may ultimately result in an increase in the
uncertainty of the FA estimation, and so may not prove useful
when sensitivity to cross-subject changes is the most important
factor in analysis success. Furthermore, such research is certainly not intended to supplant more experimentally driven
investigations into the relationship between the underlying
biophysical processes and the diffusion MRI acquisition physics, which in the long term may provide better-founded corrections for effects such as the tract-thinning and partial-voluming
in general, as well as better interpretability of changes in diffusion parameters such as FA, MD and the tensor eigenvalues.
30
30
40
R1
R2
R3
R1
True FA
20
20
10
10
(e)
(d)
True FA
(c)
R2
40
50
60
60
50
R3
70
(f)
70
10
20
30
40
Apparent FA
50
60
70
(g)
10
20
30
40
Reconstructed FA
50
60
70
Figure 14 Modeling of FA and partial-volume estimation (PVE) in order to attempt to estimate true underlying FA from normal resolution diffusion data. (a) The original (high) resolution MD image, showing
excellent gray-white contrast. This is fed this into tissue-type segmentation to give white matter PVE, which was blurred to obtain the equivalent PVE that we would obtain in normal resolution data, shown
in (b) (dark blue small white matter partial volume fraction; bright blue pure white matter voxels). We assume that the high resolution FA image (c) represents the true underlying FA; red lowest
FA, yellow highest FA. (d) FA derived by downsampling the raw diffusion data and computing the FA, simulating FA that would be achieved at normal resolution acquisition, and skeletonized in order to only
consider tract-center voxels. Comparing colors with (c), it is clear that FA has been reduced by the downsampling. After modeling apparent FA as a function of true FA and PVE, we can reconstruct an
estimate of true underlying FA, shown in (e). In an alternative approach, we use some components of the tensor covariance (h) instead of PVE in our modeling, and in (f) and (g) show the improved
correspondence between reconstructed FA and true FA with such an approach. Data kindly provided by Jennifer McNab and Karla Miller.
(b)
(a)
455
456
Standard Space Templates and Atlases

Standard-space template images are either single-subject or
multi-subject-averaged images having a specified field of
view, resolution, brain position (within the image) and coordinate system (origin and orientation). The most well-known
coordinate systems are the Talairach and MNI definitions
(these are close to each other but not exactly the same), with
the most widely used template being the MNI152 template,
corresponding to an average of 152 T1-weighted structural
images in MNl space. The primary purpose of such coordinate
systems and templates is to allow the researcher to align data
into a common space, and report voxel coordinates in a way
that is meaningful to other researchers.
An example diffusion-related template is the FMRIB58_FA
image supplied with FSL. This was created by taking FA images
from 58 healthy adults, linearly aligning them to the MNIl52
T1-weighted template image and creating a mean FA from
these. This process was then iterated several times using nonlinear registration, regenerating a new mean FA template on
each iteration, with ever-increasing sharpness. Such iterative
template creation can be carried out with varying degrees of
sophistication, including avoidance of initialization bias
through the averaging of registration warp fields; for example,
see Goodlett, Davis, Jean, Gilmore, and Gerig (2006) and
Guimond, Meunier, and Thirion (2000). The MNIl52 and
FMRIB58_FA template images can be seen in the top two
rows of Figure 15.
A standard-space atlas is usually based upon a specific template and contains richer information than just the original
template image intensities. For example, the atlas may contain
specific information about the probability of different tissue
types (or structural or functional brain regions) at each template voxel. Probabilistic atlases contain population probabilities rather than hard labelings, for example, telling the
researcher that a given voxel is found in the putamen in 67%
of subjects and in the pallidum in the other 33%.
Atlases can be useful in a number of ways. The most obvious is as an aid to the researcher in interpreting the location of
interesting diffusion results (e.g., the location of voxels where
FA is significantly different between two groups of subjects).
Care must be taken though, as the alignment between the
study data and the template/atlas space may be inaccurate,
possibly leading to incorrect conclusions about location. A
second example usage of atlases is to provide ROIs within
which to average diffusion information such as FA, before
carrying out cross-subject statistics. This can help reduce the
effect of noise in the data, reduce the conservativeness of
multiple comparison correction, and aid in interpretability of
spatial location; however, an obvious disadvantage with such
an approach is the loss of spatial detail/richness.
Several complementary atlases of relevance to white matter
connectivity have recently become available. One is the Julich
histological (cyto- and myelo-architectonic) atlas created by
the team of Profs Karl Zilles and Katrin Amunts at the Research
Center Julich and coordinated by Simon Eickhoff. The atlas
currently contains 68 GM structures and ten white matter
structures. It is based on the miscroscopic and quantitative
histological examination of ten human postmortem brains.
The histological volumes of these brains were 3D reconstructed
and spatially normalized into the space of a single subject

template in MNI space, to create a probabilistic map of each
area (Amunts & Zilles, 2006; Eickhoff et al., 2007, 2005; Toga,
Thompson, Mori, Amunts, & Zilles, 2006).
A second atlas is the JHU DTI-based white-matter atlas,
created by Susumu Mori, laboratory of brain anatomical MRI,
Johns Hopkins University. This comprises two subatlases: In
the ICBM-DTI-81 white-matter labels atlas, 50 white-matter
tract labels were created by hand segmentation of a standardspace average of diffusion MRI tensor maps from 81 adults. In
the tractography atlas, 20 structures were identified probabilistically by averaging the results of running deterministic tractography on 28 normal subjects (Mori, Wakana, van Zijl, &
Nagae-Poetscher, 2005; Wakana et al., 2007).
Empirical Studies of Gaussianity and Repeatability in

Diffusion MRI Data
As discussed earlier, it is of interest to characterize variability
and Gaussianity of diffusion data across subjects, and how this
is affected by different voxelwise preprocessing approaches. In
this section, we first report tests of cross-subject Gaussianity,
and then tests of cross-session and cross-subject variability.
Testing for Gaussianity

Jones et al. (2005) evaluated cross-subject Gaussianity across all
brain voxels in a VBM-style voxelwise analysis. It was found that
there was a large number of voxels whose cross-subject distribution was significantly non-Gaussian approximately 717%
of voxels, depending on the amount of spatial smoothing
employed. Smith et al. (2006) tested two datasets one comprising 36 controls and the other comprising 33 schizophrenics,
using the Lilliefors modification of the KolmogorovSmirnov
test (Lilliefors, 1967) to find voxels where the cross-subject
distribution was significantly non-Gaussian. The test threshold
was set at 0.05. Therefore we expect to find 5% of voxels failing
the test by chance; a much higher number of voxels is evidence
for non-Gaussianity.
We ran the test on each dataset in three ways. Firstly, we
tested all voxels after the initial nonlinear registration (and
before skeletonization); this is similar therefore to the VBMbased investigation reported in Jones et al. (2005). Secondly,
we masked this aligned data with the mean FA skeleton, and
investigated just these voxels i.e., looking at skeleton voxels,
but before projecting the aligned data onto the skeleton.
Finally, we tested the skeletonized data after full TBSS preprocessing, that is, after projection onto the skeleton.
The percentages of voxels found to be non-Gaussian in the
controls dataset were (respectively for the three tests): 17.8, 7.0,
and 6.6. In the schizophrenics dataset, the percentages were:
19.2, 8.1, and 7.5. Thus, it is clear that with the VBM-style
analysis, we find a large number of voxels with a non-Gaussian
distribution (nearly four times more than predicted by chance,
in exact agreement with the figure found in Jones et al. (2005)
for unsmoothed VBM-preprocessed data). Interestingly, the
spatial distribution of these tends to be away from the tract
centers, as judged visually, and as shown by the great reduction
in the percentages in the other tests, where the aligned data is
457
Figure 15 Slices through several MNIl52-space templates and atlases. From top to bottom: MNl152 template image, formed by averaging 152
T1-weighted structural images (nonlinear version of MNI152 kindly provided by Andrew Janke and Louis Collins). FMRlB58_FA, formed by averaging
58 FA images. Julich histological atlas; solid colors show the maximum-probability classification of all current GM and WM structures
(thresholded at 25% probability) and the probability image for the left corticospinal tract (shown in red-yellow, thresholded at 5%). Johns Hopkins
DTI-based white matter labels atlas, created from hand segmentation of an average tensor map from 81 subjects. Johns Hopkins DTI-based probabilistic
tractography atlas, created by averaging tractography results from 28 subjects; shown is the maximum-probability classification of tracts and
the probability image for the left corticospinal tract.
458
only tested at the skeleton voxels. For the fully TBSS-processed

data, the test failure rate is reduced still further, to rates not far
above the 5% expected by chance.
Repeatability Tests
Cross-session and cross-subject repeatability is also of great
interest. In Smith et al. (2006), we investigated the repeatability of FA values, both across sessions and across subjects. We
analyzed data from eight healthy subjects, each scanned on
three separate occasions. We estimated % coefficient of variation (CoV: 100 standard deviation/mean) across sessions or
subjects as the measure of repeatability.
We first measured CoV at seven voxels placed in the center
of various white matter tracts on the mean FA image; the genu
of the CC, left and right optic radiation, left and right pyramidal tract in the cerebral peduncle, and left and right superior
cingulum bundle. The exact positioning of the points is
described in Heiervang, Behrens, Mackay, Robson, and
Johansen-Berg (2006). As well as estimating CoV for the
TBSS-preprocessed data at these points, we also found CoV

for data before the skeletonization, after the nonlinear registration stage, which we therefore refer to as being VBMpreprocessed (though note that no spatial smoothing was
applied with either approach). Thirdly, we estimated CoV by
carefully choosing the relevant voxels of interest by hand on
each original FA image separately. Ideally, this hand placing
has the advantage of adapting to tract localization changes
across subjects, but potentially suffers from subjectivity/usererror. In the easiest to define, thickest tracts, hand definition of
the voxel in this way should give a close to optimal CoV.
We also obtained global summary statistics (median and
mode) across the whole brain for CoV in the TBSS and VBMpreprocessed cases. VBM-preprocessed results are only reported
for voxels where the mean FA across all subjects and all sessions is >0.2, to avoid bias through inclusion of potentially
high CoV values in low mean FA voxels. Likewise, the TBSS
skeleton was thresholded at the default of 0.2.
Figure 16 shows the intersession and inter-subject variability results. Cross-session variability with TBSS preprocessing is
Figure 16 Intersession and inter-subject variability results. Eight subjects were scanned three times each. Percentage coefficient of variation (CoV)
variability results are shown at seven white matter positions of interest and also using summary statistics for the whole brain. Data kindly
provided by Einar Heiervang and Heidi Johansen-Berg.
Figure 17 Coronal views through the controls > schizophrenics group comparison of FA. (a) TBSS analysis showing the FA skeleton in blue and
significant group difference in red, in the corpus callosum and fornix. (b) VBM-style analysis, with no spatial smoothing; as well as the corpus callosum
and fornix, a group difference is suggested running along the underside of the ventricles. (The 5 mm and 10 mm FWHM smoothing analyses
showed the same general pattern, though even more diffuse.) (c, d) The mean FA images for the controls and schizophrenics, respectively. It is clear that
while the corpus callosum is well aligned between the two groups, the lower edge of the ventricles is not, due to larger ventricles in the patient
group. This has given rise to a spurious result in the VBM-style analyses. (e) Atlas-based confirmation of structures. The Julich histological probabilistic
atlas shows the cingulum bundles in green, the callosal body in red-yellow, the fornix in light-blue, the corticospinal tract in yellow and the superior
occipito-frontal fascicle in red. The Harvard-Oxford probabilistic subcortical structural atlas shows the thalamus in copper, the ventricles in dark-blue
and the caudate in pink. Data kindly provided by Clare Mackay.
generally slightly lower than VBM preprocessing and generally
considerably lower than with hand-placing. Cross-subject variability with TBSS preprocessing is consistently lower than with
VBM preprocessing and lower than hand-placing in four out of
seven positions of interest. The results suggest that TBSS is
successful in aligning equivalent structures across sessions/
459
subjects and that it improves alignment further than pure nonlinear registration has achieved here. With TBSS the intersession CoV is generally between 3% and 5% (mode 3%),
and the inter-subject CoV is generally between 5% and 15%
(mode 12%). These figures should prove useful when carrying
out power calculations for planned DTI studies. For example,
Figure 18 TBSS results from 15 MS patients. (a, b) 3D surface renderings of the mean FA skeleton. Blue shows the group mean lesion probability
distribution, thresholded at 20%. Red shows voxels where FA correlates negatively (across subjects) with subject total lesion volume. (b) is a 3D
stereo pair. (c) Yellow shows where FA correlates negatively with EDSS disability score. (d) Red as above (negative correlation with lesion volume).
In (c) and (d), green shows the mean FA skeleton, blue shows the group mean lesion distribution, and the background image is the MNI152.
Data kindly provided by Heidi Johansen-Berg and Zaheer Cader.
460
aging (between the ages of 40 and 70) might be expected to

reduce FA from 0.8 to 0.7 in the genu of the CC, and so one
might plan to recruit ten subjects for each age group to have an
80% chance of finding a significant group difference at the
p < 0.05 level. Note though that this simple example does not
take into account multiple comparisons across space, and if the
difference was localized in just a very few voxels, the difference
found in this example might not reach significance after correction for multiple comparisons.
Example Multi-Subject Studies

In this section, we present example results from studies of three
pathologies schizophrenia, MS, and Alzheimers disease
(AD). In the first, we present results from both VBM-style and
TBSS analyses, and illustrate the problems of interpreting the
VBM-style analysis. In the second, we illustrate the use of other
diffusion-related parameters than just FA, in order to help
obtain a richer understanding of the biophysical processes
involved in the pathology. In the third study, we illustrate the
use of crossing-fiber information to help interpret FA changes
in regions of complex WM organization. The diffusion acquisition parameters for these studies are reported in detail in
Smith et al. (2006) and Douaud et al. (2009).
Comparison of Voxel-Based and Tract-Based Analyses in

Schizophrenia
We analyzed data from 33 schizophrenics and 36 age-matched
controls, applying both VBM-style and TBSS preprocessing,
before looking for group differences using cluster-based thresholding. Cluster p-values were obtained using permutation testing, with cluster-forming threshold t > 3, and cluster significance
p < 0.05 corrected for multiple comparisons across space.
For the VBM analysis, we smoothed the data at a range of
spatial extents (0, 5, and 10 mm FWHM) before running the
cross-subject analysis. The VBM-style analysis was only performed at voxels where the mean FA across subjects (after
nonlinear alignment) was > 0.15. We considered that any
mean FA lower than this is dangerous to consider for a group
difference, as such a voxel must be considered to be potentially
dominated by GM or CSF partial voluming.
TBSS found reduced FA in patients in right-superior, medial
and anterior CC, superior and right-inferior fornix and in long
association fibers near the junction of the right superior and
inferior longitudinal fasciculi. In the majority of these areas the
VBM-style analysis also found a group difference at all three
spatial smoothing extents, though with much less precision
about the exact localization of group difference. However, in
addition, several spurious results were generated by the VBMstyle analyses, for example, just below the ventricles, as seen in
coronal view in Figure 17. It is clear from inspecting the mean
FA images for the controls and schizophrenics that while the
CC is well aligned between the two groups, the lower edge of
the ventricles is not, due to larger ventricles in the patient
group. This has given rise to a result which could easily be
misinterpreted as a group difference in FA in the VBM-style
analyses. TBSS did not show any spurious effect, as it was not
sensitive to the between-group shift in this area. For the
significant TBSS result in the fornix, we confirmed, through

looking at the skeleton-projection vectors, that this result was
not spurious, that is, that any inter-subject movement in the
fornix was correctly dealt with via the final projection of maximum FA onto the skeleton.
Using Multiple Diffusion Parameters to Interpret White Matter

Change in MS
In Smith et al. (2006) and Cader et al. (2007), a study of 15
patients with MS was presented. After applying TBSS preprocessing, we carried out two GLM analyses. In the first, we
correlated FA (voxelwise, across subjects) with each subjects
EDSS score (Expanded Disability Status Scale, a common measure of disability), using permutation-based inference on cluster size (t > 1, p < 0.05 corrected). In the second analysis, we
correlated FA across subjects with total lesion volume (measured by hand segmentation of T2-weighted images), again
with permutation-based inference on cluster size (t > 2,
p < 0.05 corrected).
Figure 18 shows the mean lesion probability distribution
in blue: For each subject, a binary lesion mask is created by
hand. All subjects lesion masks are then transformed into
standard space and averaged. The figure shows this mean
lesion distribution thresholded at 20% (i.e., at any given
blue voxel, 20% of the subjects had a lesion present). Red
voxels on the mean FA skeleton show where FA correlates
negatively across subjects with subject total lesion volume.
There is strong negative correlation in left superior cingulum
and many parts of the CC, including midline parts of the CC,
Figure 19 TBSS results illustrating spatial distributions of white matter

voxels showing significant correlation between diffusion measures and
callosal cross-sectional area, global T2 lesion load, and EDSS.
Correlations are shown for FA (top row), axial diffusivity (Ax, middle
row), and radial diffusivity (Ra, bottom row). Here, decreases in FA were
predominantly associated with increases in radial diffusivity. Two axial
slices are shown, at the level of Z 24 and Z 28 (MNI152 space).
Figure kindly provided by Heidi Johansen-Berg and Zaheer Cader.
461
AF
PF
1850
4400
1700
4200
1550
4000
1400
3800
1250
3600
1100
3400
3200
950
CON
AD
800
NS
CON
3000
AD
Figure 20 Top: location of significant increase in MO between controls and MCIs (pink). Superposed is the location of increase in FA (redyellow).
Middle: probabilistic tractography of motor (pinkblue) and association (redyellow) pathways in controls. Bottom: connection probabilities
(unnormalized number of streamlines) from the centrum-semiovale to target ROIs that isolate association (left) and motor (right) pathways. Only the
association pathways are significantly different between controls and AD. Figure kindly provided by Gwenaelle Douaud.
462
well away from areas of lesion. This suggests that FA is

reduced even in normal appearing white matter as disease
progresses. Yellow voxels show where FA correlates negatively
with EDSS disability. Affected areas include superior cingulum, CC, pyramidal/corticospinal tract and inferior frontooccipital/longitudinal fasciculus.
Further analyses investigated the separate behavior of the
axial diffusivity (i.e., the first tensor eigenvalue, describing
diffusion parallel to principal fiber direction) and the radial
diffusivity (the average of the second and third eigenvalues,
describing diffusion perpendicular to the principal fiber direction). These diffusion parameters were fed into the TBSS analysis, using the nonlinear registration warps and tract-center
projections as previously estimated using the FA data. Figure 19
shows these parameters in rows 2 and 3, respectively, with
similar results found whether the model covariate used was
CC area, total lesion volume or disability score. While both
diffusivities are increased as a result of the pathology, the radial
diffusivity is increasing much more quickly than the axial; this
mismatch is what gives rise to the decrease in FA. This is
suggestive of demyelination (which would affect radial diffusivity more than axial), as well as more general axonal
degeneration.
Interpreting FA Changes of Crossing Fiber Regions in Mild

Cognitive Impairment and Mild Alzheimers
In Douaud et al. (2009), a study of 61 healthy control subjects,
56 mild cognitive impairment (MCI) patients, and 53 AD
patients was presented. The study uses TBSS to compare various DTI-derived parameters between the three groups. The key
finding of this study is that MCI patients only differed significantly from controls in a region of the centrum semiovale,
where motor and association pathways intersect. In this region,
there was an increase in FA in MCIs relative to controls; see
Figure 20. The same region also showed further increase in FA
between MCI and AD. As the mode (MO) of anisotropy was
also increased between the two groups (see Figure 11), the
authors suspected a selective degeneration of one of the two
intersecting pathways. A probabilistic tractography analysis,
seeded from the location of this FA increase, showed that the
connection probability from the association but not the motor
pathways was significantly reduced between controls and AD.
This provided further evidence that the apparent increase in FA
could not be interpreted as an increase in WM integrity, but
rather as a probable selective degeneration of the superior
longitudinal fasciculus, and a relative preservation of the
motor projections.
Conclusions
Localized/voxelwise analysis of multi-subject diffusion MRI
data has a clear role to play in neuroimaging, for example, in
tracking changes in white matter caused by disease. Although
careful tractography-based analyses will increasingly have great
value, whole-brain voxelwise analyses provide a powerful complement to such approaches, by allowing the entire dataset to
be investigated in a straightforward manner. Much has already
been achieved in developing such methodologies, but issues of
robustness, accuracy, and interpretability are crucial, and

researchers need to be aware of the limitations of the different
approaches. While analysis methodology researchers are continuing to develop improved approaches to address such concerns, they are also making rapid advances in the kinds of
questions that can be asked at the highest level (such as
looking at the entire pattern of voxelwise changes, can we
accurately classify subjects into different pathology groups)
and also at the lowest (such as what are the many diffusionderived parameters telling us about the biological nature of the
pathology). This is an exciting area in which to be carrying out
research, and one that still has much needing to be done!

Tissue Microstructure Imaging with Diffusion MRI.
References
Alexander, D. C., Pierpaoli, C., Basser, P. J., & Gee, J. C. (2001). Spatial
transformations of diffusion tensor magnetic resonance images. IEEE Transactions
Amunts, K., & Zilles, K. (2006). In L. Zaborszky, F. G. Wouterlood & J. L. Lanciego
(Eds.), Neuroanatomical tract-tracing: Molecules, neurons, and systems,
Chapter 18. Berlin: Springer.
Andersson, J., Jenkinson, M., & Smith, S. (2007). Non-linear registration aka spatial
normalisation. Internal technical report TR07JA2, Oxford Centre for Functional
Magnetic Resonance Imaging of the Brain, Department of Clinical Neurology,
Oxford University, Oxford, UK. Available at www.fmrib.ox.ac.uk/analysis/techrep for
downloading.
Andersson, J., Smith, S., & Jenkinson, M. (2007). Non-linear optimisation. Internal
technical report TR07JA1. Oxford Centre for Functional Magnetic Resonance
Imaging of the Brain, Department of Clinical Neurology, Oxford University, Oxford,
UK. Available at www.fmrib.ox.ac.uk/analysis/techrep for downloading.
Ashburner, J., & Friston, K. J. (2000). Voxel-based morphometry The methods.
Ashburner, J., & Friston, K. J. (2001). Why voxel-based morphometry should be used.
NeuroImage, 14(6), 12381243.
Ashburner, J., & Friston, K. J. (2004). Generative and recognition models for
neuroanatomy. NeuroImage, 23(1), 2124.
Barnea-Goraly, N., Eliez, S., Hedeus, M., Menon, V., White, C. D., Moseley, M., et al.
(2003). White matter tract alterations in fragile X syndrome: Preliminary evidence
from diffusion tensor imaging. American Journal of Medical Genetics Part B:
Neuropsychiatric Genetics, 118B, 8188.
Beckmann, C. F., & Smith, S. M. (2004). Probabilistic independent component analysis
for functional magnetic resonance imaging. IEEE Transactions on Medical Imaging,
23(2), 137152.
Behrens, T. E. J., Johansen-Berg, H., Jbabdi, S., Rushworth, M. F. S., &
Woolrich, M. W. (2007). Probabilistic diffusion tractography with multiple fibre
orientations. What can we gain? NeuroImage, 23, 144155.
Behrens, T. E. J., Johansen-Berg, H., Woolrich, M. W., Smith, S. M.,
Bengtsson, S. L., Nagy, Z., Skare, S., Forsman, L., Forssberg, H., & Ullen, F. (2005).
Extensive piano practicing has regionally specific effects on white matter
development. Nature Neuroscience, 8(9), 11481150.
Bookstein, F. L. (2001). Voxel-based morphometry should not be used with
imperfectly registered images. NeuroImage, 14(6), 14541462.
Buchel, C., Raedler, T., Sommer, M., Sach, M., Weiller, C., & Koch, M. A. (2004). White
matter asymmetry in the human brain: A diffusion tensor MRI study. Cerebral
Cortex, 14, 945951.
Cader, S., Johansen-Berg, H., Wylezinska, M., Palace, J., Behrens, T. E., Smith, S., et al.
(2007). Discordant white matter N-acetylasparate and diffusion MRI measures
suggest that chronic metabolic dysfunction contributes to axonal pathology in
multiple sclerosis. NeuroImage, 36(1), 1927.
Cercignani, M., Bammer, R., Sormani, M. P., Fazekas, F., & Filippi, M. (2003). Intersequence and inter-imaging unit variability of diffusion tensor MR imaging
histogram-derived metrics of the brain in healthy volunteers. American Journal of
Neuroradiology, 24, 638643.
Cercignani, M., Inglese, M., Pagani, E., Comi, G., & Filippi, M. (2001). Mean diffusivity
and fractional anisotropy histograms of patients with multiple sclerosis. American
Journal of Neuroradiology, 22, 952958.
Ciccarelli, O., Behrens, T. E., Johansen-Berg, H., Talbot, K., Orrell, R. W., Howard, R. S.,
et al. (2009). Investigation of white matter pathology in ALS and PLS using tractbased spatial statistics. Human Brain Mapping, 30(2), 615624.
1042210427.
Corouge, I., Fletcher, P. T., Joshi, S., Gouttard, S., & Gerig, S. (2006). Fiber tractoriented statistics for quantitative diffusion tensor MRI analysis. Medical Image
Analysis, 10, 786798.
Davatzikos, C. (2004). Why voxel-based morphometric analysis should be used
with great caution when characterizing group differences. NeuroImage, 23(1),
1720.
de Groot, M., Vernooij, M. W., Klein, S., Ikram, A., Vos, F. M., Smith, S. M., et al.
(2013). Improving alignment in tract-based spatial statistics: Evaluation and
optimization of image registration. NeuroImage, 76, 400411.
Douaud, G., Mackay, C., Andersson, J., James, S., Quested, D., Kar Ray, M., et al.
(2009). Schizophrenia delays and alters maturation of the brain in adolescence.
Brain, 132, 24372448.
Durrleman, S., Fillard, P., Pennec, X., Trouv, A., & Ayache, N. (2011). Registration, atlas
estimation and variability analysis of white matter fiber bundles modeled as
currents. NeuroImage, 55(3), 10731090.
Eberly, D. (1996). Ridges in image and data analysis. Dordrecht: Kluwer Academic
Publishers.
Eberly, D., Gardner, R., Morse, B., & Pizer, S. (1994). Ridges for image analysis.
Journal of Mathematical Imaging and Vision, 4(4), 353373.
Eickhoff, S. B., Paus, T. P., Evans, A. C., Jenkinson, M., Smith, S., Saad, Z. S., et al.
(2007). The anatomy toolbox for functional neuroimaging - new developments.
In Thirteenth annual meeting of the organization for human brain mapping.
functional imaging data. NeuroImage, 25(4), 13251335.
Ellis, C. M., Simmons, A., Jones, D. K., Bland, J., Dawson, J. M., & Horsfield, M. A.
(1999). Diffusion tensor MRI assesses corticospinal tract damage in ALS.
Neurology, 53, 10511058.
Ennis, D. B., Kindlman, G., Rodriguez, I., Helm, P. A., & McVeigh, E. R. (2005).
Visualization of tensor fields using superquadric glyphs. Magnetic Resonance in
Medicine, 53, 169176.
Ennis, D. B., & Kindlmann, G. (2006). Orthogonal tensor invariants and the analysis of
diffusion tensor magnetic resonance images. Magnetic Resonance in Medicine,
55(1), 136146.
Eriksson, S. H., Rugg-Gunn, F. J., Symms, M. R., Barker, G. J., & Duncan, J. S. (2001).
Diffusion tensor imaging in patients with epilepsy and malformations of cortical
development. Brain, 124, 617626.
Everitt, B. S., & Bullmore, E. T. (1999). Mixture model mapping of brain activation in
functional magnetic resonance images. Human Brain Mapping, 7, 114.
Gong, G., Jiang, T., Zhu, C., Zang, Y., Wang, F., Xie, S., et al. (2005). Asymmetry
analysis of cingulum based on scale-invariant parameterization by diffusion tensor
imaging. Human Brain Mapping, 24, 9298.
Good, C. D., Johnsrude, I. S., Ashburner, J., Henson, R. N., Friston, K. J., &
Frackowiak, R. S. (2001). A voxel-based morphometric study of ageing in 465
normal adult human brains. NeuroImage, 14(1), 2136.
Goodlett, C., Davis, B., Jean, R., Gilmore, J., & Gerig, G. (2006). Improved correspondence
for DTI population studies via unbiased atlas building. In Medical image computing
and computer-assisted intervention (pp. 260267). Berlin: Springer.
Groves, A. R., Beckmann, C. F., Smith, S. M., & Woolrich, M. W. (2011). Linked
independent component analysis for multimodal data fusion. NeuroImage, 54(3),
21982217.
Groves, A. R., Smith, S. M., Fjell, A. M., Tamnes, C. K., Walhovd, K. B., Douaud, G.,
et al. (2012). Benefits of multi-modal fusion analysis on a large-scale dataset: Lifespan patterns of inter-subject variability in cortical morphometry and white matter
microstructure. NeuroImage, 63(1), 365380.
Guevara, P., Duclap, D., Poupon, C., Marrakchi-Kacem, L., Fillard, P., Le Bihan, D.,
et al. (2012). Automatic fiber bundle segmentation in massive tractography datasets
using a multi-subject bundle atlas. NeuroImage, 61(4), 10831099.
Guevara, P., Poupon, C., Rivire, D., Cointepas, Y., Descoteaux, M., Thirion, B., et al.
(2011). Robust clustering of massive tractography datasets. NeuroImage, 54(3),
19751993.
463
Guimond, A., Meunier, J., & Thirion, J.-P. (2000). Average brain models: A
convergence study. Computer Vision and Image Understanding, 77, 192210.
Hayasaka, S., Luan Phan, K., Liberzon, I., Worsley, K. J., & Nichols, T. E. (2004).
NeuroImage, 22(2), 676687.
Heiervang, E., Behrens, T. E. J., Mackay, C. E., Robson, M. D., & Johansen-Berg, H.
(2006). Between session reproducibility and between subject variability of diffusion
MR and tractography measures. NeuroImage, 33(3), 867877.
Horsfield, M. A., & Jones, D. K. (2002). Application of diffusion weighted and diffusion
tensor MRI to white matter diseases. NMR in Biomedicine, 15, 570577.
Hyvarinen, A., Karhunen, J., & Oja, E. (2001). Independent component analysis. New
Jersey: Wiley.
Jbabdi, S., Behrens, T. E., & Smith, S. M. (2010). Crossing fibres in tract-based spatial
statistics. NeuroImage, 49, 249256.
Jbabdi, S., Sotiropoulos, S. N., Savio, A. M., Grana, M., & Behrens, T. E. (2012).
over fitting problems. Magnetic Resonance in Medicine, 68(6), 18461855.
Jenkinson, M., & Smith, S. M. (2001). A global optimisation method for robust affine
registration of brain images. Medical Image Analysis, 5(2), 143156.
kurtosis imaging: The quantification of non-Gaussian water diffusion by
means of magnetic resonance imaging. Magnetic Resonance in Medicine, 53,
14321440.
Jones, D. K., Catani, M., Pierpaoli, C., Reeves, S. J. C., Shergill, S. S., OSullivan, M.,
et al. (2006). Age effects on diffusion tensor magnetic resonance imaging
tractography measures of frontal cortex connections in schizophrenia. Human Brain
Mapping, 27(3), 230238.
Jones, D. K., Griffin, L. D., Alexander, D. C., Catani, M., Horsfield, M. A., Howard, R.,
et al. (2002). Spatial normalisation and averaging of diffusion tensor MRI data sets.
Jones, D. K., Symms, M. R., Cercignani, M., & Howard, R. J. (2005). The effect of filter
size on VBM analyses of DT-MRI data. NeuroImage, 26, 546554.
Kindlmann, G., Ennis, D. B., Whitaker, R. T., & Westin, C.-F. (2007). Diffusion tensor
analysis with invariant gradients and rotation tangents. IEEE Transactions on
Kindlmann, G. L., San Jose Estepar, R., Smith, S. M., & Westin, C.-F. (2009). Sampling
and visualizing creases with scale-space particles. IEEE Transactions on
Visualization and Computer Graphics, 15(6), 14151424.
Kindlmann, G., Tricoche, X., & Westin, C.-F. (2007). Delineating white matter structure
in diffusion tensor MRI with anisotropy creases. Medical Image Analysis, 11,
492502.
Kubicki, M., Westin, C.-F., Nestor, P. G., Wible, C. G., Frumin, M., Maier, S. E., et al.
(2003). Cingulate fasciculus integrity disruption in schizophrenia: A
magnetic resonance diffusion tensor imaging study. Biological Psychiatry, 54,
11711180.
Lee, J. E., Chung, M. K., Lazar, M., DuBray, M. B., Kim, J., Bigler, E. D., et al. (2009). A
study of diffusion tensor imaging by tissue-specific, smoothing-compensated
voxel-based analysis. NeuroImage, 44(3), 870883.
Li, H., Xue, Z., Guo, L., Liu, T., Hunter, J., & Wong, S. T. C. (2010). A hybrid
approach to automatic clustering of white matter fibers. NeuroImage, 49(2),
12491258.
Li, Y.-O., Yang, F. G., Nguyen, C. T., Cooper, S. R., LaHue, S. C., Venugopal, S., et al.
(2012). Independent component analysis of DTI reveals multivariate microstructural
correlations of white matter in the human brain. Human Brain Mapping, 33(6),
14311451.
Lilliefors, H. (1967). On the KolmogorovSmirnov test for normality with mean and
variance unknown. Journal of the American Statistical Association, 62, 399402.
Lim, K. O., & Helpern, J. A. (2002). Neuropsychiatric applications of DTI A review.
NMR in Biomedicine, 15, 587593.
Lin, F., Yu, C., Jiang, T., Li, K., Li, X., Qin, W., et al. (2006). Quantitative analysis along
the pyramidal tract by length-normalized parameterization based on diffusion tensor
tractography: Application to patients with relapsing neuromyelitis optica.
Metzler-Baddeley, C., OSullivan, M. J., Bells, S., Pasternak, O., & Jones, D. K. (2012).
How and how not to correct for CSF-contamination in diffusion MRI. NeuroImage,
59(2), 13941403.
Miller, K. L., Stagg, C. J., Douaud, G., Jbabdi, S., Smith, S. M., Behrens, T. E., et al.
(2011). Diffusion imaging of whole, post-mortem human brains on a clinical MRI
scanner. NeuroImage, 57(1), 167181.
Mori, S., Wakana, S., van Zijl, P. C. M., & Nagae-Poetscher, L. M. (2005). MRI atlas of
human white matter. Elsevier.
Moseley, M. E. (2002). Diffusion tensor imaging and aging A review. NMR in
464
Neil, J., Miller, P., Mukherjee, P. S., & Huppi, P. S. (2002). Diffusion tensor imaging of
normal and injured developing human brain A technical review. NMR in
neuroimaging: A primer with examples. Human Brain Mapping, 15, 125.
ODonnell, L. J., Westin, C.-F., & Golby, A. J. (2009). Tract-based morphometry for
white matter group analysis. NeuroImage, 45(3), 832844.
Pagani, E., Filippi, M., Rocca, M. A., & Horsfield, M. A. (2005). A method for obtaining
tract-specific diffusion tensor MRI measurements in the presence of disease:
Application to patients with clinically isolated syndromes suggestive of multiple
sclerosis. NeuroImage, 26(1), 258265.
Pajevic, S., & Pierpaoli, C. (1999). Color schemes to represent the orientation of
anisotropic tissues from diffusion tensor data: Application to white matter fiber
tract mapping in the human brain. Magnetic Resonance in Medicine, 42(3),
526540.
Park, H.-J., Kubicki, M., Shenton, M. E., Guimond, A., McCarley, R. W., Maier, S. E.,
et al. (2003). Spatial normalization of diffusion tensor MRI using multiple channels.
Park, H.-J., Westin, C.-F., Kubicki, M., Maier, S. E., Niznikiewicz, M., Baer, A., et al.
(2004). White matter hemisphere asymmetries in healthy subjects and in
schizophrenia: A diffusion tensor MRI study. NeuroImage, 23, 213223.
Pasternak, O., Sochen, N., Gur, Y., Intrator, N., & Assaf, Y. (2009). Free water
elimination and mapping from diffusion MRI. Magnetic Resonance in Medicine,
62(3), 717730.
Pierpaoli, P., & Basser, P. J. (1996). Toward a quantitative assessment of diffusion
anisotropy. Magnetic Resonance in Medicine, 36, 893906.
Rueckert, D., Sonoda, L. I., Hayes, C., Hill, D. L. G., Leach, M. O., & Hawkes, D. J.
(1999). Nonrigid registration using free-form deformations: Application to breast
MR images. IEEE Transactions on Medical Imaging, 18(8), 712721.
Rugg-Gunn, F. J., Eriksson, S. H., Symms, M. R., Barker, G. J., & Duncan, J. S. (2001).
Diffusion tensor imaging of cryptogenic and acquired partial epilepsies. Brain, 124,
627636.
Salimi-Khorshidi, G., Smith, S. M., & Nichols, T. E. (2011). Adjusting the effect of
nonstationarity in cluster-based and TFCE inference. NeuroImage, 54(3), 20062019.
Simon, T. J., Ding, L., Bish, J. P., McDonald-McGinn, D. M., Zackai, E. H., & Gee, J.
(2005). Volumetric, connective, and morphologic changes in the brains of children
with chromosome 22q11.2 deletion syndrome: An integrative study. NeuroImage,
25, 169180.
Smith, S. M., Jenkinson, M., Johansen-Berg, H., Rueckert, D., Nichols, T. E.,
Mackay, C. E., et al. (2006). Tract-based spatial statistics: Voxelwise analysis of
multi-subject diffusion data. NeuroImage, 31, 14871505.
Smith, S. M., Johansen-Berg, H., Jenkinson, M., Rueckert, D., Nichols, T. E.,
Miller, K. L., et al. (2007). Acquisition and voxelwise analysis of multi-subject
diffusion data with tract-based spatial statistics. Nature Protocols, 2(3), 499503.
Smith, S. M., & Nichols, T. E. (2009). Threshold-free cluster enhancement: Addressing

Sommer, M., Koch, M. A., Paulus, W., Weiller, C., & Buchel, C. (2002). Disconnection
of speech-relevant brain areas in persistent developmental stuttering. The Lancet,
360, 380383.
Toga, A. W., Thompson, P. M., Mori, S., Amunts, K., & Zilles, K. (2006). Towards
multimodal atlases of the human brain. Nature Reviews. Neuroscience, 7, 952966.
Tuch, D. S. (2004). Q-ball imaging. Magnetic Resonance in Medicine, 52(6),
13581372.
Tuch, D. S., Salat, D. H., Wisco, J. J., Zaleta, A. K., Hevelone, N. D., & Rosas, H. D.
(2005). Choice reaction time performance correlates with diffusion anisotropy in
white matter pathways supporting visuospatial attention. Proceedings of the
Wakana, S., Caprihan, A., Panzenboeck, M. M., Fallon, J. H., Perry, M., Gollub, R. L.,
et al. (2007). Reproducibility of quantitative tractography methods applied to
cerebral white matter. NeuroImage, 36(3), 630644.
Woolrich, M. W., Behrens, T. E. J., Beckmann, C. F., & Smith, S. M. (2005). Mixture
models with adaptive spatial regularization for segmentation with an application to
FMRI data. IEEE Transactions on Medical Imaging, 24(1), 111.
Worsley, K. J., Evans, A. C., Marrett, S., & Neelin, P. (1992). A three-dimensional
statistical analysis for CBF activation studies in human brain. Journal of Cerebral
Yendiki, A., Panneck, P., Srinivasan, P., Stevens, A., Zollei, L., Augustinack, J., et al.
(2011). Automated probabilistic reconstruction of white-matter pathways in health
and disease using an atlas of the underlying anatomy. Frontiers in
Neuroinformatics, 5, 00023.
Yue, C., Zipunnikov, V., Bazin, P.-L., Pham, D., Reich, D., Crainiceanu, C., et al. (2013)
Parametrization of white matter manifold-like structures using principal surfaces.
ArXiv e-prints, April.
Yushkevich, P. A., Zhang, H., Simon, T. J., & Gee, J. C. (2008). Structure-specific
statistical mapping of white matter tracts. NeuroImage, 41(2), 448461.
Zhang, H., Awate, S. P., Das, S. R., Woo, J. H., Melhem, E. R., Gee, J. C., et al. (2010). A
tract-specific framework for white matter morphometry combining macroscopic and
microscopic tract features. Medical Image Analysis, 14(5), 666673.
hidden Markov random field model and the expectation maximization algorithm.
Zhu, H., Kong, L., Li, R., Styner, M., Gerig, G., Lin, W., et al. (2011). FADTTS:
Functional analysis of diffusion tensor tract statistics. NeuroImage, 56(3),
14121425.
Zhu, H., Styner, M., Tang, N., Liu, Z., Lin, W., & Gilmore, J. H. (2010). FRATS:
Functional regression analysis of DTI tract statistics. IEEE Transactions on Medical
Imaging, 29(4), 10391049.
The General Linear Model

SJ Kiebel, Technische Universitat Dresden, Dresden, Germany
K Mueller, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
Glossary
Contrast Linear combination of parameter estimates.

Covariance Measure of how much two random variables
change together.
Degrees of freedom Number of parameters of within a
statistical model that may vary independently.
Design matrix A matrix of explanatory variables used in
certain statistical models.
F-test Statistical test in which the test statistic has an
F-distribution under the null hypothesis.
General linear model Statistical linear model for the
analysis of multivariate measurements.
Introduction
Classical analyses of functional brain signals (EEG/MEG/fMRI/
PET) are based on the general linear model. Model specification,
as an equation, or as a so-called design matrix, is a crucial step
in the analysis of imaging data and precedes parameter estimation. Finally, inferences are made using voxel-wise statistical
tests. This article is based on more extensive presentations in
Kiebel and Holmes (2003, 2007). Newcomers to statistical
methods are directed toward Moulds excellent text Introductory Medical Statistics (Mould, 1998), while the more
mathematically experienced will find Chatfields Statistics for
Technology (Chatfield, 1983) useful. Draper and Smith
(1998) gave a good exposition of matrix methods for the
general linear model and went on to describe regression analysis in general. A rather advanced, but very useful, text on linear
models is Christensen (1996).
Suppose we are to conduct an experiment during which we
will measure a response variable (such as BOLD signal at a
particular voxel) Yj, where j 1, . . ., J indexes the observation.
Yj is a random variable, conventionally denoted by a capital
letter. Suppose also that for each observation, we have a set of L
(L < J) explanatory variables (each measured without error)
denoted by xjl, where l 1, . . ., L indexes the explanatory variables. The explanatory variables may be continuous (or sometimes discrete) covariates, functions of covariates, or dummy
variables indicating the levels of an experimental factor.
A general linear model explains the response variable Yj in
terms of a linear combination of the explanatory variables plus
an error term:
Yj xj1 b1 xjl bl xjL bL ej
[1]
Here, the bl are (unknown) parameters, associated with

each of the L explanatory variables xjl. The errors ej are independent and identically distributed normal random variables
with zero mean and variance s2, written ej N 0, s2 .
Maximum likelihood Method of estimating the parameters

of a statistical model.
Null hypothesis General position in inferential statistics
that there is no relationship between measurements
(response variables) and their underlying cause (explanatory
variables).
Pseudoinverse Generalization of the inverse matrix for a
wider class of noninvertible matrices.
Rank of matrix Number of linearly independent column
vectors.
t-test Statistical test in which the statistic follows a Students
t-distribution under the null hypothesis.
A simple example is linear regression, where only one continuous explanatory variable xj is measured (without error) for
each observation j 1, . . ., J. The model is usually written as
Yj m xj b ej
where the unknown parameters are m, a constant term in the
model, the regression slope b, and ej N 0, s2 . This can be
rewritten as a general linear model by the use of a dummy
variable taking the value xj1 1 for all j:
Yj xj1 m xj2 b2 ej
which is of the form of eqn [1] on replacing b1 with m.
Similarly, the two-sample t-test is a special case of a general
linear model: suppose Yj1 and Yj2 are two independent groups
of random

variables. The two-sample t-test assumes
Yqj N mq , s2 , for q 1, 2, and assesses the null hypothesis
: m1 m2. The index j indexes the data points in both groups.
The standard statistical way of writing the model is
Yqj mq eqj
[2]
The q subscript on the mq indicates that there are two levels

to the group effect, m1 and m2. Here, eqj N 0, s2 . This can be
rewritten using two dummy variables xqj1 and xqj2 as
Yqj xqj1 m1 xqj2 m2 eqj
which is of the form of eqn [1] after reindexing for qj. Here, the
dummy variables indicate group membership, where xqj1 indicates whether observation Yqj is from the first group, in which
case it has the value 1 when q 1 and 0 when q 2. Similarly,
xqj2 has the value 0 when q 1 and 1 when q 2.
Matrix Formulation
Here, we use the general linear model in its matrix formulation, present its least squares parameter estimation, and
http://dx.doi.org/10.1016/B978-0-12-397025-1.00317-1
465
466
INTRODUCTION TO METHODS AND MODELING | The General Linear Model
describe how one can make inferences based on a contrast of

the parameters. This theoretical treatment of the model is
useful to derive a set of equations that can be used for the
analysis of any data set that can be formulated in terms of the
general linear model (eqn [1]).
The general linear model can be expressed using matrix
notation. Consider writing out eqn [1] in full, for each observation Yj, giving a set of simultaneous equations:
Y1 x11 b1 x1l bl x1L bL e1
Yj xj1 b1 xjl bl xjL bL ej
YJ xJ1 b1 xJl bl xJL bL eJ

This has an equivalent matrix form
0
1
x11 x . . . x
0 1
0 1 0 1
1L
1l
B
C b1
Y1
e1
.
B
C
..
B C B ..
CB C B C
. CB b C B e C
B C B
B Yj C B
CB l C B j C
@ A B xj1 xjl xjL C@ A @ A
B
C
.
.
@ ..
A b
eJ
YJ
..
L
xJ1 xJl xJL
which can be written in matrix notation as
Y Xb e
where Y is the column vector of observations, e the J 1 column
vector of error terms, and b the L 1 column vector of parameters; b [b1, . . ., bl, . . ., bL]T. The J L matrix X, with jlth element
xjl, is the so-called design matrix. It has one row per observation
and one column (explanatory variable) per model parameter.
The important point about the design matrix is that it is a near
complete description of our model with the remainder of the
model comprising an error term. The design matrix is where the
experimental knowledge about the expected signal is expressed.
Parameter Estimation
Once an experiment has been completed, we have observations of the random variables Yj, which we denote by yj. Usually, the simultaneous equations implied by the general linear
model (eqn [1] with e 0) cannot be solved, because the
number of parameters L is typically chosen to be less than the
number of observations J. Therefore, some method of estimating parameters that best fit the data is required. This is
achieved by the method of ordinary least squares.
Denote a set of parameter estimates by b0 [b10 , . . ., bL0 ]T.
These parameters lead to fitted values y0 [y10 , . . ., yJ0 ]T Xb0 ,
giving residual errors e [e1, . . ., eJ]T y y0 y Xb0 . The residP
ual sum of squares S Jj1 e2 eT e is the sum of the square
differences between the actual and fitted values and thus measures the fit of the model with these parameter estimates. The
least squares estimates are the parameter estimates that minimize the residual sum of squares. In full,
S
J
X
yj xj1 b1 xjL bL
2
j1
This is minimized when the partial derivatives of S with

respect to each parameter become 0:
J
2
X

0
0
@S
xjl yj xj1 b1 xjL bL 0
0 2
@bl
j1
This equation is the lth row of XTy (XTX)b0 . Thus, the least
^ satisfy the normal equations:
squares estimates, denoted by b,

XT y X T X b^
[3]
For the general linear model, the least squares estimates are
the maximum likelihood estimates and are the best linear unbiased
estimates. That is, of all linear parameter estimates consisting of
linear combinations of the observed data whose expectation is
the true value of the parameters, the least squares estimates
have the minimum variance. If (XTX) is invertible, in which it is
if and only if the design matrix X is of full (column) rank, then
the least squares estimates are

1
b^ XT X XT y
If X has linearly dependent columns, it is rank-deficient,
and (XTX) is singular and has no inverse. In this case, the
model is overparameterized: there are infinitely many parameter sets describing the same model. Correspondingly, there are
infinitely many least squares estimates b^ satisfying the normal
equations (eqn [3]). In this case, a pseudoinverse method can
be used for parameter estimation. Let (XTX) denote the
pseudoinverse of (XTX). Then, we can use (XTX) in place of
(XTX)1. A set of least squares estimates are given by
b^ XT X X T y where often the MoorePenrose pseudoinverse

is used.
Statistical Inference
After parameter estimation, t- and F-statistics can be derived,
which are used to test for a linear combination of parameter
estimates. It can be shown that the parameter estimates
are normally
distributed:
if X is full rank, then

1
. From this, it follows that for a column
b^ N b, s2 X T X
vector c containing L weights, then

1
cT b^ N cT b, s2 cT X T X c
For an independent and identical error, the residual variance s^2 is estimated by the residual sum of squares divided by
the appropriate degrees of freedom:
s^2
X 2Jp
eT e
s2
Jp
Jp
where p rank(X). Furthermore, if b^ and s^2 are assumed to be

independent (Fischers law), prespecified hypotheses in
terms of linear compounds of the model parameters can be
assessed using
cT b^ cT b
q tJp
s^2 cT XT X1 c
where tJp is a Students t-distribution with J p degrees of
freedom. For example, the hypothesis : cTb d can be
assessed by computing
467
cT b d
T q
s^2 cT XT X1 c
true, then S(b1|b2) has a noncentral chi-square distribution,

still independent of S(b). Therefore, the following F-statistic
expresses evidence against :
A p-value can be computed by comparing T with a

t-distribution having J p degrees of freedom. Often, null
hypotheses are of the form cTb 0.
As an example, we will consider the two-sample t-test. The
model (eqn [2]) leads to a design matrix X with two columns of
dummy variables indicating group membership and parameter
vector b [m1, m2]T. Thus, the null hypothesis : m1 m2 is
equivalent to : cTb 0 with c [1, 1]T.
The first column of the design matrix contains J1 1s
and J2 0s, indicating the measurements from group one,
while the second column contains J1 0s and J2 1s for group

J 0
1=J1 0
1
two. Thus, XT X 1
, X T X
, and
0 J2
0 1=J2
Sb2 Sb
p p2
F
Fpp2 , Jp
Sb
Jp
1
cT XT X c J11 J12 , giving the t-statistic

m^1 m^2
T s

tJ1 J2 2
1
2 1
s^
J1 J2
which is the standard formula for the two-sample t-statistic,
with a Students t-distribution of J1 J2 2 degrees of freedom
under the null hypothesis.
If the model is overparameterized (i.e., X is rank-deficient),
then there are infinitely many parameter sets describing
the same model. Constraints or the use of a pseudoinverse
selects a unique set of parameters. Therefore, when examining
linear compounds cTb of the parameters, it is imperative to
consider only compounds that are invariant over the space
of possible parameters. Such linear compounds are called
contrasts.
F-statistics
The extra sum-of-squares principle provides a method for
assessing general linear hypotheses, where inference is based
on an F-statistic. Here, we will describe the classical F-test based
on the assumption of an independent identically distributed
error. We first present the classical F-test as found in introductory statistical texts. After that, we will derive an equivalent but
more useful implementation of the F-test for typical models in
neuroimaging.
Suppose we have a model with parameter vector b that can
be partitioned into b [bT1, bT2]T, and suppose we wish to test
: b1 0. The corresponding partitioning of the design matrix
is X [X1 X2], and the full model is
2 3
b1
Y X1 X2 4 5 E
b2
which when is true reduces to the reduced model Y X2b2 E.
Denote the residual sum of squares for the full and reduced
models by S(b) and S(b2), respectively. The extra sum of squares
due to b1 after b2 is then defined as S(b1|b2) S(b2) S(b).
Under , S(b1|b2) s2w2p independent of S(b), where the
degrees of freedom are p rank(X) rank(X2). If is not
[4]
where p rank(X) and p2 rank(X2). The larger F gets, the

more unlikely it is that F was sampled under the null hypothesis . Significance can then be assessed by comparing this
statistic with the appropriate F-distribution (Draper & Smith,
1998).
This formulation of the F-statistic has two disadvantages.
The first is that both the full model and the reduced model
have to be fitted to the data. In practice, this would be implemented by a two-pass procedure on a, typically, large data set
(e.g., fMRI) with potentially ten thousands of voxels. The
second disadvantage is that a partitioning of the design matrix
into two blocks of regressors is not the only way one can
partition the design matrix space. In general, one can partition
X into two sets of linear combinations of the regressors. For
example, one might be interested in the difference between two
effects. If each of these two effects is modeled by one regressor,
a simple partitioning is not possible. Rather, one has to reparameterize the model such that the differential effect is
explicitly modeled by a single regressor.
Consequently, the F-test in eqn [4] can be reformulated by
using contrast matrices: A contrast matrix is a generalization of
a contrast vector. Each column of a contrast matrix consists of
one contrast vector. Importantly, the contrast matrix controls
the partitioning of the design matrix X. A user-specified contrast matrix c is used to determine a subspace of the design
matrix, that is, Xc Xc. The orthogonal contrast to c is given by
c0 Ip cc. Then, let X0 Xc0 be the design matrix of the
reduced model. We wish to compute what effects Xc explain,
after first fitting the reduced model X0. Although c and c0 are
orthogonal to each other, Xc and X0 are possibly not, because
the relevant regressors in the design matrix X can be correlated.
In this correlated case, the subsequent fitting procedure attributes their shared variance to X0. The explicit fitting procedure
can be avoided by constructing a projection matrix from the
data to the subspace of Xc, which is orthogonal to X0. We
denote this subspace by Xa.
The projection matrix M due to Xa can be derived from the
residual forming matrix of the reduced model X0 that is given
by R0 IJ X0X
0 . The projection matrix is then M R0 R,
where R is the residual forming matrix of the full model, that
is, R IJ XX. The F-statistic can then be written as
F
MY T MY J p Y T MY J p
T
Fp1 , Jp
Y RY p1
RY T RY p1
where p1 rank(Xa). Since M projects onto a subspace within

X, we can also write
F
b^T X T MX b^ J p
Fp1 , Jp
Y T RY
p1
This equation means that after a single initial parameter

estimation step, one can conveniently compute an F-statistic
468
for any user-specified contrast without a reparameterization as

suggested by eqn [4]. In addition, F-statistics are based on the
full model so that YTRY needs only to be estimated once and
can be subsequently interrogated with various contrasts testing
different hypotheses.
not be tenable, for example, when comparing normal subjects

with patients, and an unequal variance model should be used
(see Glaser & Friston, 2007).
Paired t-Test
Examples
One-Sample t-Test
In this section, we will discuss basic statistical tests as special
cases of the general linear model. The simplest model is the
one-sample t-test used to test the null hypothesis that the mean
of J observations equals zero. In that case, the design matrix
consists of just a constant regressor. The model is
Y x1 b1 e
where x1 is a constant vector of ones and e N 0,s2 IJ . The
null hypothesis is : b1 0 and the alternative hypothesis is
: b1 > 0. Then, the t-value is computed as
b^1
T q
tJ1
s^2 =J
where s^2 yT Ry=J 1, where R is the residual forming matrix
(see above) and yTRy are the sum of squares
J of theresiduals.
X
2
Thiscould also be expressed as yT Ry
yj y^j , where
j1
y^j x1 b^1 b^1 .
j
The model underlying the paired t-test is an extension of the

two-sample t-test model. It is assumed that observations come
in pairs, that is, one observation of each pair is in the first
group and the other is in the second group. The extension is
that the means over pairs are not assumed to be equal, that
is, the mean of each pair is modeled separately. For instance,
let the number of pairs be Npairs 5, that is, the number of
observations is J 10. The design matrix consists of seven
regressors. The first two model the deviation from the pairwise
mean within group and the last five model the pair-specific
means. The model has degrees of freedom one less than
the number of regressors. Let the contrast vector be
c [1, 1, 0, 0, 0, 0, 0]T, that is, the alternative hypothesis is
: b1 < b2 . This leads to
b^2 b^1
T s

tJ2J 1
1 1
s^2 =
J1 J2
The difference to the unpaired two-sample t-test lies in the
degrees of freedom J J/2 1. The paired t-test can be a more
appropriate model for a given data set, but more effects are
modeled, that is, there are less error degrees of freedom.
Two-Sample t-Test
As another example, we use the two-sample t-test again (see
above) but in an overparameterized version. The resulting
design matrix consists of three columns: the first two encode
as above the group membership of each observation and the
third models a common constant across all observations of
both groups. Let the number of observations in the first and
second groups be J1 and J2, where J J1 J2. The three regressors consist of ones and zeros, where the first regressor consists
of J1 ones, followed by J2 zeros. The second regressor consists
of J1 zeros, followed by J2 ones. The third regressor contains
ones only. Let the contrast vector be c [1, 1, 0]T, that is, the
alternative hypothesis is : b1 < b2 . Then,
0
1
J1 0 J1
T
@
X X 0 J2 J2 A
J1 J2 J
This model is overparameterized so we use the pseudoinverse (XTX) to compute the t-statistic. We sandwich
(XTX) with the contrast and get cT X T X c J11 J12 . The

t-statistic is then given by
b^2 b^1
T s

tJ2
1 1
2
s =
J1 J2
and s^2 yT Ry=J 2. We implicitly made the assumption that
we have equal variance in both groups. This assumption may
Analysis of Covariance
A one-way analysis of covariance (ANCOVA) allows one to
model group effects, that is, the mean of each of Q groups.
This model includes the one-sample and two-sample t-tests,
that is, the cases when 1 Q 2. In our example, let the number of groups be Q 3, where there are five scans within each
group, that is, Jq 5 for q 1, . . ., Q. There are a range of different contrasts available. For instance, we could test the null
hypothesis that the group means are all equal using the Fcontrast as described earlier. Here, we wish to test the null
hypothesis, whether the mean of the first two groups is equal
to the mean of the third group, that is, : (b1 b2)/2 b3 0,
and our alternative hypothesis is : b1 b2 =2 <
Tb3 . This can

be tested using a t-statistic, where c 12 , 12 , 1, 0 . The resulting t-statistic and its distribution is

b^1 b^2 =2 b^3
T s

tJ3
1 1 1
2
s^ =

J1 J2 J3

Analysis of Variance (ANOVA); Contrasts and Inferences; Convolution
Models for FMRI; Design Efficiency; False Discovery Rate Control;
Topological Inference.
References
Chatfield, C. (1983). Statistics for technology. London: Chapman & Hall.
Christensen, R. (1996). Plane answers to complex questions: The theory of linear
models. Berlin: Springer-Verlag.
Draper, N., & Smith, H. (1998). Applied regression analysis (3rd ed.). New York: Wiley.
Glaser, D., & Friston, K. (2007). Covariance components. In K. Friston, J. Ashburner,
S. Kiebel, T. Nichols, & W. D. Penny (Eds.), Statistical parametric mapping: The
analysis of functional brain images (1st ed.). London: Elsevier.
469
Kiebel, S., & Holmes, A. (2003). The general linear model. In R. Frackowiak,
K. Friston, C. Frith, R. Dolan, C. Price, S. Zeki, J. Ashburner, & W. Penny (Eds.),
Human brain function (2nd ed.). Amsterdam: Elsevier.
Kiebel, S., & Holmes, A. (2007). The general linear model. In K. Friston,
J. Ashburner, S. Kiebel, T. Nichols, & W. D. Penny (Eds.), Statistical
parametric mapping: The analysis of functional brain images (1st ed.).
London: Elsevier.
Mould, R. (1998). Introductory medical statistics (3rd ed.). London: Institute of Physics
Publishing.
Contrasts and Inferences

JA Mumford, University of Texas, Austin, TX, USA
J-B Poline, University of California, Berkeley, CA, USA
Glossary
Autoregressive model A model that assumes past

observations predict current observations based on a linear
relationship.
Collinear One vector is collinear with another set of vectors
if the single vector is equal to some linear combination of
the other vectors.
Introduction
Understanding how to construct and test a contrast of parameters in a linear model requires understanding what they represent in the model and how they are estimated. This article
presents a few examples of models and contrasts of interest for
these models. It covers issues such as near collinearity and
orthogonalization of regressors. We also discuss how to test
combinations of estimated parameters to form either t- or
F-statistics and how these statistics are related.
Linear combination Combining multiple variables by

premultiplying by a constant and summing. For example, a
linear combination of x and y would be ax by for some
constants a and b.
Orthogonalization Orthogonalization of vector A to vector
B is the projection of A into the space orthogonal, or
perpendicular, to B.
during fixation. Likewise, for t during the squeeze stimulus,

X1(t) 1 and Y(t) b0 b1 e(t); hence, b1 represents change
in BOLD during the task compared to baseline.
Model 1 will not fit the data well if the BOLD response
varies according to force. It may be fair to assume a linear
relationship between BOLD activation and force. This is modeled using a parametrically modulated regressor, created by
convolving the HRF with a boxcar whose heights reflect the
modulation value (Figure 1, model 2). The unmodulated
regressor must also be included to model the overall mean
task activation. The model is
Y t b0 X1 t b1 X2 t b2 Et
Setting Up the Design Matrix

Stage 1 Analysis: Modeling the BOLD Time Series
With multiple subjects, data are analyzed in stages (Mumford &
Nichols, 2006; Worsley et al., 2002). Stage 1 analyzes each
subjects data, independently, and stage 2 combines activation
estimates over subjects to obtain group results. The design
matrix at any stage must describe the data as thoroughly as
possible, since undescribed signal increases the error variance.
Consider an experiment where a subject is cued to squeeze a
rubber ball at four force levels, alternating with fixation stimuli.
We will illustrate three stage 1 models with varying flexibility. At
the minimum, the model needs a regressor for the stimulus and
a constant regressor, following model 1 (Figure 1).
The stimulus regressor is created by convolving a boxcar
regressor (dashed line), where boxes of height equal to 1
indicate the stimuli, with a canonical hemodynamic response
function (HRF). The constant regressor models the baseline
activation, in this case the fixation. A linear model assumes
that, given some explanatory variables (X1, X2, . . .), over many
experiments, the average data Y will be a linear combination of
the Xi (b1X1 b2X2 . . .). The interpretation of the model
parameters can be understood through the models equation
at time t,
Y t b0 X1 t b1 Et
where Y(t) is the blood oxygenation level dependent (BOLD)
time series, X1(t) is the convolved regressor, and E(t) is the error
term. If t is a point during fixation, ignoring convolution,
X1(t) 0 and Y(t) b0 e(t); thus, b0 is the BOLD activation
where X1(t) and X2(t) are the unmodulated and modulated

regressors, following Figure 1. The interpretation of b1
depends on the parameterization of the modulation. Consider
a time point, t s, during the task where the modulation has
magnitude ms. Ignoring convolution, X1(s) 1 and X2(s) ms
so Y(s) b0 b1 msb2. Therefore, b1 is the difference between
task activation and baseline when ms 0. If ms 0 is out of the
range of possible values, this may not be interpretable. Instead,
if the force values are mean-centered ( 1.5, 0.5, 0.5, and
1.5), b2 now represents only the variation of the force around
the average modulation and b1 is the magnitude for the average
BOLD response. Instead of mean centering the modulation
values, another approach is to orthogonalize the modulated
regressor with respect to the constant duration regressor, which
is discussed later. It is also possible to model higher-order
polynomial relationships, such as quadratic or cubic effects
by adding the modulation values after squaring or cubing.
Without a hypothesis about the functional relationship
between BOLD activation and force, the most flexible model
includes a separate regressor for each force level and can
accommodate any variation between force levels. Differences
between levels are tested using linear contrasts, as described in
the next section. The model is
Y t b0 X 1 t b1 X 2 t b2 X3 t b3 X 4 t b4 Et [1]
where Xi(t) follow model 3 of Figure 1. b0 is the fixation
activation and b1 is force 1 versus fixation, b2 is force 2 versus
fixation, and so on.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00318-3
471
472
INTRODUCTION TO METHODS AND MODELING | Contrasts and Inferences
Model 2
Model 3
0
40
40
40
80
120
Time (s)
Time (s)
Time (s)
Model 1
0
80
120
160
120
160
X1
80
160
X1
X2
X1
X2
X3
X4
Figure 1 Three different model examples for force data example. In each case, the y-axis is the time in seconds, where the beginning of the run starts
at the top of the axis. The first regressor in each case is the constant regressor, which corresponds to the b0 parameter. Model 1 models all trials
under the assumption that the BOLD response to all forces will be equal. Model 2 assumes a linear relationship between the BOLD response and
force through the modulated regressor, X2. Model 3 models each force using a separate regressor, where forces 14 are modeled in X1X4.
Known noise sources should additionally be modeled. fMRI

data have low-frequency artifacts due to subject motion and
scanner noise (Zarahn, Aguirre, & DEsposito, 1997). A portion
of this noise is removed using high-pass filters. One approach is
to add a series of cosine functions of varying frequencies to
model low-frequency drift. Task signal will be lost if it falls
into the range of low-frequency noise, so typically a task period
equal to or shorter than 30 s (15 s on/15 s off) and specifying
the filter cutoff to avoid task frequencies are recommended.
Prior to modeling the BOLD time series, images are aligned
over time to a template, using a six-degrees-of-freedom spatial
transformation. This results in six time series representing the
registrations translation and rotation parameters in the 3 spatial dimensions. These time series, and their rates of change,
often describe noise in the data and it is common to include
motion parameters and their derivatives to remove nuisance
signal from the data.
Stage 2 Analysis: The Group Model

Once the subject-specific contrast estimates have been created,
the group model combines these estimates to obtain group
inferences. For example, assume a study using a stop-signal
task-analyzed successful versus unsuccessful stops in stage 1 analysis for subjects in one of three groups: healthy control, bipolar,
or attention deficit hyperactivity disorder (ADHD). Stage 2 analysis goal is to run the 1-way analysis of variance (ANOVA) to
analyze the group effect. There are multiple ways of parameterizing this model, including the two models shown in Figure 2.
The left panel illustrates what is commonly called the cell means
model, which models the mean for each group; X1 models the
mean of the controls; while X2 and X3 model the bipolar and
ADHD means. Each of b1, b2, b3 is interpreted as the corresponding group mean. The second model in Figure 2 is parameterized
differently, where the column of 1s represents the unmodeled
baseline group, the healthy controls, while b2 and b3 model
differences between bipolar versus controls and ADHD versus
controls.
Parameter and Contrast Estimation

Estimating the Model Parameters
The model can be expressed in matrix notation as Y Xb e,
where Y is a vector containing the T time points of the data for a
voxel, b is a vector containing the p parameters of the model, X
is the T p design matrix, and e is the noise vector of length T
that follows a Gaussian distribution with a mean of 0 and a
T T covariance matrix, s2S. The correlation structure, S, is
typically assumed to follow an autoregressive model with 1
parameter with additive white noise (Bullmore et al., 1996).
The temporal autocorrelation is modeled through the use of
prewhitening, which we will not discuss here, but see
Woolrich, Ripley, Brady, and Smith (2001) for further details.
Assuming S is the identity matrix, the estimate for b can be
obtained using matrix algebra:
Y Xb
X T Y X T Xb
T 1 T
^
X X X Yb
where XT represents the transpose of X. The estimate of e is
given by
ê Y Y^
^2 êT ê=T p.
and the estimated noise variance is s
T 1
The matrix inverse (X X) only exists when X is full rank.
Rank deficiency means one column can be recreated using linear
combinations of other columns in the matrix. The most obvious
case occurs when two regressors are identical, say,
Y b0 b1X1 b2X2 e and X1 X2. There are infinite solutions
^ 5, b
^ 10, and b
^ 30 yield the
to this problem since if b
0
1
2
^ 5, b
^ 5, and b
^ 35 will be equally
^ then b
best-fitting Y,
0
1
2
good estimates, as 5 10X1 30X2 5 40X1 5 5X1 35X2.
Since a unique solution cannot be obtained, the model is not
estimable; however, some combination of the parameters may
still be estimable. For example, the sum, or contrast, of the
473
Healthy controls
Bipolar
ADHD
X1
X2
X3
Hypothesis
X2
X3
[ 1
[ 1
[ 0
0
0
0
0 ]
1 ]
1 ]
X1
Contrasts
H0: HC 0 HA: HC > 0 [ 1

H0: ADHD 0 HA: ADHD > 0 [ 0
H0: ADHD HC 0 HA: ADHD HC< 0 [ 1
0
0
0
0 ]
1 ]
1 ]
H0: HC =0 AND Bipolar = 0 AND ADHD = 0

HA: HC 0 OR Bipolar 0 OR ADHD 0
1
0
0
0
1
0
0
0
1
1
1
1
0
1
0
0
0
1
H0: HC = Bipolar AND HC = ADHD AND Bipolar = ADHD

HA: HC Bipolar OR HC ADHD OR Bipolar ADHD
1
0
0
1
1
1
0
0
0
1
1
1
Figure 2 Two parameterizations of a 1-way ANOVA with three levels. The top, left panel is the cell means model approach and models a separate mean
for each group. The top, right panel is an equivalent parameterization that models the controls as the baseline. In the succeeding text, the design
matrices three t-tests and two F-tests are illustrated.
effects of b1 and b2 is estimable as will be described in the next

section.
t-Tests
A contrast is most often defined in neuroimaging as a linear
combination of the parameters of the model, quantifying the
effect of interest. As we do not know the true parameters,
contrasts are estimated using the estimates of the parameters,
^ . Since contrasts are used to test hypotheses about linear
the b
i
combinations of the bis, they are created by premultiplying b
by a row vector, lT. This vector, the contrast weights, is also
often called a contrast, by extension. The contrast can also be
thought as a model restriction, which would be expressed as a
linear combination of the columns of the design matrix X.
Recall model 1 in Figure 1, modeling the intercept and the
squeeze task in Y b0 X1b1 E. Since b1 indicates whether the
task activation is greater than baseline, the task effect would be
tested using H0 : b1 0 versus HA : b1 > 0. Rejecting the null
hypothesis concludes that the activation during the task is
greater than baseline. The contrast for this test would be
lT [01], since lTb 0 b0 1 b1 b1.
Model 3 in Figure 1 models each level of force according to
eqn [1], where b1b4 represent the activation of forces 14
versus baseline, respectively. The test of force 1 versus baseline
would use lT [0 1 0 0 0]. To test if the activation for force 4 is
larger than force 1, lT [0 1 0 0 1] would be used. The negative of this contrast, lT [0 1 0 0 1], tests if force 1 has larger
activation than force 4.
For the right-hand side model in Figure 2, constructing the
contrast to test H0 : ADHD 0 versus HA : ADHD > 0 will not be
intuitive, but can be understood by constructing the average of
the model-based values of Y. The predicted value of Y for each of
the ADHD entries (Y(9) to Y(12)) is b1 b3; hence, the average
would be the same and the contrast of interest is lT [1 0 1]. For
models that are not full rank, this procedure gives us a way of
finding the estimable contrasts we need to test the groups means
or differences between group means. Although the strictest

requirement is that the design matrix must be full rank, in
some cases, rank-deficient, or rank-degenerated, models can be
used given the contrast of interest is estimable. For example,
in
the
rank-deficient
model
described
earlier,
Y b0 b1X1 b2X2 e, where X1 X2, the contrast lT [01 1]
is estimable, since there is a unique solution for b1 b2. Generally, if a contrast is in the form of a combination of the lines of
X : l Xtc for some vector c, the contrast is estimable. Parameters
in these degenerated models are estimated using the Moore
Penrose pseudoinverse X (Moore, 1920) in place of (XTX)1XT
and p is set to the rank of X, or the maximum number of linearly
independent columns in the matrix.
These vector contrasts are known as t-contrasts, since the
corresponding test statistic follows the t-distribution. The
statistics is given by the contrast estimate divided by its standard deviation

^ SD
^
^ lT b
t df lT b=
where

1
^ s
^ lT b
^ 2 XT X
SD
The degrees of freedom of the statistics are df T p.
F-Tests
Using the group 1-way ANOVA with three levels (Figure 2), the
hypothesis may be whether any of the group means differ from
0, corresponding to
H0 : HC 0 and Bipolar 0 and ADHD 0
HA : HC 6 0 or Bipolar 6 0 or ADHD 6 0
There are two important aspects of the F-test. Firstly, rejecting the F-test concludes that at least one of the alternative
474
possibilities must be true. Additionally, the F-test is a two-sided

test, so whether the effect is positive or negative is unknown
and further testing is required.
The F-test uses a contrast matrix and the bottom of Figure 2
illustrates the contrast matrices for both models. The test statistic for the F-test is given by

T h
1 i1 T
^
^ =r s
^2
f df 1, df 2 DT b
DT X T X D
D b
[2]

T h
1 i1 T
^
^ MSEX0 MSEX
DT b
DT X T X D
D b
[3]
leading to the same F-statistics as in the preceding text. For a

specific contrast, D, one can find the corresponding X0 (e.g.,
taking X0 XtD and reciprocally, such that the two formulations of the F-test are exactly equivalent).
Although, for df1 1, the significance of the F-test implies
that the one-sided t-tests will be significant, with p-values half
as large, the connection between an F-test and t-tests is not
always this clear. The significance of an F-test does not always
imply one of the related t-tests will be significant. Likewise, the
significance of an individual t-test does not imply the significance of the F-test. To understand this concept, consider the
1-way ANOVA (left panel, Figure 2), but the null of whether
either of the first two means is 0, H0 : b1 b2 0. From eqn [2],
the corresponding F-statistics are
f df 1, df 2

0.1
0.0
-0.1
-0.2
-0.3
-0.3
-0.2
-0.1
0.0
b1
0.1
0.2
0.3
Figure 3 Demonstration of hypothesis bounds for F-test of two

parameters versus 0 (circle) and corresponding 1-sided t-test hypothesis
bounds. In this case, the variances for the two estimated parameter
are equal and the regressors are uncorrelated. If the variance differs, the
F-test boundary will be an ellipse, and if they are correlated, the ellipse
will be rotated. The colored points illustrate the different test outcomes:
None of the tests are significant (green), F- and t-tests are both
significant (red), F-test and one t-test are significant (orange), F-test is
insignificant while one t-test is significant (blue), and F-test is significant
while neither t-test is significant (magenta).
1.
2.
3.
4.
5.
No test is significant (green).

The F-test and both t-tests are significant (red).
The F-test is significant and one t-test is significant (orange).
The F-test is insignificant, but one t-test is significant (blue).
The F-test is significant, but neither t-test is significant
(magenta).
One last possibility, not illustrated in Figure 3, occurs when X1

and X2 are correlated and have differing variabilities, in which
case the significance boundary is a rotated ellipse, allowing the
F-test to be insignificant while both t-tests are significant.
From the F-statistics in eqn [4], it can be seen that the
numerator is a weighted sum of the squared values of the bis.
When this weighted sum is high compared to the noise variance, s2, the F-value is high. It is possible for the F-test to be
significant because either one of the contrast components is
large or the cumulative effects of several components are large,
in which case the F-test may be significant while none of the
t-tests are.

X1 T X1 b1 2 X2 T X 2 b2 2 2 X1 T X2 b1 b2 =2s2
[4]
Since X 1 X 2 0 and X1 X1 X2 X2 4, this simplifies to

the equation for a circle, as shown in Figure 3 (assuming
^ and b
^ that fall outside of
^2 1). Any combination of b
s
1
2
the circle would yield a significant F-statistics. The solid horizontal and vertical lines are the significance boundaries for the
1-sided t-tests given by t Xi T Xi bi =s and together illustrate
five of the six possibilities for the results:
T
0.2
b2
where r is the number of rows, or the rank, of the contrast

^2 is the error variance
matrix, D; X is the design matrix; and s
estimate. The degrees of freedom are df1 r and df2 N p,
where N is the length of Y, and the test statistic follows the F
distribution, fdf1,df2 Fdf1,df2. The simplest F-test contrast has a
single row and is equivalent to a 2-sided t-test.
The test of the main group effect, following the model in
the left panel of Figure 2, is H0 : b1 b2 b3, and the alternative is that at least one pair of betas differ from each other.
The contrast matrix tests each row against 0, and to formulate
the contrast matrix, it is helpful to rewrite the hypothesis so
the equalities are set to 0. This can be done by subtracting b3
from the system of equations giving H0 : b1 b3 b2 b3 0,
leading to the contrast matrix shown in the bottom of Figure 2. There are multiple equivalent contrasts that can be
used, since any of the bis can be subtracted and multiplication of D by a constant will not change the resulting test
statistic.
Another view of the F-test is using nested models, the full
model X and a reduced model X0. What is tested is what is in X
and not in X0. The F-test looks at the mean error sum of squares
assuming X0 is the right model (H0) versus assuming that X is
the right model (HA). It can be shown that
0.3
Other Considerations
Near Collinearity
Each parameter, or contrast of parameters, from the model is
adjusted for all other effects in the model. Hence, if effect 1 is
very correlated to effect 2, what is tested is only the aspect of
effect 1 not present in effect 2. This can be seen by looking at
the more traditional way of expressing the numerator of the

F-test as the difference between the residual sum of square of
the reduced model and the full model (eqn [3]). When two
effects are highly correlated, a near collinearity can occur, and
although the model is estimable, it results in highly variable,
unstable estimates. Running efficiency calculations during the
study planning phase can decrease collinearity through stimulus order randomization and jittering or lengthening the duration of baseline between trials (Birn, Cox, & Bandettini, 2002;
Liu, 2004).
Near collinearity among regressors for which no inferences
will be carried out, for example, motion parameters, can be
ignored. Although if regressors of interest are affected, the
model must be reduced, removing regressors until near collinearity is resolved. The interpretation is that the results can be
due to the modeled or the removed, correlated, effect(s).
The variance inflation factor (VIF) can be used to assess the
degree of near collinearity in the model. The VIF for a regressor
is associated with the overall model fit, or R2, from the model
of that regressor as a function of all other regressors in the
model. One interpretation of R2 is the correlation between the
data and the projection of the data into the space spanned by
the contrast of interest, which can have 1 or multiple dimensions. The VIF is 1/(1 R2) and will be 1 in the best case
scenario (R2 0) and will tend toward infinity as R2
approaches 1. A typical rule of thumb is a VIF larger than 5
indicates problematic near collinearity. If the effect of interest
is a contrast of the parameters or several contrasts (F-test), then
the VIF should be computed with the corresponding R2 in
which the regressor of interest is replaced with the space of
interest spanned by the corresponding contrast.
Orthogonalization
Orthogonalization involves assigning shared variability
between regressors to one of the regressors. For example, in a
model adjusting for height and weight, it would be expected
that these two regressors would be highly correlated.
Orthogonalization assigns the shared variability to one of the
regressors, so orthogonalization of height with respect to
weight would assign shared variability to weight. The height
effect is still adjusted for weight, but the weight effect is no
longer adjusted for height, in this scenario. Since weight is no
longer adjusted for height, the corresponding p-value for the
weight effect will likely decrease. This is often, incorrectly,
viewed as a benefit due to a misinterpretation of the result as
an adjusted effect, when, in fact, the significance of the weight
effect could be due to height.
There are few acceptable uses of orthogonalization. When
parametrically modulated regressors are included, one
475
alternative to mean centering parametric modulation values

is to orthogonalize the parametrically modulated regressor
with respect to the constant duration regressor, which means
that the constant duration regressor reflects the mean activation while the modulated regressor reflects the effect of modulation, adjusted for the overall mean activation.
Conclusion
While the general linear model (GLM) is widely used in neuroimaging for inference with t- and F-tests on the effects of
interest, it is important to realize that the validity of these
inferences will rely on the models assumptions: that the
model is correct the expected Y is Xb and that the noise is
normally distributed. Model checking tools should therefore
be used as much as possible (Luo & Nichols, 2003). For more
details on the flexibility and limitations of the GLM for fMRI,
see Poline and Brett (2012).

Analysis of Variance (ANOVA); Convolution Models for FMRI; Design
Efficiency; Rigid-Body Registration; The General Linear Model.
References
Birn, R. M., Cox, R. W., & Bandettini, P. A. (2002). Detection versus estimation in eventrelated fMRI: Choosing the optimal stimulus timing. Neuroimage, 15(1), 252264.
Bullmore, E., Brammer, M., Williams, S. C., Rabe-Hesketh, S., Janot, N., David, A., et al.
(1996). Statistical methods of estimation and inference for functional MR image
analysis. Magnetic Resonance in Medicine, 35(2), 261277.
Liu, T. T. (2004). Efficiency, power, and entropy in event-related fMRI with multiple trial
types. Part II: Design of experiments. Neuroimage, 21(1), 401413.
Luo, W. L., & Nichols, T. E. (2003). Diagnosis and exploration of massively univariate
neuroimaging models. Neuroimage, 19(3), 10141032.
Moore, E. (1920). On the reciprocal of the general algebraic matrix. Bulletin of the
American Mathematical Society, 26(9), 394395.
Mumford, J. A., & Nichols, T. (2006). Modeling and inference of multisubject fMRI data.
IEEE Engineering in Medicine and Biology Magazine, 25(2), 4251.
Poline, J. B., & Brett, M. (2012). The general linear model and fMRI: Does love last
forever? Neuroimage, 62(2), 871880.
Woolrich, M. W., Ripley, B. D., Brady, M., & Smith, S. M. (2001). Temporal
autocorrelation in univariate linear modeling of FMRI data. Neuroimage, 14(6),
13701386.
Worsley, K. J., Liao, C. H., Aston, J., Petre, V., Duncan, G. H., Morales, F., et al. (2002).
A general statistical analysis for fMRI data. Neuroimage, 15(1), 115.
Zarahn, E., Aguirre, G. K., & DEsposito, M. (Apr 1997). Empirical analyses of BOLD
fMRI statistics. I. Spatially unsmoothed data collected under null-hypothesis
conditions. Neuroimage, 5(3), 179197.
Analysis of Variance (ANOVA)

RN Henson, MRC Cognition and Brain Sciences Unit, Cambridge, UK
Abbreviations
ANCOVA
ANOVA
df
Analysis of covariance
Analysis of variance
Degrees of freedom
Introduction
Analysis of variance (ANOVA) is simply an example of the
general linear model (GLM) that is commonly used for factorial
designs. A factorial design is one in which the experimental
conditions can be categorized according to one or more factors,
each with two or more levels (Winer, Brown, & Michels, 1991).
For example, an experiment might present two types of visual
stimuli (e.g., faces and houses), each at three different levels of
eccentricity. This would correspond to a 2 3 ANOVA, in
which the six conditions correspond to unique combinations
of each level of the stimulus-type and eccentricity factors.
In univariate ANOVA, each condition furnishes one measurement (e.g., BOLD response at a given voxel) for each of
multiple replications (e.g., subjects). When each level of one or
more factors is measured on the same thing, for example, the
same subject contributes data to each level, the ANOVA is
called a repeated-measures ANOVA. Such factors are also called
within-subject factors, as distinct from between-subject factors, for
which the levels can be considered independent (ANOVAs that
contain both within-subject and between-subject factors are
sometimes called mixed ANOVAs). A 1 2 repeated-measures
ANOVA corresponds to a paired (or dependent samples) t-test;
1 2 between-subject ANOVA corresponds to an unpaired (or
independent samples) t-test. Repeated-measures ANOVAs
include additional covariates in the GLM to capture variance
across measurements (e.g., between-subject variance), normally reducing the residual error and hence improving statistics for the effects of interest. This is in fact one type of analysis
of covariance, or ANCOVA, in which the data are adjusted for
covariates of no interest (another example covariate might be,
e.g., the order in which conditions were measured). Analysis
of multiple measurements per condition is also possible
(multivariate ANOVA, or MANOVA), though this can be formally reduced to a univariate ANOVA with additional factors
and proper treatment of the error term (see Kiebel, Glaser, &
Friston, 2003), so is not discussed further here. Finally,
ANOVA (and the GLM) can be considered special cases of
linear mixed-effects (LMEs) models (Chen, Saad,
Britton, Pine, & Cox, 2013), though many of the issues to do
with error covariance modeling are generalized later in the text.
What characterizes ANOVA is the focus on a specific set of
statistical tests across the conditions (contrasts), designed to test
the main effects of each factor and interactions between factors.
So in the 2 3 ANOVA example earlier in the text, there would
be three such treatment effects: (1) the main effect of stimulus
GLM
MANOVA
OLS
ReML
General linear model

Multivariate analysis of variance
Ordinary least squares
Restricted maximum likelihood
type, (2) the main effect of eccentricity, and (3) the interaction
between stimulus type and eccentricity. A significant main
effect of a factor means that the differences between the levels
of that factor are significant (relative to the variability across
replications) when averaging over the levels of all other factors.
So the main effect of stimulus type would correspond to the
difference between faces and houses, regardless of eccentricity.
A significant interaction between two factors means that the
effect of one factor depends on the levels of the other factor. So
an interaction between stimulus type and eccentricity would
mean that the difference between faces and houses depends on
their eccentricity (or equivalently, that the effect of eccentricity
depends on whether the stimulus is a face or house). So, for
example, there might be a large difference between faces and
houses at low eccentricity but less of a difference (or even a
difference in the opposite direction) at high eccentricity
(a result that can be followed up by more focused contrasts
within each level of a factor, sometimes called simple effects). It
is arguably difficult to interpret the main effect of a factor if it
interacts with other factors (or more generally, to interpret an
mth-order interaction if one of the factors is also involved in a
significant (m 1)-th-order interaction). In such cases, a common strategy is to repeat separate ANOVAs on each level of one
of the factors in that interaction, after averaging over the levels
of factors not involved in that interaction. More generally, for a
K-way ANOVA with K factors, there are K main effects, K
(K 1)/2 two-way or second-order interactions, K(K 1)
(K 2)/6 three-way or third-order interactions, etc., and one
highest-order K-way interaction (see Section Generalization
to K-Way ANOVAs).
Example 1 4 Between-Subject ANOVA

Consider an ANOVA with one factor A of four levels, each level
measured on an independent group of ten subjects. This can be
expressed formally as the following GLM:
ys, a x1 b1 x 2 b2 x3 b3 x4 b4 es, a
where ys,a refers to the data from the sth subject in the group
who received the ath level of factor A, concatenated into a
column vector (with n 1 . . . 40 values in this case); xa is a
regressor, here an indicator variable whose values of 0 or 1
code whether the nth measurement in y comes from the ath
level of A; ba is the parameter for the ath level of A (whose
http://dx.doi.org/10.1016/B978-0-12-397025-1.00319-5
477
478
INTRODUCTION TO METHODS AND MODELING | Analysis of Variance (ANOVA)
values are estimated from fitting the model and here correspond to the mean across subjects for that level); and es,a is the
residual error for the sth subject and ath level (again derived
from fitting the model). Sometimes, a fifth regressor would be
added to capture the grand mean across all the data, but this is
not necessary for the F-contrasts considered later in the text.
Fitting the model entails estimating the values of the four
parameters such that the sum of the squares of the residuals
is minimized (the so-called ordinary least squares, or OLS,
estimates).
The same equation can be written in matrix format as
y Xb e
e N 0; Ce
Ce s 2 I
[1]
where X is the design matrix in which the four regressors have

been combined (shown graphically in Figure 1(a)). The second expression in eqn [1] denotes that the residuals are
assumed to be drawn from a zero-mean, multivariate normal
(Gaussian) distribution with covariance Ce. In fact, ANOVA
normally assumes that the residuals are drawn independently
from the same distribution (often termed independent and identically distributed (IID), or white, residuals), which is what is
captured by the third expression in eqn [1], where the error
covariance matrix is an N-by-N identity matrix (I) scaled by a
single variance term s2. One example where this assumption
might not hold is when the conditions differ in the variance
across replications within each condition (homogeneity of variance or heteroscedasticity). For example, patients within one
group (level) may be more variable than controls in another
group (level). Another example arises in repeated-measures
ANOVAs, where the conditions may differ in the pairwise
covariance between them. Both of these require some form of
correction (see Section Nonsphericity).
expressed in several ways. One way is the mean sum of squares

of the treatment effects (b14 here) divided by the mean sum of
squares of the residuals:
Fdf A ; df e
SSA =df A
SSe =df e
where SS are the sums of squares and df are the degrees of freedom.
In the present example, with L 4 levels of the factor,
dfA L 1 3 (since there are three ways that four things can
differ) and dfe N L 36 (i.e., the df in the data minus the df in
the model). Given those df, the probability of obtaining that
value of F or larger under the null hypothesis, p, can be calculated
from the standard F-distribution and declared significant if p is
less than a certain value, for example, p < 0.05. Note that a
significant main effect could result from any pattern of difference
across the four means (e.g., there is no requirement of an ordinal
relationship across the levels). Note also that F-tests are twotailed, but there is nothing to prohibit a one-tailed (directional)
test of a main effect or interaction if there is only one numerator
df in the contrast.
The F-statistic can also be specified by a contrast matrix, c, or
the so-called F-contrast. For the main effect of A in the present
example, c can be expressed in a number of ways (as long as
rank(c) 3 to reflect dfA), such as three pairwise differences
between the four levels:
2
3
1 1 0 0
c 4 0 1 1 0 5
0 0 1 1
The F-statistic can then be expressed in terms of the param^ full design matrix (X), data y, and contrast c
eter estimates (b),
(see Appendix A of Henson & Penny, 2003). Once the use of
such F-contrasts is understood, more complicated ANOVAs
can be considered, as next.
Significance and F-Contrasts

Having fit the model, the main effect of factor A corresponds to
the classical statistical test of the null hypothesis that four
means of each level are identical, that is, that b1 b2 b3 b4.
This is tested by constructing an F-statistic, which can be
Example 2 2 Within-Subject ANOVA

Consider an ANOVA with two factors A and B, each with two
levels, and the resulting four conditions this time measured on
y1,1,1(s1)
...
y1,1(s1)
...
yA(s1)
yA(s2)
yA(s10)
y10,2,2(s10)
y10,4(s40)
x1(a1) x2(a2) x3(a3) x4(a4)
(a)
...
y1,1,2(s1)
...
y1,2(s11)
...
x11 x12 x21 x22 s1
(b)
s2
...
cA
s10
(c)
Figure 1 GLM design matrices for example ANOVAs, where white 1, gray 0: (a) A 1 4 between-subject ANOVA, (b) a 2 2 within-subject ANOVA
with pooled error, and (c) one of the main effects (or interaction effect) in (b), after premultiplying the data by the contrast for that effect, corresponding
to a partitioned error.

each of ten subjects. One possible GLM for this repeatedmeasures ANOVA (which uses a single pooled error; as
explained later) is
ys, a, b x11 b11 x12 b12 x 21 b21 x22 b22 X s bs es, a, b
where x12, for example, indicates whether or not the nth measurement comes from the first level of A and second level of B.
The corresponding design matrix is shown in Figure 1(b) (note
the order of conditions, in which factor A rotates slowest across
columns). The matrix Xs, which has one column per subject,
captures the mean across conditions for each subject. These
covariates of no interest capture a source of variance (betweensubject variance) that would otherwise be likely to inflate the
residual error (at the price of extra df in the model, i.e., now
dfe N rank(X) 40 13 27 for estimating the residuals).
Within this model, we want to test three F-contrasts, where
cA 1 1
1
1
[2]
corresponds to the main effect of A (ignoring an extra ten zeros

for the subject effects); the main effect of B is
cB 1
1
1
1
1
479
can be achieved by premultiplying the data by the F-contrast

for each ANOVA effect, for example, for the main effect of A:

1
y A cA In y
where is the Kronecker product, In is an n-by-n identity
matrix for the n subjects per level of A (n 10 here), and c(1)
A
is as defined in eqn [2]. The new data, yA, can then be fit by the
simple design matrix shown in Figure 1(c), with the corresponding F-contrast c(2)
A 1. The advantage of this procedure
is that the error covariance of the new GLM can be estimated as
a single scalar, that is, Ce s2In, and hence, there are no concerns about nonsphericity, at least for effects like this with one
numerator df (i.e., rank(c(1)
A ) 1). For ANOVA effects with
more than one df (e.g., repeated-measures factors with more
than two levels), the partitioned error covariance matrices can
still be nonspherical (so some form of correction is still necessary), but the degree of nonsphericity is nonetheless normally
reduced, owing to the smaller dimensionality of Ce. However,
partitioning the error results in less sensitive tests compared
with a single pooled error, providing the nonsphericity of that
error can be estimated accurately, as discussed next.
and the interaction is

cAB 1
1
(see Section Generalization to K-Way ANOVAs).
Nonsphericity
As mentioned in the preceding text, a second consequence of
ANOVAs with repeated measures is that the IID assumption in
eqn [1] is unlikely to hold, in that the residual for one measurement on one subject is likely to be similar to the residuals
for other measurements on that subject, that is, the residuals
for repeated measurements are likely to be positively correlated
across subjects. This inhomogeneity of covariance is another case
of nonsphericity (in fact, IID is a special case of a spherical Ce; for
more precise definition of nonsphericity, see Appendix C of
Henson & Penny, 2003). Nonsphericity implies that the effective df in the data is less than the number of observations.
Standard approximations exist to estimate the degree of
nonsphericity and associated loss of df, by estimating a proportion 1/df < e < 1 by which the numerator and denominator df of the F-ratio are scaled (e 1 corresponding to
spherical residuals). Common approximations include the
GreenhouseGeisser or HuynhFeldt corrections (Howell,
2002). One problem with these post hoc df corrections however is that they tend to be conservative, since there are rarely
sufficient data to estimate e efficiently (Kiebel et al., 2003).
Error Covariance Modeling

Another solution to the nonsphericity problem is to employ a
more complex model of Ce:
X
lQ
Ce
i i i
where Qi are called (co)variance components and li are their relative
weightings, or hyperparameters. So for the GLM in Figure 1(b),
where there is a single pooled error, the structure of the error can
be modeled by ten covariance components: four modeling the
variance for each condition and six modeling the covariance
between each pair of conditions (Figure 2). The hyperparameters (l) can be estimated simultaneously with the parameters (b) using an iterative algorithm, such as ReML (Friston
et al., 2002). Once the hyperparameters are estimated, the
Q5
Q1
Q2
Q3
Q4
Q6
Q7
Q8
Q9
Q10
Pooled and Partitioned Errors

One way of reducing the nonsphericity problem is to partition
the GLM error term into separate components, with one error
term per ANOVA effect. So for the 2 2 ANOVA example
earlier in the text, dfe 27 for the single pooled error becomes
dfe 9 for each of the three ANOVA effects. This partitioning
Figure 2 Covariance components for modeling error nonsphericity in a

repeated-measures ANOVA with four conditions and ten subjects
(data assumed to rotate fastest with subject): Q14 model inhomogeneity
of variance, while Q510 model inhomogeneity of covariance.
480
estimated error covariance can be constructed, inverted, and

multiplied by the data (and model) to prewhiten both. This is
the most statistically efficient solution, recovering the full df in
the data.
However, as also the case for the post hoc df corrections
considered in the preceding text, the efficiency with which the
hyperparameters can be estimated depends on the precision
with which the true error covariance can be estimated from the
sample residuals, that is, depends on the amount of data
(Kiebel et al., 2003). For neuroimaging data, one approach is
to combine data across a large number of voxels, in order to
increase the precision of the sample estimate of Ce. These
voxels can be selected once as all those showing some evidence
of an omnibus experimental effect (Friston et al., 2002), or
iteratively in the context of a local neighborhood in a spatially
regularized (Bayesian) framework (Woolrich, Jenkinson,
Brady, & Smith, 2004). Friston et al. (2002), for example,
assumed that the error correlation matrix is identical across
those voxels, differing only in a single scaling factor, s2, which
can be estimated at a voxel-wise level when refitting the model
to the prewhitened data, as in eqn [1]. If this assumption
holds, then this approach provides maximal sensitivity for
the ANOVA effects. (The greater dfs also tend to produce
smoother maps of residuals, rendering corrections for multiple
comparisons across voxels like random field theory less
stringent.) Figure 3(a) shows, for example, how this prewhitened, voxel-wide pooled-error approach increases sensitivity to a true effect (blue solid line), relative to partitioning the
error (blue dotted line) while maintaining appropriate falsepositive control when there is no true effect (overlapping green
solid and dotted lines at p 0.05). On the other hand, if one
tries to estimate the error correlation voxel-wise rather than
Prop. voxels with p < 0.05
Voxelwide ReML, voxelwide eror
voxel-wide, or the true error correlation is not constant across

voxels, this approach can produce an increased false-positive
rate (red solid and green dotted lines in Figure 3(b) and 3(c)).
In sum, this approach to combining data across voxels is more
sensitive, but less robust, than partitioning the error or post
hoc df corrections.
Generalization to K-Way ANOVAs

The examples in the preceding text can be generalized to K-way
ANOVAs, with K factors each with Lk levels. Thus, for an L1-byK
Y
Lk conditions, K !/(m !
L2-by. . . LK ANOVA, there are
k1
(K m) !) treatment effects of the mth order (where the firstorder effects are the main effects), and 2K 1 treatment effects
in total. (One should therefore consider correcting the p-values
for the number of treatment effects tested, i.e., to allow for the
multiple comparison problem in classical statistics.)
The F-contrasts for each treatment effect can be built from
two types of component contrast matrix mk and dk for the kth
factor:
where 1Lk is a row vector of Lk ones, ILk is an Lk-by-Lk identity

matrix, PT is the transpose of matrix P, diff(P) is a matrix of
column differences of a matrix P, and orth(P) is the orthonormal basis of P. The component mk can be thought of as the
common effect of the kth factor and the component dk can be
thought of as the differential effect for the kth factor. The
F-contrast for the mth-order interaction between the first f
Voxelwise ReML, voxelwide eror
Voxelwide ReML, voxelwise error
0.8
0.8
0.8
0.6
True Pool
True Part
Null Pool
Null Part
0.4
0.2
0.05
0
0.6
True Pool
True Part
Null Pool
Null Part
0.4
0.2
10 12 14 16 18 20 22 24
Number of subjects
0.05
0
dk orthdiff ILk T
mk 1Lk
0.6
True Pool
True Part
Null Pool
Null Part
0.4
0.2
10 12 14 16 18 20 22 24
Number of subjects
0.05
0
10 12 14 16 18 20 22 24
Number of subjects
Figure 3 Sensitivity and bias for various treatments of the error in a 2 2 repeated-measures ANOVA, in which there is a true main effect of A (blue lines),
but no main effect of B (red or green lines). The proportion of 10 000 voxels whose p-values exceed p < 0.05 are plotted against the number of subjects. In
(a), the true error correlation is constant across voxels. The solid lines arise when averaging residual covariances across all voxels and estimating the
nonsphericity of the single pooled-error term (Pool) using ReML and the ten covariance components depicted in Figure 2 (see text for details); the dotted
lines reflect the same effects estimated using a partitioned error (Part). Note the pooled error is more sensitive to the main effect of A while maintaining the
same control of false-positives (at expected chance proportion of 0.05) for the main effect of B. In (b), the error nonsphericity is estimated for each voxel
separately, and the inefficiency of this estimation no longer results in a gain in sensitivity for the pooled relative to partitioned error, and there is now an
increased false-positive rate (red line). In (c), the true error correlation varies across voxels but is still estimated by averaging residuals across voxels. This
also results in a loss of sensitivity and (modest) increase in false-positive rates for pooled relative to partitioned error. The code for these simulations is
available at http://www.mrc-cbu.cam.ac.uk/wp-content/uploads/2013/05/check_pooled_error.m.

factors (assuming that the first factor rotates slowest in the data
and design matrix) is then given by
c d1 d2 . . . df mKf 1 mKf 2 . . . mK
So for the 2 2 ANOVA considered previously in the text,

p
p
mk 1 1 dk 1= 2 1= 2
1 1
(the latter equivalence shown for simplicity, since the sign and
overall scaling of an F-contrast do not matter). We can then
construct the previous F-contrasts for the 2 2 example, with
the main effect of factor A:
cA d1 m2 1
1 1
1 1
1
1
1
the main effect of factor B:

cB m1 d2 1
1 1
1 1
1
and the interaction:

cAB d1 d2 1 1 1 1 1
1 1 0 0 0 0 1 1
1
1
1
(where the final equivalence indicates how such an interaction

can be thought of as a difference of differences, or difference of
two simple effects). This procedure can be generalized to any
ANOVA, and the resulting contrasts can be used to partition
the error (for repeated measures) and/or construct an F-statistic
and corresponding p-value.
Acknowledgments
This work was supported by the UK Medical Research Council
(MC_US_A060_5PR10).
481

Contrasts and Inferences; The General Linear Model; Topological
Inference.
References
Chen, G., Saad, Z. S., Britton, J. C., Pine, D. S., & Cox, R. W. (2013). Linear mixedeffects modeling approach to FMRI group analysis. NeuroImage, 73, 176190.
Friston, K. J., Glaser, D. E., Henson, R. N., Kiebel, S., Phillips, C., & Ashburner, J.
(2002). Classical and Bayesian inference in neuroimaging: Applications.
Henson, R. N., & Penny, W. (2003). ANOVAs and SPM. Technical Report, Wellcome
Department of Imaging Neuroscience.
Howell, D. C. (2002). Statistical methods for psychology (5th ed.). Belmont, CA:
Duxbury Press.
Kiebel, S. J., Glaser, D. E., & Friston, K. J. (2003). A heuristic for the degrees of freedom
of statistics based on multiple hyperparameters. NeuroImage, 20, 466478.
Winer, B. J., Brown, D. R., & Michels, K. M. (1991). Statistical principles in
experimental design. McGraw-Hill.
Woolrich, M. W., Jenkinson, M., Brady, J. M., & Smith, S. M. (2004). Fully Bayesian
spatio-temporal modeling of FMRI data. IEEE Transactions on Medical Imaging, 23,
213231.
Relevant Websites
http://afni.nimh.nih.gov/sscc/gangc/ANOVA.html ANOVA in AFNI software, and
extension to LME models: http://afni.nimh.nih.gov/sscc/gangc/lme.html.
https://en.wikipedia.org/wiki/Analysis_of_variance wikipedia, classical perspective.
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM ANOVA in FSL.
http://www.mrc-cbu.cam.ac.uk/wp-content/uploads/2013/05/check_pooled_error.m
Matlab code used to calculate efficiency in examples here.
http://www.mrc-cbu.cam.ac.uk/personal/rik.henson/personal/
HensonPenny_ANOVA_03.pdf GLM perspective and implementation in SPM.
http://nmr.mgh.harvard.edu/harvardagingbrain/People/AaronSchultz/GLM_Flex.html
software toolbox for partitioned error models in SPM.
http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels LME in
Freesurfer.
Convolution Models for FMRI

DR Gitelman, Professor of Neurology, Chicago Medical School at Rosalind Franklin University, Park Ridge, IL, USA
Glossary
BOLD Blood oxygen level dependent imaging: An MRI

imaging technique that uses changes in the ratio of oxy- to
deoxyhemoglobin due to changes in blood flow as an
indirect measure of neuronal activity.
Convolution A mathematical operation on two functions
that acts to blend one function with another.
Deconvolution A process for reversing the effects of
convolution on recorded data.
Functional magnetic resonance imaging A magnetic
resonance imaging technique that provides an indirect
measure of brain activity by detecting changes in brain
blood flow.
General linear model Statistical linear model of data

analysis.
Repetition time (TR) The time between successive pulse
sequences being applied to a slice or in the case of the
rapid imaging sequences use for fMRI, the entire
image.
Wavelet A mathematical function that is used to divide data
into different frequency components and then analyze each
component at a resolution matched to its scale (Graps, A.
(1995). An introduction to wavelets. IEEE Computational
Science & Engineering, 2(2), pp. 5061).
Wiener filter A type of linear time-invariant filter.
Introduction
LTI Models
Since the first studies in the early 1990s, functional magnetic

resonance imaging (fMRI) using blood oxygen leveldependent (BOLD) contrast has provided a powerful means
of examining brain function (Belliveau et al., 1992; Kwong
et al., 1992; Ogawa, Lee, Kay, & Tank, 1990). However, it is
well known that the recorded BOLD signal is only an indirect
measure of neuronal activity (Ogawa, Lee, Kay, & Tank, 1990;
Ogawa, Lee, Nayak, & Glynn, 1990). Detailed biophysical
models have been described that relate BOLD signal to underlying neural events (Buxton, Wong, & Frank, 1998; Ogawa
et al., 1993; Sotero & Trujillo-Barreto, 2007), but these biophysical models are not used in typical fMRI analyses (except
for specialized applications such as dynamic causal modeling;
Friston, Harrison, & Penny, 2003). Instead, the relationship
between neural events and BOLD data is usually modeled
using principles of linear systems analysis.
Early on in the development of fMRI technology, it was
realized that BOLD signal appeared to be a smoothed and
delayed (i.e., filtered) representation of neural activity
(Bandettini, Jesmanowicz, Wong, & Hyde, 1993). A relatively
straightforward and mathematically tractable way of analyzing
a system in which the input is transformed into an output is to
model the data as a linear time-invariant (LTI) system. Such a
system shows a linear relationship between its output and its
input as characterized by its impulse response function. In the
case of fMRI, the input is neural activity, the output is measured BOLD signal, and the impulse response is better known
as the hemodynamic response function (HRF). Linear systems
analysis combines the input signal and impulse response function using the mathematical technique of convolution. The
details will be reviewed later, but intuitively, convolution can
be thought of as repeatedly combining or blending one function with another (Figure 1).
LTI systems must by definition have properties of both linearity and time invariance. In order to apply these principles to
fMRI analysis, let us say we have a function f that transforms
neural activation X(t) into BOLD output y(t). Then,
yi t f Xi t
[1]
Linearity means that the data obey principles of (1) scaling

and (2) superposition. The scaling principle states that scaling
the inputs will identically scale the outputs. So, for the real
constant, a, the scaling principle means that
ayi t f aX i t
The superposition principle says that the sum of the outputs
is equal to the sum of the inputs. Therefore, if one is given
y1 t f X1 t and y2 t f X2 t
then
y1 t y2 t f X1 t X2 t
The property of time invariance implies that the response to
an input at time t is the same at a later time t. Following from
eqn [1], then for all times t,
yi t t f Xi t t
[2]
In order to apply these equations to analyzing fMRI data,

they should be written with time as a discrete variable, rather
than a continuous variable, since the BOLD signal is sampled
at discrete intervals (i.e., the TR). To formulate these equations
in discrete time, it is important introduce the concept of a delta
(
1if t t
function dt t
:
0if t 6 t
http://dx.doi.org/10.1016/B978-0-12-397025-1.00320-1
483
484
INTRODUCTION TO METHODS AND MODELING | Convolution Models for FMRI
Input function
(neural activity)
Impulse response
function (HRF)
Predicted BOLD
timecourse
0
0
20
40
60
Time (s)
80
5 10 15 20 25 30
Peristimulus time (s)
0 10 20 30 40 50 60 70
Time (s)
Figure 1 Convolution example: The stimulus function (a surrogate for neural activity) is combined, using convolution, with the hemodynamic
response function (HRF) to produce a predicted time course of BOLD signal. Notice that convolution acts to blend repeatedly the impulse response
function with the input function. is the symbol for convolution. Adapted from Henson, R., & Friston, K. (2006). Convolution models for fMRI.
In W. D. Penny, K. J. Friston, J. T. Ashburner, S. J. Kiebel, & T. E. Nichols (Eds.), Statistical parametric mapping: The analysis of functional brain images.
London: Academic Press, with permission from Elsevier.
Xt x1 dt 1 x2 dt 2 . .. n9 t 9
d(t t)
This definition says the value of the delta function is 1

whenever the variable, t, is equal to the specified time point,
t; otherwise, the value is 0. Figure 2 graphically illustrates a
delta function.
Using the principle of superposition, neural activation can
be written as the weighted sum of a series of delta functions
(Ashby, 2011; Figure 3):
[3]
t
Time (t)
Equation [3] can now be rewritten as a sum:

X t
1
X
xt dt t
[4]
t0
Note that neural activation is 0 both before time 0 (x0 0)

and after time interval 9 (xi 0 for all i > 9). Equation [4] can
be substituted into eqn [1] with the conditions that f[X(t)]
0 for t < 0, since the BOLD response cannot start before neural
activation, and f[d(t t)] 0 for t > t:
y t
t
X
Figure 2 Graphical demonstration of a delta function, which takes on

the value of 1 when t t, otherwise it is 0. Adapted from Ashby, F. G.
(2011). Modeling the BOLD response. Statistical analysis of fMRI data.
Cambridge, MA: MIT Press. 2011 Massachusetts Institute of
Technology, by permission of The MIT Press.
x4
Xt f dt t
[5]
t0
Recall that an LTI systems response to an impulse is always

the same regardless of when that impulse occurs. Therefore, the
response of the system to the delta function d(t t) can be
written as h(t t) f[d(t t)], where h(t) is the HRF to a single
idealized neural activation. Substituting this expression into
eqn [5] produces
yt
Xt
0
Xtht t
and taking the limit as t ! 0, the sum can be rewritten as an

integral:
Z
yt
Xtht tdt
This equation corresponds to the well-known convolution

integral. Thus, the LTI system model of BOLD fMRI data (y) is
the convolution of the HRF with an estimate of the neural
activity. This can be written as y(t) x(t) * h(t) (with convolution denoted as *) or as
x(t)
x3
x2
x1
5 6
T (TR)
Figure 3 A series of delta functions approximating neural activation

in discrete time. The delta function takes on different values x1, x2, . . ., xn
at each MRI measurement time (TR). Adapted from Ashby, F. G.
(2011). Modeling the BOLD response. Statistical analysis of fMRI data.
Cambridge, MA: MIT Press. 2011 Massachusetts Institute of
Technology, by permission of The MIT Press.
y HX
with H in Toeplitz matrix form.
[6]
485
1997; Friston, Fletcher, et al., 1998; Friston, Frith, Turner, &

Frackowiak, 1995; Henson & Friston, 2006; Hinrichs et al.,
2000; Ollinger, Corbetta, & Shulman, 2001; Ollinger, Shulman,
& Corbetta, 2001). Temporal basis functions can be understood
as comprising a set of linearly independent vectors or waveforms
that span the space of possible fMRI hemodynamic responses.
Spanning the space means that every potential response can be
expressed as a linear combination of these vectors.
An expanded temporal basis set can take a variety of forms
including three gamma density functions to model the early,
middle, and late forms of the BOLD response (Figure 4(a);
Friston, Josephs, Rees, & Turner, 1998), or a canonical HRF
together with its first (temporal) and sometimes second (dispersion) derivatives (Figure 4(b)) to model shifts in the
latency and duration of the HRF, respectively (Henson, Price,
Rugg, Turner, & Friston, 2002; Liao et al., 2002). More flexible
models that make few assumptions about the HRF response
shape are the finite impulse response (FIR; Figure 4(c)) and
Fourier (Figure 4(d)) basis sets (Henson & Friston, 2006;
Ollinger, Corbetta, et al., 2001; Ollinger, Shulman, et al.,
2001). The FIR model consists of a series of extended delta
functions or boxcars each usually 1 TR seconds in length
(TR repetition time). The entire series of boxcars or bins is
assumed to last for the duration of the HRF (designated as T ),
which is generally the time it would take for the HRF to return
to baseline, or around 2432 s. Because the FIR model does
not assume any specific shape for the HRF, other than that, the
response is linear; another use of this basis set is in analyzing
the shape of the HRF. In this case, the parameter estimate for
each vector in the FIR basis set can be plotted in order to
reproduce the HRF. The Fourier basis set includes a constant
term and a user-specified number of sine and cosine functions
up to a sampling frequency of N/T where N is the number of
Using the Convolution Equation

The most widely used and simplest method of analyzing BOLD
fMRI data is by using a standard function to approximate the
HRF and then convolving it with an estimate of the neural
signal. Note that the neural signal itself cannot be practically
measured in people, so it is generally modeled as a series of
delta functions based on the temporal sequence of the task
design. The predicted BOLD signal can then be compared with
the measured BOLD signal using the general linear model
(Friston, Holmes, et al., 1995). Previous studies have proposed
several different functions as approximations to the HRF. (A
discussion of the advantages and disadvantages of each function is beyond the scope of this article.) The functions have
included a Poisson function (Friston, Jezzard, & Turner, 1994),
gamma distribution function (Boynton, Engel, Glover, & Heeger, 1996; Cohen, 1997; Lange & Zeger, 1997), double gamma
distribution function (Friston, Fletcher, et al., 1998), and
Gaussian function (Rajapakse, Kruggel, Maisog, & Von
Cramon, 1998). Current fMRI analysis software including
SPM (http://www.fil.ion.ucl.ac.uk/spm), FSL (http://fsl.fmrib.
ox.ac.uk/fsl), and AFNI (http://afni.nimh.nih.gov/afni) as the
three most popular packages use the double gamma function
as the canonical HRF, since it reproduces the shape of the
physiological HRF including the late undershoot. These software programs also allow a variety of other choices.
Although the single-function approach to approximating the
HRF generally works well, its two main disadvantages are that
any single function may not model the HRF very well, particularly in patient populations, and that all voxels are constrained to
use the same HRF model. To finesse these limitations, one can
use an expanded set of temporal basis functions to model
the hemodynamic response more flexibly (Dale & Buckner,
0
0
(a)
0
(c)
10
15
20
25
30
10
15
20
25
30
10
15
20
25
30
10
15
20
25
30
(b)
0
(d)
Figure 4 Temporal basis sets for fMRI analysis. The waveforms or vectors in each graph are convolved with the experimental stimulus function
(i.e., a surrogate for neural activity) to produce a predicted time course. Each time course constitutes a separate column of the design matrix. (a) Three
gamma functions modeling early (blue), middle (red), and late (green) responses. (b) Canonical HRF (blue), temporal derivative (red), and
dispersion derivative (green). (c) Boxcar functions for the FIR model. Each boxcar is generally designed to last for TR seconds. (d) Sine and cosine
waveforms comprise the Fourier basis set. Adapted from Henson, R., & Friston, K. (2006). Convolution models for fMRI. In W. D. Penny, K. J. Friston,
J. T. Ashburner, S. J. Kiebel, & T. E. Nichols (Eds.) Statistical parametric mapping: The analysis of functional brain images. London: Academic
Press, with permission from Elsevier.
486
sine and cosine functions and T is the duration of the HRF. The
number of basis functions is 2N 1. In Figure 4(d), N is 8. The
Fourier basis set may be most appropriate when peristimulus
time sampling, which is the temporal relationship between
event onset times and the MR sampling time (TR), is not
uniform (Henson & Friston, 2006).
Although all of these extended temporal basis sets generally
provide a better fit to the BOLD signal than using a single
waveform to model the HRF, the main disadvantage is the
greater complexity of analyzing the multiple parameter estimates associated with each of the vectors in the temporal basis
set at the second (i.e., multiple subject) level. In some cases,
such as the basis set of three gamma functions, the parameter
estimates associated with each function can be analyzed separately, as each vector has a biologically interpretable meaning,
for example, early versus middle versus late responses. On the
other hand, the parameter estimates for the Fourier or FIR basis
sets must be analyzed as a group using second-level F-tests and
repeated measures ANOVAs. This limits the ability to make
statistical inferences about specific task differences using contrasts and t-tests (Henson & Friston, 2006).
In cases where the HRF may have a significant nonlinear
component, the chosen basis set can be further expanded as a
Volterra series (Friston, Josephs, et al., 1998; Henson & Friston,
2006). Friston et al. noted that a Volterra series is similar to a
Taylor series model that has been extended for dynamic (i.e.,
nonlinear) systems (Friston, Josephs, et al., 1998). In general, a
second-order Volterra model is sufficient for most nonlinear
fMRI analyses (Friston, Josephs, et al., 1998).
Deconvolution
Sometimes, rather than using the convolution equation to
estimate the BOLD response, the goal of the analysis is to
estimate the neural response itself. In such cases, one
must calculate the inverse transform of the convolution operation or deconvolution. Estimates of neural activity are particularly relevant when using fMRI for calculating measures of
effective connectivity or the influences between neural systems. In such analyses, although fMRI signal is measured as
BOLD data, interactions take place at the neuronal level,
hence the need for an estimate of the underlying neural
activity. Mathematically, it is also critical to deconvolve
BOLD to neuronal signal because interactions calculated at
a hemodynamic level are not equivalent to those calculated at
a neuronal level (Gitelman, Penny, Ashburner, & Friston,
2003). For example, let us examine the interaction of neural
activity between two regions, A and B. Note that the interaction term for two vectors is simply their Hadamard product
(i.e., their element-by-element multiplication). If BOLD signals, yAand yB, are measured, then forming the interaction
term at the BOLD level is not equivalent to forming that
term at the neuronal level. Let XA and XB represent the
neuronal activity in each region. Then,
yA yB HXA HXB 6 HXA XB
H is the hemodynamic response function. Therefore, HXA and
HXB represent the BOLD signal from regions A and B, respectively, and H(XA XB) is the BOLD signal resulting from
the interaction of neural activities from each region.Thus, it is

necessary to deconvolve the BOLD signal to obtain a model of
the underlying neuronal activity. Similar logic applies to generating interaction terms between a behavioral state vector and
regional signal in psychophysiological interactions (Gitelman
et al., 2003).
Although simple in concept, deconvolution of fMRI signal
turns out to be problematic because the mapping between
fMRI and neural signals is nonunique. What this means is
that any number of neural waveforms could appear to have
the same BOLD signal, making it difficult to find an inverse
transform or deconvolution. This follows from the HRF acting
like a low-pass filter and removing the high frequencies from
the neural signal, or as described by Zarahn, the transfer function (i.e., the HRF) has zero values for the high-frequency
components, making the mapping nonunique (Zarahn,
2000). Figure 5 illustrates this by showing nearly identical
simulated BOLD signals resulting from convolution of the
HRF with a low-frequency input signal (0.05 Hz) versus a
mixed-frequency input signal (0.05 0.2 Hz). In the latter
case, the higher frequencies are being filtered out by the HRF.
Several methods of handling the problem of fMRI deconvolution have been described. Glover used a Wiener filter and
found relatively good performance as long as the temporal
spacing of the events was > 4 s (Glover, 1999). However, the
technique required separately measuring both the impulse
response and an estimate of the noise from the data. Zarahn
was able to use least squares deconvolution but had to carefully select the temporal components in the trial design
(Zarahn, 2000). The use of an empirical Bayesian estimator
was outlined by Gitelman et al. (2003). This technique did not
require prespecification of the experimental design or a measure of the noise variance. Instead, it dealt with the loss of
high frequencies in the BOLD data by setting the prior covariances for the high-frequency components to infinity, corresponding to a prior precision of 0. This effectively removed
the high frequencies from the model without having to alter
the design matrix of the Fourier temporal basis set used in the
Bayesian estimator (Gitelman et al., 2003). The noise variance
was also estimated from the data. Although this approach
was formally shown to be similar to those of Glover (1999)
and Zarahn (2000), it allowed more flexibility in the experimental design. Another technique for deconvolution using
Fourier regularized wavelets may have an advantages in
better separation of signal from noise and better performance,
even for rapid event-related designs (Wink, Hoogduin, &
Roerdink, 2008).
Nonlinearities and Other Variations of the BOLD

Response
An important question when analyzing fMRI data using an LTI
model is how well the data conform to the principles of linearity and time invariance. Although multiple studies have
shown nonlinearities in BOLD fMRI data (Boynton et al.,
1996; Buxton et al., 1998; Vazquez & Noll, 1998), departures
from linearity are usually not severe for many standard fMRI
experiments. Nevertheless, studies have found nonlinear fMRI
responses due to changes in stimulus timing and/or
487
Input signal 1
1
0.5
0
0.5
1
0
0
10
20
30 40
Time (s)
50
60
10 15 20 25 30
0.5
0
Input signal 2
2
0.5
1
0
10
20
30
40
50
60
Time (s)
1
2
Predicted time courses (simulated BOLD)

1
0
0
10
20
30 40
Time (s)
50
60
10 15 20 25 30
Figure 5 Low-pass filter effects of the HRF. Two different neural input signals and their convolution with an HRF are shown. Input signal 1 is sin
(2pt/20). Input signal 2 is sin(2pt/20)sin(2pt/5). Note that the higher frequencies of input signal 2 are filtered out after convolution with the HRF
so that the predicted time courses look nearly identical. Obviously, deconvolution of the predicted time courses would produce results similar to input
signal 1, demonstrating the nonunique mapping between the input signals (i.e., neural signals) and predicted time courses (i.e., simulated BOLD).
Adapted from Zarahn, E. (2000). Testing for neural responses during temporal components of trials with BOLD fMRI. Neuroimage, 11, 783796,
with permission from Elsevier.
presentation. For example, BOLD responses that are larger in

amplitude but shorter in duration than expected have been
noted as visual stimuli are shortened to less than approximately 4 s (Boynton et al., 1996; Vazquez & Noll, 1998) or
auditory stimulus trains are shortened to < 6 s (Robson, Dorosz,
& Gore, 1998). Boynton et al. (1996) illustrated this in the visual
system by summing hemodynamic responses to checkerboard
patterns for stimuli of shorter duration (3, 6, or 12 s) to estimate
corresponding responses to stimuli of longer duration 6 s (3 s
response shifted 3 s response), 12 s (four shifted copies of the
3 s response, or two shifted copies of the 6 s response), or 24 s (8
of the 3 s, 4 of the 6 s, or 2 of the 12 s responses). They found that
responses to the shortest duration stimuli (3 s) overestimated
responses to longer-duration stimuli (6, 12, or 24 s). Other
changes to visual stimuli that have resulted in nonlinearities
include presenting stimuli every 500 ms or less. This led to
responses that were lower in amplitude and slightly more
delayed than would be predicted by a linear model (Huettel &
McCarthy, 2000). Using visual stimuli with a contrast of < 40%
also leads to nonlinear behavior (Boynton et al., 1996; Vazquez
& Noll, 1998).
Even when stimulus characteristics and timing are held
constant, variations in the hemodynamic response are not
constant across the brain, but can change by region (Birn,
Saad, & Bandettini, 2001). Miezin, Maccotta, Ollinger,
Petersen, and Buckner (2000), for example, found nonlinear
responses in visual but not motor cortex (Miezin et al., 2000).
Another study found variations by region in hemodynamic
response latency (Huettel & McCarthy, 2001). Also, the amplitude and timing of responses in one region may not predict the
responses in other regions (Miezin et al., 2000). Despite
variations in the absolute timing of the HRF between regions,

however, relative differences in timing may be fairly constant at
least for simple visual and motor tasks (Menon, Luknowsky, &
Gati, 1998).
Intersubject differences are another source of HRF variation
to be considered. Although central tendencies tend to minimize the average intersubject differences within young, normal
subject groups (Miezin et al., 2000), the same cannot be said if
subjects have changes in their cerebral vasculature
(Bonakdarpour, Parrish, & Thompson, 2007) or subject groups
are of widely differing ages (DEsposito, Deouell, & Gazzaley,
2003). In such cases, alternative analysis strategies may be
needed such as using flexible models for deconvolution
(Ollinger, Corbetta, et al., 2001; Ollinger, Shulman, et al.,
2001) or looking at interaction effects across groups, rather
than the main effect of group itself (DEsposito et al., 2003).
There is evidence that both neural and hemodynamic factors may contribute to nonlinear hemodynamic responses and
their relative contributions may vary by the stimulus type,
presentation rate, and region of the brain. For example, successive presentations of a visual stimulus result in a decreased
amplitude of the second BOLD response when the interstimulus interval is < 4 s (Huettel & McCarthy, 2000). Similarly,
Puce, Allison, and McCarthy (1999) showed reduced amplitudes of event-related response components to successive presentations of visual stimuli (Puce et al., 1999), and suppression
of a second somatosensory evoked potential to a preceding
stimulus has also been shown (Ogawa et al., 2000). Because
the decremented evoked potential responses do not depend on
hemodynamics, this implies that there must be at least a partial
neural basis for this phenomenon.
488
Conclusions
This article has reviewed techniques for analyzing BOLD fMRI
data using the concepts of LTI systems. The power of this
technique lies in its ability to model a wide variety of experimental designs. Moreover, the use of various basis sets for the
systems impulse response function allows the user to focus on
different temporal aspects of the data and even to analyze
nonlinear responses all within the same flexible framework.

Analysis of Variance (ANOVA); Design Efficiency; Models of fMRI
Signal Changes; The General Linear Model.
References
Ashby, F. G. (2011). Modeling the BOLD response. Statistical analysis of fMRI data.
Bandettini, P. A., Jesmanowicz, A., Wong, E. C., & Hyde, J. S. (1993). Processing
strategies for time-course data sets in functional MRI of the human brain. Magnetic
Belliveau, J. W., Kwong, K. K., Kennedy, D. N., Baker, J. R., Stern, C. E., Benson, R.,
et al. (1992). Magnetic resonance imaging mapping of brain function. Investigative
Radiology, 27, S59S65.
Birn, R. M., Saad, Z. S., & Bandettini, P. A. (2001). Spatial heterogeneity of the
nonlinear dynamics in the FMRI BOLD response. NeuroImage, 14, 817826.
Bonakdarpour, B., Parrish, T. B., & Thompson, C. K. (2007). Hemodynamic response
function in patients with stroke-induced aphasia: Implications for fMRI data
analysis. NeuroImage, 36, 322331.
Boynton, G. M., Engel, S. A., Glover, G. H., & Heeger, D. J. (1996). Linear systems
analysis of functional magnetic resonance imaging in human V1. Journal of
Cohen, M. S. (1997). Parametric analysis of fMRI data using linear systems methods.
Dale, A. M., & Buckner, R. L. (1997). Selective averaging of rapidly presented individual
trials using fMRI. Human Brain Mapping, 5, 329340.
DEsposito, M., Deouell, L. Y., & Gazzaley, A. (2003). Alterations in the BOLD fMRI
signal with ageing and disease: A challenge for neuroimaging. Nature Reviews.
Friston, K. J., Fletcher, P., Josephs, O., Holmes, A., Rugg, M. D., & Turner, R. (1998).
Event-related fMRI: Characterizing differential responses. NeuroImage, 7, 3040.
Friston, K. J., Frith, C. D., Turner, R., & Frackowiak, R. S.J (1995). Characterizing
evoked hemodynamics with fMRI. NeuroImage, 2, 157165.
Friston, K. J., Harrison, L., & Penny, W. (2003). Dynamic causal modeling.
Frackowiak, R. S.J (1995). Statistical parametric maps in functional imaging: A
Friston, K. J., Jezzard, P., & Turner, R. (1994). Analysis of functional MRI time-series.
Friston, K. J., Josephs, O., Rees, G., & Turner, R. (1998). Nonlinear event-related
responses in fMRI. Magnetic Resonance in Medicine, 39, 4152.
Gitelman, D. R., Penny, W. D., Ashburner, J., & Friston, K. J. (2003). Modeling regional
and psychophysiologic interactions in fMRI: The importance of hemodynamic
deconvolution. NeuroImage, 19, 200207.
Glover, G. H. (1999). Deconvolution of impulse response in event-related BOLD fMRI.
Henson, R., & Friston, K. (2006). Convolution models for fMRI. In W. D. Penny, K. J.
Friston, J. T. Ashburner, S. J. Kiebel & T. E. Nichols (Eds.), Statistical parametric
mapping: The analysis of functional brain images. London: Academic Press.
Henson, R. N., Price, C. J., Rugg, M. D., Turner, R., & Friston, K. J. (2002). Detecting
latency differences in event-related BOLD responses: Application to words versus
nonwords and initial versus repeated face presentations. NeuroImage, 15, 8397.
Hinrichs, H., Scholz, M., Tempelmann, C., Woldorff, M. G., Dale, A. M., & Heinze, H. J.
(2000). Deconvolution of event-related fMRI responses in fast-rate experimental
designs: Tracking amplitude variations. Journal of Cognitive Neuroscience,
12(Suppl. 2), 7689.
Huettel, S. A., & McCarthy, G. (2000). Evidence for a refractory period in the
hemodynamic response to visual stimuli as measured by MRI. NeuroImage, 11,
547553.
Huettel, S. A., & McCarthy, G. (2001). Regional differences in the refractory period of the
hemodynamic response: An event-related fMRI study. NeuroImage, 14, 967976.
Lange, N., & Zeger, S. L. (1997). Non-linear Fourier time series analysis for human
brain mapping by functional magnetic resonance imaging. Journal of the Royal
Statistical Society: Series C: Applied Statistics, 46, 129.
Liao, C. H., Worsley, K. J., Poline, J. B., Aston, J. A., Duncan, G. H., & Evans, A. C.
(2002). Estimating the delay of the fMRI response. NeuroImage, 16, 593606.
Menon, R. S., Luknowsky, D. C., & Gati, J. S. (1998). Mental chronometry using
latency-resolved functional MRI. Proceedings of the National Academy of Sciences
Miezin, F. M., Maccotta, L., Ollinger, J. M., Petersen, S. E., & Buckner, R. L. (2000).
Characterizing the hemodynamic response: Effects of presentation rate, sampling
procedure, and the possibility of ordering brain activity based on relative timing.
in magnetic resonance image of rodent brain at high magnetic fields. Magnetic
Ogawa, S., Lee, T. M., Stepnoski, R., Chen, W., Zhu, X. H., & Ugurbil, K. (2000). An
approach to probe some neural systems interaction by functional MRI at neural time
scale down to milliseconds. Proceedings of the National Academy of Sciences of the
Ollinger, J. M., Corbetta, M., & Shulman, G. L. (2001). Separating processes within a
trial in event-related functional MRI: II. Analysis. NeuroImage, 13, 218229.
Ollinger, J. M., Shulman, G. L., & Corbetta, M. (2001). Separating processes within
a trial in event-related functional MRI: I. The method. NeuroImage, 13,
210217.
Puce, A., Allison, T., & McCarthy, G. (1999). Electrophysiological studies of human face
perception. III: Effects of top-down processing on face specific potentials. Cerebral
Cortex, 9, 445458.
Rajapakse, J. C., Kruggel, F., Maisog, J. M., & Von Cramon, D. Y. (1998). Modeling
hemodynamic response for analysis of functional MRI time-series. Human Brain
Mapping, 6, 283300.
Robson, M. D., Dorosz, J. L., & Gore, J. C. (1998). Measurements of the temporal
fMRI response of the human auditory cortex to trains of tones. NeuroImage, 7,
185198.
Sotero, R. C., & Trujillo-Barreto, N. J. (2007). Modelling the role of excitatory and
inhibitory neuronal activity in the generation of the BOLD signal. NeuroImage, 35,
149165.
Vazquez, A. L., & Noll, D. C. (1998). Nonlinear aspects of the BOLD response in
functional MRI. NeuroImage, 7, 108118.
Wink, A. M., Hoogduin, H., & Roerdink, J. B. (2008). Data-driven haemodynamic
response function extraction using Fourier-wavelet regularised deconvolution. BMC
Zarahn, E. (2000). Testing for neural responses during temporal components of trials
with BOLD fMRI. NeuroImage, 11, 783796.
Relevant Websites
http://afni.nimh.nih.gov/afni AFNI software.
http://www.fil.ion.ucl.ac.uk/spm SPM software.
http://fsl.fmrib.ox.ac.uk/fsl FSL software.
Design Efficiency
RN Henson, MRC Cognition and Brain Sciences Unit, Cambridge, UK
Abbreviations
AR(p)
BOLD
DCT
FIR
fMRI
GLM
HRF
ReML
SOA
Autoregressive model of order p

Blood oxygenation level-dependent (signal
normally measured with fMRI)
Discrete cosine transform
Finite impulse response (basis set)
TR
General linear model

Restricted maximum likelihood
Stimulus-onset asynchrony (SOAmin minimal
SOA)
Interscan interval (repetition time)

1
e 1= c X T X cT
Formal Definition of Efficiency

The general linear model (GLM) normally used for massunivariate statistical analysis of functional magnetic resonance
imaging (fMRI) data can be written for a single voxel as
y Xb e,

e N 0, s2 Ce
[1]
where y is an N 1 column vector of the data time series

sampled every TR for N scans, X is an N P design matrix in
which the P columns are regressors for the time series of predicted experimental effects, b is a P 1 column vector of
parameters for each regressor in X (whose values are estimated
when fitting the model to the data), and e is N 1 vector of
residual errors. The second expression in eqn [1] denotes that
the residuals come from a zero-mean, multivariate normal
(Gaussian) distribution with covariance Ce. Normally, the
residuals are assumed to be drawn independently from the
same distribution (white residuals), or if not, then the data
and model are filtered, or prewhitened, by an estimate of the
error covariance (see later). This means that Ce s2I, corresponding to an N N identity matrix (I) scaled by a single
variance term s2.
Assuming white residuals, the parameters can be estimated by
minimizing the sum of squares of the residuals, to give the so^ The planned comcalled ordinary least squares (OLS) estimates, b.
parisons we want to test with our experiment are a linear combination of these parameter estimates, specified by a 1 P contrast
vector, c. For example, c 1 1 would test whether the
parameter estimate for the first of two regressors is greater than
the second. Significance can be assessed by a T-statistic, defined by
^
cb
T df q
T 1
^2
c X X cT s
[2]
^2 is the error variance estimated by eTe/df (whereT

where s
denotes the transpose of a matrix) and the degrees of freedom,
df, are defined by N rank(X). The probability, p, of getting a
^ 0,
value of T or greater under the null hypothesis that cb
given the df, can then be calculated from Students T-distribution, and the null hypothesis rejected if, for example, p < 0.05.
We are now in the position to define the efficiency of a
contrast, e, as
[3]
which can be seen as inversely related to the denominator of

the T-statistic in eqn [2]. Thus, if we increase e, we also increase
T. (For multiple contrasts, where c is an M P matrix of M
contrasts, such as an F-contrast, we can define the average
efficiency as 1/trace{c(XTX)1cT)}.)
Note that the scaling of e is arbitrary (depending on the
scaling of the contrast, scaling of regressors, and number of
scans), so the precise relationship between e and T is best
assumed only to be monotonic. Note also that this statement
assumes that the estimate of the error variance (^
s2 ) is independent of the design (X), which may not always be true (see
later). Given these assumptions, and that the contrasts are
specified a priori, then to maximize the efficiency of our
design, we simply need to vary X. We now consider how X is
defined for fMRI.
HRF Convolution
We can start by assuming that stimuli elicit brief bursts of
neural activity, or events, which are modeled by delta functions
every time a stimulus is presented. Then, for the jth of Nj event
types (conditions), the neural activity over time, or neural time
course, uj(t), can be expressed as
uj t
iN
i j
X

d t T ji
i1
where Tji is a vector of i 1 . . . Ni(j) onset times and d is the

Dirac delta function. With fMRI, we do not measure neural
activity directly, but rather the delayed and dispersed BOLD
impulse response, b(t), where t indexes poststimulus time
(e.g., from 0 to 30 s). Given that b(t) may vary across voxels
(and individuals), it can be modeled by linear combination of
Nk hemodynamic response functions (HRFs), hk(t):
bj t
kN
Xk
bkj hk t
k1
where bkj are the parameters to be estimated for each HRF and
condition (and voxel).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00321-3
489
490
INTRODUCTION TO METHODS AND MODELING | Design Efficiency
Assuming that BOLD responses summate linearly (though

see later), the predicted BOLD time course over the experiment, x(t), can then be expressed as the convolution of the
neural time courses by the HRFs:
x t
jN
Xj
uj t bt
j1
jN
i j
Xj kN
Xk iN
X

bkj hk t T ji
[4]
i1
j1 k1
resulting in a linearly separable equation that can be represented by a design matrix X with P NjNk columns.
At one extreme, we can assumed a fixed shape for the BOLD
response by using a single canonical HRF (i.e., Nk 1). At the
other extreme, we can make no assumptions about the shape
of the BOLD response (up to a certain frequency limit) by
using a so-called finite impulse response (FIR) set (see Figure 1;
for multiple basis functions, the contrasts become cINk ,
where c is a contrast across the Nj event types and INk is an
Nk Nk identity matrix for the Nk basis functions). Normally,
one is only interested in the magnitude of a BOLD response,
in which case a single canonical HRF is sufficient to estimate
efficiency a priori (by assuming that a canonical HRF is a
sufficient approximation on average across voxels and individuals). If however one is interested in estimating the shape
of the BOLD impulse response, then a more general set such

as an FIR is necessary. Using a canonical HRF would correspond to what Liu, Frank, Wong, and Buxton (2001) called
detection power, while using an FIR would correspond to what
they called estimation efficiency. This is important because
the choice of HRF affects the optimal experimental design
(see later).
Filtering
So far, we have considered definition of the signal, x(t), but the
other factor that affects the T-statistic in eqn [2] is the noise
^2 . fMRI is known to have a preponderance of lowvariance, s
frequency noise, caused, for example, by scanner drift and by
biorhythms (e.g., pulse and respiration) that are aliased by
slower sample rates (1/TR). A common strategy therefore is to
high-pass filter the data. An example matrix, F, for implementing high-pass filtering within the GLM using a discrete cosine
transform (DCT) set is shown in Figure 1. The reduction in
noise will improve sensitivity, as long as the filtering does not
remove excessive signal too. Heuristics suggest that an
Amplitude (a.u.)
Canonical HRF
and
u2 (t)
Transition
table
or
hk(t )
0
0
200
x1 (t)
400 600
Time (s)
5 10 15 20 25 30
Post-stimulus time (s)
800 1000
x2 (t)
FIR HRF set

Amplitude (a.u.)
u1 (t)
Amplitude (a.u.)
SOAmin
hk(t )
Scans
5 10 15 20 25
Post-stimulus time (s)
F
0
e = 1/(c((KX)T (KX))-1cT )
1
Figure 1 Ingredients for efficiency: the minimal SOA, SOAmin, and stimulus transition table determine the neural time course, uj(t), which is convolved
with HRFs of poststimulus time, hk(t), to create the design matrix, X. This, together with an a priori contrast, c, and any (high-pass) filter matrix,
K (here generated by K IN FF1), then determines the efficiency, e.

approximate inflection in the noise power spectrum typically
occurs at around 1/120 s, which is why it is inadvisable to have
designs with changes in signal slower than this (e.g., alternating blocks of more than 60 s; see later).
High-pass filtering also helps render the noise white, that is,
constant across frequencies, though there is often still temporal
autocorrelation (color) in the residuals. A common strategy to
deal with this is to hyperparameterize the error covariance
matrix Ce using an AR(p) model, which can be estimated
using ReML (Friston et al., 2002). Once estimated, Ce can be
inverted in order to prewhiten the data and model, which
therefore also affects efficiency. Mathematically, both highpass filtering and prewhitening can be implemented by multiplying data and model by a single filter matrix, K, such that
efficiency becomes

1
1
c KXT KX cT
[5]
Parameterizing Experimental Designs

For events, the neural time course is determined by Tji in
eqn [4], which itself can be captured by two parameters: (1)
the minimal time between events, or minimal stimulus-onset
asynchrony, SOAmin, and (2) a transition table, which can be
defined by two matrices, an NP NH matrix, TM(p), describing
the history of the previous NH event types, of which there are NP
possible sequences (in the extreme case NP NJ NH , though it
can be smaller), and an NP NJ matrix, TM(n), describing the
probability of the next event being one of the NJ event types,
given each of those possible previous sequences. So for a fully
randomized design, where the probability of each event is
equal and independent of previous events (NH 1), TM(p)
would be NJ 1 matrix and TM(n) would be NJ NJ matrix
with values of 1/NJ for each event type. So for j 1, 2 event
types,

1
0:5 0:5
TMp
TMn
2
0:5 0:5
This implies that there is an equal chance of event type 1
being followed by event type 1 as there is for it being followed
by event type 2 and likewise for what follows event type 2.
Specifying a design in terms of probabilistic transition matrices
allows one to treat the design matrix as a random variable and
derive the expected efficiency by averaging over all possible
design matrices (see Friston, Zarahn, Josephs, Henson, &
Dale, 1999, for details). In other words, one can express design
efficiency in terms of the probabilistic contingencies entailed
by the design matrix.
Randomized Designs
For a randomized design with two event types, we can plot the
efficiency against SOAmin for each of 2 contrasts, c 1 1 ,
the differential effect of event types 1 and 2, and c 1 1 , the
common effect of event types 1 and 2 versus the interstimulus
491
baseline. For a canonical HRF, the efficiency of these two

contrasts is plotted against SOAmin in Figure 2(a). As can be
seen, the optimal SOA for the common effect is around 18 s,
whereas the optimal SOA for the differential effect increases
exponentially as SOAmin decreases.
The basic reason for these results is that higher efficiency
corresponds to greater variability of the signal over time (where
the signal is a function of the contrast and regressors). At short
SOAs, the sluggish (low-pass) nature of the HRF means that
when we do not distinguish the two event types (by using a
contrast for their common effect), the BOLD responses for
successive events summate to give a small oscillation around
a raised baseline (leftmost inset in Figure 2(a)), that is, low
signal variance. The random ordering of the two event types
means that for the differential effect, however, there is a large
variance in signal. At longer SOAs, there is time for the BOLD
response to return to baseline between events, so signal variance (efficiency) is increased for the common effect, but the
variance for the differential effect decreases relative to short
SOAs (rightmost inset in Figure 2(a)). For further explanations
of this behavior of efficiency, for example, in terms of signal
processing or correlations between regressors, see http://imaging.mrc-cbu.cam.ac.uk/imaging/DesignEfficiency. The important point of Figure 2(a) is that if one is interested in the
difference between two randomly ordered event types, then a
shorter SOA is generally better, though the price one pays is
reduced efficiency to detect the common effect of both versus
baseline. In reality though, this increasing efficiency with
decreasing SOAmin (for a differential effect) cannot occur indefinitely, because at some point, there will be saturation of the
neural and/or hemodynamic response to stimuli that are too
close together in time, an example of nonlinear behavior that is
ignored under the linear superposition assumptions made so
far (see later).
One can improve efficiency for the common effect versus
baseline at short SOAs by ensuring that the probabilities in
TM(n) do not sum to 1 (across columns). This means that for
some SOAmin, no event occurs (sometimes called a null-event or
fixation trial, Dale, 1999). This effectively produces a stochastic
distribution of SOAs, with an exponentially decreasing probability of each SOA. The efficiency for the common effect now
also increases as SOAmin decreases, at a cost to the efficiency of
the differential effect (Figure 2(b)). These types of design are
suitable for an FIR basis set (insets in Figure 2(b)) because a
stochastic distribution of SOAs allows the BOLD response
shape to be estimated, particularly with short SOAmin. (Note
that efficiency is not directly comparable across canonical and
FIR HRFs, since it depends on the scaling of the basis functions,
and an FIR will also entail a reduction in the df, which will
affect the final T-statistic in eqn [2].)
Blocked Designs
Events of the same type can be blocked into short sequences,
which can increase the detection power relative to a randomized design. For a blocked design with two event types, there
would be NH events per block; for example, for blocks of three
events,
Time (s)
Signal (X) (a.u.)
Signal (X) (a.u.)
Signal (X) (a.u.)
Signal (X) (a.u.)
492
Time (s)
Time (s)
Efficiency (a.u.)
Efficiency (a.u.)
Time (s)
18
14
20
SOA (s)
Signal (X) (a.u.)
Signal (X) (a.u.)
Signal (X) (a.u.)
20
Time (s)
Time (s)
Time (s)
Efficiency (a.u.)
Efficiency (a.u.)
Time (s)
18
14
SOA (s)
(b)
Signal (X) (a.u.)
2
(a)
10 18
(c)
30
50
70
(d)
Block length (SOA = 2 s)
14
20
SOA (s)
Figure 2 Efficiency for various possible contrasts and designs. (a) Efficiency (arbitrary units) as a function of SOAmin in a randomized design using a
canonical HRF for a differential [1 1] contrast between two event types (dashed magenta line) and the common [1 1] contrast versus baseline
(solid cyan line). Insets are sections of corresponding contrasts of regressors (predicted signal) for SOAmin 4 (left) and SOAmin 18 (right). Efficiency
for the differential effect is higher at short SOAs owing to the greater signal variance caused by the random ordering of event types. (b) Similar to (a), but
now including null events with probability 1/3 and an FIR basis set (dashed red differential effect; solid blue common effect). The stochastic
distribution of SOAs caused by null events increases efficiency for common effect versus baseline even at short SOAmin. (c) Efficiency as function of
block length for a differential contrast between two event types in a blocked design (and high-pass filter cutoff of 120 s). The dashed magenta line and
left inset correspond to a canonical HRF; the dashed cyan line and right inset correspond to an FIR basis set. Maximal efficiency with a canonical
HRF arises for a block length of 18 s; for an FIR basis set, blocks shorter than the FIR duration are inefficient, owing to linear dependence between the
basis functions. (d) Efficiency for the unique effect of the second of two event types ([0 1] contrast) using a canonical HRF in a design where the
second event type can only follow the first event type. The dashed blue line and rightmost inset show an alternating design in which the second event
type always follows the first; the solid blue line and left inset show a design in which the second event type follows the first 50% of the time (the
red dashed line in the insets corresponds to the regressor for the first event type). For SOAmin below approximately 10 s (e.g., 6 s), the 50% design is
more efficient (despite fewer events of the second type in total), because it decorrelates the two regressors. In all panels, 2000 scans with TR 2 s
were simulated, with the first 30 s discarded to remove transient effects.
TMp
1
61
6
61
6
62
6
42
2
1
1
2
2
2
1
3
2
1
0
7
60
27
6
6
27
7 TMn 6 0
7
61
27
6
41
15
1
1
3
1
17
7
17
7
07
7
05
0
The magenta dashed line in Figure 2(c) shows efficiency for

the differential effect between two event types as a function of
block length using a canonical HRF when SOAmin is 2 s and the
high-pass cutoff is 120 s. Short blocks (in the extreme case,
alternating event types when block length is 1) have low efficiency, for the same reason that the main effect is inefficient at
short SOAs: any variance in neural activity is smoothed out by
the HRF. As in Figure 2(a), efficiency is maximal for block
lengths around 18 s (since 1/18 Hz is close to the highest passband of the canonical HRF filter; Josephs & Henson, 1999), but
for block lengths of 30 s of more, efficiency plummets again
because of the high-pass filter: for such long blocks, most of the
signal variance (particularly that at the fundamental frequency of
the block alternation) is low enough to be removed by the high-
493
pass filter, which is appropriate since it is likely to be masked by

fMRI noise anyway. In short, one does not want fMRI designs
where the signal changes too fast (since it will be attenuated by
the sluggish BOLD response) or where it changes too slow (since
it will be removed by any high-pass filtering or swamped by
noise).
The blue dotted line in Figure 2(c) shows efficiency as a
function of block length when using an FIR basis set rather
than canonical HRF. In this case, efficiency is low, at least until
the block length exceeds the duration of the assumed BOLD
response (30 s here). This is because of the high covariance
between regressors for each basis function (rightmost inset in
Figure 2(c)), as explained later. This illustrates that, while
blocked designs are efficient for estimating the amplitude of a
known BOLD response, they are not efficient for estimating the
unknown shape of a BOLD response (Liu et al., 2001).
example, genetic algorithms (Wager & Nichols, 2003). Additional constraints are often needed however, such as limits on
runs of the same event type; otherwise, an optimization
scheme is likely to converge on a blocked design, which is
always most efficient (for detection power) from the fMRI
perspective, but may not be appropriate from the psychological perspective (e.g., if the presence of structure in the sequence
of events affects brain activity). An interesting class of
pseudorandomized design that has optimal estimation efficiency is an m-sequence (Buracas & Boynton, 2002). This is a
deterministic sequence that presents all combinations of event
histories up to NH m (i.e., has a large, deterministic transition
matrix) but that is nonetheless effectively unpredictable to
participants. Such sequences have been computed for NJ 2,
3, and 5 event types but require a fixed number (NJ NH 1) of
events in total.
Unique Effects
Nonlinearities and Assumptions
In addition to the differential and common effects for two

event types, one might be interested in the unique effect
of each event type, having adjusted for effects of the other
event type, which corresponds to contrasts of 1 0 or
0 1 . A common example is when one type of event must
always follow another type, such as a motor act that is contingent on a stimulus (e.g., a working memory trial). The
dashed line in Figure 2(d) shows that, for SOAs below 9 s,
efficiency is low for a 0 1 contrast in such an alternating
design. To improve efficiency, one needs to reduce the correlation between the two event types (since the term XTX in
eqn [3] relates to the covariance of the regressors in the design
matrix). One way to do this is to randomize the SOA between
stimuli and motor acts; another is to only require a motor
act on a random fraction, say 50%, of trials, as shown in the
solid line in Figure 2(d). Although this entails fewer motor
events in total, the efficiency for separating the BOLD
response to the motor act from that to the stimulus is
increased at short SOAs.
A similar issue arises in so-called mixed designs, in which
one wishes to separate a sustained, or state, effect from a
transient, or item, effect (Chawla, Rees, & Friston, 1999). This
requires blocks of events, in which the SOA is varied within
each block so as to reduce the correlation between the (epoch)
regressor modeling the state effect and the (event) regressor
modeling the item effect. The downside of such designs is that
this requirement to decorrelate the two regressors, in order to
estimate both unique effects reasonably efficiently, considerably reduces the efficiency for estimating either effect alone,
relative to designs with only epochs, or only events.
The main assumption made in the examples mentioned earlier

is that the brains response to successive events is a linear
superposition of responses that would occur to each event on
its own. Of course, this is unlikely in practice, particularly for
short SOAs, where there is likely to be saturation of neural and/
or hemodynamic responses. Such saturation has been demonstrated empirically and can be modeled with the GLM by using
Volterra kernels (Friston, Josephs, Rees, & Turner, 1998). Once
fit, these kernels can be used to adjust predictions for efficiency. For kernels fit to auditory cortex responses to auditory
stimuli of varying SOAs, the negative impact of saturation
on efficiency still only became appreciable for SOAs below
2 s: that is, there was still an advantage of short SOAs down
to 2 s in randomized designs.
A second assumption is that changing the design (X in
eqn [5]) does not affect the estimation of the error (^
s2 in
eqn [2] or even K in eqn [5]). Different SOAs (even across
trials within a design) may entail differences in HRF shape, or
different nonlinearities, resulting in inaccurate model fits and
therefore different residuals. Indeed, when comparing blocked
and randomized designs, differences in the error estimate have
been shown empirically (Mechelli, Price, Henson, & Friston,
2003). Nonetheless, without such a priori knowledge about
the noise, one can only rely on the general heuristics about
maximizing the signal outlined earlier.
Optimizing Designs
The examples in Figure 2 represent just a subspace of possible
designs, chosen to help illustrate some of the properties of
eqn [5]. Other formal explorations of design space can be
found in, for example, Dale (1999), Josephs and Henson
(1999), Friston et al. (1999), and Hagberg, Zito, Patria, and
Sanes (2001). There are automated ways of maximizing efficiency by searching through possible designs, using, for
Summary
Efficiency is a well-defined mathematical property of the GLM,
and under the linear assumptions of a convolution model for
the BOLD response, efficiency can be optimized for a priori
contrasts of the conditions of an fMRI experiment by selecting
the optimal SOAmin and stimulus transition table.
Acknowledgments
This work was supported by the UK Medical Research Council
(MC_US_A060_5PR10).
494

Contrasts and Inferences; Convolution Models for FMRI; The General
Linear Model.
References
Buracas, G. T., & Boynton, G. M. (2002). Efficient design of event-related fMRI
experiments using M-sequences. NeuroImage, 16, 801813.
Chawla, D., Rees, G., & Friston, K. J. (1999). The physiological basis of attentional
modulation in extrastriate visual areas. Nature Neuroscience, 2, 671676.
Dale, A. M. (1999). Optimal experimental design for event-related fMRI. Human Brain
Mapping, 8, 109114.
Friston, K. J., Josephs, O., Rees, G., & Turner, R. (1998). Non-linear event-related
responses in fMRI. Magnetic Resonance in Medicine, 39, 4152.
Friston, K. J., Zarahn, E., Josephs, O., Henson, R. N., & Dale, A. M. (1999). Stochastic
designs in event-related fMRI. NeuroImage, 10, 607619.
Hagberg, G. E., Zito, G., Patria, F., & Sanes, J. N. (2001). Improved detection of eventrelated functional MRI signals using probability functions. Neuroimage, 14,
11931205.
Josephs, O., & Henson, R. N. (1999). Event-related fMRI: Modelling, inference and
optimisation. Philosophical Transactions of the Royal Society, London, 354,
12151228.
Liu, T. T., Frank, L. R., Wong, E. C., & Buxton, R. B. (2001). Detection power, estimation
efficiency, and predictability in event-related fMRI. Neuroimage, 13, 759773.
Mechelli, A., Price, C. J., Henson, R. N., & Friston, K. J. (2003). Estimating efficiency a
priori: A comparison of blocked and randomised designs. Neuroimage, 18,
798805.
Wager, T. D., & Nichols, T. E. (2003). Optimization of experimental design in fMRI: A
general framework using a genetic algorithm. Neuroimage, 18, 293309.
Relevant Websites
http://www.cabiatl.com/CABI/resources/fmrisim/ Tool for simulating fMRI designs.
http://www.mrc-cbu.cam.ac.uk/wp-content/uploads/2013/09/fMRI_GLM_efficiency.m
Matlab code used to calculate efficiency in examples here.
http://imaging.mrc-cbu.cam.ac.uk/imaging/DesignEfficiency General advice about
how to optimise an fMRI experiment.
http://psych.colorado.edu/tor/Software/genetic_algorithms.html Genetic algorithm
for optimising fMRI designs.
http://surfer.nmr.mgh.harvard.edu/optseq/ Tool for optimising randomised designs.
G Flandin and KJ Friston, UCL Institute of Neurology, London, UK
Glossary
Euler characteristic A topological invariant that describes

the shape or structure of an excursion set regardless of the
way it is stretched or distorted. Also called the Euler
Poincare characteristic.
Excursion set Subset of a random field that exceeds a
threshold level.
Conventional whole-brain neuroimaging data analysis uses
some form of statistical parametric mapping (SPM) (Flandin
& Friston, 2008; Friston, 2007). This entails the creation of a
parametric model (usually a general linear model (GLM)) of
data at each point in search space (voxel or vertex) to produce a
SPM: these are fields that are, under the null hypothesis, distributed according to a known probability density function,
usually the Students t- or FisherSnedecor F-distributions
(Friston et al., 1995; Worsley et al., 2002). Topological inference
is then used to test hypotheses about regionally specific effects
attributable to the experimental manipulation (Friston, Frith,
Liddle, & Frackowiak, 1991). By referring to the probabilistic
behavior of random fields, topological features of the SPM are
assigned adjusted p-values, controlling for the implicit multiple
testing problem that occurs when making inference over the
search space (Adler, 1981; Friston, Holmes, Poline, Price, &
Frith, 1996; Friston, Worsley, Frackowiak, Mazziotta, & Evans,
1994; Worsley, Evans, Marrett, & Neelin, 1992; Worsley et al.,
1996).
Multiple Testing
If one knows precisely where to look in the search space,
inference can be based on the value of the statistic at the
specific location in the SPM (sometimes referred to as the
uncorrected p-value). Otherwise, an adjustment for multiple
dependent testing has to be made to the p-values (Hochberg &
Tamhane, 1987). One such adjustment is to control for the
familywise error rate (FWER), that is, the rate of making one or
more false-positive declarations over the search space (Nichols
& Hayasaka, 2003).
A standard approach in the context of discrete statistical
tests is the Bonferroni correction (Shaffer, 1995). There is,
however, a fundamental difference between an SPM and a
collection of discrete statistic values. The data we consider
here are images that can be treated as discrete sampling from
a continuous function of some underlying support. The activation or effect of interest corresponds to some topological
feature of this function. This can be a peak (a local maximum)
or a cluster (a connected component of the excursion set above
some threshold). By doing so, we convert a continuous process
Multiple testing The process of considering a set of

statistical inferences simultaneously.
Random field A stochastic process defined on a manifold.
Resolution element (resel) A unitless quantity,
generalization of a voxel (volume element) whose
dimensions are given by the smoothness of a random field.
Topology The mathematical study of shapes and spaces.
(signal) to a topological feature (activation) that does or does

not exist (Chumbley & Friston, 2009; Chumbley, Worsley,
Flandin, & Friston, 2010). This is of particular relevance
because neighboring tests are not independent, by virtue of
continuity of the original data. Provided the data are smooth, a
topological adjustment is less severe (i.e., more sensitive) than
a Bonferroni correction for the number of tests. When declaring a peak or cluster of the SPM to be significant, we refer
collectively to all the voxels associated with that feature. If the
SPM is smooth, one false-positive peak may be associated with
hundreds of voxels.
With topological inference, we therefore aim to control the
false-positive rate of a discrete set of topological features (peaks
and clusters) rather than discrete tests (voxels). An intuitive
explanation of the increased sensitivity of topological inference
goes as follows: the expected number of false-positive voxels
depends on the false-positive rate of peaks times the expected
number of voxels subtending one peak. As the expected number of voxels per peak is always greater than one, the expected
false-positive rate of voxels is always greater than the falsepositive rate of peaks. Topological inference deals with the
multiple testing problem in the context of continuous statistical fields in a way analogous to the Bonferroni procedure for
families of discrete statistical tests (Friston, 2007).
Random Field Theory

Given the controversies about the multiple testing problem
that recently appeared in the neuroimaging community as
reviewed in Nichols (2012), it is somehow refreshing to
point out that the methods commonly used nowadays to
perform topological inference were actually designed in the
early 1990s, shortly after the inception of SPM. This highlights
the fact that some control over the number of false positives
was of primary concern for neuroscientists from the very early
days. In 1991, Friston et al. (1991) proposed a first approach
based on the theory of level crossings (Adler & Hasofer, 1976;
Hasofer, 1978), and the following year, Worsley et al. (1992)
showed in a seminal paper that random field theory (RFT,
Adler, 1981) could be used to provide adjusted p-values for
local maxima based on the expected Euler characteristic (EC)
(this will be described in the next section). New distributional
results quickly emerged generalizing the approach to any
http://dx.doi.org/10.1016/B978-0-12-397025-1.00322-5
495
496
INTRODUCTION TO METHODS AND MODELING | Topological Inference
number of dimensions and for all sorts of statistical fields

(Siegmund & Worsley, 1995; Worsley, 1994; Worsley, Taylor,
Tomaiuolo, & Lerch, 2004; Worsley et al., 1996). This list of
references is a testimony to the key contributions Keith Worsley made to this field until his death in 2009 (Taylor, Evans, &
Friston, 2009). The next main contribution was to extend the
results to consider another topological feature: the spatial
extent of a cluster of voxels defined by a height threshold
(Friston et al., 1994). In Friston et al. (1996), a further level
of inference, this time concerning the number of clusters
(defined by a height threshold and an extent threshold), was
introduced, giving rise to a hierarchy of levels of inference
targeting different aspects of the signal and therefore having
different sensitivities and regional specificities.
In what follows, we review the main results of the RFT in the
light of recent work from Adler and Taylor (2007) and Taylor
and Worsley (2007). These results are then used to provide a
closed-form equation for the probability of observing c or
more clusters with k or more voxels (or resels as we shall see
later) above a threshold u in an SPM. This allows one to assign
adjusted p-values to topological features of the SPM (peak
height, cluster extent, or number of clusters) and interpret
unlikely ones as regionally specific effects, that is, activations.
Geometry of Random Fields

SPMs are interpreted as continuous statistical processes by
referring to the probabilistic behavior of random fields
(Adler, 1981; Worsley et al., 1992). In essence, the RFT models
both the univariate probabilistic characteristics of an SPM and
any nonstationary spatial covariance structure. It is used here
to generate distributional approximations for the maximum of
topological features of random field statistics that is simply and
directly related to the control of the FWER over the search space
(Nichols & Hayasaka, 2003). A gentle (but fascinating!) introduction to the theory of random fields can be found in Worsley
(1996), while avid readers will hopefully find satiety in Adler
and Taylor (2007). In this section, we review the main theoretical results used to provide a general expression for the
probability of getting any excursion set defined by three
(a)
(b)
quantities: a height threshold, a spatial extent threshold, and

a threshold on the number of clusters.
The Euler Characteristic

Let us consider a smooth random field T(s), s 2 S D ,
defined in a D-dimensional space. For example, S might be a
regular grid approximating a three-dimensional search space
(i.e., a volumetric image made of cuboid voxels) or a triangular
mesh modeling a surface (a curved 2-D manifold embedded in
a 3-D structure). The RFT allows one to make predictions about
a specific topological invariant, the EC of the excursion set,
produced by thresholding a random field. Intuitively, in two
dimensions, the EC counts the number of blobs minus the
number of holes in the set, while in three dimensions, it counts
the number of blobs minus the number of handles plus the
number of hollows (Worsley, 1996). This prediction is of
particular interest because, at high thresholds, handles and
hollows disappear, and the EC then counts the number of
blobs or local maxima, while at very high thresholds, the
excursion set is almost empty with an EC of 0 or 1, such that
the expected EC becomes the probability of getting a peak
above threshold by chance. This furnishes a very accurate
approximation of the p-value of the maximum of a smooth
random field:

max T s u s 2 S : T s u
[1]
s2S
This is the expected EC heuristic, as validated for Gaussian

fields in Taylor, Takemura, and Adler (2005) and illustrated in
Figure 1. It is only valid for high threshold u but nevertheless
provides a crucial link between a topological measure of the
search space (the expected EC) and the p-value based on the
distribution of the maximum statistic over the search space.
The ensuing p-values can then be used to assign adjusted (or
corrected) p-values to any observed peak.
Gaussian kinematic formula

The expected EC of the excursion set at threshold u has an
explicit parametric closed form given by the Gaussian
(c)
Figure 1 Illustration of the Euler characteristic (EC) heuristic. A two-dimensional Gaussian random field is displayed as a three-dimensional
surface where color is a function of amplitude. The excursion set for increasing thresholds (depicted as a blue plane) is represented underneath.
(a) Intuitively, the EC is counting the number of blobs minus the number of holes; (b) at high threshold, the EC counts the number of blobs; (c) at very
high threshold, the EC is zero or one.

kinematic formula (Taylor, 2006; Taylor & Worsley, 2007;
Worsley et al., 1996):
XD
L S; Lrd u
[2]
s 2 S : T s u
d0 d
This remarkable result is an exact expression for the
expected EC at all thresholds. It is the sum over all dimensions
of the product of two important quantities: one, Ld S, L,
measuring the topologically invariant volume of the search
space and the other, rd(u), measuring the density of events
(excursion or peaks per unit volume). Effectively, their product
is the number of events one would expect by chance (the
expected EC).
LipschitzKilling curvature and resel count

Ld S, L is called the dth LipschitzKilling curvature (LKC) of
S. It is a function of the search space S and its variogram L, the
variance of the spatial

derivatives of the component or error
fields Z: L var Z_ s . Essentially, the LKC measures the effective volume in each dimension after accounting for nonstationary smoothness of the field. When the spatial correlations
are uniform, that is, in the isotropic case L IDD, the LKCs
Ld S; L reduce to the intrinsic volumes md(S), a generalization
of the volume of S to lower-dimensional measures. An example of the intrinsic volumes for a ball of radius r is given in
Table 1. Of interest, the Dth LKC of S is the term that makes the
largest contribution in the sum of Eqn [2] and corresponds to
the volume term (Taylor & Worsley, 2007)
[3]
LD S det Ls1=2 ds 4 log 2D=2 reselD S
497
the Euclidean coordinates with the normalized residuals of the

GLM and proceed as if the data were stationary. This independence of the LKCs from the actual spatial coordinates of s 2 S
highlights their fundamental topological nature.
EC density
rd(u) is the dth EC density of the random field T(s) above u. It
corresponds to the concentration of events (excursion or
peaks) per resel. It depends on the type of statistic and threshold, but not on the geometry and smoothness. Closed-form
expressions for the EC density are available for all univariate
(Adler, 1981; Worsley, 1994; Worsley et al., 1996) and multivariate (Carbonell, Worsley, & Galan, 2008; Worsley et al.,
2004) statistics in common use. An example of the EC densities
for a t-statistic in three dimensions is given in Table 1.
Size of the Connected Components of an Excursion Set

Another topological feature of interest is the size of the connected components of an excursion set (Forman et al., 1995;
Friston et al., 1994; Poline & Mazoyer, 1994; Roland, Levin,
Kawashima, & Akerman, 1993). For a Gaussian random field,
it has been shown that, at high threshold u, the distribution of
the size of a cluster in resels, Ku, can be approximated by
(Friston et al., 1994; Nosko, 1969)

2=D

1
D
G
1
K u k exp bk2=D , where b

2
[4]
This provides a simple connection between the LKC and the

resel count introduced by Worsley et al. (1992). A resel (resolution element) is a voxel whose dimensions are commensurate with smoothness, such that the resel count reflects the
number of effectively independent observations in S (appropriately combining volume and smoothness).
An unbiased estimator of the LKCs for stationary random
fields sampled on a regular lattice is available in Kiebel, Poline,
Friston, Holmes, and Worsley (1999) and Worsley et al.
(1996). It relies on the computation of the spatial partial
derivatives of the standardized residual fields. In the nonisotropic or nonstationary case, the LKCs can be estimated by
means of statistical flattening (Taylor & Worsley, 2007; Worsley, Andermann, Koulis, MacDonald, & Evans, 1999). This
implies that one can simply estimate the LKCs by replacing
where is the expected number of resels per cluster, obtained

by computing the ratio between the expected suprathreshold
volume in resels (the product of the resel count with (1 F(u))
where F is the cumulative density function for the unit Gaussian distribution) and the expected number of clusters (approximated by the expected EC from Eqn [2]). Results for t-, w2-, and
F-fields are readily available in Cao (1999) and Cao and
Worsley (2001).
Equation [4] corresponds to the approximate p-value of the
spatial extent Ku of a single cluster (i.e., the uncorrected
p-value). In the next section, this result will be used to provide
a p-value for the largest cluster size of the excursion set, therefore providing p-values adjusted for the search space and controlling for the FWER of clusters. An empirical validation of
these results is available in Hayasaka and Nichols (2003).
Table 1
Intrinsic volumes of a ball S of radius r and EC densities for a t-statistic random field with n degrees of freedom in three dimensions (D 3).
Ft denotes the cumulative density function for the statistic in question, t here. G is the gamma function
md(S)
d
0
1
2
3
[Euler characteristic (S)]

4r
[2 caliper diameter(S)]
2pr2
[1/2 surface area(S)]
(4/3)pr3
[volume(S)]
rd(u)
1 Ft(u)

2 n1=2
2p1 1 un

Gn1
2 n1=2
2
2p3=2
u 1 un
n=21=2 Gn=2
n1=2

u2
2
2p2 n1
n u 1 1 n
498
Note that cluster sizes are here measured in resel units so

that the equation accommodates nonstationary fields where
the size of clusters in voxels might vary according to the local
smoothness of the field (Worsley et al., 1999). A correction for
the uncertainty in the estimate of the size in resels of small
clusters is given in Hayasaka, Phan, Liberzon, Worsley, and
Nichols (2004). While stationarity assumptions might be reasonable for fMRI or PET data, images, for example, from voxelbased morphometry, are known to exhibit profound nonstationarity and extent units in resels therefore have to be considered (Ashburner & Friston, 2000; Ridgway et al., 2008;
Salmond et al., 2002).
RFT Assumptions
expectation c0. The proportion of these rare events that meet

the spatial extent criterion will be K u k. These criterion
events will themselves occur according to a Poisson distribution with expectation c0 :K u k. The probability that the
number of events will be c or more is simply one minus the
probability that the number of events lies between 0 and c
minus 1. Distributional results are also available in the context
of conjunctions (Friston, 2007; Worsley & Friston, 2000).
In summary, the SPM is thresholded to make inferences
about regionally specific effects using some height and spatial
extent thresholds that are chosen by the user. Adjusted p-values
can then be derived that pertain to various topological features
of the excursion set (i.e., subset of the SPM above threshold):
The RFT results presented here rely on two main assumptions

(Worsley et al., 1996):
The component (error) fields conform to a reasonable lattice approximation of an underlying random field with a
multivariate Gaussian distribution.
These fields are continuous, with an autocorrelation function twice differentiable at the origin (not necessarily
Gaussian).
In practice, for neuroimaging data, the inference is appropriate

if (i) the threshold chosen to define the clusters is high enough
such that the expected EC is a good approximation to the
number of clusters; (ii) the lattice approximation is reasonable,
which implies the smoothness is relatively large compared to
the voxel size; and (iii) the errors of the specified statistical
model are normally distributed, which implies the model not
is not misspecified.
In order to ensure that the smoothness assumptions of the
RFT are not violated, it is common practice to smooth the data
as a preprocessing procedure: this is however not an inherent
part of topological inference as smoothness is taken into
account when estimating the resel counts. While an isotropic
Gaussian kernel is often used, it is worth noting that any type
of filtering can be used, in particular one that emphasizes the
data features of interest such as anisotropic diffusion.
Levels of Inference
A General Formulation
Under the assumptions of the Poisson clumping heuristic
(Aldous, 1989), connected components can be viewed as
clumps centered at points of a multidimensional Poisson process. Building on the results presented in the preceding text,
this allows us to construct a general expression for the probability of observing c or more clusters with k or more resels
above a threshold u in an SPM (Friston et al., 1996):
Xc1
u; k; c 1
Poisi, c0 :K u k
[5]
i0
where c0 is the expected number of maxima, approximated by
the expected EC (Eqn [2]), and Pois(.; l) is the Poisson probability density function with mean l. An intuitive interpretation
of Eqn [5] is as follows: consider clusters as rare events that
occur in a volume according to a Poisson distribution with
Set-level inference: the number of activated regions (i.e., the

number of connected subsets above some height and volume threshold). This is a statement about the activation
profile as characterized by its constituent regions (Friston
et al., 1996).
Cluster-level inference: the number of activated voxels or
resels (i.e., extent) comprising a particular connected subset
(i.e., cluster). This is a special case of set-level inference,
which can be obtained when the number of clusters c is
equal to 1:
u; k; 1 1 exp c0 :K u k c0 :K u k
[6]
This is the corrected p-value based on spatial extent (Friston

et al., 1994). An approximation is found by taking the uncorrected p-value from Eqn [4] and adjusting it using a simple
Bonferroni correction:
Peak-level inference: the height of maxima within that cluster. This is a special case of cluster-level inference that
results when the cluster can be small (i.e., k 0):
u; 0; 1 1 exp c0 c0
[7]
This is simply the corrected p-value based on the expected

number of maxima or EC (Friston et al., 1991; Worsley et al.,
1992, 1996).
A discussion on the form of control (strong or weak) over
familywise error of these procedures is available in Friston
(2007) and Nichols and Hayasaka (2003).
Several variants of the cluster-level inference presented
here have been proposed in the literature including the use
of cluster mass (Bullmore et al., 1999; Zhang, Nichols, &
Johnson, 2009), a bivariate test combining spatial extent and
peak intensity (Poline, Worsley, Evans, & Friston, 1997), and a
threshold-free approach (Smith & Nichols, 2009).
Sensitivity and Regional Specificity

On the basis of an analytical power analysis in the context of
distributed signals, Friston et al. (1996) showed that set-level
inferences are more powerful than cluster-level inferences and
that cluster-level inferences are themselves more powerful than
peak-level inferences. The price paid for the increased sensitivity is reduced localizing power. Peak-level tests permit

individual maxima to be identified as significant features, providing the highest regional specificity. Cluster- and set-level
inferences only allow clusters or a set of clusters to be identified, with a loss of anatomical precision.
In some cases, however, focal activation might actually be
detected with greater sensitivity using tests based on peak
height (with a spatial extent threshold of zero). In practice,
this is the most commonly used level of inference, reflecting
the fact that characterization of functional anatomy is generally
more useful when specified with a high degree of anatomical
precision.
Despite their lack of regional specificity, set-level inferences
can still sometimes be useful when characterizing distributed
activation patterns in studies of high-level cognitive functions
or for studies of degenerative neurological disorders with widespread pathology. Importantly, set-level inferences do not preclude lower-level inferences, as long as they are performed in a
nested, step-down fashion. All levels can be reported, each
higher level providing protection for the lower level, allowing
for a better characterization of the significance of the results
obtained (Friston, 2007).
499
Chumbley et al., 2010) and therefore still relies on the distributional results from the RFT, as opposed to controlling the
FDR of point tests (e.g., t-tests at each voxel or vertex)
(Genovese, Lazar, & Nichols, 2002).
Topological inference is nowadays a standard practice in
the analysis of imaging modalities such as functional magnetic
resonance imaging (fMRI) and positron emission tomography
(PET) (Nichols, 2012) and electroencephalography (EEG)
and magnetoencephalography (MEG) (Kilner & Friston,
2010; Kilner, Kiebel, & Friston, 2005). Interestingly, thanks
to the generality of the RFT and its suitability to any type
of smooth data lying on a manifold, it has also found applications in numerous fields such as cosmology (Worsley, 1995),
meteorology (Worsley, 2002), and pedobarography (Pataky,
2008).

Analysis of Variance (ANOVA); Contrasts and Inferences; False
Discovery Rate Control; Posterior Probability Maps; The General Linear
Model.
Anatomically Closed Hypotheses

The p-value adjustment is based explicitly on the search space,
giving the researcher the latitude to restrict the search space to
the extent that prior knowledge imposes. If one has as is often
the case some a priori idea of where the activation should be,
one can prespecify a small search space and make the appropriate correction instead of having to control for the entire
search space (Worsley et al., 1996). Note that it is sometimes
more appropriate to surround a small but highly convoluted
search space by an encompassing sphere with slightly higher
volume but less surface area: this is because the lowerdimension terms of the Gaussian kinematic formula play a
larger role in this setting. An alternative approach is to use
the uncorrected p-value based on the spatial extent of the
nearest cluster (Friston, 1997).
Final Remarks
RFT can be adopted in any situation in which one would
normally perform parametric statistical tests, such as t- or
F-tests. When these cannot be used, for example, when the
errors are not normally distributed, the requisite null distribution of the maximum statistic can be estimated using nonparametric procedures, such as resampling (Hayasaka & Nichols,
2003; Maris & Oostenveld, 2007; Nichols & Holmes, 2002).
Permutation methods also offer substantial improvements
over the RFT for extreme situations such as low smoothness
or low degrees of freedom (Nichols & Hayasaka, 2003). In such
settings, a Bonferroni correction can be used as a safeguard for
overconservativeness of the RFT.
Note that we have here focused on the use of the RFT for
controlling the FWER of topological features in statistical
maps; similar ideas can also be used to control the false discovery rate (FDR) (Benjamini & Hochberg, 1995). Crucially,
topological FDR controls for the expected FDR of features
(such as peaks or clusters) (Chumbley & Friston, 2009;
References
Adler, R. J. (1981). The geometry of random fields. New York: Wiley.
Adler, R. J., & Hasofer, A. M. (1976). Level crossings for random fields. The Annals of
Probability, 4(1), 112.
Adler, R. J., & Taylor, J. E. (2007). Random fields and geometry. New York: Springer.
Aldous, D. J. (1989). Probability approximations via the Poisson clumping heuristic.
New York: Springer-Verlag.
Ashburner, J., & Friston, K. J. (2000). Voxel-based morphometry The methods.
NeuroImage, 11(6 Pt 1), 805821.
Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical
and powerful approach to multiple testing. Journal of the Royal Statistical Society:
Series B Methodological, 57(1), 289300.
Bullmore, E. T., Suckling, J., Overmeyer, S., Rabe-Hesketh, S., Taylor, E., &
Brammer, M. J. (1999). Global, voxel, and cluster tests, by theory and permutation,
for a difference between two groups of structural MR images of the brain. IEEE
Cao, J. (1999). The size of the connected components of excursion sets of w2, t and F
fields. Advances in Applied Probability, 31(3), 579595.
Cao, J., & Worsley, K. J. (2001). Applications of random fields in human brain
mapping. In M. Moore (Ed.), Spatial statistics: Methodological aspects and
applications (pp. 169182). New York: Springer.
Carbonell, F., Worsley, K. J., & Galan, L. (2008). The geometry of the Wilkss L random
field. Annals of the Institute of Statistical Mathematics, 63(1), 127.
Chumbley, J., & Friston, K. J. (2009). False discovery rate revisited: FDR
and topological inference using Gaussian random fields. NeuroImage, 44(1),
6270.
Chumbley, J., Worsley, K. J., Flandin, G., & Friston, K. J. (2010). Topological FDR for
Flandin, G., & Friston, K. J. (2008). Scholarpedia, 3(4), 6232.
Forman, S. D., Cohen, J. D., Fitzgerald, M., Eddy, W. F., Mintun, M. A., & Noll, D. C.
(1995). Improved assessment of significant activation in functional magnetic
resonance imaging (fMRI): Use of a cluster-size threshold. Magnetic Resonance in
Medicine, 33(5), 636647.
Friston, K. J. (1997). Testing for anatomically specified regional effects. Human Brain
Mapping, 5(2), 133136.
Friston, K. J. (2007). Statistical parametric mapping: The analysis of functional brain
images. Amsterdam/Boston, MA: Elsevier/Academic Press.
Friston, K. J., Frith, C. D., Liddle, P. F., & Frackowiak, R. S.J (1991). Comparing
functional (PET) images: The assessment of significant change. Journal of Cerebral
Blood Flow & Metabolism, 11(4), 690699.
Friston, K. J., Holmes, A., Poline, J. B., Price, C. J., & Frith, C. D. (1996). Detecting
activations in PET and fMRI: Levels of inference and power. NeuroImage, 4(3),
223235.
500
Frackowiak, R. S. J. (1995). Statistical parametric maps in functional imaging: A
general linear approach. Human Brain Mapping, 2(4), 189210.
Friston, K. J., Worsley, K. J., Frackowiak, R. S.J, Mazziotta, J. C., & Evans, A. C. (1994).
Assessing the significance of focal activations using their spatial extent. Human
Genovese, C. R., Lazar, N. A., & Nichols, T. N. (2002). Thresholding of statistical maps
in functional neuroimaging using the false discovery rate. NeuroImage, 15(4),
870878.
Hasofer, A. M. (1978). Upcrossings of random fields. Advances in Applied Probability,
10, 14.
Hayasaka, S., & Nichols, T. E. (2003). Validating cluster size inference: Random field
and permutation methods. NeuroImage, 20(4), 23432356.
Hayasaka, S., Phan, K. L., Liberzon, I., Worsley, K. J., & Nichols, T. E. (2004).
NeuroImage, 22(2), 676687.
Hochberg, Y., & Tamhane, A. C. (1987). Multiple comparison procedures. New York:
Wiley.
Kiebel, S. J., Poline, J. B., Friston, K. J., Holmes, A. P., & Worsley, K. J. (1999). Robust
smoothness estimation in statistical parametric maps using standardized residuals
from the general linear model. NeuroImage, 10(6), 756766.
Kilner, J. M., & Friston, K. J. (2010). Topological inference for EEG and MEG. Annals of
Applied Statistics, 4(3), 12721290.
Kilner, J. M., Kiebel, S. J., & Friston, K. J. (2005). Applications of random field theory to
electrophysiology. Neuroscience Letters, 374(3), 174178.
Maris, E., & Oostenveld, R. (2007). Nonparametric statistical testing of EEG- and MEGdata. Journal of Neuroscience Methods, 164(1), 177190.
Nichols, T. E. (2012). Multiple testing corrections, nonparametric methods, and random
field theory. NeuroImage, 62(2), 811815.
Nichols, T. E., & Hayasaka, S. (2003). Controlling the familywise error rate in functional
neuroimaging: A comparative review. Statistical Methods in Medical Research,
12(5), 419446.
Nosko, V. P. (1969). Local structure of Gaussian random fields in the vicinity of high
level shines. Soviet Mathematics Doklady, 10, 14811484.
Pataky, T. C. (2008). Assessing the significance of pedobarographic signals using
random field theory. Journal of Biomechanics, 41(11), 24652473.
Poline, J. B., & Mazoyer, B. M. (1994). Analysis of individual brain activation maps
using hierarchical description and multiscale detection. IEEE Transactions on
Poline, J. B., Worsley, K. J., Evans, A. C., & Friston, K. J. (1997). Combining spatial
extent and peak intensity to test for activations in functional imaging. NeuroImage,
5(2), 8396.
Ridgway, G. R., Henley, S. M.D, Rohrer, J. D., Scahill, R. I., Warren, J. D., & Fox, N. C.
(2008). Ten simple rules for reporting voxel-based morphometry studies.
NeuroImage, 40(4), 14291435.
Roland, P. E., Levin, B., Kawashima, R., & Akerman, S. (1993). Three-dimensional
analysis of clustered voxels in 15O-butanol brain activation images. Human Brain
Mapping, 1(1), 319.
Salmond, C. H., Ashburner, J., Vargha-Khadem, F., Connelly, A., Gadian, D. G., &
Friston, K. J. (2002). Distributional assumptions in voxel-based morphometry.
NeuroImage, 17(2), 10271030.
Shaffer, J. P. (1995). Multiple hypothesis testing. Annual Review of Psychology, 46(1),

561584.
Siegmund, D. O., & Worsley, K. J. (1995). Testing for a signal with unknown location
and scale in a stationary Gaussian random field. The Annals of Statistics, 23(2),
608639.
Smith, S., & Nichols, T. N. (2009). Threshold-free cluster enhancement: Addressing
Taylor, J. E. (2006). A Gaussian kinematic formula. The Annals of Probability, 34(1),
122158.
Taylor, J. E., Evans, A. C., & Friston, K. J. (2009). A tribute to: Keith Worsley 1951
2009. NeuroImage, 46(4), 891894.
Taylor, J. E., Takemura, A., & Adler, R. J. (2005). Validity of the expected Euler
characteristic heuristic. The Annals of Probability, 33(4), 13621396.
Taylor, J. E., & Worsley, K. J. (2007). Detecting sparse signals in random fields, with an
application to brain mapping. Journal of the American Statistical Association,
102(479), 913928.
Worsley, K. J. (1994). Local maxima and the expected Euler characteristic of excursion
sets of w2, F and t fields. Advances in Applied Probability, 26, 1342.
Worsley, K. J. (1995). Boundary corrections for the expected Euler characteristic of
excursion sets of random fields, with an application to astrophysics. Advances in
Applied Probability, 27(4), 943.
Worsley, K. J. (1996). The geometry of random images. Chance, 9(1), 2740.
Worsley, K. J. (2002). Gaussian random field. In A. H. El-Shaarawi & W. W. Piegorsch
(Eds.), Encyclopedia of environmetrics (p. 1674). Chichester, NY: Wiley.
Worsley, K. J., Andermann, M., Koulis, T., MacDonald, D., & Evans, A. C. (1999).
Detecting changes in nonisotropic images. Human Brain Mapping, 8(23), 98101.
Worsley, K. J., & Friston, K. J. (2000). A test for a conjunction. Statistics & Probability
Letters, 47(2), 135140.
Worsley, K. J., Liao, C. H., Aston, J., Petre, V., Duncan, G. H., Morales, F., & Evans, A. C.
(2002). A general statistical analysis for fMRI data. NeuroImage, 15(1), 115.
of cerebral activation. Human Brain Mapping, 4(1), 5873.
Worsley, K. J., Taylor, J. E., Tomaiuolo, F., & Lerch, J. (2004). Unified univariate and
multivariate random field theory. NeuroImage, 23, S189S195.
Zhang, H., Nichols, T. E., & Johnson, T. D. (2009). Cluster mass inference via random
field theory. NeuroImage, 44(1), 5161.
Relevant Websites
Neuroimaging software implementing topological inference using random
field theory
http://www.math.mcgill.ca/keith/fmristat FMRISTAT.
http://fsl.fmrib.ox.ac.uk FSL.
http://nipy.org NIPY.
http://www.fil.ion.ucl.ac.uk/spm SPM.
http://www.math.mcgill.ca/keith/surfstat SurfStat.
False Discovery Rate Control

CR Genovese, Carnegie Mellon University, Pittsburgh, PA, USA
Glossary
Bonferroni correction A simple (and somewhat

conservative) method for controlling the familywise error
rate.
Density function A representation of the probability
distribution for a continuous random variable. For a random
variable X with a continuous distribution, the density
function describes the limiting probability mass per unit
length over shrinking intervals around a point. It can be
computed as the derivative of the distribution function.
Distribution function A representation of the probability
distribution for a random variable. For a random variable X,
the distribution function of X is given by G(t) {X t}.
False discovery rate The expected proportion of false
discoveries relative to the total number of rejected null
hypotheses.
False-negative, false nondiscovery, or type II error A
testing error in which one retains the null hypothesis when it
is in fact false.
False-positive, false discovery, or type I error A testing
error in which one rejects the null hypothesis when it is in
fact true.
Familywise error rate The probability that any
of a set (or family) of null hypotheses are incorrectly
rejected.
Per-comparison error rate The expected number of false
discoveries made during multiple testing divided by the
number of tests.
The Multiple-Testing Problem

A common and fundamental statistical operation is to decide
between two possible hypotheses for explaining the observed
data. Is there a difference between treatment groups? Was there
activity associated with this voxel? Does the response tend to
increase with the value of a specified covariate? The statistical
procedure used to make such a decision is called a hypothesis test.
In the frequentist paradigm, the logic of hypothesis testing
is based on surprise. One starts with the assumption that the
true data-generating mechanism belongs to a specified collection of default models, called the null hypothesis. (In practice,
the null hypothesis often consists of only one model. Models
not in the null hypothesis are called alternative hypotheses.)
Then one asks whether the observed data are surprising enough
under this assumption that one would rather change the
assumption than ascribe the observation to chance.
There is an intrinsic asymmetry between these two outcomes. If the observations are sufficiently surprising, we reject
the null hypothesis, concluding that the data are not explained by
one of its constituent models. If the observations are not
sufficiently surprising, we merely retain the null hypothesis;
Per-family error The expected number of false discoveries

made during multiple testing.
Power The probability of correctly rejecting a false null
hypothesis or one minus the probability of a type II error.
p-Value The probability under the null distribution that a
test statistic is more surprising (e.g., more extreme) than the
value of the test statistic that was observed. A test can be
performed by comparing the p-value to a significant level,
rejecting the null when p a. In the idealized version of
hypothesis testing, one picks ahead of time and performs
the test, but in practice, one computes a p-value and anyone
can compare that to a chosen significance level.
Sampling distribution The probability distribution of a
statistic under repeated random sampling of the data.
Significance level, a level A measure of how surprised one
needs to be to reject the null hypothesis. In most practical
cases, this is the specified probability under the null
hypothesis at which one would reject the null (see also
p-value). More generally, the level is a bound on the
probability of rejecting across all models within null
hypothesis.
Test statistic A random quantity computed from the data
that is used to perform a hypothesis test. The distribution of
a test statistic should be known (at least to good
approximation) when the null distribution is true, allowing
one to determine the threshold for a specified a level.
Voxel A three-dimensional volume element in
neuroimaging.
we do not know whether the null hypothesis is true or the

data are just not informative enough to reject it. The level of
surprise is gauged by comparing the value of a test statistic,
computed from the data, to a reference distribution derived
under the null hypothesis. Values in the tails of the reference
distribution are considered more surprising.
The threshold of what is sufficiently surprising to reject the
null hypothesis is arbitrary, ostensibly chosen by subject-matter
considerations and subjective needs but usually chosen by
convention. This choice governs a critical trade-off between
two types of errors: rejecting the null hypothesis when it is
true (false-positive, false discovery, or type I error) or retaining
the null hypothesis when it is false (false-negative, false nondiscovery, or type II error). The threshold for the test is given as a
bound on the probability of rejecting the null hypothesis under
each model in the null hypothesis, called the significance level
and usually denoted by a. The smaller a, the more surprising the
value of the test statistic needs to be to reject the null hypothesis. A small a protects against a false discovery but gives the test
poorer resolving power for distinguishing models in the null
hypothesis (null models) from models outside it (alternative
models). (In practice, it is more common to compute p-values
http://dx.doi.org/10.1016/B978-0-12-397025-1.00323-7
501
502
INTRODUCTION TO METHODS AND MODELING | False Discovery Rate Control
Type I
error rate
Type II
error rate
Threshold
Figure 1 The sampling distributions under the null and alternative

hypotheses and the tail areas representing error probabilities of each
type. The threshold is specified by the choice of , the probability of a
rejection under the null hypothesis.
from the test statistics, which can be used to perform the test at
any specified level.).
Figure 1 illustrates this trade-off. It shows the sampling
distribution of the test statistic under both a null and alternative model and a choice of significance level, with the probabilities of false discovery (type I error) and false nondiscovery
(type II error) depicted as shaded areas under the corresponding distributions. These probabilities vary with both a and the
difficulty of distinguishing between null and alternative distributions (e.g., the separation between the two distributions in
the figure).
In practice, the problem of performing a single hypothesis
test reduces to a problem of error control. (It should be noted
that the description of hypothesis testing here is based on the
frequentist paradigm. The Bayesian approach to statistics leads
to a different perspective on testing.) It is true that the resolving
power of a hypothesis test can be improved by increasing the
amount of data used, by reducing the intrinsic variability
(noise) in the measurements, and sometimes by choosing
a more effective test statistic. But for a given data set and in a
common situation where good tests have been constructed
(e.g., t-test for comparing group means), a practitioners only
real choice is how to balance the two types of errors, with the
choice of mediating the trade-off between false discoveries
and false nondiscoveries.
However, it is rare for a practitioner to need only a single
hypothesis test, and error control becomes much more complicated when performing many tests simultaneously. Consider, for instance, the case in functional neuroimaging where
we want to test for a treatment effect at each voxel in some
region of interest. A test of the null hypothesis that no voxels
exhibit a treatment effect is of some interest but limited usefulness. There are many interesting alternatives to the null
hypothesis (corresponding to nonzero effects at different combinations of voxels), but a single hypothesis test does not
distinguish among them. Instead, we can perform a test at
each voxel of the null hypothesis that the signal at that voxel
exhibits no treatment effect. Controlling the error rate for each
test in isolation will lead to an effective error rate that scales
with the number of tests performed. So we need an error
control strategy for the individual tests that guarantees control
of some measure of error for the combined inference. Ideally,
this strategy would account for statistical dependence among
the test statistics and structural relations (e.g., spatial contiguity) among the inferences. This is the multiple-testing problem.
As an illustration of the problem, consider m simultaneous
level a tests with test statistics that are statistically independent.
Then, under the null hypothesis for every test, the probability
that there will at least one false discovery among the m tests is
no bigger than 1 (1 a)m, which is approximately ma when a
is small. When a 0.05 and m 1000, the probability of a false
discovery is close to 1 when all the null hypotheses are true,
and the expected number of false discoveries is 50. Setting
a 5.13 105 0.05/1000 reduces the probability of false
discoveries to 0.05. Thus, controlling the combined measure
of error requires a much more stringent threshold for surprise
in the individual tests, with a consequent loss of power for
detecting small deviations from the null hypotheses. Traditional approaches to error control in multiple testing have
centered on maximizing detection power while guaranteeing
control of the probability of making any errors.
Benjamini and Hochberg (BH) (1995) introduced a new
criterion for control the false discovery rate (FDR) which is
the expected portion of rejected null hypotheses that were false
rejected. This allows a multiple-testing strategy to increase
detection power while maintaining principled control of a
combined error measure. BH also introduced a simple method
that guarantees control of FDR under certain assumptions (see
Genovese, Lazar, & Nichols, 2002 for a neuroimaging-focused
review).
Figure 2 illustrates the difference between traditional error
control and FDR error control on the same data. Each panel
shows the results of tests for 20 batches of data. Every batch
contains 1000 points independently drawn from a Gaussian
whose mean increases toward the center of the gray circle and
is zero outside it. The points shown for each batch are those for
which the null hypothesis of zero mean is rejected. The traditional (familywise) control correctly captures points near the
middle of the circle where the signal is highest and, with one
exception, correctly ignores points outside the gray signal
where the signal is truly zero. But it misses most of the points
on the margin of the circle where the signal is weaker but
potentially interesting. In contrast, FDR control not only captures points all the way toward the edges of the circle but also
incorrectly captures a small portion of points outside the circle.
Both the traditional and the BH approaches will be discussed
in detail in the ensuing sections.
Traditional Error-Control Methods

To appreciate the advantages and disadvantages of FDR control, it is helpful to consider traditional approaches to error
control in multiple testing. Suppose we are testing m null
hypotheses simultaneously. A multiple-testing procedure is
an algorithm for determining from the data which of the m
null hypotheses to reject so as to control some combined
measure of error. For any fixed multiple-testing procedure, we
can decompose the results of each hypothesis test according to
the result of the test and the truth, as in Table 1.
We will need some further notation for what follows. Let
Z1, Z2, . . ., Zm denote the values of the test statistics (computed
from the data) for each test, and let P1, P2, . . ., Pm denote the
corresponding p-values. The p-values are the probabilities
under the null hypothesis of observing a value of the test
statistic at least as surprising as what was observed. We will
also denote the sorted p-values by 0 < P(1) P(2) . . . P(m).
503
Figure 2 Tests were performed on 20 batches of data using both a traditional familywise error-controlling procedure and an FDR-controlling
procedure. In each batch, 1000 test statistics are drawn from normal distributions with means corresponding to their location on the plot. Points outside
the gray circle have mean 0 (no signal); points inside the circle have mean rising smoothly as their position moves closer to the center. The points
shown correspond to rejected null hypotheses.
Table 1
Breakdown of m hypothesis tests according to whether the
null hypothesis is true or false and whether the null hypothesis is rejected
or retained
Null hypothesis
true
Null hypothesis
false
Total
Null hypothesis
rejected
Null hypothesis
retained
Total
m0 V
m0
m m0 S
m m0
mR
The entries in the cells denote the corresponding counts.
For any i, let Hi and H(i) denote the null hypothesis corresponding to Pi and P(i), respectively.
The most often considered traditional criteria for error control are
1. familywise error rate (FWER), {V 1}, the probability of
at least one false discovery;
2. per-family error rate (PFER), V , the expected number of
false discoveries; and
3. per-comparison error rate (PCER), V =m, the proportion
of false discoveries relative to the total number of tests.
These rates satisfy PCER FWER PFE. While arguments have
been made for controlling all of these rates, FWER is the most
commonly used and will be the focus here. See Hochberg and
Tamhane (1987) and Shaffer (1995) for a discussion of the
relative merits of the criteria and of the meaning of a family of
tests. See also Nichols and Hayasaka (2003) for a review of
FWER control in neuroimaging.
FWER is a stringent criterion, requiring a small probability
of any false discoveries no matter how many tests are performed. This is a valuable guarantee, but it makes detection
power a primary concern. This has spurred the search for FWERcontrolling procedures that improve power, both for general
use and for target situations (e.g., contrasts in normal linear

models). More recently, modifications of the criteria itself have
been considered to allow for principled control with greater
power. For instance, Lehman and Romano (2005) and Van der
Laan, Dudoit, and Pollard (2004) generalized the FWER to
{V k} for each fixed integer k 1, with the idea that one
specifies a criterion in advance. In a neuroimaging context,
Forman et al. (1995) extended FWER with a contiguity criterion
designed to improve power. The random field-based
approaches to multiple testing (e.g., Worsley, 2005; Worsley,
Evans, Marrett, & Neelin, 1992) capture contiguity in a different
way with effective tests for coherent regions of large signal; this
is analogous to FWER control targeted to meaningful
alternatives.
The classical method for FWER control is the simple Bonferroni correction: perform each test at level a/m. (More generP
ally, test i can be performed at level ai where
iai a.)
Bonferroni guarantees that FWER a for any configuration of
true and false null hypotheses, though the FWER will often be
strictly less than a as in the independent example in the preceding text. (This is called strong control of FWER; weak control
only guarantees FWER a when all m null hypotheses are
true.)
An improvement on Bonferroni was given in Holm (1979)
and is sometimes called the HolmBonferroni method. Unlike
Bonferroni, which decides upon all the hypotheses at once, the
Holms method proceeds through the ordered p-values sequentially, beginning with P(1). If P(1) > a/m, then all null hypotheses are retained. Otherwise, if P(2) > a/(m 1), then H(1) is
rejected and the rest retained, and so on. More succinctly,
H(1), . . ., H(k1) are rejected and the remaining null hypotheses
a
are retained where 1 k m is the first index with Pk > mk1
.
This guarantees FWER a for all configuration of true and false
null hypotheses and, like Bonferroni, makes no assumptions
about statistical (in)dependence among the test statistics.
A wide variety of alternative FWER-controlling methods
have been developed (Hochberg & Tamhane, 1987; Shaffer,
1995). Many of these have more power than HolmBonferroni
504
but at the cost of more stringent assumptions (for instance, on

the dependence structure of the tests). One approach to constructing high-power FWER-controlling procedures is the
closure principle (Finner & Roters, 2002; Marcus, Peritz, &
Gabriel, 1976), which requires that a hypothesis be rejected if
and only if all intersections of hypotheses that imply it are also
rejected. The HolmBonferroni method is a closed procedure
in this sense.
The FDR and the BenjaminiHochberg Algorithm

The FDR is an alternative criterion introduced by Benjamini
and Hochberg (1995) to allow for meaningful error control
with greater detection power than FWER-controlling methods.
The FDR is defined as the expected proportion of false discoveries relative to all discoveries (rejections of the null).
Mathematically,
FDR
V
;
min R, 1
[1]
which gives 0 FDR 1 with FDR 0 when no null hypotheses are rejected. Comparing the FWER and FDR criteria shows
how FDR control can achieve more power at the cost of more
type I errors. While a small FWER ensures that V 0 with high
probability, a small FDR allows V to be large as long as (on
average) the number of rejections is substantially larger. Metaphorically, FWER control yields smaller servings of wheat
nearly free of chaff, while FDR control yields a larger serving
of wheat with some but not too much chaff mixed in.
The expectation in the definition [1] makes FDR a population quantity. In particular, knowing that FDR a means that if
one were to repeat the tests every day with new data (but the
same configuration of true and false null hypotheses), the
proportions of false discoveries relative to the number of rejections would average approximately a over many days. For any
specific data set, the proportion could be higher or lower than
the controlled level.
The BH Procedure
Building on the observations of Simes (1986), BH developed a
procedure for controlling FDR at a specified level under some
assumptions about the dependence of the tests. The procedure
is computationally simple: reject all Hi for which Pi TBH,
where

i
TBH max Pi : Pi a , for 0 i m
[2]
m
defining P(0) 0.
BH proved that for independent test statistics, this procedure guarantees
FDR
m0
a
m
[3]
for any configuration of true and false null hypotheses. When

the test statistics have continuous distributions (as opposed to
discrete), BH prove that the inequality in eqn [3] is actually an
equality.
This shows that the BH procedure overcontrols FDR, with

corresponding loss of detection power, and that the procedure
performs best in the sparse case m0 m, where most of the null
hypotheses are true. Benjamini and Yekutielii (2001) showed
that the BH procedure controls the FDR at level a whenever the
test statistics are positively dependent in a specific sense that
includes the case of Gaussian variables that are all positively
correlated. Benjamini and Yekutielii (2001) also
showed that
Xm
1
for any
the BH procedure controls FDR at level amm0
i1 i
dependence relations among the test statistics. Applying the
P
BH procedure with level a/ i(1/i) is a general technique for
controlling FDR at level a, but unfortunately, this can be very
conservative, often more so than the Bonferroni correction.
Why the BH Procedure Works

To understand why the BH method works, it helps to consider
a useful model for the p-values first proposed by Efron,
Tibshirani, Storey, and Tusher (2001). In this two-group
model, each null hypothesis is false with probability
0 a 1, independently. Hypotheses with a true null hypothesis have p-values drawn from a uniform distribution; those
with a false null hypothesis are drawn marginally from an
arbitrary distribution. So, marginally, the p-values P1, . . ., Pm
are independent and identically distributed draws from a
cumulative distribution function G. See Genovese and
Wassermann (2002, 2004) for more details on this setup.
For a fixed value 0 < t < 1, if we reject all null hypotheses for
which Pi t, the resulting FDR(t) is
FDRt
1 at
Gt
[4]
for large m. On the other hand, the BH p-value threshold is the

largest value of t for which
d t 1 a^t
FDR
G^m t
[5]
where we have estimated a^ 0 and G^m t #fPmi t g. The latter,

the proportion of p-values smaller than t, is an estimate of G(t)
that gets better and better as m grows.
Thus, the BH procedure works by estimating the FDR from
the data and picking the largest threshold at which the estimated FDR is controlled. The estimates use the marginal,
empirical distribution of the p-values and the assumption of
no false null hypotheses. This explains the better performance of
the procedure in the sparse case (m0 m) and its asymptotic
performance for large m. It also points to ways to improve
power, as described in the succeeding text.
Choosing Levels and Drawing Conclusions

The choice of level at which FDR is controlled is an arbitrary
and subjective one that must be made a priori. Interpretation
of the level is complicated by the ratio in the definition of FDR
and by its coupling all the tests. In particular, it has different
implications for the number of errors when there are few versus
many rejections. A common way to choose the bound is to use
simple, conventional values like 0.01, 0.05, and 0.1. This has
the advantage of limiting the opportunity for special, post hoc

tuning. An alternative is to use the expected number of rejections (from experience, pilot data, or an educated guess) to set
a tolerable bound for the number of false discoveries. In the
end, having a consistent approach is probably more important
than trying to optimize the choice on a case-by-case basis.
Because FDR is a population quantity, FDR control does
not lead to any sharp conclusions about the true number of
false discoveries. For example, having guaranteed FDR < 0.01
and rejecting 100 null hypotheses, one cannot claim that there
is at most one false discovery.
Extensions of False Discovery Control

The broad success of the BH method has led to efforts to
broaden its applicability, increase its power, and generalize
the criterion in scientifically useful ways.
Adaptive FDR control. The tendency of the BH method to
overcontrol by the factor m0/m, thus losing power, suggests a
correction: estimate the number of true null hypotheses via
^0 and then apply the BH method with level
some statistic m
^0 . This is the template on which several adaptive, or multia=m
stage, FDR-controlling methods are based. Several estimates
of the number of true (or false) null hypotheses have been
constructed, not only most notably Jin and Cai (2007),
Meinshausen and Rice (2006), and Storey, Taylor, and
Siegmund (2004) but also Benjamini and Hochberg (2000),
Genovese and Wasserman (2004), Meinshausen and
Buhlmann (2005), Nettleton and Hwang (2003), Schweder
and Spjotvoll (1982), and Storey (2002). The second and
third of these are computed directly from the empirical distribution function of the p-values G^m introduced earlier.
Benjamini, Krieger, and Yekutieli (2006) used the BH method
twice, taking the number of nonrejected nulls at one level as a
first-stage estimate of m0 to be used in the BH method at the
second stage. Simulations and asymptotic theory support the
claim that these methods can improve power over standard
BH, although the robustness of these gains under variations in
the assumptions (e.g., dependence) is not fully understood.
Reiss, Scwartzman, Lu, Huang, and Proal (2012) discussed the
paradoxical results that can arise when applying these adaptive
methods to neuroimaging data and made recommendations
on how best to use them in that context.
Dependence. The validity of FDR control under the BH
method depends on the statistical dependence relations
among the test statistics. As mentioned earlier, BH gives valid
control with positively dependent or independent test statistics and controls at a level above nominal in general. Guo and
Raoo (2008) constructed a distribution where the FDR is
P
a i1/i, showing that the general bound is sharp. But such a
distribution is difficult to construct from standard test statistics, and in practice, the BH method is hard to break too badly.
Simulations and asymptotic analysis in Finner, Dickhaus, and
Roters (2007) show that the distribution V/min(R, 1), and thus
the power of FDR-controlling procedures, can be highly sensitive to small changes in the dependence relations among the
test statistics. Troendle (2000), Yekutieli and Benjamini
(1999), and Romano, Shaikh, and Wolf (2008) developed
resampling-based methods. The first is restricted to normal/t
models. The third incorporates information on the
505
dependence structure and can be extended to tail-control criteria, but the theory behind it is only asymptotic.
Tail control. An alternative to controlling the expectation of
V/min(R,
1) is to
n
o control the probability that this ratio is large,
V
> c for a specified c. Methods for controlling this
min R, 1
measure were introduced by Genovese and Wasserman (2004)
and Dudoit, Van Der Laan, and Pollard (2004), and such
tail control has received substantial attention in the literature
(Genovese & Wasserman, 2004, 2006; Guo, He, & Sarkar,
2014; Guo & Rao, 2010; Guo & Roman, 2007; Hommel &
Hoffmann, 1987; Lehman & Romano, 2005; Romano &
Shaikh, 2006).
False nondiscovery rate. Analogous to type II error, a complement to the FDR is the false nondiscovery rate where
m m0 S=m R is the proportion of incorrectly retained
null hypotheses relative to the total number of retained nulls.
This was introduced in Genovese and Wassermann (2002)
with the goal of choosing a threshold that minimizes this rate
subject to specified control of FDR. The criterion has been the
subject of active study, including Genovese and Wasserman
(2004), Jichun Xie, Cai, Maris, and Li (2011), Sarkar (2002,
2007), and Sun and Cai (2007).
Positive FDR. Storey (2002, 2003) introduced (and developed a method to control) an alternative error criterion called the
positive false discovery rate (pFDR). The pFDR is defined by

V
R > 0
[6]
pFDR
min R, 1
and is related to the FDR by FDR pFDR {R > 0}. The pFDR
has a nice Bayesian interpretation: assuming that all null
hypotheses have the same prior probability of being true, the
pFDR is the posterior probability of an incorrect rejection of a
null hypothesis.
Local FDR. Building on the two-group model for p-values
described earlier, Efron et al. (2001) introduced the local FDR
as an alternative criterion where FDR is based on distribution
functions (recall FDR(t) (1 a)t/G(t)), or equivalently tail
areas, derived from the null and marginal test-statistic density
functions, which are more difficult to estimate. The local FDR
is an empirical Bayesian posterior probability of a true null
given the observed test statistic and thus has the advantage of
ease of interpretation and amenability to theoretical analysis.
Empirical null distributions. Efron (2004, 2007a, 2007b)
pointed out that in many large-scale studies, the theoretical
null distribution of the test statistics is misspecified, due, for
instance, to hidden dependencies, artifacts, and other factors.
This bias can adversely affect the performance of multipletesting methods. These papers describe an empirical Bayesian
approach to multiple testing that involves estimating the null
distribution and using the estimated null distribution for testing. While this necessarily involves some loss of power relative
to the theoretical ideal, it improves performance relative to the
case where the theoretical null is significantly misspecified.
Schwartzman (2008) extended empirical-null procedures to
general exponential-family distributions.
Spatial contiguity and random fields. In many applications,
most notably functional neuroimaging, the unit of testing (e.g.,
the voxel) is not the same as the unit of inference (e.g., the
region). Control of voxelwise error measures such as FDR need
not relate in a simple way to the corresponding regional error
506
measures, and indeed, Chumbley and Friston (2009)

demonstrated that voxelwise FDR control can induce large
region FDR levels. Several related methods have been developed for controlling regional FDR (Benjamini & Heller, 2007;
Chumbley & Friston, 2009; Friedenberg & Genovese, 2013;
Heller, Stanley, Yekutieli, Rubin, & Benjamini, 2006; Perone
Pacifico, Genovese, Verdinelli, & Wasserman, 2004, 2007). For
instance, Benjamini and Heller (2007) used a hierarchical
approach, first controlling FDR on regions and then cleaning
locations with no signal with a voxelwise analysis. Perone
Pacifico et al. (2004) and Chumbley and Fristonn (2009)
developed methods based on random fields with different
notions of erroneous regions.
Alternative Approaches to the Multiple-Testing

Problem
Higher criticism. Donoho and Jinn (2008) introduced an
approach for detecting rare and weak signals, called the
higher criticism after Tukey, that can be adapted to multiple
testing. This constructs a function of the threshold

G^m t t
p
[7]
HCt m q

G^m t 1 G^m t
and defines the testing threshold THC to be the value of P(i)
achieving maxiHC(P(i)). One rejects all Hi for which Pi THC.
The higher criticism has advantages in improved (and in some
sense optimal) classification performance under certain
regimes with few nonzero signals of small magnitude, making
it a worthwhile alternative to FWER- and FDR-based multipletesting approaches in some situations.
Eschewing p-values. Sun and Cai (2007) developed a compound decision framework for multiple testing and showed
that simple rules based on p-values (as in the methods
described earlier in the text) do not lead to statistically efficient
procedures. Their compound rule estimates the distribution of
test statistics from the data and uses this to construct a test.
They showed that their method achieves an optimality (oracle)
bound and outperforms BH and related adaptive methods. Sun
and Cai (2009) extended this idea to show how to exploit
structural information about dependence in the data to
improve multiple-testing performance further. Sun, Reich,
Cai, Guindani, and Schwartzman (2014) provided compound
decision rules for FDR control, tail control, and regional FDR
control.
Conclusions
Procedures for controlling FDR in multiple testing provide a
principled way to improve detection power and are useful in
large-scale testing regimes like those found in functional neuroimaging. The standard BenjaminiHochberg method is a
computationally simple and broadly applicable procedure
that performs well in variety of realistic situations. Substantial
research has extended this procedure in a variety of ways to
handle alternative dependence structures, increase power with
multistage decisions, and provide alternative error measures
that may be relevant to practitioners. Extensions beyond simple p-value-based rules promise further improvements in statistical efficiency and the ability to target new kinds of
dependence structures in data.
References
Benjamini, Y., & Heller, R. (2007). False discovery rates for spatial signals. Journal of
the Acoustical Society of America, 102, 12721281.
Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical
and powerful approach to multiple testing. Journal of the Royal Statistical Society,
Series B: Statistical Methodology, 57(1), 289300.
Benjamini, Y., & Hochberg, Y. (2000). The adaptive control of the false discovery rate in
multiple comparison problems. Journal of Educational and Behavioral Statistics,
25(1), 6083.
Benjamini, Y., Krieger, A. M., & Yekutieli, D. (2006). Adaptive linear step-up procedures
that control the false discovery rate. Biometrika, 93(3), 491507.
Benjamini, Y., & Yekutieli, D. (2001). The control of the false discovery rate in multiple
testing under dependency. Annals of Statistics, 29, 11651188.
Chumbley, J. R., & Friston, K. J. (2009). False discovery rate revisited: FDR and
topological inference using Gaussian random fields. NeuroImage, 44, 6270.
Donoho, D., & Jin, J. (2008). Higher criticism thresholding: Optimal feature selection
when useful features are rare and weak. Proceedings of the National Academy of
Sciences, 105(32), 1479014795.
Dudoit, S., Van Der Laan, M., & Pollard, K. (2004). Multiple testing. I. Single-step
procedures for the control of general type I error rates. Statistical Applications in
Genetics and Molecular Biology, 3, 1041, Available at www.bepress.com/sagmb/
vol3/iss1/art13.MR2101462.
Efron, B. (2004). Large-scale simultaneous hypothesis testing: The choice of a null
hypothesis. Journal of the Acoustical Society of America, 99(465), 96104.
Efron, B. (2007a). Correlation and large-scale simultaneous significance testing.
Journal of the Acoustical Society of America, 102, 93103.
Efron, B. (2007b). Size, power, and false discovery rates. Annals of Statistics, 35(4),
13511377.
Efron, B., Tibshirani, R., Storey, J., & Tusher, V. (2001). Empirical Bayes analysis of a
microarray experiment. Journal of the Acoustical Society of America, 96,
11511160.
Finner, H., Dickhaus, T., & Roters, M. (2007). Dependency and false discovery rate:
Asymptotics. Annals of Statistics, 35(4), 14321455.
Finner, H., & Roters, M. (2002). Multiple hypotheses testing and expected number of
type I errors. Annals of Statistics, 30, 220238.
Forman, S. D., Cohen, J. D., Fitzgerald, M., Eddy, W. F., Mintun, M. A., & Noll, D. C.
(1995). Improved assessment of significant activation in functional magnetic
resonance imaging (fMRI): Use of a cluster-size threshold. Magnetic Resonance in
Medicine, 33, 636647.
Friedenberg, D. A., & Genovese, C. R. (2013). Straight to the source: Detecting
aggregate objects in astronomical images with proper error control. Journal of the
American Statistical Association, 108(502), 456468.
Genovese, C. R., Lazar, N. A., & Nichols, T. E. (2002). Thresholding of statistical maps
in functional neuroimaging using the false discovery rate. NeuroImage, 15,
870878.
Genovese, C., & Wasserman, L. (2002). Operating characteristics and extensions of the
false discovery rate procedure. Journal of the Royal Statistical Society, Series B:
Statistical Methodology, 64, 499517.
Genovese, C., & Wasserman, L. (2004). A stochastic process approach to false
discovery control. Annals of Statistics, 32, 10351061.
Genovese, C. R., & Wasserman, L. (2006). Exceedance control for the false discovery
proportion. Annals of Statistics, 101(476), 14081417.
Guo, W., He, L., & Sarkar, S. K. (2014). Further results on controlling the false
discovery proportion. Annals of Statistics, 42, 10701101.
Guo, W., & Rao, M. B. (2008). On control of the false discovery rate under no
assumption of dependency. Journal of Statistical Planning and Inference, 138,
31763188.
Guo, W., & Rao, M. (2010). On stepwise control of the generalized familywise error rate.
Electronic Journal of Statistics, 4, 472485.
Guo, W., & Romano, J. (2007). A generalized Sidak-Holm procedure and control of
generalized error rates under independence. Statistical Applications in Genetics and
Molecular Biology, 6(1).
Heller, R., Stanley, D., Yekutieli, D., Rubin, N., & Benjamini, Y. (2006). NeuroImage, 33,
599608.

Hochberg, H., & Tamhane, A. (1987). Multiple comparison procedures. New York: Wiley.
Holm, S. (1979). A simple sequentially rejective multiple test procedure. Scandinavian
Journal of Statistics, 6, 6570.
Hommel, G., & Hoffmann, T. (1987). Controlled uncertainty. Springer.
Jichun Xie, T., Cai, T., Maris, J., & Li, H. (2011). Optimal false discovery rate control for
dependent data. Statistics and Its Interface, 4, 417430.
Jin, J., & Cai, T. T. (2007). Estimating the null and the proportion of nonnull effects in
large-scale multiple comparisons. Journal of the Acoustical Society of America,
102, 495506.
Lehman, E. L., & Romano, J. (2005). Generalizations of the familywise error rate. Annals
of Statistics, 33, 11381154.
Marcus, R., Peritz, E., & Gabriel, K. R. (1976). On closed testing procedures with special
relevance to ordered analysis of variance. Biometrika, 63, 655660.
Meinshausen, N., & Buhlmann, P. (2005). Lower bounds for the number of false null
hypotheses for multiple testing of associations under general dependence
structures. Biometrika, 92, 893907.
Meinshausen, N., & Rice, J. (2006). Estimating the proportion of false null
hypotheses among a large number of independently tested hypotheses. Annals of
Statistics, 34.
Nettleton, D. & Hwang, J. (2003). Estimating the number of false null hypotheses when
conducting many tests. Technical report, Department of Statistics, Iowa State
University.
Nichols, T., & Hayasaka, S. (2003). Controlling the family-wise error rate in functional
12(5), 419446.
Perone Pacifico, M., Genovese, C. R., Verdinelli, I., & Wasserman, L. (2004). False
discover control for random fields. Journal of the American Statistical Association,
99, 10021014.
Perone Pacifico, M., Genovese, C. R., Verdinelli, I., & Wasserman, L. (2007). Scan
clustering: A false discovery approach. Journal of Multivariate Analysis, 98,
14411469.
Reiss, P. T., Scwartzman, A., Lu, F., Huang, L., & Proal, E. (2012). Paradoxical results of
adaptive false discovery rate procedures in neuroimaging studies. NeuroImage,
63(4), 18331840.
Romano, J. P., & Shaikh, A. M. (2006). Stepup procedures for control of generalizations
of the familywise error rate. Annals of Statistics, 34, 18501873.
Romano, J. P., Shaikh, A. M., & Wolf, M. (2008). Formalized data snooping based on
more generalized error rates. Econometric Theory, 24, 404447.
Sarkar, S. K. (2002). Some results on false discovery rate in stepwise multiple
comparison procedures. Annals of Statistics, 30, 239257.
507
Sarkar, S. K. (2007). Stepup procedures controlling generalized fewer and generalized

FDR. Annals of Statistics, 35, 24052420.
Schwartzman, A. (2008). Empirical null and false discovery rate inference for
exponential families. Annals of Applied Statistics, 2(4), 13321359.
Schweder, T., & Spjotvoll, E. (1982). Plots of p-values to evaluate many tests
simultaneously. Biometrika, 69, 402493.
Shaffer, J. (1995). Multiple hypothesis testing: A review. Annual Review of Psychology,
46, 561584.
Simes, R. J. (1986). An improved Bonferroni procedure for multiple tests of
significance. Biometrika, 73, 751754.
Storey, J. (2002). A direct approach to false discovery rates. Journal of the Royal
Statistical Society, Series B: Statistical Methodology, 64, 479498.
Storey, J. (2003). The positive false discovery rate: A Bayesian interpretation and the
q-value. Annals of Statistics, 31, 20132035.
Storey, J. D., Taylor, J. E., & Siegmund, D. (2004). Strong control, conservative point
estimation and simultaneous conservative consistency of false discovery rates: A
unified approach. Journal of the Royal Statistical Society, Series B: Statistical
Methodology, 66, 187205.
Sun, W., & Cai, T. T. (2007). Oracle and adaptive compound decision rules for
false discovery control. Journal of the American Statistical Association, 102,
901912.
Sun, W., & Cai, T. (2009). Large scale multiple testing under dependence. Journal of
the Royal Statistical Society, Series B: Statistical Methodology, 71, 393424.
Sun, W., Reich, B., Cai, T., Guindani, M., & Schwartzman, A. (2014). False discovery
control in large-scale spatial multiple testing. Journal of the Royal Statistical
Society, Series B: Statistical Methodology, http://dx.doi.org/10.1111/rssb.12064.
Troendle, J. F. (2000). Stepwise normal theory multiple test procedures controlling
the false discover rate. Journal of Statistical Planning and Inference, 84(12),
139158.
Van der Laan, M., Dudoit, S., & Pollard, K. (2004). Augmentation procedures for control
of the generalized familywise error rate and tail probabilities for the proportion of
false positives. Statistical Applications in Genetics and Molecular Biology, 3.
Worsley, K. J. (2005). An improved theoretical p value for SPMS based on discrete local
maxima. NeuroImage, 28(4), 10561062.
Worsley, K. J., Evans, S., Marrett, A. C., & Neelin, P. (1992). A three-dimensional
statistical analysis of CBF activation studies in human brain. Journal of Cerebral
Yekutieli, D., & Benjamini, Y. (1999). Resampling-based false discovery rate controlling
multiple test procedures for correlated test statistics. Journal of Statistical Planning
and Inference, 82, 171196.
Bayesian Model Inversion

MW Woolrich and MA Chappell, University of Oxford, Oxford, UK
Introduction
What is the unique perspective that Bayes has to offer, when
compared with the widely used classical approaches? As
Kershaw et al. (1999) put it: With [Bayesian] methodology it
is possible to derive a relevant statistical test for activation in an
fMRI time series no matter how complicated the parameters of
the model are. The derivation is usually quite straightforward
and results may be extracted from it without first having to find
estimates for all of the parameters. In other words, Bayes
provides you with a mathematically principled framework, in
which you can probabilistically infer on model parameters no
matter what, or how complicated, the model is.
In this article, we will explore how Bayes provides a framework within which we can attempt to infer on models of
neuroimaging data while allowing us to incorporate our prior
knowledge of the brain and the neuroimaging equipment in
the form of biophysically informed or regularizing priors. It
allows us to extract probabilistic information from the data, for
example, calculate confidence measures for our estimates, and
can be used to combine information from multiple modalities.
Bayes can also be used to compare and select between models.
that is, white, and is an example of a maximum likelihood

approach.) However, this approach has limitations. Firstly,
extracting a single best guess (or point estimate) for a parameter completely ignores the presence of, or extent of, the uncertainty that we have in that parameter. Secondly, how do we
systematically combine the information in the data with any
prior knowledge that we have about the parameters in the
model? Bayesian statistics offers a solution to these problems
and also provides a framework in which we can do much more.
Bayes Inference
Bayes provides the only generic framework for the adjustment
of belief (in the form of probability density functions (PDFs))
in the presence of new information (Cox, 1946). It gives us a
tool for inferring on any model we choose and guarantees that
uncertainty will be handled correctly.
Bayes rule tells us how (for a model M, with model parameters Y) we should use the data, Y, to update our prior belief in
the values of the parameters, p(Y|M), to get a posterior distribution of the parameter values, p(Y|Y, M):
pYjY, M
Generative Models
In a typical neuroimaging scenario, we are looking to extract
some pertinent information about the brain from noisy data.
Mapping measured data to brain characteristics is generally
difficult to do directly. For example, since fMRI data are
noisy, we cannot directly set up a rule that states, If the fMRI
data look exactly like X, then the brain is definitely active in area
Y. However, it is comparatively easy to turn the problem
around and specify, If the brain is active in area Y, then the
fMRI data should look like X, that is, if we know what the
brain is doing, then we can predict what our neuroimaging
data should look like. This is what we refer to as a generative
model, which sits at the heart of all Bayesian neuroimaging
analysis methods. Figure 1 illustrates an example of a generative model for predicting task fMRI data using linear convolution of a known stimulus time course with a parameterized
hemodynamic response function (HRF).
Generative models are a natural way for us to incorporate
our understanding of the brain and of different neuroimaging
modalities to make predictions about what neuroimaging data
look like. However, in practice, we want to do the opposite. We
want to be able to take acquired data and, using a generative
model, extract pertinent information about the brain (i.e.,
infer on the model and its parameters). The classical approach
to doing this is to fit the generative models to the data, for
example, by minimizing the squared difference between the
data and the generative model to estimate each of the model
parameters. (This approach assumes that the noise is Gaussian,
pYjY, MpYjM
pYjM
[1]
The term p(Y|Y, M) is the likelihood and typically corresponds to the generative model. The numerator in this equation, p(Y|M), is the model evidence, which can be ignored when
inferring on the model parameters, but, as we shall see later,
can come into play when performing model selection.
Often in neuroimaging, data from different voxels are considered to be conditionally independent, that is, conditioned
on the parameters, the data are independent across voxels. This
means that the likelihood can be factorized over voxels:
Y
pY i jYi , M
pYjY, M
i
The voxelwise likelihood, p(Yi|Yi, M), is then specified by a

voxelwise generative model. Figure 2 illustrates just such a case
for the application of Bayesian inference on task fMRI data
using the generative model from Figure 1.
Unfortunately, calculating the joint posterior PDF given in
eqn [1] is seldom straightforward. The denominator in eqn [1]
is
[2]
pYjM pYjY, MpYjM dY
Y
an integral that is often not tractable analytically. Furthermore,

the joint posterior PDF on all parameters is often not the
distribution that we are most interested in. We are often interested in the posterior PDF on a single parameter or an interesting subset of parameters, YI.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00325-0
509
510
INTRODUCTION TO METHODS AND MODELING | Bayesian Model Inversion
Generative model
Convolved
with
Gaussian
noise
m
Haemodynamic
response function
m=6s
h=1
Predicited data
Stimulus
time-course
m=9s
h=1
Predicited data
Figure 1 Generative models are at the core of all Bayesian neuroimaging analysis techniques. This figure shows an example of a simple voxelwise
generative model for predicting fMRI data. It consists of an HRF parameterized using the time-to-peak, m, and the height, h. The HRF is convolved
with a time course of the known experimental stimulus (in this case a boxcar stimulus) and then added to Gaussian noise. For the sake of
simplicity, we are assuming that the variance of the Gaussian noise is known. The only unknown parameters in the model are m and h. For
different values for m and h, we can predict what the fMRI data look like in a voxel.
Point Estimation
One approximate method for getting a posterior distribution
on the parameters of interest is by conditioning on the estimates of the other nuisance parameters, YI. This requires
that you have a way of getting point estimates of the nuisance
^ I . Typically, point estimates are obtained using
parameters, Y
techniques such as maximum likelihood, maximum a posteriori, or a maximum marginal likelihood (evidence optimization) approach. The conditional posterior on the parameters of
interest is then given by

^ I , M p YjYI , YI Y
^ I , M
p YI jY, YI Y

^ I
p YI jM, YI Y
[3]
Crucially, these point estimation approaches do not incorporate the uncertainty we have in the nuisance parameters into
the uncertainty we have in the parameters of interest, whereas
marginalization does.
Marginalization
The principled way for getting posteriors on the parameters of
interest is to integrate over the nuisance parameters; this is the
process of marginalization in order to obtain marginal posterior
distributions. This incorporates the uncertainty there is in the
unknown nuisance parameters into the uncertainty we have in
the parameters of interest. This fully Bayesian approach is the
one we will focus on in this article.
The downside of obtaining marginal posterior distributions
is that it involves performing often complicated, highdimensional integrals, that is,
pYI jY, M
pYjY, M dYI
[4]
YI
where YI are the parameters of interest and YI are all other
parameters. As with obtaining the model evidence, these integrals are seldom tractable analytically. But as we shall see later,
this can be handled with approximations and numerical integration techniques.
Analytic (Exact) Inference Example

In this section, we will walk through an example where the
required integrations are tractable, that is, fitting a Gaussian
distribution to infer a mean from some data.
We start by specifying clearly what our generative model is.
In this case, we assume that the N 1 data vector, Y, is generated from a normal distribution with a mean, m, and variance,
b1, where each of the N observations is conditionally independent from each other given the model parameters. This gives
us our likelihood:
Y
pYjm, b
pY i jm, b
i

1
pY i jm, b N Y i ; m, b0
1
[5]
p
b
b
2A
@
pY i jm, b p exp Y i m
2
2p
We now need to specify our priors on the model parameters
Y {m, b}. We will discuss the choice of prior later; for now,
we simply state that we use a noninformative Jeffreys prior
(Jeffreys priors are designed to make the posterior invariant to
reparameterization. This means that the prior can change if
you integrate over different parameterizations of your model
511
P (h)
P (m)
Priors
3 2 1 0
h (a.u.)
10
12
m (s)
Acquired data, Y
Generative
model
Likelihood P(Y|m,h)
ye
Ba
10
10
2
3
P(mly)
P(hly)
h (a.u.)
m (s)
12
Marginal posterior
12
m (s)
Joint posterior P (m,h|Y)
h (a.u.)
Marginal posterior
Figure 2 Schematic of the process of Bayesian inference on the generative model in Figure 3. The ingredients consist of the acquired fMRI data, the
generative model, and the priors. The generative model provides us with the likelihood term in Bayes rule. Bayes combines these ingredients to
give us probabilistic inference on the model parameters in the form of the joint posterior distribution across all parameters in the model. However, we are
often interested in the posterior distribution on a single parameter or a subset of parameters. This can be obtained by integrating (i.e., averaging)
over parameters to obtain the marginal distribution.
parameters. For example, in the example here (fitting a Gaussian), if we integrate over log(b) rather than b, then the Jeffreys
prior, p(log(b)), becomes uniform, but the posterior distribution is unchanged):
pm; b 1=b
[6]
where
1X
Yi
N i
X
S
Y i x2
x
The aim in this example is to invert the generative model

described in eqn [5] to get a probabilistic inference on the
mean, m. However, we need to deal with the unknown, nuisance variable, b. The poor mans Bayesian approach would be
to use a point estimate of b obtained from some other method,
for example, Maximum a Posteriori (MAP) estimation, and to
insert that into eqn [3]. For example, this would result in the
following conditional posterior over the mean:

^ M N m; x, S=N 1
p mjY, b b,
[7]
However, here, we are going to focus on using full Bayes to

do probabilistic inference on the model to get at the marginal
posterior distribution on m. To get this, we need to perform the
integral in eqn [4], that is,
1
pmjY, M
pm, bjY, M db
0
where, using Bayes rule (eqn [1]), dropping the dependency

on the model M, and keeping only the terms that depend on
the model parameters, we have
512

pm, bjY pYjm, b pm; b
[8]
We can now insert the expressions for the likelihood, p

(Y|m, b), (from eqn [5]) and the prior, p(m, b), (from eqn [6])
to get
pmjY, M
1
0
N
b 2 1 Y
2pN=2

b
exp Y i m2 db
2
This integral can be solved analytically and results in a noncentral t-distribution (see Appendix)
pmjY, M T m; x, S=N 1, n
where n is the degrees of freedom:
nN1
Note that this is an alternative, more accurate reflection of
the posterior distribution over the mean m than can be
obtained using the conditional posterior approach from
eqn [7]. Most notably, the mean is now distributed as a
t-distribution with an increased fatness in its tails (where
lower degrees of freedom results in fatter tails) compared to
a normal distribution; this reflects the extra uncertainty we
have on m given the uncertainty in b. In contrast, the conditional posterior approach from eqn [7] is just a normal distribution, by virtue of not taking the uncertainty in b into
account.
Grid Enumeration
This is a brute force method, only useful for low-dimensional
parameter spaces (i.e., models with low numbers of unknown
parameters). As a rough rule of thumb, it can work up to about
P 6 model parameters (depending on the ease of computation of the generative model), but beyond this, the curse of
dimensionality kicks in, rendering it computationally impractical. In practical neuroimage analysis, it is rarely the case that
this is appropriate. However, we include it here as it is an
excellent toy inference method to play with, and putting the
size of the parameter space aside, it can be used with any
generative model.
The method simply amounts to setting up an appropriate Pdimensional grid for all possible values of your P model
parameters within appropriate ranges. For continuous variables (e.g., the mean of a Gaussian distribution), this requires
the continuous space to be discretized. The unnormalized joint
posterior can then be calculated exhaustively at every point in
the discrete grid.
For example, consider a model with P 2 continuous
parameters, y and l. These can be discretized within appropriate ranges and with appropriate coarseness to give yi and lj,
where i and j index the grid points. We can then compute the
unnormalized joint posterior, Qij, at every grid point using
eqn [8]. Crucially, computing the unnormalized joint posterior
is fairly easy, because it does not require the difficult integration implicit in computing the normalization constant or
model evidence. The normalized joint posterior distribution is
then obtained by

Qij
p y yi , l lj jY X
Q
ij ij
and the marginal posterior distribution for y is given by (with
an analogous expression for l)
X
Q
j ij
py yi jY X
Q
ij ij
Example: Inferring the HRF Delay and Amplitude in fMRI Data

This example infers on a generative model of task fMRI data (at
a single spatial location) and corresponds to the generative
model shown in Figure 1. The model consists of a known
stimulus (as in a task fMRI experiment) convolved with an
HRF of unknown amplitude, h, and delay, m; that is,
Y t hf t t; m et
where et N(0, s2e ) and ft(t; m) is the continuous function
f(t; m) sampled at time t, where
f t; m gt; mst
where s(t) is the known stimulus (or task) time course and
g(t; m) is the HRF modeled as a two-parameter Gamma distribution (see Appendix) parameterized with a mean delay of m.
Note that the standard deviation of the gamma HRF is fixed to
1. We also assume that we have a normal prior distribution on
m (the HRF delay):

pm N m; mm ; s2m
and the prior distribution on h (the size of the response) is a
uniform noninformative prior.
Simulated data can be generated from this assumed generative model for different true values of m and h. Figure 1
shows an example of doing this. Inference can then be carried
out using exhaustive enumeration over a 2-dimensional grid.
An example of doing this is shown in Figure 2. The MATLAB
script used to produce this can be downloaded from
http://www.fmrib.ox.ac.uk/woolrich/demo_exhaustive_
grid_enum.m.gz
This script can be used to produce joint and marginal
posterior distribution values for different realizations of simulated data and can be called using different values for the true
values of m and h, different prior means and variances on m,
and different amounts of noise, s2e .
Practical Bayesian Inference

In most practical neuroimage analysis situations, either the
integrals in Bayes rule are intractable, or we have too many
parameters (>6) to make grid enumeration (full evaluation)
practical. As such, other inference approaches are required.
Figure 3 shows just some of the options available. We separate
these into two approaches: those that solve the integrals
numerically and those that use parametric approximations to
the posterior.
513
Accuracy
Speed
Numerical integrat on
Posterior approximation
Conjugate priors?
Number of model parameters
Yes
Full
evaluation
Rejection
sampling
MCMC
Variational
bayes
No
Variational
laplace
Figure 3 The use of Bayes requires integrations to be performed that are seldom tractable, in which case there are broadly speaking two separate
approaches used: (1) solve the integrals numerically and (2) make approximations to the posterior distribution.
Numerical Integration
Sampling methods draw samples in parameter space from the
joint posterior distribution, implicitly performing the integrals
numerically. For example, we may repetitively choose random
sets of parameter values and choose to accept or reject these
samples according to a criterion based on the value of the
numerator in eqn [1]. Examples of schemes such as this are
rejection sampling and importance sampling (Gamerman,
1997). However, these kinds of sampling schemes tend to be
very slow, particularly in high-dimensional parameter spaces,
as samples are proposed at random, and thus, each has a very
small chance of being accepted.
Markov chain Monte Carlo (MCMC; Gilks, Richardson, &
Spiegelhalter, 1996) is a sampling technique that addresses the
problem of having a large number of parameters by proposing
samples preferentially in areas of high probability. Samples
drawn from the posterior are no longer independent of one
another, but the high probability of accepting samples allows
for many samples to be drawn and, in many cases, for the
posterior PDF to be built in a relatively short period of time
(compared with other numerical integration approaches).
While MCMC is a powerful technique that can be used on a
wide variety of models, it is time-consuming when compared
with posterior approximation approaches.
Gaussian noise (e.g., as in Figure 1), in which case other

approximations are needed. One option is often referred to as
variational Laplace, which approximates the posterior for nonconjugate parameters as being multivariate Gaussian. This can
be achieved by applying first- or second-order Taylor expansions of the problem terms in Bayes rule and relates to the
Laplace approximation. The problem can then be solved using
variational Bayes in the normal way (Woolrich & Behrens,
2006). Variational Laplace can be applied (in principle) to
any generative model, with or without conjugate priors.
Priors
Bayesian statistics requires that we specify our prior probabilistic belief about the model parameters. This requirement has
often been a source of criticism of the Bayesian approach.
However, Bayesians support the view that we cannot infer
from data without making assumptions; indeed, the act of
choosing a generative model itself constitutes an assumption
(which the model provides a good description of reality). It
turns out that having a framework within which we can specify
prior assumptions can be a big advantage. As we shall see, this
can serve to augment the assumptions already made in the
generative model with complementary knowledge of the
system.
Posterior Approximations
The intention here is to make approximations such that the
integrals become analytically tractable. These approaches generally optimize the posterior PDF with respect to variational
free energy (an upper bound on the log of the model evidence). This tends to be less accurate, but computationally
faster, than numerical integration and typically requires more
work to be done mathematically rather than computationally.
A key issue is whether or not the model has conjugate
priors. Conjugacy exists for a model if the posteriors have the
same distributional form as the prior. If this is the case, then a
technique known as variational Bayes or ensemble learning can
be employed. Typically, this approximates the true posterior
distribution by estimating it using a posterior factorized over
subsets of the model parameters.
However, models are often not conjugate, for example,
when we have nonlinear generative models with additive
Biophysical Priors
Biophysical priors are priors that encode what we understand
as being biologically plausible. For example, we know that a
value of 1.3 s at 3 T for the T1 of gray matter is plausible,
whereas values of 0.3 s and 2.3 s are not. Within Bayes, we
can encode this information in the form of prior PDFs.
Earlier, in Figures 1 and 2, we saw in a fairly simple example how priors could be used to constrain the HRF shape to
have delays that are biologically plausible. In practice, more
complex and more highly parameterized HRF models can be
used. For example, in Woolrich, Behrens, and Smith (2004a),
priors were placed on the basis function regression parameters
such that the variational Bayes inference is constrained to only
those combinations of parameters that give biophysically plausible HRF shapes; and in Friston (2002), Bayesian inference
514
was deployed on a biologically informed nonlinear model of

the BOLD response based on the balloon model.
Biophysical priors have proved particularly useful in the
more quantitative brain mapping modalities. For example,
they have been used in the analysis of arterial spin labeling
(ASL) data. ASL can be used to quantify cerebral blood flow
(CBF); however, the generative model for ASL includes other
model parameters, such as the T1 or mean transit time of
blood. These other nuisance parameters are known to some
extent, but not precisely, and this partial knowledge can be
incorporated into the Bayesian model inversion via priors to
give more realistic probabilistic inference on the CBF
(Chappell, Okell, Jezzard, & Woolrich, 2010).
previous in the chain, with the data at the head of the chain
and the priors at the tail.
In brain mapping, one of the best examples of this is in
multisession/subject modeling. Consider a group analysis of
some functional neuroimaging data, Ys (e.g., task M/EEG,
fMRI), for subject s, for which the within-subject generative
model for Ys (the likelihood) is p(Ys|bs, ys), where bs is the effect
size and ys are some (nuisance) model parameters. In the group
analysis, we want to be able to infer a group average (population
average) effect size. To do this, we assume a group-level generative
model in which the population distribution is normally distributed with group mean, B, and between-subject variance, s2B:

pbs jB, sB N bs ; B; s2B
Regularization Priors
Using Bayes rule, we can chain together the within-subject

generative models for each of our subjects, with the group-level
generative model, to get a hierarchical all-in-one model:
Priors can also be used to regularize (or to improve the stability

in the estimation of) parameters in the generative model.
Regularization priors tend to contain hyperparameters that control the strength of the regularization. Crucially, these hyperparameters are typically inferred via the Bayesian inference
framework at the same time as the rest of the model another
example of the ability of Bayesian approaches to adapt to the
information content in the data.
An early example of the use of temporal regularization priors
was in the use of semiparametric Bayesian approaches for HRF
modeling in fMRI data (Ciuciu et al., 2003; Goutte, Nielsen, &
Hansen, 2000; Marrelec, Benali, Ciuciu, Pelegrini-Issac, &
Poline, 2003). Semiparametric refers to the idea that the
HRF does not have a fixed parameterized form. Instead the
HRF is allowed to have any form with a parameter describing
the size of the HRF at each time point. Without temporal
regularization, these models have too many parameters for
stable inference. Regularization is also related to the idea of
online model selection, for example, shrinkage or automatic
relevance determination (ARD) priors (see later).
One of the first approaches to spatial regularization used
spatial Markov random field (MRF) priors, with inference via
numerical integration approaches such as MCMC (Gossl et al.,
2001; Woolrich, Jenkinson, Brady, & Smith, 2004). More computationally efficient variational Bayesian approaches have
since been developed (Penny, Trujillo-Barreto, & Friston, 2005;
Woolrich, Behrens, & Smith, 2004). This work on MRFs has also
been generalized within the more flexible framework of spatial
Gaussian process priors, allowing for the modeling of spatial
nonstationarities (Harrison, Penny, Ashburner, Trujillo-Barreto,
& Friston, 2007; Harrison, Penny, Daunizeau, & Friston, 2008),
and the combination of spatial and nonspatial prior information
(Groves, Chappell, & Woolrich, 2009).
Bayesian spatial regularization has also seen widespread use
in the source reconstruction of electrophysiological data. See
the corresponding article for more on this.

p b, y, B, s2B jY pY s jbs , ys pbs jB, sB p y; B; s2B
where b {bs 8 s} and p(y, B, s2B) are the priors. The conditional
probability distributions sandwiched between the first (likelihood) and last (full prior) terms in hierarchical models are
commonly referred to as empirical priors. These can be thought
of as prior beliefs that are conditioned on other unknown
parameters. Inference on the group mean, B, can then be
obtained via marginalization over all of the other model
parameters:

pBjY p b, y, B, s2B jY dbdyds2B
Inference on any individual subjects effect size, bs, can be
obtained in an analogous way. This approach ensures that the
group mean effect size regularizes the individual subject effect
sizes and vice versa, and inference takes into account the
uncertainty on all of the other model parameters. This kind
of hierarchical model has been used to infer upon task fMRI
group analysis (Ahn, Krawitz, Kim, Busmeyer, & Brown, 2011;
Friston et al., 2002a, 2002b; Sanyal & Ferreira, 2012; Woolrich,
Behrens, Beckmann, Jenkinson, & Smith, 2004), to model the
relationship between local (e.g., voxelwise) and global parameters (Chappell et al., 2010; DuBois Bowman, Caffo, Bassett, &
Kilts, 2008; Groves, Beckmann, Smith, & Woolrich, 2011;
Jbabdi, Woolrich, Andersson, & Behrens, 2007), and has
been proposed as general mechanism of how the brain itself
infers information from the environment (Friston, 2008).
Hierarchical models also offer a route to properly handle
inference of multimodal data, using symmetrical generative
models that simultaneously predict the different data modalities (Daunizeau et al., 2007; Groves et al., 2011; Henson,
Mouchlianitis, & Friston, 2009; Luessi, Babacan, Molina,
Booth, & Katsaggelos, 2011; Valdes-Sosa et al., 2009; Woolrich
& Stephan, 2013).
Hierarchical Bayes
A useful concept when constructing generative models is that
of hierarchical Bayes. This corresponds to the idea that an
overall generative model can be broken down into a chain of
subgenerative models, each conditionally dependent on the
Model Selection and Averaging

Bayesian data analysis is the process of fitting a probabilistic
model to a set of data and encompasses the following three

main steps: (i) setting up a full probabilistic model, including a
data generative model (likelihood function) and a set of priors
on model parameters; (ii) conditioning on observed data
(model inversion) to obtain the posterior distributions; and
(iii) evaluating the performance of the model in comparison
with other models. This last step is one of the perceived
strengths of Bayesian techniques.
In order to evaluate a model using Bayes, the quantity that
needs to be evaluated is the (up to this point mostly ignored)
denominator of the posterior distribution given in eqn [1], that
is, the probability of the data given the model. (Although a
pure Bayesian would actually calculate the posterior distribution p(M|Y) p(Y|M)p(M) provided an appropriate choice for
the priors p(M). Typically, it is implicitly assumed that all
models are a priori equally likely, that is, p(M) is equal for
all models. p(M|Y) is then proportional to the evidence, p(Y|
M).) This quantity, often termed the marginal likelihood, or
model evidence, accounts for both the accuracy (data fit) and
complexity of the model given the observed data. Model selection consists of calculating this quantity for a given number of
models and selecting the model with highest marginal likelihood. In particular, this has seen widespread use in selecting
between different models of effective connectivity when using
dynamic causal modeling (DCM; Penny, Stephan, Mechelli, &
Friston, 2004; Stephan & Harrison et al., 2007; Stephan, Weiskopf, Drysdale, Robinson, & Friston, 2007). See the corresponding article on Model Selection.
The downside of model selection is when a large space of
models needs to be explored, in which case inferring the model
evidence for all models can become computationally prohibitive. A good example of this is when trying to use approaches
like DCM in network discovery (i.e., inferring connectivity
between a large number of brain areas using evidence from
functional neuroimaging data; Smith et al., 2011). A potential
solution is the idea of post hoc Bayesian model comparison
(Friston, Li, Daunizeau, & Stephan, 2011; Friston & Penny,
2011). However, it remains to be seen if this can reliably
work on network models with large numbers of nodes (>10).
An alternative to doing full model selection is to do online
model selection using approaches such as shrinkage priors or
ARD priors (Mackay, 2005). In its most straightforward form,
ARD consists of placing a Gaussian prior, with zero mean and
unknown variance, on any model parameter in question. The
key is that the variance is probabilistically inferred alongside
the parameter: If the ARD variance is inferred to be small, then
the parameter is shrunk to near zero, effectively knocking it
out of the model; otherwise, the ARD variance is inferred to be
large and the parameter is free to be inferred as nonzero. ARD
has found a number of uses in brain mapping, including in M/
EEG and fMRI analysis (Wipf & Nagarajan, 2009; Woolrich,
Jenkinson, Brady, & Smith, 2004), and in the selection of the
number of crossing fibers in the local diffusion models of
diffusion MRI data (Behrens, Berg, Jbabdi, Rushworth, &
Woolrich, 2007).

Bayesian Model Inference; Distributed Bayesian Inversion of MEG/EEG
Models; Dynamic Causal Models for fMRI; Posterior Probability Maps;
Variational Bayes.
515
Appendix: Function Definitions

The two-parameter Gamma distribution may be defined as
Gax; b; c
1 xc1 x
e b
Gc bc
[A1]
The univariate noncentral t-distribution may be defined as

n1
x m2
T x; m; s ; n
n 1
1
s2 n
nps2 2 G 2
!n1
2
where n are the degrees of freedom and the distribution has a

mean of m and a variance of s2n/(n 2) for n > 2.
References
Ahn, W.-Y., Krawitz, A., Kim, W., Busmeyer, J. R., & Brown, J. W. (2011). A modelbased fMRI analysis with hierarchical Bayesian parameter estimation. Journal of
Neuroscience, Psychology, and Economics, 4, 95110.
Bartsch, A., Homola, G., Biller, A., Solymosi, L., & Bendszus, M. (2006). Diagnostic
functional MRI: Illustrated clinical applications and decision-making. Journal of
Behrens, T. E. J., Berg, H. J., Jbabdi, S., Rushworth, M. F. S., & Woolrich, M. W.
(2007). Probabilistic diffusion tractography with multiple fibre orientations: What
can we gain? Neuroimage, 34, 144155.
Chappell, M. A., Okell, T. W., Jezzard, P., & Woolrich, M. W. (2010). A general
framework for the analysis of vessel encoded arterial spin labeling for vascular
territory mapping. Magnetic Resonance in Medicine, 64, 15291539.
Ciuciu, P., Poline, J.-B., Marrelec, G., Idier, J., Pallier, C., & Benali, H. (2003).
Unsupervised robust nonparametric estimation of the hemodynamic response
function for any fMRI experiment. IEEE Transactions on Medical Imaging, 22,
12351251.
Cox, R. (1946). Probability, frequency, and reasonable expectation. American Journal of
Physics, 14, 110.
Daunizeau, J., Grova, C., Marrelec, G., Mattout, J., Jbabdi, S., Pelegrini-Issac, M., et al.
(2007). Symmetrical event-related EEG/fMRI information fusion in a variational
Bayesian framework. Neuroimage, 36, 6987.
DuBois Bowman, F., Caffo, B., Bassett, S. S., & Kilts, C. (2008). A Bayesian hierarchical
framework for spatial modeling of fMRI data. Neuroimage, 39, 146156.
Flandin, G., & Penny, W. D. (2007). Bayesian fMRI data analysis with sparse spatial
basis function priors Neuroimage, 34, 11081125.
Friston, K. (2002). Bayesian estimation of dynamical systems: An application to fMRI.
Friston, K. (2008). Hierarchical models in the brain. PLOS Computational Biology, 4,
e1000211.
Friston, K. J., Li, B., Daunizeau, J., & Stephan, K. E. (2011). Network discovery with
DCM. Neuroimage, 56, 12021221.
Friston, K., & Penny, W. (2011). Post hoc Bayesian model selection. Neuroimage, 56,
20892099.
Friston, K. J., Penny, W., Phillips, C., Kiebel, S., Hinton, G., & Ashburner, J. (2002a).
Classical and Bayesian inference in neuroimaging: Theory. Neuroimage, 16,
465483.
Friston, K. J., Penny, W., Phillips, C., Kiebel, S., Hinton, G., & Ashburner, J. (2002b).
Classical and Bayesian inference in neuroimaging: Theory. Neuroimage, 16,
465483.
Gamerman, D. (1997). Markov chain Monte Carlo. London: Chapman and Hall.
Gilks, W., Richardson, S., & Spiegelhalter, D. (1996). Markov chain Monte Carlo in
practice. London: Chapman and Hall.
Gossl, C., Auer, D. P., & Fahrmeir, L. (2001). Bayesian spatiotemporal inference in
functional magnetic resonance imaging. Biometrics, 57, 554562.
Goutte, C., Nielsen, F. A., & Hansen, L. K. (2000). Modeling the haemodynamic
response in fMRI using smooth FIR filters. IEEE Transactions on Medical Imaging,
19, 11881201.
Groves, A. R., Beckmann, C. F., Smith, S. M., & Woolrich, M. W. (2011). Linked
independent component analysis for multimodal data fusion. Neuroimage, 54,
21982217.
516
Groves, A., Chappell, M., & Woolrich, M. (2009). Combined spatial and non-spatial
prior for inference on MRI time-series. Neuroimage, 45, 795809.
Harrison, L. M., Penny, W., Ashburner, J., Trujillo-Barreto, N., & Friston, K. J. (2007).
Diffusion-based spatial priors for imaging. Neuroimage, 38, 677695.
Harrison, L., Penny, W., Daunizeau, J., & Friston, K. (2008). Diffusion-based spatial
priors for functional magnetic resonance images. Neuroimage, 41, 408423.
Hartvig, N. V., & Jensen, J. L. (2000). Spatial mixture modeling of fMRI data human
brain mapping, 11, 233248.
Henson, R. N., Mouchlianitis, E., & Friston, K. J. (2009). MEG and EEG data fusion:
Simultaneous localisation of face-evoked responses. Neuroimage, 47, 581589.
Jbabdi, S., Woolrich, M. W., Andersson, J. L.R, & Behrens, T. E.J (2007). A Bayesian
framework for global tractography. Neuroimage, 37, 116129.
Luessi, M., Babacan, S. D., Molina, R., Booth, J. R., & Katsaggelos, A. K. (2011).
Bayesian symmetrical EEG/fMRI fusion with spatially adaptive priors. Neuroimage,
55, 113132.
Mackay, D. (2005a). Information theory, inference, and learning algorithms. Cambridge
University Press, p. 640.
Marrelec, G., Benali, H., Ciuciu, P., Pelegrini-Issac, M., & Poline, J.-B. (2003). Robust
Bayesian estimation of the hemodynamic response function in event-related BOLD
fMRI using basic physiological information. Human Brain Mapping, 19, 117.
Penny, W. D., Stephan, K. E., Mechelli, A., & Friston, K. J. (2004). Comparing dynamic
causal models. Neuroimage, 22, 11571172.
Penny, W. D., Trujillo-Barreto, N. J., & Friston, K. J. (2005). Bayesian fMRI time series
analysis with spatial priors. Neuroimage, 24, 350362.
Sanyal, N., & Ferreira, M. A.R (2012). Bayesian hierarchical multi-subject multiscale
analysis of functional MRI data. Neuroimage, 63, 15191531.
Smith, S. M., Miller, K. L., Salimi-Khorshidi, G., Webster, M., Beckmann, C. F.,
Nichols, T. E., et al. (2011). Network modelling methods for FMRI. Neuroimage, 54,
875891.
Stephan, K. E., Harrison, L. M., Kiebel, S. J., David, O., Penny, W. D., & Friston, K. J.
(2007). Dynamic causal models of neural system dynamics: Current state and future
extensions. Journal of Biosciences, 32, 129144.
Stephan, K. E., Weiskopf, N., Drysdale, P. M., Robinson, P. A., & Friston, K. J. (2007).
Comparing hemodynamic models with DCM. Neuroimage, 38, 387401.
Valdes-Sosa, P. A., Sanchez-Bornot, J. M., Sotero, R. C., Iturria-Medina, Y.,
Aleman-Gomez, Y., Bosch-Bayard, J., et al. (2009). Model driven EEG/fMRI fusion
of brain oscillations. Human Brain Mapping, 30, 27012721.
Wipf, D., & Nagarajan, S. (2009). A unified Bayesian framework for MEG/EEG source
imaging. Neuroimage, 44, 947966.
Woolrich, M. W., & Behrens, T. E. (2006). Variational Bayes inference of spatial
mixture models for segmentation. IEEE Transactions on Medical Imaging, 25,
13801391.
Woolrich, M. W., Behrens, T. E. J., Beckmann, C. F., Jenkinson, M., & Smith, S. M.
(2004). Multilevel linear modelling for FMRI group analysis using Bayesian
inference. Neuroimage, 21, 17321747.
Woolrich, M. W., Behrens, T. E. J., Beckmann, C. F., & Smith, S. M. (2005). Mixture
models with adaptive spatial regularization for segmentation with an application to
FMRI data. IEEE Transactions on Medical Imaging, 24, 111.
Woolrich, M. W., Behrens, T. E. J., & Smith, S. M. (2004). Constrained linear basis sets
for HRF modelling using variational Bayes. Neuroimage, 21, 17481761.
Woolrich, M. W., Jenkinson, M., Brady, J. M., & Smith, S. M. (2004). Fully Bayesian
spatio-temporal modeling of FMRI data. IEEE Transactions on Medical Imaging, 23,
213231.
Woolrich, M., & Stephan, K. (2013). Biophysical network models and the human
connectome. Neuroimage, 80, 330338.
Further Reading
Mackay, D. (2005b). Information Theory, Inference, and Learning Algorithms.
Cambridge University Press In particular chapters: 2.02.3, 3, 24, 27, 28; and for
extra fun: 29,33.
Posterior Probability Maps

MJ Rosa, University College London, London, UK
Glossary
Empirical Bayes Statistical procedure in which the prior

density is estimated from the data.
Expectation-Maximization (EM) Iterative algorithm for
finding the maximum likelihood or a posteriori estimates of
statistical model parameters.
Likelihood Probability of the data given the parameters of
the model.
Posterior density Conditional probability of the model
parameters given the observed data.
Prior density A priori (before observing the data)
distribution of the parameters of the model.
Introduction
From a historical perspective, brain research has focused on
identifying functional features, such as perceptual or motor processing, that can be anatomically segregated within the cortex.
This perspective, known as functional specialization, suggests
that experimental manipulation leads to activity changes in,
and only in, certain specialized brain areas. Presently, given the
availability of noninvasive imaging techniques, such as functional magnetic resonance imaging (fMRI), functional specialization studies, or functional brain mapping, typically amount
to the production of three-dimensional images of neuronal activation showing which parts of the brain respond to a given
cognitive or sensory challenge. This procedure is traditionally
based on some form of statistical parametric mapping (SPM).
SPM is a modeling framework used to test hypotheses
about regionally specific effects in the brain, also known as
brain activations (Friston et al., 1995). The idea behind this
framework is quite simple: the data from each and every voxel
are analyzed independently using a general linear model
(GLM) and standard univariate (parametric) statistical tests.
The resulting voxel-wise statistics are assembled into an
image and interpreted as continuous statistical processes, by
referring to the probabilistic behavior of random fields, modeled by random field theory (RFT) (Worsley, Evans, Marrett, &
Neelin, 1992; Worsley et al., 1996).
Classical inferences about the GLM parameter estimates are
made using their estimated variance, allowing one to test the
null hypothesis, that all the estimates are zero, using the
F-statistic or that some particular linear combination (e.g., a
subtraction) of the estimates is zero, using a t-test (Poline,
Holmes, Worsley, & Friston, 1997). The t-statistic obtains by
dividing a contrast vector of the ensuing parameter estimates
by the standard error of that contrast (Poline, 2003). However,
in classical inference, without any a priori anatomical hypothesis, a correction for multiple comparisons over the volume
analyzed is necessary to ensure that the probability of rejecting
Posterior Probability Maps (PPMs) Three-dimensional

images of the posteriorprobability that the effect at a
particular voxel exceeds some specified threshold, given the
data.
Random Field theory Mathematical theory to deal with
smooth statistical maps.
Statistical Parametric Maps (SPMs) Three-dimensional
images where the value at each voxel, under the null
hypothesis, is distributed according to a known probability
function (such as Students t or F distribution).
the null hypothesis incorrectly (false positives) is maintained at

a small rate. RFT provides a way to accommodate this problem
by adjusting the voxel-wise p-values, while taking into account
the fact that neighboring voxels are not independent by virtue of
continuity in the original data (Worsley et al., 1992, 1996).
An alternative approach to classical inference is to use
Bayesian inference (Friston et al., 2002). This approach is
based upon the posterior distribution of the effect, that is,
activation, given the data. Bayesian inference relies on the
specification of a prior probability distribution, which comprises knowledge or beliefs about the effect that have been
obtained before observing the data. After observing the data,
these priors are updated into the posterior distribution. A
common way to summarize this posterior is to compute the
probability that the effect of interest exceeds some threshold.
By computing this probability for each voxel, one can again
assemble the voxel-wise statistics into a three-dimensional
image in this case known as a posterior probability map
(PPM) (Friston & Penny, 2003).
The motivation for using Bayesian inference is that it has
high face validity (Gelman, Carlin, Stern, & Rubin, 1995). This
is because the inference is about an effect being greater than
some specified size that has some meaning in relation to the
underlying neurophysiology. This contrasts with classical inference, in which the inference is about the effect being significantly different from zero. The problem with classical inference
is that, with sufficient data or sensitivity, trivial departures from
the null hypothesis can be declared significant. Another advantage of using Bayesian inference in neuroimaging is the fact
that it does not contend with the multiple comparisons
problem. The probability that activation has occurred, given
the data, at any particular voxel is the same, irrespective of
whether one has analyzed that voxel or the entire brain.
Because there is no need for false positive rate correction,
PPMs can be relatively more powerful than SPMs (Friston &
Penny, 2003). However, see Woolrich (2012) for an alternative view.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00326-2
517
518
INTRODUCTION TO METHODS AND MODELING | Posterior Probability Maps
In this article, we introduce Bayesian inference and present

the construction of PPMs, including an empirical Bayes
approach to determine the prior density over the model
parameters. We then contrast PPMs and SPMs for the same
effect in the same single-subject fMRI dataset.
Bayesian Inference
In Bayesian inference, prior beliefs about parameters, y, of model,
m, are quantified by the prior density, p(y|m). Inference on the
parameters, y, after observing data, y, is based on the posterior
density, p(y|y, m). These densities are related through Bayes rule:

p yy, m p ym

[1]
pyj y,m
p ym
where p(y|y, m) is the probability of the data (likelihood)
conditioned upon the model and its parameters. The normalization factor, p(y|m), is called the model evidence and plays a
central role in model selection. The maximum a posteriori
estimate of the model parameters is simply:
yMAP arg max y pyj y, m
[2]
The posterior density is an optimal combination of prior

knowledge and new observations, and provides a complete
description of uncertainty about the model parameters. Generally, the choice of priors reflects either empirical knowledge
(e.g., previous or simply other measurements from the same
data) or formal considerations (e.g., biological or physical
constraints).
Given a GLM at each voxel from brain imaging data
sequences, y:
y Xy e
[3]
where X is the design matrix, under Gaussian assumptions (N

(m, C) denotes a multivariate normal distribution with mean m
and covariance C) about the error, e N(0, Ce), the likelihood,
p(y|y) N(Xy, Ce), and priors, p(y) N(, S), can be written as:

1
pyj yexp y XyT C1
e y Xy
2
[4]

1
pyexp y T S1 y
2
where the dependency on m was dropped in order to simplify
the notation. Using eqns [4] and [1], the posterior density also
has a Gaussian form, p(y|y) N(m, C):

1
pyj yexp y mT C1 y m
[5]
2
and the posterior mean and covariance are given by (if we
assume that the parameters y have a prior mean of 0):

1 1
C XT C1
e XS
[6]
m CX T C1
e y
See Bishop (2006) for a derivation. To compute the posterior
moments, one needs to know or estimate the error covariance
matrix, Ce. Friston et al. (2002) consider linear Gaussian models
in which the error covariance can be specified in terms of the
hyperparameter, le, where Ce leV. The matrix V is the correlation
or nonsphericity matrix and specifies the covariance structure. The
hyperparameter can be estimated using restricted maximum
likelihood (ReML) or, equivalently, in an Expectationmaximization (EM) algorithm as follows (Friston et al., 2002):
untilconvergence f E step
Ce le V
T 1
1
C X Ce X S1
m CX T C1
e y
M step
1
T 1
U C1
e Ce XCX Ce

1
1 T
g trUV tr U VUyyT
2
2
1
H trUVUV
2
le le H1 g
[7]
The matrix U is the residual forming matrix, pre-multiplied by

the error precision. This projector matrix restricts the estimation
of variance components to the null space of the design matrix.
The quantities g and H are the first- and expected second-order
derivatives (i.e., gradients and expected negative curvature) of the
ReML objective function. This objective function is a special case
of the variational free energy function (Friston, Mattout, TrujilloBarreto, Ashburner, & Penny, 2007). To summarize, the M-step
calculates the hyperparameter by maximizing the ReML objective
function. In the E-step, the hyperparameter estimate is then used
to update the posterior mean and covariance. This procedure is
repeated until convergence.
Once the moments are known (from eqn [6]), the posterior
probability, p, that a particular effect or contrast c exceeds some
threshold g can be easily obtained:

g cT m
p 1 F p
[8]
cT Cc
where F is the cumulative density function of the normal
distribution. An image of these probabilities can be constructed by inverting a linear model in all voxels of the volume
analyzed. The corresponding maps are called PPMs (Friston &
Penny, 2003) and comprise an alternative approach to the
t- and F-maps used in SPM.
Empirical Bayes Approach

The approach to estimate the posterior moments presented in
the previous section assumes that we know the prior covariance of the parameters (fully Bayesian approach), which in
general is not known. Here we briefly introduce a modeling
framework for estimating the prior covariance directly from the
data (empirical Bayes approach), which was proposed originally in SPM2 (see Relevant Websites ) for the construction of
PPMs. For a derivation of the whole framework please consult
Friston and Penny (2003).
In brief, this framework uses an empirical Bayes algorithm
with global shrinkage priors. Global shrinkage priors embody a
prior belief that, on average over all voxels, there is no net experimental effect. Some voxels will respond negatively and some
positively with a variability determined by the prior precision,
which can be estimated from the data. The estimation relies on a
two-level procedure, where eqns [3] and [7] are the voxel-wise
first level, and a similar but voxel-wide second level is introduced
to estimate the prior variance from the data over all voxels. In
other words, in the voxel-specific estimation step (first level) we

use a prior over the parameters that has been estimated at the
second level from all voxels in the data. Similarly to the error
covariance matrix, the prior covariance matrix, S, can be conP
structed as a sum of m structure matrices, S jljQj, where the
hyperparameters, lj, are estimated from the data in all voxels. In
the absence of confounds, the estimation is done using a simple
maximum likelihood approach that minimizes the difference
between the estimated and observed covariances of the data,
averaged over voxels. In the presence of confounds, one can
write the design matrix as X [X0, X1], where X0/X1 correspond
to the regressors of no interest/interest, respectively. Treating
confounds as fixed effects (i.e., having infinite prior precision)
and the rest as random effects, we can write the GLM as

y
y X1 , X0 1 e1
y0
[9]
y1 0 e2
where e(1) is the observation error and e(2) the error on the
parameters of interest. By definition, the parameters of interest
sum to zero over all the search volume. Inverting this model for
all voxels at once is computationally infeasible. One efficient
solution is to collapse eqn [9] into the following single-level
model (Friston & Penny, 2003):
y X0 y0 x
x X1 e2 e1
[10]
The error covariance Cx is estimated by pooling the data from

all voxels and now includes a component for the observation
error and m components for each parameter y1, such that
P
Cx E xxT li Qi

Q X1 Q1 X1T , . .., X1 Qm X1T , V
519
[11]
l l1 , ... , lm , le T
Cx and l in eqn [11] can be estimated using a very similar EM
framework as in eqn [7], where we replace yyT by the sample
mean over voxels, 1n YY T (n is the total number of voxels), Ce by
Cx, and X by X0. See Friston and Penny (2003) for the full
equations. The estimated prior covariance S is then used in eqn
[7], where the error covariance is reestimated to obtain the posterior distribution at each voxel, as described in the preceding text.
More recently, other approaches have been proposed
to estimate the voxel-wise posteriors for PPMs, such as the
variational Bayes approach based on the use of the GLM and
autoregressive error processes. This method is described in
Penny, Kiebel, and Friston (2003).
PPMs: Empirical Demonstration

In this section, we present PPMs obtained from a single-subject
fMRI dataset. We contrast these maps with SPMs for the same
effect obtained with the same data. The data can be downloaded from the SPM software website (see Relevant
Websites). The preprocessing and maps were constructed
using SPM8 (revision number 5236).
The data were acquired by Buchel and Friston (1997) during an attention to visual motion paradigm from a normal
Motion
[0, 0, 0]
Contrast
PPM
Height threshold p = 0.95

Extent threshold K = 0 voxels
Design matrix
z = 3mm
z = 0mm
z = 3mm
Effect size
1
0
Figure 1 Posterior probability map for the effect of motion. The map was created using a threshold of g 0 for the effect size and a threshold of 0.95
for the posterior probability (only for display purposes).
520
subject with a 2 T whole-body MRI system. Four consecutive

100 scan sessions were acquired, comprising a sequence of ten
scan blocks of five conditions. The first was a dummy condition to allow for magnetic saturation effects. In the second,
fixation, the subject viewed a fixation point at the center of a
screen. In an attention condition, the subject viewed 250 dots
moving radially from the center and was asked to detect
changes in radial velocity. In no attention, the subject was
asked simply to view the moving dots. In a static condition,
the subject viewed stationary dots. The order of the conditions
alternated between fixation and visual stimulation (static, no
attention, or attention). The data were preprocessed (realigned,
normalized, and smoothed with a 6 mm Gaussian kernel)
using the conventional SPM (see Relevant Websites) analysis
pipeline, as described in Buchel and Friston (1997).
Here, we look at the effect of visual motion above and
beyond that due to photic simulation with stationary dots.
Figure 1 shows the PPM for this effect. PPMs were obtained
using the empirical Bayes approach described earlier and a
threshold of g 0. We present only voxels for which the posterior is above 0.95. The PPM can be seen as a way of summarizing the confidence that the effect at each voxel exceeds the
specified threshold (in this case 0).
The corresponding SPM (Figure 2) was obtained for the
same effect of motion, with a family wise error (FWE) correction threshold of p 0.05. As can be seen in Figures 1 and 2,
the PPM and SPM for the same effect are very similar, allowing
to make very similar spatial inferences about the effect in this
case (this similarity might not be present in other datasets).
However, the SPM tends to be more conservative and identifies
a smaller number of voxels than the PPM (Figures 1 and 2).
This is because, as discussed earlier, the classical approach of
testing the null hypothesis of no activation at each voxel
induces a multiple comparison problem that calls for a procedure to control the rate of false positives. This procedure
depends on the search volume, which means that in large
search volumes, such as in whole-brain analyses, the correction
can be very severe and therefore some of the voxels seen in an
uncorrected SPM disappear when corrected. In contrast, a PPM
that does not label the voxels as activated does not need to be
corrected for multiple comparisons. See Woolrich (2012) for
more discussion.
Conclusions
PPMs correspond to three-dimensional images of the posterior
probability that the effect at a particular voxel exceeds some
specified threshold, given the data. PPMs allow imaging neuroscientists to make Bayesian inferences about regionally specific effects in the brain. As exemplified in this article, using a
single-subject fMRI dataset, they can be similar to SPMs for the
Motion
[0, 0, 0]
Contrast
SPM(T338)
Height threshold T= 4.87

Extent threshold K = 0 voxels
Design matrix
z = 3 mm
z = 0 mm
z = 3 mm
T-value
7
0
Figure 2 Corresponding statistical parametric map for the same effect of motion (Figure 1). The map has been thresholded at p 0.05
(FWE-corrected).

same effect. However, in general, PPMs tend to be more sensitive since they do not need to be corrected for multiple comparisons as discussed earlier. In other words, the probability
that activation has occurred, given the data, at any particular
voxel is the same, irrespective of whether one has analyzed that
voxel or the entire brain (see Woolrich, 2012, for an alternative
view).
A disadvantage of using PPMs is the fact that these maps are
more computationally intensive to construct. Some critics of
Bayesian inference also mention the need to specify a prior
density over the model parameters as a caveat of this approach
and Bayesian inference in general. However, Bayesian statisticians defend that one cannot make inferences without making
assumptions (e.g., the type of generative model), even when
using classical statistics. As presented earlier, one can estimate
the prior density over the parameters directly from the data,
using an empirical Bayes algorithm. Alternatives to this
method, based on fully Bayesian approaches, are available,
such as the variational Bayes framework described in Penny
et al. (2003) or the multilevel approach described in Woolrich,
Behrens, Beckmann, Jenkinson, and Smith (2004).
Finally, in addition to the effect size PPMs presented here,
which represent posterior probabilities over the model parameters, one can also create PPMs for Bayesian model selection.
These maps correspond to three-dimensional images of the
posterior probability of one model being better than another
model to explain the data at a particular voxel. These maps
are analogous to the F-tests used to construct SPMs, with
the advantage that the models to be compared do not need
to be nested. Additionally, an arbitrary number of models can
be compared together. The construction of PPMs for model
selection is described in Rosa, Bestmann, Harrison, and
Penny (2010).

Bayesian Model Inference; Contrasts and Inferences; The General
Linear Model; Topological Inference; Variational Bayes.
521
References
Bishop, C. M. (2006). Pattern recognition and machine learning (2nd ed.). New York:
Springer.
Buchel, C., & Friston, K. J. (1997). Modulation of connectivity in visual pathways by
attention: Cortical interactions evaluated with structural equation modelling and
fMRI. Cerebral Cortex, 7(8), 768778.
Friston, K. J., Holmes, A. P., Worsley, K. J., Poline, J. B., Frith, C., &
Frackowiak, R. S. J. (1995). Statistical parametric maps in functional imaging: A
Friston, K. J., Mattout, J., Trujillo-Barreto, N., Ashburner, J., & Penny, W. (2007).
Variational free energy and the Laplace approximation. NeuroImage, 34, 220234.
Friston, K. J., & Penny, W. D. (2003). Posterior probability maps and SPMs.
NeuroImage, 19(3), 12401249.
Friston, K. J., Penny, W. D., Phillips, C., Kiebel, S. J., Hinton, G., & Ashburner, J.
(2002). Classical and Bayesian inference in neuroimaging: Theory. NeuroImage, 16,
465483.
Gelman, A., Carlin, J., Stern, H., & Rubin, D. (Eds.). (1995). Bayesian data analysis.
London: Chapman and Hall.
Penny, W. D., Kiebel, S. J., & Friston, K. J. (2003). Variational Bayesian inference for
fMRI time series. NeuroImage, 19(3), 727741.
Poline, J. B. (2003). Contrasts and classical inference. In R. S. J. Frackowiak, K. J.
Friston, C. Frith, R. Dolan & J. C. Mazziotta (Eds.), Human brain function (2nd ed.).
New York: Academic Press.
Poline, J. B., Holmes, A. P., Worsley, K. J., & Friston, K. J. (1997). Making statistical
inferences. In R. S. J. Frackowiak, K. J. Friston, C. Frith, R. Dolan & J. C. Mazziotta
(Eds.), Human brain function (pp. 85106). USA: Academic Press.
Rosa, M. J., Bestmann, S., Harrison, L., & Penny, W. (2010). Bayesian model selection
maps for group studies. NeuroImage, 49(1), 217224.
Woolrich, M. W. (2012). Bayesian inference in fMRI. NeuroImage, 62(2), 801810.
Woolrich, M. W., Behrens, T. E., Beckmann, C. F., Jenkinson, M., & Smith, S. M.
(2004). Multilevel linear modelling for FMRI group analysis using Bayesian
inference. NeuroImage, 21(4), 17321747.
Blood Flow & Metabolism, 12, 900918.
of cerebral activation. Human Brain Mapping, 4, 5873.
Relevant Websites
http://www.fil.ion.ucl.ac.uk/spm/ Statistical parametric mapping software.
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ FSL software library.
Variational Bayes
MA Chappell and MW Woolrich, University of Oxford, Oxford, UK
Glossary
Bayes theory A mathematical formulation that permits the

updating of belief. It relates prior knowledge, likelihood
(observed data), and evidence terms to the posterior
allowing inference of unknown parameters of a system
(Bayesian inference).
Calculus of variations A field of mathematics dealing with
maximization or minimization of functionals (functions of
functions).
Conjugate prior (conjugate prior distribution) A
probability distribution chosen as a prior is said to be
conjugate to the likelihood if the posterior takes the same
parametric form as the prior.
EM (expectationmaximization) An iterative method for
finding the maximum likelihood or maximum a posteriori
estimate.
Evidence (model evidence) The normalizing constant in
Bayes theorem, formally the probability of the model
chosen to describe the system for all possible values of the
parameters, it does not directly depend upon the parameters
but only the observed data. Since the evidence does depend
upon the choice of model, but not specific values of
parameters in the model, it can be seen as means to compare
different models when applied to observed data for their
ability to appropriately model the system.
Factorized posterior An approximate posterior distribution
composed of the product of distributions on groups of the
parameters of the full distribution. The specification of a
factorized posterior is seen as taking a mean-field
approximation.
Forward model A mathematical model of the system under
analysis that gives a deterministic predication of the
observed data in terms of a number of unknown parameters.
Free energy (variational free energy) A quantity for
comparing two probability distributions that gives a lower
bound on the log evidence where another distribution is
being sued to approximate the true posterior distribution.
The equation is identified as being equivalent to the concept
of free energy in physics. Variational Bayes takes the
approach of maximizing the free energy.
General linear model A statistical linear model that
describes a series of multi-variate measurements in terms of
a design matrix and associated parameters to be estimated
from observed data, plus noise.
Hyperparameter A parameter of the prior distribution, sued
to distinguish these from the parameters of the system under
analysis.
Inference (Bayesian inference) In the context of data
analysis, the process of deriving information about a system
from observed data, including prior knowledge of the

system.
KullbackLeibler distance (KL divergence) A quantity for
comparing two probability distributions supplying a
distance (or divergence) between them. It is a measure of the
information lost when one distribution is used to
approximate another. Thus variation Bayes seeks to
minimize the KL distance, but typically does so via a
maximization of the free energy.
Laplace approximation An approximate approach to full
Baeysian inference based on MAP in which an
approximation to the full posterior is sought around the
maximum (mode) of the distribution based on the local
curvature.
Likelihood (Likelihood function) A function of both the
system parameters and the data that describes how likely
the observed data were given a choice of system
parameters. Unlike the other terms in Bayes theorem the
Likelihood is not a probability distribution (on the
observed data).
MAP (maximum a posteriori) A form of inference (not
always regarded as fully Bayesian inference) in which the
maximum of the posterior distribution is sought rather than
the full distribution. This produces a point estimate of the
parameters of the system under observation.
Mean-field approximation The process of approximating a
multi-variate (posterior) distribution via the product of
lower dimensional distributions on the parameters, creating
a factorized (posterior) distribution. Its use in variational
Bayes has parallels with the mean-field approximation taken
in physics problems.
MLE (maximum Likelihood estimation) Estimation of the
maximum of the Likelihood function, produces a point
estimate for the parameters of the system under observation
without inclusion of prior information. This is not
considered Bayesian inference since Bayes theory is not
employed (there is no update of belief).
Posterior (posterior probability
distribution) Information that has been inferred about the
parameter(s) of interest of the system from observed data
and prior knowledge via the application of Bayes theorem.
This will take the form of a probability distribution on the
parameter(s).
Prior (prior probability distribution) Existing knowledge
about the system on which inference is to be performed. In
the context of Bayesian inference this will be captured in a
probability distribution on the parameter(s) of interest.
Informally the idea of prior information might also include
the choice of model used to describe the system.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00327-4
523
524
INTRODUCTION TO METHODS AND MODELING | Variational Bayes
Introduction
Bayesian methods have proved powerful in many applications, including brain mapping, for the inference of model
parameters from data. These methods are based on Bayes
theorem, which itself is deceptively simple. However, in
practice, the computations required are intractable even for
simple cases. While alternative methods for the Bayesian
inference exist, many of these either make too crude an
approximation, for example, point estimation using maximum a posteriori (MAP) estimators, or attempt to estimate
full posterior distributions by sampling from the exact solution that can be computationally prohibitive (e.g., Markov
chain Monte Carlo (MCMC) methods).
However, more recently, the variational Bayes (VB) method
has been proposed (Attias, Leen, & Muller, 2000) that facilitates analytic calculations of the posterior distributions over a
model. The method makes use of the mean field approximation, which approximates the true posterior as the product of
several marginal posteriors. Practical implementations of VB
typically make use of factorized approximate posteriors and
priors that belong to the conjugate-exponential family, making the requisite integrals tractable. The procedure takes an
iterative approach resembling an expectationmaximization
method and whose convergence (albeit to a local minima) is
guaranteed. Since the method is approximate, the computational expense is significantly less than MCMC approaches.
Attias et al. (2000) provided the original derivation of the VB
framework for graphical models (although were not the first to
take such an approach). They introduced the concept of freeform selection of the posterior given the chosen model and
priors, although this is ultimately limited by the need for the
priors and factorized posteriors to belong to the conjugateexponential family (Beal, 2003). A comprehensive example of
the application of VB to a one-dimensional Gaussian mixture
model has been presented in Penny and Roberts (2000). Beal
(2003) has provided a thorough description of VB and its relationship to MAP and maximum likelihood estimation (MLE), as
well as its application to a number of standard inference problems. He has shown that expectationmaximization algorithm
is a special case of VB. In Friston, Mattout, Trujillo-Barreto,
Ashburner, & Penny (2007), they additionally considered the
VB approach and variational free energy in the context of the
Laplace approximation and restricted maximum likelihood
(ReML); this is known as variational Laplace. In this context,
they used a fixed multivariate Gaussian form for the approximate posterior, in contrast to the free-form approach.
This article sets out to provide an introduction to VB starting
from the principles of the Bayesian inference and thus following
on from the previous article in this work on Bayesian model
inversion. The essential principles for constructing a VB inference algorithm are outlined and this is followed by a number of
examples. These include a toy mathematical example for the
inference of the parameters of a Gaussian distribution.
Subsequently, a VB algorithm is developed for inference from
the widely used general linear model (GLM), and a number of
applications and extensions from the brain mapping literature
are highlighted. The VB scheme for the GLM is then used as a
basis for extensions to nonlinear models to provide methods
that can be used relatively widely in various brain mapping
applications, particularly those involving time series data. Examples of its use from the literature are also included. Finally, some
other literature examples are provided demonstrating the application of VB inference in brain mapping.
Variational Bayes
Bayesian Inference
The basic Bayesian inference problem is one where there are a
series of measurements, y, and they are to be used determine
the parameters, w, of the chosen model M. The method is
based on Bayes theorem:
P wjy, M
P y, wjM P yjw, MP wjM
P yjM
P yjM
[1]
which gives the posterior probability of the parameters given the

data and the model, P wjy, M, in terms of the likelihood of the
data given the model with parameters w, P yjw, M; the prior
probability of the parameters for this model, P wjM; and the
evidence for the measurements given the chosen model,
P yjM. Often, the correct normalization of the posterior probability distribution is not important. Hence, the evidence term
can be ignored to give
P wjy P yjwP w
[2]
where the dependence upon the model is implicitly assumed.

P(y|w) is calculated from the model and P(w) incorporates
prior knowledge of the parameter values and their variability.
For a general model, it may not be possible (let alone easy) to
evaluate the posterior probability distribution analytically. In
which case, one might approximate the posterior with a simpler
form q(w), which itself will be parameterized by a series of
hyperparameters. A measurement of the fit of this approximate
distribution to the true distribution is the free energy:

PyjwP w
F qw log
dw
qw
[3]
Inferring the posterior distribution P(w|y) is now a matter

of estimation of the correct q(w), which is achieved by maximizing the free energy over q(w): as Attias et al. (2000) put it,
Optimising [F] produces the best approximation to the true
posterior . . ., as well as the tightest lower bound on the true
marginal likelihood.
Derivation for Equation [3]

Consider the log evidence
log P y log P yjwP w dw
[4]
Introduce another (at this stage arbitrary) probability distribution q(w) that is to be compared with (or in this case used
to approximate) P(w|y), to get
P yjwP w
log Py log qw
dw
[5]
qw
Now using Jensens inequality, this can be written as

P yjwP w
dw
log Py qw log
qw
[6]
This latter quantity is identified from physics as the free

energy and the equality holds when q(w) P(w|y). Thus, the
process of seeking the best approximation, q(w), becomes a
process of maximization of the free energy.
Derivation for Equation [10]

We can define the free energy as
F f w, qw dw
The maximization of F is equivalent to minimizing the

KullbackLeibler (KL distance), also known as the relative
entropy (Penny, Kiebel, & Friston, 2006), between q(w) and
the true posterior. Start with the log evidence
log P y log
P y; w
P wjy
[7]
take the expectation with respect to the (arbitrary) density q(w)
P y; w
dw
qw log
P wjy
2
3
y;
w
5 dw
qw log 4

P wjy qw
[8]
P y; w
qw
dw qw log
dw
qw log
qw
Pwjy
F KL
where KL is the KL distance between q(w) and P(w|y). Since KL
satisfies Gibbs inequality, it is always positive; hence, F is a
lower bound for the log evidence. Thus, to achieve a good
approximation, we either maximize F or minimize KL, only
the former being possible in this case.
[12]
which is a functional (a function of a function) where

f w, qwdw qw log
Alternative interpretation
525
PyjwP w
qw
[13]
We wish to maximize the free energy with respect to each

factorized posterior distribution in turn; to do so, we need to
turn to the calculus of variations. We require the maximum of F
with respect to the approximate posterior of a subset of the
parameters, qwi wi ; thus, we write the functional in terms of
these parameters alone as
F gwi , qwi wi dwi

where
g (wi, qwi (wi))
14
f (w, q(w)) dwi .
From variational calculus, the maximum of F with respect

to the approximate posterior, qwi wi , is the solution of the
Euler differential equation
(
)
@
d
@
g
w
gwi ,qwi
,q

0 [15]
i
i
@qwi wi
dwi @q0wi wi
where the second term is zero, in this case, as g is not dependent upon q0wi wi . Using eqn [14], this can be written as (note
that this
is
equivalent to the form used in (Friston et al., 2007)
@
@F
@qwi @wi 0)
qw (wi)
i
q (w) log
P (y | w) P (w)
dw
i
q (w)
0.
16
Variational Approach
To make the integrals tractable, the variational method chooses
mean field approximation for q(w):
Y
q w i
(9)
qw
i wi
where the parameters in w have been collected into separate
groups wi, each with their own approximate posterior distribution q(wi). This is the key restriction in the VB method, making
q approximate. It assumes that the parameters in the separate
groups are independent, although it does not require complete
factorization of all the individual parameters (Attias et al.,
2000). The computation of q(wi) proceeds by the maximization of q(wi) over F; by application of the calculus of
variations, this gives
log qwi ( wi ) qwi ( wi ) log P (y | w) P (w) dwi
10
qwi ( wi ) log P (y | w) P (w) dwi
qwi ( wi ) log qwi ( wi ) dwi
qwi ( wi ) log qwi ( wi ) dwi 0.
17
Hence,
log qwi
qwi ( wi ) log P (y | w) P (w) dwi constant,
18
which is the result in eqn [10]. Since qwi wi is a probability

distribution, it should be normalized, although often, the form
of q is chosen (e.g., use of factorized posteriors conjugate to the
priors) such that the normalization is unnecessary. A derivation that incorporates the normalization, using Lagrange multipliers, is given by Beal (2003).
where wi refer to the parameters not in the ith group. It is

possible to write eqn [10] in terms of an expectation as
log qwi ( wi ) log P (y | w) P (w) qw ,
i
11
where h iX is the expectation of the expression taken with

respect to X.
Conjugate-Exponential Restriction
Commonly, the approach referred to by Attias et al. (2000) as
free-form optimization is used, whereby rather than assuming a specific parametric form for the posteriors, we let them
526
fall out of free-form optimisation of the VB objective function.

A further restriction is to only employ priors that are conjugate
with the complete data likelihood. The prior is said to be
conjugate to the likelihood if and only if (Beal, 2003) the
posterior (in this case, we are interested in the approximate
factorized posterior) is the same parametric form as the prior:
qwi wi P YjwPwi
[19]
This naturally simplifies the computation of the factorized

posteriors, as the VB update becomes a process of updating the
posteriors hyperparameters. A few example conjugate priors are
given in Table 1. In general, this restriction requires that the
complete data likelihood comes from the exponential family:
In general the exponential families are the only classes of
distributions that have natural conjugate prior distributions
because they are the only distributions with a fixed number of
sufficient statistics apart from some irregular cases (Beal, 2003).
Additionally, the advantage of requiring an exponential distribution for the complete data likelihood can be seen by examining eqn [10], where this choice naturally leads to an exponential
form for the factorized posterior allowing a tractable VB solution. Hence, VB methods typically deal with models that are
conjugate exponential, where setting the requirement that the
likelihood come from the exponential family usually allows the
conjugacy of the prior to be satisfied. In general, the restriction to
models whose likelihood is from the exponential family is not
restrictive as many models of interest satisfy this requirement
(Beal, 2003). Neither does this severely limit the choice of priors
(which by conjugacy will also need to be from the exponential
family), since this still leaves a large family including noninformative distributions as limiting cases (Attias et al., 2000).
Equation [10] now provides a series of equations for the
hyperparameters of each qwi wi in terms of the parameters of
the priors and potentially of the other factorized posteriors.
The resultant VB scheme involves computing the hyperparameters for each set using the values calculated for the
other sets. These variational updates are iterated until convergence, typically in a number of variational steps. Classical
algorithms like the expectationmaximization algorithm can
be seen as special cases of these variational updates. The VB
updates are guaranteed to converge because the scheme can be
formulated as a coordinate descent.
Table 1
A Simple Example: Inferring a Single Gaussian

The procedure of arriving at a VB algorithm from eqn [10] is
best illustrated by a trivial example. Penny and Roberts (2000)
provided the VB update equations for a Gaussian mixture
model including inference on the structure of the model.
They also provided the results for the simple example of inferring on a single Gaussian. Drawing measurements from a
Gaussian distribution with mean m and precision b,
p
2
b b
P yn jm, b p e2yn m
2p
[20]
If N samples are drawn that are identically independently

distributed (i.i.d.),
P yjm, b
YN
n1
P yn jm, b
[21]
To infer the two Gaussian parameters, factorize the approximate posterior as

qm; b qmqb
[22]
Factorized posteriors for both parameters need to be chosen. Restricting this choice to priors that belong to the
conjugate-exponential family, choose prior distributions as
normal for m and gamma for b:
2
1
1
qmjm, n Nm; m; n p e2nmm
2pn
qbjb, c Gab; b; c
1 bc1 b
e b
Gc bc
[23]
[24]
Thus, there are four hyper-parameters (m, n, b, c) over the

parameters of the posterior distribution. The log factorized
posteriors (which will be needed later) are given by
log qm
m m2
constfmg
2n
b
log qb c 1 log b constfbg
b
[25]
[26]
Some conjugate priors for typical likelihood for data analysis problems
Likelihood
Model parameters

Bernoulli
Poisson
Normal
with known precision, n
Normal
with known mean, m
Multivariate normal
with known precision matrix, L
1 p
p
x0
x1
Conjugate prior distribution
Prior parameters
b1
x a1 1 x
Ba; b
a, b
Beta
Gamma
Normal
2
n
n
p e2xm
2p
Gamma
1 nc1 n
e b
Gc bc
b, c
2
L
L
p e 2 xm
2p
Normal
L0 L0 mm0 2
p
e 2
2p
m0, L0
lx l
e
x!
2
n
n
p e2xm
2p
x, is the measured quantity and may be discrete or continuous according to the situation.
1 lc1 l
e b
Gc bc
n0 n0 mm0 2
p
e 2
2p
b, c
m0, n0

where const{X} contains all terms constant with respect to X.
Likewise, the log priors are given by
m m0 2
constfmg
2n0
[27]
b
c0 1 log b constfbg
b0
[28]
log P m
log P b
P m, bjY P Yjm, bPmP b
[29]
from which the log posterior up to a proportion can be defined

as
L log P Yjm, n log P m log Pb constfm; bg
N
bX
b
log b
y m2 c0 1 log b
n n
2
2
b0

m m0 2
constfm; bg
2n0
Rearrange this equation to be in the form of the log

factorized posterior for m from eqn [25], which is a log
normal distribution, noting that
X
X
X
y m2 Nm2 2m n yn
y2
n n
n n
[34]
Nm2 2ms1 s2
with
XN
s1
where prior values for each of the hyperparameters are denoted

by a 0 subscript.
Bayes theorem gives
527
Xn1
N
yn
y2
n1 n
s2
Hence, using this result and completing the square,

1 Nn0 bc
m0 n0 bcs1 2
m
Lqb db
1 Nn0 bc
2n0
constfmg
[35]
[36]
Comparing coefficients with the expression for the log

factorized posterior for m in eqn [25] finally gives
m
n
[30]
m0 n0 bcs1
1 Nn0 bc
[37]
n0
1 Nn0 bc
[38]
Note that having ignored the terms, which are constant in m,

is only possible to define q(m) up to scale.
Update on m
From eqn [10],
log qm Lqb db
[31]
Performing the integral on the right-hand side,
Lqb db
8
<
N
bX
b
log b
yn m2 c0 1 log b
:2
2 n
b0

Starting from eqn [10], again,
log qb Lqm dm
8
<
N
bX
b
y m2 c0 1 log b
log b
n n
:2
2
b0
m m0 2

2n0
m m0
gGab; b; c db
2n0
[32]
This simplifies by noting that the second and third terms

are constant with respect to m, that the integral of a probability
distribution is unity, and that the integral in the final term is
simply the expected value (the mean) of the gamma distribution. Hence,
bc X
m m0
Lqb db

2n0
2
constfmg
Nm; m; n dm
N
b
log b c0 1 log b
2
b0
b X

y m2 Nm; m; n dm constfbg
n n
2
0
1
0
1
N
1
X
[39]
@ c0 1A log b @ Ab
2
b0 2
m m0 2
Gab; b; c db
2n0
0
1
N
@ c0 1A log bGab; b; c db
2
1

bGab; b; c db
b0
1X
2
bGab; b; c db
y

m

n n
2
Update on b
yn m
[33]
where X is a function of m only
X s2 2ms1 Nm2 Nm; m; n dm
s2 2s1 mNm; m; n dm N m2 Nm; m; n dm

s2 2s1 m N m2 n
[40]
Comparing coefficients with the log factorized posterior for

m, eqn [28], gives the updates for b:
1
1 X

b b0 2
[41]
N
c0
2
[42]
528
These are the updates, informed by the data, for the hyperparameters. Since the update equations for the hyperparameters
for m depend on the hyperparameter values for b and vice versa,
these updates have to proceed as an iterative process.
prior values were used: m0 0, n0 1000, b0 1000,

c0 0.001. The VB updates were run over 1000 iterations
(more than sufficient for convergence) giving estimates for
the mean of the distribution as 0.0918 and variance as
1.1990. Figure 2 compares the approximate posterior for m to
the true marginal posterior arrived at by analytically evaluating
the posterior, showing that as the size of the data increases, the
approximation improves.
Numerical Example
Since this example is sufficiently simple, it is possible to plot
the factorized approximation to the posterior against the true
posterior, as is done in Figure 1, where 100 samples were
drawn from a normal distribution with zero mean and unity
variance and where the following relatively uninformative
Free Energy
The expression for the free energy (eqn [13]) for this problem is
given by Penny and Roberts (2000):
F Lav KLqmjjpm KLqbjjpb
(43)
where the average likelihood is

Posterior (a.u.)
Lav 0:5Ncc log b

0:5bc s2 N m2 n 2ms1
(44)
The KL divergence between the factorized posteriors and

priors is given by
1
KLqmjjpm 0:5 log
0.5
1.5
b
0.5
0.5
0
n0 m2 m20 n 2mm0
0:5
n
2v0
KLqbjjpb c 1cc log b c log Gc log Gc0

bc
c0 log b0 c0 1cc0 log b0
b0
Figure 1 Comparison of (log) true posterior (wireframe) with the

factorized approximation (shaded) for variational Bayesian inference of
the parameters of a single Gaussian. Reproduced with permission from
The FMRIB Variational Bayes Tutorial, Chappell, M. A., Groves, A. R., &
Woolrich, M. W. (2007). A technical report of the Analysis Group, FMRIB
Centre, University of Oxford, TR07MC1.
[45]
and c(x) is the digamma function evaluated at x (see
Appendix). The free energy provides a way to monitor the
convergence of the update equations and is an approximation
to the model evidence.
N = 5 approximate
N = 5 true
N = 10 approximate
0.9
Marginal posterior for m
N = 10 true
0.8
N = 100 approximate
0.7
N = 100 true
0.6
0.5
0.4
0.3
0.2
0.1
0
1
0.8 0.6 0.4 0.2
0
m
0.2
0.4
0.6
0.8
Figure 2 Accuracy of the marginal posterior for m as the size of the data increases. Reproduced with permission from the The FMRIB Variational Bayes
Tutorial, Chappell, M. A., Groves, A. R., & Woolrich, M. W. (2007). A technical report of the Analysis Group, FMRIB Centre, University of Oxford,
TR07MC1.
log qyjy Lqfjy df
VB Updates for the GLM

In this section, the VB scheme for the inference of the parameters for the GLM with additive noise is derived. The model for
the measurements, y, is
y yx e
[46]
where x is the design matrix, y are the parameters, and e is the

additive Gaussian noise with precision f:

e N 0; f1
[47]
Hence,

P yn jf
f
2p
1=2
e1=2e
fe
N
1
log f y yxT fy yx
2
2
[49]
[50]
From here on, the subscripts on q will be dropped as the

function should be clear from the domain of the function. The
following distributions are chosen for the priors:

1
1
1
1
log qyjy yT Ly yT Lm mT Ly constfyg [58]
2
2
2
and the right-hand side of eqn [57] as
Lqfjy df
0
1
1
@ fy yxT y yx y m0 T L0 y m0
2
2
!
constfyg Gaf; s; c df
1
y m0 T L0 y m0
2
1
y yxT y yx fGaf; s; c df constfyg
2
where Y {y, f} is the set of all the parameters to be inferred:

those of the model and the noise.
Factorize the approximate posterior separately over the
model parameters y and the noise parameter f:
qY qy yqf f
[57]
The factorized log posterior on the left-hand side is (from

eqn [56])
[48]
Thus, for N observations, the log likelihood is

log P yjY
529
P y MVN y; m0 ; L0
[51]
Pf Gaf; s0 ; c0
[52]
The factorized posteriors are chosen conjugate with the

factorized posteriors as

qyjy MVN y; m; L1
[53]
qfjy Gaf; s; c
[54]
1
1
y m0 T L0 y m0 scy yxT y yx
2
2
constfyg
[59]
Rearranging this to be in the form of eqn [58] and then

comparing coefficients give the following updates for m and L:
L scxT x L0
[60]
Lm scx T y L0 m0
[61]
Note that the precision matrix for the model parameters

given by eqn [60] is a weighted sum of the prior precision
matrix and the inner product of the design matrix, where the
weighting is determined by the amount of noise, as given by
the mean of the gamma posterior for the noise precision: the
product sc. Hence, as in all Bayesian inferences, there is a
balance struck between the prior information and the measured data depending upon how informative and noisy those
data are. Likewise, this can be seen in the update equation for
the parameter means.
Updates for the Noise Precision

Now, using Bayes theorem (eqn [1]) to get the log posterior
[55]
For the noise precision posterior distribution, we have from

eqn [10]
log qfjy Lqyjy dy

[62]
where any terms that are constant in y, f appear in the final

term. Hence,
The factorized log posterior on the left-hand side is (from

eqn [56])
L log P Yjy log P yjY log Py log Pf

constfy; fg
1
N
L y yx T y yx log f
2
2
1
1
y m0 T L0 y m0 c0 1 log f f
2
s0
constfy; fg
log qfjy c 1 log f

[56]
[63]
and the right-hand side of eqn [62] as

8
<
1
N
fy gyT y gy log f c0 1 log f

: 2
2
Updates for Forward Model Parameters

From eqn [10],
f
constffg
s
)
1
f constffg qy dy
s0
530

0
N
1
1
@ c0 1A log f f f y gyT y gy
2
s0
2
MVNy; m; L dy
[64]
Equation [64] becomes

N
1
c0 1 log f f
2
s0

o
1 n
f y mxT y mx Trace L-1 xT x
2
[65]
Rearranging this to be in the form of eqn [63] and then

comparing coefficients give the following update equations:
c
N
co
2
1 1 1
1
y mxT y mx Trace L-1 xT x
s s0 2
2
[66]
[67]
In this case, the update for c is not dependent upon the

hyperparameters for y; hence, it does not need to be iteratively
determined. Notice also that the estimate of the noise precision
parameters is dictated by the prior and the data: being affected
by the number of measurements in the data, the error between
the model and measured data (ymx) and the effect on the
predicted signal brought about by uncertainty in the model
parameters: Tr(L1xTx).
Convergence
The expression for the free energy for this case can be derived
from eqn [13] and is given by
0
1
sc @N
F
c0 1A log s cc
s0
2

o
1n

mm0 T L0 mm0 Tr L-1 L0
2

o
1n
y mxT y mx Tr L-1 xT x s log c

2
0
1
N
log Gc c @ c 1A log s cc
2
1
log det L constant
2
[68]
The free energy can, as in the simple case, be used to

monitor convergence. The free energy should always be monotonic making it a useful diagnostic tool for debugging update
equations and ensuring that the implementation is correct.
While convergence with VB is guaranteed, this is only to a
local rather than the global minimum, so the initialization of
the updates calls for careful consideration.
Applications in Brain Mapping

Penny, Kiebel, and Friston (2003) have provided an introduction to VB specifically for functional MRI (fMRI) data using the
GLM; they went beyond the simple derivation earlier and
included an autoregressive noise model making it more applicable to blood oxygenation level-dependent (BOLD) fMRI data.
Penny et al. (2006) included a comparison of the VB solution to
the classical Laplace approximation approach, widely used in
Bayesian inference, of finding the maximum a posteriori solution and locally approximating the posterior distribution using a
Gaussian distribution based on the local curvature. Woolrich,
Behrens, and Smith (2004) extended the framework of Penny
et al. (2003) to include the inference of the hemodynamic
response function via a constrained basis set and spatial priors
on the autoregressive noise parameters. Penny, Trujillo-Barreto,
and Friston (2004) further extended the method to include
spatial priors on the regression coefficients and Penny, Kilner,
and Blankenburg (2007) modeled the noise as a mixture of
Gaussians to derive robust inference scheme. Groves, Chappell,
and Woolrich (2009) implemented a combined spatial and
biophysical prior using a combination of evidence optimization
and a VB solution for inference under the GLM. Makni, Beckmann, Smith, & Woolrich (2008) derived a VB deconvolution
method for fMRI data, permitting the hemodynamic response
function to be inferred from the data, based on the bilinear
dynamic systems model. Chaari, Vincent, Forbes, Dojat, &
Ciuciu (2013) have also taken a variational approach to the
joint detection of hemodynamics and activity in event-related
fMRI.
VB Updates for Nonlinear Forward Models

To ensure tractability of the VB approach, the models to
which it can be applied are limited (Beal, 2003), for example,
a linear model in the previous section. There are several
generalizations of the variational updates described earlier
to accommodate nonlinear models. For example, one can
retain the variational steps under a local linearization
assumption (Woolrich & Behrens, 2006). Alternatively, one
can optimize the hyperparameters of the approximate marginals with respect to variational free energy using a gradient
descent or other optimization scheme. Crucially, the solution
to this optimization corresponds to eqn [10] that forms the basis
of variational updates. The advantage of explicitly optimizing
variational free energy (as exploited in variational Laplace) is
that the analytic solution is not required explicitly and
therefore, the priors do not have to be conjugate to the likelihoods. As an example of these generalizations, we will focus on
the local linearization and second-order approximation to analytic variational updates.
The model for the measurements, y, is now
y gy e
[69]
where g(y) is the nonlinear forward model for the measurements and e is the additive Gaussian noise with precision f as
in eqn [46]. The specification of the priors and the derivation
of the log likelihood proceed as in the previous section (eqns
[50][56]). Unlike the case for the GLM, L (eqn [56]) may not
produce tractable VB updates for any general nonlinear model.
In this case, tractability will be achieved by considering a linear
approximation of the model. Approximating g(y) by a firstorder Taylor expansion about the mode of the posterior

distribution, which for an multivariate normal (MVN) is also
the mean,
gy gm Jy m
[70]
where J is the Jacobian (matrix of partial derivates)

d gyx
Jx, y

dyy

N
1
c0 1 log f f
2
s0

1
f kT k Trace L-1 JT J
2
[71]
ym
Following exactly the same procedure as in Section Updates

for Forward Model Parameters under VB Updates for the
GLM, but now using the linearization of g(y) from eqn [70],
(72)
Equation [59] becomes
1 T
y L0 scJT J y yT L0 m0 scJk Jm
2
L0 m0 scJk JmT yg
[73]
Rearranging this in the form of eqn [58] and comparing

coefficients give the updates for m and L:
L scJT J L0
T
Lmnew scJ k Jmold L0 m0
[74]
[75]
Note that in eqn [61], the new value of m is dependent

upon its previous value. This is unlike VB for linear forward
models (and all the other updates for this formulation), where
the new value for each hyperparameter is only dependent upon
the other hyperparameters and hyperparameter priors. Notice
also that the set of equations are very similar to the GLM case
with the same weighting of new and prior information but the
Jacobian matrix has taken the role of the design matrix.
Updates for the Noise Precision

Following the same procedure as the linear model in Section
Updates for the Noise Precision under VB Updates for the
GLM and using the linearization as in eqn [72], eqn [64]
becomes
(y g(q))T (y g(q)) MVN (q;m,)dq,
kTk (q m)TJTk kTJ (q m) (q m)TJTJ (q m) MVN (q)dq,
T
kk
Trace ( 1JTJ).
76
whereR the indicated terms are zero after the integration (since,
e.g., (y m)MVN(y; m, L) dy m m 0) and the following result has been used:
y mT Uy mMVN y; m; L1 dy Tr L-1 U 8U [77]

Hence, eqn [76] becomes
N
co
2
1 1 1 T
1
k k Tr L-1 JT J
s s0 2
2
Updates for Forward Model Parameters
[78]
Rearranging this in the form of eqn [63] and comparing

coefficients give the following update equations:
y gy y gm Jy m
k Jy m
531
[79]
[80]
Convergence
The expression for F is given by
0
1
sc @N
F
c0 1A log s cc
s0
2

o
1n

mm0 T L0 mm0 Tr L-1 L0
2

1 T

k k Tr L-1 JT J s log c log Gc
2
0
1
N
1
c @ c 1A log s cc log det L
2
2
constant
(81)
In pure VB the free energy, F should increase at every iteration. However, since the nonlinear version of VB deviates from
an EM approach, the value of F during iteration may pass through
a maximum and actually start to decrease again. The issue of
convergence for this nonlinear inference scheme is discussed
further in Chappell, Groves, Whitcher, & Woolrich (2009).
Applications in Brain Mapping

Chappell et al. (2009) originally applied the previous derivation to arterial spin labeling (ASL) MRI for the quantification of
perfusion in the brain using a nonlinear kinetic model. They
included a comparison with an MCMC-derived posterior and
showed good agreement between it and the approximation for
the nonlinear model employed. The algorithm was extended
to model variations in the noise within the signal by including multiple separable noise components. The use of automatic
relevancy determination (or shrinkage priors) was also
investigated for the selective inclusion of further sources of
signal in the ASL model; this was included by a further factor
within the factorized approximation posterior and its efficacy
was demonstrated in Chappell et al. (2010). In Groves et al.
(2009), a combined spatial and biophysical prior was derived
and implemented within the VB framework for nonlinear
models. The algorithm can be extended to autoregressive (AR)
noise as with the linear model and has been applied to dualecho fMRI (Woolrich, Chiarelli, Gallichan, Perthen, & Liu,
2006). The framework has also been applied to pH mapping
using chemical exchange saturation transfer MRI, using a model
based on the BlochMcConnell equations (Chappell et al.,
2013), and to perfusion quantification using dynamic
susceptibility contrast MRI using a semiparametric model that
532
afforded a form of constrained deconvolution (Mehndiratta,

MacIntosh, Crane, Payne, & Chappell, 2013).
Further Applications of VB in Brain Mapping

MEG/EEG
Sato et al. (2004) has proposed a VB method for magnetoencephalography (MEG) data with a hierarchical prior incorporating structural and functional MRI data. The VB approach
was compared and contrasted with an MCMC solution
highlighting issues related to the unimodal approximation of
the VB approach by Nummenmaa et al. (2007). Subsequently,
Kiebel, Daunizeau, Phillips, and Friston (2008) have derived a
VB algorithm for the inversion of dipole models in electroencephalography (EEG) and MEG. More recently, Mohseni et al.
(2010) have applied VB to the detection of event-related
potentials.
Dynamic Causal Mappings

Dynamic causal mapping (DCM) has been widely applied to
fMRI data using the Bayesian inference (Friston, Harrison, &
Penny, 2003) and a VB scheme has been proposed by
Daunizeau, Friston, & Kiebel (2009). In Friston et al. (2007),
the variational free energy for the Laplace approximation was
derived and simple relationships between VB, expectation
maximization, and ReML were found. This permitted ReML
to be applied to DCMs while including model selection, and
Penny (2012) further investigated model selection concluding
that the free energy was the most appropriate metric to use for
model comparisons.
Structural MRI and Registration

Woolrich and Behrens (2006) applied VB to mixture modeling
for application to segmentation and made use of a Taylor
expansion to the second order to make the calculations tractable. Their comparisons to an equivalent MCMC inference
scheme demonstrated an order of magnitude increase in computational speed. Simpson, Schnabel, Groves, Andersson, &
Woolrich (2012) derived a Bayesian framework to nonrigid
registration incorporating the inference of the degree of spatial
regularization to be applied and exploited the VB approach.
Acknowledgments
A large portion of this work originally appeared as the FMRIB
Variational Bayes Tutorial and the authors are grateful to
Adrian Groves, Saad Jbabdi, and Salima Makni for helpful
comments and advice in preparing that work.

Obtaining Quantitative Information from fMRI; Perfusion Imaging with
Arterial Spin Labeling MRI; INTRODUCTION TO METHODS AND
MODELING: Bayesian Model Inference; Bayesian Model Inversion;
Contrasts and Inferences; Convolution Models for FMRI; Distributed
Bayesian Inversion of MEG/EEG Models; Dynamic Causal Models for
fMRI; Dynamic Causal Models for Human Electrophysiology: EEG,

MEG, and LFPs; Forward Models for EEG/MEG; Models of fMRI Signal
Changes; Posterior Probability Maps; The General Linear Model.
Appendix.
Function Definitions
The gamma distribution may be defined as

Gax; b; c
1 xc1 x
e b
Gc bc
[82]
The digamma function is defined as

cx
d
G0 x
ln Gx
Gx
dx
[83]
References
Attias, H., Leen, T., & Muller, K.-L. (2000). A variational Bayesian framework for
graphical models. Advances in Neural Information Processing Systems, 12, 4952.
Beal, M. (2003). Variational algorithms for approximate Bayesian inference. PhD Thesis,
Gatsby Computational Neurosicence Unit.
Chaari, L., Vincent, T., Forbes, F., Dojat, M., & Ciuciu, P. (2013). Fast joint detectionestimation of evoked brain activity in event-related fMRI using a variational
approach. IEEE Transactions on Medical Imaging, 32(5), 821837. http://dx.doi.
org/10.1109/TMI.2012.2225636.
Chappell, M. A., Donahue, M. J., Tee, Y. K., Khrapitchev, A. A., Sibson, N. R.,
Jezzard, P., et al. (2013). Quantitative Bayesian model-based analysis of amide
proton transfer MRI. Magnetic Resonance in Medicine, 70(2), 556567. http://dx.
doi.org/10.1002/mrm.24474.
Chappell, M. A., Groves, A. R., Whitcher, B., & Woolrich, M. W. (2009). Variational
Bayesian inference for a nonlinear forward model. IEEE Transactions on Signal
Processing, 57(1), 223236.
Chappell, M. A., MacIntosh, B. J., Donahue, M. J., Gunther, M., Jezzard, P., &
Woolrich, M. W. (2010). Separation of macrovascular signal in multi-inversion time
arterial spin labelling MRI. Magnetic Resonance in Medicine, 63(5), 13571365.
http://dx.doi.org/10.1002/mrm.22320.
Daunizeau, J., Friston, K. J., & Kiebel, S. J. (2009). Variational Bayesian identification
and prediction of stochastic nonlinear dynamic causal models. Physica D: Nonlinear
Phenomena, 238(21), 20892118. http://dx.doi.org/10.1016/j.physd.2009.08.002.
Friston, K., Harrison, L., & Penny, W. (2003). Dynamic causal modelling. NeuroImage,
19, 12731302.
Friston, K., Mattout, J., Trujillo-Barreto, N., Ashburner, J., & Penny, W. (2007).
Variational free energy and the Laplace approximation. NeuroImage, 34(1),
Groves, A. R., Chappell, M. A., & Woolrich, M. W. (2009). Combined spatial and nonspatial prior for inference on MRI time-series. NeuroImage, 45(3), 795809. http://
Kiebel, S. J., Daunizeau, J., Phillips, C., & Friston, K. J. (2008). Variational Bayesian
inversion of the equivalent current dipole model in EEG/MEG. NeuroImage, 39(2),
Makni, S., Beckmann, C., Smith, S., & Woolrich, M. (2008). Bayesian deconvolution
fMRI data using bilinear dynamical systems. NeuroImage, 42(4), 13811396. http://
Mehndiratta, A., MacIntosh, B. J., Crane, D. E., Payne, S. J., & Chappell, M. A. (2013).
A control point interpolation method for the non-parametric quantification of
cerebral haemodynamics from dynamic susceptibility contrast MRI. NeuroImage,
64, 560570. http://dx.doi.org/10.1016/j.neuroimage.2012.08.083.
Mohseni, H. R., Ghaderi, F., Wilding, E. L., & Sanei, S. (2010). Variational Bayes for
spatiotemporal identification of event-related potential subcomponents. IEEE
Transactions on Biomedical Engineering, 57(10), 24132428.
Nummenmaa, A., Auranen, T., Hamalainen, M. S., Jaaskelainen, I. P., Lampinen, J.,
Sams, M., et al. (2007). Hierarchical Bayesian estimates of distributed MEG
sources: Theoretical aspects and comparison of variational and MCMC methods.

Penny, W. D. (2012). Comparing dynamic causal models using AIC, BIC and free
energy. NeuroImage, 59(1), 319330. http://dx.doi.org/10.1016/j.
Penny, W., Kiebel, S., & Friston, K. (2003). Variational Bayesian inference for fMRI time
series. NeuroImage, 19(3), 727741.
Penny, W., Kiebel, S., & Friston, K. (2006). Variational Bayes. In K. Friston, J.
Ashburner, S. Kiebel, T. Nichols & W. Penny (Eds.), Statistical parametric mapping:
The analysis of functional brain images. London: Elsevier.
Penny, W. D., Kilner, J., & Blankenburg, F. (2007). Robust Bayesian general linear
models. NeuroImage, 36(3), 661671. http://dx.doi.org/10.1016/j.
Penny, W., & Roberts, S. (2000). Variational Bayes for 1-dimensional mixture models.
Technical Report PARG-200001, Department of Engineering Science, University
of Oxford. Available from http://www.fil.ion.ucl.ac.uk/~wpenny/publications/vbmog.
ps.
Penny, W. D., Trujillo-Barreto, N. J., & Friston, K. J. (2004). Bayesian fMRI time series
analysis with spatial priors. NeuroImage, 24, 350362.
Sato, M.-a, Yoshioka, T., Kajihara, S., Toyama, K., Goda, N., Doya, K., et al. (2004).
Hierarchical Bayesian estimation for MEG inverse problem. NeuroImage, 23(3),
Simpson, I. J. A., Schnabel, J. A., Groves, A. R., Andersson, J. L. R., & Woolrich, M. W.
(2012). Probabilistic inference of regularisation in non-rigid registration.
Woolrich, M. W., & Behrens, T. E. J. (2006). Variational Bayes inference of spatial
mixture models for segmentation. IEEE Transactions on Medical Imaging, 25(10),
13801391.
Woolrich, M. W., Behrens, T. E. J., & Smith, S. M. (2004). Constrained linear basis sets
for HRF modelling using variational Bayes. NeuroImage, 21(4), 17481761. http://
533
Woolrich, M. W., Chiarelli, P., Gallichan, D., Perthen, J., & Liu, T. T. (2006). Bayesian
inference of hemodynamic changes in functional arterial spin labeling data.
Magnetic Resonance in Medicine, 56(4), 891906. http://dx.doi.org/10.1002/
mrm.21039.
Further Reading
Bishop, C. (2006). Pattern recognition and machine learning. New York: Springer http://
research.microsoft.com/cmbishop/PRML.
Mackay, D. (2003). Information theory, inference, and learning algorithms. Cambridge:
Cambridge University Press http://www.inference.phy.cam.ac.uk/mackay/itila/.
Relevant Websites
http://www.fmrib.ox.ac.uk/fsl The FMRIB Software Library incorporating various MR
neuroimaging tools that use VB methods.
http://www.fmrib.ox.ac.uk/fsl/fabber An implementation of the VB technique for the
fitting of a non-linear model to series image data. Includes an application to dualecho functional MRI, but is extendable to other models.
http://www.fmrib.ox.ac.uk/fsl/basil A toolbox for perfusion quantification using
arterial spin labelling MRI incorporating model-based analysis using the VB method
in fabber.
http://www.fmrib.ox.ac.uk/fsl/baycest A tool for the quantification of chemical
exchange saturation transfer MRI using the VB method in fabber.
http://vbmeg.atr.jp A Matlab toolbox for VB MEG analysis.
http://en.wikipedia.org/wiki/Conjugate_prior Contains an extensive table of conjugate
priors.

NJ Trujillo-Barreto, Institute of Brain, Behaviour and Mental Health, The University of Manchester, UK
pyjmk pyjyk , mk pyk jmk dyk
Introduction
Much of modern neuroscience is concerned with the question of
model choice. A researcher collects data, often in the form of
measurements on many different aspects of the observed units,
and wants to study how these variables affect some outcome of
interest: Which measures are important to the outcome? Which
are not? Are there interactions between the variables that need to
be taken into account? From the statistical point of view, this
enterprise rests on the solution of an inference problem while
accommodating model uncertainty (Clyde & George, 2004). In
many cases, the models (or hypotheses) considered are nonnested or acceptance of the null model is required, which are
unnatural situations in classical hypothesis testing (Kass &
Raftery, 1995). For such setups, the Bayesian approach provides
a natural and general probabilistic framework that simultaneously accommodates both model and parameter
uncertainties.
[3]
is the evidence or marginal likelihood of mk. Under the full

three-stage hierarchical model interpretation for the data,
p(mk|y) is the conditional probability that mk was the actual
model generated at the first stage. This posterior distribution
provides a complete representation of post-data model uncertainty that can be used for a variety of inferences and decisions.
For example, one may be interested in testing a theory represented by one of a set of carefully studied models, or one
simply wants to discard many speculative models to find a
single useful model. However, in problems where no single
model stands out, it may be preferable to report a set of models
with high posterior probability along with their probabilities,
to convey the model uncertainty. These two setups concern two
types of inference, namely, Bayesian model selection and
Bayesian model averaging (BMA).
Bayesian Model Selection

The Probabilistic Setup for Model Uncertainty
Suppose that a set of K 1 models {m0, m1, . . ., mK} are under
consideration for data y and that under mk, y has a probability
distribution p(y|yk, mk), where yk is a vector of unknown parameters that indexes the members of mk (more precisely, mk is a
model class). The comprehensive Bayesian approach for multiple model setups proceeds by assigning a prior probability distribution p(yk|mk) to the parameters of each model and a prior
probability p(mk) to each model. This complete specification can
be understood as a three-stage hierarchical mixture model for
generating the data (Clyde & George, 2004): First, the model mk
is generated from p(m0),. . ., p(mK); second, the parameter vector
yk is generated from p(yk|mk); and third, the data y are generated
from p(y|yk, mk). This prior formulation induces a joint distribution over the data, parameters, and models:
py, yk , mk pyjyk , mk pyk jmk pmk
[1]
Through conditioning and marginalization, the joint distribution p(y, yk, mk) can be used to obtain posterior summaries of
interest.
Under the full three-stage hierarchical mixture formulation, the

model selection problem becomes that of finding the model mk
that actually generated the data in the first step (Chipman et al.,
2001). By treating p(mk|y) as a measure of the truth of model mk,
a natural strategy for model selection is to choose the mk that
maximizes the posterior p(mk|y). However, basing inferences on
a single model alone is risky because uncertainty about the
model selection process is not considered.
Bayesian Model Averaging

BMA (Hoeting, Madigan, Raftery, & Volinsky, 1999) provides
solutions to the prediction, decision making, and inference problems that incorporate rather than ignoring model uncertainty.
Given a magnitude of interest D (such as an effect size, a future
observable, or the utility of a course of action) that is well defined
for every model, its posterior distribution given the data is
pDjy
K
X
pDjy, mk pmk jy
[4]
k0

If the goal is model inference, attention focuses on the posterior distribution p(mk|y), which is obtained by margining out
the parameters yk and conditioning on the data y:
pyjmk pmk
pmk jy X
pyjmi pmi
i
where
[2]
This is an average of the posterior distributions under each of

the models considered, weighted by their posterior model
probability. Moreover, averaging over all the models in this
fashion provides better average predictive ability, as measured
by a logarithmic scoring rule, than using any single model
(Madigan & Raftery, 1994).
Interpretation of BMA
BMA can be thought of as a method for soft model selection.
Equation [4] expresses the probability of observing D given
http://dx.doi.org/10.1016/B978-0-12-397025-1.00328-6
535
536
INTRODUCTION TO METHODS AND MODELING | Bayesian Model Inference
that the data were generated by exactly one of the models. The
soft weights p(mk|y) only reflect a statistical inability to distinguish the generative model based on limited data. As more data
arrive, the model becomes more distinguishable and BMA will
focus its weight on the most probable model. In this view, the
posterior model probabilities used in BMA account for the
uncertainty on the model selection process. Under complete
certainty about a specific model mi,

1 if k i
pmk jy
[5]
0 if k 6 i
pyjmk
Bk:j
p y mj
which is the Bayes factor (Good, 1958; Kass & Raftery, 1995).
Hence, the Bayes factor Bk:j is the ratio of the posterior odds of
mk versus mj to its prior odds, regardless of the value of its prior
odds. When models are equally probable a priori, the Bayes
factor is equal to the posterior odds. Note that the posterior
model probabilities (eqn [2]) can be expressed entirely in
terms of Bayes factors and prior odds as
Bk:0 ak:0
pmk jy X
Bi:0 ai:0
and BMA reduces to model selection

pDjy pDjy, mi
[6]
That is, inference about D is conditional on the selected model.

However, BMA can also be used for model combination as
long as the right question is posed. For example, one might be
interested in the probability of observing D given that the data
were generated by a linear combination of models. This can be
addressed by applying BMA to a new model space of stacked
models.
Managing the Summation

The size of the model space M often renders the exhaustive
summation in eqn [4] impractical. There are two main
approaches to deal with this problem. The first approach is to
average over a subset O of models that are supported by the
data, so that eqn [4] is replaced by
X
pDjy, mk pmk jy
[7]
pDjy
mk 2O
The problem then reduces to constructing efficient algorithms

to search for the models in O. Two of these algorithms are the
Occams window method (Madigan & Raftery, 1994) and a
variant of the leaps and bounds algorithm (Volinsky, Madigan,
Raftery, & Kronmal, 1997).
The second approach uses Markov Chain Monte Carlo
(MCMC) methods to directly approximate eqn [4]. Several
MCMC methods for model uncertainty have been proposed
such as the reversible jump sampler (Green, 1995), the sampling algorithm of Carlin and Chib (1995), the stochastic
search variable selection method (George & McCulloch,
1993), and the MCMC model combination (MC3) method
(Madigan & York, 1995). A good review of many of these
methods can be found in Godsill (2011).
Posterior Odds and Bayes Factors

Based on eqn [2], pairwise comparison of models is summarized by their posterior odds:
pmk jy pyjmk pmk

p mj jy
p ymj p mj
[8]
This expression reveals how the data update the prior

pmk
odds ak:j to yield the posterior odds, through multiplip mj
cation by
[9]
[10]
where, without losing generality, model m0 is taken as a reference model to which m1, . . ., mK are compared. It is reasonable
to assume that ak:0 1 (all models are equally probable a
priori), but other values may be used to reflect prior information about relative plausibility of competing models.
Interpretation of Bayes Factors

The Bayes factor summarizes the evidence provided by the data
in favor of one scientific theory, represented by a statistical
model, as opposed to another. Additionally, given that the
logarithm of the marginal probability of the data (the log
evidence) can be viewed as a predictive score, eqn [9] means
that the Bayes factor can also be interpreted as measuring the
relative success of mk and mj at predicting the data. This interpretation avoids viewing one model as true. Conventional
rules of thumb for interpreting the evidence for one model
provided by the Bayes factor are shown in Table 1 (taken from
Kass and Raftery (1995)), although originally expressed in half
units on the log10 scale by Jeffreys (1961)).
Bayes Factor Approximations

Computation of the Bayes factors (eqn [9]) requires evaluating
the integral eqn [3] that defines the evidence of the model. For
this, the prior distribution on the parameters p(yk|mk) has to be
specified. The latter is a difficult task per se and, more often
than not, renders the analytic evaluation of the evidence intractable. There are a plethora of approximations available to the
Bayes factors, which differ in the way they deal with the prior
distribution of the parameters. They can be divided into
Table 1
Interpretation of Bayes factors
2 log Bk:j
Bk:j
p(mk|y) (%)
Evidence in favor of mk
(against mj)
02
26
610
10
13
320
20150
150
5075
7595
9599
99
Barely worth a mention

Positive
Strong
Very strong
A Bayes factor of 20 corresponds to a belief of 95% in the statement mk is the actual

model that generated the data. This corresponds to strong evidence in favor of mk.
Posterior probabilities were calculated assuming that candidate models are equally
probable a priori.

methods that avoid the specification of the prior completely or
those that approximate the integrand in eqn [3] directly so that
the integral can be evaluated analytically. Usually, the approximated log evidence can be written as
log pyjmk Accuracy mk Complexity mk
[11]
The accuracy is a measure of data fit (usually the best-fit loglikelihood), and the complexity is interpreted as a penalty term
for the number of parameters used by the model to explain the
data. The log evidence as given by eqn [11] optimizes a tradeoff between accuracy and complexity of the model that can be
understood in the following way: A more complex model can
always fit the data better, but it risks overfitting (it fits signal
and noise), while a too simple model has little flexibility and
therefore has a low goodness-of-fit and generalizes poorly to
new data sets. The optimal model must be accurate and simple.
Complexity KLqyk kpyk jmk
537
[19]
is the KL divergence between the approximate posterior and

the prior distributions.
Laplaces method
By definition, the evidence in eqn [3] is the normalization
constant of the posterior distribution of the parameters. By
conditioning eqn [1] on the data and the model, the Bayes
rule for the parameters is
pyk jy, mk
pyjyk , mk pyk jmk

pyjmk
[20]
Approximating the Posterior Distribution
Assuming that the posterior distribution eqn [20] is

highly peaked about its mode ~
yk , the Laplaces method
(Tierney & Kadane, 1986) can be used to approximate the
numerator of eqn [20] as a normal distribution with mean ~
yk
and covariance:
The negative free energy approximation
~ k rr log fpyjyk , mk pyk jmk gj ~

S
yk yk
Without losing generality, the log evidence can be written as
where
log pyjmk F mk KLqyk kpyk jy, mk
[12]
py,yk jmk
dyk
Fmk qyk log
qyk
[13]
is the negative variational free energy and
qyk
dyk
KLqyk kpyk jy, mk qyk log
pyk jy, mk
[14]
is the KullbackLeibler (KL) divergence between the arbitrary

function q(yk) and the posterior distribution of the parameters
p(yk|y, mk). The KL divergence is a measure of distance between
two functions that satisfies the Gibbs inequality
KLqyk kpyk jy, mk 0
[15]
being zero when q(yk) p(yk|y, mk). Therefore, the function q

(yk) that minimizes the KL eqn [14] can be considered as an
approximation to the true posterior. From eqn [12] follows
that, for a given model and data set, minimizing the KL is
equivalent to maximizing F(mk). The variational optimization
of F(mk) to obtain the approximate posterior q(yk) is known as
variational Bayes (Attias, 2000). After optimization, the
negative variational free energy can be used as an approximation to the log evidence of the model:
log pyjmk Fmk
[16]
Additionally, by using inequality eqn [15] in eqn [12], it

follows
log pyjmk Fmk
[17]
which means that F(mk) is actually a lower bound on log p(y|mk).

The negative free energy can also be rewritten in terms of accuracy and complexity as in eqn [11], where
Accuracy qyk log pyjyk , mk dyk

[18]
is the expectation of the log-likelihood under model mk taken
over the approximate posterior and
[21]
where rrf xjx~x denotes the Hessian of second derivatives of

f(x), evaluated at x x~. Integrating this approximation yields

yk , mk log p ~
yk jmk
log pyjmk log p y~

dk
1
~ k
[22]
log 2p log S
2
2
where dk is the dimension of yk. An important variant of eqn
[22] is

log pyjmk log p yy^k , mk log p y^k jmk

dk
1
log 2p log S^k
[23]
2
2
(Tierney, Kass, & Kadane, 1989) where y^k is the maximum
1
likelihood estimator of yk and S^ is the observed information
k
matrix; that is the negative Hessian matrix of the log-likelihood

evaluated at y^k . Although eqn [23] is expected to be less accurate than eqn [22] when the prior is somewhat informative
relative to the likelihood, it has the advantage that it can be
easily computed.
Avoiding the Prior Distribution

The Schwarz criterion or Bayesian information criterion
Assuming that the prior distribution over parameters is broad
in relation to the likelihood (which is usually the case for large
sample sizes) and that the Hessian has full rank, it is possible to
avoid the use of the prior densities p(yk|mk) in eqn [9] by
dropping all terms in eqn [22] that do not scale with the
sample size n, that is,

Sk:j log p y~
yk , mk log p y~
yj , mj

1
dk dj log n
[24]
2
This is known as the Schwarz criterion (Schwarz, 1978),
and it converges asymptotically to the logarithm of the Bayes
factor as n increases. Twice Sk:j is also known as the Bayesian
information criterion.
538
The Akaike information criterion

The Akaike information criterion (AIC; Akaike, 1974) is not a
formal approximation to the evidence, but it is derived by
minimizing the KullbackLeibler divergence between the true
and estimated predictive distributions. One justification for
AIC is Bayesian (Akaike, 1983), that is, asymptotically, comparisons based on Bayes factors and on AIC are equivalent if
the precision of the prior is comparable to the precision of the
likelihood. However, this requires the prior to change with
sample size, which is usually not the case. Rather, the data
tend to provide more information than the prior. The AIC is
defined as

[25]
AICk:j 2 log p yy^k log p yy^k 2 dk dj
For small sample sizes (roughly n/dk < 40), a corrected form
is recommended (Sugiura, 1978):

2dk dk 1 2dj dj 1

[26]
AICck:j AICk:j
n dj 1
n dk 1
AICck:j converges to AICk:j as n gets large. To account for
model uncertainty, one can define Akaikes weights
(Burnham, 2004):
expAICk:0 =2
wk X
expAICk:0 =2
[27]
which can be used to define model averaging estimators of the

form
y^
K
X
wk y^k
[28]
k0
where y^k is the maximum likelihood estimator of the parameters under model mk. The Akaikes weights are interpreted as
the probability that model mk is, in fact, the KL best model for
the data. Although the wk values depend on the full models set,
their ratios wk/wj are identical to the original likelihood ratios,
and therefore, they are invariant to the models set.
Bayes Factors for Improper Priors

Objective priors such as the so-called reference and noninformative priors are often improper. The difficulty with calculating the evidence eqn [3] in this case is that the prior p(yk|
mk) is defined only up to an arbitrary constant ck and, therefore, the Bayes factor in eqn [9] is only defined up to ck/cj that is
itself arbitrary. Dependence of the Bayes factor on the specified
priors and the difficulties of calculating and interpreting the
Bayes factor at all when improper priors are placed on the
parameters of the models have led some authors to seek automatic Bayesian methods for model selection. Two of these
approaches are the intrinsic Bayes factors and the fractional
Bayes factors, which are discussed in the succeeding text.
Intrinsic Bayes factors

Calculation of the intrinsic Bayes factors (Berger & Pericchi,
1996) proceeds as follows:
Divide the data into a training set and a testing set.
On the training set, convert the (improper) prior distributions to proper posterior distributions as
pyk jy , mk
py jyk , mk pyk jmk

py jmk
[29]
Since both p(yk|mk) and p(y*|mk) are affected by the

same arbitrary constant, they cancel out.
Compute the Bayes factor using the testing data and compute the posterior distributions from the training set as the
new priors.
Letting y and y denote the minimal training set and the

testing set, respectively, the intrinsic Bayes factor is defined as
pyjy , mk

Bk:j y
p y y , mj
where
[30]
pyjy , mi pyjyi , mi pyi ,yj,mi dyi , i j, k
[31]
Importantly, a minimal training set needs to be found. For a

given dataset, there will be many minimal training samples;
the intrinsic Bayes factor can be calculated for each one, and
then, an average of these factors, either arithmetic or geometric,
is taken, yielding the arithmetic intrinsic and geometric intrinsic Bayes factors, respectively.
Fractional Bayes factors

For large datasets, there are many minimal training sets over
which to average, making the intrinsic Bayes factor approach
cumbersome. In this case, asymptotic considerations lead to
the definition of the fractional Bayes factors (OHagan, 1995).
Let n* denote the size of the training set, let n denote the size of
the entire dataset, and let b n*/n. For large n* and n, the
likelihood based on the training set only will approximate
the likelihood based on all the data, raised to the bth power.
The fractional Bayes factor is defined as
f y, bjmk
Bbk:j
f y,b mj
where
[32]
f y, bjmi
pyjyi , mi pyi jmi dyi

pyjyi , mi i pyi jmi dyi
, ij, k
Fractional Bayes factors have several desirable properties in

common with ordinary Bayes factors that are not shared by
intrinsic Bayes factors, such as they satisfy the likelihood principle and are invariant to transformations of the data.
Applications to Neuroimaging
The Bayesian treatment of model uncertainty, coupled with
advances in posterior search and computation, has led to an
explosion of research in model selection and model averaging.
In neuroimaging, Bayesian model selection and BMA have been
used to deal with uncertainty about the forward model and/or

the prior distributions used for Bayesian source reconstruction of
encephalography data (Friston et al., 2008; Henson, Mattout,
Phillips, & Friston, 2009; Mattout, Phillips, Penny, Rugg, &
Friston, 2006; Sato et al., 2004; Trujillo-Barreto, Aubert-Vazquez,
& Valdes-Sosa, 2004); selection among different dynamical
causal models (Penny et al., 2010, Penny, Stephan, Mechelli, &
Friston, 2004); selection of the number of activated clusters and
dynamical regimes in dynamical source reconstruction methods
(Daunizeau & Friston, 2007; Olier, Trujillo-Barreto, & El-Deredy,
2013); selection among alternative neurovascular coupling
mechanisms underlying the generation of the hemodynamic
response (Rosa, Kilner, & Penny, 2011; Sotero, Trujillo-Barreto,
Jimenez, Carbonell, & Rodrguez-Rojas, 2009); model selection
for group studies (Stephan, Penny, Daunizeau, Moran, & Friston,
2009); and estimation of the autoregressive model order used to
model hemodynamic signals (Penny, Kiebel, & Friston, 2003),
among others. Although new model uncertainty challenges continue to arise in a wide variety of areas, the potential of Bayesian
methods under model uncertainty has only begun to be realized.

Bayesian Model Inversion; Distributed Bayesian Inversion of MEG/EEG
Models; Dynamic Causal Models for fMRI; Dynamic Causal Models for
Human Electrophysiology: EEG, MEG, and LFPs; Information
Theoretical Approaches; Variational Bayes.
References
Akaike, H. (1974). A new look at the statistical model identification. IEEE Transactions
on Automatic Control, 19, 716723.
Akaike, H. (1983). Information measures and model selection. Bulletin of the
International Statistical Institute, 50, 277290.
Attias, H. (2000). A variational Bayesian framework for graphical models. Advances in
Neural Information Processing Systems, 12, 209215.
Berger, J. O., & Pericchi, L. R. (1996). The intrinsic Bayes factor for model selection and
prediction. Journal of the American Statistical Association, 91, 109.
Burnham, K. P. (2004). Multimodel inference: Understanding AIC and BIC in model
selection. Sociological Methods & Research, 33, 261304.
Carlin, B. P., & Chib, S. (1995). Bayesian model choice via Markov chain Monte Carlo
methods. Journal of the Royal Statistical Society: Series B: Methodological, 57,
473484.
Chipman, H. A., George, E. I., Mcculloch, R. E., Clyde, M., Foster, D. P., & Stine, R. A.
(2001). The practical implementation of Bayesian model selection. IMS Lecture
Notes-Monograph Series, 38, 65134.
Clyde, M., & George, E. I. (2004). Model uncertainty. Statistical Science, 19, 8194.
Daunizeau, J., & Friston, K. J. (2007). A mesostate-space model for EEG and MEG.
Friston, K., Harrison, L., Daunizeau, J., Kiebel, S., Phillips, C., Trujillo-Barreto, N. J.,
et al. (2008). Multiple sparse priors for the M/EEG inverse problem. NeuroImage,
39, 11041120.
George, E. I., & McCulloch, R. E. (1993). Variable selection via Gibbs sampling. Journal
of the American Statistical Association, 88, 881889.
539
Godsill, S. J. (2011). On the relationship between Markov Chain Monte Carlo methods
for model uncertainty. Journal of Computational and Graphical Statistics, 10,
230248.
Good, I. J. (1958). Significance tests in parallel and in series. Journal of the American
Statistical Association, 53, 799813.
Green, P. J. (1995). Reversible jump Markov chain Monte Carlo computation and
Bayesian model determination. Biometrika, 82, 711732.
Henson, R. N., Mattout, J., Phillips, C., & Friston, K. J. (2009). Selecting forward
models for MEG source-reconstruction using model-evidence. NeuroImage, 46,
168176.
Hoeting, J. A., Madigan, D., Raftery, A. E., & Volinsky, C. T. (1999). Bayesian model
averaging: A tutorial. Statistical Science, 14, 382417.
Jeffreys, H. (1961). Theory of probability (3rd ed.). Oxford, UK: Oxford University Press.
Kass, R. E., & Raftery, A. E. (1995). Bayes factors. Journal of the American Statistical
Association, 90, 773795.
Madigan, D., & Raftery, A. E. (1994). Model selection and accounting for model
uncertainty in graphical models using Occams window. Journal of the American
Statistical Association, 89, 15351546.
Madigan, D., & York, J. (1995). Bayesian graphical models for discrete data.
International Statistical Review/Revue, 63, 215232.
Mattout, J., Phillips, C., Penny, W. D., Rugg, M. D., & Friston, K. J. (2006). MEG source
localization under multiple constraints: An extended Bayesian framework.
OHagan, A. (1995). Fractional Bayes factors for model comparisons. Journal of the
Royal Statistical Society, Series B, 57, 99138.
Olier, I., Trujillo-Barreto, N. J., & El-Deredy, W. (2013). A switching multi-scale
dynamical network model of EEG/MEG. NeuroImage, 83, 262287.
Penny, W., Kiebel, S., & Friston, K. (2003). Variational Bayesian inference for fMRI time
series. NeuroImage, 19, 727741.
Penny, W. D., Stephan, K. E., Daunizeau, J., Rosa, M. J., Friston, K. J., Schofield, T. M.,
et al. (2010). Comparing families of dynamic causal models. PLoS Computational
Biology, 6, e1000709.
causal models. NeuroImage, 22, 11571172.
Rosa, M. J., Kilner, J. M., & Penny, W. D. (2011). Bayesian comparison of
neurovascular coupling models using EEG-fMRI. PLoS Computational Biology,
7, e1002070.
Sato, M., Yoshioka, T., Kajihara, S., Toyama, K., Goda, N., Doya, K., et al. (2004).
Hierarchical Bayesian estimation for MEG inverse problem. NeuroImage, 23,
806826.
Schwarz, G. (1978). Estimating the dimension of a model. The Annals of Statistics, 6,
461464.
Sotero, R. C., Trujillo-Barreto, N. J., Jimenez, J. C., Carbonell, F., &
Rodrguez-Rojas, R. (2009). Identification and comparison of stochastic metabolic/
hemodynamic models (sMHM) for the generation of the BOLD signal. Journal of
Computational Neuroscience, 26, 251269.
Stephan, K. E., Penny, W. D., Daunizeau, J., Moran, R. J., & Friston, K. J. (2009).
Bayesian model selection for group studies. NeuroImage, 46, 10041017.
Sugiura, N. (1978). Further analysis of the data by Akaikes information criterion and the
finite corrections. Communications in Statistics, Theory and Methods, A7, 1326.
Tierney, L., & Kadane, J. B. (1986). Accurate approximations for posterior moments and
marginal densities. Journal of the American Statistical Association, 81, 8286.
Tierney, L., Kass, R. E., & Kadane, J. B. (1989). Fully exponential Laplace
approximations to expectations and variances of nonpositive functions. Journal of
the American Statistical Association, 84, 710716.
Trujillo-Barreto, N. J., Aubert-Vazquez, E., & Valdes-Sosa, P. A. (2004). Bayesian
model averaging in EEG/MEG imaging. NeuroImage, 21, 13001319.
Volinsky, C. T., Madigan, D., Raftery, A. E., & Kronmal, R. A. (1997). Bayesian model
averaging in proportional hazard models: Assessing the risk of a stroke. Journal of
the Royal Statistical Society, Series C, 46, 433448.
Models of fMRI Signal Changes

RB Buxton, University of California, San Diego, CA, USA
Glossary
Arterial spin labeling (ASL) An MRI method for measuring

CBF noninvasively.
Blood oxygenation level-dependent (BOLD) signal A
small change in the measured MR signal due to changes in
the local blood oxygenation, specifically the change in total
deoxyhemoglobin.
Cerebral blood flow (CBF) The rate of delivery of arterial
blood to an element of brain tissue, often expressed in units
of milliliters of arterial blood per 100 g of tissue per minute,
and a typical value for human gray matter is about 60 ml
(100 g)1 min1.
Abbreviation
ASL
BOLD
CBF
CBVV
Arterial spin labeling

Blood oxygenation level-dependent
Cerebral blood flow
Venous cerebral blood volume as a fraction of
total tissue volume
Modeling the BOLD Response

As neural activity in a part of the brain changes, the local blood
flow and oxygen metabolism also change, but with the flow
change much larger (Fox & Raichle, 1986), producing a change
in local blood oxygenation. This in turn translates to a small
change in the magnetic resonance (MR) signal near the site of
the neural activity change. This unexpected effect on the MR
signal called the blood oxygenation level-dependent (BOLD)
effect was discovered in 1992 (Kwong et al., 1992; Ogawa
et al., 1992) and is the basis of functional magnetic resonance
imaging (fMRI) for mapping patterns of activity in the human
brain in response to a stimulus or during ongoing spontaneous
activity. Figure 1 illustrates the experimentally measured
BOLD response to a short stimulus (2 s) and a long stimulus
(20 s). The figure also shows the cerebral blood flow (CBF)
response to the two stimuli measured with a different MRI
method called arterial spin labeling (ASL). The advantage of
ASL methods is that they are sensitive specifically to blood
flow and in combination with BOLD measurements provide
a way to untangle the more complicated BOLD response.
However, the disadvantage of ASL methods is that the measurement is intrinsically noisier than the BOLD response measurement, as can be seen in Figure 1. In this example, a brief
stimulus evokes a 30% blood flow change accompanied by
a BOLD signal change of less than 1%. The BOLD response
is delayed 12 s and takes 68 s to return to baseline. With
a longer duration stimulus, the BOLD response looks like a
Cerebral metabolic rate of oxygen (CMRO2) The rate

of oxygen metabolism within an element of brain tissue,
often expressed in units of micromoles of O2
metabolized per 100 g of tissue per minute, and a typical
value for human gray matter is about 160 mmol
(100 g)1 min1.
Deoxyhemoglobin Hemoglobin with unoccupied
oxygen binding sites. The paramagnetic effects of
deoxyhemoglobin lead to the MR signal being
sensitive to changes in the local deoxyhemoglobin
concentration.
CMRO2
EEG
fMRI
HRF
MEG
Cerebral metabolic rate of oxygen

Electroencephalography
Magnetoencephalography
delayed and smoothed version of the stimulus block, but with

an additional distinctive feature: a pronounced undershoot
during the poststimulus period.
There are several reasons for trying to model the BOLD
response. A basic goal is to understand the physiological origins of this effect and, if possible, use the BOLD signal, in
addition to the ASL signal, as a quantitative probe of the
underlying blood flow and oxygen metabolism changes. That
is, an appropriate model can provide a mathematical framework for interpreting these measured signals in terms of those
physiological changes. In most applications of fMRI, though,
the goal is not to investigate blood flow and oxygen metabolism, but rather to infer something useful about the underlying
neural activity that drives these physiological changes. To that
end, a model of the BOLD response provides a bridge from the
neural activity to the measured signals. The most basic question asked in an fMRI experiment is whether a particular image
volume element (voxel) is activated during a particular task,
based on a correlation of the measured signal with an expected
response to the stimulus. The sensitivity of this test is optimized
by building into the analysis the knowledge that the expected
BOLD response will not look like the stimulus itself, but rather a
delayed and smoothed version of that stimulus. In more sophisticated applications such as dynamic causal modeling (DCM),
computational neuroscience models of the interactions of
brain regions are combined with a forward model that translates the dynamic neural activity into the signals that can be
measured, which could include electroencephalography (EEG)
http://dx.doi.org/10.1016/B978-0-12-397025-1.00329-8
541
542
INTRODUCTION TO METHODS AND MODELING | Models of fMRI Signal Changes
BOLD response
Stimulus
Change (%)
(a)
40
30
20
10
0
10
20
Change (%)
0.8
0.6
0.4
0.2
0.0
0.2
0.4
10
Time (s)
15
20
CBF response
Stimulus
(c)
10
Time (s)
2.0
1.5
1.0
0.5
0.0
0.5
1.0
BOLD response
Stimulus
20
(b)
Change (%)
Change (%)
BOLD and CBF responses
15
20
(d)
80
60
40
20
0
20
40
40
Time (s)
60
80
CBF response
Stimulus
20
40
Time (s)
60
80
Figure 1 Stimulus responses. The figures show experimental measurements of the BOLD response in the primary motor cortex to a 2 s finger-tapping
stimulus (a) and in the primary visual cortex to a 20 s flickering checkerboard stimulus (b). The corresponding CBF responses measured with ASL
are shown in (c) and (d). Note the pronounced BOLD poststimulus undershoot for the longer stimulus. Motor cortex data are from Miller, K. L.,
Luh, W. M., Liu, T. T., Martinez, A., Obata, T., Wong E. C., et al. (2001). Nonlinear temporal dynamics of the cerebral blood flow response. Human Brain
Mapping, 13(1), 112 and visual cortex data are from Perthen, J. E., Lansing, A. E., Liau, J., Liu, T. T., & Buxton, R. B. (2008). Caffeine-induced
uncoupling of cerebral blood flow and oxygen metabolism: A calibrated BOLD fMRI study. Neuroimage, 40(1), 23747.
or magnetoencephalography (MEG) signals as well as fMRI

signals in multimodal applications (Friston & Dolan, 2010).
The goal of these studies is to estimate (or deconvolve) the
neural activity that drives the measured signals to test models
of neuronal interactions.
Origins of the BOLD Effect

The BOLD effect occurs because of two phenomena, one physiological and one biophysical (Buxton, 2013). The physiological phenomenon is that neural activation leads to a blood flow
response 23 times larger than the oxygen (O2) metabolism
response. The biological benefit of this imbalance is not well
understood, although it may reflect a mechanism to preserve
the oxygenation of the tissue (Buxton, 2010). The somewhat
counterintuitive effect of the large blood flow change is that the
capillary and venous blood are more oxygenated during activation because the delivery of O2 has increased more than the
consumption of O2, leading to a change in the O2 saturation of
hemoglobin. Most of the oxygen in the blood is bound to
hemoglobin, and typically, in arterial blood, the hemoglobin
is nearly saturated with O2 molecules (98%). As the blood
reaches the smallest vessels, O2 diffuses into the tissue leaving
behind hemoglobin with empty O2 binding sites, referred to as
deoxyhemoglobin. Because neural activation leads to a larger
blood flow change than oxygen metabolism change, the local
deoxyhemoglobin concentration decreases with increased neural activity. Put another way, the fundamental physiological
phenomenon is that the fraction of delivered O2 that is
extracted and metabolized, called the oxygen extraction fraction (E), decreases when neural activity increases.
The change of deoxyhemoglobin concentration ties in with
the second phenomenon underlying the BOLD signal, based
on a biophysical effect: Deoxyhemoglobin is paramagnetic,

and its presence leads to a slight reduction of the MR signal
imaged with MRI. The MR signal arises from the precession of
hydrogen nuclei in a magnetic field due to the interaction of
the hydrogen magnetic moment with the main magnetic field
of the MR system. Thinking of the hydrogen magnetic moment
as a vector, precession is a steady rotation of that vector at a
frequency proportional to the local magnetic field, and the net
MR signal is proportional to the sum of these precessing vectors. The presence of paramagnetic deoxyhemoglobin makes
the local magnetic field somewhat inhomogeneous, so that
hydrogen nuclei in different locations near the blood vessels
precess at different rates. The precessing vectors then get out of
phase with each other, reducing the net signal to a degree that
is proportional to the deoxyhemoglobin concentration.
In a typical resting human brain, about 40% of the oxygen
delivered by blood flow is extracted and metabolized. The
associated deoxyhemoglobin in the veins leads to the MR signal
being reduced at baseline by roughly 10% compared with what
the signal would be if there was no deoxyhemoglobin. The
basic chain of events underlying the dynamic BOLD response
(Figure 2) is then the following: (1) Increased neural activity
triggers a CBF change that is larger than the oxygen metabolism
(cerebral metabolic rate of oxygen (CMRO2)) change; (2) the
deoxyhemoglobin content of the veins (and to a lesser extent
the capillaries) decreases because the blood is more oxygenated; and (3) the decrease of deoxyhemoglobin causes a slight
increase of the local MRI signal as the signal reduction effect of
deoxyhemoglobin is partially lifted. In physiological terms, the
BOLD response is a complex phenomenon, because the change
in deoxyhemoglobin concentration depends on the balance of
the changes in CBF, CMRO2, and also venous blood volume
(CBVV). With neural activation, each of these physiological
variables increases, but with conflicting effects on the BOLD
543
The BOLD response

Stimulus
CBF
E
Neural response
CMRO2
CBV
BOLD
Figure 2 Schematic illustration of the pathway from a stimulus to the BOLD response. A stimulus triggers a neural response, which then drives
changes in blood flow (CBF), oxygen metabolism (CMRO2), and venous blood volume (CBV). The imbalance of changes in flow and metabolism leads to
a change in the oxygen extraction fraction (E), and the combined changes in E and CBV determine the net change in deoxyhemoglobin, resulting in
the measured BOLD response. Curves show possible responses for each physiological variable, including adaptation of the neural response and a slow
recovery of venous CBV leading to a poststimulus undershoot (as in the balloon model). Note that an undershoot of CBF or a slow recovery of
CMRO2 (not shown) also could create a BOLD poststimulus undershoot, and these may be the more dominant effects.
response. The deoxyhemoglobin concentration is decreased by

increased blood flow, but increased by increased oxygen
metabolism and venous blood volume. The complexity of the
BOLD response has led to a long-lasting fundamental ambiguity for interpreting the BOLD response in physiological terms:
increases in CMRO2 and venous blood volume cannot be
distinguished, because both effects serve to increase local
deoxyhemoglobin.
The Linear Hemodynamic Response Function

In the most basic application of BOLD signal models, the
physiological origins are not as important as simply having a
mathematical function that captures the appearance of the
BOLD response to improve detection of a BOLD response to
a stimulus. The general linear model (GLM) provides a framework for detecting a known response pattern in noisy data, and
the goal is to use a delayed and smoothed version of the
stimulus as the expected response as in Figure 1. In most
fMRI studies, the expected response is treated as a linear convolution of the stimulus pattern with a hemodynamic response
function (HRF). The key idea here is the assumption of linearity: that the net response of very brief stimuli presented back
to back is simply the sum of the individual responses to each
of the brief stimuli. Then, the only information needed to
construct an expected response is a definition of the HRF, the
response to a very brief stimulus (known as the impulse
response function in other fields). Mathematically, the
expected BOLD response is then the convolution of the HRF
with the stimulus pattern.
The HRF is often modeled as a gamma-variate function, a
mathematical function of time (t) of the form (t exp[t/t])n, a
function that initially increases and then smoothly returns to
baseline at a rate that depends on the time constant t. A poststimulus undershoot can be included by adding a second
broader gamma-variate function with a negative amplitude. A
standard HRF of this form is illustrated in Figure 3, along with
simulations of the BOLD response for a block stimulus and an
event-related design. The modeled BOLD responses look plausible compared with experimental data, but there is a second
feature of the response that needs to be modeled: the delay from
the beginning of the stimulus to the initial rise of the BOLD
response. The presence of an unknown delay complicates the
analysis with the GLM, because a delay is not easily modeled as
a linear effect. One approach is to add additional functions that
approximate a time shift of the basic HRF. Alternatively, a delay
is simply assumed, or the data are analyzed individually with
different HRFs corresponding to different delays.
The HRF approach is widely used, but these models of the
BOLD response are essentially just mathematical approximations of experimental data and do not attempt to model the
underlying physiological changes nor the physics of how those
changes translate to a change in the magnitude of the BOLD
signal. In addition, the use of a simple linear model for the
BOLD response fails to describe several interesting nonlinear
effects that have been observed.
Nonlinearities of the BOLD Response

Although the BOLD response is often approximated as a linear
response to the stimulus, experimental studies have found
nonlinear effects: (1) The response to a brief stimulus, when
used as a linear HRF to predict the response to a longer sustained stimulus, tends to overestimate the response to the
longer stimulus; and (2) when two brief stimuli are presented
close together in time, the net response is weaker than twice the
544
The hemodynamic response function (HRF)

Block stimulus
1
0
HRF
0.2
20
(b)
40
Time (s)
60
80
Event-related stimulus
1
0
0
(a)
10
15
20
25
30
Time (s)
0
20
(c)
40
Time (s)
60
80
Figure 3 Typical assumed form of the HRF. In many fMRI analyses, the BOLD response is modeled as a convolution of the HRF (a) with the stimulus
pattern, illustrated here with the resulting BOLD responses for a simple block design (b) and for an event-related design (c). The stimulus pattern
is shown as the lower gray line in (b) and (c). Mathematically, this HRF is a sum of two gamma-variate functions with different signs and widths to model
a primary positive response followed by a weaker negative response, producing a poststimulus undershoot of the BOLD signal. An HRF such as
this is not a physiological model, but simply a convenient mathematical shape that approximates the data.
response to a single stimulus. (Figure 4 illustrates these effects

with simulations based on ideas developed in the following
sections.) It is important to remember that studies such as
these are testing whether the BOLD response can be described
as a linear function of the stimulus and that nonlinearities
could enter at any stage of the events diagrammed in Figure 2,
including the neural activity response to the stimulus. For
example, adaptation could lead the neural response to be
reduced for a sustained stimulus compared with a brief stimulus, and this would translate to nonlinearity in the BOLD
response even if the translation from neural activity to a CBF
response and on to a BOLD response is entirely linear. Given
the potential for such nonlinear neural effects, experimental
data are at least consistent with the idea that the transformation from neural activity to CBF is reasonably linear but there is
a nonlinear step to the BOLD response.
BOLD response nonlinearities
(a)
Time (s)
Linear
prediction
Actual
Physical Models of the BOLD Response

Ultimately, the goal is to have an accurate model of the BOLD
response grounded in the underlying physiology and physics.
Such a model would describe how different aspects of neural
activity drive blood flow and oxygen metabolism measurements and how these changes combine in a nonlinear way to
produce the BOLD response. A complete model then requires
two components: a mechanistic physiological model that captures the interrelationships of the physiological variables (e.g.,
how neural activity drives CBF and CMRO2) and a physical
model that relates the BOLD response to those physiological
variables. At this point, the physical model of the BOLD effect
is better understood (see Buxton, 2013, for a recent review),
(b)
Time (s)
Figure 4 Nonlinearities of the BOLD response. In these simulations,

CBF is assumed to be a linear convolution with a damped oscillator HRF,
and the step from the physiological response to the BOLD response is
modeled by the nonlinear dependence in eqn [1]: the BOLD ceiling effect.
The resulting nonlinearities are as follows: (a) For two brief closely
spaced stimuli, the net response is weaker than the sum of the two
individual responses; and (b) the response to a sustained stimulus is
weaker than what would be predicted from a brief stimulus. In each plot,
the response of the first isolated brief stimulus is used to make a
linear prediction of the following more extended stimulus (shown in red),
and the actual net BOLD response is shown in blue.

providing a description of the BOLD signal magnitude in terms
of the underlying changes in CBF, CMRO2, and CBVV. How
these physiological variables are driven by neural activity is still
an active area of research.
The physical models, relating the BOLD signal to given
physiological variables, began with early and influential
models of the extravascular BOLD effect (i.e., the BOLD signal
change of the extravascular signal) based on Monte Carlo
numerical simulations and analytic models of the evolution
of the MR signal in inhomogeneous magnetic fields created by
idealized vascular beds (random infinitely long cylinders)
(Davis, Kwong, Weisskoff, & Rosen, 1998; Ogawa et al.,
1993; Yablonskiy & Haacke, 1994). Later models built on
these models included additional factors that affect the BOLD
signal, such as intravascular signal changes and volume
exchange effects as blood volume expands and displaces extravascular tissue generating a different intrinsic MR signal
(Buxton, Uludag, Dubowitz, & Liu, 2004; Griffeth & Buxton,
2011; Obata et al., 2004). One of the complexities of the
physical modeling is that diffusion of water molecules around
the smallest blood vessels tends to weaken the effect of deoxyhemoglobin in these vessels on the resulting BOLD response.
The result is that the BOLD response is more strongly affected
by venous deoxyhemoglobin, particularly in larger veins, than
by deoxyhemoglobin in the smallest vessels.
Despite this physical complexity of the BOLD response, a
relatively simple heuristic model captures the basic effects in a
simple way and is also reasonably accurate when compared
with more sophisticated models (Griffeth, Blockley, Simon, &
Buxton, 2013):
dB A1 l aV 1 1=f
[1]
All variables describe the change from a baseline state, but

defined in different ways. The BOLD signal change, dB, is the
fractional change in the MR signal from baseline (usually
expressed as a percent signal change), while the CBF change,
f, is the new value of CBF divided by the baseline value (e.g., for
a 40% increase of CBF from baseline, f 1.4). The three additional parameters describe the three additional effects that
modulate the BOLD signal: (1) the local concentration of
deoxyhemoglobin in the baseline state, which is the primary
determinant of the scaling factor A; (2) the change in CMRO2,
which is described by l, the fractional change in CMRO2
divided by the fractional change in CBF (e.g., if CMRO2
changes by 20% from baseline, while CBF changes by 40%,
l 0.5); and (3) the change in CBVV, here described by the
parameter aV, which is approximately the fractional change in
CBVV divided by the fractional change in CBF (e.g., if CBVV
changes by 8%, while CBF changes by 40%, aV 0.2).
The heuristic model captures the basic effects contributing
to the BOLD response and, in particular, captures the essential
nonlinearity of the BOLD response: there is a ceiling on how
large the BOLD signal can be. If we temporarily ignore any
effects of changes in CMRO2 or CBVV (aV l 0), the maximum possible BOLD signal change is A, corresponding to very
large CBF changes (f 1) that wash out all of the deoxyhemoglobin. Looked at in reverse, the presence of deoxyhemoglobin
in the baseline state creates a finite reduction of the MR signal,
and the most that could ever happen is an elimination of that
545
reduction, creating the ceiling on the BOLD signal. The addition of changes in CMRO2 and CBVV further modifies the
amplitude of the BOLD response, with these changes generally
opposing the CBF change. In short, we can think of the BOLD
response as primarily driven by the CBF change, but strongly
modulated by the baseline state (A) (essentially the local concentration of deoxyhemoglobin), the change in CMRO2 (l),
and the change in CBVV (aV).
Equation [1] exhibits a basic nonlinearity due to the BOLD
ceiling effect: if the CBF response is doubled, the BOLD
response is increased by less than a factor of 2. That is, the
fundamental nonlinearity in the way the BOLD response
depends on f in eqn [1] leads to nonlinearities similar to
what have been observed, as illustrated in Figure 4. However,
it is important to note that such nonlinear effects could arise
from other factors in Figure 2 as well. For example, if venous
blood volume increases slowly, then a growing CBVV could
also lead to a reduction of the amplitude of a sustained stimulus compared with a brief stimulus.
Finally, a cautionary note is needed about BOLD signal
models such as eqn [1] or other proposed models currently
in use: They are steady-state models, and their application to
rapid dynamics could produce errors. That is, an abrupt change
in oxygen metabolism will require a few seconds to fully translate into deoxyhemoglobin changes, depending on the time
constants for O2 transport and blood clearance. More detailed
models treating these effects are needed for a full dynamic
BOLD model. Nevertheless, the steady-state assumption is
likely to be reasonably accurate for most applications.
Physiological Models of the BOLD Response

The physiological component of a BOLD signal model, relating the dynamics of the physiological variables to each other
and to neural activity, is still not well understood. As illustrated
in Figure 2, neural activity leads to changes in CBF, CMRO2,
and CBVV, but a quantitative understanding of the mechanisms underlying these effects is still lacking. The simplest
picture of these effects would be that one of these physiological
variables is driven by the neural activity, and the other two
follow the first in a well-defined way, and most current models
have adopted this assumption (e.g., in eqn [1], the CMRO2 and
CBVV changes are referenced to the CBF change by the parameters l and aV).
The balloon model (Buxton, Wong, & Frank, 1998) was
originally proposed as a dynamic model for the BOLD
response that treated the dynamic CBF as the driver of the
system, with CMRO2 and CBVV driven by the CBF dynamics.
This model was motivated by an attempt to understand the
BOLD poststimulus undershoot (illustrated in Figure 1) and
contained two components: an updated physical model for the
BOLD signal amplitude that included intravascular signal
changes and a set of differential equations for the evolution
of CBVV and local deoxyhemoglobin. Specifically, the model
described a slow return of CBVV to baseline as the origin of the
poststimulus undershoot (see also Mandeville et al., 1999, for
a similar model of this effect).
In a later application (Friston, Mechelli, Turner, & Price,
2000), the basic components of the balloon model were
546
combined with an additional neural driver of the CBF. In this

model, neural activity drives a signal that in turn drives CBF.
The mathematical structure is equivalent to CBF being treated
as a linear convolution of the neural activity with an HRF, but
with a different and more mechanistic form than earlier mathematical HRFs: the response is modeled as a damped harmonic
oscillator. The mathematical form of the response is exp[t/t]
sin[ot], a signal rise and fall followed by decaying oscillations
with angular frequency o and decay time t. More recently,
additional support for CBF responding like a damped oscillator has been reported (Ress, Thompson, Rokers, Khan, & Huk,
2009). Variations of this model have been used in a number of
DCM applications, where modeling the dynamics and nonlinearities of the BOLD response is critical for separating other
physiological effects from neural effects (Stephan, Weiskopf,
Drysdale, Robinson, & Friston, 2007).
Although the CBF damped oscillator model adopts aspects
of the balloon model, particularly the transformation of physiological changes to a BOLD signal, there is an important
difference related to the physiological origin of the poststimulus undershoot. In the original balloon model, the goal
was to test whether a slow recovery of CBVV could account for
the poststimulus undershoot. In the damped oscillator model,
the origin of the undershoot is an undershoot of CBF itself.
One limitation of the mathematical form of the damped oscillator model is that the HRF cannot have an undershoot much
longer than the primary positive part of the response, because
essentially the positive and negative components of the
response are one cycle of the oscillation, and in contrast,
observed undershoots can be quite long. Nevertheless, the
BOLD poststimulus undershoot may in fact have a strong
component from a CBF undershoot (Buxton, 2012).
Limitations and Challenges

The basic challenge for fMRI studies is that the BOLD HRF,
while reproducible within subjects, varies across a subject population (Aguirre, Zarahn, & DEsposito, 1998; Handwerker,
Gonzalez-Castillo, DEsposito, & Bandettini, 2012; Handwerker,
Ollinger, & DEsposito, 2004). Within individuals, the BOLD
response also can vary due to changes in the baseline state
(Behzadi & Liu, 2006; Cohen, Ugurbil, & Kim, 2002). Estimating individual BOLD responses and using these individual HRFs
to remove the blurring (deconvolving the underlying driving
signal) can improve the sensitivity of fMRI studies (Glover,
1999). One area where the careful consideration of the BOLD
HRF has proven useful is in multimodal studies using EEG or
MEG signals as the measured drivers of the BOLD response
(David et al., 2008; Storti et al., 2013).
A limitation of the current physiological BOLD signal
models is the assumption that CMRO2 and CBVV changes are
tightly tied to the CBF change, so that the latter can be taken as
the physiological driver of the system. Current thinking is that
CBF and CMRO2 are driven in parallel by neural activity and
possibly by different aspects of neural activity: CMRO2 may
simply follow the energy costs of the evoked neural activity,
but there is substantial evidence that CBF is driven in a feedforward manner by the neural activity itself (Attwell &
Iadecola, 2002), particularly excitatory neural activity, rather

than in a feedback manner driven by the CMRO2.
Recently, a more sophisticated model (Sotero & TrujilloBarreto, 2007) was proposed in which neural activity is considered as both excitatory activity and inhibitory activity, each
driving both CBF and CMRO2 but in different ways. This is an
important step toward a more realistic model of the complexities of the BOLD response, although the specific assumptions
are based on ideas about the physiology that are still speculative. As new experimental results present a clearer picture of the
oxygen metabolism demands of excitatory and inhibitory
activity and how each contributes to CBF changes, this model
can be improved.
Empirically, recent studies suggest that the coupling ratio l
of CMRO2 changes to CBF changes is altered in several situations: with increasing stimulus amplitude (Liang et al., 2013),
with modulatory effects of attention (Moradi, Buracas, &
Buxton, 2012) and adaptation (Moradi & Buxton, 2013), and
in response to a drug (caffeine) (Griffeth, Perthen, & Buxton,
2011). The basic pattern suggested by these initial studies is
that when the stimulus is modulated to create a larger evoked
response, CBF is modulated more than CMRO2. However,
when the brain state is modulated to change the evoked
response to the same stimulus (e.g., by attention or adaptation), the pattern is opposite: CMRO2 is modulated more than
CBF. Thinking of CMRO2 as perhaps the closet reflection of the
magnitude of neural activity, this pattern suggests that the
BOLD response exaggerates the underlying physiological
changes when the stimulus amplitude is changed, but underestimates these changes when the brain state is manipulated to
create a different evoked response to the same stimulus. The
implications of these observations for modeling the BOLD
response remain to be worked out.
Remarkably, after more than 20 years of fMRI studies, there
is still no consensus on whether the BOLD poststimulus undershoot is a neural, vascular, or metabolic effect (see Buxton,
2012; van Zijl, Hua, & Lu, 2012, for recent reviews), because
each could provide a mechanism for reducing total deoxyhemoglobin in the undershoot period. While the duration of the
undershoot seems too long to be a neural effect, a recent study
suggests there could be a connection (Mullinger, Mayhew,
Bagshaw, Bowtell, & Francis, 2013). Most explanations assume
that the undershoot is due to a transient of the other physiological parameters, either an undershoot of CBF or a slow
return of CMRO2 or CBVV to baseline. For many applications
of fMRI, the exact source of the undershoot may not matter if
the BOLD response, the primary measured variable, is accurately modeled. Nevertheless, there is the potential suggested
in the preceding text that different aspects of neural activity
drive CBF and CMRO2 in different ways. If true, future combined studies using both BOLD and ASL acquisitions that
make it possible to separate CBF and CMRO2 effects could
potentially provide a more nuanced picture of the underlying
neural activity.
In short, modeling the BOLD response is a work in progress, because the physiological mechanisms are still not well
understood. The challenge for developing accurate models of
the BOLD response is to understand in a quantitative way the
path illustrated in Figure 2. As current experimental research
makes clearer the mechanistic connections between neural

activity, blood flow, and oxygen metabolism, new models will
better capture the transformation from underlying neural activity to measureable signals.

Functional MRI Dynamics; INTRODUCTION TO METHODS AND
MODELING: Convolution Models for FMRI; Dynamic Causal Models
for fMRI.
References
Aguirre, G. K., Zarahn, E., & DEsposito, M. (1998). The variability of human, BOLD
hemodynamic responses. NeuroImage, 8, 360376.
Attwell, D., & Iadecola, C. (2002). The neural basis of functional brain imaging signals.
Trends in Neurosciences, 25(12), 621625.
Behzadi, Y., & Liu, T. T. (2006). Caffeine reduces the initial dip in the visual BOLD
response at 3 T. NeuroImage, 32(1), 915.
Buxton, R. B. (2010). Interpreting oxygenation-based neuroimaging signals: The
importance and the challenge of understanding brain oxygen metabolism. Frontiers
in Neuroenergetics, 2, 8.
Buxton, R. B. (2012). Dynamic models of BOLD contrast. NeuroImage, 62(2), 953961.
Buxton, R. B. (2013). The physics of functional magnetic resonance imaging (fMRI).
Reports on Progress in Physics, 76, 096601.
Buxton, R. B., Uludag, K., Dubowitz, D. J., & Liu, T. T. (2004). Modeling the
hemodynamic response to brain activation. NeuroImage, 23(Suppl. 1), S220S233.
Cohen, E. R., Ugurbil, K., & Kim, S. G. (2002). Effect of basal conditions on the
David, O., Guillemain, I., Saillet, S., Reyt, S., Deransart, C., Segebarth, C., et al. (2008).
Identifying neural drivers with functional MRI: An electrophysiological validation.
PLoS Biology, 6(12), 26832697.
Fox, P. T., & Raichle, M. E. (1986). Focal physiological uncoupling of cerebral blood
flow and oxidative metabolism during somatosensory stimulation in human
subjects. Proceedings of the National Academy of Sciences of the United States of
America, 83, 11401144.
Friston, K. J., & Dolan, R. J. (2010). Computational and dynamic models in
Friston, K. J., Mechelli, A., Turner, R., & Price, C. J. (2000). Nonlinear responses in
fMRI: The balloon model, Volterra kernels, and other hemodynamics. NeuroImage,
12(4), 466477.
Glover, G. H. (1999). Deconvolution of impulse response in event-related fMRI.
Griffeth, V. E., Blockley, N. P., Simon, A. B., & Buxton, R. B. (2013). A new functional
MRI approach for investigating modulations of brain oxygen metabolism. PLoS
One, 8(6), e68122.
Griffeth, V. E., & Buxton, R. B. (2011). A theoretical framework for estimating cerebral
oxygen metabolism changes using the calibrated-BOLD method: Modeling the
effects of blood volume distribution, hematocrit, oxygen extraction fraction, and
tissue signal properties on the BOLD signal. NeuroImage, 58(1), 198212.
Griffeth, V. E., Perthen, J. E., & Buxton, R. B. (2011). Prospects for quantitative fMRI:
Investigating the effects of caffeine on baseline oxygen metabolism and the response
to a visual stimulus in humans. NeuroImage, 57(3), 809816.
547
Handwerker, D. A., Gonzalez-Castillo, J., DEsposito, M., & Bandettini, P. A. (2012). The
continuing challenge of understanding and modeling hemodynamic variation in
fMRI. NeuroImage, 62(2), 10171023.
Handwerker, D. A., Ollinger, J. M., & DEsposito, M. (2004). Variation of BOLD
hemodynamic responses across subjects and brain regions and their effects on
statistical analyses. NeuroImage, 21(4), 16391651.
Liang, C. L., Ances, B. M., Perthen, J. E., Moradi, F., Liau, J., Buracas, G. T., et al.
(2013). Luminance contrast of a visual stimulus modulates the BOLD response
more than the cerebral blood flow response in the human brain. NeuroImage, 64,
104111.
Mandeville, J. B., Marota, J. J.A, Ayata, C., Zaharchuk, G., Moskowitz, M. A.,
Rosen, B. R., et al. (1999). Evidence of a cerebrovascular post-arteriole Windkessel
679689.
Miller, K. L., Luh, W. M., Liu, T. T., Martinez, A., Obata, T., Wong, E. C., et al. (2001).
Nonlinear temporal dynamics of the cerebral blood flow response. Human Brain
Mapping, 13(1), 112.
Moradi, F., Buracas, G. T., & Buxton, R. B. (2012). Attention strongly increases oxygen
metabolic response to stimulus in primary visual cortex. NeuroImage, 59(1),
601607.
Moradi, F., & Buxton, R. B. (2013). Adaptation of cerebral oxygen metabolism and
blood flow and modulation of neurovascular coupling with prolonged stimulation in
human visual cortex. NeuroImage, 82, 182189.
Mullinger, K. J., Mayhew, S. D., Bagshaw, A. P., Bowtell, R., & Francis, S. T. (2013).
Poststimulus undershoots in cerebral blood flow and BOLD fMRI responses are
modulated by poststimulus neuronal activity. Proceedings of the National Academy
of Sciences of the United States of America, 110(33), 1363613641.
Obata, T., Liu, T. T., Miller, K. L., Luh, W. M., Wong, E. C., Frank, L. R., et al. (2004).
Discrepancies between BOLD and flow dynamics in primary and supplementary
motor areas: Application of the balloon model to the interpretation of BOLD
transients. NeuroImage, 21(1), 144153.
Ogawa, S., Menon, R. S., Tank, D. W., Kim, S.-G., Merkle, H., Ellerman, J. M., et al.
(1993). Functional brain mapping by blood oxygenation level Dependent contrast
magnetic resonance imaging: A comparison of signal characteristics with a
biophysical model. Biophysical Journal, 64(3), 803812.
Perthen, J. E., Lansing, A. E., Liau, J., Liu, T. T., & Buxton, R. B. (2008). Caffeineinduced uncoupling of cerebral blood flow and oxygen metabolism: A calibrated
BOLD fMRI study. NeuroImage, 40(1), 237247.
Ress, D., Thompson, J. K., Rokers, B., Khan, R. K., & Huk, A. C. (2009). A model for
transient oxygen delivery in cerebral cortex. Frontiers in Neuroenergetics, 1, 3.
Sotero, R. C., & Trujillo-Barreto, N. J. (2007). Modelling the role of excitatory and
inhibitory neuronal activity in the generation of the BOLD signal. NeuroImage,
35(1), 149165.
Comparing hemodynamic models with DCM. NeuroImage, 38(3), 387401.
Storti, S. F., Formaggio, E., Bertoldo, A., Manganotti, P., Fiaschi, A., & Toffolo, G. M.
(2013). Modelling hemodynamic response function in epilepsy. Clinical
Neurophysiology, 124(11), 21082118.
van Zijl, P. C., Hua, J., & Lu, H. (2012). The BOLD post-stimulus undershoot, one of the
most debated issues in fMRI. NeuroImage, 62(2), 10921102.
Yablonskiy, D. A., & Haacke, E. M. (1994). Theory of NMR signal behavior in
magnetically inhomogeneous tissues: The static dephasing regime. Magnetic
Forward Models for EEG/MEG

F Lecaignard, Lyon Neuroscience Research Center (CRNL), Lyon, France; University Lyon 1, Lyon, France; Cermep Imagerie du
vivant, Lyon, France
J Mattout, Lyon Neuroscience Research Center (CRNL), Lyon, France; University Lyon 1, Lyon, France
This article is composed of three sections. The first section

describes our current knowledge of what most contributes to
EEG/MEG signals and how laws of physics enable us to quantify this contribution. The second section covers the main steps
and assumptions that yield the computation of EEG/MEG
forward models. It also stresses the main factors of uncertainty
in this computation. Finally, the third section emphasizes
the difference between forward model (computational) complexity and the generative model (probabilistic) complexity.
This notion becomes particularly important when one wants to
evaluate different forward models of EEG/MEG data.
The Origin of EEG and MEG Signals

From Microscopic (Single-Neuron) Activity to Macroscopic
(Population-Level) Currents
Neurons have the property to be electrically excitable and to
produce and propagate nerve impulses. Neuronal activity is
expressed as transmembrane electric currents, which contribute to the macroscopic electric potential differences and magnetic fields measurable on the scalp and its vicinity.
Pyramidal and stellate cells are the two main types of neurons. They mostly differ in shape and orientation relative to the
cortical surface. Whatever their functional specialization, their
typical structure consists of a cell body (soma) surrounded by
dendritic branches and extending in a nerve fiber, the axon,
which projects onto other neurons through synaptic junctions
(Figure 1(a)).
The neurons membrane contains pores that are selectively
permeable to ions.
In the absence of excitation, continuous ionic exchanges
across the pores maintain the membrane potential Vm at a
resting value Vm Vr Vintra Vextra 70 mV, with Vintra
and Vextra referring to intracellular and extracellular potentials, respectively.
Typical dendrites receive inputs from presynaptic neurons
by way of a chemical exchange called neurotransmission
(Figure 1(b)). Fixation of released neurotransmitters on postsynaptic receptors triggers the opening of specific pores, allowing for ionic movements across the membrane. These currents
cause the postsynaptic (membrane) potentials (PSP). Synaptic
integration of PSP over time and space results in an action
potential (AP) propagating along the axon toward the apical
dendrites Figure 1(c), upon condition that a depolarization
threshold has been reached (Vm > Vt 50 mV). Excitatory
synapses tend to evoke a local membrane depolarization
(Vm > Vt), whereas inhibitory synapses cause local membrane
hyperpolarization (Vm < Vt).
From the extracellular medium, a site along the membrane
where ions move into the cell corresponds to a sink current
(current disappearance), whereas a site where ions go out

of the cell defines a source current (current appearance). At the
microscale (neuronal level) and more generally at the mesoscale (cell assembly level), transmembrane and intracellular
currents are referred to as primary currents, Jp. These are often
described as currents related to postsynaptic activity. They
produce an electric field in the medium, which in turn gives
rise to conduction currents Je sE, also referred to as volume or
secondary currents. In every point within the head, the electric
current can be described as J Jp sE.
Source and sink current distributions on the membrane can
be modeled by multipolar (Taylor) developments (Mosher,
Leahy, Shattuck, & Baillet, 1999). Simple dipole models capture
well the contribution of PSPs (Koles, 1998), whereas APs are well
described by quadrupole models whose contribution decreases
rapidly with distance and can be neglected in the context of EEG
and MEG (Crouzeix, 2001; Figure 2). Furthermore, approximately 50 000 neurons with simultaneous activity and similar
orientation are required to be picked up by MEG and EEG
sensors (Pernier, 2007). Consequently, it is usually assumed
that only the primary currents produced by a synchronous population of neurons with a preferred orientation, as with pyramidal cells, contribute to the electric potentials and magnetic fields
measurable on scalp (Crouzeix, 2001; Nunez, 1981).
From Macroscopic Currents to Observed Electric and Magnetic

Activities
!
Predicting the electric (E ) and magnetic (B ) fields produced by

neuronal activity on EEG and MEG sensors requires solving
Maxwells equations in head tissues. In their general form,
Maxwells equations can be written as
!
! r
!
!
@B
, r B 0,
r E , r E
@t
e
!!
!
!
@E
r B m J e
@t
[1]
where J and r indicate the volume density of current and

volume density of charge, respectively, and e and m are the
electric permittivity and magnetic permeability of the medium,
respectively.
The head is composed of several tissues with various conductivities and therefore can be described as a finite inhomogeneous conducting volume. It is commonly accepted that e
and m are equal to free space value (e0 and m0, respectively)
(Malmivuo & Plonsey, 1995).
Given that the frequency spectra of EEG and MEG signals are
much below 1 kHz, capacitive effects can be neglected (Schwan
& Kay, 1957). The duration of the electromagnetic wave propagation (from neuronal sources to sensors) is negligible
http://dx.doi.org/10.1016/B978-0-12-397025-1.00330-4
549
550
INTRODUCTION TO METHODS AND MODELING | Forward Models for EEG/MEG
Presynaptic
neuron
Neurotransmitters
Presynaptic
membrane
Postsynaptic
neuron
Postsynaptic
membrane
Extracellular
medium
Soma
+ + +
+ + +
Intracellular
medium
ion channel
+
+
ions
(b)
Axon
Nucleus
Extracellular medium
++ ++
++ +
K+
(a)
Basal dendrites
Na+
Apical dendrites
Na+/K+ pump
+ +
+ + + +

+ + +
Extracellular medium
(c)
Figure 1 Schematic view of a neuron. (a) Basic parts of the neuron structure (orange), in connection to other neurons (blue). (b) Neurotransmission at
a chemical synapse. Presynaptic action potential triggers the release of neurotransmitters that bind to receptors on postsynaptic (ligand-gated) ion
channels (blue), hence inducing ionic exchanges across the postsynaptic membrane.(c) Schematic view of the axonal membrane. Sodium-potassium
pumps (red), achieving ionic equilibrium at rest, and (voltage-gated) ion channels (green) involved in the propagation of action potential along the axon, are
represented.
Current
sink
Conduction currents
Current sink
Primary currents Na+
Conduction currents
Na+
(b)
Current lines
Current dipole
(a)
Current sources
Primary currents
Current quadrupole
Figure 2 Schematic view of typical distributions of current sinks and sources (red and black dots respectively). (a) Due to their asymetrical
distribution, postsynaptic currents are fairly approximated by current dipoles. Action potential expresses as two equivalent current dipoles with opposite
directions, leading to a quadrupolar approximation. (b) Illustration of an excitatory synapse. Local sink currents induce primary currents across the
membrane and within the cell. The conducting currents close the loop in the extracellular space, hence creating a distribution of source currents along
the membrane. In the same way, an inhibitory synapse creates a source current.
compared to physiological time constants; hence, scalp measures appear as instantaneous and synchronous, and the quasistatic approximation holds (Plonsey & Heppner, 1967). Under
this regime, Maxwells equations simplify as follows:
!
r E
! !
!
!
!
r
, r E 0 , r B 0, r B m0 J
e0
[2]
The electric and magnetic fields are now decoupled, and

importantly, the forward computation has become independent of time. The latter means that only the location,
orientation, and amplitude of the neuronal sources need to
be known to compute the sensor signals.
Since the electric potential simply relates to the electric
field by

!
E r, t grad V r, t
[3]
and accounting for Ohms law, the law of conservation of

charge and the BiotSavart law that relates magnetic fields to
the underlying currents, eqn [2] yields the following formulations for the electric potential V(r, t) and the magnetic field B(r,
t) distributions, given a time-varying source distribution Jp(r, t)
and tissue conductivity s(r):
!
!
sr r grad V r, t r Jp r, t
[4]
!

h! 0
0 ! 0 i
!
0
Jp r , t s r grad V r , t r r
m
0
0
Br, t 0
dr
r rj3
4p
[5]
at spatial location r and time t. Electrical and magnetical fields
generated by a single ECD are illustrated in Figure 3(a). In
addition, Figure 3(b,c) shows an example of the difference
between EEG and MEG data generated by the same underlying
sources.
The Main Forward Model Assumptions

A forward model of EEG and MEG data calls for a description
of the neuronal current distribution (referred to as the source
distribution), a specification of the conducting properties of
the head tissues and some information about the sensors
(locations and orientations in the case of MEG). A large
551
number of models have been proposed in the literature.

They differ by the realism with which they account for the
physical and geometric properties of head tissues. In other
words, the practicality of deriving EEG and MEG forward
models often boils down to trading off between the complexity of computing a fine individual structural and physical
model and the accuracy of the ensuing forward prediction.
In addition, contrary to simple models, complex ones will not
have analytic solutions and numerical approximations will be
needed.
The Source Model

At the macroscale, the coherent activity of a neuronal assembly
is most commonly modeled by an equivalent current dipole
(ECD) (Figure 3(a)). Higher-order models have also been
explored (Nolte & Curio, 2000), mostly as an attempt to better
capture the extent of active cortical areas. However, such
models introduce a higher number of unknown parameters
that are also difficult to interpret. Nevertheless, quadrupoles
may be of interest, particularly in MEG, to model the complex
fields generated by extended and deep cortical sources (Jerbi
et al., 2004).
Two main approaches can be distinguished when considering the ECD as a unitary source model:
The dipolar approach relies on the assumption that a fairly

small number of ECDs (fixed a priori, typically less than 8)
contribute simultaneously and significantly to the scalp
data. Each ECD is fully described by six parameters, three
for its location and three for its orientation and magnitude.
Scalp
Skull
B
Cortical ribbon
(b)
J2
s2
J1
s1
Current distorsion
(a)
(c)
Figure 3 (a) Current dipole with electric field lines (red) and magnetic field lines (green). Because of different conductivities in different head tissues,
current lines are distorted when they cross tissue boundaries. (b) Scalp topography of real EEG data (auditory evoked response N100). (c)
Corresponding scalp topography of MEG data (from simultaneously recorded EEG and MEG responses to auditory tones).
552
This yields a well-conditioned system where the number of

unknown parameters to be fitted is smaller than the number of independent data points (which at each point in time
roughly corresponds to the number of sensors).
The distributed or imaging approach relaxes the strong constraint on the number of active regions. A few thousands
ECDs are typically used to model the entire source space
with fixed positions, either distributed over a 3-D regular
grid covering the whole brain volume or limited to the
cortical sheet with a possible normal orientation constraint.
For the latter, only each ECD magnitude is left to be estimated, yielding a linear but ill-conditioned system to be
solved. A unique solution to the ill-posed EEG/MEG inverse
problem will be obtained here by incorporating additional
constraints about the source configuration. This source
model enables one to produce images of cortical or brain
activity, which makes statistical inference at the subject or
group level more tractable and more sensitive (Litvak &
Friston, 2008; Mattout, Henson, & Friston, 2007).
The Head Model

This is another critical part of the forward model. It embeds our
knowledge and assumptions on head tissue geometry and
conducting properties.
Head geometry models

Spherical models are the simplest ones, consisting of concentric
spheres with homogeneous and isotropic conductivity in each
compartment or layer (de Munck, van Dijk, & Spekreijse, 1988;
Rush & Driscoll, 1968). Although the head is not spherical,
these models are attractive because of the ensuing exact analytic
expressions for the electric potential and magnetic field on the
head surface. They have been extensively evaluated empirically.
The three-shell model distinguishes between the scalp,
skull, and brain layers with radius ratio and isotropic conductivities as proposed in Rush and Driscoll (1969). It is largely
used for EEG and available in most routine softwares.
Since the magnetic permeability is homogenous over tissues and since volume currents barely contribute to the external magnetic field, spherical models appear more suitable for
MEG than EEG. MEG spherical models are blind to volume
current contributions but present the advantage that neither
tissue conductivity knowledge nor the radius of the sphere is
needed. The overlapping spheres model, which refines the
single-sphere model by fitting a sphere to each sensor location,
provides a better MEG forward solution (Huang, Mosher, &
Leahy, 1999).
Realistic models are numerical models that have been mostly
developed for EEG, to better account for the shape and electrical properties of the tissues, namely, their electrical conductivity as with the boundary element method (BEM) (Hamalainen
& Sarvas, 1989) and their anisotropy as with the finite element
method (FEM) (Marino, Halgren, Badier, Gee, & Nenov, 1993)
or the finite difference method (FDM) (Lemieux, McBride, &
Hand, 1996).
The BEM relies on surface meshes derived from MRI segmentation and assigns each layer with homogenous and isotropic conductivity. Studies comparing spherical and BEM
models in EEG and MEG obtained better source estimates
using BEM for dipoles below the supratemporal plane

(Crouzeix, Yvert, Bertrand, & Pernier, 1999; Yvert, Bertrand,
Thevenet, Echallier, & Pernier, 1997). FEM and FDM rely on
3-D meshes where each finite element can be ascribed with a
different, anisotropic conductivity tensor matrix. Models then
differ in their number of compartments, conductivity values,
anisotropic ratios, and tensor orientations. The latter can be
derived from diffusion tensor imaging (DTI) (Tuch, Wedeen,
Dale, George, & Belliveau, 2001).
We refer the reader to Hamalainen, Hari, Ilmoniemi, Knuutila,
and Lounasmaa (1993), Meijs, Weier, Peters, and van Oosterom
(1989), Mosher, Leahy, and Lewis (1999), Rush and Driscoll
(1969), and Sarvas (1987) for a detailed description of the
forward model computation, under the spherical assumption
(analytic form) and the more realistic assumption (numerical
form).
Head tissue conductivities

Individual conductivity values are of high importance, particularly for realistic models. Estimations from dead tissues have
proved very different from in vivo values and first in vivo observations have come from anesthetized animals (Robillard &
Poussart, 1977). More recently, in vivo measures have been
made possible in humans thanks to the advent of electric
impedance tomography (Ferree, Eriksen, & Tucker, 2000;
Goncalves, de Munck, Heethaar, Lopes da Silva, & van Dijk,
2000) and DTI (Tuch, Wedeen, Dale, George, & Belliveau,
1999), but these techniques can still hardly be used routinely.
Hence, empirical values reported in experimental studies are
largely used as a first approximation (Rush & Driscoll, 1968).
Several studies based on simulated data have compared the
relative sensitivity of EEG and MEG forward solutions to conductivities. Critically, EEG is highly sensitive to the brain/skull
conductivity ratio (Vallaghe & Clerc, 2009) as well as to
white matter anisotropy (Gullmar, Haueisen, & Reichenbach,
2010). MEG is particularly sensitive to brain tissue conductivity (Gencer & Acar, 2004; Van Uitert & Johnson, 2003) and
white matter anisotropy (Gullmar et al., 2010).
Sensor Registration
Sensor description relative to the head model is achieved by
means of a spatial transformation based on head landmarks
(least-square fitting) or head surface (surface-matching
methods) or both, identified in both the MRI and the electrophysiological coordinate systems.
Various sources of errors are associated with sensor coregistration, particularly landmark identification on MR images,
electrode and landmark digitization, and head movements
during MEG acquisition. Typically, coregistration errors range
between 5 and 10 mm (Hillebrand & Barnes, 2011; Whalen,
Maclin, Fabiani, & Gratton, 2008), with moderate consequences on EEG inverse solutions (Acar & Makeig, 2013;
Wang & Gotman, 2001) but potentially dramatic effects on
MEG ones (Hillebrand & Barnes, 2003). Interestingly, uncertainty about the forward model, due to coregistration, could be
accounted for in the source reconstruction process thanks to
probabilistic or Bayesian methods (Lopez, Penny, Espinosa, &
Barnes, 2012).
Empirical Evaluation of Forward Model Assumptions

From Forward to Generative Models
The forward relationship between source parameters y and
observed EEG or MEG data Y is of the general form
Y Ly
[6]
where L indicates the lead-field operator and embodies all the

precited anatomical and biophysical assumptions one needs to
account for in the forward model. Data Y is an N T matrix,
where N is the number of sensors and T the number of time
samples. y is a P-long vector made of all source location,
orientation, and amplitude parameters.
Forward models have in themselves barely no interest; they
are only useful and even mandatory when one aims at reconstructing brain activity from scalp recordings, that is, inverting
eqn [6] to estimate y. Contrary to the forward computation of
L, this inverse problem is ill-posed and requires additional
(prior) information or constraints to ensure a unique solution.
Two types of additional assumptions can be specified: assumptions about measurement noise and prior knowledge about
parameters y. In particular, when source locations are fixed as
in distributed approaches, eqn [6] becomes linear:
Y Ly e
[7]
where L is the N P lead-field (or gain) matrix operator and e

models an additive measurement noise, which is usually
assumed to follow a Gaussian distribution with zero mean
and a fully known or parameterized variance structure
(Mattout, Phillips, Penny, Rugg, & Friston, 2006).
This highlights the fact that solving the inverse problem
requires the specification of not only the lead-field operator
L but also the prior distributions over noise e and parameters y. Altogether, those assumptions make a full generative
model, which could be used to simulate realistic EEG or
MEG data.
The probabilistic or Bayesian framework is very much
appropriate to define and invert generative models. Indeed,
probabilistic distributions can flexibly describe our knowledge
or uncertainty about a phenomenon. Moreover, advanced
inference techniques have been developed to invert complex
probabilistic models.
Bayesian (Forward) Model Comparison

Importantly, the Bayesian framework enables formal model
comparison given empirical observations. Since the forward
model is part of the generative model, Bayesian model comparison offers a principled way of comparing forward model
assumptions, as long as all other assumptions (viz., priors over
noise and source parameters) are kept the same for each compared generative model and provided that all models are fitted
to the same dataset.
This is a recent and important extension to previous evaluation approaches of EEG and MEG forward models, which
mostly rested on numerical simulations (Acar & Makeig,
2013; Crouzeix et al., 1999; Vatta, Meneghini, Esposito,
Mininel, & Di Salle, 2010) and on a few empirical measures
553
using biophysical phantoms (Baillet et al., 2001; Leahy,

Mosher, Spencer, Huang, & Lewine, 1998).
Bayesian model comparison rests on computing the model
evidence p(Y| M). The higher the model evidence, the better the
model. A useful approximation to the log evidence is the free
energy (F) (Penny, 2012). It can be obtained using variational
techniques and has already been used to compare forward
models of EEG and MEG data.
Namely, it could show that canonical cortical meshes may
carry sufficient structural information to solve the MEG inverse
problem (Henson, Mattout, Phillips, & Friston, 2009; Mattout
et al., 2007).
A Note on Model Complexity

Given data Y and model M with parameters y, the free energy
can be written as
F h ln pYj y, Miq KLqyj pyj M
[8]
where
p(Y| y, M) and p(y| M) are the likelihood and prior distributions, respectively (they fully define the generative
model M),
q(y) is the approximate posterior distribution over model
parameters (the outcome of the inverse inference process),
KL is the KullbackLeibler divergence, which can be interpreted as a statistical distance between two distributions.
Here, it quantifies the distance between the posterior and
the prior distribution over y.
Importantly, the first term in eqn [8] corresponds to model

accuracy, while the second term quantifies model complexity.
In the general case of Gaussian distributions, this term can be
written as
KLqyj pyj M

1
1
ln jCy j ln Cy=Y
2
2

T
1
my=Y my
my=Y my C1
y
2

Trace C1
y Cy=Y cst
[9]
where my, Cy and my/Y, Cy/Y are the mean and variance of the
prior and posterior distributions, respectively.
Given those equations, changing the lead-field operator by
moving from a simple spherical head model to a more realistic
one might increase the free energy in two ways:
By improving the fit of the data (increasing model accuracy)

By reducing model complexity through a posterior distribution that would decrease the earlier-mentioned KullbackLeibler divergence. Namely, this could be the case if
the realistic model would yield a smaller posterior correlation between parameters (Penny, 2012).
Importantly, this means that a more realistic model, although

more complex in a computing sense (because it requires the
fine extraction of individual anatomical and biophysical
features), might yield a significantly higher free energy.
However, this will be the case only if such a model offers a
more realistic and higher spatial resolution that the data can
accommodate. In other words, whether it is worth deriving a
554
fine and realistic head model for source reconstruction

depends on the spatial precision that the data can offer.
In Henson et al. (2009), using data from a face perception
MEG experiment, it was shown that a BEM model should be
preferred to a spherical one, provided that individually defined
inner skull and scalp meshes were used.
Finally, besides head models, Bayesian model comparison
can also be used to evaluate the ability of EEG and MEG data to
inform advanced source models based on neural masses.
Recent developments of dynamic causal models to study
brain effective connectivity have led to more biologically plausible models of neuronal populations. As an example, a recent
study suggests that EEG data can distinguish between the
dynamics of local neuronal excitatory and inhibitory subpopulations (Moran et al., 2013).

Principles of Electroencephalography; Basic Principles of
Magnetoencephalography; INTRODUCTION TO METHODS AND
MODELING: Bayesian Model Inference; Bayesian Model Inversion;
Distributed Bayesian Inversion of MEG/EEG Models; Dynamic Causal
Models for Human Electrophysiology: EEG, MEG, and LFPs; Neural
Mass Models; Variational Bayes.
References
Acar, Z. A., & Makeig, S. (2013). Effects of forward mod el errors on EEG source
localization. Brain Topography, 26(3), 378396.
Baillet, S., Riera, J. J., Marin, G., Mangin, J. F., Aubert, J., & Garnero, L. (2001).
Evaluation of inverse methods and head models for EEG source localization using a
human skull phantom. Physics in Medicine and Biology, 46(1), 7796.
Crouzeix, A. (2001). Methodes de localisation des generateurs de lactivite electrique
cerebrale a` partir de signaux electro- et magneto-encephalographiques (pp. 1264).
PhD Thesis, University Lyon 1, France.
Crouzeix, A., Yvert, B., Bertrand, O., & Pernier, J. (1999). An evaluation of dipole
reconstruction accuracy with spherical and realistic head models in MEG. Clinical
de Munck, J. C., van Dijk, B. W., & Spekreijse, H. (1988). Mathematical dipoles are
adequate to describe realistic generators of human brain activity. IEEE Transactions
on Biomedical Engineering, 35(11), 960966.
Ferree, T. C., Eriksen, K. J., & Tucker, D. M. (2000). Regional head tissue conductivity
estimation for improved EEG analysis. IEEE Transactions on Biomedical
Engineering, 47(12), 15841592.
Gencer, N. G., & Acar, C. E. (2004). Sensitivity of EEG and MEG measurements to tissue
conductivity. Physics in Medicine and Biology, 49(5), 701717.
Goncalves, S., de Munck, J. C., Heethaar, R. M., Lopes da Silva, F. H., & van Dijk, B. W.
(2000). The application of electrical impedance tomography to reduce systematic
errors in the EEG inverse problem A simulation study. Physiological
Measurement, 21(3), 379393.
Gullmar, D., Haueisen, J., & Reichenbach, J. R. (2010). Influence of anisotropic
electrical conductivity in white matter tissue on the EEG/MEG forward and inverse
solution. A high-resolution whole head simulation study. NeuroImage, 51(1),
145163.
Hamalainen, M. S., Hari, R., Ilmoniemi, R. J., Knuutila, J., & Lounasmaa, O. (1993).
Magnetoencephalography Theory, instrumentation, and applications to
noninvasive studies of the working human brain. Reviews of Modern Physics, 65(2),
413497.
Hamalainen, M. S., & Sarvas, J. (1989). Realistic conductivity geometry model of the
human head for interpretation of neuromagnetic data. IEEE Transactions on
Biomedical Engineering, 36(2), 165171.
Henson, R. N., Mattout, J., Phillips, C., & Friston, K. J. (2009). Selecting forward
models for MEG source-reconstruction using model-evidence. NeuroImage, 46(1),
168176.
Hillebrand, A., & Barnes, G. R. (2003). The use of anatomical constraints with MEG
beamformers. NeuroImage, 20(4), 23022313.
Hillebrand, A., & Barnes, G. R. (2011). Practical constraints on estimation of source

extent with MEG beamformers. NeuroImage, 54(4), 27322740.
Huang, M. X., Mosher, J. C., & Leahy, R. M. (1999). A sensor-weighted overlappingsphere head model and exhaustive head model comparison for MEG. Physics in
Medicine and Biology, 44(2), 423440.
Jerbi, K., Baillet, S., Mosher, J. C., Nolte, G., Garnero, L., & Leahy, R. M. (2004).
Localization of realistic cortical activity in MEG using current multipoles.
NeuroImage, 22(2), 779793.
Koles, Z. J. (1998). Trends in EEG source localization. Electroencephalography and
Clinical Neurophysiology, 106(2), 127137.
Leahy, R. M., Mosher, J. C., Spencer, M. E., Huang, M. X., & Lewine, J. D. (1998). A
study of dipole localization accuracy for MEG and EEG using a human skull
phantom. Electroencephalography and Clinical Neurophysiology, 107(2), 159173.
Lemieux, L., McBride, A., & Hand, J. W. (1996). Calculation of electrical potentials on
the surface of a realistic head model by finite differences. Physics in Medicine and
Biology, 41(7), 10791091.
Litvak, V., & Friston, K. J. (2008). Electromagnetic source reconstruction for group
studies. NeuroImage, 42(4), 14901498.
Lopez, J. D., Penny, W. D., Espinosa, J. J., & Barnes, G. R. (2012). A general Bayesian
treatment for MEG source reconstruction incorporating lead field uncertainty.
NeuroImage, 60(2), 11941204.
Malmivuo, J., & Plonsey, R. (1995). Bioelectromagnetism. New-York: Oxford University
Press.
Marino, F., Halgren, E., Badier, J.-M., Gee, M., & Nenov, V. (1993). A finite difference
model of electric field propagation in the human head: Implementation and validation.
In: The IEEE annual northeast bioengineering conference, New Jersey (pp. 8286).
Mattout, J., Henson, R. N., & Friston, K. J. (2007). Canonical source reconstruction for
MEG. Computational Intelligence and Neuroscience, Article ID 67613. http://dx.doi.
org/10.1155/2007/67613.
Mattout, J., Phillips, C., Penny, W. D., Rugg, M. D., & Friston, K. J. (2006). MEG source
localization under multiple constraints: An extended Bayesian framework.
NeuroImage, 30(3), 753767.
Meijs, J. W., Weier, O. W., Peters, M. J., & van Oosterom, A. (1989). On the numerical
accuracy of the boundary element method. IEEE Transactions on Biomedical
Engineering, 36(10), 10381049.
Moran, R. J., Stephan, K. E., Campo, P., Symmonds, M., Dolan, R. J., & Friston, K. J.
(2013). Free energy, precision and learning: the role of cholinergic
neuromodulation. Journal of Neuroscience, 33(19), 82278236.
Mosher, J. C., Leahy, R. M., & Lewis, P. S. (1999). EEG and MEG: Forward solutions
for inverse methods. IEEE Transactions on Biomedical Engineering, 46(3),
245259.
Mosher, J. C., Leahy, R. M., Shattuck, D. W., & Baillet, S. (1999). MEG source imaging
using multipolar expansions. Lecture notes in computer science, (pp. 98111).
Berlin: Springer.
Nolte, G., & Curio, G. (2000). Current multipole expansion to estimate lateral extent of
neuronal activity: A theoretical analysis. IEEE Transactions on Biomedical
Engineering, 47(10), 13471355.
Nunez, P. L. (1981). Electric fields of the brain: The neurophysics of EEG, (pp. 8391).
New-York: Oxford University Press.
Penny, W. D. (2012). Comparing dynamic causal models using AIC, BIC and free
energy. NeuroImage, 59(1), 319330.
Pernier, J. (2007). Electro et magneto encephalographie Biophysique, techniques et
methodes, (pp. 1248). Paris: Herme`s Science, Editions Lavoisier.
Plonsey, R., & Heppner, D. B. (1967). Considerations of quasi-stationarity
in electrophysiological systems. Bulletin of Mathematical Biophysics, 29(4),
657664.
Robillard, P. N., & Poussart, Y. (1977). Specific-impedance measurements of brain
tissues. Medical & Biological Engineering & Computing, 15(4), 438445.
Rush, S., & Driscoll, D. A. (1968). Current distribution in the brain from surface
electrodes. Anesthesia and Analgesia, 47(6), 717723.
Rush, S., & Driscoll, D. A. (1969). EEG electrode sensitivity An application of
reciprocity. IEEE Transactions on Biomedical Engineering, 16(1), 1522.
Sarvas, J. (1987). Basic mathematical and electromagnetic concepts of the biomagnetic
inverse problem. Physics in Medicine and Biology, 32(1), 1122.
Schwan, H. P., & Kay, C. F. (1957). Capacitive properties of body tissues. Circulation
Research, 5(4), 439443.
Tuch, D. S., Wedeen, V. J., Dale, A. M., George, J. S., & Belliveau, J. W. (1999).
Conductivity mapping of biological tissue using diffusion MRI. Annals of the
New York Academy of Sciences, 888, 314316.
Tuch, D. S., Wedeen, V. J., Dale, A. M., George, J. S., & Belliveau, J. W. (2001).
Conductivity tensor mapping of the human brain using diffusion tensor MRI.
98(20), 1169711701.

Vallaghe, S., & Clerc, M. (2009). A global sensitivity analysis of three- and four-layer
EEG conductivity models. IEEE Transactions on Biomedical Engineering, 56(4),
988995.
Van Uitert, R., & Johnson, C. (2003). Influence of brain conductivity on
magnetoencephalographic simulations in realistic head models. In: Proceedings of
the 25th annual international conference of the IEEE engineering in medicine and
biology society, pp. 14.
Vatta, F., Meneghini, F., Esposito, F., Mininel, S., & Di Salle, F. (2010). Realistic
and spherical head modeling for EEG forward problem solution: A comparative cortexbased analysis. Computational Intelligence and Neuroscience, 2010(1), 111.
555
Wang, Y., & Gotman, J. (2001). The influence of electrode location errors on EEG dipole
source localization with a realistic head model. Clinical Neurophysiology, 112(9),
17771780.
Whalen, C., Maclin, E. L., Fabiani, M., & Gratton, G. (2008). Validation of a method for
coregistering scalp recording locations with 3D structural MR images. Human Brain
Mapping, 29(11), 12881301.
Yvert, B., Bertrand, O., Thevenet, M., Echallier, J. F., & Pernier, J. (1997). A systematic
evaluation of the spherical model accuracy in EEG dipole localization.
Electroencephalography and Clinical Neurophysiology, 102(5), 452459.
Distributed Bayesian Inversion of MEG/EEG Models

JD Lopez and JF Vargas, Universidad de Antioquia UDEA, Medelln, Colombia
GR Barnes, University College London, London, UK
Glossary
Current dipole Two electric charges that have equal

magnitudes but opposite signs and are separated by an
infinitely small distance.
Abbreviations
BEM
EEG
LORETA
Boundary element method

Electroencephalography
Low-resolution brain electromagnetic
tomography
Introduction
Magnetoencephalography (MEG) and electroencephalography
(EEG) give us measures of magnetic field or electric potential
difference at the surface of the head due to neuronal current
flow. Estimating this current flow can give us estimates of brain
function, which update millisecond by millisecond. Figure 1
shows the distribution of magnetic field change outside the
head at a specific time instant. Based on a mathematical model
of the head and its relationship to the MEG sensors, it is
possible to estimate which part of the brain caused this changing field and, if necessary, superimpose this on an anatomical
image or structural MRI.
The estimation of cortical current flow based on MEG/EEG
data is an ill-posed inverse problem, that is, there is an infinity
of possible distributions of current flow that will generate the
same measured data. The accuracy of the solution to this
inverse problem depends both on the accuracy of the forward
model of the head and on the prior information used to reduce
the uncertainty (Baillet & Garnero, 1997).
One form of prior information is to assume that the data
can be explained by a small number of current elements of
dipoles (Supek & Aine, 1993); this is extremely powerful but is
a nonlinear problem that entails the fit of location, orientation,
and dipole magnitude and therefore becomes unstable as the
number of dipoles increases. One popular way to avoid this
problem is to consider that the locations and orientations of
all sources are known and simply estimate their magnitude
(Dale & Sereno, 1993; Grech et al., 2008; Hamalainen & Ilmoniemi, 1984).
There are numerous algorithms each involving different
prior assumption sets and cost functions (see Baillet, Mosher,
and Leahy (2001) for review). They range from the well-known
minimum norm estimation (MNE) algorithm (Hamalainen &
Ilmoniemi, 1984), in which the assumption is that all sources
are active but with minimum energy, to approaches such as
Lead-field matrix A gain matrix defining the sensitivity of

sensors outside the head to current dipoles on the gray
matter sheet.
MEG
MSP
PDF
WMNE
Magnetoencephalography
Multiple sparse priors
Probability density function
Weighted minimum norm estimation
Low-resolution brain electromagnetic tomography (LORETA;

Pascual-Marqui, Michel, & Lehmann, 1994) and standardized
LORETA (sLORETA; Pascual-Marqui, 2002) that include
assumptions about smoothness on the cortical surface. Some
classes of algorithms such as beamformers require no prior
anatomical information but make strong functional assumptions about the underlying current flow (Sekihara, Poeppel,
Marantz, Koizumi, & Miyashita, 1999; van Veen, van Drongelen,
Yuchtman, & Suzuki, 1997). All these approaches are based on
defining the neural activity as Gaussian distributed with a known
fixed prior covariance (Idier, 2008). Mosher, Baillet, and Leahy
(2003) were the first to point out that fundamentally, all of these
algorithms differ only in the choice of prior source covariance
matrix.
The representation of the MEG/EEG inverse problem within
the Bayesian framework has been widely studied (Baillet &
Garnero, 1997; Schmidt, George, & Wood, 1999; TrujilloBarreto, Aubert-Vasquez, & Valdes-Sosa, 2004).
(Auranen et al., 2005; Sato et al., 2004; Wipf & Nagarajan,
2009). In order to generalize these approaches, this fixed prior
covariance can be replaced by a weighted sum of a set of
possible covariance components. Each covariance component
might, for example, describe the sensor-level covariance one
would expect due to an active patch of the cortex (Harrison,
Penny, Ashburner, Trujillo-Barreto, & Friston, 2007). A good
example of this solution is the multiple sparse priors (MSP)
algorithm (Friston et al., 2008; Henson, Wakeman, Litvak, &
Friston, 2011) that uses the negative variational free energy as
cost function to weight the candidate covariance matrices
(Friston, Mattout, Trujillo-Barreto, Ashburner, & Penny,
2007).
In this article, the theoretical framework of the MEG/EEG
inverse problem is explained, demonstrating with an illustrative example how the definition of the prior covariance matrix
varies the solution. Finally, the MSP algorithm is presented as a
generalization of the Bayesian inversion schemes.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00331-6
557
558
INTRODUCTION TO METHODS AND MODELING | Distributed Bayesian Inversion of MEG/EEG Models
Figure 1 The left panel shows the distribution of magnetic field measured outside the head. The middle panel shows the distribution of these
magnetic field measurements relative to the head and cortical surface. The right panel shows an estimate (based on additional prior information) of the
current flow that gave rise to the magnetic field change.
The MEG/EEG Inverse Problem

The magnitude of the electromagnetic fields observed over the
scalp with MEG/EEG can be obtained from the quasi-static
approximation of Maxwell and Poissons equations (Hallez
et al., 2007). For fixed current sources, this comes down to a
linear model:
Y LJ e
[1]
where Y 2 RNc Nt is the MEG/EEG dataset of Nc sensors and

Nt time samples and J 2 Nd Nt is the amplitude of Nd current
dipoles distributed evenly across and oriented normal to the
cortical surface. Both data and dipoles are related by the gain
matrix L 2 Nc Nd (also known as the lead field matrix). Sensor
noise and uncertainty on the propagation model are represented by the random variable e 2 Nc Nt .
In the linear model of eqn [1], the lead field matrix L
(propagation model) is noninvertible because the dipoles outnumber the sensors (Nd Nc), that is, an estimate of ^J J
cannot be directly recovered without additional assumptions
(see Liu, Dale, and Belliveau (2002) (Appendix) for demonstrations of four different approaches).
The prior probability density function (PDF) of the source
activity p(J), based on prior knowledge, is weighted by the
likelihood p(Y|J) (or fit to the data), allowing us to estimate
the posterior source distribution using the Bayes theorem:
pJjY
pYjJpJ
pY
The estimated current density

can
be recovered through the
expectation operator ^J E p JY . Initially, the evidence p(Y)
is considered constant given that the dataset is fixed, but it will
be included later for optimization purposes.
Typically, MEG/EEG measurement noise is considered to be
white and Gaussian pe N e; 0, Se , with Se 2 Nc Nc the
posterior covariance of the measurement. Making similar
Gaussian assumptions on the distribution of the likelihood
and the prior probabilistic model, pJ N J; 0, Q, with
Q 2 Nd Nd the prior covariance of the neural activity. For
uninformative priors, this reduces to (Grech et al., 2008)

^J QLT Se LQLT 1 Y
[2]
with ()T the transpose operator. In similar way, the posterior

covariance of p(J|Y) is

1
1
[3]
covpJjY SJ LT S1
e LQ
The source estimate is highly dependent on the assumptions made about the source- and sensor-level covariance
matrices Q and Se, respectively. In the absence of prior information about noise over sensors or their gain differences, one
typically assumes a sensor noise covariance matrix of the form
Se h0 INc , where INc 2 Nc Nc is an identity matrix and
h0 2 is the sensor noise variance. It can also be viewed as a
regularization parameter (Golub, Heath, & Wahba, 1979; Hansen, 2000) or hyperparameter (Phillips, Rugg, & Friston,
2002b).
Fixed Bayesian Inversion Approaches

There are multiple constraints that can be used as prior source
covariance matrix, Q. In this section, the most widely used
approaches (distributed within open-source software packages) are briefly explained, in the context of a toy example.
A single-trial dataset of Nt 161 samples over Nc 274
MEG sensors was generated with the single source of neural
activity shown in Figure 1 into sensor space. White random
noise with signal-to-noise ratio (SNR) of zero decibels was
added to the data, with SNR 10 log10|std(Y)/std(e)|. The
reconstruction algorithms were implemented over a mesh of
Nd 8196 dipoles distributed over and oriented normal to
the cortical surface (Phillips, Rugg, & Friston, 2002a). The
forward modeling was performed over the single-shell forward model (Nolte, 2003) implemented in the Statistical
Parametric Mapping (SPM) 8 software package. Source
codes similar to this example can be downloaded as supplementary material of Lopez, Litvak, Espinosa, Friston, &
Barnes, 2013a (http://www.fil.ion.ucl.ac.uk/spm).
(Weighted) Minimum Norm

The simplest (minimum norm) assumption is that all sources
have approximately the same prior variance and no covariance:
Q I Nd

Figure 2(a) shows an image of Q with equal weighting on
all source locations and no off-diagonal elements (no covariance). In Figure 2(b), the focal dipolar source that generated
the data is shown as a red circle. Note that the estimate of
neural activity (gray color scale) is generally more superficial as
the algorithm is trying to minimize energy, and the closer the
sources to the sensors, the smaller the current flow needs to be.
Smoother-Based Approaches
Harrison et al. (2007), a Greens function based on a graph

Laplacian was solved using the vertices and faces provided by
the structural MRI, taking into account the intervoxel distance
and connections between sulci. Greens function QG 2 Nd Nd
is defined as
QG esg GL
where sg is a positive constant value that determines the
size of the activated regions and GL 2 Nd Nd is a graph Laplacian with interdipole connectivity information. A Gaussian
smoothed solution, for example, can be directly formed by
Greens function, Q QG; Figure 3(a) shows an image of the
prior source covariance matrix for this case, and its solution is
shown in Figure 3(b). As expected, the solution is smoother
yet still displaced slightly superficially.
# dipoles
One can build on the minimum norm assumptions to include

a constraint that the neuronal activity is smooth, rather than
point-like, on the cortical surface. The LORETA algorithm
(Pascual-Marqui et al., 1994) makes this assumption. One
way to obtain the smoothing function was proposed in
559
# dipoles
(a)
(b)
# dipoles
Figure 2 (a) The minimum norm assumption is based on an identity matrix. (b) The red circles show the location of the simulated source; the
translucent glass brain shows the frontal, lateral, and superior views of the dipoles with the highest variance during the time windows of interest. Note
that the minimum norm solution tends to be displaced superficially.
(a)
# dipoles
(b)
Figure 3 (a) Gaussian smoothed prior covariance matrix. (b) The smoothed solution (also called LORETA-like) still has a large localization error for
deep sources.
560
Data-Based Approaches
Up until now, the choice of Q has not depended on the data. It
is also possible to use empirical Bayes to estimate these prior
(source noise and sensor noise) covariance matrices from the
data. At the simplest level, one can make an estimate of the
source covariance matrix empirically and use empirical Bayes
to provide the optimal weighting between source and sensor
noise matrices.
For example, beamformer algorithms make a direct estimate of source covariance based on the assumption that there
are no zero-lag correlated sources (Sekihara et al., 1999; van
Veen et al., 1997). The beamforming solution can be introduced into the Bayesian framework as a single covariance
matrix, Q B, where B 2 Nd Nd is a diagonal matrix formed
directly from the data, and it is projected into the source space
with the lead field matrix and normalized (Belardinelli, Ortiz,
Barnes, Noppeney, & Preissl, 2012). Each diagonal element of
B is defined as
1 T T 1 1
Bii
L YY
Li
, 8i 1, . . . , Nd
di i
with Bii the ith main diagonal element of B, and Li the ith
column of L, and the normalization parameters d is defined as
di
1
, 8i 1, . . . , Nd
LTi Li
Figure 4(a) shows the beamformer estimate of the prior

source covariance matrix Q; note that only diagonal elements
are active as the underlying assumption is that there is no
covariance between sources. Figure 4(b) shows the neural
activity reconstruction using this single beamforming prior
although a still relatively diffuse estimate.
MSP Algorithm
Nq
X
hi Ci
[4]
i1
Here, each Ci 2 Nd Nd is a prior source covariance matrix

that can take any form. For simplicity, we consider the case
where a prior component corresponds to a single potentially
activated
region

of the cortex. The hyperparameters

h h1 ; . . . ; hNq
weight these covariance components.
Regions with large hyperparameters will have large prior variances. Note that these components may embody different
types of informative priors, for example, different smoothing
functions, medical knowledge, and fMRI priors (Henson et al.,
2011). The choice of the set of prior components C used in
eqn [4] determines the sets of prior assumptions that define the
model; and specific forms of C can be used to emulate standard
source reconstruction approaches. For the minimum norm
solution, for example, the set is just one identity matrix
C INd , and for the LORETA-like solution, it will be a
smoothed version C QG.
In the absence of prior information, the most inclusive set C
should have the same number of components as there are
dipoles distributed through the source space (around 8000).
However, this (overcomplete) set precludes beliefs or constraints on source activity: the number of components usually
considered is of the same order as the number of channels
(<500). As we know a priori that neuronal current flow has
some local coherence, we model the basic unit of current flow
as a spatially smooth impulse (Greens) function at selected
vertices on the cortical surface. The size and the number of the
ensuing patches can be defined based on prior knowledge
(Belardinelli et al., 2012; Lopez et al., 2012). Current implementations are based on fixed sets of patches. For example, the
SPM software package uses a set of Nq 512 patches covering
the entire cortical surface.
# dipoles
The single prior-based approaches presented in the preceding

text can be generalized by considering the prior source
covariance
as the
weighted sum of multiple prior components

C C1 ; . . . ; CNq , which is commonly known as empirical
Bayes (see Wipf and Nagarajan (2009) for a review on its
treatment in source reconstruction):
(a)
# dipoles
(b)
Figure 4 (a) Prior covariance matrix formed with the weighted covariance of the data. (b) The beamforming reconstruction is highly smoothed but with
small localization error for single sources of neural activity.
561
# dipoles
# dipoles
(a)
(b)
Figure 5 (a) Set of covariance components that form the matrix Q. (b) The optimization of the MSP can achieve zero localization error if the source of
neural activity coincides with one of the covariance components or a linear mixture of them.
For a given set of covariance components C, the optimization of hyperparameters is performed with an iterative process
called variational Laplace approximation (Friston et al., 2008),
which maximizes the model evidence p(Y), by computing the
gradient and Hessian of the negative variational free energy
(Friston et al., 2007). The free energy is used as the cost function to fit the modeled covariance (determined
by the hyperparameters h) to the data covariance SY 1 Nt YY T . The free
energy can be expressed in words as (Lopez, Litvak et al.,
2013a)

Model
Size of model
Num of data
F

covariance
samples
error

Error in
Error in covariance

hyperparameters
of hyperparameters
The MSP is based on a library of hundreds of covariance
components, each corresponding to a different locally smooth
focal region (or patch) of the cortex (for implementation details
of the MSP algorithm, see Friston et al. (2008), Lopez, Litvak
et al. (2013a), and Belardinelli et al. (2012)). Figure 5(a) shows
how the set of covariance components is formed with diagonal
smoothers representing focal active regions. Figure 5(b)
shows the MSP reconstruction after the optimization process
performed over the hyperparameters; note that zero localization
error may be achieved if the source of neural activity coincides
with one of the active regions in the dictionary of covariance
components C. Finally, the localization error given by each of
the algorithms and their resultant free energy are shown in
Figure 6.
Concluding Remarks
In this article, a brief review of the most widely used Bayesian
distributed inversion approaches for solving the MEG/EEG
inverse problem has been presented. Fundamentally, all
schemes can be put into a common mathematical framework
differing only in the prior assumptions about the source covariance matrix. Here, the mathematical assumptions underlying
30
Localisation error(mm)
Log model evidence
20
10
0
MMN
Loreta
BMF
MSP
Figure 6 Blue bars show the localization error (the distance between
the peak of the estimated current distribution and the simulated source
location) for the four different algorithms used. Red bars show the
relative log model evidence for the four solutions. Note that normally,
localization error is not available but model evidence seems to be a good
proxy with which to judge between prior assumptions.
the classical minimum norm, the smoothed LORETA-like, and

the beamforming estimations have been revisited; and the MSP
algorithm has been introduced as a generalization of these
approaches. It should be noted that we provide only a toy
example of a focal single source; some methods like MSP will
perform well by definition; how well each method performs on
neurophysiological data will depend on how the brain works. In
these cases, we rarely have access to the ground truth, but do
have access to model evidence, which appears to be a good
proxy.
All the methods described have been the inherently static,
that is, they assume stationarity of the signal over the period of
interest. However, temporal information can be included by
decomposing the time window of interest into independent
components (Phillips et al., 2002a, 2002b; Trujillo-Barreto,
Aubert-Vazquez, & Penny, 2008), and more recent advances
(Daunizeau and Friston, 2007; Olier, Trujillo-Barreto, & ElDeredy, 2013) point the way towards the incorporation of
both temporal priors into these spatial models. Similarly,
there is a great deal of ongoing work in this field including
incorporating realistic sets of covariance components
(Chowdhury, Lina, Kobayashi, & Grova, 2013), reducing the
effect of errors in the forward model (Lopez, Troebinger,
562
Penny, Espinosa, & Barnes, 2013b), and taking advantage of

noise properties (Zhang, Raij, Hamalainen, & Yao, 2013).

Bayesian Model Inference; Bayesian Model Inversion; Forward Models
for EEG/MEG; The General Linear Model.
References
Auranen, T., Nummenmaa, A., Hamalainen, M. S., Jaaskelainen, I. P., Lampinen, J.,
Vehtari, A., et al. (2005). Bayesian analysis of the neuromagnetic inverse problem
with Lp-norm priors. Neuroimage, 26, 870884.
Baillet, S., & Garnero, L. (1997). A Bayesian approach to introducing anatomofunctional priors in the EEG/MEG inverse problem. IEEE Transactions on
Biomedical Engineering, 44, 5.
Baillet, S., Mosher, J. C., & Leahy, R. M. (2001). Electromagnetic brain mapping. IEEE
Signal Processing Magazine, 18(6), 1430.
Belardinelli, P., Ortiz, E., Barnes, G., Noppeney, U., & Preissl, H. (2012). Source
reconstruction accuracy of MEG and EEG Bayesian inversion approaches. PLoS
One, 7, 12.
Chowdhury, R. A., Lina, J. M., Kobayashi, E., & Grova, C. (2013). MEG source
localization of spatially extended generators of epileptic activity: Comparing entropic
and hierarchical bayesian approaches. PLoS One, 8(2), e55969.
Dale, A. M., & Sereno, M. I. (1993). Improved localization of cortical activity by
combining EEG and MEG with MRI cortical surface reconstruction: A linear
approach. Journal of Cognitive Neuroscience, 5, 162176.
Daunizeau, J., & Friston, K. J. (2007). A mesostate-space model for EEG and MEG.
Friston, K., Harrison, L., Daunizeau, J., Kiebel, S., Phillips, C., Trujillo-Barreto, N., et al.
(2008). Multiple sparse priors for the M/EEG inverse problem. NeuroImage, 39,
11041120.
Variational free energy and the Laplace approximation. NeuroImage, 34, 220234.
Golub, G. H., Heath, M., & Wahba, G. (1979). Generalized cross-validation as a method
for choosing a good ridge parameter. Technometrics, 21, 215223.
Grech, R., Cassar, T., Muscat, J., Camilleri, K., Fabri, S., Zervakis, M., et al. (2008).
Review on solving the inverse problem in EEG source analysis. Journal of
NeuroEngineering and Rehabilitation, 5, 25.
Hallez, H., Vanrumste, B., Grech, R., Muscat, J., De Clercq, W., Vergult, A., et al. (2007).
Review on solving the forward problem in EEG source analysis. Journal of
NeuroEngineering and Rehabilitation, 4, 46.
Hamalainen, M. S., & Ilmoniemi, R. J. (1984). Interpreting measured magnetic fields of
the brain: Estimates of current distributions. Technical Report, Helsinki University of
Technology.
Hansen, P. C. (2000). Computational inverse problems in electrocardiology: The Lcurve and its use in the numerical treatment of inverse problems. In P. Johnston
(Ed.), Advances in Computational Bioengineering. Computational inverse problems
in electrocardiology (pp. 119142). WIT Press.
Harrison, L., Penny, W., Ashburner, J., Trujillo-Barreto, N., & Friston, K. (2007).
Diffusion-based spatial priors for imaging. NeuroImage, 38, 677695.
Henson, R. N., Wakeman, D. G., Litvak, V., & Friston, K. J. (2011). A parametric
empirical Bayesian framework for the EEG/MEG inverse problem: Generative models
for multi-subject and multi-modal integration. Frontiers in Human Neuroscience, 5,

16.
Idier, J. (2008). Bayesian approach to inverse problems. Hoboken, NJ: Wiley, 381 pages.
Liu, A. K., Dale, A. M., & Belliveau, J. W. (2002). Monte Carlo simulation studies of EEG
and MEG localization accuracy. Human Brain Mapping, 16, 4762.
Lopez, J. D., Barnes, G., & Espinosa, J. (2012). Single MEG/EEG source reconstruction
with multiple sparse priors and variable patches. DYNA, 174, 136144.
Lopez, J. D., Litvak, V., Espinosa, J., Friston, K., & Barnes, G. R. (2013a). Algorithmic
procedures for Bayesian MEG/EEG source reconstruction in SPM. Neuroimage, 84,
476487.
Lopez, J. D., Troebinger, L., Penny, W., Espinosa, J., & Barnes, G. (2013b). Cortical
surface reconstruction based on MEG data and spherical harmonics. In: 35th annual
international conference of the IEEE EMBC.
Mosher, J. C., Baillet, S., & Leahy, R. M. (2003). Equivalence of linear approaches in
bioelectromagnetic inverse solutions. In IEEE workshop on statistical, signal
processing (abstract).
Nolte, G. (2003). The magnetic lead field theorem in the quasi-static approximation and
its use for magnetoencephalography forward calculation in realistic volume
conductors. Physics in Medicine and Biology, 48(22), 36373652.
Olier, I., Trujillo-Barreto, N. J., & El-Deredy, W. (2013). A switching multi-scale
dynamical network model of EEG/MEG. Neuroimage, 83, 262287.
Pascual-Marqui, R. (2002). Standardized low resolution brain electromagnetic
tomography (sLORETA): Technical details. Methods & Findings in Experimental &
Clinical Pharmacology, 24, 524.
Pascual-Marqui, R., Michel, C. M., & Lehmann, D. (1994). Low resolution
electromagnetic tomography: A new method for localizing electrical activity in the
brain. International Journal of Psychophysiology, 18, 4965.
Phillips, C., Rugg, M., & Friston, K. (2002a). Anatomically informed basis functions for
EEG source localization: Combining functional and anatomical constraints.
Phillips, C., Rugg, M., & Friston, K. (2002b). Systematic regularization of linear inverse
solutions of the EEG source localization problem. NeuroImage, 17, 287301.
Sato, M., Yoshioka, T., Kajihara, S., Toyama, K., Goda, N., Doya, K., et al. (2004).
Hierarchical Bayesian estimation for MEG inverse problem. Neuroimage, 23(3),
806826.
Schmidt, M., George, J. S., & Wood, C. C. (1999). Bayesian inference applied to the
electromagnetic inverse problem. Human Brain Mapping, 7(3), 195212.
Sekihara, K., Poeppel, D., Marantz, A., Koizumi, H., & Miyashita, Y. (1999). MEG
spatio-temporal analysis using a covariance matrix calculated from nonaveraged multiple-epoch data. IEEE Transactions on Biomedical Engineering,
46, 515521.
Supek, S., & Aine, C. J. (1993). Simulation studies of multiple dipole neuromagnetic
source localization: Model order and limits of source resolution. IEEE Transactions
on Biomedical Engineering, 40, 529540.
Trujillo-Barreto, N. J., Aubert-Vasquez, E., & Valdes-Sosa, P. A. (2004). Bayesian
model averaging in EEG/MEG imaging. Neuroimage, 21, 13001319.
Trujillo-Barreto, N. J., Aubert-Vazquez, E., & Penny, W. D. (2008). Bayesian M/
EEG source reconstruction with spatio-temporal priors. NeuroImage, 39,
318335.
van Veen, B. D., van Drongelen, W., Yuchtman, M., & Suzuki, A. (1997). Localization of
brain electrical activity via linearly constrained minimum variance spatial filtering.
IEEE Transactions on Biomedical Engineering, 44, 867880.
Wipf, D., & Nagarajan, S. (2009). A unified Bayesian framework for MEG/EEG source
Zhang, J., Raij, T., Hamalainen, M., & Yao, D. (2013). MEG source localization using
invariance of noise space. PLoS One, 8(3), e58408.
Neural Mass Models

O David, Universite Joseph Fourier, Grenoble, France
Introduction
Organization of Cortical Microcircuits
The neocortex is commonly described as a six-layered structure
(DeFelipe, Alonso-Nanclares, & Arellano, 2002). Spiny neurons (pyramidal cells and spiny stellate cells) and smooth
neurons are the two major groups of cortical neurons. The
majority of cortical neurons are pyramidal cells that are
found in layers 26. Most spiny stellate cells are interneurons
that are located in the middle cortical layers. Smooth neurons
are essentially GABAergic interneurons distributed in all layers.
In general, cortical neurons are organized into multiple, small
repeating microcircuits. In spite of cortical heterogeneity, a
common basic microcircuit has emerged. Its skeleton is formed
by a pyramidal cell, which receives excitatory inputs that originate from extrinsic afferent systems and spiny cells. Inhibitory
inputs originate mostly from GABAergic interneurons. These
microanatomical characteristics have been found in all cortical
areas and species examined so far, and, therefore, they can be
considered as fundamental aspects of cortical organization
(DeFelipe et al., 2002). These basic microcircuits are commonly referred to as cortical minicolumns (50 mm diameter,
containing about 400 principal cells), which themselves
grouped into cortical macrocolumns (900 mm diameter)
(Jones, 2000). Eventually, a cortical area (12 cm diameter)
is composed of several cortical macrocolumns.
Magnetoencephalographic/Electroencephalographic Signals
Magnetoencephalographic/electroencephalographic
(MEG/
EEG) signals result mainly from primary intracellular (MEG)
and extracellular (EEG) current flow, created by massively
summed postsynaptic potentials in synchronously activated
and vertically oriented neurons, which constitute the dendritic
activity of macrocolumns of pyramidal cells. Spontaneous
MEG/EEG activity is often decomposed into distinct frequency
bands (e.g., delta, 14 Hz; theta, 48 Hz; alpha, 812 Hz; beta,
1230 Hz; and gamma, 3070 Hz; Nunez & Srinivasan, 2005),
which are robust correlates of subjects states and can be readily
used, for example, to define sleep stages. The exact neurophysiological mechanisms, which constrain this synchronization to a
given frequency band, have remained obscure. It is clear though
that the generation of oscillations appears to depend on interactions between large populations of inhibitory and excitatory
neurons, whose kinetics determine their oscillation frequency
(David & Friston, 2003). Event-related fields (ERFs) and potentials (ERPs) are obtained by averaging MEG and EEG signals in
relation to some transient stimulus or task (Coles & Rugg, 1995;
DeFelipe et al., 2002). They have been used for decades as
putative electrophysiological correlates of perceptual and cognitive operations because they last often less than a few seconds
and are correlated with stimulus changes or cognitive set. However, like MEG/EEG oscillations, the exact neurobiological
mechanisms underlying their generation have remained largely

unknown for decades. Understanding the neuronal biophysics
of MEG/EEG signals and predicting oscillatory patterns that
could emerge from large-scale neuronal networks have been
the main motivation for the development of neural mass
models in the 1970s (DeFelipe et al., 2002; Wilson & Cowan,
1972). Advances in computational modeling initiated a revival
of those models in the 2000s that has not diminished since.
Neural Mass Models and the Mean Field Approximation

There are several ways to model neural signals. One may want
to model as best as possible the neurophysiology of the system
by taking into account every process. Though it is very interesting for the biological plausibility of those models, this
approach may lead to the study of very complex systems, in
which many processes interact on different timescales so that it
is difficult to determine the exact influence of each model
parameter. The other possibility is to adopt a simplified
approach, in which realism is sacrificed for a more parsimonious description of key mechanisms. Because the complexity of
neural networks generating MEG/EEG signals is considerable
(DeFelipe et al., 2002; Jones, 2000; Thomson & Deuchars,
1997), the second option is usually more viable, particularly
if model parameters are estimated from experimental data.
This involves modeling neuronal activity with simplifying
assumptions and empirical priors to emulate realistic signals.
Neural mass models are based upon this approach (David &
Friston, 2003; Freeman, 1978; Lopes da Silva, 1974; Nunez &
Srinivasan, 2005; Robinson et al., 2001; Stam et al., 1999;
Valdes et al., 1999; van Rotterdam et al., 1982; Wendling
et al., 2000). These models usually comprise cortical macrocolumns, which can be thought of as cortical areas, and, sometimes, thalamic nuclei. They use only one or two state variables
to represent the mean activity of a whole neuronal population.
These states summarize the behavior of thousands of interacting neurons. This procedure, sometimes referred to loosely as a
mean field approximation (MFA; Figure 1), is very efficient for
determining the steady-state behavior of neuronal systems. Its
utility in a dynamic or nonstationary context is less established
because neural mass models are unable to say anything about
more complex behaviors within a single population, such as
phase-locked states (away from synchrony) or transient clustering (Coombes, 2010; David & Friston, 2003; Deco et al.,
2008; Haskell, Nykamp, & Tranchina, 2001).
Structure of a Neural Mass Model

Neural mass models usually describe the activity of a neuronal
population by its mean membrane potential (Figure 2). The
population receives an input in terms of the mean firing rate of
all afferent axons. This input and the membrane potential of
the population are causally related to each other by synaptic
http://dx.doi.org/10.1016/B978-0-12-397025-1.00333-X
563
564
INTRODUCTION TO METHODS AND MODELING | Neural Mass Models
u1
u1
v1
0
u2
u2
v1
w1
v2
0
w2 v2
MFA
0
w
u, v
un
un
vn
1
0
wn
vn
Figure 1 Mean field approximation (MFA). The left-hand side illustrates a neuronal population composed n neurons. vi, mi, and wi denote the membrane
potential, the normalized firing rate, and the firing threshold of the ith neuron, respectively. The output relations in the graphs show that, in this
example, the neurons fire at 1 or do not fire (0), depending on the threshold of firing, which may exhibit some variation between neurons. On the righthand side, the MFA of the neural mass models stipulates that the dynamics of that neuronal ensemble, or neuronal mass, is sufficiently described by the
mean of the state variables (v and m), using the mean relationship between v and m (the step function is transformed into a sigmoid function by the
averaging). Thus, the effect of the MFA, which is practically very important as n is on the order of a million, is that it reduces a huge system (3*n variables:
wi, vi, mi, i [1,. . .,n]) into a small one (4 variables: w, r, m, and v). The drawback of this approach is that the reconstructed dynamics might not be
accurate, in part because the information about the synchronization among neurons is lost by the averaging step. Adapted with permission from David, O.,
Harrison, L., & Friston, K. (2007). Neuronal models of EEG and MEG. In K. Friston et al. (Eds.), Statistical parametric mapping: The analysis of
functional brain images (pp. 414440). London, Academic Press.
Mean
membrane
potential
Mean
firing
rate
Input
synapses
Mean
firing
rate
Axons
Dendrites
and somas
Figure 2 In neural mass models, a neuronal population is usually
described by its mean membrane potential, which receives incoming
inputs (mean firing rate of all afferent axons) and sends output
signals (mean firing rate of the neurons belonging to the population).
Adapted with permission from David, O., Harrison, L., & Friston, K.
(2007). Neuronal models of EEG and MEG. In K. Friston et al. (Eds.),
Statistical parametric mapping: The analysis of functional brain images
(pp. 414440). London, Academic Press.
responses that are modeled with an input conversion operator,

usually a linear low-pass filter. The shape of the implicit convolution kernel embodies the synaptic and dendritic kinetics
belonging to that population. The output of the neuronal
population is modeled as the mean firing rate of the neurons
belonging to the population. It is generally assumed that the
mean firing rate is an instantaneous nonlinear function (often
a sigmoid as in Figure 1) of the mean membrane potential.
Depending upon the level of integration of the model, the
functional unit of interest represented by a neural mass model
can be any elementary neuronal circuit (cortical minicolumn,

macrocolumn, or area). For example, if one is interested in
cognitive neuroscience using noninvasive measurements, the
highest level of integration may be preferred, and therefore, an
adequate neural mass model should be able to reflect the
activity of a whole cortical area. Neural mass models thus
connect together several neuronal populations to constitute a
functional unit. Several functional units can also be coupled
together to model large-scale integration.
Applications of Neural Mass Models

Neural mass models of MEG/EEG were first used to study alpha
rhythms (Jansen & Rit, 1995; Lopes da Silva, 1974; Stam et al.,
1999; van Rotterdam et al., 1982). More recent studies have
shown that it is possible to reproduce the whole spectrum of
MEG/EEG oscillations, using appropriate values of model
parameters within a physiological range (David & Friston,
2003; Robinson et al., 2001). In addition, these models have
been used to test specific hypotheses about brain processes, for
example, resonance phenomena (Spiegler et al., 2011), habituation (Laxminarayan et al., 2012), aging (Pons et al., 2010),
focal attention (Suffczynski et al., 2001), and vision (Nguyen
Trong, Bojak, & Knosche, 2012). Pathological activity such as
epilepsy can also be emulated. In principle, this means that
generative models such as neural mass models could be used to
characterize the pathophysiological mechanisms underlying
seizure activity (Blenkinsop et al., 2012; Robinson, Rennie, &
Rowe, 2002; Wendling et al., 2002, 2012).
a bifurcation analysis (Spiegler et al., 2010), and it has been

extended to reproduce various induced and evoked responses
(David, Kilner, & Friston, 2006) and epileptic signals (Wendling
et al., 2002). We develop in the succeeding text the equations of
the model used in David et al. (2005).
Event-related activity can also be modeled using transient

inputs (David, Harrison, & Friston, 2005; David, Kilner, & Friston, 2006; Jansen & Rit, 1995; Rennie, Robinson, & Wright,
2002; Suffczynski et al., 2001). An early attempt, in the context
of visual ERPs, showed that it was possible to emulate ERP-like
damped oscillations (Jansen & Rit, 1995). A more sophisticated
thalamocortical model has been used to simulate event-related
synchronization and event-related desynchronization, commonly found in the alpha band (Suffczynski et al., 2001). An
extended discussion on how neural mass models can be used to
decipher mechanisms of induced and evoked has also been
proposed in David, Kiebel, et al. (2006). In this work, the authors
distinguished dynamic causes (changes of neuronal input) from
structural causes (changes of model parameters) of the observed
dynamics because they have different actions on the phase reset
of oscillations in response to a stimulus. Importantly, it has been
shown that model parameters can be adjusted to fit real ERPs
using thalamocortical models (Rennie et al., 2002) or corticocortical models (David, Kiebel, et al., 2006).
To sum up, neural mass models offer a unified view on
MEG/EEG oscillations and event-related activity. As an illustration, we describe in the succeeding text the model we have
been using to develop dynamic causal modeling for ERP
(David, Kiebel, et al., 2006). This is just a model among others
as there is no unique way to capture the full complexity of
brain networks with simple models.
Model of a Neuronal Population

The Jansen and Rit model specifies the evolution of the dynamics of a neuronal population using two operators (Figure 3):
The first transforms u, the average density of presynaptic input
arriving at the population, into v, the average postsynaptic
membrane potential (PSP). This is modeled by the linear
transformation
v hu
The kernel h is parameterized by H and t modeling specific

properties of synapses. The parameter H tunes the maximum
amplitude of PSPs, and t is a lumped representation of the sum
of the rate constants of passive membrane and other spatially
distributed delays in the dendritic tree. Equations [1] and [2]
are mathematically equivalent to the following state equations:
H
2
1
x_ u x 2 v
t
t
t
v_ x
The Jansen and Rit model was initially developed to model

alpha rhythms within a cortical minicolumn of the visual cortex
(Jansen & Rit, 1995). It has been extensively characterized using
Input
synapses
h(t) =
h
t0
t<0
uo
Axons
Dendrites
and somas
t
t
H exp
t
t
uo = S(v)
S(v) =
2e0
1 + exp( rv)
e0
uo
0
0
[3]
Let us consider that u is an external input to the neuronal

population with a known time course u(t). Then, it is possible
v = h ui
[1]
where denotes the convolution operator in the time domain

and h is the impulse response or first-order kernel:
(
t
t
H
exp

t0
h t
[2]
t
t
0
t<0
A Neural Mass Model of a Cortical Area
ui
565
Figure 3 Model of a neuronal population that rests on two operators: the first transforms ui, the average density of presynaptic input arriving at the
population, into v, the average postsynaptic membrane potential (PSP). This is modeled by a linear transformation. The kernel h is parameterized by
H and t modeling specific properties of synapses. The parameter H tunes the maximum amplitude of PSPs and t is a lumped representation of the sum
of the rate constants of passive membrane and other spatially distributed delays in the dendritic tree. The second operator transforms the average
membrane potential of the population into an average rate of action potentials fired by the neurons. This transformation is assumed to be instantaneous
and is described by a sigmoid function parameterized with e0 and r. Adapted with permission from David, O., Harrison, L., & Friston, K. (2007).
Neuronal models of EEG and MEG. In K. Friston et al. (Eds.), Statistical parametric mapping: The analysis of functional brain images (pp. 414440).
London, Academic Press.
566
to obtain the time course of the membrane potential v(t) by

integrating the differential equations eqn [3].
The second operator transforms the average membrane
potential of the population into an average rate of action
potentials fired by the neurons. This transformation is assumed
to be instantaneous and is described by the sigmoid function
Sv
2e0
e0
1 exprv
[4]
where e0 and r are parameters that determine its shape (e.g.,

voltage sensitivity). It is this function that endows the simulation with nonlinear behaviors that are critical for phenomena
like phase resetting of the EEG/MEG (David et al., 2005). Note
that the expression of S in eqn [4], which is different from the
original version of (Jansen & Rit, 1995), implicitly specifies
that the resting state for the mean membrane potential v and
the mean firing rate u S(v) is zero. This means that we are
looking at variations of v around a given resting value, which is
negative (tens of mV) but unknown. In other words, every
modeled signal is to be considered as small perturbations
around the resting potential. Therefore, all the variables in
the following equations are zero mean, centered on the resting
state we assumed to be zero.
Model of a Cortical Area

A cortical area, understood here as an ensemble of strongly
interacting macrocolumns, is modeled by a population of excitatory pyramidal cells, receiving (i) inhibitory and excitatory
feedback from local (i.e., intrinsic) interneurons and (ii) excitatory input from neighboring or remote (i.e., extrinsic) areas. It
is composed of three subpopulations (Figure 4): a population
of excitatory pyramidal (output) cells receives inputs from

inhibitory and excitatory populations of interneurons, via
intrinsic connections (intrinsic connections are confined to the
cortical sheet). Within this model, excitatory interneurons can
be regarded as spiny stellate cells found predominantly in layer
4 and in receipt of forward connections (Miller, 2003). Excitatory pyramidal cells and inhibitory interneurons will be considered to occupy agranular layers and receive backward and
lateral inputs. Interactions, among the different subpopulations,
depend on the constants gi, which control the strength of intrinsic connections and the total number of synapses expressed by
each subpopulation. The state equation describing the activity of
one cortical area can be summarized as
x_ f x, u, y
where the function f represents the differential equations

shown in Figure 4, x are the states of the system, u are the
extrinsic inputs, and y are the various parameters of the model.
The MEG/EEG signal is assumed to be modeled by the
average depolarization of pyramidal cells (x0(t) in Figure 4).
For the sake of simplicity, here, we ignore the observation
equation, that is, how x0(t) is measured. This includes not
only the effects of amplifiers (which are an additional bandpass filter) but also the MEG/EEG lead fields that indicate the
spatial distribution of the electromagnetic field in the head
using Maxwells equations and suitable head models (Baillet,
Mosher, & Leahy, 2001). For given synaptic responses h and
sigmoid functions S, the model of Figure 4 can produce a large
variety of MEG/EEG-like waveforms (physiological and
epileptic-like spontaneous activity) when extrinsic inputs u
are random processes or event-related activity like ERP/ERF
when extrinsic inputs contain fast transients (Figure 5).
C1
x7 = x8
.
H
2x
x
x8 = e (g3S(x0)+ c1u) 8 72
te
te te
Inhibitory
interneurons
Spiny
stellate
cells
g4
g3
.
x1 = x4
2x
x
.
H
x4 = e (g 1S(x0)+ c2u) 4 12
te
te te
g 1 Intrinsic
connections
C2
Extrinsic
connections
u
g2
Pyramidal
cells
[5]
x0 = x5 x6
C3
x2 = x5
.
x
H
2x
x5 = e (g 2S(x1)+ c3u) 5 22
te te
te
.
x3 = x6
2x x
.
H
x6 = i (g 4S(x7) 6 32
ti
ti
ti
Figure 4 State space representation of the Jansen and Rit model of a cortical area. Three neuronal subpopulations are considered to model a cortical
area. Pyramidal cells interact with both excitatory and inhibitory interneurons with the connectivity constants g2 0.8g1, g3 g4 0.25g1. The
parameters He,i and te,i control the expression of postsynaptic potentials as shown in equation. Subscripts e and i denote excitatory and inhibitory,
respectively. Adapted with permission from David, O., Harrison, L., & Friston, K. (2007). Neuronal models of EEG and MEG. In K. Friston et al. (Eds.),
Statistical parametric mapping: The analysis of functional brain images (pp. 414440). London, Academic Press.
Inhibitory
interneurons
567
4
2
Spiny
stellate
cells
0
2
Pyramidal
cells
Inhibitory
interneurons
Spiny
stellate
cells
Pyramidal
cells
100
200
300
400
500
600
Time (ms)
700
800
900
1000
100
200
300
400
500
600
Time (ms)
700
800
900
1000
6
4
2
0
Figure 5 Effect of the shape of extrinsic inputs u on the dynamic of a cortical area (Figure 4). Top: MEG/EEG-like oscillations are obtained when u is
stochastic (Gaussian in this simulation). Bottom: ERP/ERF-like waveforms are obtained when u contains a fast transient (a delta function in this
simulation). This simulation used the model described in Figure 4, with extrinsic inputs entering on spiny stellate cells only, with the following
parameters: He 3.25, Hi 29.3, te 10 ms, ti 15 ms, d d(ij) 10 ms, g1 50, g2 40, g3 g4 12, e0 2.5, v0 0, r 0.56. Adapted
with permission from David, O., Harrison, L., & Friston, K. (2007). Neuronal models of EEG and MEG. In K. Friston et al. (Eds.), Statistical parametric
mapping: The analysis of functional brain images (pp. 414440). London, Academic Press.
Model of Two Coupled Cortical Areas

Neurophysiological studies have shown that cortical outputs to
distant targets are exclusively excitatory. Moreover, experimental evidence suggests that MEG/EEG activity is generated by
strongly coupled but remote cortical areas (Buzsaki, Anastassiou, & Koch, 2012; Varela et al., 2001). Fortunately, modeling
excitatory coupling is straightforward using neural mass
models, and some consequences of excitatory to excitatory
coupling have been described already (Jansen & Rit, 1995;
Wendling et al., 2000). Here, we describe how the coupling
between two cortical areas, each one modeled as mentioned
earlier, is operationally defined. In addition, we illustrate what
are the effects of such coupling, both on MEG/EEG oscillations
and on ERP/ERF.
Coupling two cortical areas is performed by injecting the
activity of one cortical area into the extrinsic input of the other
area. The efferent activity is the mean firing of pyramidal cells
weighted by the connection strength (effective connectivity) a,
that is, aS(x0). The state equations of areas 1 and 2 can be
written as follows:

2
x_1 f x1 , a12 S x0 t d12 c1 u, y1

[6]
1
x_2 f x2 , a21 S x0 t d21 c2 u, y2
where x(1) and x(2) are the states of areas 1 and 2, a21 and a12 are
the effective connectivity from 1 to 2 and from 2 to 1, c1 and c2
are the extrinsic effective connectivity (weight of u) on areas 1
x02
c2u(t)
2
x2,q 2
a21S(x01(t d21))
a12S(x0(t d12))
1
c1u(t)
x1,q 1
x10
Figure 6 Graphical representation of the connection between two

cortical areas. Coupling coefficient assembled into matrices A and C
tunes the coupling strength (see main text). Adapted with permission
from David, O., Harrison, L., & Friston, K. (2007). Neuronal models of
EEG and MEG. In K. Friston et al. (Eds.), Statistical parametric mapping:
The analysis of functional brain images (pp. 414440). London,
Academic Press.
and 2, y(1) and y(2) are the neuronal parameters of areas 1 and
2, and d(12) and d(21) are the propagation delay from 2 to 1 and
from 1 to 2 (Figure 6). In matrix form and ignoring the
propagation delays for simplicity, eqn [6] is equivalent to
x_ f x, ASx0 Cu,y
[7]
with
"
#

1

1
0 a12
c
x0
x1
x 2 , x0 2 , y y2 , A
, C 1
a
0
c2
x
y
21
x0
568
1
c1
a21
c1
c2
a12
0.6
0.4
0.2
0
0.2
0.4
a12 = 0; a21 = 0
a21
a12
a12 = 0; a21 = 0
6
4
2
0
1.5
1
0.5
0
0.5
1
1.5
a12 = 15; a21 = 40
a12 = 0; a21 = 60
6
4
2
0
2
200 400 600 800 1000 1200 1400 1600 1800 2000
Time (ms)
100 200 300 400 500 600 700 800 900 1000
Time (ms)
Figure 7 Relationships between effective connectivity (coupling parameters) and functional connectivity (observed correlations between signals). The
model is composed of two areas, asymmetrically coupled. Left: Ongoing activity was simulated using a different stochastic input entering on each area,
which generated synchronous oscillations when increasing neuronal coupling between cortical areas. Right: A fast transient (delta function) was
assumed to occur at the extrinsic input of area 1. When areas are not coupled (left-hand side), the evoked response does not propagate to area 2,
whereas one can observe a late activity in area 2 because of a coupling from area 1 towards area 2 on the right-hand side. Adapted with permission from
David, O., Harrison, L., & Friston, K. (2007). Neuronal models of EEG and MEG. In K. Friston et al. (Eds.), Statistical parametric mapping: The analysis of
functional brain images (pp. 414440). London, Academic Press.
In other words, coupling is specified using connectivity

matrices. In this simple model, there are two of them: the
matrix A that specifies the connectivity between cortical areas
and the matrix C that specifies where other extrinsic inputs,
such as stimuli, enter in the model.
The coupling between areas in a neuronal model is the
effective connectivity, that is, the influence of one system on
the other (Friston, Moran, & Seth, 2013). Using a model composed of two areas, it is easy to look at the effect of effective
connectivity on functional connectivity, that is, the correlation
between generated signals. To this end, a simulation was performed with the same parameters as in Figure 5. The connections between areas were asymmetrical (forward from 1 to 2 and
backward from 2 to 1; see David et al., 2005). Extrinsic inputs u
were applied to spiny stellate cells only. A propagation delay of
10 ms between areas has been assumed. The left-hand side of
Figure 7 shows that synchronous oscillations appear when
increasing neuronal coupling between cortical areas. Thus, neuronal coupling and synchrony of the EEG/MEG signals (Varela
et al., 2001) can be tightly related to each other. The right-hand
side of Figure 7 shows that coupling between areas ensures the
propagation of neuronal transients such as ERP/ERF. The important point here is that changes in neuronal coupling are the
main cause of many features of event-related responses and
bridge between ERP/ERF research and the study of induced
and ongoing EEG/MEG activity (David, Kilner, & Friston, 2006).
Conclusion
Neural mass models afford a straightforward approach to
modeling the activity of populations of neurons. Their main
assumption is that the state of a neuronal population can be

approximated using very few state variables (generally limited
to mean membrane currents, potentials, and firing rates).
Given a macroscopic architecture, describing the overall connectivity (i) between populations of a given cortical area and
(ii) between different cortical areas, it is possible to simulate
the steady-state dynamics of the system or even the transient
response to a perturbation of extrinsic input or connectivity.
Consequently, neural mass models are useful to describe and
predict the macroscopic electrical activity of the brain. Since
the early 1970s, they have been used to study electrophysiological processes. More recently, they have been introduced
into neuroimaging to understand the underlying neuronal
mechanisms of fMRI and PET data (Almeida & Stetter, 2002;
Friston & Dolan, 2010; Horwitz & Tagamets, 1999; Riera et al.,
2006; Sotero & Trujillo-Barreto, 2008; Valdes-Sosa et al., 2009;
Voges et al., 2012).
Despite their relative simplicity, neural mass models can
reproduce a large variety of MEG/EEG signals and can exhibit
complex dynamic behavior reminiscent of actual large-scale
brain networks. Biological plausibility can even be improved
using mean field models, which account for the dispersion of
activity within each neuronal population but at the expense of
computational burden (Bojak & Liley, 2010; Coombes, 2010;
Deco et al., 2008; Friston & Dolan, 2010; Pinotsis & Friston,
2011). The potential advantage neural mass models afford, in
comparison to standard data analysis, is their ability to pinpoint specific neuronal mechanisms underlying normal or
pathological activity. Effort is needed to incorporate them,
more systematically, in MEG/EEG analyses to enable inquiry
into mechanistic questions about macroscopic neuronal processes. Importantly, several groups have demonstrated that the

parameters of neural mass models can be estimated from
recorded data (Babajani-Feremi & Soltanian-Zadeh, 2011;
David, Kiebel, et al., 2006; Moran et al., 2008; Valdes et al.,
1999). This is a critical step to prove the face validity of neural
mass models.

Magnetoencephalography; INTRODUCTION TO ANATOMY AND
PHYSIOLOGY: Cell Types in the Cerebral Cortex: An Overview from
the Rat Vibrissal Cortex; Columns of the Mammalian Cortex; Cortical
GABAergic Neurons; Cytoarchitectonics, Receptorarchitectonics, and
Network Topology of Language; Cytoarchitecture and Maps of the
Human Cerebral Cortex; Functional and Structural Diversity of
Pyramidal Cells; Functional Connectivity; Synaptic Organization of the
Cerebral Cortex; Transmitter Receptor Distribution in the Human Brain;
Von Economo Neurons; INTRODUCTION TO METHODS AND
MODELING: Distributed Bayesian Inversion of MEG/EEG Models;
Dynamic Causal Models for fMRI; Dynamic Causal Models for Human
Electrophysiology: EEG, MEG, and LFPs; Effective Connectivity;
Forward Models for EEG/MEG; Graph-Theoretical Analysis of Brain
Networks; Methodological Issues in fMRI Functional Connectivity and
Network Analysis; Models of fMRI Signal Changes; Resting-State
Functional Connectivity; The Emergence of Spontaneous and Evoked
Functional Connectivity in a Large-Scale Model of the Brain.
References
Almeida, R., & Stetter, M. (2002). Modeling the link between functional imaging and
neuronal activity: Synaptic metabolic demand and spike rates. NeuroImage, 17(2),
10651079.
Babajani-Feremi, A., & Soltanian-Zadeh, H. (2011). Development of a variational
scheme for model inversion of multi-area model of brain. Part I: Simulation
evaluation. Mathematical Biosciences, 229(1), 6475.
Baillet, S., Mosher, J., & Leahy, R. (2001). Electromagnetic brain mapping. IEEE Signal
Processing Magazine, 18(6), 1430.
Blenkinsop, A., et al. (2012). The dynamic evolution of focal-onset epilepsies
Combining theoretical and clinical observations. European Journal of Neuroscience,
36(2), 21882200.
Bojak, I., & Liley, D. T. J. (2010). Axonal velocity distributions in neural field equations.
PLoS Computational Biology, 6(1), e1000653.
Buzsaki, G., Anastassiou, C. A., & Koch, C. (2012). The origin of extracellular fields and
currents EEG, ECoG, LFP and spikes. Nature Reviews Neuroscience, 13(6), 407420.
Coles, M. G. H., & Rugg, M. D. (1995). Event-related brain potentials: An introduction.
In Electrophysiology of mind (pp. 126). Oxford: Oxford University Press.
Coombes, S. (2010). Large-scale neural dynamics: Simple and complex. NeuroImage,
52(3), 731739.
David, O., & Friston, K. J. (2003). A neural mass model for MEG/EEG: Coupling and
neuronal dynamics. NeuroImage, 20(3), 17431755.
David, O., Harrison, L., & Friston, K. J. (2005). Modelling event-related responses in
the brain. NeuroImage, 25(3), 756770.
David, O., Kiebel, S. J., et al. (2006). Dynamic causal modeling of evoked responses in
EEG and MEG. NeuroImage, 30(4), 12551272.
David, O., Kilner, J. M., & Friston, K. J. (2006). Mechanisms of evoked and induced
responses in MEG/EEG. NeuroImage, 31(4), 15801591.
Deco, G., et al. (2008). The dynamic brain: From spiking neurons to neural masses and
cortical fields. PLoS Computational Biology, 4(8), e1000092.
DeFelipe, J., Alonso-Nanclares, L., & Arellano, J. I. (2002). Microstructure of the
neocortex: Comparative aspects. Journal of Neurocytology, 31(35), 299316.
Freeman, W. J. (1978). Models of the dynamics of neural populations.
Electroencephalography and Clinical Neurophysiology, 34(Suppl.), 918.
Friston, K. J., & Dolan, R. J. (2010). Computational and dynamic models in
569
Friston, K., Moran, R., & Seth, A. K. (2013). Analysing connectivity with Granger
causality and dynamic causal modelling. Current Opinion in Neurobiology, 23(2),
172178.
Haskell, E., Nykamp, D. Q., & Tranchina, D. (2001). Population density methods for
large-scale modelling of neuronal networks with realistic synaptic kinetics:
Cutting the dimension down to size. Network (Bristol, England), 12(2),
141174.
Horwitz, B., & Tagamets, M.-A. (1999). Predicting human functional maps with neural
net modeling. Human Brain Mapping, 8(23), 137142.
Jansen, B. H., & Rit, V. G. (1995). Electroencephalogram and visual evoked potential
generation in a mathematical model of coupled cortical columns. Biological
Cybernetics, 73(4), 357366.
Jones, E. G. (2000). Microcolumns in the cerebral cortex. Proceedings of the
National Academy of Sciences of the United States of America, 97(10),
50195021.
Laxminarayan, S., et al. (2012). Modeling habituation in rat EEG-evoked responses via a
neural mass model with feedback. Biological Cybernetics, 105(56), 371397.
Lopes da Silva, F. H. (1974). Model of brain rhythmic activity. The alpha-rhythm of the
thalamus. Kybernetik, 15(1), 2737.
Miller, K. D. (2003). Understanding layer 4 of the cortical circuit: A model based on cat
V1. Cerebral Cortex (New York, NY: 1991), 13(1), 7382.
Moran, R. J., et al. (2008). Bayesian estimation of synaptic physiology from the spectral
responses of neural masses. NeuroImage, 42(1), 272284.
Nguyen Trong, M., Bojak, I., & Knosche, T. R. (2012). Associating spontaneous with
evoked activity in a neural mass model of visual cortex. NeuroImage, 66C, 8087.
Nunez, P. L., & Srinivasan, R. (2005). Electric fields of the brain. New York: Oxford
University Press.
Pinotsis, D. A., & Friston, K. J. (2011). Neural fields, spectral responses and lateral
connections. NeuroImage, 55(1), 3948.
Pons, A. J., et al. (2010). Relating structural and functional anomalous connectivity in
the aging brain via neural mass modeling. NeuroImage, 52(3), 848861.
Rennie, C. J., Robinson, P. A., & Wright, J. J. (2002). Unified neurophysical model of
EEG spectra and evoked potentials. Biological Cybernetics, 86(6), 457471.
Riera, J. J., et al. (2006). Nonlinear local electrovascular coupling. I: A theoretical
model. Human Brain Mapping, 27(11), 896914.
Robinson, P., Rennie, C., & Rowe, D. (2002). Dynamics of large-scale brain activity in
normal arousal states and epileptic seizures. Physical Review E, 65(4), 041924.
Robinson, P., et al. (2001). Prediction of electroencephalographic spectra from
neurophysiology. Physical Review E, 63(2), 021903.
Sotero, R. C., & Trujillo-Barreto, N. J. (2008). Biophysical model for integrating
neuronal activity, EEG, fMRI and metabolism. NeuroImage, 39(1), 290309.
Spiegler, A., et al. (2010). Bifurcation analysis of neural mass models: Impact of
extrinsic inputs and dendritic time constants. NeuroImage, 52(3), 10411058.
Spiegler, A., et al. (2011). Modeling brain resonance phenomena using a neural mass
model. PLoS Computational Biology, 7(12), e1002298.
Stam, C. J., et al. (1999). Dynamics of the human alpha rhythm: Evidence for nonlinearity? Clinical Neurophysiology, 110(10), 18011813.
Suffczynski, P., et al. (2001). Computational model of thalamo-cortical networks:
Dynamical control of alpha rhythms in relation to focal attention. International
Journal of Psychophysiology, 43(1), 2540.
Thomson, A. M., & Deuchars, J. (1997). Synaptic interactions in neocortical local
circuits: Dual intracellular recordings in vitro. Cerebral Cortex (New York, NY:
1991), 7(6), 510522.
Valdes, P. A., et al. (1999). Nonlinear EEG analysis based on a neural mass model.
Biological Cybernetics, 81(56), 415424.
Valdes-Sosa, P. A., et al. (2009). Model driven EEG/fMRI fusion of brain oscillations.
van Rotterdam, A., et al. (1982). A model of the spatialtemporal characteristics of the
alpha rhythm. Bulletin of Mathematical Biology, 44(2), 283305.
Varela, F., et al. (2001). The brainweb: Phase synchronization and large-scale
integration. Nature Reviews Neuroscience, 2(4), 229239.
Voges, N., et al. (2012). Modeling of the neurovascular coupling in epileptic discharges.
Brain Topography, 25(2), 136156.
Wendling, F., et al. (2000). Relevance of nonlinear lumped-parameter models in the
analysis of depth-EEG epileptic signals. Biological Cybernetics, 83(4),
367378.
Wendling, F., et al. (2002). Epileptic fast activity can be explained by a model of
impaired GABAergic dendritic inhibition. The European Journal of Neuroscience,
15(9), 14991508.
Wendling, F., et al. (2012). Interictal spikes, fast ripples and seizures in partial
epilepsies Combining multi-level computational models with experimental data.
European Journal of Neuroscience, 36(2), 21642177.
Wilson, H. R., & Cowan, J. D. (1972). Excitatory and Inhibitory interactions in localized
populations of model neurons. Biophysical Journal, 12(1), 124.
The Emergence of Spontaneous and Evoked Functional Connectivity

in a Large-Scale Model of the Brain
A Ponce-Alvarez and G Deco, Universitat Pompeu Fabra, Barcelona, Spain
Glossary
Bifurcation A change in the qualitative behavior of a

dynamic system under the change of one or more
parameters of the system, called bifurcation parameters.
Parameter values at which the bifurcation occurs are called
critical or bifurcation values.
Bifurcation diagram A diagram showing the fixed points of a
dynamic system, as a function of the bifurcation parameters.
BOLD signal The blood oxygen level-dependent (BOLD)
signal is the image contrast obtained using fMRI resulting from
changes in blood flow. How the neural activity is related to the
BOLD signal is modeled by the hemodynamic model.
Conjugate transpose The conjugate transpose of a given
matrix A is a matrix A* obtained by first taking the transpose
of A and then tacking the complex conjugate of each
element.
Diffusion imaging The diffusion-weighted magnetic
resonance (MR) imaging technique allows mapping the
restricted diffusion of water through myelinated nerve fibers
in the brain. The combination of this technique and fiber
tractography is used to estimate the anatomical connectivity
between brain areas, that is, the density of fibers connecting
two given brain regions.
Effective connectivity How different cortical areas influence
each other, even in the absence of direct connection between
them. The effective connectivity is known to be dynamic and
dependent on the context or the previous brain activity, due
to synaptic plasticity, neuromodulation, or even the
interplay between excitation and inhibition.
Eigenvectors/eigenvalues An eigenvector v of a matrix A is a
nonzero vector that satisfies Av lv, where the scalar l is the
associated eigenvalue.
Fiber tractography A rendering method for reconstructing
the fiber tracts from diffusion-imaging data. Tractography
tracks the maximum orientation of diffusion, from voxel to
voxel. The paths obtained by following the local diffusion
maxima are assumed to represent nerve fibers.
Fisher information A measure that quantifies the encoding
accuracy of the network response, that is, how well the
network encodes a variation of an input. For a multivariate
Gaussian distribution, the Fisher information (FI) can be
written as the sum of two terms: FI FImean FIcov, given by
1 0
FImean f0 (y)TQ(y)
0 f (y) and 2
=2, where f(y) and Cv(y)
FIcov y Trace Cv yCv y1
are the networks mean response and covariance matrix
evoked by the input y, respectively; f(y) and Cv(y) are the
first derivatives with respect to the input. FImean and FIcov
represent the contribution to the FI of the mean response
and the covariance, respectively.
Functional connectivity The statistical relation between
activities in two or more neural sources. Functional
connectivity (FC) usually refers to the temporal correlation

between sources but has been extended to include
correlations across trials or different subjects. Standard FC
measures include correlations, coherence, and phase
synchrony.
Hemodynamic model It describes the coupling of neuronal
activity and observed BOLD signals with a dynamic model
of the transduction of neural activity to perfusion changes.
The dynamic model uses the BalloonWindkessel model to
transform the perfusion into an observed BOLD signal,
through a model of blood flow and deoxyhemoglobin
content dynamics. This provides a complete dynamic model
of neurovascular coupling.
Jacobian matrix It is given by the first-order partial
derivative of the nonlinear function f with respect to each
variable, evaluated at an equilibrium point x*: Jij @fi/@xj.
Note that the Jacobian matrix depends on the point x* at
which it is evaluated.
Linear stability (theorem) An equilibrium point x* of the
nonlinear dynamic system x_ f x is stable if all the
eigenvalues of J, the Jacobian matrix evaluated at x*,
have negative real parts. The equilibrium point is
unstable if at least one of the eigenvalues has a positive
real part.
Linearized system Let x_ f x be a nonlinear dynamic
system. Near any point x*, the system can be linearized by
considering the small variations around x*, that is,
x x* dx. As a result, the dynamics governing dx are linear
and given by dx_ Jdx, where J is the Jacobian matrix of the
system, evaluated at x*.
Mean-field approximation The mean-field approximation
ignores the interaction between single neurons within the
network and instead considers the ensemble dynamics
(ergodicity assumption).
Resting-state activity The intrinsic activity of the brain in
the absence of stimuli, movements, or task. It is also called
spontaneous or ongoing activity. However, there is no
clear consensus on which experimental protocol leads to a
better approximation of the genuine resting-state
condition. For this reason, experimental paradigms for
studying the resting condition are diverse, such as the awake
with either closed eyes or open/fixating eyes, light sleep in
humans, or under anesthesia in animals.
Spiking network A network in which individual neurons
(usually expressed by integrate-and-fire or HodgkinHuxley
models) interact with each other through different types of
dynamic synapse (e.g., AMPA, NMDA, or GABA) that react
to the incoming spikes to each neuron.
Transpose The transpose of a given matrix A is a matrix AT
such that (AT)ij (A)ji (rows of A become columns of AT, and
columns of A become rows of AT).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00334-1
571
572
INTRODUCTION TO METHODS AND MODELING | Spontaneous and Evoked Functional Connectivity Modeling of the Brain
Introduction: Spontaneous and Evoked Brain Activity

and Anatomical Connectivity
During the last decade, the spontaneous activity of the brain its
activity in the absence of sensory inputs and movement
production and its interplay with the external world, during
active cognition, have been revisited. In early works, spontaneous fluctuations have been often dismissed as background noise
and assumed to be sufficiently random for it to be averaged out
in statistical analyses. However, activation studies generally
compare task-related activity between conditions while trying
to control for differences in cognitive processing (or other attributes of brain states). This acknowledges that the experimental
control or baseline state is itself an active state. The notion that
baseline states are active has been subsequently endorsed by
neuroimaging and electrophysiological experiments. There are
several lines of evidence supporting this idea. First, early studies
reported systematic patterns of deactivation with increasing cognitive demands (Andreasen et al., 1995; Shulman et al., 1997).
Second, most of the brains energy consumption is used to
maintain the spontaneous metabolic activity (Raichle & Mintun,
2006). Third, the brain at rest displays spatial patterns of correlated activity across different brain areas known as resting-state
networks (RSNs; Biswal, Yetkin, Haughton, & Hyde, 1995;
Deco & Corbetta, 2011; Fox and Raichle, 2007; Fox et al.,
2005; Fransson, 2005; Greicius, Krasnow, Reiss, & Menon,
2003), and the spatial distribution of the RSNs resembles the
pattern of activation seen during cognitive tasks (Biswal et al.,
1995; Fox et al., 2005; Greicius et al., 2003), suggesting and
intrinsic link between spontaneous and evoked activity.
In the monkey, by combining fMRI and retrograde tracer
maps, Vincent et al. (2007) showed that correlated spontaneous blood oxygen level-dependent (BOLD) fluctuations closely
relate to those of task-evoked responses and anatomical connectivity. This suggests that RSNs arise from correlations of
neuronal noise between brain areas that are coupled by the
underlying anatomical connectivity. Nevertheless, how both
the spontaneous and evoked patterns relate to the anatomical
connectivity has remained an open question that has motivated several experimental and theoretical studies to understand structure/function relationships (Bullmore & Sporns,
2009; Cabral, Hugues, Sporns, & Deco, 2011; Deco and Jirsa,
2012; Deco, Jirsa, & McIntosh, 2011; Deco, Jirsa, McIntosh,
Sporns, & Kotter, 2009; Freyer et al., 2011; Ghosh, Rho,
McIntosh, Kotter, & Jirsa, 2008; Honey, Kotter, Breakspear, &
Sporns, 2007; Honey et al., 2009; Pernice, Staude, Cardanobile,
& Rotter, 2011; Robinson, 2012).
Neural Dynamics: The Missing Link

The spontaneous activity patterns of the brain are typically
characterized by the resting functional connectivity (FC) in
neuroimaging experiments. Theoretical models allow us to
investigate explicitly the link between FC and the underlying
anatomical connectivity (Figure 1(a)). Resting-state models are
constrained by the empirical anatomical matrix that expresses
the density of white matter fiber tracts connecting two given
brain areas. Here, we used a 66 66 cortical anatomical matrix,
obtained by averaging the tractography on diffusion-imaging
data of five healthy human subjects (Hagmann et al., 2008).

This anatomical architecture interconnects the different brain
areas or local nodes (Table 1), whose activities are governed
by neural dynamics. Different models for the local nodes have
been proposed, with different levels of details, such as simple
oscillators (Cabral et al., 2011; Daffertshofer & van Wijk, 2011;
Deco et al., 2009; Ghosh et al., 2008), chaotic dynamic systems
(Honey et al., 2007), and biophysically inspired canonical networks composed of excitatory and inhibitory spiking neurons
coupled through NMDA, AMPA, and GABA synapses (Deco &
Jirsa, 2012). The resulting anatomically constrained networks
are then simulated to generate a prediction of the FC. Since one
common conclusion of previous modeling studies is that the FC
is strongly dependent on the local dynamics and the global
dynamic state of the network, it is fundamental to describe the
local dynamics as realistically as possible. For this reason, we
concentrate here on the realistic large-scale model formulated by
Deco and Jirsa (2012) (Figure 1(b)). The canonical local network used in this model is known to reproduce the observed
asynchronous spontaneous state in vivo, in which spiking activity is irregular, weakly correlated, and comprised between 3 and
10 Hz (Burns & Webb, 1976; Koch & Fuster, 1989; Wilson,
Scalaidhe, & Goldman-Rakic, 1994). Combining both structure
and dynamics in the models, the next step is to find the region of
model parameters that leads to the best match between the
model predictions and the empirical data. Here, we used the
empirical FC, given by averaging the correlation matrices of
fMRI BOLD signals obtained from 24 healthy human subjects,
during resting-state conditions (Hlinka, Palus, Vejmelka,
Mantini, & Corbetta, 2011). To allow comparison between the
model and the empirical functional data, the model synaptic
activity was transformed to BOLD signals using the hemodynamic model (Friston, Harrison, & Penny, 2003).
The large-scale spiking model requires the solution of many
hundreds of thousands of coupled nonlinear differential equations corresponding to each single neuron and each single
synapse. This renders the model computationally very complex
and its numerical simulations very time-consuming. Thus,
there is a need for reducing the spiking model into an efficient
simplified model that, while keeping the realism of the dynamics, allows for analytic insights.
Reduced Brain Model: Dynamic Mean-Field

Approximation
The spiking model can be simplified by using a dynamic meanfield (DMF) technique (Wong & Wang, 2006) that approximates the average ensemble behavior, instead of considering
the detailed interactions between individual neurons. A succession of approximations is used to summarize the dynamics
(Wong & Wang, 2006). First, the inputoutput function of
inhibition can be linearized, eliminating its self-dependence.
Second, because the synaptic gating variable (i.e., the fraction
of open channels) of NMDA receptors has a much longer decay
time constant (100 ms) than AMPA (2 ms) and GABA (10 ms)
receptors, one can assume that the dynamics of the NMDA
gating variable dominates the time evolution of the system,
while the other synaptic variables instantaneously reach their
steady state. Finally, the effect of AMPA-mediated self-
DSI-tractography
Resting-state BOLD signals
573
excitation is absorbed in a constant input. This leads to a

system of N-coupled nonlinear differential equations, where
N is the number of brain areas considered (in our case N 66),
expressing the dynamics of NMDA gating variables:
dSi t
Si
1 Si Hxi i t
tS
dt
X
xi wKSi GK
Cij Sj I0
[1]
[2]
Structural
connectivity
Dynamical
model
Model
FC
Empirical FC
(a)
where Si denotes the average synaptic gating variable at the local

cortical area i, i is the uncorrelated Gaussian noise of amplitude
s, w is the local excitatory recurrence, Cij is the structural connectivity matrix expressing the neuroanatomical links between
the areas i and j, and K is a constant equal to 0.2609 (nA). The
factor G is a global scaling parameter that determines the
strength specified in the matrix C. The transfer function H is a
sigmoid function that converts the input synaptic activity xi into
an output population firing rate function. The timescale of the
dynamics is one of the NMDA synaptic receptors: tS 100 ms. I0
is the overall effective external input, which value was tuned, in
order to compensate the neglect of AMPA receptors, to obtain a
bifurcation diagram of the DMF model similar to the one
obtained for the spiking model (Figure 2).
The bifurcation diagrams characterizing the stationary
states of the brain system for both the spiking (Figure 2(a))
and the reduced DMF models (Figure 2(b)) are determined by
G, the control parameter that changes the network from weakly
to strongly connected. If the network nodes are weakly
interconnected, only one stable state exists, characterized by a
low firing activity in all cortical areas. For a critical value of G, a
first bifurcation occurs where new multistable states of high
activity coexist with the stable state of low activity. If large-scale
connections are sufficiently strong, a second bifurcation
appears where the state of low activity becomes unstable. In
the following, we examined how the network correlations
change with G and for which values of G the matching between
the model FC and the empirical FC is the highest.
Empirical FC Versus Model FC
GABA
(b)
NMDA
AMPA
AMPA
Figure 1 Linking anatomical connections and functional connectivity

(FC). (a) Neuroanatomical connectivity data were obtained by diffusion
imaging and tractography. Parcellation provides a connectivity matrix
C linking the N cortical areas cortical regions with clear anatomical
landmarks. A neurodynamic model was then constructed using a set of
stochastic differential equations coupled according to the connectivity
matrix C. To validate the model, the model FC was compared to the
empirical one. This framework enables us to study the link between
anatomical structure and resting-state dynamics. (b) The model for each
local brain area consists of one population of excitatory neurons and
one population of inhibitory neurons recurrently connected. Local
excitation is mediated by AMPA and NMDA synaptic receptors, largescale excitation is AMPA-mediated, and local inhibition is GABAmediated. Local parameters were such that, when isolated, the local
The predictions of the spiking model, the reduced DMF model,

and its linearized version were tested by calculating the agreement between the empirical FC and the FC of simulated BOLD
signals. As the control parameter G increases, the agreement
between the model and the empirical data increases, up to the
destabilization of the spontaneous state (Figure 3(a)). Indeed,
a common characteristic of all resting-state models is that the
optimal match between the models predictions and the empirical data is found for a parameter region near criticality, that
is, near a bifurcation. Interestingly, this is the case even for
different types of bifurcations, such as Hopf bifurcation,
network emulates the neurophysiological characteristics of the empirical
observed spontaneous state, that is, low correlations between the
spiking activity of the neurons and low firing rate. Panel (a): figure
modified from Deco, G., Ponce-Alvarez, A., Mantini, D., Romani, G.L.,
Hagmann, P., & Corbetta, M. (2013). Resting-state functional
connectivity emerges from structurally and dynamically shaped slow
linear fluctuations. Journal of Neuroscience, 33, 1123911252.
574
Table 1
Names and abbreviations of the brain regions considered in
the human connectome from Hagmann et al. (2008) (in alphabetical
order)
Abbreviation
Brain region
BSTS
CAC
CMF
CUN
ENT
FP
FUS
IP
ISTC
IT
LING
LOCC
LOF
MOF
MT
PARC
PARH
PC
PCAL
PCUN
POPE
PORB
PREC
PSTC
PTRI
RAC
RMF
SF
SMAR
SP
ST
TP
TT
Bank of the superior temporal sulcus

Caudal anterior cingulate cortex
Caudal middle frontal cortex
Cuneus
Entorhinal cortex
Frontal pole
Fusiform gyrus
Inferior parietal cortex
Isthmus of the cingulate cortex
Inferior temporal cortex
Lingual gyrus
Lateral occipital cortex
Lateral orbitofrontal cortex
Medial orbitofrontal cortex
Middle temporal cortex
Paracentral lobule
Parahippocampal cortex
Posterior cingulate cortex
Pericalcarine cortex
Precuneus
Pars opercularis
Pars orbitalis
Precentral gyrus
Postcentral gyrus
Pars triangularis
Rostral anterior cingulate cortex
Rostral middle frontal cortex
Superior frontal cortex
Supramarginal gyrus
Superior parietal cortex
Superior temporal cortex
Temporal pole
Transverse temporal cortex
Taken from Deco, G., Ponce-Alvarez, A., Mantini, D., Romani, G.L., Hagmann, P., &
Corbetta, M. (2013). Resting-state functional connectivity emerges from structurally and
dynamically shaped slow linear fluctuations. Journal of Neuroscience, 33,
1123911252.
saddle-nodes, and metastable synchronized states (Deco &

Jirsa, 2012; Deco et al., 2009; Ghosh et al., 2008; Honey
et al., 2007; Robinson, 2012). Consistent with this view, it
has been shown that features of the spontaneous activity in
the frequency and time-frequency domain, such as the lowfrequency 1/f behavior of EEG spectrum (Aburn, Holmes,
Roberts, Boonstra, & Breakspear, 2012; Robinson, Rennie, &
Wright, 1997) and the bistability of alpha power fluctuations
(Freyer et al., 2011), are captured by critical dynamics.
StructureFunction Relation
Given that the linearized version of the DMF model fairly
reproduces the resting global dynamics, we can further simplify
the system of stochastic differential equations by expressing it
in terms of the first- and second-order statistical moments
means and covariances of network activity. In general, the
analysis of nonlinear stochastic differential equations, as those

of eqns [1] and [2], requires extensive numerical simulations to
precisely estimate the meaningful statistics of the stochastic
dynamic system. However, assuming that noise is sufficiently
weak to confine the gating variables around their mean values,
one can derive deterministic differential equations for the firstand second-order moments of the distribution of the gating
variables. This method is referred to as the moments method
(Rodriguez & Tuckwell, 1996) and uses a Taylor expansion of
the equations of the stochastic system to concentrate on the
fluctuations around the mean values. In this way, one can
derive motion equations (deterministic) for the means and
covariances (for details, see Deco et al. (2013)). Alternatively,
equations for moments can be obtained using the Laplace
transform (Marreiros, Kiebel, Daunizeau, Harrison, & Friston,
2009). Within this approximation, it can be shown that the
covariance matrix of fluctuations around the stationary spontaneous state, noted Cv, is given by the algebraic equation
JCv Cv JT Qn 0
[3]
where J is the Jacobian matrix evaluated at the steady spontaneous state and Qn is the covariance matrix of the noise.
Equation [3] is solved using the eigendecomposition of the
Jacobian matrix J LDL1, where D is a diagonal matrix containing the eigenvalues of J, noted li, and the columns of
matrix L are the eigenvectors of J. Using the inverse and the
conjugate transpose of L, noted L1 and L{, respectively, we get
Cv LML{
[4]

*
1
{
~ = li l and QL
~
where M is given by Mij Q
Qn L .
ij
j
Equation [4] can be seen as a linear noise propagation
equation: An initial uncertainty or noise (M) is propagated
through the dynamic system and is mapped to its approximated linear output (Cv). It expresses the contribution to the
mapping of the intrinsic noise into the resulting functional
correlations of both the dynamics and the anatomical structure, since the Jacobian matrix is explicitly determined by the
connectivity matrix and the network dynamic state at which
it is evaluated. Hence, eqn [4] gives a direct relation between
the correlation structure, the underlying connectivity, and
dynamics. Finally, using this method, we estimated the
correlation q
structure
between
gating variables, defined as
Qij Cv ij = Cv ii Cv jj .
FC Emerges from Structurally Shaped and Dynamically

Slowdown Linear Fluctuations
Figure 3(b) shows the fitting between the empirical FC and the
stationary correlation structure of gating variable fluctuations
obtained using the moments method. Note that, here, we
concentrate on the correlation matrix Q between the fluctuations of the gating variables of each cortical area, defined
earlier, and not directly on the FC based on the model BOLD
signals. This is justified because the hemodynamic model used
here is a temporal convolution that applies independently to
each neural source, and thus, it does not actively couple the
activity between different brain areas although, recently, the
model has been extended to incorporate spatial dependencies
575
100
Single
state
150
Multistability
(with spont.
state)
Multi-stability
(high firing rate)
0
100
0
100
100
0
Spikes .s-1
Max r (spikes .s-1)
200
50
10
0
Area #
0
1
(a)
2
3
Coupling strength (G)
Single
state
0
100
100
0
100
0
50
10
0
1
66
Area #
0
1
(b)
100
Multi-stability
Multi(high firing rate)
stability
(with spont.
state)
Spikes .s-1
Max r (spikes .s-1)
150
66
2
3
Coupling strength (G)
Figure 2 Mean-field approximation. Bifurcation diagrams of the cortical spiking network (a) and the reduced DMF model (b) as a function of the global
coupling strength. Each point represents the maximum firing rate activity among all nodes. In both cases, depending on the coupling strength (G)
and the initial conditions, the network converges to one of the three possible dynamic regimes: For low values of G, the network settles into a single
stable state of low firing activity (i.e., the spontaneous state); for increasing values of G, new stable states of high activity (blue histograms in the
Insets) coexist together with the spontaneous state (yellow histogram in the Insets); or for even larger values of G, the spontaneous state becomes
unstable. Figure modified from Deco, G., Ponce-Alvarez, A., Mantini, D., Romani, G.L., Hagmann, P., & Corbetta, M. (2013). Resting-state functional
connectivity emerges from structurally and dynamically shaped slow linear fluctuations. Journal of Neuroscience, 33, 1123911252.
(Drysdale, Huber, Robinson, & Aquino, 2010). We found that

the fitting between the correlation matrix Q and the empirical
FC is maximal near the destabilization of the spontaneous
state, as for the correlation structure of BOLD from the DMF.
Notice, however, that, opposite to Figure 3(a), the decrease
of the fitting for low values of G is not as substantial using the
correlation matrix Q instead of the FC of model BOLD signals.
This arises from the filtering effect of the hemodynamic model,
which can be seen as a low-pass filter that lets frequencies under
1 Hz pass (Robinson et al., 2006). Thus, gating variable correlations at slow timescales are transmitted through the BOLD
model, while correlations at fast timescales are attenuated. Slow
fluctuations are expected to be amplified close to the bifurcation, since the timescale of dynamics increases when the spontaneous state loses attraction close to the instability. This effect
can be quantified by computing the power spectrum of fluctuations around the spontaneous state, which can be derived by
taking the Fourier transform of the equation governing the time
evolution of fluctuations. As expected, the power of low frequencies (<1 Hz) increases when the global coupling increases
(Figure 3(c)), making the correlation structure Q observable

after applying the BOLD model. In summary, these results
indicate that FC arises from reverberation of noise in the linearized dynamic system, which is constrained by the anatomical
connections and which is subject to a dynamic slowdown due to
the loss of stability of the spontaneous state.
Finally, we compared the correlation structure generated by
the different models, that is, the spiking model, the DMF, and
the moments approximation of the DMF, by plotting the FC
between one seed region and all other brain regions, for the
optimal value of G (i.e., at the edge of the second bifurcation;
Figure 3(d)). The seed region was the left posterior cingulate
(lPC), which is component of the well-known default-mode
network, a set of correlated brain regions that are more activated
at rest than during the performance of cognitive goal-directed
tasks (Raichle et al., 2001; Shulman et al., 1997; Snyder &
Raichle, 2012). As shown in Figure 3(d), the linearized reduction in form of the moments method is an analytic model that
captures excellently the dynamics of both DMF and spiking
models and the empirical resting-state activity.
576
Figure 3 Prediction of the FC. (a) The fitting of empirical data as a function of the global coupling parameter G was calculated for the spiking (red stars)
and for both the reduced DMF models (blue points) and its linearized version around the spontaneous state (gray squares). As a measure of
similarity, we used the Pearson correlation coefficient between the Fisher z-transformed pairwise correlation coefficients of both the empirical and the
simulated FC matrix. In the detailed spiking model, simulated BOLD signals were obtained by transforming the synaptic activity summed over the excitatory
and inhibitory populations in each cortical area by the hemodynamic model, while for the DMF, the synaptic gating variables of each cortical area were
used as input to the hemodynamic model. (b) Similarity between the empirical FC and the correlation structure of gating variable fluctuations obtained using
the moments method. (c) Averaged power spectrum of gating variable fluctuations around the spontaneous state, as a function of the global coupling
and frequency. (d) Comparison between the neuroanatomical and functional connections linking the left posterior cingulate (lPC). Gray bars indicate the
seed. Figure modified from Deco, G., Ponce-Alvarez, A., Mantini, D., Romani, G.L., Hagmann, P., & Corbetta, M. (2013). Resting-state functional
connectivity emerges from structurally and dynamically shaped slow linear fluctuations. Journal of Neuroscience, 33, 1123911252.
Dynamic Changes of Effective Connectivity

Examination of eqn [4] shows that the networks covariance is
determined by (the eigenvectors of) the Jacobian matrix that
depends on the fixed point at which it is evaluated. Thus, the
covariance depends on the global state of the network. As we

show in the succeeding text, this state dependence of the network covariance is an essential feature when considering the
evoked activity of the brain. For instance, if external inputs/
stimuli are applied to a set of cortical areas, the brain network
would change its dynamic state and settle to a new created fixed
point, for which the Jacobian matrix is different, and consequently, the correlations between areas would change. To illustrate this, we applied an arbitrary input to both left and right
lateral occipital cortices and compared the resulting evoked
correlation structure of gating variables with the one obtained
in the spontaneous (or rest) condition (Figure 4(a) and 4(b)).
The stimulus substantially increases or decreases the pairwise
correlations between cortical areas with respect to the spontaneous condition and, therefore, generates a different effective connectivity by changing the network interactions. Effective
connectivity refers to how different cortical areas influence
each other, even in the absence of direct connection between
them (Aertsen et al., 1989; Bullmore & Sporns, 2009; Friston,
2011; Robinson, 2012). Several studies have shown that the
effective connectivity of the brain during cognitive tasks can
change depending on the context (e.g., Friston & Buchel, 2000;
Rowe, Stephan, Friston, Frackowiak, & Passingham, 2005; Toni
et al., 2012). Dynamic changes of effective connectivity are
expected to arise due to activity- and context-dependent brain
dynamics, mediated by synaptic plasticity, neuromodulation, or
even the interplay between excitation and inhibition (Vogels &
Abbott, 2009). The effective connectivity has been efficiently
577
estimated using dynamic causal modeling (Friston, 2011), a

method that uses Bayesian inversion of observed data to estimate the effective connectivity, while anatomical connectivity
can be used for constraining prior distribution of effective
connectivity weights (Stephan, Penny, Daunizeau, Moran, &
Friston, 2009). Here, we used a different and complementary
approach in which effective connectivity is assumed to emerge
from changes in the dynamic state of the brain network built
on the anatomical connectivity, due to changes of activity in
a set of cortical areas subject to external inputs, attention, or
learning. A linear approximation of the effective connectivity is
given by the Jacobian matrix that maps the propagation of
noise to the observed correlations (FC; eqn [4]).
Effect of Effective Connectivity on Coding Accuracy

The question arises whether the state dependence of the
second-order statistics impairs or improves the encoding of
the stimulus. This can be elucidated by calculating the Fisher
information (FI), which gives an upper bound to the accuracy
that any population code can achieve (Abbott & Dayan, 1999).
The FI takes into account the change of the mean activity and
Figure 4 Spontaneous versus evoked correlations. (a) The correlation matrix evoked by an external stimulus (upper triangular part of the matrix) was
compared to the spontaneous correlation matrix (lower triangular part of the matrix); both matrices were calculated using the moments method. In
both conditions, the global coupling was G 2.2, for which the agreement between the spontaneous correlation matrix and the empirical FC was
maximum. In the evoked condition, the right and left lateral occipital cortices (LOCC) received an augmented constant input, equal to I0 dI, with I0 0.3
(nA) and dI 0.05 (nA), while all other cortical areas received the baseline input I0 (see eqn [2]). The stationary states, at which correlations are
calculated, in both spontaneous and evoked conditions, are represented by the histograms. Red bars indicated the stimulated nodes (rLOCC and lLOCC).
(b) Element-by-element difference (Drc) between evoked correlation matrix and spontaneous (rest) correlation matrix. (c) The Fisher information
(FI) was calculated in response to an infinitesimal variation of the stimulus (dI 0.001; black trace). Both the contribution to the FI of the mean response
(FImean; red trace) and the contribution to the FI of the covariance (FIcov; blue trace) present a maximum near the instability. Panels (a) and (b) were
taken from Deco, G., Ponce-Alvarez, A., Mantini, D., Romani, G.L., Hagmann, P., & Corbetta, M. (2013). Resting-state functional connectivity
emerges from structurally and dynamically shaped slow linear fluctuations. Journal of Neuroscience, 33, 1123911252.
578
covariances with respect to a variation in the stimulus. It can be

written as a sum of two quantities, FImean and FIcov, representing the contribution of the mean response and the covariance,
respectively. FImean and FIcov were calculated as a function of G,
using the moments method (Figure 4(c)). This analysis shows
that the FI increases close to the bifurcation, with a major
contribution of the covariance term. Therefore, depending of
the network parameters, a substantial part of the information
can come from the effective connectivity. This shows that the
working point of the network (close to the bifurcation) is
functionally meaningful: near criticality, the system is maximally sensitive to external stimulations and able to efficiently
encode the incoming information.
Conclusions and Outlook

The previously mentioned results show that resting FC emerges
from linear fluctuations that are dynamically slowed down,
due to loss of attraction near criticality, and shaped by noise
propagation through the network architecture. The results were
obtained by using an anatomically constrained large-scale
model of the brain. The model initially considered the entire
spiking and synaptic dynamics of the canonical excitatory
inhibitory cortex module. To get more theoretical insights,
the model was simplified using, first, a DMF approximation
and, second, a reduction on first- and second-order network
statistics. This allows expressing analytically the contribution
to the FC of both the anatomical structure and relevant neural
dynamics and reveals the inherent state-dependent property of
the network covariance. Finally, we showed that operating near
the bifurcation has a functional advantage in the sense that, in
this parameter region, the accuracy of the neural code is
increased due to an increase of the information content of
both the mean network response and the evoked covariance.
The model and its approximations allow a comprehensive
theoretical framework for investigating how the brain dynamics are affected by anatomical lesions (through selectively deleting the anatomical connections) and by pharmacological
treatments or neuromodulation (through incorporation of
the dynamic equations of specific neurotransmitters). Indeed,
spiking models with neuromodulation are amenable to meanfield reductions (Eckhoff, Wong-Lin, & Holmes, 2011) that
would provide a low-dimensional description of the model.

Diffusion MRI; Functional MRI Dynamics; INTRODUCTION TO
ANATOMY AND PHYSIOLOGY: Cell Types in the Cerebral Cortex:
An Overview from the Rat Vibrissal Cortex; Columns of the Mammalian
Cortex; Cytoarchitectonics, Receptorarchitectonics, and Network
Topology of Language; Functional Connectivity; Synaptic Organization
of the Cerebral Cortex; INTRODUCTION TO METHODS AND
Diffusion Tensor Imaging; Dynamic Causal Models for fMRI; Effective
Connectivity; Fiber Tracking with DWI; Neural Mass Models;
Probability Distribution Functions in Diffusion MRI; Q-Space Modeling
in Diffusion-Weighted MRI; Resting-State Functional Connectivity.
References
Abbott, L. F., & Dayan, P. (1999). The effect of correlated variability on the accuracy of a
population code. Neural Computation, 11, 91101.
Aburn, M. J., Holmes, C. A., Roberts, J. A., Boonstra, T. W., & Breakspear, M. (2012).
Critical fluctuations in cortical models near instability. Frontiers in Fractal
Physiology, 3, 331.
Aertsen, A., Gerstein, G., Habib, M., & Palm, G. (1989). Dynamics of neuronal firing
correlation: modulation of effective connectivity. Journal of Neurophysiology, 61,
900917.
Andreasen, N. C., OLeary, D. S., Cizadlo, T., Arndt, S., Rezai, K., Watkins, G. L., et al.
(1995). Remembering the past: Two facets of episodic memory explored with
positron emission tomography. American Journal of Psychiatry, 152, 15761585.
Biswal, B., Yetkin, F., Haughton, V., & Hyde, J. (1995). Functional connectivity in the
motor cortex of resting human brain using echo-planar MRI. Magnetic Resonance in
Medicine, 34, 537541.
Bullmore, E., & Sporns, O. (2009). Complex brain networks: Graph theoretical
analysis of structural and functional systems. Nature Reviews Neuroscience, 10,
186198.
Burns, N., & Webb, A. (1976). The spontaneous activity of neurons in the cats cerebral
cortex. Proceedings of the Royal Society of London Series B-Biological Sciences,
194, 211223.
Cabral, J., Hugues, E., Sporns, O., & Deco, G. (2011). Role of network oscillations in
resting-state functional connectivity. Neuroimage, 57, 130139.
Daffertshofer, A., & van Wijk, B. C.M (2011). On the influence of amplitude on the
connectivity between phases. Frontiers in Neuroinformatics, 5, 6.
Deco, G., & Corbetta, M. (2011). The dynamical balance of the brain at rest. The
Neuroscientist, 17, 107123.
Deco, G., & Jirsa, V. (2012). Ongoing cortical activity at rest: Criticality, multistability
and ghost attractors. Journal of Neuroscience, 32, 33663375.
Deco, G., Jirsa, V., & McIntosh, A. (2011). Emerging concepts for the dynamical organization
of resting-state activity in the brain. Nature Reviews Neuroscience, 12, 4356.
Deco, G., Jirsa, V., McIntosh, A. R., Sporns, O., & Kotter, R. (2009). Key role of
coupling, delay, and noise in resting brain fluctuations. Proceedings of the National
Deco, G., Ponce-Alvarez, A., Mantini, D., Romani, G. L., Hagmann, P., & Corbetta, M.
(2013). Resting-state functional connectivity emerges from structurally and dynamically
shaped slow linear fluctuations. Journal of Neuroscience, 33, 1123911252.
Drysdale, P., Huber, J. P., Robinson, P. A., & Aquino, K. M. (2010). Spatiotemporal
BOLD hemodynamics from a poroelastic hemodynamic model. Journal of
Theoretical Biology, 265, 524534.
Eckhoff, P., Wong-Lin, K. F., & Holmes, P. (2011). Dimension reduction and dynamics
of a spiking neuron model for decision making under neuromodulation. Journal on
Applied Dynamical Systems, 10, 148188.
Fox, M., & Raichle, M. (2007). Spontaneous fluctuations in brain activity observed
with functional magnetic resonance imaging. Nature Reviews Neuroscience, 8,
700711.
Fox, M., Snyder, A., Vincent, J., Corbetta, M., Van Essen, D., & Raichle, M. (2005). The
human brain is intrinsically organized into dynamic, anticorrelated functional
networks. Proceedings of the National Academy of Sciences of the United States of
America, 102, 96739678.
Fransson, P. (2005). Spontaneous low-frequency BOLD signal fluctuations: An fMRI
investigation of the resting-state default mode of brain function hypothesis. Human
Freyer, F., Roberts, J. A., Becker, R., Robinson, P. A., Ritter, P., & Breakspear, M.
(2011). Biophysical mechanisms of multistability in resting-state cortical rhythms.
Friston, K. (2011). Functional and effective connectivity: A review. Brain Connectivity, 1,
1336.
Friston, K., & Buchel, C. (2000). Attentional modulation of effective connectivity from
V2 to V5/MT in humans. Proceedings of the National Academy of Sciences of the
Friston, K., Harrison, L., & Penny, W. (2003). Dynamic causal modelling. Neuroimage,
19, 12731302.
Ghosh, A., Rho, Y., McIntosh, A., Kotter, R., & Jirsa, V. (2008). Noise during rest
enables the exploration of the brains dynamic repertoire. PLoS Computational
Biology, 4, e1000196.
Greicius, M., Krasnow, B., Reiss, A., & Menon, V. (2003). Functional connectivity
in the resting brain: A network analysis of the default mode hypothesis.
100, 253258.
Hagmann, P., Cammoun, L., Gigandet, X., Meuli, R., Honey, C., Wedeen, V. J., et al.
(2008). Mapping the structural core of human cerebral cortex. PLoS Biology, 6, e159.
Hlinka, J., Palus, M., Vejmelka, M., Mantini, D., & Corbetta, M. (2011). Functional
connectivity in resting-state fMRI: Is linear correlation sufficient? Neuroimage, 54,
22182225.
Honey, C., Kotter, R., Breakspear, M., & Sporns, O. (2007). Network structure of
cerebral cortex shapes functional connectivity on multiple time scales. Proceedings
1024010245.
Honey, C., Sporns, O., Cammoun, L., Gigandet, X., Thiran, J., Meuli, R., et al. (2009).
Predicting human resting-state functional connectivity from structural connectivity.
106, 20352040.
Koch, K., & Fuster, J. (1989). Unit activity in monkey parietal cortex related to
haptic perception and temporary memory. Experimental Brain Research, 76,
292306.
Marreiros, A. C., Kiebel, S. J., Daunizeau, J., Harrison, L. M., & Friston, K. J. (2009).
Population dynamics under the Laplace assumption. Neuroimage, 44,
701714.
Pernice, V., Staude, B., Cardanobile, S., & Rotter, S. (2011). How structure
determines correlations in neuronal networks. PLoS Computational Biology, 7,
e1002059.
Raichle, M. E., MacLeod, A. M., Snyder, A. Z., Powers, W. J., Gusnard, D. A., &
Shulman, G. L. (2001). A default mode of brain function. Proceedings of the
Raichle, M. E., & Mintun, M. A. (2006). Brain work and brain imaging. Annual Review of
Robinson, P. A. (2012). Interrelating anatomical, effective, and functional brain
connectivity using propagators and neural field theory. Physical Review E, 85,
011912.
Robinson, P. A., Drysdale, P. M., Van der Merwe, H., Kyriakou, E., Rigozzi, M. K.,
Germanoska, B., et al. (2006). BOLD responses to stimuli: Dependence on
frequency, stimulus form, amplitude, and repetition rate. Neuroimage, 31, 585599.
579
Robinson, P. A., Rennie, C. J., & Wright, J. J. (1997). Propagation and

stability of waves of electrical activity in the cerebral cortex. Physical Review E, 56,
826840.
Rodriguez, R., & Tuckwell, H. (1996). Statistical properties of stochastic nonlinear
dynamical models of single spiking neurons and neural networks. Physical Review
E, 54, 55855590.
Rowe, J. B., Stephan, K. E., Friston, K., Frackowiak, R. S., & Passingham, R. E. (2005).
The prefrontal cortex shows context-specific changes in effective connectivity to
motor or visual cortex during the selection of action or colour. Cerebral Cortex, 15,
8595.
Shulman, G. L., Corbetta, M., Buckner, R. L., Raichle, M. E., Fiez, J. A., Miezin, F. M.,
et al. (1997). Top-down modulation of early sensory cortex. Cerebral Cortex, 7,
193206.
Snyder, A., & Raichle, M. (2012). A brief history of the resting state: The Washington
University perspective. Neuroimage, 62, 902910.
Bayesian model selection for group studies. Neuroimage, 46, 10041017.
Toni, I., Rowe, J., Stephan, K. E., & Passingham, R. E. (2012). Changes of corticostriatal effective connectivity during visuomotor learning. Cerebral Cortex, 12,
10401047.
Vincent, J., Patel, G., Fox, M., Snyder, A., Baker, J., Van Essen, D., et al. (2007).
Intrinsic functional architecture in the anaesthetized monkey brain. Nature, 447,
8386.
Vogels, T. P., & Abbott, L. F. (2009). Gating multiple signals through detailed balance
of excitation and inhibition in spiking networks. Nature Neuroscience, 12, 483491.
Wilson, F., Scalaidhe, S., & Goldman-Rakic, P. (1994). Functional synergism between
putative gamma-aminobutyrate-containing neurons and pyramidal neurons in
prefrontal cortex. Proceedings of the National Academy of Sciences of the United
Wong, K., & Wang, X. (2006). A recurrent network mechanism of time integration in
perceptual decisions. Journal of Neuroscience, 26, 13141328.

Bharat Biswal, New Jersey Medical School, Rutgers University, NJ, USA
Introduction
Functional magnetic resonance imaging (fMRI) due to its high
spatial and temporal resolution in addition to its noninvasiveness has become the method of choice for studying
systems-level brain function. MRI in general can generate the
anatomy of different tissue types in the brain; however, it takes
minutes to generate one structural brain image with great
contrast of the different tissue types in the brain. Using
fMRIs, on the other hand, a series of images of the brain are
acquired over time; each individual functional brain image is
acquired within seconds typically with lower spatial resolution.
At its core, fMRI uses the blood oxygen level-dependent
(BOLD) signal, which was discovered by Seiji Ogawa in
1991. It is currently understood that task activation or stimulus
presentation leads to an increase in neuronal firing in the
eloquent regions of the brain. Increased neuronal firing leads
to an increase in oxygen consumption and leads to vasodilation. The activation-induced increase in brain oxygenation
decreases intravascular deoxyhemoglobin and, therefore,
decreases susceptibility-induced intravoxel dephasing. Spin
coherence increases, resulting in increased signal intensity.
Brain activation is observed as localized signal enhancement.
Task Activation Design

Brain mapping experiment typically consists of alternating
periods of stimulus task and control state and the cycle is
repeated several times. Images are collected throughout the
cycles and the image acquisition is repeated at several intervals
of the time of repetition throughout the experiment, while the
subject alternates between the stimulus and control task. In
every experiment, it is assumed that the magnitude of the
BOLD effect reflects the magnitude of the neural activity
change [34]. A standard method of task presentation uses a
boxcar or block design where blocks of the stimulus or task are
presented typically for 2030 s, alternating with periods of rest
or a control condition. Throughout these stimulus/control
cycles, dynamic echo planar images are collected covering all
or part of the brain. The control task is chosen carefully such
that it activates all of the neural processes common to the
stimulus task. By subtracting the brain regions recruited during
the performance of the control task from the brain regions
recruited during the test condition, the areas of the brain
whose activity is associated specifically with the cognitive process of interest can be identified. An alternative experimental
approach is to present stimuli as isolated brief events separated
in time so that the individual response to single events can be
identified. Another advantage of this event-related approach is
that it avoids the potential confounding factors of habituation
or fatigue that may arise in a block design as a consequence of
the presentation of repeated identical stimuli. The primary
objective in the experiment is to find the regions of the brain

that are activated for a given task and the activation maps can
be generated by correlating the time series with the given task.

Resting-state connectivity (RSC) may be defined as significant
correlated signal between functionally related brain regions in
the absence of any stimulus or task. This correlated signal arises
from spontaneous low-frequency signal fluctuations (SLFs). We
first demonstrated a significant temporal correlation of SLFs
both within and across hemispheres in the primary sensorimotor cortex during rest. Seventy four percent of the time series
from these voxels correlated significantly (after filtering the
fundamental and harmonics of respiration and heart rates)
while only a few voxel time courses (<3%) correlated with
those in regions outside of the motor cortex. Subsequently,
Hampson et al. (2002) demonstrated the presence of RSC in
sensory cortices, specifically auditory and visual cortices. In their
studies, signal from visual cortex voxels during rest (first scan)
was used as a reference and correlated with every other voxel in
the brain. A significant number of voxels from the visual cortex
passed a threshold of 0.35, while only a few voxels from outside
the visual cortex passed the threshold. They have demonstrated
similar results in the auditory cortex (Hampson et al., 2004).
Lowe et al. (1997) extended Biswal and Hydes (1995)
results by showing such correlations over larger regions of the
sensorimotor cortex (i.e., across multiple slices). Xiong, Fox,
and colleagues (1998, 1999) established relationships between
motor and association cortices. Similar to earlier results, they
observed RSC between the sensorimotor cortex areas (primary,
premotor, and secondary somatosensory). Further, however,
they observed RSC relationships between these motor areas
and association areas, specifically anterior and posterior cingulate cortices, regions known to be involved in attention.
Greicius et al. (2004) observed RSC in the anterior and posterior cingulate areas. Subsequent observation of activation during a visual attention task indicated similar cingulate activity.
These studies have established the foundation for restingstate functional connectivity studies using fMRI (e.g., Biswal
et al., 1995; Grecius et al., 2004; Gusnard and Raichle, 2002;
Hampson et al., 2002; Lowe et al., 1997). Results from these
studies form the basis for speculation regarding the functional
role of RSC. Bressler et al. (1996) had suggested that such
correlated SLFs may be a phenomenon representing the functional connection of cortical areas analogous to the phenomenon of effective connectivity defined by Friston et al. (1993).
Spontaneous Low-Frequency Physiological Fluctuations

Low-frequency SLFs were first observed by Davies and Bronk
(1957) in cerebral oxygen availability using polarographic
techniques. These low-frequency spontaneous fluctuations
http://dx.doi.org/10.1016/B978-0-12-397025-1.00335-3
581
582
INTRODUCTION TO METHODS AND MODELING | Resting-State Functional Connectivity
have also been observed by several investigators using animal

models and a variety of measurement techniques, including
laser Doppler flowmetry (LDF) (Hudetz et al., 1992), fluororeflectometry of NADH and cytochrome-aa3 (Vern et al., 1998),
and polarographic measurement of brain tissue PO2 with
microelectrodes. These fluctuations appear to be independent
of cardiac and respiratory fluctuations and hence are termed
spontaneous.
Biophysical-Origin Hypotheses of RSC

Testing these hypotheses of the role of SLFs has involved
attempts to determine their physiological origins. Cooper
et al. (1966) hypothesized that these fluctuations represent
cellular maintenance of an optimum balance between blood
flow and cerebral metabolic rate. Testing this hypothesis has
involved the manipulation of cerebral metabolism with anesthesia. These studies have involved the comparison of activity
during waking and anesthetized states in animals using various
techniques including LDF (Hudetz et al., 1992) and functional
MRI in humans (Biswal et al., 1993; Weisskoff et al., 1993).
Signal oscillations in the rodent brain vary with differing levels
of halothane anesthesia, PCO2, and nitric oxide synthase
blockade LDF (Hudetz et al., 1992). These results suggest support for the biophysical-origin hypothesis that affects the neural vasculature. The neural mechanisms of slow rhythmic
fluctuations have not yet been clearly defined yet though studies indicate they may be both neuronal and glial in origin
(Zonta et al., 2003).
In spectrophotometric studies of the intramitochondrial
redox state of enzyme cytochrome aa3 (CYT) and cerebral
blood volume (CBV), continuous slow oscillations and interhemispheric synchrony have been observed between these variables (Vern et al., 1998). The relationship between CYT and CBV
oscillations seems to be independent of the physiological state
as they have been observed during both awake state and sleep
(Vern et al., 1997a, 1988, 1998), during anesthesia (Dora and
Kovach, 1981; Hudetz et al., 1992), and during cerebral ischemia (Golanov, 1994; Mayevsky and Ziv, 1991). Though there
have been studies indicating the presence of metabolic oscillations in the absence of CBF oscillations (indicating that metabolic oscillations may be primary in origin), there is no concrete
evidence to indicate so. On the contrary, flow oscillations can
be linked to metabolic oscillations in the presence of evidence
indicating that NADH and cytochrome aa3 oscillations lagged
behind CBV oscillations (Vern et al., 1997a, 1998). These results
indicate that spontaneous oscillations in the intramitochondrial
redox state may at least in part be linked to a rhythmic variation
in oxygen consumption of the tissue.
It should be emphasized that the origin of the slow cerebral fluctuations of CBV and CYTox remains to be determined. It is unlikely to be entirely vascular (vasomotion),
in view of the complex frequency/time and interhemispheric
architecture of these fluctuations in cats and rabbits (Vern
et al., 1997a, 1998). There are a variety of neuronal, glial,
and vascular phenomena that may offer their contributions to
what finally appears as a measurable fluctuation (Berridge
and Rapp, 1979). For instance, glutamate-induced intracellular calcium waves within the glial syncytium may represent an
energy-dependent indirect reflection of activity within focal
neuronal fields. Such factors would need to be carefully dissected by future efforts. An interesting example of such multifactorial components of the slow fluctuations emerges from
the study of CBV and CYTox during the transition from slowwave sleep to REM sleep in the cat, as will be discussed in the
following sections.
Cognitive-Origin Hypotheses of RSC

In contrast to biophysical-origin hypotheses, others have proposed cognitive-origin hypotheses, based on observations that
low-frequency SLFs appear to correlate between functionally
connected brain areas (e.g., Biswal & Hyde, 1997a). Testing
these hypotheses has involved the observation of resting-state
activity between functionally connected regions and contrasts
between. Thus, a family of cognitive-origin hypotheses (in
contrast to biophysical-origin hypotheses) have emerged.
Gusnard and Raichle (2001), for instance, had suggested that
such coherence indicates the presence of a default mode of
brain function in which a default network continuously monitors external (e.g., visual stimuli) and internal (e.g., body
functions and emotions) stimuli. Other cognitive-origin
hypotheses suggest that low-frequency fluctuation is related
to ongoing problem solving and planning (Greicius et al.,
2004). Biswal and Hyde (1995) and Xiong, Fox, and colleagues
(1998,1999) observed that analyses of resting-state physiological fluctuations reveal many more functional connections
than those revealed by task-induced activation analysis. They
hypothesized that task-induced activation maps underestimate
the size and number of functionally connected areas and that
functional networks are more fully revealed by RSC analysis.
Comparisons of RSC and Task-Induced Activity

Skudlarski and Gore (1998) compared RSC and SLFs in the
olfactory cortex during three sustained passive stimuli: a pleasant odor, an unpleasant odor, and no odor. They reported that
the presentation of odor altered the strength of correlation in
some regions, compared to rest. Biswal and Hyde (1998) studied low-frequency physiological fluctuations in the motor cortex during a sustained 6 min period of bilateral finger tapping.
In all four subjects, the frequency and phase of low-frequency
fluctuations were similar. The magnitude of the low-frequency
fluctuations, however, was significantly enhanced during continuous finger tapping. In addition, RSC maps produced by
correlation of low-frequency fluctuations between motor-cortex
voxels had an improved coincidence with task-activation maps
compared to the RSC. These results suggest that attention to a
prolonged task spontaneously fluctuates and that RSC is modulated by attention. These three studies involved a sustained
active task or a sustained change in environment or a sustained
task that was repeated twice with different instructions.
Numerous other variants and extensions of these ideas are
immediately apparent. However, in each case, one is comparing differences between small effects. There is a significant
challenge to improve experimental methodologies for these
kinds of experiments.
We have carried out a study to test the reliability of restingstate functional connectivity maps in fMRI using testretest
analysis. Five resting-state data sets were collected from each

subject in addition to bilateral finger tapping to activate the
sensorimotor cortex. The reliability of the resting-state data sets
was obtained using different measures:
(1) Voxel precision: The ratio of the number of specific activated sensorimotor voxels that passed the threshold in
each of the five rest scans to the number that passed the
threshold in at least one of the 5 rest scans.
(2) First-order precision and second-order precision: The numerator of the earlier-mentioned ratio is modified to include
voxels that passed the threshold in 4 out of 5 rest scans and
3 out of 5 rest scans.
It was observed in all subjects that all five resting-state functional connectivity maps of the sensorimotor cortex had substantial overlap with the corresponding bilateral finger-tapping
task. It was seen that while voxel precision was about 60%, the
first-order precision and second-order precision were about
70% and 80%, respectively. This suggests that while there is
variability between the resting-state functional connectivity
maps, most of it can be accounted by simply taking into
account the neighboring voxels.
Voxel time-course intensities from the sensorimotor cortex
increased by about 5% during finger tapping, and the same
voxel time courses during rest varied by 1% (Biswal et al.,
1996). A significant correlation was obtained between the
percent signal change in an activated voxel from the sensorimotor voxel and the percent signal change during rest in the
corresponding voxels. Average regression coefficients of about
0.55 were seen. These results show that the percent increase in
voxel activation during task is inherently correlated with
underlying low-frequency physiological fluctuations.
Finally, Lowe et al. (1997b) sought to examine the role of
attention in RSC. They compared correlations during rest and
during stimulation in three subjects. Following the rest scan,
subjects were presented with sequences of tones and circular
symbols. The sequences of tone and symbol presentation were
randomly out of phase with each other. Attention was manipulated by requiring subjects in one condition to press a button
when the auditory tone was heard and to press a button when
the symbol appeared in another condition.
They reasoned that, since all stimuli and responses were
identical between the two scans, any change in correlation
between motor, visual, and auditory regions across the two
scans should be due to the effects of attention on neuronal
connectivity. They observed slight increases in intraregional
correlations during task performance. Specifically, correlations
between visual cortex voxels were increased, compared to rest
and to auditory-task performance, while subjects attended to
symbols. Similarly, correlations between auditory cortex voxels
were increased, compared to rest and to visual-task performance, while subjects attended to tones.
The results of the studies presented in the preceding text
suggest intriguing clues about the relationship between RSC,
functional activity, and the role of attention in mediating these
relationships. Thus, Gusnard and Raichle (2001), for instance,
had argued that the set of brain regions showing correlated
activity at rest (the default network) continuously monitors
external (e.g., visual stimuli) and internal (e.g., body functions
and emotions) stimuli. On the basis of similar observations
and apparent hippocampal involvement, Greicius et al. (2004)
583
had argued that RSC may be related to episodic memory

retrieval in the service of ongoing problem solving and planning (Greicius et al., 2003). Moreover, such activity may be
suppressed or suspended (Gusnard and Raichle, 2001) under
conditions of demanding cognitive activity. Such accounts are
intriguing because they suggest that presumed baseline activity
may not be as random as has been nearly universally presumed. Others have argued that RSC represents the tonic activation of networks that are brought on line during cognitive
task performance. All of these hypotheses suggest that meaningful functional activity may be occurring during rest. Understanding the mechanisms and the functional and clinical
relevance of such activity may have profound effects on our
understanding of functional neuroimaging results, leading to
explanations, for instance, of many poorly understood phenomena including the up-to-date inexplicable negative activation results that have bedeviled neuroimaging research.
Further, understanding RSCactivation relationships could
lead to plausible accounts for patterns and age-related differences in BOLD activity as well (e.g., Cabeza, 2001; Grady et al.,
1995; Rypma & DEsposito, 2000; Rypma et al., 2001, 2005)
because older adults often show greater activation than younger adults. Cognitive accounts of this phenomenon, such as
age-related compensation, have been unsatisfactory thus far
because age-related activation increases have not been consistently related to performance improvements in older adults
(e.g., Grady et al., 1995; Rypma et al., 2001). The idea that
such age-related activation increases are related to a RSC network that must be inhibited for successful task performance is
compelling because older adults are known to have deficits in
inhibitory functions at the cellular (i.e., neuronal), structural
(i.e., glial), and cognitive (i.e., behavioral; Hasher et al., 1991)
levels. Greicius et al. (2004), however, had observed decreased
hippocampal involvement in comparisons between older
healthy and Alzheimers disease (AD) patients.
Effective-state connectivity results from interactions between

brain regions during task performance
Effective-state connectivity (ESC) may be defined as the influence that one region or system exerts over another during task
performance (Buchel et al., 2004; Friston et al., 1993). ESC may
be modeled with a number of functions (e.g., linear or quadratic) to characterize the nature of interactions between brain
regions (usually specified a priori or on the basis of level 1,
traditional massive univariate analysis). ESC models reflect the
hemodynamic change in a given voxel or region as the weighted
sum of changes in other regions. More complex structural equation models reflect the relationships between regions by minimizing the least-squared difference between an observed
covariance structure and the structure of a theoretical model.
The necessary multimodal imaging work has not yet been done
to determine the neural substrate of effective connectivity. It is
presumed to reflect propagating neurotransmission between
brain regions via white-matter tracts.
ESC reveals functional activity between regions showing RSC

Biswal et al. (1997) had shown (1) that BOLD signal is more
sensitive to RSC than flow-based signal implicating a neural
basis for RSC and (2) that motor regions evincing RSC show
increased BOLD activity during finger-tapping performance.
584
Biswal and Hyde (), for instance, studied physiological fluctuations in the motor cortex during rest and during a sustained
6 min period of bilateral finger tapping. They observed that the
magnitude of low-frequency physiological fluctuations
observed at rest was enhanced during continuous finger tapping. In addition, maps of these motor cortex-based lowfrequency fluctuations had significantly greater coincidence
with task-activation maps than those in other brain regions.
These results suggest that functionally active networks are
chronically active at rest. Recently, Gao and Fox had hypothesized that ESC represents a subset of the RSC network. Analyzing the sensorimotor cortex, they found a number of
additional regions, including the premotor region, to be connected that are not typically connected during bilateral finger
tapping.
Task-related patterns of BOLD activity may represent acute
activation of the circuits necessary for the task at hand. Such
circuitry may be revealed in ESC analysis models advanced by a
number of researchers (e.g., Buchel & Friston, 2000; Goebel
et al., 2003; McIntosh et al., 1996). ESC analyses have revealed
interconnections between brain regions known to be active during cognitive task performance. In one WM study, for instance,
McIntosh et al. (1999) had observed increases in interactions
among PFC regions and between PFC and corticolimbic regions
with increasing delay intervals. ESC studies comparing younger
and older adults have indicated that older adults show increased
ESC during cognitive task performance. Their results indicated
that, whereas younger adults showed hippocampal interactions
with ventral PFC, during memory encoding, older adults showed
hippocampal interactions with both dorsal and ventral and parietal interactions. At present, the meaning of this age- and diseaserelated increased ESC remains poorly understood. The best evidence suggests that either (1) it may reflect compensatory activity
in the service of optimizing memory performance (Grady et al.,
1999) or (2) it may reflect a decreased inhibition of the default
mode, as Greicius et al. (2004) had suggested. Little leverage
may be gained on these questions because the results come from
different groups of subjects performing different tasks.
In recent years, there has been a renewed interest in lowfrequency spontaneous fluctuations. Using a variety of neuroimaging methodologies in animals (e.g., LDF, reflectance
oximetry, and fMRI), studies have reported spontaneous fluctuations in the 412 cpm range when cerebral perfusion was
challenged by systemic and local manipulations. Hypotension,
hyperventilation, and cerebral artery occlusion substantially
modulate the magnitude of these spontaneous fluctuations.
These studies clearly challenge our current understanding of
CBF autoregulation and demonstrate the dynamic nature of
regional CBF. The work proposed here will contribute to our
understanding of the basic neurophysiology of these phenomena and to our basic understanding of brain function.
The literature reviewed in the preceding text indicates that
RSC and ESC have been used separately to examine differences
between young and old and between old and AD patient
groups.
Neuropsychological and functional neuroimaging studies
indicate that attention is subserved by anatomically overlapping but functionally dissociable networks in the brain (Posner
& Petersen, 1990). A posterior network that includes the superior parietal lobe and its connections to inferior temporal and
lateral premotor regions is important for voluntary detection of

target stimuli in space (termed selective attention; Corbetta
et al., 1998). An anterior network that includes the anterior
cingulate and its connections to the dorsolateral prefrontal
cortex is important for monitoring target detection and maintaining target- and goal-related information in the working
memory while resisting interference from competing information (termed executive control). The parietal and frontal cortices are anatomically connected directly and indirectly via the
anterior cingulate gyrus (Goldman-Rakic, 1988). The anatomical connectivity facilitates goal-directed behavior that is
accomplished by continuous interaction of operations of selective attention and executive control.
Life-span development appears to reflect disproportionate
changes in anterior attentional networks. Cognitive development from childhood to adulthood includes improved executive control of action and attention. These cognitive
improvements are subserved by functional anatomical maturation of the prefrontal cortex and associated anterior cingulate circuitry (Bunge et al., 2002). Conversely, normal aging is
marked by declines in executive control that are related to
reductions in inhibitory functions (e.g., Hasher, Stoltzfus,
Zacks, & Rypma, 1991) and functional changes in the prefrontal cortex and associated circuitry (Rypma & DEsposito,
2000; Rypma et al., 2004). These findings suggest that the
anterior attentional network may be relatively more affected
by the deleterious effects of adult aging. These findings suggest that anterior rather than posterior attentional networks
are more influenced by neural changes associated with childhood development and aging.
Evidence suggests that, whereas the anterior attentional network is disproportionately affected by diseases of childhood,
diseases of aging may affect both anterior and posterior attention networks (e.g., Castellanos, 2007; Vaidya, Rombouts, et al.,
2005). Clinically, ADHD is characterized by impulsivity,
inattention, and hyperactivity. In the laboratory, it is characterized by reductions in performance on anterior attention tasks
(e.g., go/no-go and n-back; Shallice et al., 2002; Vaidya et al.,
1999), but relatively preserved performance on visual search
tasks (Aman, Roberts, & Pennington, 1998). AD patients, on
the other hand, tend to show deficits in both kinds of tasks
(Backman et al., 2005; Drzezga et al., 2005; Rosler et al., 2005).
In order to examine how functional connectivity is modulated by attention over the life span, we will implement attention tasks that show region-specific activation in posterior and
anterior attentional networks. The posterior attention network
will be examined by a selective attention task that is modeled
after the conjunction visual search paradigm introduced by
Triesman (1991). This paradigm has been used in fMRI studies
of typically developing children of the same ages as included
here (Booth et al., 2003) and in adults (e.g., Corbetta &
Shulman, 1998). The anterior attention network will be studied using an n-back task that involves maintenance, updating,
and suppression of interference, operations that constitute
executive control. This paradigm has been used in fMRI studies
of typically developing children of the same ages as the subjects
in our proposed studies (Casey et al., 1995), young adults
(Nyberg et al., 2003), and elderly (Verhaegen & Basak, 2005).
Analyses that combine ESC and RSC will permit investigators to observe attentional changes associated with childhood

and aging. First, both childhood and aging groups should
show greater changes in anterior than in posterior attentional
networks compared with their control groups. Second, the
anterior attentional network that is weaker in both populations differs in the underlying developmental sequel, specifically immature myelination and pruning in childhood and
deteriorating myelination in aging (e.g., Madden et al., 2004;
Peters & Sethares, 2004). We expect that relationships between
frontal and parietal cortices will be affected in different ways in
these two anatomical scenarios. Analysis of RSCESC in
healthy and diseased children, healthy young adults, and
healthy and diseased elderly will permit us to assess the effects
of developing, intact, and deteriorating connections between
brain regions and their associated behavioral consequences.
Improved understanding of RSC could benefit the diagnosis of age-related disorders across the life span. We have
recently demonstrated altered RSC between hippocampal
585
regions in AD patients (Li et al.; see succeeding text). In AD

patients, we observed significantly fewer resting-state correlations between hippocampal regions than in controls. Moreover, there were minimal differences between AD patients
and controls in resting-state correlations in the visual cortex
between these two groups. We have also carried out a study
on a diverse group of five patients with Tourettes syndrome.
The results of these investigations are reported in a paper in
AJNR (Biswal et al., 1998b), which describes motor taskactivation studies, and in two abstracts (Biswal et al., 1997c,
1997d) that report on functional connectivity using analysis
of physiological fluctuations. Comparisons were made with
age- and gender-matched controls. A bilateral finger-tapping
paradigm was used for task activation. We believe that there is
a high likelihood, based on these studies, that analysis of
resting-state physiological fluctuations will contribute to clinical practice.
Effective Connectivity
B Misic and AR McIntosh, Rotman Research Institute, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
Glossary
Autoregressive model (Granger) A model in which the

present value of a time-varying process (e.g., the activity of a
brain region) linearly depends on some number of its own
previous values.
Bayesian model inversion (DCM) An optimization
procedure in which the data are used to update the
unknown parameters of the causal model, subject to the
constraints imposed by the prior distribution, resulting in
the posterior distribution.
Effective connectivity Direct influence of one neural
element on another.
Forward model (DCM) A mapping from the underlying
neural activity generated by the causal model to some
observable data feature, such as BOLD, EEG, and MEG
activity.
Functional connectivity A temporal association
(e.g., correlation and covariance) between the time courses
of two neural elements.
Modification index (SEM) The potential improvement in
model fit if a parameter of the model (e.g., path coefficient)
were allowed to freely vary.
Network Analysis and Effective Connectivity

A fundamental challenge in neuroscience is to understand how
neural operations engender mental phenomena, from sensation to perception to higher cognition. Early clinical studies
looking at cognitive deficits following lesions often attributed
discrete mental operations to specific brain regions. Modern
neuroimaging techniques, which can simultaneously measure
activity in the whole brain during some mental function, have
reinforced neurobiological theories that emphasize the distributed and integrative nature of neural operations. Brain regions
do not operate in isolation, but as part of an interacting network, and the contribution of a particular region must depend
on the status of the other elements of the network (neural
context; Bressler & McIntosh, 2007; McIntosh, 2000).
In neuroimaging, neural interactions are conceptualized
and estimated in terms of two distinct but related notions of
connectivity. Functional connectivity refers to temporal associations between neural elements and may be estimated using
correlation or covariance, as well as coherence and mutual
information. Thus, two elements with statistical interdependency are said to be functionally connected. Yet a functional
connection between two neural elements does not imply that
they are communicating directly, as their covariation may be
due to common inputs from another source. Effective connectivity is a logical progression from functional connectivity and
refers to the direct influence of one neural element on another
(Aertsen, Gerstein, Habib, & Palm, 1989; Friston, 1994).
Path coefficient (SEM) A regression weight (beta) that

describes the strength of a particular effective connection.
Posterior distribution (DCM) An updated distribution for
each parameter that reflects both prior beliefs and empirical
knowledge.
Prior distribution (DCM) A distribution for each
parameter (e.g., synaptic couplings) that reflects prior
beliefs about that parameter and serves as a soft
constraint in the ensuing optimization
procedure.
Spectral Granger causality (Granger) Total power
in one signal that can be attributed to another
signal.
Stacked run (SEM) A framework for testing for group and
condition differences, wherein several alternative models are
simultaneously fitted.
Structural equations (SEM) A set of linear regression
equations that describe how much of the variance in a target
region is accounted for by the activity in other regions that
project to it.
Transfer entropy (Granger) Total information in one signal
that can be attributed to another signal.
The key distinction between functional and effective connectivity lies in the levels of inference they allow. Functional
connectivity, estimated as statistical dependencies between
neural elements, does not allow inference on the directionality
of influence. Effective connectivity is estimated by formulating
an explicit causal model of how neural elements influence one
another, thereby allowing inference about directional influences. This is illustrated in Figure 1, wherein the two anatomical networks differ in one aspect: the presence of a direct
projection from node A to node B (McIntosh & Korostil,
2008). Nodes A and B receive common inputs, and as a result,
they would display functional connectivity in both networks.
Thus, the two networks could not be differentiated in terms of
functional connectivity, but could in terms of effective connectivity. The purpose of effective connectivity is to explicitly
model directionality in the network.
In this article, we give an overview of three techniques for
estimating effective connectivity. Two are confirmatory, in
the sense that an explicit model of element interactions is
formulated and tested to see whether it fits the observed
data and/or whether it fits the observed data better than
alternative models (structural equation modeling, (SEM)
and dynamic causal modeling (DCM)). The third (Granger
causality) is also used to estimate causal influence but is
usually applied in an exploratory fashion to any pair of neural
elements. Indeed, Granger causality can also be thought of as
an assessment of directed functional connectivity, because it
tests for dependencies over time.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00336-5
587
588
INTRODUCTION TO METHODS AND MODELING | Effective Connectivity

causal order of the network is given by the system of structural
equations
Network 1
x1 c x1
x2 px1 cx2
x3 qx1 rx2 cx3
x4 sx2 tx3 cx4
Network 2
C
This system of equations is used to generate a predicted or

implied covariance matrix (McArdle & McDonald, 1984). The
implied covariance matrix is a prediction of the variances of
neural elements and their mutual covariances, parameterized
by the path coefficients. For example, the pairwise correlations
Rxi , xj predicted by eqn [1] are
Rx1 , x2 p
Rx1 , x3 q pr
Rx1 , x3 ps prt qt
Rx2 , x3 r pq
Rx2 , x3 s rt pqt
Rx3 , x4 t sr qps
Figure 1 Two different network configurations. The networks have

similar topologies, save for a projection from A to B, which is absent in
network 1 and present in network 2. Because A and B receive common
inputs from C, functional connectivity would not be able to distinguish
between the two configurations. Effective connectivity, which explicitly
models the directionality of influence, would be able to determine if
there is any residual influence from A and B, once the intervening effects
of C are accounted for. Adapted from McIntosh, A. R., & Korostil, M.
(2008). Interpretation of neuroimaging data based on network concepts.
Brain Imaging and Behavior, 2(4), 264269.
Structural Equation Models

The goal of SEM is to test whether a hypothesized causal
structure is consistent with the empirical data (Joreskog,
Sorbom, Magidson, & Cooley, 1979; Loehlin, 1987). In neuroimaging, SEM models are usually a subset of brain regions
and the patterns of causal influence among them (McIntosh &
Gonzalez-Lima, 1991; McIntosh et al., 1994; Mclntosh &
Gonzalez-Lima, 1994). Regions to be included in the model
are typically selected based on prior hypotheses or analytic
outcomes. Patterns of influence between regions are anatomically constrained, such that effective connectivity between two
regions is possible only if there is a direct anatomical link
(although indirect effects are possible).
Model Specification
The path diagram in Figure 2 (left) illustrates how a structural
model is mathematically formulated (McIntosh and Misic,
2013). The activity of each region is treated as a variable.
Effective connectivity between elements is specified by a system
of linear regression equations, termed structural equations, that
define the sources of variance for each region. In the present
example, xi represents the variance of each region, which is
partitioned into variance explained
by other regions, as well as

an error or residual term cxi . Residual terms represent exogenous influences from other regions that could not be included
in the model, as well as the influence of a region on itself. The
regression weights p, q, r, s, and t (also known as path coefficients) represent the strength of each effective connection. The
[1]
[2]
Model Estimation
Path coefficients and residual variances are estimated recursively by fitting the implied covariance matrix to the empirical
covariance matrix. Thus, SEM uses patterns of functional connectivity (covariances) to estimate effective connectivity (path
coefficients).
Path coefficients represent the proportion of activity in one
area that is determined by the activity of other areas that project
to it. For example, in Figure 2, the structural equation for any
given connection (e.g., x1x3) contains terms that represent the
influence of other areas (e.g., the path coefficients for x1x2 and
x2x3), in addition to the path coefficient for that connection.
As a result, a path coefficient can be thought of as a semipartial
correlation, because it reflects the influence of one area on
another, with influences from other areas held constant.
Model Inference
The simplest question that can be addressed with SEM is
whether the model fits the observed data. Here, the discrepancy between the implied and empirical covariance matrices is
assessed using some goodness-of-fit statistic, such as the w2. A
model that is not consistent with the data would yield a large
w2 value, indicating a significant departure from the empirical
(i.e., expected) covariance matrix.
A principal strength of SEM is that it can be extended to
compare multiple models that represent competing hypotheses. For instance, if two regions are reciprocally connected,
SEM can be used to test whether the effective connections
between them are equal (i.e., symmetrical) or unequal
(i.e., asymmetrical). The implied covariance matrices for the
symmetrical and asymmetrical models are compared to the
empirical covariance matrix, generating two separate statistics,
w2symmetric and w2asymmetric, for their respective goodness of fit.
The model fits are then compared directly using the w2 difference test; the difference w2asymmetric w2symmetric is computed and
assessed with respect to the difference in degrees of freedom for
the two models. The test assesses whether the modification of
SEM
DCM
x1
x1
x1
x3
p
r
x3
x4
x2
x4
x1
x2
x3
x4
DCM
x1
x2
x3
x4
0 0 0
p 0 0
r 0
0 s t
0
0
0
0
a12 a13
0 a23
0
0
0
0
x1
x2
x3
x4
0
0
a34
0
a34
x4
X
t
0
0
0
0
x3
a24
u2
X= X+
SEM
a23
b24
u1
a13
x2
c11
a12
x2
589
= AX + uBX + Cu
x1
x2
x3
x4
+ u2
0
0
0
0
0
0
0
0
0
0
0
0
0
b24
0
0
x1
x2
x3
x4
c11
0
0
0
0
0
0
0
u1
u2
Figure 2 Similarities and differences between SEM and DCM. In SEM (left), causal order is specified by a system of linear regression equations with
one set of path coefficients (b) and error terms (c). In DCM (right), causal order is specified by a system of differential equations parameterized
in terms of synaptic couplings (A), as well as exogenous inputs (u) that may influence either the synaptic couplings between regions (B) or intrinsic
activity in individual regions (C). Adapted from McIntosh, A., & Misic, B. (2013). Multivariate statistical analyses for neuroimaging data.
Annual Review of Psychology, 64, 499525.
allowing asymmetrical effects for reciprocal connections significantly improves model fit. A significant difference would
imply that the additional path coefficient improved the overall
model fit, providing evidence that the path coefficients are
different for the two connections. Functional connectivity,
which is symmetrical by definition, could not be used to
make inferences on these competing hypotheses (Mclntosh &
Gonzalez-Lima, 1994).
The hierarchical approach we have just described can also
be used to test whether effective connections differ between
conditions or groups. To test for group differences for specific
connections, several models can be nested in a single multigroup (stacked) run (McIntosh, Cabeza, & Lobaugh, 1998). In
a null model, path coefficients are constrained to be the same
for all groups, yielding the same implied covariance matrix for
each group. The alternative model allows path coefficients for
those connections to vary, yielding a separate implied covariance matrix for each group. If the fit is significantly improved
by allowing path coefficients to vary, then there is a significant
difference in those effective connections between conditions.
So far, we have described how SEM can be used in a confirmatory manner, where the causal structure is predefined
based on known anatomy and the inferential focus is on
whether specific effective connections change between tasks.
Bullmore et al. (2000) proposed a more relativistic approach to
model selection, where only the nodes of the network are
specified a priori, while the connectivity of the model is filled
out in a data-driven manner. The procedure starts with a null
model, in which all path coefficients are set to zero. At each
iteration, the path coefficient with the largest modification
index (the improvement in model fit if that path coefficient
were allowed to freely vary) is temporarily unconstrained and

added to the model. Since the addition of any path will
improve the w2 value, the modification is evaluated using a
parsimonious fit index, which is high for models that have
both a well-fitting implied covariance matrix and the fewest
paths (Bollen, 1986). A path is added permanently only if
it improves the fit index; otherwise, the path with the next
highest modification index is unconstrained and evaluated.
The procedure continues until the fit index cannot be increased
further by adding paths, resulting in a model that optimally
fits the observed data. There is a distinct possibility of capitalization on chance with such an iterative fitting procedure,
however, cross-validation either within the sample or on a
new sample is necessary.
Dynamic Causal Modeling

DCM is a Bayesian framework for estimating experimentally
induced changes in effective connectivity. Unlike SEM and
Granger causality, it seeks to estimate causal influence at the
level of the underlying neuronal dynamics, rather than at the
level of the observations (e.g., fMRI BOLD signal or EEG/MEG)
(Friston, Harrison, & Penny, 2003).
Causal Model
As with SEM, an initial model of causal influence is defined by
specifying a set of regions, which may be chosen based on
hypotheses or analyses. Each region in the model is composed
of neuronal subpopulations intrinsically coupled to each
590
other. Neuronal populations at each region are extrinsically

coupled to each other, forming a network. The activity of
each neuronal population is governed by a set of coupled
stochastic or ordinary differential
equations that relate the

rate of change of activity @x
to
current
activity (x):
@t
@x
f x, u, yc
@t
[3]
Synaptic coupling between populations is mathematically

represented by introducing terms for the state of one population into the equation for the state of another population,
thereby allowing the former to influence the latter. The speed
with which one population influences another is described by
a set of coupling parameters (yc). The coupling parameters yc
are unknown, and the purpose of DCM is to infer them,
analogous to path coefficients in SEM but focusing on the
observed time series. Exogenous influences (u), representing
experimental manipulations, manifest as external inputs that
induce changes in an individual population or in the coupling
between populations.
Forward Model
The underlying causal model describes the temporal evolution
of neuronal activity. To allow comparison between the causal
model and the observed data, a forward model is used to
translate this neural activity into predicted neuroimaging measurements, analogous to the implied covariance matrices in
SEM. The forward model is a mapping (g) from the underlying
neuronal activity (x) to some feature of the data (y):

y g x, yf
[4]
The forward model is chosen according to the imaging
modality used in the experiment. If the data are evoked
responses, such as event-related potentials or fields, the
forward model g is the lead field matrix, modeling the
propagation of electric current or magnetic fields though
the brain, cerebrospinal fluid, skull, and scalp. The location
and orientation of the source dipole are parameterized by yf
(Kiebel, David, & Friston, 2006). If the data are BOLD
contrast, g models the hemodynamic response by mapping
local neuronal activity to changes in blood flow, blood
volume, and deoxygenated hemoglobin (Buxton, Wong, &
Frank, 1998). In that case, parameters yf represent rate
constants of vasodilatory signal decay and autoregulatory
feedback by blood flow (Stephan, Weiskopf, Drysdale,
Robinson, & Friston, 2007).
Figure 2 demonstrates that SEM and DCM have much in
common (McIntosh and Misic, 2013). From the perspective of
SEM, the extrinsic synaptic couplings implemented in DCM
can be thought of as the grand average effective connectivity
across all conditions and the modulatory effects as the changes
in extrinsic connectivity due to experimental manipulation.
From the perspective of DCM, SEM can be thought of as a
special case in which the system is driven by noise rather than
systematic exogenous inputs (Figure 2), while the interactions
are linear and take place at the level of the observations, rather
than at the neural level (McIntosh and Misic, 2013).
Model Inversion
Once the causal model has been translated from neuronal
activity to predicted data (e.g., ERPs and BOLD signal), it can
be compared to the observed data to estimate the unknown
parameters of the model, including the synaptic couplings. In
DCM, the comparison between predicted and observed data is
done within a Bayesian framework. Unknown model parameters are assumed to be random variables. Before the experiment
is performed, these parameters have a prior distribution, which
reflects a priori knowledge about their values. A prior distribution constrains the unknown parameters to an interval or to a
fixed value. For instance, if two regions share no known anatomical connection, their synaptic coupling may be assumed
to be zero. Likewise, prior empirical knowledge may be used to
set the likely range of values of some hemodynamic
parameters.
Following the experiment, the data are used to update the
model (i.e., estimate the parameters), resulting in a posterior
distribution for each parameter, which reflects both prior
beliefs and empirical knowledge. This updating procedure
(Bayesian model inversion) seeks to maximize the model evidence, defined as the probability of the data given the present
model. Model evidence is highest for models that explain the
data accurately and have the fewest parameters.
Inference
DCMs allow statistical inference on models and on parameters
(Stephan et al., 2007, 2010). Two models can be compared
directly by taking either the ratio of their respective evidence
(Kass & Raftery, 1995) or the difference in their respective log
evidence. A model with evidence more than 20 times greater
than another model is considered stronger. This procedure
(Bayesian model selection) can be used to make a wide variety
of comparisons, such as DCMs with different inputs, different
anatomical connections, and different priors. Models with
different numbers of parameters can be compared directly
because evidence takes into account model complexity. Once
the optimal model is selected, specific parameters can be statistically assessed with respect to their posterior densities.
Note that the relative log evidence (or log Bayesian factor)
plays exactly the same role as the difference in w2 goodness-offit statistics in SEM. As we will see in the next section, in
Granger causality, the implicit likelihood of two models is
indexed by the F-statistic. Thus, all of these statistics can be
regarded as comparing the likelihood of models with and
without particular connections or dependencies.
Granger Causality
Autoregressive Models
If the past of signal x1 contains information that can help to
predict the future of another signal x2 above and beyond
information contained in the past of x2 itself, then x1 is said
to have causal influence on x2 (Wiener, 1956). Assuming that it
is purely linear, this causal relationship can be mathematically
represented as a linear regression, where the past values of x1
are used to predict the present value of x2 (Granger, 1969). In

other words, if the prediction error for present values of x2 is
reduced by inclusion of past values of x1, x1 exerts causal
influence on x2 (Ding, Chen, & Bressler, 2006; Seth, 2007).
Notice that time is important in making inferences about
effective connectivity, similar to DCM with time delays, but
unlike SEM, which focuses on zero-order covariances. For any
given pair of signals, causal influence can be assessed in both
directions by reversing their roles, allowing causal effects (i.e.,
effective connectivity) to be either reciprocal or unidirectional.
In the context of neuroimaging, where the focus is on causal
relationships within a network of brain regions, this definition
can be extended to the multivariate case, such that the present
activity of all regions is predicted by the past activity of all other
regions. Maintaining the assumption that they are linear, these
causal relationships can be mathematically represented as a
multivariate linear regression, also known as a multivariate
vector autoregressive (MVAR) model (Goebel, Roebroeck,
Kim, & Formisano, 2003). At the outset, the model will contain
terms for every possible connection in the network, with each
connection tested individually to determine if it is significantly
different from zero. In this manner, a directed subnetwork
depicting causal flow can be extracted without an a priori
hypothesis about precise pattern of effective connectivity
among regions, analogous to the relativistic SEM approach
(Bullmore et al., 2000).
An MVAR model of order m seeks to predict the present
(tth) values of p variables (e.g., brain regions) as a linear
combination of their m previous values. The tth sample from
the multivariate time series is represented as a p-dimensional
vector X(t):
X t
m
X
AiX t i Et
[5]
i1
The ith matrix A(i) has dimensions p p and contains autoregressive coefficients for time lag i, which can be estimated by
ordinary least squares. E(t) is a vector of residuals. The present
value of the jth region xj(n) is a linear combination of m past
values of all other regions, weighted by the elements of the jth
column of matrix A(i). Thus, for an individual effective connection, the influence of all other regions in the network is
accounted for and partialled out. Since the effective connections are formulated as regression equations, their significance
is typically assessed via the F-test. Alternatively, a confidence
interval on the autoregressive coefficients can be constructed
by bootstrapping (Roebroeck, Formisano, & Goebel, 2005).
591
power in some signal x1 that can be attributed to another signal

x2. Spectral Granger causality is closely related to the directed
transfer function (Kaminski et al., 2001) and partial directed
coherence (Baccala & Sameshima, 2001).
The second innovation extends Granger causality to include
nonlinear causal influences between signals. Here, the extent to
which past values of one signal predict the present value of
another is assessed by conditional mutual information, rather
than linear regression known as transfer entropy (TE). This
formulation defines causal influence as a directed exchange
of information (Schreiber, 2000; Vicente, Wibral, Lindner, &
Pipa, 2011). Specifically, TE from x1 to x2 is the decrease of
uncertainty in future values of x2 due to knowledge of past
values of x1, given past values of x2. The advantage of this
approach is that it does not assume any particular causal
order (TE is computed for all pairwise connections) nor any
particular type of causal influence (TE is sensitive to linear and
nonlinear effects). Although TE was a bivariate measure in its
initial formulation, it has been extended to the multivariate
case such that confounding influences from intervening
regions (i.e., indirect coupling) are accounted for and partialled out (Vakorin, Krakovska, & McIntosh, 2009).
Summary
Effective connectivity describes the distributed network interactions that give rise to mental operations. A diverse repertoire
of techniques has been developed to accommodate different
assumptions, imaging modalities, and experimental questions.
The techniques we have outlined often differ mathematically
and sometimes philosophically, but they all represent specific
and complementary models of how patterns of influence are
established within a network of neural elements and how these
patterns support mental function.

Bayesian Model Inversion; Bayesian Model Inference; Distributed
Bayesian Inversion of MEG/EEG Models; Dynamic Causal Models for
fMRI; Dynamic Causal Models for Human Electrophysiology: EEG,
MEG, and LFPs; Forward Models for EEG/MEG; Granger Causality;
Models of fMRI Signal Changes; Neural Mass Models; Resting-State
Functional Connectivity.
Spectral and Nonlinear Extensions
References
The Granger framework has been further developed and

adapted for specific types of signals and causal relationships,
two of which we outline here. The first innovation concerns
signals that naturally contain strong oscillatory components in
specific bands, such as electromagnetic neural activity. The
Granger framework can be extended to the frequency domain,
allowing a spectral representation of causal influence (Ding
et al., 2006; Geweke, 1982; Kaminski, Ding, Truccolo, &
Bressler, 2001). Spectral Granger causality is applied to signals
that have been transformed to the frequency domain; it is
calculated for each frequency and interpreted as the total
Aertsen, A., Gerstein, G., Habib, M., & Palm, G. (1989). Dynamics of neuronal firing
correlation: modulation of effective connectivity. Journal of Neurophysiology,
61(5), 900917.
Baccala, L., & Sameshima, K. (2001). Partial directed coherence: A new concept in
neural structure determination. Biological Cybernetics, 84(6), 463474.
Bollen, K. (1986). Sample size and bentler and bonetts nonnormed fit index.
Psychometrika, 51(3), 375377.
Bressler, S., & McIntosh, A. (2007). The role of neural context in large-scale
neurocognitive network operations. In V. Jirsa & A. McIntosh (Eds.), Handbook of
brain connectivity (pp. 403419). Berlin: Springer.
Bullmore, E., Horwitz, B., Honey, G., Brammer, M., Williams, S., & Sharma, T. (2000).
How good is good enough in path analysis of fmri data? NeuroImage, 11(4),
289301.
592
Buxton, R., Wong, E., & Frank, L. (1998). Dynamics of blood flow and oxygenation
changes during brain activation: The balloon model. Magnetic Resonance in
Medicine, 39(6), 855864.
Ding, M., Chen, Y., & Bressler, S. (2006). Granger causality: Basic theory and
application to neuroscience. In S. Schelter, N. Winterhalder & J. Timmer (Eds.),
Handbook of time series analysis (p. 437). Wiley-VCH.
Friston, K. J. (1994). Functional and effective connectivity in neuroimaging: A
synthesis. Human Brain Mapping, 2(12), 5678.
19(4), 12731302.
Geweke, J. (1982). Measurement of linear dependence and feedback between multiple
time series. Journal of the American Statistical Association, 77(378), 304313.
Goebel, R., Roebroeck, A., Kim, D., & Formisano, E. (2003). Investigating directed
cortical interactions in time-resolved fmri data using vector autoregressive modeling
and granger causality mapping. Magnetic Resonance Imaging, 21(10), 12511261.
Granger, C. (1969). Investigating causal relations by econometric models and crossspectral methods. Econometrica, 37, 424438.
Joreskog, K., Sorbom, D., Magidson, J., & Cooley, W. (1979). Advances in factor
analysis and structural equation models. Cambridge, MA: Abt Books.
Kaminski, M., Ding, M., Truccolo, W., & Bressler, S. (2001). Evaluating causal relations
in neural systems: Granger causality, directed transfer function and statistical
assessment of significance. Biological Cybernetics, 85(2), 145157.
Kass, R., & Raftery, A. (1995). Bayes factors. Journal of the American Statistical
Association, 90(430), 773795.
Kiebel, S., David, O., & Friston, K. (2006). Dynamic causal modelling of evoked
responses in eeg/meg with lead field parameterization. NeuroImage, 30(4),
12731284.
Loehlin, J. (1987). Latent variable models: An introduction to factor, path, and structural
equation analysis. Hillsdale, NJ: Lawrence Erlbaum.
McArdle, J., & McDonald, R. (1984). Some algebraic properties of the reticular action
model for moment structures. British Journal of Mathematical and Statistical
Psychology, 37(2), 234251.
McIntosh, A. (2000). Towards a network theory of cognition. Neural Networks, 13(89),
861870.
McIntosh, A., Cabeza, R., & Lobaugh, N. (1998). Analysis of neural interactions
explains the activation of occipital cortex by an auditory stimulus. Journal of
McIntosh, A., & Gonzalez-Lima, F. (1991). Structural modeling of functional neural
pathways mapped with 2-deoxyglucose: Effects of acoustic startle habituation on the
auditory system. Brain Research, 547(2), 295302.
McIntosh, A., Grady, C., Ungerleider, L., Haxby, J., Rapoport, S., & Horwitz, B. (1994).
Network analysis of cortical visual pathways mapped with pet. Journal of
McIntosh, A. R., & Korostil, M. (2008). Interpretation of neuroimaging data based on
network concepts. Brain Imaging and Behavior, 2(4), 264269.
McIntosh, A., & Misic, B. (2013). Multivariate statistical analyses for neuroimaging
data. Annual Review of Psychology, 64, 499525.
Mclntosh, A., & Gonzalez-Lima, F. (1994). Structural equation modeling and its
application to network analysis in functional brain imaging. Human Brain Mapping,
2(12), 222.
Roebroeck, A., Formisano, E., & Goebel, R. (2005). Mapping directed influence over the
brain using granger causality and fmri. NeuroImage, 25(1), 230242.
Schreiber, T. (2000). Measuring information transfer. Physical Reviews Letters, 85(2),
461464.
Seth, A. (2007). Granger causality. Scholarpedia, 2(7), 1667.
Stephan, K., Penny, W., Moran, R., den Ouden, H., Daunizeau, J., & Friston, K.
(2010). Ten simple rules for dynamic causal modeling. NeuroImage, 49(4),
30993109.
Stephan, K., Weiskopf, N., Drysdale, P., Robinson, P., & Friston, K. (2007). Comparing
hemodynamic models with dcm. NeuroImage, 38(3), 387401.
Vakorin, V., Krakovska, O., & McIntosh, A. (2009). Confounding effects of
indirect connections on causality estimation. Journal of Neuroscience, 184(1),
152160.
Vicente, R., Wibral, M., Lindner, M., & Pipa, G. (2011). Transfer entropyA model-free
measure of effective connectivity for the neurosciences. Journal of Computational
Wiener, N. (1956). The theory of prediction. In E. Beckenbach (Ed.), Modern
mathematics for engineers (pp. 165190). New York: McGraw-Hill.
Granger Causality
A Roebroeck, Maastricht University, Maastricht, The Netherlands
Glossary
Nonstationarity In time series; exhibiting changing

statistical properties over time.
Order Of an autoregressive model; the number of past time
points (in discrete time) or order of the differential equation
(in continuous time) considered in the regression.
WAGS influence WienerAkaikeGrangerSchweder
influence; a generalized concept of causality applicable to
Markovian and non-Markovian processes, in discrete or
continuous time.
Abbreviations
ARMA Autoregressive moving average
Aggregation In time series; a process of creating a new time

series by summing or integrating values in nonoverlapping
windows.
Autoregressive model A time series model predicting values
from past observations.
G-causality Granger causality (synonym).
Markovian process A time series generating process in
which the conditional probability distribution of future
values depends only upon the present value.
AR
Autoregressive
Introduction
Granger causality or G-causality is named after econometrist
Clive Granger and designates a measurable concept of causality
or directed influence for time series data. G-causality is rooted
in econometric and time-series analysis and is defined using
predictability and temporal precedence. Grangers idea
(Granger, 1969) was to give a concrete operational and testable
(in a statistical sense) definition of causality for time series
data, based on earlier ideas of mathematician Wiener (1956).
Specifically, a variable y G-causes another variable x if the
prediction of xs values improves when we use past values of
y, given that all other relevant information z is taken into
account. Here x, y, and z can be multivariate, that is, sets of
variables, such that we can talk about a set of variables jointly
G-causing another set, conditioned on a third set. In the context of neuroimaging, these could be sets of electrodes, sensors,
voxels, or sources. The greater the number of relevant time
series is contained in z, the more strict the test of G-causality
between x and y becomes. This is because our confidence
increases that y contains unique predictive information for xs
future, which we could consider a necessary (but perhaps not
sufficient) condition for a cause of x. Omitting sources of
common influence or intervening variables could lead to spurious causality findings between x and y. A prominent attraction of G-causality over measures of instantaneous (in time)
correlation or statistical dependence is its model-based assessment of direction of influence or causality, independently in
both directions between two time series. The reliance on temporal precedence to define this direction ensures that this
direction is largely derived from information in the data
record, that is, from the dynamics of the time series. Moreover,
G-causality can be formulated in the frequency and the combined timefrequency domain, such that we can talk about, for
example, the G-causality from y to x at 40 Hz, 500 ms

post stimulus.
In brain imaging, early contributions applied G-causality to
animal electrophysiology (Bernasconi & Konig, 1999; Ding,
Bressler, Yang, & Liang, 2000; Freiwald et al., 1999) after
which it started to find applicability in neuroimaging analysis
of fMRI (Goebel, Roebroeck, Kim, & Formisano, 2003; Roebroeck, Formisano, & Goebel, 2005; Valdes-Sosa, 2004), EEG
(Astolfi et al., 2004), and MEG (Gow, Segawa, Ahlfors, & Lin,
2008; Kujala et al., 2007) signals as a tool to assess functional
or effective connectivity in task-related brain networks. Its
independent assessment of causal directions allow tests of
hypotheses concerning bottom-up and top-down, feedforward and feed-back or fully reciprocal information flow
between brain systems. In electrophysiological modalities,
these can then be associated with frequency ranges of oscillatory activity, through the possibility of frequency decomposition of G-causality. Furthermore, a fully multivariate (and
conditional) implementation of G-causality allows testing
these hypotheses in the context of a full multi-area or multisource brain network.
Implementation Using Autoregressive Models

The basic G-causality concept is general enough to allow usage
of a wealth of different predictive models to implement the
concept (see in the succeeding text), but discretetime multivariate (or vector) autoregressive (AR) models are mostly used.
Important contributions in this respect were made by Geweke
(1982, 1984) when he rigorously showed how time-domain
and frequency-domain directed influence (or feedback, as he
calls it) in the G-causal sense can be defined for vector AR
processes. In his definitions, the linear dependence between
http://dx.doi.org/10.1016/B978-0-12-397025-1.00337-7
593
594
INTRODUCTION TO METHODS AND MODELING | Granger Causality
discrete multivariate time-series x[n] and y[n] is completely

decomposed into three independent components: influence
from x to y, influence from y to x, and instantaneous correlation without direction in time, all possibly conditional on z[n].
Mathematically, this is most insightfully formulated in
terms of three vector AR processes of order p involving x[n], y
[n], and z[n]:

x n
x 0 n
zn

p
X
S Cxz
x 0 n
Ax0 ix 0 n i u0 n varu0 n T3
Cxz Szx
i1
y
n

y 0 n
zn

p
X
T3 Cyz
0
y n
Ay0 iy 0 n i v 0 n varv 0 n CT S
zy
yz
2i1 3
x n
q0 n 4 y n 5
zn
2
3
Cxyz
p
0
X
Y
0
0
0
0
Cyxz 5
q n
Aq0 iq n i w n varw n 4
i1
CTxyz CTyxz Szxy

S C0
Y 0 0T4
C T4
[1]
The measures of total linear dependence between x and y
conditional on z, linear influence from x to y conditional on
z, linear influence from y to x conditional on z, and instantaneous correlation between x and y conditional on z are defined
to be, respectively (Geweke, 1984):

Fx, yjz ln jS3 jjT3 j=Y0
Fx!yjz ln jT3 j=jT4 j
[2]
Fy!xjz ln jS3 j=jS4 j
0

Fxyjz ln jS4 jjT4 j=Y
The completeness in the decomposition of total linear
dependence follows from these definitions:
Fx, yjz- Fx!yjz- Fy!xjz- Fxyjz-
[3]
Each of these measures ranges from 0 to infinity. The two

directed measures implement G-causality by quantifying the
decrease in residual variance (in a multivariate sense as the
determinant of a covariance matrix) when adding the other
causing variable to the AR prediction model, in a loglikelihood ratio form. The inclusion of z[n] in all three AR
processes ensures proper conditioning on information in zs
past. Frequency-domain compositions of each of these measures can be derived from the matrix-valued transfer function
of the AR processes (Chen, Bressler, & Ding, 2006):
!1
p
X
Aiexpj2pfi
[4]
H f I
i1
Gewekes frequency-domain measures have the property of

integrating (over all frequencies) to their corresponding timedomain measures making it true frequency decompositions of
the measures defined above. Other frequency-decomposed
measures of influence or causality, such as the directed transfer
function (Kaminski, Ding, Truccolo, & Bressler, 2001) and
partial directed coherence (Sameshima & Baccala, 1999) are

also derived from the transfer function and are closely related.
Concrete estimation of G-causality can proceed by estimating AR models of appropriate order p from recorded brain
imaging data, for instance by linear regression or solving the
YuleWalker equations on the datas autocovariance series
(Reinsel, 1997). Although formulation in terms of three AR
processes makes Gewekes influence measures insightful, they
can be also identified from a data record by spectral factorization rather than AR model estimation (Bernasconi & Konig,
1999; Dhamala, Rangarajan, & Ding, 2008).
Limitations, Invariances, and Extensions of the AR

Formulation
The AR model implementation of G-causality has its shortcomings including limited robustness against nonstationarity,
additive noise and aggregation (time-window averaging).
Many of these have been recognized in econometric literature
early on and proposed solutions consist in using preprocessing
strategies such as detrending or differencing, and particularly
in more sophisticated time series models, such as
autoregressive moving average (ARMA) models (Granger,
1980). In brain imaging, proposals for more sophisticated
G-causality modeling have included state-space ARMA formulations (Nalatore, Ding, & Rangarajan, 2007; Solo, 2006), nonlinear basis function models (Freiwald et al., 1999), switching
linear systems (Smith, Pillai, Chen, & Horwitz, 2009), and
time-varying models (Havlicek, Jan, Brazdil, & Calhoun,
2010; Hesse, Moller, Arnold, & Schack, 2003) for nonstationary data.
Brain imaging signals can indeed be nonstationary over
sufficiently long time periods and the acquisition instrumentation invariably adds noise to the recorded signals, making
these important considerations in G-causality analysis. The
usage of G-causality for fMRI signals is particularly challenging
since neuronal signals are essentially low-pass filtered and
temporally undersampled and the hemodynamic low-pass filter can differ between brain areas in the same subject
(Roebroeck et al., 2005; Roebroeck, Formisano, & Goebel,
2009). However, it has been shown that unbiased G-causality
estimators can be constructed in the bivariate case (Roebroeck
et al., 2005) and that, principally, AR G-causality is robust
against hemodynamic filtering (Deshpande, Sathian, & Hu,
2010; Ryali, Supekar, Chen, & Menon, 2010; Schippers,
Renken, & Keysers, 2011; Stevenson & Kording, 2010). In
fact, Seth, Chorley, and Barnett (2013) show that, rather than
hemodynamic low-pass filtering, it is slow temporal sampling
in fMRI acquisition that can lead to spurious causality in the
multivariate AR implementation.
The robustness of a G-causality estimate largely derives
from invariance properties of the prediction model underlying
the estimate. The AR formulation of G-causality has the property of invariance under invertible linear filtering. More precisely, the above measures of influence remain unchanged if
variables are each premultiplied with different invertible lag
operators (Geweke, 1982). In practice the order of the estimated VAR model would need to be sufficient to accommodate these operators. Beyond invertible linear filtering, an
595
P X1 1, t jX1 t, 1, X2 t, 1, X3 t, 1

P X1 1, t jX1 t, 1,X3 t, 1
[5]
ARMA formulation has further invariances. Solo (2006)

showed that causality in an ARMA model is preserved under
sampling and additive noise. Finally, Amendola, Niglio, and
Vitale (2010) show the class of ARMA models to be closed
under aggregation operations, which include both sampling
and time-window averaging.
Formal Definitions and Generalization

Almost simultaneous with Grangers work, Akaike (1968),
and Schweder (1970) introduced similar concepts of influence, prompting (Valdes-Sosa, Roebroeck, Daunizeau, &
Friston, 2010) to coin the general term WAGS influence (for
WienerAkaikeGrangerSchweder). This is a generalization
of a proposal by Aalen (1987) and Aalen and Frigessi (2007)
who was among the first to point out the connections
between Grangers and Schweders influence concepts. Within
this framework we can define several general types of WAGS
influence, which are applicable to both Markovian and
non-Markovian processes, in discrete or continuous time.
Introducing notation for both continuous and discrete
time, for three vector time series X1(t), X2(t), X3(t) we wish
to know if time series X1(t) is influenced by time series X2(t)
conditional on X3(t). Let X[a, b] {X(t), t 2 [a, b]} denote the
history of a time series in the discrete or continuous time
interval [a, b]. The first categorical distinction is based on
what part of the present or future of X1(t) can be predicted by
the past or present of X2(t2) t2 t. This leads to the following
classification (Florens, 2003; Florens & Fougere, 1996):
If X2(t2) : t2 < t, can influence any future value of X1(t) it is a

global influence.
If X2(t2) t2 < t, can influence X1(t) at time t it is a local
influence.
If X2(t2) t2 t, can influence X1(t) it is a contemporaneous
influence.
A second distinction is based on predicting the whole probability distribution (strong influence) or only given moments
(weak influence). Since the most natural formal definition is
one of independence, every influence type amounts to the
negation of an independence statement. The two classifications
give rise to six types of independence and corresponding influence as set out in Table 1.
To illustrate, X1(t) is strongly, conditionally, and globally
independent of X2(t) given X3(t), if
Table 1
That is, the probability distribution of the future values of X1

does not depend on the past of X2, given that the information in
the past of both X1 and X3 has been taken into account. When
this condition does not hold we say X2(t) strongly, conditionally, and globally influences (SCGi) X1(t) given X3(t). Here, we
use a convention for intervals [a, b] which indicates that the left
endpoint is included but not the right and that b precedes a.
Note that the whole future of Xt is included (hence the term
global), and the whole past of all time series is considered. This
means these definitions accommodate non-Markovian processes (for Markovian processes, we only consider the previous
time point). Furthermore, these definitions do not depend on
an assumption of linearity or any given functional relationship
between time series. Note also that this definition is appropriate
for point processes, discrete and continuous time series, even for
categorical (qualitative-valued) time series. The challenge with
this formulation is that it calls on the whole probability distribution and therefore its practical assessment requires the use of
measures such as mutual information that estimate the probability densities nonparametrically.
Concepts of influence in the G-causality tradition are
defined based on expectations, making them measures of
weak independence as defined above. Consider weak conditional local independence in discrete time, which is defined:
EX1 t DtjX1 t, 1,X2 t, 1,X3 t, 1
EX1 t DtjX1 t, 1, X3 t, 1
When this condition does not hold we say X2 weakly,

conditionally, and locally influences (WCLi) X1 given X3. This
is the case tested with the discrete AR (or ARMA) implementation discussed earlier.
In comparison weak conditional local independence in
continuous time is defined:
EY1 t jY1 t, 1, Y2 t, 1, Y3 t, 1
EY1 t jY1 t, 1, Y3 t, 1
Local (immediate
future)
Contemporaneous
[7]
To test this continuous WAGS influence concept, we could

consider a first-order stochastic differential equation model for
Y [Y1Y2Y3]:
dY BYdt dv
[8]
When the goal is to estimate WAGS influence for discrete

data starting from a continuous time model in eqn [8], one has
Types of influence defined by absence of the corresponding independence relations
Global (all horizons)
[6]
Strong (probability distribution)
Weak (expectation)
By absence of strong, conditional, global independence:

X2(t)SCGi X1(t) k X3(t)
By absence of strong, conditional, local independence:
X2(t)SCLi X1(t) k X3(t)
By absence of strong, conditional, contemporaneous
independence:
X2(t)SCCi X1(t) k X3(t)
By absence of weak, conditional, global independence:

X2(t)WCGi X1(t) k X3(t)
By absence of weak, conditional, local independence:
X2(t)WCLi X1(t) k X3(t)
By absence of weak, conditional, contemporaneous
independence:
X2(t)WCCi X1(t) k X3(t)
Strong and weak conditional global influence (SCGi and WCGi); strong and weak conditional local influence (SCLi and WCLi); strong and weak conditional contemporaneous
influence (SCCi and WCCi).
596
to explicitly model the mapping to discrete time. Mapping

continuous time predictions to discrete samples is a wellknown topic in engineering and can be solved by explicit
integration over discrete time steps (Roebroeck, Seth, &
Valdes-Sosa, 2011). Although this uniquely defines the mapping from continuous to discrete parameters, it does not solve
the reverse assignment of estimating continuous model parameters from discrete data. Doing so requires a solution to the
aliasing problem (Mccrorie, 2003) in continuous stochastic
system to estimate continuous time AR models (McCrorie,
2002), and continuous time ARMA models (Chambers &
Thornton, 2012) from discrete data (Bergstrom, 1966, 1984;
Phillips, 1973, 1974). This relates generalized WAGS influence
to causal modeling frameworks formulated in continuous
time, such as dynamic causal modeling (Friston, Harrison, &
Penny, 2003), as further explored in Valdes-Sosa et al. (2010).

Magnetoencephalography; Functional MRI Dynamics; High-Speed,
High-Resolution Acquisitions; Temporal Resolution and Spatial
Resolution of fMRI; INTRODUCTION TO ANATOMY AND
PHYSIOLOGY: Functional Connectivity; INTRODUCTION TO
METHODS AND MODELING: Dynamic Causal Models for fMRI;
Dynamic Causal Models for Human Electrophysiology: EEG, MEG, and
LFPs; Effective Connectivity; Methodological Issues in fMRI Functional
Connectivity and Network Analysis; Resting-State Functional
Connectivity; INTRODUCTION TO SYSTEMS: Network
Components.
References
Aalen, O. O. (1987). Dynamic modeling and causality. Scandinavian Actuarial Journal,
1987(34), 177190.
Aalen, O. O., & Frigessi, A. (2007). What can statistics contribute to a causal
understanding? Scandinavian Journal of Statistics, 34, 155168.
Akaike, H. (1968). On the use of a linear model for the identification of feedback
systems. Annals of the Institute of Statistical Mathematics, 20, 425439.
Amendola, A., Niglio, M., & Vitale, C. (2010). Temporal aggregation and closure of
VARMA models: Some new results. In M. Greenacre, N. C. Lauro, & F. Palumbo
(Eds.), Data analysis and classification: Studies in classification, data analysis, and
knowledge organization (pp. 435443): Springer.
Astolfi, L., Cincotti, F., Mattia, D., Salinari, S., Babiloni, C., Basilisco, A., et al. (2004).
Estimation of the effective and functional human cortical connectivity with structural
equation modeling and directed transfer function applied to high-resolution EEG.
Bergstrom, A. R. (1966). Nonrecursive models as discrete approximations to systems of
stochastic differential equations. Econometrica, 34, 173182.
Bergstrom, A. R. (1984). Continuous time stochastic models and issues of aggregation.
In : Z.Griliches, & M. D. Intriligator (Eds.), Handbook of econometrics: Vol. II.
Amsterdam: Elsevier.
Bernasconi, C., & Konig, P. (1999). On the directionality of cortical interactions studied
by structural analysis of electrophysiological recordings. Biological Cybernetics,
81, 199210.
Chambers, M. J., & Thornton, M. A. (2012). Discrete time representation of continuous
time ARMA processes. Econometric Theory, 28, 219238.
Chen, Y., Bressler, S. L., & Ding, M. (2006). Frequency decomposition of conditional
Granger causality and application to multivariate neural field potential data. Journal
of Neuroscience Methods, 150, 228237.
Deshpande, G., Sathian, K., & Hu, X. (2010). Effect of hemodynamic variability on
Granger causality analysis of fMRI. NeuroImage, 52, 884896.
Dhamala, M., Rangarajan, G., & Ding, M. (2008). Analyzing information flow in brain
networks with nonparametric Granger causality. NeuroImage, 41, 354362.
Ding, M., Bressler, S. L., Yang, W., & Liang, H. (2000). Short-window spectral analysis
of cortical event-related potentials by adaptive multivariate autoregressive modeling:
Data preprocessing, model validation, and variability assessment. Biological
Cybernetics, 83, 3545.
Florens, J. (2003). Some technical issues in defining causality. Journal of
Econometrics, 112, 127128.
Florens, J. P., & Fougere, D. (1996). Noncausality in continuous time. Econometrica,
64, 11951212.
Freiwald, W. A., Valdes, P., Bosch, J., Biscay, R., Jimenez, J. C., Rodriguez, L. M., et al.
(1999). Testing non-linearity and directedness of interactions between neural
groups in the macaque inferotemporal cortex. Journal of Neuroscience Methods,
94, 105119.
Geweke, J. F. (1982). Measurement of linear dependence and feedback
between multiple time series. Journal of the American Statistical Association, 77,
304324.
Geweke, J. F. (1984). Measures of conditional linear dependence and feedback between
time series. Journal of the American Statistical Association, 79, 907915.
Goebel, R., Roebroeck, A., Kim, D. S., & Formisano, E. (2003). Investigating directed
cortical interactions in time-resolved fMRI data using vector autoregressive
modeling and Granger causality mapping. Magnetic Resonance Imaging, 21,
12511261.
Gow, D. W., Jr., Segawa, J. A., Ahlfors, S. P., & Lin, F. H. (2008). Lexical influences on
speech perception: A Granger causality analysis of MEG and EEG source estimates.
Granger, C. W. J. (1969). Investigating causal relations by econometric models and
cross-spectral methods. Econometrica, 37, 424438.
Granger, C. W. J. (1980). Testing for causality: A personal viewpoint. Journal of
Economic Dynamics and Control, 2, 329352.
Havlicek, M., Jan, J., Brazdil, M., & Calhoun, V. D. (2010). Dynamic Granger causality
based on Kalman filter for evaluation of functional network connectivity in fMRI data.
Hesse, W., Moller, E., Arnold, M., & Schack, B. (2003). The use of time-variant EEG
Granger causality for inspecting directed interdependencies of neural assemblies.
Journal of Neuroscience Methods, 124, 2744.
Kaminski, M., Ding, M., Truccolo, W. A., & Bressler, S. L. (2001). Evaluating causal
relations in neural systems: Granger causality, directed transfer function and
statistical assessment of significance. Biological Cybernetics, 85, 145157.
Kujala, J., Pammer, K., Cornelissen, P., Roebroeck, A., Formisano, E., & Salmelin, R.
(2007). Phase coupling in a cerebro-cerebellar network at 8-13 Hz during reading.
McCrorie, J. R. (2002). The likelihood of the parameters of a continuous time
vector autoregressive model. Statistical Inference for Stochastic Processes, 5,
273286.
Mccrorie, J. R. (2003). The problem of aliasing in identifying finite parameter
continuous time stochastic models. Acta Applicandae Mathematica, 79, 916.
Nalatore, H., Ding, M., & Rangarajan, G. (2007). Mitigating the effects of measurement
noise on Granger causality. Physical Review E: Statistical, Nonlinear, and Soft
Matter Physics, 75, 031123.
Phillips, P. C. B. (1973). The problem of identification in finite parameter continuous
time models. Journal of Econometrics, 1, 351362.
Phillips, P. C. B. (1974). The estimation of some continuous time models.
Econometrica, 42, 803823.
Reinsel, G. C. (1997). Elements of multivariate time series analysis. New York: SpringerVerlag.
Roebroeck, A., Formisano, E., & Goebel, R. (2005). Mapping directed influence over the
brain using Granger causality and fMRI. NeuroImage, 25, 230242.
Roebroeck, A., Formisano, E., & Goebel, R. (2009). The identification of interacting
networks in the brain using fMRI: Model selection, causality and deconvolution.
Neuroimage, 58(2), 296302.
Roebroeck, A., Seth, A. K., & Valdes-Sosa, P. (2011). Causal time series analysis of
functional magnetic resonance imaging data. Journal of Machine Learning
Research: Workshop and Conference Proceedings, 12, 6594.
Ryali, S., Supekar, K., Chen, T., & Menon, V. (2010). Multivariate dynamical
systems models for estimating causal interactions in fMRI. Neuroimage, 54(2),
807823.
Sameshima, K., & Baccala, L. A. (1999). Using partial directed coherence to
describe neuronal ensemble interactions. Journal of Neuroscience Methods, 94,
93103.
Schippers, M. B., Renken, R., & Keysers, C. (2011). The effect of intra- and inter-subject
variability of hemodynamic responses on group level Granger causality analyses.

Schweder, T. (1970). Composable Markov processes. Journal of Applied Probability, 7,
400410.
Seth, A. K., Chorley, P., & Barnett, L. C. (2013). Granger causality analysis of fMRI
BOLD signals is invariant to hemodynamic convolution but not downsampling.
Smith, J. F., Pillai, A., Chen, K., & Horwitz, B. (2009). Identification and validation of
effective connectivity networks in functional magnetic resonance imaging using
switching linear dynamic systems. NeuroImage, 52, 10271040.
Solo, V. (2006). On causality I: Sampling and noise. In Proceedings of the 46th IEEE
conference on decision and, control (pp. 36343639).
Stevenson, I. H., & Kording, K. P. (2010). On the similarity of functional connectivity
between neurons estimated across timescales. PLoS One, 5, e9206.
597
Valdes-Sosa, P. A. (2004). Spatio-temporal autoregressive models defined over brain

manifolds. Neuroinformatics, 2, 239250.
Valdes-Sosa, P., Roebroeck, A., Daunizeau, J., & Friston, K. (2010). Effective
connectivity: Influence, causality and biophysical modeling. Neuroimage, 58,
339361.
Wiener, N. (1956). The theory of prediction. In E. F. Berkenbach (Ed.), Modern
mathematics for engineers. New York: McGraw-Hill.
Relevant Websites
http://www.scholarpedia.org/article/Granger_causality.
Information Theoretical Approaches

M Wibral, Goethe University, Frankfurt, Germany
V Priesemann, Max Planck Institute for Brain Research, Frankfurt, Germany
Nomenclature
d

AXt a1 , . . . aj , . . . aJ
aj
H(X)
H(X|Y)
h(x)
h(x|y)
I(X; Y)
I(X; Y|Z)
i(x, y)
i(x; y|z)
Notes regarding t
Physical or true interaction delay

between two processes
Set of all possible outcomes of Xt
Specific outcome of a random
variable x
Entropy
Conditional entropy
Information content
Conditional information content
Mutual information
Conditional mutual information
Local mutual information
Local conditional mutual
information
Whenever necessary, the index t is
detailed as t1, t2,..., tk. In contrast,
for stationary processes, the index
t can be omitted
Information, Meaning, and Neuroscience

Meaning Versus Information
Information theory in neuroscience is often misunderstood.
At the heart of the confusion lies the fact that in everyday
language, we use information and meaning as synonymous.
However, meaning is ultimately relative to the human receiver
of information. Information that is meaningful for one person
say a message with a reply to a question the receiver sent earlier
may be meaningless for an accidental receiver of the message
who does not know the initial question or even how to read.
The information content of the message however should stay
the same independent of who receives it. Hence, information
theory devised a measure of information content that is independent of the receiver. In the following paragraphs, we will
provide an intuitive introduction to this measure.
The fundamental definition of information content was
given by Shannon in Shannon (1948) and relies on the
notion that an event that we observe reduces the uncertainty
(about what is still possible). In the following, we give a
heuristic derivation of the Shannon information based on
this general intuition about information. Assume, for
example, that the message in the example earlier in the text
contained the six-digit winning number sequence of a lottery
(where the six numbers were drawn at random). Then, before
reading the first digit, we are uncertain about which of 106
possible (and equally likely) number sequences the message
contains. After reading the first digit of our message, which
pXt (xt aj)

R {R1, R2}
Si, Rj
u
X(c), X(c)
t
X(s), X(s)
Xt, xt
X , Y, Z
X,Y,Z
X, Y, Z or Xt, Yt, Zt
x, y, z or xt, yt, zt
Probability that Xt has a specific

outcome aj
Joint variable (in this example of
two responses)
Random variables referring to
stimuli (Si) or responses (Rj)
Assumed interaction delay
between two processes
Cyclostationary process
and cyclostationary random
variable
Stationary process and stationary
random variable
State space representation of X at t
System
Random process
Random variable (at time point t)
Realization of the random
variable (at time point t)
will be one number between 0 and 9, only 105 possibilities

are left, and our uncertainty about the overall possible
six-digit sequences in the message is reduced. Finally, after
reading the last digit, only one six-digit sequence remains
possible, now with a probability equal to unity, and there is
no remaining uncertainty.
In this example, each time we read a digit, our uncertainty
was reduced. However, the amount of uncertainty reduction
needs to be defined. At first, it might seem that reading the first
digit reduces our uncertainty most, because it eliminated
106 105 9 105 possibilities while reading the last digit
removed only nine possibilities. Intuition however tells us
that in this example, all digits should carry equal amounts of
information. How can we define a measure that appeals to
our intuition?
The correct way to look at the earlier-mentioned problem is
in terms of the fractional change in the number of possibilities
that reading a digit provides: We see that reading the first digit
removes a fraction f of 9/10 of all possibilities, and so do all
others, including the last digit. In other words, reading the first
digit informs us about which one out of ten equiprobable
partitions of the space of all six-digit sequences of numbers
the winning number is in. The probability of being in any
one partition is 1/10. Upon reading that number, we only
have 1/10 of the initial possibilities remaining.
If we repeated the lottery with drawing six-digit codes composed of letters a, b, . . ., z, then our initial uncertainty would be
clearly bigger as there are now 266 possibilities to begin with.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00338-9
599
600
INTRODUCTION TO METHODS AND MODELING | Information Theoretical Approaches
Nevertheless, after reading all six letters in the sequence, our

uncertainty would be again zero, because only one possibility
remained. Hence, compared to the example with the numbers,
the reading of each letter must provide a greater reduction in
uncertainty. And, indeed, each letter lets us decide between one
of 26 equiprobable partitions of the remaining possibilities now,
since each letter has a probability of 1/26. Thus, reading a letter
reduces the space of potential outcomes to a fraction of f 1/26.
Therefore, it makes sense to define the information in an
event in relation to the fraction f of the original space of outcomes
or possibilities that observing this event confines us to. The
smaller this fraction, the more possibilities are excluded, the
more uncertainty is reduced, and therefore, the larger the information content of the event. The fraction of the space of all
possible events that an event ai (e.g., obtaining the letter i when
reading the first digit) takes can be measured by its probability
p(ai). Furthermore, before an event, all (remaining) possibilities
are available p(ai any event) 1. Hence, the reduction
of uncertainty by an event ai is related to the fraction f(ai)
p(any event)/p(specific event) 1/p(ai). Interestingly, this quantity f can be defined in a meaningful way even when the events in
question are no longer equiprobable, as we are only interested in
the fraction of possibilities that remain after observing a specific
event with probability p(ai).
If, in a next step, we consider the reduction of uncertainty
provided by reading two consecutive letters ai, aj at the same
time, we see that this reduces our possibilities to a fraction of
f(ai, aj) 1/p(ai, aj). As the letters were drawn independently,
this amounts to f(ai, aj) (1/p(ai))(1/p(aj)). This shows that f
itself cannot be a measure of information content, because our
intuition tells us that such a measure should be additive for
independent events and not multiplicative. A measure that
complies with the requirements in the preceding text and is
also additive is the logarithm of the fraction f(ai):
hai log f ai log
1
pai
[1]
Here, the logarithm can in principle be taken to any base.

The resulting quantity h is called the Shannon information
(content). This definition of information content also has
the desirable property that it is continuous in the changes
of the underlying probabilities. This means that if the probability of an event ai slightly changes, the corresponding
change of h(ai) is also small, that is, our measure does not
jump around with slight changes of the probability distributions. As a consequence, small errors in our assumptions
about the necessary probability distributions will not produce
arbitrarily large errors in our assessment of the information
content.
Here, we chose an intuitive introduction of the Shannon
information. Nevertheless, the definition given in Eqn [1] is
precisely the definition of the Shannon information that can
also be axiomatically derived via the average information content, called entropy (see Shannon, 1948).
Information Theory in Neuroscience

To see what information theory can add to our understanding
in neuroscience, it is useful to first define the general questions
we want to address in neuroscience. What kinds of questions

would we like to have answers to? At first glance, questions in
neuroscience seem to separate well into three levels of
understanding that have been repeatedly described (e.g.,
Marr, 1982) and that are generally considered useful:
At the functional level (originally called computational

level), we ask what information processing problem a neural system (or a part of it) tries to solve. Such problems
could, for example, be the detection of edges or objects in a
visual scene or the maintenance of information about an
object after the object is no longer in the visual scene. It is
important to note that questions at the functional level
typically revolve around entities that have a direct meaning
to us, for example, objects or specific object properties used
as stimulus categories, or operationally defined states or
concepts such as attention or working memory. An example
of an analysis carried out purely at this level is the analysis
whether a person behaves as an optimal Bayesian observer
(see references in Knill & Pouget, 2004).
At the algorithmic level (in complex systems science, this
would be called the computational perspective on a system
(Crutchfield, Ditto, & Sinha, 2010), one reason to largely
avoid the use of the word computation here), we ask what
entities or quantities of the functional level are represented by the neural system and how the system operates
on these representations using algorithms. For example,
detection of an object in noisy visual input might in
principle be solved algorithmically either by a parallel or
by a sequential search of all memories of objects ever seen
for the best match.
At the (biophysical) implementation level, we ask how the
representations and algorithms are implemented in biological neural systems. Descriptions at this level are given in
terms of the relationship between various biophysical properties of the neural system or its components, for example,
membrane currents or voltages, the morphology of neurons, and spike rates. A typical study at this level might
aim, for example, at reproducing observed physical behavior of neural circuits, such as gamma-frequency (>40 Hz)
oscillations in local field potentials by modeling the biophysical details of these circuits from the ground up
(Markram, 2006).
While this separation of levels of understanding initially

served to resolve important debates in neuroscience, there is
a growing awareness of a specific shortcoming of this classic
view: results obtained by careful study at any single one of
these levels do not constrain the possibilities at any other
level (see, e.g., the afterword by Poggio in Marr, 1982). For
example, the goal of winning a game of tic-tac-toe at the
functional level can be reached by a brute force strategy at
the algorithmic level that is implemented in a mechanical
computer (Dewdney, 1993), but it can also be reached by a
different algorithm carried out by the biological brains of
children.
As we will see, information theory serves to address the
relationships between the levels. For example, a measure called
mutual information offers powerful tools to link entities defined
at the functional level to physical quantities observed at the
implementation level. Furthermore, measures from a subfield

of information theory, called local information dynamics
(Lizier, 2013), link the algorithmic to the implementation
level. Local information dynamics establishes this link by
deriving constraints for possible algorithms from the physical
quantities (implementation level). Such constraints can be
derived, for example, by comparing the relative amounts of
stored or transferred information or by identifying the
sequence of information transfers between various parts of
the brain.
More specifically, using information theory, we can address
the following main questions:
1. How much information does a specific neural response
provide about a stimulus or experimental condition? This
question clearly relates quantities at the implementation
level, that is, physical indices of neural responses, to entities
defined by the experimenter at the functional level, such as
certain stimulus classes (for example faces, objects, and
animals) or operationally defined states such as attention.
The benefit of information theory here is that we can measure not only that a response conveys information about a
stimulus but also how much. Moreover, this can be done
without explicit knowledge of the neural encoding.
2. Which stimulus leads to responses (implementation level)
that are relatively unique for this stimulus? In other words,
which stimulus is well encoded, in the sense that the system
does indeed represent it? Again, this question asks about
entities defined at the functional level, that is, stimuli, tasks,
or states, but this time relates them to properties at the
algorithmic level, that is, how well they are represented by
the neural system.
3. If we accept the notion that the brain performs information
processing in the form of a (distributed) computation, then
this computation can be decomposed into the components
of information storage, information transfer, and
information modification to improve our understanding
of it. We may therefore ask how this computation is carried
out, that is, which biological phenomena at the implementation level subserve information storage, information transfer,
and information modification at the algorithmic level?
Clearly, this question uses data at the implementation
level (neural activity) to provide constraints for possible
algorithms. For example, if we observe no signs of information storage in the system, this may rule out algorithms that
rely heavily on storing intermediate information.
In the following sections, we will first introduce the necessary
information theoretical concepts and then proceed to answer
questions one and two that belong to the domain of neural
(en)coding and representations. Finally, we show how question three can be addressed using information theory in the
form of (local) information dynamics.
Information Theoretical Preliminaries

In this section, we introduce the necessary notation and basic
information theoretical concepts that are indispensable to
understand information theoretical analyses in neuroscience.
This is done to obtain a self-contained presentation of the
601
material for readers without a background in information

theory. Readers familiar with elementary information theory
and readers who are not interested in the precise definitions at
first reading may skip ahead to the next section.
Notation and Basic Information Theory

Notation
To avoid confusion, we first have to state what systems we wish
to apply our measures to and how we formalize observations
from these systems mathematically. We define that a system
of interest (e.g., neuron and brain area) X produces an
observed time series {x1, . . ., xt, . . ., xN} that is sampled at time
intervals D. For simplicity, we choose our temporal units such
that D 1 and hence index our measurements by t 2
{1 . . . N} . The full time series is understood as a realization
of a random process X, unless stated otherwise. This random
process is nothing but a collection of random variables Xt,
sorted by an integer index (t in our case). Each random variable
Xt, at a specific time
t, is described
by the set of all its J possible
outcomes AXt a1 , . . . aj . . . aJ and their associated probabilities pXt xt aj . Since the probabilities of a specific outcome pXt xt aj may change with t, that is, when going from
one random variable to the next, we have to indicate the
random variable Xt the probabilities belong to hence the
subscript in pXt . In sum, in this notation, the individual
random variables Xt produce realizations xt, and each of
the realizations has J different possible outcomes aj. Furthermore, the time index of a random variable Xt is necessary,
because the random variables Xt1 and Xt2 with t1 6 t2 can have
different probability distributions. When using more than
one system, the notation is generalized to multiple systems
X , Y, Z, . . . .
To clarify the conceptual distinction between a random
variable Xt and a random process X, think about the following
example. Assume one would like to obtain 20 random numbers between 1 and 6 by throwing (biased) dice. One could
do this, for example, by throwing one dice twenty times or by
throwing twenty dice, each one time. The first case represents
20 realizations of a single random variable X1. The six possible outcomes for each of these 20 realizations of the random
variable are AX1 f1; 2; 3; 4; 5; 6g, and the probability distribution of the random variable is pX1 . Here, the random
process X consists of only one random variable X1, that is, it
is of length one. In contrast, in the second case, where twenty
different dice are thrown, each dice represents a random
variable Y1, . . ., Yt, . . ., Y20, and the length of the random process Y is 20. Here, each of the random variables Yt is realized
only once and has its own probability distribution pYt . The
important difference between the two examples is that in the
second case, each of the dice in principle can have a different
bias, for example, the probability distributions pYt1 and
pYt2 can differ for t1 6 t2. Thus, in the second case, we
could bias the first dice to always yield 1 and the last dice
to always yield 6. This is impossible with the single dice of
the first example. The distinction between a random process
and a random variable is very important in the context of
stationarity, which will be discussed next.
602
Estimation of probability distributions for stationary

and nonstationary random processes
Often, the probability distributions of our random variables Xt
are unknown. Since knowledge of these probability distributions is essential to computing any information theoretical
measure, the probability distributions have to be estimated
from the observed realizations of the random variables xt.
This is only possible if we have some form of replication of
the processes we wish to analyze. From such replications, the
probabilities are estimated, for example, by counting relative
frequencies or, more generally, by a density estimation.
In general, the probability pXt xt aj to obtain the jth outcome xt aj at time t has to be estimated from replications of the
processes at the same time point t, that is, via an ensemble of
physical replications of the systems in question. Generating a
sufficient number of such physical replications of a process is
often impossible in neuroscience. For example, to obtain 105
samples, we would have to record from this number of subjects
at time t, given that the subjects were similar enough to count as
replications of a single random variable at all. Therefore, to
generate sufficient data for the estimation of pXt , one either
resorts to repetitions of parts of the process in time (often called
trials), resorts to the generation of cyclostationary processes, or
even assumes stationarity. All three possibilities will be discussed
in the following.
In neuroscience, experiments are often organized in repeated
parts (e.g., trials and stimulation blocks). The random process X
therefore repeats at tk (we do not require evenly spaced trials in
time). Thus, the probability to obtain the value xt aj can be
estimated from observations made at a sufficiently large set M
of time points tk, where we know by design of the experiment
that the process repeats itself, that is, that random variables Xtk at
certain time points tk have probability distributions identical to
the distribution at t that is of interest to us:
8 t M M 6 : pXt aj pXt aj
2 AXt
8 t k 2 M, aj
Basic information theory

Based on the previously mentioned definitions, we now define
the necessary basic information theoretical quantities. We
assume the reader is familiar with the basic concepts of probability theory. If this is not the case, the treatment in
Effenberger (2013) offers a well-written introduction. Assume
a random variable X with possible outcomes x 2 AX and a
probability distribution p(x) over these outcomes. As stated
before, the information content is the reduction in uncertainty
linked to the occurrence of a specific outcome x aj (with
probability p(x aj)) that we obtain when aj is observed. As
shown in the introduction, this uncertainty reduction entirely
depends on the probability of the event x, and the events
information content h is defined as
hx log
8n 2 , aj 2 AXt
[3]
This condition guarantees that we can estimate the necessary probability distributions pXt of the random variable X(c)
t
(c)
by looking at other random variables XtnT
of the process X(c).
Finally, for stationary processes X(s), we can substitute T in
Eqn [3] by T 1 and
pXt aj pXtn aj 8t, n 2 , aj 2 AXt
[4]
In the stationary case, the probability distribution pXt can

be estimated from the entire set of measured realizations xt.
1
log px
px
[5]
While the last term in the equation appears simpler and is

more commonly used, we will use the middle term in the
following, because it stresses that the information content of
an event is related to the inverse of its probability.
The average information content of a random variable X is
called the entropy H of the random variable:
HX
px log
x2Ax
1
px
[6]
The information content of a specific outcome x aj of X,

given we already know the outcome y ak of another variable
Y, which is not necessarily independent of X, is called conditional information content:
[2]
If the set M of time points tk that the process is repeated at

is large enough, we obtain a reliable estimate of pXt .
Cyclostationarity can be understood as a specific form of
repeating parts of the random process, where the repetitions
occur after regular intervals T. For cyclostationary processes
X(c), we assume (Gardner, 1994; Gardner, Napolitano, &
(c)
Paura, 2006) that there are random variables XtnT
at times
t nT that have the same probability distribution as X(c)
t :
8t T 2 : pXt aj pXtnT aj
From now on, we assume stationarity of all involved processes,

unless stated otherwise. Accordingly, we drop the subscript
index indicating the specific random variable, that is,
pXt p, Xt X, and xt x.
hxjy log
1
pxjy
[7]
Averaging this for all possible outcomes of X, given their

probabilities p(x|y) after the outcome y was observed, and then
averaging over all possible outcomes y that occur with p(y)
yields the conditional entropy
X
1
pxjy
y2AY
x2AX
X
1
px; y log
pxjy
x2A , y2A
HXjY
py
pxjy log
[8]
The conditional entropy H(X|Y) can be described from

various perspectives: H(X|Y) is the average amount of information that we get from making an observation of X after having
already made an observation of Y. In terms of uncertainties,
H(X|Y) is the average remaining uncertainty in X once Y was
observed. We can also say that H(X|Y) is the information in X
that cannot be obtained from Y.
The conditional entropy is used to derive the amount of
information shared between the two variables X, Y. This is
because this shared or mutual information I(X; Y) is the total
average information in one variable (H(X)) minus the average

information that is unique to this very variable (H(X|Y)).
Hence, the mutual information is defined as
IX; Y HX HXjY HY HYjX
[9]
Clearly, the mutual information is symmetrical, that is,

I(X; Y) I(Y; X).
Similarly to conditional entropy, we can also define a conditional mutual information between two variables X, Y, given the
value of a third variable Z is known:
IX; YjZ HXjZ HXjY, Z
[10]
The earlier-mentioned measures of mutual information are

averages, but they can also be used without taking the expected
value, that is, in their localized form. Although average values
like the mutual information or entropy are used more often than
their localized equivalents, it is perfectly valid to inspect local
values like the information content h. This localizability was in
fact a requirement both Shannon and Fano postulated for proper
information theoretical measures (Fano, 1961; Shannon, 1948),
and there is a growing trend in neuroscience (Lizier, Heinzle,
Horstmann, Haynes, & Prokopenko, 2011a; Wibral et al., 2014)
and in the theory of distributed computation (Boedecker, Obst,
Lizier, Mayer, & Asada, 2012; Lizier, 2013) to return to local
values. For the previously mentioned measures of mutual
information, the localized forms are listed in the following:
The local mutual information i(x; y) is defined as
ix; y log
px; y
pxpy
[11]
The local conditional mutual information is defined as

ix; yjz log
pxjy, z
pxjz
[12]
Hence, mutual information and conditional mutual information are just the expected values of these local quantities.
These quantities are called local, because they allow to quantify
mutual and conditional mutual information between single
realizations. Note however that the probabilities p() that enter
Eqns [11] and [12] are global in the sense that they are representative of all possible outcomes. In this sense, the use of local
information measures is complementary to the evaluation of
probability distributions of single random variables Xt of a
nonstationary process X via an ensemble of realizations. In
other words, a valid probability distribution has to be estimated irrespective of whether we are interested in average or
local information measures.
603
time, then the position xt1 matters for our information about
the next position xt1 of the pendulum at time t 1. Here,
analyzing just xt is not enough to describe the next position.
For example, assume xt 0 and xt1 < 0. In this case, we have a
zero crossing of the pendulum and in the next step xt1 > 0.
Conversely, if xt 0 and xt1 0 as well, the pendulum does
not move at all and the future state of the pendulum is xt1 0.
Clearly, analyzing a single position xt is not enough to inform
us about the next position of the pendulum. In this example,
looking at just one past value together with the present one (xt,
xt1) is sufficient to predict the next position xt1. Therefore,
(xt, xt1) describes the state of the pendulum at time t. In the
next paragraph, we will translate the concept of a state to our
framework of random processes.
In general, if there is any dependence between the Xt, we
have to form the smallest collection of variables
X t Xt ; Xt1 ; Xt2 ; . . . ; Xti ; . . . with ti < t that jointly make Xt1
conditionally independent of all Xtk with tk < min(ti), that is,
pxt1 , xtk jxt pxt jxt pxtk jxt
[13]
8tk < min ti 8xt1 2 AXt1 , xtk 2 AXtk , xt 2 Axt

A realization of Xt is called a state of the random process X
at time t. To obtain the states of a random process, the time
intervals between ti need not be uniform (Faes, Nollo, & Porta,
2012; Small & Tse, 2004). The process of obtaining Xt from
data is called state space reconstruction. For state space reconstruction, various optimization routines exist (Ragwitz &
Kantz, 2002; Small & Tse, 2004).
Without proper state space reconstruction, information
theoretical analyses of computational processes of a system
that are carried out will almost inevitably miscount information in the random process. Indeed, the importance of state
space reconstruction cannot be overstated; for example, a failure to reconstruct states properly leads to false-positive findings and reversed directions of information transfer as
demonstrated in Vicente, Wibral, Lindner, and Pipa (2011).
Imperfect state space reconstruction is also the underlying
principle of various modes of failure of information transfer
analysis recently demonstrated analytically (circumventing
trivial estimation problems) by Smirnov (2013).
For the remainder of the text, we therefore assume a proper
state space reconstruction. The resulting state space representations are indicated by bold case letters, that is, Xt and xt refer to
the state variables of X and their realizations, respectively. For
stationary processes, again, pXt1 pXt2 for all t1, t2 and the
indices in principle can be omitted.
Analyzing Neural Coding

Signal Representation and State Space Reconstruction
The neural signals (i.e., the random process) that we analyze
usually show history dependence. This means that the random
variables that form the random process are no longer independent, but depend on variables in their past. In this setting, a
proper description of the process requires to look at the present
and past random variables jointly. A simple example may
illustrate this: if we record the position xt of a pendulum over
As introduced in the preceding text, information theory can

serve to bridge the gap between the functional level, where we
deal with properties of a stimulus or task that bear a direct
meaning to us, and the implementation level, where we
recorded physical indices of neural activity, such as action
potentials. To this end, we use mutual information (Eqn
[10]) and derivatives thereof to answer questions like the
following:
604
1. Which (features of) neural responses (R) carry information

about (which features of) a class of stimuli (S)?
2. How much does an observer of a specific neural response r,
that is, a receiving brain area, change its beliefs about the
identity of a stimulus s, from the initial belief p(s) to the
posterior belief p(s|r) after receiving the neural response r?
3. Which specific neural response r is particularly informative
about an unknown stimulus from a certain set of stimuli?
4. Which stimulus s leads to responses that are informative
about this very stimulus, that is, to responses that can
transmit the identity of the stimulus to downstream
neurons?
In the following sections will show how to answer these questions one by one using information theory.
1. Which features of neural responses (R) carry information
about which features of a certain class of stimuli (S)?
This question can be easily answered by computing the
mutual information I(S; R) between stimulus features in an
experiment and specific features of the neural responses
(such as spike rates). Despite its deceptive simplicity, computing this mutual information can be very informative
about neural codes. For example, if we only extract certain
features Fi(r) of neural responses r, such as the time of the
first spike (e.g., Johansson & Birznieks, 2004) or the relative
spike times (Havenith et al., 2011), also with respect to an
oscillation cycle (OKeefe & Recce, 1993), and compare the
resulting mutual information for both features I(S; F1(R)),
and I(S; F2(R)), then we can see which feature carries more
information. The feature carrying more information is
potentially the one also read out by the neural system. In
general, these mutual information values give us upper
bounds on what downstream neural circuits can possibly
extract from a certain response feature dimension, such as
spike times or rate, alone. Nevertheless, one has to keep in
mind that several response features might have to be considered jointly and carry synergistic information (see
Section The Question of Ensemble Coding, below).
2. How much does an observer of a specific neural response r,
that is, a receiving brain area, change its beliefs about the
identity of a stimulus s, from the initial belief p(s) to the
posterior belief p(s|r) after receiving the neural response r?
This question is natural to ask in the setting of Bayesian
brain theories (Knill & Pouget, 2004). Since this question
addresses a quantity associated with a specific response (r),
we have to decompose the overall mutual information
between the stimulus variable and the response variable
(I(S; R)) into more specific information terms. As this question is about a difference in probability distributions,
before and after receiving r, it is naturally expressed in
terms of a KullbackLeibler divergence between p(s) and
p(s|r). The resulting measure is called the specific surprise
isup (DeWeese & Meister, 1999):
isup S; r
X
s
psjr log
psjr
ps
[14]
P
It can be easily verified that I(S; R) r p(r)isup(S; r).

Hence, isup is a valid decomposition of the mutual information
into
more
specific,
response-dependent
contributions. As a KullbackLeibler divergence, isup is

always positive or zero:
isup S; r 0
[15]
this simply indicates that any incoming response will either

update our beliefs leading to a positive KullbackLeibler
divergence or not, in which case the KullbackLeibler
divergence will be zero. From this, it immediately follows
that isup cannot be additive: if of two subsequent responses
r1, r2, the first leads us to update our beliefs about s from p
(s) to p(s|r1), but the second leads us to revert this update,
that is, p(s|r1, r2) p(s), then isup(S; r1, r2) 0 6 isup(S; r1)
isup(S; r2|r1). Loosely speaking, a series of surprises and
belief updates do not necessarily lead to a better estimate.
3. Which specific neural response r is particularly informative
about an unknown stimulus from a certain set of stimuli?
This question asks how much the knowledge about r
and the update of our beliefs about s from p(s) to p(s|r) is
worth in terms of an uncertainty reduction about s, that is, an
information gain. In contrast to the question about an
update of our beliefs earlier in the text, we here ask whether
this update increases or reduces uncertainty about s. This
question is naturally expressed in terms of conditional
entropies, comparing our uncertainty before the response,
H(S), with our uncertainty after receiving the response,
H(S|r). The resulting difference is called the response specific information ir(S; r) (DeWeese & Meister, 1999):
ir S; r HS HSjr
[16]
P
Again, it is easily verified that I(S; R) r p(r)ir(S; r).

However, here, ir(S; r) is not necessarily positive: As a
response r can lead from probability distributions p(s)
with a low entropy H(S) to one with a high entropy H(S|
r), and vice versa, the measure can be positive or negative.
What is gained by accepting negative information gains in
the sum, that is, accepting that results may be misinformative in terms of an increase in uncertainty, is that the measure is additive for two subsequent responses:
ir S; r1 ; r2 ir S; r1 ir S; r2 jr1
[17]
4. Which stimulus s leads to responses r that are informative

about the stimulus itself?
In other words, which stimulus is reliably associated to
responses that are relatively unique for this stimulus, so that
we know about the occurrence of this specific stimulus from
the response unambiguously? Here, we ask about stimuli
that are being encoded well by the system, in the sense that
they lead to responses that are informative to a downstream
observer. In this type of question, a response is considered
informative if it strongly reduces the uncertainty about the
stimulus, that is, if it has a large ir(S; r). Thus, we ask how
informative the responses for a given stimulus s are on
average over all responses that the stimulus elicits with p(r|s):
iSSI s; R
prjsir S; r
[18]
r2Ar
The resulting measure iSSI(s; R) is called the stimulusspecific information (SSI) (Butts, 2003). Again, it can be

P
verified easily that I(S; R) s p(s)iSSI(s; R), meaning that
iSSI is another valid decomposition of the mutual information. Just as the response-specific information terms that it
is composed of, the SSI can be negative.
The SSI has been used to investigate which stimuli are
encoded well in neurons with a specific tuning curve; it was
demonstrated that the specific stimuli that were encoded
best changed with the noise level of the responses (Butts &
Goldman, 2006).
RF1
1
+1
RF3
Receptive fields
RF2
Another question that is often asked in neuroscience is whether

an ensemble of neurons codes individually or jointly for a
stimulus. For example, after recording from an ensemble of
two neurons {R1, R2} after stimulation with stimuli
s 2 AS fs1 ; s2 ; . . .g, we may ask the following:
RF3
Interestingly, only questions one and two can be answered

using standard tools of information theory such as the (conditional) mutual information. In fact, the answers to questions
three to five, that is, the quantification of unique, redundant,
and synergistic information, are still a field of active research.
While at the time of writing no agreement about a solution
of this problem has been reached, it is clear that early attempts
at quantifying synergies or redundancies, for example, by the
interaction information I(S; R2|R1) I(S; R1) (McGill, 1954),
are imperfect in that they let synergistic and redundant information cancel each other in the measure when both are present
(Williams & Beer, 2010). The fact that interaction information
has been widely used in neuroscience makes it important to
have closer look at the problem even in the absence of a
solution.
Before we present more details, we would like to improve
the understanding of the previously mentioned questions by
looking at a thought experiment where three neurons in visual
area V1 are recorded simultaneously while being stimulated
with one of a set of four stimuli (Figure 1(a) and 1(b)). Two of
the neurons have almost identical receptive fields (RF1, RF2),
while the third one has a collinear but spatially displaced
receptive field (RF3). These neurons are stimulated with one
of the following stimuli: s1 does not contain anything at the
receptive fields of the three neurons, and the neurons stay
RF2
(b)
(c)
1
+1
The Question of Ensemble Coding
1. What information does Ri provide about S? This is the

mutual information I(S; Ri).
2. What information does the joint variable R {R1, R2} provide about S? This is the mutual information I(S; {R1, R2}).
3. What information does the joint variable R {R1, R2} have
about S that we cannot get from observing both variables
R1, R2 separately? This information is called the synergy of
{R1, R2} with respect to S.
4. What information does one of the variables, say R1, have
about S that we cannot obtain from any other variable (R2
in our case)? This information is the unique information of
R1 about S.
5. What information does one of the variables, again say R1,
have about S that we could also obtain by looking at
another variable R2 alone? This information is the redundant information of R1 and R2 about S.
(a)
RF1
605
+1
+1
+1
R1
R3
+1
RF1
RF2
RF3
Stimulus s1
Stimulus s2
1
2
3
RF1
RF1
RF2
RF3
RF2
Stimulus s3
RF3
Stimulus s4
Figure 1 Redundant and synergistic neural coding. (a) Receptive fields

(RFs) of three neurons R1, R2, R3. (b) Set of four stimuli. (c) Circuit for
synergistic coding. Responses of neurons R1, R2 determine the response
of neuron N via an XOR function. In the hidden circuit in between (gray
box), open circles denote excitatory neurons; filled circles, inhibitory
neurons. Numbers in circles are activation thresholds; signed numbers at
connecting arrows are synaptic weights.
inactive; s2 is a small bar moving with the preferred orientation

of neurons 1 and 2 and is moving in their preferred direction;
s3 is a similar small bar, but now moving over the receptive
field of neuron 3, instead of 1 and 2; and s4 is a long bar
covering all receptive fields in the example.
To make things easy, let us encode responses that we get
from these three neurons (colored traces in Figure 1) in binary
form, with 1 simply indicating that there was a response in
our response window (gray boxes behind the activity traces in
Figure 1). If we assume the stimuli to be presented with equal
probability (p(s si) 1/4), then the entropy of the stimulus
set is H(S) 2 (bit). Obviously, none of the information terms
in the preceding text can be larger than these 2 bits. We also see
that each neuron shows activity (binary response 1) in half of
the cases, yielding an entropy H(Rj) 1 for the responses of
each neuron. The responses of the three neurons fully specify
the stimulus, and therefore, I(S; R1, R2, R3) 2). To see the
mutual information between an individual neurons response
606
and the stimulus, we may compute I(S; Ri) H(S) H(S|Ri).

To do this, we remember H(S) 2 and use that the number of
equiprobable outcomes for S drops by half after observing a
single neuron (e.g., after observing a response r1 1 of neuron
1, two stimuli remain possible sources of this response s2 or
s4). This gives H(S|Ri) 1, and I(S; Ri) 1. Hence, each neuron
provides 1 bit of information about the stimulus when considered individually.
What happens if we consider joint variables formed from
pairs of neurons? If we look at neurons 1 and 2, their responses
to each stimulus are identical. Each of the neurons provides 1 bit
of information about the stimulus. Even if we look at the two of
them jointly {R1, R2}, we still get only one bit: I(S; {R1, R2}) 1.
This is because the information carried by their responses is
redundant. To see this, consider that we cannot decide between
stimuli s1 and s3 if we get the result (r1 0,r2 0), and we can
also not decide between stimuli s2 and s4 when observing
(r1 1,r2 1). (Other combinations of responses do not occur
by the construction of this example.) We see that neurons 1 and
2 seem to have the same information about the stimulus; hence,
we suspect that a measure of redundant information should
show nonzero values in this case.
To understand the concept of synergy, we next consider the
output of our two example neurons 1 and 3 being further
transformed by a network that implements the mathematical
XOR function, such that a downstream neuron N gets activated
only if there is one small bar on the screen (i.e., one of our
neurons R1 or R3 gets activated, but not both), but neither for

no stimulus nor for the long bar (Figure 1(c)). In this case, the
individual mutual information of each neuron R1, R3 with the
downstream neuron N is zero (I(N; Ri) 0). However, the
mutual information between our two neurons considered
jointly and the downstream neuron is still 1 bit, because the
response of N is fully determined by its two inputs: I(N; {R1,
R3}) 1. In this case, there is only synergistic information.
In general, the total information I(Y; {X1, X2}) that two variables X1, X2 have about a third variable Y can be decomposed
into the unique information of each Xi about Y, the redundant
information that both variables share about Y, and the synergistic information that can only be obtained by considering {X1,
X2} jointly. Figure 2 shows this so-called partial information
decomposition (Williams & Beer, 2010). One easily sees that the
redundant, unique, and synergistic information cannot be
obtained by simply subtracting classical mutual information
terms, without double counting. However, if we were given a
measure of either redundancy or synergy (or even unique information) (Bertschinger et al., 2014), the other parts of the
decomposition can be computed. Therefore, Williams and
Beer recently suggested a specific measure of redundant information, called Imin, that measures the redundant information
about a variable Y that is contained in a set of source variables
X {X1, X2, . . ., Xr} (Williams & Beer, 2010):
Imin X; fX 1 ; X 2 ; . . . ; X r g
X
y2AY
I(Y; X1)
Ird
[19]
Iuq
I(Y; X1X2)
Mutual information
between Y and the set
{X1X2}
I(Y; X1)
Mutual information
between Y and X1
Iuq(Y; {X1}) = ?
Unique information
about Y from X1, which
cannot be obtained
from X2.
Ird(Y; {X1}{X2}) =
Isyn(Y; {X1X2}) = ?
Xi
I(Y;X1X2)
I(Y; X2)
Isyn
Iuq
py min IY y; X i
Redundant information
about Y can be
obtained either from X1
or from X2.
Synergetic information
can only be obtained from
X1 and X2 together (red
area).
The definitions of these information measures are currently debated.
Figure 2 Partial information decomposition for three variables: one target Y and two sources X1 and X2. The original partial information decomposition
diagram is a modified version of the one first presented in Williams and Beer (2010).
[20]
{X1}{X2}
{X
1
}{X
2
X3
{X1}
{X1}{X2}{X3}
{X2}
{X2}{X3}
{X1}{X3}
{X
{X3}{X1X2}
2X
3}
}
X2
}
X3
}{X 2
X2
{X 1
It may not be visible immediately in the preceding equations,

but central quantities of the previous treatment, such as H(S),
}
X3
}{X 1
{X 2
Importance of the Stimulus Set and Response Features
{X1X2}
}
X3
{X 1
However, this measure has been criticized for sometimes

showing redundant information even if source variables X1, X2
have no mutual information or showing synergy when the target
variable (Y in the preceding text) is just a collection of the source
variables (Griffith & Koch, 2014). For example, when considering neurons 1 and 3 jointly, we can fully decode the 2 bit of
stimulus information. At first sight, it seems clear in this example that each neuron contributes 1 bit of unique information,
because the responses of neurons 1 and 3 are independent on
the randomly chosen stimuli of our set. Therefore, it was
axiomatically proposed that in this case, each neuron should
contribute 1 bit of unique information (Griffith & Koch, 2014;
Harder, Salge, & Polani, 2013). In this view, there is no synergy,
in contrast to the results that Imin provides. However,
positive synergy has also been proposed as a mathematically
sound alternative result for this example (Bertschinger, Rauh,
Olbrich, & Jost, 2013). To see the rationale for this alternative
proposal, consider that after observing r1 1, we (and also
neuron 1) know that the two events (r1 0,r2 0) and (r1 0,
r2 1) are both impossible. Interestingly, after observing just
r2 1, we (and also neuron 2) know that (r1 0,r2 0) and
(r1 1,r2 0) are both impossible. The sets of events known
to each neuron to be impossible intersect. Hence, although the
two neurons do not share any information about each others
responses, they have information in common about impossible
states of the world. Therefore, a nonzero synergy for this case has
been considered, albeit less than the one bit that Imin measures
for the example. Obviously, if a measure is used that provides
nonzero synergy in the example, then each neuron will contribute less than 1 bit of unique information.
It should be noted that Imin has also been criticized for not
having a continuous local counterpart in contrast to mutual
information (see Eqn [11]) (Lizier, Flecker, & Williams, 2013).
It should also be noted that the problem of assigning
redundant or synergistic information quickly increases in complexity when the number of variables increases (see Figure 3
for the decomposition of I(Y; {X1, X2, X3})).
In sum, there is currently no generally accepted measure,
neither of redundancy nor of synergy (Bertschinger et al., 2013;
Lizier et al., 2013). Various candidate measures (Griffith &
Koch, 2014; Harder et al., 2013; Williams & Beer, 2010) have
been proposed, but so far, most of them seem have considerable shortcomings, and it is even unclear whether all the properties that we intuitively assign to redundancies or synergies are
compatible with each other (Bertschinger et al., 2013). For
neuroscience, this means that older accounts of synergy
(Brenner, Strong, Koberle, Bialek, & Van Steveninck, 2000;
Gawne & Richmond, 1993; Han, 1978; McGill, 1954) have
to be carefully reconsidered as they may (or may not) double
count redundancies, while a mathematically rigorous replacement is missing for now.
{X1X2X3}
}{X
1
xi 2AXi

1
1
log
pxi jy log
py
pyjxi
X3
{X
1
IY y; X i
607
{X3}
{X1X3}{X2X3}
{X
1X2}{X1X3}{X2X3}
Figure 3 Partial information decomposition for four variables: one

target variable Y can receive information from various combinations of
the three source variables X1, X2, X3. Comparing with Figure 2, one sees
that the number of partial information contributions rises very rapidly
with the number of source variables. Modified from Williams, P.L., &
Beer, R.D. (2010). Nonnegative decomposition of multivariate
information. ArXiv e-print No. 1004.2515.
H(S|r), depend strongly on the choice of the stimulus set AS .

For example, if one chooses to study the human visual
system with a set of visual stimuli in the far infrared end
of the spectrum, I(S; R) will most likely be very small and
analysis futile (although done properly, a zero value of
iSSI(s; R) for all stimuli will correctly point out that the
human visual system does not care or code for any of the
infrared stimuli). Hence, characterizing a neural code properly hinges to a large extent on an appropriate choice of
stimuli. In this respect, it is safe to assume that a move
from artificial stimuli (such as gratings in visual neuroscience) to more natural ones may dramatically alter our view
of neural codes in the future. A similar argument holds for
the response features that are selected for analysis. If any
feature is dropped or not measured at all, this may distort
the information measures in the preceding text. This may
even happen, if the dropped feature, say the exact spike
time variable RST, seems to carry no mutual information
with the stimulus variable when considered alone, that is,
I(S; RST 0). This is because there may still be synergistic
information that can only be recovered by looking at other
response variables jointly with RST. For example, it would be
possible in principle that neither spike time RST nor spike
rate RSR carry mutual information with the stimulus variable
when considered individually, that is, I(S; RST) I(S; RSR) 0.
Still, when considered jointly, they may be informative:
I(S; {RST, RSR})> 0! The problem of omitted response features
is almost inevitable in neuroscience, as the full sampling of all
parts of a neural system is typically impossible, and we have to
work with subsampled data. Considering only a subset of
608
(response) variables may dramatically alter the apparent

dependency structure in the neural system (see Priesemann,
Munk, & Wibral, 2009, for an example). Therefore, the effects
of subsampling should always be kept in mind when interpreting results of studies on neural coding.
Analyzing Distributed Computation in Neural Systems

The analysis of neural coding strategies presented in the preceding text relies on our knowledge of the (stimulus) features
at the functional level that are encoded in neural responses
that we record at the implementation level. If we have this
knowledge, information theory will help us link these two
levels. This is somewhat similar to the situation in cryptography where we consider a code cracked if we obtain a humanreadable plain text message, that is, we move from the implementation level (encrypted message) to the functional level
(meaning).
However, what happens if the plain text were in a language that bears no resemblance to ours? In this case, we
would potentially crack the code without ever realizing it, as
the plain text still has no meaning for us. This is the situation we face currently in neuroscience if we move beyond
early sensory or motor areas. Beyond these areas, our knowledge of what is actually encoded in those neural signals gets
vague. As a result, proper stimulus sets get hard to choose. In
this case, the gap between the functional level and the
implementation level may actually become too wide for
meaningful analyses, as also noticed recently by Carandini
(2012). As shown in this section, we may try instead to use
information theory to link the implementation level and
algorithmic level, by retrieving the information processing
footprint of the computation carried out by a neural circuit
in terms of information storage, information transfer, and
information modification.
There is considerable agreement that neural systems perform some kind of information processing or computation.
Information processing in general can be decomposed into the
component processes of (1) information storage, (2) information transfer, and (3) information modification. This decomposition had already been formulated by Turing (see Langton,
1990):
Information storage quantifies the information contained in

the past of a process that is used by the process (e.g., a
neuron or a brain area) in its future. This relatively abstract
definition means that we will see at least a part of the past
information again in the future of the process, but potentially transformed. Hence, information storage can be naturally quantified by a mutual information between the past
and the future of a process. If this mutual information is
nonzero, we can predict a part of the future information in
the process, that is, there is information storage.
Information transfer quantifies the information contained in
the past state variables X t-u of one source process X that can
be used to predict information in future variables Yt of a
target process Y, while this information is not contained in
the past state variables Yt1 of the target process.
Information modification quantifies the combination of

information from various source processes into a new
form that is not (trivially) predictable from any subset of
these source processes (Lizier, Prokopenko, & Zomaya,
2010; Lizier et al., 2013).
A thought experiment may serve to illustrate that information

theory serves as an analysis at the algorithmic level rather than
at the implementation level. Assume a very capable neuroscientist working with a small neural system, for example, the
nervous system of the worm Caenorhabditis elegans. Let us also
assume that she has sorted out the anatomical setup of this
nervous system in such detail that he can simulate the realistic
dynamics of this system in a computer. At this stage, our
researcher may actually perform an analysis to understand
the causal role elements of the nervous system play for its
dynamic behavior. To do this, she may intervene in the biological system, for example, by injecting a current into a specific cell (there are roughly 300 neurons in C. elegans, each with
its own identity), and observe how the dynamics change. She
may then proceed to (virtually) inject the same current in his
modeled neurons. If the modeled dynamics reflect the biological dynamics, she may rightfully claim to have a causal understanding of the systems dynamics at the implementation level.
Note that at this level, the interventions used are very different
(injecting a current vs. changing some lines of code in the
model).
Interestingly, both interventions would look indistinguishable at the algorithmic level. This is because the nervous system
and its model produce identical behavior in the sense that the
activities recorded in vivo and in silico and then stored on disk
look identical (we assume a perfect model here). Accordingly,
an information theoretical analysis would not be able to tell
the difference between the model and the real thing. At first
sight, this may seem rather disappointing so is there any
insight we potentially gain by shedding biological/modeling
detail using information theoretical analysis?
To see what insights can be gained about the information
processing in a neutral system using information theory,
assume that a set of neurons only contributes to support processes, for example, as pacemaker cells that keep this system in
an operational dynamic activity regime. Assume that these
neurons do not contribute anything else to the computation
proper. Telling these neurons apart from other parts of network
convincingly may be hard at the implementation level, analyzing only the dynamics. It may even be hard to detect their
particular role in the first place, performing an analysis at the
implementation level. In contrast, an information theoretical
analysis at the algorithmic level may easily identify them by
their lack of information storage, their lack of mutual information with input, or their high values of information modification (they would modify any potential input to random output
in our scenario). Thus, information theory helps to unravel the
role each component has in information processing at each
point in time.
Based on Turings general decomposition of computation
into component processes of storage, transfer, and modification (Langton, 1990), Lizier and colleagues recently proposed
an information theoretical framework to quantify distributed
computations in terms of all three component processes locally

for each part of the system (e.g., neurons or brain areas) and
each time step (Lizier, 2013; Lizier, Prokopenko, & Zomaya,
2008, 2012; Lizier et al., 2010). This framework is called local
information dynamics and has been successfully applied to
unravel computation in swarms (Wang, Miller, Lizier,
Prokopenko, & Rossi, 2012), in Boolean networks (Lizier,
Pritam, & Prokopenko, 2011b), and in neural data (Lizier
et al., 2011a).
In the following, we present both global and local measures
of information transfer, information storage, and information
modification, beginning with the well-established measures of
information transfer and ending with the highly dynamic field
of information modification.
609
variables is appropriate in a neural setting must be checked

carefully for each case. In fact, it was found that electroencephalography (EEG) source signals are not Gaussian: When decomposing EEG activity in its independent components, which are
by definition as non-Gaussian as possible, then these results
match well with a decomposition into electric dipoles, which
are physical approximations to neural sources. The close match
between the non-Gaussian decomposition and the dipole
decomposition indicates that neural signals may often be nonGaussian (Wibral, Turi, Linden, Kaiser, & Bledowski, 2008).
Therefore, the results of a linear Granger causality analysis
should be interpreted with care.
TE estimation
Information Transfer
The analysis of information transfer was formalized initially by
Schreiber using the transfer entropy (TE) functional (Schreiber,
2000) and has seen a rapid surge of interest in neuroscience
(Amblard & Michel, 2011; Barnett, Barrett, & Seth, 2009; Battaglia, Witt, Wolf, & Geisel, 2012; Besserve, Scholkopf, Logothetis,
& Panzeri, 2010; Buehlmann & Deco, 2010; Chavez, Martinerie,
& Le Van Quyen, 2003; Garofalo, Nieus, Massobrio, &
Martinoia, 2009; Gourevitch & Eggermont, 2007; Ito et al.,
2011; Li & Ouyang, 2010; Lindner, Vicente, Priesemann, &
Wibral, 2011; Lizier et al., 2011b; Ludtke et al., 2010; Neymotin,
Jacobs, Fenton, & Lytton, 2011; Palus, Komarek, Hrncr, &
Sterbova, 2001; Staniek & Lehnertz, 2009; Stetter, Battaglia,
Soriano, & Geisel, 2012; Vakorin, Misic, Krakovska, & McIntosh,
2011; Vakorin, Kovacevic, & McIntosh, 2010; Vakorin, Krakovska, & McIntosh, 2009; Vicente et al., 2011; Wibral et al.,
2013; Wibral et al., 2011) and general physiology (Faes & Nollo,
2006; Faes, Nollo, & Porta, 2011; Faes et al., 2012).
Definition
Information transfer from a random process X (the source) to
another random process Y (the target) is measured by the TE
functional (Schreiber, 2000):
TEXtu ! Yt IX tu ; Yt jY t1
or, equivalently:
TEX tu ! Yt
[21]
X
yt 2AYt , yt1 2AY t1 , x tu 2AXtu
pyt ; yt1 ; xtu log
pyt jyt1 , xtu

pyt jyt1
[22]
where I(;|) is the conditional mutual information, Yt is

the random variable of process Y at time t, and Xtu, Yt1 are
the past state random variables of processes X and Y, respectively. The delay variable u in Xtu indicates that the past
state of the source is to be taken u time steps into the past to
account for a potential physical interaction delay between the
processes.
The TE functional can be linked to WienerGranger-type
causality (Barnett et al., 2009; Wiener, 1956). More precisely,
for systems with jointly Gaussian variables, TE is equivalent to
linear Granger causality (see Barnett et al., 2009 and references
therein). However, whether the assumption of Gaussian
When the probability distributions entering Eqn [21] are

known (e.g., in an analytically tractable neural model), TE
can be computed directly. However, in most cases, these probability distributions would have to be derived from data to be
inserted into Eqn [21] for an estimate of TE. Indeed, this
approach has been used in the past and leads to a so-called
plug-in estimator (see Panzeri, Senatore, Montemurro, and
Petersen, 2007). However, these plug-in estimators have serious bias problems (Panzeri et al., 2007). Therefore, newer
approaches to TE estimation rely on more direct estimations
of the entropies that TE can be decomposed into (Kraskov,
Stogbauer, & Grassberger, 2004; Vicente et al., 2011). These
estimators have better bias properties and we therefore restrict
our presentation to these approaches.
As pointed out in the preceding text, we will have to reconstruct the states of the processes before we can proceed to
estimate information theoretical quantities. One approach to
state reconstruction is time delay embedding (Takens, 1981). It
uses past variables Xtnt, n 1, 2, . . . that are spaced in time by
an interval t. The number of these variables and their optimal
spacing can be determined using established criteria (Faes
et al., 2012; Lindner et al., 2011; Ragwitz & Kantz, 2002;
Small & Tse, 2004). The realizations of the states variables
can be represented as vectors of the form
x dt xt , xtt , xt2t , . . .
, xtd1t
[23]
where d is the dimension of the state vector. Using this vector

notation, the TE estimator for an interaction with assumed
delay u is
X
dy
x
TESPO X tu ! Yt
pyt ; yt1
; x dtu
dy
dx
yt , yt1 , xtu
d
log
y
x
pyt jyt1
, xdtu
[24]
y
pyt jyt1
where the subscript SPO (for self-prediction optimal) is a

d
y
, has to be constructed
reminder that the past state of Yt, y t1
such that conditioning on the past of the target process is
optimal (see Wibral et al., 2013, for details). Or saying it
y
y
instead of y t1
,
differently, if one would condition on y tu
then the self-prediction for Yt is not optimal and the TE will
be overestimated.
The parameter u is the assumed time that the information
transfer needs to get from process X to Y. It was recently proven
610
for bivariate systems that the previously mentioned estimator

assumes its maximum value if the parameter u is equal to the
true delay d of the information transfer from X to Y (Wibral
et al., 2013). This relationship allows to estimate the interaction delay d by scanning the assumed delay u:
d argmax TESPO X tu ! Yt
u
[25]
We can rewrite Eqn [24] using a representation in the form

of four entropies (for continuous-valued random variables,
these entropies are differential entropies) H() as
d
y
y
x
x
TESPO X tu ! Yt Hyt1
; x dtu
Hyt ; y t1
; xdtu
dy
Hyt ; yt1
dy
Hy t1
[26]
This shows that TESPO estimation is equal to computing a

combination of different joint and marginal entropies. Entropies can be estimated efficiently by nearest-neighbor techniques. These techniques exploit the fact that the distances
between neighboring data points in a given embedding space
are related to the local probability density: the higher the local
probability density around an observed data point, the closer
the next neighbors. Since next neighbor estimators are dataefficient (Kozachenko & Leonenko, 1987; Victor, 2002), they
allow to estimate entropies in high-dimensional spaces from
limited real data.
Unfortunately, it is problematic to estimate TE by simply
applying a naive nearest-neighbor estimator for the entropy,
such as the KozachenkoLeonenko estimator (Kozachenko &
Leonenko, 1987), separately to each of the terms appearing in
Eqn [26]. The reason is that the dimensionality of the state
spaces involved in Eqn [26] differs largely across terms. In Eqn
x
[26], the term x dtu
has the highest dimensionality. Because of
the different dimensionalities, fixing a given number of neighbors for the search will set very different spatial scales (range of
distances) for each term (Kraskov et al., 2004). Since the error
bias of each term is dependent on these scales, the errors would
not cancel each other but accumulate. The Kraskov
GrassbergerStogbauer estimator handles this problem by
only fixing the number of neighbors k in the highestdimensional space and by projecting the resulting distances
to the lower-dimensional spaces as the range to look for neighbors there (Kraskov et al., 2004). After adapting this technique
to the TE formula (Wollstadt et al., 2014; Vicente et al., 2011),
the suggested estimator can be written as
D
TESPO X tu ! Yt ck cnydy 1
t1
cny ydy 1 cnydy

t t1
dx
t1 x tu
[27]
where c denotes the digamma function, the angle brackets

(h i) indicate an averaging over different time points for stationary systems or an ensemble average for nonstationary ones,
and k is the number of nearest neighbors used for the estimation. n() refers to the number of neighbors that are within a
hypercube around a state vector, where the size of the hypercube in each of the marginal spaces is defined based on the
distance to the kth nearest neighbor in the highest-dimensional
dy
x
, xdtu
).
space (spanned by yt , yt1
Interpretation of TE as a measure at the algorithmic level

In line with what was said in the introduction, it is important
to note that TE analyzes distributed computation at the algorithmic level, not at the level of a physical dynamic system. As
such, it is not well suited for inference about causal interactions
although it has been used for this purpose in the past. The
fundamental reason for this is that information transfer relies
on causal interactions, but causal interactions do not necessarily lead to nonzero information transfer (Ay & Polani, 2008;
Chicharro & Andrzejak, 2009; Lizier & Prokopenko, 2010).
Instead, causal interactions may serve active information storage alone (see next section) or force two systems into identical
synchronization, where information transfer becomes effectively zero. This might be summarized by stating that TE is
limited to effects of a causal interaction from a source to a
target process that are unpredictable given the past of the target
process alone. In this sense, TE may be seen as quantifying
causal interactions currently in use for the communication aspect
of distributed computation. Therefore, one may say that TE
measures predictive or algorithmic information transfer.
The difference between an analysis of information transfer
in a computational sense and causality analysis based on interventions has been clarified recently by Lizier and colleagues
(2010). The same authors also demonstrate why an analysis of
information transfer is sometimes more important than the
analysis of causal interactions if the computation of the system is
to be understood.
Common problems and solutions

Typical problems in TE estimation encompass (1) finite sample
bias, (2) the need for multivariate analyses, and (3) the presence of nonstationarities in the data. In recent years, all of these
problems have been addressed satisfactorily:
1. Finite sample bias can be overcome by using surrogate data,
dy
x
, x dtu
of the random
where the observed realizations yt , yt1
dy
dx
variables Yt , Y t1 , X tu are reassigned to other random variables of the process, such that the temporal order underlying the information transfer is destroyed (for an example,
see the procedures suggested in Lindner et al., 2011). This
reassignment should conserve as many data features of the
single process realizations as possible.
2. So far, we have restricted our presentation of TE estimation
to the case of just two interacting random processes X, Y,
that is, a bivariate analysis. In a setting that is more realistic
for neuroscience, one deals with large networks of interacting processes X, Y, Z, . . .. In this case, various complications
arise if the analysis is performed in a bivariate manner. For
example, a process Z could transfer information with two
different delays dZ!X, dZ!Y to two other processes X, Y. In
this case, a pairwise analysis of TE between X and Y will
yield an apparent information transfer from the process
that receives information from Z with the shorter delay to
the one that receives it with the longer delay (common
driver effect). A similar problem arises if information is
transferred first from a process X to Y and then from Y to
Z. In this case, a bivariate analysis will also indicate information transfer from X to Z (cascade effect). Moreover, two
sources may transfer information purely synergistically,
that is, the TE from each source alone to the target is zero,

and only considering them jointly reveals the information
transfer. Again, cryptography may serve as an example here.
If an encrypted message is received, there will be no discernible information transfer from encrypted message to
plain text without the key. In the same way, there is no
information transfer from the key alone to the plain text. It
is only when encrypted message and key are combined that
the relation between the combination of encrypted message
and key on the one side and the plain text on the other side
is revealed.
From a mathematical perspective, this problem seems to
be easily solved by introducing the complete TE (Lizier &
Prokopenko, 2010):
TEcompl X tu ! Yt jV
log
X
yt , yt1 , x tu , v
pyt ; yt1 ; xtu ; v
pyt jyt1 , xtu , v

pyt jy t1 , v
[28]
Here, the state random variable V is a collection of the

past states of all processes in the network other than X, Y.
However, there is often a practical problem with this
approach, because even for small networks of random
processes, the joint state space of the variables Yt, Yt1, Xtu,
V is intractably large from the estimation perspective.
Moreover, the problem of finding all information transfers
in the network, from either single source variables into the
target or synergistic transfer from collections of source variables to the target, is in principle NP-complete and can
therefore typically not be solved in a reasonable time.
Therefore, Faes and colleagues (2012), Lizier and Rubinov (2012), and Stramaglia, Wu, Pellicoro, and Marinazzo
(2012) suggested to analyze the information transfer in a
network iteratively, selecting information sources for a target in each iteration based on either the magnitude of
apparent information transfer (Faes et al., 2012) or its
significance (Lizier & Rubinov, 2012; Stramaglia et al.,
2012). In the next iteration, already selected information
sources are added to the conditioning set (V in Eqn [28]),
and the next search for information sources is started. The
approach of Stramaglia and colleagues is particular here in
that the conditional mutual information terms are computed at each level as a series expansion, following a suggestion by Bettencourt, Gintautas, and Ham (2008). This
allows for an efficient computation as the series may truncate early, and the search can proceed to the next level.
Importantly, these approaches also consider synergistic
information transfer from more than one source variable
to the target. For example, a variable transferring information purely synergistically with V maybe included in the
next iteration, given that the other variables it transfers
information with are already in the conditioning set V.
However, there is currently no explicit indication in the
approaches of Faes and colleagues (2012) and Lizier and
Rubinov (2012) as to whether multivariate information
transfer from a set of sources to the target is in fact synergistic, and redundant links will not be included. In contrast,
both redundant and synergistic multiplets of variables
transferring information into a target may be identified in
611
the approach of Stramaglia and colleagues (2012) by looking at the sign of the contribution of the multiplet.
Unfortunately, there is also the possibility of cancellation
if both types of multivariate information (redundant and
synergistic) are present.
3. As already explained in Section Basic information theory,
nonstationary random processes in principle require that
the necessary estimates of the probabilities in Eqn [21] be
based on physical replications of the systems in question.
Where this is impossible, the experimenter should design
the experiment in such a way that the processes are repeated
in time. If such cyclostationary data are available, then TE
should be estimated using ensemble methods as described
in Wollstadt et al., 2014 and implemented in the TRENTOOL toolbox (Lindner et al., 2011).
Local information transfer

As TE is formally just a conditional mutual information, we
can obtain the corresponding local mutual information (Eqn
[12]) from Eqn [24]. This quantity is called the local information transfer te (Lizier et al., 2008). For realizations xt, yt of two
processes X, Y at time t, it reads
d
teX tu xtu ! Yt yt log
y
x
pyt jyt1
, xdtu
y
pyt jyt1
[29]
As said earlier in Section Basic information theory, the use

of local information measures does not eliminate the need for
an appropriate estimation of the probability distributions
involved. Hence, for a nonstationary process, these distributions will still have to be estimated via an ensemble approach
for each time point for the random variables involved for
example, via physical replications of the system or via enforcing cyclostationarity by the design of the experiment.
The analysis of local information transfer has been applied
with great success in the study of cellular automata to prove the
conjecture that certain coherent spatiotemporal structures traveling through the network are indeed the main carriers of
information transfer (Lizier et al., 2008). In addition in the
study of random Boolean networks, it was shown that the local
information transfer and the local active information storage
(see next section) are in an optimal balance near the critical
point (Lizier et al., 2011b). These theoretical findings on computational properties at the critical point are of great relevance
to neuroscience, as it has been conjectured that the brain may
operate in a self-organized critical state (Beggs & Plenz, 2003),
and recent evidence demonstrates that the human brain is at
least very close to criticality, albeit slightly subcritical
(Priesemann, Valderrama, Wibral, & Le Van Quyen, 2013;
Priesemann et al., 2014).
Information Storage
Before we present explicit measures of information storage, a
few comments may serve to avoid misunderstanding. Since
this article is about the analysis of neural activity, measures of
information storage are concerned with information stored in
this activity rather than in synaptic properties, for example.
As laid out in the preceding text, information storage is
612
conceptualized here as a mutual information between past and

future states of neural activity. From this, it is clear that there
will not be much information storage if the information contained in the future states of neural activity is low in general. If,
on the other hand, these future states are rich in information
but bear no relation to past states, that is, are unpredictable,
again information storage will be low. Hence, large information storage occurs for activity that is rich in information but, at
the same time, predictable.
Thus, information storage gives us a way to define the
predictability of a process that is independent of the prediction
error: Information storage quantifies how much future information of a process can be predicted from its past, whereas the
prediction error measures how much information cannot be
predicted. If both are quantified in information measures, the
error and the predicted information add up to the total amount
of information (technically: the entropy rate; also see Eqn
[40]). Importantly, since the entropy rate can vary considerably, these two measures can lead to quite different views
about the predictability of a process. As predictability (in the
sense of the amount of predicted information) in turn plays a
crucial role in current theories of brain function, such as predictive coding, we expect to see a rise in the application of this
measure to neural data in the near future (Wibral et al., 2014;
Gomez et al., 2014).
Before turning to the explicit definition of measures of
information storage, it is also worth to consider different perspectives on the temporal extent of past and future states that
we are interested in: Most globally, excess entropy (Crutchfield &
Packard, 1982; Grassberger, 1986) is the mutual information
between the semi-infinite past and future of a process before
and after time point t. In contrast, if we are interested in the
information currently used for the next step of the process, the
mutual information between the semi-infinite past and the next
step of the process, the active information storage is of greater
interest.
k
eXt ixk
t ; xt
[32]
The limit of k ! 1 can be replaced by a finite kmax if a kmax

exists such that conditioning on X kt max renders X kt max conditionally independent of any Xl with l t kmax.
Local active information storage

From a perspective of the dynamics of information processing,
we might not be interested in information that is used by a
process at some time far in the future, but at the next point in
time, that is, information that is said to be active or currently
in use for the computation of the next step (the realization of
the next random variable) in the process (Lizier et al., 2012).
To quantify this information, a different mutual information is
computed, namely, the active information storage:
AXt lim IX k
t1 ; Xt
[33]
k!1
Again, if the process in question is stationary, then

AXt const: AX and the expected value can be obtained
from an average over time instead of an ensemble of realizations of the process as

;
x
[34]
AX lim ix k
t1 t
k!1
which can be read as an average over local active storage values

aXt :
AX haXt it
[35]
aXt lim ix k
t1 ; xt
[36]
k!1
Even for nonstationary processes, we may investigate local

active storage values, given the corresponding probability distributions are properly obtained from an ensemble of realizak
:
tions of Xt, Xt1
aXt lim ix k
t1 ; xt
k!1
Excess entropy
Excess entropy is formally defined as
k
EXt lim IX k
t ; Xt
[30]
k!1
k
where Xk
t {Xt, Xt1, . . ., Xtk1} and Xt {Xt1, . . ., Xtk}
indicate collections of the past and future k variables of the
k
process X. These collections of random variables, (Xk
t , Xt ), in
the limit k ! 1 span the semi-infinite past and future,
respectively. In general, the mutual information in Eqn [30]
has to be evaluated over multiple realizations of the process.
For stationary processes, however, EXt is a constant, EX, and
Eqn [30] may be rewritten as an average over time points t and
computed from a single realization of the process (at least in
principle, as we have to take into account that the process must
run for an infinite time to allow the limit lim for all t):
k!1

k
EX lim ix k
[31]
t ; xt
k!1
where i(;) is the local mutual information from Eqn [11], and
k
k
xk
are realizations of Xk
t , xt
t , Xt . Even if the process in
question is nonstationary, we may look at values that are
local in time as long as the probability distributions are derived
appropriately (see Section Basic information theory):
[37]
Again, the limit of k ! 1 can be replaced by a finite kmax if a

max
renders Xt condikmax exists such that conditioning on X kt1
tionally independent of any Xl with l t kmax.
Interpretation of information storage as a measure

at the algorithmic level
As laid out in the preceding text, information storage is a
measure of the amount of information in a process that is
predictable from its past. As such, it quantifies, for example,
how well activity in one brain area A can be predicted by
another area, for example, by learning its statistics. Hence,
questions about information storage arise naturally when asking about the generation of predictions in the brain.
Information Modification
Langton (1990) described information modification as an interaction between transmitted information and stored information
that results in a modification of one or the other. Attempts to
define information modification more rigorously implemented
this basic idea. First attempts at defining a quantitative measure
of information modification resulted in a heuristic measure
termed local separable information (Lizier et al., 2010), where

the local active information storage and the sum over all pairwise local transfer entropies into the target was taken:
sXt aXt
X
Zt , i 6X t1
ixt ; zt , i jxt1
[38]
with Zt , i indicating the past state variables of all processes that
transfer information into the target variable Xt and where the
index t is a reminder that only past state variables are taken
into account, that is, t < t. As shown previously in the text, the
local measures entering the sum are negative if they are misinformative about the future of the target. Eventually, the
overall sum, or separable information, might also be negative,
indicating that neither the pairwise information transfers nor
the history could explain the information contained in the
targets future. This was seen as an indication of a modification
of either stored information or transferred information.
At the same time, the overall information in the future of
the target can of course be explained by looking at the sources
of information and the history of the target jointly, at least up
to the genuinely stochastic part (innovation) in the target, as
shown in Lizier et al. (2010). Even a decomposition of the
overall information into storage, transfer terms, and the innovation is possible for considering the sources jointly (Lizier
et al., 2010). To see why this is possible when considering
the source variables and the history of the target jointly, but
not when we look at pairwise local mutual information terms,
it is instructive to consider a series of subsets formed from the
(ordered) set of all variables Zt , i that can transfer information
into the target, except variables from the targets own history.
Following the derivation in Lizier et al. (2010) (with the exception of adding the variable index t to account for nonstationary
processes), we denote this set as V Xt nX t1 fZt , 1 ; . . . ; Zt , G g,
where G is the number of variables in the set and Xt is the
target. Xt1, the history of the target, is not part of the set. The
bold typeface in Zt , i is a reminder that we work with a state
space representation where necessary. Next,
we create a series

g
g
of subsets V Xt nX t1 such that V Xt nX t1 Zt , 1 ; . . . ; Zt , g1 ,
that is, the gth subset only contains the first g 1 sources. As
the TE is a mutual information, we can decompose the collective TE from all our source variables, TEV Xt nX t1 ! Xt , as a
series of conditional mutual information terms, incrementally
increasing the set that we condition on
TEV Xt nX t1 ! Xt
G
X
g
IXt ; Zt , g jX t1 , V Xt nX t1
[39]
g1
The total entropy of the target H(Xt) can then be written as

HXt AX
G
X
IXt ; Zt , g jXt1 , V Xt nX t1 WXt
[40]
g1
where WXt is the genuine innovation in Xt. If we rewrite the

decomposition in Eqn [41] in its local form,
hxt aXt
G
X
ixt ; zt , g jxt1 , vXt nxt1 wXt
613
context that the source variables provide for each other is

neglected in (Eqn 38) and synergies and redundancies are not
properly accounted for. Importantly, the results of both Eqns
[38] and [41] are only identical, if no information is provided
either redundantly or synergistically by the sources Zt , g . This
observation led Lizier and colleagues to propose a more rigorously defined measure of information modification based on
the synergistic part of the information transfer from the source
variables Zt , g and the targets history Xt1 to the target Xt
(Lizier et al., 2013). This definition of information modification has several highly desirable properties. However, it relies
on a suitable definition of synergy, which is currently not
available. As there is currently a considerable debate on how
to define the part of a the mutual information I(Y; {X1, . . .,
Xi, . . .}) that is synergistically provided by joint source variables Xi about the target Y, the question of how to best measure
information modification remains an open one.
Conclusion and Outlook

Neural systems undoubtedly perform acts of information processing in the form of distributed (biological) computation.
This computation can be decomposed into its component
processes of information storage, information transfer, and
information modification using information theoretical tools.
This allows us to derive constraints on possible algorithms
served by the observed neural dynamics. The representations
that these algorithms operate on, on the other hand, can be
guessed by analyzing the relation between meaningful quantities in our experiments or the outside world and indices of
neural activity. This is done via an analysis of mutual information between these indices of neural activity and these meaningful quantities. In this article, we have shown how to
rigorously define the necessary information theoretical
quantities and how to apply them to neuroscientific questions.
Due to the dynamic development of the field, not all questions
have found their definitive answers yet in terms of information
theory. Especially the question of how to measure nontrivial
information modification remains open at the time of writing
but is bound to see further progress in the future.

Magnetoencephalography; Functional Near-Infrared Spectroscopy;
INTRODUCTION TO ANATOMY AND PHYSIOLOGY: Functional
Connectivity; INTRODUCTION TO COGNITIVE NEUROSCIENCE:
Uncertainty; INTRODUCTION TO METHODS AND MODELING:
Dynamic Causal Models for Human Electrophysiology: EEG, MEG, and
LFPs; Effective Connectivity; Multi-voxel Pattern Analysis; RestingState Functional Connectivity; INTRODUCTION TO SYSTEMS:
Motion Perception; Neural Correlates of Motor Deficits in Young
Patients with Traumatic Brain Injury.
[41]
g1
and compare to Eqn [38], we see that the difference between

the potentially misinformative sum in Eqn [38] and the fully
accounted for information in h(xt) from Eqn [41] lies in the
conditioning of the local transfer entropies. This means the
References
Amblard, P.-O., & Michel, O. J. (2011). On directed information theory and Granger
causality graphs. Journal of Computational Neuroscience, 30, 716.
Ay, N., & Polani, D. (2008). Information flows in causal networks. Advances in Complex
Systems, 11, 1741.
614
Barnett, L., Barrett, A. B., & Seth, A. K. (2009). Granger causality and transfer entropy
are equivalent for Gaussian variables. Physical Reviews Letters, 103, 238701.
Battaglia, D., Witt, A., Wolf, F., & Geisel, T. (2012). Dynamic effective connectivity of
inter-areal brain circuits. PLoS Computational Biology, 8, e1002438.
Beggs, J. M., & Plenz, D. (2003). Neuronal avalanches in neocortical circuits. The
Journal of Neuroscience: The Official Journal of the Society for Neuroscience, 23,
1116711177.
Bertschinger, N., Rauh, J., Olbrich, E., & Jost, J. (2013). Shared information-new insights
and problems in decomposing information in complex systems. In Proceedings of the
European Conference on Complex Systems 2012 (pp. 251269). Springer
International Publishing.
Bertschinger, N., Rauh, J., Olbrich, E., Jost, J., & Ay, N. (2014). Quantifying unique
information. Entropy, 16, 21612183.
Besserve, M., Scholkopf, B., Logothetis, N. K., & Panzeri, S. (2010). Causal
relationships between frequency bands of extracellular signals in visual cortex
revealed by an information theoretic analysis. Journal of Computational
Bettencourt, L. M., Gintautas, V., & Ham, M. I. (2008). Identification of functional
information subgraphs in complex networks. Physical Reviews Letters, 100, 238701.
Boedecker, J., Obst, O., Lizier, J. T., Mayer, N. M., & Asada, M. (2012). Information
processing in echo state networks at the edge of chaos. Theory in Biosciences, 131,
205213.
Brenner, N., Strong, S. P., Koberle, R., Bialek, W., & Van Steveninck, R. R. D. R. (2000).
Synergy in a neural code. Neural Computation, 12, 15311552.
Buehlmann, A., & Deco, G. (2010). Optimal information transfer in the cortex through
synchronization. PLoS Computational Biology, 6, e1000934.
Butts, D. A. (2003). How much information is associated with a particular stimulus?
Network: Computation in Neural Systems, 14, 177187.
Butts, D. A., & Goldman, M. S. (2006). Tuning curves, neuronal variability, and sensory
coding. PLoS Biology, 4, e92.
Carandini, M. (2012). From circuits to behavior: A bridge too far? Nature Neuroscience,
15, 507509.
Chavez, M., Martinerie, J., & Le Van Quyen, M. (2003). Statistical assessment of
nonlinear causality: Application to epileptic EEG signals. Journal of Neuroscience
Methods, 124, 113128.
Chicharro, D., & Andrzejak, R. G. (2009). Reliable detection of directional couplings
using rank statistics. Physical Review E, 80, 026217.
Crutchfield, J. P., Ditto, W. L., & Sinha, S. (2010). Introduction to focus issue: intrinsic
and designed computation: Information processing in dynamical systems-beyond
the digital hegemony. Chaos, 20, 037101-1037101-6.
Crutchfield, J. P., & Packard, N. H. (1982). Symbolic dynamics of one-dimensional
maps: Entropies, finite precision, and noise. International Journal of Theoretical
Physics, 21, 433466.
Dewdney, A. K. (1993). The Tinkertoy computer and other machinations. New York:
W.H. Freeman.
DeWeese, M. R., & Meister, M. (1999). How to measure the information gained from
one symbol. Network: Computation in Neural Systems, 10, 325340.
Effenberger, F. (2013). A primer on information theory, with applications to
neuroscience. In Computational biomedicine: Data mining and modeling (135192).
Berlin: Springer-Verlag.
Faes, L., & Nollo, G. (2006). Bivariate nonlinear prediction to quantify the strength of
complex dynamical interactions in short-term cardiovascular variability. Medical
and Biological Engineering and Computing, 44, 383392.
Faes, L., Nollo, G., & Porta, A. (2011). Information-based detection of nonlinear
Granger causality in multivariate processes via a nonuniform embedding technique.
Physical Review E, 83, 051112.
Faes, L., Nollo, G., & Porta, A. (2012). Non-uniform multivariate embedding to assess
the information transfer in cardiovascular and cardiorespiratory variability series.
Computers in Biology and Medicine, 42, 290297.
Fano, R. M. (1961). Transmission of Information: A statistical theory of
communications. Cambridge, MA: Massachusetts Institute of Technology Press.
Gardner, W. A. (1994). An introduction to cyclostationary signals. Cyclostationarity in
Communications and Signal Processing, 190.
Gardner, W. A., Napolitano, A., & Paura, L. (2006). Cyclostationarity: Half a century of
research. Signal Processing, 86, 639697.
Garofalo, M., Nieus, T., Massobrio, P., & Martinoia, S. (2009). Evaluation of the
performance of information theory-based methods and cross-correlation to estimate
the functional connectivity in cortical networks. PloS One, 4, e6482.
Gawne, T. J., & Richmond, B. J. (1993). How independent are the messages carried by
adjacent inferior temporal cortical neurons? Journal of Neuroscience, 13, 27582771.
Gomez, C., Lizier, J. T., Schaum, M., Wollstadt, P., Grutzner, C., Uhlhaas, P., et al.
(2014). Reduced predictable information in brain signals in autism spectrum
disorder. Frontiers in neuroinformatics, 8.
Gourevitch, B., & Eggermont, J. J. (2007). Evaluating information transfer between

auditory cortical neurons. Journal of Neurophysiology, 97, 25332543.
Grassberger, P. (1986). Toward a quantitative theory of self-generated complexity.
International Journal of Theoretical Physics, 25, 907938.
Griffith, V., & Koch, C. (2014). Quantifying synergistic mutual information. In Guided
Self-Organization: Inception (pp. 159190). Berlin Heidelberg: Springer.
Han, T. S. (1978). Nonnegative entropy measures of multivariate symmetric
correlations. Information and Control, 36, 133156.
Harder, M., Salge, C., & Polani, D. (2013). Bivariate measure of redundant information.
Havenith, M. N., Yu, S., Biederlack, J., Chen, N.-H., Singer, W., & Nikolic, D. (2011).
Synchrony makes neurons fire in sequence, and stimulus properties determine who
is ahead. Journal of Neuroscience, 31, 85708584.
Ito, S., Hansen, M. E., Heiland, R., Lumsdaine, A., Litke, A. M., & Beggs, J. M. (2011).
Extending transfer entropy improves identification of effective connectivity in a
spiking cortical network model. PloS One, 6, e27431.
Johansson, R. S., & Birznieks, I. (2004). First spikes in ensembles of human tactile
afferents code complex spatial fingertip events. Nature Neuroscience, 7, 170177.
Knill, D. C., & Pouget, A. (2004). The Bayesian brain: The role of uncertainty in neural
coding and computation. Trends in Neurosciences, 27, 712719.
Kozachenko, L. F., & Leonenko, N. N. (1987). Sample estimate of the entropy of a
random vector. Problems of Information Transmission, 23, 95101.
Kraskov, A., Stogbauer, H., & Grassberger, P. (2004). Estimating mutual information.
Langton, C. G. (1990). Computation at the edge of chaos: Phase transitions and
emergent computation. Physica D: Nonlinear Phenomena, 42, 1237.
Li, X., & Ouyang, G. (2010). Estimating coupling direction between neuronal
populations with permutation conditional mutual information. NeuroImage, 52,
497507.
Lindner, M., Vicente, R., Priesemann, V., & Wibral, M. (2011). TRENTOOL: A Matlab
open source toolbox to analyse information flow in time series data with transfer
entropy. BMC Neuroscience, 12, 119.
Lizier, J., & Rubinov, M. (2012). Multivariate construction of effective computational
networks from observational data. Max Planck Institute for Mathematics in the
Sciences Preprint 25/2012.
Lizier, J. T. (2013). The local information dynamics of distributed computation in
complex systems. Heidelberg/New York/Dordecht/London: Springer.
Lizier, J.T., Flecker, B., & Williams, P.L. (2013). Towards a synergy-based approach to
measuring information modification. Artificial Life (ALIFE), IEEE Symposium on
artificial life. IEEE.
Lizier, J. T., Heinzle, J., Horstmann, A., Haynes, J.-D., & Prokopenko, M. (2011).
Multivariate information-theoretic measures reveal directed information structure
and task relevant changes in fMRI connectivity. Journal of Computational
Lizier, J. T., Pritam, S., & Prokopenko, M. (2011). Information dynamics in small-world
Boolean networks. Artificial Life, 17, 293314.
Lizier, J. T., & Prokopenko, M. (2010). Differentiating information transfer and causal
effect. European Physical Journal B, 73, 605615.
Lizier, J. T., Prokopenko, M., & Zomaya, A. Y. (2008). Local information transfer as a
spatiotemporal filter for complex systems. Physical Review E, 77, 026110.
Lizier, J. T., Prokopenko, M., & Zomaya, A. Y. (2010). Information modification and
particle collisions in distributed computation. Chaos: An Interdisciplinary Journal of
Nonlinear Science, 20, 037109.
Lizier, J. T., Prokopenko, M., & Zomaya, A. Y. (2012). Local measures of
information storage in complex distributed computation. Information Sciences, 208,
3954.
Ludtke, N., Logothetis, N. K., & Panzeri, S. (2010). Testing methodologies for the
nonlinear analysis of causal relationships in neurovascular coupling. Magnetic
Markram, H. (2006). The blue brain project. Nature Reviews Neuroscience, 7, 153160.
Marr, D. (1982). Vision: A computational investigation into the human representation
and processing of visual information. San Francisco, CA: W.H. Freeman.
McGill, W. J. (1954). Multivariate information transmission. Psychometrika, 19,
97116.
Mitchell, M. (2011). Ubiquity symposium: Biological computation. Ubiquity, 2011, 3.
Neymotin, S. A., Jacobs, K. M., Fenton, A. A., & Lytton, W. W. (2011). Synaptic
information transfer in computer models of neocortical columns. Journal of
Computational Neuroscience, 30, 6984.
OKeefe, J., & Recce, M. L. (1993). Phase relationship between hippocampal place units
and the EEG theta rhythm. Hippocampus, 3, 317330.
Palus, M., Komarek, V., Hrncr, Z., & Sterbova, K. (2001). Synchronization as
adjustment of information rates: Detection from bivariate time series. Physical
Review E, 63, 046211.

Panzeri, S., Senatore, R., Montemurro, M. A., & Petersen, R. S. (2007). Correcting for
the sampling bias problem in spike train information measures. Journal of
Priesemann, V., Munk, M. H.J, & Wibral, M. (2009). Subsampling effects in neuronal
avalanche distributions recorded in vivo. BMC Neuroscience, 10, 40.
Priesemann, V., Valderrama, M., Wibral, M., & Le Van Quyen, M. (2013). Neuronal
avalanches differ from wakefulness to deep sleep Evidence from intracranial depth
recordings in humans. PLoS Computational Biology, 9, e1002985.
Priesemann, V., Wibral, M., Valderrama, M., Propper, Le Van Quyen, M., Geisel, T.,
et al. (2014). Spike avalanches in vivo suggest a driven, slightly subcritical brain
state. Frontiers in Systems Neuroscience, 8, 108.
Ragwitz, M., & Kantz, H. (2002). Markov models from data by simple nonlinear time
series predictors in delay embedding spaces. Physical Review E, 65, 056201.
Schreiber, T. (2000). Measuring information transfer. Physical Reviews Letters, 85, 461.
Shannon, C. E. (1948). A mathematical theory of communication. Bell System Technical
Journal, 27, 379423.
Small, M., & Tse, C. K. (2004). Optimal embedding parameters: A modelling paradigm.
Physica D: Nonlinear Phenomena, 194, 283296.
Smirnov, D. A. (2013). Spurious causalities with transfer entropy. Physical Review E,
87, 042917.
Staniek, M., & Lehnertz, K. (2009). Symbolic transfer entropy: Inferring directionality in
biosignals. Journal of Biomedical Engineering and Technology, 54, 323328.
Stetter, O., Battaglia, D., Soriano, J., & Geisel, T. (2012). Model-free reconstruction of
excitatory neuronal connectivity from calcium imaging signals. PLoS Computational
Biology, 8, e1002653.
Stramaglia, S., Wu, G.-R., Pellicoro, M., & Marinazzo, D. (2012). Expanding the transfer
entropy to identify information circuits in complex systems. Physical Review E, 86,
066211.
Takens, F. (1981). Detecting strange attractors in turbulence. In Dynamical systems and
turbulence, Warwick 1980 (pp. 366381). New York: Springer.
Vakorin, V. A., Kovacevic, N., & McIntosh, A. R. (2010). Exploring transient transfer
entropy based on a group-wise ICA decomposition of EEG data. NeuroImage, 49,
15931600.
615
Vakorin, V. A., Krakovska, O. A., & McIntosh, A. R. (2009). Confounding effects of

indirect connections on causality estimation. Journal of Neuroscience Methods,
184, 152160.
Vakorin, V. A., Misic, B., Krakovska, O., & McIntosh, A. R. (2011). Empirical and
theoretical aspects of generation and transfer of information in a neuromagnetic
source network. Frontiers in Systems Neuroscience, 5, 96.
Vicente, R., Wibral, M., Lindner, M., & Pipa, G. (2011). Transfer entropy A model-free
measure of effective connectivity for the neurosciences. Journal of Computational
Victor, J. D. (2002). Binless strategies for estimation of information from neural data.
Wang, X. R., Miller, J. M., Lizier, J. T., Prokopenko, M., & Rossi, L. F. (2012).
Quantifying and tracing information cascades in swarms. PloS One, 7, e40084.
Wibral, M., Lizier, J. T., Vogler, S., Priesemann, V., & Galuske, R. (2014). Local active
information storage as a tool to understand distributed neural information
processing. Frontiers in neuroinformatics, 8.
Wibral, M., Pampu, N., Priesemann, V., Siebenhuehner, F., Seiwert, H., Lindner, M.,
et al. (2013). Measuring information-transfer delays. PloS One, 8, e55809.
Wibral, M., Rahm, B., Rieder, M., Lindner, M., Vicente, R., & Kaiser, J. (2011). Transfer
entropy in magnetoencephalographic data: Quantifying information flow in cortical
and cerebellar networks. Progress in Biophysics and Molecular Biology, 105, 8097.
Wibral, M., Turi, G., Linden, D. E., Kaiser, J., & Bledowski, C. (2008). Decomposition
of working memory-related scalp ERPs: Crossvalidation of fMRI-constrained
source analysis and ICA. International Journal of Psychophysiology, 67,
200211.
Wiener, N. (1956). The theory of prediction. In E. F. Beckenback (Ed.), Modern
mathematics for engineers (pp. 165190). New York: McGraw-Hill.
Williams, P.L., & Beer, R.D. (2010). Nonnegative decomposition of multivariate
information. ArXiv e-print No. 1004.2515.
Wollstadt, P., Martnez-Zarzuela, M., Vicente, R., Daz-Pernas, F. J., & Wibral, M.
(2014). Efficient Transfer Entropy Analysis of Non-Stationary Neural Time
Series. PLoS ONE, 9(7), e102833. http://dx.doi.org/10.1371/journal.
pone.0102833.
Dynamic Causal Models for fMRI

KE Stephan, University of Zurich & Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland;
Neuronal State Equations

The general idea of DCM (dynamic causal modeling) was introduced in 2003 and demonstrated in application to fMRI (Friston,
Harrison, & Penny, 2003). This article represented a significant
deviation from existing perspectives on estimating effective connectivity from fMRI data and introduced a number of important
themes that have since greatly influenced modeling approaches
to neuroimaging data. In brief, this article pointed out that
physiological mechanisms (such as effective connectivity) do
not live at the level of the measured data; instead, they exist at
the hidden (unobservable) neuronal level and must be inferred
upon, from the available measurements, by means of a model
how neuronal activity causes blood oxygen level-dependent
(BOLD) signals. More technically, it suggested that one needs to
formulate a hierarchical generative model of measured BOLD
data that links the neuronal level to the measurement level
through a biophysical forward model. This allows for model
inversion and thus for inference on hidden neurophysiological
mechanisms that underlie the observed data.
Given that hemodynamic signals only convey information
about low-frequency aspects of neuronal activity (cf. low-pass
filter properties of the hemodynamic response function), DCM
for fMRI requires a model of neuronal processes that is simple
and generic and captures key aspects of any neuronal system. A
suitable low-order approximation can be motivated from basic
systems theory considerations about nonautonomous systems
(Stephan, 2004), postulating two main components: a simple
neuronal state vector x (with one state per region, representing a
coarse summary of overall synaptic activity in this region) and a
vector of known inputs u (perturbations or experimental manipulations, such as sensory stimulation or task conditions). Modeling the rate of change in the neuronal state vector under the
influence of the known perturbations and performing a Taylor
series approximation up to bilinear order around the resting state
(x 0, u 0), one obtains (cf. Stephan et al., 2008)
f x; u
dx
dt
f 0; 0
@f
@f
@2f
x u
xu
@x
@u
@x@u
[1]
Setting
A @f =@xju0 , Bi @ 2 f =@x@ui , C @f =@ujx0
leads to the neuronal state equation of DCM for fMRI:
!
m
X
dx
i
f x; u
A
x Cu
ui B
dt
i1
[2]
(3)
Here, the A matrix represents the endogenous (fixed) connectivity (i.e., when the system is not being perturbed), the B
matrices represent context-dependent modulation of coupling

(i.e., plasticity), and the C matrix represents the strength of
direct influences on regional activity (e.g., sensory inputs; see
Figure 1).
A few things are worth noting here. First, the interpretation
of the A matrix depends on the nature of the input vector. If, for
example, the inputs are defined such that u 0 denotes the
absence of inputs, then the endogenous coupling refers to the
resting (unperturbed) state of the system and signal changes
induced by inputs lead to positive or negative deflections away
from rest. By contrast, if the input vector is mean-corrected, the
endogenous coupling refers to the state of the system when it
experiences average perturbation, and signal changes evoked
by inputs are caused by deviations from this average stimulation. Second, the C matrix can, to some degree, absorb missing
inputs to the regions considered in the model. This is analogous to conventional general linear model (GLM) analyses of
fMRI data where voxel interactions are absorbed into the driving inputs that are the sole influence each voxel experiences.
Given the previously stated equation, one would like to
obtain estimates of the connectivity parameters. In DCM, this
is done using a variational Bayesian approach, which is discussed in more detail later in the text. In a first step, however,
we require a forward model, that is, a link from the modeled
neuronal dynamics to the measured BOLD data.
From Hidden Neuronal Dynamics to BOLD Data:

The Hemodynamic Model
Standard analyses of fMRI data based on the GLM typically
employ a convolution model of BOLD data, assuming that the
hemodynamic response function represents the impulse
response of a linear time-invariant system (Friston, Frith, Turner,
& Frackowiak, 1995). An alternative perspective is to model the
mechanistic chain, from neuronal activity to the BOLD signal to
biophysically motivated differential equations. This has the
advantage that one can estimate hemodynamic parameters in
a region- and subject-specific fashion, thus eschewing any
assumptions about canonical forms and strict linearity. The
hemodynamic model employed by DCM rests on pioneering
work by Buxton, Wong, and Frank (1998) who introduced the
so-called Balloon model that suggests differential equations for
changes in blood volume and deoxyhemoglobin content under
neuronal activation, explaining the measured BOLD signal as a
nonlinear mixture of the two. This model was subsequently
augmented by differential equations that linked neuronal activity to volume and deoxyhemoglobin content via changes in
vasodilation and blood flow (Friston, Mechelli, Turner, &
Price, 2000). Further refinements of the nonlinear output equation and systematic model comparisons (Stephan, Weiskopf,
Drysdale, Robinson, & Friston, 2007) led to the form used in
http://dx.doi.org/10.1016/B978-0-12-397025-1.00339-0
617
618
INTRODUCTION TO METHODS AND MODELING | Dynamic Causal Models for fMRI
Nonlinear DCM
Bilinear DCM
u2
u2
u1
u2
Bilinear state equation

dx
=
dt
m
A + ui
i=1
B(i) x + Cu
Nonlinear state equation

dx
=
dt
A + ui
i=1
j=1
B(i) + xj D( j) x + Cu
Figure 1 A summary of the neuronal state equations in bilinear and nonlinear DCMs for fMRI, respectively. This figure is reproduced, with permission,
from Figure 1 in Stephan, K. E., Kasper, L., Harrison, L. M., Daunizeau, J., den Ouden, H. E., Breakspear, M., & Friston, K. J. (2008). Nonlinear
dynamic causal models for fMRI. Neuroimage, 42, 649662.
the present implementation DCM. A graphic summary of this

hemodynamic model is contained by Figure 2. Finally, it is
worth mentioning that the forward model can also account for
slice-wise differences in sampling time (Kiebel, Kloppel, Weiskopf, & Friston, 2007).
Model Inversion
Together with parametric assumptions about observation noise
and its serial correlation (Friston et al., 2002), the set of differential equations representing neuronal and hemodynamic processes (with a joint parameter vector y) constitutes a model of
the likelihood of the data y, p(y|y, m). Combined with suitably
chosen priors on the neuronal and hemodynamic parameters,
this results in a full generative model of measured data, that is, a
full probabilistic model specifying the joint probability of all
variables (observations, parameters, and hyperparameters).
Given some measured fMRI data, this model can be inverted
in order to provide posterior estimates of the parameters. In
DCM, this proceeds under Gaussian assumptions about the
posterior (Laplace assumption). However, instead of optimizing
the posterior probabilities directly, for example, through Markov chain Monte Carlo techniques, DCM rests on a variational
Bayesian approach that optimizes the (negative) free energy as a
lower-bound approximation to the log model evidence. This has
the advantage of being computationally efficient and providing
an estimate of the log evidence that serves as the basis for model
comparison, as described later in the text.
The variational Laplace algorithm employed by DCM is
computationally efficient and robust in many situations
(Friston, Mattout, Trujillo-Barreto, Ashburner, & Penny,
2007). However, as it relies on a gradient ascent scheme, it
can be susceptible to local minima; this can become a serious
problem when moving from simple bilinear DCMs for fMRI
data to more complex nonlinear models (Daunizeau, David, &
Stephan, 2011). For this reason, ongoing developments are
concerned with global optimization approaches for DCM
inversion, for example, on the basis of Gaussian processes.
Extensions of the Neuronal State Equation

Following the initial formulation of DCM on the basis of a
bilinear differential equation, several extensions have been
suggested that greatly expand the scope of DCM for fMRI. For
example, Stephan et al. (2008) had extended the underlying
Taylor approximation to second-order, allowing for multiplicative interactions between neuronal states. This enables one to
infer on how synaptic coupling between two populations
changes as a function of the activity in a third population.
Such estimates of the nonlinear gating of connection strengths
represent synaptic interactions that underlie different forms of
short-term synaptic plasticity. An example of such effects,
based on simulations, is provided in Figure 3.
The initial formulation of DCM assumed a single neuronal
state variable per population (region). This basic DCM was
finessed by Marreiros, Kiebel, and Friston (2008) who modeled two state variables per region, representing excitatory and
inhibitory neuronal populations, respectively. This extension
allowed for modeling intraregional interactions and for enforcing excitatory long-range connections, in accordance with the
general wiring rules of the isocortex.
Finally, an important extension of DCM concerned random
fluctuations in neuronal and hemodynamic states. This treatment rests on random or stochastic differential equations that
account for state noise and its temporal smoothness. This type
of DCM is numerically considerably more challenging for
model inversion and led to the development of new procedures, such as dynamic expectation maximization (Friston,
Trujillo-Barreto, & Daunizeau, 2008), variational Bayesian filtering techniques for nonlinear stochastic state-space models
(Daunizeau, Friston, & Kiebel, 2009; Friston, 2008), and, more
recently, generalized filtering (Friston, Stephan, et al., 2010).
A major advantage of stochastic DCMs is that they allow
DCM to be applied to resting state data, which had not been
possible with conventional deterministic DCMs: since resting
state data are acquired in the absence of experimental control,
there are no inputs that could inform a deterministic DCM.
Since their recent introduction, stochastic DCMs have already
619
Stimulus functions
m
= A + uj B( j ) x + Cu
j=1
dt
dx
Neural state equation
Vasodilatory signal
s = x ks g ( -1)
s
s
Flow induction (rCBF)
=s
Hemodynamic
state equations
Balloon model
Changes in volume
t n = - n1/a
Changes in dHb
t q = E (, E0) /E0 - n1/a q/n
l (q,n) =
DS
V0 k1(1- q) + k2 1- n + k3(1-n)
S0
k1 = 4.3J0E0TE
k2 = e r0E0TE
k3 = 1-e
BOLD signal
change equation
Figure 2 A graphic summary of the hemodynamic modeling DCM for fMRI. This figure is reproduced, with permission, from Figure 1 in Stephan, K. E.,
Weiskopf, N., Drysdale, P. M., Robinson, P. A., & Friston, K. J. (2007). Comparing hemodynamic models with DCM. Neuroimage, 38, 387401.
been applied by several studies, to both resting state data (e.g.,

Di & Biswal, 2013; Rehme, Eickhoff, & Grefkes, 2013) and task
fMRI data (e.g., Bernal-Casas et al., 2013; Daunizeau, Stephan,
& Friston, 2012; Li et al., 2011; Li, Wang, Yao, Hu, & Friston,
2012; Ma et al., 2012). For task fMRI, both deterministic DCM
and stochastic DCM are now available options, and an important task for the future is to clarify which version is more
appropriate in which particular situation (see Daunizeau
et al. (2012) for an initial analysis).

For any given experimental observation, in principle, an infinite number of possible explanations exist. Generally, the scientific process consists in selecting a finite subset of these
possible hypotheses, based on prior beliefs about what constitutes a plausible explanation. Formally, this corresponds to
defining a prior on model space, such that all but a finite

number of models are assigned a prior probability of zero.
Given this hypothesis set or model space, one then proceeds
by evaluating the evidence, that is, the probability of the data
given the model p(y|m), with regard to each of the models m
considered. The evidence corresponds to the probability of
observing the data when integrating out the dependency on
the model parameters. In other words, it represents the
expected data under random sampling from the priors. It can
be shown that the evidence represents a principled index for
the goodness or generalizability of a model, that is, the tradeoff between its accuracy (fit) and complexity. The evidence
thus provides a rational basis for comparing different models
(Pitt & Myung, 2002); critically, these do not need to be nested
and may differ to an arbitrary extent in their formulation and
complexity (Penny, Stephan, Mechelli, & Friston, 2004a).
Comparing different models on the basis of their (log)
model evidence is also referred to as Bayesian model selection
620
0.4
0.3
0.2
0.1
0
u2
+++
Neural population activity
10
20
30
40
50
60
70
80
90
100
10
20
30
40
50
60
70
80
90
100
10
20
30
40
50
60
70
80
90
100
0.6
0.4
x3
0.2
0
+++
0.3
0.2
0.1
u1
+++
x1
x2
+
BOLD signal change (%)
1
0
Neuronal state equation
dx
dt
a11
= a21
a12
a22
a32
(3)
a23 + x3 d21
0
a33
0
0
0
0
x1
x +
2
x3
c11
0
u1
0
u
2
c32
0
4
3
2
1
0
-1
10
20
30
40
50
60
70
80
90
100
10
20
30
40
50
60
70
80
90
100
10
20
30
40
50
60
70
80
90
100
3
2
1
0
Figure 3 A simulation of nonlinear gating of connections, as modeled by a nonlinear DCM for fMRI. This figure is reproduced, with permission, from
Figure 2 in Stephan, K. E., Kasper, L., Harrison, L. M., Daunizeau, J., den Ouden, H. E., Breakspear, M., & Friston, K. J. (2008). Nonlinear dynamic
causal models for fMRI. Neuroimage, 42, 649662.
(BMS). While BMS has been a long-standing tool in machine

learning (Mac Kay, 1992), it was introduced to neuroimaging
only relatively recently (Penny et al., 2004a). This introduction
was motivated by the desire to compare alternative DCMs of
fMRI data and has since spawned a considerable literature. One
major challenge was to develop BMS procedures that would
account for heterogeneity across subjects. This is a critical issue
because subjects may differ greatly, in either how a particular
cognitive process is implemented neurobiologically or which
of several cognitive strategies is being deployed in a particular
task. In other words, when conducting model comparison at
the group level, one faces the possibility that the model itself is
a random variable in the population. This led to the development of a random effects BMS procedure that employs a hierarchical model to infer, from the profile of log evidences across
subjects, on the frequencies of models in the sample of subjects
studied (Stephan, Penny, et al., 2009). This explicit account of
intersubject heterogeneity is particularly important for clinical
applications, for example, in the investigation of psychiatric
spectrum disorders. However, random effects BMS has found
widespread application beyond neuroimaging, for example, in
computational modeling of behavioral data, such as learning
and decision-making models in neuroeconomics and cognitive
science (e.g., Tricomi, Rangel, Camerer, & ODoherty, 2010).
Since model parameter estimates are conditional on the
chosen model, the typical sequence in a DCM (and any other
modeling study with a focus on inference) is the following

(Stephan et al., 2010): first, the definition of the model space
(hypothesis set); second, model comparison; and third, statistical analysis of parameter estimates from the winning model
(see Figure 4 for a graphic summary). However, the data may
not always contain sufficient information to allow for disambiguating competing models clearly. Furthermore, when considering a large number of models, one faces the problem of
dilution, that is, posterior model probabilities monotonically
decrease with the number of models considered (since each
model in the hypothesis set has nonzero prior probability and
posterior model probabilities must sum to unity). These problems can be addressed in two ways: either by model space
partitioning or family-level inference (Penny et al., 2010; Stephan, Penny, et al., 2009) or by Bayesian model averaging
(BMA; Hoeting, Madigan, & Raftery, 1999), which delivers a
weighted average of the posterior probability of each parameter across models (weighted by the posterior probability of
each model).
The most recent extension to BMS procedures is the introduction of post hoc procedures (Friston & Penny, 2011; Rosa,
Friston, & Penny, 2012). These provide estimates of the log
evidence for any reduced model as a function of the posterior
density over the parameters of the full model. This radically
reduces the computational complexity of computing the log
evidence for a set of models and has enabled the development
621
Definition of model space
Inference on model structure or Inference on model parameters?
Inference on
individual models or model space partition?
Optimal model structure assumed

to be identical across subjects?
Comparison of model
families using
FFX or RFX BMS
Inference on
parameters of an optimal model or parameters of all models?
Optimal model structure assumed

to be identical across subjects?
Yes
Yes
No
No
FFX BMS
FFX BMS
BMA
RFX BMS
FFX analysis of
parameter estimates
(e.g., BPA)
RFX BMS
RFX analysis of
parameter estimates
(e.g., T-test, ANOVA)
Figure 4 A flowchart of the analysis options available in DCM. This figure is reproduced, with permission, from Figure 1 in Stephan, K. E., Penny, W. D.,
Moran, R. J., den Ouden, H. E., Daunizeau, J., & Friston, K. J. (2010). Ten simple rules for dynamic causal modeling. Neuroimage, 49, 30993109.
of network identification procedures, which, depending on the

size of the model, can perform an exhaustive search of model
space, comprising all possible combinations of connections for
a given network (Friston, Li, et al., 2010).
Model Validation
Careful validation is crucial for any modeling approach, not
just DCM, and requires multiple studies that address different
aspects of validity (e.g., face validity, construct validity, and
predictive validity). Concerning DCM for fMRI, its face validity
has been examined by several simulation studies that tested
whether known parameter estimates or model structure could
be recovered (Daunizeau, 2013; Friston et al., 2003; Friston &
Penny, 2011; Stephan, Friston, et al., 2009; Stephan et al.,
2008; Stephan, Penny, et al., 2009). Construct validity has
also been examined, for example, by testing whether DCMbased estimates of effective connectivity were compatible with
estimates obtained by other methods (e.g., structural equation
modeling; Penny, Stephan, Mechelli, & Friston, 2004b) or with
known neurophysiological effects, such as mutual inhibition
of motor areas via interhemispheric connections (Grefkes,
Eickhoff, Nowak, Dafotakis, & Fink, 2008). Finally, predictive
validity has been established in rodent studies where DCM was
challenged to detect known mechanisms, such as the experimentally induced origin of epileptic seizures (David et al.,
2008) or effects of vagal nerve stimulation (Reyt et al., 2010).
It is worth noting that physiological validation studies of this

sort have particularly been performed with respect to DCM for
electrophysiological data, using pharmacological manipulations in both animals and humans (Moran, Jung, et al., 2011;
Moran et al., 2007, 2008; Moran, Symmonds, et al., 2011).
An additional aspect of model validation concerns test
retest reliability. This has been addressed by several studies.
For example, Schuyler et al. demonstrated that for simple
visual and auditory tasks, within-subject parameter estimates
are highly reproducible across separate sessions (Schuyler,
Ollinger, Oakes, Johnstone, & Davidson, 2010). Another
reproducibility study using a more complex action selection
task found less reproducibility of connectivity estimates; by
contrast, model selection results were highly reproducible
(Rowe, Hughes, Barker, & Owen, 2010). Most recently, a multisite reproducibility study of stochastic DCM, involving 180
subjects over three different centers, found very good reproducibility, in terms of both parameter estimates and model
selection results (Bernal-Casas et al., 2013).
Application to Clinical Applications

Although DCM for fMRI goes far beyond the type of inference
afforded by models of functional connectivity and more traditional models of effective connectivity, from a neurophysiological perspective, DCM still only provides a relatively simple
representation of mechanisms. For example, it does not
622
(or only to a very limited degree, as in two-state DCMs) distinguish between different types of neurons. Similarly, its inference on synaptic plasticity rests on observing changes in the
effective strength of connections due to experimental factors
known to elicit plasticity (such as learning or pharmacology),
but does not reveal the exact type of plasticity nor the neurotransmitter systems.
Despite this coarse physiological representation, DCM for
fMRI can produce meaningful insights into the pathophysiology of brain diseases. Taking the dysconnection hypothesis
of schizophrenia and (Friston, 1998; Stephan, Baldeweg, &
Friston, 2006) as an example, a recent fMRI study on chronic
schizophrenic patients found that while the degree of prefrontal activation during a working memory task depended on task
performance, the prefrontalparietal connection strength was
uniformly diminished across patients, regardless of task performance, representing a functional dysconnection between
these two areas during working memory (Deserno, Sterzer,
Wustenberg, Heinz, & Schlagenhauf, 2012). In a separate
study (Schmidt et al., 2013), the same connection was found
to be progressively diminished in strength across disease stages
in schizophrenia, with successive reductions from healthy participants via at-risk mental state subjects to untreated firstepisode schizophrenic patients. However, in medicated firstepisode patients, the strength of this connection recovered to
normal levels, indistinguishable from healthy controls
(Schmidt et al., 2013). Other notable work on schizophrenia
examined possible mechanisms why perceptual illusions are
less impaired in schizophrenic patients. Two separate studies,
applying DCM to fMRI and EEG data from the hollow-mask
illusion paradigm, found increased strength of bottom-up but
decreased strength of top-down connections (Dima, Dietrich,
Dillo, & Emrich, 2010; Dima et al., 2009). This replicated
finding nicely agrees with predictions from theories of
impaired perceptual inference in schizophrenia, which posit a
Step 1
model inversion
reduction in the precision of perceptual priors (for a recent

review, see Adams, Stephan, Brown, Frith, and Friston (2013)).
Beyond its potential utility for pathophysiological studies,
DCM might also provide a foundation for establishing modelbased diagnostic tools. Ideally, prospective studies that challenge DCM (or any other model) to predict, from measured
neuroimaging data, the future expression of clinically relevant
variables (such as outcome or treatment response) could further demonstrate its predictive validity and, at the same time,
directly establish its utility as a clinical tool. In a first and less
ambitious step, if it can be shown that DCM can predict
independent clinical variables from fMRI data, this would
demonstrate that the models estimates of physiology meaningfully relate to the disease process studied. Indeed, the latter
sort of validation has been achieved in two initial studies on
generative embedding. Generative embedding integrates generative models of brain physiology or behavior with (un)supervised learning techniques from machine learning, such as
support vector machines for classification (Figure 5). In brief,
the idea is to use the model as a hypothesis-led denoising tool
that provides a low-dimensional summary, in terms of the
model parameter estimates, of the mechanisms that generated
the observed data. This summary can then be used to specify a
feature space for subsequent clustering or classification. Critically, this feature space is interpretable mechanistically, in the
frame of reference provided by the model. The utility of this
approach was demonstrated by a recent study that tested
whether the absence or presence of a hidden (out of the
field of view) brain lesion could be predicted from connectivity
estimates in the healthy part of the brain (Brodersen et al.,
2011). In this study, the lesion was a stroke located in prefrontal or anterior temporal cortex (rendering the patients aphasic)
while DCM was applied to fMRI data from the nonaffected
early auditory system (primary and secondary auditory cortices
and auditory thalamus) during a passive speech listening task.
Step 2
kernel construction
c MQ
B
C
p(q |x,m)
MQ Rd
AB
AC
BB
BC
k : Rd Rd R
Rd
km : MQ MQ R
Measurements from
an individual subject
Subject representation in the

generative score space
Subject-specific
inverted generative model
A
Step 3
support vector classification
Step 4
interpretation
B
C
c^ = sgn S ai*k(xi, x) + b*
Jointly discriminative
model parameters
Separating hyperplane fitted to

discriminate between groups
Figure 5 A graphic summary of the idea behind generative embedding. This figure is reproduced, with permission, from Figure 1 in Brodersen, K. H.,
Schofield, T. M., Leff, A. P., Ong, C. S., Lomakina, E. I., Buhmann, J. M., & Stephan, K. E. (2011). Generative embedding for model-based classification
of fMRI data. PLoS Computational Biology, 7, e1002079.

Indeed, estimates of synaptic coupling from a simple six-region
DCM allowed for almost perfect (98%) prediction of whether
or not the individual subjects suffered from a remote lesion.
This performance was far superior to classification results
obtained by more conventional means, for example, based
on regional activity (searchlight classification) or functional
connectivity estimates.
More recent work on generative embedding has extended it
to the unsupervised domain, using DCM parameter estimates
for detecting unknown subgroups in psychiatric spectrum diseases by clustering (Brodersen et al., 2013). In this proof of
concept study, a simple three-area DCM of interactions
between visual, parietal, and prefrontal cortices during working memory was combined with variational Gaussian mixture
modeling and applied to 41 schizophrenic patients (data from
Deserno et al., 2012). The results indicated the presence of
three subgroups, distinguished by different connectivity patterns. Most importantly, these three neurophysiologically
defined subgroups differed significantly with regard to the
level of negative symptoms expressed clinically. In other
words, the purely physiology-based definition of subgroups,
informed only by estimates of coupling derived from fMRI
data, allowed a prediction of clinical symptoms. While this
study does not have any clinical utility, it provides a blueprint
for future studies in which models whose parameters map onto
therapeutically accessible mechanisms (e.g., dopaminergic
transmission; Moran, Symmonds, et al., 2011) and could be
used to designate subgroups with specific treatment recommendations. This notion of model-based assays for
individualized predictions may become an important strategy
for enhancing the direct clinical utility of neuroimaging and for
providing physiological markers that may serve to dissect psychiatric spectrum disorders into mechanistically more distinct
subgroups (cf. Stephan, Friston, et al., 2009).
Summary
This article has summarized the conceptual and mathematical
basis of DCM for fMRI and outlined its development over the
past decade. It is probably fair to say that, by highlighting the
importance of forward models and emphasizing the utility of a
Bayesian approach, DCM has introduced some important
changes in the development of fMRI connectivity analyses
(for discussions of different approaches and their interactions,
see Stephan and Roebroeck (2012) and Valdes-Sosa, Roebroeck, Daunizeau, and Friston (2011)). More generally, it has
brought several themes to the attention of the neuroimaging
community that are of critical importance for modeling
approaches in general but had previously been somewhat
neglected, such as the importance of model selection and the
need for validation studies.
Importantly, DCM does not refer to one specific model, but
represents a modeling framework that evolves as new numerical techniques and measurement modalities become available. Model validation is and will remain an important
component in these ongoing developments. In particular,
studies that evaluate the feasibility of model-based predictions,
with respect to independent data, not only provide important
validation but also may establish practical applications that
623
tackle important problems in basic neuroscience and clinical

neuroscience.

Functional MRI Dynamics; INTRODUCTION TO ANATOMY AND
PHYSIOLOGY: Cytoarchitectonics, Receptorarchitectonics, and
Network Topology of Language; Functional Connectivity;
INTRODUCTION TO CLINICAL BRAIN MAPPING: Schizophrenia;
Model Inference; Bayesian Model Inversion; Convolution Models for
FMRI; Dynamic Causal Models for Human Electrophysiology: EEG,
MEG, and LFPs; Effective Connectivity; Granger Causality; Models of
fMRI Signal Changes; Resting-State Functional Connectivity;
Variational Bayes.
References
Adams, R. A., Stephan, K. E., Brown, H. R., Frith, C. D., & Friston, K. J. (2013). The
computational anatomy of psychosis. Frontiers in Psychiatry, 4, 47.
Bernal-Casas, D., Balaguer-Ballester, E., Gerchen, M. F., Iglesias, S., Walter, H.,
Heinz, A., et al. (2013). Multi-site reproducibility of prefrontalhippocampal
connectivity estimates by stochastic DCM. Neuroimage, 82, 555563.
Brodersen, K. H., Deserno, L., Schlagenhauf, F., Lin, Z., Penny, W. D., Buhmann, J. M.,
et al. (2013). Dissecting psychiatric spectrum disorders by generative embedding.
Brodersen, K. H., Schofield, T. M., Leff, A. P., Ong, C. S., Lomakina, E. I.,
Buhmann, J. M., et al. (2011). Generative embedding for model-based classification
of fMRI data. PLoS Computational Biology, 7, e1002079.
Daunizeau, J., David, O., & Stephan, K. E. (2011). Dynamic causal modelling: A critical
review of the biophysical and statistical foundations. Neuroimage, 58, 312322.
Daunizeau, J., Friston, K. J., & Kiebel, S. J. (2009). Variational Bayesian identification
and prediction of stochastic nonlinear dynamic causal models. Physica D, 238,
20892118.
Daunizeau, J., Stephan, K. E., & Friston, K. J. (2012). Stochastic dynamic causal modelling
of fMRI data: Should we care about neural noise? Neuroimage, 62, 464481.
Daunizeau, J., Lemieux, L., Vaudano, A. E., Friston, K. J., & Stephan, K. E. (2013). An
electrophysiological validation of stochastic DCM for fMRI. Frontiers in
Computational Neuroscience, 6(103).
David, O., Guillemain, I., Saillet, S., Reyt, S., Deransart, C., Segebarth, C., et al. (2008).
Identifying neural drivers with functional MRI: An electrophysiological validation.
PLoS Biology, 6, 26832697.
Deserno, L., Sterzer, P., Wustenberg, T., Heinz, A., & Schlagenhauf, F. (2012). Reduced
prefrontalparietal effective connectivity and working memory deficits in
schizophrenia. Journal of Neuroscience, 32, 1220.
Di, X., & Biswal, B. B. (2013). Identifying the default mode network structure using
dynamic causal modeling on resting-state functional magnetic resonance imaging.
Dima, D., Dietrich, D. E., Dillo, W., & Emrich, H. M. (2010). Impaired top-down
processes in schizophrenia: A DCM study of ERPs. Neuroimage, 52, 824832.
Dima, D., Roiser, J. P., Dietrich, D. E., Bonnemann, C., Lanfermann, H., Emrich, H. M.,
et al. (2009). Understanding why patients with schizophrenia do not perceive the
hollow-mask illusion using dynamic causal modelling. Neuroimage, 46, 11801186.
Friston, K. J. (1998). The disconnection hypothesis. Schizophrenia Research, 30,
115125.
Friston, K. J. (2008). Variational filtering. Neuroimage, 41, 747766.
Friston, K. J., Frith, C. D., Turner, R., & Frackowiak, R. S. (1995). Characterizing evoked
hemodynamics with fMRI. Neuroimage, 2, 157165.
Friston, K. J., Li, B., Daunizeau, J., & Stephan, K. E. (2010). Network discovery with
DCM. Neuroimage, 56, 12021221.
624
Variational free energy and the Laplace approximation. Neuroimage, 34, 220234.
Friston, K. J., Mechelli, A., Turner, R., & Price, C. J. (2000). Nonlinear responses in
fMRI: The Balloon model, Volterra kernels, and other hemodynamics. Neuroimage,
12, 466477.
Friston, K., & Penny, W. (2011). Post hoc Bayesian model selection. Neuroimage, 56,
20892099.
Friston, K., Stephan, K. E., Li, B., & Daunizeau, J. (2010). Generalised filtering.
Mathematical Problems in Engineering, 621670, .
Friston, K. J., Trujillo-Barreto, N., & Daunizeau, J. (2008). DEM: A variational treatment
of dynamic systems. Neuroimage, 41, 849885.
Grefkes, C., Eickhoff, S. B., Nowak, D. A., Dafotakis, M., & Fink, G. R. (2008). Dynamic
intra- and interhemispheric interactions during unilateral and bilateral hand
movements assessed with fMRI and DCM. Neuroimage, 41, 13821394.
Hoeting, J. A., Madigan, D., & Raftery, A. E. (1999). Bayesian model averaging: A
tutorial. Statistical Science, 14, 382401.
Kiebel, S. J., Kloppel, S., Weiskopf, N., & Friston, K. J. (2007). Dynamic causal
modeling: A generative model of slice timing in fMRI. Neuroimage, 34, 14871496.
Li, B., Daunizeau, J., Stephan, K. E., Penny, W., Hu, D., & Friston, K. (2011).
Generalised filtering and stochastic DCM for fMRI. Neuroimage, 58, 442457.
Li, B., Wang, X., Yao, S., Hu, D., & Friston, K. (2012). Task-dependent modulation of
effective connectivity within the default mode network. Frontiers in Psychology, 3, 206.
Ma, L., Steinberg, J. L., Hasan, K. M., Narayana, P. A., Kramer, L. A., & Moeller, F. G.
(2012). Stochastic dynamic causal modeling of working memory connections in
cocaine dependence. Human Brain Mapping, 35, 760778.
Mac Kay, D. J.C (1992). A practical bayesian framework for Backpropagation networks.
Neural Computation, 4, 448472.
Marreiros, A. C., Kiebel, S. J., & Friston, K. J. (2008). Dynamic causal modelling for
fMRI: A two-state model. Neuroimage, 39, 269278.
Moran, R. J., Jung, F., Kumagai, T., Endepols, H., Graf, R., Dolan, R. J., et al. (2011).
Dynamic causal models and physiological inference: A validation study using
isoflurane anaesthesia in rodents. PLoS One, 6, e22790.
Moran, R. J., Kiebel, S. J., Stephan, K. E., Reilly, R. B., Daunizeau, J., & Friston, K. J.
(2007). A neural mass model of spectral responses in electrophysiology.
Moran, R. J., Stephan, K. E., Kiebel, S. J., Rombach, N., OConnor, W. T., Murphy, K. J.,
et al. (2008). Bayesian estimation of synaptic physiology from the spectral
responses of neural masses. Neuroimage, 42, 272284.
Moran, R. J., Symmonds, M., Stephan, K. E., Friston, K. J., & Dolan, R. J. (2011). An
in vivo assay of synaptic function mediating human cognition. Current Biology, 21,
13201325.
Penny, W. D., Stephan, K. E., Daunizeau, J., Rosa, M. J., Friston, K. J., Schofield, T. M.,
et al. (2010). Comparing families of dynamic causal models. PLoS Computational
Biology, 6, e1000709.
Penny, W. D., Stephan, K. E., Mechelli, A., & Friston, K. J. (2004a). Comparing dynamic
causal models. Neuroimage, 22, 11571172.
Penny, W. D., Stephan, K. E., Mechelli, A., & Friston, K. J. (2004b). Modelling
functional integration: A comparison of structural equation and dynamic causal
models. Neuroimage, 23(Suppl. 1), S264S274.
Pitt, M. A., & Myung, I. J. (2002). When a good fit can be bad. Trends in Cognitive
Sciences, 6, 421425.
Rehme, A. K., Eickhoff, S. B., & Grefkes, C. (2013). State-dependent differences between
functional and effective connectivity of the human cortical motor system.
Reyt, S., Picq, C., Sinniger, V., Clarencon, D., Bonaz, B., & David, O. (2010). Dynamic
causal modelling and physiological confounds: A functional MRI study of vagus
nerve stimulation. Neuroimage, 52, 14561464.
Rosa, M. J., Friston, K., & Penny, W. (2012). Post-hoc selection of dynamic causal
models. Journal of Neuroscience Methods, 208, 6678.
Rowe, J. B., Hughes, L. E., Barker, R. A., & Owen, A. M. (2010). Dynamic causal
modelling of effective connectivity from fMRI: Are results reproducible and
sensitive to Parkinsons disease and its treatment? Neuroimage, 52,
10151026.
Schmidt, A., Smieskova, R., Aston, J., Simon, A., Allen, P., Fusar-Poli, P., et al. (2013).
Brain connectivity abnormalities predating the onset of psychosis: Correlation with
the effect of medication. JAMA Psychiatry, 70, 903912.
Schuyler, B., Ollinger, J. M., Oakes, T. R., Johnstone, T., & Davidson, R. J. (2010).
Dynamic Causal Modeling applied to fMRI data shows high reliability. Neuroimage,
49, 603611.
Stephan, K. E. (2004). On the role of general system theory for functional neuroimaging.
Journal of Anatomy, 205, 443470.
Stephan, K. E., Baldeweg, T., & Friston, K. J. (2006). Synaptic plasticity and
dysconnection in schizophrenia. Biological Psychiatry, 59, 929939.
Stephan, K. E., Friston, K. J., & Frith, C. D. (2009). Dysconnection in schizophrenia:
From abnormal synaptic plasticity to failures of self-monitoring. Schizophrenia
Bulletin, 35, 509527.
Stephan, K. E., Kasper, L., Harrison, L. M., Daunizeau, J., den Ouden, H. E.,
Breakspear, M., et al. (2008). Nonlinear dynamic causal models for fMRI.
Bayesian model selection for group studies. Neuroimage, 46, 10041017.
Stephan, K. E., Penny, W. D., Moran, R. J., den Ouden, H. E., Daunizeau, J., &
Friston, K. J. (2010). Ten simple rules for dynamic causal modeling. Neuroimage,
49, 30993109.
Stephan, K. E., & Roebroeck, A. (2012). A short history of causal modeling of fMRI data.
Comparing hemodynamic models with DCM. Neuroimage, 38, 387401.
Tricomi, E., Rangel, A., Camerer, C. F., & ODoherty, J. P. (2010). Neural evidence for
inequality-averse social preferences. Nature, 463, 10891091.
Valdes-Sosa, P. A., Roebroeck, A., Daunizeau, J., & Friston, K. (2011). Effective connectivity:
Influence, causality and biophysical modeling. Neuroimage, 58(2), 339361.
Dynamic Causal Models for Human Electrophysiology: EEG, MEG, and LFPs
R Moran, Virginia Tech Carilion Research Institute, Roanoke, VA, USA; Bradley Department of Electrical and Computer
Engineering, Roanoke, VA, USA
LFPS Local Field Potentials

MEG Magnetoencephalography
Glossary
DCM Dynamic Causal Modeling

EEG Electroencephalography
Introduction
Connectivity estimates using dynamic causal modelings (DCMs)
for EEG have been used to inform the mechanisms underlying
Parkinsons disease, epilepsy, the vegetative state, and schizophrenia. Application rests upon a plausible generative model
of neuronal dynamics between connected brain sources and
nodes. These models describe not directly observable mechanisms for example, the strength of synaptic connections along
extrinsic cortico-cortical pathways, using differential equations.
Bayesian inference is then used to map from recorded responses
(electroencephalographic/magnetoencephalographic/local field
potential (EEG/MEG/LFP) data) to their underlying cause.
Hence, the estimates of intrinsic (within-region) and extrinsic
(region-to-region) connections are deemed effective or modelbased assessments. This DCM procedure (Friston, Harrison, &
Penny, 2003) of proposing a generative architecture and then
fitting the model to data can be applied to a range of electrophysiological data features, including event-related potentials
(ERPs), spectral densities, and cross-spectral densities (CSDs),
induced responses (IRs) (timefrequency), and phase coupling
(PHA). DCMs for ERPs and CSDs use neural mass models to
describe active brain sources. In contrast, DCMs for IR and PHA
use phenomenological models to describe interregional effects
using more abstract parameters. This article will first outline the
types of neural mass models used in DCM for ERP/CSDs. The
second section outlines the forward mapping that allows these
models to generate scalp- and sensor-level EEG and MEG data or
invasive LFPs and describes how Bayesian inversion procedures
are used to test competing hypotheses regarding the generative
processes. The following section then demonstrates how these
models and procedures can be applied in the context of either
ERP or CSD data. The final section outlines the phenomenological class of DCMs.
Neural Mass Models

Since Hodgkin and Huxley developed their biophysical model
of ionic currents and action potential generation in the squid
axon, scientists have considered how similar membrane potential mechanisms can be described at the level of neuronal
populations. This pursuit of describing neuronal activity in
concert has led to the development of neural mass models
and their application in DCMs for EEG. Neural mass models
use principles of statistical physics to mathematically
describe how population dynamics emerge from single-cell

dynamics. In particular, mean field reductions use probability densities to represent salient features, such as the average
current flow induced by particular ions. Neural mass models
reduce the interaction of these types of neuronal states to
interactions among the means, or modes, of their densities.
This simplification reduces a potentially large parameter space
(describing interactions among many neurons) to a simpler,
one-dimensional (ensemble) characterization. DCMs for
ERPs and CSDs use these first-order neural mass models
(with options to include second-order statistics). From this
dynamic and statistical starting point, the neural mass models
that represent dynamics within a source are further elaborated.
Three important neurobiological properties are represented
in DCMs neural mass models, namely, laminar-specific cellular
subtypes within a region, laminar-specific extrinsic connections
between sources, and glutamate and GABAergic receptor
dynamics. Based on histological data, it is known that the cortex
has a layered structure (six-layered neocortex and the less layered
allocortex) with different cell types populating these layers. The
neural mass models used in DCM capture this anatomical structure by specifying (currently three or four) subpopulations of cell
types, occupying the granular, supragranular, and infragranular
layers. These are interconnected through plausible intrinsic connectivity structures and include populations of pyramidal cells,
inhibitory interneurons, and spiny stellate cells. It is worth noting that these architectures are designed to be rearranged for
particular investigations, for example, in a granular primary
motor cortex, by disconnecting certain layers/populations.
While synapses formed by local gray matter axons are represented within a region, as intrinsic connections, network-based
brain dynamics (where multiple sources are coactivated) are
generated through interregional (myelinated) connections.
These extrinsic connections have the same mathematical form
as intrinsic connections but are exclusively glutamatergic (excitatory) and impinge upon cell populations in particular layers.
For example, a thalamocortical or forward cortico-cortical connection will excite granular layer IV stellate cells. In contrast,
other backward, modulatory extrinsic connections will excite
pyramidal cells and inhibitory interneurons outside of layer IV.
Neural mass models also allow one to infer the synaptic
connections, mediated by different neurotransmitters and receptor types, for example, GABAergic and glutamatergic processes.
This third component of biophysical plausibility provides different dynamic effects at, for example, an AMPA receptor (fast
excitatory) versus an NMDA receptor (slow, excitatory, and
http://dx.doi.org/10.1016/B978-0-12-397025-1.00340-7
625
626
INTRODUCTION TO METHODS AND MODELING | Dynamic Causal Models for Human Electrophysiology: EEG, MEG, and LFPs
gated). Describing these different channel responses generates

more realistic brain dynamics and provides for fine-grained
inference on different contributions to EEG recordings. From
this perspective, DCM represents a mathematical microscope
and can assess local synaptic physiology.
Together, these dynamic descriptions, comprising coupled
nonlinear differential equations, form a mathematical state
space. These states of a neural mass, such as fluctuations in
membrane depolarization, evolve over time according to
the model parameters. Overall, these parameters include the
strength of intrinsic connections within each region, the
strength of extrinsic connections, and parameters controlling
synaptic adaptation (time constants of AMPA, NMDA, and
GABAA receptors), membrane capacitance, and axonal delays
(Figure 1). A forward observation model then transforms these
depolarizations into the observed EEG or MEG output.
Forward Models, Model Comparison, and Hypothesis

Testing
Forward models in these DCMs comprise a linear mixture of
depolarizations, which are then transformed via a
parameterized lead field into scalp- or sensor-level data

(Figure 2). This mapping can accommodate different lead
fields that are dependent on the imaging modality (invasive
LFPs or noninvasive EEG and MEG). Since dendrites of interneurons are roughly symmetrically positioned around the cell
body, while dendrites of pyramidal cells align tangentially to
the cortical surface, the net dipolar output is modeled as primarily the output of these pyramidal subpopulations. This
fully parameterized model can then generate electrophysiological data.
An inversion routine can then be applied to a particular
model given empirical EEG/MEG or LFP recordings. The inversion routine is the key component of DCM. So far, this article
has outlined a generative model of electrophysiological data.
DCM is designed to map back from real measured responses to
the underlying neuronal generators (Figure 2). This inverse
mapping or model inversion provides an estimation of the
model parameters conditional on a given set of data. In
DCM, this procedure is prescribed by a variational scheme,
which optimizes the conditional density of parameters under
a fixed-form (Laplace) assumption. This optimization entails
maximizing a free-energy bound on the log evidence using
variational Laplace. The inversion scheme requires a form for
Figure 1 This figure shows a neural mass model used in DCM for EEG to represent an active brain source. This 4-subpopulation model uses
MorrisLecar-type differential equations to describe the time evolution of current and conductance states at different cell types. (Cells can possess
AMPA, GABAA, and NMDA receptors with ion-channel time constants (1/k). Layers and sources are connected with strengths parameterized by g.
VREV are reversal potentials for ions through these channels, and VT is the threshold potential.) The neuronal architecture comprises interconnected
neuronal subpopulations, including inhibitory interneurons and pyramidal cells (supragranular and infragranular layers) and spiny stellate cells
(granular layer IV). Pyramidal cells send signals outside of the neural mass. These deliver forward signals (from superficial layer) and backward signals
(from deep layers). The spiny stellate cells, in turn, receive extrinsic forward connections, while the inhibitory cells and superficial pyramidal cells
are in receipt of extrinsic backward connections.
627
DCM framework
Model structure/ Model parameters
Parameterized
lead field
Parameterized
interconnected
Neural mass models
Generative model
Bayesian inversion
Empirical data
Figure 2 This figure outlines the elements that comprise the DCM framework. Generative models (physiological for DCM for ERP/CSD and
phenomenological for DCM for IR/PHA) produce a repertoire of empirical recordings. A particular dataset acquired in humans (or animals) can then be
fitted to these models using a variational Bayesian inversion, to reveal the density of model parameters conditional on those particular data.
the observation noise to produce a likelihood function of the

modeled parameters and also requires prior probabilities on
model parameters. These priors are specified in terms of a prior
mean and variance. The prior variance determines how far the
parameter can move from its prior mean during inversion.
Parameters that have been investigated empirically, like the
time constants of different receptors, are given relatively small
prior variance, while in contrast, flat (higher variance) priors
are used for effective connectivity measures.
Once optimized, the inversion routine returns both an
approximation to the log model evidence, known as the free
energy, and a set of posterior or conditional model parameters.
The first of these is used to assess competing hypotheses regarding the structure of a model, independent of their parameters.
This is used to identify the most plausible architecture. Individual parameter posteriors can then be investigated to assess
relative contributions to network dynamics or to compare
across populations (e.g., using an identical model but fitted
to data from healthy controls and a pathological cohort).
inversion procedure will then determine how parameters are

weighted (including biophysical and forward parameters) to
best fit the empirical scalp/sensor/electrode ERPs.
CSDs are modeled in the same way, with the exception of
specific exogenous inputs. Instead, a mixture of parameterized
scale-free or power law noise components provides the input
to the neural mass equations. This system of differential equations is linearized around a fixed point, to describe the
response of a node in the frequency domain. This linearization
allows one to compute the transfer function mapping from the
endogenous (neuronal) fluctuations to the scalp/sensor/electrode data. This transformation assumes that the system operates in a stationary regime, with fluctuations around a stable
fixed point. DCM for CSDs also returns coherence, covariance,
and phase lags at the level of neuronal sources and scalp or
sensor level.
DCMs for ERPs and CSDs
DCM for IRs (Chen, Kiebel, & Friston, 2008) (timefrequency)

and DCM for PHA (Penny, Litvak, Fuentemilla, Duzel, &
Friston, 2009) are based on identical principles to those
previously in the text, comprising the description of a generative model, priors on model parameters, and Bayesian model
inversion. They are distinct from DCM for ERPs and DCM for
CSDs in two ways. The first difference is that they do not
explicitly describe a neurobiological architecture in the generative model but prescribe instead an abstracted mathematical
form. This is flexible enough to accommodate highly nonlinear
generative mechanisms. The second difference is that data are
Both DCM for ERPs (Kiebel, David, & Friston, 2006) and DCM
for CSDs (Moran et al., 2009) use the neural mass models outlined earlier in the text. For ERPs, exogenous inputs, timed
according to experimental stimuli, serve as the input to the
neural masses. This is represented as a thalamic input volley,
with the form of a delayed (by a few tens of milliseconds) narrow
Gaussian impulse function. This can be entered into plausible
cortical nodes. From these sources, dynamics will propagate
throughout connected nodes in the modeled network. The
DCM for IRs and DCM for Phase Coupling
628
modeled in source space directly so they require preliminary

source localization and time-series extraction.
Frequency-to-frequency interactions are a popular topic in
human electrophysiological research, for example, assessing
whether alpha spectra suppress other spectral features locally
or at different regions of the brain. This type of hypothesis can
be addressed formally using DCM for IR where a full time
frequency interaction can be deconstructed using a model of
connected brain sources. DCM for IR models spectral dynamics in terms of a mixture of frequency modes obtained from a
singular value decomposition of a sources time series. The
differential equations employed in this routine are the time
evolution of energy interactions across all frequencies where
linear or nonlinear source interactions can produce within and
between frequency effects.
In order to understand how sources of electrophysiological
activity become phase-locked or drift out of phase, DCM for
phase coupling optimizes a generative model comprising
weakly coupled oscillators. These sets of differential equations
describe how the phase of one region (modeled as an oscillator) influences the change of phase of another. These timeevolving phase couplings are described in terms of a Fourier
series to any order. Given empirical data series from EEG/MEG
or LFP, a Hilbert transform of source space time-series data
(band-passed to a frequency of interest) reveals how networks
interact in that spectral domain. This is an increasingly studied
principle of cortical organization, one prominent example
being the investigation of hippocampal-based network interactions in theta and gamma bands.
Conclusion
The DCM approach to analyzing electrophysiological data
takes advantage of the large and rich prior literature on
neuronal physiology and codes. It is an informed analysis

method that allows us to formally address how our EEG/
MEG/LFP data could have been generated by the brain.

Cell Types in the Cerebral Cortex: An Overview from the Rat Vibrissal
Cortex; Synaptic Organization of the Cerebral Cortex;
Model Inference; Bayesian Model Inversion; Distributed Bayesian
Inversion of MEG/EEG Models; Dynamic Causal Models for fMRI;
Effective Connectivity; Forward Models for EEG/MEG; Neural Mass
Models; The Emergence of Spontaneous and Evoked Functional
Connectivity in a Large-Scale Model of the Brain; Variational Bayes.
References
19, 12731302.
Kiebel, S., David, O., & Friston, K. (2006). Dynamic causal modelling of evoked
responses in EEG/MEG with lead field parameterization. NeuroImage, 30,
12731284.
Moran, R., et al. (2009). Dynamic causal models of steady-state responses.
Chen, C., Kiebel, S., & Friston, K. (2008). Dynamic causal modelling of induced
responses. NeuroImage, 41, 12931312.
Penny, W., Litvak, V., Fuentemilla, L., Duzel, E., & Friston, K. (2009). Dynamic causal
models for phase coupling. Journal of Neuroscience Methods, 183, 1930.
Relevant Websites
http://www.fil.ion.ucl.ac.uk/spm/software/spm12/ Written by members of the FIL
Methods group at University College London. All the DCM components described
in this article can be implemented using Matlab routines that are available as part of
the academic freeware package SPM.
Graph-Theoretical Analysis of Brain Networks

O Sporns, Indiana University, Bloomington, IN, USA
Glossary
Centrality Measures the influence or importance of a node

or edge within the network, e.g. the node degree,
betweenness, eigenvector, and pagerank centrality.
Clustering The tendency of nodes to form connected
triangles, i.e. a configuration where neighbors of a node are
also neighbors of each other, forming a cluster or clique.
Community In networks, communities correspond to
modules, and represent densely interconnected sets of
nodes.
Connector hub A hub node that maintains a diverse
connectivity profile across several different network
modules.
Degree The number of edges attached to a given node.
Edge A network link or connection.
Graph A mathematical representation of a network,
comprising a collection of nodes and edges.
Hub A node that is highly connected or highly central
within the overall network.
Introduction
The human brain is a complex network of neural elements
(neurons and brain regions) interconnected by a large number
of connections (synaptic links and interregional pathways)
(Bullmore & Sporns, 2009). In recent years, network
approaches to understanding human brain structure and function have been driven by two parallel developments. On one
side, networks have become an object of intensive investigation across many disciplines, from information technology to
the social and biological sciences (Boccaletti, Latora, Moreno,
Chavez, & Hwang, 2006). On the other side, modern brain
imaging techniques have begun to reveal the architecture of
human brain networks in increasing detail. Diffusion imaging
and tractography deliver estimates of anatomical connections
comprising large-scale structural networks (Johansen-Berg &
Rushworth, 2009). Functional magnetic resonance imaging
(fMRI), especially the growing use of resting-state fMRI
(Raichle, 2011), provides neural time series data that can be
processed into a network form, most commonly expressing the
pairwise similarity (cross correlation) of spontaneous signal
fluctuations during rest or coactivation patterns during task
conditions. The confluence of network approaches and neuroimaging technology has catalyzed a new network perspective
on the human brain (Sporns, 2011).
Structural and functional networks can be rendered as connection matrices. Such matrices correspond to graphs comprising sets of network nodes and edges whose configuration
represents the networks topology (Figure 1). In large-scale
human brain networks, nodes generally represent distinct
regions or parcels, while edges express their mutual
Module A cluster of nodes that are densely interconnected,

while being only sparsely connected to nodes in other
modules.
Motif A subset of nodes and their interconnections.
Node A network element, e.g. a neuron or brain region in a
brain network.
Path A sequence of unique edges that link a source node to a
target node.
Provincial hub A hub node that predominantly connects to
other nodes within its own module.
Shortest path length The shortest path length between
two nodes corresponds to the minimal number of edges
that have to be traversed to travel from one node to the
other.
Small-world organization A network that shows a level of
clustering much higher than observed in random
networks, and an average shortest path length that is
approximately equal to that observed in random
networks.
connections, which can be binary (1 or 0 for connections

that are present or absent, respectively) or weighted (with
weights representing connection density or strength). One
major goal of graph-theoretical network analysis is to characterize the architecture of networks with a set of compact and
neurobiologically interpretable measures. These measures can
then serve to compare networks across individuals, across
developmental time, or across disease states, in order to assess
network differences that can be related to differences in behavioral and cognitive performance. Going beyond descriptive
tools, network science offers a number of additional opportunities, including the combined analysis of structural and functional networks to reveal how dynamic brain responses are
shaped by the anatomical substrate (Deco, Jirsa, & McIntosh,
2011) and the investigation of the role of spatial embedding
and wiring minimization constraints on network topology
(Bullmore & Sporns, 2012). In this brief overview, we will
focus on a set of graph measures that are currently widely
used as tools to describe large-scale brain networks (see also
Rubinov and Sporns (2010)). Open-source algorithmic tools
for computing these measures are available as part of the Brain
Connectivity Toolbox (see Relevant Websites).
Defining Brain Networks

Fundamental first steps toward constructing brain networks are
the definition of network nodes and the selection of appropriate measures for expressing their connectivity. Node definition
is important because the sensitivity of subsequent network
analyses depends on accurate definition of parcel boundaries
http://dx.doi.org/10.1016/B978-0-12-397025-1.00341-9
629
630
INTRODUCTION TO METHODS AND MODELING | Graph-Theoretical Analysis of Brain Networks
Node
Edge
Low degree
Path
High degree
Module 1
Connector hub
Module 2
Provincial hub
Figure 1 Schematic illustration of a graph and some basic graph measures. The graph consists of a set of nodes and edges (top), here represented as
a binary undirected network. Based on the number of edges, nodes can be low-degree or high-degree (middle). Paths connect nodes to each other.
The example shown here is the shortest path (three edges) linking node A to node B (and B to A, since the edges are undirected). The network
can be partitioned into two modules (bottom), and high-degree nodes can be classified as either connector hubs or provincial hubs, based on the pattern
of connections within and between modules.
(Wig, Schlaggar, & Petersen, 2011), and network measures

generally take on different values for different parcellations of
the same imaging data set (Zalesky et al., 2010). Large-scale
networks that span across the entire human brain require a
neurobiologically sound strategy to subdivide gray matter
regions, especially the cerebral cortex, into discrete and nonoverlapping parcels that represent network nodes. Ideally, such
parcels should maintain a coherent pattern of extrinsic anatomical and functional connections. Numerous parcellation
strategies have been proposed (De Reus & van den Heuvel,
2013), including atlas-based approaches, network construction from individual voxels, and random partitions across
different scales (Cammoun et al., 2012). Other approaches
are more directly data-driven, such as network-based detection
of regional centers (Wig et al., 2013), clustering approaches
(Blumensath et al., 2013), and boundary mapping based on
detecting transitions in cortical connection profiles (Cohen
et al., 2008).
In the simplest case, edges represent binary relationships,
indicating the presence or absence of a connection. Binary
networks discard all information about the strength of an
anatomical or functional connection and generally require
the application of a threshold. Thresholding can be problematic if there is no clear rationale for threshold selection, and
many studies that employ thresholding therefore explore network topologies over a range of threshold values. In structural
networks derived from diffusion imaging and tractography, the
number or density of tractography streamlines linking pairs of

nodes, or their connection probability, is often used to define
edge weights. It should be noted that this practice makes
several assumptions that ideally should be validated against
more traditional anatomical measures (Jones, Knosche, &
Turner, 2013). Other edge measures of structural networks
may incorporate the myelination status or other aspects of
the axonal microstructure. In functional networks, particularly
those extracted from resting-state fMRI, the most commonly
used measure of edge weight is the Pearson cross correlation. It
should be noted that this linear measure is acausal and makes
no statement about actual functional interaction, only about
the similarity of nodal time courses. More sophisticated measures of pairwise dynamic coupling include partial correlations
(Smith et al., 2011), nonlinear measures such as mutual information, and directed measures based on temporal precedence
cues (Friston, Moran, & Seth, 2013). The latter are problematic
in fMRI due to unknown regional variability of hemodynamic
delays (Friston, 2009).
Measures of Network Topology

Many measures of network topology can be computed for each
network element, that is, for each node or each edge, thus
quantifying the contribution this element makes to the network as a whole. One of the simplest measures is the node

degree, given as the number of distinct edges each node maintains. The node strength is the sum of all the edge weights of
each node, a nodal measure that is analogous to degree in
weighted networks. Another simple nodal measure is the clustering coefficient, which for a given node corresponds to the
fraction of all possible connections among the nodes topological neighbors that are actually found. High clustering implies
that the node is at the center of a network clique, with many
nodes interconnected in triangles. Triangles are examples of
network motifs, sets of generally small (3- or 4-node) subgraphs that define local patterns of connectivity. Motifs may
be thought of as a networks building blocks (Milo, Shen-Orr,
Itzkovitz, Kashtan, Chklovskii, et al., 2002). Every network can
be uniquely decomposed into a set of motifs, and the frequency with which certain motifs occur characterizes ways in
which locally connected nodes interact.
Paths in a network refer to sequences of unique edges that
link two nodes (Figure 1). In a fully (or strongly) connected
network, all pairs of nodes are linked by at least one path of
finite length. The path length may be computed as the number
of discrete steps or in a weighted network as the sum of the
individual edge lengths (often expressed as the inverse of the
edge weight). The length of the shortest path between two
nodes defines their topological distance, and all pairwise distances are collectively represented by the networks distance
matrix. The mean (or median) of the finite off-diagonal
elements of the distance matrix is also called the networks
path length, often interpreted as indicative of the networks
capacity to transmit information. Indeed, a networks global
communication efficiency can be captured by a measure that is
closely related to the inverse of the path length (Latora &
Marchiori, 2001).
High clustering and short path length, both expressed relative to appropriate random null models, are the hallmarks of
small-world organization (Watts & Strogatz, 1998). It has been
suggested that small-worldness can be quantified as a ratio
between scaled versions of the networks average clustering
coefficient and its path length (Humphries & Gurney, 2008;
Telesford, Joyce, Hayasaka, Burdette, & Laurienti, 2011). While
small-world organization was among the very first universal
attributes shared across many technological, social, and biological networks, it should be noted that the presence of smallworld attributes is insufficient to fully characterize network
architecture. For example, equivalent levels of small-worldness
can be found in lattice networks with random shortcuts and in
networks composed of distinct but interlinked clusters (i.e.,
modules) (see the succeeding text).
All network measures discussed so far vary widely across
networks of different size, density, or architecture. From the
perspective of analyzing brain networks, it is important to measure network properties relative to suitable random models that
are constructed to test specific null hypotheses. Most commonly
used null models preserve the network size and density and the
specific degree sequence (i.e., the degrees of each node) while
randomizing the global network topology. These null models
essentially allow statements about the degree to which empirically observed network attributes deviate from a null model that
accounts for size, density, and degree sequence but is random
otherwise. Other null models are possible, including lattice
models that induce spatial neighborhood relationships
among nodes (Sporns & Kotter, 2004). Future developments
631
in graph theory applications to brain network will likely include

the development of more specific and sensitive null models to
probe for significant network attributes.
Measures of Centrality
The centrality of a node (or edge) quantifies its importance or
influence within the global network architecture. This definition immediately suggests multiple ways by which centrality
may be captured. Perhaps, the simplest measure of node centrality is the node degree, as it specifies the number of neighbors of each node and hence defines the size of the
neighborhood it can directly influence. Node degree is often
(but not always) highly correlated with betweenness centrality,
defined as the fraction of all shortest paths across the network
that each node (or edge) participates in. A node through which
many short paths must pass is centrally embedded within the
networks topology, potentially acting as a point of convergence or divergence. Another measure of centrality takes into
account how quickly (i.e., in how few steps) a given node can
communicate with all other nodes. This measure, called closeness centrality, is easily computed from the networks distance
matrix. Other topological centrality measures include the
eigenvector centrality (Lohmann et al., 2010) and one of its
variants, the PageRank centrality. According to these measures,
nodes have high centrality if they are connected to other highly
central nodes. Finally, centrality can be measured in relation to
a networks communities or modules, essentially quantifying
the extent to which a given node enables communication
across module boundaries (see the succeeding text).
Another approach for defining centrality is to quantify the
effect on network integrity that results from the removal of a
given node or edge. Computationally, node or edge removal is
easily implemented, and effects on network integrity can be
derived from comparing measures of communication such as
global efficiency before and after node/edge deletion. Generally (but not in all cases), such nodal vulnerability measures
correlate strongly with node degree and/or betweenness. In
addition to providing an indication of centrality for each
node and edge, removal of network elements can reveal important additional information about how networks might
respond to local damage, by rerouting of short communication
paths or readjustments in module boundaries.
Measures of centrality are critical for defining putative network hubs. In brain networks, hubs have been detected in
virtually all anatomical and functional networks, across species
and independent of recording or measuring modality. Despite
the ubiquity of hubs, hub detection does not always lead to
consistent results, in part due to dissociations among multiple
measures of centrality (e.g., degree, betweenness, and closeness). Robust hub detection is best carried out with a combination of measures (Sporns, Honey, & Kotter, 2007), including
nodal degree, path-based betweenness centrality, and measures
that assess vulnerability.
Community Detection
Many networks, including most brain networks, can be partially
decomposed into clusters of nodes that are more densely
632
interconnected among each other, with less dense connections

between clusters (Figure 1). These clusters are also referred to as
network communities or modules, and module detection is an
extremely active area of theoretical network science (Fortunato,
2010). Numerous methods are available, based on diffusive
random walks (Rosvall & Bergstrom, 2007), the graph eigenspectrum (Newman, 2006), or optimization of a modularity metric
expressing the ratio of within- to between-module edge density
(Newman & Girvan, 2004). The latter approach utilizes highly
effective optimization strategies to identify module partitions for
which the modularity metric becomes maximized (Blondel,
Guillaume, Lambiotte, & Lefebvre, 2008). Extensions of the
metric to include directed networks (Leicht & Newman, 2008)
and networks with both positive and negative edges (Rubinov &
Sporns, 2011) have been proposed. Once a module partition has
been defined, highly connected nodes can be classified based on
their connection profile across modules, computed as the participation coefficient (Guimera & Amaral, 2005). Nodes with high
participation tend to connect multiple modules and are therefore
called connector hubs, while nodes with low participation tend
to connect nodes within a single module, as provincial hubs.
Applications of community detection methods in neuroscience data sets have raised several methodological issues that are
particularly salient for functional brain networks. The first issue
relates to the common practice of applying a threshold to the
functional connectivity matrix such that only a small percentage
(often in the range of 510%) of all functional connections are
retained. In addition, after subjecting the primary data matrix to a
threshold, the remaining connections are often set to unity, resulting in a greatly sparsified binary network, which is then subjected
to standard graph analysis. This widespread practice of thresholding functional networks removes all negative edges and most
importantly results in a topology that is much sparser than that
of the original network. This leads to the detection of a greater
number of more distinctly separated clusters or modules than
would be obtained from the original (unthresholded) data set.
The second issue has to do with the optimization of the
module partition given an appropriate modularity metric. It
turns out not only that in most real-world networks, the identification of an optimal module partition is computationally
challenging but also that such networks can be partitioned at
near-optimal levels in a number of different or degenerate ways
(Good, de Montjoye, & Clauset, 2010). Combining these degenerate solutions into a so-called agreement matrix can provide
important information about the consistency (across all solutions) with which a given node pair is assigned to the same or a
different module. This idea has been developed further into a
quantitative approach called consensus clustering (Lancicinetti
& Fortunato, 2012), which when applied to brain networks can
provide information about the strength with which individual
brain regions affiliate with their home community. Regions that
show relatively weak affiliation may be considered candidates for
putative hub regions, since they are more likely to cross-link
multiple and functionally diverse modules.
Conclusion
This article has provided a brief overview of a number of commonly used measures to describe the topology of brain networks.
A number of issues remain for future work, including the careful
interpretation of graph measures in the context of neurobiology

and the construction of null models that probe specific hypotheses about network architecture. As complex systems approaches
to brain function gain ground, there is an urgent need for more
sophisticated generative and dynamic models to understand
brain function (Fornito, Zalesky, & Breakspear, 2013; Lohmann,
Stelzer, Neumann, Ay, & Turner, 2013).
Acknowledgment
The authors work was supported by the James S. McDonnell
Foundation.

Language; Functional Connectivity; INTRODUCTION TO METHODS
AND MODELING: Effective Connectivity; Methodological Issues in
fMRI Functional Connectivity and Network Analysis; Resting-State
Functional Connectivity; INTRODUCTION TO SYSTEMS: Hubs and
Pathways; Large-Scale Functional Brain Organization; Network
Components.
References
Blondel, V., Guillaume, J. L., Lambiotte, R., & Lefebvre, E. (2008). Fast unfolding of
communities in large networks. Journal of Statistical Mechanics, 2008, P10008.
Blumensath, T., Jbabdi, S., Glaser, M. F., et al. (2013). Spatially constrained
hierarchical parcellation of the brain with resting-state fMRI. NeuroImage, 76,
313324.
Boccaletti, S., Latora, V., Moreno, Y., Chavez, M., & Hwang, D. U. (2006). Complex
networks: Structure and dynamics. Physics Reports, 424, 175308.
Bullmore, E., & Sporns, O. (2009). Complex brain networks: Graph theoretical analysis
of structural and functional systems. Nature Reviews Neuroscience, 10, 186198.
Bullmore, E., & Sporns, O. (2012). The economy of brain network organization. Nature
Reviews Neuroscience, 13, 336349.
Cammoun, L., Gigandet, X., Meskaldji, D., et al. (2012). Mapping the human
connectome at multiple scales with diffusion spectrum MRI. Journal of
Cohen, A. L., Fair, D. A., Dosenbach, N. U. F., et al. (2008). Defining functional areas in
individual human brains using resting state functional connectivity MRI.
de Reus, M. A., & Van den Heuvel, M. P. (2013). The parcellation-based connectome:
Limitations and extensions. NeuroImage, 80, 397404. http://dx.doi.org/10.1016/j.
Deco, G., Jirsa, V. K., & McIntosh, A. R. (2011). Emerging concepts for the dynamical
organization of resting-state activity in the brain. Nature Reviews Neuroscience, 12,
4356.
Fornito, A., Zalesky, A., & Breakspear, M. (2013). Graph analysis of the human
connectome: Promise, progress, and pitfalls. NeuroImage, 80, 426444. http://dx.
doi.org/10.1016/j.neuroimage.2013.04.087.
Fortunato, S. (2010). Community detection in graphs. Physics Reports, 486, 75174.
Friston, K. (2009). Causal modeling and brain connectivity in functional magnetic
resonance imaging. PLoS Biology, 7, e1000033.
Friston, K., Moran, R., & Seth, A. K. (2013). Analysing connectivity with Granger causality
and dynamic causal modeling. Current Opinion in Neurobiology, 23, 172178.
Good, B. H., de Montjoye, Y. A., & Clauset, A. (2010). Performance of modularity
maximization in practical contexts. Physical Review E, 81, 046106.
Guimera, R., & Amaral, L. A.N (2005). Functional cartography of complex metabolic
networks. Nature, 433, 895900.
Humphries, M. D., & Gurney, K. (2008). Network small-world-ness: A quantitative
method for determining canonical network equivalence. PLoS One, 3, e0002051.
Johansen-Berg, H., & Rushworth, M. F.S (2009). Using diffusion imaging to study
human connectional anatomy. Annual Reviews in Neuroscience, 32, 7594.
Jones, D. K., Knosche, T. R., & Turner, R. (2013). White matter integrity, fiber count,
and other fallacies: The dos and donts of diffusion MRI. NeuroImage, 73, 239254.

Lancicinetti, A., & Fortunato, S. (2012). Consensus clustering in complex networks.
Scientific Reports, 2, 336.
Latora, V., & Marchiori, M. (2001). Efficient behavior of small-world networks. Physical
Review Letters, 87, 198701.
Leicht, E. A., & Newman, M. E. (2008). Community structure in directed networks.
Physical Review Letters, 100, 118703.
Lohmann, G., Margulies, D. S., Horstmann, A., et al. (2010). Eigenvector centrality
mapping for analyzing connectivity patterns in fMRI data of the human brain. PLoS
One, 5, e10232.
Lohmann, G., Stelzer, J., Neumann, J., Ay, N., & Turner, R. (2013). More is different in
functional magnetic resonance imaging: A review of recent data analysis techniques.
Brain connectivity, 3(3), 223239. http://dx.doi.org/10.1089/brain.2012.0133.
Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., & Alon, U. (2002).
Network motifs: Simple building blocks of complex networks. Science, 298, 824827.
Newman, M. E. (2006). Finding community structure in networks using the eigenvectors
of matrices. Physical Review E, 74, 036104.
Newman, M. E.J, & Girvan, M. (2004). Finding and evaluating community structure in
networks. Physical Review E, 69, 026113.
Raichle, M. E. (2011). The restless brain. Brain Connectivity, 1, 312.
Rosvall, M., & Bergstrom, C. T. (2007). An information-theoretic framework for
resolving community structure in complex networks. Proceedings of the National
Academy of Sciences USA, 104, 73277331.
Rubinov, M., & Sporns, O. (2010). Complex network measures of brain connectivity:
Uses and interpretations. NeuroImage, 52, 10591069.
Rubinov, M., & Sporns, O. (2011). Weight-conserving characterization of complex
functional brain networks. NeuroImage, 56, 20682079.
Smith, S. M., Miller, K. L., Salimi-Khorshidi, G., et al. (2011). Network modeling
methods for FMRI. NeuroImage, 54, 875891.
Sporns, O. (2011). Networks of the brain. Cambridge: MIT Press.
633
Sporns, O., Honey, C. J., & Kotter, R. (2007). Identification and classification of hubs in
brain networks. PLoS ONE, 2, e1049.
Sporns, O., & Kotter, R. (2004). Motifs in brain networks. PLoS Biology, 2, e369.
Telesford, Q. K., Joyce, K. E., Hayasaka, S., Burdette, J. H., & Laurienti, P. J. (2011). The
ubiquity of small-world networks. Brain Connectivity, 1, 367375.
Watts, D. J., & Strogatz, S. H. (1998). Collective dynamics of small-worldnetworks.
Nature, 393, 440442.
Wig, G. S., Laumann, T. O., Cohen, A. L., et al. (2013). Parcellating an individual
subjects cortical and subcortical brain structures using snowball sampling of
resting-state correlations. Cerebral Cortex, http://dx.doi.org/10.1093/cercor/
bht056.
Wig, G. S., Schlaggar, B. L., & Petersen, S. E. (2011). Concepts and principles in the
analysis of brain networks. Annals of the New York Academy of Sciences, 1224,
126146.
Zalesky, A., Fornito, A., Harding, I. H., et al. (2010). Whole-brain anatomical networks:
Does the choice of nodes matter? NeuroImage, 50, 970983.
Relevant Websites
http://www.biological-networks.org/ Biological Networks, with resources and data
sets maintained by Marcus Kaiser.
www.brain-connectivity-toolbox.net Brain Connectivity Toolbox, a matlab graph
analysis toolset maintained by Olaf Sporns and Mika Rubinov.
http://cocomac.g-node.org Cocomac, an online database of macaque anatomical
connectivity.
http://www.humanconnectome.org/ Human Connectome Project website, with
extensive datasets recorded from the human brain.
Crossvalidation
N Kriegeskorte, Medical Research Council, Cambridge, UK
Glossary
Generalization performance The quality of the predictions

about new data afforded by a model fitted with a given data
set.
Independence (statistical independence) The absence of
any relationship, linear or nonlinear, determininstic or
stochastic, between two variables. Independence implies
Empirical science often involves an informal process of

hypothesis generation followed by a formal experimental test
of a specific hypothesis. Both hypothesis generation and testing are empirical processes, but the first is exploratory and
inconclusive, and the second is confirmatory and supported
by formal statistical inference. This two-stage procedure is
mirrored in data analysis, where exploratory analyses can
help generate specific hypotheses and the latter are subjected
to formal inference. Similarly, the fitting of the parameters of a
model can convert a vague and difficult-to-test hypothesis into
a specific and testable hypothesis.
Crossvalidation is a statistically efficient method for using
the cycle of fitting (i.e., generation of a specific hypothesis) and
testing within the analysis of a single data set. More specifically,
crossvalidation can be used to estimate the predictive performance of alternative models that require parameter fitting. The
method can also be used to adjudicate between different
models. One element of crossvalidation is the division of the
data set into independent subsets used for generation of a
specific hypothesis (also known as parameter estimation,
fitting or training) and validation (also known as testing).
(Some authors use the term validation set, and reserve the term
test set for a third independent subset of the data, used when a
second level of validation is required. Here, we use the concepts
of validation and test interchangeably.) The other element is
the use of each data subset for training and testing on different
folds of the process. This reuse of the data for the purposes of
training and testing is what the prefix cross in crossvalidation
refers to. It renders the process statistically efficient.
Let us first consider the case of twofold crossvalidation. The
data are divided into two subsets, typically of equal size. One
set is designated as the training set, the other as the test set. The
training could consist in fitting the weights of a linear model.
The testing might involve measuring the accuracy of the predictions of the model (e.g., the classification accuracy or the
coefficient of determination). More generally, model fitting
can be thought of as the generation of a specific hypothesis
(the fitted model) from a general space of hypotheses (the
models parameter space). After using one set of data to generate the hypothesis, using the same set to test the hypothesis
would be circular (Kriegeskorte, Simmons, Bellgowan, &
Baker, 2009): The specific hypothesis (the fitted model) will
reflect the noise to some extent. New data with independent
noise can serve to test the specific hypothesis. The use of an
that learning either variable does not change our belief

(expressed as a probability distribution) about the other
variable.
Overfitting The inevitable effect of measurement error on
the estimates of parameters obtained by fitting a model to a
given data set.
independent data set for testing ensures that overfitting does

not positively bias the estimate of predictive performance.
Using independent data sets simply enables us to perform an
empirical test of predictive performance.
Using one half of the data for training and the other half for
testing provides a valid test. However, we might have designated the training set as the test set and vice versa. Swapping
the two sets will give slightly different, but equally valid results.
This motivates using each subset as the test set once and
averaging the estimates of predictive performance. Note that
(a) the training data are independent of the test data on each
fold, (b) the test data are independent between folds, and (c)
the training data are independent between folds in twofold
crossvalidation. Nevertheless, the estimates of predictive performance obtained on different folds are not independent,
because each fold uses all data. For an intuition on this dependency of the results of different folds, consider the effect of the
noise on the estimates of predictive performance. If the noise
makes data set 1 appear slightly more consistent with data set
2, then predictive performance is likely to appear slightly
greater on both folds of crossvalidation. Conversely, if the
noise makes data set 1 appear slightly less consistent with
data set 2, then predictive performance is likely to appear
slightly smaller on both folds of crossvalidation. If the estimates of predictive performance across folds were independent, we would expect averaging of the estimates across folds
to reduce the variance of the overall estimate by a factor equal
to the square root of the number of folds. Because the folds are
dependent, averaging of the estimates across folds improves
the estimate by a smaller, but typically still substantial, factor.
There is an obvious disadvantage to twofold crossvalidation. Although all the data contribute to the estimate of predictive performance, the training set comprises only half the
data on each fold. This typically means that the model is not
fitted as well as it would be if all data had been used. Our
crossvalidation estimate of predictive performance is therefore
negatively biased in the sense that it will tend to underestimate
the predictive performance our model would achieve on new
data if it were fitted with all our data. This motivates the use
of a greater portion of the data as training data on each fold. In
k-fold crossvalidation (Figure 1), the data are divided into k
independent subsets. On each fold, one subset is held out as
the test set, the others are used for training. As before, the
estimates of predictive performance are averaged across folds.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00344-4
635
636
INTRODUCTION TO METHODS AND MODELING | Crossvalidation
Figure 1 The division of the data into independent training and test sets
in fivefold crossvalidation.
What Is the Optimal Number of Folds?

Consider the case of k 10. In this case, 90% of the data is used
for training on each fold. As a result the negative bias of the
crossvalidation estimate of predictive performance will typically
be small. Although the test set is smaller by factor k/2 on each
fold (compared to twofold crossvalidation), there are also k/2
times as many folds, across which the evidence will be combined to reduce the variance of the estimate of predictive performance. Using k > 2, thus, appears statistically advantageous.
However, more computation is required, because the model
needs to be fitted k times.
Beyond the higher computational demands, there is another
disadvantage, however, to increasing k. For k 2, the two training sets are independent between folds. For k > 2, the training
sets are overlapping, and thus dependent, between folds. As
explained above, the predictive-performance estimates will
always be dependent across folds, even for nonoverlapping
training sets. However, their dependence grows with the dependence of the training sets across folds. This reduces the benefit of
averaging the performance estimates across folds.
The extreme case is n-fold crossvalidation, where n is the
number of data points. This is also known as leave-one-out
crossvalidation. One data point (or the smallest quantum of
data on which predictive performance can be tested in a given
scenario, e.g., one subject) is held out on every fold. The training
sets, then, are identical for all but one data point and the fitted
models will be very similar across folds. The estimate of predictive performance will be optimal in terms of its bias (the conservative bias will be minimized), but not in terms of its variance,
which will be larger than for smaller settings of k. Empirical
studies suggest that choices of k in the range of 510, yield
good results in practice (Hastie, Tibshirani, & Friedman, 2002).
Important Things to Keep in Mind When Using

Crossvalidation
(1) Training and test data must be independent. It is essential to
ensure that the subsets the data are divided into are statistically independent. For example, fMRI time series are
serially autocorrelated in terms of both the underlying
signals and the noise. Two time points in the same temporal neighborhood therefore must never straddle a division into training and test sets. To avoid this, the data can
be divided into scanner runs (or subruns, with an appropriate hemodynamic safety margin), and two disjoint
sets of runs designated as the training and test data on
each fold.
(2) The folds yield dependent performance estimates. Any inferential procedures must not assume that the performance
estimates obtained on different folds are independent.
For example, when response patterns are classified and
counts of correct and incorrect classifications summed
over folds, a binomial test of the null hypothesis that
performance is at chance level is not appropriate. A good
approach is to obtain a single unbiased performance estimate for each subject, then use a non-parametric test (e.g.,
Wilcoxons signed-rank test) to test whether performance
exceeds chance level. This approach can also be extended
to model comparisons (using performance differences as
the test statistic). It has the additional advantage of treating
the variation across subjects as a random effect, and thus
supports inferences about the population.
(3) Multiple nested levels of crossvalidation might be needed.
Crossvalidation serves the purpose to obtain estimates of
predictive performance that are not biased by overfitting.
In many scenarios, there is more than one level of parameters to be fitted. In a linear pattern classification analysis,
for example, the classifier might have hyperparameters in
addition to the weights associated with each response
channel (e.g., each voxel). If the hyperparameters are to
be chosen so as to maximize the crossvalidation estimate
of performance, the maximum performance estimate will
be biased by overfitting of the hyperparameters. A second
level of crossvalidation is therefore needed. On each fold
of the outer crossvalidation loop, the hyperparameter can
be determined by nested crossvalidation within the training set. The optimal setting is then used to predict the test
set (which has not been used to optimize the
hyperparameter).
Examples of Brain Imaging Analyses that Do or Do Not

Require Crossvalidation
Example 1: Univariate Activation Analysis
The effects of experimental conditions on activation within a
predefined brain region are often analyzed with linear models.
The framework of univariate linear regression does not require
us to divide the data or perform crossvalidation. In the analysis
of functional magnetic resonance imaging data, for example, it
is typically reasonable to assume that the errors are univariate
normal and to account for temporal autocorrelation of the
time series by pre-whitening or pre-coloring. The predictor
weights and any linear contrasts of interest, along with their
standard errors, can then be estimated and inference can be
performed using a single data set. This approach is generally
preferred to a crossvalidation approach for its power, elegance,
and convenience.
Even in univariate activation analysis, however, the use of
independent validation sets can be essential. For example,

when a given data set is used to explore the brain for locations
exhibiting a particular effect (to define regions of interest) and
statistically related activation effects are then to be analyzed for
the region thus defined. In this scenario, independent data are
needed to ensure valid statistical inference and unbiased estimates of effect sizes (Kriegeskorte, Lindquist, Nichols, Poldrack,
& Vul, 2010; Kriegeskorte et al., 2009; Vul, Harris, Winkielman, &
Pashler, 2009). Independent validation data are also needed
when a large number of univariate activation predictors is fitted
using regularization terms, and when the models ability to
generalize to a different set of stimuli is to be tested (e.g. Huth,
Nishimoto, Vu, & Gallant, 2012; Kay, Naselaris, Prenger, &
Gallant, 2008).
Example 2: Univariate Activation Mapping

In the previous example, we assumed a single predefined region
of interest on whose regional-average activation was analyzed
by univariate regression. Let us consider the brain mapping
problem. The hypothesis that contrasting two cognitive states
will reveal greater activity somewhere in the brain is more difficult to test than the hypothesis that there will be brain activity in
a specific region. We need to analyze all locations and perform
inference on the map as a whole. The field has developed
powerful techniques for mapping activation contrasts throughout a measured volume, while accounting for temporal and
spatial dependencies, and for the multiple testing across locations. One approach relies on Gaussian field theory (Friston
et al., 1994; Worsley et al., 1996), another uses nonparametric
permutation tests (Nichols & Holmes, 2002). Both of these aim
to control the familywise error rate (Nichols & Hayasaka,
2003). An alternative approach to the multiple-testing problem
is to control the false-discovery rate (Genovese, Lazar, &
Nichols, 2002). None of these approaches require crossvalidation. Classical brain mapping is an example of a scenario where
the complication of crossvalidation can be avoided. Many of
the established methods rely on particular assumptions (e.g.,
univariate normal errors), which are justified and which
increase the power of the statistical inference.
Example 3: Multivariate Pattern-Information Analysis

Analyses of multivariate activity patterns within a predefined
region of interest can reveal the information contained in local
brain representations (for a tutorial introduction, see Mur,
Bandettini, & Kriegeskorte, 2009). One approach to detecting
information in patterns would be multivariate linear regression
(Krzanowski, 1988), the multivariate generalization of the analysis framework used for univariate activation analysis. However,
this framework relies on the assumption that the errors are
normally distributed. Whereas the normal assumption is reasonable for the univariate scenario, it is not in general safe to rely on
multivariate normal errors in pattern analyses (Kriegeskorte,
Goebel, & Bandettini, 2006). This is one reason why the field
has preferred permutation tests and crossvalidation-based
approaches including linear discriminant analysis. When a
Fisher linear discriminant or linear support-vector machine
(Bishop, 2006) is fitted with one data set and its performance
compared to chance level using independent data, the assumptions of the model are implicitly tested. For example, the Fisher
637
linear discriminant is based on a multivariate normal model of

the errors, much like the multivariate regression framework.
However, a violation of multinormality would only decrease
predictive performance. Inference on crossvalidated performance estimates therefore provides a valid test of pattern information that does not rely on the multinormal assumption. This
illustrates how crossvalidation can reduce our reliance on questionable assumptions.
Example 4: Multivariate Pattern-Information Mapping

As for univariate activation, it is useful to map an imaged volume
continuously so as to locate brain regions containing a particular
kind of information in their local multivariate patterns
(Kriegeskorte et al., 2006). One approach relies on nonparametric permutation tests (as used in univariate mapping), where the
stimulus labels are permuted to simulate the null hypothesis.
Such tests do not require distributional assumptions and enable
us to use the most suitable test statistics including those provided
by classical multivariate statistics (Krzanowski, 1988), measures
of the similarity structure of the patterns (Kriegeskorte, Mur, &
Bandettini, 2008), or crossvalidated pattern-classifier performance estimates. Another approach is to enter multiple singlesubject descriptive pattern-information maps into a multisubject
inferential mapping procedure, treating subject as a random
effect. As for the permutation approach, the pattern-information
statistics may or may not involve crossvalidation.
Example 5: Selection Among Multiple Nonlinear

Computational Models
A major goal of brain science is to test computational models
of brain information processing. Brain imaging studies have
begun to incorporate such models into the data analysis (e.g.,
Kay et al., 2008; for a review see Kriegeskorte, 2011). In contrast to the generic statistical models discussed in the previous
examples, a model of this type mimics the actual information
processing performed by the brain. For example, it may take
stimuli in the form of bitmap images as its input and predict
their representation in a visual area. Interesting models of
brain information processing are typically complex and nonlinear. In order to test and compare models, we need to determine the extent to which they can predict brain representations
of arbitrary novel stimuli (or novel stimuli within a predefined
population of stimuli). When models of this type have parameters to be fitted, the use of independent validation sets (data
for different stimuli) is essential. Current analyses of this type
typically require crossvalidation procedures.
What Are the Alternatives to Crossvalidation and What

Are Their Advantages and Disadvantages?
Evaluation of the predictive performance of a model and selection among alternative models can be approached using probability theory. The predictive performance of a model m on a
data set d can be measured as p(d|m), the probability of the
data given the model. The philosophically most compelling
way to select a model is by its probability given the data,
638
p(m|d), which can be computed using Bayes theorem (Bishop,

2006; MacKay, 2003). A fully probabilistic treatment of model
selection requires explicit representation of all sources of
uncertainty including a prior probability distribution over the
model space. This approach requires no fitting. It therefore
does not suffer from overfitting, and does not require empirical
validation on independent data (Ghahramani, 2013). A fully
probabilistic approach, while simple in theory, can be daunting in practice. First, modeling all sources of uncertainty is
often difficult, and results will depend on the assumptions
made. A second challenge is probabilistic inference. A growing
literature on stochastic and deterministic approximate inference algorithms, including Markov chain Monte Carlo sampling, provides powerful and general solutions to this
challenge. However, the particular problem at hand may
require a custom-built solution for inference and fully automatic methods are not yet widely used. Fitting a models
parameters greatly simplifies inference and can render an otherwise untestable model testable. Therefore, empirical tests
on independent data (as efficiently implemented by crossvalidation) remain an important tool for scientific data analysis
whether the inference framework adopted is Bayesian or
frequentist, or a combination of both. Assumptions implicit
to the models, then, are continually confronted with the ultimate challenge: predicting new data.
Minimum Description Length

Another criterion for model selection is the minimum description length (MDL) principle. The MDL principle states that the
best model is the one that enables the most efficient compression of the data. The compressed data must describe the model,
its parameters, and the residuals of the fit to the data. Complex
models are implicitly penalized because their description takes
more space. The winning model best balances its own complexity against the size of the residuals (and thus the number of
bits needed to transmit them at a specified precision). The
preference for models that can be concisely described can be
interpreted as a prior favoring simple models. The MDL principle then turns out to be equivalent to Bayesian inference
(MacKay, 2003). In practice, determining the MDL by optimally encoding models, parameters, and residuals for compressed transmission is a nontrivial engineering challenge.
The explicitly Bayesian approach may be easier to implement
and preferable for its conceptual clarity.
Information Criteria
In certain scenarios, we can avoid both the challenge of a fully
Bayesian approach and the computational demands of crossvalidation. The Akaike information criterion (AIC) and the
Bayesian information criterion (BIC) provide measures of
model performance that account for model complexity. AIC
and BIC combine a term reflecting how well the model fits the
data with a term that penalizes the model in proportion to its
number of parameters. These criteria are easier to compute
than a crossvalidation estimate of predictive performance and
they enable accurate model selection when the assumptions
they are based on hold. The AIC relies on an asymptotic
approximation that may not hold for a given finite data set,
and the BIC relies on the assumption that the model errors are
independent and normally distributed. Both AIC and BIC are
functions of the parameter count and the maximized likelihood, that is, the probability of the data given the maximumlikelihood fit of the model. Counting parameters is not in
general a good method of estimating model complexity. For
example, the effective number of parameters is reduced when
the hypothesis space is regularized using an explicit prior or by
including a penalty on undesirable parameter combinations in
the cost function minimized by the fitting procedure. The
effective number of parameters can be difficult to estimate
accurately. Nevertheless, where applicable, AIC and BIC provide a quick and easy way to compare models.
Concluding Remarks
Statistical inference, whether Bayesian or frequentist, necessarily combines data with (explicit or implicit) prior assumptions.
Prior assumptions can stabilize our estimates and guide our
inferences. In Bayesian inference, an accurate prior will pull our
estimates toward the true value and an inaccurate prior will
pull them away from the true value. In frequentist inference, the
assumption of a particular error distribution lends us power.
Unsurprisingly, nonparametric inference techniques that make
no distributional assumptions tend to have less power. The
classical frequentist statistical approach is to fit and perform
inference on the basis of a single data set. Overfitting can be
accounted for in estimating the error variance. This obviates the
need for checking predictive performance on independent data.
When the inference is performed on a likelihood ratio comparing two point hypotheses, this approach has been shown to be
optimally powerful (Neyman & Pearson, 1933).
Without tests of predictive performance on independent
data, however, the classical statistical approach to inference is
severely limited, for two reasons. First, our assumptions are
usually not exactly true, and therefore our inferences are not
necessarily reliable. Second, the classical statistical approach is
only feasible for a very restricted class of models. This is the
reason why the field that has led the development of the most
complex models, machine learning, heavily relies on crossvalidation. In science our models should mirror the mechanisms
we hypothesize, and not be limited to a small set we happen to
know how to test with a single data set. Our goal is not
mathematical elegance, but learning about nature. Testing
effects and selecting models according to their actual predictive
power on new data puts all assumptions to the test and keeps
us firmly grounded in empirical reality.
In sum, the advantage of crossvalidation over alternative
methods is its generality: It can be applied when other methods
cannot and it does not rely on assumptions or approximations.
For many of the most interesting and well-motivated models in
brain science, a fully Bayesian approach is daunting and the
assumptions required for classical frequentist inference and for
information criteria for model selection may not hold. Crossvalidation enables us to develop our models as motivated by
the science (rather than the statistics) and to employ the familiar procedure of first defining a hypothesis specific enough to
be testable and then testing it empirically within the analysis of
a single data set.

Bayesian Model Inference; Bayesian Model Inversion; False Discovery
Rate Control; Information Theoretical Approaches.
References
Bishop, C. M. (2006). Pattern recognition and machine learning. New York: Springer.
Friston, K. J., Holmes, A. P., Worsley, K. J., Poline, J. P., Frith, C. D., &
Frackowiak, R. S. (1994). Statistical parametric maps in functional imaging: A
general linear approach. Human Brain Mapping, 2(4), 189210.
Genovese, C. R., Lazar, N. A., & Nichols, T. (2002). Thresholding of statistical maps in
functional neuroimaging using the false discovery rate. NeuroImage, 15(4),
870878.
Ghahramani, Z. (2013). Bayesian non-parametrics and the probabilistic approach to
modelling. Philosophical Transactions of the Royal Society A: Mathematical,
Physical and Engineering Sciences, 371(1984). http://rsta.royalsocietypublishing.
org/content/371/1984/20110553.full.
Hastie, T., Tibshirani, R., & Friedman, J. (2002). Elements of statistical learning.
New York: Springer.
Huth, A. G., Nishimoto, S., Vu, A. T., & Gallant, J. L. (2012). A continuous semantic
space describes the representation of thousands of object and action categories
across the human brain. Neuron, 76(6), 12101224.
Kay, K. N., Naselaris, T., Prenger, R. J., & Gallant, J. L. (2008). Identifying natural
images from human brain activity. Nature, 452(7185), 352355.
Kriegeskorte, N. (2011). Pattern-information analysis: From stimulus decoding to
computational-model testing. NeuroImage, 56(2), 411421.
Kriegeskorte, N., Goebel, R., & Bandettini, P. (2006). Information-based functional brain
mapping. Proceedings of the National Academy of Sciences of the United States of
America, 103(10), 38633868.
639
Kriegeskorte, N., Lindquist, M. A., Nichols, T. E., Poldrack, R. A., & Vul, E. (2010).
Everything you never wanted to know about circular analysis, but were afraid to ask.
Journal of Cerebral Blood Flow & Metabolism, 30(9), 15511557.
Kriegeskorte, N., Mur, M., & Bandettini, P. (2008). Representational similarity
analysis Connecting the branches of systems neuroscience. Frontiers in
Systems Neuroscience, 2(4). http://www.ncbi.nlm.nih.gov/pmc/articles/
PMC2605405/.
Kriegeskorte, N., Simmons, W. K., Bellgowan, P. S., & Baker, C. I. (2009). Circular
analysis in systems neuroscience: The dangers of double dipping. Nature
Krzanowski, W. J. (1988). Principles of multivariate analysis: A users perspective.
Oxford: Clarendon Press.
MacKay, D. J. (2003). Information theory, inference and learning algorithms. New York:
Mur, M., Bandettini, P. A., & Kriegeskorte, N. (2009). Revealing representational content
with pattern-information fMRI An introductory guide. Social Cognitive and
Affective Neuroscience, 4(1), 101109.
Neyman, J., & Pearson, E. S. (1933). On the problem of the most efficient
tests of statistical hypotheses. Philosophical Transactions of the Royal
Society A: Mathematical, Physical and Engineering Sciences, 231(694706),
289337.
Nichols, T., & Hayasaka, S. (2003). Controlling the familywise error rate in functional
12(5), 419446.
Vul, E., Harris, C., Winkielman, P., & Pashler, H. (2009). Puzzlingly high correlations in
fMRI studies of emotion, personality, and social cognition. Perspectives on
Psychological Science, 4(3), 274290.
of cerebral activation. Human Brain Mapping, 4(1), 5873.
Multi-voxel Pattern Analysis

C Allefeld, Universitatsmedizin Berlin, Berlin, Germany
J-D Haynes, Universitatsmedizin Berlin, Berlin, Germany; Humboldt-Universitat zu Berlin, Berlin, Germany
Background and Motivation

For many years, the analysis of fMRI data was mainly based
on univariate methods. In the dominant mass-univariate
approach, a general linear model (GLM; Friston, Holmes,
et al., 1995) is estimated separately for each voxel in the brain,
and the result is shown as an image of model parameters or
derived statistics. In contrast, multivariate analysis allows to
jointly examine brain signals recorded at multiple spatial locations. Though multivariate approaches had been present since
the beginning of fMRI research (Friston, Frith, Frackowiak, &
Turner, 1995; McIntosh, Bookstein, Haxby, & Grady, 1996),
they were never widely adopted. Only in recent years, multivariate analyses have gained traction and are now frequently used
to complement univariate analyses, especially in studies aiming
at neural coding.
The renewed interest in multivariate analysis has a number
of reasons: (1) Invasive studies have shown that in many cases,
the brain represents a single mental state in a form that involves
multiple neurons (Georgopoulos, Schwartz, & Kettner, 1986),
and these representations can be spatially distributed (Fujita,
Tanaka, Ito, & Cheng, 1992). The separate analysis of data from
single locations might thus not capture the true nature of
neural representations. (2) Computational neuroscience has
provided information-theoretic analyses that allow to identify
the information encoded in entire ensembles of neurons (e.g.,
Nevado, Young, & Panzeri, 2004). (3) Univariate analyses
ignore the dependencies between voxels as a source of information. Two voxels, which appear not to be linked to an experimental variable when analyzed separately, might encode
information by their joint activity (see, e.g., Haynes & Rees,
2006, Box 2). (4) Advances in MR methodology at higher
field strengths are substantially increasing the spatial resolution
of fMRI (Triantafyllou, Hoge, & Wald, 2006), which provides
better access to representational information contained in finegrained activity patterns in unsmoothed fMRI data.
The adoption of multivariate analysis methods was further
fostered by the biased sampling model (Haynes & Rees, 2005;
Kamitani & Tong, 2005), which aims to provide a link between
the information sampled by single fMRI voxels and the topographies of cortical columns as observed by invasive techniques.
The model explains the subtle variations in response amplitude for homogeneous classes of stimuli (e.g., orientations) by
voxel-by-voxel differences in the sampling of underlying cortical columns. While there has been considerable debate on the
exact nature of single-voxel response biases, the currently
emerging picture is that multiple causes contribute to the
response variability and resulting formation of patterns across
neighboring voxels (Chaimow, Yacoub, Ugurbil, & Shmuel,
2011; Freeman, Brouwer, Heeger, & Merriam, 2011; Kamitani
& Sawahata, 2010; Kriegeskorte, Cusack, & Bandettini, 2010;
Op de Beeck, 2010; Shmuel, Chaimow, Raddatz, Ugurbil, &
Yacoub, 2010; Swisher et al., 2010).
Pattern analysis is the common term for a number of related

multivariate analysis methods with the aim of accessing and
assessing the information contained in multiple variables
called features which have been jointly measured under
different circumstances called classes (see Bishop, 2006;
Hastie, Tibshirani, & Friedman, 2009). The methods seek to
combine the feature values in a way that enables to link them
to particular classes. In the application to neuroimaging data,
called multi-voxel pattern analysis (MVPA), classes most often
correspond to experimental conditions, and in the simplest
case, features are single-trial BOLD signal values in different
voxels or estimates of the parameters of a GLM.
MVPA differs from mass-univariate analysis not just insofar
as data from multiple voxels are analyzed jointly instead of in
parallel. Pattern analysis also drops the assumption that the
effect of an experimental manipulation must be similar in
different voxels of the same region, which is implicit in the
univariate analysis of smoothed fMRI data, and instead,
searches for complex patterns of localized increases and
decreases of the observed signal. By combining those local
effects in a way that adjusts for their possibly different signs,
MVPA results in a multivariate measure that does not allow for
a distinction between a positive and a negative effect. Since
pattern analysis simply indicates whether a difference in the
experimental manipulation makes a difference in the distribution of the observed data, MVPA has been interpreted as a shift
from activation- to information-based imaging (Kriegeskorte,
Goebel, & Bandettini, 2006).
Methodology of Pattern Analysis

Feature Definition
The first step to perform MVPA is to define and extract the
features the pattern analysis algorithm should operate on.
There are three common approaches: (1) the use of voxel
data from the whole brain, (2) the use of voxel data from a
region of interest defined anatomically or localizer-based, or
(3) the searchlight method. A searchlight (Kriegeskorte et al.,
2006) is a small group of voxels centered on a brain voxel,
typically a sphere of a given radius, where the center voxel is
moved through the brain such that for each possible location,
one pattern analysis is performed. While whole-brain and
region-of-interest analyses result in a single value, the searchlight analysis delivers one value for each center voxel location,
which can then be attributed to this center voxel to form a
statistical map of local multivariate effects. For this reason,
searchlight analysis is also referred to as mass-multivariate
analysis.
BOLD signal values or GLM parameter estimates are
collected from all voxels in the given area and concatenated
to form a voxel activation vector for each trial or run and for
each experimental condition (Figure 1). Each vector
http://dx.doi.org/10.1016/B978-0-12-397025-1.00345-6
641
INTRODUCTION TO METHODS AND MODELING | Multi-voxel Pattern Analysis
Searchlight
Whole
brain
Voxel activation vectors
Condition A
Condition B
Voxel activation space
Voxel 2
642
Region of
interest
Voxel 1
Figure 1 Definition of voxel activation space. Voxelwise data to be used for pattern analysis are extracted from a given area (white outlines), which
can be the whole brain, a region of interest, or a searchlight, that is, a small area that is moved throughout the brain. The extracted data are
concatenated to form voxel activation vectors, which are associated with experimental conditions (blue and orange). The components of vectors can be
interpreted as coordinates into a high-dimensional voxel activation space (only two dimensions shown). In this space, the similarity between
multivariate responses within a condition and the difference between conditions lead to the formation of clusters of data points, which
can be discriminated by pattern analysis.

T
x x1 , x2 , . .., xp comprises values from p different voxels. In
the following, we will denote the vectors for the two conditions
!
!
A and B with x Ai and x Bi , respectively, where i 1 ... n enumerates the data points in each class.
!
These vectors x can then be interpreted as the locations of
points in a p-dimensional voxel activation space. Pattern analysis
algorithms operate on this space trying to identify different
regions where data points belonging to a particular condition
occur more often than those belonging to another condition.
!
Informative Directions in Voxel Activation Space

The simplest way to distinguish different regions in voxel activation space is to define a linear function of the measurements,
a discriminant:
!
! !
d x w1 x1 w2 x2 . .. wp xp wT x
centroid distance direction, thereby improving the class separation. As a consequence, the single coefficients of the optimal
!
weight vector w cannot be interpreted as a measure of singlevoxel informativeness.
Fishers linear discriminant

The first method to find an optimal linear discriminant was
proposed by Fisher (1936), using the ratio of the between-class
variance to the within-class variance of the projected data,
!
d x , as a criterion. Expressed in terms of the sample proper!
!
ties, the p-dimensional centroids
and the p p
! x A and x B!
covariance matrices SA cov x Ai and SB cov x Bi , the optimal direction is given by

SA SB 1 !
!
!
xB xA
w
2
The weight vector w that defines the discriminant corresponds to a direction in voxel activation space, and the com!
putation of d x is equivalent to a projection of the data onto
this direction.
Figure 2 illustrates how the choice of this direction determines how well data points from the two classes can be sepa!
rated. An alignment of w with one of the two axes, that is, using
only data from one of the voxels, results in not only some
discrimination but also a large overlap of the projected class
distributions. Using the sum of the values from voxels 1 and 2
(corresponding roughly to the univariate analysis of smoothed
data) makes the situation worse because the experimental
manipulation has effects of different signs in the two voxels.
Choosing the direction such that the projected distance
between the two class means (centroids) is maximized gives
an improved result, but there is still overlap. In contrast, the
!
optimal choice w cleanly separates data belonging to the two
classes.
The direction orthogonal to the centroid distance contains
no discriminative information at all (pure noise in Figure 2);
all the variation in this direction is accounted for by the withinclass variance. The reason why the optimally informative direction is still not identical to maxim centroid distance is that the
noise is correlated between voxels 1 and 2. The optimal direction includes part of the pure noise direction to compensate
for that noise which is corrupting information along the
Classification and Cross-Validated Accuracy

!
! !
The discriminant d x wT x can be used to classify new data
!0
points x based on a threshold:
!
!
x 0 is assigned to class A if d x 0 b < 0,
!
!
x 0 is assigned to class B if d x 0 b 0,
where the bias b is the negative of the classification threshold;

!
the quantity d x 0 b is also called decision value. One choice
for b derives from the value of the discriminant at the centroid
of the complete data set:

1 !
!
b d
xA xB
2
In applications in cognitive neuroscience, classification of
single data points is not normally the final goal of pattern
analysis. Instead, the interesting question is how well data
from two classes can be discriminated, as an indication of how
strongly the multivariate distribution is influenced by the experimental manipulation. One way to quantify discriminability is
to assess the performance of a classifier by its classification accuracy, the proportion of data points correctly classified.
However, the accuracy cannot be correctly assessed on the
!
data used to compute the classifier parameters w and b (the
training data). This becomes apparent in the case of perfectly
643
pt
im
Pure
nois
Voxel 2
Vo
xe
l1
Vo
xe
l2
al
Max
im.
cen
troid
dist
anc
Voxel 1
Figure 2 Directions in voxel activation space. Data points from two classes (conditions; blue and orange) can be discriminated differently well
depending on the direction that is considered (arrows). If data points are projected onto a direction (gray lines), one-dimensional distributions arise
(colored ticks), which show different degrees of overlap between the classes. The optimal direction is not exclusively determined by the class centroids
(maximizing their projected distance) but also takes the within-class distribution or noise into account.
All data
Fold 1
Fold 2
Fold 3
Fold 4
Fold 5
Figure 3 Cross-validated classification accuracy. To correctly assess a classifiers performance, it has to be tested on data not used for training.
A common way to achieve this with limited data is to partition the data set (leftmost panel) into k subsets. The classification algorithm is then trained on
data from k 1 of the parts (open circles) and tested on the remaining part (filled circles). This is repeated such that each part is once used for
testing (k-fold cross-validation). The classification performance is assessed by the number of test data points correctly classified, the cross-validated
accuracy (here: 7 out of 10 70%).
separable data: The classifier performs at 100% accuracy on the

training data, but there is no guarantee that this performance
generalizes to new data points. The standard method to estimate classification accuracy given a limited amount of data is
cross-validation (Figure 3): The data set is separated into k parts

of (approximately) the same size, and the classifier is trained
on data from k 1 of these parts and tested on the last part.
This is repeated in turn such that each part is once used for
644
testing (cross-validation folds), and the estimated accuracy is

the number of data points correctly classified.
There are a number of precautions that have to be taken in
order to obtain a valid assessment of classifier performance using
cross-validation: (1) Testing data should be statistically independent of training data to prevent a carry-over of information; this
should ideally be approximated by partitioning the data according to recording sessions (runs). In contrast, neighboring trials
within a run cannot be considered independent due to the
temporal autocorrelation of the BOLD signal and the temporal
smoothing induced by the hemodynamic response. (2) The
number of data points should be the same for both classes in
the whole data set and in each part because an imbalance may be
exploited by the classifier to achieve a classification accuracy
above chance (50%) without a real class difference. (3) Data in
each part should follow the same distribution, which is representative of the whole (stationarity).
Note that the estimate provided by cross-validation
depends on the amount of data available as well as its partitioning, and it underestimates the performance of the best
classifier possible. Moreover, the statistical significance of an
observed cross-validated accuracy cannot be assessed by the
binomial distribution because the cross-validation folds are
not mutually statistically independent.
Classification Methods
In the following, we briefly describe three approaches to classification; they are illustrated in Figure 4.
Linear discriminant analysis

LDA uses the same discriminant as Fishers approach but motivates it with a generative model, that is, a model of the probability distribution of the data. The assumption is that data
belonging to the two classes come from multivariate normal
!
!
distributions with different means, m A and m B , but the same
within-class covariance matrix:

!
!
!
!
X A N m A , S and X B N m B , S
This model allows to compute the probability that a new
!
data point x 0 belongs to class A or B, the posterior probabilities
(for equal priors)
LDA
Logistic regression

!
P Bj x 0
1

! !
1 exp w T x b
and

!
!
P Aj x 0 1 P Bj x 0
where

1 ! !
!
!
!
w S1 m B m A and b wT m A m B
2
!
!
!
!
^
^
can be estimated based on m A x A ; m B x B , and
1
^
S 2 SA SB . The optimal classifier under these assumptions
is the one that chooses the class that has the largest posterior
! !
probability, which is equivalent to using wT x b as the decision value.
An important limitation of LDA is that it is necessary
to estimate the within-class covariance matrix, which has
1
2 p1 p free entries, a number that for higher dimensionalities of the voxel activation space can quickly get larger than the
number of data points available to calculate it. In this case,
the estimate becomes singular, which means its inverse cannot
be computed. Even if the number of data points is formally
sufficient, S^1 becomes an unreliable estimator of S1 for
increasing dimensionality, degrading the performance of the
classifier. Two common ways to cope with this problem are
regularization of the model via a shrinkage estimator (Schafer
& Strimmer, 2005) or reduction of dimensionality via principal component analysis (see Jolliffe, 2002).
!
Logistic regression
Another way to circumvent the covariance estimation problem
is to directly fit the equation for the posterior class probabilities
to the data, that is, to treat it as a discriminative model that does
not make an explicit statement about the distribution of the
!
data x . This approach is called logistic regression because
1/(1 exp(s)) is known as the logistic function. It is important to note that despite of its name, logistic regression is not a
form of regression but a classification method.
The advantage of logistic regression over LDA is that it is not
necessary to estimate the within-class covariance but only the
!
p-dimensional weight vector w and scalar bias b. Moreover, the
SVM
Mahalanobis distance
Figure 4 Approaches to pattern analysis. Each panel shows the defining elements of the respective method in black and the resulting posterior class
probabilities or binary classification as a colored background. Linear discriminant analysis assumes multivariate normal distributions for the two
classes and estimates their class means (centroids; dots) and common covariance (ellipses) to compute the posterior probabilities. Logistic regression
directly models the posterior distribution using only a weight vector and bias (arrow with intercept). The support vector machine achieves
classification by searching for a separating area without data points (between colored lines), which is as wide as possible (margin width; double-sided
arrow). This separating area is defined by the data points at the edge, the support vectors (circled). Mahalanobis distance directly quantifies the
distinctness of the two distributions by the distance of the centroids measured in units of the within-class standard deviation (ellipses).

logistic regression model is not bound to the assumption of
normally distributed data but extends to discrete data as well
as a subset of the family of exponential distributions (see
Bishop, 2006).
Support vector machine

A nonprobabilistic approach to classification is given by the
support vector machine, which is based on the principle of
margin maximization. The SVM searches for a linear classification boundary that separates the training data of the two
classes and then chooses an orientation and position of that
separating hyperplane such that it has the maximally possible
distance from the nearest training data points (Vapnik, 1982).
The trained classifier is defined by only those data points that
!
lie at the edge of the margin, the so-called support vectors z j :
!
m
X
j1
ai z j and b wT

1 !
!
zA zB
2
where ai is positive for support vectors of class B and negative for

!
!
support vectors of class A and where z A and z B are each one
arbitrarily chosen support vector of each class. The soft margin
classifier (Cortes & Vapnik, 1995) extends the original approach
of margin maximization by a penalty for misclassified data
points so that it can be applied to nonseparable training data.
The advantages of the SVM classifier are that it does not
depend on specific assumptions about the distribution of the
data and that it can be applied without special precautions to
small data sets of high dimensionality. Through the kernel
trick, which implicitly applies a nonlinear mapping to the
input data (Boser, Guyon, & Vapnik, 1992), the algorithm
can be simply extended in order to obtain a nonlinear classifier. A drawback of the approach to directly find a separating
hyperplane is that classifications are not qualified by a probability (but see Platt, 2000). Moreover, there exists no simple
generalization to the case of multiple classes, which is straightforward for LDA as well as logistic regression.
Alternatives to Classification Accuracy

Cross-validated classification accuracy is the most commonly
used method to quantify discriminability in MVPA, but not the
only one. A direct way to measure the degree to which the
multivariate data distributions associated with two different
classes are different from each other is the Mahalanobis distance
(Figure 4):
s

T S S 1

!
!
!
!
A
B
DM
xB xA
xB xA
2
the distance between the class means measured in units of the
within-class standard deviation (Mahalanobis, 1936). 14 D2M
coincides with the optimal value of between-class variance to
!
within-class variance of d x , achieved by Fishers linear discriminant, and for the two-class normal distribution model of
LDA, it is directly related to the information-theoretic distinctness of the two distributions (Kullback & Leibler, 1951). A
generalization to the case of multiple classes as well as graded
class membership (regression) is given by statistics used in the
multivariate analysis of variance (MANOVA; see Timm, 2002).
645
The drawback of both Mahalanobis distance and multivariate

statistics, that they severely overestimate the true effect size, can
be corrected by cross-validation (Allefeld & Haynes, 2014).
One step beyond pattern analysis goes the approach to
compare the similarity structure of a psychological variable
with the similarity structure of the corresponding neural activation patterns (Edelman, Grill-Spector, Kushnir, & Malach,
1998). In the recent formulation of this approach as representational similarity analysis (Kriegeskorte, Mur, & Bandettini,
2008), the (dis)similarity matrix plays the role of a unified
tool that facilitates comparisons between different neurophysiological modalities, different brain areas, and different species, as well as with behavioral data, and can be used to
evaluate theoretical predictions. Such matrices may be built
using not only pattern correlations but also classification accuracies or Mahalanobis distances, and the underlying representational space can be reconstructed using techniques like
multidimensional scaling (see Timm, 2002).
Acknowledgments
Thanks to Fonov et al. (2009) for the brain template for
Figure 1, rendered with C. Rordens MRIcroGL.

Crossvalidation; Information Theoretical Approaches; Reverse
Inference; The General Linear Model.
References
Allefeld, C., & Haynes, J.-D. Haynes. (2014). Searchlight-based multi-voxel pattern
analysis of fMRI by cross-validated MANOVA. NeuroImage, 345357. http://dx.doi.
org/10.1016/j.neuroimage.2013.11.043.
Bishop, C. M. (2006). Pattern recognition and machine learning. New York: Springer.
Boser, B. E., Guyon, I., & Vapnik, V. (1992). A training algorithm for optimal margin
classifiers. In Proceedings of the fifth annual workshop of computational learning
theory (pp. 144152). Pittsburgh: Association for Computing Machinery.
Chaimow, D., Yacoub, E., Ugurbil, K., & Shmuel, A. (2011). Modeling and analysis of
mechanisms underlying fMRI-based decoding of information conveyed in cortical
columns. NeuroImage, 56, 627642.
Cortes, C., & Vapnik, V. (1995). Support vector networks. Machine Learning, 20,
273297.
Edelman, S., Grill-Spector, K., Kushnir, T., & Malach, R. (1998). Towards direct
visualization of the internal shape space by fMRI. Psychobiology, 26, 309321.
Fisher, R. A. (1936). The use of multiple measurements in taxonomic problems. Annals
of Eugenics, 7, 179188.
Fonov, V. S., Evans, A. C., McKinstry, R. C., Almli, C. R., & Collins, D. L. (2009).
Unbiased nonlinear average age-appropriate brain templates from birth to
adulthood. NeuroImage, 47, S102.
Freeman, J., Brouwer, G. J., Heeger, D. J., & Merriam, E. P. (2011). Orientation
decoding depends on maps, not columns. Journal of Neuroscience, 31,
47924804.
Friston, K. J., Frith, C. D., Frackowiak, R. S., & Turner, R. (1995). Characterizing
dynamic brain responses with fMRI: A multivariate approach. NeuroImage, 2,
166172.
Friston, K. J., Holmes, A. P., Poline, J. B., Grasby, P. J., Williams, S. C., Frackowiak, R. S.,
et al. (1995). Analysis of fMRI time-series revisited. NeuroImage, 2, 4553.
Fujita, I., Tanaka, K., Ito, M., & Cheng, K. (1992). Columns for visual features of objects
in monkey inferotemporal cortex. Nature, 360, 343346.
Georgopoulos, A. P., Schwartz, A. B., & Kettner, R. E. (1986). Neuronal population
coding of movement direction. Science, 233, 14161419.
Hastie, T., Tibshirani, R., & Friedman, J. (2009). The elements of statistical learning:
Data mining, inference, and prediction (2nd ed.). New York: Springer.
646
Haynes, J.-D., & Rees, G. (2005). Predicting the orientation of invisible

stimuli from activity in human primary visual cortex. Nature Neuroscience, 8,
686691.
Haynes, J.-D., & Rees, G. (2006). Decoding mental states from brain activity in humans.
Nature Reviews Neuroscience, 7, 523534.
Jolliffe, I. T. (2002). Principal component analysis (2nd ed.). New York: Springer.
Kamitani, Y., & Sawahata, Y. (2010). Spatial smoothing hurts localization but not
information: Pitfalls for brain mappers. NeuroImage, 49, 19491952.
Kamitani, Y., & Tong, F. (2005). Decoding the visual and subjective contents of the
human brain. Nature Neuroscience, 8, 679685.
Kriegeskorte, N., Cusack, R., & Bandettini, P. (2010). How does an fMRI voxel sample
the neuronal activity pattern: Compact-kernel or complex spatiotemporal filter?
Kriegeskorte, N., Goebel, R., & Bandettini, P. (2006). Information-based functional brain
mapping. Proceedings of the National Academy of Sciences of the United States of
America, 103, 38633868.
Kriegeskorte, N., Mur, M., & Bandettini, P. (2008). Representational similarity
analysis Connecting the branches of systems neuroscience. Frontiers in Systems
Neuroscience, 2. http://dx.doi.org/10.3389/neuro.06.004.2008.
Kullback, S., & Leibler, R. A. (1951). On information and sufficiency. Annals of
Mathematical Statistics, 22, 7986.
Mahalanobis, P. C. (1936). On the generalized distance in statistics. Proceedings of the
National Institute of Sciences of India, 2, 4955.
McIntosh, A. R., Bookstein, F. L., Haxby, J. V., & Grady, C. L. (1996). Spatial pattern analysis
of functional brain images using partial least squares. NeuroImage, 3, 143157.
Nevado, A., Young, M. P., & Panzeri, S. (2004). Functional imaging and neural
information coding. NeuroImage, 21, 10831095.
Op de Beeck, H. P. (2010). Against hyperacuity in brain reading: Spatial smoothing
does not hurt multivariate fMRI analyses? NeuroImage, 49, 19431948.
Platt, J. C. (2000). Probabilities for SV machines. In A. J. Smola, et al. (Eds.), Advances
in large margin classifiers (pp. 6174). Cambridge: The MIT Press.
Schafer, J., & Strimmer, K. (2005). A shrinkage approach to large-scale covariance
matrix estimation and implications for functional genomics. Statistical Applications
in Genetics and Molecular Biology, 4, 32.
Shmuel, A., Chaimow, D., Raddatz, G., Ugurbil, K., & Yacoub, E. (2010). Mechanisms
underlying decoding at 7 T: Ocular dominance columns, broad structures, and
macroscopic blood vessels in V1 convey information on the stimulated eye.
Swisher, J. D., Gatenby, J. C., Gore, J. C., Wolfe, B. A., Moon, C. H., Kim, S. G., et al.
(2010). Multiscale pattern analysis of orientation-selective activity in the primary
visual cortex. Journal of Neuroscience, 30, 325330.
Timm, N. H. (2002). Applied multivariate analysis. New York: Springer.
Triantafyllou, C., Hoge, R. D., & Wald, L. L. (2006). Effect of spatial smoothing on
physiological noise in high-resolution fMRI. NeuroImage, 32, 551557.
Vapnik, V. (1982). Estimation of dependences based on empirical data, Addendum 1.
New York: Springer.
Reverse Inference
RA Poldrack, Stanford University, Stanford, CA, USA
Glossary
Bayes rule The equation that describes how to optimally

update a conditional probability based on new evidence.
Cross validation A strategy to assess the generalization
accuracy of a statistical method, in which the model is
On 30 September 2011, an Op-Ed was published in the New

York Times by Martin Lindstrom, a self-styled neuromarketer.
In it, he described an fMRI study in which individuals were
presented with audio and video of an iPhone as it vibrated and
rang, with the following results:
. . .most striking of all was the flurry of activation in the insular
cortex of the brain, which is associated with feelings of love and
compassion. The subjects brains responded to the sound of their
phones as they would respond to the presence or proximity of a
girlfriend, boyfriend, or family member.
In short, the subjects did not demonstrate the classic brainbased signs of addiction. Instead, they loved their iPhones.
This is a classic example of what has come to be called
reverse inference, which is the use of activation to infer the
presence of a specific cognitive function (in this case, the rather
ill-founded inference that insular activity reflected the fact that
subjects were experiencing feelings of love when viewing the
iPhone).
In this article, I will first outline an analysis of reverse
inference that highlights its problematic logical status and
show how meta-analyses can be used to examine its evidentiary
power. I will also outline how meta-analysis has been formalized using large-scale databases and how the tools of machine
learning provide the potential to perform reverse inference in a
defensible, albeit more limited, manner.
Forward versus Reverse Inference

The conceptual approach of most neuroimaging studies has
been labeled forward inference (Henson, 2006) and proceeds
as follows: A researcher is interested in understanding the brain
systems that support some particular cognitive process, say,
memory retrieval. He or she performs fMRI, while the subject
performs a task in which the presence or level of engagement of
memory retrieval is manipulated and examines the fMRI data
in order to find regions whose level of activity is related to the
level of engagement of the cognitive process. This requires a
number of assumptions (Poldrack, 2010), but under those
assumptions, the researcher can then infer that the regions
showing differences in activity related to the task manipulation
are somehow involved in memory retrieval. This is termed
successively fit on subsets of the data and tested on the

remaining left-out data.
Machine learning A field of statistics and computer science
concerned with the development of methods to learn and
generalize from data.
forward inference because it reasons forward from an experimental manipulation to a brain function.
Instead of inferring on the basis of an experimental manipulation, reverse inference proceeds in the opposite direction:
The researcher performs an fMRI study and finds that some
area is activated. Instead of inferring the function of the region
based on the task manipulation, the researcher instead infers
the function of the region via a comparison with other studies
in which the same area was active. For example, given activation in the left inferior frontal region (Brocas area), a
researcher might infer that the subject is engaging language
processes in relation to the manipulation that drove the
activation.
An Analysis of Reverse Inference

Concerns about reverse inference were raised early in the
course of the rise of neuroimaging (Aguirre, 2003), noting
that its logical status is tenuous. Taken as a deductive logical
claim, it is an example of the logical fallacy of affirming the
consequent: If X (cognitive process), then g (activation); g,
therefore X. The reason for this is intuitive; one can only reason
from the presence of activation to the presence of a process if
that process is the only one that results in that specific activation. If every task activates a region reliably, then its activation
is not indicative of any task in particular.
A probabilistic analysis (Poldrack, 2006) allows one to
better understand this relation to the base rate of activation,
specifically using Bayes rule:

P AM PM

P MA
P AM PM P A M P M
where M refers to the engagement of a particular mental process and A refers to the presence of activation in a specific
region. This equation highlights that the probability that a
reverse inference is correct relies not only on the likelihood
that the mental process in question activates the region but
also on the base rate of activation of that region across all
mental processes. This formulation makes the untenable
assumption that mental tasks map directly to (unobservable)
mental processes; in principle, one also needs to include a
conditional probability for mental process engagement given
http://dx.doi.org/10.1016/B978-0-12-397025-1.00346-8
647
648
INTRODUCTION TO METHODS AND MODELING | Reverse Inference
a particular task (Poldrack, 2006), but this value is almost

certainly unknowable.
While these analyses cast doubt on strong interpretations of
reverse inference, it is important to highlight that it also shows
that they are not completely invalid either (as is sometimes
now assumed in the literature). This was made clear in
Poldrack (2006):
It is crucial to note that this kind of reverse inference is not deductively
valid, but rather reflects the logical fallacy of affirming the consequent. . .However, cognitive neuroscience is generally interested in a
mechanistic understanding of the neural processes that support cognition rather than the formulation of deductive laws. To this end,
reverse inference might be useful in the discovery of interesting new
facts about the underlying mechanisms. Indeed, philosophers have
argued that this kind of reasoning (termed abductive inference by
Pierce [8]), is an essential tool for scientific discovery [9].
Others have also highlighted the potential utility of reverse

inference for discovery, both in domains where the inferences can
be tightly constrained by prior knowledge (Hutzler, 2013; Poldrack
& Wagner, 2004) and in domains where the inferences are
less tightly constrained by prior knowledge (Young & Saxe, 2009).
Meta-Analytic Approaches to Reverse Inference

The foregoing probabilistic framework highlights a way forward toward the assessment of any particular reverse inference
using meta-analysis. Poldrack (2006) presented a proof of
concept of such an analysis using the BrainMap database to
assess the reverse inference that activation in the left inferior
frontal cortex (Brocas area) implied the engagement of language processing. This analysis showed that activation in this
region did indeed provide evidence for the engagement of
language but that this evidence was relatively weak. This
reflected the fact that while activation was slightly more likely
in language-related tasks than non-language-related tasks, it
still occurred often enough in non-language-related tasks that
Syntax
it undercuts any strong predictions about the involvement of

language. There are of course a number of significant caveats to
this analysis; in particular, the fact that an experiment is not
coded as being related to language in the BrainMap database
does not mean that subjects did not engage language in relation to the experimental manipulation, such that one has to
place a fairly wide confidence interval around any estimates of
reverse inference accuracy. Others have performed similar
meta-analyses in different domains and found stronger evidence for those reverse inferences, such as the inference from
ventral striatum activation to reward processing Ariely and
Berns (2010).
A limitation of the BrainMap database is that it requires
manual annotation of each paper, which limits the number of
studies in the database. Yarkoni, Poldrack, Nichols, Van Essen,
and Wager (2011) developed an alternative approach that was
based on the assumption that the mental concepts being studied in each paper would be reflected in the words used in the
paper, in conjunction with an automated method for extracting activation coordinates from published papers. This
method, which has been implemented in the online Neurosynth database (http://neurosynth.org), allows one to quantify
both forward inference (i.e., the likelihood of activation in a
particular region given that a paper contains a particular word
at high frequency) and reverse inference (i.e., the likelihood
that a paper uses a particular word at high frequency given that
a region is activated). The openly accessible site also provides
access to other analyses, such as results from topic modeling
that highlight the degree that different words are used together
in relation to specific conceptual topics (Poldrack et al., 2012).
Figure 1 shows an example of a set of forward and reverse
inference maps for several concepts. This figure highlights the
fact that the relation between forward and reverse inference
differs greatly between regions; for regions that are activated
very often (such as the anterior cingulate or anterior insula),
very strong forward inference results can be associated
with very weak reverse inference maps, whereas for other
regions, the maps are much more similar. One very promising
Reward
Figure 1 Neurosynth meta-analytic maps for the terms syntax and reward. The voxels shown in red are those for which there was a significant
forward inference association (i.e., the voxel is active when the term appears often in a paper), whereas the voxels in blue are those for which
there was also a significant reverse inference association (i.e., activation in the voxel was predictive of the word appearing in the paper). Note that in both
maps, the anterior cingulate and anterior insula show forward inference activation but no significant reverse inference association, reflecting the fact
that they are activated across a very broad set of tasks.

aspect of the Neurosynth site is that it allows one to easily
output an image for any meta-analysis, which can then be
used as a region of interest for further analysis. In addition,
the Neurosynth software tools (available at https://github.
com/neurosynth/neurosynth) can be used to perform
decoding analyses that can provide the most likely reverse
inferences for any particular activation image.
While very useful, meta-analytic approaches have inherent
challenges that limit their interpretability. First, because they
are based on the labeling that gets used in published papers,
they may themselves be influenced by informal reverse
inferences and thus could result in circular inferences. For
example, if researchers interpret ventral striatal activation as
reflecting reward, then papers with activation in this region
are more likely to use the term reward even if there is no direct
manipulation of reward in the task. For this reason, it is useful to
find convergent results between literature mining analyses and
analyses of manually curated databases like BrainMap. Second,
these methods inherit all of the problems with literature mining;
since papers are treated as a bag of words, contextual information (such as negation) is not reflected in the analysis. For
example, a paper claiming that the ventral striatum is not
involved in reward will still contribute to associations between
ventral striatum and reward in the meta-analysis. Despite the
limitations, these meta-analytic approaches provide important
new ways to test reverse inferences in a more formal way.
Reverse Inference by Formal Decoding

The development of methods for decoding of mental states
using machine learning methods has provided a new set of
approaches for the formal testing of reverse inferences. In this
case, rather than using a meta-analytic database to obtain
patterns for each cognitive concept, one instead uses data
from individual subjects and trains a classifier to decode either
the task or the cognitive concept that is expressed in a new test
dataset. Whereas most studies using decoding methods have
applied them within subjects, a growing set of studies have
shown that it is possible to decode mental tasks and states
using classifiers trained on different individuals (Davatzikos
et al., 2005; Mourao-Miranda, Bokde, Born, Hampel, & Stetter,
2005; Poldrack, Halchenko, & Hanson, 2009; Shinkareva et al.,
2008). This provides the potential for even more powerful
decoding and potentially alleviates some of the problems
with meta-analytic reverse inference, though at the cost of
necessarily narrower inferences.
Early work (Poldrack et al., 2009) showed that it was possible to decode which of eight different tasks an individual was
engaged in, using a leave-one-subject-out cross validation
strategy. Using a relatively homogenous dataset, the task
being performed could be decoded with > 70% accuracy
using a whole-brain classifier. In addition, the classifier structure was decomposed in order to understand the latent structure of the neural space with regard to mental concepts. More
recent work has expanded this out to much larger set of tasks
and concepts, which is necessary in order to make compelling
claims regarding large-scale decoding of mental processes from
imaging data. Using the OpenfMRI database, Poldrack et al.
(2013) examined the ability to classify the task being
649
performed by subjects out of a total of 26 different possible

tasks (which varied greatly in their similarity across tasks) and
found that it was possible to classify the task being performed
with about 50% accuracy. Analyses of classifier confusions
showed that the classifier tended to confuse similar tasks,
highlighting the potential utility of these methods to identify
similarities between tasks in terms of their underlying neural
subspaces. These findings highlight the potential utility of
decoding-based reverse inference methods; ongoing work
aims to decompose the tasks further into their underlying
cognitive components, so that one can classify psychological
processes rather than tasks, which is the ultimate aim of reverse
inference.
Conclusion
The neuroimaging literature has become increasingly sensitive
to the difficulties of interpreting reverse inferences, with some
arguing that this backlash has actually gone too far (e.g.,
Hutzler, 2013). It is clear that this strategy may be useful in
inspiring novel hypotheses regarding brain function, particularly in new areas of study, but its use must be tempered by the
heavy sensitivity upon base rates of activation. There is great
hope that large-scale databasing, particularly databases of full
datasets such as OpenFMRI, may provide the basis for much
more powerful decoding of mental function from brain activation, providing reverse inferences whose evidence is directly
quantifiable.

BrainMap Database as a Resource for Computational Modeling;
Crossvalidation; Databases; Meta-Analyses in Functional
Neuroimaging; Multi-voxel Pattern Analysis.
References
Aguirre, G. K. (2003). Functional imaging in behavioral neurology and cognitive
neuropsychology. In T. E. Feinberg, & M. J. Farah (Eds.), Behavioral neurology and
cognitive neuropsychology. New York: McGraw-Hill.
Ariely, D., & Berns, G. S. (2010). Neuromarketing: The hope and hype of neuroimaging
in business. Nature Reviews Neuroscience, 11(4), 284292.
Davatzikos, C., Ruparel, K., Fan, Y., Shen, D. G., Acharyya, M., Loughead, J. W., et al.
(2005). Classifying spatial patterns of brain activity with machine learning methods:
Application to lie detection. NeuroImage, 28(3), 663668.
Henson, R. (2006). Forward inference using functional neuroimaging: Dissociations
versus associations. Trends in Cognitive Sciences, 10(2), 6469.
Hutzler, F. (2013). Reverse inference is not a fallacy per se: Cognitive processes can be
inferred from functional imaging data. Neuroimage, 84, 10611069.
Mourao-Miranda, J., Bokde, A. L. W., Born, C., Hampel, H., & Stetter, M. (2005).
Classifying brain states and determining the discriminating activation
patterns: Support vector machine on functional mri data. NeuroImage, 28(4),
980995.
Poldrack, R. A. (2006). Can cognitive processes be inferred from neuroimaging data?
Trends in Cognitive Sciences, 10(2), 5963.
Poldrack, R. A. (2010). Subtraction and beyond: The logic of experimental designs for
neuroimaging. In S. J. Hanson, & M. Bunzl (Eds.), Foundational issues in human
brain mapping (pp. 147160). Cambridge, MA: MIT Press.
Poldrack, R. A., Barch, D. M., Mitchell, J. P., Wager, T. D., Wagner, A. D., Devlin, J. T.,
et al. (2013). Toward open sharing of task-based fMRI data: the openfMRI project.
Frontiers in Neuroinformatics, 7, 12.
650
Poldrack, R. A., Halchenko, Y. O., & Hanson, S. J. (2009). Decoding the large-scale
structure of brain function by classifying mental states across individuals.
Psychological Science, 20, 13641372.
Poldrack, R. A., Mumford, J. A., Schonberg, T., Kalar, D., Barman, B., & Yarkoni, T.
(2012). Discovering relations between mind, brain, and mental disorders using
topic mapping. PLoS Computational Biology, 8(10), e1002707.
Poldrack, R. A., & Wagner, A. D. (2004). What can neuroimaging tell us about the
mind? insights from prefrontal cortex. Current Directions in Psychological Science,
13, 177181.
Shinkareva, S. V., Mason, R. A., Malave, V. L., Wang, W., Mitchell, T. M., & Just, M. A.
(2008). Using fMRI brain activation to identify cognitive states associated with
perception of tools and dwellings. PLoS One, 3(1), e1394.
Methods, 8, 665670.
Young, L., & Saxe, R. (2009). An fMRI investigation of spontaneous mental state
inference for moral judgment. Journal of Cognitive Neuroscience, 21(7),
13961405.
Computational Modeling of Responses in Human Visual Cortex

BA Wandell, Stanford University, Stanford, CA, USA
J Winawer, New York University, New York, NY, USA
KN Kay, Stanford University, Stanford, CA, USA; Washington University, St. Louis, MO, USA
Glossary
ECoG Electrocorticography (electrical recordings from

intracranial electrodes).
Extrastriate cortex Visual cortex outside of V1, including
V2, V3, and so forth.
fMRI Functional magnetic resonance imaging.
Introduction
Many fields of investigation, spanning medicine, science, and
humanities, have an interest in the spatially localized measurements of human brain activity provided by functional magnetic resonance imaging (fMRI). These fields use a diverse array
of experimental, statistical and computational methods to analyze and interpret fMRI responses, and this diversity reflects the
questions of interest to each field.
The approach in vision science differs substantially from
that taken in most other fields. Most disciplines use neuroimaging designs based on between-group or between-condition
comparisons; the primary aim of these experiments is to find
statistically significant group differences that localize function
by combining weak signals. But the fMRI signals in visual
cortex are relatively strong, so that experiments can be performed in individual subjects using a wide range of stimuli.
Further, the spatial organization and high degree of connectivity across visual cortex is clear, so that localization is not a
driving factor. Instead, the principal goals of neuroimaging in
vision science are (a) to develop computational models that
predict fMRI responses for a wide range of stimuli, and (b) to
integrate neuroimaging measurements with data from other
techniques (psychophysics, intracranial recordings, singleunit physiology, and so forth). To support these goals, neuroimaging designs for vision science use parametric variations of
the stimulus and computational models that compute the
mapping from stimuli to fMRI time series. In vision science,
computational modeling is central and statistical analyses are
secondary.
We illustrate and explain the approach in the following
sections. First, we introduce visual field maps (also called
retinotopic maps). This background section provides the
reader with a sense of the cortical locations where we measure
fMRI responses and the quality of the fMRI time series in visual
cortex. Second, we describe the importance of stimulusreferred measurement in vision science. This approach is critical for integrating different types of measurements. Third, we
describe the current generation of computational models of
the fMRI time series. These models extend conventional visual
field mapping and analyze the time series more fully. Finally,
Stimulus-referred Experimental designs that characterize

the neural response with respect to the stimulus properties.
Striate cortex V1
Visual field map (retinotopic map) Spatial representation
of the visual field within visual cortex.
Visual receptive field The region of space in which the
presence of a stimulus elicits a response.
we illustrate how these models and stimulus-referred methods

have clarified the relationship between fMRI and intracranial
data obtained from human visual cortex.
Visual Field Maps

In the mid-1800s, biologists began examining the responses in
animal brains to localize various stimulus-driven responses.
Visual cortex was localized rather early, though not without
some serious disputes (Phillips, Zeki, & Barlow, 1984; Munk,
1881; Zeki, 1993). The biologists were joined in the late
nineteenth and early twentieth centuries by neurologists and
ophthalmologists (Inouye, 1909; Henschen, 1893; Holmes,
1918; Holmes & Lister, 1916). The clinicians treated soldiers
who had occipital head wounds that caused blindness in
restricted regions of the visual field. By mapping correspondences between the wound location and the visual field loss,
Inouye, Holmes and others showed that the position of the
wound corresponded to the location of the visual field loss.
They correctly concluded that there is at least one topographic
map of the contralateral visual hemifield in each hemisphere.
In the 1940s, electrophysiology in animal brains revealed
that there are multiple sensory maps. It is challenging to measure visual field maps using single-unit electrophysiology. The
experiment requires a series of electrode penetrations through
the folded cortical sheet, followed by a histological reconstruction so that the electrode positions might be integrated with
the responses. Hubel and Wiesel characterized the work as a
dismaying exercise in tedium, like trying to cut the back lawn
with a pair of nail scissors (Hubel & Wiesel, 1977; p. 28). Even
so, good progress was made, and by the early 1990s electrophysiologists and anatomists identified dozens of maps in
various species (Felleman & Essen, 1991; Zeki, 1993).
The first human fMRI experiments measured cortical
responses to visual stimuli that covered a large part of the
visual field (Ogawa et al., 1992; Kwong et al., 1992). These
stimuli elicited responses in a broad swath of occipital cortex.
Shortly thereafter, fMRI measurements clarified the relationship between stimulus visual field position and cortical
responses (DeYoe, Bandettini, Neitz, Miller, & Winans, 1994;
http://dx.doi.org/10.1016/B978-0-12-397025-1.00347-X
651
652
INTRODUCTION TO METHODS AND MODELING | Computational Modeling of Responses in Human Visual Cortex
Engel, Glover, & Wandell, 1997; Engel et al., 1994; Sereno

et al., 1995). In one widely adopted method, the experimenter
presents a contrast pattern within a series of concentric rings of,
say, increasing inner and outer diameters (Warnking et al.,
2002). Such an expanding ring stimulus generates a traveling
wave of activity that begins at the occipital pole when the ring
diameter is small and travels to the peripheral representation as
the ring diameter increases; these responses define the eccentricity dimension. In a separate experiment, the experimenter
presents a contrast pattern within a wedge that rotates around
fixation. This stimulus elicits responses that are specific to
certain angles and these responses define the angle dimension.
Together, the ring and wedge measurements determine the
most effective visual field position for each voxel.
The images in Figure 1 show fMRI eccentricity and angle
maps in the most posterior portion of occipital cortex. The
color overlay specifies angle on the left mesh and eccentricity
on the right mesh. There is a single, integrated eccentricity map
near the occipital pole. A great deal of the cortical surface area
at the pole represents the fovea, and there is a systematic shift
toward more peripheral representations in the posterior-toanterior direction. The integrated eccentricity representation
includes V1, V2, V3, and hV4, although the hV4 part of the
map is a bit compressed. Based on the eccentricity data alone,
one would have no basis for segregating the activated cortex
into different regions.
The segregation into multiple maps becomes clear from

examining the angle representations. The V1 map has a continuous angle representation of the contralateral visual field,
spanning the lower vertical meridian (green in the pseudocolor
map) to the upper vertical meridian (red). The angle representation reverses at the vertical meridians, and this marks
the boundary with V2. The V1 map is surrounded by a dorsal
and ventral section of V2, which represent the lower
(greencyan) and upper (redblue) visual field. The V2 map
is, in turn, surrounded by dorsal and ventral sections of V3.
This nested organization for V1V3 is typical of nonhuman
primates. But the confirmation that this organization is present
in human was only made in the early 1990s by a combination
of neurology and fMRI (DeYoe et al., 1996; Engel et al., 1997;
Horton & Hoyt, 1991a, 1991b; Sereno et al., 1995).
Visual stimuli elicit activity in about 20% of the human
brain, covering the entire occipital lobe and extending into
portions of temporal and parietal cortex (Wandell, Dumoulin,
& Brewer, 2009). It is likely that occipital cortex is completely
covered by maps, though some regions have proven difficult to
measure (Winawer, Horiguchi, Sayres, Amano, & Wandell,
2010). Identifying the organization within human visual cortex is essential for interpreting fMRI data from visual cortex and
for building meaningful computational theories of vision. This
project has had excellent progress. Measurements like those in
Figure 1 show that the general spatial layout of early human
Figure 1 Visual field maps in occipital cortex. The small inset at the upper right is a smoothed rendering of the surface boundary between gray
matter and white matter in a right hemisphere, and the dotted rectangle is shown in the magnified and further smoothed images. The dark and light
gray shading indicates sulci and gyri, respectively. The two main images show visual cortex rendered from a point behind the occipital pole. The
underlying anatomy is the same for the two meshes, differing only in the color overlays. The color overlays show the most effective angle (left) or
the most effective eccentricity (right). Colors are shown only for voxels where the data are well fit by a population receptive field model, as explained
below. The solid black lines and labels indicate the positions of ten visual field maps. The view and data were selected to provide a large field of
view spanning most of the occipital lobe. Additional maps have been identified, including some on the intraparietal sulcus (IPS) and anterior ventral
surface (Arcaro, McMains, Singer, & Kastner, 2009; Dechent & Frahm, 2003; Kolster, Peeters, & Orban, 2010; Konen & Kastner, 2008; Sereno,
Pitzalis, & Martinez, 2001). The uncolored region on the ventral surface is close to a large sinus that limits the ability to measure the BOLD signal
(Winawer, Horiguchi, Sayres, Amano, & Wandell, 2010).
visual maps V1, V2, and V3 is similar to nonhuman
primate. However, research has revealed substantial differences
in the size, spatial layout, and responsiveness between human
and nonhuman primate extrastriate maps (e.g., V3, hV4, V3A/
B, and VO-1). These findings have been reviewed recently, and
we refer the reader to these reviews to learn more about this
work (Silver & Kastner, 2009; Wandell, Dumoulin, & Brewer,
2007; Wandell & Winawer, 2011).
Stimulus-Referred Measurements
It is worthwhile to step back and consider what exactly is measured when a visual field map is defined: the map specifies which
stimulus position most effectively drives the response at each
cortical location. Thus, the map characterizes cortex in terms of
the stimulus. Such stimulus-referred (also called input-referred)
descriptions of neural responses play a key role in vision science.
The great majority of visual neuroscience measurements use a
stimulus-referred approach to characterize neural responses.
Receptive field (RF) measurement is a classic and particularly clear example (Hartline, 1938). Suppose one measures
the response of a V1 neuron to a small spot presented at
different locations in the visual field. The cell will respond
when the spot is within a small region of the visual field, and
this region is called the RF. Note that the RF is a description of
the stimulus properties (locations) that evoke a response.
There is no description of the proximal inputs to the cell
lateral geniculate neurons, other V1 neurons, feedback signals
from extrastriate cortex, and inputs received from the pulvinar.
Stimulus-referred descriptions are a theoretical construct; a V1
neuron lives and dies in the dark, never being directly stimulated by photons. In describing the RF of a cell, the optical
components of the eye and the extensive neural and glial
network that give rise to the RF are not explicitly characterized.
Stimulus-referred descriptions can be applied to many
properties in addition to visual field position, such as orientation, direction, and wavelength (Wandell, 1995). Stimulusreferred measurements summarize neural circuit responses
without requiring the construction of a circuit model. This
capability is important because such circuit models are presently beyond the reach of neuroscience methods.
Perhaps the most valuable aspect of stimulus-referred measurement is that it supports the coordination of insights from
many parts of vision science including optics, retinal processing, cortical circuitry, local field potentials, scalp recordings,
and perception. Integration across these measures is challenging because each samples the nervous system in its own way
and produces outputs with different units. For example, microelectrodes measure voltages or spike rates, calcium imaging
measures photons, fMRI measures modulation in blood oxygenation, and perception measures subject reports. The stimulus is a unifying framework for vision science; the stimulus
representation serves as a common ground where results
from very different measures are compared.
The use of stimulus-referred measurements is very common
in vision science, just as input-referred measurements are very
common in engineering (Wandell, 1995). They are so ubiquitous
that the beauty and value of the approach is rarely taught. One
objective of this article is to make the idea and its value explicit.
653
Population RF Models
The success in the parcellation of visual cortex into maps provides a foundation for a new phase of investigation: building
computational models of fMRI responses to visual stimuli. The
goal of this work is to precisely express and test neural processing principles. Stimulus-referred computational models offer
the best hope for coordinating different types of visual measures into a unified theory. This new phase of modeling could
not take place without the first phase. Response properties
differ across maps; interpreting a set of measurements is difficult unless one knows which map is the source of the
measurements.
In an early step toward theory, Tootell et al. (1997) observed
that reducing the width of a contrast pattern, such as an expanding ring contrast pattern, substantially reduced the duration of
the V1 on-response but had little effect on the V3A on-response.
They explained the difference by the hypothesis that V3A receptive fields cover more of the visual field than V1 receptive fields.
Qualitatively, the on-response in V1 was governed by the stimulus width but in V3A the on-response was governed by the RF
width. Smith, Singh, Williams, and Greenlee (2001) systematically investigated this idea, quantifying the proportion of the
time that the fMRI response is elevated compared to baseline
(the duty cycle) as thin rings or wedges traversed the visual field.
The duty cycle differed substantially between cortical locations,
and they explained these differences in terms of the size of the
RF of neurons in each cortical location.
Construction of a Linear Population RF Model

Dumoulin and Wandell (2008) built upon the prior work in
several ways. First, they defined an explicit computational
model to predict the fMRI response at each voxel. The key
element of the model was the concept of the population RF
(pRF), named by Victor, Purpura, Katz, and Mao (1994) who
used the approach in local field potential measurements in
macaque. The pRF summarizes the collective RFs of all the
cells giving rise to the response within a voxel.
The initial models approximated the pRF by a twodimensional Gaussian, characterized by a center position,
(x,y), and spread (s). These parameters are specified in the
visual field relative to the gaze location (fixation). By using a
stimulus-referred description, Smith et al. (2001) and
Dumoulin and Wandell (2008) were able to compare fMRI
measurements with data obtained using other brain measurement methods. For example, the pRF spread measured using
fMRI could be plotted against the single-unit RF size measured
using macaque electrophysiology.
Second, Dumoulin and Wandell implemented a computational model of the fMRI time series. A model of the fMRI
time series is possible in visual cortex because the response
amplitude in individual subjects is large and there is no
need to average across subjects. Implementing a full model
provides the investigator with an opportunity to predict
fMRI time series to different types of stimuli. Dumoulin and
Wandell took advantage of the model implementation to
measure maps using a new type of stimulus. The model also
made possible the quantification of a new stimulus feature
(pRF size) within maps.
654
pRF profile
8
Coods: [163 267 154]

Variance explained: 64.32%
y (deg)
x = 2.5, y = 0.1 ()
r = 2.5 , theta= 269

Sigma = 0.5
Beta = 9.4% /sec
8
4
0
x ()
5
0
5
0
24
48
72
96
Time (s)
120
144
168
192
pRF profile
V2
y ()
Coods: [153 269 154]

4
0
r = 3.7, theta= 87
Sigma = 1.2

x = 6.5, y = 0.7 ()
r = 6.5, theta= 84
Sigma = 5.0
Beta = 4.5% /sec
Beta = 0.8% /sec
8
15
0
x ()
8
BOLD Signal (%)
8
BOLD Signal (%)
Coods: [123 261 157]
x = 3.7, y = 0.2 ()
10
5
0
5
0
pRF profile
V3A
y (deg)
BOLD Signal (%)
24
48
72
96
Time (s)
120
144
168
192
0
x ()
48
72
10
0
10
0
24
96
Time (s)
120
144
168
192
Figure 2 A tool to analyze the population receptive field (pRF). The fMRI time series were measured with a 7 Tesla scanner at a resolution of 1 mm3
voxels. The stimulus was a contrast pattern within a slowly translating bar aperture. The aperture swept through the visual field at different angles;
occasionally the contrast pattern was turned off. The three plots show the fMRI signal measured at voxels located in three different locations
(white circles in V1, V2, and V3A; upper right image). The dashed black lines are measurements and the solid blue lines are pRF model fits. The estimated
pRF for each voxel is shown in the image panels. The three time series responses to the same pattern differ in timing and width. This time series
difference is modeled by the center position and size of the pRF. The tool is part of the open source vistasoft package (http://github.com/vistalab). Data
obtained in collaboration with E. Yacoub and K. Ugurbil.
Figure 2 shows a pRF analysis tool, implemented by Rory

Sayres, that several groups have used to examine and interpret
fMRI time series. The three panels show responses and analyses
for voxels in V1, V2, and V3A. The stimulus was a set of
oriented bars that moved slowly across the visual field along
eight different trajectories. Occasionally, the bars were
removed so that the observer simply viewed a zero contrast
field (Dumoulin & Wandell, 2008). The estimated pRF and the
predicted and measured time series responses are shown for
each voxel. Plainly, the predicted time series are in good agreement with the measurements. The estimated pRF sizes differ
substantially across maps, confirming the prior work.
What Does a pRF Measure?

Human cortex contains 50 000 neurons per mm3 so that a
typical 2 mm isotropic voxel contains about 400 000 neurons
(Braitenberg & Schuz, 1998); the 1 mm isotropic voxels
depicted in Figure 2 contain about 50 000 neurons each. A

subset of these neurons, as well as the local glial cells, respond
to any given stimulus, and it is this population response that
determines the voxels RF. Furthermore, pRF parameters will
depend on the specific population of neurons stimulated by
the pattern that defines the texture within the moving bar.
Features such as the temporal frequency, wavelength composition, and so on may excite different populations and influence
the pRF parameters.
The RF measured using single-unit physiology has a related
theoretical status. Each neuron in V1 is contacted by about
10 000 other neurons, and cells in their neighborhood in
turn contact these neurons. When a small point is presented
in the visual field, voltage sensitive dye measurements show
that activity in the superficial layers of cortex spreads over a
distance of several millimeters, commensurate with the size
of an fMRI voxel (Grinvald, Lieke, Frostig, & Hildesheim,
1994). Hence, the RF measured in a single V1 cell in layers 2/
3 reflects the pooled activity of its inputs and its role in the
neural circuit.
The principal difference between the single-unit RF and the
pRF is that RF measurements tap into circuit activity at a single
point within the neural plexus, while the pRF is a mean-field
measurement of the circuit activity. The key limitation of
mean-field fMRI measurements is obvious spatial resolution.
However, an advantage is that fMRI measurements provide a
much larger field of view and can reveal coordinated activity in
remote sites. The fMRI measurement is also sensitive to signals
that are missed by single unit RF measurements. In some cases
where BOLD and single unit measurements diverge, the BOLD
signal correlates best with perceptual judgments (Maier et al.,
2008). The BOLD signal is also sensitive to glial responses
(Schulz et al., 2012), a cell class often neglected in electrophysiological measurements in animals. Finally, fMRI provides
direct information about human, while single-unit physiology
is carried out in animal models whose circuits may differ.
The pRF framework has been applied usefully in a number
of studies. For example, the framework has been used to clarify
certain visual field maps (Amano, Wandell, & Dumoulin,
2009; Arcaro et al., 2009; Winawer et al., 2010) and to compare pRF sizes between controls and subjects with neurological
conditions (Hoffmann et al., 2012; Levin, Dumoulin, Winawer,
Dougherty, & Wandell, 2010). The method has been applied
to measure plasticity (Brewer, Barton, & Lin, 2012) and the effect
of task-demands (de Haas, Schwarzkopf, Anderson, & Rees,
2013). It has been used in fMRI studies of visual cortex in animal
models (Shao et al., 2013; Smirnakis, Keliris, Shao, Papanikolaou, & Logothetis, 2012) and to elucidate the relationship with
655
anatomy (Benson, Butt, Jain, Brainard, & Aguirre, 2013). Finally,

the pRF framework has been used as a means for decoding the
contents of visual cortical activity (Kay, Naselaris, Prenger, &
Gallant, 2008; Nishimoto, Vu, Naselaris, Benjamini, Yu, &
Gallant, 2011).
Improving the Linear pRF Model

It is a truism that all models are wrong, but some are useful
(Box & Draper, 1987). The first pRF models are useful, but
they are inaccurate in several ways. Our group and others
continue to work to identify and reduce the model deficiencies
(Alvarez, De Haas, Clark, Rees, & Schwarzkopf, 2013; Binda,
Thomas, Boynton, & Fine, 2013; Zuiderbaan, Harvey, &
Dumoulin, 2012).
The failures become apparent when we use the pRF model
to predict the fMRI time series response to a larger range of
visual stimuli. Returning to the original measurements by
Tootell et al. (1997), Winawer set out to use the pRF model
to predict responses to both thin and thick bars. It became
apparent that the Dumoulin and Wandell pRF model could
not account for even such a modest increase in the range of
stimuli.
Kay, Winawer, Mezer, and Wandell (2013a) show that the
failure arises from a basic assumption: linear summation of
contrast across the spatial RF. The failure of spatial linearity can
be measured in a simple experiment (Figure 3). Consider a
voxel that responds to contrast near the horizontal midline. We
can present a stimulus that fills either the upper half of the pRF
or the lower half. If spatial linearity holds, the response to a
Figure 3 Spatial summation of contrast fails to predict the fMRI signal in human visual cortex. The upper bar plots show the measured responses
to a lower field stimulus, an upper field stimulus, and the combination of the two. For the voxel in V1 (upper left) and V3 (upper right), the
response to the full aperture is less than the sum of the responses to the two partial apertures, and hence less than the linear prediction (indicated by
the black lines). The failure of linearity is more severe for V3 than for V1. The lower images show the 2-s circle for the pRF for the two voxels
(dark line V1; light line V3). Reproduced from Kay, K., Winawer, J., Mezer, A., & Wandell, B. A. (2013). Compressive spatial summation in human visual
cortex. Journal of Neurophysiology, 110, 481494.
656
stimulus that fills both the upper and lower portions of the pRF
should equal the sum of the responses to upper and lower
separately. This spatial summation prediction is somewhat
inaccurate in the posterior maps, V1 and V2, and it misses
substantially in anterior extrastriate maps (Kay et al., 2013a).
Kay et al. showed that incorporating a static nonlinearity into
the standard pRF model remedies the failure of spatial linearity. Furthermore, Kay et al. showed that the specific form of the
nonlinearity fit to the BOLD signal is compatible with existing
models of single neuron spike rates, such as divisive normalization (Carandini & Heeger, 2012).
Connecting these two very different kinds of measurements, fMRI and single unit spiking, is possible because
stimulus-referred models are fit in both domains. It is tempting
to think of divisive normalization as a circuit model rather
than a stimulus-referred model because there has been substantial work trying to explain normalization in terms of circuit
properties such as shunting inhibition, resistance, and capacitance (Ferster, 2010). But in fact divisive normalization model
parameters are specified in the stimulus domain, including
contrast and orientation, and the circuits giving rise to normalization are largely unknown (Carandini & Heeger, 2012). Normalization, like linear filtering, is an application of the
stimulus-referred approach.
In a separate study, Kay, Winawer, Rokem, Mezer, &
Wandell (2013b) further extended the modeling effort by
developing a new pRF model that accounts for measurements
of responses to an even wider range of stimuli. The new model
is also distributed as a full computation (http://kendrickkay.
net/socmodel/). This model is much more complex than the
Dumoulin and Wandell formulation, allowing it to predict the
responses to a much wider range of stimuli.
Integration of fMRI and ECoG Data

There has been remarkable progress in inventing new ways to
measure neural signals. Modern methods range from wellisolated single units to local field potentials, calcium imaging,
voltage sensitive dyes, and intrinsic functional measures such
as fMRI. These methods provide different types of information
about neural circuitry, and there is much to be gained by
understanding how to combine insights from different
methods (Goense & Logothetis, 2008; Mukamel et al., 2005;
Niessing et al., 2005).
The stimulus-referred measurement approach integrates the
diverse measures made by visual neuroscientists. In a recent
study we measured pRFs using both ECoG and fMRI, and we
asked whether the two data sets might be explained by the
same pRF model (Winawer et al., 2013). The ECoG data are a
voltage time series captured at millisecond resolution, while
the fMRI signal is a modulation in the local oxygenation sampled every second or two. By using stimulus-referred measurements, we can compare the measurements in a common
reference frame, bypassing the problem of incommensurate
units.
There were several straightforward findings (Figure 4). First,
the ECoG signal contains responses from at least two neural
sources, broadband and stimulus-locked, and we created accurate pRF models of each response component. Second, the RF
position and size derived from the ECoG and the fMRI
responses agreed. Third, the spatial summation properties of
broadband, but not stimulus-locked, ECoG signals match the
spatial summation measured in the fMRI signal. From this
stimulus-referred analysis we concluded that the fMRI signal
arises principally from the broadband ECoG component.
Discussion
As computational models of vision increase in accuracy and
power (i.e., account for a larger range of stimuli), they become
more complex. The original Tootell et al. and Smith et al.
papers could reason correctly and informally about RF sizes.
But they accounted for very few stimuli and relied on summary
measures of the response time series. Modern computational
models that account for a much larger range of stimuli and
predict the full time series are significantly more complex
(Figure 5). These models are not captured in a small set of
formulae, and it is necessary to use software implementations
to generate predictions.
Computational modeling is a cumulative process that
expands the domain of application by accounting for an
increasing range of experimental conditions. This differs from
experimental work focused on hypothesis testing. Computational models are built by testing new features while always
checking for the impact of the new features on previous predictions; new data are not viewed as a hypothesis test that
results in accepting or rejecting the model by a statistical test.
Rather, computational model development is a process that
yields increasingly refined predictions from a sustained effort;
we believe this is one of its great benefits.
Finally, we note that even if a computational model is
imperfect, it can still be useful. For example, it is reasonable
to use linear pRF models to estimate RF center positions when
using a single bar width, even though the model does not
generalize to multiple bar widths. The use of a model that is
adequate for a given objective is common in other branches of
science and engineering. After all, we do not calculate local
travel time using relativity and the Earths curvature.
Which Brain Measurements Are Best?

We have emphasized the value of stimulus-referred models for
integrating data from different types of measurements. We are
aware that an alternative scientific approach is to deny the
validity of all but one measure:
Any analysis of plastic reorganization at a neuronal locus needs a
veridical measure of changes in the functional output that is,
spiking responses of the neurons in question.
Calford, M. B., et al. (2005). Neuroscience: rewiring the adult
brain. Nature, 438(7065): E3; discussion E3-4.
We think it is best to be open to the value of many measurement methods. In fact, we dont think there is a strong
alternative to this approach because it is illusory to think that
even within a measurement domain the signals form a single,
unitary class. For example, in the retina, the same stimulus
produces different responses in different cell types, such as
657
Figure 4 Stimulus-referred models integrate different measurement modalities. (a) A stimulus-referred pRF model (Kay, Winawer, Mezer, & Wandell,
2013) was applied to V1, V2, and V3 responses from retinotopic stimuli. Measurements were obtained using both ECoG and fMRI, and we further
separated the ECoG signal into two components an asynchronous broadband signal that measured a stimulus-driven increase in response variance,
and a stimulus-locked response that modulated in synchrony with each contrast reversal. The CSS model fit the measured time series of all three
signals. (b) The estimated pRF centers to the two types of ECoG are similar (filled and open symbols; lines connect estimates from a single electrode).
These pRF centers also match the fMRI estimates (not shown). (c) The estimated spatial summation exponent, n, from the pRF model is highly
compressive (n < 1) for fMRI and for ECoG broadband responses. The exponent is close to linear (n 1) for the stimulus-locked response. Hence, fMRI
spatial summation matches broadband ECoG, but not stimulus-locked ECoG. Reproduced from Winawer J., et al. (2013). Asynchronous broadband
signals are the principal source of the BOLD response in human visual cortex. Current Biology, 23, 11451153. See also Harvey et al. (2013) for a
stimulus-referred approach to understanding the relationship between ECoG and fMRI pRF measurements.
Figure 5 A modern computational model of fMRI signals in visual cortex. The model developed by Kay et al. integrates an array of widely used
visual neuroscience computations (energy, divisive normalization, spatial summation, second-order contrast, and compressive nonlinearity). These
operations are organized into two stages of sequential linear, nonlinear, nonlinear (LNN) operations. To develop models of this complexity which are
surely much simpler than what will ultimately be required requires software implementations and the ability to test different forms of the model
on multiple classes of stimuli. Reproduced from Kay, K. N., Winawer, J., Rokem, A., Mezer, A., & Wandell, B.A. (2013). A two-stage cascade model of
BOLD responses in human visual cortex. PLoS Computational Biology, 9(5), e1003079.
658
Neural measures
Single unit action potentials,
MUA
EcoG, EEG, LFP, MEG
BOLD, Optical imaging
Voltage sensitive dyes
Calcium imaging
Neurons, glia and

circuits
Stimulus
Neurons, glia and

circuits
Neurons, glia and
circuits
Perceptual measures
Sensitivity, discrimination, response time,
similarity, appearance
Figure 6 An integrative view of modeling visual brain function. Computational models of visual neuroscience must take a broad view that spans
the stimulus, brain systems, and perceptual measures. Because visual responses arise from a well-characterized physical stimulus, we can use
stimulus-referred theories to integrate information from many measurement modalities and better understand many aspects of brain circuits.
retinal ganglion cells of the parasol and midget classes. The

voltage response in the ECoG signal arises from multiple
sources with distinct properties. In cortex some spikes are
relevant for only local calculations, while others are communicated by long-range projections to other cortical regions.
Thus, it is incorrect to expect that the fMRI response or a
perceptual judgment will match spiking responses when
there are so many different types of neurons and so many
different types of spikes.
Further, the modern neuroscientist should consider the
likelihood that cortical function depends importantly on several types of cells. There are many reasons to believe that
responses in other brain cells, such as the many types of glia
present in the human brain, are important for brain function
(Bullock et al., 2005). If the fMRI signal informs us about these
responses as well as neuronal responses, should we complain?
Or should we be grateful to have this additional information?
We advocate for an integrative view of the visual system
(Figure 6). We suggest that a goal of visual neuroscience would
be to develop models that begin with a careful description of
the stimulus, integrate experimental observations derived from
multiple measures of brain activity and circuitry, model these
multiple types of responses, and characterize the relationship
between certain brain responses and perception.

INTRODUCTION TO ANATOMY AND PHYSIOLOGY: Functional
Organization of the Primary Visual Cortex; Topographic Layout of
Monkey Extrastriate Visual Cortex; INTRODUCTION TO SOCIAL
COGNITIVE NEUROSCIENCE: Action Perception and the Decoding
of Complex Behavior; INTRODUCTION TO SYSTEMS: Face
Perception; Visuomotor Integration.
References
Alvarez, I., De Haas, B., Clark, C. A., Rees, G., & Schwarzkopf, D. S. (2013). Optimal
stimulation for population receptive field mapping in human fMRI. Journal of
Vision, 13(9), 31.
Amano, K., Wandell, B. A., & Dumoulin, S. O. (2009). Visual field maps, population
receptive field sizes, and visual field coverage in the human MT complex. Journal
of Neurophysiology, 102(5), 27042718.
Arcaro, M. J., McMains, S. A., Singer, B. D., & Kastner, S. (2009). Retinotopic
organization of human ventral visual cortex. The Journal of Neuroscience, 29(34),
1063810652.
Benson, N. C., Butt, O. H., Jain, S., Brainard, D. H., & Aguirre, G. K. (2013). Cortical surface
structure predicts extrastriate retinotopic function. Journal of Vision, 13(9), 271.
Binda, P., Thomas, J. M., Boynton, G. M., & Fine, I. (2013). Minimizing biases in
estimating the reorganization of human visual areas with BOLD retinotopic mapping.
Journal of Vision, 13(7), 13.
Box, G., & Draper, N. (1987). Empirical model-building and response surfaces.
New York: Wiley.
Braitenberg, V., & Schuz, A. (1998). Cortex: Statistics and geometry of neuronal
connectivity (2nd ed.). Heidelberg: Springer-Verlag.
Brewer, A. A., Barton, B., & Lin, L. (2012). Functional plasticity in human parietal
visual field map clusters: Adapting to reversed visual input. Journal of Vision,
12(9), 1398.
Bullock, T. H., et al. (2005). Neuroscience. The neuron doctrine, redux. Science,
310(5749), 791793.
Calford, M. B., et al. (2005). Neuroscience: Rewiring the adult brain. Nature, 438(7065),
E3, discussion E34.
Carandini, M., & Heeger, D. J. (2012). Normalization as a canonical neural
computation. Nature Reviews. Neuroscience, 13(1), 5162.
de Haas, B., Schwarzkopf, D. S., Anderson, E. J., & Rees, G. (2013). Effects of
perceptual load on population receptive fields. Journal of Vision, 13(9), 290.
Dechent, P., & Frahm, J. (2003). Characterization of the human visual V6 complex by
functional magnetic resonance imaging. The European Journal of Neuroscience,
17(10), 22012211.
DeYoe, E. A., Bandettini, P., Neitz, J., Miller, D., & Winans, P. (1994). Functional
magnetic resonance imaging (FMRI) of the human brain. Journal of Neuroscience
Methods, 54(2), 171187.
DeYoe, E. A., et al. (1996). Mapping striate and extrastriate visual areas in human
cerebral cortex. Proceedings of the National Academy of Sciences of the United
Dumoulin, S. O., & Wandell, B. A. (2008). Population receptive field estimates in human
visual cortex. NeuroImage, 39(2), 647660.
visual cortex and the spatial precision of functional MRI. Cerebral Cortex, 7(2),
181192.
Engel, S. A., et al. (1994). fMRI of human visual cortex. Nature, 369(6481), 525.
Felleman, D. J., & Essen, D. C.V (1991). Distributed hierarchical processing in the
Ferster, D. (2010). Diverse mechanisms of contrast normalization in primary visual
cortex. Journal of Vision, 10(15), 29.
Goense, J., & Logothetis, N. K. (2008). Neurophysiology of the BOLD fMRI signal in
awake monkeys. Current Biology, 18(9), 631640.
Grinvald, A., Lieke, E. E., Frostig, R. D., & Hildesheim, R. (1994). Cortical point-spread
function and long-range lateral interactions revealed by real-time optical imaging of
macaque monkey primary visual cortex. The Journal of Neuroscience, 14,
25452568.
Hartline, H. K. (1938). The response of single optic nerve fibers of the vertebrate
eye to illumination of the retina. The American Journal of Physiology, 121,
400415.
Harvey, B. M., et al. (2013). Frequency specific spatial interactions in human
electrocorticography: V1 alpha oscillations reflect surround suppression.
Henschen, S. E. (1893). On the visual path and centre. Brain, 16, 170180.
Hoffmann, M. B., et al. (2012). Plasticity and stability of the visual system in human
achiasma. Neuron, 75(3), 393401.
Holmes, G. (1918). Disturbances of vision by cerebral lesions. British Journal of
Ophthalmology, 2, 353384.
Holmes, G., & Lister, W. T. (1916). Disturbances of vision from cerebral lesions, with
special reference to the cortical representation of thc macula. Brain, 39, 3473.
Horton, J. C., & Hoyt, W. F. (1991a). Quadrantic visual field defects: A hallmark of
lesions in extrastriate (V2/V3) cortex. Brain, 114, 17031718.
Horton, J. C., & Hoyt, W. F. (1991b). The representation of the visual field in human
striate cortex. A revision of the classic Holmes map. Archives of Ophthalmology,
109(6), 816824.
Hubel, D. H., & Wiesel, T. N. (1977). Ferrier lecture. Functional architecture of macaque
monkey visual cortex. Proceedings of the Royal Society of London. Series B:
Biological Sciences, 198(1130), 159.
Inouye, T. (1909). Die Sehstorungen bei Schussverletzungen der kortikalen Sehsphare.
Leipzig, Germany: W. Engelmann.
Kay, K. N., Naselaris, T., Prenger, R. J., & Gallant, J. L. (2008). Identifying natural
images from human brain activity. Nature, 452, 352355.
Kay, K., Winawer, J., Mezer, A., & Wandell, B. A. (2013). Compressive spatial
summation in human visual cortex. Journal of Neurophysiology, 110, 481494.
Kay, K. N., Winawer, J., Rokem, A., Mezer, A., & Wandell, B. A. (2013). A two-stage
cascade model of BOLD responses in human visual cortex. PLoS Computational
Biology, 9(5), e1003079.
Kolster, H., Peeters, R., & Orban, G. A. (2010). The retinotopic organization of the
human middle temporal area MT/V5 and its cortical neighbors. The Journal of
Neuroscience, 30(29), 98019820.
Konen, C. S., & Kastner, S. (2008). Representation of eye movements and stimulus
motion in topographically organized areas of human posterior parietal cortex. The
Kwong, K. K., et al. (1992). Dynamic magnetic resonance imaging of human brain
Levin, N., Dumoulin, S. O., Winawer, J., Dougherty, R. F., & Wandell, B. A. (2010).
Cortical maps and white matter tracts following long period of visual deprivation and
retinal image restoration. Neuron, 65(1), 2131.
659
Maier, A., et al. (2008). Divergence of fMRI and neural signals in V1 during
perceptual suppression in the awake monkey. Nature Neuroscience, 11(10),
11931200.
Mukamel, R., et al. (2005). Coupling between neuronal firing, field potentials, and FMRI
in human auditory cortex. Science, 309(5736), 951954.
Munk, H. (1881). On the functions of the cortex. In G. Von Bonin (Ed.), The Cerebral
Cortex (pp. 97117). Springfield, Illinois: Charles C. Thomas.
Niessing, J., et al. (2005). Hemodynamic signals correlate tightly with synchronized
gamma oscillations. Science, 309(5736), 948951.
Nishimoto, S., Vu, A. T., Naselaris, T., Benjamini, Y., Yu, B., & Gallant, J. L. (2011).
Reconstructing visual experiences from brain activity evoked by natural movies.
Current Biology, 21, 16411646.
Ogawa, S., et al. (1992). Intrinsic signal changes accompanying sensory stimulation:
Functional brain mapping with magnetic resonance imaging. Proceedings of the
Phillips, C. G., Zeki, S., & Barlow, H. B. (1984). Localization of function in the cerebral
cortex. Past, present and future. Brain, 107(Pt 1), 327361.
Schulz, K., et al. (2012). Simultaneous BOLD fMRI and fiber-optic calcium recording in
rat neocortex. Nature Methods, 9(6), 597602.
Sereno, M. I., Pitzalis, S., & Martinez, A. (2001). Mapping of contralateral space in
retinotopic coordinates by a parietal cortical area in humans. Science, 294(5545),
13501354.
Sereno, M. I., et al. (1995). Borders of multiple human visual areas in humans revealed
by functional MRI. Science, 268, 889893.
Shao, Y., et al. (2013). Visual cortex organisation in a macaque monkey with macular
degeneration. European Journal of Neuroscience, 38, 34563464.
Silver, M. A., & Kastner, S. (2009). Topographic maps in human frontal and parietal
cortex. Trends in Cognitive Sciences, 13(11), 488495.
Smirnakis, S. M., Keliris, G., Shao, Y., Papanikolaou, A., & Logothetis, N. (2012).
Population receptive field measurements in macaque visual cortex. Journal of
Vision, 12(9), 1397.
Smith, A. T., Singh, K. D., Williams, A. L., & Greenlee, M. W. (2001). Estimating
receptive field size from fMRI data in human striate and extrastriate visual cortex.
Cerebral Cortex, 11(12), 11821190.
Tootell, R. B., et al. (1997). Functional analysis of V3A and related areas in human
visual cortex. The Journal of Neuroscience, 17(18), 70607078.
Victor, J. D., Purpura, K., Katz, E., & Mao, B. (1994). Population encoding of spatial
frequency, orientation, and color in macaque V1. Journal of Neurophysiology,
72(5), 21512166.
Wandell, B. A. (1995). Foundations of vision. Sunderland, MA: Sinauer Press.
Wandell, B. A., Dumoulin, S. O., & Brewer, A. A. (2007). Visual field maps in human
cortex. Neuron, 56(2), 366383.
Wandell, B. A., Dumoulin, S. O., & Brewer, A. A. (2009). Visual cortex in humans. In L.
Squire (Ed.), Encyclopedia of neuroscience. New York: Elsevier.
Wandell, B. A., & Winawer, J. (2011). Imaging retinotopic maps in the human brain.
Vision Research, 51(7), 718737.
Warnking, J., et al. (2002). fMRI retinotopic mapping step by step. NeuroImage,
17(4), 16651683.
Winawer, J., Horiguchi, H., Sayres, R. A., Amano, K., & Wandell, B. A. (2010).
Mapping hV4 and ventral occipital cortex: The venous eclipse. Journal of Vision,
10, 1.
Winawer, J., et al. (2013). Asynchronous broadband signals are the principal
source of the BOLD response in human visual cortex. Current Biology, 23,
11451153.
Zeki, S. (1993). A vision of the brain. London: Blackwell Scientific Publications.
Zuiderbaan, W., Harvey, B. M., & Dumoulin, S. O. (2012). Modeling centersurround configurations in population receptive fields using fMRI. Journal of
Vision, 12(3), 10.
Meta-Analyses in Functional Neuroimaging

MA Lindquist, Johns Hopkins University, Baltimore, MD, USA
TD Wager, University of Colorado at Boulder, Boulder, CO, USA
Glossary
Coordinate-based meta-analysis A meta-analysis

performed using the spatial locations of peaks of activation,
reported in a standard coordinate system, across multiple
neuroimaging studies.
Meta-analysis The statistical analysis of multiple separate
but similar studies with the goal of testing the combined
data for statistical significance.
Introduction
In recent years, there has been an explosive growth in both the
number and variety of neuroimaging studies being performed
around the world. This is illustrated in Figure 1, which shows
the rapid increase in the yearly number of publications related
to functional magnetic resonance imaging (fMRI) since 1993.
With this growing body of knowledge comes a need to both
integrate and synthesize research findings. Performing metaanalyses has arguably become the primary research tool for
accomplishing this goal (Wager, Lindquist, & Kaplan, 2007;
Wager, Lindquist, Nichols, Kober, & Van Snellenberg, 2009).
They allow for the pooling of multiple separate but similar
studies and can be used to evaluate the consistency of findings
across labs, scanning procedures, and task variants, as well as
the specificity of findings in different brain regions or networks
to particular task types. Meta-analyses have already been used
to study many types of psychological processes, including cognitive control, working memory, decision-making, language,
pain, and emotion (Laird et al., 2005; Phan, Wager, Taylor, &
Liberzon, 2002; Wager, Jonides, & Reading, 2004). They have
also been used to summarize structural and functional brain
correlates of disorders such as attention deficit disorder,
schizophrenia, depression, chronic pain, anxiety disorders,
and obsessivecompulsive disorder (Dickstein, Bannon, Xavier
Castellanos, & Milham, 2006; Etkin & Wager, 2007; Glahn
et al., 2005; Menzies et al., 2008).
To date, the primary goal of meta-analyses has been to
provide summaries of the consistency of regional brain activation for a set of studies of a particular task type, thereby
providing a consensus regarding which regions are likely to
be truly activated by a given task (see Figure 2 for an
illustration). Evaluating consistency across studies is critical
because false-positive rates in neuroimaging are likely to be
significantly higher than in many other fields. In previous
work, we estimated the false-positive rates to lie somewhere
between 10% and 40% (Wager et al., 2009). These inflated
false-positive rates are a by-product of poor control for multiple comparisons combined with the small sample sizes typically used in neuroimaging studies. Though these rates may be
decreasing over time as sample sizes increase and more
Monte Carlo methods A class of computational algorithms

that use repeated re-sampling of the available data to obtain
numerical results.
Ontology A representation of a domain of knowledge.
Reverse inference Using observed brain activity to infer a
particular cognitive process not directly tested, drawing on
other research implicating that brain area with that cognitive
process.
rigorous statistical thresholding procedures are becoming

more common (Woo, Krishnan, & Wager, 2014), it remains
important to assess which findings have been replicated and
have a higher probability of being true activations.
The goals of meta-analysis can be extended beyond regional
activation to also identify groups of consistently coactivated
regions that may form spatially distributed functional networks in the brain (Kober et al., 2008). If two regions are
coactivated, then studies that activate one region are more
likely to activate the other. Thus, the analysis of coactivation
can be viewed as a meta-analytic analogue to functional connectivity, which can provide the basis for testing them as units
of analysis in individual studies and lead to the development
of testable hypotheses about functional connectivity in specific
tasks.
Evaluating the specificity of activation patterns for particular psychological processes is also important in order to understand whether a particular brain region is unique to a certain
psychological domain or whether it is shared by a larger set of
cognitive processes. For example, this is critical for determining
whether activity in some region implies the involvement of a
given psychological process (so-called reverse inference;
Poldrack, 2006; Yarkoni, Poldrack, Nichols, Van Essen, &
Wager, 2011). Specificity can only be examined across a
range of tested alternative tasks. However, different psychological domains are typically studied in isolation, and it is nearly
impossible to compare a wide range of tasks within the scope
of a single study. However, meta-analytic activation patterns
can be compared across the entire range of tasks studied using
neuroimaging techniques, providing a unique way to evaluate
activation specificity across functional domains.
Meta-Analytic Data
In an ideal setting, meta-analysis would be performed using
the full statistical maps made available from each study and fit
using a mixed-effects model that aggregates the effect size at
each individual voxel. However, in practice, this information is
not readably available from individual studies. There has been
some movement toward creating such databases, and the
http://dx.doi.org/10.1016/B978-0-12-397025-1.00348-1
661
662
INTRODUCTION TO METHODS AND MODELING | Meta-Analyses in Functional Neuroimaging
The growth of fMRI

3500
Number of publications
3000
2500
2000
1500
1000
500
0
1995
2000
2005
Publication year
2010
Figure 1 A graph showing the rapid increase in the number of publications that mention the term fMRI in either the title or abstract for the years
19932013 according to PubMed.
Reported peaks
Meta-analysis
results
performing large-scale, automated synthesis of neuroimaging

data extracted from published articles.
Meta-Analytic Methods
Figure 2 (Left) Peak activation coordinates from 163 studies on

emotion. (Right) A summary of consistently activated regions computed
using MKDA analysis.
increased availability of such data promises to fundamentally

change the manner in which meta-analysis is performed. However, in practice, individual imaging studies often use very
different analyses, and effect sizes are only reported for a
small number of activated locations, making combined
effect-size maps across the brain impossible to reconstruct
from published reports.
Instead, coordinate-based meta-analysis is typically performed using the spatial locations of peaks of activation
(peak coordinates), reported in the standard coordinate systems of the Montreal Neurological Institute (MNI) and combined across studies. Figure 2 (left) shows the reported peaks
from 163 studies of emotion. This information is typically
provided in most neuroimaging papers, and in early work,
peak coordinates were manually harvested from articles.
Today, there exist electronic databases, such as BrainMap
(Fox & Lancaster, 2002) and Neurosynth (Yarkoni et al.,
2011), of published functional and structural neuroimaging
experiments with coordinate-based results reported in MNI
space. Both databases are easily searchable by paradigm, cognitive domain, region of interest, and anatomical labels. While
the papers are added manually to BrainMap, Neurosynth uses
text mining algorithms to automatically harvest peak coordinates from journal articles and provides a platform for
A typical neuroimaging meta-analysis studies the locations of

peak activations from a large number of studies and seeks to
identify regions of consistent activation in a set of studies that
use a particular task or are related to the same psychological state
(see Figure 2). Meta-analytic methods that have been proposed
include combining effect-size data (Van Snellenberg, Torres, &
Thornton, 2006), analyzing the frequencies of reported peaks
within anatomically defined regions of interest (Phan et al.,
2002), performing cluster analyses (Northoff et al., 2006;
Wager et al., 2004) and using various Bayesian methods
(Kang, Johnson, Nichols, & Wager, 2011; Yue, Lindquist, &
Loh, 2012). However, the most popular approaches toward
performing meta-analysis on functional neuroimaging data are
the so-called kernel-based methods. These include activation
likelihood estimation (ALE; Turkeltaub, Eden, Jones, & Zeffiro,
2002) and kernel density approximation (KDA; Wager et al.,
2004), as well as their extensions modified ALE (modALE;
Eickhoff et al., 2009) and multilevel KDA (MKDA; Wager
et al., 2007). Though the current standards in the field are
MKDA and modALE, we begin by discussing their precursors
for historical reasons.
Kernel-Based Methods
In ALE and KDA, the peak coordinates are the basic units of
analyses. Both methods measure consistency by counting the
number of peak activations in each voxel, convolving the
results with a kernel, and comparing the number of observed
peaks to a null-hypothesis distribution (see Figure 3 for an
illustration). In KDA, the kernel is spherical with radius r, and
the resulting maps are interpreted as the number of peaks
Study-specific Peak coordinates

across studies
peaks
Kernel convolution
Peak density or
ALE map
663
Significant results
Density kernel
1
0
1
1
1 1
OR
ALE kernel
1
0
1
1
1 1
Figure 3 Example of meta-analysis using KDA or ALE on three studies. The three small maps on the left show peaks reported in each study for a
representative axial brain slice. Peaks are combined across studies and the resulting map is smoothed with either a spherical kernel (KDA) or a Gaussian
kernel (ALE). The resulting peak density map or ALE map is thresholded, resulting in a map of significant results.
within r mm. In ALE, the kernel is Gaussian, with a prespecified

full width at half maximum value. The smoothed values are
then treated at each voxel as estimates of the probability that
each peak lays within r mm, and their union is computed to
give the activation likelihood. This is interpreted as the probability that at least one of the peak activations lays within this
voxel.
For both methods, Monte Carlo methods are used to find an
appropriate threshold to test the null hypothesis that the n
reported peak coordinates are uniformly distributed throughout
the gray matter. A permutation distribution is computed by
repeatedly generating n peaks at random locations and performing the smoothing operation to obtain a series of statistical maps
under the null hypothesis that can be used to compute voxel-wise
p values. In KDA, the maximum density value from each permutation is saved, and a maximum density distribution is computed
under the null hypothesis. This allows one to determine thresholds that ensure strong control over the family-wise error rate
(FWER). In contrast, ALE identifies voxels where the union of
probabilities exceeds that expected by chance and subsequent p
values are subjected to false discovery rate correction.
Both approaches have a number of shortcomings. For
example, neither method takes into account which study the
peaks came from. Thus, KDA and ALE summarize consistency
across peak coordinates, rather than across studies. The consequence is that a significant result can be driven primarily by a
single study. In addition, they assume no interstudy differences
and that the peaks are spatially independent within and across
studies under the null hypothesis. Hence, both approaches are
designed to perform fixed-effects analysis and the results are
not generalizable outside of the studies under consideration.
MKDA and modALE were developed to circumvent these
shortcomings. Both take into consideration the multilevel
nature of the data and nest peak coordinates within studyspecific contrast maps. This allows study-specific maps to be
treated as random effects and ensures that no single map can
disproportionately contribute to the results, allowing for a
transition from fixed-effects to random-effects analysis. In
addition, study-specific maps are weighed by measures of
both study quality (MKDA) and sample size (both MKDA

and modALE), ensuring that larger and more rigorously performed studies exert more influence on the final results.
For both methods, the contrast maps serve as the unit of
analysis rather than the peak coordinates. Similar to KDA, in
MKDA, the peaks are convolved with a spherical kernel of
radius r mm. However, here, the convolution occurs within
each subject-specific map rather than across all the included
peaks. This results in the creation of new maps where a voxel
value of 1 represents the presence of a peak within r mm and
0 represents the absence of a peak within r mm. These maps are
thereafter weighed depending on the criteria mentioned in the
preceding text, giving rise to a map representing the weighted
proportion of study-specific maps activated within r mm of that
particular voxel. In modALE, the peaks are convolved with a
Gaussian kernel. In contrast to ALE, the width of the kernel
depends upon empirical estimates of the between-subject and
between-template variabilities that are used to model the spatial uncertainty associated with each coordinate. The modeled
probabilities are then combined over all studies by taking the
voxel-wise union of their probability values.
Similar to their predecessors, the MKDA and modALE
methods use Monte Carlo simulations to obtain a threshold
and establish statistical significance. However, there are a few
important differences. In MKDA, the null hypothesis is that the
distribution of blobs, or coherent regions of activation, within
each convolved study-specific map is randomly distributed. In
each Monte Carlo iteration, the number and shape of the
activation blobs are held constant within each study-specific
map, while their location is randomly distributed throughout
the gray matter. This preserves the spatial clustering of nearby
peaks within each contrast and avoids the assumption of independent peak locations within contrasts. After each Monte
Carlo iteration, the maximum density statistic across all studies
is saved and used to choose an appropriate threshold that
controls the FWER (see Figure 4 for an illustration). For
modALE, the permutation testing is limited to regions of gray
matter and modified to test for significant clustering between
experiments.
664
Study-specific Comparison
indicator maps
peaks
Weighted
average
Significant results
Weighted
average
Figure 4 Example of meta-analysis using MKDA on three studies. The three small maps on the left show peaks reported in each study for a
representative axial brain slice. Each map is separately convolved with a spherical kernel, generating indicator maps for each study contrast map. The
weighted average of the indicator maps is computed and thresholded to produce a map of significant results.
Investigating Coactivation
Meta-analysis can also be used to reveal consistent patterns of
coactivation. For example, in MKDA, the data can be organized
as an n v indicator matrix consisting of information about
how the n different study-specific maps activate in the neighborhood of each of the v voxels in the brain. The resulting
connectivity profiles across voxels can be summarized to a
smaller set of structurally or functionally defined regions.
Hypothesis tests can then be performed on connectivity, and
relationships among multiple regions can be summarized and
visualized. There exist several potential measures of association
for bivariate, binomial data that are applicable, including Kruskals gamma, Kendalls tau, and Fishers exact test.
Evaluating Specificity
Meta-analysis provides perhaps the only way to compare neuroimaging results across a wide variety of tasks. For example,
within the kernel-based methods, separate maps can be constructed for each of two task types and subtracted to yield
difference maps. The same procedure can be used in the
Monte Carlo randomization to perform inference. Locations
of contiguous activation blobs (or peaks in ALE/KDA) are
randomized, providing simulated null-hypothesis conditions
that we can use to decide on a threshold for determining
significant differences. These difference maps allow one to
test the relative frequency of activating a given region, compared with the overall frequencies in the rest of the brain. Thus,
a reliable concentration of peaks in a certain brain area for a
specific task type will increase the marginal activation frequencies for that task, which in turn affects the null-hypothesis
difference in the Monte Carlo simulations. A caveat is that for
task types with relatively few peaks, there need not be a greater
absolute probability of activating a region to achieve a significant density for that region relative to other task types.
To test the absolute difference in activation in one condition compared with another, one can alternatively perform a
nonparametric chi-square test (Wager et al., 2007). This allows
one to test whether there is a systematic association between
activation in a particular voxel and a set of tasks.
Software
In recent years, a number of user-friendly software solutions
have been introduced that have simplified the process of performing a meta-analysis. For example, GingerALE is the BrainMap application that is used to perform an ALE meta-analysis
on coordinates in Talairach or MNI space. Neurosynth uses text
mining to automatically harvest peak coordinates from journal
articles and provides a platform for performing large-scale,
automated synthesis of neuroimaging data extracted from published articles. Through a Web interface, simple but useful
analyses of fMRI data can be run on a very large scale. Neurosynth currently contains coordinates from 6000 published
studies, along with words from the full text of the published
papers. Meta-analytic maps of the relationships between brain
activation and use of 10 000 key terms in the papers are available online, as well as online coactivation analyses, topic-based
brain maps, and other features under development. Users can
view lists of papers that activate a given location, create a map
of regions that coactivate with a location, download activation
and coactivation maps for use in studies, and download
feature sets of many commonly used maps (e.g., face,
place, working memory, and reward). Maps for each term
can be forward inference maps, a chi-square test on the likelihood of activation in each brain location given studies that
frequently use a particular term, and reverse inference maps
a chi-square test for independence on the likelihood of a study
involving a term or not, given activation at each location. These
maps can be used for exploration, hypothesis generation, and
inference about activation across domains (e.g., Roy, Shohamy, & Wager, 2012). They can also be used as quantitative
masks for selection of a priori regions of interest (e.g., Wager
et al., 2013). Finally, both KDA and MKDA are available in a
Matlab toolbox.
Future Developments
Meta-analyses have become increasingly popular in recent
years, and there is promise of many interesting developments

in the coming years. One exciting direction is that analyses
across study types can be used to develop brain-based psychological ontologies that allow for the grouping of different kinds
of tasks and psychological functions together based on the
similarity of their brain patterns (Poldrack, 2008; Turner &
Laird, 2012). Another promising future direction is the development of meta-analysis-based classifier techniques that allow
quantitative inferences to be made from brain activation to
psychological states (Yarkoni et al., 2011). This could allow
formal predictions to be made about psychological states
based on brain activation.
A few Bayesian methods have recently appeared in the
statistics literature. The first (Kang et al., 2011) proposes a
Bayesian spatial hierarchical model using a marked independent cluster process. Interestingly, this provides a generative
model that allows for prediction of peak locations from new
studies. The second (Yue et al., 2012) suggests a nonparametric
binary regression method where each location (or voxel) has a
probability of being truly activated, and the corresponding
probability function is based on a spatially adaptive Gaussian
Markov random field. Finally, the results of meta-analysis can
potentially be used to create priors for Bayesian analysis as they
provide information about the current state-of-the-art knowledge of a certain psychological process under study. In addition, they show great promise as tools for performing feature
selection in multivoxel pattern analysis (Wager et al., 2013).

BrainMap Database as a Resource for Computational Modeling;
Contrasts and Inferences; Databases; Reverse Inference; The General
Linear Model.
References
Dickstein, S. G., Bannon, K., Xavier Castellanos, F., & Milham, M. P. (2006). The neural
correlates of attention deficit hyperactivity disorder: An ALE meta-analysis. Journal
of Child Psychology and Psychiatry, 47(10), 10511062.
Eickhoff, S. B., Laird, A. R., Grefkes, C., Wang, L. E., Zilles, K., & Fox, P. T. (2009).
Coordinate-based activation likelihood estimation meta-analysis of neuroimaging
data: A random-effects approach based on empirical estimates of spatial uncertainty.
Etkin, A., & Wager, T. (2007). Functional neuroimaging of anxiety: A meta-analysis of
emotional processing in PTSD, social anxiety disorder, and specific phobia.
American Journal of Psychiatry, 164(10), 14761488.
Fox, P. T., & Lancaster, J. L. (2002). Mapping context and content: The BrainMap
model. Nature Reviews Neuroscience, 3(4), 319321.
Glahn, D. C., Ragland, J. D., Abramoff, A., Barrett, J., Laird, A. R., Bearden, C. E., et al.
(2005). Beyond hypofrontality: A quantitative meta-analysis of functional neuroimaging
studies of working memory in schizophrenia. Human Brain Mapping, 25(1), 6069.
Kang, J., Johnson, T. D., Nichols, T. E., & Wager, T. D. (2011). Meta analysis of
functional neuroimaging data via Bayesian spatial point processes. Journal of the
American Statistical Association, 106(493), 124134.
665
Kober, H., Barrett, L. F., Joseph, J., Bliss-Moreau, E., Lindquist, K., & Wager, T. D.
(2008). Functional grouping and corticalsubcortical interactions in emotion: A
meta-analysis of neuroimaging studies. NeuroImage, 42, 9981031.
Laird, A. R., McMillan, K. M., Lancaster, J. L., Kochunov, P., Turkeltaub, P. E.,
Pardo, J. V., et al. (2005). A comparison of label-based review and ALE metaanalysis in the Stroop task. Human Brain Mapping, 25(1), 621.
Menzies, L., Chamberlain, S. R., Laird, A. R., Thelen, S. M., Sahakian, B. J., &
Bullmore, E. T. (2008). Integrating evidence from neuroimaging and
neuropsychological studies of obsessivecompulsive disorder: the orbitofrontostriatal model revisited. Neuroscience & Biobehavioral Reviews, 32(3),
525549.
Northoff, G., Heinzel, A., de Greck, M., Bermpohl, F., Dobrowolny, H., & Panksepp, J.
(2006). Self-referential processing in our brain A meta-analysis of imaging
studies on the self. NeuroImage, 31(1), 440457.
Phan, K. L., Wager, T., Taylor, S. F., & Liberzon, I. (2002). Functional neuroanatomy of
emotion: A meta-analysis of emotion activation studies in PET and fMRI.
NeuroImage, 16(2), 331348.
Trends in Cognitive Sciences, 10(2), 5963.
Poldrack, R. A. (2008). The role of fMRI in cognitive neuroscience: Where do we stand?
Current Opinion in Neurobiology, 18(2), 223227.
Roy, M., Shohamy, D., & Wager, T. D. (2012). Ventromedial prefrontalsubcortical
systems and the generation of affective meaning. Trends in Cognitive Sciences,
16(3), 147156.
Turkeltaub, P. E., Eden, G. F., Jones, K. M., & Zeffiro, T. A. (2002). Meta-analysis of the
functional neuroanatomy of single-word reading: Method and validation.
NeuroImage, 16(3), 765780.
Turner, J. A., & Laird, A. R. (2012). The cognitive paradigm ontology: Design and
application. Neuroinformatics, 10(1), 5766.
Van Snellenberg, J. X., Torres, I. J., & Thornton, A. E. (2006). Functional neuroimaging
of working memory in schizophrenia: Task performance as a moderating variable.
Neuropsychology, 20(5), 497.
Wager, T. D., Atlas, L. Y., Lindquist, M. A., Roy, M., Woo, C. W., & Kross, E. (2013). An
fMRI-based neurologic signature of physical pain. New England Journal of
Medicine, 368(15), 13881397.
Wager, T. D., Jonides, J., & Reading, S. (2004). Neuroimaging studies of shifting
attention: A meta-analysis. NeuroImage, 22(4), 16791693.
Wager, T. D., Lindquist, M., & Kaplan, L. (2007). Meta-analysis of functional
neuroimaging data: Current and future directions. Social Cognitive and Affective
Wager, T. D., Lindquist, M. A., Nichols, T. E., Kober, H., & Van Snellenberg, J. (2009).
Evaluating the consistency and specificity of neuroimaging data using metaanalysis. NeuroImage, 45(1), S210S221.
Woo, C. W., Krishnan, A., & Wager, T. D. (2014). Cluster-extent based
thresholding in fMRI analyses: Pitfalls and recommendations. NeuroImage, 91,
412419.
Methods, 8(8), 665670.
Yue, Y. R., Lindquist, M. A., & Loh, J. M. (2012). Meta-analysis of functional
neuroimaging data using Bayesian nonparametric binary regression. Annals of
Applied Statistics, 6(2), 697718.
Relevant Websites
http://brainmap.org Brainmap.
http://neurosynth.org Neurosynth.
http://sumsdb.wustl.edu/sums/index.jsp Surface Management System Database.
http://wagerlab.colorado.edu/tools Matlab toolbox.
Integrative Computational Neurogenetic Modeling

NK Kasabov, Auckland University of Technology, Auckland, New Zealand
Introduction
The brain is a complex spatio-temporal neurogenetic information processing machine that processes information at different
functional levels (Figure 1). Spatio-temporal activity in the
brain depends on the internal brain structure, on the external
stimuli and also very much on the dynamics at gene-protein
level. Methods for measuring activity of the brain, such as EEG
(electroencephalogram), fMRI (functional magneto resonance
images), MEG (magneto-encephalograms), PET (positron emission technology), and DTI (diffusion tensor imaging), have
been widely used, some of them presented in this encyclopedic
volume. Integrative computational neurogenetic modeling
(CNGM) go one step further integrating these data with
relevant genetic data for a better understanding of the brain.
Genes are both the result of the evolution of species and
the functioning of an individual brain during a life time.
Different genes express as different mRNA, microRNA and
proteins in different areas of the brain and are involved in all
information processes, from spiking activity, to perception,
decision making, and emotions. Functional connectivity
develops in parallel with structural connectivity during brain
maturation where a growth-elimination process (synapses are
created and eliminated) depends on the gene expression and
environment. For example, postsynaptic AMPA-type glutamate
receptors (AMPARs) mediate most fast excitatory synaptic
transmissions and are crucial for many aspects of brain functioning, including learning, memory, and cognition (Henley
et al., 2011). Kang et al. (2011) performed weighted gene
co-expression network analysis to define modules of coexpressed genes and identified 29 such modules, associated
with distinct spatio-temporal expression patterns and biological processes in the brain. The genes in each module form a
gene regulatory network (GRN).
The spiking activity of a neuron may act as a feedback and
affect the expression of genes. As pointed out in Zhdanov
(2011) on a time scale of minutes and hours the function of
neurons may cause changes in the expression of hundreds of
genes transcribed into mRNAs and also in microRNAs. This
links together the short-term, the long-term and the genetic
memories of the neurons representing the global memory of
the whole neuronal system.
The anatomically comprehensive atlas of the adult human
brain trascriptome (www.brain-map.org) is a rich repository of
bran-gene data that will definitely trigger new directions for
research and computational modeling of neurogenetic data
(Hawrylycz et al., 2012; Kasabov, 2014a). Example of a gene
expression brain map is given in Figure 2. Gene expression is
clearly distinguished between structural and functional areas of
the brain. Specific genes define specific functions of different
sections of the brain. Specific genes relate to specific types
of neurons and types of connections. For example, the gene
expression level of genes related to dopamine-signaling (e.g.
DRD5DRD1, COMPT, MAOB, DDC, TH, etc.) is higher in

areas of a normal subject brain that consist of neurons with
larger number of dopamine regulated ion channels. These areas
relate to dopamine-driven cognition, emotion, and addiction.
Such areas are: hippocampus, striatum, hypothalamus, amygdala, and pons. If these areas are activated normally it means
that there is a sufficient dopamine signaling. In a diseased
brain, a nonactivated area may suggest lack of dopamine.
Zilles and Amunts (2010), for example, demonstrated that
changes in the neurotransmitter receptor densities for important neurotransmitters coincide mostly with the Brodmann
cytoarchitectonic borders. These neurotransmitter receptors
are: a1, noradrenergic a1 receptor; a2A noradrenergic a2A
receptor; AMPAR, a-amino-3-hydroxy-5-methyl-4-isoxazole
propionic acid receptor; GABAB, GABA (g-aminobutyric
acid)-ergic GABAB receptor; M2, cholinergic muscarinic M2
receptor; M3 cholinergic muscarinic M3 receptor; NMDAR,
N-methyl-D-aspartate receptor.
The enormousness of brain data available and the complexity of the research questions that need answering through
integrated models for brain data analysis are grand challenges
for the areas of machine learning and information science in
general (Gerstner et al., 2012; Koch & Reid, 2012; Poline &
Poldrack, 2012; VanEssen et al., 2012). And this is where
CNGM can help.
CNGM, as defined and proposed in Kasabov (2007) and
Benuskova and Kasabov (2007) are based on computational
models of spiking neurons, linked in a spiking neural network
(SNN). A single spiking neuron model can integrate gene and
spiking information related to spiking activity of the neuron,
while a SNN can represent a pattern of brain activity. Something more, a probabilistic neurogenetic spiking neuron model
can manifest quantum information processing characteristics.
Probabilistic Neurogenetic Model of a Spiking Neuron

Several spiking neuronal models have been proposed so far
(e.g. Gerstner, 2001; Hodgkin & Huxley, 1952; Izhikevich,
2006; Maass et al., 2002). Figure 3(a) and 3(b) illustrates the
structure and the functionality of the popular Leaky-Integrateand Fire Model (LIFM). The neuronal postsynaptic potential
(PSP), also called membrane potential u(t), increases with
every input spike at a time t, multiplied by the synaptic efficacy
(strength), until it reaches a threshold y. After that, an output
spike is emitted and the membrane potential is reset to an
initial state. The membrane potential can have certain leakage
between spikes, which is defined by a temporal parameter t.
The LIFM has been extended to probabilistic neurogenetic
model (PNGM) (Benuskova & Kasabov, 2007; Kasabov, 2010,
2014b; Kasabov et al., 2005) Figure 4(a) and 4(b). As a
partial case, when no probability parameters and no genetic
parameters are used, the model is reduced to the LIFM (Figure
3(a) and 3(b)).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00349-3
667
668
INTRODUCTION TO METHODS AND MODELING | Integrative Computational Neurogenetic Modeling
6. Evolutionary (population/generation) processes
__________________________________________________
5. Brain cognitive processes
_________________________________________________
4. System information processing (e.g. neural ensembles)
_________________________________________________
3. Information processing in a cell (neuron)
_________________________________________________
2. Molecular information processing (genes, proteins)
_________________________________________________
1. Quantum information processing
Figure 1 Different levels of information processing in the brain. Reproduced from Kasabov, N. (2007). Evolving connectionist systems: The
knowledge engineering approach. London: Springer (first edition 2002).
The PNGM is a probabilistic model. In addition to the

connection weights wj,i(t), three probabilistic parameters are
defined:
Figure 2 From the brain explorer: the expression level of several genes
(on the vertical axis) in different areas of the brain (horizontal axis): ABAT
A_23_P152505, ABAT A_24_P330684, ABAT CUST_52_PI416408490,
ALDH5A1 A_24_P115007, ALDH5A1 A_24_P923353, ALDH5A1
A_24_P3761, AR A_23_P113111, AR CUST_16755_PI416261804, AR
CUST_85_PI416408490, ARC A_23_P365738, ARC
CUST_11672_PI416261804, ARC CUST_86_PI416408490, ARHGEF10
A_23_P216282, ARHGEF10 A_24_P283535, ARHGEF10 CUST_) (from
www.brain-map.org and http://www.alleninstitute.org).
In the PNGM, four types of synapses for fast excitation, fast

inhibition, slow excitation, and slow inhibition are used. The contribution of each one to the PSP of a neuron is defined by the
level of expression of different genes/proteins along with the
presented external stimuli. The model utilizes known information about how proteins and genes affect spiking activities of a
neuron. Figure 4(b) shows what proteins affect each of the
four types of synapses. This information is used to calculate the
contribution of each of the four different synapses j connected
to a neuron i to its post synaptic potential PSPi(t):
!

!
S
S
synapse
synapse
eij
s A
exp synapse exp synapse
[1]
tdecay
trise
where tsynapse
decay/rise are time constants representing the rise and fall
of an individual synaptic PSP; A is the PSPs amplitude; eijsynapse
represents the type of activity of the synapse between neuron j
and neuron i that can be measured and modeled separately for
a fast excitation, fast inhibition, slow excitation, and slow
inhibition (it is affected by different genes/proteins). External
inputs can also be added to model background noise, background oscillations or environmental information. Genes that
relate to the parameters of the neurons are also related to the
activity of other genes, thus forming a GRN.
A probability pcj,i(t) that a spike emitted by neuron nj will

reach neuron ni at a time moment t through the connection
between nj and ni. If pcj,i(t) 0, no connection and no spike
propagation exist between neurons nj and ni. If pcj,i(t) 1 the
probability for propagation of spikes is 100%.
A probability psj,i(t) for the synapse sj,i to contribute to the
PSPi(t) after it has received a spike from neuron nj.
A probability pi(t) for the neuron ni to emit an output spike
at time t once the total PSPi(t) has reached a value above the
PSP threshold (a noisy threshold).
The total PSPi(t) of the spiking neuron ni is now calculated
using the following formula:
X
X

PSPi t
ej f1 pcj, i t p f2 psj, i t p
pt0 , ..., t j1, ..., m
wj, i t t t0
[2]
where ej is 1, if a spike has been emitted from neuron nj, and

0 otherwise; f1(pcj,i(t)) is 1 with a probability pcji(t), and 0 otherwise; f2(psj,i(t)) is 1 with a probability psj,i(t), and 0 otherwise;
t0 is the time of the last spike emitted by ni; (t t0) is an
additional term representing decay in the PSPi. As a special
case, when all or some of the probability parameters are fixed
to 1, the above probabilistic model will be simplified and will
resemble the LIFM.
The probabilistic parameters of the PNGM of a neuron have
also their biological analogs and are controlled by specific
genes (Kasabov et al., 2011). For example, the probability of
a synapse to contribute to the postsynaptic potential after it has
received a spike from a presynaptic neuron may be affected by
different proteins, e.g., proteins that affect the transmitter
release mechanism from the presynaptic terminal such as the
SNARE proteins (Syntaxin, Synaptobrevin II, SNAP-25), SM
proteins (Munc181), the sensor Synaptotagmin, and Complexin, and also the proteins such as PSD-95 and Transmembrane AMPA receptor regulatory proteins (TARPs) in the
postsynaptic site. The probability for a neuron to emit an
output spike at the time when the PSP has reached a value
above the threshold may be affected by different proteins, e.g.,
669
Spikes Stimulus
Integration
+leakage
1.0
Spike
Refractory period
u(t)
0.8
0.4
2
Binary events
0.6
0.2
0.0
4
(a)
(b)
Figure 3 (a) The structure of a LIFM. (b) Functionality of a LIFM.
Psij (t)
ni
,Wij (t)
nj
Pcij (t)
Pi (t)
(a)
Pj (t)
Different types of action potential

of a spiking neuron
Related neurotransmitters and ion

channels
Fast excitation PSP

Slow excitation PSP
Fast inhibition PSP
Slow inhibition PSP
Modulation of PSP
Firing threshold
A MPA R
NM D A R
GABAAR
GABABR
mGluR
Ion channels SCN, KCN, CLC
(b)
Figure 4 (b) Neuronal action potential parameters and related proteins and ion channels in the computational neuro-genetic model of a spiking
neuron: AMPAR (amino-methylisoxazole- propionic acid) AMPA receptor; NMDR (N-methyl-D-aspartate acid) NMDA receptor; GABAAR (gammaaminobutyric acid) GABAA receptor; GABABR GABAB receptor; SCN sodium voltage-gated channel; KCN kalium (potassium) voltage-gated
channel; CLC chloride channel. Reproduced from Benuskova, L., & Kasabov, N. (2007). Computational neuro-genetic modelling. New York:
Springer, p. 290.
density of the sodium channels in the membrane of the triggering zone. The time decay parameter in a LIFM may be
affected by different genes and proteins depending on the
type of the neuron. Such proteins are transporters in the presynaptic membrane, the glial cells and the enzymes, which
uptake and break down the neurotransmitters in the synaptic
cleft (BAX, BAD, DP5); metabotropic GABAB Receptors; KCNK
family proteins that are responsible for the leak conductance of
the resting membrane potential.
Spiking Neural Networks: Structures and Learning

Algorithms
Many spiking neuron models can be connected to form different computational architectures, e.g., simple one-layer feedforward network, recurrent network, reservoir type network,
3D cube that maps the structure of the brain (Kasabov, 2014b;
also see Figure 7 in this article).
Different learning rules for SNN have been introduced to
make the SNN structure learn from data, mimicking learning
in the brain. The STDP (Spike Timing Dependant Plasticity)
learning rule (Song et al., 2000) utilizes Hebbian plasticity
(Hebb, 1949) in the form of long-term potentiation (LTP)
and depression (LTD) (Figure 5(a)). Efficacy of synapses is
strengthened or weakened based on the timing of postsynaptic
action potential in relation to the presynaptic spike. If the
difference in the spike time between the presynaptic and postsynaptic neurons is negative (presynaptic neuron spikes first)
then the connection weight between the two neurons
increases, otherwise it decreases. Connected neurons, trained

with STDP learning rule, learn consecutive temporal associations from data. New connections can be generated based on
activity of consecutively spiking neurons. Presynaptic activity
that precedes postsynaptic firing can induce LTP, reversing this
temporal order causes LTD.
STDP and other fundamental learning methods have
been recently used to develop new types of eSNN models
for spatio-temporal pattern recognition: SPAN (Mohemmed
et al., 2012, 2013); dynamic eSNN (deSNN) (Kasabov et al.,
2013); reservoir eSNN (Schliebs, Kasabov, & DefoinPlatel, 2010; Kasabov, 2014b); ReSuMe (Gutig & Sompolinsky,
2006; Ponulak & Kasinski, 2010). The deSNN (Kasabov
et al., 2013) combines rank-order and temporal (e.g. STDP)
learning rules. The initial values of synaptic weights are set
according to the rank-order learning assuming the first incoming spikes are more important than the rest. The weights
are further modified to accommodate following spikes activated by the same stimulus, with the use of a temporal learning rule STDP.
The rank-order learning rule (Thorpe & Gautrais, 1998)
uses important information from the input spike trains,
namely the rank of the first incoming spikes on the neuronal
synapses (Figure 5(b)). It establishes a priority of inputs (synapses) based on the order of the spike arrival on these synapses
for a particular pattern. This is a phenomenon observed in
biological systems. The rank-order learning has several advantages when used in SNN, mainly: fast, one-pass learning (as it
uses the extra information of the order of the incoming spikes)
and asynchronous data entry (synaptic inputs are accumulated
670
0.4
F (%)
PSP
W
0.2
t (ms)
40
20
20
PSPTh
PSPTh
PSP
40
0.2
Output
Input
0.4
(a)
time
Output
(b)
Figure 5 (a) Synaptic change in a STDP learning neuron (Song et al., 2000); (b) rank-order learning neuron.
Analysis of patterns of spiking

activity and connectivity
SNN model
Other relevant gene/

protein information
GRN model
Molec. model
M1
M2
Mp
Figure 6 A general diagram of a CNGM.
into the neuronal membrane potential in an asynchronous

way). The PSP of a neuron i at a time t is calculated as:
X
[3]
PSPi, t
mod order j wj, i
where mod is a modulation factor, that has a value between
0 and 1; j is the index for the incoming spike at synapse j,i and
wj,i is the corresponding synaptic weight; order(j) represents
the order (the rank) of the spike at the synapse j,i among all
spikes arriving from all m synapses to the neuron i. The order(j)
has a value 0 for the first spike and increases according to the
input spike order. An output spike is generated by neuron i if
the PSP(i,t) becomes higher than a threshold PSPTh(i). During
the training process, for each training input pattern there is a
new output neuron created and its connection weights are
calculated based on the order of the incoming spikes:
Dwj, i t mod orderj, it
[4]
Computational Neurogenetic Models (CNGM)

Figure 6 is a general diagram of a CNGM that consists of
several modules hierarchically connected: a low molecular
level modeling modules; GRN modules; SNN; high level of
SNN activity analysis module.
An example of a CNGM is shown in Figure 7(a), called

NeuCube (Kasabov, 2014b). It consists of the following functional modules: input data encoding module; 3D SNN reservoir module (SNNr); output function (classification) module;
GRN module; optimization module.
Continuous value input data is transformed into spikes
(e.g. pixel, EEG channel, fMRI voxel) using population rank
coding (Bothe, 2004), address event representation (AER)
method (Delbruck, 2007) or other methods, e.g. Bens Spike
Algorithm (BSA) (Nuntalid et al., 2011).
The transformed input data is entered (mapped) into spatially located neurons from the SNNr. Brain data sequences
are mapped to spatially located neurons in the SNNr that
represent spatially brain areas where data is collected. Spike
trains are continuously fed into the SNNr in their temporal
order. The SNNr is structured to spatially map brain areas for
which STBD or/and gene data is available using some of the
brain templates, such as Talairach (Talairach & Tournoux,
1988), Montreal Neurological Institute template (MNI)
(Evans et al., 1993) or other. A neuronal SNNr structure can
include known structural or functional connections between
different areas of the brain represented in the data. Setting up
a proper initial structural connectivity in a model, is important in order to learn properly spatio-temporal data, to capture functional connectivity and to interpret the model
(Honey et al., 2007). More specific structural connectivity
671
Figure 7 (a) A diagram of the general NeuCube architecture, consisting of input data encoding module, 3D SNNr module, output function module
(e.g. for classification or prediction), gene regulatory networks (GRN) module. (b) Spiking activity in the SNNr during learning of brain data.
(c) Connectivity in the SNNr before training with EEG brain data small world connectivity. (d) Connectivity of the SNNr after training with EEG brain data
using STDP. Reproduced from Kasabov, N. (2014). NeuCube: A spiking neural network architecture for mapping, learning and understanding of
spatio-temporal brain data. Neural Networks, 52, 6276.
data can be obtained using, for example, diffusion tensor

imaging (DTI) method.
The input STBD is propagated through the SNNr and a
method of unsupervised learning is applied, such as STDP. The
neuronal connections are adapted and the SNNr learns to
generate specific trajectories of spiking activities when a particular input pattern is entered. The SNNr accumulates temporal
information of all input spike trains and transforms it into
dynamic states that can be classified over time. The recurrent
reservoir generates unique neuronal spike time responses
for different classes of input spike trains which effect is
called polychronization (Izhikevich, 2006). As an illustration,
Figure 7(b)7(d) shows the spiking activity (b) and connectivity of a SNNr before training (c) and after training (d) on
illustrative EEG data, where the SNNr has 1471 neurons
and the coordinates of these neurons correspond directly to
the Tailarach template coordinates with a resolution of approximately 1 cm3. It can be seen that as a result of training new
connections have been created that represent spatio-temporal
interaction between input variables captured in the SNNr

from the data.
After the SNNr is trained in an unsupervised model, the
same input data is propagated again through the SNNr and an
output classifier is trained to recognize the patterns of activity
of the SNNr in a predefined output class for this input pattern.
Modeling the Effect of Genes on the Activity of a CNGM

Since the NeuCube structure maps brain structural areas
through standard stereotaxic coordinates (e.g. MNI, Talairach,
etc.) gene data can be added to the NeuCube architecture if
such data is available. Gene expression data can be mapped to
neurons and areas from a NeuCube as a fifth dimension, in
addition to the three spatial and one temporal dimensions, so
that a vector of gene expression can be allocated for every
neuronal group. Some of these genes would be directly
involved in the function of the PNGM of the neurons. Neurons
672
can share same expression vectors in a cluster. This is possible

because spatial locations of neurons in the SNNr correspond to
stereotaxic coordinates of the brain (Hawrylycz et al., 2012).
Furthermore, there are known chemical relationships between
genes, or between groups of genes related to same brain
function, forming GRN (Schliebs, 2005, see also Figure 9).
Therefore, the fifth dimension in a SNNr can be represented
as a GRN.
The relationship between genes and spiking neuronal activities can be explored through varying gene expression levels
and performing simulations, especially when both gene and
brain data are available for some special cognitive or abnormal
brain states. Some data related to expression of genes in different areas of the brain under different conditions are available
from the Brain Atlas of the Allen Brain Institute (see Figure 2).
This is illustrated with a simple example shown in Figure 8.
Neurogenetic Modeling of Brain Diseases
Neurogenetic Modeling for Cognitive Robotics

and Emotional Computing
Building artificial cognitive systems (e.g. robots, AI agents) that
are able to communicate with humans in a human-like way has
been a goal for computer scientists for decades now. Cognition
is closely related with emotions. Basic emotions are happiness,
sadness, anger, fear, disgust, surprise, but other human emotions play role in cognition as well (pride, shame, regret, etc.).
Some primitive emotional robots or simulation systems have
already been developed (e.g., see Meng et al., 2010). The area of
affective computing, where some elements of emotions are
modeled in a computer system, is growing (Picard, 1997).
Based on prior information and available data, different

CNGM models can be created for the study of various brain
states, conditions, and diseases (Benuskova & Kasabov, 2007;
Genes and Diseases), such as epilepsy, schizophrenia, mental
retardation, brain aging, Parkinson disease, clinical depression,
stroke, and AD (Kasabov, 2014b; Kasabov et al., 2011;
Morabito et al., 2012; Schliebs, 2005). Once learned in a
CNGM model, the already known two-way links between
spiking activity of the brain and gene transcription and translation, can be potentially used to evaluate gene mutations and
the effects of drugs.
One of the most studied brain disease is Alzheimers disease
(AD). Gene expression data at a molecular level from both
healthy and AD patients have been published in the Brain
Atlas (www.brain-map.org). Interactions between genes in
AD subjects have been studied and published (e.g., Schliebs,

2005). An example of a GRN related to AD is given in Figure 9.
Atlases of structural and functional pathways data of both
healthy and AD subjects have also been made available (Toga
et al., 2006).
A possible scenario of studying AD through neurogenetic
modeling in a NeuCube model will involve the GRIN2B gene.
It has been found that subjects affected by AD have a deficit of
NMDAR subunit, with GRIN2B level decreased in the hippocampus. A GRN of NMDAR will be constructed as the synthesis
of this receptor is possible only due to the simultaneous expression of different genes, which are responsible for the subunits
that form the macromolecule. Such genes are GRIN1-1a,
GRIN2A, GRIN2B, GRIN2D, and GRIN3A. A GRN of AMPAR
genes can also be developed and the two GRNs connected in a
NeuCube SNNr.
A similar approach can be applied for modeling data for
Parkinsons disease, multiple sclerosis, stroke, and other brain
diseases for which both molecular and STBD is available.
1000
Neuron
800
600
400
200
1000
2000
3000
4000
5000
Time
Figure 8 A single gene expression level over time can affect the pattern of activity of a whole SNNr of 1000 neurons. The gene controls the t parameter
of all 1000 LIF neurons over a period of 5 s. The top diagram shows the evolution of the t parameter. The response of the 10 000 spiking neurons
is shown as a raster plot of spike activity. A black point in this diagram indicates a spike of a specific neuron at a specific time in the simulation
(the x axis). The bottom diagram presents the evolution of the membrane potential of a single neuron from the network (green curve) along
with its firing continuous noisy threshold (red curve). Output spikes of the neuron are indicated as black vertical lines in the same diagram (from
Kasabov, 2014). Reproduced from Kasabov, N. (Ed.) (2014). Springer handbook of bio-/neuroinformatics. Heidelberg: Springer.
APP
Vascular component
VEGF
trkA
M1/M3-mR; nR
IL-1
NGF
p75NTR
-amyloid
7 nR
AChE
Cholinergic
system
IL-1 TNF
Inflammation/
cytokines
Figure 9 Genes related to AD form a GRN that can be modeled as

part of a CNGM. Reproduced from Schliebs, R. (2005). Basal forebrain
cholinergic dysfunction in Alzheimers disease interrelationship
with b-amyloid, inflammation and neurotrophin signalling.
Neurochemical Research, 30, 895908.
A CNGM would make it possible to model cognitionemotion brain states that could further enable the creation of
human-like cognitive systems. That would require understanding relevant brain processes as different levels of information
processing. For example, it is known that human emotions
depend on the expression and the dynamic interaction of
neuromodulators (serotonin, dopamine, noradrenalin, and
acetylcholine) and some other relevant genes and proteins
(e.g., 5-HTTLRP, DRD4, DAT), that are functionally linked to
the spiking activity of the neurons in certain areas of the brain.
They have wide ranging effects on brain functions. For example, Noradrenaline is important to arousal and attention mechanisms. Acetylcholine has a key role in encoding memory
function. Dopamine is related to aspects of learning and
reward seeking behavior and may signal probable appetitive
outcome, whereas serotonin may affect behavior with probable aversive outcome. Modifying gene and protein expression
levels of genes used in a particular CNGM would affect the
learning and pattern recognition properties of that model. For
example, the modification could cause connections and functional pathways to become stronger or weaker, which could be
observed and further interpreted in terms of cognitive and
emotional states.
Acknowledgements
This work was supported by the Knowledge Engineering and
Discovery Research Institute (KEDRI, http://www.kedri.info)
of the Auckland University of Technology and partially by the
EU FP7 Marie Curie project EvoSpike PIIF-GA-2010-272006,
hosted by the Institute for Neuroinformatics at ETH/UZH
Zurich (http://ncs.ethz.ch/projects/evospike).

Anatomical MRI for Human Brain Morphometry; Basic Principles of
Electroencephalography; Basic Principles of Magnetoencephalography;
fMRI at High Magnetic Field: Spatial Resolution Limits and
Applications; Functional MRI Dynamics; Molecular fMRI; MRI and fMRI
Optimizations and Applications; Obtaining Quantitative Information
673
from fMRI; INTRODUCTION TO ANATOMY AND PHYSIOLOGY:

Development of Structural and Functional Connectivity; Functional
Connectivity; Motor Cortex; Somatosensory Cortex; INTRODUCTION
TO CLINICAL BRAIN MAPPING: Alzheimers Disease; Basic
Concepts of Image Classification Algorithms Applied to Study
Neurodegenerative Diseases; Brain Mapping Techniques Used to Guide
Deep Brain Stimulation Surgery; Imaging Genetics; Organic Amnesia;
Primary Progressive Aphasia; INTRODUCTION TO COGNITIVE
NEUROSCIENCE: A Frontostriatal Circuit for Timing the Duration of
Events; Music; Prediction and Expectation; The Neural Underpinnings
of Spatial Memory and Navigation; INTRODUCTION TO METHODS
AND MODELING: Diffusion Tensor Imaging; Modeling Brain Growth
and Development; Models of fMRI Signal Changes; INTRODUCTION
TO SOCIAL COGNITIVE NEUROSCIENCE: Genetic Neuroimaging
of Social Perception; INTRODUCTION TO SYSTEMS: Memory;
Neural Networks Underlying Novelty Processing.
References
Benuskova, L., & Kasabov, N. (2007). Computational neuro-genetic modelling.
New York: Springer, p. 290.
Bothe, S. M. (2004). The evidence for neural information processing with precise spiketimes: A survey. Natural Computing, 3, .
Delbruck, T. (2007). jAER open source project. http://jaer.wiki.sourceforge.net.
Evans, A. C., Collins, D. L., Mills, S. R., Brown, E. D., Kelly, R. L., & Peters, T. M.
(1993). 3D statistical neuroanatomical models from 305 MRI volumes.
In: IEEE-nuclear science symposium and medical imaging conference. IEEE Press.
Gerstner, W. (2001). Whats different with spiking neurons? In H. Mastebroek & H. Vos
(Eds.), Plausible neural networks for biological modelling (pp. 2348). Dordrecht:
Kluwer Academic Publishers.
Gerstner, W., Sprekeler, H., & Deco, G. (2012). Theory and simulation in neuroscience.
Science, 338, 6065.
Gutig, R., & Sompolinsky, H. (2006). The Tempotron: A neuron that learns spike
timing-based decisions. Nature Neuroscience, 9(3), 420428.
Hawrylycz, M., et al. (2012). An anatomically comprehensive atlas of the adult human
brain transcriptome. Nature, 489, 391399.
Hebb, D. (1949). The organization of behavior. New York: John Wiley and Sons.
Henley, J. M., Barker, E. A., & Glebov, O. O. (2011). Routes, destinations and delays: Recent
advances in AMPA receptor trafficking. Trends in Neuroscience, 34(5), 258268.
Hodgkin, A. L., & Huxley, A. F. (1952). A quantitative description of membrane current
and its application to conduction and excitation in nerve. Journal of Physiology,
117, 500544.
Honey, C. J., Kotter, R., Breakspear, M., & Sporns, O. (2007). Network structure of
of the National Academy of Sciences, 104, 1024010245.
Izhikevich, E. (2006). Polychronization: Computation with spikes. Neural Computation,
18, 245282.
Kang, H. J., et al. (2011). Spatio-temporal transcriptome of the human brain. Nature,
478, 483489.
Kasabov, N. (2007). Evolving connectionist systems: The knowledge engineering
approach. London: Springer (first edition 2002).
Kasabov, N. (2010). To spike or not to spike: A probabilistic spiking neuron model.
Neural Networks, 23(1), 1619.
Kasabov, N. (Ed.), (2014). Springer handbook of bio-/neuroinformatics. Heidelberg:
Springer.
Kasabov, N. (2014b). NeuCube: A spiking neural network architecture for mapping,
learning and understanding of spatio-temporal brain data. Neural Networks, 52,
6276.
Kasabov, N., Benuskova, L., & Wysoski, S. (2005). A computational neurogenetic
model of a spiking neuron. In: Proc. IJCNN, vol. 1, IEEE Press.
Kasabov, N., Dhoble, K., Nuntalid, N., & Indiveri, G. (2013). Dynamic evolving spiking
neural networks for on-line spatio- and spectro-temporal pattern recognition. Neural
Networks, 41, 188201.
Kasabov, N., Schliebs, R., & Kojima, H. (2011). Probabilistic computational
neurogenetic framework: From modelling cognitive systems to Alzheimers disease.
IEEE Transactions of Autonomous Mental Development, 3(4), 3003011.
Koch, C., & Reid, R. (2012). Nature, 483, 397.
674
Maass, W., Natschlaeger, T., & Markram, H. (2002). Real-time computing without stable
states: A new framework for neural computation based on perturbations. Neural
Computation, 14(11), 25312560.
Meng, Y., Jin, Y., Yin, J., & Conforth, M. (2010). Human activity detection using spiking
neural networks regulated by a gene regulatory network. In: Proc. IJCNN, IEEE
Press.
Mohemmed, A., Schliebs, S., Matsuda, S., & Kasabov, N. (2012). SPAN: Spike pattern
association neuron for learning spatio-temporal sequences. Intenational Journal of
Neural Systems, 22(4), 116.
Mohemmed, A., Schliebs, S., Matsuda, S., & Kasabov, N. (2013). Evolving spike pattern
association neurons and neural networks. Neurocomputing, 107, 310.
Morabito, F. C., Labate, D., La Foresta, F., Morabito, G., & Palamara, I. (2012).
Multivariate, multi-scale permutation entropy for complexity analysis of AD EEG.
Entropy, 14(7), 11861202.
Nuntalid, N., Dhoble, K., & Kasabov, N. (2011). EEG classification with BSA spike
encoding algorithm and evolving probabilistic spiking neural network. In LNCS
(vol. 7062, pp. 451460). Springer.
Picard, R. (1997). Affective computing. Cambridge: MIT Press.
Poline, J.-B., & Poldrack, R. A. (2012). Frontiers in brain imaging methods grand
challenge. Frontiers in Neuroscience, 6, 96. http://dx.doi.org/10.3389/
fnins.2012.00096.
Ponulak, F., & Kasinski, A. (2010). Supervised learning in spiking neural networks with
ReSuMe: Sequence learning, classification, and spike shifting. Neural Computation,
22(2), 467510.
Schliebs, R. (2005). Basal forebrain cholinergic dysfunction in Alzheimers disease
Interrelationship with b-amyloid, inflammation and neurotrophin signalling.
Neurochemical Research, 30, 895908.
Schliebs, S., Kasabov, N., & Defoin-Platel, M. (2010). On the probabilistic optimization
of spiking neural networks. International Journal of Neural Systems, 20(6),
481500.
Song, S., Miller, K., Abbott, L., et al. (2000). Competitive Hebbian learning through
spike-timing-dependent synaptic plasticity. Nature Neuroscience, 3, 919926.
Talairach, J., & Tournoux, P. (1988). Co-planar stereotaxic atlas of the human brain: 3dimensional proportional systemAn approach to cerebral imaging. New York:
Thieme Medical Publishers.
Thorpe, S., & Gautrais, J. (1998). Rank order coding. Computational Neuroscience:
Trends in Research, 13, 113119.
Toga, A., Thompson, P., Mori, S., Amunts, K., & Zilles, K. (2006). Towards multimodal
atlases of the human brain. Nature Reviews. Neuroscience, 7, 952966.
VanEssen, et al. (2012). The human connectome project: A data acquisition perspective.
NeuroImage, 62(4), 22222231.
Zilles, K., & Amunts, K. (2010). Centenary of Brodmanns mapConception and fate.
Zhdanov, V. P. (2011). Kinetic models of gene expression including non-coding RNAs.
Physics Reports, 500, 142.
Relevant Websites
http://www.brain-connectivity-toolbox.net/ Brain Connectivity Toolbox.
http://braincorporation.com BrainCorporation.
http://www.nitrc.org/projects/brainwaver/ BrainwaveR Toolbox.
http://bluebrainproject.epfl.ch The Blue Brain Project.
http://ncs.ethz.ch/projects/EvoSpike EvoSpike Project, EU FP7.
BrainMap Database as a Resource for Computational Modeling

DS Barron, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
PT Fox, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA; South Texas Veterans Health
Care System, San Antonio, TX, USA
Glossary
Spatial normalization The process of transforming brain

images from native space into registration with a 3-D
template used to define a reference space.
Statistical parametric imaging (or mapping) Transforming
brain images from raw, individual (per subject) data sets in
native space to 3-D images of statistical parameters (Z score,
T scores, F values, R values, p values, etc.) in a standard
coordinate space.
Stereotactic coordinates 3-D anatomical addresses (x, y, z)
defined relative to a reference space and used for analysis
and reporting of functional and structural brain-imagederived observation.
Voxel A data point within a 3-D image-data array, a volume
element. 3-D image datasets statistically analyzed in the
same manner at every voxel and analyzed voxel-wise.
Voxel-based morphometry A voxel-wise analysis method
for detecting between-group (e.g., patients versus controls)
differences in brain anatomy within a standardized
coordinate space.
Abbreviations
fMRI
ICA
MACM
SPI
SPM
VBM
Activation likelihood estimation A widely used family of

algorithms for coordinate-based meta-analysis of functional
and structural neuroimaging observations.
Coordinate space Any of a number of references spaces
defined by an anatomical template and used for analysis and
reporting of neuroimaging data, the two most widely used
being Talairach space and MNI space.
Coordinate-based meta-analysis Meta-analytic method
developed specifically for use with functional and structural
neuroimaging data reported within a standardized
coordinate space.
Meta-analysis Retrospective combination of previously
reported results to better estimate the reliability of those
results.
Metadata Standardized descriptors of data sets stored in
electronic databases for purposes of data retrieval and
filtering studies for inclusion in a meta-analysis.
ALE
CBMA
CBP
Activation likelihood estimation (for functional

meta-analyses) or anatomical likelihood
estimation (for anatomical meta-analyses)
Coordinate-based meta-analysis
Coactivation-based parcellation
Data Types and Sources

Thirty years of neuroimaging have produced a massive amount
of data about the human brain. Poline et al. (2012) recently
reported that from the early 1990s to 2011, over 22 000 studies
were published using functional magnetic resonance imaging
(fMRI) alone. They presented a conservative estimate that, combined, these studies represent 144 000 scan hours (12 000
datasets 12 subjects each 1 h scan time per subject $300
USD/h) at a cost of US$43 million. They also argued that,
combined, these studies represented around 144 terabytes of
raw data and up to 1.5 petabytes (1 PB 1000 TB) of processed
data (Poline et al., 2012). These are huge numbers and they
only represent fMRI! Understandably, much effort has gone into
archiving and databasing this information that represents
millions of dollars and man-hours.
Archives and databases have been created to store and
facilitate intra- and interlaboratory syntheses of neuroimaging
data (Fox & Friston, 2012). Such efforts focus on both

Independent components analysis
Meta-analytic connectivity model
Statistical parametric image
Statistical parametric map
Voxel-based morphometry
functional and structural imaging data; MRI and PET data are
discussed here. Data storage can take place at various stages of
the neuroimaging analysis pipeline: as primary, raw data; as
derived, statistical parametric image (SPI) data; and as reduced,
coordinate data, published in journal articles (see Figure 1).
The advantages and disadvantages of each data type (or even
database) are beyond the scope of this article; we will briefly
discuss primary and derived data archives followed by a deeper
discussion of reduced data archives.
Primary, Raw Data

Primary, raw data archives are most common. Typically, each
neuroimaging center will maintain an archive of all subject
scans on a mass storage device or hard drive as either DICOM
or NifTI files (cf. http://www.nitrc.org/). Individual subject
scans are listed with nonidentifiable alphanumeric names,
per ethical standards (Institutional Review Board, IRB, or otherwise). A spreadsheet or list of scans is typically used to
http://dx.doi.org/10.1016/B978-0-12-397025-1.00350-X
675
676
INTRODUCTION TO METHODS AND MODELING | BrainMap Database as a Resource for Computational Modeling
Figure 1 Data types in typical neuroimaging analysis pipeline. Left: Acquisition of primary, raw data as shown by photograph of Sarabeth Pridgen
Fox playing the piano during PET acquisition of primary, raw data; photograph taken by Dr. Stephan Elleringmann. Middle: Example of derived, statistical
parametric data representing statistical differences in primary data image volumes. Right: Table from Petersen et al. (1988) reporting local
maximum of statistical parametric data as reduced, coordinate data.
reference this archive and, if relevant, contains information

about individual subjects such as age, gender, cognitive test
scores, paradigm/task used during scan, and diagnosis. This
additional information is known as metadata and is important
for classifying and interpreting neuroimaging data, as will be
discussed in the succeeding text.
While there have been many large-scale efforts by the neuroimaging community to promote open sharing of primary
data, this progress has been slow limited by the variability
among sites in instrumentation and data-acquisition parameters, by the sheer size of the data sets, by patient confidentiality
issues, and by the desire of investigators to protect their
invested effort (and grant money) by maintaining access control. Despite these barriers, large, primary datasets are becoming steadily more accessible. The International Consortium for
Brain Mapping (ICBM) was a pioneer in this effort (Mazziotta,
Toga, Evans, Fox, & Lancaster, 1995), with the ICBM data still
being actively downloaded. Another early effort was the fMRI
Data Center, which gathered, curated, and openly shared the
complete datasets from published research articles (Van Horn
& Gazzaniga, 2013). Other more recent efforts include the
Biomedical Informatics Research Network (Keator et al.,
2008), the OpenfMRI Project (http://openfmri.org/; Poldrack
et al., 2013), the 1000 Functional Connectomes Project (http://
fcon_1000.projects.nitrc.org/), and the Laboratory of NeuroImaging (http://www.loni.usc.edu/Research/Databases/). Diseasespecific archives include the Alzheimers Disease Neuroimaging
Initiative (http://www.adni-info.org) and National Database
for Autism Research (http://ndar.nih.gov) among others. Many
datasets and neuroimaging tools are hosted on the NIHsponsored Neuroimaging Informatics Tools and Resources
Clearinghouse (http://www.nitrc.org/).
While access to these archives is free-of-charge, the construction and maintenance of these archives are not. Registration is typically required for access, mainly to allow funding
sources know where and how often their product is being
appreciated. In addition, registration allows both the data

user and the data provider to fulfill government regulations
(e.g., United States 21 CFR Part 50: http://www.hhs.gov/ohrp/
humansubjects/; 45 CFR Parts 160, 162, 164: http://www.hhs.
gov/ocr/privacy/) regarding patient privacy and to fulfill institutional ethical obligations (e.g., IRB; US 21 CFR Part 56,
http://www.accessdata.fda.gov/) to maintain data in a secure
REPOSITORY. Given these regulations, a common datasharing model is to provide open access to online descriptions
of available data, with comprehensive access being managed
by an over-site committee.
Derived, Statistical Parametric Data

Derived, statistical parametric data are three-dimensional (3-D)
images that represent the statistical measures derived from a
group of spatially normalized, raw data scans. Parametric data
can represent statistical differences in brain structure or function, depending on the analysis. Although all studies reporting
coordinates have, in some way, utilized statistical parametric
data, there are relatively few examples of derived data archives.
The Surface Management System Database (SumsDB) is an
online environment that allows users to search for fMRI parametric images that have activation levels within a selected
range located within a selected region of interest (http://
sumsdb.wustl.edu/sums/; Van Essen, 2009). This repository
also includes a large number (40 000 foci representing
1300 studies) of reduced, coordinate data (described in the
succeeding text).
Reduced, Coordinate Data

Coordinate-based databases represent spatially normalized,
statistically significant results from individual studies. Each
xyz coordinate references a template space (i.e., Talairach,
MNI) and most commonly represents the regional maximum
value from a corresponding SPI; for this reason, coordinate
data are considered a reduced version of a derived SPI. A
number of reduced data repositories exist: BrainMap, SumsDB
(Dickson, Drury, & Van Essen, 2001), Brede, AMAT, and Neurosynth. The former four were reviewed in Derrfuss and Mar
(2009); Neurosynth and BrainMap will be described in the
succeeding text.
Neurosynth was recently created as an online, open-source
resource that uses a parsing engine to automatically extract
reduced, coordinate data from the columns reported in tables
in neuroimaging articles (Yarkoni, Poldrack, Nichols, Van
Essen, & Wager, 2011). Such an automated approach allows
coordinates to be rapidly retrieved. This approach does not
distinguish activations from deactivations, different experimental contrasts, or coordinate space; however, because of
the sheer number of foci gathered, Neurosynth has shown
capable of producing informative brain-wide meta-analyses
(Yarkoni et al., 2011). Neurosynth uses text-mining and
machine-learning techniques to extract metadata and provides
frequency-based weightings for behavioral and cognitive terms
appearing in the coordinate-containing articles. These weightings are used to drive meta-analyses that can be performed
directly from the Neurosynth web interface. At time of writing,
Neurosynth reported 200 000 foci representing 6000 studies (http://neurosynth.org/).
BrainMap (Fox & Lancaster, 1994, 2002; Fox, Mikiten, Davis,
& Lancaster, 1994) was the first online reduced, coordinate
database. From the outset, the BrainMap strategy was to provide
coordinate-based results linked to experimental metadata that
emphasize experimental designs and behavioral conditions (Fox
& Lancaster, 1994). Each neuroimaging experiment is manually
coded and verified by the BrainMap team before being loaded
into the database. It takes a research assistant approximately
3060 min to enter the details of a single publication into
Scribe, the BrainMap data entry application (Laird, 2009).
While this is a time-consuming process, such manual duration
allows a depth and accuracy of coding that provides diverse data
mining opportunities and increases the value of the BrainMap
database; in addition, manual entry is necessary to insure accurate representation of experimental design, coordinate space,
data interpretation, and other aspects per the BrainMap coding
scheme (described in the succeeding text).
BrainMap contains two separate databases: a functional
database (representing fMRI and PET studies) and a voxelbased morphometry (VBM) database (representing structural
data). At time of writing, the BrainMap functional database
contained 90 000 foci representing 2300 papers; the BrainMap VBM database contained 18 000 foci representing 900
papers (http://brainmap.org/).
Finding the Data You Want: Metadata Taxonomies

Retrieving archived data can be a formidable challenge. This
challenge can be minimized with the use of general organizing
principles that clearly explain archive contents and allow users
to flexibly search, retrieve, and pool images or studies to
answer specific questions. The BrainMap database organizes
reduced, coordinate data into taxonomic categories based on
metadata descriptions. The BrainMap coding scheme includes
a detailed taxonomy of experimental design that provides
677
metadata descriptors intended not simply for retrieval of like

studies but for data-driven inferences concerning the functional properties of specific brain regions and networks (Fox
et al., 1994). Such metadata-driven analyses have allowed
emergent, database properties of neuroimaging data to be
modeled (see in the succeeding text) in both primary data
repositories and coordinate-based databases. Occasional tests
of the BrainMap taxonomy have shown that its organizing
principles are intuitive and readily applied by the neuroimaging community (Fox et al., 2005). The BrainMap taxonomy has
also helped inform comparable taxonomies for primary, raw
data repositories (Turner & Laird, 2011).
Data-Mining in a Coordinate Space: BrainMap at Work

We now outline several types of analysis that can be performed
using the BrainMap database. We begin with coordinate-based
analyses that synthesize results from specific experiments and
move to metadata analyses that reveal emergent, functional
properties of the human brain.
Paradigm and Disease-Level Analysis

The primary use of meta-analysis has been to synthesize the
published literature (of significant results) for the purposes of
computing consensus effects and, thereby, for placing constraints on the interpretation, design and analysis of subsequent
studies (Fox, Parsons, & Lancaster, 1998). Neuroimaging metaanalyses can serve as quantitative reviews and for hypothesis
generation. For example, to review where the brain is most
commonly active across single-word reading tasks, one can
search within the BrainMap fMRI database for all studies that
published single-word reading tasks. Meta-analysis of these
studies using activation likelihood estimation (ALE) will provide a quantitative review of brain activation in single-word
reading tasks. Other fMRI meta-analyses represent stuttering
(Brown, Ingham, Ingham, Laird, & Fox, 2005), depression
(Fitzgerald, Laird, Maller, & Daskalakis, 2008), and obsessive
compulsive disorder (Menzies et al., 2008) have also been
performed.
To review where structural damage is most common in
medial temporal lobe epilepsy, one could meta-analyze VBM
studies of gray matter reduction in this patient population
(Barron, Fox, Laird, Robinson, & Fox, 2013). Such an ALE
meta-analysis of these studies can inform the hypothesis of
where structural damage is most likely to be found in future
studies. Other VBM meta-analyses represent autism spectrum
disorder (Nickl-Jockschat et al., 2011), Huntingtons disease
(Dogan et al., 2013; Lambrecq et al., 2012), and anorexia
nervosa (Titova, Hjorth, Schioth, & Brooks, 2013).
The most interesting ALE applications do not merely merge
previous results, but also highlight previously ignored regions,
resolve conflicting views, validate new paradigms, and generate
new hypotheses for experimental testing. A more extensive list
of ALE studies and algorithms is available at www.brainmap.
org/pubs. Both the functional and VBM BrainMap databases
can be freely accessed at this level through Sleuth, the BrainMap
search engine (http://brainmap.org/tools).
678
Volume-Level Analysis: Connectivity

BrainMap can also be searched by volumes, that is, by which
studies report results within a specified volume of interest. This
allows one to meta-analytically assess interregional connectivity in a manner that is conceptually similar to functional, nonmeta-analytic approaches (e.g., resting-state fMRI; Biswal,
Zerrin Yetkin, Haughton, & Hyde, 1995). In these nonmetaanalytic approaches, temporal covariations in regional activation are used to detect connectivity; in the meta-analytic
approach, however, the unit of time is the study rather than
the second. Regions in which activations co-occur across studies (i.e., regions that are mutually predictive) are functionally
connected; regions that do not co-occur are not connected.
Higher probability of co-occurrence should reflect great
strength of functional connectivity. Functional connectivity
can be computed and exploited in different ways.
Region to region
The concept of coactivation-based, meta-analytic connectivity
model (MACM) was introduced by Koski and Paus (2000). To
identify frontal lobe projections to the anterior cingulate gyrus,
they manually collected and examined data from 107 studies,
reporting differential connection patterns within different subregions of the anterior cingulate. While regarding their new
approach as intrinsically plausible, Koski and Paus (2000)
acknowledged that it lacked formal validation. In view of this
shortcoming, they recommended replications using larger data
sets, the development of statistically more sophisticated
approaches, and validating the approach against alternative
connectivity measure, all of which eventually came to pass.
Note that this application was region to region in that it limited
its scope to connections between the frontal lobe and the
anterior cingulate gyrus; such an analysis can be performed
within Sleuth by searching the BrainMap database with
Sleuths anatomical label AND function (e.g., searching BrainMap for activations within frontal lobe AND anterior
cingulate).
Region-to-whole-brain
The first region-to-whole-brain coactivation meta-analysis was
reported by Postuma and Dagher (2006). Having identified
126 peer-reviewed, whole-brain studies with activations in
caudate or putamen, the authors computed the first wholebrain, meta-analytic functional connectivity images. In these
images, coactivation patterns were observed that were consistent with the concept of spatially segregated corticostriatal
connections as predicted by previous anatomical labeling studies in nonhuman primates. As with Koski and Paus (2000), no
validation other than plausibility was offered.
The region-to-whole-brain analysis strategy was adopted
and extended by Robinson, Laird, Glahn, Lovallo, and Fox
(2010). Using the Harvard/Oxford atlas to define the amygdala, the entire BrainMap database as the data source, and ALE
to compute co-occurrence spatial probabilities, Robinson
mapped the coactivation profile of the left and right amygdalae.
By way of validation of the approach, she termed MACM,
Robinson compared the amygdala MACM results with those
obtained by various tract-tracing methods in rhesus monkeys,
as reported in the CoCoMac database (Stephan et al., 2000),
finding startlingly good correspondence. Robinson et al.
(2012) applied a similar strategy to the caudate nuclei, adding
functional filtering using BrainMap behavioral domain metadata (Figure 2). MACM connectivity profiles have been validated by reference to resting state (Cauda et al., 2011; Cieslik
et al., 2012; Rottschy et al., 2012; Smith et al., 2009), diffusion
tractography (Eickhoff et al., 2010; Robinson et al., 2012), and
electrophysiology (Narayana et al., 2012). MACM analyses are
performed by searching for BrainMap subsets within Sleuth.
Left hemisphere
Right hemisphere
Action specific
Cognition specific
Perception specific
Emotion specific
Figure 2 MACM with behavioral domain filtering. The images illustrate the regional and behavioral specificities of the connections of the caudate
nucleus. Connectivity was computed as coactivations frequency with seed region (caudate nucleus), sampling across the entire BrainMap database.
ALE was used to compute statistical significance of co-occurrences. Behavioral filtering used the top tier of the BrainMap behavioral domain hierarchy.
The projection patterns closely matched those established in the primate literature and were confirmed by DTI tractography. Images are reproduced
with permission from Robinson et al. (2010), the original report of behaviorally filtered MACM connectivity mapping.
Coactivation-based parcellation
679
Entire Database Analysis: Brain-Wide Functional Ontologies
Coactivation-based parcellation (CBP) is an exciting extension

of the region-to-whole-brain MACM approach and is based on
the ability to create a voxel-to-whole-brain MACM. Because of
this ability, individual voxels within a larger volume of interest
can be redistricted into regions of similar whole-brain connectivity patterns, with the most similar voxels forming clusters.
CBP of primary structural (DTI) data has been shown to provide a close correspondence between structurally and functionally defined borders, using the boundary between SMA and
pre-SMA as a demonstration case (Johansen-Berg et al., 2004).
Eickhoff et al. (2011) applied CBP to BrainMaps reduced data
for the same brain regions (SMA and pre-SMA) and obtained
the virtually identical borders (Eickhoff et al., 2011). In an
even more telling validation, Bzdok, Laird, Zilles, Fox, and
Eickhoff (2012) applied CBP to the amygdala (cf. Figure 3),
demonstrating a close correspondence to previously defined
cytoarchitectonic borders (Amunts et al., 2005). Additional
studies have successfully classified subregions of the dorsolateral prefrontal cortex (Cieslik et al., 2012) and Brocas area
(Clos, Amunts, Laird, Fox, & Eickhoff, 2013) corroborated
the BrainMap-derived connectivity patterns with resting-state
functional connectivity using fMRI. Because MACM-CBP analyses require comprehensive use of the BrainMap database,
such analyses are performed in the context of collaboration
with the BrainMap team, which is free-of-charge.
In section Volume-Level Analysis: Connectivity, we reviewed

methods that drew connectivity inferences between two seed
regions (less complex) and between a seed region and the
whole brain (more complex). Here, we review methods that
draw connectivity inferences by comparing coactivations
between every brain voxel and every other voxel (all-to-all)
both within and across paradigm classes. The two most-general
classes of network discovery methods addressed are graph
theoretical modeling and independent components analysis
(ICA). Both approaches have been applied to the entire BrainMap database (or large subsets thereof), that is, across behaviorally inhomogeneous paradigms. The remaining analyses
require comprehensive use of the BrainMap database, which
is granted freely in the context of collaboration with the BrainMap team.
Graph theory modeling approaches

Graph theoretical constructs have been applied meta-analytically for voxel-wise, all-to-all (whole-brain to whole-brain)
network discovery. Neumann, Fox, Turner, and Lohmann
(2010) used Bayesian network discovery to model the underlying coactivation structure of brain regions across imaging
studies. This analysis involved a large subset (2505 experiments) of the BrainMap database and showed that serial,
data-driven reductions in the scope of analysis revealed different levels of commonly co-occurring regions, indicating that
certain brain areas were more likely to coactivate at different
levels.
Crossley, Mechelli, and Vertes (2013) extended the all-to-all
graph theory approach to estimate the relative frequency that
each pair of regions in standard space was coactivated by
multiple tasks reported in the primary literature. As show in
Figure 4, this large-scale topological modeling revealed complex hubs, functionally specialized modules (for perception,
action, emotion, etc.), and a rich club that was more diversely
coactivated by tasks requiring both action and cognition.
Independent components analysis
Cytoarchitectonic
parcellation
Coactivation-based
parcellation
Figure 3 Coactivation-based parcellation. The coactivation-based

parcellation of the amygdala as derived using the BrainMap database
(right panels) proved highly similar to that observed (in a separate post
mortem sample) using cytoarchitecture (left panel). Blue laterobasal
nuclei group, red centromedial nuclei group, green superficial nuclei
group. Reproduced from Bzdok, D., Laird, A. R., Zilles, K., Fox, P. T., &
Eickhoff, S. B. (2012). An investigation of the structural, connectional,
and functional subspecialization in the human amygdala. Human Brain
Mapping, 34, 32473266, with permission.
Toro, Fox, and Paus (2008) used the BrainMap database to

generate a comprehensive connectivity atlas. At the time,
BrainMap included 3402 experiments (conditional contrasts)
reporting a total of 27 909 activated locations. For each experiment, a binary, per-study activation volume was generated.
From these, the co-occurrence pattern likelihood was computed between all voxels and demonstrated a robust structure
in the meta-analytic functional connectivity that can be recovered even with only a moderate subset of studies.
Intrigued by Toros observations, Smith et al. (2009) took
this strategy a step further and applied ICA to the entire BrainMap data volume. ICA has been widely used to demonstrate
intrinsic connectivity networks in the resting brain using fMRI
(i.e., resting-state networks or RSNs). Although observed at
rest, Fox and Raichle (2007) proposed that RSNs represent
basic organizational units of the brain, being functional networks drawn upon during task performance. Smith tested this
hypothesis by comparing ICA decompositions of resting-state
fMRI to those derived from the BrainMap data. In parallel, ICA
analyses were performed using resting-state fMRI data from 36
Figure 4 Topological analysis. The comparability of topological networks derived from meta-analysis of the BrainMap database (top row) and
resting-state fMRI in 27 subjects (middle row) is illustrated. In anatomical space (a; upper two rows), the size of the nodes is proportional to their
weighted degree (strength), and their color corresponds to module membership. The relationship between the coactivation metric (Jaccard index; b) and
the connectivity metric for every pair of regions is graphed (b). The degree and distance distributions for both networks are plotted (c and d,
respectively). Reproduced from Crossley, N. A., Mechelli, A., & Vertes, P. E. (2013). Cognitive relevance of the community structure of the human
brain functional coactivation network. Proceedings of the National Academy of Sciences of the United States of America, 110, 1158311588, with
permission.
Figure 5 ICA. The comparability of independent components derived from meta-analysis and resting-state networks is illustrated. Each of the ten
panels shows one well-matched pair of networks from two, 20-component ICA analyses. In each panel, the left-side images are derived from a metaanalysis of the BrainMap database (30 000 subjects); the right-side images are from a 36-subject resting-state fMRI database. Reproduced from
Smith, S. M., Fox, P. T., Miller, K. L., Glahn, D. C., Fox, P. M., Mackay, et al. (2009). Correspondence of the brains functional architecture during
activation and rest. Proceedings of the National Academy of Sciences of the United States of America, 106, 1304013045, with permission.
healthy volunteers. Decompositions were performed into both
20 and 70 components.
Of the 20 components generated separately from the two
datasets, ten maps from each set were unambiguously paired
between datasets, with a minimum correlation r 0.25
(p < 105, corrected for multiple comparisons and for spatial
smoothness). These ten well-matched pairs of networks are
shown in Figure 5. With an ICA dimensionality of 70, the
primary networks split into subnets in similar (but not identical) ways, continuing to show close correspondence between
BrainMap and RSN components. This argues that the full
repertoire of functional networks utilized by the brain in action
(coded in BrainMap) is continuously and dynamically active
even when at rest and, vice versa, that RSNs represent an
intrinsic functional architecture of the brain that is drawn
upon to support task performance.
Behavioral Interpretation
Automated, anatomical labeling machines like the Talairach
Daemon have been widely embraced by the neuroimaging
community (Lancaster et al., 2000). Such a machine returns
an anatomical label for an xyz coordinate location or a 3-D
volume within a standardized space. Automated, behavioral
machines are similar in that they provide behavioral descriptions for locations or volumes and can be produced by referencing the BrainMap metadata. Behavioral descriptions are
681
especially useful to describe the results of studies that have no

behavioral component, such as structural or resting-state functional MRI studies, or system modeling studies that delineate
brain-wide network organization.
BrainMaps behavioral metadata can be used to characterize
the behavioral properties of specific networks (Cauda et al.,
2011; Robinson et al., 2010). Statistical methods to test for
between-region differences in behavioral domain profiles have
been developed (Lancaster et al., 2012) and are currently being
extended to paradigm class data. Using this approach, it
appears that given sufficient numbers of experiments and
well-developed behavioral metadata unique behavioral characterization of individual brain regions is a viable possibility.
An extension of the behavioral domain profile approach is to
extract profiles for multiple regions jointly, that is, to characterize a functional network. This strategy was employed by
Laird et al. (2009), in work that behaviorally categorized the
default mode network, examining behavioral domain profiles
of individual areas and of groups of areas (i.e., subnetworks).
Another strategy for meta-analytic structurefunction inference was pioneered by Smith et al. (2009), in the context of
applying ICA to the BrainMap database. Figure 6 (left side) is a
heat map showing the respective contributions of BrainMap
behavioral domains to individual components in the ICA
shown in Figure 5. Close inspection reveals that some components have very high behavioral specificity, while other
Figure 6 BrainMap metadata behavioral interpretations. The mapping of BrainMap metadata onto ICA components is shown. Note that behavioral
metadata form discrete groupings that functionally characterize the spatial groupings provided by ICA. In the left panel, 20 behavioral domain
categorizations were correlated with the ten ICA-derived components shown in Figure 5. In the right panel, the metadata analysis has been extended to
include 50 behavioral domain categories and 75 paradigm class categories. Hierarchical clustering was used to group the ICA into spatially and
behaviorally related clusters for all 20 ICA components. (a) Reproduced from Smith, S. M., Fox, P. T., Miller, K. L., Glahn, D. C., Fox, P. M., Mackay, et al.
(2009). Correspondence of the brains functional architecture during activation and rest. Proceedings of the National Academy of Sciences of the
United States of America, 106, 1304013045, with permission; (b) Reproduced from Laird, A. R., Eickhoff, S. B., Fox, P. M., Uecker, A. M., Ray, K. L.,
Saenz, J. J., et al. (2011). The BrainMap strategy for standardization, sharing, and meta-analysis of neuroimaging data. BMC Research Notes, 4,
349; Laird, A. R., Fox, P. M., Eickhoff, S. B., Turner, J. A., Ray, K. L., McKay, D. R., et al. (2011). Behavioral interpretations of intrinsic connectivity
networks. Journal of Cognitive Neuroscience, 23, 40224037, with permission.
682
components have contributions from a wide range of

behavioral domains. The ICA-based strategy of Smith and
colleagues has been extended by Laird et al. (2011) both by
enriching the metadata included in the analysis and by applying hierarchical clustering analysis to sort components into
functionally related groupings (Figure 6, right side).
Caveat: While this approach provides a much more refined
association of components with behaviors, some components
still show limited behavioral specificity. The most likely explanations for this lack of behavioral specificity in some networks
are twofold: First, the behavioral specificity of some regions
and networks (hubs in the terminology of topological modeling) is almost certainly low. Hub regions are engaged in a wide
variety of tasks and will defy precise behavioral characterization. Second, a more evolved functional ontology is needed, as
has been argued (Poldrack, 2006; Price, Devlin, Moore, Morton, & Laird, 2005). Relative to the second cause, the
approaches illustrated here, we would suggest, provide the
tools for ontology development to proceed programmatically.
This can be determined by targeting networks that show limited behavioral domain specificity and enriching the metadata,
for example, by adding levels to the coding hierarchy. This
work is ongoing (Fox et al., 2005; Laird et al., 2011) and calls
for deeper, more evolved tools. Ultimately, categorizations of
behavior that are reflected in the network properties of the
brain will have superior intrinsic validity and utility as compared to those based solely on cognitive theory.
Conclusion
A closing point of some importance is that databases allow
many rich sources of analysis, as exemplified by the BrainMap
database. Since its inception, BrainMap has evolved with a
family of coordinate-based meta-analysis (CBMA) methods,
described in the preceding text. While these may appear to be
conceptually discrete methods, in practice, they tend to be
applied serially, with simpler forms of meta-analysis providing
input for more advanced forms.
CBMA methods are used as hypothesis generators within
larger-scope studies to define regions of interest for subsequent, extra-BrainMap methods like diffusion tractography
and resting-state fMRI. In addition, rigorous paradigm taxonomy allows BrainMap meta-analysis to offer a versatile, powerful approach for discovering the behavioral significance of
networks mapped using anatomical or functional techniques
that contain no explicit behavioral information.
Acknowledgments
This work was supported by awards from the National Institutes
of Health (MH74457, RR024387, MH084812, NS062254,
AA019691, and EB015314) and the Congressionally Directed
Medical Research Program (W81XWH0820112). Portions of
this article were adapted from Fox and Friston (2012) and
from Fox et al. (2014).
The BrainMap database is an electronic compilation of the
results of peer-reviewed, published neuroimaging studies
(both functional and structural) that utilized standardized
coordinates to analyze and report their results (Fox & Lancaster, 2002). The BrainMap data (as an electronic compilation)
and the coding taxonomy are protected by copyrights held by
the University of Texas Board of Regents (see http://brainmap.
org for the entire BrainMap Database Collaborative-Use
License Agreement).

Rigid-Body Registration; Nonlinear Registration Via Displacement
Fields; Diffeomorphic Image Registration; Voxel-Based Morphometry;
Bayesian Multiple Atlas Deformable Templates; Resting-State
Functional Connectivity; Effective Connectivity; Graph-Theoretical
Analysis of Brain Networks; Reverse Inference; Meta-Analyses in
Functional Neuroimaging; Databases.
References
Amunts, K., Kedo, O., Kindler, M., Pieperhoff, P., Mohlberg, H., Shah, N. J., et al.
(2005). Cytoarchitectonic mapping of the human amygdala, hippocampal region
and entorhinal cortex: Intersubject variability and probability maps. Anatomy and
Embryology, 210, 343352.
Barron, D. S., Fox, P. M., Laird, A. R., Robinson, J. L., & Fox, P. T. (2013). Thalamic
medial dorsal nucleus atrophy in medial temporal lobe epilepsy: A VBM metaanalysis. NeuroImage: Clinical, 2, 2532.
Biswal, B., Zerrin Yetkin, F., Haughton, V. M., & Hyde, J. S. (1995). Functional
connectivity in the motor cortex of resting human brain using echo-planar mri.
Brown, S., Ingham, R. J., Ingham, J. C., Laird, A. R., & Fox, P. T. (2005). Stuttered and
fluent speech production: An ALE meta-analysis of functional neuroimaging studies.
Bzdok, D., Laird, A. R., Zilles, K., Fox, P. T., & Eickhoff, S. B. (2012). An investigation of
the structural, connectional, and functional subspecialization in the human
amygdala. Human Brain Mapping, 34, 32473266, http://www.ncbi.nlm.nih.gov/
pubmed/22806915.
Cauda, F., Cavanna, A. E., Dagata, F., Sacco, K., Duca, S., & Geminiani, G. C. (2011).
Functional connectivity and coactivation of the nucleus accumbens: A combined
functional connectivity and structure-based meta-analysis. Journal of Cognitive
Cieslik, E. C., Zilles, K., Caspers, S., Roski, C., Kellermann, T. S., Jakobs, O., et al.
(2012). Is there one DLPFC in cognitive action control? Evidence for heterogeneity
from co-activation-based parcellation. Cerebral Cortex, 23, 26772689, http://www.
ncbi.nlm.nih.gov/pubmed/22918987.
Clos, M., Amunts, K., Laird, A. R., Fox, P. T., & Eickhoff, S. B. (2013). Tackling the
multifunctional nature of Brocas region meta-analytically: Co-activation-based
parcellation of area 44. NeuroImage, 83, 174188, http://www.ncbi.nlm.nih.gov/
pubmed/23791915.
Crossley, N. A., Mechelli, A., & Vertes, P. E. (2013). Cognitive relevance of the
community structure of the human brain functional coactivation network.
110(28), 1158311588.
Derrfuss, Marr (2009). Lost in localization: The need for a universal coordinate
database. Neuroimage, 48, 17.
Dickson, J., Drury, H., & Van Essen, D. C. (2001). The surface management system
(SuMS) database: A surface-based database to aid cortical surface reconstruction,
visualization and analysis. Philosophical Transactions of the Royal Society, B:
Biological Sciences, 356, 12771292.
Dogan, I., Eickhoff, S. B., Schulz, J. B., Shah, N. J., Laird, A. R., Fox, P. T., et al. (2013).
Consistent neurodegeneration and its association with clinical progression in
Huntingtons disease: A coordinate-based meta-analysis. Neurodegenerative
Diseases, 12, 2335.
Eickhoff, S. B., Bzdok, D., Laird, A. R., Roski, C., Caspers, S., Zilles, K., et al. (2011).
Co-activation patterns distinguish cortical modules, their connectivity and
functional differentiation. NeuroImage, 57, 938949.
Eickhoff, S. B., Jbabdi, S., Caspers, S., Laird, A. R., Fox, P. T., Zilles, K., et al. (2010).
Anatomical and functional connectivity of cytoarchitectonic areas within the human
parietal operculum. Journal of Neuroscience, 30, 64096421.
Fitzgerald, P. B., Laird, A. R., Maller, J., & Daskalakis, Z. J. (2008). A meta-analytic
study of changes in brain activation in depression. Human Brain Mapping, 29,
683695.
Fox, P. T., & Friston, K. J. (2012). Distributed processing: Distributed functions?
Fox, P. T., Laird, A. R., Fox, S. P., Fox, P. M., Uecker, A. M., Crank, M., et al. (2005).
Brainmap taxonomy of experimental design: Description and evaluation. Human
Fox, P., & Lancaster, J. (1994). Neuroscience on the net. Science, 266, 994996.
Fox, P. T., & Lancaster, J. L. (2002). Mapping context and content: The BrainMap
model. Nature Reviews Neuroscience, 3, 319321.
Fox, P. T., Lancaster, J. L., Laird, A. R., & Eickhoff, S. B. (2014). Meta-analysis in
human neuroimaging: Computational modeling of large-scale databases. Annual
Review of Neuroscience, 37, 1.
Fox, P. T., Mikiten, S. A., Davis, G., & Lancaster, J. L. (1994). BrainMap: A database of
human functional brain mapping. In R. W. Thatcher, W. Hallet, T. A. Zeffiro, E. R.
John & M. Huerta (Eds.), Functional neuroimaging. San Diego: Academic Press,
Elsevier.
Fox, P. T., Parsons, L. M., & Lancaster, J. L. (1998). Beyond the single study: Function/
location metanalysis in cognitive neuroimaging. Current Opinion in Neurobiology,
8, 178187.
Fox, M. D., & Raichle, M. E. (2007). Spontaneous fluctuations in brain activity observed
700711.
Johansen-Berg, H., Behrens, T. E. J., Robson, M. D., Drobnjak, I.,
Rushworth, M. F. S., Brady, J. M., et al. (2004). Changes in connectivity profiles
define functionally distinct regions in human medial frontal cortex. Proceedings of
1333513340.
Keator, D. B., Grethe, J. S., Marcus, D., Ozyurt, B., Gadde, S., Murphy, S., et al. (2008).
A national human neuroimaging collaboratory enabled by the Biomedical
Informatics Research Network (BIRN). IEEE Transactions on Information Technology
in Biomedicine, 12, 162172.
Koski, L., & Paus, T. (2000). Functional connectivity of the anterior cingulate cortex
within the human frontal lobe: A brain-mapping meta-analysis. Experimental Brain
Research, 133, 5565.
Laird, A. R. (2009). ALE meta-analysis workflows via the BrainMap database:
Progress towards a probabilistic functional brain atlas. Frontiers in
Neuroinformatics, 3, 23, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715269/.
Laird, A. R., Eickhoff, S. B., Fox, P. M., Uecker, A. M., Ray, K. L., Saenz, J. J., et al.
(2011). The BrainMap strategy for standardization, sharing, and meta-analysis of
neuroimaging data. BMC Research Notes, 4, 349.
Laird, A. R., Eickhoff, S. B., Li, K., Robin, D. A., Glahn, D. C., & Fox, P. T. (2009).
Investigating the functional heterogeneity of the default mode network using
coordinate-based meta-analytic modeling. Journal of Neuroscience, 29,
1449614505.
Laird, A. R., Fox, P. M., Eickhoff, S. B., Turner, J. A., Ray, K. L., McKay, D. R., et al.
(2011). Behavioral interpretations of intrinsic connectivity networks. Journal of
Cognitive Neuroscience, 23, 40224037.
Lambrecq, V., Langbour, N., Guehl, D., Bioulac, B., Burbaud, P., & Rotge, J. Y. (2012).
Evolution of brain gray matter loss in Huntingtons disease: A meta-analysis.
European Journal of Neurology, 20, 315321.
Lancaster, J. L., Laird, A. R., Eickhoff, S. B., Martinez, M. J., Fox, P. M., & Fox, P. T.
(2012). Automated regional behavioral analysis for human brain images. Frontiers
in Neuroinformatics, 6, 23.
Lancaster, J. L., Woldorff, M. G., Parsons, L. M., Liotti, M., Freitas, C. S., Rainey, L.,
et al. (2000). Automated Talairach atlas labels for functional brain mapping. Human
Mazziotta, J. C., Toga, A. W., Evans, A., Fox, P., & Lancaster, J. (1995). A probabilistic
atlas of the human brain: Theory and rationale for its development the international
consortium for brain mapping (ICBM). NeuroImage, 2, 89101.
683
Menzies, L., Chamberlain, S. R., Laird, A. R., Thelen, S. M., Sahakian, B. J., &
Bullmore, E. T. (2008). Integrating evidence from neuroimaging and
neuropsychological studies of obsessivecompulsive disorder: The orbitofrontostriatal model revisited. Neuroscience & Biobehavioral Reviews, 32, 525549.
Narayana, S., Laird, A. R., Tandon, N., Franklin, C., Lancaster, J. L., & Fox, P. T. (2012).
Electrophysiological and functional connectivity of the human supplementary motor
area. NeuroImage, 62, 250265.
Neumann, J., Fox, P. T., Turner, R., & Lohmann, G. (2010). Learning partially directed
functional networks from meta-analysis imaging data. NeuroImage, 49, 13721384.
Nickl-Jockschat, T., Habel, U., Maria Michel, T., Manning, J., Laird, A. R., Fox, P. T.,
et al. (2011). Brain structure anomalies in autism spectrum disorder A metaanalysis of VBM studies using anatomic likelihood estimation. Human Brain
Mapping, 33, 14701489.
Petersen, S. E., Fox, P. T., Posner, M. I., Mintun, M., & Raichle, M. E. (1988). Positron
emission tomographic studies of the cortical anatomy of single-word processing.
Nature, 331(6157), 585589.
Trends in Cognitive Sciences, 10, 5963.
et al. (2013). Toward open sharing of task-based fMRI data: The OpenfMRI project.
Frontiers in Neuroinformatics, 7, 12, http://www.ncbi.nlm.nih.gov/pmc/articles/
PMC3703526/.
Poline, J.-B., Breeze, J. L., Ghosh, S., Gorgolewski, K., Halchenko, Y. O., Hanke, M.,
et al. (2012). Data sharing in neuroimaging research. Frontiers in Neuroinformatics,
6, 9, http://www.ncbi.nlm.nih.gov/pubmed/22493576.
Postuma, R. B., & Dagher, A. (2006). Basal ganglia functional connectivity based on a
meta-analysis of 126 positron emission tomography and functional magnetic
resonance imaging publications. Cerebral Cortex, 16, 15081521.
Price, C. J., Devlin, J. T., Moore, C. J., Morton, C., & Laird, A. R. (2005). Meta-analyses
of object naming: Effect of baseline. Human Brain Mapping, 25, 7082.
Robinson, J. L., Laird, A. R., Glahn, D. C., Blangero, J., Sanghera, M. K., Pessoa, L., et al.
(2012). The functional connectivity of the human caudate: An application of metaanalytic connectivity modeling with behavioral filtering. NeuroImage, 60, 117129.
Robinson, J. L., Laird, A. R., Glahn, D. C., Lovallo, W. R., & Fox, P. T. (2010).
Metaanalytic connectivity modeling: Delineating the functional connectivity of the
human amygdala. Human Brain Mapping, 31, 173184.
Rottschy, C., Caspers, S., Roski, C., Reetz, K., Dogan, I., Schulz, J. B., et al. (2012).
Differentiated parietal connectivity of frontal regions for what and where
memory. Brain Structure and Function, 218, 15511567.
Smith, S. M., Fox, P. T., Miller, K. L., Glahn, D. C., Fox, P. M., Mackay, C. E., et al.
(2009). Correspondence of the brains functional architecture during activation and
rest. Proceedings of the National Academy of Sciences of the United States of
America, 106, 1304013045.
Stephan, K. E., Hilgetag, C. C., Burns, G. A. P. C., ONeill, M. A., Young, M. P., &
Kotter, R. (2000). Computational analysis of functional connectivity between areas
of primate cerebral cortex. Philosophical Transactions of the Royal Society, B:
Titova, O. E., Hjorth, O. C., Schioth, H. B., & Brooks, S. J. (2013). Anorexia nervosa is
linked to reduced brain structure in reward and somatosensory regions: A metaanalysis of VBM studies. BMC Psychiatry, 13, 110.
Toro, R., Fox, P. T., & Paus, T. (2008). Functional coactivation map of the human brain.
Turner, J. A., & Laird, A. R. (2011). The cognitive paradigm ontology: Design and
application. Neuroinformatics, 10, 5766.
Van Essen, D. C. (2009). Lost in localization But found with foci?!. NeuroImage, 48,
1417.
Van Horn, J. D., & Gazzaniga, M. S. (2013). Why share data? Lessons learned from the
fMRIDC. NeuroImage, 82, 677682.
Methods, 8, 665670.
Databases
JD Van Horn, University of Southern California, Los Angeles, CA, USA
Introduction
Organizing, annotating, archiving, and distributing biomedical data in usable and structured frameworks have become
critical elements across a range of scientific efforts. Driven by
advances in clinical, genetic, and imaging electronic data collection, research data are being gathered at an increasing rate.
The need to store and exchange data in meaningful ways in
support of data analysis, rigorous hypothesis testing, and subsequent analysis is considerable. While a spectrum of infrastructures for neuroimaging databasing exist (Van Horn et al.,
2001), from summary findings to fully curated archives, largescale computing and storage have clear advantages for study
information fidelity (Van Horn & Gazzaniga, 2005), distributed computation (Van Horn et al., 2006), and data reuse (Van
Horn & Ishai, 2007).
There are, however, many challenges to achieving valueadded data sharing, which become more obvious as data are
collected variably, where documentation is insufficient, some
postprocessing and/or data analysis has already occurred, or
the coordination among multiple sites is poor. If processed
versions of data are to be shared, the problem can often be
compounded because knowledge of which version of data was
used for a particular analysis and the order of processing steps
is highly important to the interpretation and reuse of derived
results (Van Horn & Toga, 2009a). Table 1 provides an overview of advantages/drawbacks across the database spectrum.
Nevertheless, advantages of distributed science in the form
of multisite consortia and accompanying databases have
continued to push this approach in many population-level
investigations.
Several noteworthy examples illustrate the breadth of neuroimaging databases. The BrainMap database (Fox & Lancaster,
2002; Fox, Mikiten, Davis, & Lancaster, 1994b; Laird, Eickhoff,
et al., 2011) is among the most well-known and longest-running
brain imaging results database. Recording brain activation focal
statistical results as Talairach/Montreal Neurological Institute
(MNI) space coordinates, BrainMap has systematically evolved
over time (Laird, Lancaster, & Fox, 2005) to incorporate new and
diverse information on study experimental design (Fox et al.,
2005). Now encompassing the results from many thousands of
brain mapping studies, BrainMap is an essential tool for metaanalytic assessments of the neuroimaging literature (Laird, Lancaster, & Fox, 2009; Laird et al., 2009; Laird, Fox, et al., 2011;
Torta & Cauda, 2011).
The fMRI Data Center (fMRIDC) project (Van Horn et al.,
2001) conducted active curation of complete datasets from
functional neuroimaging studies of cognition and behavior
between 2000 and 2007. Despite early misgivings from the
community (Governing Council of the Organization for
Human Brain Mapping, 2001; Toga, 2002b), this database
of functional and structural datasets, accompanied by subject
and paradigm metadata, from over 100 peer-reviewed studies
even now still represents one of the largest collections

of neuroimaging undertaken. Data contributed to the
fMRIDC have been used in the reanalyses of fMRI results in
Alzheimers disease (Greicius, Srivastava, Reiss, & Menon,
2004), examinations of effective connectivity in visual object
recognition (Mechelli, Price, Noppeney, & Friston, 2003),
comparison of dynamic causal models (Penny, Stephan,
Mechelli, & Friston, 2004), and neural decoding (Carlson,
Schrater, & He, 2003), among other applications (Van Horn
& Gazzaniga, 2012). The fMRIDC to record and disseminate
study data helped to solidify the notion that fMRI data reuse
and repurposing beyond the scope of its original application
could result in wide-ranging applications and interesting
results (Van Horn & Ishai, 2007).
Encouraged by these outcomes, the neuroscientific community has seen increased numbers of large-scale databases, each
with varying degrees of success, driven in part by advances in
infrastructure technologies, the demand for multiscale data in
the investigation of fundamental disease processes, the need for
cooperation across disciplines to integrate and interpret the
data, and the movement of science in general toward freely
available information (Van Horn & Toga, 2009b). Numerous
imaging examples can be found in the ubiquitous application
of neuroimaging to the study of brain structure and function in
health and disease. A simple Internet search finds several wellknown cooperative efforts to construct and populate large brain
databases (Mazziotta et al., 2001), develop databases of cortical
surfaces and atlas their features (Van Essen, 2005), and provide
insights into brain genetics (Saykin et al., 2010). What is more,
the development of databasing tools such as XNAT (Marcus,
Olsen, Ramaratnam, & Buckner, 2007) has allowed individual
labs or collections thereof to actively archive and share data.
Databasing initiatives spearheaded by government agencies
like the National Institutes of Health (NIH) in the United
States are also underway to gather data on a diverse range of
neurological topics including autism (the National Database
for Autism Research (NDAR); http://www.ndar.gov) and neurotrauma (the Federal Interagency Traumatic Brain Injury
Research (FITBIR); http://fitbir.nih.gov). The recent Human
Brain Project effort underway in Europe (http://www.humanbrainproject.eu/; Markram, 2012) also has plans to gather,
database, and share larger-scale brain imaging data through
its informatics activities. Leading grassroots examples of open
neuroimaging databasing and sharing include the OpenfMRI
project (https://openfmri.org/) (Poldrack et al., 2013), for
cognitive task-based activation studies, and the 1000 Functional Connectomes Project (http://fcon_1000.projects.nitrc.
org/) (Milham, 2012), for datasets relevant to resting-state
connectivity analysis. Inherent in these community-driven,
multilaboratory, and governmentally driven projects are sociologic, legal, and even ethical concerns that must be resolved
satisfactorily before they can work effectively or be widely
accepted by the scientific community.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00351-1
685
686
Table 1
INTRODUCTION TO METHODS AND MODELING | Databases

Attributes of functionality across the spectrum of neuroimaging databases
Staffed?
Metadata?
User-side
resources?
Web?
Accessibility?
Log-in?
Provenance?
HIPAA?
QC?
Single
site/multisite?
Published study
datasets?
Robust
infrastructure?
Published
description?
Processing tools?
Upload cost?
Download cost?
Customizable
interface?
CD/DVD/
USB
Anonymous
FTP/SCP
Advertised
metadata
Activation
loci only
Statistical
maps
Personal data
repository
Fully curated archive
No
Maybe
Yes
Unlikely
Maybe
No
Partially
Maybe
No
Partially
Yes
No
Partially
Study level
No
No
Yes
Yes
Yes
Yes
No
No
One-toone
N/A
Yes
Open
Yes
Open
Yes
Open
Yes
Open
Possibly
Possibly
Yes
Open/partial
No
Unlikely
Yes
Unlikely
Likely
Maybe
Single
Unlikely
Likely
Maybe
Single/multi
Not
required
Unlikely
N/A
N/A
Single
No
Unlikely
Maybe
Unlikely
Single
Software
needed
Unlikely
N/A
N/A
Single
Yes
Possibly
User-driven
Single
Yes
Yes
Curated
Single/multi
Maybe
Maybe
Maybe
Yes
Yes
Possibly
Published/nonpublished
N/A
Maybe
Maybe
Partially
Partially
Maybe
Yes
No
Unlikely
Maybe
Yes
Yes
Maybe
Yes
No
No
Maybe
Workflows
Unlikely
Unlikely
Unlikely
Unlikely
Metaanalytic
None
None
Possibly
None
Only for
media
No
Metaanalytic
None
none
None
None
Possibly
None
No
No
No
No
Possibly
Possibly
While not intended to be an exhaustive list, per se, Table 2

presents a brief list of several ongoing or newly developed
multisite trials or collaborations working toward applying
neuroimaging methods for mapping the normal brain and
sharing brain imaging data in various neurological diseases.
Each effort maintains explicit requirements for the sharing of
data and making their databases openly accessible to outside
researchers.
Neuroimaging Databasing: A Particular Example

As a particular example of neuroimaging databases in action,
the Image Data Archive (IDA) from the Laboratory of Neuro
Imaging (LONI) is highlighted that serves as a leading example
of a fully curated multimodal neuroimaging archive used as a
resource for active data sharing. LONI has been serving as a
repository for single-site and multisite neuroimaging research
studies for many years (Toga, 2002a). The LONI IDA (Toga &
Crawford, 2010) provides a comprehensive and interactive
environment for safely archiving, querying, visualizing, and
sharing neuroimaging clinical and neurocognitive data. It represents a user-friendly environment to archive, search, share,
track, and disseminate neuroimaging data, accommodating
magnetic resonance imaging (MRI), functional magnetic resonance imaging (fMRI), positron emission tomography (PET),
MRA, diffusion tensor imaging (DTI), and other imaging data
types (Figure 1).
Archiving data in the IDA is designed to be straightforward

and secure, requiring no specialized hardware or software. The
IDA employs a flexible data deidentification engine and
encrypted file transmission to ensure compliance with
patient-privacy regulations and data are stored on redundant
servers with daily and weekly on- and off-site backups. Additionally, the IDA automatically extracts relevant metadata from
deidentified image files, saving the contributor from having to
enter this information manually and allowing data to be
searched within moments of archival.
Once archived, data can be downloaded and/or streamed
into the data processing workflow environments for processing
and analysis (Dinov et al., 2009, 2010). Integration of an
automated file format translation engine (Neu et al., 2005)
allows users to download image data converted into several
commonly used file formats. The archive facilitates the deidentification and pooling of data from multiple institutions,
protecting data from unauthorized access while providing the
ability to share data among collaborative investigators.
The data from studies contained in the IDA include over
14 000 imaging series for thousands of subjects, from different
age groups, disease states, and species (Table 2), with growth
averaging >380 new image series per month. Study investigators
may perform textual queries across the clinical and imaging
data, browse, update, and organize the data. A basic image viewer
allows the image data to be visually inspected. Users may form
data collections and download the data locally or pass the
collections to the LONI Pipeline, which provides a graphical
interface to a dynamic suite of image processing software.
Table 2
Neuroimaging trials or collaborative efforts involving multiple research sites

Imaging
modalities
Participating institutions
Subject population
Alzheimers Disease
Neuroimaging
Initiative (ADNI)
UCSF, NCIRE, VA, University of California, San Diego; Arizona

State University; Banner Good Samaritan Medical Center; UC
Davis; Mayo Clinic, Rochester, Minnesota; University of
California, Berkeley
Mild cognitive impairment;

Alzheimers disease;
normal control subjects
sMRI,
PET
Autism Centers of
Excellent (ACE)
network
Collaborative
Initiative on Fetal
Alcohol Spectrum
Disorder (CIFASD)
Yale, Harvard, UCLA, USC, and Seattle Childrens Research

Institute
Children with autism

spectrum disorder
MRI, EEG
San Diego State University; Indiana University School of

Medicine; University of California, San Diego; University of
California, Los Angeles; University of New Mexico; Texas
A&M, Indiana UniversityPurdue University School of
Science; Ukrainian-American Birth Defects Program;
University of North Carolina at Chapel Hill; Harvard; UC
Davis; Folkhalsan Research Center, Helsinki; University of
Cape Town, South Africa; Emory University; Moscow
Regional Research Institute of Obstetrics and Gynaecology
University of California, Los Angeles; Montreal Neurological
Institute; University of Texas, San Antonio; Vogt Institute,
Julich, Germany
Fetal alcohol syndrome

children (with and without
facial dysmorphia),
normal control subjects
Normal subjects;
methamphetamine
patients; HIV; children;
and Williams syndrome
International
Consortium for
Brain Mapping
(ICBM)
Functional Imaging
Research in
Schizophrenia
Testbed
(FIRSTBIRN)
Pediatric Brain
Tumor
Consortium
(PBTC)
University of California, Irvine; University of California, San

Diego; University of California, Los Angeles; Stanford
University; University of New Mexico; University of
Minnesota; Massachusetts General Hospital; Brigham and
Womens Hospital; Duke University; University of North
Carolina; University of Iowa
Childrens Memorial Hospital, Chicago; Duke University
Medical Center; Texas Childrens Cancer Center; St. Jude
Childrens Research Hospital; The Childrens Hospital of
Philadelphia; Childrens Hospital of Pittsburgh; University of
California, San Francisco; Childrens National Medical
Center; NCI
URL
References
www.adniinfo.org
www.
loni.ucla.
edu/
ADNI/
index.
shtml
ace.loni.
ucla.edu
Boyes et al. (2008); Fletcher, Powell, Foster, and Joshi

(2007); Hua et al. (2008); Jack et al. (2008); Leow et al.
(2006); Morra et al. (2008); Mueller et al. (2005b); and
Yanovsky et al. (2008)
sMRI,
fMRI,
DTI
www.
cifasd.
org
Moore et al. (2007)
www.loni.
ucla.edu/
ICBM/
Mazziotta, Toga, Evans, Fox, and Lancaster, (1995);

Mazziotta et al. (2001); and Mazziotta et al. (2009)
Schizophrenia spectrum
disorders, normal control
subjects
sMRI;
MRS;
MRA;
DTI/
DWI;
PET
sMRI;
fMRI;
DTI
www.
nbirn.
net/
research/
function
Friedman et al. (2008), Kim et al. (2009), and Potkin and

Ford (2009)
Children with primary brain

tumors
sMRI;
PET
www.pbtc.
org
Mulkern et al. (2008) and Poussaint et al. (2007)
N/A
Multisite trial
687
688
Figure 1 The LONI IDA web interface provides users with the means to both upload, search for, and (in the case of approved users) download
neuroimaging datasets or link to their collections via LONI Pipeline. Archiving data in the IDA is straightforward and secure and requires no specialized
hardware, software, or personnel. All that is required is a computer with Internet access and web browser. The IDA automatically extracts relevant
metadata from the deidentified image files allowing data to be searched within moments of archival. Once archived, data may be downloaded and/or
streamed into the LONI Pipeline processing environment. Integration of the LONI Debabeler file format translation engine (Neu, Valentino, & Toga, 2005)
allows users to download image data in a number of file formats in addition to the original file format.
The Information Flow of Neuroimaging Data Sharing

Many open-site and multisite projects seek to draw in data
from the scientific community while meeting the needs of the
core investigators. This process is streamlined through the
choices made in the curation model that governs the flow of
data into the database (see Figure 2, based on the IDA model).
For instance, each contributing investigator or acquisition site
might upload image data to the repository through a dedicated
web-based application that incorporates a number of data
validation and data deidentification operations, including validation of the subject identifier, validation of the dataset as
human or phantom, validation of the file format, image file
deidentification, encrypted data transmission, database population, secure storage of the image files, and metadata and
tracking of data accesses. The image archiving portion of the
system is expected to be both robust and extremely easy to use
with the bulk of new users requiring little, if any, training. Key
elements of such a curation system might include the following: (1) the subject identifier being validated against a set of
acceptable, site-specific IDs; (2) potentially patient-identifying
information being removed or replaced; (3) image data are
checked by trained curators to see that they look appropriate
and possess all relevant image metadata; (4) image files should
be transferred in the repository in compliance with patientprivacy regulations; (5) it is helpful if metadata elements are
extracted from the image files instead of manual entry where

transcription error is likely. Customized database mappings
can be constructed for the various image file information to
provide consistency across scanners and image file formats; (6)
newly received study data might be placed into a quarantined
status and/or the images held for quality control assessment;
and (7) images passing quality assessments might be made
available, whereas images not passing quality control might
be flagged as failing so that they can be assessed more carefully
or removed from the archive altogether. These represent but a
small set of overall steps for ensuring the fidelity in a curated
neuroimaging database but illustrate the degree of detail often
needed to provide an accurate and reliable resource to the
public.
Databasing Infrastructure
For curated databases, a robust and reliable computational
infrastructure is a necessity for supporting a resource intended
to serve the needs and requirements of a broadly based
research community. The hardware infrastructure behind a
database must provide high performance, security, and reliability at each level being fault-tolerant with no single points
of failure. A firewall appliance would need to protect and
segment network traffic, permitting only authorized ingress
Deidentification
HIPAA
compliance
Data types
Imaging
Biospecimen
Genetic
Clinical
689
Website
Study tracking
Queries
Requests
Downloads
Co
llec
ta
ted
da
Qu
ara
nti
Upload
data
QA and
validation
Acquisition
sites
ta
ne
da
ved
da
Ap
pro
Download
data
ta
Multi-format
downloads
Coriell
Clinical
coordinating
center
De
rive
ta
da
Data
repository
Post
processing
Analysis workflows
Scientific
investigators
and study pls
Figure 2 This figure illustrates a comprehensive model for database deposition and download. Secure uploads from data acquisition sites, data
coordinating centers, or individual investigators are run through deidentification software to remove any sensitive patient information. Data are
compartmentalized into their various data types and subject to quality assurance and validation. Analysis workflows might access the repository directly
for use in processing and novel analyses. Downloads are strictly monitored and data conversions may be performed in multiple file formats.
and egress. Multiple redundant databases, applications, and

web servers help to ensure service continuity in the event of a
single-system failure and also provide improved performance
through load balancing of requests across the multiple
machines. To augment the network-based security practices,
database servers might utilize only secure encryption for all
data transfers. This multipronged approach (Figure 3) minimizes the risk of loss, ensuring that a pristine copy of the data
archive is always available. As expected, dedicated IT personnel
would be needed to ensure system uptime, maintenance and
upgrading when needed.
Data Access and Security

Access to a database may be restricted to those who are site
participants and/or those who have applied for access and
received approval from the projects data sharing and publications representatives. Different levels of user access may be
available to an individual. Those at the acquisition sites
might be able to upload data for subjects from their site but
then not able to access data from other sites, whereas the
imaging core leaders may upload, download, edit, or delete
data. Such policies vary from archive to archive but provide a
level of comfort and control for investigators and database
managers as to who is accessing and using the data in the
database (Smith et al., 2004).
For some archives, particularly those large projects with
unique cohorts (e.g., the Alzheimers Disease Neuroimaging
Initiative (ADNI); Weiner et al., 2012), a specific data processing
core might oversee access by external investigators. An online

application and review process might be needed so that applicant information and committee decisions are recorded into
their own database. Approved users might be required to
submit annual progress reports, and the online system provides
mechanisms for this function along with related tasks, such as
adding team members to an approved application and receiving
manuscripts for review by designated project officers (Toga
& Crawford, 2010).
Unlike anonymous file transfer protocol (FTP) sites or data
access through simple URLs embedded in a webpage, logging
data access can be illustrative for how much the data are being
used. For the LONI IDA, over 100 000 image datasets (more than
5 million total files) and related clinical imaging, biomarker, and
genetic datasets are presently available to approved investigators
(Table 3).
Access records indicate that greater than 800 000 downloads of raw, preprocessed, and postprocessed scans have
been provided to investigators worldwide at all times of the
day for use in new research and for use in education. Downloads of the clinical, biomarker, image analysis results and
genetic data have been provided more than 4300 times. The
trends in IDA data download activity have increased each year
since the data became available, increasing from 154 200
image datasets downloaded in 2007 to almost 290 000 image
datasets downloaded in 2009 (Figure 4).
Such activity is indicative not only (1) that the resource has
value to researchers looking for access to data upon which
novel analyses can be conducted but also that (2) the database
is gaining trust, which can be a major factor in its continued
success (see succeeding text).
690
Load
balancing
layer
Security
layer
Online
users
Load balancer
User
authentication
protocol
Request
Website
interface
Authentication server
Authentication key
Writeable
databases
Write request
Web
server
Tomcat servers
Application and
redundancy
layer
Disaster recovery
layer
Sync
Read-only
database
Read request
Backup
Data
Offsite disk
Onsite tapes
Offsite data vault
Data bunker
Figure 3 The compute infrastructure for a fully curated neuroimaging database might be composed of (a) a load-balancing layer, designed to
ensure limited bottleneck accessibility to compute resources; (b) a rigorous security layer, managing access requests, user authentication, and user
privileges; (c) an application and redundancy layer, for data deposition and database management; and (d) a disaster recovery layer, comprising on-site
tape backup, off-site disk mirroring and archiving, and periodic caching into offsite high-stability data bunkers.
Table 3
Domain
Research projects utilizing the LONI Image Data Archive (IDA)

Project utilizing LONI IDA resources
Aging and dementia

Age Moderates HIV-Related CNS Dysfunction
Alzheimers Disease Neuroimaging Initiative
(ADNI)
Modifiers of Brain Aging and Alzheimers
Disease
PET Study of 5-HT1A Receptors in AD
UCLA Alzheimers Disease Research Center
(ADRC)
Primary institution
References
University of Pittsburgh School of

Medicine
University of California, San Francisco
Lepore et al. (2006)
University of Kansas
Burns et al. (2005)
University of Toronto, Toronto, Ontario,

Canada
University of California, Los Angeles
Lanctot et al. (2007)
Universite de Montreal, Montreal, Quebec,

Canada
University of Washington
N/A
Shandong University, China

N/A
Mazziotta et al. (2001)
University of California, San Diego

Sowell, Trauner, Gamst, and Jernigan

(2002)
N/A

National Institutes of Mental Health
N/A
Gogtay et al. (2004)
Narr et al. (2007)
Mueller et al. (2005a)
Cummings, Miller, Christensen, and

Cherry (2008)
Anatomy
Anatomy of the Corpus Callosum
BrainInfo
Brain atlasing
Chinese Digitized Standard Brain Atlas
International Consortium for Brain Mapping
Development
Development
Caring for a child with a serious illness
Mental health
Bipolar Endophenotypes in Population Isolates
Childhood-Onset Schizophrenia
First-Episode Schizophrenia
Bowden and Dubach (2003)

Table 3
Domain
691
(Continued)
Project utilizing LONI IDA resources
Neurogenomics
ApoE and Alzheimers Disease
Genetic influences on the brain: A twin study
Neurogenomics Investigation of Depression
Neurology
Hippocampal Volume Loss in Multiple
Sclerosis
Human Epileptic Brain: 3D MRI
Huntingtons Disease Neuroimaging Project
Neural Bases of Lexical Processes in H. Stroke
Neuropsychological Progression of New Onset
Epilepsy
Volumetrics in Brain Trauma
Primary institution
References

University of Queensland, Australia
Oxford University, the United Kingdom
Chou et al. (2008)

N/A
Sicotte et al. (2008)

University College London, the United
Kingdom
Johns Hopkins University
University of WisconsinMadison
Lin et al. (2007)

Holmes, Tsang, and Tabrizi (2006)
Hillis et al. (2005)

Hermann, Jones, Sheth, and Seidenberg
(2007)
Wu et al. (2004)
Cryosection
Mouse BIRN

N/A
MacKenzie-Graham et al. (2007)
Minority Populations TS-Marina

Multi-center Estriol Study
Santa Fe Institute Consortium

N/A
N/A
N/A
Nonhuman
Other
Alzheimers Disease
Neuroimaging Initiative
International Consortium
for Brain Mapping
Huntingtons Disease
Neuroimaging project
Australian Imaging,
Biomarkers and Lifestyle
Multi-center
Estriol Study
North American Prodrome
Longitudinal Study
Bipolar Endophenotypes in
Population Isolates
Multi-Disciplinary Approach
Study of Pelvic Pain
Consortium for
Neuropsychiatric Phenomics
Cardiovascular & HIV/AIDS
Effects on Brain & Cognition
Imaging & Genetic
Biomarkers for AD
Modifiers of Brain Aging &
Alzheimers Disease
Pediatric Thought
Disorder
Neuropsychological Progression
New Onset Epilepsy
00
70
10
00
00
00
10
ill TOTALS
1m
Download
+upload
1 273 730
61 809
23 856
16 458
10 920
10 664
8167
2844
2420
Downloads
Uploads
# of data sets
uploaded and
downloaded
2007-2011
Other 31 data sets
Figure 4 Total transaction activity (uploads and downloads) from the LONI IDA between 2007 and 2011 by differing LONI IDA projects.
1749
1641
1603
1622
1301
11 840
692
Interoperability with Analysis Workflow Tools

A significant challenge in computational neuroimaging studies
is the problem of reproducing findings and validating analyses
described by different investigators. Frequently, methodological details described in research publications may be insufficient to accurately reconstruct the analysis protocol used to
study the data. Such methodological ambiguity or incompleteness may lead to misunderstanding, misinterpretation, or
reduction of the usability of newly proposed techniques.
Interactive workflow environments for automated data
analysis are critical in many research studies involving complex
computations and large datasets (Kawas, Senger, & Wilkinson,
2006; Myers et al., 2006; Oinn et al., 2005; Taylor, Shields,
Wang, & Harrison, 2006). There are three distinct necessities
that underlie the importance of such graphic frameworks for
the management of novel analysis strategies high data volume and complexity, sophisticated study protocols, and
demands for distributed computational resources. These three
fundamental needs are evident in most modern neuroimaging,
bioinformatics, and multidisciplinary studies.
The LONI Pipeline environment (http://pipeline.loni.ucla.
edu), for example, provides distributed access to various computational resources via a graphical interface. Pipeline has been
used in a number of neuroimaging applications including
health (Sowell et al., 2007), disease (Thompson et al., 2003),
and animal models (MacKenzie-Graham et al., 2006) and
volumetric (Luders et al., 2006), functional (Rasser et al.,
2005), shape-based (Narr et al., 2007), and tensor-based
(Chiang et al., 2007) studies. Increasingly, the program is

being utilized in the performance of neurogenetic analyses
(Dinov et al., 2011). Other workflow tools, such as Nipype
(Gorgolewski et al., 2011), also provide clear, functional, and
complete records of the methodological and technological
protocols employed in the analysis. This provenance forms
an important element to just how data have been processed
and analyzed (MacKenzie-Graham, Payan, Dinov, Van Horn,
& Toga, 2008; MacKenzie-Graham, Van Horn, Woods, Crawford, & Toga, 2008; Figure 5).
Discussion
Though keen interest in databasing neuroimaging results (Fox,
Mikiten, Davis, & Lancaster, 1994a), derived information (Van
Essen, Drury, Joshi, & Miller, 1998), and raw data (Van Horn
et al., 2001) has existed for some time, databases have now
emerged as valid and much sought after resources for access to
brain imaging data. Their increased importance for providing a
comprehensive mechanism to gather, distribute and share
data, results, and information not only between and among
project participants but also to the scientific community has set
the stage for neuroimaging as a big data science. Maturing
informatics models will enable a far more extensive array of
analytic strategies and approaches to interpreting these data.
Successful databasing solutions must build a trust with the
communities they seek to serve and provide dependable
services and open policies to researchers. Several factors
Figure 5 Data processing workflow technologies provide a natural linkage to database resources. For instance, (a) the LONI Pipeline provides
direct connectivity to LONI IDA collections and other web-based data resources, which may be selected to (b) create a Pipeline module group that, at run
time, makes the connection to the database and submits the selected data for processing.

contribute to a databases utility, including whether it actually
contains viable data, and these are accompanied by a detailed
description of their acquisition (e.g., metadata); whether the
database is well organized and the user interface is easy to
navigate; whether the data are derived versions of raw data or
the raw data itself, the manner in which the database addresses
the sociological and bureaucratic issues that can be associated
with data sharing; and whether it has a policy in place to ensure
that requesting authors give proper attribution to the original
collectors of the data and the efficiency of secure data transactions. These systems must provide flexible methods for data
description and relationships among various metadata characteristics (Bug et al., 2008). Moreover, those that have been
specifically designed to serve a large and diverse audience
with a variety of needs and that possess the qualities described
earlier represent the types of databases that can have the greatest benefit to scientists looking to study the disease, assess new
methods, and examine previously published data or with interests in exploring novel ideas using the data (Van Horn &
Gazzaniga, 2005).
A list of lessons learned through the development of the IDA,
fMRIDC, and other archives follows many of the same principles identified by Arzberger et al. (2004) and Beaulieu (2001).
These are as follows: (1) The data archive information should
be open and unrestricted. (2) The database should be transparent in terms of activity and content. (3) The individuals and
institutions responsible for what should be clear. The exact
formal responsibilities among the stakeholders should be stated.
(4) Technical and semantic interoperability between the
database and other online resources (data and analyses) should
be possible through community and open standards (for review,
see Neu, Crawford, & Toga, 2012). (5) Clear curation systems
governing quality control, data validation, authentication, and
authorization must be in place. (6) The systems must be
operationally efficient and flexible. (7) There should be clear
policies of respect for intellectual property and other ethical and
legal requirements. (8) The needs for management accountability and authority. (9) A solid technological architecture and
expertise are essential. (10) There should be systems for reliable
user support. Additional issues involve Health Insurance Portability and Accountability Act (HIPAA) compliance (Hansen,
1997) and concern over incidental findings (Illes & Borgelt,
2009), anonymization of facial features (Bischoff-Grethe et al.,
2007), and skull stripping (Shattuck, Prasad, Mirza, Narr, &
Toga, 2009). The most trusted and hence successful informatics
solutions tend to be those that meet these principles and have
archival processes that are sufficiently mature and demonstrate
solid foundation and trust.
Directions for Future Development

Scientific research is increasingly data-intensive and collaborative, yet the infrastructure needed for supporting data-intensive
research is still maturing. An effective neuroimaging database
should strive to blur the boundary between the data and the
analyses, providing data exploration, statistics, and graphic
presentation as embedded toolsets for interrogating data. Interactive, iterative interrogation, and visualization of scientific
693
data lead to enhanced analysis and understanding and lower

the usability threshold (Joshi, Van Horn, & Toga, 2009). The
next steps for neuroimaging database development will involve
the construction of novel tools and services for data discovery,
integration, and visualization. Components for discovering
data resources must include contextual information that allows
data to be understood, reused, and the results reproduced.
Integrating a broader spectrum of neuroscience data and providing tools for interrogating and visualizing those data will
enable investigators to more easily and interactively investigate
broader scientific questions. Integration of additional clinical
and biochemical data and analysis results into disease-specific
databases with novel tools for interactively interrogating and
visualizing the data in tabular and graphic forms (Bowman,
Joshi, & Van Horn, 2012; Joshi, Bowman, & Van Horn, 2010)
will set the stage for rapid exploration of the brain in form and
function by students and experts alike.
Acknowledgments
The work of preparing this article was supported through a P41
(P41EB015922) resource award from the National Institute of
Biomedical Imaging and Bioengineering (NIBIB) of the
National Institutes of Health (NIH) to Dr. Arthur W. Toga.
The LONI Image Data Archive (IDA) featured as an example
herein is expertly supervised by Dr. Scott Neu and Ms. Karen
Crawford. Gratitude is expressed to the faculty and staff of the
Laboratory of Neuro Imaging (LONI) now based at the University of Southern California in Los Angeles, CA.

Information from fMRI; Positron Emission Tomography and
Neuroreceptor Mapping In Vivo; Temporal Resolution and Spatial
Resolution of fMRI; INTRODUCTION TO ANATOMY AND
PHYSIOLOGY: Gyrification in the Human Brain; INTRODUCTION TO
CLINICAL BRAIN MAPPING: Alzheimers Disease; Basic Concepts of
Image Classification Algorithms Applied to Study Neurodegenerative
Diseases; Huntingtons Disease for Brain Mapping: An Encyclopedic
Reference; Imaging Genetics; INTRODUCTION TO METHODS AND
MODELING: Analysis of Variance (ANOVA); Automatic Labeling of the
Human Cerebral Cortex; BrainMap Database as a Resource for
Computational Modeling; Computing Brain Change over Time; Cortical
Thickness Mapping; Diffusion Tensor Imaging; False Discovery Rate
Control; Meta-Analyses in Functional Neuroimaging; Tissue
Classification; Tissue Properties from Quantitative MRI; Voxel-Based
Morphometry; INTRODUCTION TO SOCIAL COGNITIVE
NEUROSCIENCE: Neural Correlates of Social Cognition Deficits in
Autism Spectrum Disorders.
References
Arzberger, P., Schroeder, P., Beaulieu, A., Bowker, G., Casey, K., Laaksonen, L., et al.
(2004). Science and government: An international framework to promote access to
data. Science, 303(5665), 17771778.
Beaulieu, A. (2001). Voxels in the brain: Neuroscience, informatics and changing
notions of objectivity. Social Studies of Science, 31(5), 635680.
Bischoff-Grethe, A., Ozyurt, I. B., Busa, E., Quinn, B. T., Fennema-Notestine, C.,
Clark, C. P., et al. (2007). A technique for the deidentification of structural brain MR
images. Human Brain Mapping, 28, 892903.
694
Bowden, D. M., & Dubach, M. F. (2003). NeuroNames 2002. Neuroinformatics, 1(1),

4359.
Bowman, I., Joshi, S. H., & Van Horn, J. (2012). Visual systems for interactive
exploration and mining of large-scale neuroimaging data archives. Frontiers in
Neuroinformatics, 6, 11.
Boyes, R. G., Gunter, J. L., Frost, C., Janke, A. L., Yeatman, T., Hill, D. L., et al. (2008).
Intensity non-uniformity correction using N3 on 3-T scanners with multichannel
phased array coils. NeuroImage, 39(4), 17521762.
Bug, W. J., Ascoli, G. A., Grethe, J. S., Gupta, A., Fennema-Notestine, C., Laird, A. R.,
et al. (2008). The NIFSTD and BIRNLex vocabularies: Building comprehensive
ontologies for neuroscience. Neuroinformatics, 6(3), 175194.
Burns, J. M., Church, J. A., Johnson, D. K., Xiong, C., Marcus, D., Fotenos, A. F., et al.
(2005). White matter lesions are prevalent but differentially related with cognition in
aging and early Alzheimer disease. Archives of Neurology, 62(12), 18701876.
Carlson, T. A., Schrater, P., & He, S. (2003). Patterns of activity in the categorical
representations of objects. Journal of Cognitive Neuroscience, 15(5), 704717.
Chiang, M.-C., Dutton, R. A., Hayashi, K. M., Lopez, O. L., Aizenstein, H. J., Toga, A. W.,
et al. (2007). 3D pattern of brain atrophy in HIV/AIDS visualized using tensor-based
morphometry. NeuroImage, 34(1), 4460.
Chou, Y. Y., Lepore, N., de Zubicaray, G. I., Carmichael, O. T., Becker, J. T., Toga, A. W.,
et al. (2008). Automated ventricular mapping with multi-atlas fluid image alignment
reveals genetic effects in Alzheimers disease. NeuroImage, 40(2), 615630.
Cummings, J. L., Miller, B. L., Christensen, D. D., & Cherry, D. (2008). Creativity and
dementia: Emerging diagnostic and treatment methods for Alzheimers disease. CNS
Spectrums, 13(2 Suppl. 2), 120, quiz 22.
Dinov, I., Lozev, K., Petrosyan, P., Liu, Z., Eggert, P., Pierce, J., et al. (2010).
Neuroimaging study designs, computational analyses and data provenance using
the LONI pipeline. PloS One, 5(9).
Dinov, I. D., Torri, F., Macciardi, F., Petrosyan, P., Liu, Z., Zamanyan, A., et al. (2011).
Applications of the pipeline environment for visual informatics and genomics
computations. BMC Bioinformatics, 12(1), 304.
Dinov, I., Van Horn, J., Lozev, K., Magsipoc, R., Petrosyan, P., Liu, Z., et al. (2009).
Efficient, distributed and interactive neuroimaging data analysis using the LONI
pipeline. Frontiers in Neuroinformatics, 3(22), 110.
Fletcher, P. T., Powell, S., Foster, N. L., & Joshi, S. C. (2007). Quantifying metabolic
asymmetry modulo structure in Alzheimers disease. Information Processing in
Fox, P. T., Laird, A. R., Fox, S. P., Fox, P. M., Uecker, A. M., Crank, M., et al. (2005).
BrainMap taxonomy of experimental design: Description and evaluation. Human
Fox, P., & Lancaster, J. (2002). Mapping context and content: The BrainMap model.
Nature Reviews. Neuroscience, 3(4), 319321.
Fox, P. T., Mikiten, S., Davis, G., & Lancaster, J. (1994a). BrainMap: A database of
human function brain mapping. In R. W. Thatcher, M. Hallett, T. Zeffiro, E. R. John &
M. Heurta (Eds.), Functional neuroimaging technical foundations (pp. 95105). San
Diego, CA: Academic Press.
Fox, P. T., Mikiten, S., Davis, G., & Lancaster, J. L. (1994b). BrainMap: A database of human
functional brain mapping. In R. W. Thatcher, M. Hallett, T. Zeffiro, E. R. John & M.
Huerta (Eds.), Functional neuroimaging (pp. 95106). San Diego, CA: Academic Press.
Friedman, L., Stern, H., Brown, G. G., Mathalon, D. H., Turner, J., Glover, G. H., et al.
(2008). Test-retest and between-site reliability in a multicenter fMRI study. Human
Gogtay, N., Giedd, J. N., Lusk, L., Hayashi, K. M., Greenstein, D., Vaituzis, A. C., et al.
(2004). Dynamic mapping of human cortical development during childhood
through early adulthood. Proceedings of the National Academy of Sciences of the
Gorgolewski, K., Burns, C. D., Madison, C., Clark, D., Halchenko, Y. O., Waskom, M. L.,
et al. (2011). Nipype: A flexible, lightweight and extensible neuroimaging data
processing framework in python. Frontiers in Neuroinformatics, 5, 13.
Governing Council of the Organization for Human Brain Mapping, (2001).
Neuroimaging databases. Science, 292, 16731676.
Greicius, M. D., Srivastava, G., Reiss, A. L., & Menon, V. (2004). Default-mode network
activity distinguishes Alzheimers disease from healthy aging: Evidence from
functional MRI. Proceedings of the National Academy of Sciences of the United
States of America, 101(13), 46374642.
Hansen, E. (1997). HIPAA (Health Insurance Portability and Accountability Act) rules:
Federal and state enforcement. Medical Interface, 10(8), 9698, 101102.
Hermann, B. P., Jones, J., Sheth, R., & Seidenberg, M. (2007). Cognitive and magnetic
resonance volumetric abnormalities in new-onset pediatric epilepsy. Seminars in
Pediatric Neurology, 14(4), 173180.
Hillis, A. E., Newhart, M., Heidler, J., Barker, P., Herskovits, E., & Degaonkar, M. (2005).
The roles of the "visual word form area" in reading. NeuroImage, 24(2), 548559.
Holmes, E., Tsang, T. M., & Tabrizi, S. J. (2006). The application of NMR-based
metabonomics in neurological disorders. NeuroRx, 3(3), 358372.
Hua, X., Leow, A. D., Parikshak, N., Lee, S., Chiang, M. C., Toga, A. W., et al. (2008).
Tensor-based morphometry as a neuroimaging biomarker for Alzheimers
disease: An MRI study of 676 AD, MCI, and normal subjects. NeuroImage, 43,
458469.
Illes, J., & Borgelt, E. (2009). Brain imaging: incidental findings: In practice and in
person. Nature Reviews. Neurology, 5(12), 643644.
Jack, C., Bernstein, M., Fox, N., Thompson, P., Alexander, G., Harvey, D., et al. (2008).
The Alzheimers disease neuroimaging initiative (ADNI): MRI methods. Journal of
Joshi, S. H., Bowman, I., & Van Horn, J. D. (2010). Large-scale neuroanatomical
visualization using a manifold embedding approach. In: Proceedings of the IEEE
Symposium on Visual Analytics Science Technology 2010 (2526 Oct. 2010), (p. 237).
Joshi, S. H., Van Horn, J. D., & Toga, A. W. (2009). Interactive exploration of
neuroanatomical meta-spaces. Frontiers in Neuroinformatics, 3, 38.
Kawas, E., Senger, M., & Wilkinson, M. (2006). BioMoby extensions to the Taverna
workflow management and enactment software. BMC Bioinformatics, 7(1), 523.
Kim, D. I., Mathalon, D. H., Ford, J. M., Mannell, M., Turner, J. A., Brown, G. G., et al.
(2009). Auditory oddball deficits in schizophrenia: An independent component analysis
of the fMRI multisite function BIRN study. Schizophrenia Bulletin, 35(1), 6781.
Laird, A. R., Eickhoff, S. B., Fox, P. M., Uecker, A. M., Ray, K. L., Saenz, J. J., Jr., et al.
(2011). The BrainMap strategy for standardization, sharing, and meta-analysis of
neuroimaging data. BMC Research Notes, 4, 349.
Laird, A. R., Eickhoff, S. B., Kurth, F., Fox, P. M., Uecker, A. M., Turner, J. A., et al.
(2009). ALE meta-analysis workflows via the BrainMap database: Progress towards
a probabilistic functional brain atlas. Frontiers in Neuroinformatics, 3, 23.
Laird, A. R., Fox, P. M., Eickhoff, S. B., Turner, J. A., Ray, K. L., McKay, D. R., et al.
(2011). Behavioral interpretations of intrinsic connectivity networks. Journal of
Cognitive Neuroscience, 23, 40224037.
Laird, A. R., Lancaster, J. L., & Fox, P. T. (2005). BrainMap: The social evolution of a
human brain mapping database. Neuroinformatics, 3(1), 6578.
Laird, A. R., Lancaster, J. L., & Fox, P. T. (2009). Lost in localization? The focus is
meta-analysis. NeuroImage, 48(1), 1820.
Lanctot, K. L., Hussey, D. F., Herrmann, N., Black, S. E., Rusjan, P. M., Wilson, A. A.,
et al. (2007). A positron emission tomography study of 5-hydroxytryptamine-1A
receptors in Alzheimer disease. The American Journal of Geriatric Psychiatry,
15(10), 888898.
Leow, A. D., Klunder, A. D., Jack, C. R., Jr., Toga, A. W., Dale, A. M., Bernstein, M. A.,
et al. (2006). Longitudinal stability of MRI for mapping brain change using tensorbased morphometry. NeuroImage, 31(2), 627640.
Lepore, N., Brun, C. A., Chiang, M. C., Chou, Y. Y., Dutton, R. A., Hayashi, K. M., et al.
(2006). Multivariate statistics of the Jacobian matrices in tensor based morphometry
and their application to HIV/AIDS. Medical Image Computing and ComputerAssisted Intervention, 9(Pt 1), 191198.
Lin, J. J., Salamon, N., Lee, A. D., Dutton, R. A., Geaga, J. A., Hayashi, K. M., et al.
(2007). Reduced neocortical thickness and complexity mapped in mesial temporal
lobe epilepsy with hippocampal sclerosis. Cerebral Cortex, 17(9), 20072018.
Luders, E., Narr, K. L., Thompson, P. M., Rex, D. E., Woods, R. P., DeLuca, H., et al.
(2006). Gender effects on cortical thickness and the influence of scaling. Human
MacKenzie-Graham, A., Lee, E.-F., Dinov, I. D., Yuan, H., Jacobs, R. E., & Toga, A. W.
(2007). Multimodal, multidimensional models of mouse brain. Epilepsia, 48, 7581.
MacKenzie-Graham, A., Payan, A., Dinov, I., Van Horn, J., & Toga, A. (2008).
Neuroimaging data provenance using the LONI pipeline workflow environment.
Provenance and Annotation of Data and Processes, 5272, 208220.
MacKenzie-Graham, A., Tinsley, M., Shah, K., Aguilar, C., Strickland, L., Boline, J.,
et al. (2006). Cerebellar cortical atrophy in experimental autoimmune
encephalomyelitis. NeuroImage, 32, 10161023.
Mackenzie-Graham, A. J., Van Horn, J. D., Woods, R. P., Crawford, K. L., & Toga, A. W.
(2008). Provenance in neuroimaging. NeuroImage, 42(1), 178195.
Marcus, D. S., Olsen, T. R., Ramaratnam, M., & Buckner, R. L. (2007). The extensible
neuroimaging archive toolkit: An informatics platform for managing, exploring, and
sharing neuroimaging data. Neuroinformatics, 5(1), 1134.
Markram, H. (2012). The human brain project. Scientific American, 306(6), 5055.
atlas of the human brain: Theory and rationale for its development. The International
Consortium for Brain Mapping (ICBM). NeuroImage, 2(2), 89101.
Mazziotta, J., Toga, A., Evans, A., Fox, P., Lancaster, J., Zilles, K., et al. (2001).
A probabilistic atlas and reference system for the human brain: International
Consortium for Brain Mapping (ICBM). Philosophical Transactions of the Royal
Society of London. Series B: Biological Sciences, 356(1412), 12931322.

Mazziotta, J. C., Woods, R., Iacoboni, M., Sicotte, N., Yaden, K., Tran, M., et al. (2009).
The myth of the normal, average human brain The ICBM experience: (1) subject
screening and eligibility. NeuroImage, 44(3), 914922.
Mechelli, A., Price, C. J., Noppeney, U., & Friston, K. J. (2003). A dynamic causal
modeling study on category effects: Bottom-up or top-down mediation? Journal of
Cognitive Neuroscience, 15(7), 925934.
Milham, M. P. (2012). Open neuroscience solutions for the connectome-wide
association era. Neuron, 73(2), 214218.
Moore, E. S., Ward, R. E., Wetherill, L. F., Rogers, J. L., Autti-Ramo, I., Fagerlund, A.,
et al. (2007). Unique facial features distinguish fetal alcohol syndrome patients and
controls in diverse ethnic populations. Alcoholism, Clinical and Experimental
Research, 31(10), 17071713.
Morra, J. H., Tu, Z., Apostolova, L. G., Green, A. E., Avedissian, C., Madsen, S. K., et al.
(2008). Validation of a fully automated 3D hippocampal segmentation method using
subjects with Alzheimers disease mild cognitive impairment, and elderly controls.
Mueller, S. G., Weiner, M. W., Thal, L. J., Petersen, R. C., Jack, C., Jagust, W., et al.
(2005a). The Alzheimers disease neuroimaging initiative. Neuroimaging Clinics of
North America, 15(4), 869877, 1112.
Mueller, S. G., Weiner, M. W., Thal, L. J., Petersen, R. C., Jack, C. R., Jagust, W., et al.
(2005b). Ways toward an early diagnosis in Alzheimers disease: The Alzheimers
Disease Neuroimaging Initiative (ADNI). Alzheimers & Dementia, 1(1), 5566.
Mulkern, R. V., Forbes, P., Dewey, K., Osganian, S., Clark, M., Wong, S., et al. (2008).
Establishment and results of a magnetic resonance quality assurance program
for the pediatric brain tumor consortium. Academic Radiology, 15(9), 10991110.
Myers, J., Allison, T. C., Bittner, S., Didier, B., Frenklach, M., Green, W. H., et al. (2006).
A collaborative informatics infrastructure for multi-scale science. Cluster
Computing, 8(4), 243253.
Narr, K., Bilder, R., Luders, E., Thompson, P., Woods, R., Robinson, D., et al. (2007).
Asymmetries of cortical shape: Effects of handedness, sex and schizophrenia.
NeuroImage, 34(3), 939948.
Neu, S. C., Crawford, K. L., & Toga, A. W. (2012). Practical management of
heterogeneous neuroimaging metadata by global neuroimaging data repositories.
Neu, S. C., Valentino, D. J., & Toga, A. W. (2005). The LONI Debabeler: A mediator for
neuroimaging software. NeuroImage, 24(4), 11701179.
Oinn, T., Greenwood, M., Addis, M., Alpdemir, M. N., Ferris, J., Glover, K., et al. (2005).
Taverna: Lessons in creating a workflow environment for the life sciences.
Concurrency and Computation: Practice and Experience, 18(10), 10671100.
causal models. NeuroImage, 22(3), 11571172.
et al. (2013). Toward open sharing of task-based fMRI data: The OpenfMRI project.
Potkin, S. G., & Ford, J. M. (2009). Widespread cortical dysfunction in schizophrenia:
The FBIRN imaging consortium. Schizophrenia Bulletin, 35(1), 1518.
Poussaint, T. Y., Phillips, P. C., Vajapeyam, S., Fahey, F. H., Robertson, R. L.,
Osganian, S., et al. (2007). The Neuroimaging Center of the Pediatric Brain Tumor
Consortium-collaborative neuroimaging in pediatric brain tumor research: A work
in progress. AJNR. American Journal of Neuroradiology, 28(4), 603607.
Rasser, P., Johnston, P., Lagopoulos, J., Ward, P. B., Schall, U., Thienel, R., et al. (2005).
Functional MRI BOLD response to Tower of London performance of first-episode
schizophrenia patients using cortical pattern matching. NeuroImage, 26(3), 941951.
Saykin, A. J., Shen, L., Foroud, T. M., Potkin, S. G., Swaminathan, S., Kim, S., et al.
(2010). ADNI biomarkers as quantitative phenotypes: Genetics core aims, progress,
and plans. Alzheimers & Dementia, 6(3), 265273.
Shattuck, D. W., Prasad, G., Mirza, M., Narr, K. L., & Toga, A. W. (2009). Online resource
for validation of brain segmentation methods. NeuroImage, 45(2), 431439.
Sicotte, N. L., Kern, K. C., Giesser, B. S., Arshanapalli, A., Schultz, A., Montag, M., et al.
(2008). Regional hippocampal atrophy in multiple sclerosis. Brain, 131(Pt 4),
11341141.
695
Smith, K., Jajodia, S., Swarup, V., Hoyt, J., Hamilton, G., Faatz, D., et al. (2004).
Enabling the sharing of neuroimaging data through well-defined intermediate levels
of visibility. NeuroImage, 22(4), 16461656.
Sowell, E., Peterson, B. S., Kan, E., Woods, R. P., Yoshii, J., Bansal, R., et al. (2007).
Sex differences in cortical thickness mapped in 176 healthy individuals between 7
and 87 years of age. Cerebral Cortex, 17(7), 15501560.
Sowell, E. R., Trauner, D. A., Gamst, A., & Jernigan, T. L. (2002). Development of
cortical and subcortical brain structures in childhood and adolescence: A structural
MRI study. Developmental Medicine and Child Neurology, 44(1), 416.
Taylor, I., Shields, M., Wang, I., & Harrison, A. (2006). Visual grid workflow in Triana.
Journal of Grid Computing, 3, 153169.
Thompson, P., Hayashi, K. M., de Zubicaray, G., Janke, A. L., Rose, S. E., Semple, J.,
et al. (2003). Dynamics of gray matter loss in Alzheimers disease. Journal of
Toga, A. W. (2002a). The Laboratory of Neuro Imaging: What it is, why it is, and how it
came to be. IEEE Transactions on Medical Imaging, 21(11), 13331343.
Toga, A. W. (2002b). Neuroimage databases: The good, the bad and the ugly. Nature
Reviews. Neuroscience, 3(4), 302309.
Toga, A. W., & Crawford, K. L. (2010). The informatics core of the Alzheimers Disease
Neuroimaging Initiative. Alzheimers & Dementia, 6(3), 247256.
Torta, D. M., & Cauda, F. (2011). Different functions in the cingulate cortex, a metaanalytic connectivity modeling study. NeuroImage, 56(4), 21572172.
Van Essen, D. C. (2005). A Population-Average, Landmark- and Surface-based (PALS)
atlas of human cerebral cortex. NeuroImage, 28(3), 635662.
Van Essen, D. C., Drury, H. A., Joshi, S., & Miller, M. I. (1998). Functional and
structural mapping of human cerebral cortex: Solutions are in the surfaces.
95(3), 788795.
Van Horn, J. D., Dobson, J., Woodward, J., Wilde, M., Zhao, Y., Voeckler, J., et al.
(2006). Grid-based computing and the future of neuroscience computation. In C.
Senior, T. Russell, & M. S. Gazzaniga (Eds.), Methods in mind (pp. 141170).
Van Horn, J. D., & Gazzaniga, M. S. (2005). Maximizing information content in shared
neuroimaging studies of cognitive function. In S. H. Koslow, & A. Subramanian
(Eds.), Databasing the brain: From data to knowledge (pp. 449458). New York:
Wiley.
Van Horn, J. D., & Gazzaniga, M. S. (2012). Why share data? Lessons learned from the
fMRIDC. NeuroImage, 82, 677682.
Van Horn, J. D., Grethe, J. S., Kostelec, P., Woodward, J. B., Aslam, J. A., Rus, D., et al.
(2001). The Functional Magnetic Resonance Imaging Data Center (fMRIDC): The
challenges and rewards of large-scale databasing of neuroimaging studies.
Philosophical Transactions of the Royal Society of London. Series B: Biological
Sciences, 356, 13231339.
Van Horn, J. D., & Ishai, A. (2007). Mapping the human brain: New insights from FMRI
data sharing. Neuroinformatics, 5(3), 146153.
Van Horn, J. D., & Toga, A. W. (2009a). Is it time to re-prioritize neuroimaging
databases and digital repositories? NeuroImage, 47(4), 17201734.
Van Horn, J. D., & Toga, A. W. (2009b). Multisite neuroimaging trials. Current Opinion
in Neurology, 22(4), 370378.
Weiner, M. W., Veitch, D. P., Aisen, P. S., Beckett, L. A., Cairns, N. J., Green, R. C.,
et al. (2012). The Alzheimers Disease Neuroimaging Initiative: A review of
papers published since its inception. Alzheimers & Dementia, 8(1 Suppl),
S1S68.
Wu, H. M., Huang, S. C., Hattori, N., Glenn, T. C., Vespa, P. M., Yu, C. L., et al. (2004).
Selective metabolic reduction in gray matter acutely following human traumatic
brain injury. Journal of Neurotrauma, 21(2), 149161.
Yanovsky, I., Thompson, P. M., Osher, S., Hua, X., Shattuck, D., Toga, A. W., et al.
(2008). Validating unbiased registration on longitudinal MRI scans from
the Alzheimers Disease Neuroimaging Initiative (ADNI). In: 5th IEEE
International Symposium on Biomedical Imaging: From Nano to Macro, Paris,
France: IEEE.
Methodological Issues in fMRI Functional Connectivity and Network Analysis

ES Finn, D Scheinost, X Shen, X Papademetris, and RT Constable, Yale University School of Medicine, New Haven, CT, USA
Introduction
Functional connectivity has opened up another dimension for
analysis of fMRI data. Instead of simply examining the magnitude of activation in individual areas, one can now examine the
synchrony of activity between distinct areas in the brain. Particularly powerful are network analyses, which divide the brain
into a set of regions of interest (ROIs), or nodes, and use
temporal similarity in signal fluctuations between pairs of
nodes to determine the strength of the functional connections,
or edges, between them. As functional connectivity is easily
measured while subjects are at rest that is, in the absence of
any externally imposed cognitive task it holds great promise
as a clinical tool as well as a means to basic scientific discovery.
There remain several important methodological concerns
with functional connectivity and network analysis using fMRI
data, and researchers must take caution when conducting and
interpreting such studies. Some of these methodological issues
are the focus of this article, which consists of three parts. In the
section Network Measures and (In)stability Across
Thresholds, we review issues related to the use of graph theory/network measures, in particular the sensitivity of these
measures to the choice of threshold for converting
continuous-valued correlations to a binary connection graph.
In the section Defining Network Nodes, we examine the
issue of defining nodes for network analysis and demonstrate
that using advanced brain parcellation algorithms significantly
improves connectivity results compared to the same analysis
using nodes defined anatomically. Finally, in the section
Motion Confounds for Connectivity Analyses, we describe
motion confounds and related preprocessing concerns. While
functional connectivity and network measures represent a
potentially powerful approach to understanding brain functional architecture, care must be taken in the application of
such analysis techniques to fMRI data in order to accurately
elucidate the large-scale organization of the brain.
Network Measures and (In)stability Across Thresholds

While whole-brain network analyses provide a wealth of information, a major challenge is to summarize this data into a
manageable number of observations that can be meaningfully
contrasted between subject groups and/or related to behavior.
The desire for such summary statistics has led to widespread
interest in the application of a branch of mathematics called
graph theory. Graph theory provides a sophisticated yet intuitive
set of measures with which to describe the topology of networks.
Used correctly, graph theory, or network analysis, is an effective
way to characterize interactions between brain regions. A number of recent studies have investigated network properties in
conditions such as schizophrenia (Alexander-Bloch et al.,
2012; Liu et al., 2008; Lynall et al., 2010; van den Heuvel,
Mandl, Stam, Kahn, & Hulshoff Pol, 2010) and Alzheimers

disease (Supekar, Menon, Rubin, Musen, & Greicius, 2008), as
well as in development across the lifespan (Power et al., 2010)
and in healthy subjects as they relate to cognitive measures like
IQ (van den Heuvel, Mandl, Kahn, & Hulshoff Pol, 2009) and
performance on working memory tasks (Stevens, Tappon, Garg,
& Fair, 2012). In each, group or individual differences in network topology were related to disease phenotypes and behavioral measures of cognition.
For a comprehensive yet nontechnical review of network
measures as they apply to fMRI data, the reader is referred to
Rubinov and Spornss (2010). See Sidebar 1 for some commonly used network measures appearing in the examples in
this article.
A central concern with applying graph theory to fMRI data
is that measures such as the ones described in Sidebar 1 were
designed to be calculated on binary graphs that is, graphs in
which connections between nodes are either present or absent.
(Think of a social network, in which people either are
acquainted or do not know one another, or a disease network
in which a person either contracts a disease or does not.)
However, connections in fMRI are measured on a continuous
scale, as correlations of temporal signal fluctuations that could
theoretically fall anywhere between 1 and 1.
Thus, to construct a binary graph from fMRI data, then, an
arbitrary threshold must be applied to decide what constitutes
a connection. This threshold can be correlation-based that is,
setting a value for the correlation coefficient between two
nodes, above which they are considered connected and
below which not connected or it can be sparsity-based, in
which a set percentage of the strongest connections are considered edges (e.g., the top 10% of correlation values throughout
the network). Both approaches have advantages and disadvantages. For example, if one wishes to contrast network properties
between a patient group and a control group, using a sparsitybased threshold ensures that both networks have an equal
overall number of connections, or global degree, which in
turn allows for more meaningful comparisons of other network measures that vary significantly with degree (e.g., characteristic path length or clustering coefficient). However, because
sparsity-based thresholds fail to take into account absolute
differences in correlation values, information about overall
increased or decreased connectivity in one group relative
to the other may be lost. Correlation-based thresholds may
enable detection of such overall differences, but if applying
such thresholds results in networks with significantly different
numbers of edges, differences in other network measures that
rely heavily on degree may be more difficult to interpret.
Many studies choose a single threshold at which to report
results, often (in the case of correlation-based thresholds)
r 0.25 (Buckner et al., 2009; Stevens et al., 2012); others
report results across a range of thresholds but usually a narrow
one (Liu et al., 2008, r 0.270.32; and van den Heuvel et al.,
http://dx.doi.org/10.1016/B978-0-12-397025-1.00352-3
697
698
INTRODUCTION TO METHODS AND MODELING | fMRI Functional Connectivity and Network Analysis
2009, r 0.30.5). However, these approaches can make

results incomplete at best and misleading at worst if there
are changes in or a complete reversal of group differences in network measures at different thresholds (Scheinost
et al., 2012).
Network measures can be unstable across thresholds in a
number of ways. This instability is demonstrated here, using
examples from a dataset of resting-state fMRI scans from 85
healthy volunteers across a wide age range. The comparison
at hand is males versus females. Connectivity analysis was
done using a whole-brain functional parcellation generated
using the Shen et al. method described in the section below,
titled Defining Network Nodes (Shen, Tokoglu, Papademetris, & Constable, 2013). Connectivity matrices were
thresholded at a range of correlation values from 0.10 to
0.50 in order to examine changes in group differences across
thresholds.
Group differences can be present at some thresholds but

not others. For example, in Figure 1(a), if one were to examine
this node at the commonly chosen threshold of r 0.25, no
significant group differences in clustering coefficient would be
detected but at virtually every other threshold, a significant
difference exists. In other cases, group differences appear only
at lower thresholds (Figure 1(b); difference significant at
thresholds <0.25) or only at higher ones (Figure 1(c); difference significant at thresholds >0.25). Finally, in perhaps the
most problematic examples, group differences can reverse
entirely across thresholds (Figure 1(d) and (e)).
Thus, it is clear that the choice of threshold can dramatically
impact results. Yet, there is no biologically principled way to
select a threshold, and experimenters must avoid simply
choosing one that provides them with the desired result. A
recently proposed approach, the intrinsic connectivity
distribution (Scheinost et al., 2012), parameterizes the degree
0.6
Clustering coefficient, node 86

0.55
0.5
0.45
0.4
0.35
0.3
(a)
Females
Males
0.25
0.1
0.2
0.3
0.4
0.5
0.56
1200
Betweenness centrality, node 101
0.54
1000
0.52
800
0.5
0.48
600
0.46
400
0.44
0.42
200
0.4
Females
Males
0.38
(b)
0.1
0.2
0.3
0.4
0.5
(c)
4.5
0
0.1
Females
Males
0.2
0.3
0.4
0.5
0.6
Char. path length, node 51
0.58
4
0.56
3.5
0.54
0.52
0.5
2.5
0.48
2
(d)
0.46
Females
Males
1.5
0.1
0.2
0.3
0.4
0.5
Females
Males
0.44
(e)
0.1
0.2
0.3
0.4
0.5
Figure 1 Instability of network measures across thresholds. Group differences in network measures for individual nodes may be present only at
certain thresholds (a), that is, only lower thresholds (b) or only higher thresholds (c), or may even reverse across thresholds (d and e). In all graphs, the
x-axis represents correlation threshold, while the y-axis represents the network measure indicated in the graph title. Crosses () indicate a p-value
<0.05 for difference between males and females; asterisks (*) indicate p < 0.01. Location of nodes is provided with sagittal and axial slices to the left of
the respective graph; axial slices are in radiological convention (image-left is subject-right). Char. path length, characteristic path length.
Sidebar 1
699
Network Measures Appearing in the Examples in This Article
Degree. Perhaps the most fundamental network property, degree is a measure of the number of edges connected to a node. On a node-wise level, it reflects how well
linked the node is to the rest of the network. A networks global degree may be computed by averaging degrees of all individual nodes to give an estimate of overall
network connectivity.
Characteristic path length. A nodes characteristic path length is the average shortest distance between it and all other nodes in the network. Short characteristic path
length is taken to represent a node that is well positioned within the network, able to efficiently exchange information with a variety of other nodes. Characteristic path
length may be computed for the whole network by averaging all of the individual nodes characteristic path lengths.
Clustering coefficient. Clustering coefficient is equal to the fraction of a nodes neighbors that are also connected to each other (Watts & Strogatz, 1998). For
instance, if node A is connected to node B, node B is connected to node C, and node C is connected to node A, these three nodes form a triangle. Clustering coefficient
is calculated by dividing the number of triangles around a node by that nodes total number of connections (degree). A high clustering coefficient therefore reflects the
presence of clustered connectivity around that individual node (Rubinov & Sporns, 2010).
Betweenness centrality. A nodes betweenness centrality is defined as the fraction of all shortest paths in the network that pass through it. Nodes that connect
distinct parts of the network often have a high betweenness centrality (Rubinov & Sporns, 2010).
curve across the full range of positive correlation thresholds

(i.e., r 0 to r 1) using a stretched exponential fit, akin to a
survival curve for degree, and thus avoids the need for choosing
an arbitrary connectivity threshold:
bx
t
dt, x, ax,bx exp
a x
The curve-fit parameters (a and b) can then be used, for
example, to compare connectivity between groups or to relate
degree across a range of thresholds to behavior or other variables. Multithreshold graphs such as those in Figure 1 can also
be visually examined to ensure that, in the case of group
comparisons, lines do not cross (i.e., that group differences
do not reverse depending on threshold). An important future
direction is to parameterize curves representing other network
measures across a range of thresholds to provide a more robust,
rigorous means of comparison than choosing a single arbitrary
threshold.
There has been some interest in modifying network measures for use on weighted graphs, that is, graphs that are not
binary but instead allow edges to carry some sort of continuous
weight value. However, how best to set weights that reflect the
relative strengths of connections is not straightforward
(Fornito, Zalesky, & Breakspear, 2013). Does a correlation
value between two nodes that is twice as high as the correlation
value between two other nodes imply that one connection is
slightly stronger than the other, twice as strong, or ten times as
strong? The answer to this remains unclear; thus the ideal
transfer function between correlation values and edge weights
for a weighted graph is difficult to determine.
Defining Network Nodes

Before conducting any network analysis, first and foremost, a
set of predefined nodes is required; each nodes mean timecourse is computed and used for subsequent correlation-based
connectivity analyses. It is crucial that all voxels within a node
share similar temporal patterns of activation; otherwise, the
nodes mean timecourse might not reflect any of the component timecourses within. A simple example might be that of a
node containing two sine waves 180 out of phase: the mean of
these signals is a straight line that contains no information on
either component.
Voxel-based analyses, which circumvent the problem of

averaging distinct timecourses, provide an attractive means to
survey whole-brain intrinsic connectivity and/or to identify
seed regions for more detailed analysis (van den Heuvel
et al., 2009, 9500 voxels; and Martuzzi et al., 2011, 135 000
voxels). For simple network measures such as degree, analyses
at the voxel level are tractable and perhaps even preferable to
using large ROIs; however, calculating network measures
beyond degree on individual voxels becomes computationally
cumbersome and difficult to interpret or visualize. To delineate
nodes larger than single voxels, many studies have used atlases
such as Brodmann areas (Baria et al., 2011) or the Brodmannbased automated anatomical labeling (AAL) atlas (Achard
et al., 2006; Tzourio-Mazoyer et al., 2002). The AAL atlas
results in a parcellation on the order of 100 regions, though
different investigators have used different numbers of regions
(van den Heuvel et al., 2010, 108 regions; Lynall et al., 2010,
72 regions; Liu et al., 2008, 90 regions; and Supekar et al.,
2008, 90 regions). Other studies have relied on parcellation
algorithms independent of anatomy or function that divide the
brain into regions according to a set of basic parameters that
is, that nodes do not span hemispheres, and there is no more
than a twofold difference in size between any two nodes
(Alexander-Bloch et al., 2012, 278 regions). Still other analyses
have defined nodes using task-based fMRI studies (Arfanakis
et al., 2000; Biswal et al., 1995; Fair et al., 2007; Hoffman et al.,
2011; Stevens et al., 2012), but as tasks typically differentially
activate only a very limited fraction of the brain, this approach
is not appropriate for whole-brain network analyses. While
apparently meaningful results have been obtained with such
approaches, they are not ideal because of the risk of mixing
different timecourses within a single node.
Group-level independent component analysis (ICA) offers
another option for whole-brain delineation of functional networks (Beckmann, DeLuca, Devlin, & Smith, 2005; Chen et al.,
2008). However, not all components found using ICA are
functionally meaningful (some, e.g., may represent different
artifacts); thus, manual inspection is often needed to select the
components.
A number of data-driven voxel-wise approaches have been
applied to parcellate either the whole brain or a selected part of
the cortex. For example, van den Heuvel et al. (2008) showed
that the normalized cut algorithm (Shi & Malik, 2000) was
capable of identifying seven consistent functionally connected
networks across a group of subjects. Yeo et al. (2011) obtained
both a 7-node network and a 17-node network whole-brain

parcellation by applying a mixture model-based clustering
algorithm (Lashkari, Vul, Kanwisher, & Golland, 2010) to a
seed-to-whole-brain correlation matrix. Cohen et al. (2008)
presented a correlation pattern classification/edge detection
approach and applied it to delineate functional boundaries
in a region near the left cingulate sulcus and adjacent medial
cortex.
Recently, a novel group-wise whole-brain parcellation
scheme optimized to yield nodes containing voxels with similar timecourses was proposed by Shen et al. (2013). In this
approach, functional data from each subject are organized as
an individual graph where the vertex set corresponds to all the
voxels and the edge set represents the connections (similarity)
between any pair of voxels. The parcellation algorithm jointly
segments the set of graphs from all subjects by simultaneously
maximizing the similarity within each subgraph (node) and
minimizing the similarity between any two subgraphs across
the group. The resulting group parcellation shows significantly
higher functional homogeneity than the AAL atlas, where the
homogeneity is measured by the signal variation within each
node. The Euclidean distance between the resting-state timecourse from a single voxel and the mean timecourse of the
node to which it belongs (defined by either the AAL atlas or the
above group-wise graph parcellation approach) is calculated,
and for a whole-brain evaluation, the Euclidean distances are
averaged across all voxels to form the so-called whole-brain
inhomogeneity index; a smaller index indicates higher functional homogeneity. Figure 2 shows the comparison between
the AAL atlas containing 114 regions and the group-wise parcellations using the Shen et al. method containing 100, 200,
and 300 regions. At the whole-brain level, the group-wise
parcellations have better functional coherence within regions
for all subjects. (It is noted that the anatomical atlas has an
advantage in the subcortical regions where function aligns
nicely with clearly delineated structures.)
This greater within-region functional coherence has a significant impact on connectivity analyses. Figure 3 demonstrates how defining nodes using a connectivity-based
parcellation as opposed to anatomical constraints (Brodmann areas) or task-based fMRI localization (peaks of activation) can make for more precise and stable results. Left panels
show a comparison between the connectivity profiles of seeds
placed in Brodmann area 19 (a) and two nodes that are subcomponents of this region in a connectivity-based parcellation
(b and c) using resting-state fMRI data from 15 healthy subjects. Brodmann area 19 is a wide swath of the cortex in the
occipital lobe that parcellation subdivides into distinct functional units, and it is clear that each of these units has different
patterns of connectivity; grouping them together as a single
seed dilutes both sets of results. Furthermore, higher-order
network measures are often more stable across thresholds
when nodes are defined using a parcellation as opposed to
peaks of functional activation. The right panel in Figure 3
compares the measure of clustering coefficient for a single
node between nonimpaired readers and dyslexic readers across
thresholds using a 30-node network defined on task-based
activation peaks or using a parcellation. While group differences are less significant and even switch direction at certain
thresholds in the activation-defined network (Figure 3(d)), the
30
AAL
K = 100
Whole brain inhomogeneity
700
K = 200
25
K = 300
20
15
10
11
21
31
41
Subjects
51
61
71
Figure 2 Comparison of inhomogeneity indices between nodes defined

using the AAL atlas versus a data-driven parcellation scheme. Wholebrain inhomogeneity indices for 79 healthy subjects were calculated as
described in the section Defining Network Nodes for four different brain
parcellations, namely, the AAL atlas (red line) and the multigraph
clustering scheme described in Shen et al. (2013) at three different
resolutions: K 100 (blue; 50 nodes per hemisphere), K 200 (green;
100 nodes per hemisphere), and K 300 (magenta; 150 nodes per
hemisphere). The x-axis is the subject index, ordered according to wholebrain inhomogeneity index based on the AAL atlas. The graph
demonstrates uniformly lower inhomogeneity that is, better
functional coherence for nodes defined using the data-driven
parcellation scheme over the AAL atlas.
network of parcellated nodes shows clear and consistent group

differences that are significant across thresholds and never
reverse (Figure 3(e)).
Many parcellation algorithms, including the one described
in Shen et al. (2013), require an input, K, for a target number
of nodes. The ideal value of K is an open question. It has been
shown that the resolution of the brain parcellation that is,
the number of nodes can affect the results of network
analyses. While certain gross observations of network topology, such as small worldness (see Rubinov & Sporns, 2010),
may be robust to parcellation resolution, absolute values
of and individual differences in specific network measures
such as path length and clustering coefficient may vary
across resolutions (Fornito, Zalesky, & Bullmore, 2010;
Zalesky et al., 2010). Preliminary work has shown that a
parcellation on the order of 200 nodes provides a good balance between homogeneity within nodes and reproducibility
across subjects (Shen et al., 2013), but more work is needed to
determine the optimal parcellation resolution for various
population groups and research goals.
Overall, it is recommended that researchers carefully
consider how to define nodes for network analyses. While
some questions remain as to the optimal parcellation scheme
and resolution, using advanced functional data-driven parcellation algorithms, as opposed to anatomically or arbitrarily
defined regions, can produce more coherent timecourses
for individual nodes and therefore more meaningful connectivity results.
Seed = Brodmann area 19 (green)
701
Single-node clustering coefficient

Nodes defined based on activation
0.7
NI
DYS
0.6
0.5
(a)
0.4
0.3
Seed = Parcellation node A (purple)
0.2
0.1
0
(d) 0.1
0.2
0.3
0.4
0.5
Nodes defined using parcellation

0.7
(b)
Seed = Parcellation node B (blue)
NI
DYS
0.6
0.5
0.4
0.3
0.2
0.1
(c)
(e) 0.1
0.2
0.3
0.4
0.5
Figure 3 Comparison of connectivity results derived from nodes defined using the AAL atlas versus a data-driven parcellation scheme. Left panels:
(a) Connectivity profile of a seed placed in Brodmann area 19 (green) using data from 15 healthy subjects (showing all voxels correlated with the seed at
r 0.25). Compare (A) to connectivity profiles of two nodes representing functional subdivisions of Brodmann area 19 in a data-driven parcellation
scheme (b, purple seed; c, blue seed). (b and c) Divergent patterns of connectivity that are diluted when the two seed areas are lumped together in (a).
Right panel: (d) Clustering coefficient for a single node using a network of 30 nodes defined based on peaks of task-based activation, compared
between nonimpaired (NI) readers and dyslexic (DYS) readers in a study of brain activity to a reading task; (e) clustering coefficient for a node with
similar coordinates defined using the data-driven whole-brain parcellation scheme described in Shen et al. (2013). As in Figure 1, x-axis represents
correlation threshold, y-axis represents clustering coefficient, crosses () indicate a group difference at p < 0.05, and asterisks (*) indicate p < 0.01.
While group differences are less significant and even switch direction in the task-defined network, the whole-brain data-driven parcellation gives clear
and consistent group differences that are significant across thresholds and do not reverse.
Motion Confounds for Connectivity Analyses

Even as resting-state functional connectivity finds increasing
application in basic science and clinical investigations, there
are a number of preprocessing concerns that may influence
results. Specifically, subject motion and motion-related confounds remain a challenge. It has recently been shown that
most functional connectivity measures can be confounded by
head-movement artifacts even after taking conventional steps
to control for motion artifacts. Results from ROI-based
methods (Power, Barnes, Snyder, Schlaggar, & Petersen,
2012; Van Dijk, Sabuncu, & Buckner, 2012), network analyses
(Van Dijk et al., 2012), and ICA methods (Satterthwaite et al.,
2012) have all been shown to correlate with subject head
movement. High-motion subjects tend to show increased
strength of local connections and decreased strength of remote
connections (Power et al., 2012; Van Dijk et al., 2012). Furthermore, head movement varies with age, with children and
elderly subjects tending to move the most (Hampson et al.,
2012; Satterthwaite et al., 2012; Van Dijk et al., 2012). Reports
have suggested that censoring high-motion time points (Power
et al., 2012), regressing a summary of motion at the group
level (Satterthwaite et al., 2012), balancing motion across
groups (Tian et al., 2006), regressing motion parameters
based on autoregressive models (Friston, Williams, Howard,

Frackowiak, & Turner, 1996; Satterthwaite et al., 2013), and
regressing the global signal from each time point (Yan et al.,
2013) can help mitigate motion artifacts in connectivity analysis.
The aforementioned studies suggest that head movement
has a nonlinear effect on connectivity, as evidenced by the fact
that standard regression of motion parameters is not sufficient
to remove motion confounds. Even with rigid-body motion,
different regions of the brain travel different distances during
head movement due to the head pivoting on the neck
(Satterthwaite et al., 2013). Thus, regression of motion parameters, which parameterize the motion of the whole head, cannot account for the different distances that different brain
regions may have traveled. Unfortunately, regression of voxelspecific distance metrics does not markedly reduce motion
confounds (Satterthwaite et al., 2013; Yan et al., 2013). Likewise, regression of metrics that summarize motion for each
subject at the group level may not completely account for this
nonlinear effect. As shown in Hampson et al. (2012), the
relation between age and degree of connectivity (Martuzzi
et al., 2011) was similar with and without regression of motion
at the group level. Conversely, when data were removed such
that motion and age were not correlated, the relation between
age and degree of connectivity showed different patterns than
702
the previous analysis in regions of the default-mode network.

Due to such nonlinear effects, it cannot be assumed that
regression of simple summaries of head movement will
remove or minimize motion confounds.
The current approaches to reducing motion artifacts do not
attempt to directly correct the causes of motion confounds but
simply to minimize their impact on group statistics. The distinction between correcting for motion confounds and minimizing their impact on group statistics is important. While
some effects are certainly artifacts and errors, other effects
may reflect true differences in functional connectivity. A recent
resting-state fMRI study showed a high correlation between the
timecourse of movement parameters and the timecourse of
typical motor areas (Scheinost, Papademetris, & Constable,
2013); see Figure 4. While, in some ways, it seems obvious
that motion would be correlated with connectivity in motor
areas, this finding demonstrates that it is difficult to differentiate which portions of the data represent changes in brain
activity associated with motion and which represent artifacts.
Thus, simply removing high-motion time points (Carp, 2013;
Power et al., 2012) or regressing several orders of motion
parameters (Satterthwaite et al., 2012, 2013) may occlude
interesting changes in brain function. Nevertheless, distinguishing artifacts from true differences in connectivity due to
motion remains an open question in connectivity analysis.
Head movement may be a greater concern for functional
connectivity than conventional fMRI studies based on the
general linear model (GLM). In GLM analyses, a task vector

is used to describe the data. This task vector is independent
from the collected data and, thus, free of any motion confounds. The primary concern in GLM analysis is if the subject
moves in synchrony with the task, which makes it is difficult to
differentiate between signal changes due to head motion and
the task. Random motion throughout the experiment not correlated with the task will cause a reduction in detection power
but not systematic confounds due to motion. In contrast,
functional connectivity lacks the external task vector and uses
the data itself as a model. In this case, motion confounds are
present in both the independent and dependent variables. If
motion caused spikes in these two timecourses at approximately the same time points, the correlation between the two
time series would substantially increase in magnitude. Because
there is no external reference such as a task, functional connectivity analysis is more susceptible to systematic confounds due
to motion. It is important to note that solutions designed for
task-based analysis will not necessarily translate to connectivity
analysis given these differences, and thus, continued development of connectivity-specific methods for handling subject
motion is necessary.
While motion is a great concern for resting-state functional
connectivity, careful data processing and good quality control
can minimize the impact of motion on group analysis. Based
on the literature, the current recommendations to minimize
motion confounds are to first balance motion across the group,
Figure 4 Areas where BOLD signal is significantly correlated with subject head motion. Areas positively correlated with motion include the
supplementary motor area, primary motor cortex, primary sensory cortex, cerebellum, thalamus, and visual cortex. Areas negatively correlated with
motion include several areas of the medial and lateral frontal lobe and lateral portions of the parietal lobe. Results shown at p < 0.05 corrected for
multiple comparisons.
possibly removing subjects/data if necessary, and, second, if
concerns about motion still exist, to perform one or more of
the advanced techniques listed in the preceding text including
censoring, regression of higher-order motion terms, and regression of motion at the group level. New evidence also suggests
that smoothing all images to a uniform degree helps attenuate
the systematic effects of head motion on functional connectivity analyses (Scheinost et al., 2014).
Conclusion
In conclusion, functional connectivity and network analyses
present exciting new opportunities for characterizing the largescale organization of the brain and how this organization
varies with individuals, cognitive states, development, or
disease. While methodological concerns require researchers to
make informed choices about data analysis and preprocessing,
the explosion of interest in these techniques ensures that the
field of brain mapping will continue to refine and optimize
such methods to apply to clinical problems and research goals
in basic neuroscience.

Functional Connectivity; INTRODUCTION TO METHODS AND
Effective Connectivity; Graph-Theoretical Analysis of Brain Networks;
Resting-State Functional Connectivity; INTRODUCTION TO
SYSTEMS: Hubs and Pathways; Large-Scale Functional Brain
Organization; Network Components.
References
Achard, S., Salvador, R., Whitcher, B., Suckling, J., & Bullmore, E. (2006). A resilient,
low-frequency, small-world human brain functional network with highly connected
association cortical hubs. Journal of Neuroscience, 26(1), 6372.
Alexander-Bloch, A., Lambiotte, R., Roberts, B., Giedd, J., Gogtay, N., & Bullmore, E.
(2012). The discovery of population differences in network community structure:
New methods and applications to brain functional networks in schizophrenia.
Arfanakis, K., Cordes, D., Haughton, V. M., Moritz, C. H., Quigley, M. A., &
Meyerand, M. E. (2000). Combining independent component analysis and
correlation analysis to probe interregional connectivity in fMRI task activation
datasets. Magnetic Resonance Imaging, 18(8), 921930.
Baria, A. T., Baliki, M. N., Parrish, T., & Apkarian, A. V. (2011). Anatomical and
functional assemblies of brain BOLD oscillations. Journal of Neuroscience, 31(21),
79107919.
Beckmann, C., DeLuca, M., Devlin, J., & Smith, S. (2005). Investigations into restingstate connectivity using independent component analysis. Philosophical Transactions
of the Royal Society of London, Series B: Biological Sciences, 360, 10011013.
Biswal, B., Zerrin Yetkin, F., Haughton, V. M., & Hyde, J. S. (1995). Functional
connectivity in the motor cortex of resting human brain using echo-planar mri.
Buckner, R. L., Sepulcre, J., Talukdar, T., Krienen, F. M., Liu, H., Hedden, T., et al.
(2009). Cortical hubs revealed by intrinsic functional connectivity: Mapping,
assessment of stability, and relation to Alzheimers disease. Journal of
Carp, J. (2013). Optimizing the order of operations for movement scrubbing: Comment
on Power et al. NeuroImage, 76, 436438.
Chen, S., Ross, T., Zhan, W., Myers, C., Chuang, K.-S., Heishman, S., et al. (2008).
Group independent component analysis reveals consistent resting-state networks
across multiple sessions. Brain Research, 1239, 141151.
703
Cohen, A., Fair, D., Dosenbach, N., Miezin, F., Dierker, D., Essen, D. V., et al. (2008).
Defining functional areas in individual human brains using resting functional
connectivity MRI. NeuroImage, 41, 4557.
Fair, D. A., Dosenbach, N. U. F., Church, J. A., Cohen, A. L., Brahmbhatt, S.,
Miezin, F. M., et al. (2007). Development of distinct control networks through
segregation and integration. Proceedings of the National Academy of Sciences of
the United States of America, 104, 1350713512.
Fornito, A., Zalesky, A., & Breakspear, M. (2013). Graph analysis of the human
connectome: Promise, progress, and pitfalls. NeuroImage, 80, 426444.
Fornito, A., Zalesky, A., & Bullmore, E. T. (2010). Network scaling effects in graph
analytic studies of human resting-state fMRI data. Frontiers in Systems
Friston, K. J., Williams, S., Howard, R., Frackowiak, R. S., & Turner, R. (1996).
Movement-related effects in fMRI time-series. Magnetic Resonance in Medicine, 35,
346355.
Hampson, M., Tokoglu, F., Shen, X., Scheinost, D., Papademetris, X., &
Constable, R. T. (2012). Intrinsic brain connectivity related to age in young and
middle aged adults. PLoS One, 7, e44067.
Hoffman, R. E., Fernandez, T., Pittman, B., & Hampson, M. (2011). Elevated functional
connectivity along a corticostriatal loop and the mechanism of auditory/verbal
hallucinations in patients with schizophrenia. Biological Psychiatry, 69(5),
407414.
Lashkari, D., Vul, E., Kanwisher, N., & Golland, P. (2010). Discovering structure in the
space of fMRI selectivity profiles. NeuroImage, 50, 10851098.
Liu, Y., Liang, M., Zhou, Y., He, Y., Hao, Y., Song, M., et al. (2008). Disrupted smallworld networks in schizophrenia. Brain, 131, 945961.
Lynall, M.-E., Bassett, D. S., Kerwin, R., McKenna, P. J., Kitzbichler, M., Muller, U.,
et al. (2010). Functional connectivity and brain networks in schizophrenia. Journal
Martuzzi, R., Ramani, R., Qiu, M., Shen, X., Papademetris, X., & Constable, R. T. (2011).
A whole-brain voxel based measure of intrinsic connectivity contrast reveals local
changes in tissue connectivity with anesthetic without a priori assumptions on
thresholds or regions of interest. NeuroImage, 58, 10441050.
Power, J. D., Barnes, K. A., Snyder, A. Z., Schlaggar, B. L., & Petersen, S. E. (2012).
Spurious but systematic correlations in functional connectivity MRI networks arise
from subject motion. NeuroImage, 59, 21422154.
Power, J. D., Fair, D. A., Schlaggar, B. L., & Petersen, S. E. (2010). The development of
human functional brain networks. Neuron, 67(5), 735748.
Rubinov, M., & Sporns, O. (2010). Complex network measures of brain connectivity:
Uses and interpretations. NeuroImage, 52, 10591069.
Satterthwaite, T. D., Elliott, M. A., Gerraty, R. T., Ruparel, K., Loughead, J.,
Calkins, M. E., et al. (2013). An improved framework for confound regression and
filtering for control of motion artifact in the preprocessing of resting-state functional
connectivity data. NeuroImage, 64, 240256.
Satterthwaite, T. D., Wolf, D. H., Loughead, J., Ruparel, K., Elliott, M. A.,
Hakonarson, H., et al. (2012). Impact of in-scanner head motion on multiple
measures of functional connectivity: Relevance for studies of neurodevelopment in
youth. NeuroImage, 60, 623632.
Scheinost, D., Benjamin, J., Lacadie, C. M., Vohr, B., Schneider, K. C., Ment, L. R., et al.
(2012). The intrinsic connectivity distribution: A novel contrast measure reflecting
voxel level functional connectivity. NeuroImage, 62, 15101519.
Scheinost, D., Papademetris, X., & Constable, R. T. (2013). Correlation of head
movement and fMRI temporal signal in motor processing areas: What is artifact?
Seattle, WA: Human Brain Mapping.
Shen, X., Tokoglu, F., Papademetris, X., & Constable, R. T. (2013). Groupwise wholebrain parcellation from resting-state fMRI data for network node identification.
Shi, J., & Malik, J. (2000). Normalized cuts and image segmentation. IEEE Transactions
on Pattern Analysis and Machine Intelligence, 22, 888905.
Stevens, A. A., Tappon, S. C., Garg, A., & Fair, D. A. (2012). Functional brain network
modularity captures inter- and intra-individual variation in working memory
capacity. PLoS One, 7, e30468.
Supekar, K., Menon, V., Rubin, D., Musen, M., & Greicius, M. D. (2008). Network
analysis of intrinsic functional brain connectivity in Alzheimers disease. PLoS
Computational Biology, 4, e1000100.
Tian, L., Jiang, T., Wang, Y., Zang, Y., He, Y., Liang, M., et al. (2006). Altered
resting-state functional connectivity patterns of anterior cingulate cortex in
adolescents with attention deficit hyperactivity disorder. Neuroscience Letters, 400,
3943.
704
van den Heuvel, M. P., Mandl, R. C. W., Kahn, R. S., & Hulshoff Pol, H. E. (2009).
Functionally linked resting-state networks reflect the underlying structural connectivity
architecture of the human brain. Human Brain Mapping, 30, 31273141.
Van Den Heuvel, M., Mandl, R., & Pol, H. H. (2008). Normalized cut group clustering of
resting-state FMRI data. PLoS One, 3(4), e2001.
van den Heuvel, M. P., Mandl, R. C. W., Stam, C. J., Kahn, R. S., & Hulshoff Pol, H. E.
(2010). Aberrant frontal and temporal complex network structure in schizophrenia: A
graph theoretical analysis. Journal of Neuroscience, 30, 1591515926.
Van Dijk, K. R., Sabuncu, M. R., & Buckner, R. L. (2012). The influence of head motion
on intrinsic functional connectivity MRI. NeuroImage, 59, 431438.
Watts, D. J., & Strogatz, S. H. (1998). Collective dynamics of small-world networks.
Nature, 393, 440442.
Wilke, M. (2012). An alternative approach towards assessing and accounting for

individual motion in fMRI timeseries. NeuroImage, 59, 20622072.
Yan, C. G., Cheung, B., Kelly, C., Colcombe, S., Craddock, R. C., Di Martino, A.,
et al. (2013). A comprehensive assessment of regional variation in the impact
of head micromovements on functional connectomics. NeuroImage, 76,
183201.
Yeo, B., Krienen, F., Sepulcre, J., Sabuncu, M., Lashkari, D., Hollinshead, M., et al.
(2011). The organization of the human cerebral cortex estimated by intrinsic
Zalesky, A., Fornito, A., Harding, I. H., Cocchi, L., Yucel, M., Pantelis, C., et al. (2010).
Whole-brain anatomical networks: Does the choice of nodes matter? NeuroImage,
50, 970983.
BRAIN MAPPING
AN ENCYCLOPEDIC
REFERENCE
Volume 2
Anatomy and Physiology
Systems
BRAIN MAPPING
AN ENCYCLOPEDIC
REFERENCE
Volume 2
Systems
EDITOR-IN-CHIEF
ARTHUR W. TOGA
SECTION EDITORS
KARL ZILLES
Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Julich, Julich, Germany
KATRIN AMUNTS
Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Julich, Julich, Germany
MARSEL MESULAM
Northwestern University, Chicago, IL, USA
SABINE KASTNER
Princeton University, Princeton, NJ, USA
AMSTERDAM BOSTON HEIDELBERG LONDON

NEW YORK OXFORD PARIS SAN DIEGO
SAN FRANCISCO SINGAPORE SYDNEY TOKYO

32 Jamestown Road, London NW1 7BY, UK
525 B Street, Suite 1800, San Diego, CA 92101-4495, USA
225 Wyman Street, Waltham, MA 02451, USA
The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, UK
The following articles are US government work in the public domain and are not subject to copyright:
Contrast Agents in Functional Magnetic Resonance Imaging; Distribution of Estrogen Synthase (Aromatase) in the Human Brain; Evolution
of Instrumentation for Functional Magnetic Resonance Imaging; Temporal Resolution and Spatial Resolution of fMRI
The following articles are not part of Elsevier:
Cytoarchitectonics, Receptorarchitectonics, and Network Topology of Language; Expertise and Object Recognition; Hemodynamic and
Metabolic Disturbances in Acute Cerebral Infarction; Inflammatory Disorders in the Brain and CNS; Neuropsychiatry; Primary Progressive
Aphasia; Puberty, Peers, and Perspective Taking: Examining Adolescent Self-Concept Development Through the Lens of Social Cognitive
Neuroscience
No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means electronic,
mechanical, photocopying, recording or otherwise without the prior written permission of the publisher.
Permissions may be sought from Elseviers Science & Technology Rights department in Oxford, UK: phone (44) (0) 1865 843830;
fax (44) (0) 1865 853333; email: permissions@elsevier.com
Alternatively you can submit your request online by visiting the Elsevier website at http://elsevier.com/locate/permissions and selecting
Obtaining permission to use Elsevier material.
Notice
No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability,
negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein.
British Library Cataloguing in Publication Data
A catalogue record for this book is available from the British Library
Library of Congress Cataloging-in-Publication Data
A catalog record for this book is available from the Library of Congress
ISBN: 978-0-12-397025-1
For information on all Elsevier publications
visit our website at store.elsevier.com
15 16
17 18 19
10 9 8 7 6 5 4 3 2 1
Publisher: Lisa Tickner

Acquisitions Editor: Ginny Mills
Content Project Manager: Will Bowden Green
Production Project Manager: Paul Prasad
Cover Designer: Alan Studholme
CONTRIBUTORS
K Amunts
Institute of Neuroscience and Medicine (INM-1), Julich,
Germany; JARA Julich-Aachen Research Alliance,
Aachen, Germany; University of Dusseldorf, Dusseldorf,
Germany
E Armstrong
Troy University, Troy, AL, USA
A Aron
Stony Brook University, Stony Brook, NY, USA
G Auzias
MN Baliki
K-J Bar
Jena University Hospital, Jena, Germany; Psychiatry,
Brighton and Sussex Medical School, Falmer, UK
S Bludau
Aachen, Germany
D Caplan
Neuropsychology Laboratory, Boston, MA, USA
S Caspers
Germany
M Catani
NatBrainLab, Department of Forensic and
Neurodevelopmental Sciences, Institute of Psychiatry
PO50 Kings College London, London, United Kingdom
JL Chan
University of Western Ontario, London, ON, Canada
JT Coull
Aix-Marseille Universite & CNRS, Marseille Cedex 3,
France
O Coulon
H Critchley
University of Sussex, Falmer, UK
E Borra
Universita` di Parma, Parma, Italy
JC Culham
University of Western Ontario, London, ON, Canada
AD (Bud) Craig
Barrow Neurological Institute, Phoenix, AZ, USA
KR Daffner
Harvard Medical School, Brigham and Womens
Hospital, Boston, MA, USA
A Butt
University of Portsmouth, Portsmouth, UK
C Butti
Icahn School of Medicine at Mount Sinai, New York, NY,
USA
DP Buxhoeveden
University of South Carolina, Columbia, SC, USA
G Dehaene-Lambertz
INSERM-CEA, Cognitive Neuroimaging Unit,
NeuroSpin, Gif-sur-Yvette, France; University Paris Sud,
Orsay, France
JFX DeSouza
York University, Toronto, ON, Canada
D Bzdok
Institut fur Neurowissenschaften und Medizin (INM-1),
Julich, Germany
AS Dick
Florida International University, Miami, FL, USA
K Caeyenberghs
University of Ghent, Ghent, Belgium
M DEsposito
vi
Contributors
J Dubois
INSERM-CEA, Cognitive NeuroImaging Unit,
NeuroSpin, Gif-sur-Yvette, France; University Paris Sud,
Orsay, France
R Egger
Max Planck Institute for Biological Cybernetics,
Tubingen, Germany
J Gooijers
KU Leuven, Leuven, Belgium
MSA Graziano
Princeton University, Princeton, NJ, USA
MT Herrero
University of Murcia, Murcia, Spain
T Egner
Duke University, Durham, NC, USA
G Hickok
University of California, Irvine, CA, USA
SB Eickhoff
Research Centre Julich, Julich, Germany; HHU
Dusseldorf, Dusseldorf, Germany; Institut fur
Neurowissenschaften und Medizin (INM-1),
Julich, Germany
AB Hillis
MD, USA
C Estrada
University of Murcia, Murcia, Spain
PR Hof
USA
AC Evans
McGill University, Montreal, QC, Canada
CF Horton
University of California, San Diego, La Jolla, CA, USA
HC Evrard
Center for Integrative Neuroscience and Max Planck
Institute for Biological Cybernetics, Tubingen, Germany
AC Huk
The University of Texas, Austin, TX, USA
L Fadiga
University of Ferrara, Ferrara, Italy; Istituto Italiano di
Tecnologia; Genova, Italy
MA Farmer
D Feldmeyer
Institute of Neuroscience and Medicine, Research Center
Julich, Julich, Germany; RWTH Aachen University,
Aachen, Germany; Julich-Aachen Research Alliance,
Translational Brain Medicine (JARA Brain), Aachen,
Germany
A Flinker
New York University, New York, USA
S Francis
University of Nottingham, Nottingham, UK
I Gauthier
Vanderbilt University, Nashville, TN, USA
M Gerbella
R Insausti
University Castilla La Mancha, Albacete, Spain
SJ Joo
The University of Texas, Austin, TX, USA
M Judas
University of Zagreb Croatian Institute for Brain
Research, Zagreb, Croatia; University of Zagreb, Zagreb,
Croatia
JH Kaas
Vanderbilt University, Nashville, TN, USA
RT Knight
I Kostovic
University of Zagreb Croatian Institute for Brain
Research, Zagreb, Croatia; University of Zagreb, Zagreb,
Croatia
Z Kourtzi
University of Cambridge, Cambridge, UK
CR Gillebert
University of Leuven, Leuven, Belgium; University of
Oxford, Oxford, UK
ML Kringelbach
Aarhus University, Aarhus, Denmark; University of
Oxford, Oxford, UK
R Goebel
A Kucyi
J Goni
Indiana University, Bloomington, IN, USA
KS LaBar
Duke University, Durham, NC, USA
Contributors
C Lopez
Centre National de la Recherche Scientifique (CNRS),
Marseille, France; Aix Marseille Universite, Marseille,
France
JHR Lubke
Institute of Neuroscience and Medicine INM-2, Julich,
Germany; Rheinisch-Westfalische Technische
Hochschule/University Hospital Aachen, Aachen,
Germany; Julich-Aachen Research Alliance Translational
Brain Medicine, Aachen, Germany
G Luppino
J-F Mangin
CEA Saclay, Gif-sur-Yvette, France
W Matchin
MM McCarthy
University of Maryland School of Medicine, Baltimore,
MD, USA
V Menon
Stanford University School of Medicine, Stanford, CA,
USA
H Mohlberg
Aachen, Germany
VI Muller
Research Centre Julich, Julich, Germany; HHU
Dusseldorf, Dusseldorf, Germany
S Nasr
Martinos Center for Biomedical Imaging, Charlestown,
MA, USA; Harvard Medical School, Boston, MA, USA
DE Nee
M Noda
Kyushu University, Fukuoka, Japan
M Oberlaender
Max Planck Institute for Biological Cybernetics,
Tubingen, Germany; Bernstein Center for Computational
Neuroscience, Tubingen, Germany
N Palomero-Gallagher
Aachen, Germany
V Parpura
University of Alabama, Birmingham, AL, USA;
University of Rijeka, Rijeka, Croatia
vii
BN Pasley
M Petrides
McGill University, Montreal, Quebec, Canada
TC Pritchard
The Pennsylvania State University College of Medicine,
Hershey, PA, USA
L Puelles
University of Murcia, Murcia, Spain; Instituto Murciano
de Investigacion Biosanitaria [IMIB], Murcia, Spain
DS Race
MD, USA
MA Raghanti
Kent State University, Kent, OH, USA
S Raj
Harvard Medical School, Brigham and Womens
Hospital, Boston, MA, USA
JP Rauschecker
Georgetown University Medical Center, Washington,
DC, USA
PJ Reber
Northwestern University, Evanston, IL, USA
J Regis
CHU La Timone, Marseille, France
D Rivie`re
G Rizzolatti
University of Parma, Parma, Italy
JJ Rodriguez
IKERBASQUE, Basque Foundation for Science, Bilbao,
Spain; University of the Basque Country UPV/EHU,
Leioa, Spain
A Rollenhagen
Institute of Neuroscience and Medicine, INM-2, Julich,
Germany
ET Rolls
Oxford Centre for Computational Neuroscience, Oxford,
UK
B Rossion
Universite catholique de Louvain, Louvain-la-Neuve,
Belgium
Y Roth
Edith Wolfson Medical Center, Holon, Israel
S Rozzi
viii
Contributors
MR Sabuncu
Athinioula A. Martinos Center for Biomedical Imaging,
B Tia
D Schluppeck
University of Nottingham, Nottingham, UK
R Tootell
Martinos Center for Biomedical Imaging, Charlestown,
MA, USA; Harvard Medical School, Boston, MA, USA
O Schmitt
University Medical Center Rostock, Rostock, Germany
W Schultz
University of Cambridge, Cambridge, UK
K Semendeferi
University of California, San Diego, La Jolla, CA, USA
J Sepulcre
Massachusetts General Hospital and Harvard Medical
School, Boston, MA, USA; Athinioula A. Martinos Center
for Biomedical Imaging, Charlestown, MA, USA
CC Sherwood
The George Washington University, Washington, DC,
USA
S Shushan
Weizmann Institute of Science, Rehovot, Israel; Edith
Wolfson Medical Center, Holon, Israel
HM Sigurdardottir
Brown University, Providence, RI, USA; University of
Iceland, Reykjavk, Iceland
SL Small
N Sobel
Weizmann Institute of Science, Rehovot, Israel
LB Spurlock
Kent State University, Kent, OH, USA
JF Staiger
University Medicine Gottingen, Gottingen, Germany
F Sultan
HIH for Clinical Brain Research, Tuebingen, Germany
ZY Sun
SP Swinnen
Group Biomedical Sciences, KU Leuven, Belgium; KU
Leuven, Leuven, Belgium
HJ ten Donkelaar
Radboud University Nijmegen Medical Centre,
Nijmegen, The Netherlands
P Tetreault
J Ullmann
University of Queensland, Brisbane, Australia
N Uppal
USA
E Vachon-Presseau
TJ van Hartevelt
Aarhus University, Aarhus, Denmark; University of
Oxford, Oxford, UK
R Vandenberghe
University of Leuven, Leuven, Belgium; University
Hospitals Leuven, Leuven, Belgium
W Vanduffel
KU Leuven Medical School, Leuven, Belgium; Harvard
Medical School, Boston, MA, USA; Massachusetts
General Hospital, Charlestown, MA, USA
A Vania Apkarian
L Vasung
University of Zagreb, Zagreb, Croatia; University of
Geneva, Geneva, Switzerland
JH Venezia
A Verkhratsky
The University of Manchester, Manchester, UK;
IKERBASQUE, Basque Foundation for Science, Bilbao,
Spain; University of the Basque Country UPV/EHU,
Leioa, Spain
R Viaro
BA Vogt
Cingulum NeuroSciences Institute, Manlius, NY, USA;
Germany; Boston University School of Medicine, Boston,
MA, USA
C Watson
Curtin University, Perth, Australia; Neuroscience
Research Australia, Sydney, Australia
Contributors
ix
X Weng
Hangzhou Normal University, Hangzhou, China
L Zaborszky
The State University of New Jersey, Newark, NJ, USA
A Wree
University Medical Center Rostock, Rostock, Germany
Q Zhu
KU Leuven Medical School, Leuven, Belgium
X Xu
Idaho State University, Pocatello, ID, USA
K Zilles
Aachen, Germany; RWTH University Aachen, Aachen,
Germany
D Yilmazer-Hanke
Creighton University, Omaha, NE, USA
VOLUME 2 TABLE OF CONTENTS

Preface
xv
Editor-in-Chief
xvii
Section Editors
xix
Acknowledgments
xxiii
INTRODUCTION TO ANATOMY AND PHYSIOLOGY
Evolution of the Cerebral Cortex
K Semendeferi and CF Horton
Fetal and Postnatal Development of the Cortex: MRI and Genetics
11
J Dubois and G Dehaene-Lambertz
Quantitative Data and Scaling Rules of the Cerebral Cortex
21
E Armstrong
Brain Sex Differences
27
MM McCarthy
Gyrification in the Human Brain
37
K Zilles and N Palomero-Gallagher
Sulci as Landmarks
45
J-F Mangin, G Auzias, O Coulon, ZY Sun, D Rivie`re, and J Regis
Columns of the Mammalian Cortex
53
DP Buxhoeveden
Cell Types in the Cerebral Cortex: An Overview from the Rat Vibrissal Cortex
59
R Egger and M Oberlaender
Functional and Structural Diversity of Pyramidal Cells
65
D Feldmeyer
Cortical GABAergic Neurons
69
JF Staiger
Von Economo Neurons
81
MA Raghanti, LB Spurlock, N Uppal, CC Sherwood, C Butti, and PR Hof
Synaptic Organization of the Cerebral Cortex
93
A Rollenhagen and JHR Lubke
Astrocytes, Oligodendrocytes, and NG2 Glia: Structure and Function
101
A Verkhratsky, A Butt, JJ Rodriguez, and V Parpura
Microglia: Structure and Function
109
A Verkhratsky, M Noda, and Vladimir Parpura
xi
xii
Cytoarchitecture and Maps of the Human Cerebral Cortex
115
K Zilles, N Palomero-Gallagher, S Bludau, H Mohlberg, and K Amunts
Myeloarchitecture and Maps of the Cerebral Cortex
137
K Zilles, N Palomero-Gallagher, and K Amunts
Cortical Surface Morphometry
157
AC Evans
Embryonic and Fetal Development of the Human Cerebral Cortex
167
I Kostovic and M Judas
Cytoarchitectonics, Receptorarchitectonics, and Network Topology of Language
177
K Amunts and M Catani
Functional Connectivity
187
SB Eickhoff and VI Muller
The Resting-State Physiology of the Human Cerebral Cortex
203
D Bzdok and SB Eickhoff
Genoarchitectonic Brain Maps
211
L Puelles
Basal Ganglia
217
A Wree and O Schmitt
Thalamus: Anatomy
229
MT Herrero, R Insausti, and C Estrada
Cerebellum: Anatomy and Physiology
243
F Sultan
The Brain Stem
251
C Watson and J Ullmann
Transmitter Receptor Distribution in the Human Brain
261
N Palomero-Gallagher, K Amunts, and K Zilles
Motor Cortex
277
E Borra, M Gerbella, S Rozzi, and G Luppino
Somatosensory Cortex
283
JH Kaas
Functional Organization of the Primary Visual Cortex
287
R Goebel
Topographic Layout of Monkey Extrastriate Visual Cortex
293
W Vanduffel and Q Zhu
Auditory Cortex
299
JP Rauschecker
Vestibular Cortex
305
C Lopez
Gustatory System
313
TC Pritchard
Posterior Parietal Cortex: Structural and Functional Diversity
317
S Caspers
Mapping Cingulate Subregions
325
BA Vogt
Amygdala
D Yilmazer-Hanke
341
The Olfactory Cortex
xiii
347
TJ van Hartevelt and ML Kringelbach
Development of the Basal Ganglia and the Basal Forebrain
357
HJ ten Donkelaar
Development of the Diencephalon
367
HJ ten Donkelaar and L Vasung
Development of the Brain Stem and the Cerebellum
377
HJ ten Donkelaar
Insular Cortex
387
HC Evrard and AD (Bud) Craig
Basal Forebrain Anatomical Systems in MRI Space
395
L Zaborszky, K Amunts, N Palomero-Gallagher, and K Zilles
Anatomy and Physiology of the Mirror Neuron System
411
L Fadiga, B Tia, and R Viaro
Lateral and Dorsomedial Prefrontal Cortex and the Control of Cognition
417
M Petrides
Development of Structural and Functional Connectivity
423
J Dubois, I Kostovic, and M Judas
INTRODUCTION TO SYSTEMS
439
Hubs and Pathways
441
J Sepulcre, MR Sabuncu, and J Goni
Large-Scale Functional Brain Organization
449
V Menon
Neural Correlates of Motor Deficits in Young Patients with Traumatic Brain Injury
461
K Caeyenberghs and SP Swinnen
Visuomotor Integration
469
JC Culham
Bimanual Coordination
475
SP Swinnen and J Gooijers
Oculomotor System
483
JL Chan, A Kucyi, and JFX DeSouza
Primate Color Vision
489
R Tootell and S Nasr
Motion Perception
507
AC Huk and SJ Joo
Neural Codes for Shape Perception
511
Z Kourtzi
Face Perception
515
B Rossion
Expertise and Object Recognition
523
HM Sigurdardottir and I Gauthier
Visuospatial Attention
529
R Vandenberghe and CR Gillebert
Early Auditory Processing

JP Rauschecker
537
xiv
Functional Brain Imaging of Human Olfaction
543
S Shushan, Y Roth, and N Sobel
Somatosensory Processing
549
D Schluppeck and S Francis
Pain: Acute and Chronic
553
A Vania Apkarian, MN Baliki, MA Farmer, P Tetreault, and E Vachon-Presseau
Multisensory Integration and Audiovisual Speech Perception
565
JH Venezia, W Matchin, and G Hickok
Taste, Flavor, and Appetite
573
ET Rolls
Brain Mapping of Control Processes
581
T Egner
Working Memory
589
DE Nee and M DEsposito
Salience Network
597
V Menon
Neural Networks Underlying Novelty Processing
613
S Raj and KR Daffner
Emotion
619
KS LaBar
Memory
625
PJ Reber
The Mesolimbic Dopamine Pathway and Romantic Love
631
X Xu, X Weng, and A Aron
Autonomic Control
635
K-J Bar and H Critchley
Reward
643
W Schultz
Structural and Functional Components of Brain Networks for Language
653
AS Dick and SL Small
Speech Sounds
661
BN Pasley, A Flinker, and RT Knight
Grammar and Syntax
667
D Caplan
Naming
671
DS Race and AB Hillis
Action Understanding
677
G Rizzolatti
Cortical Action Representations
683
MSA Graziano
Directing Attention in Time as a Function of Temporal Expectation

JT Coull
687
PREFACE
The contributions of brain mapping are self-evident. Perhaps only a few areas of science have been applied as
broadly and deeply as brain mapping. In less than 50 years, it has revolutionized the study of brain structure
and function as well as the practice of clinical neuroscience. The resulting images derived from brain mapping
studies can be found everywhere. They grace the covers of many scientific journals, and even permeate the lay
media. The arresting imagery derived from sophisticated brain mapping methodologies and applied to
previously intractable problems has transformed neuroscience like no other specialty.
Brain mapping is a field that encompasses a wide range of scientific areas from MR physics, molecular
dynamics, and the mathematical modeling of data to the anatomical and physiological measurement of brain
systems and the study of complex cognitive functions. These all have been applied to understand the human
condition in health and disease. Advances have led to new effective treatments in stroke and improved
therapeutic intervention in many diseases affecting the brain. New approaches have enabled measures that
differentiate us as individuals anatomically and functionally. Maps that represent whole populations of people
of a certain age, gender, handedness, suffering from a particular neurological or psychiatric condition or even
genetic cohorts with a particular single nucleotide polymorphism can be created. The utility of these maps as
biomarkers or as guides in clinical trials has become a reality. Brain mapping is as vibrant and dynamic as ever
and increasingly links to other paths of discovery including genetics, proteomics, biologics, and big data.
The creation of this encyclopedia comes at a time that acknowledges the spectacular growth and important
contributions already made and the promise for ever more exciting and significant discoveries. It was just about
20 years ago that the first of the Brain Mapping Trilogy was published with the title, Brain Mapping: The Methods.
At about the same time, a group of brain imaging scientists decided it would be a good idea to form a new
society and the Organization for Human Brain Mapping was born. There are now several journals devoted to
neuroimaging and brain mapping. Other periodicals focused on more general neuroscience invariably include
a considerable number of papers on brain mapping. For the last couple of decades the number of brain
mapping publications grew from around 3200 in 1996 to about 14 000 in 2013, more than a 400% increase!
What a remarkable 20 years it has been. No longer can the breadth of brain mapping be covered in a traditional
text book style. The field has grown just too large.
Given the fact that there are well over 100 000 published papers on brain mapping, an encyclopedic
reference system to navigate these numbers is sorely needed. The three volumes of this encyclopedia fill that
need and consist of a comprehensive collection of thoughtful and informative descriptions of each topic. Well
referenced and written by recognized authorities, each article provides a wealth of information for the novice
and expert alike.
We organized the encyclopedia into seven sections. Volume 1 includes sections entitled Acquisition Methods
edited by Peter Bandettini and another entitled Methods and Modeling edited by Karl Friston and Paul Thompson. Acquisition Methods includes descriptions of magnetic resonance imaging (MRI), functional magnetic
resonance imaging (fMRI), magnetoencephalography (MEG), positron emission tomography (PET), and
near-infrared spectroscopy (NIRS). Most of the articles focus on variations in fMRI acquisition, given the
range and extent of this brain imaging method. However, it is clear that other approaches covered in this section
have lots to offer in the study of brain, each with its own advantages and disadvantages and each method has its
limitations, no one is a panacea. All are highly complementary and benefit from the synergy of multimodal
integration described further in Methods and Modeling. Here, Friston and Thompson selected papers describing advances in analytics built upon novel mathematics for representing and modeling signals, detecting
patterns, and understanding causal effects. These have accelerated the contributions of imaging and brain
xv
xvi
Preface
mapping significantly. Creative applications of random fields to dynamic causal models, graph theory,
networks, and topological measures of connectomes, to chart connections inferred from functional synchrony
or anatomical circuitry. Continuum mechanics fluid flow, differential geometry, and relativity all have been
used to model and manipulate anatomical surfaces in the brain, and to align and compare observations from
whole populations.
Volume 2 includes a section on Anatomy and Physiology edited by Karl Zilles and Katrin Amunts and another
devoted to Systems edited by Marsel Mesulam and Sabine Kastner. In the Anatomy and Physiology section, the
functional, cellular, and molecular basics along with organizational principles of brain structure provide a solid
foundation for models and simulations. This section goes on to provide an overview of brain development
beginning with the evolution of the cerebral cortex as well as embryonic and fetal development of the human
brain. Finally, the last part of this section is dedicated to different brain regions with emphasis focused on
functional systems and a superb lead into Systems. The section on Systems edited by Mesulam and Kastner is
comprised of articles that address the functional anatomy of action, perception, and cognition in multiple
modalities and domains.
Volume 3 contains sections on Cognitive Neuroscience edited by Russ Poldrack and another focused on Social
Cognitive Neuroscience edited by Matthew Lieberman and a third covering Clinical Brain Mapping edited by
Richard Frackowiak. The section on Cognitive Neuroscience covers a broad range of topics on mapping cognitive
functions including attention, learning and memory, decision making, executive function, and language. There
are articles on neuroeconomics, a field that combines neuroscience, psychology, and economics to better
understand the neural mechanisms for decision making. There is also a series of papers on memory, including
episodic memory, familiarity, semantic memory, and nondeclarative forms of learning. Language is covered in
this section as well, with articles on speech perception and production, syntax, semantics, and reading.
Poldrack also included studies of unique populations such as sign language speakers, bilinguals, and individuals with reading disabilities.
The section on Social Cognitive Neuroscience deals with how our brain responds to our social world. There are
papers that chart the different ways in which people respond to the rewards and punishments of social living
such as perceptions of unfair treatment, social rejection, or other negative social influences. There are also
articles describing neural mechanisms for reward and incentive motivation that respond to reinforcers like
money or sexual cues. Another part of this section deals with the concept of self. And another explores the
basic mechanisms of social perception. These articles focus on the perception of faces, bodies, and emotions as
basic cues. Also included are articles about social thinking and attitudinal and evaluative processes that keep
track of what matters to us and who or what we align ourselves with or against. Clinical Brain Mapping provides
numerous examples of the translational value of brain mapping. For example, the time course and cascade of
stroke pathophysiology pointed to the need for hyperacute treatment with thrombolytics. The contribution of
functional imaging first with PET and subsequently with fMRI, forever altered clinical neurology, neurosurgery
and other clinical neuroscience specialties. The ability to perform scans repetitively gave insights into functional
dynamics in the human brain enabling investigations of neurodegenerative disease, psychiatric disorders, and
the efficacy of therapeutic intervention.
Each of these sections stands alone as a comprehensive collection of articles describing the how, why, and
what brain mapping has contributed to these areas. Each article introduces the topic and brings the reader up to
date with the latest in findings and developments. We deliberately structured the encyclopedia so that readers
can peruse the material in any order or concentrate on a particular set of topics from methods to applications.
We kept the articles concise and suggest further reading to those who desire a more extensive review. They are
well referenced and illustrated appropriately.
Together these articles comprise a unique and rich resource for anyone interested in the science of mapping
the brain.
Arthur W. Toga
EDITOR-IN-CHIEF
Arthur W. Toga is the director, Laboratory of Neuro Imaging; director, Institute
of Neuroimaging and Informatics; provost professor, Departments of Ophthalmology, Neurology, Psychiatry, and the Behavioral Sciences, Radiology
and Engineering at the Keck School of Medicine of USC. His research is focused
on neuroimaging, informatics, mapping brain structure and function, and
brain atlasing. He has developed multimodal imaging and data aggregation
strategies and applied them in a variety of neurological diseases and psychiatric
disorders. His work in informatics includes the development and implementation of some of the largest and most widely used databases and data mining
tools linking disparate data from genetics, imaging, clinical and behavior,
supporting global efforts in Alzheimers disease, Huntingtons, and Parkinsons
disease. He was trained in neuroscience and computer science and has written
more than 1000 papers, chapters, and abstracts, including eight books. Recruited to USC in 2013, he directs the
Laboratory of Neuro Imaging. This 110-member laboratory includes graduate students from computer science,
biostatistics, and neuroscience. It is funded with grants from the National Institutes of Health grants as well as
industry partners. He has received numerous awards and honors in computer science, graphics, and neuroscience. Prior to coming to USC he was a distinguished professor of Neurology at UCLA, held the Geffen Chair of
Informatics at the David Geffen School of Medicine at UCLA, associate director of the UCLA Brain Mapping
Division within the Neuropsychiatric Institute, and associate dean, David Geffen School of Medicine at UCLA.
He is the founding editor-in-chief of the journal NeuroImage and holds the chairmanship of numerous
committees within NIH and a variety of international task forces.
xvii
SECTION EDITORS
Peter A. Bandettini is chief of the section on Functional Imaging Methods and
director of the Functional MRI Core Facility at the National Institutes of
Health. He is also editor-in-chief of the journal NeuroImage. He received his
BS from Marquette University in 1989 and his PhD from the Medical College
of Wisconsin in 1994, where he pioneered the development of magnetic
resonance imaging of human brain function using blood oxygenation contrast.
During his postdoctoral fellowship at the Massachusetts General Hospital with
Bruce Rosen, he continued his investigation of methods to increase the interpretability, resolution, and applicability of functional MRI techniques. In
1999, he joined NIMH as an investigator in the Laboratory of Brain and
Cognition and as the director of the NIH Functional MRI Core Facility. In
2001, he was awarded the Scientific Directors Merit Award for his efforts in
establishing the NIH FMRI Core Facility. In 2002, he was conferred the Wiley
Young Investigators Award at the Annual Organization for Human Brain
Mapping meeting. His section on Functional Imaging Methods is currently
developing MRI methods to improve the spatial resolution, temporal resolution, sensitivity, interpretability, and applications of functional MRI. Recently,
his research has focused specifically on improving general methodology for
fMRI applications at 3 and 7 T, investigation of fMRI-based functional connectivity methodology and applications, and investigation of fMRI decoding
methodology and applications. He has published over 120 papers and 20
book chapters and has given over 300 invited presentations. Recently, his
paper Time course EPI of Human Brain Function during Task Activation was
honored by the journal, Magnetic Resonance in Medicine, as one of their 30
papers in the past 30 years that helped shape the field.
Marsel Mesulam is director of Cognitive Neurology and Alzheimers Disease
Center, Northwestern University. He has completed his MD in medicine from
Harvard Medical School in 1972, received his postdoctoral fellow ship from
Harvard University in 1977. He was conferred with Bengt Winblad Lifetime
Achievement Award from Alzheimers Association in 2010 and Lishman Lectureship Award from International Neuropsychiatric Association. His research
interests are neural networks, functional imaging, dementia, cerebral cortex,
and cholinergic pathways. Also he has received Distinguished Career Contribution Award from the Cognitive Neuroscience Society and the Potamkin Prize
from the American Academy of Neurology.
xix
xx
Section Editors
Sabine Kastner is professor at the Princeton Neuroscience Institute and Department of Psychology, Princeton University, Princeton, NJ. She has received her
M.D. from the University of Dusseldorf (Germany) in 1993 and her Ph.D from
the University of Gottingen (Germany) in 1994, and did postdoctoral training at
NIMH. She was conferred with Young Investigator award from the Cognitive
Neuroscience Society (2005), the John Mclean, Jr., Presidential University
Preceptorship from Princeton University (2003), and is a fellow of the American
Psychological Society. Her research interests include the neural basis of visual
perception, attention and awareness, studied in two primate brain models
(monkey and human) with functional brain imaging and electrophysiology.
Richard Frackowiak studied medicine at the University of Cambridge where he
first became interested in the neurosciences. He joined the Medical Research
Councils Cyclotron Unit at Hammersmith Hospital, London, in 1979, under
Professor Terry Jones, who had just installed one of Britains first Positron Emission Tomography (PET) scanners. Richard Frackowiak is director at Department of
Clinical Neuroscience and Head of Service of Neurology, CHUV University Hospital, Lausanne, Switzerland. Frackowiak has won the IPSEN and Wilhelm Feldberg prizes and during the 1990s was the fourth most highly cited British
biomedical scientist. His books include Human Brain Function and Brain Mapping:
The Disorders. He is currently setting up a new Clinical Neuroscience Department
at the University of Lausanne. His research interest has been the functional and
structural architecture of the human brain in health and disease. He has pioneered
the development and introduction of positron emission tomography and magnetic resonance imaging and prosecuted a research programme dedicated to
understanding the organization of human brain functions, but his focus has
been on plasticity and mechanisms for functional recuperation after brain injury
and the patho-physiology of cerebral neurodegenerations. He has become interested in the use of MR-based morphometry especially in the study of genetic
influences on brain disease and in a search for biomarkers and endophenotypes
of neurodegenerative disorders. Most recently he has introduced computerized
image classification for diagnosis and treatment monitoring into clinical science.
Matthew Lieberman received his PhD from Harvard University. Lieberman,
with Kevin Ochsner, coined the term Social Cognitive Neuroscience, an area of
research that integrates questions from the social sciences which the methods
of cognitive neuroscience and has become a thriving area of research.
Lieberman has been a professor at UCLA in the Departments of Psychology,
Psychiatry and Biobehavioral Sciences since 2000. His work uses functional
magnetic resonance imaging (fMRI) to examine the neural bases of social
cognition and social experience. In particular, his work has examined the
neural bases of social cognition, emotion regulation, persuasion, social rejection, self-knowledge, and fairness. His research has been published in top
scientific journals including Science, American Psychologist, and Psychological
Science. His research has been funded by grants from the National Institute of
Mental Health, National Science Foundation, Guggenheim Foundation, and
Defense Advanced Research Projects Agency. His work has received coverage by
HBO, The New York Times, Time magazine, Scientific American, and Discover
Magazine. Lieberman is also the founding editor of the journal Social Cognitive
and Affective Neuroscience and helped create the Social and Affective Neuroscience
Society. Lieberman won the APA Distinguished Scientific Award for Early
Career Contribution to Psychology (2007) and campus wide teaching awards
from both Harvard and UCLA. He is the author of the book Social: Why Our
Brains Are Wired to Connect (finalist for the LA Times Book Prize and winner of
the Society for Personality and Social Psychology Book Prize).
Section Editors
xxi
Karl Zilles, MD, PhD, graduated from the University of Frankfurt, medical
faculty, and received the MD (1971) and the PhD (1977) in anatomy from the
Hannover Medical School, Germany. He was full professor of anatomy and
neuroanatomy at the University of Cologne between 1981 and 1991 and at
the University of Dusseldorf between 1991 and 2012. Additionally, he was
director of the C. & O. Vogt-Brain Research Institute, Dusseldorf, from 1991 to
2012, and of the Institute of Neuroscience and Medicine, Research Center Julich,
Germany, from 1998 to 2012. He is currently JARA senior professor at the
Research Center Julich and at the RWTH Aachen University, Germany. He serves
as editor-in-chief of the journal Brain Structure and Function and was member of
editorial boards of various scientific journals (e.g., NeuroImage). Karl Zilles is
fellow of the German National Academy of Sciences Leopoldina and fellow of
the North-Rhine Westphalia Academy of Science and Arts. His research focus is
on the structural (cyto- and myeloarchitecture), molecular (receptor architecture), and functional (neuroimaging using MRI, fMRI, and PET) organization of
the mouse, rat, nonhuman primate, and human cerebral cortex. He pioneered
brain mapping based on the regional and laminar distribution of transmitter
receptors in the healthy and pathologically impaired human brains and brains
of genetic mouse and models. He recently introduced, together with Katrin
Amunts, Markus Axer, and colleagues, an ultra-high-resolution method for
nerve fiber and fiber tract visualization based on polarized light imaging in the
human, monkey, mouse, and rat brains. He published more than 590 original
articles in nature, science, neuron, brain, and other peer-reviewed journals.
Katrin Amunts, MD, PhD, graduated in 1987 from the Pirogov Medical School
in Moscow, Russia. She received the PhD (1989) in neuroscience, anatomy from
the Institute of Brain Research at the Lumumba University in Moscow, Russia.
After her postdoc at the C. & O. Vogt Institute for Brain Research of the HeinrichHeine-University Dusseldorf, Germany, and at the Institute of Neuroscience and
Medicine, Research Center Julich, she became associate professor for StructuralFunctional Brain Mapping (2004), and full professor at the Department of
Psychiatry, Psychotherapy, and Psychosomatics of the RWTH Aachen University
(2008) as well as director of the Institute of Neuroscience and Medicine (INM-1)
at the Research Centre Julich. Since 2013, she is additionally full professor for
Brain Research and director of the C. & O. Vogt Institute for Brain Research, at the
Heinrich-Heine-University Dusseldorf. She is a member of the editorial board of
Brain Structure and Function. Currently, she is member of the German Ethics
Council and speaker for the programme Decoding the Human Brain of the
Helmholtz Association, Germany. Katrin Amunts is interested in understanding
the relationship between the microstructure of the human brain and functional
systems such as motor control, language, and vision. Although scientists have
been studying brain cytoarchitecture for over 100 years, its importance has
increased rapidly with the advance of modern imaging techniques. This led,
together with Karl Zilles and his team, to the development of a novel, observerindependent and functionally relevant cytoarchitectonic mapping strategy resulting in freely available brain maps comprising approximately 200 areas and
nuclei, as well as the anatomy toolbox software, developed with Simon Eickhoff,
for co-localizing functional activations and cytoarchitectonically defined brain
regions. The Julich atlas JuBrain as a multimodal human brain model will replace
during the next decade the cytoarchitectonic brain atlas, which Korbinian Brodmann published in 1909 (Zilles and Amunts, Nature Reviews Neuroscience,
2010). Recently, the group has provided the first ultra-high resolution model of
the human brain, the BigBrain (Amunts et al., Science, 2013).
xxii
Section Editors
Russell A. Poldrack is Professor of Psychology at Stanford University. He has

previously held academic posts at the University of Texas, UCLA, and Harvard
Medical School. His lab uses the tools of cognitive neuroscience to understand
how decision making, executive control, and learning and memory are implemented in the human brain. They also develop neuroinformatics tools
and resources to help researchers make better sense of data, with involvement
in projects including the Cognitive Atlas, OpenfMRI, Neurosynth, and
Neurovault.
Paul Thompson directs the ENIGMA Consortium, a global alliance of 307

scientists in 33 countries who study ten major diseases ranging from schizophrenia, depression, ADHD, bipolar illness, and OCD, to HIV and addiction.
ENIGMAs genomic screens of over 31 000 peoples brain scans and genomewide data (published in Nature Genetics, 2012; Nature, 2015) bring together
experts from 185 institutions to unearth genetic variants that affect the brain
structure, and discover factors that help or harm the brain. At USC, Thompson
is associate dean for Research at the Keck School of Medicine and a Professor of
Neurology, Psychiatry, Radiology, Pediatrics, Engineering, and Ophthalmology. Thompson also directs the USC Imaging Genetics Center a group of 35
scientists in Marina del Rey, California. His team also studies aging and
Alzheimers disease, as well as brain growth in children. Thompson has an
MA in mathematics and Greek and Latin Languages from Oxford University,
and a PhD in neuroscience from UCLA.
Karl Friston is a theoretical neuroscientist and authority on brain imaging. He
invented statistical parametric mapping (SPM), voxel-based morphometry
(VBM), and dynamic causal modeling (DCM). These contributions were motivated by schizophrenia research and theoretical studies of value-learning
formulated as the dysconnection hypothesis of schizophrenia. Mathematical
contributions include variational Laplacian procedures and generalized filtering for hierarchical Bayesian model inversion. Friston currently works on
models of functional integration in the human brain and the principles that
underlie neuronal interactions. His main contribution to theoretical neurobiology is a free-energy principle for action and perception (active inference).
Friston received the first Young Investigators Award in Human Brain Mapping
(1996) and was elected a fellow of the Academy of Medical Sciences (1999). In
2000, he was president of the International Organization of Human Brain
Mapping. In 2003, he was awarded the Minerva Golden Brain Award and was
elected a fellow of the Royal Society in 2006. In 2008, he received a Medal,
Colle`ge de France and an Honorary Doctorate from the University of York in
2011. He became a fellow of the Society of Biology in 2012 and received the
Weldon Memorial prize and Medal in 2013 for contributions to mathematical
biology.
ACKNOWLEDGMENTS
Sometimes, the scope and structure of a book is clear from the outset, other times it evolves as the outlines are
written or because contributors with different perspectives suggest new and different things. This book
occasionally took on a life of its own, morphing into something greater than the original concept. But that
was because of the hundreds (literally) of people who contributed to it. Working independently and together
we created a one-of-a-kind collection of excellent articles on brain mapping, from data generation to knowledge
about the brain. This collaborative effort is one of the greatest joys in working on project of this magnitude. The
end result is a mix of all this expertise into a single product. While such a process could easily produce chaos, in
this case each editor had a clear vision that complemented the other sections of the book. Each contributor
produced a superb article and collectively they cover the field.
One of the most difficult aspects of this project was limiting the scope because its magnitude kept getting
larger the more we all talked about it. There are so many new areas within brain mapping. There are so many
creative ways to apply the ever increasing number of methods to study the structure and function of brain in
health and disease. This scope further motivated us to create an encyclopedia because the field was not only
ready for such a thing, it needed it.
Many of us who worked on this book have known each other for a long time. Others of you are new
acquaintances, but to each of you I owe my sincerest gratitude. You are among the best and brightest minds in
neuroscience and your participation made this book. Your research and writing will be appreciated by the
readers for many years to come.
In addition to all the contributors writing and editing chapters and sections there are many others who
deserve mention. At the Laboratory of Neuro Imaging at the University of Southern California I am privileged
to have a spectacular staff. Grace Liang-Franco manages the lab with an efficiency and deftness that defies limits.
Sandy, Diana, and Catalina all keep things moving smoothly and professionally so I can work on projects like
this encyclopedia. Thanks to you all. The team at Elsevier has been terrific. They have tolerated the fits and starts
associated with a project like this and helped usher into the world an important and substantial work. Thanks
to Mica Haley, Ashlie Jackman, Will Bowden-Green, Erin Hill-Parks, and many others.
Finally, I always express gratitude to my family. They do not help me write or edit or even read the things I
write but somehow they make it possible. I work at home in the evenings and on weekends, just like many of
you reading this book. I guess I could be doing other things but my family tolerates this behavior and has for
decades. Perhaps they are happy I am preoccupied with academic pursuits. It keeps me busy and out of their
hair. But for whatever the real reason, my wife Debbie, and my children Nicholas, Elizabeth, and Rebecca let me
work on these things and I appreciate them more than can be stated here.
Arthur W. Toga
Los Angeles, CA
xxiii
INTRODUCTION TO ANATOMY AND PHYSIOLOGY
With the advent of structural and functional imaging, additional research fields were opened for neurophysiology and particularly neuroanatomy as basic sciences in brain mapping, since solid knowledge of the
underlying structure and function is required for the meaningful interpretation of structural MRI, activation
spots in fMRI, resting-state networks, modeled fiber tracts of diffusion-weighted imaging, and functional
connectivity models. This need has recently become even more acute because the development of highresolution neuroimaging and the modeling and simulation approaches encroach more and more onto the
interface between mesoscopic and microscopic scales. Therefore, detailed data of the functional, cellular, and
molecular basics are necessary to provide solid foundations for models and simulations. We did not intend to
provide a short version of a traditional neuroanatomy textbook, and this section cannot give a comprehensive
review of all necessary details, but aims to build an introduction into the organizational principles of brain
structure.
The first articles in this section provide an overview of brain development beginning with the evolution of
the cerebral cortex and the underlying scaling rules. Variation in cortical microstructure indicates cognitively
significant evolutionary shifts rather than large-scale changes in size (Semendeferi and Horton, Evolution of
the Cerebral Cortex). This is supported by the fact that anthropoids differ from other eutherians in gaining
less mass for every unit increase in isocortical neuron numbers, which probably reflects a relative increase in
the number of interneurons (Armstrong, Quantitative Data and Scaling Rules of the Cerebral Cortex). The
following articles summarize principal aspects of brain morphology. Sex differences in the brain and
the cellular mechanisms of how they are established during development are described (McCarthy, Brain
Sex Differences). Gyrification is a major morphological hallmark of the human cerebral cortex. A detailed
anatomical identification of the sulci and gyri of the probably most frequently used reference brain in
neuroimaging is provided, and two major hypotheses of gyrification mechanisms are discussed (Zilles and
Palomero-Gallagher, Gyrification in the Human Brain). Since sulci are frequently used as landmarks for
anatomical localization of functional neuroimaging data, new computational methods have been designed to
support those activities for improving the role of sulci as landmarks, including models of intersubject variability
of the shape of the sulci (Mangin et al., Sulci as Landmarks). Cortical morphometric methods enable crosssectional and longitudinal studies of large sample sizes of both healthy human subjects and patients. Cortical
thickness, surface and volume are frequently used to analyze anatomical changes. A description of recent
developments and caveats is provided here (Evans, Cortical Surface Morphometry).
The second part of this section deals with the embryonic and fetal development of the human brain. An
obvious feature of the developing human cerebral cortex is the prolonged coexistence of transient fetal and
adultlike circuitry. This enables a considerable plasticity during ontogeny and its surprising reorganization
capacity during brain evolution (Kostovic and Judas, Embryonic and Fetal Development of the Human
Cerebral Cortex). The development of the human cerebral cortex can now be analyzed in-vivo using MRI,
and the impact of the relationships between MRI markers, genetic and environmental factors, and cognitive
development can be studied (Dubois and Dehaene-Lambertz, Fetal and Postnatal Development of
the Cortex: MRI and Genetics). These articles are followed by descriptions of the development of the
basal ganglia and the basal forebrain (ten Donkelaar, Development of the Basal Ganglia and the Basal
Forebrain), the diencephalon (ten Donkelaar and Vasung, Development of the Diencephalon), and the
brain stem and the cerebellum (ten Donkelaar, Development of the Brainstem and the Cerebellum). The
developmental part is concluded by an article on the maturation of structural and functional connectivity,
which starts during the early fetal period and extends until the end of adolescence (Dubois, Kostovic and
Judas, Development of Structural and Functional Connectivity).
Introduction to Anatomy and Physiology
A series of articles focus on cell types in the cerebral cortex. The major goal of cell-typing is to understand
functional principles of cortical organization. Some general aspects of somatodendritic cell type classification
are described and how they relate to cell type-specific computations is discussed (Egger and Oberlaender, Cell
Types in the Cerebral Cortex: An Overview from the Rat Whisker System). Since the pyramidal cells are the
most frequent neurons in the cerebral cortex, the correlation between their considerable diversity in function
and structure is important. The enhancement of synaptic response to prior activity enabled by the somatodendritic, axonal, and synaptic organization of these neurons may constitute a mechanism for learning and
memory (Feldmeyer, Functional and Structural Diversity of Pyramidal Neurons). Cortical GABAergic neurons are key players in the organization of intracortical microcircuits. They show a large variety of different cell
types, with differential distribution patterns throughout cortical layers and target specificities. Six of these
GABAergic interneurons are presented here (Staiger, Cortical GABAergic Neurons). The von Economo neurons, which were already described at the beginning of the twentieth century but never analyzed in more detail,
recently raised attention, because of their significance in brain evolution and neurological and psychiatric
illnesses. Their morphology, distribution in the brain, and functional role are described here (Raghanti et al.,
Von Economo Neurons). The elucidation of the synaptic organization in the cerebral cortex is still a work in
progress because of the incredible complexity of synaptic varieties and their involvement in connectivity
(Rollenhagen and Lubke, Synaptic Organization of the Cerebral Cortex). The neurons of the cerebral cortex
are distributed in horizontal (layers) and vertical (columns) structures. The columns can be interpreted as
cortical modules, which are not uniform in composition, but are highly complex and show variations of the
basic columnar concept (Buxhoeveden, Columns of the Mammalian Cortex). The glial cells were interpreted
for a long time as being mere scaffolding elements. This concept is no longer sustainable as shown in the two
articles on the variety of the morphology and functions of macroglial cells and microglia (Verkhratsky et al.,
Astrocytes, Oligodendrocytes and NG2-Cells: Structure and Function; Verkhratsky, Noda, Parpura, Microglia: Structure and Function). Macroglial cells express neurotransmitters and can influence local and remote
neural activity via metabolic and/or signaling pathways. Microglial cells differ from macroglial cells by their
origin from the mesoderm and play various roles during physiological, defensive, and pathological processes
including antigen presentation, phagocytosis, and cytotoxicity.
Brain maps are crucial for the interpretation of the anatomical localization of neuroimaging data. The
pioneering cytoarchitectonic observations of Brodmann are of major importance in this respect; however, the
imaging community unfortunately uses in most cases only his schematic 2-D drawings or the 3-D interpretation
by Talairach and Tournoux. The underlying descriptions by Brodmann and, particularly, the vast cyto- and
myeloarchitectonic literature of the Vogt and von Economo schools published since his pioneering monography
are often neglected or completely forgotten. Brodmanns schematic drawing alone does not provide a sufficient
basis for localization and understanding of the anatomical organization behind the functional imaging data!
Therefore, we have included six articles that describe the often forgotten or recently developed maps of the
human cerebral cortex (Zilles et al., Cytoarchitecture and Maps of the Human Cerebral Cortex), myeloarchitecture (Zilles, Palomero-Gallagher and Amunts, Myeloarchitecture of the Human Cerebral Cortex), receptor
architecture (Palomero-Gallagher, Amunts and Zilles, Transmitter Receptor Distribution in the Human
Brain), and genoarchitecture (Puelles, Genoarchitectonic brain maps). Furthermore, advantages and drawbacks
of different approaches to functional connectivity (Eickhoff and Muller, Functional Connectivity) and the
physiology of the cerebral cortex based on resting-state signal, connectivity, and networks as well as the
dimensions of metabolism (Bzdok and Eickhoff, The Resting-State Physiology of the Human Cerebral Cortex)
are also described.
The last part of this section is dedicated to different brain regions with emphasis on functional systems. It
starts with a article on the brain stem in light of recent gene expression and inducible genetic fate mapping
(Watson and Ullmann, The Brainstem), followed by an article on the anatomy and physiology of the
cerebellum based on connectivity mapping and the cerebellar microcircuitry as well as comparative anatomical
considerations (Sultan, Cerebellum: Anatomy and Physiology). After descriptions of the anatomy, connectivity and function of the basal ganglia (Wree, Basal Ganglia), amygdala (Yilmazer-Hanke, Amygdala), and the
magnocellular structures of the basal forebrain (Zaborszky et al., Basal Forebrain Anatomical Systems in MRI
Space), presentations of various cortical sensory (van Hartevelt and Kringelbach, The Olfactory Cortex; Kaas,
Somatosensory Cortex; Goebel, Functional Organization of the Primary Visual Cortex; Vanduffel and Zhu,
Topographic Layout of Monkey Extrastriate Visual Cortex; Rauschecker, Auditory Cortex; Lopez, Vestibular
Cortex; Pritchard, Gustatory System), motor (Borra et al., Motor Cortex), and higher multimodal systems
(Caspers, Posterior Parietal Cortex; Vogt, Mapping Cingulate Subregions; Evrard and Craig, Insular Cortex;
Fadiga, Tia and Viaro, Anatomy and Physiology of the Mirror Neuron System; Petrides, Lateral and Dorsomedial Prefrontal Cortex and the Control of Cognition; Amunts and Catani, Cytoarchitectonics, Receptorarchitectonics, and Network Topology of Language) conclude this section.
Karl Zilles
Katrin Amunts
Evolution of the Cerebral Cortex

K Semendeferi and CF Horton, University of California, San Diego, La Jolla, CA, USA
Glossary
Derived trait Traits that are newly acquired and did not exist
in the last common ancestor.
Embryonic zone Neural regions present in the developing
embryo which contain progenitor cells and generate cortical
neurons.
GABA-ergic interneuron A neuron that modulates activity
of other neurons using GABA neurotransmitter; typically
inhibitory.
Gyral white matter White matter immediately under the
cortex.
Homoplasy Similar traits in different species that have
evolved independent of ancestral lineage.
Minicolumn Vertically oriented conglomerates of cells that
extend through layers II through VI of the cortex, and serve
Definition of Cerebral Cortex

The mammalian cortex is a multilayered cellular sheet of neural
tissue that makes up the outermost surface of the brain. It is
largely comprised of the neocortex or isocortex, which consists
of six horizontally organized layers (Figure 1(a) and 1(b)).
Some cortical regions have fewer layers, such as the allocortex
(the hippocampus), periallocortex (the entorhinal cortex), and
proisocortex (the posterior orbitofrontal cortex). Cortical neurons in the mammalian cortex fall under two major classes
excitatory neurons and inhibitory interneurons. These classes
can be further divided into a wide array of subtypes defined by
size, shape, morphology, connectivity, and protein expression
and are distributed differentially in cortical layers and cortical
regions and across species. The cortex is characterized by conglomerates of vertically organized cells (minicolumns), which
operate as the basic computational unit and functionally integrate the cortical layers. Within these vertical units, afferent
signals to cortical layers are thalamic (targeting layer IV), subcortical (targeting layers II, III, and IV), or corticocortical (connectivity between layers II, III, and IV) (Figure 1(b)). Efferent
outgoing signals are sent from layer II or III to other cortical
areas (intra- or interhemispherically), from layer V to subcortical
structures, and from layer VI to the thalamus (Buxhoeveden &
Casanova, 2002; Purves, 2008). Minicolumns are modified by
various modalities, including inhibitory neurons, horizontal
connections between minicolumns, feedback connections from
subcortical and other cortical regions, and neurotransmitter
inputs from the brainstem and thalamus. Such modifications
can induce long-term changes over a lifetime that contribute to
neuronal plasticity, perceptual learning, and behavioral
flexibility and are also subject to evolutionary changes that alter
and adjust functional connectivity for adaptive modification.
The neocortex is further organized by cortical areas that are
functionally and cytoarchitectonically distinct from other areas
as the basic anatomical and physiological unit of the

mammalian cortex.
Monotreme Egg-laying mammals.
Primitive trait Traits that were retained from the last
common ancestor.
Progenitor cell: A cell that has the ability to differentiate
later into one or more specific cell types; is more specific
than a stem cell.
Pyramidal neuron Neurons with distinct pyramidal-shaped
soma (cell body). These are found in the cortex,
hippocampus, and amygdala and are the most numerous
excitatory cell type in the mammalian cortex.
(Figure 1(c)). Interacting neurons that share a particular set of

inputs and signal targets constitute a cortical area and give the
area distinct functional significance. A well-known example of a
cortical area is V1/Brodmanns area 17, the primary visual cortex,
which receives most output from the lateral geniculate nucleus of
the thalamus and provides visual input to other higher-order
visual regions of the cortex. Such differentiation of cortical
areas contributes to the functional flexibility of the neocortex.
Origins of the Cerebral Cortex

Comparative studies suggest that regions of the mammalian
neocortex are homologous to the reptilian dorsal cortex
(Figure 2; Molnar, 2011), as well as the avian dorsomedial
pallium (Karten, 1969), and have a similar columnar structure
as the avian auditory cortex (Wang, Brzozowska-Prechtl, &
Karten, 2010). The mammalian neocortex also contains
many structural, functional, and physiological features that
can be found in other more conserved areas of the brain,
suggesting that the mammalian neocortex is not a completely
new structure. However, certain distinct features found in the
mammalian neocortex are not present in reptiles or birds. One
uniquely mammalian trait is the cortical magnification of sensory receptors, in which sensory receptors are distributed differently depending on behavioral significance, so that more
significant sensory cortical areas have a greater number of
receptors. The mammalian cortex is also unique in that it has
a thicker structure and contains more neurons and a greater
diversity in neur.onal types compared to homologous structures in birds and reptiles (Figure 2; Molnar, 2011).
Fossil record endocasts suggest early mammals were very
small with small brains, a large olfactory bulb and piriform
cortex, and little neocortex. The mass extinction of dinosaurs
around 65 MYA was followed by rapid radiation of
http://dx.doi.org/10.1016/B978-0-12-397025-1.00192-5
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Evolution of the Cerebral Cortex
II
III
Pyramidal cell
Local axon
collateral (local
circuitry)
IV
4
Other
cortical
areas
Thalum
V
Descending axon
(output)
VI
White
matter
(a)
Other cortical
areas, opposite
hemisphere
Subvertical
structures
(e.g., striatum
superior
colliculum)
(b)
Other
cortical
areas
Brainstem
modulatory
systems
(c)
Figure 1 (a) Figure depicting the cytoarchitectonic distinctions of the six layers of the cortex. (b) Figure depicting the input/output specializations of the
cortical layers. (c) Figure depicting the cortical areas (Brodmanns areas) in a human brain. Adapted from Purves, D. (2008). Neuroscience (4th ed.).
Sunderland, MA: Sinaur Associates, Inc. (Figure 26.2 A,B, p. 568; Figure 26.3, p. 269), with permission.
Layers
I
Vertical expansion
Layers
I, V, and VI
IIIII
IV
V
evolved later in placental mammals. Furthermore, the corpus

callosum is a new trait in placental mammalian brains, given its
absence in monotremes, marsupials, reptiles, or any other
vertebrates (Keeler, 1933). Despite these differences, extant
species with varying degrees of cortical size and complexity
do not represent stages of mammalian evolution, but are
instead a mix of both primitive and derived traits (Kaas, 2007).
VI
(a)
Scaling and Development

Horizontal expansion
(b)
Figure 2 (a) The comparison between the dorsal cortices of an adult

turtle, which has a single cell-dense layer, and an adult rat, which has the
typical mammalian pattern of six distinct cellular layers. Comparative
studies suggest that many of the cells of the infragranular layers in
mammals (V and VI) were already present in the single cellular layer of
the reptilian dorsal cortex. In (b), an adult mouse and adult human are
compared, in which cortical surface area is greatly increased in the
human. Adapted from Molnar, Z. (2011). Evolution of cerebral cortical
development. Brain, Behavior and Evolution, 78(1), 94107 (Figure 3,
p. 96), with permission.
mammalian species, resulting in great physical variation,

including increases in brain size and other neural modifications (Figure 3; Jerison, 1963). Comparative observations of
extant species suggest that three neocortical sensory areas, V1
(primary visual), S1 (primary somatosensory), and A1 (primary auditory), present in all living mammals, are premammalian and may have been critical to the emergence and
organization of the neocortex (Krubitzer & Kaas, 2005). However, M1 (the primary motor cortex) is absent in marsupials
(Beck, Pospichal, & Kaas, 1996), which suggests this region
Neurogenesis in mammalian development occurs in transient

embryonic zones (i.e., the ventricular zone or the subventricular zone) that lie along the surface of the lateral ventricles of the
cerebrum. Neurons migrate from these embryonic zones
through long-distance radial (vertical) and tangential (horizontal) migration (Rakic, 2009). The radial unit, which contains all
precursor cells for the adult cortical minicolumn, is the fundamental unit of neuronal proliferation in the cortex (Rakic,
1990). A greater number of radial units generated results in
more cortical columns and therefore greater horizontal expansion of the cortex (Rakic, 2009). Recent studies suggest that the
compartmentalization of the embryonic zone and the differential regulation of progenitor cells are of key evolutionary importance in increasing cortical expansion and specialization
(Molnar, 2011). Furthermore, much of neural migration patterning and maturation are mediated by cell-specific and cortical layer-specific transcription factors, which can also
determine axonal connectivity (Kwan, Sestan, & Anton, 2012).
While the chronology of stages in neurogenesis is highly
conserved across mammals, the length of neurogenesis itself is
highly variable, ranging from 10 days (mouse) to 100 days
(monkeys) (Clancy, Darlington, & Finlay, 2001). The scale of
neurogenesis is nonlinear and increases exponentially with
extended periods of development, which differentially affects
the total number of neurons in structures with early termination of neurogenesis (i.e., the medulla), versus later neurogenesis termination (i.e., the cortex), such that structures that
Modern mammal brain
Fossil mammal brain

Oligocene sabertooth:
Hoplophoneus
E = 50 g; P = 25000 g
domestic cat
E = 30 g; P = 3000 g
Endocast
Endocast
Brain
Brain and endocasts

Reduced 0.72
(a)
(b)
Figure 3 Endocast of a modern (a) and a fossil (b) mammalian brain. E brain weight, P body weight. Reproduced from Jerison, H. (1963).
Interpreting the evolution of the brain. Human Biology, 35(3), 263291, with permission.
appear later have more neurons (Finlay & Brodsky, 2007). In

general, cell groups that are more lateral (alar) along the
embryonic axis have later neurogenesis termination, while
cell groups that are more basal have earlier neurogenesis termination. The two exceptions to this pattern are the olfactory
bulb and the hippocampus, which continue neurogenesis
throughout life (Finlay & Brodsky, 2007).
A related source of cortical variability across mammalian
species is the scale of component parts. Most variability in
homologous brain regions of mammals is predicted by total
brain size (Finlay & Brodsky, 2007). However, neural components scale at different rates; in mammals, brain volume
becomes dominated by the neocortex as the brain increases
in size (Finlay & Darlington, 1995; Figure 4). The individual
scaling of brain regions is thought to be critical to primate
brain evolution and attracted considerable attention with
respect to human brain evolution, particularly in the frontal
lobe. The cognitive specializations that make primates and
particularly humans unique are often attributed to the functions of the frontal lobe; however, it must be emphasized that
the brain is organized in neural systems, not isolated components. Humans and apes do not deviate from the primate trend
in expected frontal lobe volume, frontal gray matter volume, or
frontal white matter volume when taking into account overall
brain size, relative measurements, allometric scaling, and phylogeny (Barton & Venditti, 2013; Semendeferi, Damasio,
Frank, & Van Hoesen, 1997; Semendeferi, Lu, Schenker, &
Damasio, 2002; Smaers et al., 2011). It has been suggested
instead that the cognitive specializations in humans result
from the evolution of multiple specific cortical and subcortical
regions of the brain in concert to form larger and more
complex distributed networks (Barger et al., 2012; Barton &
Venditti, 2013).
Changes in Microanatomy
Changes in brain size had significant effect on neural reorganization in mammalian evolution. Larger brains have more
cortical surface area and more neurons than smaller brains,
but there is little difference in terms of neuronal body size or
axonal length (Bekkers & Stevens, 1970). Brain tissue is
extremely costly, so efficiency is critical with increasing brain
size. One such high cost is long axon lengths, which are both
spatially expensive and metabolically expensive (Swindale,
2001). In larger brains, there is a decrease in the ratio of
soma to axons and a necessary shift in cortical wiring (Zhang
& Sejnowski, 2000), suggesting that network organization may
be different in the scaling of large and small brains. One
reorganizational consequence is that as brain size increases,
each neuron is in contact with a smaller proportion of total
neurons. Therefore, larger brains necessitate more modular
organization through an increase in local processing, a
decrease in long-range connections including interhemispheric
connections through the corpus callosum, and an increase in
hemispheric independence (Kaas, 2000; Ringo, Doty, Demeter,
& Simard, 1994). This also results in larger brains having
relatively more white matter than the cortex in comparison to
smaller brains (Figure 5).
Comparisons across mammalian taxa show that brain size has
a positive correlation with number of cortical areas (Figure 6),
suggesting that size-necessitated modular organization results in
more distinct cortical regions, which may in turn allow more
flexible and refined processing. However, large brain size has a
cost: aside from energetic costs of generating and maintaining
an increasingly large brain (Leonard, Robertson, Snodgrass, &
Kuzawa, 2003), other restraints to brain size are infant head size,
which is constrained by the width of the birth canal (Leutenegger,
30.00
Neocortex (+16)
Striatum (+15)
Diencephalon (+13)
In (structure size (mm3))
Cerebellum (+10)
20.00
Schizocortex (+10)
Hippocampus (+7)
Septum (+6.5)
Mesencephalon (+3)
10.00
Medulla (+0.5)
Paleocortex (-2)
0.00
4.00
6.05
8.10
10.15
12.20
14.25
In (brain size (mm3))

Figure 4 Sizes of ten measure brain subdivisions from 131 species plotted as a function of total brain size (orange squares, simians; green circles,
prosimians; red circles, insectivores; and blue squares, bats). Compared to other brain regions, the neocortex scales with the steepest slope
compared to overall brain size. Reproduced from Finlay, B. L., & Darlington, R. B. (1995). Linked regularities in the development and of mammalian
brains evolution. Science, 268(5217), 15781584. with permission.
Neocortical white vs. gray matter
Ln white matter
Primates
Carnivores
Others
2
0
-2
All mammals: 1.28 (95%: 1.24-1.33)

Primates: 1.33 (95%: 1.23-1.43)
-4
Carnivores: 1.17 (95%: 1.05-1.3)

All non-primates: 1.26 (95%: 1.21-1.31)
-2
2
Ln gray matter
Figure 5 Ln neocortical gray matter plotted against Ln neocortical

white matter in mammals, with major axis regression slopes and 95%
confidence intervals. White matter is disproportionately scaled in larger
brains. Reproduced from Bush, E. C., & Allman, J. M. (2003). The scaling
of white matter to gray matter in cerebellum and neocortex. Brain,
Behavior and Evolution, 61(1), 15 (Figure 2, p. 4), with permission.
1982; Trevathan, 1988), and the gravitational costs of increasing

head weight (Kaas, 2007).
The modular organization of larger brains allows for more
complex regional neural processing (Kaas, 1989; Mitchison,
1991) such that different trends of cortical disproportionality

and modification across mammals likely reflect functional
adaptations for ecological variation (Figure 7). For example,
chimpanzees, bonobos, and humans have a specialized frontal
lobe, with modifications such as increased gyral white matter
in humans and increased gyral white to gray matter ratio in the
frontal lobe in chimpanzees and bonobos compared to other
apes (Schenker, Desgouttes, & Semendeferi, 2005), disproportionate enlargement in the left prefrontal cortex (PFC) of apes
and humans compared to monkeys (Smaers et al., 2011),
and differences in size of individual cortical areas in humans
(Semendeferi, Armstrong, Schleicher, Zilles, & Van Hoesen,
1998; Semendeferi et al., 2011). However, most cortical specializations are likely not changes in relative size, but changes
in functional allocation of cortical areas, so that even basic
cortical processing might vary in cortical areas for animals of
different ecological niches. This type of specialization is not
determined at neurogenesis, but during later development,
with neural resources being variably allocated to new functions
as needed in response to the environment (Kaas, 2007).
Species-specific differences in layer, or laminar, structure
are another form of cortical specialization. While some claim
that the number of neurons vertically spanning the cortex of
each homologous functional area varies little across species
(Carlo & Stevens, 2013; Rockel, Hiorns, & Powell, 1980),
recent observations in mammals reveal variation in neuronal
density and minicolumn spacing. For example, several microanatomical differences in humans and apes suggest the human
60
Rhesus
50
Number of areas
40
Owl monkey
Marmoset
30
Squirrel monkey
Cat
Galago
20
Squirrel
10
Various shrews, rat
0
0
2000
4000
6000
8000
10 000
12 000
Cortical areas (mm2)

Figure 6 The number of cortical areas plotted against cortical surface area in select mammal species. Reproduced from Finlay, B. L., & Brodsky, P.
(2007). Cortical evolution as the expression of a program for disproportionate growth and the proliferation of areas. In J. H. Kass (Ed.), Evolution
of nervous systems in mammals (pp. 7496). Academic Press, with permission.
Mouse
V
S
A
Ghost bat
S
asymmetry (Schenker et al., 2010). In addition to an increase

in its size, BA 10 in humans has significantly more neuropil
space (cortical space not occupied by cell bodies) (Spocter
et al., 2012), wider minicolumns (Semendeferi et al., 2011),
and lower cell density in supragranular layers (Semendeferi,
Armstrong, Schleicher, Zilles, & Van Hoesen, 2001) compared
to apes and selected other primates. These findings point to
possible differences in arborization of specific neuronal subpopulations and increases in connectivity that may be critical
to human brain evolution.
Cellular Phenotypes and Distribution

Short-tailed opossum
V
S
m
A
r
1mm
Figure 7 Primary sensory areas in three species (A, auditory cortex; S,

somatosensory cortex; and V, visual cortex) with the same size
cortical sheet. Differentially sized cortical areas reflect specific ecological
adaptations. Reproduced from Krubitzer, L., & Kahn, D. M. (2003).
Nature versus nurture revisited: An old idea with a new twist. Progress in
Neurobiology, 70(1), 3352, with permission.
PFC is marked by a decrease in cell density. In Brocas area (BA

44 and 45), a prefrontal region implicated in language production, humans demonstrate decreased neuronal density and
greater horizontal spacing between minicolumns compared
to other apes, which suggests that humans have more space
available for inter-minicolumn connectivity (Schenker et al.,
2008). Compared to other great apes, humans also demonstrate the most individual variation in asymmetry in Brocas
area and show a population-level presence of leftward
There are several types of neurons in the cortex. Excitatory

pyramidal neurons comprise the most abundant morphological class of neurons in the cortex. They are oriented orthogonally toward the pial surface and have pyramidal-shaped soma
with typically one apical and several highly branched basal
dendritic projections that often span across cortical layers.
Layers II and III of the neocortex have several small- to
medium-sized pyramidal neurons with restricted dendritic
trees that form connections with nearby cortical regions,
while larger pyramidal neurons of some areas deep in layers
III and V have expansive dendritic trees that allow for longdistance connections. Neuronal morphology in layer V is most
varied, with neurons that are involved in both corticocortical
connectivity and corticothalamic connectivity. Horizontal projections serve primarily to interconnect related cortical
modules, which allows for regional and functional specificity
of excitatory patterns (Figure 1(b)).
Pyramidal neuron morphology mirrors patterns of
connectivity a dendritic tree restricted to a single cortical
layer is receptive to few afferents while a large dendritic tree
that spans the cortex is receptive to a wide variety of inputs. The
size and branching pattern of dendritic trees, as well as the
distribution of pyramidal neurons, have significant variability
across species and cortical regions. The total number of dendritic spines, that is, the number of synaptic inputs onto the
dendrites of a particularity neuron (DeFelipe & Farinas, 1992)
in different cortical regions of the primate cortex, varies significantly. For example, in humans and other primates, spine
density differences between cortical areas can vary by tenfold
(Elston, 2007). These differences have great functional significance and reflect differences in computational capability of a
neuron; for instance, differences in spine number reflect the
amount of excitatory inputs, and differences in length, number
of arborizations, and axonal thickness reflect profound physiological differences in synaptic connectivity (Spruston, 2008).
Species-specific chemical signatures of pyramidal neuron subtypes are another source of pyramidal variation (see Hof &
Sherwood, 2007).
Inhibitory GABAergic interneurons are the second major
class of neurons in the cortex and broadly function to regulate
pyramidal cell activity. Interneurons are difficult to classify
because subtypes are identified by numerous characteristics,
such as size, morphology, calcium-binding proteins (parvalbumin (PV), calbindin (CB), and calretinin (CR)), neuropeptide
content (Andressen, Blumcke, & Celio, 1993; Hendry et al.,
1989; Markram et al., 2004), and other protein expression. The
role of interneuron subtype distribution in cortical evolution is
equally unclear. For example, interneurons expressing the
enzyme tyrosine hydroxylase (TH) are very common in cortical
layers VVI and at the white matter boundary of humans
(Benavides-Piccione & DeFelipe, 2007) and are present in the
same layers of old-world monkeys (Benavides-Piccione &
DeFelipe, 2007; Kohler, Everitt, Pearson, & Goldstein, 1983;
Lewis, Foote, Goldstein, & Morrison, 1988; Raghanti et al.,
2009), but are not present in the great apes (Raghanti et al.,
2009) and have varying abundance and distribution in
nonprimates.
Comparisons of GABAergic interneuron distribution across
species may reflect shifts in cortical evolution. The primate
cortex has a significantly greater proportion of GABAergic
interneurons compared to rodents (Beaulieu, 1993; Beaulieu,
Kisvarday, Somogyi, Cynader, & Cowey, 1992; Hendry,
Schwark, Jones, & Yan, 1987; Meinecke & Peters, 1987). Evidence of different developmental origins of GABAergic interneurons in these mammalian groups (Letinic, Zoncu, & Rakic,
2002; Rakic & Zecevic, 2003) suggests there were a greater
number and a greater variety of newer types of GABAergic
interneurons in primate evolutionary history compared to
rodents or carnivores (DeFelipe, Alonso-Nanclares, & Arellano,
2002). The distribution of interneuron subtypes may also
reflect phylogenetic relationships. For example, the rarity of
PV-immunoreactive interneurons in cetaceans and artiodactyls
may be an ancestrally conserved trait for Laurasiatheria (placental mammals originating from Laurasia) because other laurasiatherians that have many ancestral features also have few
PV-immunoreactive interneurons (Glezer, Jacobs, & Morgane,
1988). Convergent evolution may also be reflected in interneuron subtype distribution. For instance, the calcium-binding
protein interneurons have similar type and distribution in
both Carnivora and Euarchontoglires (rodents, tree shrews,
primates, lagomorphs, and colugos), despite great phylogenetic distance (Ballesteros-Yanez et al., 2005; Glezer, Hof,
Leranth, & Morgane, 1993; Hof et al., 1999). While cell
distribution, organization, and morphology of neurochemical

types are highly varied across mammals, neuronal mechanisms
are often more conserved (Ballesteros-Yanez et al., 2005).
There are other types of specialized neurons in the mammalian cortex that do not fall under these two major neuronal
classes yet may play an important role in mammalian cortical
evolution. For example, many large-brained animals, including humans, apes, macaques, cetaceans, and elephants, possess
large bipolar spindle neurons in the frontoinsular cortex and
limbic anterior area that are not present in other species
(Allman et al., 2011; von Economo, 2009). These variations
possibly reflect differences in learning, memory, and cognitive
ability.
Humans do not differ significantly from other primates in
ways that would be expected given their distinct cognitive
phenotype. The human PFC glianeuron ratio, while higher
than other primates, scales proportionately to the increase in
brain size (Sherwood et al., 2006). Acetylcholine (ACh), dopamine (DA), and serotonin (5HT), three neurotransmitters that
modulate neural activity and are commonly implicated in
complex cognitive function, do not have greater quantity or
distribution in human PFC regions compared to chimpanzees
and macaques, with the exception of DA innervation in BA 32.
However, all three species demonstrate unique distribution
patterns of innervation within the cortical layers by all three
neuromodulatory systems in the PFC, while distribution patterns in BA 4 are relatively conserved across species. Furthermore, humans and chimpanzees, but not macaques,
demonstrate coils of innervated axon fibers associated with
cortical plasticity in layer III for all three neurotransmitter subtypes (Raghanti, Stimpson, Marcinkiewicz, Erwin, & Hof,
2008; Raghanti et al., 2008a, 2008b). Observations such as
these across mammalian species demonstrate a substantial
amount of homoplasy and species-specific specializations, suggesting that subtle yet unique variations in neuronal phenotype and distribution may underlie significant differences in
neural processing.

Cortex; Columns of the Mammalian Cortex; Cortical GABAergic
Neurons; Cortical Surface Morphometry; Cytoarchitecture and Maps of
the Human Cerebral Cortex; Development of the Basal Ganglia and the
Basal Forebrain; Embryonic and Fetal Development of the Human
Cerebral Cortex; Functional and Structural Diversity of Pyramidal Cells;
Lateral and Dorsomedial Prefrontal Cortex and the Control of
Cognition; Quantitative Data and Scaling Rules of the Cerebral Cortex;
Synaptic Organization of the Cerebral Cortex; Von Economo Neurons.
References
Allman, J. M., Tetreault, N. A., Hakeem, A. Y., Manaye, K. F., Semendeferi, K.,
Erwin, J. M., et al. (2011). The von Economo neurons in the frontoinsular and
anterior cingulate cortex. Annals of the New York Academy of Sciences, 1225,
5971.
Andressen, C. I., Blumcke, I., & Celio, M. R. (1993). Calcium-binding proteins:
Selective markers of nerve cells. Cell and Tissue Research, 271, 181208.
Ballesteros-Yanez, I., Munoz, A., Contreras, J., Gonzalez, J., Rodriguez-Veiga, E., &
DeFelipe, J. (2005). The double bouquet cell in the human cerebral cortex and a

comparison with other mammals. Journal of Comparative Neurology, 486,
344360.
Barger, N., Stefanacci, L., Schumann, C. M., Sherwood, C. C., Annese, J., Allman, J. M.,
et al. (2012). Neuronal populations in the basolateral nuclei of the amygdala are
differentially increased in humans compared with apes: A stereological study. The
Barton, R. A., & Venditti, C. (2013). Human frontal lobes are not relatively large.
10(22), 16.
Beaulieu, C. (1993). Numerical data on neocortical neurons in adult rat, with special
reference to the GABA population. Brain Research, 609, 284292.
Beaulieu, C., Kisvarday, Z., Somogyi, P., Cynader, M., & Cowey, A. (1992).
Quantitative distribution of GABA-immunopositive and -immunonegative neurons and
syn-apses in the monkey striate cortex (area 17). Cerebral Cortex, 2, 295309.
Beck, P. D., Pospichal, M. W., & Kaas, J. H. (1996). Topography, architecture, and
connections of somatosensory cortex in opossums: Evidence for five
somatosensory areas. Journal of Comparative Neurology, 366, 109133.
Bekkers, J. M., & Stevens, C. F. (1970). Two different ways evolution makes neurons
larger. Progress in Brain Research, 83, 3745.
Benavides-Piccione, R., & DeFelipe, J. (2007). Distribution of neurons expressing
tyrosine hydroxylase in the human cerebral cortex. Journal of Anatomy, 211,
212222.
Bush, E. C., & Allman, J. M. (2003). The scaling of white matter to gray matter in
cerebellum and neocortex. Brain, Behavior and Evolution, 61(1), 15.
Buxhoeveden, D. P., & Casanova, M. F. (2002). The minicolumn and evolution of the
brain. Brain, Behavior and Evolution, 60(3), 125151.
Carlo, C., & Stevens, C. (2013). Structural uniformity of neocortex, revisited.
Proceedings of the National Academy of Science, 110(4), 16.
Clancy, B., Darlington, R. B., & Finlay, B. L. (2001). Translating developmental time
across mammalian species. Neuroscience, 105(1), 717.
DeFelipe, J., Alonso-Nanclares, L., & Arellano, J. I. (2002). Microstructure of the
neocortex: Comparative aspects. Journal of Neurocytology, 31, 299316.
DeFelipe, J., & Farinas, I. (1992). The pyramidal neuron of the cerebral cortex:
Morphological and chemical characteristics of the synaptic inputs. Progress in
Neurobiology, 39, 563607.
Elston, G. N. (2007). Specialization of the neocortical pyramidal cell during
primate evolution. In J. H. Kaas & T. M. Preuss (Eds.), Evolution of nervous
systems: Evolution of the primate nervous systems (pp. 191253). Oxford:
Elsevier.
Finlay, B. L., & Brodsky, P. (2007). Cortical evolution as the expression of a program
for disproportionate growth and the proliferation of areas. In J. H. Kass (Ed.),
Evolution of nervous systems in mammals (pp. 7496): Academic Press.
Finlay, B. L., & Darlington, R. B. (1995). Linked regularities in the development and of
mammalian brains evolution. Science, 268(5217), 15781584.
Glezer, I. I., Jacobs, M. S., & Morgane, P. J. (1988). Implications of the initial brain
concept for brain evolution in Cetacea. Behavioral and Brain Sciences, 11, 75116.
Glezer, I. I., Hof, P. R., Leranth, C., & Morgane, P. J. (1993). Calcium-binding
protein-containing neuronal populations in mammalian visual cortex: A
comparative study in whales, insectivores, bats, rodents, and primates. Cerebral
Cortex, 3, 249272.
Hendry, S. H. C., Jones, E. G., Emson, P. C., Lawson, D. E.M, Heizmann, C. W., &
Streit, P. (1989). Two classes of cortical, GABA neurons defined by differential
calcium-binding protein immunoreactivities. Experimental Brain Research, 76,
467472.
Hendry, S. H., Schwark, H. D., Jones, E. G., & Yan, J. (1987). Numbers and proportions of GABA-immunoreactive neurons in different areas of monkey cerebral
cortex. Journal of Neuroscience, 7, 15031519.
Hof, P. R., Glezer, I. I., Conde, F., Flagg, R. A., Rubin, M. B., Nimchinsky, E. A., et al.
(1999). Cellular distribution of the calcium-binding proteins parvalbumin,
calbindin, and calretinin in the neo-cortex of mammals: Phylogenetic and
developmental patterns. Journal of Chemical Neuroanatomy, 16, 77116.
Hof, P., & Sherwood, C. (2007). The evolution of neuron classes in the neocortex of
mammals. In J. Kaas (Ed.), Evolution of nervous systems in mammals
(pp. 113124): Academic Press.
Jerison, H. (1963). Interpreting the evolution of the brain. Human Biology, 35(3),
263291.
Kaas, J. H. (1989). Why does the brain have so many visual areas? Journal Cognitive
Kaas, J. H. (2000). Why is brain size so important: Design problems and solutions as
neocortex gets bigger or smaller. Brain Mind, 1, 723.
Kaas, J. (2007). Reconstructing the organization of neocortex of the first mammals and
subsequent modifications. In J. Kaas (Ed.), Evolution of nervous systems in
mammals (pp. 2648): Academic Press.
Karten, H. (1969). The organization of the avian telencephalon and some speculations
on the phylogeny of the amniote telencephalon. Annals of the New York Academy of
Sciences, 167, 164180.
Keeler, C. E. (1933). Absence of corpus callosum as mendelizing character in the house
mouse. Proceedings of the National Academy of Sciences of the United States of
America, 19(6), 609611.
Kohler, C., Everitt, B. J., Pearson, J., & Goldstein, M. (1983). Immunohistochemical
evidence for a new group of catecholamine-containing neurons in the basal
forebrain of the monkey. Neuroscience Letters, 37, 161166.
Krubitzer, L., & Kaas, J. H. (2005). The evolution of the neocortex in mammals:
How is phenotypic diversity generated? Current Opinion in Neurobiology, 15,
44453.
Krubitzer, L., & Kahn, D. M. (2003). Nature versus nurture revisited: An old idea with a
new twist. Progress in Neurobiology, 70(1), 3352.
Kwan, K. Y., Sestan, N., & Anton, E. S. (2012). Transcriptional co-regulation of
neuronal migration and laminar identity in the neocortex. Development, 139(9),
15351546.
Leonard, W. R., Robertson, M. L., Snodgrass, J., & Kuzawa, C. W. (2003). Metabolic
correlates of hominid brain evolution. Comparative Biochemistry and Physiology,
Part A: Molecular & Integrative Physiology, 136, 515.
Letinic, K., Zoncu, R., & Rakic, P. (2002). Origin of GABAergic neurons in the human
neocortex. Nature, 417, 645649.
Leutenegger, W. (1982). Encephalization and obstetrics in primates. In E. Armstrong, &
D. Falk (Eds.), Primate brain evolution: Methods and concepts (pp. 4396): New
York: Plenum.
Lewis, D. A., Foote, S. L., Goldstein, M., & Morrison, J. H. (1988). The dopaminergic
innervation of monkey prefrontal cortex: A tyrosine hydroxylase
immunohistochemical study. Brain Research, 449, 225243.
Markram, H., Toledo-Rodriguez, M., Wang, Y., Gupta, A., Silberberg, G., & Wu, C.
(2004). Interneurons of the neocortical inhibitory system. Nature Reviews.
Meinecke, D. L., & Peters, A. (1987). GABA immunoreactive neurons in rat visual
cortex. Journal of Comparative Neurology, 261, 388404.
Mitchison, G. (1991). Neuronal branching patterns and the economy of cortical wiring.
Proceedings of the Royal Society of London B, 245, 151158.
Molnar, Z. (2011). Evolution of cerebral cortical development. Brain, Behavior and
Evolution, 78(1), 94107.
Purves, D. (2008). Neuroscience (4th ed.). Sunderland, MA: Sinaur Associates, Inc.
Raghanti, M. A., Spocter, M. A., Stimpson, C. D., Erwin, J. M., Bonar, C. J.,
Allman, J. M., et al. (2009). Species-specific distributions of tyrosine hydroxylaseimmunoreactive neurons in the prefrontal cortex of anthropoid primates.
Raghanti, M. A., Stimpson, C. D., Marcinkiewicz, J. L., Erwin, J. M., & Hof, P. R. (2008).
Cholinergic innervation of the frontal cortex: Differences among humans,
chimpanzees, and macaque monkeys. Journal of Comparative Neurology, 506,
409424.
Raghanti, M. A., Stimpson, C. D., Marcinkiewicz, J. L., Erwin, J. M., Hof, P. R., &
Sherwood, C. C. (2008a). Cortical dopaminergic innervation among humans,
chimpanzees, and macaque monkeys: A comparative study. Neuroscience, 155(1),
203220.
Raghanti, M. A., Stimpson, C. D., Marcinkiewicz, J. L., Erwin, J. M., Hof, P. R., &
Sherwood, C. C. (2008b). Differences in cortical serotonergic innervation among
humans, chimpanzees, and macaque monkeys: A comparative study. Cerebral
Cortex, 18(3), 584597.
Rakic, P. (1990). Critical cellular events in cortical evolution: Radial unit hypothesis. In
B. L. Finlay, G. Innocenti, & H. Scheich (Eds.), The neocortex: Ontogeny and
phylogeny (pp. 2132): Plenum.
Rakic, P. (2009). Evolution of the neocortex: A perspective from developmental biology.
Nature Reviews. Neuroscience, 2009, 724735.
Rakic, S., & Zecevic, N. (2003). Emerging complexity of layer I in human cerebral
cortex. Cerebral Cortex, 13, 10721083.
Ringo, J. L., Doty, R. W., Demeter, S., & Simard, P. Y. (1994). Time is of the essence: A
conjecture that hemispheric specialization arises from interhemispheric conduction
delay. Cerebral Cortex, 4, 331343.
Rockel, A. J., Hiorns, R. W., & Powell, T. P. (1980). The basic uniformity in structure of
the neocortex. Brain, 103, 221244.
Schenker, N. M., Buxhoeveden, D. P., Blackmon, W. L., Amunts, K., Zilles, K., &
Semendeferi, K. (2008). A comparative quantitative analysis of cytoarchitecture and
minicolumnar organization in Brocas area in humans and great apes. The Journal of
Comparative Neurology, 510(1), 117128.
Schenker, N. M., Desgouttes, A. M., & Semendeferi, K. (2005). Neural connectivity and
cortical substrates of cognition in hominoids. Journal of Human Evolution, 49(5),
547569.
10
Schenker, N. M., Hopkins, W. D., Spocter, M. A., Garrison, A. R., Stimpson, C. D.,
Erwin, J. M., et al. (2010). Brocas area homologue in chimpanzees (Pan
troglodytes): probabilistic mapping, asymmetry, and comparison to humans.
Cerebral Cortex, 20(3), 730742.
Semendeferi, K., Armstrong, E., Schleicher, A., Zilles, K., & Van Hoesen, G. W. (1998).
Limbic frontal cortex in hominoids: A comparative study of area 13. American
Journal of Physical Anthropology, 106(2), 129155.
Semendeferi, K., Armstrong, E., Schleicher, A., Zilles, K., & Van Hoesen, G. W. (2001).
Prefrontal cortex in humans and apes: A comparative study of area 10. American
Journal of Physical Anthropology, 114(3), 224241.
Semendeferi, K., Damasio, H., Frank, R., & Van Hoesen, G. W. (1997). The evolution of
the frontal lobes: A volumetric analysis based on three-dimensional reconstructions
of magnetic resonance scans of human and ape brains. Journal of Human Evolution,
32, 375388.
Semendeferi, K., Lu, A., Schenker, N., & Damasio, H. (2002). Humans and great apes
share a large frontal cortex. Nature Neuroscience, 5(3), 272276.
Semendeferi, K., Teffer, K., Buxhoeveden, D. P., Park, M. S., Bludau, S., Amunts, K.,
et al. (2011). Spatial organization of neurons in the frontal pole sets humans apart
from great apes. Cerebral Cortex, 21(7), 14851497.
Sherwood, C. C., Stimpson, C. D., Raghanti, R. A., Wildman, D. E., Uddin, M.,
Grossman, L. I., et al. (2006). Evolution of increased glia-neuron ratios in the
human frontal cortex. Proceedings of the National Academy of Sciences of the

Smaers, J. B., Steele, J., Case, C. R., Cowper, A., Amunts, K., & Zilles, K. (2011).
Primate prefrontal cortex evolution: Human brains are the extreme of a lateralized
ape trend. Brain, Behavior and Evolution, 77(2), 6778.
Spocter, M. A., Hopkins, W. D., Barks, S. K., Bianchi, S., Hehmeyer, A. E.,
Anderson, S. M., et al. (2012). Neuropil distribution in the cerebral cortex differs
between humans and chimpanzees. The Journal of Comparative Neurology,
520(13), 29172929.
Spruston, N. (2008). Pyramidal neurons: Dendritic structure and synaptic integration.
Swindale, N. V. (2001). Keeping the wires short: A singularly difficult problem. Neuron,
29, 316317.
Trevathan, W. R. (1988). Fetal emergence patterns in evolutionary perspective.
American Anthropologist, 90, 674681.
von Economo, C. (2009). Cellular structure of the human cerebral cortex. Basel: Karger,
Translated by L.C. Triarhou.
Wang, Y., Brzozowska-Prechtl, A., & Karten, H. J. (2010). Laminar and columnar
auditory cortex in avian brain. PNAS, 107(28), 1267612681.
Zhang, K., & Sejnowski, T. J. (2000). A universal scaling law between gray matter and
white matter of cerebral cortex. Proceedings of the National Academy of Sciences,
97, 56215626.
Fetal and Postnatal Development of the Cortex: MRI and Genetics

J Dubois and G Dehaene-Lambertz, INSERM-CEA, Cognitive Neuroimaging Unit, NeuroSpin, Gif-sur-Yvette, France; University
Paris Sud, Orsay, France
Glossary
Folding of the cortex Process including the formation of

the cortical sulci and gyri during brain development.
Nomenclature
DTI
GA
MRI
Diffusion tensor imaging

Gestational age
Introduction
PTA
STS
T1w/T2w images
w GA
Post-term age
Superior temporal sulcus
T1-/T2-weighted images
Weeks of gestational age
The Early Cerebral Organization
In the human brain, development of the cortex is a complex

and long-lasting process that begins during the first weeks of
pregnancy and lasts until the end of adolescence. It involves
several overlapping mechanisms that proceed at different times
and speeds among the cortical regions (e.g., the sensory regions
develop early on and quickly, whereas the associative regions,
like the frontal ones, develop later on and slowly). Since
understanding normal development is essential before
considering the complexity of pathological conditions, this
article focuses on studies using magnetic resonance imaging
(MRI) in healthy fetuses, newborns, infants, and children. In
most of these studies, the main goal is to uncover in the human
brain in vivo the well-known developmental processes
described in the immature animal brain, despite challenges to
test young children and especially infants (Dubois et al.,
2014). Although the relationship between MRI structural
markers and infant cognitive development is still unclear,
these studies provide a first description of human cerebral
maturation, useful for clinics. We here mainly review studies
on the structural development of the cortex, assessed by T1and T2-weighted (T1w and T2w) images and diffusion tensor
imaging (DTI). We successively detail (1) how the cortex grows
and gets convoluted, (2) the microstructural maturation of the
gray matter, (3) the interhemispheric asymmetries in cortical
development, and (4) how this development might be
impacted by genetic, epigenetic, and environmental factors.
The Cortex Development: Structure and Morphology

The last weeks of pregnancy and the first postnatal months are
marked by an intense increase in cortical volume and surface
area, which progressively slows down after 2 years of age until
adolescence.
Primary, secondary, and tertiary folds Cortical folds that

appear from 20w GA, from 32w GA, and around term age
(40w GA) respectively.
Due to the differences in cellularity, membrane density, and

water content of the different tissue compartments that affect
contrasts and diffusion parameters, the last waves of neuronal
migration are clearly visible with T1w and T2w MRI in fetuses
as young as 20 weeks of gestational age (w GA) (Girard,
Raybaud, & Poncet, 1995; Scott et al., 2011) and with DTI in
preterm newborns (Maas et al., 2004; Figure 1). Successive
layers are described from the center of the brain to its surface:
the germinal matrix from where neuroblasts migrate in the
subventricular and periventricular zones, the intermediate
zone that gathers radial glia and the developing axonal fibers
of the future white matter, the subplate zone where migrating
neurons are waiting until reaching their final location in the
cortical plate, and finally the thin cortical plate. Between 20w
GA and 26w GA, the subplate is seen as a hyperintense layer
whose volume increases, first globally in proportion with the
supratentorial volume and secondly at different rates among
brain regions (Corbett-Detig et al., 2011). It becomes progressively isointense and thus difficult to identify from 35w GA on,
although it might still be present until the end of the first year,
notably in the frontal regions (Kostovic et al., 2014).
Cortical Growth
Because contrasts in T1w and T2w images evolve with maturation (Dubois et al., 2014), the comparison of cortical volume
across ages (Figure 2(a)) should remain cautious. In utero, the
volume of the cortical plate increases from around 10 ml at
21w GA to 70 ml at 31w GA (Scott et al., 2011), and developmental rates differ among brain regions, with higher volume
increases in the parietal and occipital regions than in the
frontal lobe (Rajagopalan et al., 2011). In preterm newborns,
the volume increases from around 25 ml at 29w GA to 250 ml
at 48w GA (Kuklisova-Murgasova et al., 2011). During the first
2 years after term birth, brain growth is mainly due to gray
http://dx.doi.org/10.1016/B978-0-12-397025-1.00194-9
11
12
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Fetal and Postnatal Development of the Cortex: MRI and Genetics
T2w
28w GA
31w GA
35w GA
4w PTA
(a)
DTI-RGB
(b)
Inner cortical surface
(c)
Figure 1 Structural imaging of the developing brain. T2w images (a), DTI-RGB directionality maps (b), and inner cortical surfaces (Dubois, Benders,
Cachia, et al., 2008; Leroy, Mangin, et al., 2011) are presented for three preterm newborns of different ages and an infant aged 4w old
(PTA: postterm age). Note that anisotropy decreases with age in the preterm cortex (b).
matter development (Gilmore et al., 2007; Knickmeyer et al.,

2008) contrarily to the following years (Matsuzawa et al.,
2001). The cortical volume increases much more during the
first postnatal year (by around 106%) than during the second
year (by 18%) and faster in the association cortices, particularly in the frontal and parietal lobes, relatively to the primary
motor and sensory cortices (Gilmore et al., 2012; Figure 3(a)).
The preadolescent increase in cortical volume is followed
by a postadolescent decrease, with different growth peaks
across brain regions, varying from around 10 years (the female
parietal lobe) to 17 years (the female temporal lobe) (Giedd
et al., 1999; Figure 2(a)). Higher-order association cortices
mature after lower-order somatosensory and visual cortices,
and phylogenetically older regions mature earlier than newer
regions (Gogtay et al., 2004).
Cortical Folding
Concurrently with brain growth, the cortex is getting folded
during the last trimester of pregnancy. Dedicated tools and
morphometric analyses have enabled to map in detail the developing cortical surface and growth patterns in fetuses as young as
20w GA (Habas et al., 2012) and in preterm newborns imaged
shortly after birth (Dubois, Benders, Cachia, et al., 2008; Figure 1
(c)). These in vivo studies confirm earlier postmortem observations (Chi, Dooling, & Gilles, 1977a) and show a precise calendar (with the appearance of primary folds around 20w GA,
secondary folds around 32w GA, and tertiary folds around
term), which can be used as a robust marker of brain maturation.
Gyrification becomes manifest after 24w GA (Rajagopalan et al.,
2011) and greatly heightens during the last weeks before term
(Figure 2(b); Angleys et al., 2014; Dubois, Benders, Cachia,
et al., 2008). Although some variability is observed among individuals, the regional pattern is consistent over the brain surface:
sulcation starts in the central region and proceeds first toward the
parietal, temporal, and occipital lobes and second toward the
frontal lobe (Dubois, Benders, Cachia, et al., 2008; Ruoss, Lovblad, Schroth, Moessinger, & Fusch, 2001).
At term, the cortical surface area is three times smaller
than in adults, but the cortex is roughly similarly folded,
13
Changes in the volume of cortex during childhood

Preterm newborns
350
Children
Infants
800
140
Volume (ml)
Cortex
Male
600
250
120
400
150
100
200
50
WM
25
30
(a)
40
35
GA (weeks)
45
50
Female
Parietal lobe
80
0
12
24
Post-natal age (months)
Development of the cortical surface in newborns

Inner cortical surface
18
10
14
Post-natal age (years)
22
Folding of the cortical surface
250
200
4.4
Born at term
Area (log)
Area (cm2)
300
Preterm
150
Sulcation index
4.5
4.3
4.2
4.1
4.0
100
3.9
28 30 32 34 36 38 40
(b)
1.7
1.7
1.5
1.5
1.3
1.3
1.1
1.1
4.6 4.7 4.8 4.9 5.0 5.1 5.2
GA (weeks)
28 30 32 34 36 38 40
Brain size (log)
GA (weeks)
40
60
80 100 120 140 160
Brain size (mL)
Figure 2 Changes in cortical volume, surface area, and folding during development. Cortical volume (a) increases during the preterm period
(Kuklisova-Murgasova et al., 2011), infancy (Knickmeyer et al., 2008), and childhood, before decreasing during adolescence (Giedd et al., 1999).
The increases in surface area and sulcation (b) are major during the last gestational weeks, going with the growth in brain size (Angleys et al., 2014).
Regional rates in cortical volume growth
T2w
%
01 year
150
110
(a)
70
Maturation index
Maturation
7w PTA
(b)
Figure 3 Asynchronous development of brain regions. During the first postnatal year, cortical regions demonstrate different rates of volume increase
(a) (Gilmore et al., 2012) and maturation (b) (Leroy, Glasel, et al., 2011): primary sensorimotor regions grow less and appear more mature
(red arrows on T2w images) than associative regions.
and the most variable regions among individuals are the

same across newborns and adults (Hill, Dierker, et al.,
2010). Noticing the nonuniform pattern of cortical growth
among brain regions, Hill and colleagues proposed that it
resembles the pattern of evolutionary expansion between

human and macaque monkey, with phylogenetically recent
regions being the least developed at birth (Hill, Inder, et al.,
2010).
14
Modeling Cortical Development

Why does the human brain fold? The cortical structure appears
as a closed surface, with fundamental mechanical properties of
elasticity and plasticity (Toro & Burnod, 2005). Glial and
axonal fibers might apply tension radially to this surface
while it grows and consequently folds (Van Essen, 1997).
According to genetic control or mechanistic constraints, the
folding may organize around stable points, also called sulcal
roots (Regis et al., 2005) or pits (Lohmann, Von Cramon, &
Colchester, 2008) in the adult brain. So far, this hypothesis has
been confirmed in preterm newborns, in whom stable interindividual pits have been revealed along the central and superior temporal sulci using analyses of the surface curvature and
depth (Operto et al., 2012) and also in infants in whom
displacement field analyses have detected growth seeds on
longitudinal data (Lefe`vre et al., 2009).
The Maturation of Cortical Microstructure

These macrostructural changes are the visible marker of the
microstructural evolution, marked by synaptic outburst and
pruning, modifications in dendritic branching, and fiber
myelination.
Changes in Cortical Microstructure During the Preterm Period

In the developing brain of preterm newborns, DTI provides
valuable information on cortical architecture and is sensitive to
the regional heterogeneity in cortical development. The diffusion of water molecules is anisotropic in the cortical plate
around 26w GA presenting a radial orientation of the tensor
main direction and then becomes isotropic from around 36w
GA (Dudink et al., 2010; Mckinstry et al., 2002; Figure 1(b)).
This change is explained by the early radial deployment of glial
fibers and apical dendrites of pyramidal neurons, followed by
the elongation and complex branching of neuronal connections (basal dendrites for the pyramidal neurons and thalamocortical afferents). Besides, mean diffusivity increases between
26w GA and 32w GA and decreases thereafter, suggesting competing mechanisms (Mckinstry et al., 2002): decrease in cell
density associated with programmed cell death, addition of
neuropils between the neuronal somas, and decrease in water
content. These changes are not uniform over the brain (Ball
et al., 2013; Deipolyi et al., 2005), and they are not linear at
least for some regions, such as the right superior temporal
sulcus (STS) and lateral occipitotemporal gyrus (Aeby
et al., 2012).
studies (Figure 3(b)), and further uncovered a gradient of

maturation within the linguistic network, the STS appearing
less mature than the inferior frontal region (Leroy, Glasel,
et al., 2011). Travis and colleagues also measured significant
age effects within bilateral inferior lateral and anteroventral
temporal regions and dorsomedial frontal and superior parietal cortices during the second postnatal year (Travis et al.,
2013). T1w signal intensity and T1w/T2w myelin mapping
reveal that cortical maturation is ongoing until 30 years of
age in some brain regions and that occipital visual cortices
display the earliest maturation, while superior frontal regions
have the most protracted maturation (Grydeland, Walhovd,
Tamnes, Westlye, & Fjell, 2013; Westlye et al., 2010). Besides,
the magnetic susceptibility displays an exponential growth,
suggesting a continuous increase in iron content (Li, Wu,
et al., 2013).
Changes in Cortical Thickness During Childhood

and Adolescence
In newborns, average cortical thickness is around 1.3 mm
between 27 and 45w GA (Xue et al., 2007). It further increases
with age, ranging from 1.5 mm in the occipital regions to
5.5 mm in the dorsomedial frontal cortex during childhood
(Sowell et al., 2004). As for the cortical volume, this increase is
followed during adolescence by an asynchronous decrease
across brain regions (Shaw et al., 2007, 2008; Sowell et al.,
2004). These thickness changes are correlated across regions
linked with rich structural and functional connectivity
(e.g., frontotemporal association regions; Raznahan, Lerch,
et al., 2011).
It has been argued that cortical thinning would be an artifactual observation resulting from myelination that would
blur the segmentation of the gray/white matter boundary on
MR images. However, age-related evolutions of thickness and
maturation are distinct over the life span (Westlye et al., 2010),
and developmental patterns of superficial white matter diverge
from the widespread changes in thickness (Wu et al., 2013).
Relationships between cortical thickness, volume, surface area,
and folding are also a matter of debate. Between 7 and 23 years
of age, the regional patterns and timings of developmental
trajectories differ for thickness and surface area, suggesting
that these parameters rely on different mechanisms
(Wierenga, Langen, Oranje, & Durston, 2013). Nevertheless,
thinning seems associated with sulcal widening and gyral white
matter expansion during adolescence, period when the cortex
flattens (Aleman-Gomez et al., 2013). Nonlinear changes in
cortical volume emerge from the complex age-dependent interactions of changes in thickness and surface area, also relying on
gyrification (Raznahan, Shaw, et al., 2011).
Cortical Maturation During Infancy

Accompanying the complex evolution of cortical microstructure, the dendritic and axonal fibers get myelinated. It is now
possible to quantify this maturation in vivo by taking advantages of the changes in T1 and T2 signals induced by modifications in water and iron contents. For example, using
normalized T2w images in infants, Leroy and colleagues recovered the regional asynchrony of maturation between primary
and associative regions, as first described in postmortem
Interhemispheric Asymmetries in Cortical

Development
The two cerebral hemispheres do not develop symmetrically
during the fetal and postnatal life, suggesting early structural
bases of functional lateralization. Postmortem studies have
described that the right hemisphere shows gyral complexity
earlier than the left, while Heschls gyrus and the planum
15
Whole-brain analyses of inter-hemispheric asymmetries

Preterm newborns
t=6
Term newborns
Infants 1-year-old
Infants 2-year-old
6
(a)
Inter-hemispheric asymmetries of the superior temporal sulcus

STS depth
t score
***
Right
10
Left
5
0.53
16
0
28 40 mm
Front
Left
Dorsal
STS
Front
5
30 19
0.55
Right
Depth (mm)
20
15
10
Maturation index
STS maturation
24 13 2
Front
0
Ventral
STS
Left
0.51
0.49
20 30 mm
Front
0.55
Right
Right
0.53
Maturation index +
Left
24 13 2
(b)
0.51
0.49
20 30 mm
Figure 4 Interhemispheric asymmetries in cortical development. The cortex folds asymmetrically in perisylvian regions (a), as shown in preterm
newborns (Dubois et al., 2010) and infants (Li, Nie, et al., 2013). Notably, the STS (b) is deeper (Glasel et al., 2011) and more mature (Leroy, Glasel,
et al., 2011) on the right side than on the left.
temporale are more developed on the left side by 31w GA (Chi

et al., 1977a; Chi, Dooling, & Gilles, 1977b). In vivo studies
have confirmed these cortical asymmetries (Figure 4). STS
folds earlier on the right side than on the left side in in utero
fetuses (Habas et al., 2012; Kasprian et al., 2011) and in
preterm newborns (Dubois, Benders, Cachia, et al., 2008),
and the right STS remains deeper than the left in newborns at
term (Hill, Dierker, et al., 2010), infants (Glasel et al., 2011; Li,
Nie, et al., 2013), children, and adults (Leroy et al., in preparation), in association with an advanced maturation during
infancy (Leroy, Glasel, et al., 2011).
The leftward elongation of the planum temporale and
thickening of Heschls gyrus are also detected early on (Dubois
et al., 2010; Glasel et al., 2011; Hill, Dierker, et al., 2010; Li,
Nie, et al., 2013). The posterior end of the sylvian fissure is
shifted forward and upward in the right hemisphere of infants
(Glasel et al., 2011; Li, Nie, et al., 2013), and this asymmetry
increases with age (Sowell et al., 2002). Furthermore, the anterior region of the sylvian fissure seems to grow earlier on the
left side (Dubois et al., 2010; Li, Nie, et al., 2013), close to
Brocas region that matures before its right counterpart (Leroy,
Glasel, et al., 2011). These maturational asymmetries in the
posterior STS and Brocas region are finally associated with
asymmetries in the arcuate fasciculus connecting these cortical
areas (Dubois et al., 2009; Leroy, Glasel, et al., 2011).
Thus perisylvian regions involved in language processing in
the left hemisphere and in social contact in the right hemisphere follow a different developmental calendar. The relation
between structural and functional lateralization is still not clear
(Dehaene-Lambertz, Hertz-Pannier, & Dubois, 2006), but
early asymmetric expression of several genes, like LMO4 that
is consistently more expressed in the right superior temporal
regions than in the left regions of human embryos (Sun et al.,
2005), suggests an evolutionary pressure on these regions.
Influence of Genetic, Epigenetic, and Environmental

Factors
Several studies have related differences in cognitive performances with variations in cortical development during childhood and adolescence (Lu et al., 2007; Shaw et al., 2006).
Nevertheless, the variability of detailed relationships among
studies suggests that numerous factors affecting cognitive performances and brain development (e.g., socioeconomic status,
education, birth weight, nutrition, and stress) should be taken
into account. Furthermore, since age is the main variable driving brain changes, longitudinal studies should be preferred to
isolate the crucial factors and their impact on precise structures
along the developmental trajectory (Raznahan, Shaw, et al.,
2011). Too numerous pathologies disrupt development;
therefore, we will only focus on normal development, except
for prematurity, a major societal issue.
Sexual Dimorphism
Whereas no difference in folding is detected among fetuses of
the same age (Chi et al., 1977a), males already have larger
cortical volumes than females after preterm (Dubois, Benders,
Cachia, et al., 2008) or term birth (Gilmore et al., 2007).
During childhood and adolescence, this dimorphism
strengthens, with volumes being 10% larger in boys (Giedd
et al., 1999) correlating with body mass index (Brain
Development Cooperative Group, 2012). The age-related
changes in volume peak slightly earlier (12 years) in girls,
but the curve shape does not differ among genders (Giedd
et al., 1999; Lenroot et al., 2007).
Girls tend to have larger gray matter volume relative to
brain size than boys (Groeschel, Vollmer, King, & Connelly,
16
2010), and gender differences are more pronounced for volume and surface area than for cortical thickness (Wierenga
et al., 2013), for which sex differences are region-specific
(Sowell et al., 2007). During adolescence, the pattern of differences in cortical thickness between genders accelerates, notably
a wave of maturation sweeps frontal subregions with a delay in
males compared with females (Raznahan et al., 2010) probably related to the earlier female puberty. The acceleration of
cortical thickness changes during this period is different across
regions and is modulated by the level of cerebral androgen
receptor signaling in both males and females (Raznahan et al.,
2010). The effect of gender is strikingly different in the superior
frontal region (accelerated loss in males relatively to females)
and the parietal lobule (reverse pattern), suggesting possible
relationship with gender cognitive differences (e.g., better
social cognition in females versus better visuospatial cognition
in males; Raznahan et al., 2010) despite no direct established
correlation.
Besides hormonal influence, sex chromosome gene expression also directly influences gray matter volume in different
brain regions (parietooccipital and temporoinsular), as demonstrated during the early stages of puberty in normal children
and children with Turner syndrome (females missing one X
chromosome) and Klinefelter syndrome (males having an
additional X chromosome) (Hong et al., 2014). These developmental studies demonstrate the robust influence of hormones and sex chromosome gene dosages on cortical
development and underscore the need to precisely match gender and age when evaluating normal or pathological brain
functioning.
Genetic Influences
To assess how genetics and environment influence cortical
development, most MRI studies have relied on the longitudinal
follow-up of pediatric monozygotic and dizygotic twins. Cortical volume and depth are highly correlated within monozygotic twin pairs, but surface measures are more prone to
environmental influences (White, Andreasen, & Nopoulos,
2002). The volume heritability decreases with age (Wallace
et al., 2006), differently among brain regions (Giedd, Schmitt,
& Neale, 2007). Cortical density is increasingly similar in subjects with increasing genetic affinity, particularly in the frontal,
sensorimotor, and perisylvian language regions (Thompson
et al., 2001). The degree of genetic influence on cortical thickness also differs among brain regions (Van Soelen et al., 2012):
regions that develop earlier show greater genetic effects during
early childhood, while later-developing regions are more heritable in adolescents than children (Lenroot et al., 2009).
So far, the heritability in cortical patterning has not been
studied during development, but in adults, the similarity in
sulcal graphs is higher in twin pairs than in unrelated pairs,
suggesting a genetic influence on cortical folding (Im et al.,
2011). Finally, genetics also influences interhemispheric asymmetries: asymmetries in the planum temporale and sylvian
fissure are slightly heritable during childhood. However, heritability decreases when twins with discordant writing hand or
large birth weight differences are included (Eckert et al., 2002),
suggesting that prenatal and postnatal factors should not be
neglected.
Intrauterine Environment and Gestational Duration

In agreement with postmortem studies (Chi et al., 1977a), an
in vivo study of preterm newborns has shown a delayed but
harmonious maturation in twins at birth in comparison with
singletons (Dubois, Benders, Borradori-Tolsa, et al., 2008),
whereas the gyrification of newborns with intrauterine growth
restriction is discordant to the normal developmental trajectory.
Within monozygotic pairs in a normal birth weight range, higher
birth weight is associated with higher intelligence quotient in
adolescence and with higher cortical volume and surface area
notably in several perisylvian regions (Raznahan, Greenstein,
Lee, Clasen, & Giedd, 2012). This relation is not observed in
singletons and is weaker in dizygotic twins. These results highlight that a slightly more difficult prenatal environment interacting with genetic expression has a durable effect (although weak:
two points of IQ in the aforementioned study).
Premature birth also strongly modifies subsequent brain
growth, even in the absence of major destructive brain lesions.
In comparison with normal newborns, preterm newborns at
term-equivalent age show alterations in cortical volume
(reductions in most brain regions except increases in occipital
regions) (Padilla, Alexandrou, Blennow, Lagercrantz, & Aden,
2014), folding (Melbourne et al., 2014), and maturation (Ball
et al., 2013), in a dose-dependent fashion related to the premature exposure to extrauterine environment (development
increases with gestational age at birth). From 23 to 48w GA,
the scaling exponent relating surface area and volume
decreases with increasing prematurity (Kapellou et al., 2006).
Prematurity consequences further stretch to infancy and
childhood, with early brain measures predicting future cognitive development. Cortical folding in preterms at birth correlates with cortical volume and neurobehavioral development
at term-equivalent age (Dubois, Benders, Borradori-Tolsa,
et al., 2008). Language abilities of 2-year-old infants born
preterm are negatively correlated with DTI diffusivities measured in the left superior temporal gyrus at term-equivalent
age, suggesting that the early stage of development of this
region is crucial for later language acquisition (Aeby et al.,
2013). The rate of microstructural maturation assessed
between 27 and 46w GA predicts neurodevelopmental scores
at 2 years of age (Ball et al., 2013). At 8 years of age, children
born preterm demonstrate increased bilateral temporal lobe
gyrification compared with term controls, and the left increase
is negatively correlated with reading recognition scores (Kesler
et al., 2006). Even in children born full term, a longer duration
of gestation (until 41w GA) seems beneficial, being associated
with region-specific increases in cortical density (Davis et al.,
2011). These studies outline that cognitive functions have their
roots in early development, but questions remain on the causal
disturbing mechanisms of exposure, notably on the respective
roles of microscopic brain lesions, to the too stimulating outside world versus to the maternal protective and filtering
environment.
Conclusion
MRI now enables to map and characterize the dynamics of
cortical development and the development of structural and
functional connectivity, highlighting the structural bases of
cognitive development. These studies are challenging in healthy
infants and require dedicated methodologies for image acquisition and postprocessing (Dubois et al., 2014), but it is worth the
effort since markers of maturation are required to better understand pathological mechanisms or the deleterious effects of early
disturbances such as prematurity. However, if clear effects of age,
genes, hormonal status, or nutrition are observed on structural
images, the causal relationships between these observations and
cognition are still unknown due to the complex interactions
between these factors and the delicacy of the neural circuitry
still not captured by MR images.
Acknowledgment
The authors thank P. S. Huppi for the images of preterm
newborns (Figure 1) and F. Leroy for images of cortical maturation (Figure 3). The finalization of this work received support from the European Union Seventh Framework Program
(FP7/20072013, grant agreement n 604102), the French
National Agency for Research, the Fyssen Foundation, the
Fondation de France, the Ecole des Neurosciences de Paris,
the Fondation Motrice, and the McDonnell Foundation.

Anatomical MRI for Human Brain Morphometry; Diffusion MRI; Myelin
Imaging; INTRODUCTION TO ANATOMY AND PHYSIOLOGY:
Brain Sex Differences; Cortical Surface Morphometry; Development of
Structural and Functional Connectivity; Development of the Basal
Ganglia and the Basal Forebrain; Embryonic and Fetal Development of
the Human Cerebral Cortex; Gyrification in the Human Brain; Sulci as
Landmarks; INTRODUCTION TO CLINICAL BRAIN MAPPING:
Developmental Brain Atlases; INTRODUCTION TO METHODS AND
MODELING: Cortical Thickness Mapping; Diffusion Tensor Imaging;
Modeling Brain Growth and Development; Tissue Properties from
Quantitative MRI.
References
Aeby, A., De Tiege, X., Creuzil, M., David, P., Baleriaux, D., Van Overmeire, B., et al.
(2013). Language development at 2 years is correlated to brain microstructure in the
left superior temporal gyrus at term equivalent age: A diffusion tensor imaging
study. NeuroImage, 78, 145151.
Aeby, A., Van Bogaert, P., David, P., Baleriaux, D., Vermeylen, D., Metens, T., et al.
(2012). Nonlinear microstructural changes in the right superior temporal sulcus and
lateral occipitotemporal gyrus between 35 and 43 weeks in the preterm brain.
Aleman-Gomez, Y., Janssen, J., Schnack, H., Balaban, E., Pina-Camacho, L.,
Alfaro-Almagro, F., et al. (2013). The human cerebral cortex flattens during
adolescence. Journal of Neuroscience, 33, 1500415010.
Angleys, H., Germanaud, D., Leroy, F., Hertz-Pannier, L., Mangin, J. F., Lazeyras, F.,
et al., (2014). Successive waves of cortical folding in the developing brain revealed
by spectral analysis of gyrification. Proceedings of OHBM, #4431.
Ball, G., Srinivasan, L., Aljabar, P., Counsell, S. J., Durighel, G., Hajnal, J. V., et al.
(2013). Development of cortical microstructure in the preterm human brain.
110, 95419546.
Brain Development Cooperative Group, (2012). Total and regional brain volumes in a
population-based normative sample from 4 to 18 years: The NIH MRI Study of
Normal Brain Development. Cerebral Cortex, 22, 112.
Chi, J. G., Dooling, E. C., & Gilles, F. H. (1977a). Gyral development of the human
brain. Annals of Neurology, 1, 8693.
17
Chi, J. G., Dooling, E. C., & Gilles, F. H. (1977b). Left-right asymmetries

of the temporal speech areas of the human fetus. Archives of Neurology, 34,
346348.
Corbett-Detig, J., Habas, P. A., Scott, J. A., Kim, K., Rajagopalan, V., Mcquillen, P. S.,
et al. (2011). 3D global and regional patterns of human fetal subplate growth
determined in utero. Brain Structure and Function, 215, 255263.
Davis, E. P., Buss, C., Muftuler, L. T., Head, K., Hasso, A., Wing, D. A., et al. (2011).
Childrens brain development benefits from longer gestation. Frontiers in
Psychology, 2, 1.
Dehaene-Lambertz, G., Hertz-Pannier, L., & Dubois, J. (2006). Nature and nurture in
language acquisition: Anatomical and functional brain-imaging studies in infants.
Trends in Neurosciences, 29, 367373.
Deipolyi, A. R., Mukherjee, P., Gill, K., Henry, R. G., Partridge, S. C., Veeraraghavan, S.,
et al. (2005). Comparing microstructural and macrostructural development of the
cerebral cortex in premature newborns: Diffusion tensor imaging versus cortical
gyration. NeuroImage, 27, 579586.
Dubois, J., Benders, M., Borradori-Tolsa, C., Cachia, A., Lazeyras, F.,
Ha-Vinh Leuchter, R., et al. (2008). Primary cortical folding in the human newborn:
An early marker of later functional development. Brain, 131, 20282041.
Dubois, J., Benders, M., Cachia, A., Lazeyras, F., Ha-Vinh Leuchter, R.,
Sizonenko, S. V., et al. (2008). Mapping the early cortical folding process in the
preterm newborn brain. Cerebral Cortex, 18, 14441454.
Dubois, J., Benders, M., Lazeyras, F., Borradori-Tolsa, C., Leuchter, R. H.,
Mangin, J. F., et al. (2010). Structural asymmetries of perisylvian regions in the
preterm newborn. NeuroImage, 52, 3242.
Dubois, J., Dehaene-Lambertz, G., Kulikova, S., Poupon, C., Huppi, P. S., &
Hertz-Pannier, L. (2014). The early development of brain white matter: A review of
imaging studies in fetuses, newborns and infants. Neuroscience, 276, 4871.
Dubois, J., Hertz-Pannier, L., Cachia, A., Mangin, J. F., Le Bihan, D., &
Dehaene-Lambertz, G. (2009). Structural asymmetries in the infant language and
sensori-motor networks. Cerebral Cortex, 19, 414423.
Dudink, J., Buijs, J., Govaert, P., Van Zwol, A. L., Conneman, N., Van Goudoever, J. B.,
et al. (2010). Diffusion tensor imaging of the cortical plate and subplate in
very-low-birth-weight infants. Pediatric Radiology, 40, 13971404.
Eckert, M. A., Leonard, C. M., Molloy, E. A., Blumenthal, J., Zijdenbos, A., &
Giedd, J. N. (2002). The epigenesis of planum temporale asymmetry in twins.
Giedd, J. N., Blumenthal, J., Jeffries, N. O., Castellanos, F. X., Liu, H., Zijdenbos, A.,
MRI study. Nature Neuroscience, 2, 861863.
Giedd, J. N., Schmitt, J. E., & Neale, M. C. (2007). Structural brain magnetic resonance
imaging of pediatric twins. Human Brain Mapping, 28, 474481.
Gilmore, J. H., Lin, W., Prastawa, M. W., Looney, C. B., Vetsa, Y. S.,
Knickmeyer, R. C., et al. (2007). Regional gray matter growth, sexual dimorphism,
and cerebral asymmetry in the neonatal brain. Journal of Neuroscience, 27,
12551260.
Gilmore, J. H., Shi, F., Woolson, S. L., Knickmeyer, R. C., Short, S. J., Lin, W., et al.
(2012). Longitudinal development of cortical and subcortical gray matter from birth
to 2 years. Cerebral Cortex, 22(11), 24782485.
Girard, N., Raybaud, C., & Poncet, M. (1995). In vivo MR study of brain maturation in
normal fetuses. American Journal of Neuroradiology, 16, 407413.
Glasel, H., Leroy, F., Dubois, J., Hertz-Pannier, L., Mangin, J. F., &
Dehaene-Lambertz, G. (2011). A robust cerebral asymmetry in the infant brain: The
rightward superior temporal sulcus. NeuroImage, 58, 716723.
Groeschel, S., Vollmer, B., King, M. D., & Connelly, A. (2010). Developmental changes
in cerebral grey and white matter volume from infancy to adulthood. International
Journal of Developmental Neuroscience, 28, 481489.
Grydeland, H., Walhovd, K. B., Tamnes, C. K., Westlye, L. T., & Fjell, A. M. (2013).
Intracortical myelin links with performance variability across the human lifespan:
Results from T1- and T2-weighted MRI myelin mapping and diffusion tensor
imaging. Journal of Neuroscience, 33, 1861818630.
Habas, P. A., Scott, J. A., Roosta, A., Rajagopalan, V., Kim, K., Rousseau, F., et al.
(2012). Early folding patterns and asymmetries of the normal human brain detected
from in utero MRI. Cerebral Cortex, 22, 1325.
Hill, J., Dierker, D., Neil, J., Inder, T., Knutsen, A., Harwell, J., et al. (2010). A surfacebased analysis of hemispheric asymmetries and folding of cerebral cortex in termborn human infants. Journal of Neuroscience, 30, 22682276.
Hill, J., Inder, T., Neil, J., Dierker, D., Harwell, J., & Van Essen, D. (2010). Similar
patterns of cortical expansion during human development and evolution.
18

107, 1313513140.
Hong, D. S., Hoeft, F., Marzelli, M. J., Lepage, J. F., Roeltgen, D., Ross, J., et al. (2014).
Influence of the x-chromosome on neuroanatomy: Evidence from turner and
klinefelter syndromes. Journal of Neuroscience, 34, 35093516.
Im, K., Pienaar, R., Lee, J. M., Seong, J. K., Choi, Y. Y., Lee, K. H., et al. (2011).
Quantitative comparison and analysis of sulcal patterns using sulcal graph
matching: A twin study. NeuroImage, 57, 10771086.
Kapellou, O., Counsell, S. J., Kennea, N., Dyet, L., Saeed, N., Stark, J., et al. (2006).
Abnormal cortical development after premature birth shown by altered allometric
scaling of brain growth. PLoS Medicine, 3, e265.
Kasprian, G., Langs, G., Brugger, P. C., Bittner, M., Weber, M., Arantes, M., et al.
(2011). The prenatal origin of hemispheric asymmetry: An in utero neuroimaging
study. Cerebral Cortex, 21, 10761083.
Kesler, S. R., Vohr, B., Schneider, K. C., Katz, K. H., Makuch, R. W., Reiss, A. L., et al.
(2006). Increased temporal lobe gyrification in preterm children. Neuropsychologia,
44, 445453.
Knickmeyer, R. C., Gouttard, S., Kang, C., Evans, D., Wilber, K., Smith, J. K., et al.
(2008). A structural MRI study of human brain development from birth to 2 years.
Kostovic, I., Jovanov-Milosevic, N., Rados, M., Sedmak, G., Benjak, V.,
Kostovic-Srzentic, M., et al. (2014). Perinatal and early postnatal reorganization of the
subplate and related cellular compartments in the human cerebral wall as revealed by
histological and MRI approaches. Brain Structure and Function, 219, 231253.
Kuklisova-Murgasova, M., Aljabar, P., Srinivasan, L., Counsell, S. J., Doria, V.,
Serag, A., et al. (2011). A dynamic 4D probabilistic atlas of the developing brain.
Lefe`vre, J., Leroy, F., Khan, S., Dubois, J., Huppi, P. S., Baillet, S., et al. (2009).
Identification of growth seeds in the neonate brain through surfacic Helmholtz
decomposition. Information Processing in Medical Imaging, 21, 252263.
Lenroot, R. K., Gogtay, N., Greenstein, D. K., Wells, E. M., Wallace, G. L., Clasen, L. S.,
et al. (2007). Sexual dimorphism of brain developmental trajectories during
childhood and adolescence. NeuroImage, 36, 10651073.
Lenroot, R. K., Schmitt, J. E., Ordaz, S. J., Wallace, G. L., Neale, M. C., Lerch, J. P., et al.
(2009). Differences in genetic and environmental influences on the human cerebral
cortex associated with development during childhood and adolescence. Human
Leroy, F., Cai, Q., Bogart, S., Dubois, J., Coulon, O., Monzalvo, K., et al., (accepted for
publication). A new human-specific brain landmark: The depth asymmetry of the
superior temporal sulcus. Proceedings of the National Academy of Sciences United
States of America.
Leroy, F., Glasel, H., Dubois, J., Hertz-Pannier, L., Thirion, B., Mangin, J. F., et al.
(2011). Early maturation of the linguistic dorsal pathway in human infants. Journal
Leroy, F., Mangin, J. F., Rousseau, F., Glasel, H., Hertz-Pannier, L., Dubois, J., et al.
(2011). Atlas-free surface reconstruction of the cortical grey-white interface in
infants. PLoS One, 6, e27128.
Li, G., Nie, J., Wang, L., Shi, F., Lyall, A. E., Lin, W., et al. (2013). Mapping longitudinal
hemispheric structural asymmetries of the human cerebral cortex from birth to 2
years of age. Cerebral Cortex, 24(5), 12891300.
Li, W., Wu, B., Batrachenko, A., Bancroft-Wu, V., Morey, R. A., Shashi, V., et al. (2013).
Differential developmental trajectories of magnetic susceptibility in human brain
gray and white matter over the lifespan. Human Brain Mapping, 35(6), 26982713.
Lohmann, G., Von Cramon, D. Y., & Colchester, A. C. (2008). Deep sulcal landmarks provide
an organizing framework for human cortical folding. Cerebral Cortex, 18, 14151420.
Lu, L., Leonard, C., Thompson, P., Kan, E., Jolley, J., Welcome, S., et al. (2007).
Normal developmental changes in inferior frontal gray matter are associated with
improvement in phonological processing: A longitudinal MRI analysis. Cerebral
Cortex, 17, 10921099.
Maas, L. C., Mukherjee, P., Carballido-Gamio, J., Veeraraghavan, S., Miller, S. P.,
Partridge, S. C., et al. (2004). Early laminar organization of the human cerebrum
demonstrated with diffusion tensor imaging in extremely premature infants.
Matsuzawa, J., Matsui, M., Konishi, T., Noguchi, K., Gur, R. C., Bilker, W., et al. (2001).
Age-related volumetric changes of brain gray and white matter in healthy infants and
children. Cerebral Cortex, 11, 335342.
Mckinstry, R. C., Mathur, A., Miller, J. H., Ozcan, A., Snyder, A. Z., Schefft, G. L., et al.
(2002). Radial organization of developing preterm human cerebral cortex revealed
by non-invasive water diffusion anisotropy MRI. Cerebral Cortex, 12, 12371243.
Melbourne, A., Kendall, G. S., Cardoso, M. J., Gunny, R., Robertson, N. J., Marlow, N.,
et al. (2014). Preterm birth affects the developmental synergy between cortical
folding and cortical connectivity observed on multimodal MRI. NeuroImage, 89,
2334.
Operto, G., Auzias, G., Le Troter, A., Perrot, M., Rivie`re, D., Dubois, J., et al. (2012).
brain. In: Meeting IEEE ISBI (pp. 422425).
Padilla, N., Alexandrou, G., Blennow, M., Lagercrantz, H., & Aden, U. (in press). Brain
growth gains and losses in extremely preterm infants at term. Cerebral Cortex, Jan 31
Rajagopalan, V., Scott, J., Habas, P. A., Kim, K., Corbett-Detig, J., Rousseau, F., et al.
(2011). Local tissue growth patterns underlying normal fetal human brain
gyrification quantified in utero. Journal of Neuroscience, 31, 28782887.
Raznahan, A., Greenstein, D., Lee, N. R., Clasen, L. S., & Giedd, J. N. (2012). Prenatal
growth in humans and postnatal brain maturation into late adolescence.
109, 1136611371.
Raznahan, A., Lee, Y., Stidd, R., Long, R., Greenstein, D., Clasen, L., et al. (2010).
Longitudinally mapping the influence of sex and androgen signaling on the
dynamics of human cortical maturation in adolescence. Proceedings of the
National Academy of Sciences of the United States of America, 107,
1698816993.
Raznahan, A., Lerch, J. P., Lee, N., Greenstein, D., Wallace, G. L., Stockman, M.,
et al. (2011). Patterns of coordinated anatomical change in human cortical
development: A longitudinal neuroimaging study of maturational coupling.
Neuron, 72, 873884.
Raznahan, A., Shaw, P., Lalonde, F., Stockman, M., Wallace, G. L., Greenstein, D., et al.
(2011). How does your cortex grow? Journal of Neuroscience, 31, 71747177.
Regis, J., Mangin, J. F., Ochiai, T., Frouin, V., Riviere, D., Cachia, A., et al. (2005).
"Sulcal root" generic model: A hypothesis to overcome the variability of the human
cortex folding patterns. Neurologia Medico-Chirurgica (Tokyo), 45, 117.
Ruoss, K., Lovblad, K., Schroth, G., Moessinger, A. C., & Fusch, C. (2001). Brain
development (sulci and gyri) as assessed by early postnatal MR imaging in preterm
and term newborn infants. Neuropediatrics, 32, 6974.
Scott, J. A., Habas, P. A., Kim, K., Rajagopalan, V., Hamzelou, K. S.,
Corbett-Detig, J. M., et al. (2011). Growth trajectories of the human fetal brain
tissues estimated from 3D reconstructed in utero MRI. International Journal of
Developmental Neuroscience, 29, 529536.
Shaw, P., Eckstrand, K., Sharp, W., Blumenthal, J., Lerch, J. P., Greenstein, D., et al.
(2007). Attention-deficit/hyperactivity disorder is characterized by a delay in cortical
maturation. Proceedings of the National Academy of Sciences of the United States of
America, 104, 1964919654.
Shaw, P., Greenstein, D., Lerch, J., Clasen, L., Lenroot, R., Gogtay, N., et al. (2006).
Intellectual ability and cortical development in children and adolescents. Nature,
440, 676679.
Shaw, P., Kabani, N. J., Lerch, J. P., Eckstrand, K., Lenroot, R., Gogtay, N., et al. (2008).
Neurodevelopmental trajectories of the human cerebral cortex. Journal of
Sowell, E. R., Peterson, B. S., Kan, E., Woods, R. P., Yoshii, J., Bansal, R., et al. (2007).
Sex differences in cortical thickness mapped in 176 healthy individuals between 7
and 87 years of age. Cerebral Cortex, 17, 15501560.
children. Journal of Neuroscience, 24, 82238231.
Sowell, E. R., Thompson, P. M., Rex, D., Kornsand, D., Tessner, K. D., Jernigan, T. L.,
et al. (2002). Mapping sulcal pattern asymmetry and local cortical surface gray
matter distribution in vivo: Maturation in perisylvian cortices. Cerebral Cortex, 12,
1726.
Sun, T., Patoine, C., Abu-Khalil, A., Visvader, J., Sum, E., Cherry, T. J., et al. (2005).
Early asymmetry of gene transcription in embryonic human left and right cerebral
cortex. Science, 308, 17941798.
Thompson, P. M., Cannon, T. D., Narr, K. L., Van Erp, T., Poutanen, V. P., Huttunen, M.,
et al. (2001). Genetic influences on brain structure. Nature Neuroscience, 4,
12531258.
Toro, R., & Burnod, Y. (2005). A morphogenetic model for the development of cortical
convolutions. Cerebral Cortex, 15, 19001913.
Travis, K. E., Curran, M. M., Torres, C., Leonard, M. K., Brown, T. T., Dale, A. M., et al.
(2013). Age-related changes in tissue signal properties within cortical areas
important for word understanding in 12- to 19-month-old infants. Cerebral Cortex,
24(7), 19481955.
in the central nervous system. Nature, 385, 313318.
Van Soelen, I. L., Brouwer, R. M., Van Baal, G. C., Schnack, H. G., Peper, J. S.,
Collins, D. L., et al. (2012). Genetic influences on thinning of the cerebral cortex
during development. NeuroImage, 59, 38713880.
Wallace, G. L., Eric Schmitt, J., Lenroot, R., Viding, E., Ordaz, S., Rosenthal, M. A., et al.
(2006). A pediatric twin study of brain morphometry. Journal of Child Psychology
and Psychiatry, 47, 987993.
Westlye, L. T., Walhovd, K. B., Dale, A. M., Bjornerud, A., Due-Tonnessen, P., Engvig, A.,
et al. (2010). Differentiating maturational and aging-related changes of the cerebral
cortex by use of thickness and signal intensity. NeuroImage, 52, 172185.
White, T., Andreasen, N. C., & Nopoulos, P. (2002). Brain volumes and surface
morphology in monozygotic twins. Cerebral Cortex, 12, 486493.
Wierenga, L. M., Langen, M., Oranje, B., & Durston, S. (2013). Unique developmental
trajectories of cortical thickness and surface area. NeuroImage, 87, 120126.
Wu, M., Lu, L. H., Lowes, A., Yang, S., Passarotti, A. M., Zhou, X. J., et al. (2013).
Development of superficial white matter and its structural interplay with cortical gray
matter in children and adolescents. Human Brain Mapping, 35(6), 28062816.
Xue, H., Srinivasan, L., Jiang, S., Rutherford, M., Edwards, A. D., Rueckert, D., et al.
(2007). Automatic segmentation and reconstruction of the cortex from neonatal
MRI. NeuroImage, 38, 461477.
Further Reading
Dubois, J., Dehaene-Lambertz, G., Soare`s, C., Cointepas, Y., Le Bihan, D., &
Hertz-Pannier, L. (2008). Microstructural correlates of infant functional
development: Example of the visual pathways. Journal of Neuroscience, 28,
19431948.
19
Dubois, J., Dehaene-Lambertz, G., Perrin, M., Mangin, J. F., Cointepas, Y.,
Duchesnay, E., et al. (2008). Asynchrony of the early maturation of white matter
bundles in healthy infants: Quantitative landmarks revealed non-invasively by
diffusion tensor imaging. Human Brain Mapping, 29, 1427.
Kouider, S., Stahlhut, C., Gelskov, S. V., Barbosa, L. S., Dutat, M., De Gardelle, V., et al.
(2013). A neural marker of perceptual consciousness in infants. Science,
340(6130), 376380.
Mahmoudzadeh, M., Dehaene-Lambertz, G., Fournier, M., Kongolo, G., Goudjil, S.,
Dubois, J., et al. (2013). Syllabic discrimination in premature human infants prior to
complete formation of cortical layers. Proceedings of the National Academy of
Dehaene-Lambertz, G., Hertz-Pannier, L., Dubois, J., Meriaux, S., Roche, A.,
Sigman, M., et al. (2006). Functional organization of perisylvian activation during
presentation of sentences in preverbal infants. Proceedings of the National Academy
Dehaene-Lambertz, G., Dehaene, S., & Hertz-Pannier, L. (2002). Functional
neuroimaging of speech perception in infants. Science, 298, 20132015.
Dehaene-Lambertz, G., & Dehaene, S. (1994). Speed and cerebral correlates of syllable
discrimination in infants. Nature, 370, 292295.
Quantitative Data and Scaling Rules of the Cerebral Cortex

E Armstrong, Troy University, Troy, AL, USA
Glossary
Afrotherians A superorder branch of mammals that

originated in Africa. It includes many differently sized large
animals ranging from elephants to tenrecs.
Anthropoids Monkeys, apes, and humans.
The size of the isocortex is important to its processing information, but like other biological structures, its size is constrained by those of interrelated structures. Consequently,
size is analyzed in association with a reference metric, which
in biology typically uses the bivariate allometric formula
Y bX a
where Y is the metric of some feature, X is the reference metric, b
is the intercept of the derived slope, and a is the coefficient of
allometry (the slope or scaling factor). Because allometry does
not assume an isometric (one-to-one) relationship, it can determine the regularity of associated change even when altered
ratios suggest otherwise. When parallel lines describe different
taxonomic groups, those differences are considered to be grade
shifts of the same type of structure (Barton & Harvey, 2000;
Huxley, 1932). Groups that differ in slopes have altered some
intrinsic factors within the compared structures and alert scientists of the need to investigate the biology in more detail.
Although allometry cannot identify the cause of the relationship, it can eliminate complex explanations by showing that a
simple scaling factor produces the observed size. The sizes of
brain regions with direct interconnections are usually correlated.
Dendritic trees in the cortex are intimately involved with the
cortical microcircuitry. The lengths of dendrites scale at 0.67
with numbers of synapses and branch points in logarithmically
transformed data. The design constraints of dendritic branching
may reflect the function of neurons to both process and distribute information. The dendritic design minimizes the amount of
energy required for recharging synapses and for maintaining
membrane potentials (Cuntz, Mathya, & Haussera, 2012).
Each isocortical neuron may expend the same amount of energy,
but the energy used by the isocortex scales isometrically with
numbers of neurons and not neuronal density (HerculanoHouzel et al., 2011). This can be explained by larger dendritic
and axonal trees having lower energy costs (Karbowski, 2014).
Quantitative data of the isocortex consist mostly of volumetric data and number of neurons. The volumetric data come
from measuring structures identified on histological slides and
the numbers of neurons from the isotropic fractionator.
Both the total volume of the isocortex and its surface area
scale with brain weight among mammals. That is, differences
in absolute volume of the isocortex correlate with that of the
rest of the brain. Despite the coarseness of the measure, some
taxonomic groups differ in relative amounts of cortex after
Glires A superorder of rodents and lagomorphs.

Haplorhines Anthropoids plus tarsiers.
Hominoids Humans and apes.
Prosimians Lemurs, lorises, and tarsiers.
Strepsirhines Lemurs and lorises.
accounting for brain size; primates have relatively more neocortex than insectivores and within primates, haplorhines have
more neocortex than strepsirhines. The separations appear
robust with parallel slopes and no overlapping values between
taxa (Barton & Harvey, 2000; Stephan, Frahm, & Baron, 1981).
Whereas the total amount of cortex among mammals
ranges by a magnitude of approximately five, cortical thickness, the span of cortex from the pial surface to the white
matter, is relatively stable and differs among extant mammals
by a magnitude of less than one. Constancy in cortical thickness is thought to reflect the conservation of important elements of the microcircuitry of cortical columns, possibly the
lengths of pyramidal apical dendrites (Allman, 1990).
Cortical thickness varies within a brain; in convoluted
mammalian brains, the neocortex is thinnest at the depths of
sulci and widest at the crowns of gyri (Bok, Kip, & Taalman,
1939). Studies using magnetic resonance images have
found that the neocortices of normal adult human and chimpanzee brains have regional, gender, maturational, aging,
neuropathologic, and hemispheric differences in thickness. It
is thickest in association and motor regions and thinnest in
sensory regions (Hopkins & Avants, 2013). The variation is
best known in humans and very little is known how it varies
in smaller-brained and lissencephalic mammals.
Scaling studies of cortical thickness use global or average
values, and these have been determined by dividing the surface
area of a brain by the brains volume. Average isocortical
thicknesses scale with brain weight, but the correlation is rather
low. This may reflect the use of an average value. Small lissencephalic terrestrial mammals have an allometric scaling of
approximately 0.08, whereas mammals with larger brains,
including those with convoluted surfaces, have a higher slope
(0.17). Aquatic mammals have surprisingly thin cortices and
scale separately from other mammals (Haug, 1987; Hofman,
1988). The differences suggest that for every unit increase in
brain weight, small-brained terrestrial mammals increase both
surface area and cortical thickness, whereas mammals with
convoluted brains increase just surface area; that is, add repetitive units (Ventura-Antunes, Mota, & Herculano-Houzel,
2013; Hofman, 1988).
A larger isocortex is also associated with convolutedness
(gyrification) of the cortex. Unlike a grade difference, measurements of gyrification show different allometric exponents
between prosimians and anthropoids and between rodents
http://dx.doi.org/10.1016/B978-0-12-397025-1.00195-0
21
22
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Quantitative Data and Scaling Rules of the Cerebral Cortex
and primates (Ventura-Antunes et al., 2013; Zilles, Armstrong,

Moser, Schleicher, & Stephan, 1989). The difference in slopes
suggests that the cortical architecture differs in some relevant
dimension. One relevant architectural difference is the relative
enlargement of the outer cortical laminae II and III vis-a`-vis the
inner ones, V and VI. Compared to anthropoids, prosimians
have smaller ratios between the outer and inner laminae.
Furthermore, they have fewer small stellate cells in layers
IIIV and relatively less neuropil. The altered laminar ratios
between prosimians and anthropoids and/or increased numbers of small neurons in anthropoids may produce the shift in
the allometric coefficient either directly or by altering the elasticity and resistance to tension (Armstrong et al., 1991;
Ventura-Antunes et al., 2013; Zilles et al., 1989).
Expansion in gray matter breadth is the expansion that is
perpendicular to cortical thickness and parallel to the cortical
surface. The number of neurons within the isocortex correlates
with isocortical mass with a slope above isometry (Gabi et al.,
2010; Herculano-Houzel, Collins, Wong, & Kaas, 2007;
Herculano-Houzel et al., 2011; Neves et al., 2014; Sarko,
Catania, Leitch, Kaas, & Herculano-Houzel, 2009; Seelke,
Dooley, & Krubitzer, 2014). Restricting the analyses to taxonomic groups shows that anthropoids have the shallowest
slope of studied mammals, about half of that of non-eutherians
(glires, afrotherians, and insectivores) that have overlapping
values. The flatter the slope, the less neuropil is accumulated
per unit gain in number of neurons, suggesting that nonanthropoids gain more connections for every unit increase of the
isocortex than anthropoids (Herculano-Houzel et al., 2011) or
that anthropoids may have added a significant population of
small interneurons.
Cortical lobe volumes scale with brain size. Much of this
work has focussed on the human brain in efforts to determine
how we differ from great apes. The prefrontal lobes are the
most studied, and most analyses show that their sizes in primates, including humans, are predicted by that of the brain.
Additional complexities arise from lateralization and smaller
regional differences within the prefrontal cortex (Ribeiro et al.,
2013; Semendeferi, Lu, Schenker, & Damasio, 2002; Smaers
et al., 2011). The temporal lobe scales differently with brain
weight between monkeys and apes with the monkey trajectory
being above that of apes (Rilling & Seligman, 2002). Conflict
remains as to whether the ape allometric exponent of temporal
lobe to brain weight predicts human values (Rilling &
Seligman, 2002; Semendeferi and Damasio, 2000). The insula,
with its role in social awareness, has recently been analyzed.
Overall, its size in the human brain is predicted by its hyperallometric scaling in nonhuman primates. Within the hominoid insula the region containing large von Economo neurons
is relatively enlarged when the human brain is compared with
that of the chimpanzee (Bauernfeind et al., 2013).
A few studies have analyzed the sizes of regions within lobes
and most of those have focussed on differences between human
and nonhuman primate brains. A detailed analysis of visual areas
shows that both scaling and changes independent of reference
sizes occur in primates. Motor regions, including the primary
motor cortex (Brodmanns area 4), scale among primates with
human values being predictable from primate scaling. The primate association cortices expand more than the sensorimotor
cortices, but the increases appear predictable by scaling relationships with brain weight (Passingham, 1975; Sanides, 1975).
Except for anthropoid primates, which do not have a statistically significant association, larger cortices have decreased
neuronal densities (Figure 1). The association between neuronal density and cortical mass is much less tight than that found
between number of neurons and cortical mass. The decline in
cortical neuronal densities has overlapping values among
glires, afrotherians, and insectivores, suggesting that they may
2.5
Log cortical mass
2
Afrotheria
1.5
Anthropoids
Prosimians
0.5
Glires
Insectivores
0.5
Marsupial
Tree shrew
1.5
Naked mole rat

0.5
1.5
Log neuronal density, number (mg)

Figure 1 Neuronal densities as a function of neocortical mass in mammals. There appear to be three clusters: anthropoids, nonanthropoid eutherians,
and the marsupial. Anthropoids have the highest densities for their brain sizes, and the two variables are not significantly associated. The
association between the two variables is strongest for the glires. Values for afrotherians, glires, and insectivores overlap. The marsupial has the lowest
neuronal density for its brain weight. Data from Herculano-Houzel, S., Ribeiro, P., Campos, L., Valotta da Silva, A., Torres, L. B., Catania, K. C. H.,
et al. (2011). Updated neuronal scaling rules for the brains of glires (rodents/lagomorphs). Brain, Behavior and Evolution, 78, 302314; Gabi, M.,
Collins, C. E., Wong, P., Torres, L. B., Kaas, J. H., & Herculano-Houzel, S. (2010). Cellular scaling rules for the brains of an extended number of primate
species. Brain, Behavior and Evolution, 76, 3244; Sarko, D. K., Catania, K. C., Leitch, D. B., Kaas, J. H., & Herculano-Houzel, S. (2009). Cellular
scaling rules of insectivore brains. Frontiers in Neuroanatomy, 3, 112; Seelke, A. M., Dooley, J. C., & Krubitzer, L. A. (2014). The cellular composition of
the marsupial neocortex. Journal of Comparative Neurology, 522, 22862298; Neves, K., Ferreira, F. M., Tovar-Moll, F., Gravett, N., Bennett, N. C.,
Kaswera, C., et al. (2013) Cellular scaling rules for the brain of afrotherians. Frontiers in Neuroanatomy, 5, 113.
form a single nonanthropoid eutherian group. The marsupial
is quite distinct in its low value.
The findings that anthropoid primates diverge from other
mammals by having smaller differences in cortical mass given
similar changes in neuronal densities (Figure 1) corroborate the
observations of many classical and comparative neuroanatomists, who determined that primate brains have a surprisingly
dense isocortex. Lorent de No (1938) was so impressed by the
difference in densities between mouse and human brains that
he called the mouse organization a skeletal version of humans.
The increase in primate neuronal density occurs primarily
through an increase in small neurons, primarily interneurons
(Golgi II and stellate cells) and small pyramidal cells. The
appearance of very small neurons is more prominent in anthropoid than prosimian brains; the visual cortex suggests that the
difference may be one between haplorhines and strepsirhines.
The anthropoid increase in granularization (small pyramidal
cells and interneurons) is observed primarily in the outer cortical laminae, and while found in various degrees throughout the
isocortex, granularization reaches its apex in the sensory koniocortex (hypergranularized; powdery cortex). Given the small
size of these neurons, their increase in numbers affects the
cortical mass much less than pyramidal cells. Furthermore,
because their axons are often local (intrinsic) or of short range,
their numbers do not increase the white matter mass or cells (see
in the succeeding text). These factors skew the relationship of
neuron numbers to mass and features of the white matter.
At the same time, morphometric analysis of histological
material definitely shows that neuropil expands in primate
cortices often as a function of increased brain size and sometimes independent of it. An automated measure of the proportion of neuropil occupied by stained neuronal cell bodies, glial
and endothelial nuclei compared with the total amount of
tissue, the gray level index (GLI) estimated neuronal density
in the primate posterior cingulate cortex and found that larger
23
primate brains have relatively more neuropil (Armstrong,

Zilles, Schlaug, & Schleicher, 1986; Zilles, Armstrong, Schlaug,
& Schleicher, 1986).
Nonneuronal (other) cells, which are predominantly glia,
increase as a function of number of cortical neurons in rodents
but only slightly more than isometry in anthropoids. Given the
greater decrease in neuronal density in larger rodent brains, the
glia-to-neuron ratio also increases more in rodents than primates (Herculano-Houzel et al., 2011). In both cases, the
observed increases in glia-to-neuron ratios are smaller than
classically thought (Hilgetag & Barbas, 2009).
In a series of mammals of different brain sizes, white matter
volume is highly correlated with that of the gray matter, and for
every unit increase in brain size, white matter expands more
than gray matter. The scaling relationship is a bit higher than
isometry (Frahm, Stephan, & Baron, 1982; Hofman, 1988;
Ventura-Antunes et al., 2013). Total white matter is a rather
coarse metric and several groups have analyzed it further.
Rodent white matter scales with the surface area of the cortex
at approximately the expected geometric rate of volume to surface (3/2). Primates, on the other hand, have a greater amount
of surface area for any difference in the white matter as shown by
the lower scaling, approximately 1.2. Rodents increase white
matter volume more for every increase in number of neurons
than primates do (Ventura-Antunes et al., 2013).
The data about numbers of neurons have not yet separated
interneurons from large pyramidal (projection) neurons. Since
large pyramidal neurons are the likely source for axons in the
white matter, it follows that an association between white
matter mass and pyramidal neurons is to be expected whereas
none is expected between interneurons and white volume.
The accumulation of more interneurons in anthropoids than
in rodents weakens and lowers the association between number of neurons and white matter volume in anthropoids
(Figure 2).
4.50
4.00
Log volume white matter
3.50
3.00
2.50
Anthropoid
2.00
Prosimian
Rodent
1.50
Scandentia
1.00
0.50
0.00
0
0.5
1
1.5
2
2.5
Log number of neurons (g+w)
3.5
Figure 2 The volume of the white matter regressed against number of neurons. Rodents have a strong association. Anthropoids have no statistically
significant association. Data from Ventura-Antunes, L., Mota, B., & Herculano-Houzel, S. (2013). Different scaling of white matter volume, cortical
connectivity, and gyrification across rodent and primate brains. Frontiers in Neuroanatomy, 7, 3.
24
Log number of other cells (glia) in white matter
3.5
3
2.5
2
Anthropoids
Prosimian
1.5
Rodents
Scandentia
1
0.5
0
0
0.5
1.5
2
2.5
Log number of neurons (g+w)
3.5
Figure 3 The number of nonneuronal nuclei (oligodendrocytes and astrocytes) regressed against number of neurons. When rodents are compared
with anthropoids, rodents have more glia for their numbers of neurons, have a steeper slope, and have a tighter association than anthropoids. An
increase in intrinsic neurons moves the anthropoid values away from those of rodents. Data from Ventura-Antunes, L., Mota, B., & Herculano-Houzel, S.
(2013). Different scaling of white matter volume, cortical connectivity, and gyrification across rodent and primate brains. Frontiers in
Neuroanatomy, 7, 3.
There was no marked difference in scalings between rodents

and anthropoids when the correlation between glial cells and
white matter mass was studied as the predominant source of
glia is the white matter. Once the data include the effects of
both interneurons and pyramidal cells, as when other cells in
the white matter are analyzed as a function of numbers of
neurons in the isocortex, the association again weakens in
anthropoids (Figure 3). The lower slope of anthropoids
shows that for every unit gain in numbers of neurons, anthropoids increase other cells (glia) in the white matter less than
rodents, a finding consistent with an increase in interneurons
among anthropoids.

Columns of the Mammalian Cortex; Cortical GABAergic Neurons;
Cortical Surface Morphometry; Evolution of the Cerebral Cortex;
Gyrification in the Human Brain; Insular Cortex; Lateral and
Dorsomedial Prefrontal Cortex and the Control of Cognition; The
Resting-State Physiology of the Human Cerebral Cortex.
References
Allman, J. (1990). Evolution of neocortex. In: E. G. Jones & A. Peters (Eds.), Cerebral
cortex Vol. 8A. New York: Plenum.
Armstrong, E., Curtis, M., Buxhoeveden, D. P., Fregoe, C., Zilles, K., Casanova, M.,
et al. (1991). Cortical gyrification in the rhesus monkey: A test of the mechanical
folding hypothesis. Cerebral Cortex, 1, 426432.
Armstrong, E., Zilles, k., Schlaug, G., & Schleicher, A. (1986). Comparative aspects of the
primate posterior cingulate cortex. Journal of Comparative Neurology, 253, 539548.
Barton, R. A., & Harvey, P. H. (2000). Mosaic evolution of brain structure in mammals.
Nature, 405, 10551058.
Bauernfeind, A. L., de Sousa, A. A., Avasthi, T., Dobson, S. D., Raghanti, M. A.,
Lewandowski, A. H., et al. (2013). A volumetric comparison of the insular cortex and
its subregions in primates. Journal of Human Evolution, 64, 263279.
Bok, S. T., Kip, M. J., & Taalman, V. E. (1939). The size of the body and the size and
number of the nerve cells in the cerebral cortex. Acta Neerlandica Morphologiae
Normalis et Pathologicae, 3, 122.
Cuntz, H., Mathya, A., & Haussera, M. (2012). A scaling law derived from optimal
dendritic wiring. PNAS, 109, 1101411018.
Frahm, H., Stephan, H., & Baron, G. (1982). Comparison of brain structures in
insectivores and primates neocortex. Journal fur Hirnforschung, 23, 375389.
Gabi, M., Collins, C. E., Wong, P., Torres, L. B., Kaas, J. H., & Herculano-Houzel, S.
(2010). Cellular scaling rules for the brains of an extended number of primate
species. Brain, Behavior and Evolution, 76, 3244.
Haug, H. (1987). Brain sizes, surfaces, and neuronal sizes of the cortex cerebri: A
stereological investigation of man and his variability and a comparison with some
mammals (primates, whales, marsupials, insectivores, and one elephant). American
Journal of Anatomy, 180(2), 126142.
Herculano-Houzel, S. (2011). Scaling of brain metabolism with a fixed energy budget
per neuron: Implications for neuronal activity, plasticity, and evolution. PLoS One,
6, e17514.
Herculano-Houzel, S., Collins, C. E., Wong, P., & Kaas, J. H. (2007). Cellular scaling
rules for primate brains. Proceedings of the National academy of Sciences of the
Herculano-Houzel, S., Ribeiro, P., Campos, L., Valotta da Silva, A., Torres, L. B.,
Catania, K. C.H, et al. (2011). Updated neuronal scaling rules for the
brains of glires (rodents/lagomorphs). Brain, Behavior and Evolution, 78, 302314.
Hilgetag, C. C., & Barbas, H. (2009). Are there ten times more glia than neurons in the
brain? Brain Structure and Function, 213, 365366.
Hofman, M. A. (1988). Size and shape of the cerebral cortex in mammals II. The cortical
volume. Brain, Behavior and Evolution, 32, 1726.
Hopkins, W. D., & Avants, B. B. (2013). Regional and hemispheric variation in cortical
thickness in chimpanzees (Pan troglodytes). Journal of Neuroscience, 33,
52415248.
Huxley, J. S. (1932). Problems of relative growth. London: Methuen.
Karbowski, J. (2014). Constancy and trade-offs in the neuroanatomical and metabolic
design of the cerebral cortex. Frontiers in Neural Circuits, 9, 116.
Lorente de No, R. (1938). The cerebral cortex: Architecture, intracortical connections
and motor projections. In J. F. Fulton (Ed.), Physiology of the Nervous System
(pp. 291339). London: Oxford University Press.
Neves, K., Ferreira, F. M., Tovar-Moll, F., Gravett, N., Bennett, N. C., Kaswera, C., et al.
(2014). Cellular scaling rules for the brain of afrotherians. Frontiers in
Neuroanatomy, 5, 113.
Passingham, R. E. (1975). Changes in the size and organisation of the brain in man and
his ancestors. Brain, Behavior and Evolution, 11, 7390.
Ribeiro, P. F.M, Ventura-Antunes, L., Gabi, M., Mota, B. M., Grinberg, L. T.,
Farfel, J. M., et al. (2013). The human cerebral cortex is neither one nor many:
Neuronal distribution reveals two quantitatively different zones in the gray matter,
three in the white matter, and explains local variations in cortical folding. Frontiers
in Neuroanatomy, 7, 120.
Rilling, J. K., & Seligman, R. A. (2002). A quantitative morphometric
comparative analysis of the primate temporal lobe. Journal of Human Evolution, 42,
505533.
Sanides, F. (1975). Comparative neurology of the temporal lobe in primates including
man with reference to speech. Brain and Language, 2, 396419.
Sarko, D. K., Catania, K. C., Leitch, D. B., Kaas, J. H., & Herculano-Houzel, S. (2009).
Cellular scaling rules of insectivore brains. Frontiers in Neuroanatomy, 3, 112.
Seelke, A. M., Dooley, J. C., & Krubitzer, L. A. (2014). The cellular composition of the
marsupial neocortex. Journal of Comparative Neurology, 522, 22862298.
25
Semendeferi, K., & Damasio, H. (2000). The brain and its main anatomical subdivisions
in living hominoids using magnetic resonance imaging. Journal of Human
Evolution, 38(2), 317332.
Semendeferi, K., Lu, A., Schenker, N., & Damasio, H. (2002). Humans and great apes
share a large frontal cortex. Nature Neuroscience, 5, 272276.
Smaers, J. B., Steele, J., Case, C. R., Cowper, A., Amunts, K., & Zilles, K. (2011).
Primate prefrontal cortex evolution: Human brains are the extreme of a lateralized
ape trend. Brain, Behavior and Evolution, 77, 6778.
Stephan, H., Frahm, H., & Baron, G. (1981). New and revised data on
volumes of brain structures in insectivores and primates. Folia Primatologica, 35,
129.
Ventura-Antunes, L., Mota, B., & Herculano-Houzel, S. (2013). Different scaling of
white matter volume, cortical connectivity, and gyrification across rodent and
primate brains. Frontiers in Neuroanatomy, 7, 3.
Zilles, K., Armstrong, E., Moser, K. H., Schleicher, A., & Stephan, H. (1989). Gyrification
in the cerebral cortex of primates. Brain, Behavior and Evolution, 34, 143150.
Zilles, K., Armstrong, E., Schlaug, G., & Schleicher, A. (1986). Quantitative
cytoarchitectonics of the posterior cingulate cortex in primates. Journal of
Brain Sex Differences

MM McCarthy, University of Maryland School of Medicine, Baltimore, MD, USA
Glossary
Amygdala A brain region important to social behaviors,

including juvenile play and mating behavior, as well as fear
and anxiety behaviors.
Aromatase (Cyp19) Aromatase is an enzyme that converts
testosterone into estradiol. Cyp19 is the name of the gene
that codes for the enzyme. Aromatase is found in the brain
as well as in the ovary of females. In males, aromatase in the
brain generates high levels of estradiol during early
development by converting the testosterone made by the
testis.
AVPV Anteroventral periventricular nucleus. The AVPV is a
small region in the preoptic area that sends projections to
the GnRH neurons which control gonadotropin secretion.
The control of gonadotropin secretion is sexually dimorphic
and this brain region is also sexually dimorphic, thereby
connecting form and function.
Chromosome Complement Refers to the presence of XX
versus XY.
Connectome Refers to the compilation of connections
between neurons and the patterns of activity associated with
those connections.
Endocannabinoids These are short distance rapid signaling
molecules made from lipid membranes. Sometimes referred
to as the brains own marijuana, these molecules activate
receptors in the brain that control neurotransmitter release
and can impact the proliferation of cells, including neurons.
Epigenetics Literally means above the genome and refers to
changes to the genome that alter gene expression but do not
change the nucleotide base sequence. Epigenetic changes
Introduction
Your gender, whether you are a boy or girl, man or woman, is
one of the most salient and enduring identifying features one
possesses. The term gender is unique to humans as it incorporates both self and societal perceptions of ones sex, which is
either male or female. Thus, studies of animals address sex
differences, whereas studies of humans may involve either or
both gender and sex. Ones sex is determined on several levels
that can be summarized as the three Gs genes, gonads, and
genitalia (Joel, 2012). In the overwhelming majority of cases,
these three variables align such that an XX individual will
develop ovaries and female genitalia whereas an XY individual
will develop testis and male genitalia and this will in turn
inform gender. Thus, sex and gender are internally consistent.
But is this also true for the sex/gender of the brain? That boys
and girls, men and women, behave differently is so self-evident
as to be hardly worth stating. But this easy generality is in
reality highly nuanced and complex in both its origins and
may be direct to the DNA via methylation, or indirect to the

surrounding chromatin by changing acetylation or other
modifiers on the histones. Epigenetic changes are induced
by the environment, including experience, hormones, toxins
etc., and may or may not be heritable depending upon
whether they occur in germ cells.
FSH Follicle stimulating hormone. FSH is a gonadotropin
made in the pituitary that stimulates growth of ovarian
follicles in females and spermatogenesis in males.
LH Luteinizing hormone. LH is a gonadotropin released
from the pituitary in response to its releasing factor, GnRH,
which is made by neurons in the preoptic area. LH
stimulates the ovary and promotes ovulation of a ripened
follicle and its subsequent transformation into the hormone
producing gland called a corpus luteum. In males, LH
promotes steroidogenesis by the testis.
Nociception Is the perception of pain.
Prostaglandins Prostaglandins are short distance rapid
signaling molecules made from lipid membranes by the
cyclooxygenase enzymes. They are considered inflammatory
mediators but are emerging as important regulators of
normal brain development.
SDN-POA Sexually dimorphic nucleus of the preoptic area.
The preoptic area is a critical brain region anterior to the
optic chiasm which controls sexual behavior, maternal
behavior, gonadotropin secretion, and body temperature.
The SDN is a collection of cells noted for being large and
densely clustered. There are more of these cells in the male
rodent brain than the female and an analogous nucleus has
been described in the hypothalamus of humans.
manifestations. In what ways are men and womens brains

really different? And why are they different? Is it biology?
Culture? Society? Experience? Or some combination thereof?
Only in animals can we hope to tease out truly biological
sources of variation in male and female brains and the first
experimental evidence of this comes from the publication of
the now iconic paper of Phoenix, Goy, Gerall, and Young
(1959). This study of guinea pigs established that the sensitivity
of adult animals to either male (testosterone) or female (estradiol and progesterone) hormones and the induction of sexual
behavior were dependent upon the hormonal milieu experienced early in life, with the authors asserting that the neural
substrate controlling behavior had been organized (Figure 1).
This was a heretical idea at the time but in hindsight is entirely
consistent with other sensitive periods in brain development
that alter adult neural function, as well as newly emerging ideas
about early life programming that impacts all manners of adult
responding including energy utilization, stress responding, and
immune system activation (Bale et al., 2010). The authors made
http://dx.doi.org/10.1016/B978-0-12-397025-1.00196-2
27
28
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Brain Sex Differences
Ovary
Default
Bipotential
gonad
Aromatase
SRY Gene
E2
T
Y Chromosome
Testis
Masculinization
Default
Bipotential
brain
Feminization
Figure 1 Sexual differentiation of the brain. The bipotential gonad is programmed to form an ovary by default but will differentiate into a testis in
response to the activation of the SRY gene on the Y chromosome. The bipotential brain is also programmed towards feminization in the absence of
testosterone (T), which is a precursor to estradiol (E2). In rodents, E2 masculinizes the brain, one manifestation of which is adult male sexual behavior.
In the absence of exposure to high levels of E2 early in development during a sensitive period, often referred to as the organizational phase, the
neural circuits that control sex behavior are feminized. Both male and female adult sex behaviors require activation by the appropriate hormonal milieu.
Via this mechanism of differentiation, a match between gonadal sex and reproductive behavior is assured.
the even further heretical assertion that testosterone and its

metabolites alter the structure or function of the neural correlates of sexual behavior. Today, we fully embrace the notion
that steroids act on the brain to modify neural structure and
function, regardless of whether one accepts this contributes to
sex differences in behavior. In fact, the more we look, the more
we find. But not all sex differences are made equal, and some
may have evolved in order to appear only in response to challenge or to compensate for the costs of reproduction that differ
in males and females (McCarthy, Arnold, Ball, Blaustein, & De
Vries, 2012; McCarthy & Konkle, 2005).
Following publication of Phoenix, Goy, Gerall, and Young
(1959) the next decades saw an accelerating interest in the
hormonal control of behavior. Convincing evidence of neuroanatomical sex differences was not apparent until the early
1970s with the description of song control nuclei in canaries
and zebra finches that were visibly larger in males, who sing
complex songs with regularity, compared to females who sing
infrequent and simple songs (Nottebohm & Arnold, 1976).
This discovery led to a reexamination of mammalian brains,
in particular the laboratory rat, in which it was assumed that
sex differences in morphology would be small, subtle, and
infrequent. The discovery of the sexually dimorphic nucleus
of the preoptic area (SDN-POA) (Gorski, Gordon, Shryne, &
Southam, 1978) spawned a cottage industry of research into
volumetric sex differences in specific nuclei. Several were
found, and in each case, the sex difference in volume is determined by gonadal steroid exposure during the perinatal sensitive period.
Around the same time that the organizational/activational
hypothesis was being formulated and conceptually integrated
into research on sex behavior, a different group of scientists
were focusing on the neural control of the anterior pituitary
and the release of the gonadotropins, LH and FSH, which in
turn regulate the gonads. In females, the pattern of LH release
is distinctly different from that of males because it is a critical

driver of the reproductive cycle, the midpoint of which is
demarcated by ovulation. In males, reproductive readiness is
constant, and so, LH is released in a pulsatile but consistent
pattern. The release of LH from the anterior pituitary is controlled by neurons that express gonadotropin-releasing factor
(GnRH) and the firing pattern of these neurons differs in males
and females, although the neurons themselves show little sex
differences in terms of number or morphology. The sex difference in pattern of LH release is organized neonatally just as sex
behavior is and involves multiple nuclei making up a neural
network controlling the final output, the GnRH neuron
(Clarkson & Herbison, 2006).
For many years, decades actually, these two end points, sex
behavior and gonadotropin secretion, and the two brain
regions controlling them, the POA and hypothalamus, were
the dominant focus of neuroendocrinological study. This
began to change with the discovery of a profound impact of
the steroid estradiol on the density of synapses in the adult rat
hippocampus (Gould, Woolley, Frankfurt, & Mcewen, 1990)
and brings us to the current era in which sex differences in the
brain are known to be pervasive, multifactorial, and often
unrelated to reproduction.
Multiple Mechanisms and Influences Establish and

Maintain Sex Differences in the Brain
One thing that has become clear is that there is no one thing
that establishes sex differences in the brain. On the broad
spectrum, we know steroids are important, both androgens
and estrogens (McCarthy, 2008; Zuloaga, Puts, Jordan, &
Breedlove, 2008), and more recently, we know that chromosome compliment is also important, that is, XX versus XY
(Arnold & Burgoyne, 2004). We also know that experience

matters, that moms or dams treat their male offspring differently than their female offspring (Bowers, Perez Pouchoulen,
Edwards, & McCarthy, 2013; Moore, 1984). But we have also
learned a great deal at the cellular level about the myriad of
ways that the multiple end points that are different in male and
female brains can come about.
Cell Death Proteins Mediate Volumetric Sex Differences

Returning to the volumetric sex differences and the SDN, it was
apparent that this difference could come about in one of three
different ways: (1) cell genesis, (2) cell migration, or (3) cell
death. The latter seemed like the least likely of the three but in
fact turned out to be true (Figure 2). Estradiol, the aromatized
end product of testosterone, is a survival factor for SDN neurons. Males and females make the same number of neurons
initially, but since only males make estradiol in the POA from
their testicular androgens, the neurons begin to die in the
females a few days after birth. If newborn female pups are
given injections of estradiol, the neurons will survive and
they will have a male-sized SDN (Davis, Popper, & Gorski,
1996; Rhees, Shryne, & Gorski, 1990a, 1990b). If the injections
of estradiol are not given until after a week of life, the neurons
have already died and cannot be replaced. A similar scenario
occurs in the principle nucleus of the bed nuclei of the stria
terminalis (BNSTp) that is larger in males than in females and
is increased in volume in females by estradiol injections early,
but not late (De Vries & Simerly, 2002; Forger et al., 2004;
Polston & Simerly, 2003; Simerly, 2002). Interestingly, however, in both cases, what would appear to be a one-time permanent change, dead cells can only die once after all, is
actually a dynamic process in that ongoing cell genesis will
maintain the larger volume SDN and BNSTp in the postpubertal male (Ahmed et al., 2008).
The anteroventral periventricular nucleus (AVPV) also
shows a sex difference in overall volume only reversed, being
Male
Female
SDN
Healthy cells
Dead and dying cells
E2
Medial preoptic nucleus
Figure 2 The size of the sexual dimorphic nucleus (SDN) is determined

by cell death. The SDN is a collection of Nissl dense cells located in
the medial preoptic nucleus that is 35 times larger in males. Both sexes
begin with the same number of neurons in the SDN, but cells die in
females due to a lack of stimulation by estradiol (E2), which in this brain
region is a cell survival factor. In other regions, E2 initiates cell death
cascades or cell proliferation, highlighting the importance of regional
specificity in brain sex differences.
29
larger in females (Davis, Shryne, & Gorski, 1996; Gorski, Harlan, Jacobson, Shryne, & Southam, 1980; Simerly, Swanson,
Handa, & Gorski, 1985). Here, estradiol is a cell death signal
and induces both GABAergic and dopaminergic cells to die but
via a distinct cellular cascade for each. In GABAergic neurons,
females have higher levels of TNF-a, which activates NF-kB, a
cell survival protein. Male GABAergic neurons downregulate
this pathway via estradiol-induced expression of TRIP (TNF
receptor-associated factor 2-inhibiting protein). Starved of
NF-kB, the cells die in males (Krishnan, Intlekofer, Aggison,
& Petersen, 2009). In the dopamine neurons, estradiol activates a classic caspase-3 apoptotic cascade (Simerly, Zee, Pendleton, Lubahn, & Korach, 1997; Waters & Simerly, 2009), the
result being that males have fewer GABA and dopamine neurons in the AVPV and thus an overall smaller volume.
Target-Derived Growth Factors Induce Sex Differences

in Projections
Just as important as the number and phenotypes of cells in a
particular nucleus are the afferent projections they receive.
Functionally connecting the BNSTp and the AVPV is a direct
GABAergic projection that is up to 10 times larger in males
than in females (Hutton, Gu, & Simerly, 1998; Polston, Gu, &
Simerly, 2004; Polston & Simerly, 2006). Such a sex difference could also arise from a variety of sources, but the use of
explant cultures established that estradiol-induced growth
factors in the target, the AVPV, are released from the neurons
and attract the growth cones of the axons extending from the
BNSTp neurons (Ibanez, Gu, & Simerly, 2001). In the
absence of this growth factor, many fewer axons find their
way to the target, resulting in a marked sex difference in
innervation. This is one component of a circuit that controls
the surge release of LH from the anterior pituitary that is
essential for ovulation. Each node in the circuit shows
marked sex differences, but each one is derived via a different
mechanism, beginning with the BNSTp that is larger in males
and that makes an even larger GABAergic projection to the
AVPV, which is smaller in males and sends a direct glutamatergic innervation to the GnRH neurons, thereby regulating
their activity. This is just one component of a complex
and still emerging network of neurons controlling GnRH
firing rate, including an essential role for yet another neural
type, the kisspeptin neurons (Clarkson, Danglemont De
Tassigny, Moreno, Colledge, & Herbison, 2008; Clarkson &
Herbison, 2006).
Astrocytes and GABA Regulate Synapse Repression

in the Arcuate Nucleus
The arcuate nucleus located in the mediobasal hypothalamus
is a key region for control of the anterior pituitary and the
release of critical trophic factors such as LH, FSH, GnRH,
somatostatin, and prolactin. There are also important populations of arcuate neurons involved in feeding and metabolism,
two end points that also vary in males and females. Mong and
colleagues morphologically characterized arcuate neurons and
found that neonatal females had twice as many dendritic spine
synapses as males (Mong, Roberts, Kelly, & McCarthy, 2001).
Interestingly, the morphology of the resident astrocytes was
30

learned in the arcuate nucleus, a first line of inquiry
was whether the astrocytes of the POA also differ in their
morphology between males and females, and indeed, they
do, again being more complex and stellate in males
(Amateau & McCarthy, 2002b). However, the key player here
is a most unlikely candidate, the prostaglandin PGE2. Prostaglandins are membrane-derived lipid-signaling molecules normally associated with injury and inflammation but are
emerging as important signaling molecules in neural plasticity
as well as brain development. In males, estrogens from testicularly derived androgens upregulate PGE2 synthesis and release
(Amateau & McCarthy, 2004). This is believed to occur predominantly in neurons where ER are readily detected. The
PGE2 then has two critical actions. One is the activation of
the EP2 and EP4 receptors that are adenylate cyclase-linked,
leading to the activation of PKA that phosphorylates a key
residue of the GluR2 subunit of AMPA receptors that promotes
their trafficking to the membrane (Lenz, Wright, Martin, &
McCarthy, 2011; Wright, Burks, & McCarthy, 2008). Second
is that the small initial amount of PGE2 activates microglia, the
brain-resident immune cells, and evokes the synthesis and
release of still more PGE2 in a positive feed-forward mechanism (Lenz, Nugent, Haliyur, & McCarthy, 2013). The additional PGE2 is sufficient to induce calcium-dependent release
of glutamate from the neighboring astrocytes (and contribute
to their morphological masculinization), and the released glutamate activates the now membrane-clustered AMPA receptors
leading to the formation and stabilization of new dendritic
spines (Figure 3). So in this case, a two-cell system has evolved
to a three-cell scenario in which neurons, astrocytes, and microglia all play essential parts in the process of masculinization.
also markedly different, with female astrocytes being relatively

simple and bipolar in shape while male astrocytes were highly
stellate, with multiple bifurcating branches (Mong, Glaser, &
McCarthy, 1999). It is speculated that the more highly ramified
astrocytes of males physically repress the formation of synapses
and maintain this pattern throughout life. The change in astrocyte morphology is induced by estrogens derived from testicular androgens during the perinatal period, but there is no
evidence of estrogen receptor (ER) within the astrocytes themselves (McCarthy, Amateau, & Mong, 2002). The mystery of
how a steroid could alter the morphology of a cell that does not
have a receptor for it was solved with the discovery that estradiol upregulates production of the enzyme glutamic acid
decarboxylase, the rate-limiting enzyme in GABA synthesis.
Astrocytes also express GABA-A receptors that when activated
lead to process growth and branching, that is, stellation. Thus,
a pathway that begins with steroid-induced transcription in a
neuron changes a neighboring astrocyte, which then feeds back
into the morphology of that or other neurons, demonstrating
the role of cell-to-cell communication in sexual differentiation
(Mong, Nunez, & McCarthy, 2002).
Immune and Inflammatory Mediators Regulate Sex

Differences in Synaptogenesis
The POA was discussed earlier as the sight of the SDN and a
critical brain region for control of male sexual behavior.
However, there is an additional sex difference in the POA that
is quite robust the density of dendritic spine synapses that is
twice as great on male POA neuron dendrites as females
(Amateau & McCarthy, 2002a). Borrowing from the lessons
Microglia
PGE2
ine
Sp
te
AMPA receptors
ri
nd
PGE2
De
yte
oc
tr
As
E2
ER
COX1& 2
Neuron
Figure 3 A sex difference in synaptic patterning involves immune and inflammatory mediators and cell-to-cell communication. Dendrites of POA
neurons in males have twice the density of dendritic spine synapses as females. This sex difference is the result of estradiol (E2) induction of the COX-1
and COX-2 genes that synthesize the prostaglandin PGE2, normally a proinflammatory molecule but here functioning as a regulatory component of
normal brain development. PGE2 released from neurons appears to have multiple functions including induction of increased activation of both
astrocytes and microglia, evidenced by increased stellation and amoeboid-like shape, respectively, and a further production and release of PGE2
from these cell types. This feed-forward mechanism of PGE2 production stimulates glutamate release, presumably from astrocytes, which is in turn
essential for the activation of AMPA receptors and the formation and stabilization of dendritic spine synapses.

That microglia are peripherally derived specialized macrophages
makes this a particularly interesting mechanism for establishing
sex differences and emerging evidence that mast cells may be a
fourth contributing cell type makes this system one to watch.
Hippocampal Neurogenesis Is Regulated by Endogenous

Estrogens
The sex differences in the volume of the SDN and other hypothalamic nuclei led to the perception that differential cell death
was the predominant, if not only, mechanism by which sex
differences were established in the brain. However, once attention was turned to nonreproductive telencephalic brain regions,
perceptions changed (Figure 4). During the perinatal sensitive
period, males have twice the rate of new cell genesis as females in
the developing hippocampus, including in the CA1, CA3, and
dentate gyrus (Bowers, Waddell, & McCarthy, 2010; Zhang,
Konkle, Zup, & McCarthy, 2008). As with most sex differences
during this time, administration of gonadal steroids, either estrogens or androgens, to females will increase the rate of cell genesis
to that of males. Intriguingly, close to 80% of the surviving
newborn cells in males will differentiate into neurons, whereas
only 40% will do so in females, and this too is responsive to
estradiol treatment of females (Bowers et al., 2010; Waddell,
Bowers, Edwards, Jordan, & McCarthy, 2013). This is unusual
in that most agents that promote cell proliferation repress differentiation, and vice versa, those factors that promote differentiation do so at the expense of proliferation. Precisely how it is that
estradiol does this double dance is unclear. Equally unclear is
how estradiol regulates the sex difference, but upregulation of
BDNF is emerging as a likely regulator.
T and E2
Hippocampus
Increased BDNF
Higher
endocannabinoid
tone
Amygdala
= New cells in females
= New cells in males
Figure 4 Sex differences in cell genesis in the hippocampus and

amygdala are mediated by distinct mechanisms. Cell proliferation is
emerging as an important contributor to brain sex differences outside the
preoptic area and hypothalamus. In the hippocampus, newborn males
generate up to twice as many new cells as females and the majority
will differentiate into neurons. This sex difference is induced by estradiol
(E2) and may involve induction of BDNF. In the amygdala, cell genesis
in females is higher than males at the same developmental time point.
This sex difference is also mediated by steroids and is the result of a
higher endocannabinoid tone in males, which have more 2-AG and
anandamide and lower levels of FAAH and MAGL during the first days
of life, and this then suppresses cell proliferation via a currently
unknown mechanism.
31
Endocannabinoids Mediate Cell Genesis in the Amygdala

The discovery of sex difference in cell genesis in the hippocampus sparked interest in related regions and led to the discovery
of a higher number of newborn cells in the amygdala of
females compared to males, opposite to that observed in the
hippocampus (Krebs-Kraft, Hill, Hillard, & McCarthy, 2010).
The signaling molecules mediating this difference are also
membrane-derived, the endocannabinoids 2-AG and anandamide, which bind to and activate the G protein-coupled receptors
CB1 and CB2. In the developing amygdala, endocannabinoids
suppress cell genesis (Figure 4). Males, it turns out, have a higher
endocannabinoid tone in the developing amygdala as is evident
by higher levels of 2-AG and anandamide and lower amounts of
the two degradative enzymes, FAAH and MAGL, that normally
clear the endocannabinoids and thereby contribute to the overall
tone. Treating females with CB agonists during the neonatal sensitive period decreases cell genesis to the level seen in males, and
this correlates with a behavioral change some 3 weeks later when
juvenile females show an increase in social play that brings them
on par with males (Krebs-Kraft et al., 2010). Social play, sometimes referred to as rough and tumble play, is expressed at higher
frequency and greater intensity in males of a wide range of species,
including humans, and is fascinating for its expression during a
time in life when steroid hormones are at their nadir. Thus, any
hormonal influence on play behavior must have occurred earlier
in development and organized the neural substrate controlling
this behavior. A sex difference in cell genesis in the amygdala
regulated by endocannabinoid tone is a novel mechanism for
such an organizational effect.
Epigenetic Changes Maintain Sex Differences in the Brain

and Behavior
Organization implies a degree of permanency and indeed that
was the original intent, that early hormone exposure would
organize the neural substrate for later activation following
puberty to assure a match between reproductive physiology
and behavior. But we now understand that many synapses
come and go and that neurogenesis can continue throughout
life; thus, there must be a cellular memory that is maintained
from the perinatal period until adulthood, and the best candidate for cellular memory is epigenetics.
Epigenetics means above the genome and refers to changes to
the DNA and associated chromatin that do not involve changes to
the nucleotide sequence. Modifications to the histones that surround nucleosomes and regulate transcription factor access to the
DNA and direct methylation of cytosine residues are the two
major forms of epigenetic modification. Steroid hormones are
excellent candidates for agents of epigenetic change in that their
receptors associate with enzymes that alter acetylation of histones. Referred to as HATs (histone acetyltransferases) and
HDACs (histone deacetylases), these enzymes either add or
remove acetyl groups from lysine residues that, respectively,
loosens or tightens the chromatin packing around the DNA.
The inhibition of HDAC activity in the POA during the neonatal
sensitive period disrupts sexual differentiation of masculine
behavior, and two genes central to this process, ERS1 (estrogen
receptor alpha) and CYP19 (aromatase), have more HDAC binding to their promoters in males than in females (Matsuda et al.,
32
2011). Thus, steroids may be both the targets and the regulators
of epigenetic changes that allow for organizational modifications
to endure. HDAC activity also contributes to volumetric sex
differences as it is required for steroid-induced masculinization
of the larger BNSTp found in males (Murray, Hien, De Vries, &
Forger, 2009). The importance of DNA methylation is just beginning to emerge with implications for sex differences in social play
behavior (Auger, Jessen, & Edelmann, 2011) and possibly sex
behavior (Edelmann & Auger, 2011; McCarthy et al., 2009;
Nugent & McCarthy, 2011; Nugent, Schwarz, & McCarthy, 2010).
identified, and indeed, they may be due to gene networks,

but that chromosome complement contributes to sex differences in the brain and behavior cannot be denied.
Neural Networks Mediate Sex Differences in

Physiology and Behavior
It is relatively easy to highlight specific neuroanatomical differences between the brains of a male rat (or mouse) and a
female rat (or mouse) matched for age, genetic background,
and rearing conditions (Figure 5). But what does this mean to
neural functioning? To behavior and physiology? In the reproductive axis, as discussed earlier, we can clearly point to a
neural network that controls the release of LH from the pituitary that is markedly different in males and females. Likewise,
there is a neural circuit controlling male and female sexual
behaviors, and while it involves essentially all the same brain
regions for both, there are presumably nodes of influence that
are weighted differently in the two sexes (Figure 6). Thus,
males have twice the density of excitatory input onto dendrites
of POA neurons as females, and this input most likely comes
from olfactory information integrated by the amygdala. Projections from the POA to the mediobasal hypothalamus vary in
response to the dimorphic morphology of efferent neurons in
males versus females and so on down the line. Thus, while the
circuit is in essence the same in both sexes, the integration and
management of information are different and can be due to
Chromosome Complement Matters Too

The hegemony of hormones has been challenged by a new
model, the four core genotypes in which the Y chromosome
gene coding for a testis, SRY, has been translocated to an
autosome, thereby allowing for mice that are XX but have testes
or XY but have ovaries (Arnold & Chen, 2009). While sexually
differentiated reproductive behaviors remain entirely a product
of early hormone exposure, many other behaviors and neuroanatomical end points are influenced by the chromosome
complement independently of the gonads. These include
aggression, habit formation, overall activity, nociception, progesterone receptor expression, vasopressin innervation, and
anxiety levels (Arnold, 2004; Arnold et al., 2004; Gatewood
et al., 2006; Gioiosa et al., 2008; Gioiosa, Chen, Watkins,
Umeda, & Arnold, 2008; Wagner et al., 2004). Specific genes
that can be causally tied to these effects have not yet been
Cellular endpoints
modified by
androgens and
estrogens in the
developing brain
Cell birth / cell survival / cell death

Neurogenesis
Caspases: BAX
Gliagenesis
Apoptosis
Survival
Synaptic patterning
Migration
Synapse elimination
Synaptogenesis
Epigenetics
Neurochemical phenotype
Growth and differentiation
Histone
acetylation
DNA
Methylation
Dendritic growth
Astrocyte differentiation
Figure 5 Multiple cellular end points are organized by steroids developmentally. As investigation into the biological basis of sex differences in the brain
continues, greater numbers and varieties of cellular end points that are targets of the organizational effects of steroids are emerging. Each of these
variables has been identified to be modulated by steroids and/or different in male versus female brains in rodent animal models. Importantly, the
end points that are modified are region-specific, as are the signal transduction pathways mediating them, yet most are influenced by the same hormones
(predominantly estradiol in rodents) and usually during a common sensitive window. How this high degree of specificity is achieved is unknown but
may involve a convergence between genetic factors, such as sex chromosome compliment, and hormonal action.
33
LH Release
Bnst
AVPV
Arcuate
GnRH Neuron
Sex behavior
Odors
Amygdala
Human connectome
POA
PAG
SNB
Figure 6 Connectomes and networks mediate sex differences in physiology and behavior. While sexual differentiation of specific brain regions may
occur independently, it is the interaction between regions in a network that ultimately influences physiology and behavior. In humans, the recent
findings on the human connectome by Ingalhalikar et al. (2014) using diffusion tensor imaging in almost 1000 subjects revealed that males
predominately make active connections within one cerebral hemisphere whereas females make many more cross hemispheric connections and favor
the frontal cortical areas. In rodents, there are nodes of influence in the neural circuit controlling LH release such that some areas or projections
are larger or smaller in males and females, producing a sex difference in the pattern of gonadotropin secretion. The same is true for the circuit controlling
sex behavior, which involves mostly the same regions in males and females but is differentiated by the sensitivity to specific odors, density of the
synaptic profile, number or type of neurons, etc. In this way, the same region can serve different functions for each sex depending on how it
was organized developmentally and activated in adulthood.
firing thresholds, patterns of input or variance in transcriptional activation, among others.

Recent advances in imaging are providing new insights into
the neural connectome, particularly in humans. The use of
fMRI and diffusion tensor imaging allows for weighting of
nodes of influence and patterns of connectivity. Males and
females are found to vary in many respects under both basal
and challenge conditions. There are numerous caveats and
qualifications when interpreting imaging data on humans
due to subjectivity and inherent bias that often leads to discarding of negative data regarding sex differences. Nonetheless,
there is an emerging consensus that the developmental trajectories of various neural systems vary in boys versus girls
(Lenroot et al., 2007) and that connectivity between the cortical hemispheres is markedly different in men and women and
that this begins to emerge relatively early in childhood
(Ingalhalikar et al., 2014). Females have a high degree of
cross hemisphere connectivity, whereas males have a high
degree of intrahemispheric trafficking (Figure 6). Whether
this translates into multitasking diffuse attention versus
focused systematizing thought processes remains to be seen.
Why Understanding Sex Differences in the Brain

Is Important
An unusual facet of this topic is the interest and implications
across a wide swath of disciplines, from biomedicine to education to politics. Everyone has an opinion about differences
between men and women, and the potential for inherent but
unrecognized bias must constantly be guarded against. This

bias can be both in favor of and against sex differences, with
some arguing that all men are different from all women while
others arguing that sex differences are small and largely a
product of cultural expectations. Each stand runs the risk of
committing a type II error, seeing a difference when there is not
one, or a type I error, missing a difference when it exists.
The power of studies in animals is that cultural and societal
expectations can be removed from the equation, but environment and experience can still impact sex differences in ways we
might not expect. Nonetheless, one can be generally assured
that any differences observed are biological in origin.
Understanding biology is essential for understanding why
there is such a large gender bias in the incidence of neurological and neuropsychiatric disorders (Abel, Drake, & Goldstein,
2010; Bale et al., 2010). Boys are diagnosed at substantially
higher rates than girls for autism spectrum disorder, with a
5-to-1 ratio of disparity. They are also more likely to be diagnosed with early-onset schizophrenia and to suffer from dyslexia, stuttering, Tourettes syndrome, and severe mental
retardation. All of these either are developmental in onset or
have origins in development. Girls on one hand and woman
on the other hand are about twice as likely to be diagnosed
with major depressive disorder and anxiety or panic disorders.
They are substantially more likely to suffer from anorexia
nervosa, a devastating and life-threatening eating disorder.
Men and women also differ in their risk for drug or substance
abuse and addiction, post-traumatic stress disorder, and autoimmune and neurodegenerative diseases such as Parkinsons
and Alzheimers. The risk for, severity of, and recovery from
34
stroke are so different in men and women that specific guidelines for the treatment of women have been established
(Bushnell et al., 2014). Modeling these conditions in animals
is difficult and, in some cases, impossible (i.e., stuttering or
Tourettes), but the pervasive impact of sex on biological end
points has persuaded the NIH that all preclinical research
involving animals or humans should incorporate it as an
experimental variable. Guidelines for implementation are
expected in late 2014 and promise to change the perception
of the relevance of sex differences in the brain from narrowly
defined effects on reproduction to a mainstream component of
neural functioning.

Obtaining Quantitative Information from fMRI; INTRODUCTION TO
ANATOMY AND PHYSIOLOGY: Cytoarchitectonics,
Receptorarchitectonics, and Network Topology of Language;
Development of Structural and Functional Connectivity; Functional
Connectivity; INTRODUCTION TO CLINICAL BRAIN MAPPING:
Depression; Developmental Brain Atlases; Emotion and Stress; Imaging
Studies of Anxiety Disorders; Limbic to Motor Interactions during
Social Perception; Neuroimaging Evidences of Gonadal Steroid
Hormone Influences on Reward Processing and Social DecisionMaking in Humans; INTRODUCTION TO METHODS AND
MODELING: Resting-State Functional Connectivity;
INTRODUCTION TO SOCIAL COGNITIVE NEUROSCIENCE:
Neural Correlates of Social Cognition Deficits in Autism Spectrum
Disorders; INTRODUCTION TO SYSTEMS: Hubs and Pathways.
References
Abel, K. M., Drake, R., & Goldstein, J. M. (2010). Sex differences in schizophrenia.
International Review of Psychiatry, 22, 417428.
Ahmed, E. I., Zehr, J. L., Schulz, K. M., Lorenz, B. H., Doncarlos, L. L., & Sisk, C. L.
(2008). Pubertal hormones modulate the addition of new cells to sexually dimorphic
brain regions. Nature Neuroscience, 11, 995997.
Amateau, S. K., & McCarthy, M. M. (2002a). A novel mechanism of dendritic spine
plasticity involving estradiol induction of prostglandin-E2. The Journal of
Amateau, S. K., & McCarthy, M. M. (2002b). Sexual differentiation of astrocyte
morphology in the developing rat preoptic area. Journal of Neuroendocrinology, 14,
904910.
Amateau, S. K., & McCarthy, M. M. (2004). Induction of PGE(2) by estradiol mediates
developmental masculinization of sex behavior. Nature Neuroscience, 7, 643650.
Arnold, A. P. (2004). Sex chromosomes and brain gender. Nature Reviews.
Arnold, A. P., & Burgoyne, P. S. (2004). Are XX and XY brain cells intrinsically
different? Trends in Endocrinology and Metabolism, 15, 611.
Arnold, A. P., & Chen, X. (2009). What does the "four core genotypes" mouse model tell
us about sex differences in the brain and other tissues? Frontiers in
Neuroendocrinology, 30, 19.
Arnold, A. P., Xu, J., Grisham, W., Chen, X., Kim, Y. H., & Itoh, Y. (2004). Minireview:
Sex chromosomes and brain sexual differentiation. Endocrinology, 145, 10571062.
Auger, A. P., Jessen, H. M., & Edelmann, M. N. (2011). Epigenetic organization of brain
sex differences and juvenile social play behavior. Hormones and Behavior, 59,
358363.
Bale, T. L., Baram, T. Z., Brown, A. S., Goldstein, J. M., Insel, T. R., McCarthy, M. M.,
et al. (2010). Early life programming and neurodevelopmental disorders. Biological
Bowers, J. M., Perez Pouchoulen, M., Edwards, N. S., & McCarthy, M. M. (2013).
Foxp2 mediates sex differences in ultrasonic vocalization by rat pups and directs
order of maternal retrieval. The Journal of Neuroscience, 33, 32763283.
Bowers, J. M., Waddell, J., & McCarthy, M. M. (2010). A developmental sex difference
in hippocampal neurogenesis is mediated by endogenous oestradiol. Biology of Sex
Differences, 1, 8.
Bushnell, C., McCullough, L. D., Awad, I. A., Chireau, M. V., Fedder, W. N., Furie, K. L.,
et al. (2014). Guidelines for the prevention of stroke in women: A statement for
healthcare professionals from the american heart association/american stroke
association. Stroke, 45, 15451588.
Clarkson, J., Danglemont De Tassigny, X., Moreno, A. S., Colledge, W. H., &
Herbison, A. E. (2008). Kisspeptin-GPR54 signaling is essential for preovulatory
gonadotropin-releasing hormone neuron activation and the luteinizing hormone
surge. The Journal of Neuroscience, 28, 86918697.
Clarkson, J., & Herbison, A. E. (2006). Postnatal development of kisspeptin neurons in
mouse hypothalamus; sexual dimorphism and projections to gonadotropinreleasing hormone neurons. Endocrinology, 147, 58175825.
Davis, E. C., Popper, P., & Gorski, R. A. (1996). The role of apoptosis in sexual
differentiation of the rat sexually dimorphic nucleus of the preoptic area. Brain
Davis, E. C., Shryne, J. E., & Gorski, R. A. (1996). Structural sexual dimorphisms in
the anteroventral periventricular nucleus of the rat hypothalamus are sensitive to
gonadal steroids perinatally, but develop peripubertally. Neuroendocrinology, 63,
142148.
De Vries, G. J., & Simerly, R. B. (2002). Anatomy, development and function of sexually
dimorphic neural circuits in the mammalian brain. In D. W. Pfaff, A. P. Arnold, A. M.
Etgen, S. E. A. Fahrbach, & R. T. Rubin (Eds.), Hormones, brain and behavior (1st
edn.). New York: Academic Press.
Edelmann, M. N., & Auger, A. P. (2011). Epigenetic impact of simulated maternal
grooming on estrogen receptor alpha within the developing amygdala. Brain,
Behavior, and Immunity, 25, 12991304.
Forger, N. G., Rosen, G. J., Waters, E. M., Jacob, D., Simerly, R. B., & De Vries, G. J.
(2004). Deletion of Bax eliminates sex differences in the mouse forebrain.
101, 1366613671.
Gatewood, J. D., Wills, A., Shetty, S., Xu, J., Arnold, A. P., Burgoyne, P. S., et al. (2006).
Sex chromosome complement and gonadal sex influence aggressive and parental
behaviors in mice. The Journal of Neuroscience, 26, 23352342.
Gioiosa, L., Chen, X., Watkins, R., Klanfer, N., Bryant, C. D., Evans, C. J., et al. (2008).
Sex chromosome complement affects nociception in tests of acute and chronic
exposure to morphine in mice. Hormones and Behavior, 53, 124130.
Gioiosa, L., Chen, X., Watkins, R., Umeda, E. A., & Arnold, A. P. (2008). Sex
chromosome complement affects nociception and analgesia in newborn mice. The
Journal of Pain, 9, 962969.
Gorski, R. A., Gordon, J. H., Shryne, J. E., & Southam, A. M. (1978). Evidence for a
morphological sex difference within the medial preoptic area of the rat brain. Brain
Research, 148, 333346.
Gorski, R. A., Harlan, R. E., Jacobson, C. D., Shryne, J. E., & Southam, A. M. (1980).
Evidence for the existence of a sexually dimorphic nucleus in the preoptic area of the
rat. The Journal of Comparative Neurology, 193, 529539.
Gould, E., Woolley, C. S., Frankfurt, M., & Mcewen, B. S. (1990). Gonadal steroids
regulate dendritic spine density in hippocampal pyramidal cells in adulthood.
Hutton, L. A., Gu, G., & Simerly, R. B. (1998). Development of a sexually dimorphic
projection from the bed nuclei of the stria terminalis to the anteroventral
periventricular nucleus in the rat. The Journal of Neuroscience, 18, 30033013.
Ibanez, M. A., Gu, G., & Simerly, R. B. (2001). Target-dependent sexual differentiation
of a limbic-hypothalamic neural pathway. The Journal of Neuroscience, 21,
56525659.
Ingalhalikar, M., Smith, A., Parker, D., Satterthwaite, T. D., Elliott, M. A., Ruparel, K.,
et al. (2014). Sex differences in the structural connectome of the human brain.
111, 823828.
Joel, D. (2012). Genetic-gonadal-genitals sex (3G-sex) and the misconception of brain
and gender, or, why 3G-males and 3G-females have intersex brain and intersex
gender. Biology of Sex Differences, 3, 27.
Krebs-Kraft, D. L., Hill, M. N., Hillard, C. J., & McCarthy, M. M. (2010). Sex difference
in cell proliferation in developing rat amygdala mediated by endocannabinoids has
implications for social behavior. Proceedings of the National Academy of Sciences
Krishnan, S., Intlekofer, K. A., Aggison, L. K., & Petersen, S. L. (2009). Central role of
TRAF-interacting protein in a new model of brain sexual differentiation. Proceedings of
the National Academy of Sciences of the United States of America, 106, 1669216697.
Lenroot, R. K., Gogtay, N., Greenstein, D. K., Wells, E. M., Wallace, G. L., Clasen, L. S.,
et al. (2007). Sexual dimorphism of brain developmental trajectories during
childhood and adolescence. NeuroImage, 36, 10651073.

Lenz, K. M., Nugent, B. M., Haliyur, R., & McCarthy, M. M. (2013). Microglia are
essential to masculinization of brain and behavior. The Journal of Neuroscience, 33,
27612772.
Lenz, K. M., Wright, C. L., Martin, R. C., & McCarthy, M. M. (2011). Prostaglandin E2
regulates AMPA receptor phosphorylation and promotes membrane insertion in
preoptic area neurons and glia during sexual differentiation. PLoS One, 6,
E18500.
Matsuda, K. I., Mori, H., Nugent, B. M., Pfaff, D. W., McCarthy, M. M., & Kawata, M.
(2011). Histone deacetylation during brain development is essential for permanent
masculinization of sexual behavior. Endocrinology, 152, 27602767.
McCarthy, M. M. (2008). Estradiol and the developing brain. Physiological Reviews, 88,
91124.
McCarthy, M. M., Amateau, S. K., & Mong, J. A. (2002). Steroid modulation of
astrocytes in the neonatal brain: Implications for adult reproductive function.
Biology of Reproduction, 67, 691698.
McCarthy, M. M., Arnold, A. P., Ball, G. F., Blaustein, J. D., & De Vries, G. J. (2012).
Sex differences in the brain: The not so inconvenient truth. The Journal of
McCarthy, M. M., Auger, A. P., Bale, T. L., De Vries, G. J., Dunn, G. A., Forger, N. G.,
et al. (2009). The epigenetics of sex differences in the brain. The Journal of
McCarthy, M. M., & Konkle, A. T. (2005). When is a sex difference not a sex difference?
Frontiers in Neuroendocrinology, 26, 85102.
Mong, J. A., Glaser, E., & McCarthy, M. M. (1999). Gonadal steroids promote glial
differentiation and alter neuronal morphology in the developing hypothalamus in a
regionally specific manner. The Journal of Neuroscience, 19, 14641472.
Mong, J. A., Nunez, J. L., & McCarthy, M. M. (2002). GABA mediates steroid-induced
astrocyte differentiation in the neonatal rat hypothalamus. Journal of
Neuroendocrinology, 14, 116.
Mong, J. A., Roberts, R. C., Kelly, J. J., & McCarthy, M. M. (2001). Gonadal steroids
reduce the density of axospinous synapses in the developing rat arcuate nucleus:
An electron microscopy analysis. The Journal of Comparative Neurology, 432,
259267.
Moore, C. L. (1984). Maternal contributions to the development of masculine sexual
behavior in laboratory rats. Developmental Psychobiology, 17, 347356.
Murray, E. K., Hien, A., De Vries, G. J., & Forger, N. G. (2009). Epigenetic control of
sexual differentiation of the bed nucleus of the stria terminalis. Endocrinology, 150,
42414247.
Nottebohm, F., & Arnold, A. P. (1976). Sexual dimorphism in vocal control areas of the
songbird brain. Science, 194, 211213.
Nugent, B. M., & McCarthy, M. M. (2011). Epigenetic underpinnings of developmental
sex differences in the brain. Neuroendocrinology, 93, 150158.
Nugent, B. M., Schwarz, J. M., & McCarthy, M. M. (2010). Hormonally mediated
epigenetic changes to steroid receptors in the developing brain: Implications for
sexual differentiation. Hormones and Behavior, 59, 338344.
Phoenix, C. H., Goy, R. W., Gerall, A. A., & Young, W. C. (1959). Organizing action of
prenatally administered testosterone proprionate on the tissues mediating mating
behavior in the female guinea pig. Endocrinology, 65, 369382.
35
Polston, E. K., Gu, G., & Simerly, R. B. (2004). Neurons in the principal nucleus of the
bed nuclei of the stria terminalis provide a sexually dimorphic gabaergic input to the
anteroventral periventricular nucleus of the hypothalamus. Neuroscience, 123,
793803.
Polston, E. K., & Simerly, R. B. (2003). Sex-specific patterns of galanin,
cholecystokinin, and substance P expression in neurons of the principal bed
nucleus of the stria terminalis are differentially reflected within three efferent
preoptic pathways in the juvenile rat. The Journal of Comparative Neurology, 465,
551559.
Polston, E. K., & Simerly, R. B. (2006). Ontogeny of the projections from the
anteroventral periventricular nucleus of the hypothalamus in the female rat. The
Rhees, R. W., Shryne, J. E., & Gorski, R. A. (1990a). Onset of the hormone-sensitive
perinatal period for sexual differentiation of the sexually dimorphic nucleus of the
preoptic area in female rats. Journal of Neurobiology, 21, 781786.
Rhees, R. W., Shryne, J. E., & Gorski, R. A. (1990b). Termination of the hormonesensitive period for differentiation of the sexually dimorphic nucleus of the preoptic
area in male and female rats. Developmental Brain Research, 52, 1723.
Simerly, R. B. (2002). Wired for reproduction: Organization and development of sexually
dimorphic circuits in the mammalian forebrain. Annual Review of Neuroscience, 25,
507536.
Simerly, R. B., Swanson, L. W., Handa, R. J., & Gorski, R. A. (1985). Influence of
perinatal androgen on the sexually dimorphic distribution of tyrosine hydroxylaseimmunoreactive cells and fibers in the anteroventral periventricular nucleus of the
rat. Neuroendocrinology, 40, 501510.
Simerly, R. B., Zee, M. C., Pendleton, J. W., Lubahn, D. B., & Korach, K. S. (1997).
Estrogen receptor-dependent sexual differentiation of dopaminergic neurons in the
preoptic region of the mouse. Proceedings of the National Academy of Sciences of
Waddell, J., Bowers, J. M., Edwards, N. S., Jordan, C. L., & McCarthy, M. M. (2013).
Dysregulation of neonatal hippocampal cell genesis in the androgen insensitive Tfm
rat. Hormones and Behavior, 64, 144152.
Wagner, C. K., Xu, J., Pfau, J. L., Quadros, P. S., De Vries, G. J., & Arnold, A. P. (2004).
Neonatal mice possessing an Sry transgene show a masculinized pattern of
progesterone receptor expression in the brain independent of sex chromosome
status. Endocrinology, 145, 10461049.
Waters, E. M., & Simerly, R. B. (2009). Estrogen induces caspase-dependent cell
death during hypothalamic development. The Journal of Neuroscience, 29,
97149718.
Wright, C. L., Burks, S. R., & McCarthy, M. M. (2008). Identification of prostaglandin
E2 receptors mediating perinatal masculinization of adult sex behavior and
neuroanatomical correlates. Developmental Neurobiology, 68, 14061419.
Zhang, J.-M., Konkle, A. T. M., Zup, S. L., & McCarthy, M. M. (2008). Impact of sex and
hormones on new cells in the developing rat hippocampus: A novel source of sex
dimorphism? The European Journal of Neuroscience, 27, 791800.
Zuloaga, D. G., Puts, D. A., Jordan, C. L., & Breedlove, S. M. (2008). The role of
androgen receptors in the masculinization of brain and behavior: What weve learned
from the testicular feminization mutation. Hormones and Behavior, 53, 613626.
Gyrification in the Human Brain

K Zilles, Institute of Neuroscience and Medicine (INM-1), Julich, Germany; JARA Julich-Aachen Research Alliance, Aachen,
Germany; RWTH University Aachen, Aachen, Germany
N Palomero-Gallagher, Institute of Neuroscience and Medicine (INM-1), Julich, Germany; JARA Julich-Aachen Research Alliance,
Aachen, Germany
Glossary
Gyrencephalic Folded cortical surface showing the gyri and

sulci.
Gyrification index Ratio between the total (including
sulcal) and the superficially exposed cortical surfaces.
The human brain is gyrencephalic, as are the cerebral cortices of

most other large-brained mammalian species. Small-brained
mammals show a smooth cortical surface, that is, lissencephalic.
Cortical folding is a morphological hallmark of the human
brain. The pattern of folding is extremely variable between
different individuals. For detailed descriptions, the reader is
referred to the numerous atlases describing the variability of
the gyri and sulci (Mazziotta, Toga, Evans, Fox, & Lancaster,
1995; Ono, Kubik, & Abernathey, 1990; Thompson, Schwartz,
Lin, Khan, & Toga, 1996). Since modern neuroimaging studies
frequently register their results to the Montreal Neurological
Institute reference brain (Holmes et al., 1998), we here describe
the gyri and sulci of this brain in Figures 1 and 2. A comparison
of this brain with several other human brains immediately
shows that the pattern of sulci and gyri is highly variable
between subjects. In fact, each single brain provides a personal
fingerprint based on its gyrification pattern (Figure 3).
Besides this qualitative aspect, gyrification can be quantitatively analyzed. The overall degree of cortical folding can be
measured as gyrification index (GI), whereby GI is defined by
the ratio between the total cortical surface, that is, the superficially exposed part of the cortex plus the part located within the
sulci, and the superficially exposed part of the cortex (Figure 4).
The GI can be measured using serial sections through the brain
or by surface reconstructions based on MRI data. The global GI,
averaged over the total cerebral cortex, or local GIs assigned to
specific cortical regions have been reported.
Global and Regional Gyrification

The human brain has the largest global GI among primates
(Pillay & Manger, 2007; Rilling & Insel, 1999; Zilles, Armstrong,
Moser, Schleicher, & Stephan, 1989; Zilles et al., 1988), but
some mammals with larger brains than those of humans can
reach even larger GIs (Brodmann, 1913; Elias & Schwartz, 1969;
Marino et al., 2007; Pillay & Manger, 2007). The global GI of
the human brain varies between 2.21 and 2.97 (mean
GI 2.56 0.02) in a post mortem sample of 61 female and
male brains (age range 1691 years; Zilles et al., 1988). In an
in vivo sample of 242 female and male brains (age range 1985
Lissencephalic Smooth cortical surface, without the

(prominent) gyri or sulci.
years), a mean GI of 2.29 0.08 was found based on MRI

(Rogers et al., 2010). That means that approximately two-thirds
of cortical surface are buried in the sulci. The global GI does
not correlate with body weight and length, brain weight, or
cortical thickness in the human brain (Rogers et al., 2010; Zilles
et al., 1988). Only in the male brain was a significant leftright
asymmetry of the global GI reported, with the left hemisphere
having a slightly higher GI than the right one (Zilles
et al., 1997).
The global GI differs between males and females (Rogers
et al., 2010). Greater gyrification was found in women than in
men in frontal and parietal regions (Luders et al., 2004, 2008;
Mueller et al., 2013; Toro et al., 2008). Luders et al. (2004)
interpreted this finding as a compensatory effect in females to
counteract their smaller absolute cortical volume, as compared
to males, by an increasing cortical surface and folding. This
interpretation would require a negative correlation between GI
and cerebral volume, which was reported for global GI and
cerebral volume by Rogers et al. (2010).
The GI reaches highest values over the multimodal association cortices, that is, at the levels of the prefrontal, parietal,
and temporal regions, and lowest values around the central
region and the occipital pole (Mueller et al., 2013; Toro et al.,
2008; Zilles et al., 1988; Figure 4). Notably, the regions presenting maximum gyrification coincide with the regions of
highest variability in functional connectivity (Mueller et al.,
2013). Furthermore, the regions of maximal variability in
functional connectivity are found in areas belonging to the
default, frontoparietal control, and attentional networks
(Mueller et al., 2013). Differences in regionally specific gyrification may indicate a brain size-independent plasticity that is,
among other factors, influenced by different individual environmental conditions (e.g., exercise and mediation; Hogstrom,
Westlye, Walhovd, & Fjell, 2013).
Ontogeny of the GI
Cortical folding starts at the 16th week of gestation, accelerates conspicuously as from the 28th week, and reaches a
transient maximum between the 66th and 80th weeks
http://dx.doi.org/10.1016/B978-0-12-397025-1.00197-4
37
38
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Gyrification in the Human Brain
(a)
(b)
(c)
(d)
(e)
(f)
(g)
(h)
Figure 1 Lateral (a, b), medial (c, d), dorsal (e), basal (f), frontal (g), and caudal views (h) of the Montreal Neurological Institute (MNI) single subject
template (Holmes et al., 1998), on which sulci have been identified. 1, Sylvian fissure; 2, posterior subcentral sulcus; 3, horizontal ramus of the Sylvian
fissure; 4, ascending ramus of the Sylvian fissure; 5, diagonal sulcus; 6, central sulcus; 60 , paracentral fossa; 600 , marginal precentral sulcus; 7,
precentral sulcus; 8, medial precentral sulcus; 9, medial frontal sulcus (superior frontal paramidline sulcus); 10, superior frontal sulcus; 11, intermediate
sulcus; 12, inferior frontal sulcus; 13, frontal polar sulcus; 14, frontomarginal sulcus; 15, callosal sulcus; 16, cingulate sulcus; 17, paracingulate sulcus;
18, paracentral sulcus; 19, anterior parolfactory sulcus; 20, superior rostral sulcus; 21, inferior rostral sulcus; 22, olfactory sulcus; 23, sulcus
fragmentosus; 24, medial orbital sulcus; 25, intermediate orbital sulcus; 26, lateral orbital sulcus; 27, transverse orbital sulcus; 28, postcentral sulcus;
29, supramarginal sulcus; 30, intraparietal sulcus; 31, Jensen sulcus (primary intermediate sulcus); 32, superior parietal sulcus; 33, angular sulcus; 34,
subparietal sulcus; 35, precuneal sulcus; 36, transverse temporal sulcus (Heschls sulcus); 37, superior temporal sulcus; 38, inferior temporal sulcus;
39, rhinal sulcus; 40, occipitotemporal sulcus; 41, collateral sulcus; 42, parieto-occipital sulcus; 43, anterior occipital sulcus; 44, calcarine sulcus; 45,
cuneal sulcus (paracalcarine sulcus); 46, lingual sulcus; 47, mid-fusiform sulcus; 48, inferior occipital sulcus; 49, inferior lateral occipital sulcus; 50,
superior lateral occipital sulcus; 51, superior occipital sulcus; 52, transverse occipital sulcus; 53, accessory sulcus. Arrows indicate position of the
occipitotemporal incisure, arrowheads that of the temporolimbic incisure. Circles highlight the anterior and posterior commissures, respectively. For
general aspects concerning anatomical variability, see Ono et al. (1990). For more detailed information concerning sulci, see Amunts et al. (1999),
Caspers et al. (2006), Duvernoy (1999), Malikovic et al. (2012), Tzourio-Mazoyer et al. (2002), Ongur, Ferry, and Price (2003), Petrides (2012), Vogt,
Nimchinsky, Vogt, and Hof (1995), and Weiner et al. (2014).
(a)
(b)
(c)
(d)
(e)
(f)
(g)
(h)
39
Figure 2 Lateral (a, b), medial (c, d), dorsal (e), basal (f), frontal (g), and caudal views (h) of the MNI single subject template (Holmes et al., 1998), on
which gyri have been identified. Sulci are color-coded as in Figure 1. fa, precentral gyrus; fb, superior frontal gyrus; fc, medial frontal gyrus; fd, inferior
frontal gyrus; fe, pars triangularis; ff, pars opercularis; fg, cingulate gyrus; fh, superior cingulate gyrus; fi, paraterminal gyrus; fj, subcallosal gyrus;
fk, superior rostral gyrus; fl, inferior rostral gyrus; fm, gyrus rectus; fn, medial orbital gyrus; fo, posterior orbital gyrus; fp, anterior orbital gyrus;
fq, lateral orbital gyrus; fr, frontomarginal gyrus; pa, postcentral gyrus; pb, subcentral gyrus; pc, supramarginal gyrus; pd, angular gyrus; pe, superior
parietal lobule; pf, paracentral lobule; pg, precuneus; ph, cingulate gyrus, parietal part; ta, superior temporal gyrus; tb, intermediate temporal gyrus; tc,
inferior temporal gyrus; td, temporal pole; te, gyrus ambiens; tf, gyrus semilunaris; tg, parahippocampal gyrus; th, fusiform gyrus (lateral
occipitotemporal gyrus); oa, superior occipital gyrus; ob, middle occipital gyrus; oc, inferior occipital gyrus; od, cuneus; oe, lingual gyrus (medial
occipitotemporal gyrus). For further details, see Figure 1.
(Armstrong, Schleicher, Omram, Curtis, & Zilles, 1995).

From this time on, the GI declines by 18% from a maximal
value of 3.03 to the adult value of 2.95, which is reached at
an age of approximately 23 years (Armstrong et al., 1995;
Figure 5). The folding overshoot was confirmed in a later
MRI study (Pienaar, Fischl, Caviness, Makris, & Grant,
2008). It is presently not clear which mechanisms cause

the overshoot of gyrification. Perinatal cell pruning
(Haydar, Kuan, Flavell, & Rakic, 1999) may play a role,
but the postnatal myelination of input and output fibers
in the white matter of the gyri can also influence the developmental course of cortical folding by increasing the gyral
40
Figure 3 Dorsal view of the MNI single subject template (Holmes et al.,
1998) and photographs of 16 adult human formalin-fixed brains as
examples to visualize intersubject variability in sulcal and gyral patterns.
The gyrification pattern of each human brain appears like an individual
fingerprint.
width while the sulcal depth remains constant (Kochunov

et al., 2005; Magnotta et al., 1999).
The Sylvian fissure and the callosal sulcus appear as the first
sulci in the 14th week of gestation, followed by the olfactory,
calcarine, and parieto-occipital sulci in the 16th week (Chi,
Dooling, & Gilles, 1977). In the 18th week, the cingulate sulcus
and the circular sulcus of the insular cortex are the next to
appear. The folding of the central sulcus is clearly visible in
the 20th week, followed by the superior temporal and collateral sulci in the 23rd week, the precentral sulcus in the 24th
week, the postcentral and superior frontal sulci in the 25th
week, and the intraparietal and middle temporal sulci in the
26th week. The last primary sulci appear in the 27th (lateral
occipital sulcus) and 28th (inferior frontal sulcus) weeks. The
secondary sulci and gyri start to develop between the 32nd and
34th week in the different lobes, whereas the tertiary sulci do
not appear until birth and later (Chi et al., 1977).
Gyrification and Aging

It is a frequently reported observation that sulcal width is
increased in the brains of elderly people. This impression is
substantiated by quantitative analysis of MRI data. It was
found that the sulcal width increased at a rate of approximately
0.7 mm per decade and the sulcal depth decreased at a rate of
approximately 0.4 mm per decade (Kochunov et al., 2005).
Consequently, the correlated changes of both factors lead to
a decrease of the GI. The same authors reported that this

age-related effect on sulcal width was more pronounced in
males than in females in several cortical regions. Interestingly,
the most pronounced age-related decreases of cortical depth
and increases of sulcal width were observed in multimodal
association areas, whereas the unimodal sensory cortices presented the smallest changes (Kochunov et al., 2005). A more
recent study on decreases of gyrification highlights the inferior
parietal lobule as a hot spot for age-related changes in cortical
folding (Hogstrom et al., 2013).
An important relation between the regional preferences of
decreases in gyrification and functional brain organization was
recently reported in a study comparing gyrification within the
default mode network (DMN) during aging (Jockwitz et al.,
2014). It was found that gyrification declines mainly in the
posterior part of the DMN (the posterior cingulate cortex/
precuneus and angular gyrus). In the anterior part of the
DMN (medial prefrontal cortex), such a decline was only
seen in the right hemisphere, whereas in the posterior part
it was detected in both hemispheres. This hot spot of agedependent decline in gyrification of the posterior part of the
DMN compared to its prefrontal part correlates with the agerelated shift in cognitive activity from posterior to anterior
(PASA; Davis, Dennis, Daselaar, Fleck, & Cabeza, 2008). This
posterioranterior shift in GI decline during aging further
supports the generalization of the PASA theory as proposed
by Davis et al. (2008) by structural correlates. Furthermore,
the preference of age-related GI decline to all right hemispheric
parts of the DMN matches the right hemi-aging model as
proposed by Dolcos, Rice, and Cabeza (2002).
Gyrification and Genetics

In contrast to nonhuman primates, in which approximately
70% of the intraspecies phenotypic variance can be attributed
to genetic variation, only 30% of this variance is caused by
heritability in humans (Rogers et al., 2010). Additionally, a
greater influence of environmental over genetic factors regarding
the areas, length, and depth of sulci was also found by comparisons between the brains of mono- and dizygotic human twins
(Bartley, Jones, & Weinberger, 1997; Hasan et al., 2011). The
relatively low genetic determination of gyrification is further
supported by a regionally specific comparison of the prefrontal
cortex between monozygotic and dizygotic twins. It was found
that the monozygotic twins did not present more similarity
concerning their prefrontal GI compared to dizygotic twins
(Hasan et al., 2011). Brain size, however, is more strongly
controlled by genetic factors than gyrification (Bartley et al.,
1997; Hasan et al., 2011). Thus, it can be hypothesized that
two independent sets of selective pressures produce increases in
brain size and gyrification (Rogers et al., 2010).
The Causes of Cortical Folding

The causes of cortical folding are in the center of a longstanding debate. It is clear that the enlargement of the cortical
surface provides the advantage of increasing the number of
cortical columns (modules) but requires folding of the cortex
Multimodal
Multimodal
41
Multimodal
Prefrontal
3.5
3.0
2.5
GI
2.0
1.5
(a)
1.0
(c)
Rostral
Caudal
Variability of
functional
connectivity
GI =
(b)
Length of complete contour
High variability
Low variability
Length of outer contour
(d)
Figure 4 (a) Lateral surface of a human left hemisphere. (b) Drawing of the contour of a coronal section through the human brain at the level
highlighted in (a). The lengths of the complete (red line) and outer (blue line) contours were measured and the gyrification index (GI) was calculated for
each section. (c) Course of the band that covers 95% of the single GI values from the frontal pole to the occipital pole in the left hemisphere of 61 human
brains. The approximate extent of multimodal areas is highlighted. Adapted from Zilles, K., Armstrong, E., Schleicher, A., & Kretschmann, H.-J. (1988).
The human pattern of gyrification in the cerebral cortex. Anatomy and Embryology, 179, 173179. (d) Intersubject variability in resting state functional
connectivity. Blue tones code for values below the global mean and orange tones for values above it. Figure in panel (d) was adapted from Mueller, S.,
Wang, D., Fox, M. D., Yeo, B. T., Sepulcre, J., Sabuncu, M. R., et al. (2013). Individual variability in functional connectivity architecture of the human
brain. Neuron, 77, 586595.
3.25
3
2.75
GI
2.5
2.25
66th80th
week
2
1.75
1.5
1.25
1
10
Birth
200
Age (weeks)
4000
Figure. 5 Ontogenetic development of cortical folding in humans from fetal to adult stages. Age in weeks post conception (birth at 40th week). Data
from Armstrong, E., Schleicher, A., Omram, H., Curtis, M., & Zilles, K. (1995). The ontogeny of human gyrification. Cerebral Cortex, 5, 5663;
Zilles, K., Armstrong, E., Schleicher, A., & Kretschmann, H.-J. (1988). The human pattern of gyrification in the cerebral cortex. Anatomy and Embryology,
179, 173179.
as a consequence of the restricted space in the birth channel,

which limits increases in skull size over a certain level. Thus, a
maximum surface must be packed into a minimum volume
(Mota & Herculano-Houzel, 2012; Welker, 1990). The importance of cortical columns (DeFelipe, 2011) as essential
building blocks is underlined by the fact that gyrification

and the total number of cortical neurons and cortical
volume or thickness are not simply related (HerculanoHouzel, 2011; Herculano-Houzel, Collins, Wong, Kaas, &
Lent, 2008). Regional differences in the thicknesses between
42
more superficial cortical layers (i.e., supragranular layers IIII)

and deeper layers (i.e., infragranular layers VVI) also seem to
be correlated with the intensity of cortical folding (Armstrong
et al., 1991; Richman, Stewart, Hutchinson, & Caviness, 1975).
However, these differences have yet to be comprehensively
studied throughout the human brain and precisely related to
regions of high or low GI values.
Two major hypotheses have been proposed:
The tension-based hypothesis based on the mechanical

properties of fiber tracts connecting cortical areas with
each other (van Essen, 1997, 2007).
The gray matter hypothesis. Here, neural stem and progenitor cell division during ontogeny are a major driving force
leading to an overproportional cortical surface enlargement
compared to a relatively smaller increase in volume
(Kriegstein, Noctor, & Martinez-Cerdeno, 2006).
Axonal growth or retraction depends on tension (Dennerll,

Lamoureux, Buxbaum, & Heidemann, 1989) and this finding
stimulated the tension-based hypothesis (van Essen, 1997, 2007).
The viscoelastic properties of nerve fibers that connect cortical
areas via short- and long-range fiber tracts can, therefore, lead to
folding of the cortical surface. In the human forebrain, tangentially organized corticocortical connections outnumber the radially organized corticosubcortical connections by far, thus
leading to a dominating tangential (relative to the cortical surface) tension within the tissue. An outward-directed folding is
the consequence of this mechanical force (van Essen, 1997).
However, tension is present in not only tangentially but also
radially arranged axons, and tension is not found across the
developing gyri (Xu et al., 2010). Thus, tension cannot pull on
the opposite walls of a gyrus and may not result in a general
outward folding. Complex interactions of different tension
directions may thus influence the regionally specific shape of
folding patterns (Hilgetag & Barbas, 2006; Toro et al., 2008).
Additionally, the heterochronous sequence of fiber tract development and the different regional developmental dynamics
may also be important factors in the mechanical tension-based
hypothesis (Xu et al., 2010). Cortical folding has the advantage
not only of a maximal surface in a minimal volume but also of a
minimized pathway length between the interconnected cortical
areas, which optimizes the speed of signal transmission.
The gray matter hypothesis is based on the fact that neural stem
and transit-amplifying intermediate progenitor cells are found in
the outer subventricular zone of the developing human brains
(Fietz et al., 2010; Hansen, Lui, Parker, & Kriegstein, 2010;
Kriegstein et al., 2006; Lui, Hansen, & Kriegstein, 2011; Rakic,
1995), and this zone expands considerably just before the beginning of gyrification between 11th and 16th weeks of gestation in
humans (Lui et al., 2011). Besides the frequently observed bipolar radial glial cells, a unipolar intermediate radial glial cell was
recently detected within the outer subventricular zone. This cell
type provides by its cell processes a fanlike scaffold that contacts
the pial surface. Immature neurons migrate along these processes,
and thus, the cortical surface and its folding are considerably
increased (Kriegstein et al., 2006; Molnar & Clowry, 2012;
Reillo & Borrell, 2012; Reillo, de Juan, Garcia-Cabezas, & Borrell,
2011). An experimental reduction of the proliferation in the outer
subventricular zone leads to a reduction of the cortical surface
and folding (Reillo et al., 2011).
Experiments in lissencephalic transgenic animals expressing

a stabilized b-catenin in neuronal progenitor cells demonstrated that these changes in the precursor population lead to
a horizontal expansion of the cortical surface and folding,
without increasing cortical thickness (Chenn & Walsh, 2002).
This result further supports the possible role of the gray matter
development in cortical folding.
The subplate zone may also contribute to gyrification
(Kostovic & Rakic, 1990). This zone reaches its largest thickness below the late-maturing association cortices and has
a slow and long-enduring development (Judas, Sedmak,
Pletikos, & Jovanov-Milosevic, 2010; Kostovic & Judas, 2010).
Notably, the secondary and tertiary sulci appear predominantly and late (heterochronicity of cortical folding;
Armstrong et al., 1995) in the region of association cortices,
contribute considerably to the intensity of gyrification in these
regions, and are especially prone to intersubject variability.
We think that the mechanical and the gray matter hypotheses are not necessarily contradictory, but emphasize different
important aspects underlying the increase in cortical surface
and gyrification. Cell proliferation, migration, and maturation
precede and overlap with the generation of connectivity. There
is a developmental window during which both processes can
interact. Simulation of these complex developmental mechanisms based on detailed anatomical and cellular data including
mechanical properties of the tissue and their temporal aspects
is necessary for a comprehensive understanding of the causal
mechanisms of gyrification.
Examples of Altered Gyrification in Neurological

and Psychiatric Diseases
Both reduced gyrification and pathologically increased gyrification have been described in the fetal and postnatal human
brains (Francis et al., 2006; Pang, Atefy, & Sheen, 2008) and
demonstrated in animal models (Chenn & Walsh, 2002).
A severely reduced or lacking gyrification is found in lissencephaly. This condition is caused by disturbances during late
neuronal migration. Various genetic abnormalities, such as
doublecortin (X-linked dominant; Gleeson et al., 1998),
Reelin (autosomal recessive; Bonneau et al., 2002), and
Lissencephaly1 (autosomal dominant; Reiner et al., 1993)
result in classical lissencephaly. Decreased gyrification was
found in epilepsy (Lin et al., 2007), attention-deficit/
hyperactivity disorder (Wolosin, Richardson, Hennessey,
Denckla, & Mostofsky, 2009), dementia (Lebed, Jacova,
Wang, & Beg, 2012), mental retardation (Zhang et al., 2010),
and dyslexia (Casanova, Araque, Giedd, & Rumsey, 2004).
Polymicrogyria is characterized by cortical thinning, an
abnormally high number of small gyri resulting in an increased
gyrification. It has been described in Williams syndrome
(Gaser et al., 2006), autism (Jou, Minshew, Keshavan, &
Hardan, 2010), and schizophrenia (Palaniyappan & Liddle,
2012; Schultz et al., 2013). Polymicrogyria can occur locally
restricted or diffusely distributed in one (preferentially the
right hemisphere if a deletion of 22q11.2 is found; Robin
et al., 2006) or both hemispheres. Polymicrogyria in both
hemispheres, particularly in the frontal and parietal lobes,
was found together with mutations in the G protein-coupled

receptor gene GPR56 (Piao et al., 2002, 2005). Functional
deficits in polymicrogyria can include cognitive impairment,
hemiparesis, and epilepsy (Bearden et al., 2009; Caraballo,
Cersosimo, Mazza, & Fejerman, 2000).
We have here presented only a few examples of the relations
between impaired gyrification and psychiatric and neurological diseases, since the aim of this article is the normal cortical
folding in the human brain.
Acknowledgment
This work was supported by the portfolio theme
Supercomputing and Modeling for the Human Brain of
the Helmholtz Association, Germany.
Competing financial interests: The authors declare that they
have no competing financial interests.

Columns of the Mammalian Cortex; Cortical Surface Morphometry;
Development of the Basal Ganglia and the Basal Forebrain; Embryonic
Postnatal Development of the Cortex: MRI and Genetics; Quantitative
Data and Scaling Rules of the Cerebral Cortex; Sulci as Landmarks;
INTRODUCTION TO METHODS AND MODELING: Cortical
Thickness Mapping.
References
Amunts, K., Schleicher, A., Burgel, U., Mohlberg, H., Uylings, H. B.M, & Zilles, K.
(1999). Brocas region revisited: Cytoarchitecture and intersubject variability.
Armstrong, E., Curtis, M., Buxhoeveden, D. P., Fregoe, C., Zilles, K., Casanova, M. F.,
et al. (1991). Cortical gyrification in the rhesus monkey: A test of the mechanical
folding hypothesis. Cerebral Cortex, 1, 426432.
Armstrong, E., Schleicher, A., Omram, H., Curtis, M., & Zilles, K. (1995). The ontogeny
of human gyrification. Cerebral Cortex, 5, 5663.
Bartley, A. J., Jones, D. W., & Weinberger, D. R. (1997). Genetic variability of human
brain size and cortical gyral patterns. Brain, 120(Pt 2), 257269.
Bearden, C. E., van Erp, T. G., Dutton, R. A., Lee, A. D., Simon, T. J., Cannon, T. D., et al.
(2009). Alterations in midline cortical thickness and gyrification patterns mapped in
children with 22q11.2 deletions. Cerebral Cortex, 19, 115126.
Bonneau, D., Toutain, A., Laquerriere, A., Marret, S., Saugier-Veber, P., Barthez, M. A.,
et al. (2002). X-linked lissencephaly with absent corpus callosum and ambiguous
genitalia (XLAG): Clinical, magnetic resonance imaging, and neuropathological
findings. Annals of Neurology, 51, 340349.
Brodmann, K. (1913). Neue Forschungsergebnisse der Grohirnrindenanatomie mit
besonderer Berucksichtigung anthropologischer Fragen. In A. Witting (Ed.),
Verhandlungen der Gesellschaft Deutscher Naturforscher und Arzte (pp. 200240).
Dresden: Vogel.
Caraballo, R. H., Cersosimo, R. O., Mazza, E., & Fejerman, N. (2000). Focal
polymicrogyria in mother and son. Brain and Development, 22, 336339.
Casanova, M. F., Araque, J., Giedd, J., & Rumsey, J. M. (2004). Reduced brain size and
gyrification in the brains of dyslexic patients. Journal of Child Neurology, 19,
275281.
Caspers, S., Geyer, S., Schleicher, A., Mohlberg, H., Amunts, K., & Zilles, K. (2006).
The human inferior parietal cortex: Cytoarchitectonic parcellation and interindividual
variability. NeuroImage, 33, 430448.
Chenn, A., & Walsh, C. A. (2002). Regulation of cerebral cortical size by control of cell
cycle exit in neural precursors. Science, 297, 365369.
43
Chi, J. G., Dooling, E. C., & Gilles, F. H. (1977). Gyral development of the human brain.
Annals of Neurology, 1, 8693.
Davis, S. W., Dennis, N. A., Daselaar, S. M., Fleck, M. S., & Cabeza, R. (2008). Que
PASA? The posterior-anterior shift in aging. Cerebral Cortex, 18, 12011209.
DeFelipe, J. (2011). The evolution of the brain, the human nature of cortical circuits, and
intellectual creativity. Frontiers in Neuroanatomy, 5, 29.
Dennerll, T. J., Lamoureux, P., Buxbaum, R. E., & Heidemann, S. R. (1989). The
cytomechanics of axonal elongation and retraction. Journal of Cell Biology, 109,
30733083.
Dolcos, F., Rice, H. J., & Cabeza, R. (2002). Hemispheric asymmetry and aging: Right
hemisphere decline or asymmetry reduction. Neuroscience & Biobehavioral
Reviews, 26, 819825.
Duvernoy, H. M. (1999). The human brain: Surface, blood supply, and threedimensional sectional anatomy (2nd ed.). Vienna: Springer.
Elias, H., & Schwartz, D. (1969). Surface areas of the cerebral cortex of mammals
determined by stereological methods. Science, 166, 111113.
Fietz, S. A., Kelava, I., Vogt, J., Wilsch-Brauninger, M., Stenzel, D., Fish, J. L., et al.
(2010). OSVZ progenitors of human and ferret neocortex are epithelial-like and
expand by integrin signaling. Nature Neuroscience, 13, 690699.
Francis, F., Meyer, G., Fallet-Bianco, C., Moreno, S., Kappeler, C., Cabrera Socorro, A.,
et al. (2006). Human disorders of cortical development: From past to present.
European Journal of Neuroscience, 23, 877893.
Gaser, C., Luders, E., Thompson, P. M., Lee, A. D., Dutton, R. A., Geaga, J. A., et al.
(2006). Increased local gyrification mapped in Williams syndrome. NeuroImage, 33,
4654.
Gleeson, J. G., Allen, K. M., Fox, J. W., Lamperti, E. D., Berkovic, S., Scheffer, I., et al.
(1998). Doublecortin, a brain-specific gene mutated in human X-linked
lissencephaly and double cortex syndrome, encodes a putative signaling protein.
Cell, 92, 6372.
Hansen, D. V., Lui, J. H., Parker, P. R., & Kriegstein, A. R. (2010). Neurogenic
radial glia in the outer subventricular zone of human neocortex. Nature, 464,
554561.
Hasan, A., McIntosh, A. M., Droese, U. A., Schneider-Axmann, T., Lawrie, S. M.,
Moorhead, T. W., et al. (2011). Prefrontal cortex gyrification index in twins: An
MRI study. European Archives of Psychiatry and Clinical Neuroscience, 261,
459465.
Haydar, T. F., Kuan, C. Y., Flavell, R. A., & Rakic, P. (1999). The role of cell death in
regulating the size and shape of the mammalian forebrain. Cerebral Cortex, 9,
621626.
Herculano-Houzel, S. (2011). Not all brains are made the same: New views on brain
scaling in evolution. Brain, Behavior and Evolution, 78, 2236.
Herculano-Houzel, S., Collins, C. E., Wong, P., Kaas, J. H., & Lent, R. (2008). The basic
nonuniformity of the cerebral cortex. Proceedings of the National Academy of
Hilgetag, C. C., & Barbas, H. (2006). Role of mechanical factors in the morphology of
the primate cerebral cortex. PLoS Computational Biology, 2, e22.
Hogstrom, L. J., Westlye, L. T., Walhovd, K. B., & Fjell, A. M. (2013). The structure of
the cerebral cortex across adult life: Age-related patterns of surface area, thickness,
and gyrification. Cerebral Cortex, 23, 25212530.
Holmes, C. J., Hoge, R., Collins, L., Woods, R., Toga, A. W., & Evans, A. C. (1998).
Enhancement of MR images using registration for signal averaging. Journal of
Jockwitz, C., Caspers, S., Lux, S., Jutten, K., Lenzen, S., Moebus, S., et al. (2014).
Gyrification changes in Default Mode Network as correlate of its functional
reorganization with age. Proceedings of the 20th Annual Meeting of the Organization
for Human Brain Mapping.
Jou, R. J., Minshew, N. J., Keshavan, M. S., & Hardan, A. Y. (2010). Cortical gyrification
in autistic and Asperger disorders: A preliminary magnetic resonance imaging
study. Journal of Child Neurology, 25, 14621467.
Judas, M., Sedmak, G., Pletikos, M., & Jovanov-Milosevic, N. (2010). Populations of
subplate and interstitial neurons in fetal and adult human telencephalon. Journal of
Anatomy, 217, 381399.
Kochunov, P., Mangin, J. F., Coyle, T., Lancaster, J., Thompson, P., Riviere, D., et al.
(2005). Age-related morphology trends of cortical sulci. Human Brain Mapping, 26,
210220.
Kostovic, I., & Judas, M. (2010). The development of the subplate and thalamocortical
connections in the human foetal brain. Acta Paediatrica, 99, 11191127.
Kostovic, I., & Rakic, P. (1990). Developmental history of the transient subplate zone in
the visual and somatosensory cortex of the macaque monkey and human brain.
Kriegstein, A., Noctor, S., & Martinez-Cerdeno, V. (2006). Patterns of neural stem and
progenitor cell division may underlie evolutionary cortical expansion. Nature
Reviews. Neuroscience, 7, 883890.
44
Lebed, E., Jacova, C., Wang, L., & Beg, F. (2012). Novel surface-smoothing based local
Gyrification index. IEEE Transactions on Medical Imaging, 32(4), 660669.
Lin, J. J., Salamon, N., Lee, A. D., Dutton, R. A., Geaga, J. A., Hayashi, K. M., et al.
(2007). Reduced neocortical thickness and complexity mapped in mesial temporal
lobe epilepsy with hippocampal sclerosis. Cerebral Cortex, 17, 20072018.
Luders, E., Narr, K. L., Bilder, R. M., Szeszko, P. R., Gurbani, M. N., Hamilton, L., et al.
(2008). Mapping the relationship between cortical convolution and intelligence:
Effects of gender. Cerebral Cortex, 18, 20192026.
Luders, E., Narr, K. L., Thompson, P. M., Rex, D. E., Jancke, L., Steinmetz, H., et al.
(2004). Gender differences in cortical complexity. Nature Neuroscience, 7, 799800.
Lui, J. H., Hansen, D. V., & Kriegstein, A. R. (2011). Development and evolution of the
human neocortex. Cell, 146, 1836.
Magnotta, V. A., Andreasen, N. C., Schultz, S. K., Harris, G., Cizadlo, T., Heckel, D.,
et al. (1999). Quantitative in vivo measurement of gyrification in the human brain:
Changes associated with aging. Cerebral Cortex, 9, 151160.
Malikovic, A., Vucetic, B., Milisavljevic, M., Tosevski, J., Sazdanovic, P., Milojevic, B.,
et al. (2012). Occipital sulci of the human brain: Variability and morphometry.
Anatomical Science International, 87, 6170.
Marino, L., Connor, R. C., Fordyce, R. E., Herman, L. M., Hof, P. R., Lefebvre, L., et al.
(2007). Cetaceans have complex brains for complex cognition. PLoS Biology, 5, e139.
atlas of the human brain: Theory and rationale for its development. The International
Consortium for Brain Mapping (ICBM). NeuroImage, 2, 89101.
Molnar, Z., & Clowry, G. (2012). Cerebral cortical development in rodents and primates.
Progress in Brain Research, 195, 4570.
Mota, B., & Herculano-Houzel, S. (2012). How the cortex gets its folds: An inside-out,
connectivity-driven model for the scaling of mammalian cortical folding. Frontiers in
Neuroanatomy, 6, 3.
Mueller, S., Wang, D., Fox, M. D., Yeo, B. T., Sepulcre, J., Sabuncu, M. R., et al. (2013).
Individual variability in functional connectivity architecture of the human brain.
Neuron, 77, 586595.
Ongur, D., Ferry, A. T., & Price, J. L. (2003). Architectonic subdivision of the human
orbital and medial prefrontal cortex. Journal of Comparative Neurology, 460,
425449.
Ono, M., Kubik, S., & Abernathey, C. D. (1990). Atlas of the cerebral sulci. New York:
Georg Thieme Verlag.
Palaniyappan, L., & Liddle, P. F. (2012). Aberrant cortical gyrification in schizophrenia:
A surface-based morphometry study. Journal of Psychiatry and Neuroscience, 37,
399406.
Pang, T., Atefy, R., & Sheen, V. (2008). Malformations of cortical development.
Neurologist, 14, 181191.
MNI stereotaxic space. Amsterdam: Academic Press.
Piao, X., Basel-Vanagaite, L., Straussberg, R., Grant, P. E., Pugh, E. W., Doheny, K., et al.
(2002). An autosomal recessive form of bilateral frontoparietal polymicrogyria maps to
chromosome 16q12.2-21. American Journal of Human Genetics, 70, 10281033.
Piao, X., Chang, B. S., Bodell, A., Woods, K., Benzeev, B., Topcu, M., et al. (2005).
Genotype-phenotype analysis of human frontoparietal polymicrogyria syndromes.
Annals of Neurology, 58, 680687.
Pienaar, R., Fischl, B., Caviness, V., Makris, N., & Grant, P. E. (2008). A methodology
for analyzing curvature in the developing brain from preterm to adult. International
Journal of Imaging Systems and Technology, 18, 4268.
Pillay, P., & Manger, P. R. (2007). Order-specific quantitative patterns of cortical
gyrification. European Journal of Neuroscience, 25, 27052712.
Rakic, P. (1995). A small step for the cell, a giant leap for mankind: A hypothesis of
neocortical expansion during evolution. Trends in Neurosciences, 18, 383388.
Reillo, I., & Borrell, V. (2012). Germinal zones in the developing cerebral cortex of
ferret: Ontogeny, cell cycle kinetics, and diversity of progenitors. Cerebral Cortex,
22, 20392054.
Reillo, I., de Juan, R. C., Garcia-Cabezas, M. A., & Borrell, V. (2011). A role for
Reiner, O., Carrozzo, R., Shen, Y., Wehnert, M., Faustinella, F., Dobyns, W. B., et al.
(1993). Isolation of a Miller-Dieker lissencephaly gene containing G protein betasubunit-like repeats. Nature, 364, 717721.
Richman, D. P., Stewart, R. M., Hutchinson, J. W., & Caviness, V. (1975). Mechanical
model of brain convolutional development. Science, 189, 1821.
Rilling, J. K., & Insel, T. R. (1999). The primate neocortex in comparative
perspective using magnetic resonance imaging. Journal of Human Evolution, 37,
191223.
Robin, N. H., Taylor, C. J., McDonald-McGinn, D. M., Zackai, E. H., Bingham, P.,
Collins, K. J., et al. (2006). Polymicrogyria and deletion 22q11.2 syndrome:
Window to the etiology of a common cortical malformation. American Journal of
Medical Genetics. Part A, 140, 24162425.
Rogers, J., Kochunov, P., Zilles, K., Shelledy, W., Lancaster, J., Thompson, P., et al.
(2010). On the genetic architecture of cortical folding and brain volume in primates.
Schultz, C. C., Wagner, G., Koch, K., Gaser, C., Roebel, M., Schachtzabel, C., et al.
(2013). The visual cortex in schizophrenia: Alterations of gyrification rather than
cortical thickness-a combined cortical shape analysis. Brain Structure and Function,
218, 5158.
Thompson, P. M., Schwartz, C., Lin, R. T., Khan, A. A., & Toga, A. W. (1996).
Three-dimensional statistical analysis of sulcal variability in the human brain.
Toro, R., Perron, M., Pike, B., Richer, L., Veillette, S., Pausova, Z., et al. (2008).
Brain size and folding of the human cerebral cortex. Cerebral Cortex, 18,
23522357.
van Essen, D. C. (1997). A tension-based theory of morphogenesis and compact wiring
in the central nervous system. Nature, 385, 313318.
van Essen, D. C. (2007). Cerebral cortical folding patterns in primates: Why they vary
and what they signify. In J. H. Kaas (Ed.), Evolution of nervous systems
(pp. 267276). Amsterdam: Elsevier.
Vogt, B. A., Nimchinsky, E. A., Vogt, L., & Hof, P. R. (1995). Human cingulate cortex:
Surface features, flat maps, and cytoarchitecture. Journal of Comparative Neurology,
359, 490506.
and functional divisions of human ventral temporal cortex. NeuroImage, 84,
453465.
Welker, W. (1990). Why does cerebral cortex fissure and fold? A review of determinants
of gyri and sulci. In E. G. Jones & A. Peters (Eds.), Comparative structure and
evolution of cerebral cortex (pp. 3136). New York: Plenum Press.
Wolosin, S. M., Richardson, M. E., Hennessey, J. G., Denckla, M. B., & Mostofsky, S. H.
(2009). Abnormal cerebral cortex structure in children with ADHD. Human Brain
Mapping, 30, 175184.
Xu, G., Knutsen, A. K., Dikranian, K., Kroenke, C. D., Bayly, P. V., & Taber, L. A. (2010).
Axons pull on the brain, but tension does not drive cortical folding. Journal of
Biomechanical Engineering, 132, 071013.
Zhang, Y., Zhou, Y., Yu, C., Lin, L., Li, C., & Jiang, T. (2010). Reduced cortical
folding in mental retardation. AJNRAmerican Journal of Neuroradiology, 31,
10631067.
Zilles, K., Armstrong, E., Moser, K. H., Schleicher, A., & Stephan, H. (1989). Gyrification
in the cerebral cortex of primates. Brain, Behavior and Evolution, 34, 143150.
Zilles, K., Armstrong, E., Schleicher, A., & Kretschmann, H.-J. (1988). The human pattern
of gyrification in the cerebral cortex. Anatomy and Embryology, 179, 173179.
Zilles, K., Schleicher, A., Langemann, C., Amunts, K., Morosan, P.,
Palomero-Gallagher, N., et al. (1997). Quantitative analysis of sulci in the human
cerebral cortex: Development, regional heterogeneity, gender difference, asymmetry,
intersubject variability and cortical architecture. Human Brain Mapping, 5,
218221.
Sulci as Landmarks
J-F Mangin, CEA Saclay, Gif-sur-Yvette, France
G Auzias, Aix-Marseille Universite, Marseille, France
O Coulon, Aix-Marseille Universite, Marseille, France
ZY Sun, CEA Saclay, Gif-sur-Yvette, France
D Rivie`re, CEA Saclay, Gif-sur-Yvette, France
J Regis, CHU La Timone, Marseille, France
Matching brains is a basic need in neurosciences. Brain architecture provides the guideline for this matching, because architecture stands as the topology of the underlying neural network.
Provided that the brains to be matched come from the same
species, this topology is supposed to be largely invariant across
standard subjects. With regard to the cortical surface, structural
architecture mainly amounts to multiple overlapping parcellations defining homogeneous areas for various microstructural
features (Amunts et al., 2014). Such parcellations can stem, for
instance, from cytoarchitectony, myeloarchitectony, receptor
densities, or structural connectivity profiles. One of the goals
of matching brains is the study of functional architecture, which
is supposed to fit in a way or another structural architecture.
In neuroimaging, matching brains is usually understood as
spatially normalizing images of these brains. Each brain is
warped toward a so-called standard space in which the localization of architectural modules is supposed to be stable across
subjects. Unfortunately, the T1-weighted MR scans classically
used to perform this spatial normalization include very few
architectural features relative to the cerebral cortex. The main
information included in these scans is cortical thickness and
the morphology of cortical folds. Since the link between the
cortical folding pattern and architecture is unclear except in
primary areas (Welker, 1988), the earliest spatial normalization techniques did not strongly focus on aligning cortical
sulci. This situation resulted also from the difficulties raised
by the large variability of the folding pattern across individuals.
The template brains driving the warping to the standard space
were fuzzy brain images obtained by averaging a large number
of normalized brain images without sulcal alignment. Hence,
architectural compliance of spatial normalization was poor at
the onset of the field of neuroimaging.
During the last years, however, impressive advances have
been achieved by spatial normalization technology with regard
to sulcal alignment. While our understanding of the architectural value of sulci is still weak, it did make sense to use them as
a proxy, as long as better architectural clues were missing.
Standard approaches like DARTEL in 3-D (Ashburner, 2007)
or FreeSurfer and CIVET for the cortical surface (Fischl, Sereno,
Tootell, & Dale, 1999; Lyttelton, Boucher, Robbins, & Evans,
2007) are very efficient at aligning automatically primary sulci,
which were shown to improve the alignment of primary architectonic areas (Fischl et al., 2008). Recent advances in neuroimaging will now lead to further improvement in the
architectural compliance of spatial normalization using multimodal data, for instance, myelin maps, or diffusion-based
connectivity information but also functional landmarks that
can be easier to obtain than architectural landmarks in some
areas (Robinson et al., 2014). But refining the use of the

cortical folding pattern is still possible (Yeo et al., 2010),
which is the topic of this article.
Defining Sulci and Gyri

While a hallmark of the human brain is the circonvoluted
shape of its cerebral cortex, the detailed road map of its folding
pattern is rarely a topic of interest. Folding is often only considered as an evolutionary trick increasing the surface area of
the cortex without impacting the skull volume. From this point
of view, the detailed topography of the folding pattern is
meaningless. The medicine atlases provide the nomenclature
of the primary sulci that are presented as interesting landmarks
to distinguish large brain modules like the lobes and gyri or to
localize primary functional areas. These primary sulci are the
first to develop during ontogeny. For instance, the central
sulcus (see Figure 1) delimits the frontal and parietal lobes
and hosts, respectively, primary sensory and primary motor
areas in its two walls. While actual modules of the brain are
not sulci but gyri, morphological descriptions usually focus on
sulci because they are geometrically well defined. Most gyri are
delimited by two parallel sulci, but this definition fades away at
the level of sulcal extremities or in case of sulcal interruption.
Surprisingly, the anatomical literature is rather sparse of rules
to overcome the variability of the cortical sulcal topography
across individuals. This variability, however, is very disturbing
when trying to project an atlas of the sulci onto a specific brain,
which is illustrated in Figures 13. Furthermore, the most comprehensive description of the variability of the folding patterns
has been provided for a set of only 25 brains (Ono, Kubik, &
Abarnathey, 1990), and many configurations have never been
described. Long primary sulci can be split into pieces by annectant gyri (Regis et al., 2005) (see Figure 6(a)). These pieces can
be recombined in nonstandard ways to create unusual folding
patterns without clear link with the anatomical nomenclature.
Furthermore, primary sulci are surrounded by numerous shallower folds increasing the complexity to be decrypted. While an
exquisite nomenclature of these secondary and tertiary folds has
been recently proposed (Petrides, 2012), comprehensive studies
of their variability across individuals are limited to a few areas
(Segal & Petrides, 2012; Zlatkina & Petrides, 2010).
After a careful observation of Figures 1 and 2, it becomes
clear that the reliable identification of sulci is a challenge. We
still miss a gold standard method providing a clear-cut consensual solution whatever the configuration. The following sections describe several strategies aiming at the emergence of
http://dx.doi.org/10.1016/B978-0-12-397025-1.00198-6
45
46
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Sulci as Landmarks
Figure 1 Twelve left lateral cortical surfaces with elementary folds manually labeled according to the sulcus atlas of BrainVISA (http://brainvisa.info)
(Perrot, Rivie`re et al. 2011). Reproduced from Perrot, M., Rivie`re, D., & Mangin, J. F. (2011). Cortical sulci recognition and spatial normalization.
such a method. They rely on various tools from computational

anatomy facilitating the explicit manipulation of cortical folds.
These tools support research programs aiming at testing systematically the links between the folding process and architecture, which probably differs between primary and secondary
folds. Note that in spite of our current lack of understanding of
these links, the variability of the geometry of the sulci is already
considered as a proxy of the underlying architectural variability, which is exploited for the search for developmental biomarkers (Mangin, Jouvent, & Cachia, 2010). For instance, in
epilepsy, it was shown that abnormal in utero development
leading to dysplasia can create a signature in the folding pattern (Regis et al., 2011). In schizophrenia, the shape of the
superior temporal sulcus in the right analog of Wernickes area
predicts hallucination phenomenology (Plaze et al., 2011). In
preschoolers, the folding pattern of the midcingulate cortex
influences cognitive control abilities (Borst et al., 2014).
Explicit Sulcal Constraints in Spatial Normalization

At the time where standard spatial normalization was not
satisfying in terms of gyral matching, some teams have developed alternative techniques explicitly aligning primary sulci
drawn manually on 3-D rendering of the brains (Thompson &

Toga, 1996). Whatever the progresses achieved by modern normalization tools, imposing explicitly sulcal-based constraints is
still useful to deal safely with unusual folding patterns (Van
Essen, 2012). Thanks to dedicated computer vision approaches,
it is now possible to define automatically more than 120 cortical
sulci (Perrot, Rivie`re, & Mangin, 2011) in order to provide them
to a sulcal-based normalization framework (Auzias et al., 2011)
(see Figure 4). The automatic recognition process is not errorprone and can be questioned, but once the folds have been
extracted using a computational technique (Mangin, Frouin,
Bloch, Regis, & Lopez-Krahe, 1995), they can be matched manually to any nomenclature of sulci in a reasonable time, according to the needs. Now that such a versatile framework has been
designed, the open issue is as follows: what are the sulci to be
aligned across brains?
While the interest of imposing the alignment of sulci in
primary areas has been proven (Fischl et al., 2008), the question is largely opened elsewhere. Future work will lead to assess
one by one the added value of each sulcus in the normalization
process, relative to its capacity at improving the alignment of
architectural data like postmortem architectonic maps or
in vivo fMRI maps (see Figure 4). In a context where the
amount of information planned to be used for normalization
Figure 2 Twelve left mesial cortical surfaces processed like for Figure 1.
F.C.L.a.
F.C.L.r.ant.
F.C.L.r.diag.
F.C.L.r.sc.ant.
F.C.M.ant.
F.Cal.ant.-Sc.Cal.
F.I.P.Po.C.inf.
F.I.P.r.int.l
F.P.O.
OCCIPITAL
S.C.
S.Call.
S.F.inf.
S.F.int.
S.F.marginal.
S.F.orbitaire.
S.F.sup.
S.Li.ant.
S.O.T.lat.ant.
S.O.T.lat.med.
S.O.p.
S.Or.
S.Pa.sup.
S.Pe.C.inf.
S.Pe.C.marginal.
S.Pe.C.sup.
S.R.inf.
S.T.i.ant.
S.T.pol.
S.T.s.ter.asc.ant.
S.p.C.
ventricle
Anterior lateral fissure

Anterior ramus of the lateral fissure
Diagonal ramus of the lateral fissure
Anterior sub-central ramus of the lateral fissure
Calloso-marginal anterior fissure
Calcarine fissure
Superior postcentral intraparietal superior sulcus
Primary intermediate ramus of the intraparietal sulcus
Parieto-occipital fissure
Lobe occipital
Central sulcus
Subcallosal sulcus
Inferior frontal sulcus
Infernal frontal sulcus
Marginal frontal sulcus
Orbital frontal sulcus
Superior frontal sulcus
Anterior intralingual sulcus
Anterior occipito-temporal lateral sulcus
Median occipito-temporal lateral sulcus
Occipito-polar sulcus
Orbital sulcus
Superior parietal sulcus
Inferior precentral sulcus
Marginal precentral sulcus
Superior precentral sulcus
Inferior rostral sulcus
Anterior inferior temporal sulcus
Polar temporal sulcus
Anterior terminal ascending branch of the superior temporal sulcus
Paracentral sulcus
Ventricle
Figure 3 The nomenclature used in Figures 1 and 2.
F.C.L.p.
F.C.L.r.asc.
F.C.L.r.retroC.tr.
F.C.L.r.sc.post.
F.C.M.post.
F.Coll.
F.I.P.
F.I.P.r.int.2
INSULA
S.C.LPC.
S.C.sylvian.
S.Cu.
S.F.ing.ant.
S.F.inter.
S.F.median.
S.F.polaire.tr.
S.GSM.
S.Li.post.
S.O.T.lat.int.
S.O.T.lat.post.
S.Olf.
S.Pa.int.
S.Pa.t.
S.Pe.C.inter.
S.Pe.C.median.
S.Po.C.sup.
S.Rh.
S.T.i.post.
S.T.s.
S.T.s.ter.asc.post.
S.s.P.
Posterior lateral fissure

Ascending ramus of the lateral fissure
Retro central transverse ramus of the lateral fissure
Posterior sub-central ramus of the lateral fissure
Calloso-marginal posterior fissure
Collateral fissure
Intraparietal sulcus
Secondary intermediate ramus of the intraparietal sulcus
Insula
Paracentral lobule central sulcus
Central sylvian sulcus
Cuneal sulcus
Anterior inferior frontal sulcus
Intermediate frontal sulcus
Median frontal sulcus
Polar frontal sulcus
Sulcus of the supra-marginal gyrus
Posterior intra-lingual sulcus
Internal occipito-temporal lateral sulcus
Posterior occipito-temporal lateral sulcus
Olfactory sulcus
Internal parietal sulcus
Transverse parietal sulcus
Intermediate precentral sulcus
Median precentral sulcus
Superior precentral sulcus
Rhinal sulcus
Posterior inferior temporal sulcus
Posterior terminal ascending branch of the superior temporal sulcus
Sub-parietal sulcus
47
48
IT 1
S1
Affine
Dartel
S2
IT 2
...
Disco
Dartel
IT Q
SN
t
Disco
4
(a)
(b)
(c)
Figure 4 Sulcal-driven 3-D spatial normalization. (a) Iterative refinement of a group-based sulcal template aligning individual simplified sulcal imprint.
(b) Detailed illustration in the central sulcal area using five individuals and three alternative alignment procedures. Note that explicit sulcal constraints prevent
mismatch. (c) Group-level activation maps obtained in the left hemisphere for extension of the right wrist for DARTEL (Ashburner, 2007) and DISCO
(Auzias et al., 2011). Maps from ten subjects are superimposed on the corresponding mean structural image computed for each method; t 4.0, p 0.0001
voxel-level uncorrected (Pizzagalli, Auzias, Delon-Martin, & Dojat, 2013). Explicit sulcal constraints improve t values and activation size.
is rapidly increasing, it would be important to discard the sulci

generating misleading constraints. A seminal work in this
direction has been achieved using machine learning techniques to tune the influence of the different folds in the context
of surface-based normalization (Yeo et al., 2010).
In nonprimary areas, the number of studies reporting
strong links between folding pattern and functional maps is
very low (Amiez, Kostopoulos, Champod, & Petrides, 2006;
Watson et al., 1993). Interestingly, one recent study reports
such links in the fusiform area not only with functional maps
but also with postmortem cytoarchitectonic maps (Weiner
et al., 2014). In our opinion, this global lack of knowledge
reveals the difficulty of this kind of investigations more than
the absence of link. The variability of the folding patterns in
nonprimary areas coupled with the difficult inference of individual activation maps is a huge impediment. Advanced dedicated software will help to clarify the situation.
The fact that a lot of architectonic transitions are not
marked by a fold has sometime been raised to advocate for a
poor architectural value of the folding pattern (Roland et al.,
1997). But none of the architectural hypotheses about the
causes of the folding imposes a one to one systematic relationship (Zilles, Palomero-Gallagher, & Amunts, 2013). For
instance, the idea that a protomap of the primary sulcogyral
organization with architectural flavor may exist in the outer
subventricular zone (Reillo, de Juan Romero, Garca-Cabezas,
& Borrell, 2011) or in the subplate (Kostovic & Rakic, 1990) of
the developing gyrencephalic brains would not forbid further
architectonic differentiation to occur inside primary gyri.
Another disturbing observation is the fact that the bottom
of some folds does not correspond to any architectonic borderline (Roland et al., 1997). But such folds could provide
clues about other levels of architectural segregations, related,
for instance, to connectivity profiles (Welker, 1988). The

tension-based hypothesis, which assumes that mechanical
properties of the fiber tracts are one of the causes of the folding
process, would support this idea (Van Essen, 1997). In front of
the complexity of the phenomena driving the cortical folding
process, a pragmatic approach seems mandatory. Comparing
sulcal-based normalizations using different subsets of sulci
could help decipher the contribution of each causal hypothesis
to the folding dynamics.
Patterns and Manifolds

Forcing the alignment of a sulcus across a group of subjects
raises a lot of issues. For instance, it is unclear whether the
putative associated architectural landmarks are related only to
the bottom of the sulcus or also to the top of the walls of the
sulci or even to the top of the delimited gyri. Furthermore, as
illustrated in Figures 1 and 2, a sulcus can have very different
patterns across brains. These patterns are related, for instance,
to variable interruptions or branches (Ochiai et al., 2004). In
the normalization approach described in Figure 4, branches
are automatically pruned out, and the constraint acts only on
the sulcal bottom and top lines. Nevertheless, because of interruptions, the point to point alignment between two sulcal
bottoms is an ill-posed problem that is currently overcome
through regularization of the deformation field: the warping
between the two sulci has to be very smooth and cannot afford
aligning perfectly all the details of the sulcal shapes (Auzias
et al., 2011). When a sulcus is interrupted by an annectant
gyrus (see Figure 6(a)), the two sulcal pieces often appear as
two parallel sulci at the level of the interruption. During

development, the folding process acts independently for each
piece that leads to elongation without match in continuous
sulci. The regularization of the warping deformation prevents
the spurious alignment of these supplementary parts. Similarly, manual approaches to the definition of sulcal constraints
impose smooth continuous drawing at the level of interruptions (Thompson & Toga, 1996).
Nevertheless, understanding the potential architectural
value of the different sulcal patterns is of key interest for
improving normalization. The regularization strategy mentioned earlier has few chances to be optimal in terms of architecture alignment. Hence, we have to learn explicitly how to
match different patterns to be compliant with architecture. For
this purpose, the recent success of multitemplate-based segmentation methods is suggesting a two-level strategy. This
success shows that registration techniques provide more meaningful alignment when dealing with similar patterns. Hence,
for each sulcus, normalization should be applied independently in subgroups of subjects with the same sulcal pattern,
leading to several independent standard spaces. Performing
independent group analysis of functional or architectonic
maps in each of this space would lead to pattern-specific architectural maps, as illustrated by the seminal work on the fusiform gyrus (Weiner et al., 2014). Finally, a second stage of
meta-alignment informed by architecture can be developed to
bridge the gap between these pattern-specific standard spaces.
Note that this meta-alignment stage may have to give up on
using the usual diffeomorphism framework whenever different
49
morphological patterns reveal noncompatible spatial embedding of the underlying architecture.

Applying this strategy requires the definition of patterns in
the spirit of what was done for 25 brains in the atlas of Ono
et al. (1990). Automatic data mining techniques have been
designed to extend the work of Ono to larger datasets in
order to obtain a reliable estimation of frequent sulcal patterns
(Coulon & Fonov, 2012; Sun, Perrot, Tucholka, Rivie`re, &
Mangin, 2009). Applying nonsupervised clustering to
thousands of brains, they aim at providing an exhaustive dictionary of templates of sulcal patterns to be used when designing the multitemplate normalization strategy mentioned
earlier. Several complex issues have to be addressed. First,
what should be the optimal scale for these local templates of
patterns? Ambiguities in sulcal recognition lead to split the
global folding pattern into groups of sulci minimizing intergroup mismatch rather than dealing with sulci one by one.
Second, once local templates of patterns and architecturally
compliant alignments between them have been defined, how
does one build a global standard space?
The concept of sulcal pattern is relatively easy to understand:
for instance, the central sulcus exists either as one single continuous furrow or as a split furrow in case of interruption at the level
of the middle frontoparietal pli de passage (Regis et al., 2005). In
practice, clustering techniques are challenged because of the
existence of continuous variations from one pattern to another.
With regard to the central sulcal interruption, for instance, the pli
de passage can be more or less buried, leading to a shape
Isomap axis
Weights 1:
0.1
0.3
0.99 0.85 0.4
0.06
Weights 2:
Weighted SPAM:
Iso-surface
of the weighted SPAM:
Average 1
Average 2
Hand
motion
Silent reading
Figure 5 Pattern-specific templates. Isomap manifold learning algorithm captures a 1-D approximation of the high-dimensional space spanned by the
central sulcus. Moving averages of the sulcal morphology or of registered individual fMRI maps can be computed along this manifold to get patternspecific templates (Sun, Pinel, et al., 2012). Here, using 252 subjects, the position of the putative hand knob in the pattern-specific template moves
dorsally from one side to the other side of the axis, while a second lower knob appears. The corresponding motor activation template follows the hand
knob, confirming that this well-known functional landmark holds even for extreme configurations. A reading activation template extends toward
premotor areas while the second knob appears, which could provide clues about the architectural value of this second landmark.
50
continuum between the interrupted configuration and the configuration with a very deep pli de passage. Hence, defining the
optimal number of patterns is difficult. As an alternative, it was
proposed to capture a low-dimensional manifold approximation of the high-dimensional space spanned by each sulcus (Sun,
Kloppel, et al., 2012), using Isomap algorithm, a modern version
of multidimensional scaling (Tenenbaum, de Silva, & Langford,
2000). The multitemplate-based strategy mentioned earlier has
been directly extended to this manifold strategy as illustrated in
Figure 5 (Sun, Pinel, et al., 2012). The manifold approach refines
the multitemplate strategy because it provides the transmutation
of the architectural templates along with the transmutation of
morphological patterns, which is a guideline for the second-level
alignment.
Sulcal Roots and Sulcal Pits

Primary sulcal interruption is a major difficulty for spatial
normalization whatever the strategy. The unusual fold recombinations resulting from these interruptions can puzzle the
(a1)
(a3)
(a2)
(c2)
(b)
(c1)
best experts of cortical morphology. These interruptions result

from the unusual development of annectant gyri usually buried in the depth of the sulci. Mapping these gyri often called pli
de passage (see Figure 6(a)) leads to question the scale chosen
by the first anatomists who coined the sulcal nomenclature.
Looking for an alphabet to perform a syntactic analysis of the
variability of the folding patterns led to propose the concept of
sulcal roots, indivisible atomic folding entities supposed to be
stable across subjects (Regis, 1994; Regis et al., 2005). Sulcal
roots are supposed to emerge as the primal sketch of the sulci
during development. Qualitative maps of sulcal roots were
proposed as a synthesis of embryology and pli de passage
maps (see Figure 6(b)).
Recent works on the geometry of the cortical surface have
put forward a sibling concept called sulcal pits, namely, the
deepest points of the folding pattern (Im et al., 2010; Lohmann,
von Cramon, & Colchester, 2008) (see Figure 6(c)). Sulcal pit
maps and sulcal root maps are highly similar, which is not
surprising. Note, however, that we do not know enough about
the folding process to guarantee that the deepest points are
stationary on the cortical surface during development. For
(d1)
(d2)
Figure 6 Sulcal roots and sulcal pits. (a) Qualitative maps of the pli de passage or annectant gyri leading to propose the concept of sulcal roots, the
atoms of the folding pattern supposed to stem from ontogeny (Regis, 1994). (b) A map of the lateral sulcal roots for a brain oriented according to
Talairach space (Regis et al., 2005). (c) A group map of sulcal pits, the deepest points of the folding pattern in adults (Im et al., 2010). (d) A group map of
sulcal pits in one-year-old infants (Meng, Li, Lin, Gilmore, & Shen, 2014).
51
Figure 7 Meridians and parallels. Top row: Extracting sulcal bottom lines using Morphologist pipeline of BrainVISA. Middle row left: Model of cortical
sulcal organization in meridians and parallels; center: general principle of the Hip-Hop method (Auzias et al., 2013); right: a cortical surface with sulcal
lines, flat harmonic mapping f of the same surface (sulcal lines and mean curvature of the original surface), result of the registration with the model
(mapping g), resulting coordinate system. Bottom row: sulcal lines of 62 subjects in the rectangular domain after harmonic mapping f; same after
registration with the model; same on the average surface of the 62 subjects.
instance, they could slide along the sulcal bottom. Hence, emerging studies with premature babies and infants are of high interest
(Lefe`vre et al., 2009; Meng et al., 2014; Operto & Auzias, 2012).
These mind-opening concepts provide new ways to explore
the links between morphology and architecture. For instance,
sulcal root and sulcal pit maps reveal striking alignments with
the global geometry of the cerebral cortex. This led to design
dedicated coordinate systems mimicking latitude and longitude on Earth (Auzias et al., 2013; Clouchoux et al., 2010;
Toro & Burnod, 2003) (see Figure 7). The meridians and
parallels underlying these systems can be observed in the cortex of a lot of mammals (Welker, 1988) and are supposed to
stem from phylogeny and ontogeny. They could even have an
analog in white matter organization (Wedeen et al., 2012).
Hence, they could have a strong architectural content.
la Recherche (ANR-09-BLAN-0038-01 BrainMorph and ANR12JS03-001-01 MoDeGy).
Acknowledgments
Amiez, C., Kostopoulos, P., Champod, A. S., & Petrides, M. (2006). Local morphology
predicts functional organization of the dorsal premotor region in the human brain.
The Journal of Neuroscience, 26(10), 27242731.
Amunts, K., Hawrylycz, M. J., Van Essen, D. C., Van Horn, J. D., Harel, N., Poline, J. B.,
et al. (2014). Interoperable atlases of the human brain. NeuroImage, 99, 525532.
This work was supported by the European FET flagship project

Human Brain Project (SP2), the French Agence Nationale de

Language; Development of the Basal Ganglia and the Basal Forebrain;
Embryonic and Fetal Development of the Human Cerebral Cortex; Fetal
and Postnatal Development of the Cortex: MRI and Genetics;
Gyrification in the Human Brain; INTRODUCTION TO METHODS
AND MODELING: Automatic Labeling of the Human Cerebral Cortex;
Sulcus Identification and Labeling.
References
52

38(1), 95113.
Auzias, G., Colliot, O., Glaune`s, J. A., Perrot, M., Mangin, J. F., Trouve, A., et al. (2011).
Auzias, G., Lefe`vre, J., Le Troter, A., Fischer, C., Perrot, M., Regis, J., et al. (2013).
Model-driven harmonic parameterization of the cortical surface: HIP-HOP. IEEE
Borst, G., Cachia, A., Vidal, J., Simon, G., Fischer, C., Pineau, A., et al. (2014). Folding
of the anterior cingulate cortex partially explains inhibitory control during
childhood: A longitudinal study. Developmental Cognitive Neuroscience, 9,
126135.
Clouchoux, C., Rivie`re, D., Mangin, J. F., Operto, G., Regis, J., & Coulon, O. (2010).
Model-driven parameterization of the cortical surface for localization and intersubject matching. NeuroImage, 50(2), 552566.
Coulon, O., Fonov, V., Mangin, J. -F., & Collins, D. L. (2012). Atlas-based clustering of
sulcal patterns Application to the left inferior frontal sulcus. In: Proceedings of the
ninth IEEE international symposium on biomedical imaging (ISBI) (pp. 426429).
Barcelona: IEEE.
19731980.
Fischl, B., Sereno, M. I., Tootell, R. B., & Dale, A. M. (1999). High-resolution
intersubject averaging and a coordinate system for the cortical surface. Human Brain
Mapping, 8(4), 272284.
Im, K., Jo, H. J., Mangin, J.-F., Evans, A. C., Kim, S. I., & Lee, J.-M. (2010). Spatial
distribution of deep sulcal landmarks and hemispherical asymmetry on the cortical
surface. Cerebral Cortex, 20(3), 602611.
the visual and somatosensory cortex of the macaque monkey and human brain. The
Journal of Comparative Neurology, 297(3), 441470.
Lefe`vre, J., Leroy, F., Khan, S., Dubois, J., Huppi, P., Baillet, S., et al. (2009).
Identification of growth seeds in the neonate brain through surfacic
Helmholtz decomposition. Information Processing in Medical Imaging, 5636,
252263.
Lohmann, G., von Cramon, D. Y., & Colchester, A. C. (2008). Deep sulcal landmarks
provide an organizing framework for human cortical folding. Cerebral Cortex, 18(6),
14151420.
Lyttelton, O., Boucher, M., Robbins, S., & Evans, A. (2007). An unbiased iterative group
registration template for cortical surface analysis. NeuroImage, 34(4), 15351544.
Mangin, J.-F., Frouin, V., Bloch, I., Regis, J., & Lopez-Krahe, J. (1995). From 3D
magnetic resonance images to structural representations of the cortex topography
using topology preserving deformations. Journal of Mathematical Imaging and
Vision, 5(4), 297318.
Mangin, J. F., Jouvent, E., & Cachia, A. (2010). In-vivo measurement of cortical
morphology: Means and meanings. Current Opinion in Neurology, 23(4), 359367.
Meng, Y., Li, G., Lin, W., Gilmore, J. H., & Shen, D. (2014). Spatial distribution and
longitudinal development of deep cortical sulcal landmarks in infants. NeuroImage,
100, 206218.
Ochiai, T., Grimault, S., Scavarda, D., Roch, G., Hori, T., Riviere, D., et al. (2004). Sulcal
pattern and morphology of the superior temporal sulcus. NeuroImage, 22(2),
706719.
Ono, M., Kubik, S., & Abarnathey, C. D. (1990). Atlas of the cerebral sulci. New York:
Georg Thieme.
Operto, G., Auzias, G.,Le Troter, A., Perrot, M., Riviere, D., Dubois, J., et al. (2012).
brain. In: Proceedings of the ninth IEEE international symposium on Biomedical
Imaging (ISBI) (pp. 422425). Barcelona: IEEE.
Perrot, M., Rivie`re, D., & Mangin, J. F. (2011). Cortical sulci recognition and spatial
normalization. Medical Image Analysis, 15(4), 529550.
MNI stereotaxic space. New York: Academic Press.
Pizzagalli, F., Auzias, G., Delon-Martin, C., & Dojat, M. (2013). Local landmark
alignment for high-resolution fMRI group studies: Toward a fine cortical
investigation of hand movements in human. Journal of Neuroscience Methods,
218(1), 8395.
Plaze, M., Paille`re-Martinot, M.-L., Penttila, J., Januel, D., De Beaurepaire, R.,
Bellivier, F., et al. (2011). Where do auditory hallucinations come from? A brain
morphometry study of schizophrenia patients with inner or outer space
hallucinations. Schizophrenia Bulletin, 37(1), 212.
Regis, J. (1994). Deep sulcal anatomy and functional mapping of the cerebral cortex (in
french), MD Thesis, Universite dAix-Marseille.
Regis, J., Mangin, J., Ochiai, T., Frouin, V., Riviere, D., Cachia, A., et al. (2005). "Sulcal
root" generic model: A hypothesis to overcome the variability of the human cortex
folding patterns. Neurologia Medico-Chirurgica, 45(1), 117.
Regis, J., Tamura, M., Park, M., McGonigal, A., Riviere, D., Coulon, O., et al. (2011).
Subclinical abnormal gyration pattern, a potential anatomic marker of epileptogenic
zone in patients with magnetic resonance imaging-negative frontal lobe epilepsy.
Neurosurgery, 69(1), 8093.
Reillo, I., de Juan Romero, C., Garca-Cabezas, M., & Borrell, V. (2011). A role for
cortex. Cerebral Cortex, 21(7), 16741694.
Robinson, E. C., Jbabdi, S., Glasserlabel, M. F., Andersson, J., Burgess, G. C.,
Harms, M. P., et al. (2014). MSM: A new flexible framework for Multimodal Surface
Matching. NeuroImage, 100, 414426.
Roland, P. E., Geyer, S., Amunts, K., Schormann, T., Schleicher, A., Malikovic, A., et al.
(1997). Cytoarchitectural maps of the human brain in standard anatomical space.
Segal, E., & Petrides, M. (2012). The morphology and variability of the caudal rami of
the superior temporal sulcus. The European Journal of Neuroscience, 36(1),
20352053.
Sun, Z. Y., Kloppel, S., Rivie`re, D., Perrot, M., Frackowiak, R., Siebner, H., et al. (2012).
The effect of handedness on the shape of the central sulcus. NeuroImage, 60(1),
332339.
Sun, Z., Perrot, M., Tucholka, A., Rivie`re, D., & Mangin, J.-F. (2009). Constructing a
dictionary of human brain folding patterns. Medical Image Computing and
Computer-Assisted Intervention MICCAI, 12, 117124.
Sun, Z. Y., Pinel, P., Moreno, A., Perrot, M., Rivie`re, D., Dehaene, S., et al. (2012).
Morphological manifold-based spatial normalization for fMRI group analysis.
Beijin: HBM.
Tenenbaum, J., de Silva, V., & Langford, J. (2000). A global geometric framework for
nonlinear dimensionality reduction. Science, 290(5500), 23192323.
Thompson, P., & Toga, A. W. (1996). A surface-based technique for warping threedimensional images of the brain. IEEE Transactions on Medical Imaging, 15(4),
402417.
Toro, R., & Burnod, Y. (2003). Geometric atlas: Modeling the cortex as an organized
surface. NeuroImage, 20(3), 14681484.
in the central nervous system. Nature, 385(6614), 313318.
Van Essen, D. C. (2012). Cortical cartography and Caret software. NeuroImage, 62(2),
757764.
Watson, J. D., Myers, R., Frackowiak, R. S., Hajnal, J. V., Woods, R. P., Mazziotta, J. C.,
et al. (1993). Area V5 of the human brain: Evidence from a combined study using
positron emission tomography and magnetic resonance imaging. Cerebral Cortex,
3(2), 7994.
Wedeen, V. J., Rosene, D. L., Wang, R., Dai, G., Mortazavi, F., Hagmann, P., et al.
(2012). The geometric structure of the brain fiber pathways. Science, 335(6076),
16281634.
453465.
Welker, W. (1988). Why does cerebral cortex fissure and fold? Cerebral Cortex, 8B,
3135.
Yeo, B. T., Sabuncu, M. R., Vercauteren, T., Holt, D. J., Amunts, K., Zilles, K., et al.
(2010). Learning task-optimal registration cost functions for localizing
cytoarchitecture and function in the cerebral cortex. IEEE Transactions on Medical
Imaging, 29(7), 14241441.
Zilles, K., Palomero-Gallagher, N., & Amunts, K. (2013). Development of cortical
folding during evolution and ontogeny. Trends in Neurosciences, 36(5), 275284.
Zlatkina, V., & Petrides, M. (2010). Morphological patterns of the postcentral sulcus in
the human brain. The Journal of Comparative Neurology, 518(18), 37013724.
Columns of the Mammalian Cortex

DP Buxhoeveden, University of South Carolina, Columbia, SC, USA
Glossary
Afferent Refers to fibers (dendrites) that carry input toward

or into the central nervous system. The afferent fiber of a
neuron is one that carries signals into the neuron.
Columns A form of vertical organization of the cortex.
Columns can be differentiated according to their anatomical
dimensions and physiology.
Efferent Fibers (axons) that carry input away from the neuron
to input sites like other neurons, muscles, dendrites, etc.
Fascicles A bundle or a cluster.
Inhibitory neuron A neuron that sends signals, which acts
to inhibit depolarization of another neuron. The opposite
an excitatory neuron.
Interneuron In the cortex these are small neurons with local
connectivity as contrasted with long distance fibers that carry
input to more distant regions of the cortex or outside the
cortex to other brain areas. Most but not all of them are
inhibitory.
Modules Self-contained units. As used in neuroscience

refers to units capable of function that are typically
repetitive. Modules are found in different parts of the
brain. The cortical column and barrel field cortex in
rodents are examples of modular organization in
neocortex.
Myelinated fibers Refers to axons that are coated with
myelin, a fatty substance that acts as insulation. Myelinated
fibers are found on larger long distance axons rather than
smaller, thinner, local ones.
Progenitor cells Early cells that will differentiate into
neurons.
Vertical organization Represent the anatomical and
physiological vertical organization of neurons, their
processes, and connections in the neocortex. It need not
include all six layers of cortex as some examples of vertical
units are only two or three layers deep.
Introduction
The columnar organization of the cortex refers to the vertical

organization of neuronal elements that are superimposed
upon the horizontal lamina in the mammalian cortex. There
are two basic types: the larger cortical column and the smaller
minicolumn. For clarity, use of the word column within this
section will refer to both types unless each is specified.
Columns are present across a wide spectrum of species suggesting they are phylogenetically very old.
The cortical column typically measures around 300
500 mm across and is often defined according to size of the
afferent terminal. The cortical column in turn is composed
of minicolumns that represent functional subdivisions
(Tommerdahl, Favorov, & Whitsel, 2010). Each minicolumn
contains an estimated neuron number of between 80 and 100
cells (with the exception of primary visual cortex) comprising
mostly excitatory neurons and about 1020% inhibitory
interneurons.
The larger cortical column includes specialized modules
such as the ocular dominance column in primary visual cortex
and the barrel cortex in rodents. The terms hypercolumn and
macrocolumn are also used for cortical column. The minicolumn has many names that are typically associated with anatomy, embryology, or functionality. Terms include cell
column, cell arrays, cell aggregates, microcolumn, orientation column, and ontogenetic column. In addition, minicolumns can be defined by specific features such as the apical
dendrite bundles and their neurons (Peters & Sethares, 1996)
or they can refer to specialized units that include just two layers
of cortex (Ichinohe, 2012; Innocenti & Alessandro, 2010).
The most visible components of vertical organization in cell stain

preparations consists of the pyramidal neurons of layers III, V,
and VI, which tend to be aligned in a vertical pattern (Figure 1).
In fiber stains, the vertical presence of minicolumns is readily
discerned on the basis of the afferent and efferent fibers that
derive from these neurons (Figures 24). Therefore, these pyramidal cells may be viewed as the core of the minicolumn.
There are at least three dendrite systems that arise from
pyramidal cells. What is known as the long system denotes
the apical dendrites from layer V neurons that project straight
upward to layer I. Another group of dendrites from pyramidal
cells in layers III and II also project upward to layer 1 and these
tend to merge with those of layer V creating a very notable
vertical bundle. A third system of apical dendrites derives from
layer VI pyramidal cells and terminates in layer IV. Individual
collateral fibers from some bundles can be seen to project to
neighboring bundles (Figure 5), which highlights the variation
and subtle complexity associated with information processing
at the minicolumn level (Rockland & Ichinohe, 2004).
Myelinated axons from the large pyramidal cells in layers V
and VI represent bundled efferents from a single minicolumn.
In primates, axons of the inhibitory double bouquet cells
found in the upper sections of layers III and II send their
unmyelinated axons straight down through the cortical layers
to terminate in layer V and provide lateral inhibition. There are
also local nonmyelinated vertical axon systems represented by
the smaller stellate cells of layer IV. These axons project upward
to the supragranular layers. Taken together (Figure 6), these
elements comprise the vertical anatomy of the cortex.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00199-8
53
54
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Columns of the Mammalian Cortex
Figure 1 Cell arrays or cell columns in layer III. (a) Adult rhesus monkey, (b) adult human cortex, (c) rat brain at 21 days, and (d) cell columns in
1-day-old rat cortex.
Figure 2 Apical dendrite bundles in rat cingulate cortex.
Figure 3 Stain showing cells and myelin bundles in immature rat

cortex. Yellow arrows point to lateral projections. Circles highlight
vertical bundles.
Figure 4 High magnification image (1000 total) of apical dendrite

bundles in 21-day-old rat cortex. Note the individual fibers form a bundle
rather than having a uniform or random dispersion. Reprinted with
permission from Elsevier Limited.
To be a functional unit, there must be a shared afferent

input, intrinsic connections in which the input is processed,
and a common output (Mountcastle, 1997). The anatomical
description of the minicolumn contains all these elements.
Afferent input entering layer IV is directed upward within a
minicolumn to the supragranular layers, which then send
axons down to the infragranular layers so that all the cells of
that minicolumn share the same information. The output neurons of layers V and VI provide the efferent side of the equation. Specialized groups of inhibitory interneurons, such as the
double bouquet cell, small and large basket cells, and chandelier cells, provide the intricate balance required between excitation and inhibition. The balance between excitation and
inhibition is critical to the functioning of the cortex and alterations that affect this balance are suspected of playing a role in
some brain disorders and anomalies (Raghanti, Spocter, Butti,
Hof, & Sherwood, 2010).
The physiological capability of the cortical column and minicolumn is well established and has been found in all the major
types of cortex (Mountcastle, 1997). Computer modeling studies conducted over the last two decades demonstrate that columnar structure is a logical and efficient design for information
processing. Among other advantages, placing neurons in modules that share similar inputs and outputs reduces the length of
their fibers. This in turn reduces metabolic costs while increasing
the speed of processing. This becomes more critical in a large
brain where distances between neurons increase.
Development: The Ontogenetic Column

Though not fully resolved, it is thought that minicolumns in
adult brain are founded either directly or indirectly on the
ontogenetic radial columns formed during the earliest phases
of fetal development (Costa & Hedin-Pereira, 2010). The fetal
55
cortex displays a near-homogeneous vertical arrangement (column) of cells known as ontogenetic or radial cell columns
(Rakic, 1978). The genesis of the cortex occurs in the ventricles
by a series of symmetrical and asymmetrical divisions (Rakic &
Kornack, 2001). In the first phase, cells located in the ventricular zone produce two additional progenitor cells with each
mitotic cell division. This symmetrical division is responsible
for the number of founder cells that controls the total number
of ontogenetic columns that will be produced in the cortex.
According to the radial unit hypothesis, it is the number of
these ontogenetic columns that determines the cortical surface
area (Rakic & Kornack, 2001). At some point, progenitor cells
begin to divide asymmetrically, producing one daughter cell
that becomes a neuron and will move out into the cortical
plate, and which will not undergo further division. The second
phase is responsible for the number of cells within a column
and the thickness of the cortex. Several clones of neurons that
share a common site of origin in the ventricular zone use a
common migratory pathway along the fascicles of the radial
glial cells to settle within the same column in the cortical plate
(Rakic, 2003). Radial glial cells create long fascicles that extend
from the ventricular zone to the top of the cortical plate so that
they span the entire width of the cerebral wall during corticoneurogenesis. New born nerve cells use these to traverse the
cortical plate. Though there are small differences between
radial glial cells among mammals, overall they are very similar
in morphology and chemistry. The neuronalglial unit (consisting of the radial glial cells and migrating neurons) is conserved in a variety of animals including the mouse, rat,
hamster, cat, and human fetus.
Not all cortical interneurons originate from the ventricular
zone and migrate in a radial fashion. In rodents, this is most
notable as the majority of cortical interneurons originate from
the ganglionic eminence of the ventral telencephalon and
migrate tangentially to the cortical plate (Marn & Rubenstein,
2001). In mice, up to 25% of all cortical neurons migrate
nonradially, whereas in human, this percentage is < 10% of
the total (Letinic, Zoncu, & Rakic, 2002). Thus, there are taxonomic specializations associated with this process.
The total amount of radial units that will be present in the
adult cortex are controlled during embryogenesis by a few
regulatory genes, while the final pattern and size of cytoarchitectonic regions is thought to be the work of a different set of
genes (Rakic & Kornack, 2001). The configuration of columns
within an adult cytoarchitectonic area is therefore the result of
the genetic influences described in the preceding text and
epigenetic factors such as interactions of cells, inhibitory neurons, and afferent systems. It is clear that alterations in these
genes or their influences can have profound effects on the
cortex. The increase in founder cell number is exponential so
that a small prolongation of cell division or changes in length
of the cell cycle would result in significant increases in the
number of ontogenetic units produced. The discovery of the
ontogenetic column in the process of encephalization also
elucidates how that process can lead to brain reorganization.
Minicolumn Size in Evolution

The number of ontogenetic columns produced in development
determines the cortical surface area, whereas the number of
56
Figure 5 (a)(c) Collaterals in the apical dendrite bundles. Note the distinct branching of individual fibers that connect to a neighboring bundle as
highlighted by the yellow arrows. Reprinted with permission from Elsevier Limited.
cells produced per unit affects the cortical depth. Since surface
area has increased a 1000-fold (comparing mouse to human),
while cortical depth has only increased three to four times, the
major impetus for cortical enlargement has been the addition
of new ontogenetic units. The width of minicolumns falls
within a range of 2080 mm, with the typical size being somewhere between 30 and 60. Minicolumn size varies between and
within species as do their internal components and configuration (Buxhoeveden & Casanova, 2002, 2005; HerculanoHouzel, Collins, Wong, Kaas, & Lent, 2008).
There is also no direct correlation between the size of minicolumns and brain size for animals with a diverse evolutionary
history, though it is likely that a correlation does exist for
mammals that share a close evolutionary heritage (Sarko,

Catania, Leitch, Kaas, & Herculano-Houzel, 2009; Semendeferi
et al., 2011). In general, it is not possible to predict minicolumn
size solely on the basis of brain size alone, either between species
or for brains of the same species. The small-brained primate
Saimiri has a brain weight of around 25 g with minicolumns
that are as small or smaller than those found in the brains of mice
even though the latter may have a brain weight of only 0.4 g.
The relative stability of minicolumn size when contrasted
with the huge increase in surface area may be the result of
biological restraints on the individual neuronal components
of the cortex. As a result, their dimensions stay within a limited
range, while cortical surface area can expand more freely.
57
Lamina
I.
II.
49.72
Gray value
III.
IV.
8.60
274.3
0.0
V.
Distance (mm)
(b)
VI.
(a)
Gray value
119.1
Gray value
255
78.8
0
(d)
187
Distance (mm)
0
0
(c)
456
Distance (mm)
Figure 6 (a) Vertical components of minicolumn anatomy. The following include the components that provide the anatomical and physiological basis
for verticality in the cortex. In addition, there are horizontal efferent and afferent fibers as well as local inhibitory connections occurring at different layers.
Modified from Buxhoeveden, D., & Casanova, M. F. (2002). The minicolumn hypothesis in neuroscience. Brain, 125, 935951, p. 938, with permission
from Oxford University Press. Brown: Axons from stellate cells LIV to LIII/II. Green: Apical dendrites from LII to LI that may be a subsystem within
minicolumns. Black: Long apical dendrites LV to LI. Red: Apical dendrites from LVI to LIV. Orange: Apical dendrites from LIII/LII to LI. Magenta:
Myelinated axons from LV. Blue: Myelinated axons from LVI. Purple: Axons of double bouquet cells. Gray: Pyramidal cells. (b)(d) Periodicity. (b)
Columns represent a repeating element of modules in the cortex. Plot made from binary image of pyramidal cells in layer III by running computergenerated horizontal lines across fields of cortex in human brain. Each peak represents the location of a pyramidal cell at the same horizontal level within
the layer. (c) Same analysis plot as in (b) applied to apical dendrite bundles. (d) Plot profile of the same region of interest as (c) but measured in the
horizontal plane. The periodicity is clearly in the vertical dimension only. Similar results occur with cell soma but not always as dramatically.
Minicolumn size must always be considered within the context

of the cortical surface area of a given brain in order to gauge the
relative versus absolute size of columns and the significance of
minicolumn size (Buxhoeveden, 2012).
Reducing the size of minicolumns in a given cortex results
in having more of them and they in turn interconnect with
more columns resulting in a larger number of interconnections. It is thought that small columns reflect higher resolution
in the processing of incoming information, whereas large
columns contain more cells, synapses, and fibers and represent

more generalized processors. Much of this is still speculative
but demonstrates the significance of minicolumn size.
Unresolved Issues
While the minicolumn is a common feature of cortex, the
anatomical components that constitute a column are not
58
stereotypical in all brains or in all regions of the same brain.

Debate continues regarding the ubiquity and functionality of
the minicolumn due to some conflicting results as well as
species-specific differences (Jones & Rakic, 2010). On the
basis of the variation of neuronal types and connectivity
found at the microcircuit level, it may be necessary to rule
out a universal definition. Over the last two decades, a broader
conception arose, which describes these elements as a template
for a set of shared properties of a given set of neurons across
several or more lamina. This contrast with some earlier suggestions that columns were uniform units basically identical in all
mammalian cortices. Despite the great range in microcircuitry,
some stereotypical features do exist indicating a deterministic
basis and suggest that all neocortical microcircuits may be
subtle variations of a common design (Silberberg, Gupta, &
Markram, 2002). Mountcastle (2003) noted that The important point is that columnar organization depends upon a certain set of properties common to all neurons in the elementary
unit, but that other properties may vary between different
neurons in the same minicolumn.
In summary, the columnar organization of the cortex has a
genetic basis and highly linear cell columns represent the first
organization in cortical development. Column organization
increases efficiency and processing speed and may be foundational to cortical processing (Casanova, 2010). Many details
about the intrinsic composition and various forms of columnar structure and substructure remain to be discerned. A conservative approach would be to define them as a foundational
template subject to modification on the basis of speciesspecific requirements, evolutionary history, and regional and
functional specialization.

Language; Embryonic and Fetal Development of the Human Cerebral
Cortex; Evolution of the Cerebral Cortex; Functional Connectivity;
Quantitative Data and Scaling Rules of the Cerebral Cortex.
References
Buxhoeveden, D. P. (2012). Minicolumn size and human cortex. In M. A. Hofman & D.
Falk (Eds.), Progress in brain research (Vol. 195, pp. 219235). Elsevier Limited.
Buxhoeveden, D., & Casanova, M. F. (2002). The minicolumn and evolution of the
brain. Brain, Behavior and Evolution, 60, 2551.
Buxhoeveden, D., & Casanova, M. F. (2005). The cell column in comparative anatomy,
chap. 5. Encephalization, minicolumns, and hominid evolution, chap. 6. In M. F.
Casanova (Ed.), Neocortical modularity and the cell minicolumn. Hauppauge,

New York: Nova Science Publishers.
Casanova, M. F. (2010). Cortical organization: A description and interpretation of
anatomical findings based on systems theory. Translational Neuroscience, 1,
6271.
Costa, M. R., & Hedin-Pereira, C. (2010). Does cell lineage in the developing
cortex contribute to its columnar development? Frontiers in Neuroanatomy, 4,
26.
Herculano-Houzel, S., Collins, C. E., Wong, P., Kaas, J. H., & Lent, R. (2008). The basic
nonuniformity of the cerebral cortex. Proceedings of the National Academy of
Ichinohe, N. (2012). Small-scale module of the rat granular retrosplenial cortex: An
example of the minicolumn-like structure of the cerebral cortex. Frontiers in
Innocenti, G. M., & Alessandro, V. (2010). Dendritic bundles, minicolumns, and cortical
output units. Frontiers in Neuroanatomy, 4, 17.
Johansson, C., & Lansner, A. (2007). Towards cortex sized artificial neural systems.
Neural Networks, 1, 4861.
Jones, E. G., & Rakic, P. (2010). Commentary: Radial columns in cortical architecture: It
is the composition that counts. Cerebral Cortex, 20, 22612264.
Letinic, K., Zoncu, N., & Rakic, P. (2002). Origin of GABAergic neurons in the human
neocortex. Nature, 417, 645649.
Marn, O., & Rubenstein, J. L. (2001). A long, remarkable journey: Tangential migration
in the telencephalon. Nature Reviews. Neuroscience, 2, 780790.
Mountcastle, V. B. (1997). The columnar organization of the neocortex. Brain, 120,
701722.
Mountcastle, V. B. (2003). Introduction. Computation in cortical columns. Cerebral
Cortex, 13, 24.
Peters, A., & Sethares, C. (1996). Myelinated axons and the pyramidal cell modules in
monkey primary visual cortex. The Journal of Comparative Neurology, 365,
232255.
Raghanti, M. A., Spocter, M. A., Butti, C., Hof, P. R., & Sherwood, C. C. (2010). A
comparative perspective on minicolumns and inhibitory GABAergic interneurons in
the neocortex. Frontiers in Neuroanatomy, 4, 3.
Rakic, P. (1978). Neuronal migration and conduct guidance in primate telencephalon.
Postgraduate Medical Journal, 54, 2540.
Rakic, P. (1988). The specification of cerebral cortical areas: The radial unit hypothesis.
Science, 241, 928931.
Rakic, P. (2003). Developmental and evolutionary adaptations of cortical radial glia.
Rakic, P., & Kornack, D. R. (2001). Neocortical expansion and elaboration during
primate evolution: A view from neuroembryology. In D. Falk & K. R. Gibson (Eds.),
Evolutionary anatomy of the primate cerebral cortex (pp. 3056). Cambridge:
Rockland, K. S., & Ichinohe, N. (2004). Some thoughts on cortical minicolumns.
Experimental Brain Research, 158, 265277.
Sarko, D. K., Catania, K. C., Leitch, D. B., Kaas, J. H., & Herculano-Houzel, S.
(2009). Cellular scaling rules of insectivore brains. Frontiers in Neuroanatomy,
3, 8.
Semendeferi, K., Teffer, K., Buxhoeveden, D. P., Park, M. S., Bludau, S., Amunts, K.,
et al. (2011). Spatial organization of neurons in the frontal pole sets humans apart
from great apes. Cerebral Cortex, 21, 14851497.
Silberberg, G., Gupta, A., & Markram, H. (2002). Stereotypy in neocortical
microcircuits. Trends in Neurosciences, 25, 227230 (review).
Tommerdahl, M., Favorov, O. V., & Whitsel, B. L. (2010). Dynamic representations of
the somatosensory cortex. Neuroscience and Biobehavioral Reviews, 34,
160170.
Cell Types in the Cerebral Cortex: An Overview from the Rat Vibrissal Cortex
R Egger, Max Planck Institute for Biological Cybernetics, Tubingen, Germany
M Oberlaender, Max Planck Institute for Biological Cybernetics, Tubingen, Germany; Bernstein Center for Computational
Neuroscience, Tubingen, Germany
Introduction
Historically, neuronal cell types in the cerebral cortex have
been subdivided on the basis of soma location, soma shape,
dendrite, and axon morphologies and the neurotransmitters
released at their synapses (i.e., glutamatergic and GABAergic,
reviewed in Peters and Jones (1984)). These parameters are
related to (i) the input a neuron receives; (ii) the functional
response of the neuron, for example, to sensory input; and (iii)
the neuronal populations targeted by the output of this
neuron. We regard quantitative overlap of input, functional
responses, and output measurements from different neurons
as a minimal prerequisite for assignment to a common cell
type. At the level of single cortical neurons, (i) the input can be
estimated by reconstructing their 3-D soma location in the
cortex and 3-D dendrite branching pattern; (ii) the response
can be measured by electrophysiological recording of, for
example, sensory-evoked sub- and/or suprathreshold activity;
and (iii) the output is determined by reconstructing their 3-D
axon branching pattern.
Classification of neurons with respect to inputoutput relationships has been performed in various systems. Recordings
of sensory-evoked responses and overlap of reconstructed
dendrites and axons have allowed creating a quantitative map
of cell type-specific connectivity in the cat visual cortex
(Binzegger, Douglas, & Martin, 2004). Functional imaging in
combination with electron microscopic reconstruction of neurons in the superficial cortical layers (L2/3) has allowed investigating the role of excitatory and inhibitory inputs in receptive
field formation in the mouse visual cortex (Bock et al., 2011).
Similarly, functional imaging and electron microscopic reconstruction of the mouse retina have revealed the origin of direction selectivity in ganglion cells (Briggman, Helmstaedter, &
Denk, 2011).
Additionally, the relation between input, function, and
output of different cell types has been studied in the vibrissal
part of the primary somatosensory cortex (vS1) of rodents
since its initial description (Woolsey & Van Der Loos, 1970).
Here, the one-to-one correspondence of somatotopically organized, segregated structures in vS1 cortical barrel columns
with individual facial whiskers (Welker, 1976) represents a
reliable reference frame for electrophysiological studies. Additionally, in vivo preparations of the vibrissal system allow correlating structural input and output patterns to sensory inputs
by recovering complete 3-D morphologies of dendrites and
axons of functionally characterized neurons (Brecht &
Sakmann, 2002; De Kock, Bruno, Spors, & Sakmann, 2007).
Combining these 3-D neuron morphologies with distributions
of neuron somata by registration to a standardized 3-D reference frame allows assembling an average model of a barrel
column. This allows objective classification of reconstructed

neuron morphologies into cell types and comparison with
functional profiles obtained in the anesthetized and awake
animal. These cell types and their specific inputoutput relationships, together with functional implications for different
behaviors of the animal, are summarized subsequently, introducing basic anatomical facts about excitatory cell types in the
cortex and laying the foundations for articles 206209 and
222241, which focus on brain mapping approaches in various cortical regions.
Excitatory Cell Types in the Rat Vibrissal Cortex

Classification of 95 reconstructed neuron morphologies, labeled
in vivo, objectively identified nine excitatory cell types, all previously reported as canonical elements of the cortical circuitry
(see, e.g., Binzegger et al., 2004; Feldmeyer et al., 2013; Meyer
et al., 2010; Oberlaender, De Kock, et al., 2012; Figure 1,
Table 1): two supragranular pyramidal cell types (i.e., layer (L)
2 and L3; no excitatory neurons are found in L1), two pyramidal
and one interneuron cell type in granular L4, and four pyramidal cell types in the infragranular layers (i.e., L5 and L6). In total,
there are 14981 55 excitatory neurons in an average barrel
column.
Excitatory Cell Types in Supragranular Layers

L2 pyramids (L2, Brecht, Roth, & Sakmann, 2003) can be
found in the supragranular layers between 150 and 400 mm
below the pia surface (Figure 1(a)). L2 dendrites have a short
vertical span. In contrast, dendritic arborizations (number of
dendrites, 7.1 1.7; dendrite length, 8.58 2.82 mm; number
of branch points, 59.7 13.3) in the tangential plane are elaborate, extending beyond the principal column (PC, the barrel
column in which the soma is located) border. The other cell
type in supragranular layers is L3 pyramids (L3, Brecht et al.,
2003), which are located between 300 and 550 mm below the
pia surface, resulting in spatial overlap with the population of
L2 pyramids. In contrast to L2 pyramids, they have an apical
dendrite projecting parallel to the vertical column axis and
ending with less extensive, narrower tufts in L1 (number of
dendrites, 5.6 1.8; dendrite length, 6.44 0.95 mm; number
of branch points, 42.4 10.9). Within an average barrel column, 1095 21 L2 pyramids and 1605 18 L3 pyramids are
found in supragranular layers (Oberlaender, De Kock, et al.,
2012). Spontaneous spiking activity is low for both cell types
http://dx.doi.org/10.1016/B978-0-12-397025-1.00200-1
59
60
Table 1
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Cell Types in the Cerebral Cortex

Structural and functional properties of excitatory cell types in rat vibrissal cortex
Cell
type
Number of
neurons per
barrel column
Soma location
below pia (mm)
Dendrite
length (mm)
Number of
VPM
synapses
Spontaneous spiking
activity (Hz,
anesthetized)
L2
L3
L4ss
L4sp
L4py
L5st
L5tt
L6cc
L6ct
1095 21
1605 18
2752 46
2570 17
459 18
999 25
1613 20
1661 16
2226 9
150400
300550
550900
5001000
600700
10001300
11001400
14001600
15501800
8.58 2.82
6.44 0.95
3.38 1.09
4.23 0.94
7.49 1.18
7.71 1.95
13.84 3.63
5.86 0.77
5.90 0.78
6 12
66 63
246 123
278 159
341 166
165 86
195 82
131 52
139 84
0.47 0.69
0.32 0.53
0.52 0.22
0.32 0.13
0.56 0.42
1.10 0.43
3.53 1.59
0.87 0.35
0.08 0.08
(a)
(b)
Spontaneous spiking
activity (Hz, awake)
0.23 0.19
0.25 0.20
Whisker deflectionevoked spiking activity

(050 ms, Hz)
0.26 0.66
2.88 3.75
5.08 6.05
7.40 10.81
6.80 8.53
0.97 3.60
6.69 9.19
7.69 6.67
2.36 5.39
1.16 1.58
1.64 1.26
3.77 3.25
0.38 0.19
1.08 1.91
(c)
L1
Cortical depth (mm)
L2
0.5
L3
L4
L5A
L5B
1.5
L6A
L6B
Figure 1 Excitatory cell types in the rat vibrissal cortex. (a) Cell types in supragranular layers (shaded region): layer 2 pyramid (L2), L3 pyramid (L3).
(b) Cell types in granular layer (shaded region): L4 pyramid (L4py), L4 star pyramid (L4sp), and L4 spiny stellate (L4ss). (c) Cell types in
infragranular layers (shaded region): L5 slender-tufted pyramid (L5st), L5 thick-tufted pyramid (L5tt), L6 corticocortical pyramid (L6cc), and L6
corticothalamic pyramid (L6ct). Gray bars indicate the range over which somata of the respective cell type are found (mean 1.5 SD).
(L2 pyramids, 0.47 0.69 Hz (anesthetized)/0.23 0.19 Hz

(awake); L3 pyramids, 0.32 0.53 Hz (anesthetized)/
0.25 0.20 Hz (awake); De Kock & Sakmann, 2009; Oberlaender, De Kock, et al., 2012). Change in spiking activity after
passive deflection of the principal whisker (050 ms
poststimulus) differs between the two cell types (L2 pyramids,
0.26 0.66 Hz; L3 pyramids, 2.88 3.75 Hz; De Kock et al.,
2007). Differences are also apparent at the subthreshold
level, for example, onset latency of postsynaptic potentials
(PSP): 18.3 14.8 ms (L2) and 9.9 4.0 ms (L3) (Brecht
et al., 2003).
Excitatory Cell Types in Granular Layers

The two most numerous cell types in the granular layer are L4
spiny stellates (L4ss) and L4 star pyramids (L4sp) (Figure 1(b);
Staiger et al., 2004). L4ss can be found at depths from 550 to

900 mm below the pia. They are lacking an apical dendrite and
have short, star-shaped dendrites, often oriented preferentially
toward the center of the barrel (Egger, Nevian, & Bruno, 2008;
number of dendrites, 4.9 1.3; dendrite length, 3.38 1.09 mm;
number of branch points, 25.2 15.5). L4sp can be found
between 500 and 1000 mm below the pia; have a narrow apical
dendrite extending vertically to L2/3, but not to L1; and also show
biased orientation of the basal dendrites toward the barrel center
(Egger et al., 2008; number of dendrites, 4.6 2.0; dendrite
length, 4.23 0.94 mm; number of branch points, 20.0 3.2).
The least numerous cell types in L4 are the L4 pyramidal neurons
(L4py; Staiger et al., 2004). They are located in a narrow zone
between 600 and 700 mm below the pia surface and are preferentially found at the barrel border and in the septum between
barrels. They display an apical dendrite with a small tuft ending
in L2 (number of dendrites, 6.6 0.6; dendrite length,
7.49 1.18 mm; number of branch points, 41.0 7.4). In an

average barrel column, there are 2752 46 L4ss, 2570 17 L4sp,
and 459 18 L4py, with their somata again spatially intermingling (Oberlaender, De Kock, et al., 2012). Spontaneous spiking
activity varies between different cell types in L4
(L4ss, 0.52 0.22 Hz (anesthetized); L4sp, 0.32 0.13 Hz (anesthetized); L4py, 0.56 0.42 Hz (anesthetized); 1.16 1.58 Hz
(awake, avg. across all L4 cell types); De Kock & Sakmann, 2009;
Oberlaender, De Kock, et al., 2012). However, evoked spiking
activity after passive whisker deflection is similar (L4ss,
5.08 6.05 Hz;
L4sp,
7.40 10.81 Hz;
and
L4py,
6.80 8.53 Hz; De Kock et al., 2007), as is the PSP onset latency
of the three L4 cell types (8 1.4 ms; Brecht & Sakmann, 2002).
Excitatory Cell Types in Infragranular Layers

L5 contains two pyramidal cell types, with apical dendrites
extending up to L1 (Figure 1(c); Hallman, Schofield, & Lin,
1988; Larkman & Mason, 1990). L5 slender-tufted pyramids
(L5st) can be found between 1000 and 1300 mm below the pia
surface and have an apical dendrite that branches into a narrow
tuft in L12 (number of dendrites, 7.4 1.8; dendrite length,
7.71 1.95 mm; number of branch points, 36.9 13.2). L5
thick-tufted pyramids (L5tt) are located between 1100 and
1400 mm below the pia and thus overlap spatially with L5st.
They have a long apical dendrite terminating in a more extensive
tuft in L12 (number of dendrites, 7.4 1.7; dendrite length,
13.84 3.63 mm; number of branch points, 78.5 15.5). In
contrast to L5st, the basal and apical tuft dendrites extend tangentially beyond the PC border, and oblique branches are
located along the apical trunk in upper L5 and lower L4.
Two pyramidal cell types are located in L6 (Kumar &
Ohana, 2008). L6 corticocortical pyramids (L6cc) can be
found between 1400 and 1600 mm below the pia surface.
They have a short apical dendrite without a tuft, ending at the
L45 border (number of dendrites, 6.3 0.5; dendrite length,
5.86 0.77 mm; number of branch points, 29.4 5.6). L6 corticothalamic pyramids (L6ct) are located between 1550 and
1800 mm below the pia surface, although in rare cases they
may be found in L5. They display apical dendrites extending
into L4, terminating in a narrow tuft, oblique branches along
the apical trunk, and a much narrower basal tree compared to
L6cc pyramids (number of dendrites, 7.6 1.5; dendrite length,
5.90 0.78 mm; number of branch points, 31.6 7.0).
In an average barrel column, there are 999 25 L5st pyramids, 1613 20 L5tt pyramids, 1661 16 L6cc pyramids,
and 2226 9 L6ct pyramids. Spontaneous spiking activity
is different between cell types (L5st pyramids, 1.10 0.43 Hz
(anesthetized)/1.64 1.26 Hz (awake); L5tt pyramids,
3.53 1.59 Hz (anesthetized)/3.77 3.25 Hz (awake); L6cc
pyramids,
0.87 0.35 Hz
(anesthetized)/0.38 0.19 Hz
(awake); and L6ct pyramids, 0.08 0.08 Hz (anesthetized)/
1.08 1.91 Hz (awake)), as is whisker deflection-evoked spiking activity (L5st pyramids, 0.97 3.60 Hz; L5tt pyramids,
6.69 9.19 Hz; L6cc pyramids, 7.69 6.67 Hz; and L6ct
pyramids, 2.36 5.39 Hz). However, PSP onset latencies are
comparable for the two L5 cell types (L5st pyramids,
10.0 0.7 ms; L5tt pyramids, 10.3 0.6 ms; Manns, Sakmann,
61
& Brecht, 2004), as well as L6 pyramidal neurons

(10.7 0.7 ms; Constantinople & Bruno, 2013).
Cell Type-Specific Innervation and StructureFunction

Relationships
As described earlier, these cell types not only display
characteristic dendritic morphologies but also show specific
spontaneous and sensory-evoked spiking activity in vivo (De Kock
et al., 2007; De Kock & Sakmann, 2009). Spontaneous spiking
activity is mediated by intracortical synapses (Constantinople &
Bruno, 2011) and correlates with the total dendritic length at the
level of cell types and individual neurons (Oberlaender, De
Kock, et al., 2012). Sensory-evoked spiking activity after passive
whisker touch is mediated by excitatory sensory inputs from the
thalamus to the vibrissal cortex (ventral posterior medial nucleus
(VPM); Bruno & Sakmann, 2006; Figure 2(a) and 2(b)). Axons
originate from whisker-specific neurons located within somatotopically aligned structures in VPM, called barreloids (Land,
Buffer, & Yaskosky, 1995), and project to the corresponding
barrel column in the cortex (Wimmer, Bruno, De Kock, Kuner,
& Sakmann, 2010). Vertically, they display two major innervation zones (Oberlaender, Ramirez, & Bruno, 2012). The highest
innervation density is found in L4, at a cortical depth of about
750 mm. A second, less dense innervation peak is located at
the border between L5-6, at a depth of approximately
13501400 mm. Additionally, VPM axons can be classified into
four different groups, based on the horizontal projection pattern
in L4. These groups are core, subbarrel/core, core/tail, and head
neurons (Figure 2(c) and 2(f); Furuta, Deschenes, & Kaneko,
2011; Pierret, Lavallee, & Deschenes, 2000), referring to the
position of the VPM neuron somata within the barreloid. Core
and core/tail cells display innervation of the entire barrel, reaching the highest density in the barrel center. Core/tail neurons
display additional sparse innervation of septa between barrels
and neighboring columns, particularly in infragranular layers.
Subbarrel/core axons innervate only around 3050% of the
barrel volume in L4 and may give rise to subbarrels, whose
existence was suggested previously (Land & Erickson, 2005). In
contrast, head neurons delineate the tangential barrel borders
and extend into adjacent septal regions in L4. On average, there
are 259 neurons per VPM barreloid, although this number varies
from 100 to 400, depending on the identity of the somatotopically aligned whisker (Meyer et al., 2013).
Putative synaptic inputs from VPM neurons to individual
excitatory cortical neurons could be estimated in a locationand cell type-specific manner based on 3-D overlap of axonal
(bouton) and dendritic (spine) densities (Meyer et al., 2010;
Oberlaender, De Kock, et al., 2012). L2 pyramids receive
almost no VPM synapses (on average, 6 12 synapses per
cell). L3 pyramids receive more synapses, depending on the
vertical distance between the soma and the VPM innervation
peak in L4 (66 63). In the granular layer, L4ss and L4sp
receive similar amounts of synapses (246 123 and
278 159, respectively), and L4py receive the most synapses
per cell (341 166). L5st and L5tt pyramids receive 165 86
and 195 82 synapses, respectively, while L6 pyramids receive
slightly less synapses (131 52 and 139 84 for L6cc and L6ct
62
Tangential view
ne
Midli
D1
S1
D3
2 mm
500 m
Coronal view
(c)
B3
500 m
B3 C2 D1
500 m
500 m
500 m
500 m
(e)
Midline
(a)
B1
Coronal
plane
S2
S1
VPM
2 mm
(b)
500 m
500 m
(d)
(f)
Figure 2 (a) Tangential view of the rat brain with the barrel field in the vibrissal somatosensory cortex. S1, primary somatosensory cortex; S2,
secondary somatosensory cortex. (b) Coronal view of the rat brain, showing the vertical location of barrels in vS1 and input from the thalamus (ventral
posterior medial nucleus, VPM). (c) VPM core axon in the vibrissal cortex. Left, tangential view; right, coronal view. (d) VPM core/tail axon in the
vibrissal cortex. As in (c). (e) VPM subbarrel/core axon in the vibrissal cortex. As in (c). (f) VPM head axon in the vibrissal cortex. As in (c).
pyramids, respectively). For all granular and infragranular cell

types, the average number of synapses per cell decreases with
increasing radial distance of the soma to the central barrel
column axis (Lang, Dercksen, Sakmann, & Oberlaender,
2011; Oberlaender, De Kock, et al., 2012). Additionally, for
individual neurons, the amount of VPM synapses depends on
the 3-D morphology of the dendrites and the orientation of the
dendrites with respect to the VPM axons.
These results allow correlating the structural distribution of
thalamic input with functional responses after passive whisker
deflection at the level of single neurons and cell types. In vivo
recordings of sensory-evoked activity have shown that nearsimultaneous sub- and suprathreshold responses in all cell
types, except for L2, are due to direct thalamic innervation
(Bruno & Sakmann, 2006; Constantinople & Bruno, 2013;
De Kock et al., 2007). This suggests that the cell type-specific
VPM innervation described earlier is indeed the anatomical
basis of sensory-evoked responses in the vibrissal cortex. Specifically, differences between cell types in sensory-evoked spiking (i.e., change in spiking activity 050 ms poststimulus)
correlate with differences in the amount of VPM inputs,
explaining the variability in responses of the different cell
types. However, at the level of single neurons, differences in
evoked spiking activity can only be explained for some cell
types (e.g., L4ss and L6cc pyramids) by the number of VPM
inputs each individual neuron receives (Oberlaender, De Kock,
et al., 2012). This may indicate contributions of further excitatory intracortical and/or subcortical inputs, inhibitory inputs,
or different biophysical mechanisms to sensory information
processing in these neurons (Hay, Hill, Schurmann, Markram,
& Segev, 2011; Helmstaedter, Sakmann, & Feldmeyer, 2009;
Wimmer et al., 2010).
Cell Type-Specific Intracortical Circuits

The last important feature of a neuronal cell type is its output
pathways, which are reflected in the organization of its axonal
arbor. Figure 3 shows reconstructions of the dendritic and axonal arbors of an L5st pyramid and an L5tt pyramid in vS1. These
spatially intermingling cell types display complementary intracortical axon projection patterns, with the majority of the axon
located outside of the PC. Specifically, L5st pyramids have a
total intracortical axon length of 86.8 5.5 mm, of which
16.4 6.7 mm innervate the PC and 59.9 9.7 mm the surrounding columns and septa in the vibrissal cortex. Vertically,
the innervation profiles differ inside and outside the PC. Within
the PC, axonal innervation in the supragranular, granular, and
infragranular layers is 6.2 3.6 mm, 2.1 1.1 mm, and
8.1 2.7 mm, respectively. In contrast, innervation of supragranular layers outside the PC (43.4 9.7 mm) is much higher than
innervation of granular (7.1 3.6 mm) and infragranular layers
(9.4 3.8 mm). Additionally, L5st pyramids display very specific
projections to the supragranular layers of the dysgranular
zone surrounding the vibrissal cortex (10.6 9.9 mm). L5tt
pyramids have shorter overall axon length (31.6 14.3 mm).
10.1 6.4 mm are confined to the PC and 18.6 7.5 mm to
the surrounding columns and septa of the vibrissal cortex. Vertical innervation of the PC is similar in supragranular and granular
layers (2.1 1.4 mm and 1.4 1.3 mm, respectively) and peaks
in the infragranular layers (6.6 4.1 mm). Outside of the PC, the
supragranular and granular layers show only sparse innervation
(3.0 1.9 mm and 3.3 1.8 mm, respectively), while most of
the axon targets the infragranular layers (12.2 4.4 mm).
Finally, L5tt pyramids have only very sparse innervation of
areas outside the vibrissal cortex (2.9 1.8 mm) and only
target its immediate surroundings (Oberlaender et al., 2011;
Figure 3(a) and 3(b)).
Functionally, these two cell types differ not only in their
spiking response after passive whisker deflection but also when
the animal is awake and moving its whiskers. Specifically, L5tt
pyramidal neurons respond robustly to passive whisker deflection, mediated by input from VPM mostly onto the basal
dendrites (Figure 3(c), left). In contrast, L5st pyramidal neurons increase their firing rate during whisking. The spike timing
of individual L5st pyramidal neurons carries information
63
Pia
E1
E4
D4
D3
D2
D1
Y
White
matter
A4
500 m
A1
500 m
(a)
(b)
Whisking
Passive touch
S1
S1
Active touch
S1
VPM
VPM/POm
VPM/POm
e.g., pons
e.g., striatum
e.g., pons
(c)
Figure 3 (a) Semicoronal view of intracortical projection patterns of an L5 thick-tufted (L5tt, left) and an L5 slender-tufted (L5st, right) pyramidal
neuron. Red, dendrites; blue, axon. (b) Same as in (a), tangential view. (c) L5st and L5tt pyramidal neurons report different signals during
different behavioral states of the animal (t, whisker-touch information; p, whisker-position information). These signals target different subcellular
compartments of L5tt pyramids (red). During simultaneous activation of these sensorymotor pathways, L5tt pyramidal neurons may act as
coincidence detectors and change their spiking output to bursting mode (right panel, thick arrow).
about the whisker position (Figure 3(c), center; De Kock &

Sakmann, 2009). This information reaches L5st pyramidal
neurons through thalamic and intracortical inputs (Xu et al.,
2012; Yu, Derdikman, Haidarliu, & Ahissar, 2006) and is
propagated to the supragranular layers of the PC and the
surrounding columns and to a lesser extent to the infragranular
layers of the PC.
These cell type-specific innervation patterns, functional
responses, and output pathways suggest a mechanism for
sensory processing of active whisker touch (i.e., touch of an
object while the animal is moving its whiskers): in the supragranular layers, axons from L5st pyramids may form synapses
with the apical tuft dendrites of L5tt pyramidal neurons, providing information about whisker position, similarly to the
encoding of whisker position in the membrane potential of
supragranular pyramidal neurons (Crochet & Petersen, 2006).
When the animal is whisking and touching an object at the
same time, coincident input from the whisker-touch pathway
from VPM and the whisker-position pathway from L5st
pyramids may activate the perisomatic and apical dendrite
spiking zones simultaneously, resulting in increased spiking
output and signaling location of an object (Figure 3(c), right;
Larkum, 2013; Larkum, Zhu, & Sakmann, 1999; Oberlaender
et al., 2011).
Conclusion
In summary, 3-D reconstruction of soma, dendrites, and axon
of individual cortical neuron morphologies allows objective
classification of excitatory neurons into nine different cell types
in the rat vibrissal cortex. The vertical distribution of the different cell types reveals that laminar locations of the somata do
not predict the neuron cell type. For example, L2 pyramidal
neurons may be found in the upper part of L3, and L5st
and L5tt pyramidal somata intermingle between 1100 and
1300 mm below the pia. Only by reconstructing the entire
dendrite morphology and registration of the neuron to a standardized coordinate system it is possible to unambiguously
identify neuronal cell types. These somatodendritic cell types
predict specific functional properties during different behaviors, as well as cell type-specific innervation by thalamocortical
inputs. Additionally, two cell types in L5 show specific intracortical axon projection patterns, revealing cell type-specific
pathways possibly involved in signaling of different sensory
and behavioral variables.
Thus, the correlation between input, functional responses,
and output pathways of somatodendritic cortical cell types
may provide a basis for quantitative assessment of functional,
structural, and computational studies.
64

Amygdala; Anatomy and Physiology of the Mirror Neuron System;
Auditory Cortex; Basal Forebrain Anatomical Systems in MRI Space;
Cytoarchitecture and Maps of the Human Cerebral Cortex; Development
of the Basal Ganglia and the Basal Forebrain; Functional and Structural
Diversity of Pyramidal Cells; Functional Organization of the Primary
Visual Cortex; Gustatory System; Insular Cortex; Lateral and
Dorsomedial Prefrontal Cortex and the Control of Cognition; Mapping
Cingulate Subregions; Motor Cortex; Myeloarchitecture and Maps of
the Cerebral Cortex; Posterior Parietal Cortex: Structural and
Functional Diversity; Somatosensory Cortex; Thalamus: Anatomy; The
Olfactory Cortex; Topographic Layout of Monkey Extrastriate Visual
Cortex; Vestibular Cortex.
References
Binzegger, T., Douglas, R. J., & Martin, K. A. (2004). A quantitative map of the circuit of
cat primary visual cortex. The Journal of Neuroscience, 24, 84418453.
Bock, D. D., Lee, W. C., Kerlin, A. M., Andermann, M. L., Hood, G., Wetzel, A. W., et al.
(2011). Network anatomy and in vivo physiology of visual cortical neurons. Nature,
471, 177182.
Brecht, M., Roth, A., & Sakmann, B. (2003). Dynamic receptive fields of reconstructed
pyramidal cells in layers 3 and 2 of rat somatosensory barrel cortex. The Journal of
Physiology, 553, 243265.
Brecht, M., & Sakmann, B. (2002). Dynamic representation of whisker deflection by
synaptic potentials in spiny stellate and pyramidal cells in the barrels and septa of
layer 4 rat somatosensory cortex. The Journal of Physiology, 543, 4970.
Briggman, K. L., Helmstaedter, M., & Denk, W. (2011). Wiring specificity in the
direction-selectivity circuit of the retina. Nature, 471, 183188.
Bruno, R. M., & Sakmann, B. (2006). Cortex is driven by weak but synchronously active
thalamocortical synapses. Science, 312, 16221627.
Constantinople, C. M., & Bruno, R. M. (2011). Effects and mechanisms of wakefulness
on local cortical networks. Neuron, 69, 10611068.
Constantinople, C. M., & Bruno, R. M. (2013). Deep cortical layers are activated directly
by thalamus. Science, 340, 15911594.
Crochet, S., & Petersen, C. C. (2006). Correlating whisker behavior with membrane
potential in barrel cortex of awake mice. Nature Neuroscience, 9, 608610.
De Kock, C. P., Bruno, R. M., Spors, H., & Sakmann, B. (2007). Layer and cell type
specific suprathreshold stimulus representation in primary somatosensory cortex.
The Journal of Physiology, 581, 139154.
De Kock, C. P., & Sakmann, B. (2009). Spiking in primary somatosensory cortex during
natural whisking in awake head-restrained rats is cell-type specific. Proceedings of
1644616450.
Egger, V., Nevian, T., & Bruno, R. M. (2008). Subcolumnar dendritic and axonal
organization of spiny stellate and star pyramid neurons within a barrel in rat
somatosensory cortex. Cerebral Cortex, 18, 876889.
Feldmeyer, D., Brecht, M., Helmchen, F., Petersen, C. C., Poulet, J. F., Staiger, J. F.,
et al. (2013). Barrel cortex function. Progress in Neurobiology, 103, 327.
Furuta, T., Deschenes, M., & Kaneko, T. (2011). Anisotropic distribution of
thalamocortical boutons in barrels. The Journal of Neuroscience, 31, 64326439.
Hallman, L. E., Schofield, B. R., & Lin, C. S. (1988). Dendritic morphology and axon
collaterals of corticotectal, corticopontine, and callosal neurons in layer V of primary
visual cortex of the hooded rat. The Journal of Comparative Neurology, 272,
149160.
Hay, E., Hill, S., Schurmann, F., Markram, H., & Segev, I. (2011). Models of neocortical
layer 5b pyramidal cells capturing a wide range of dendritic and perisomatic active
properties. PLoS Computational Biology, 7, e1002107.
Helmstaedter, M., Sakmann, B., & Feldmeyer, D. (2009). The relation between dendritic
geometry, electrical excitability, and axonal projections of L2/3 interneurons in rat
barrel cortex. Cerebral Cortex, 19, 938950.
Kumar, P., & Ohana, O. (2008). Inter- and intralaminar subcircuits of excitatory and
inhibitory neurons in layer 6a of the rat barrel cortex. Journal of Neurophysiology,
100, 19091922.
Land, P. W., Buffer, S. A., Jr., & Yaskosky, J. D. (1995). Barreloids in adult rat thalamus:
Three-dimensional architecture and relationship to somatosensory cortical barrels.
The Journal of Comparative Neurology, 355, 573588.
Land, P. W., & Erickson, S. L. (2005). Subbarrel domains in rat somatosensory (S1)
cortex. The Journal of Comparative Neurology, 490, 414426.
Lang, S., Dercksen, V. J., Sakmann, B., & Oberlaender, M. (2011). Simulation of signal
flow in 3D reconstructions of an anatomically realistic neural network in rat vibrissal
cortex. Neural Networks, 24, 9981011.
Larkman, A., & Mason, A. (1990). Correlations between morphology and
electrophysiology of pyramidal neurons in slices of rat visual cortex. I.
Establishment of cell classes. The Journal of Neuroscience, 10, 14071414.
Larkum, M. (2013). A cellular mechanism for cortical associations: An organizing
principle for the cerebral cortex. Trends in Neurosciences, 36, 141151.
Larkum, M. E., Zhu, J. J., & Sakmann, B. (1999). A new cellular mechanism for
coupling inputs arriving at different cortical layers. Nature, 398, 338341.
Manns, I. D., Sakmann, B., & Brecht, M. (2004). Sub- and suprathreshold receptive
field properties of pyramidal neurones in layers 5A and 5B of rat somatosensory
barrel cortex. The Journal of Physiology, 556, 601622.
Meyer, H. S., Egger, R., Guest, J. M., Foerster, R., Reissl, S., & Oberlaender, M. (2013).
Cellular organization of cortical barrel columns is whisker-specific. Proceedings of
1911319118.
Meyer, H. S., Wimmer, V. C., Hemberger, M., Bruno, R. M., De Kock, C. P., Frick, A.,
et al. (2010). Cell type-specific thalamic innervation in a column of rat vibrissal
Oberlaender, M., Boudewijns, Z. S., Kleele, T., Mansvelder, H. D., Sakmann, B., &
De Kock, C. P. (2011). Three-dimensional axon morphologies of individual layer 5
neurons indicate cell type-specific intracortical pathways for whisker motion and
touch. Proceedings of the National Academy of Sciences of the United States of
America, 108, 41884193.
Oberlaender, M., De Kock, C. P., Bruno, R. M., Ramirez, A., Meyer, H. S.,
Dercksen, V. J., et al. (2012). Cell type-specific three-dimensional structure of
thalamocortical circuits in a column of rat vibrissal cortex. Cerebral Cortex, 22,
23752391.
Oberlaender, M., Ramirez, A., & Bruno, R. M. (2012). Sensory experience restructures
thalamocortical axons during adulthood. Neuron, 74, 648655.
Peters, A., & Jones, E. G. (Eds.). (1984). Cerebral cortex 1: Cellular components of the
cerebral cortex. London, New York: Plenum Press.
Pierret, T., Lavallee, P., & Deschenes, M. (2000). Parallel streams for the relay of
vibrissal information through thalamic barreloids. The Journal of Neuroscience, 20,
74557462.
Staiger, J. F., Flagmeyer, I., Schubert, D., Zilles, K., Kotter, R., & Luhmann, H. J. (2004).
Functional diversity of layer IV spiny neurons in rat somatosensory cortex:
Quantitative morphology of electrophysiologically characterized and biocytin
labeled cells. Cerebral Cortex, 14, 690701.
Welker, C. (1976). Receptive fields of barrels in the somatosensory neocortex of the rat.
Wimmer, V. C., Bruno, R. M., De Kock, C. P., Kuner, T., & Sakmann, B. (2010).
Dimensions of a projection column and architecture of VPM and POm axons in rat
vibrissal cortex. Cerebral Cortex, 20, 22652276.
Woolsey, T. A., & Van Der Loos, H. (1970). The structural organization of layer IV in
the somatosensory region (SI) of mouse cerebral cortex. The description of a
cortical field composed of discrete cytoarchitectonic units. Brain Research, 17,
205242.
Xu, N. L., Harnett, M. T., Williams, S. R., Huber, D., Oconnor, D. H., Svoboda, K., et al.
(2012). Nonlinear dendritic integration of sensory and motor input during an active
sensing task. Nature, 492, 247251.
Yu, C., Derdikman, D., Haidarliu, S., & Ahissar, E. (2006). Parallel thalamic pathways
for whisking and touch signals in the rat. PLoS Biology, 4, e124.
Functional and Structural Diversity of Pyramidal Cells

D Feldmeyer, Institute of Neuroscience and Medicine, Research Center Julich, Julich, Germany; RWTH Aachen University, Aachen,
Germany; Julich-Aachen Research Alliance, Translational Brain Medicine (JARA Brain), Aachen, Germany
Glossary
Apical dendrite Stem dendrite of a pyramidal cell pointing

to the pia.
Apical tuft Branching in the terminal region of the apical
dendrite.
Basal dendrites Dendrites that originate at soma and
project obliquely or parallel to the pia.
Ca-spike Long-lasting action potential mediated by the
influx of Ca; action potential generated in the axon is based
on Na influx.
EPSP Excitatory postsynaptic potential.
Dendritic Morphology
Pyramidal cells take their name from their pyramid-shaped
somata and were first described by Ramon y Cajal (1893).
They can be found in vertebrates from fish to humans. Pyramidal cells are the most abundant type of excitatory projection neuron in the neocortex and hippocampus but are also
found in the amygdala (Hall, 1972). A pyramidal cell is
bipolar and has a rather stereotypical morphology: from the
base of its cell body, several, generally short basal dendrites
emerge while an apical dendrite projects from the soma top
toward the pia. However, despite their similarities, there is a
significant degree of diversity, particularly with respect to the
morphology of apical dendrites (Figure 1): some pyramidal
cells, for example, those in the CA1 and CA3 layers of the
GABAergic interneurons Inhibitory interneurons that use

g-aminobutyric acid as neurotransmitter.
IPSP Inhibitory postsynaptic potential.
LTD Long-lasting reduction of the synaptic efficacy.
LTP Long-lasting enhancement of the synaptic efficacy.
Spines Protrusion from the dendrites often mushroom-like
but structurally very variable.
Synaptic plasticity Intrinsic property of a synapse to change
its efficacy and reliability in response to certain external
stimuli.
hippocampus and in neocortical layer 5B, branch profusely in

the more distal region of the apical dendrite forming the socalled apical tufts. In contrast, pyramidal cells in neocortical
layer 5A or layer 6 have only sparse dendritic tufts with only
few branches. Finally, there are also pyramidal cells that have
apical dendrites without any tuft at all (Figure 1). These
differences suggest that different pyramidal cell types may
have different functional roles and computational powers in
the neuronal network.
Both basal and apical dendrites of pyramidal neurons are
covered with small excrescences called dendritic spines. Dendritic spines were discovered first described by Cajal in 1888
(Ramon y Cajal, 1888) and later shown to be postsynaptic
contact sites with excitatory, glutamatergic presynaptic axonal
boutons. However, excitatory contacts are established also
Pyramidal cell types
Apical
dendrite
Soma
and basal
dendrites
Hippocampus
CA1
CA3
Layer 2/3
Neocortex
Layer 5A
Layer 5B
Layer 6
Figure 1 Dendritic arbor of different pyramidal cell types in rodent hippocampus and neocortex indicating the morphological variability of this neuron
type. Basal and apical dendritic domains in the blue and red shaded area, respectively. Apical dendrites often posses very elaborate and broad tuft
regions; in others, for example, in neocortical layer 5A pyramidal cells, they are slender or even completely absent as in a subgroup of layer 6 pyramidal
cells. Note that the neurons are not drawn to scale.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00201-3
65
66
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Functional and Structural Diversity of Pyramidal Cells
with the dendritic shafts between dendritic spines. Thus, the

number of dendritic spines (typically tens of thousands)
serves as a lower-limit estimate for the number of excitatory
synapses contacting a single pyramidal neuron. In addition,
inhibitory synaptic contacts exist that are not found on dendritic spines; the vast majority of inhibitory synapses are
established with dendritic shafts and with the soma, the postsynaptic neurons.
Axonal Projection Pattern

A second highly distinctive morphological feature of pyramidal
cells is their axon morphology. For the sake of brevity, I will
concentrate on pyramidal cells in the neocortex. In general, all
pyramidal cells have two axonal domains, one that is local and
one with long-range projections to intracortical and/or subcortical target neurons. For example, layer 5 pyramidal cells have
subcortical target regions such as the thalamic nuclei, the striatum, the cerebellum, the superior colliculi, and the spinal cord.
Thus, these pyramidal cells serve as the major output neurons of
the neocortex. Pyramidal cell axons can be very long, in particular
those projecting from the motor cortex to the lumbar spinal cord;
in humans or mammals, they may extend up to 1 m or more.
In contrast, horizontal long-range projections target both
ipsi- and contralateral cortical areas. For instance, pyramidal
cells in the primary sensory cortices may establish synaptic
connections with pyramidal cells in the secondary sensory
cortices, the motor cortex, and the prefrontal and frontal cortices predominantly via layer 2/3 and layer 6 pyramidal cells.
Their axons run through cortical layers 1, 2, 3, 5, and 6. Axonal
projections to pyramidal cells in different areas of the contralateral brain hemisphere run via the corpus callosum.
In addition to long-range axonal projections, both hippocampal and neocortical pyramidal cells form local excitatory and
inhibitory neuronal networks that extend only within or across
a few cortical columns. Both excitatory and inhibitory synaptic
connections onto pyramidal cells are established with the basal
dendrites, the soma, and the apical dendrite and its tuft.
The connectivity ratio of synaptic microcircuits between
pyramidal cells and other neurons depends on the axonal
arbor of the presynaptic neuron. The connectivity in local
synaptic microcircuits is significantly higher than that of connections established by long-range axonal projections. For different pyramidal cell types, the local axonal domain can be
quite profound: Neocortical layer 5 pyramidal cells with a
slender apical tuft have very dense projections to layer 1 and
upper layer 2/3 and are therefore likely to innervate the apical
tuft of other pyramidal cells in the same cortical area. In
contrast, layer 5 pyramidal cells with a broad tuft have only
few ascending collaterals but many intracortical, horizontal
collaterals (Oberlaender et al., 2011). In conclusion, the axonal projection pattern of pyramidal cells determines which
neuron types are innervated and which dendritic compartments of the postsynaptic neurons are targeted.
Function
Pyramidal cells play important roles in learning, sensory
perception, and motor control. At the single-cell level, long-
term potentiation (LTP) of synaptic signaling between two

neurons is considered to be a correlate of the learning process
(for reviews, see Spruston, 2008, 2009).
Action Potential Firing

Generally, action potentials (APs) in pyramidal cells have a
half-width of about 2 ms and are considerably longer than
those of most GABAergic interneurons. However, AP firing in
response to prolonged current injection is rather diverse
because AP firing is dependent not only on the types of
voltage-gated ion channels present expressed by the pyramidal
cell type but also on its dendritic morphology. Most pyramidal
cells, in particular the smaller ones, respond to depolarizing
current pulses with a train of APs that show frequency adaption. In contrast, large pyramidal neurons with extensive apical
tufts display often an initial burst of two or more APs while
some pyramidal cells also show repetitive burst-like AP activity.
Synaptic Integration
The elaborate dendritic arborizations of pyramidal cells receive
functionally distinct synaptic inputs from different types of
neurons that are targeted to spatially separate region. A prerequisite for the computational power of pyramidal cells is the
integration of these synaptic inputs, a process that occurs
chiefly in the basal and apical dendrites. It has been referred
to as synaptic integration (Spruston, 2008). If dendrites
would behave like passive electric cable structures, synaptic
integration at the soma would be purely linear and proximal
30 mV
20 ms
Ca2+ spike
initiation zone
Na+ spike
initiation zone
(axon hillock)
Figure 2 Schematic drawing of a pyramidal cell. At the axon hillock, the

fast Na AP (blue) is initiated; in a region close to the dendritic tuft,
the Ca2 spike (red) is generated. Because the dendrites of the pyramidal
cell are active, Na AP and Ca2 spike can influence each other (as
indicated by the double arrows), thereby modulating the pyramidal
cell synaptic signal processing. Note the different time course of the fast
Na AP and long-lasting Ca2 spike. Scale bar applies to both signals.
67
Figure 3 Coincidence detection via backpropagation activated Ca2 spike firing. This mechanism is thought to be involved in the shaping of
synaptic integration and its plasticity. (a) Pyramidal cell in neocortical layer 5 with patch electrodes at the soma (blue), the apical dendritic trunk (gray),
and the apical tuft (red). (b) Excitatory postsynaptic potential waveform (Vm, red) evoked by a small dendritic current injection (Istim, red) causes no
dendritic Ca2 spike and has virtually no impact at the cell body (blue). (c) A somatic Na AP (blue) evoked with somatic current injection (Istim,
blue) invades the dendritic tree but still causes no dendritic spike. (d) A combination of current injections at the soma and apical tuft (as in (b) and (c))
reaches threshold for a Ca2 spike in the apical dendrite. In turn, this triggers a burst of Na AP firing. Modified from Larkum, M. E., Zhu, J. J.,
and Sakmann, B. (1999). A new cellular mechanism for coupling inputs arriving at different cortical layers. Nature, 398, 338341, with permission
from Macmillan Publishers Ltd.
synaptic inputs would dominate over distal ones because of

cable filtering. However, basal dendrites and in particular
apical dendrites are not merely passive structures. They contain
several different types of voltage-gated ion channels, for example, Na, Ca2, and K channels, and are therefore capable of
actively influencing neuronal signaling. The recruitment of
these ion channels modulates synaptic integration and may
also lead to the amplification of distal synaptic inputs (e.g.,
Stuart & Sakmann, 1995). Thus, active dendrites furnish pyramidal cells with nonlinear but powerful capabilities of processing synaptic signals.
Apical dendrites of many hippocampal and neocortical
pyramidal cells are also able to propagate the AP initiated at
the axon hillock (Stuart & Sakmann, 1994), albeit with a
reduced amplitude and a longer duration. In addition, there
is a high density of Ca2 channels in the region where the tuft
of the apical dendrite is formed. Sufficiently strong depolarizations (e.g., by strong synaptic input to the tuft) lead to the
generation of Ca2 spikes (Figure 2). Thus, pyramidal cells
with a prominent apical tuft have two regions were APs can
be generated: The normal Na AP with a short duration is
elicited at the axon initial segment of the neuron, while the
Ca2 spike (half-width 20 ms) can be evoked at the tuft.
It has been proposed that pyramidal cells respond optimally to coincident activation of several dendritic compartments. In neocortical layer 5, the distal apical dendritic tufts
are targeted, for example, by associational axons from other
cortical areas, while the proximal basal dendrites receive input
from other local pyramidal cells or from the thalamus. The
simultaneous activation of these proximal and distal dendrites
results in a burst of APs. These AP bursts are caused when a
dendritic Ca2 spike triggered by distal synaptic inputs is activated simultaneously with a backpropagating AP (Figure 3;
Larkum, 2013; Larkum, Zhu, & Sakmann, 1999); it is therefore
a coincidence detection mechanism. Such an interaction
between the Na AP and the Ca2 spike is involved in many
processes such as associative learning.
Synaptic Plasticity and Spike Timing-Dependent Plasticity

Activity-dependent synaptic plasticity is a mechanism of neuronal plasticity during which the synaptic strength of a neuronal connection changes in response to repeated synaptic
activation. It is a well-established phenomenon in pyramidal
neurons of the neocortex and hippocampus (e.g., Markram,
Lubke, Frotscher, & Sakmann, 1997). Synaptic plasticity can
68
lead to enhanced or reduced synaptic strength, processes

referred to as either LTP or long-term depression (LTD) of
synaptic signaling, respectively. The relative timing of AP firing
in both the pre- and postsynaptic neuron determines the sign
of the change in synaptic strength (for a review, see Spruston,
2008). Both LTP and LTD have been considered as key
mechanisms of learning and memory. APs backpropagate
actively (i.e., through the activation of apical dendritic Na
and K channels; see above) from their site of initiation in the
axon through the apical dendrite. Together with a dendritic
Ca2 spike may provide the postsynaptic depolarization necessary for the induction of LTP or LTD of the synaptic response
(Kampa, Letzkus, & Stuart, 2007).
Pyramidal Cells in Sensory Perception and Motor Function

Ensembles of pyramidal cells in sensory cortices play an important role in the perception and processing of sensory signals.
Many of them receive direct thalamic input from different sensory pathways. In the neocortex, sensory input from the periphery is coded spatially, that is, the information from one sensory
receptor is represented in a defined cortical space termed the
receptive field of this receptor (Hubel & Wiesel, 1962; Mountcastle, 1957). The structural correlate of a receptive field has
been defined as a so-called cortical column (Szentagothai,
1975), which is considered to be the basic module of cortical
signal processing. The major neuronal elements of these cortical
columns are networks of pyramidal cells. However, even on a
single-cell scale, pyramidal cells are able to report sensory signals. In recent studies (Houweling & Brecht, 2008; Huber et al.,
2008), it has been demonstrated that the activity of a few or even
a single pyramidal cell in rat neocortex can affect the perception
of a sensory stimulus, a finding that highlights the computational capabilities of these neurons.
Furthermore, neocortical pyramidal cells play also an
important role in the initiation of motor behavior. Pyramidal
cell activity in the motor cortex is believed to be correlated with
movements as extracellular stimulation experiments have
shown. Only recently, it has been shown that short trains of
AP firing of single pyramidal cells in neocortical layers 5 and 6
cells can affect or even initiate motor responses (Brecht,
Schneider, Sakmann, & Margrie, 2004). Thus, the activity of
single pyramidal cells in motor and sensory cortices has a
profound impact on perception and processing of sensory
signals and on the generation of movements.

Neurons; Cytoarchitecture and Maps of the Human Cerebral Cortex;
Evolution of the Cerebral Cortex; Synaptic Organization of the Cerebral
Cortex.
References
Brecht, M., Schneider, M., Sakmann, B., & Margrie, T. W. (2004). Whisker movements
evoked by stimulation of single pyramidal cells in rat motor cortex. Nature, 427,
704710.
Hall, E. (1972). The amygdala of the cat: A Golgi study. Zeitschrift fur Zellforschung und
Mikroskopische Anatomie, 134, 439458.
Houweling, A. R., & Brecht, M. (2008). Behavioural report of single neuron stimulation
in somatosensory cortex. Nature, 451, 6568.
Hubel, D. H., & Wiesel, T. N. (1962). Receptive fields, binocular interaction and
functional architecture in the cats visual cortex. Journal of Physiology, 160,
106154.
Huber, D., Petreanu, L., Ghitani, N., Ranade, S., Hromadka, T., Mainen, Z., et al. (2008).
Sparse optical microstimulation in barrel cortex drives learned behaviour in freely
moving mice. Nature, 451, 6164.
Kampa, B. M., Letzkus, J. J., & Stuart, G. J. (2007). Dendritic mechanisms controlling
spike-timing-dependent synaptic plasticity. Trends in Neurosciences, 30, 456463.
Larkum, M. (2013). A cellular mechanism for cortical associations: An organizing
principle for the cerebral cortex. Trends in Neurosciences, 36, 141151.
Larkum, M. E., Zhu, J. J., & Sakmann, B. (1999). A new cellular mechanism for
coupling inputs arriving at different cortical layers. Nature, 398, 338341.
Markram, H., Lubke, J., Frotscher, M., & Sakmann, B. (1997). Regulation of
synaptic efficacy by coincidence of postsynaptic APs and EPSPs. Science, 275,
213215.
Mountcastle, V. B. (1957). Modality and topographic properties of single
neurons of cats somatic sensory cortex. Journal of Neurophysiology, 20,
408434.
Oberlaender, M., Boudewijns, Z. S., Kleele, T., Mansvelder, H. D., Sakmann, B., &
De Kock, C. P. (2011). Three-dimensional axon morphologies of individual layer 5
neurons indicate cell type-specific intracortical pathways for whisker motion and
touch. Proceedings of the National Academy of Sciences of the United States of
America, 108, 41884193.
Ramon y Cajal, S. (1888). Estructura de los centros nerviosos de las aves. Revista
Trimestral de Histologa normal y patologica, 1, 110.
Ramon y Cajal, S. (1893). Nuevo concepto de la histologia de los centros nerviosos. La
Revista de ciencias medicas de Barcelona, 18, 2140.
Spruston, N. (2008). Pyramidal neurons: Dendritic structure and synaptic integration.
Spruston, N. (2009). Pyramidal neuron. Scholarpedia, 4, 6130.
Stuart, G. J., & Sakmann, B. (1994). Active propagation of somatic action potentials into
neocortical pyramidal cell dendrites. Nature, 367, 6972.
Stuart, G., & Sakmann, B. (1995). Amplification of EPSPs by axosomatic sodium
channels in neocortical pyramidal neurons. Neuron, 15, 10651076.
Szentagothai, J. (1975). The module-concept in cerebral cortex architecture. Brain
Research, 95, 475496.
Cortical GABAergic Neurons

JF Staiger, University Medicine Gottingen, Gottingen, Germany
Glossary
Adapting Action potential firing pattern with decreasing

frequency under steady-state depolarizing current injection.
Bursting Action potential firing pattern with an initial highfrequency burst (riding on a depolarizing envelop) under
steady-state depolarizing current injection.
Calbindin d28k Calcium-binding protein with very
heterogeneous expression pattern in cortical neurons.
Calretinin Calcium-binding protein with a preferential
expression in bipolar (putative VIP-expressing) and
multipolar (putative SOM-expressing) cortical neurons.
Fast spiking Action potential firing pattern with nearly
continuous high frequency under steady-state depolarizing
current injection.
Feedback inhibition An inhibitory action imposed by
interneurons on a local population of principal neurons,
being not the same that excited the interneurons.
Feedforward inhibition An inhibitory action imposed by
interneurons on a local population of principal neurons,
being not the same that excited the interneurons.
Irregular spiking Action potential firing pattern with
constantly changing frequencies under steady-state
depolarizing current injection.
The majority of neurons in the neocortex are excitatory principal neurons that basically come in two forms: pyramidal and
nonpyramidal cells. The excitatory nonpyramidal cells are
called spiny stellate neurons (Feldmeyer, Egger, Lubke, &
Sakmann, 1999), and as a transitional form, also, star pyramidal cells are distinguished (Oberlaender et al., 2012; Schubert,
Kotter, Zilles, Luhmann, & Staiger, 2003; Staiger, Flagmeyer,
et al., 2004). These latter cell types, at least in rodents, are
mainly found in layer IV and considered to be excitatory interneurons since they do not project out of their home area and in
most instances also not out of their home column. By contrast,
the pyramidal cells in layers II/III, V, and VI issue long-range
projections to intra- and subcortical target sites (Ahissar &
Staiger, 2010; Feldmeyer, 2012) and are considered to form
the local circuits for information processing with their recurrent axonal collaterals (Douglas & Martin, 2007; Schubert,
Kotter, & Staiger et al. 2007). Interestingly, also, the excitatory
neurons are subject to a debate as to how many types do exist
(Nelson, Sugino, & Hempel, 2006; Sorensen et al., 2013).
Inhibitory GABAergic neurons are a very diverse class of neurons that also show a great deal of regional specificity. For
example, in the archicortex, up to 21 different subtypes have
been classified (Klausberger & Somogyi, 2008), and at an extreme,
it was even concluded that each GABAergic neuron is its own type
(Parra, Gulyas, & Miles, 1998). Here, I would like to focus on the
rodent neocortex, where several groups have studied the properties
of these cells mainly in the motor cortex (or in broader terms often
called frontal cortex; Cauli et al., 1997; Fino, Packer, & Yuste,
Late spiking Action potential firing pattern with delayed

first spike under rheobase steady-state depolarizing current
injection.
Microcolumnar organization A vertical array of neurons
reaching from the pial surface to the white matter that has a
tangential size of roughly 5080 mm (as opposed to
macrocolumns that reach 300600 mm in diameter).
Oscillations Synchronous population activity in a certain
frequency band.
Parvalbumin Calcium-binding protein with a preferential
expression in bitufted axo-axonic and multipolar basket
neurons.
Somatostatin A neuropeptide with inhibitory action, in the
cortex exclusively found in GABAergic neurons.
Vasoactive intestinal (poly)peptide A neuropeptide with
mixed excitatory/inhibitory action, in the cortex exclusively
found in GABAergic neurons.
Volume transmission Signal propagation of neurons by
releasing transmitter in the extracellular space, not at specific
synaptic locations.
2013; Kawaguchi, 1995; Kawaguchi & Kondo, 2002; Otsuka &

Kawaguchi, 2009), in the primary somatosensory (barrel) cortex
(Bayraktar, Welker, Freund, Zilles, & Staiger, 2000; David, Schleicher, Zuschratter, & Staiger, 2007; Fishell & Rudy, 2011; Gupta,
Wang, & Markram, 2000; Helmstaedter, Sakmann, & Feldmeyer,
2009; Karagiannis et al., 2009; Olah et al., 2009; Pohlkamp et al.,
2013; Rudy, Fishell, Lee, & Hjerling-Leffler, 2011; Silberberg &
Markram, 2007; Staiger, Masanneck, Schleicher, & Zuschratter,
2004; Staiger, Zuschratter, Luhmann, & Schubert, 2009; Szabadics
et al., 2006; Toledo-Rodriguez, Goodman, Illic, Wu, & Markram,
2005; Wang, Gupta, Toledo-Rodriguez, Wu, & Markram, 2002;
Wang et al., 2004; Xu, Jeong, Tremblay, & Rudy, 2013; Xu, Roby,
& Callaway, 2010), and in the primary visual cortex (Dumitriu,
Cossart, Huang, & Yuste, 2007; Gonchar, Wang, & Burkhalter,
2008; McGarry et al., 2010; Pfeffer, Xue, He, Huang, & Scanziani,
2013). Some of these data were summarized in previous reviews
(Burkhalter, 2008; Fishell & Rudy, 2011; Kawaguchi & Kubota,
1997; Markram et al., 2004). For the paleocortex, also an instructive
series of publications does exist (Suzuki & Bekkers, 2010a, 2010b;
Young & Sun, 2009). The same is true for inhibitory interneurons
in primates (Conde, Lund, Jacobowitz, Baimbridge, & Lewis,
1994; De Felipe, Ballesteros-Yanez, Inda, & Munoz, 2006; De
Felipe, Gonzalez-Albo, del Rio, & Elston, 1999; Delrio & De
Felipe, 1996; Gonzalez-Burgos & Lewis, 2008; Jones, 1975,
1993; Krimer et al., 2005), topics not further covered in this
article.
In 2008, many of these scientists coauthored a consensus
paper that worked toward a universally acceptable nomenclature
http://dx.doi.org/10.1016/B978-0-12-397025-1.00202-5
69
70
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Cortical GABAergic Neurons
and classification of cortical GABAergic interneurons (Ascoli et al.,

2008). However, when these features were applied to describe a
large sample of inhibitory interneurons and statistical tools were
used to group these cells into subtypes with given names, it appeared that only a few of these reached a high degree of consensus
(De Felipe et al., 2013), which were basically only axo-axonic and
Martinotti cells due to their unique axonal morphologies (see
succeeding text). This reinforces the notion that the major defining factor for a classification of the GABAergic interneurons is the
ramification pattern and the accompanying subcellular target
specificity (axon initial segment, perisomatic area, or peripheral
dendrites) of the different (sub-)types (Freund & Buzsaki, 1996;
Freund & Katona, 2007; Klausberger & Somogyi, 2008). Based
on this assumption and review of the available literature, it is
suggested that at least these six types of GABAergic neurons do
exist and are significantly different from each other: (i) axo-axonic
(or Chandelier) cells, (ii) basket cells (BC), (iii) Martinotti
cells, (iv) bipolar/bitufted cells (BPC), (v) neurogliaform cells
(NGFC), and (vi) GABAergic projection neurons (GPC).
Nevertheless, it should be noted here that manifold other
schemes have been proposed up-to-date. These were based
on (i) embryonic origin (Brown et al., 2011; Butt et al., 2005;
Ciceri et al., 2013; Flames & Marin, 2005; Kepecs & Fishell,
2014), (ii) somatodendritic morphological archetypes (Cobas,
Welker, Fairen, Kraftsik, & van der Loos, 1987), (iii) relationship
to cortical layers and columns (Gentet, 2012; Helmstaedter,
Sakmann, & Feldmeyer, 2009), (iv) action potential firing
pattern and neurochemistry (Burkhalter, 2008; Cauli et al.,
1997; Kawaguchi & Kubota, 1997; Toledo-Rodriguez et al.,
2005), (v) pathway control (Kubota, Hatada, Kondo, Karube, &
Kawaguchi, 2007; Somogyi, Tamas, Lujan, & Buhl, 1998), (vi)
synapse dynamics (Gupta et al., 2000), and (vii) directionality
(i.e., feedforward or feedback inhibition; Isaacson & Scanziani,
2011; Suzuki & Bekkers, 2012; Yang, Carrasquillo, Hooks,
Nerbonne, & Burkhalter, 2013). It is noteworthy that also recent
mathematical and computational approaches appear, at least
partially, helpful (Battaglia, Karagiannis, Gallopin, Gutch, &
Cauli, 2013; Parekh & Ascoli, 2013; Santana, McGarry, Bielza,
Larranaga, & Yuste, 2013).
This book article is organized into three parts. In the first, a
general overview of prevailing concepts on inhibition and the
cortical GABAergic neurons is presented. In the second, a more
specific description of the six subtypes listed earlier is provided.
And in the third, a short synopsis is attempted to where recent
methodological advances have led the field in terms of a functional
understanding of these neuronal subtypes. Currently, an entire
volume of Current Opinions in Neurobiology is compiled by
Gord Fishell and Gabor Tamas on the exciting state-of-the-art of
inhibition, to which the reader interested in more details is
referred to Fishell and Tamas (2014). I also would like to give a
reference to the original work done on Golgi preparations that is so
instructively summarized in a volume of Cerebral Cortex, edited
by Ted Jones and Alan Peters (Fairen, De Felipe, & Regidor, 1984).
cells, whereas GABAergic interneurons serve this processing

only indirectly by either regulating the gain or setting the
window for temporal or spatial integration or even simply by
preventing runaway excitation. A recent paper reflected on the
potential of interneurons to actually perform information processing themselves, as exemplified for place-selective interneurons in the hippocampus and for orientation-/directionselective interneurons in the visual cortex (Hangya, Pi, Kvitsiani, Ranade, & Kepecs, 2014). This review, however, then
simply concluded that GABAergic interneurons may control
the flow of information in excitatory neuronal ensembles. It
might be an academic discussion whether this reflects information processing or not. At a most parsimonious level, due to
the indispensable contribution of GABAergic neurons to any
kind of circuit activity, they have to contribute to information
processing in yet to be determined ways. Another heuristic
argument may be that the dominant response of neocortex in
awake animals performing visual information processing is
inhibition (Haider, Hausser, & Carandini, 2013).
Another refined concept regards the GABAergic cells as an
internal clock of brain states characterized by oscillations at
different frequencies (Buzsaki & Draguhn, 2004; Klausberger &
Somogyi, 2008; Stark et al., 2013) and thereby possibly controlling behavioral state (Fu et al., 2014; Kvitsiani et al., 2013; Pi
et al., 2013). It should also be noted that there is strong evidence
that at least some of the interneurons efficiently couple neuronal
processing to metabolic demand (Buzsaki, Kaila, & Raichle,
2007; Cauli et al., 2004; Lecrux et al., 2011). This may be a
necessary prerequisite to support high-frequency firing of both
the interneurons themselves and the ensemble of principal neurons that they control or even entrain to high frequencies.
However, several recent findings have further complicated
the understanding of inhibition in the cortex. It was suggested
(and vividly debated) that GABA released by interneurons
could also have excitatory effects (even in adult brain) at
dendritic, somatic, and especially axonic initial segment
locations (Glickfeld, Roberts, Somogyi, & Scanziani, 2009;
Gulledge & Stuart, 2003; Szabadics et al., 2006; Woodruff
et al., 2011). Thus, although circuit functions get better understood, it remains open at present by what cellular, synaptic,
and molecular mechanisms these functions of GABAergic cells
could be accomplished. Furthermore, some studies have found
not only short-term but also long-term plastic modifications of
synapses onto inhibitory interneurons or the inhibitory synapses themselves, suggesting that these neurons function not only
as rigid clocks but also as fine-tuning devices, presumably in a
cell type-specific manner (Freund & Katona, 2007; Kullmann,
Moreau, Bakiri, & Nicholson, 2012; Lefort, Gray, & Turrigiano,
2013). Out of the focus of this article but highly interesting
in terms of translational neuroscience is the potential of transplantation of interneurons to treat a broad variety of neurodegenerative and neuropsychiatric diseases (Marin, 2012;
Southwell et al., 2014).
The Many Facets of Inhibition by Cortical GABAergic

Neurons
The Best-Defined Types of Cortical GABAergic Neurons

and Their Possible Subtypes
It was generally believed that information processing takes

place in ensembles of synaptically interconnected pyramidal
As stated in the Abstract, at least six different types have been

repeatedly and consistently described. The level of insight gained

mainly with Golgi staining was conclusively summarized some
20 years ago (Fairen et al., 1984). Here, we will mainly focus on
work that was done thereafter, using biocytin-filled patch or
conventional sharp electrodes in vitro or in vivo (Marx, Gunter,
Hucko, Radnikow, & Feldmeyer, 2012; Parekh & Ascoli, 2013).
Axo-Axonic (or Chandelier) Cells

The axo-axonic cell (AAC; Figure 1) is the cell type with the
highest subcellular target specificity, that is, it targets only the
axon initial segments of pyramidal cells, which was firmly
established by correlated light and electron microscopy
(Somogyi, 1977). As such, it is considered to contribute to
the so-called perisomatic inhibition (as opposed to dendritic;
see the succeeding text). Over a long period, only anecdotal
71
reports appeared on the morphology or physiology of AAC (cf.

Borrell, Yoshimura, & Callaway, 2005; Helmstaedter et al.,
2009; Kawaguchi, 1995; Xu & Callaway, 2009; Zhu, Stornetta,
& Zhu, 2004). A series of recent reports then raised the big
questions whether these cells really are the strongest inhibitors
of their target cells, effectively vetoing any attempt to generate
an action potential, or whether they actually are the most
potent excitators of cortical pyramidal cell networks (Glickfeld
et al., 2009; Howard, Tamas, & Soltesz, 2005; Szabadics et al.,
2006; Woodruff et al., 2011). It was further recognized that in
the neocortex, AACs are a rare cell type (Inda, De Felipe, &
Munoz, 2009) and only with the advent of more refined
genetic labeling techniques, this cell type can now be studied
in a controlled manner (Taniguchi, 2014; Taniguchi, Lu, &
Huang, 2013; Woodruff et al., 2011).
S1BF
I
NGFC
AAC
II/III
BPC
IV
BC
Va
MC
Vb
VI
GPC
wm
Figure 1 Graphical representation of the basic morphological features of the six types of GABAergic neurons. They are exemplified for the primary
somatosensory (barrel) cortex (S1BF). Vertical stippled lines delineate areal borders (to the left being secondary somatosensory cortex and to the
right the hindlimb area), whereas horizontal stippled lines indicate layer borders (Roman numerals indicate cortical layers; wm, white matter).
The different cell types are color-coded and placed into a most typical layer; darker hue is used for the somatodendritic domain and lighter hue for the
axon (AAC, brown; BC, green; MC, yellowish; BPC, red; NGFC, mauve; GPC, blue). Please note the much higher complexity of the arbors in the
photoreconstructions shown in Figure 2(g)2(i).
72
Axo-axonic cells have been classically called chandelier cells

due to the recurrent axonal collaterals carrying cartridges of
roughly 37 boutons. Thus, on average, the ca. 16 boutons
found on the axon initial segment (AIS) of a pyramidal cell
should converge from four neighboring AAC (Inan et al.,
2013). For still unknown functional reasons, there are two
tiers of preferential occurrence of AAC-somata, upper layers
(L) II/III and L Vb and VI (Taniguchi et al., 2013). These somata
mostly possess a bitufted or multipolar dendritic tree and often
express parvalbumin (in up to 50% of the cases), in a cortical
area-dependent manner (Taniguchi et al., 2013). Interestingly,
no matter whether they express parvalbumin or not, this landmark study found that these neurons invariably show a fastspiking action potential firing pattern. Functionally, paired
recordings or other refined electrophysiological techniques
have resolved the debate on whether AACs are only inhibitory
(Glickfeld et al., 2009) or excitatory (Szabadics et al., 2006).
They have the potential to exert both effects in neuronal networks, the actual sign of action being dependent on the membrane potential and the momentary chloride equilibrium
potential in the spatially very restricted AIS (Khirug et al.,
2008). Now the quest is on which of these potentials they use
for which of the many functions cortical networks can perform
(Douglas & Martin, 2012; Mountcastle, 1997), although a
recent notion suggests that AACs may play a dual role in the
circuit, on the one hand helping to activate quiescent pyramidal
neurons while at the same time inhibiting active ones in a
concerted and meaningful manner (Woodruff et al., 2011).
Basket Cells
BCs (Figure 1) are the second and core-contributing cell type for
perisomatic inhibition (Freund & Katona, 2007). In a broad
sense, for this type, three different subtypes were proposed: the
classical (1) small (Figure 2(d)) and (2) large BCs were recently
complemented by the so-called (3) nest BC (Wang et al., 2002),
which as a population can be found in any cortical layer except L
I. Maybe other subtypes exist as well (see succeeding text), and
thus, it is not too surprising that a recent classification attempt
found little agreement on this cell type (De Felipe et al., 2013).
However, parvalbumin seems to be a suitable neurochemical
marker (Figure 2(a)), as is the fast-spiking firing pattern
(Figure 2(g)) at the physiological level (Cauli et al., 1997;
Kawaguchi, 1995). Parvalbumin defines with a proportion of
roughly 40% the largest group of cortical GABAergic neurons
(Pfeffer et al., 2013; Rudy et al., 2011), with a preponderance in
somatic and bouton staining in layers IV and Vb. It should,
however, be noted that also nonparvalbumin, non-fast-spiking
BCs might exist (Kawaguchi & Kubota, 1998).
The main features of small BCs are a very local multipolar
dendritic tree (aspiny and beaded, typical for all axo-axonic
and BCs) and a local (i.e., intralaminar and intracolumnar)
dense axonal plexus, whose boutons form symmetrical synaptic contacts to a large degree on somata and perisomatic dendrites (Alonso-Nanclares et al., 2004; Alonso-Nanclares,
White, Elston, & De Felipe, 2004). At a single cell level, the
formation of pericellular baskets is very subtle, which makes
the morphological identification of these cells more difficult
than expected. So, it is very helpful to have the postsynaptic
target cells labeled, which can be excitatory and inhibitory
neurons (Chattopadhyaya et al., 2004; Staiger et al., 2009;

Tamas, Somogyi, & Buhl, 1998; Thomson, West, Wang, &
Bannister, 2002). However, a full quantitative analysis at the
correlated light and electron microscopic level, to clearly show
what proportion of the synapses target different subcellular
compartments, is still missing. Thus, the reported range varies
between 50% somatic targeting for the cat visual cortex
(Kisvarday, Martin, Whitteridge, & Somogyi, 1985) and just
12% (and more) for rat motor cortex (Karube, Kubota, &
Kawaguchi, 2004). Certainly, a blanket of inhibition (Packer
& Yuste, 2011) caused by cortical BCs can be imposed on
principal neurons and other BCs (Pfeffer et al., 2013) but can
be extended to more cell types, for example, to VIP-expressing
neurons (Staiger, Freund, & Zilles, 1997), as well as to Martinotti cells (own unpublished observations).
The main features of large BCs are their extensive layer- and
column-spanning dendritic and axonal arbors, which are,
however, less dense and therefore even more difficult to classify correctly at a single cell level. They have been called lateral
inhibitors (Helmstaedter et al., 2009), but in an elegant study
in the cat visual cortex, many different modes of operation
became apparent (Buzas, Eysel, Adorjan, & Kisvarday, 2001)
that do make a single mode of action unlikely.
The nest BCs are in-between in many features, and thus, it is
difficult to judge whether they are a cell type in its own right or
just the middle portion of a feature continuum (Wang et al.,
2002). Such a continuum could represent the layer-specific
needs of instantaneous excitationinhibition balance by
means of feedforward inhibition and feedback inhibition that
are considered to be the main functions of BCs (Isaacson &
Scanziani, 2011).
Interestingly, a novel fast-spiking GABAergic interneuron
was recently characterized in the visual cortex (Bortone,
Olsen, & Scanziani, 2014), which was shown to mediate a
cellular mechanism for gain control (Olsen, Bortone, Adesnik,
& Scanziani, 2012). If these cells should turn out to be BCs, an
even greater diversity of this formerly considered to be rather
homogenous cell type would become manifest.
Martinotti Cells
Because of their unique axonal ramification in layer I, Martinotti cells (MC; Figure 1) are the second best-recognizable
cell type (in terms of morphology; De Felipe et al., 2013),
and since there are very specific mouse models (Ma, Hu,
Berrebi, Mathers, & Agmon, 2006; Oliva, Jiang, Lam, Smith, &
Swann, 2000; Taniguchi et al., 2011), also, a lot has been
learned about other properties, especially functional ones.
From the present data, it can be stated that Martinotti cells
with a mainly bitufted to multipolar dendritic tree (often
being not so sparsely spiny!) can be found in all cortical layers
(again except L I) and, no matter where they are located, always
send a significant portion of their axon into L I (Figure 2(e))
where it densely ramifies (Wang et al., 2004). However,
although conceptually ignored up to now, the largest portion
of the axon stays outside of L I and has not been studied
functionally so far. Unfortunately, no detailed synaptology for
Martinotti cells does exist in the neocortex. Interestingly, data
from hippocampus strongly suggest that dendritic shafts and
spines of pyramidal cells as well as many types of interneurons
I
II/III
IV
Va
Vb
VI
wm
(a)
(b)
(c)
II/III
IV
Va
Vb
VI
Basket cell
Martinotti cell
Bitufted cell
wm
(d)
(g)
(e)
Fast spiking
(h)
(f)
Adapting
(i)
Irregular-spiking
Figure 2 Basic morphological and electrophysiological properties of the three major neurochemically defined GABAergic neurons in the barrel cortex.
(a) shows a low-magnification image of a PVcre section (pseudocolored green), which makes clear that PV cells (which should be mostly basket
cells in this stain; see Figure 2(d)) have a preferential location in layers IV and Vb. (b) shows a low-magnification image of a SOMcre section
(pseudocolored yellow), which makes clear that SOM cells (which should be mostly Martinotti cells in this stain; see Figure 2(e)) have a preferential
location in layers V and VI. (c) shows a low-magnification image of a VIPcre section (red), which makes clear that VIP cells (which should be
mostly bipolar/bitufted cells in this stain; see Figure 2(f)) have a preferential location in layer II/III. Roman numerals indicate cortical layers; scale bar,
200 mm. (df) show photoreconstructions, all in layer II/III, of a parvalbumin-expressing, fast-spiking basket cell (d), a somatostatin-expressing,
adapting Martinotti cell (e) and a VIP-expressing irregular-spiking bitufted cell (f). Please note the varicosities of the basket cell in L I, which are dendritic
and not axonal. Please also note that the axonal arbor of the Martinotti cell is artificially truncated due to restrictions of figure size but extends over
more than 2 mm tangentially below the pia. (gi) show (one of) the typical action potential firing patterns upon strong depolarizing current injections via
whole cell patch clamp electrodes (g, continuous fast-spiking; h, continuous adapting; i, irregular-spiking).
74
are postsynaptic to Martinotti cell boutons (Katona, Acsady, &

Freund, 1998). This agrees well with morphologically more
indirect but functionally conclusive results from neocortical
studies (Pfeffer et al., 2013; Silberberg & Markram, 2007).
These cells express somatostatin as a marker molecule
(Figure 2(b)) and are nearly exclusively of the adapting (regular
or low-threshold spiking; Figure 2(h) action potential firing
type; Cauli et al., 1997; Karagiannis et al., 2009; Kawaguchi &
Kubota, 1996; McGarry et al., 2010; Wang et al., 2004). It was
estimated that ca. 30% of all GABAergic neurons are
somatostatin-expressing (Pfeffer et al., 2013; Rudy et al.,
2011) and they are preferentially to be found in layers V and VI.
The best-studied circuit motif until recently was disynaptic
inhibition of neighboring pyramidal cells in layers II/III and V,
which very likely represents a form of lateral inhibition
(Berger, Perin, Silberberg, & Markram, 2009; Silberberg &
Markram, 2007). However, now, a large number of studies
covering many different cortical areas have revealed that Martinotti cells are a prime target for a disinhibitory action by which
VIP-expressing bipolar/bitufted neurons (see succeeding text)
can boost the activity in principal cell ensembles, a mechanisms
that seems to improve sensory processing and sensorydependent learning (Chamberland & Topolnik, 2012; Fu
et al., 2014; Lee, Kruglikov, Huang, Fishell, & Rudy, 2013;
Pfeffer et al., 2013; Pi et al., 2013). This will be detailed more
in the final paragraph of the article. It should be noted that we
have predicted this disinhibitory circuit, at both a morphological level and an electrophysiological level (Gentet et al., 2012;
Staiger, Masanneck, Schleicher, & Zuschratter, 2004).
Bipolar/Bitufted Cells
These BPCs (Figure 1), until very recently, were considered to
be enigmatic (Peters & Harriman, 1988) and bear a lot of
further names that are often more ornamental than scientifically helpful, like double-bouquet, arcade, or horsetail cells
(De Felipe et al., 2013; Kawaguchi & Kubota, 1996). In the
primate neocortex, however, the term double-bouquet cell is
reasonably used for a very fascinating calbindin D28kexpressing cell type that possesses a unique axonal feature
(De Felipe, Hendry, Hashikawa, Molinari, & Jones, 1990;
Yanez et al., 2005), namely, a microcolumnar organization.
Here, in rodents, the term BPC is strictly used to describe the
vertically oriented somatodendritic organization; the axon,
however, also being vertically extended, is often spanning
many or even all cortical layers in a narrow, column-restricted
manner (Bayraktar et al., 2000; Kawaguchi & Kubota, 1996).
This suggests that this cell type not only can integrate many
different inputs across all cortical layers but in a momentarily
impossible to elucidate functional logic also feeds back/
forward inhibition to all these same layers (Figure 2(f)). A
useful molecular marker is the ionotropic serotonin receptor
5HT-3 or more specifically vasoactive intestinal polypeptide
(VIP; Figure 2(c)) (Bayraktar et al., 2000; Lee, Hjerling-Leffler,
Zagha, Fishell, & Rudy, 2010; Pfeffer et al., 2013) but also
calretinin or choline acetyltransferase has been detected in
many BPCs (Bayraktar et al., 1997; Caputi, Rozov, Blatow, &
Monyer, 2009; Cauli et al., 2000; von Engelhardt, Eliava, Meyer,
Rozov, & Monyer, 2007). The electrophysiological markers
show a very high input resistance and are predominantly
adapting (previously regular-spiking nonpyramidal) and bursting (burst-spiking, BS), but very often also irregular-spiking
(Figure 2(i)) (Cauli et al., 1997; Karagiannis et al., 2009; Kawaguchi & Kubota, 1996).
We are focussing here on VIP neurons that have been relatively
neglected for a long time but are now in focus of very many
research groups, due to the availability of specific mouse models.
It was estimated that roughly 1217% of all cortical GABAergic
neurons express VIP (Pfeffer et al., 2013; Rudy et al., 2011;
Uematsu et al., 2008), which are highly concentrated in layer II/
III. In the early days, right after their initial description (Morrison,
Magistretti, Benoit, & Bloom, 1984; Sims, Hoffman, Said, &
Zimmerman, 1980), a detailed ultrastructural examination
already suggested that medium-sized smooth dendrites (i.e.,
very likely originating from other inhibitory interneurons) are
their main subcellular target structure (Connor & Peters, 1984;
Peters & Harriman, 1988). Indeed, the VIP neurons are considered
to be of the dendrite-targeting type, although at least small basket
neurons in rat also do seem to express this neuropeptide (Wang
et al., 2002). Also, from the beginning, it had been obvious that
these neurons are predominantly vertically organized, so it was
self-evident to imply them in columnar or even microcolumnar
function (Bayraktar et al., 2000; Magistretti & Morrison, 1988;
Zilles et al., 1993). In functional assays, however, surprisingly, a
net excitatory effect was often found (Haas & Gahwiler, 1992;
Sessler, Grady, Waterhouse, & Moises, 1991). This net excitation is
likely to be one of the many possible outcomes of a behaviorally
specific activation of VIP neurons by (cholinergic) arousal
mechanisms that leads to the inhibition of Martinotti cells as a
preferred target, which in turn results in disinhibition of principal
neurons (Arroyo, Bennett, Aziz, Brown, & Hestrin, 2012; Fu et al.,
2014; Gentet et al., 2012; Lee et al., 2013; Pi et al., 2013; Staiger,
Masanneck, Schleicher, & Zuschratter, 2004).
Neurogliaform Cells
The NGFCs (Figure 1) actually are still very enigmatic, although,
since the landmark papers published by Gabor Tamas group,
the notion is up that they may be an unconventional type of
volume transmission-utilizing interneuron, which not only acts
at a slower timescale via GABA-B-receptors (Olah et al., 2009;
Tamas, Lorincz, Simon, & Szabadics, 2003) but also activates
GABA-A-receptors and is promiscuously connected to other
interneurons by gap junctions (Simon, Olah, Molnar,
Szabadics, & Tamas, 2005). One of the problems of this interneuron type is that there are few specific markers to easily and
reliably identify it. They are characterized by a late-spiking
action potential firing pattern (Miyoshi et al., 2010; Tamas
et al., 2003), alpha-actinin 2, reelin, NPY, or nNOS expression
(Karagiannis et al., 2009; Kubota et al., 2011; Miyoshi et al.,
2010; Olah et al., 2009; Pohlkamp et al., 2013), and also their
unique morphology with many short primary dendrites and
among the thinnest and most densely arborizing axonal arbor
of all neurons (Kubota et al., 2011; Povysheva et al., 2007). This
morphology also led to the names dwarf cell or spiderweb cell
(Jones, 1984). In contrast to all previous cell types described in
this article, it has a frequent occurrence in layer I, which is,
however, not an exclusive location but it can be found in any
layer (Hestrin & Armstrong, 1996; Jiang, Wang, Lee, Stornetta, &
Zhu, 2013; Olah et al., 2009).

Very little is known about the precise connectivity of this
neuronal type. The available studies suggest that they are connected by chemical synapses to local pyramidal cells in a
reciprocal manner (Wozny & Williams, 2011), whereas electrical synapses are made with different interneurons (Simon
et al., 2005) and nonsynaptic communication might be effective to all somatodendritic structures located within the axonal
cloud (Olah et al., 2009). There was, however, a recent publication that questioned the universality of this indiscriminate
volume transmission scheme. McBain and colleagues reported
that NGFCs at an unusual location (i.e., layer IV of the primary
somatosensory cortex) specifically modulate feedforward thalamic inhibition on spiny stellate cells but not thalamic feedforward excitation on nearby synapses (Chittajallu, Pelkey, &
McBain, 2013). This might be only one example of a more
general scheme on how GABA-B-receptor-mediated inhibition
is able to shape the activity of larger networks of principal
neurons by diverse mechanisms (Craig & McBain, 2014).
GABAergic Projection Neurons

This GABAergic projection neuron cell type (GPC; Figure 1) is
the single reason why the whole article is not called Cortical
GABAergic interneurons. So, we should finally shortly discuss
what an interneuron is supposed to be. In my opinion, there is
no strict definition for this term, but intuitively, local interneurons should not project out of the cortex and probably also
not out of their home area (see also Introduction for the
definition of an excitatory interneuron). If this is the criterion
to be met, only the neurons to be described in this paragraph
are GABAergic projection neurons. If it is a more conservative
criterion (not outside the home column or even layer), most of
the GABAergic neurons would be projection and not local
neurons, especially Martinotti cells or the so-called elongated
NGFCs of layer I (see Figure 1), which possess horizontal
collaterals that can span more than 2 mm (Jiang et al., 2013;
Wang et al., 2004). Here, a projection neuron is defined as one
projecting into a neighboring area, no matter whether the
route taken by the axon leads through the gray or white matter.
Interestingly, one of the few studies demonstrating this type
of GABAergic neuron also established somatostatin (together
with NPY and nNOS) as their main neurochemical marker
(Tomioka et al., 2005), which is similar to Martinotti cells.
But although Martinotti cells may extend their axon for more
than 2 mm, these projection neurons were found at distances
up to 8 mm remote from the injection site of the retrograde
tracer and thus cannot be simply back-labeled classical Martinotti cells. Basically, several other groups have obtained similar
results, both for ipsilateral (Aroniadou-Anderjaska & Keller,
1996; Fabri & Manzoni, 1996; McDonald & Burkhalter,
1993) and even for callosal corticocortical projections (Fabri
& Manzoni, 2004). Very often, these cells are located deep in
layer VI or even in the white matter (Tomioka et al., 2005). To
the best of my knowledge, they have not been characterized
electrophysiologically or morphologically at an identified single cell level so far. Nothing is known about their function to
date. A look into the archicortex offers the interesting possibility that GABAergic projection neurons targeting local GABAergic interneurons can synchronize distant areas to behaviorally
relevant rhythmic discharges (Melzer et al., 2012).
75
Circuit Motifs and Putative Functions of Cortical

GABAergic Neurons
With the advent of specific cre-driver lines (Taniguchi et al.,
2011), the field recently exploded. It became clear by optogenetic manipulation of the major types of GABAergic neurons
that they participate in early and late sensory processing, support
learning, and reward mechanisms as well as motor behavior
(Abadesco et al., 2014; Adesnik, Bruns, Taniguchi, Huang, &
Scanziani, 2012; Cardin et al., 2009; Fu et al., 2014; Gentet,
Avermann, Matyas, Staiger, & Petersen, 2010; Gentet et al.,
2012; Kerlin, Andermann, Berezovskii, & Reid, 2010; Kvitsiani
et al., 2013; Lee et al., 2013, 2012; Letzkus et al., 2011; Pi et al.,
2013; Sachidhanandam, Sreenivasan, Kyriakatos, Kremer, &
Petersen, 2013; Sohal, Zhang, Yizhar, & Deisseroth, 2009;
Wilson, Runyan, Wang, & Sur, 2012; Yizhar et al., 2011). However, the precise circuit mechanisms responsible for the observed
behavior remained often but not always obscure (Figure 3).
Whereas dense local connectivity with principal cells was
interpreted as a blanket of inhibition imposed by basket and
Martinotti cells on their local circuits (Fino et al., 2013; Fino &
Yuste, 2011; Packer & Yuste, 2011), VIP-expressing bipolar/
bitufted interneurons were recently demonstrated to make a
whole in this blanket by inhibiting mainly Martinotti cells but
very likely also a subset of BCs (David et al., 2007; Karnani,
Agetsuma, & Yuste, 2014; Lee et al., 2013; Pfeffer et al., 2013).
This VIP cell-mediated disinhibition was consistently found
across many cortical areas and seems to be a very powerful
circuit motif (Fu et al., 2014; Pi et al., 2013). However, it is by
far not the only disinhibitory circuit motif that has just recently
been established. In a few circuits, we do not know both
participating interneuron types (Christophe et al., 2002;
Letzkus et al., 2011), but in others, it could be shown that (i)
somatostatin-expressing layer IV BCs are disinhibiting principal cells via their inhibition of local fast-spiking BCs (Xu et al.,
2013), (ii) NPY-expressing layer IV NGFCs disinhibit principal
cells via GABA-B-receptor-mediated suppression of fast-spiking
neurons (Chittajallu et al., 2013), and (iii) many possible
disinhibitory circuits have been proposed by the multiple
patch clamp recordings of inhibitory interneurons and several
target cells in different layers (Jiang et al., 2013).
In summary, these are exciting times for researchers interested in GABAergic (inter)neurons since all the necessary tools
for a meaningful study of structure, function, genetics, and
participation in precisely defined behaviors are available
now. Thus, with a suitable combination of these techniques,
we might soon be able to understand and then deliberately
manipulate single cells (types) to reach not only a mechanistic
understanding of basic but also more elaborate functions of
the neocortex (Feldmeyer et al., 2013; OConnor et al., 2013;
OConnor, Huber, & Svoboda, 2009).
Acknowledgments
I would like to cordially thank my former mentor, Prof. Karl
Zilles, for setting me on the track of GABAergic interneurons
and for inspiration. Many thanks are due to the members of the
Barrel Cortical Circuits Group and especially Alvar Pronneke
76
Local
cortical input
Long-range
cortical input
Subcortical
neuromodulatory
input
BPC
(VIP)
MC
(SOM)
BC
(PV)
Thalamic input
Figure 3 Circuit diagram depicting some important connectional motifs of VIP-, SOM- and PV-expressing interneurons. This diagram shows that
VIP-expressing BPC can sample input from many local and distant sources and feed forward this integrated input to SOM-expressing MC, PV-expressing
BC, and glutamatergic principal neurons (blue) to cause a complex inhibition (weak, thin line) disinhibition (strong, thick line or weak, in a target
cell type-specific manner) configuration of the local circuit. Long-range cortical input is considered to originate from other cortical areas, local cortical
input from the same area or even the same column; subcortical modulatory inputs are cholinergic from the basal forebrain, serotonergic from the
raphe nuclei, noradrenergic from the locus coeruleus, and potentially dopaminergic from the ventral tegmental area. Especially, cholinergic projections
are powerful activators of VIP neurons. Furthermore, the diagram shows thalamus-generated feedforward inhibition by basket cells. At the same time,
this neuron type is often involved in feedback inhibition, possibly of the very same neurons that excite them, thus forming reciprocal connections.
for the help with the figures. I also would like to thank the
German Research Council (DFG) for supporting this line of
research since 1997. I sincerely apologize to my colleagues
whose great research I could not refer to due to limited space
and the special focus of this book chapter.

Auditory Cortex; Basal Forebrain Anatomical Systems in MRI Space;
Cortex; Columns of the Mammalian Cortex; Cytoarchitecture and Maps
of the Human Cerebral Cortex; Functional and Structural Diversity of
Pyramidal Cells; Functional Organization of the Primary Visual Cortex;
Motor Cortex; Somatosensory Cortex; Synaptic Organization of the

Cerebral Cortex; The Olfactory Cortex; INTRODUCTION TO
CLINICAL BRAIN MAPPING: Limbic to Motor Interactions during
Social Perception; Schizophrenia.
References
Abadesco, A. D., Cilluffo, M., Yvone, G. M., Carpenter, E. M., Howell, B. W., &
Phelps, P. E. (2014). Novel disabled-1-expressing neurons identified in adult brain
and spinal cord. European Journal of Neuroscience, 39, 579592.
Adesnik, H., Bruns, W., Taniguchi, H., Huang, Z. J., & Scanziani, M. (2012). A neural
circuit for spatial summation in visual cortex. Nature, 490, 226231.

Ahissar, E., & Staiger, J. F. (2010). S1 laminar specialization. Scholarpedia, 5, 7457.
http://dx.doi.org/10.4249/scholarpedia.7457.
Alonso-Nanclares, L., Minelli, A., Melone, M., Edwards, R. H., De Felipe, J., & Conti, F.
(2004). Perisomatic glutamatergic axon terminals: A novel feature of cortical
synaptology revealed by vesicular glutamate transporter 1 immunostaining.
Alonso-Nanclares, L., White, E. L., Elston, G. N., & De Felipe, J. (2004). Synaptology of
the proximal segment of pyramidal cell basal dendrites. European Journal of
Aroniadou-Anderjaska, V., & Keller, A. (1996). Intrinsic inhibitory pathways in mouse
barrel cortex. Neuroreport, 7, 23632368.
Arroyo, S., Bennett, C., Aziz, D., Brown, S. P., & Hestrin, S. (2012). Prolonged
disynaptic inhibition in the cortex mediated by slow, non-alpha 7 nicotinic excitation
of a specific subset of cortical interneurons. Journal of Neuroscience, 32,
38593864.
Ascoli, G. A., Alonso-Nanclares, L., Anderson, S. A., Barrionuevo, G.,
Benavides-Piccione, R., Burkhalter, A., et al. (2008). Petilla terminology:
Nomenclature of features of GABAergic interneurons of the cerebral cortex. Nature
Reviews Neuroscience, 9, 557568.
Battaglia, D., Karagiannis, A., Gallopin, T., Gutch, H. W., & Cauli, B. (2013). Beyond the
frontiers of neuronal types. Frontiers in Neural Circuits, 7, 13.
Bayraktar, T., Staiger, J. F., Acsady, L., Cozzari, C., Freund, T. F., & Zilles, K. (1997).
Co-localization of vasoactive intestinal polypeptide, gamma-aminobutyric acid and
choline acetyltransferase in neocortical interneurons of the adult rat. Brain Research,
757, 209217.
Bayraktar, T., Welker, E., Freund, T. F., Zilles, K., & Staiger, J. F. (2000). Neurons
immunoreactive for vasoactive intestinal polypeptide in the rat primary
somatosensory cortex: Morphology and spatial relationship to barrel-related
columns. Journal of Comparative Neurology, 420, 291304.
Berger, T. K., Perin, R., Silberberg, G., & Markram, H. (2009). Frequency-dependent
disynaptic inhibition in the pyramidal network: A ubiquitous pathway in the
developing rat neocortex. Journal of Physiology, 587, 54115425.
Borrell, V., Yoshimura, Y., & Callaway, E. M. (2005). Targeted gene delivery to
telencephalic inhibitory neurons by directional in utero electroporation. Journal of
Bortone, D. S., Olsen, S. R., & Scanziani, M. (2014). Translaminar inhibitory cells
recruited by layer 6 corticothalamic neurons suppress visual cortex. Neuron, 82,
474485.
Brown, K. N., Chen, S., Han, Z., Lu, C. H., Tan, X., Zhang, X. J., et al. (2011). Clonal
production and organization of inhibitory interneurons in the neocortex. Science,
334, 480486.
Burkhalter, A. (2008). Many specialists for suppressing cortical excitation. Frontiers in
Butt, S. J. B., Fuccillo, M., Nery, S., Noctor, S., Kriegstein, A., Corbin, J. G., et al.
(2005). The temporal and spatial origins of cortical interneurons predict their
physiological subtype. Neuron, 48, 591604.
Buzas, P., Eysel, U. T., Adorjan, P., & Kisvarday, Z. F. (2001). Axonal topography of
cortical basket cells in relation to orientation, direction, and ocular dominance
maps. Journal of Comparative Neurology, 437, 259285.
Buzsaki, G., & Draguhn, A. (2004). Neuronal oscillations in cortical networks. Science,
304, 19261929.
Buzsaki, G., Kaila, K., & Raichle, M. (2007). Inhibition and brain work. Neuron, 56,
771783.
Caputi, A., Rozov, A., Blatow, M., & Monyer, H. (2009). Two calretinin-positive
GABAergic cell types in layer 2/3 of the mouse neocortex provide different forms of
inhibition. Cerebral Cortex, 19, 13451359.
Cardin, J. A., Carlen, M., Meletis, K., Knoblich, U., Zhang, F., Deisseroth, K., et al.
(2009). Driving fast-spiking cells induces gamma rhythm and controls sensory
responses. Nature, 459, 663667.
Cauli, B., Audinat, E., Lambolez, B., Angulo, M. C., Ropert, N., Tsuzuki, K., et al. (1997).
Molecular and physiological diversity of cortical nonpyramidal cells. Journal of
Cauli, B., Porter, J. T., Tsuzuki, K., Lambolez, B., Rossier, J., Quenet, B., et al. (2000).
Classification of fusiform neocortical interneurons based on unsupervised
clustering. Proceedings of the National Academy of Sciences of the United States of
America, 97, 61446149.
Cauli, B., Tong, X. K., Rancillac, A., Serluca, N., Lambolez, B., Rossier, J., et al. (2004).
Cortical GABA interneurons in neurovascular coupling: Relays for subcortical
vasoactive pathways. Journal of Neuroscience, 24, 89408949.
Chamberland, S., & Topolnik, L. (2012). Inhibitory control of hippocampal inhibitory
neurons. Frontiers in Neuroscience, 6, 165.
Chattopadhyaya, B., Di Cristo, G., Higashiyama, H., Knott, G. W., Kuhlman, S. J.,
Welker, E., et al. (2004). Experience and activity-dependent maturation of
77
perisomatic GABAergic innervation in primary visual cortex during a postnatal

critical period. Journal of Neuroscience, 24, 95989611.
Chittajallu, R., Pelkey, K. A., & McBain, C. J. (2013). Neurogliaform cells dynamically
regulate somatosensory integration via synapse-specific modulation. Nature
Neuroscience, 16, 13U167.
Christophe, E., Roebuck, A., Staiger, J. F., Lavery, D. J., Charpak, S., & Audinat, E.
(2002). Two types of nicotinic receptors mediate an excitation of neocortical layer I
interneurons. Journal of Neurophysiology, 88, 13181327.
Ciceri, G., Dehorter, N., Sols, I., Huang, Z. J., Maravall, M., & Marin, O. (2013).
Lineage-specific laminar organization of cortical GABAergic interneurons. Nature
Cobas, A., Welker, E., Fairen, A., Kraftsik, R., & van der Loos, H. (1987). GABAergic
neurons in the barrel cortex of the mouse An analysis using neuronal archetypes.
Journal of Neurocytology, 16, 843871.
Conde, F., Lund, J. S., Jacobowitz, D. M., Baimbridge, K. G., & Lewis, D. A. (1994).
Local circuit neurons immunoreactive for calretinin, calbindin D-28 k or
parvalbumin in monkey prefrontal cortex: Distribution and morphology. Journal of
Connor, J. R., & Peters, A. (1984). Vasoactive intestinal polypeptide-immunoreactive
neurons in rat visual cortex. Neuroscience, 12, 10271044.
Craig, M. T., & McBain, C. J. (2014). The emerging role of GABA receptors as
regulators of network dynamics: Fast actions from a slow receptor? Current
Opinion in Neurobiology, 26C, 1521.
David, C., Schleicher, A., Zuschratter, W., & Staiger, J. F. (2007). The innervation of
parvalbumin-containing interneurons by VIP-immunopositive interneurons in the
primary somatosensory cortex of the adult rat. European Journal of Neuroscience,
25, 23292340.
De Felipe, J., Ballesteros-Yanez, I., Inda, M. C., & Munoz, A. (2006). Double-bouquet
cells in the monkey and human cerebral cortex with special reference to areas 17
and 18. In Progress in Brain Research (pp. 1532). .
De Felipe, J., Gonzalez-Albo, M. C., del Rio, M. R., & Elston, G. N. (1999). Distribution
and patterns of connectivity of interneurons containing calbindin, calretinin, and
parvalbumin in visual areas of the occipital and temporal lobes of the macaque
monkey. Journal of Comparative Neurology, 412, 515526.
De Felipe, J., Hendry, S. H., Hashikawa, T., Molinari, M., & Jones, E. G. (1990). A
microcolumnar structure of monkey cerebral cortex revealed by
immunocytochemical studies of double bouquet cell axons. Neuroscience, 37,
655673.
De Felipe, J., Lopez-Cruz, P. L., Benavides-Piccione, R., Bielza, C., Larranaga, P.,
Anderson, S., et al. (2013). New insights into the classification and nomenclature of
cortical GABAergic interneurons. Nature Reviews Neuroscience, 14, 202216.
Delrio, M. R., & De Felipe, J. (1996). Colocalization of calbindin D-28 k, calretinin, and
GABA immunoreactivities in neurons of the human temporal cortex. Journal of
Douglas, R. J., & Martin, K. A. C. (2007). Mapping the matrix: The ways of neocortex.
Neuron, 56, 226238.
Douglas, R. J., & Martin, K. A. C. (2012). Behavioral architecture of the cortical sheet.
Current Biology, 22, R1033R1038.
Dumitriu, D., Cossart, R., Huang, J., & Yuste, R. (2007). Correlation between axonal
morphologies and synaptic input kinetics of interneurons from mouse visual cortex.
Fabri, M., & Manzoni, T. (1996). Glutamate decarboxylase immunoreactivity in
corticocortical projecting neurons of rat somatic sensory cortex. Neuroscience, 72,
435448.
Fabri, M., & Manzoni, T. (2004). Glutamic acid decarboxylase immunoreactivity in
callosal projecting neurons of cat and rat somatic sensory areas. Neuroscience, 123,
557566.
Fairen, A., De Felipe, J., & Regidor, J. (1984). Nonpyramidal neurons. In A. Peters &
E. G. Jones (Eds.), Cellular components of the cerebral cortex (pp. 201253).
New York: Plenum Press.
Feldmeyer, D. (2012). Excitatory neuronal connectivity in the barrel cortex. Frontiers in
Feldmeyer, D., Brecht, M., Helmchen, F., Petersen, C. C. H., Poulet, J. F. A., Staiger, J. F.,
et al. (2013). Barrel cortex function. Progress in Neurobiology, 103, 327.
Feldmeyer, D., Egger, V., Lubke, J., & Sakmann, B. (1999). Reliable synaptic
connections between pairs of excitatory layer 4 neurones within a single barrel of
developing rat somatosensory cortex. Journal of Physiology, 521, 169190.
Fino, E., Packer, A. M., & Yuste, R. (2013). The logic of inhibitory connectivity in the
neocortex. The Neuroscientist, 19, 228237.
Fino, E., & Yuste, R. (2011). Dense inhibitory connectivity in neocortex. Neuron, 69,
11881203.
Fishell, G., & Rudy, B. (2011). Mechanisms of inhibition within the telencephalon:
where the wild things are. Annual Review of Neuroscience, 34, 535567.
78
Fishell, G., & Tamas, G. (2014). Inhibition: synapses, neurons and circuits. Current
Opinion in Neurobiology, 26, vvii.
Flames, N., & Marin, O. (2005). Developmental mechanisms underlying the generation
of cortical interneuron diversity. Neuron, 46, 377381.
Freund, T. F., & Buzsaki, G. (1996). Interneurons of the hippocampus. Hippocampus, 6,
347470.
Freund, T. F., & Katona, I. (2007). Perisomatic inhibition. Neuron, 56, 3342.
Fu, Y., Tucciarone, J. M., Espinosa, J. S., Sheng, N., Darcy, D. P., Nicoll, R. A., et al.
(2014). A cortical circuit for gain control by behavioral state. Cell, 156, 11391152.
Gentet, L. J. (2012). Functional diversity of supragranular GABAergic neurons in the
barrel cortex. Frontiers in Neural Circuits, 6.
Gentet, L. J., Avermann, M., Matyas, F., Staiger, J. F., & Petersen, C. C. H. (2010).
Membrane potential dynamics of GABAergic neurons in the barrel cortex of
behaving mice. Neuron, 65, 422435.
Gentet, L. J., Kremer, Y., Taniguchi, H., Huang, Z. J., Staiger, J. F., & Petersen, C. C. H.
(2012). Unique functional properties of somatostatin-expressing GABAergic
neurons in mouse barrel cortex. Nature Neuroscience, 15, 607612.
Glickfeld, L. L., Roberts, J. D., Somogyi, P., & Scanziani, M. (2009). Interneurons
hyperpolarize pyramidal cells along their entire somatodendritic axis. Nature
Gonchar, Y., Wang, Q., & Burkhalter, A. (2008). Multiple distinct subtypes of GABAergic
neurons in mouse visual cortex identified by triple immunostaining. Frontiers in
Neuroanatomy, 1, 3.
Gonzalez-Burgos, G., & Lewis, D. A. (2008). GABA neurons and the mechanisms of
network oscillations: Implications for understanding cortical dysfunction in
schizophrenia. Schizophrenia Bulletin, 34, 944961.
Gulledge, A. T., & Stuart, G. J. (2003). Excitatory actions of GABA in the cortex. Neuron,
37, 299309.
Gupta, A., Wang, Y., & Markram, H. (2000). Organizing principles for a diversity of
GABAergic interneurons and synapses in the neocortex. Science, 287, 273278.
Haas, H. L., & Gahwiler, B. H. (1992). Vasoactive intestinal polypeptide modulates
neuronal excitability in hippocampal slices of the rat. Neuroscience, 47, 273277.
Haider, B., Hausser, M., & Carandini, M. (2013). Inhibition dominates sensory
responses in the awake cortex. Nature, 493, 97100.
Hangya, B., Pi, H. J., Kvitsiani, D., Ranade, S. P., & Kepecs, A. (2014). From circuit
motifs to computations: Mapping the behavioral repertoire of cortical interneurons.
Current Opinion in Neurobiology, 26C, 117124.
Helmstaedter, M., Sakmann, B., & Feldmeyer, D. (2009a). L2/3 interneuron groups
defined by multiparameter analysis of axonal projection, dendritic geometry, and
electrical excitability. Cerebral Cortex, 19, 951962.
Helmstaedter, M., Sakmann, B., & Feldmeyer, D. (2009b). Neuronal correlates of local,
lateral, and translaminar inhibition with reference to cortical columns. Cerebral
Cortex, 19, 926937.
Hestrin, S., & Armstrong, W. E. (1996). Morphology and physiology of cortical neurons
in layer I. Journal of Neuroscience, 16, 52905300.
Howard, A., Tamas, G., & Soltesz, I. (2005). Lighting the chandelier: New vistas for axoaxonic cells. Trends in Neurosciences, 28, 310316.
Inan, M., Blazquez-Llorca, L., Merchan-Perez, A., Anderson, S. A., De Felipe, J., &
Yuste, R. (2013). Dense and overlapping innervation of pyramidal neurons by
chandelier cells. Journal of Neuroscience, 33, 19071914.
Inda, M., De Felipe, J., & Munoz, A. (2009). Morphology and distribution of chandelier
cell axon terminals in the mouse cerebral cortex and claustroamygdaloid complex.
Isaacson, J. S., & Scanziani, M. (2011). How inhibition shapes cortical activity. Neuron,
72, 231243.
Jiang, X. L., Wang, G. F., Lee, A. J., Stornetta, R. L., & Zhu, J. J. (2013). The organization
of two new cortical interneuronal circuits. Nature Neuroscience, 16, 210218.
Jones, E. G. (1975). Varieties and distribution of non-pyramidal cells in the somatic sensory
cortex of the squirrel monkey. Journal of Comparative Neurology, 160, 205267.
Jones, E. G. (1984). Neurogliaform or spiderweb cells. In A. Peters & E. G. Jones (Eds.),
Cellular components of the cerebral cortex (pp. 409418). New York: Plenum Press.
Jones, E. G. (1993). GABAergic neurons and their role in cortical plasticity in primates.
Karagiannis, A., Gallopin, T., David, C., Battaglia, D., Geoffroy, H., Rossier, J., et al.
(2009). Classification of NPY-expressing neocortical interneurons. Journal of
Karnani, M. M., Agetsuma, M., & Yuste, R. (2014). A blanket of inhibition: Functional
inferences from dense inhibitory connectivity. Current Opinion in Neurobiology,
26C, 96102.
Karube, F., Kubota, Y., & Kawaguchi, Y. (2004). Axon branching and synaptic bouton
phenotypes in GABAergic nonpyramidal cell subtypes. Journal of Neuroscience, 24,
28532865.
Katona, I., Acsady, L., & Freund, T. F. (1998). Postsynaptic targets of somatostatinimmunoreactive interneurons in the rat hippocampus. Neuroscience, 88, 3755.
Kawaguchi, Y. (1995). Physiological subgroups of nonpyramidal cells with specific
morphological characteristics in layer II/III of rat frontal cortex. Journal of
Kawaguchi, Y., & Kondo, S. (2002). Parvalbumin, somatostatin and cholecystokinin as
chemical markers for specific GABAergic interneuron types in the rat frontal cortex.
Journal of Neurocytology, 31, 277287.
Kawaguchi, Y., & Kubota, Y. (1996). Physiological and morphological identification of
somatostatin- or vasoactive intestinal polypeptide-containing cells among
GABAergic cell subtypes in rat frontal cortex. Journal of Neuroscience, 16,
27012715.
Kawaguchi, Y., & Kubota, Y. (1997). GABAergic cell subtypes and their synaptic
connections in rat frontal cortex. Cerebral Cortex, 7, 476486.
Kawaguchi, Y., & Kubota, Y. (1998). Neurochemical features and synaptic connections
of large physiologically-identified GABAergic cells in the rat frontal cortex.
Kepecs, A., & Fishell, G. (2014). Interneuron cell types are fit to function. Nature, 505,
318326.
Kerlin, A. M., Andermann, M. L., Berezovskii, V. K., & Reid, R. C. (2010). Broadly tuned
response properties of diverse inhibitory neuron subtypes in mouse visual cortex.
Neuron, 67, 858871.
Khirug, S., Yamada, J., Afzalov, R., Voipio, J., Khiroug, L., & Kaila, K. (2008).
GABAergic depolarization of the axon initial segment in cortical principal neurons is
caused by the Na-K-2Cl cotransporter NKCC1. Journal of Neuroscience, 28,
46354639.
Kisvarday, Z. F., Martin, K. A., Whitteridge, D., & Somogyi, P. (1985). Synaptic
connections of intracellularly filled clutch cells: A type of small basket cell in the
visual cortex of the cat. Journal of Comparative Neurology, 241, 111137.
Klausberger, T., & Somogyi, P. (2008). Neuronal diversity and temporal dynamics: The
unity of hippocampal circuit operations. Science, 321, 5357.
Krimer, L. S., Zaitsev, A. V., Czanner, G., Kroner, S., Gonzalez-Burgos, G.,
Povysheva, N. V., et al. (2005). Cluster analysis-based physiological classification
and morphological properties of inhibitory neurons in layers 23 of monkey
dorsolateral prefrontal cortex. Journal of Neurophysiology, 94, 30093022.
Kubota, Y., Hatada, S., Kondo, S., Karube, F., & Kawaguchi, Y. (2007). Neocortical
inhibitory terminals innervate dendritic spines targeted by thalamocortical afferents.
Kubota, Y., Shigematsu, N., Karube, F., Sekigawa, A., Kato, S., Yamaguchi, N., et al.
(2011). Selective coexpression of multiple chemical markers defines discrete
populations of neocortical GABAergic neurons. Cerebral Cortex, 21, 18031817.
Kullmann, D. M., Moreau, A. W., Bakiri, Y., & Nicholson, E. (2012). Plasticity of
inhibition. Neuron, 75, 951962.
Kvitsiani, D., Ranade, S., Hangya, B., Taniguchi, H., Huang, J. Z., & Kepecs, A. (2013).
Distinct behavioural and network correlates of two interneuron types in prefrontal
cortex. Nature, 498, 363366, U117.
Lecrux, C., Toussay, X., Kocharyan, A., Fernandes, P., Neupane, S., Levesque, M.,
et al. (2011). Pyramidal neurons Are neurogenic hubs in the neurovascular
coupling response to whisker stimulation. Journal of Neuroscience, 31,
98369847.
Lee, S., Hjerling-Leffler, J., Zagha, E., Fishell, G., & Rudy, B. (2010). The largest group
of superficial neocortical GABAergic interneurons expresses ionotropic serotonin
receptors. Journal of Neuroscience, 30, 1679616808.
Lee, S., Kruglikov, I., Huang, Z. J., Fishell, G., & Rudy, B. (2013). A disinhibitory circuit
mediates motor integration in the somatosensory cortex. Nature Neuroscience, 16,
16621670.
Lee, S. H., Kwan, A. C., Zhang, S. Y., Phoumthipphavong, V., Flannery, J. G.,
Masmanidis, S. C., et al. (2012). Activation of specific interneurons improves V1
feature selectivity and visual perception. Nature, 488, 379383.
Lefort, S., Gray, A. C., & Turrigiano, G. G. (2013). Long-term inhibitory plasticity in
visual cortical layer 4 switches sign at the opening of the critical period.
110, E4540E4547.
Letzkus, J. J., Wolff, S. B.E, Meyer, E. M.M, Tovote, P., Courtin, J., Herry, C., et al.
(2011). A disinhibitory microcircuit for associative fear learning in the auditory
cortex. Nature, 480, 331335 U76.
Ma, Y. Y., Hu, H., Berrebi, A. S., Mathers, P. H., & Agmon, A. (2006). Distinct subtypes
of somatostatin-containing neocortical interneurons revealed in transgenic mice.
Magistretti, P. J., & Morrison, J. H. (1988). Noradrenaline- and vasoactive intestinal
peptide-containing neuronal systems in neocortex: Functional convergence with
contrasting morphology. Neuroscience, 24, 367378.

Marin, O. (2012). Interneuron dysfunction in psychiatric disorders. Nature Reviews
Markram, H., Toledo-Rodriguez, M., Wang, Y., Gupta, A., Silberberg, G., & Wu, C. Z.
(2004). Interneurons of the neocortical inhibitory system. Nature Reviews
Marx, M., Gunter, R. H., Hucko, W., Radnikow, G., & Feldmeyer, D. (2012).
Improved biocytin labeling and neuronal 3D reconstruction. Nature Protocols, 7,
394407.
McDonald, C. T., & Burkhalter, A. (1993). Organization of long-range inhibitory
connections within rat visual cortex. Journal of Neuroscience, 13, 768781.
McGarry, L. M., Packer, A. M., Fino, E., Nikolenko, V., Sippy, T., & Yuste, R. (2010).
Quantitative classification of somatostatin-positive neocortical interneurons
identifies three interneuron subtypes. Frontiers in Neural Circuits, 4, 12.
Melzer, S., Michael, M., Caputi, A., Eliava, M., Fuchs, E. C., Whittington, M. A., et al.
(2012). Long-range-projecting GABAergic neurons modulate inhibition in
hippocampus and entorhinal cortex. Science, 335, 15061510.
Miyoshi, G., Hjerling-Leffler, J., Karayannis, T., Sousa, V. H., Butt, S. J. B., Battiste, J.,
et al. (2010). Genetic fate mapping reveals that the caudal ganglionic eminence
produces a large and diverse population of superficial cortical interneurons. Journal
Morrison, J. H., Magistretti, P. J., Benoit, R., & Bloom, F. E. (1984). The distribution
and morphological characteristics of the intracortical VIP-positive cell: An
immunohistochemical analysis. Brain Research, 292, 269282.
Mountcastle, V. B. (1997). The columnar organization of the neocortex. Brain, 120,
701722.
Nelson, S. B., Sugino, K., & Hempel, C. M. (2006). The problem of neuronal cell types:
A physiological genomics approach. Trends in Neurosciences, 29, 339345.
Oberlaender, M., de Kock, C. P.J, Bruno, R. M., Ramirez, A., Meyer, H. S.,
Dercksen, V. J., et al. (2012). Cell type-specific three-dimensional structure of
thalamocortical circuits in a column of rat vibrissal cortex. Cerebral Cortex, 22,
23752391.
OConnor, D. H., Hires, S. A., Guo, Z. V., Li, N., Yu, J., Sun, Q. Q., et al. (2013). Neural
coding during active somatosensation revealed using illusory touch. Nature
OConnor, D. H., Huber, D., & Svoboda, K. (2009). Reverse engineering the mouse
brain. Nature, 461, 923929.
Olah, S., Fule, M., Komlosi, G., Varga, C., Baldi, R., Barzo, P., et al. (2009). Regulation
of cortical microcircuits by unitary GABA-mediated volume transmission. Nature,
461, 12781281.
Oliva, A. A., Jiang, M. H., Lam, T., Smith, K. L., & Swann, J. W. (2000). Novel
hippocampal interneuronal subtypes identified using transgenic mice that express
green fluorescent protein in GABAergic interneurons. Journal of Neuroscience, 20,
33543368.
Olsen, S. R., Bortone, D. S., Adesnik, H., & Scanziani, M. (2012). Gain control by layer
six in cortical circuits of vision. Nature, 483, 47U83.
Otsuka, T., & Kawaguchi, Y. (2009). Cortical inhibitory cell types differentially form
intralaminar and interlaminar subnetworks with excitatory neurons. Journal of
Packer, A. M., & Yuste, R. (2011). Dense, unspecific connectivity of neocortical
parvalbumin-positive interneurons: A canonical microcircuit for inhibition? Journal
Parekh, R., & Ascoli, G. A. (2013). Neuronal morphology goes digital: A research hub
for cellular and system neuroscience. Neuron, 77, 10171038.
Parra, P., Gulyas, A. I., & Miles, R. (1998). How many subtypes of inhibitory cells in the
hippocampus? Neuron, 20, 983993.
Peters, A., & Harriman, K. M. (1988). Enigmatic bipolar cell of rat visual cortex. Journal
of Comparative Neurology, 267, 409432.
Pfeffer, C. K., Xue, M. S., He, M., Huang, Z. J., & Scanziani, M. (2013). Inhibition of
inhibition in visual cortex: The logic of connections between molecularly distinct
interneurons. Nature Neuroscience, 16, 10681076, U130.
Pi, H. J., Hangya, B., Kvitsiani, D., Sanders, J. I., Huang, Z. J., & Kepecs, A. (2013).
Cortical interneurons that specialize in disinhibitory control. Nature, 503, 521524.
Pohlkamp, T., David, C., Cauli, B., Gallopin, T., Bouche, E., Karagiannis, A., et al.
(2013). Characterization and distribution of Reelin-positive interneuron subtypes in
the rat barrel cortex. Cerebral Cortex.
Povysheva, N. V., Zaitsev, A. V., Kroner, S., Krimer, O. A., Rotaru, D. C.,
Gonzalez-Burgos, G., et al. (2007). Electrophysiological differences between
neurogliaform cells from monkey and rat prefrontal cortex. Journal of
Rudy, B., Fishell, G., Lee, S., & Hjerling-Leffler, J. (2011). Three groups of interneurons
account for nearly 100% of neocortical GABAergic neurons. Developmental
79
Sachidhanandam, S., Sreenivasan, V., Kyriakatos, A., Kremer, Y., & Petersen, C. C.
(2013). Membrane potential correlates of sensory perception in mouse barrel
cortex. Nature Neuroscience, 16, 16711677.
Santana, R., McGarry, L. M., Bielza, C., Larranaga, P., & Yuste, R. (2013).
Classification of neocortical interneurons using affinity propagation. Frontiers in
Neural Circuits, 7.
Schubert, D., Kotter, R., & Staiger, J. F. (2007). Mapping functional connectivity in
barrel-related columns reveals layer- and cell type-specific microcircuits. Brain
Structure and Function, 212, 107119.
Schubert, D., Kotter, R., Zilles, K., Luhmann, H. J., & Staiger, J. F. (2003). Cell typespecific circuits of cortical layer IV spiny neurons. Journal of Neuroscience, 23,
29612970.
Sessler, F. M., Grady, S. M., Waterhouse, B. D., & Moises, H. C. (1991).
Electrophysiological actions of VIP in rat somatosensory cortex. Peptides, 12,
715721.
Silberberg, G., & Markram, H. (2007). Disynaptic inhibition between neocortical
pyramidal cells mediated by Martinotti cells. Neuron, 53, 735746.
Simon, A., Olah, S., Molnar, G., Szabadics, J., & Tamas, G. (2005). Gap-junctional
coupling between neurogliaform cells and various interneuron types in the
neocortex. Journal of Neuroscience, 25, 62786285.
Sims, K. B., Hoffman, D. L., Said, S. I., & Zimmerman, E. A. (1980). Vasoactive
intestinal polypeptide (VIP) in mouse and rat brain: an immunocytochemical study.
Brain Research, 186, 165183.
Sohal, V. S., Zhang, F., Yizhar, O., & Deisseroth, K. (2009). Parvalbumin neurons and
gamma rhythms enhance cortical circuit performance. Nature, 459, 698702.
Somogyi, P. (1977). A specific axo-axonal interneuron in the visual cortex of the rat.
Somogyi, P., Tamas, G., Lujan, R., & Buhl, E. H. (1998). Salient features of synaptic
organisation in the cerebral cortex. Brain Research Reviews, 26, 113135.
Sorensen, S. A., Bernard, A., Menon, V., Royall, J. J., Glattfelder, K. J., Desta, T., et al.
(2013). Correlated gene expression and target specificity demonstrate excitatory
projection neuron diversity. Cerebral Cortex.
Southwell, D. G., Nicholas, C. R., Basbaum, A. I., Stryker, M. P., Kriegstein, A. R.,
Rubenstein, J. L., et al. (2014). Interneurons from embryonic development to cellbased therapy. Science, 344, 1240622.
Staiger, J. F., Flagmeyer, I., Schubert, D., Zilles, K., Kotter, R., & Luhmann, H. J. (2004).
Functional diversity of layer IV spiny neurons in rat somatosensory cortex:
Quantitative morphology of electrophysiologically characterized and biocytin
labeled cells. Cerebral Cortex, 14, 690701.
Staiger, J. F., Freund, T. F., & Zilles, K. (1997). Interneurons immunoreactive for
vasoactive intestinal polypeptide (VIP) are extensively innervated by parvalbumincontaining boutons in rat primary somatosensory cortex. European Journal of
Staiger, J. F., Masanneck, C., Schleicher, A., & Zuschratter, W. (2004). Calbindincontaining interneurons are a target for VIP-immunoreactive synapses in rat primary
somatosensory cortex. Journal of Comparative Neurology, 468, 179189.
Staiger, J. F., Zuschratter, W., Luhmann, H. J., & Schubert, D. (2009). Local circuits
targeting parvalbumin-containing interneurons in layer IV of rat barrel cortex. Brain
Structure & Function, 214, 113.
Stark, E., Eichler, R., Roux, L., Fujisawa, S., Rotstein, H. G., & Buzsaki, G. (2013).
Inhibition-induced theta resonance in cortical circuits. Neuron, 80, 12631276.
Suzuki, N., & Bekkers, J. M. (2010a). Distinctive classes of GABAergic interneurons
provide layer-specific phasic inhibition in the anterior piriform cortex. Cerebral
Cortex, 20, 29712984.
Suzuki, N., & Bekkers, J. M. (2010b). Inhibitory neurons in the anterior piriform cortex
of the mouse: Classification using molecular markers. Journal of Comparative
Neurology, 518, 16701687.
Suzuki, N., & Bekkers, J. M. (2012). Microcircuits mediating feedforward and feedback
synaptic inhibition in the piriform cortex. Journal of Neuroscience, 32, 919931.
Szabadics, J., Varga, C., Molnar, G., Olah, S., Barzo, P., & Tamas, G. (2006). Excitatory
effect of GABAergic axo-axonic cells in cortical microcircuits. Science, 311,
233235.
Tamas, G., Lorincz, A., Simon, A., & Szabadics, J. (2003). Identified sources and targets
of slow inhibition in the neocortex. Science, 299, 19021905.
Tamas, G., Somogyi, P., & Buhl, E. H. (1998). Differentially interconnected networks of
GABAergic interneurons in the visual cortex of the cat. Journal of Neuroscience, 18,
42554270.
Taniguchi, H. (2014). Genetic dissection of GABAergic neural circuits in mouse
neocortex. Frontiers in Cellular Neuroscience, 8.
Taniguchi, H., He, M., Wu, P., Kim, S., Paik, R., Sugino, K., et al. (2011). A resource of
Cre driver lines for genetic targeting of GABAergic neurons in cerebral cortex.
Neuron, 71, 9951013.
80
Taniguchi, H., Lu, J. T., & Huang, Z. J. (2013). The spatial and temporal origin of
chandelier cells in mouse neocortex. Science, 339, 7074.
Thomson, A. M., West, D. C., Wang, Y., & Bannister, A. P. (2002). Synaptic connections
and small circuits involving excitatory and inhibitory neurons in layers 25 of adult
rat and cat neocortex: Triple intracellular recordings and biocytin labelling in vitro.
Toledo-Rodriguez, M., Goodman, P., Illic, M., Wu, C. Z., & Markram, H. (2005).
Neuropeptide and calcium-binding protein gene expression profiles predict
neuronal anatomical type in the juvenile rat. Journal of Physiology, 567, 401413.
Tomioka, R., Okamoto, K., Furuta, T., Fujiyama, F., Iwasato, T., Yanagawa, Y., et al.
(2005). Demonstration of long-range GABAergic connections distributed
throughout the mouse neocortex. European Journal of Neuroscience, 21,
15871600.
Uematsu, M., Hirai, Y., Karube, F., Ebihara, S., Kato, M., Abe, K., et al. (2008).
Quantitative chemical composition of cortical GABAergic neurons revealed in
transgenic venus-expressing rats. Cerebral Cortex, 18, 315330.
von Engelhardt, J., Eliava, M., Meyer, A. H., Rozov, A., & Monyer, H. (2007). Functional
characterization of intrinsic cholinergic interneurons in the cortex. Journal of
Wang, Y., Gupta, A., Toledo-Rodriguez, M., Wu, C. Z., & Markram, H. (2002).
Anatomical, physiological, molecular and circuit properties of nest basket cells in
the developing somatosensory cortex. Cerebral Cortex, 12, 395410.
Wang, Y., Toledo-Rodriguez, M., Gupta, A., Wu, C. Z., Silberberg, G., Luo, J. Y., et al.
(2004). Anatomical, physiological and molecular properties of Martinotti cells in the
somatosensory cortex of the juvenile rat. Journal of Physiology, 561, 6590.
Wilson, N. R., Runyan, C. A., Wang, F. L., & Sur, M. (2012). Division and subtraction by
distinct cortical inhibitory networks in vivo. Nature, 488, 343348.
Woodruff, A. R., McGarry, L. M., Vogels, T. P., Inan, M., Anderson, S. A., & Yuste, R.
(2011). State-dependent function of neocortical chandelier cells. Journal of
Wozny, C., & Williams, S. R. (2011). Specificity of synaptic connectivity between layer 1
inhibitory interneurons and layer 2/3 pyramidal neurons in the rat neocortex.
Xu, X. M., & Callaway, E. M. (2009). Laminar specificity of functional input to distinct
types of inhibitory cortical neurons. Journal of Neuroscience, 29, 7085.
Xu, H., Jeong, H. Y., Tremblay, R., & Rudy, B. (2013). Neocortical somatostatinexpressing GABAergic interneurons disinhibit the thalamorecipient layer 4. Neuron,
77, 155167.
Xu, X. M., Roby, K. D., & Callaway, E. M. (2010). Immunochemical characterization of
inhibitory mouse cortical neurons: Three chemically distinct classes of inhibitory
cells. Journal of Comparative Neurology, 518, 389404.
Yanez, I. B., Munoz, A., Contreras, J., Gonzalez, J., Rodriguez-Veiga, E., & De Felipe, J.
(2005). Double bouquet cell in the human cerebral cortex and a comparison with
other mammals. Journal of Comparative Neurology, 486, 344360.
Yang, W. G., Carrasquillo, Y., Hooks, B. M., Nerbonne, J. M., & Burkhalter, A. (2013).
Distinct balance of excitation and inhibition in an interareal feedforward and
feedback circuit of mouse visual cortex. Journal of Neuroscience, 33,
1737317384.
Yizhar, O., Fenno, L. E., Prigge, M., Schneider, F., Davidson, T. J., OShea, D. J., et al.
(2011). Neocortical excitation/inhibition balance in information processing and
social dysfunction. Nature, 477, 171178.
Young, A., & Sun, Q. Q. (2009). GABAergic inhibitory interneurons in the
posterior piriform cortex of the GAD67-GFP mouse. Cerebral Cortex, 19,
30113029.
Zhu, Y. H., Stornetta, R. L., & Zhu, J. J. (2004). Chandelier cells control excessive cortical
excitation: Characteristics of whisker-evoked synaptic responses of layer 2/3
nonpyramidal and pyramidal neurons. Journal of Neuroscience, 24, 51015108.
Zilles, K., Hajos, F., Csillag, A., Kalman, M., Sotonyi, P., & Schleicher, A. (1993).
Vasoactive intestinal polypeptide immunoreactive structures in the mouse barrel
field. Brain Research, 618, 149154.
Von Economo Neurons

MA Raghanti and LB Spurlock, Kent State University, Kent, OH, USA
N Uppal, Icahn School of Medicine at Mount Sinai, New York, NY, USA
CC Sherwood, The George Washington University, Washington, DC, USA
C Butti and PR Hof, Icahn School of Medicine at Mount Sinai, New York, NY, USA
Glossary
Cetartiodactyls Taxonomic group that includes whales and

dolphin (cetaceans) and even-toed ungulates (artiodactyls).
Frontoinsular cortex Region of the anterior insula in
humans and great apes that is characterized by the presence
of von Economo neurons within layer V.
Haplorrhines One of two taxonomic suborders within the
primate order. Haplorrhine primates include humans, great
apes, lesser apes, Old World monkeys, and the tarsier. The
term haplorrhine is in reference to the lack of a rhinarium
shared by these species.
Discovery and Rediscovery of Von Economo Neurons

In 1926, Constantin von Economo provided the first detailed
description of the morphology and cortical distribution of a
specialized spindle-shaped neuron in layer Vb of two welldefined cortical regions, the human anterior cingulate cortex
(ACC) and the frontoinsular cortex (FI; von Economo, 1926,
for a modern translation of this paper, see Seeley, Merkle, Gaus,
et al., 2012). These large spindle neurons had been sporadically
described and graphically documented in the literature following their first description in the ACC of the human by Betz
(1881), who reported their morphology as remarkably large
spindle-shaped cells in layer V. Hammarberg (1895) mentioned
the presence of spindle neurons in layer V of prefrontal polar
cortex, and spindle-shaped cells in layer V of the cingulate gyrus
were then also mentioned by Ramon y Cajal (190102, 1904)
who referred to them as giant fusiform cells. Interestingly,
Ramon y Cajal noted that their presence was not uniform
throughout the human cortex but was restricted to the cingulate
and insular cortices. During the first part of the twentieth century, the occurrence of these large spindle-shaped neurons in
either the human ACC or FI was the object of occasional reports
(De Crinis, 1933; Economo & Koskinas, 1925; Flechsig, 1897,
1920; Goldstein, 1913; Juba, 1934; Marinesco & Goldstein,
1927; Ngowyang, 1932, 1936; Nikitin, 1909; Vogt, 1903; Vogt
& Vogt, 1919). Von Economo in his 1926 paper described stick
cells or staff cells as neurons displaying a spindle-like form and
an unusual length, perpendicularly oriented to the pial surface,
harboring apical and basal dendrites almost as wide as the cell
body and sometimes branching into two, as well as rod cells
and corkscrew cells with very long rodlike or spirally winding
elements (Figure 1). Von Economo in 1927 discussed cells no
longer pyramidal, but peculiarly elongated or fusiform, to the
point of describing a cellular fusiform transformation in layers
III and V of the FI.
Hominids Taxonomic group that includes humans and

great apes.
Perissodactyls Taxonomic group that includes odd-toed
ungulates.
Strepsirrhines One of two taxonomic suborders within the
primate order. Strepsirrhine primates include lemurs,
lorises, and bushbabies. The term strepsirrhine refers to the
rhinarium (i.e., wet nose) shared by this group pf primates.
von Economo neurons Projection neurons that were
formerly known as spindle cells and were first reported in the
human anterior cingulate cortex and frontoinsular cortex.
After these initial descriptions, a few other authors acknowledged the presence of spindle cells in the human cortex
(Braak, 1980; Juba, 1934; Ngowyang, 1932; Rose, 1927,
1928; Syring, 1956). In addition, spindle neurons had been
described in the subicular cortex and entorhinal cortex of the
human hippocampal formation by Ngowyang (1936), indicating that ACC and FI are not the only limbic regions to contain
them. It was only in 1995 that the first modern study of the
morphology, distribution, and apparent numbers of the spindle neurons was performed in the human ACC (Nimchinsky,
Vogt, Morrison, & Hof, 1995), demonstrating their immunoreactivity to dephosphorylated neurofilament proteins and a
rostrocaudal gradient in their density. These authors also provided the first evidence that spindle cells are indeed projection
neurons. These spindle-shaped neurons, generally known until
1999 in the literature as spindle cells, were recently renamed
von Economo neurons (VENs) by Allman, Watson, Tetreault,
and Hakeem (2005) in tribute to Constantin von Economos
first detailed description and to avoid confusion with smaller
fusiform and spindle-shaped interneurons of layer VI.
VENs in Primates
More recently, VENs were reported as a unique neuronal morphology in the ACC of humans and their closest living relatives, the great apes: orangutans (Pongo pygmaeus and Pongo
abelii), gorillas (Gorilla gorilla), bonobos (Pan paniscus), and
chimpanzees (Pan troglodytes) (Nimchinsky et al., 1995, 1999).
Figure 2 shows representative sections in human, chimpanzee,
and gorilla. The incidence of VENs within the ACC was
observed to decrease in a rostral to caudal gradient. In humans
and bonobos, VENs were found in clusters of three to six cells
located in layer Vb of the ACC. In contrast, VENs occurred
singly or in small clusters of only two to three cells in the
http://dx.doi.org/10.1016/B978-0-12-397025-1.00203-7
81
82
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Von Economo Neurons
Figure 1 Drawings from the original work of von Economo and

Koskinas (1925, original Figure 44), showing rod and corkscrew cells in
the human anterior limbic gyrus and transverse insular cortex.
chimpanzee, gorilla, and orangutan. Humans and bonobos

possessed the highest percentage of VENs, expressed as the
percentage of pyramidal neurons in layer V (5.6% and 4.8%,
respectively). Chimpanzees and gorillas displayed an intermediate density (3.8% and 2.3%, respectively), with a relatively
sparse distribution in the orangutan (1.6%). Further, the
volume of VENs, but not other neuron types, was correlated
with relative brain size residuals among these species
(Nimchinsky et al., 1999). These findings suggested that these
unique projection neurons may have emerged within the hominid clade to support specific behavioral or cognitive functions.
Since their original description, a number of studies were
aimed at elucidating the function and phylogenetic distribution of this neuron type. Further studies revealed that humans
had significantly more VENs in the FI and ACC than great apes,
although the density of VENs relative to other neurons was
higher in the great apes (Allman, Tetreault, Hakeem, et al.,
2010; Allman et al., 2005). Humans and the African great
apes (chimpanzee, bonobo, and gorilla) show consistent presence of VENs in the FI and ACC, while the orangutan, the only
Asian great ape, shows a more sporadic distribution (Allman
et al., 2010). Also, the presence of clusters of VENs has been
used as the defining characteristic of a subdomain of the anterior agranular insular cortex called the FI that is present only in
humans and great apes, with the highest densities occurring on
the crowns of gyri (Allman et al., 2010; Bauernfeind, de Sousa,

Avasthi, et al., 2013).
Although initially considered a specialized projection neuron with restricted cortical distributions unique to humans and
great apes (Nimchinsky et al., 1999), additional analyses have
revealed the presence of VENs in other cortical regions, including human dorsolateral prefrontal cortex (Fajardo, Escobar,
Butitica, et al., 2008), superior frontal cortex (Brodmanns
area 9) (Nimchinsky et al., 1999), and subicular and entorhinal cortices (Ngowyang, 1936); in the ACC of a lesser ape
(gibbon) (Stimpson, Tetreault, Allman, et al., 2011); and in the
FI of two Old World monkey species (long-tailed and rhesus
macaques, Macaca fascicularis and Macaca mulatta, respectively)
(Bauernfeind et al., 2013; Evrard, Forro, & Logothetis, 2012).
There was one early report of VENs (or VEN-like neurons) in the
ACC of a strepsirrhine primate, the ring-tailed lemur (Lemur
catta) (Rose, 1928). However, more recent assessments of strepsirrhine primates did not find VENs within the ACC or other
cortical regions (Allman et al., 2010; Nimchinsky et al., 1999).
A comparative analysis of haplorhine primates (New World
monkeys, Old World monkeys, lesser apes, great apes, and
humans) revealed that VENs were not related to encephalization
(i.e., relative brain size to body size), as several New World
monkeys and lesser apes possess encephalization quotients
greater than those of great apes. Rather, the presence of VENs
was related to absolute brain size and only occurred in primate
brains greater than 300 g (Allman et al., 2010). Further, while a
substantial number of VENs were present in the fetal chimpanzee, fewer are present in the fetal human, with VENs emerging
predominantly during postnatal life in humans, indicating that
the morphological maturation of this neuron population is
delayed during human development (Allman et al., 2010).
There is also a rightward asymmetry present in the FI and ACC
of humans and great apes, with a higher number of VENs in the
right hemisphere. This has been interpreted as important to the
more complex nature of the sympathetic involvement in negative feedback and error-correcting behaviors that are preferentially relegated to the right hemisphere. In contrast, the left FI
and ACC are more involved in calming parasympatheticassociated emotions (Allman et al., 2010; Craig, 2005).
Allman et al. (2010) reported that human VENs were immunoreactive for the following three proteins: activating transcription factor 3 (ATF3), a protein involved in pain sensitivity;
interleukin-4 receptor alpha chain (IL4Ra), a protein that mediates allergic reactions; and neuromedin B, which is also expressed
in the gut and may be involved in mediating the connection of
visceral states and social awareness. A quantitative comparative
analysis including humans, great apes, and lesser apes (gibbon,
Hylobates muelleri, and siamang, Symphalangus syndactylus) found
that humans had a greater percentage of VENs that expressed
IL4Ra and ATF3 relative to the apes (Stimpson et al., 2011). The
authors suggested that this pattern of results, that is, differing
biochemical phenotypes, may be related to differences in interoceptive sensitivity that contribute to social behaviors.
VENs in Other Mammals

Cetartiodactyls
The discovery of VENs in cetaceans (Hof & Van der Gucht,
2007) supported the hypothesis that these neurons were
83
Figure 2 Images of Nissl-stained sections illustrating von Economo neurons (VENs) in human (a), chimpanzee (Pan troglodytes, b), and gorilla (Gorilla
gorilla, c). Arrows indicate VENs, scale bars 25 mm.
coincident with large brain size and did not negate the prospect
that they were characteristic of socially complex organisms.
Figure 3 shows representative VENs in cetacean species. While
VENs were common in the mysticetes, they were present only in
the two odontocetes with the largest absolute brain sizes. VENs
were found in regions that correspond to the FI and ACC, as well
as the frontal pole of the humpback whale (Megaptera novaeangliae), fin whale (Balaenoptera physalus), sperm whale (Physeter
macrocephalus), and killer whale (Orcinus orca) (Hof & van der
Gucht, 2007). As in primates, VENs were most common in layer
V and occasionally within layer III; there were a rostrocaudal
gradient within the ACC and a tendency for VENs to be more
prevalent in the crowns of gyri. VENs were also observed in
regions of the cetacean cortex that did not correspond to the
hominid distribution and included the inferior temporal cortex,
occipital region of the ecto- and suprasylvian cortex, and paralimbic cortex. More recently, VENs were reported in the ACC, AI,
and frontopolar cortex of smaller odontocetes, including the
bottlenose dolphin (Tursiops truncatus), the Rissos dolphin
(Grampus griseus), and the beluga whale (Delphinapterus leucas)
(Butti, Sherwood, Hakeem, et al., 2009; Hakeem et al., 2009).
Once again, there was a regionally limited neocortical distribution of VENs, with total numbers comparable to those observed
in great ape species.
More recent analyses revealed a ubiquitous and dense distribution of VENs in the cortex of the pygmy hippopotamus
(Hexaprotodon liberiensis), with VENs present in all cortical
regions (Figure 4(a)) (Butti, Fordyce, Raghanti, et al., 2014;
Butti & Hof, 2010; Butti, Raghanti, Sherwood, & Hof, 2011).
Hippopotamids are classified as artiodactyls (i.e., even-toed
ungulates) and represent the closest living relative of cetaceans
(Boisserie, Fisher, Lihoreau, and Weston, 2011); however, they
lack an enlarged brain and, while social, are not categorized as
having complex social behaviors.
To gain a better understanding of the phylogenetic distribution of this morphologically unique neuron type, we examined Nissl-stained sections from the frontopolar cortex of
additional artiodactyl species. This sample included the
domesticated pig (Sus scrofa domesticus), sheep (Ovis aries),
cow (Bos taurus), and white-tailed deer (Odocoileus virginianus).
To this end, the entire circumference of frontopolar coronal
sections was qualitatively analyzed systematically from pia to
white matter.
VENs were present in the frontal pole of each of these
species (Figure 4(b)4(f)), but the distributions and densities
of these cells revealed species-specific properties. Similar to
reports in other taxa, VENs were most numerous in the
crown gyri and absent within sulcal depths. VENs were ubiquitously distributed throughout the frontopolar cortex of the
pig and cow, but with distinctive patterns of distribution for
each species. VENs were restricted to specific regions of the
frontal pole for both deer and sheep. Remarkably, we observed
VENs within layer II of several artiodactyls, of roughly comparable appearance to the layer V VENs, with clusters of layer II
VENs present in the sheep and cow. This is a novel laminar
localization for VENs, which will deserve further investigation
in a larger number of species.
Perissodactyls and Carnivores

The cetartiodactyls are grouped together with the perissodactyls (odd-toed ungulates) and carnivores into a superordinal
clade. A ubiquitous distribution of VENs was observed in the
neocortex of the common zebra (Equus burchelli; Figure 5(a))
(Butti & Hof, 2010; Butti et al., 2011) similar to that of the
pygmy hippopotamus. We have also observed VENs in other
perissodactyls, including the black rhinoceros (Diceros bicornis;
Figure 5(b)) and horse (Equus ferus caballus; Figure 5(c)), and
84
Figure 3 Representative images of Nissl-stained sections showing VENs in (a) the minke whale (Balaenoptera acutorostrata), (b) the beluga whale
(Delphinapterus leucas), (c) the humpback whale (Megaptera novaeangliae), (d) the long-finned pilot whale (Globicephala melas), (e) bottlenose dolphin
(Tursiops truncatus), and (f) Rissos dolphin (Grampus griseus). VENs are indicated by arrows. Scale bars 25 mm.
in one carnivore, the walrus (Odobenus rosmarus; Figure 5(d)).

VENs were common throughout the frontal pole of the horse,
most frequently within layer V, but sporadically in layers II and
III. VENs were also observed throughout the frontal pole of the
walrus but were sparsely distributed. Further analyses, including additional species, are needed to clarify the distribution of
VENs within these orders.
Afrotherians
Following their discovery in cetaceans, VENs were reported to be
present in the brains of the African elephant (Loxodonta africana)
and Indian elephant (Elephas maximus; Figure 6(a)). Because
elephants independently evolved large brains and possess highly
complex social behaviors, this finding provided further opportunity for considering the role of VENs in social interactions. Their
distribution was similar to that observed in hominids and cetaceans, present in the FI, frontal pole, and dorsolateral frontal area
of the African elephant and in the ACC of the Indian elephant
(Hakeem et al., 2009). The estimated number of VENs in the
elephant ACC was less than those of humans and great apes; and
elephants were intermediate between humans and great apes in

the FI (Hakeem et al., 2009). Once again, VENs were more
common in the crowns of gyri and nearly absent in the cortex
below the fundus of each sulcus. Hakeem and colleagues (2009)
reported occasional VENs within the cortex of the manatee (Trichechus manatus latirostris; Figure 6(b)), and the absence of VENs
in a variety of mammalian species, including the rock hyrax
(Heterohyrax brucei), giant elephant shrew, xenarthrans (sloth,
armadillo, anteater, and tenrec), bontebok (Damaliscus pygargus),
brown rat (Rattus norvegicus), and paca (Cuniculus paca).
The presence of VENs within hominids, cetaceans, and elephants led to the suggestion that these neurons functioned within
the context of enlarged brains to facilitate rapid information
processing and that their presence in these distantly related taxa
may have been the result of convergent evolution. The restricted
cortical distributions further indicated that these neurons may be
particularly relevant to social behaviors and cognition (Butti,
Sherwood, Hakeem, et al., 2009; Hakeem et al., 2009). While
VENs are typically restricted in distribution to a few prefrontal
cortical regions in most species where they do occur, the ubiquitous cortical distribution of VENs reported for the pygmy
85
Figure 4 VENs are shown in (a) the pygmy hippopotamus (Hexaprotodon liberiensis), in layer II (b) and (c) of the layer V in the frontopolar cortex of
the cow (Bos taurus), (d) in the white matter of the white-tailed deer (Odocoileus virginianus), (e) in layer V of the frontopolar cortex in the domesticated
pig (Sus scrofa domesticus), and (f) sheep (Ovis aries). VENs are indicated by arrows. Scale bars 25 mm.
Figure 5 Nissl-stained sections showing VENs in (a) the common zebra (Equus burchelli), (b) black rhinoceros (Diceros bicornis), (c) horse (Equus
ferus caballus), and (d) walrus (Odobenus rosmarus). VENs are indicated by arrows. Scale bars 25 mm.
86

autism spectrum disorders, and schizophrenia, in which deficits in emotional regulation and social conduct are fundamental diagnostic features and present with dysfunctions of the
ACCFI network in functional magnetic resonance imaging
studies (Mishnew & Keller, 2010; Monk, Peltier, Wiggins,
et al., 2009; Seeley, 2008; Uddin & Menon, 2009; White,
Joseph, Francis, & Liddle, 2010). It is interesting in
this context that the ACC and FI, which are thought to provide
connections within the salience networks and to key subcortical regions such as hypothalamus, periaqueductal gray,
and autonomic nuclei, are enriched in VENs. As such, this
neuronal type may represent a crucial anatomical substrate
for these systems. The insular cortex can be envisioned as a
putative hub in networks affected in neuropsychiatric conditions such as schizophrenia (Bullmore & Sporns, 2009).
bvFTD and Alzheimers Disease
Figure 6 VENs are shown in (a) the Indian elephant (Elephas maximus)
and (b) the manatee (Trichechus manatus). VENs are indicated by
arrows. Scale bars 25 mm.
hippopotamus and common zebra indicated that a more expansive comparative analysis would be helpful in exploring the evolutionary and functional significance of this neuron type.
Recent evidence indicates that the presence of VENs is not
restricted to large-brained species with complex social organization. Based on these findings, it appears that VENs represent
a phylogenetically ancient neuron type rather than an emergent specialized neuron exclusive to encephalized or socially
complex species. Instead of parallel evolution among multiple
clades, a more parsimonious account would suggest that this
neuron type emerged very early within the mammalian radiation, but their absence in xenarthrans (e.g., anteater and sloths)
and rodents suggests that VENs, as defined by their morphology, were not present in the earliest mammals.
VENs in Neurological and Psychiatric Disorders

Studies on the involvement of VENs in psychiatric disorders are
relatively recent. Several clinicopathologic analyses of VENs in
neuropsychiatric conditions were motivated by the original
studies of Seeley, Carlin, Allman, et al. (2006) and Seeley,
Allman, Carlin, et al. (2007) that revealed significant alterations of VENs in the behavioral variant of frontotemporal
dementia (bvFTD) and possible links between alterations in
VENs and the clinical manifestations of several clinical conditions. VEN-containing cortical areas are nested in a cortical
network known as the salience network (Seeley, Menon,
Schatzberg, et al., 2007; Sridharan, Levitin, & Menon, 2008;
Taylor, Seminowicz, & Davis, 2009) in which body homeostasis information reaches the FI and is integrated into decisionmaking and value attribution processes in the ACC and
prefrontal cortex (Craig, 2003, 2009; Craig, Chen, Bandy, &
Reiman, 2000). Such functions are severely affected in bvFTD,
Seeley et al. (2006, 2008) reported a severe and early loss of

VENs in the FI of bvFTD patients and proposed a direct relationship between the vulnerability of these neurons and the
symptomatology exhibited by the patients. A more recent study
of postmortem brains of patients with bvFTD, Alzheimers
disease (AD), and controls also showed that bvFTD patients
present with an 70% decrease in numbers of VENs in ACC
and FI, in striking contrast to an absence of selective loss of
VENs in AD and in control subjects (Kim, Sidhu, Macedo,
et al., 2012). Moreover, in patients with bvFTD, the few VENs
that did not undergo degeneration showed prominent alterations in morphology (swollen soma and twisted dendrites),
distribution (very rare clustering), and presence of hyperphosphorylated tau protein, compared with controls and AD
subjects. These alterations in VEN numbers and morphology
were present even in the initial stages of bvFTD, constituting an
early pathological feature of this disease (Kim et al., 2012).
VENs are affected in AD but only in terminal stages of the
disease as shown in the ACC by Nimchinsky et al. (1995).
The results of Kim et al. (2012) are consistent with the concept
that, in contrast to AD in which VENs and social graces are
relatively spared until late stages, their selective degeneration in
early stages of bvFTD may be related to a loss of visceral
autonomic inputs to socialemotional systems in ACC and FI
and to the behavioral phenotype of this disorder.
Agenesis of the Corpus Callosum

The occurrence of major deficits in understanding nonliteral
language, humor, and scenes depicting social interactions, also
known as alexithymia, in patients with agenesis of the corpus
callosum (AgCC) (Brown & Paul, 2000), led Kaufman, Paul,
Manaye, et al. (2008) to investigate whether alterations in
VENs occurred in this congenital condition. Stereological
quantification of numbers of VENs and their ratios to pyramidal neurons in the postmortem brains of a patient with complete AgCC, a patient with partial AgCC, and a patient with
poststroke AgCC showed decreases in VENs to approximately
half their normal numbers in partial AgCC and almost absence
in complete AgCC, compared with control cases. Interestingly,
the stroke patient presented slightly higher numbers of normally distributed VENs, and the patient with partial AgCC

showed an abnormal distribution of VENs in the medial orbitofrontal gyri. Kaufman et al. (2008) suggested that VENs in
the ACC and FI are more vulnerable than other neuronal types
to the developmental defect underlying AgCC with possible
alterations in neuronal migration. The relative preservation of
VEN numbers in partial AgCC was interpreted as support for
the role of the remaining corpus callosum in preserving VEN
connectivity and survival and, together with observations from
other neuropsychiatric disorders, as indirect evidence for a role
of VENs in social cognition.
Autism Spectrum Disorders

Patients with autism spectrum disorders experience deficits in
emotional regulation and social interaction (APA, 2000).
However, Kennedy, Semendeferi, and Courchesne (2007) in
the first study of VENs in autism did not observe differences in
either total numbers or qualitatively assessed morphology in
the FI, but this study was based on a very small number of
cases. Simms, Kemper, Timbie, et al. (2009) analyzed the ACC
in a larger sample of brains from patients with autism. This
study reported a dichotomy in VEN density in patients with
autism (three patients with autism showing relatively high and
six patients relatively low VEN densities), with no overall significant differences between groups. This result further supported the notion of large heterogeneities in pathology
87
among patients with autism and that different subgroups of

patients may present with different types of alterations in VENs
(Allman et al., 2005; Kennedy et al., 2007). We conducted the
first neuropathologic study of VENs exclusively in children
with autism and matched control subjects, using stereology
to assess alterations in numbers, morphology, and distribution
of VENs over a specific developmental period. There was a
significantly higher ratio of VENs to pyramidal neurons, as
well as qualitative alterations in the cortical distribution
(frequent cortical dimple in which VENs were sparse) and in
the morphology of VENs (swollen somata and clumps of oligodendrocytes in close apposition to the soma and to the
initial segments of both basal and apical dendrites; Figure 7)
in the FI in young patients with autism (Santos, Uppal, Butti,
et al., 2011). Based on previous observations of neuronal
overgrowth in autism, possibly linked to alterations in neuronal migration, these results suggest a possible neurodevelopmental insult specifically affecting VENs. The increase in the
number of VENs was speculatively explained as a possible
factor underlying a heightened interoception often described
in clinical observations (Haag, Tordjman, Duprat, et al., 2005).
Schizophrenia and Bipolar Disorder

The ACC is consistently affected in schizophrenia as shown
by neuroimaging (Frisoni, Prestia, Adorni, et al., 2009;
Figure 7 Photomicrographs showing morphological alterations of VENs in autism. VEN with surrounding oligodendrocytes (a), corkscrew VEN (b),
and swollen VEN (c). Scale bar 10 mm.
88
Minzenberg, Laird, Thelen, et al., 2009; White et al., 2010) and

neuropathologic studies (Bouras, Kovari, Hof, et al., 2001;
Fornito, Yucel, Dean, et al., 2009). Brune, Schobel, Karau,
et al. (2010) proposed that patients with early-onset schizophrenia might present alterations of VENs in this cortical area.
A nonstereological quantification of VEN densities across
patients with schizophrenia or bipolar disorder and normal
controls failed to reveal any changes in VEN densities. However, patients with early-onset schizophrenia were characterized by a decreased density of VENs in the right ACC, especially
in patients with a longer duration of illness. These authors
interpreted these results in light of a possible distinct neurobiological correlate of early-onset schizophrenia in which
neurodevelopmental insults are thought to play a more important role, in comparison with the later-onset subtype. The
specific implication of the right ACC was explained by possible
lateralization in social information processing. This agrees with
observations by Critchley, Mathias, and Dolan (2001) that
activity in the right ACC correlates with measures of sympathetic cardiovascular arousal. Lower VEN densities in this
cortical area in schizophrenia can also be considered with
a mirror neuron model of social cognition (Gallese, Keysers,
& Rizzolatti, 2004) linking self-awareness of autonomic
arousal and empathy for social emotions, which are affected
in schizophrenia. Brune, Schobel, Karau, et al. (2011) also
looked for a link between density of VENs in the right ACC
and suicidal behavior and found a significantly higher number
of VENs in the right ACC in schizophrenia or bipolar disorder
suicide victims, further supporting the hypothesis that VENs
are involved in emotional processing and self-analysis, which
also involves negative feelings towards oneself.
Possible Functions of VENs

VENs as Specialized Pyramidal Neurons
VENs are present in relatively large and convoluted brains. This
suggests that VENs evolved from neuronal populations that likely
had a pyramidal morphology in homologue cortical areas in
ancestral mammals (Allman et al., 2010; Butti et al., 2014,
2011). Considering the relationship between morphology and
function (Larkman, Major, Stratford, & Jack, 1992; Mainen,
Carnevale, Zador, et al., 1996; Mainen & Sejnowski, 1996;
Weaver & Wearne, 2008), the remarkable spindle shape of
VENs might be related to connecting distant cortical and subcortical areas in large brains with increase in folding and modularity
(Striedter, 2005). One may then compare VENs with Betz cells in
layer Vb of the motor cortex and Meynert cells in layer VI of the
visual cortex, respectively (Hof, Nimchinsky, Young, & Morrison,
2000; Rivara, Sherwood, Bouras, & Hof, 2003), based on the fact
that VENs project out of the cerebral cortex (Nimchinsky et al.,
1995), together with their restricted regional and laminar
distribution and their size. Betz and Meynert cells similarly
have a restricted distribution, form clusters, and exhibit speciesspecific morphological and functional specialization (Hof et al.,
2000; Rivara et al., 2003; Sherwood, Lee, Rivara, et al., 2003).
Consistent with being a modified type of pyramidal neuron, VENs are thought to be involved in the fast relay of longdistance information, a concept that emerged from the finding
of their loss in AgCC, described earlier, a condition that specifically impairs interhemispheric corticocortical connectivity
(Allman et al., 2005; Kaufman et al., 2008). Interestingly, it was

proposed, in parallel to these observations in AgCC, that VENs
play a role in network switching processes in the FI and ACC
(Sridharan et al., 2008). Finally, the localization of VENs in
cortical areas in which information on the physiological states
of the body is used to guide behavioral choices (Craig, 2009)
and their position in a layer characteristically sending subcortical projections (Brodal, 1978; Glickstein, May, & Mercier,
1985, 1990) suggest an intriguing view of VENs as upper
motoneurons for corticoautonomic pathways expanding the
original insight of Constantin von Economo on the involvement of VENs in autonomic function in the conclusion of his
1926 paper (Seeley et al., 2012).
Social Awareness and Interoception

Most of the evidence for a role of VENs in social awareness
arises from neuropathologic studies of brains of patients with
neurological and psychiatric conditions resulting in deficits in
understanding social rules. It is also worth placing this issue in
the context of VEN developmental profile. VEN numbers peak
at 8 months of postnatal life in humans (Allman et al., 2010),
specifically in the right FI, a region reliably implicated in selfawareness (Craig, 2009). This coincides with the appearance of
the stranger anxiety response to nonfamiliar faces (Tennes &
Lampl, 1964) and of the no gesture that marks the beginning
of the separationindividuation from the mother (Illingworth,
1972) and of the definition of self versus others (Meissner,
2009). The fact that VENs reach adult numbers around 4
years of age in humans, when most cases of autism are diagnosed (Rice, 2011), together with our findings of increased
ratios of VENs to pyramidal neurons in children with autism
(Santos et al., 2011) also points to the possible participation of
VENs in socialemotional developmental milestones. Future
studies exploring both alterations in VENs and changes in
activation and connectivity in VEN-containing cortical areas
are needed to understand better the relationship between the
developmental patterns of these neurons and the function of
the cortical domains in which they are observed. It should be
kept in mind, nonetheless, that such observations are entirely
derived from human studies and that comparability with other
species remains highly speculative.
VENs have been implicated in the conscious perception of
bodily states and in its integration in conscious decision processing or intuition (Allman et al., 2005; Craig, 2009), based on the
expression in VENs of dopamine D3 and serotonin 2b receptors,
known to be involved in signaling the expectation of reward and
punishment (Daw, Kakade, & Dayan, 2002; Sokoloff &
Schwartz, 2002), and on the fact that serotonin 2b receptors
are found in VENs and in gastrointestinal cells (Baumgarten &
Gothert, 1997; Borman, Tilford, Harmer, et al., 2002). The
expression in VENs of high levels of bombesin-like peptides
involved in the peripheral control of digestion and, possibly,
awareness of bodily states (Allman et al., 2010; Stimpson et al.,
2011) may lend further support to this concept. Considering the
role of the right anterior insula in self-awareness (for review, see
Craig, 2009) together with the loss of VENs in the right FI
correlated with symptom severity in bvFTD (Kim et al., 2012)
also suggests a role of VENs in interoception. In fact, bvFTD is
characterized by the incapacity to represent the personal significance of internal and external events and to use them to guide
89
Cetartiodactyla
Perissodactyla
Carnivora
Laurasiatheria
Pholidota
Chiroptera
Insectivora
Rodentia
Lagomorpha
Dermoptera
Euarchontoglires
Scandentia
Primates
Pilosa
Xenarthra
Cingulata
Afrosoricida
Macroscelidea
Tubulidentata
Afrotheria
Sirenia
Hyracoidea
Proboscidea
Marsupialia
Monotremata
Figure 8 Adaptation of the phylogeny of placental mammals including orders and superorders (derived from Murphy, Eizirik, Johnson, et al., 2001).
Orders that contain at least one species in which VENs have been observed are shown in red.
behavior. This is compatible with Damasios theory of consciousness (Damasio, 1999) in which the anterior insulaACC
network plays a central role in shaping a notion of self from a
representation of integrated body. Finally, our findings of
increased VENs in the FI of children with autism (Santos,
Uppal, Butti, et al., 2011) may well be related to the concept
that such patients have difficulties distinguishing internal and
external stimuli (Haag et al., 2005), leading to increased interoception and overwhelming perceptions.
Phylogenetic Considerations
VEN function remains elusive owing to the impossibility of
performing invasive studies in the species that possess them,
making it difficult, if not impossible, to gain direct evidence on
their actual role in brain circuits and on potential speciesspecific functional differences. Their recent observation in
cercopithecine primates (Evrard et al., 2012) may open possibilities for exploratory tract-tracing investigations that may
shed light on their projections. However, as VENs are found
in an increasing number of species, including artiodactyls,
perissodactyls, sirenians, and carnivores (Figure 8) (Butti
& Hof, 2010; Butti, Santos, Uppal, & Hof, 2013), and exhibit
major differences in their distribution, their evolutionary significance needs to be revisited from early concepts such as the
neurons that make us human to a much broader interpretation, relying on a systems neuroscience-based approach. In this
context, VENs can be envisioned as part of taxon-specific,
functionally specialized networks, depending on their cortical
distribution.
Finally, it must be kept in mind that all available studies of
VENs are based solely on Nissl-stained materials and a few
immunohistochemical observations. As previously emphasized, VENs are not found in species that allow for experimental manipulations, making other approaches impractical. In
the future, the use of transcriptomics with laser capture microscopy and microarray and RNA sequencing, although depending on the availability and quality of frozen autopsy materials
from species in which VENs occur, may become an approach
to analyze VEN-specific gene expression, in a comparative
manner to enhance our understanding of the role of VENs in
brain function.
Acknowledgments
This work is supported by the James S. McDonnell Foundation
(22002078, PRH, CCS), NSF grant BCS-0921079 (MAR),
Autism Speaks (Autism Celloidin Library, PRH), and the Seaver
Foundation (NU). The authors thank Drs. J.M. Allman,
90
W.W. Seeley, A.D. Craig, M. Santos, B. Wicinski, C.D. Stimpson,

N. Heinrichs, J. Sudduth, and F.R. Treichler for their helpful
discussion and expert technical assistance.

Cortex; Evolution of the Cerebral Cortex; Functional and Structural
Diversity of Pyramidal Cells; Gustatory System; Insular Cortex;
Mapping Cingulate Subregions; Somatosensory Cortex;
INTRODUCTION TO CLINICAL BRAIN MAPPING: Frontotemporal
Dementias; Limbic to Motor Interactions during Social Perception;
Neuropsychiatry; Schizophrenia; INTRODUCTION TO COGNITIVE
NEUROSCIENCE: Salience/Bottom-Up Attention; INTRODUCTION
TO SOCIAL COGNITIVE NEUROSCIENCE: Emotion Perception and
Elicitation; Emotion Regulation; Emotional Experience; Empathy; How
the Brain Feels the Hurt of Heartbreak: Examining the Neurobiological
Overlap Between Social and Physical Pain; Neural Correlates of Social
Cognition Deficits in Autism Spectrum Disorders; Prosocial
Motivation; Puberty, Peers, and Perspective Taking: Examining
Adolescent Self-Concept Development Through the Lens of Social
Cognitive Neuroscience; Self-Knowledge; Self-Regulation and SelfRegulation Failure; Social Decision Making; Social Knowledge; Social
Reward; The Neural Correlates of Social Cognition and Social
Interaction; INTRODUCTION TO SYSTEMS: Autonomic Control;
Emotion; Hubs and Pathways; Salience Network; Somatosensory
Processing.
References
Allman, J. M., Tetreault, N. A., Hakeem, A. Y., et al. (2010). The von Economo neurons
in frontoinsular and anterior cingulate cortex in great apes and humans. Brain
Allman, J., Watson, K., Tetreault, N., & Hakeem, A. (2005). Intuition and autism: A
possible role for Von Economo neurons. Trends in Cognitive Sciences, 9, 367373.
APA, (2000). Autistic disorder. In APA (Ed.), Diagnostic and statistic manual of mental
disorders (DSM-IV-TR). Washington, DC: APA.
Bauernfeind, A. L., de Sousa, A. A., Avasthi, T., et al. (2013). A volumetric comparison
of the insular cortex and its subregions in primates. Journal of Human Evolution,
64, 263279.
Baumgarten, H., & Gothert, M. (1997). Serotoninergic neurons and 5-HT receptors in
the CNS. Springer.
Betz, W. (1881). Uber die feinere Strukture der Gehirnrinde des Menschen. Centralblatt
fur die medizinischen Wissenschaften, 19, 193195, 209234.
Boisserie, J. R., Fisher, R. E., Lihoreau, F., & Weston, E. M. (2011). Evolving between
land and water: Key questions on the emergence and history of the Hippopotamidae
(Hippopotamoidea, Cetancodonta, Cetartiodactyla). Biological Reviews of the
Cambridge Philosophical Society, 86, 601625.
Borman, R. A., Tilford, N. S., Harmer, D. W., et al. (2002). 5-HT(2B) receptors play a key
role in mediating the excitatory effects of 5-HT in human colon in vitro. British
Journal of Pharmacology, 135, 11441151.
Bouras, C., Kovari, E., Hof, P. R., Riederer, B. A., & Giannakopoulos, P. (2001). Anterior
cingulate cortex pathology in schizophrenia and bipolar disorder. Acta
Neuropathologica, 102, 373379.
Braak, H. (1980). Architectonics of the human telencephalic cortex. Berlin: Springer.
Brodal, P. (1978). The corticopontine projection in the rhesus monkey. Origin and
principles of organization. Brain, 101, 251283.
Brown, W., & Paul, L. (2000). Cognitive and psychosocial deficits in agenesis of the
corpus callosum with normal intelligence. Cognitive Neuropsychiatry, 5, 135157.
Brune, M., Schobel, A., Karau, R., et al. (2010). Von Economo neuron density in the
anterior cingulate cortex is reduced in early onset schizophrenia. Acta
Brune, M., Schobel, A., Karau, R., et al. (2011). Neuroanatomical correlates of suicide in
psychosis: The possible role of von Economo neurons. PLoS One, 6, e20936.
Bullmore, E., & Sporns, O. (2009). Complex brain networks: Graph theoretical analysis
of structural and functional systems. Nature Reviews. Neuroscience, 10, 186198.
Butti, C., Fordyce, R. E., Raghanti, M. A., et al. (2014). The cerebral cortex of the pygmy
hippopotamus, Hexaprotodon liberiensis (Cetartiodactyla, Hippopotamidae).
Anatomical Record, 297(4), 670700.
Butti, C., & Hof, P. R. (2010). The insular cortex: A comparative perspective. Brain
Butti, C., Raghanti, M. A., Sherwood, C. C., & Hof, P. R. (2011). The neocortex of
cetaceans: Cytoarchitecture and comparison with other aquatic and terrestrial
species. Annals of the New York Academy of Sciences, 1225, 4758.
Butti, C., Santos, M., Uppal, N., & Hof, P. R. (2013). Von Economo neurons: Clinical
and evolutionary perspectives. Cortex, 49, 312326.
Butti, C., Sherwood, C. C., Hakeem, A. Y., Allman, J. M., & Hof, P. R. (2009). The
number and volume of von Economo neurons in the cerebral cortex of cetaceans.
Craig, A. D. (2003). Interoception: The sense of the physiological condition of the body.
Current Opinion in Neurobiology, 13, 500505.
Craig, A. D. (2005). Forebrain emotional asymmetry: A neuroanatomical basis? Trends
in Cognitive Sciences, 912, 566571.
Craig, A. D. (2009). How do you feel now? The anterior insula and human awareness.
Craig, A. D., Chen, K., Bandy, D., & Reiman, E. M. (2000). Thermosensory activation of
insular cortex. Nature Neuroscience, 3, 184190.
Critchley, H. D., Mathias, C. J., & Dolan, R. J. (2001). Neural activity in the human brain
relating to uncertainty and arousal during anticipation. Neuron, 29, 537545.
Damasio, A. R. (1999). The feeling of what happens: Body emotion in the making of
consciousness. New York: Harcourt Brace.
Daw, N. D., Kakade, S., & Dayan, P. (2002). Opponent interactions between serotonin
and dopamine. Neural Networks, 15, 603616.
De Crinis, M. (1933). Uber die Spezialzellen in der menschlichen Grohirnrinde.
Journal fur Psychologie und Neurologie, 45, 439449.
Economo, C., & Koskinas, G. N. (1925). Die Cytoarchitektonik der Hirnrinde des
erwachsenen Menschen. Wien und Berlin: J. Springer.
Evrard, H. C., Forro, T., & Logothetis, N. K. (2012). Von Economo neurons in the
anterior insula of the macaque monkey. Neuron, 74, 428429.
Fajardo, C., Escobar, M. I., Butitica, E., Umbarila, J., Casanova, M. F., & Pimienta, H.
(2008). Von Economo neurons are present in the dorsolateral (dysgranular)
prefrontal cortex of humans. Neuroscience Letters, 435, 215218.
Flechsig, P. (1897). Zur anatomie des vorderen Sehhugelsteils, des Cingulum und der
Acusticusbahn. Neurologie Zentralblatt, 16, 290295.
myelogenetischer Grundlage. Leipzig: G. Thieme.
Fornito, A., Yucel, M., Dean, B., Wood, S. J., & Pantelis, C. (2009). Anatomical
abnormalities of the anterior cingulate cortex in schizophrenia: Bridging the gap
between neuroimaging and neuropathology. Schizophrenia Bulletin, 35, 973993.
Frisoni, G. B., Prestia, A., Adorni, A., et al. (2009). In vivo neuropathology of cortical
changes in elderly persons with schizophrenia. Biological Psychiatry, 66,
578585.
Gallese, V., Keysers, C., & Rizzolatti, G. (2004). A unifying view of the basis of social
cognition. Trends in Cognitive Sciences, 8, 396403.
Glickstein, M., May, J. G., & Mercier, B. E. (1985). Corticopontine projection in the
macaque: The distribution of labelled cortical cells after large injections of
horseradish peroxidase in the pontine nuclei. Journal of Comparative Neurology,
235, 343359.
Glickstein, M., May, J. G., & Mercier, B. E. (1990). Visual corticopontine and
tectopontine projections in the macaque. Archives Italiennes de Biologie, 128,
273293.
Goldstein, M. (1913). Contributiuni la studiul citoarchitectoniei cerebrale (Teza de
Docenta). Bucaresti: Tipografia Cultura Strada Campineana.
Haag, G., Tordjman, S., Duprat, A., et al. (2005). Psychodynamic assessment of
changes in children with autism under psychoanalytic treatment. International
Journal of Psychoanalysis, 86, 335352.
Hakeem, A. Y., Sherwood, C. C., Bonar, C. J., Butti, C., Hof, P. R., & Allman, J. M.
(2009). Von Economo neurons in the elephant brain. The Anatomical Record, 292,
242248.
Hammarberg, C. (1895). Studen uber Klinik und Pathologie der Idiotie nebst
Untersuchungen uber die normale Anatomie des Hirnrinde. Berling: Uppsala.
Hof, P. R., Nimchinsky, E. A., Young, W. G., & Morrison, J. H. (2000). Numbers of
meynert and layer IVB cells in area V1: A stereologic analysis in young and aged
macaque monkeys. Journal of Comparative Neurology, 420, 113126.
Hof, P. R., & Van der Gucht, E. (2007). Structure of the cerebral cortex of the humpback
whale, Megaptera novaeangliae (Cetacea, Mysticeti, Balaenopteridae). Anatomical
Record, 290, 131.
Illingworth, R. (1972). The development of the infant and young child normal and
abnormal (5th ed.). Baltimore: Williams and Wilkins.

Juba, A. (1934). Uber seltenere Ganglienzellformen der Grosshirnrinde. Zeitschrift fur
Zellforschung und Mikroskopische Anatomie, 21, 441447.
Kaufman, J. A., Paul, L. K., Manaye, K. F., et al. (2008). Selective reduction of von
Economo neuron number in agenesis of the corpus callosum. Acta
Kennedy, D. P., Semendeferi, K., & Courchesne, E. (2007). No reduction of spindle
neuron number in frontoinsular cortex in autism. Brain and Cognition, 64, 124129.
Kim, E. J., Sidhu, M., Macedo, M. N., et al. (2012). Frontoinsular von Economo neuron
and fork cell loss in early behavioral variant frontotemporal dementia. Cerebral
Cortex, 22, 251259.
Larkman, A. U., Major, G., Stratford, K. J., & Jack, J. J. (1992). Dendritic morphology of
pyramidal neurones of the visual cortex of the rat. IV: Electrical geometry. Journal of
Mainen, Z. F., Carnevale, N. T., Zador, A. M., Claiborne, B. J., & Brown, T. H. (1996).
Electrotonic architecture of hippocampal CA1 pyramidal neurons based on threedimensional reconstructions. Journal of Neurophysiology, 76, 19041923.
Mainen, Z. F., & Sejnowski, T. J. (1996). Influence of dendritic structure on firing
pattern in model neocortical neurons. Nature, 382, 363366.
Marinesco, G., & Goldstein, M. (1927). Nouvelles contributions a` letude de linsula de
Reil. Bulletin de la Section des Sciences de lAcademie Roumaine, 10, 10.
Meissner, W. W. (2009). I. The self and its parts. Psychoanalytic Review, 96, 187217.
Minzenberg, M. J., Laird, A. R., Thelen, S., Carter, C. S., & Glahn, D. C. (2009). Metaanalysis of 41 functional neuroimaging studies of executive function in
schizophrenia. Archives of General Psychiatry, 66, 811822.
Mishnew, N. J., & Keller, T. A. (2010). The nature of brain dysfunction in autism:
Functional brain imaging studies. Current Opinion in Neurology, 23, 124130.
Monk, C. S., Peltier, S. J., Wiggins, J. L., et al. (2009). Abnormalities of intrinsic
functional connectivity in autism spectrum disorders. NeuroImage, 47, 764772.
Murphy, W. J., Eizirik, E., Johnson, W. E., Zhang, Y. P., Ryder, O. A., & OBrien, S. J.
(2001). Molecular phylogenetics and the origins of placental mammals. Nature,
409, 614618.
Ngowyang, G. (1932). Beschreibung einer Art von Spezialzellen in der Inselrinde
zugleich Bemerkungen uber die v. Economoschen Spezialzellen. Journal fur
Psychologie und Neurologie, 44, 671674.
Ngowyang, G. (1936). Neuere Befunde uber die Gabelzellen. Cell Tissue Research, 25,
236239.
Nikitin, M. P. (1909). Die histologische Struktur des Gyrus cinguli beim Menschen.
Obozrenie Psikhiatrii Nevrologi St. Petersburg, 14, 96106.
Nimchinsky, E. A., Gilissen, E., Allman, J. M., Perl, D. P., Erwin, J. M., & Hof, P. R.
(1999). A neuronal morphologic type unique to humans and great apes.
96, 52685273.
Nimchinsky, E. A., Vogt, B. A., Morrison, J. H., & Hof, P. R. (1995). Spindle neurons of
the human anterior cingulate cortex. Journal of Comparative Neurology, 355, 2737.
Ramon y Cajal, S. (19011902). Studies on the human cerebral cortex IV: Structure of
the olfactory cerebral cortex of man and mammals. Trabajos del Laboratorio de
Investigaciones Biologicas de la Universidad de Madrid, 1, 1140.
Ramon y Cajal, S. (1904). Textura del Sistema Nervioso del Hombre y de los
Vertebrados. Madrid: Nicolas Moya.
Rice, C. E. (2011). The changing prevalence of the autism spectrum disorders.
American Family Physician, 83, 515520.
Rivara, C.-B., Sherwood, C. C., Bouras, C., & Hof, P. R. (2003). Stereologic
characterization and spatial distribution patterns of Betz cells in human primary
motor cortex. Anatomical Record, 270A, 137151.
Rose, M. (1927). Gyrus limbicus anterior und Regio retrosplenialis (Cortex
holoprotoptychos quinquestratificatus)Vergleichende Architektonik bei Tier und
Menschen. Journal fur Psychologie und Neurologie, 35, 5217.
Rose, M. (1928). Die Inselrinde des Menschen und der Tiere. Journal fur Psychologie
und Neurologie, 37, 467624.
91
Santos, M., Uppal, N., Butti, C., et al. (2011). von Economo neurons in autism: A
stereologic study of the frontoinsular cortex in children. Brain Research, 1380,
206217.
Seeley, W. W. (2008). Selective functional, regional, and neuronal vulnerability in
frontotemporal dementia. Current Opinion in Neurology, 21, 701707.
Seeley, W. W., Allman, J., Carlin, D. A., et al. (2007). Divergent social functioning in
behavioral variant frontotemporal dementia and Alzheimer disease: Reciprocal
connections and neuronal evolution. Alzheimers Disease and Associated Disorders,
21, S50S57.
Seeley, W. W., Carlin, D. A., Allman, J., et al. (2006). Early frontotemporal dementia
targets neurons unique to apes and humans. Annals of Neurology, 60,
660667.
Seeley, W. W., Menon, V., Schatzberg, A. F., et al. (2007). Dissociable intrinsic
connectivity networks for salience processing and executive control. Journal of
Seeley, W. W., Merkle, F. T., Gaus, S. E., Craig, A. D., Allman, J. M., & Hof, P. R.
(2012). Distinctive neurons of the anterior cingulate and frontoinsular cortex: A
historical perspective. Cerebral Cortex, 22, 245250.
Sherwood, C. C., Lee, P. H., Rivara, C.-B., et al. (2003). Evolution of specialized
pyramidal neurons in primate visual and motor cortex. Brain, Behavior and
Evolution, 61, 2844.
Simms, M. L., Kemper, T. L., Timbie, C. M., Bauman, M. L., & Blatt, G. J. (2009). The
anterior cingulate cortex in autism: Heterogeneity of qualitative and quantitative
cytoarchitectonic features suggests possible subgroups. Acta Neuropathologica,
118, 673684.
Sokoloff, P., & Schwartz, J. (2002). The dopamine D3 receptor and its implications in
neuropsychiatric disorders and their treatments. In G. Di Chiara (Ed.), Dopamine in
the CNS: Springer.
Sridharan, D., Levitin, D. J., & Menon, V. (2008). A critical role for the right frontoinsular cortex in switching between central-executive and default-mode networks.
105, 1256912574.
Stimpson, C. D., Tetreault, N. A., Allman, J. M., et al. (2011). Biochemical specificity
of von Economo neurons in hominoids. American Journal of Human Biology, 23,
2228.
Striedter, G. F. (2005). Principles of brain evolution. Sunderland, MA: Sinauer
Associates Inc.
Syring, A. (1956). Die Verbreitung von Spezialzellen in der Grosshirnrinde
verschiedener Saugertiergruppen. Zeitschrift fur Zellforschung und Mikroskopische
Anatomie, 45, 399434.
Taylor, K. S., Seminowicz, D. A., & Davis, K. D. (2009). Two systems of resting state
connectivity between the insula and cingulate cortex. Human Brain Mapping, 30,
27312745.
Tennes, K. H., & Lampl, E. E. (1964). Stranger and separation anxiety in infancy.
Journal of Nervous and Mental Disease, 139, 247254.
Uddin, L. Q., & Menon, V. (2009). The anterior insula in autism: Under-connected and
under-examined. Neuroscience and Biobehavioral Reviews, 33, 11981203.
Vogt, O. (1903). Zur anatomischen Gliederung des Cortex cerebri. Journal fur
von Economo, C. (1926). Eine neue Art Spezialzellen des Lobus cinguli und
Lobus insulae. Zeitschrift fur die Gesamte Neurologie und Psychiatrie, 100,
706712.
Weaver, C. M., & Wearne, S. L. (2008). Neuronal firing sensitivity to morphologic and
active membrane parameters. PLoS Computational Biology, 4, e11.
White, T. P., Joseph, V., Francis, S. T., & Liddle, P. F. (2010). Aberrant salience network
(bilateral insula and anterior cingulate cortex) connectivity during information
processing in schizophrenia. Schizophrenia Research, 123, 105115.
Synaptic Organization of the Cerebral Cortex

A Rollenhagen, Institute of Neuroscience and Medicine, INM-2, Julich, Germany
JHR Lubke, Institute of Neuroscience and Medicine INM-2, Julich, Germany; Rheinisch-Westfalische Technische Hochschule/
University Hospital Aachen, Aachen, Germany; Julich-Aachen Research Alliance Translational Brain Medicine, Aachen, Germany
Abbreviations
AMPA
ATP
BDNF
CCK
CNS
GABA
MUNC
NMDA
a-Amino-3-hydroxy-5-methyl-4isoxazolepropionic acid
Adenosine triphosphate
Brain-derived neurotrophic factor
Cholecystokinin
Central nervous system
g-Aminobutyric acid
An acronym for a family of mammalian
uncoordinated proteins located at the presynaptic
density
N-Methyl-D-aspartate
Axons are the main output structures of neurons and can be

categorized as local circuit axons (inhibitory GABAergic
interneurons and spiny stellate neurons) and projection
axons (excitatory pyramidal cells). The axon emerges either
directly from the soma or from a primary dendrite with a
thick unmyelinated initial segment that is the action potential
initiation zone. From there, numerous vertically and horizontally projecting axonal collaterals emerge; however, each neuronal cell type shows a highly specific projection pattern, for
example, within a cortical column (intracolumnar) or across
columns (transcolumnar) that is regulated by the function of
the neuron within the neocortical network.
Along the axon, presynaptic membrane specializations, socalled axonal (synaptic) boutons, are formed at relatively high
density. These boutons constitute the presynaptic elements of the
signal transduction pathway between neurons. Synaptic boutons
form either en passant or end terminal synapses with different
structural compartments of the target neurons. The establishment of synapses on a given neuron is highly target-specific
and occurs at dendrites (axodendritic contacts; Figure 1(a) and
1(b)), dendritic spines (axospinous contacts; Figure 1(a), 1(b),
and 1(e)), somata (axosomatic contacts; Figure 1(c)), and the
axon initial segment (axoaxonic contacts; Figure 1(d)). Synapses
are elementary building blocks of the nervous system and resemble independent compartments (units) with distinct structural
and functional properties.
General Structural Features of Synapses

Two fundamentally different types of synapses are found in the
neocortex.
Electrical synapses: Here, the pre- and postsynaptic opposing
cell membranes are connected by special channels so-called
gap junctions. In vertebrates, gap-junctional hemichannels are
NPY
PSD
RIM
RP
RRP
SNAP
SNARE
VIP
Neuropeptide Y
Postsynaptic density
Family of major active zone proteins
Recycling pool
Readily releasable pool
Soluble N-ethylmaleimide sensitive fusion
attachment protein
Soluble N-ethylmaleimide sensitive fusion
attachment protein receptor, an acronym derived
from SNAP superfamily of active zone proteins
Vasointestinal protein
primarily homo- or heterohexamers of connexin proteins

belonging to different families. The most common types of
connexins in the neocortex are connexin 36 expressed in neurons and connexin 43 expressed in astrocytes (Hormuzdi,
Filippov, Mitropoulou, Monyer, & Bruzzone, 2004). Electrical
synapses can serve different functions: (1) electrical and metabolic exchange through hemichannels, (2) electrical and metabolic coupling between neurons, and (3) adhesive function
independent of conductive gap-junctional channels. Electrical
synapses were long thought to be expressed only in prenatal
and early postnatal life and are involved in neuronal migration
in the neocortex. It is now established that gap junctions
connect different types of GABAergic interneurons that form
independent networks responsible for the induction of different rhythmic and oscillatory activities, thereby controlling and
modulating the behavior of the entire cortical network.
Electrical synapses are characterized by fast signal transduction
between neurons but lack synaptic plasticity (Gibson,
Beierlein, & Connors, 2005).
Chemical synapses: The second and most abundant type of
synapses in the neocortex is the chemical synapse (Figures 1
and 2(b, b1)). Here, the arriving action potential in the presynaptic neuron elicits (via the activation of voltage-gated presynaptic Ca2 channels) a chemical signal by the specific
release of either an excitatory or inhibitory neurotransmitter.
Quanta of the released neurotransmitter specifically bind to
appropriate receptors located at a highly organized membrane
complex of the postsynaptic neuron, the postsynaptic density
(PSD) (Figures 1, 2(b), and 3). The neurotransmitter may
initiate an electrical response or activate a secondary messenger
pathway that may either excite or inhibit the postsynaptic
neuron. Because of the complexity of receptor signal transduction, chemical synapses have a much broader and complex
effect on the postsynaptic neuron than electrical synapses,
namely, on synaptic transmission and plasticity (Cowan,
Sudhof, & Stevens, 2003).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00204-9
93
94
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Synaptic Organization of the Cerebral Cortex
Figure 1 Structural composition and location of synapses in the neocortex. (a) Electron micrograph showing a synaptic bouton (b1, given in
transparent yellow) establishing a synaptic contact (red arrowheads at b1 and b2) with a dendritic shaft (sh, given in transparent blue). A second bouton
(b2) terminates on a dendritic spine (sp). Note the prominent spine apparatus (framed areas) in the spine neck and head. Scale bar is 1 mm. (b) 3-D
volume reconstruction of a dendritic segment of a neocortical layer 5 pyramidal neuron with three synaptic boutons (transparent yellow) terminating on
different parts of the dendrite (blue). The synaptic boutons were made transparent to visualize important subelements within the synaptic boutons:
active zones are given in red, synaptic vesicles in green, and mitochondria in white. Note that synaptic vesicles are also frequently found in the axon
as indicated by the framed area. (c) Somatic region (so) with numerous synaptic boutons (b1b5). Scale bar is 1 mm. (d) Three synaptic boutons
(b1b3) terminating on an axon initial segment (ais) establishing axoaxonic contacts. The active zones are marked by red arrowheads. Scale bar is
0.5 mm. (e) Two axospinous synapses (b1, sp1 and b2, sp2) isolated by fine astrocytic processes (transparent green). Note that fine astrocytic
processes reach as far as the active zones (marked by red arrowheads). Scale bar is 0.5 mm. Inset: high-power electron micrograph of the active
zone composed of the pre- and postsynaptic densities and the synaptic cleft. Docked vesicles fused with the presynaptic density are marked by
asterisks. Scale bar is 0.1 mm. (f) 3-D volume reconstruction of the synaptic complex (b1 yellow; sp1 blue) in D showing the tight ensheathment
of the bouton and spine by fine astrocytic processes (green). The presynaptic density is marked by red arrowheads.
95
Figure 2 Comparison of two cortical synapses embedded in different microcircuits. (a) Two hippocampal mossy fiber boutons (MFB1 and MFB2,
transparent yellow) terminating on a large proximal dendrite (transparent blue) of a CA3 pyramidal neuron. Here, synaptic contacts are established
exclusively with the spiny excrescences (se, transparent blue), whereas puncta adherentia that are regarded as adhesion complexes (red asterisks) are
only found at the apposition zone between the two boutons and the target dendrite. Scale bar is 0.5 mm. (a1) 3-D volume reconstruction of an en
passant MFB (yellow) and its postsynaptic target dendrite. (b) Electron micrograph of a neocortical axospinous synapse with a perforated postsynaptic
density (red arrowheads). Scale bar is 0.5 mm. (b1) 3-D volume reconstruction of the synaptic complex shown in (b). Note that the mossy fiber
terminal is 20-fold larger than the neocortical bouton as indicated by the white scale bar (5 mm).
The so-called synaptic active zone, that is, the close apposition between the pre- and postsynaptic elements, is the site of
neurotransmitter release. In general, chemical synapses are
composed of three subelements: a pre- and postsynaptic compartment and a cleft between the two elements (Figures 1(e)
inset and 3(a)). The presynaptic element contains a highly
variable pool of synaptic vesicles and several mitochondria
associated with the pool of vesicles (Figure 1(ac) and 1(e)).
At the contact zone with the postsynaptic neuron, a dense
accumulation is formed, the presynaptic density (Figure 1(a),
1(c), and 1(e) inset). This density is constituted by a cocktail of
various synaptic proteins including the SNARE and SNAP
complex, various MUNC and RIM proteins, and many others
all involved in the transport, binding, and fusion of synaptic
vesicles to the presynaptic density (Sudhof, 2012). Besides

synaptic proteins, different high and low voltage-gated Ca2
channels of the N, P/Q, R, and T type exist, which are thought
to be specifically organized in clustered domains along the
presynaptic density (Stanley, 1997).
The second structural element is the synaptic cleft
(Figures 1(e) inset and 3(a)), not only a gap but also a bridge
connecting the pre- and postsynaptic density (PSD), containing a matrix of fuzzy material of still unknown function and
origin. Neurotransmitter molecules released from fused synaptic vesicles diffuse via the synaptic cleft (Figure 1(e) inset) to
the PSD and bind to appropriate neurotransmitter receptors. In
the neocortex, PSDs often are perforated by periodic interruptions of the protein matrix (Figure 2(b)). Synapses with
96
Figure 3 Distribution pattern of AMPA and NMDA receptors at neocortical synapses. (a) Intrasynaptic distribution of the AMPA receptor (subunits
GluR14, black gold grains) at a postsynaptic density (PSD) as revealed by the dense accumulation of so-called intramembranous particles on
a dendritic spine using freeze-fracture replica preparations combined with postimmunogold labeling. Here, the synaptic cleft (as marked by the
arrowheads) separating the pre- (on the left) and PSD (on the right) is clearly visible. (b) Intrasynaptic distribution of the NR1 subunit of the NMDA
receptor (black gold grains) at a PSD at a dendritic shaft. Note the clustered distribution of the NR1 subunit within the PSD. (c) Co-localization of
the AMPA receptor (labeled with 5 nm gold) and the NR1 subunit of the NMDA receptor (labeled with 10 nm gold) at a PSD located at the somatic region
of a neuron. Scale bars in (a)(c) are 100 nm.
perforated PSDs are regarded to be highly efficient in synaptic

strength and plasticity (Geinisman, 1993; Geinisman, DetoledoMorrell, & Morrell, 1991; Nicoletta, Fenghua, Gregers, Maurizio,
& Randal, 2013). Proteins at the PSD are involved in anchoring
and trafficking neurotransmitter receptors, thereby modulating
the activity of these receptors, in particular their temporal and
spatial sensitization and desensitization. The different composition and content of neurotransmitter binding sites and synaptic
proteins at the PSD is critically involved in synaptic transmission
and in the modulation of long- and short-term synaptic plasticity (Sudhof, 2012).
The so-called puncta adherentia, a second membrane
specialization that is thought to function as adhesion complexes
at large central nervous system (CNS) synapses (e.g., hippocampal
mossy fiber bouton; Rollenhagen et al., 2007), are not found at
neocortical synapses (compare Figure 2(a) with 2(b)).
Structural Composition of Chemical Neocortical

Synapses
The majority of chemical synapses in the neocortex comprise
two major groups, glutamatergic and GABAergic synapses, the
remaining contain acetylcholine, serotonin, dopamine,
adrenaline, and adenosine (Zilles, Palomero-Gallagher, &
Schleicher, 2004, reviewed by Greger & Esteban, 2007). With
respect to their structural organization, synapses were
described as asymmetrical (Gray type 1) or symmetrical (Gray
type 2) synapses (Gray, 1959a, 1959b). When examined under
an electron microscope, asymmetrical synapses are characterized by round vesicles and a prominent PSD and are established predominantly (90%) on dendritic spines (Figure 1
(a) bouton 2 and 1(d)) but to a smaller fraction also on
dendritic shafts (Figure 1(a) bouton 1 and 1(b)). Asymmetrical

synapses are typically excitatory. In contrast, symmetrical
synapses have flattened or elongated vesicles and do not contain a prominent PSD and terminate specifically on somata
and dendritic shafts (Figure 2(a) bouton 1) and only occasionally on dendritic spines. Symmetrical synapses are typically
inhibitory. The majority of neocortical synapses are excitatory
(8085%), the remaining are inhibitory GABAergic synapses
located at different parts of the dendritic tree, the somata, and
axon initial segment of their target neurons (Figure 1(c) and 1
(d); 1520%) although region- and layer-specific differences
in their distribution exist (Gray, 1959a, 1959b).
Synaptic boutons in the six layers of the neocortex differ
substantially in shape and size ranging from 0.5 to 12 mm2 in
surface area and 0.15 to 0.50 mm3 in volume and thus belong
to the smaller synapses in the CNS (Figure 2). The majority
regardless whether they are excitatory or inhibitory contain a
single but large (range 0.10.3 mm2) active zone (transmitter
release site; Figure 1(a)1(e)) when compared with other CNS
synapses. The majority of boutons contain several mitochondria (15 per synaptic bouton; Rollenhagen & Lubke, 2006).
Mitochondria are highly specialized intrinsic organelles that
act not only as energy suppliers of the nerve terminal but also
as internal calcium stores (Pozzan, Magalhaes, & Rizzuto,
2000; Rizzuto, Bernardi, & Pozzan, 2000), regulating and
adjusting internal Ca2 levels in synapses. Calcium is a key
factor in the induction, maintenance, and termination of synaptic transmission and plasticity. Mitochondria are highly
mobile (Mironov, 2006; Mironov & Symonchuk, 2006) and
may be critically involved in the mobilization of synaptic
vesicles from the reserve pool to the recycling and the readily
releasable pools (RRPs) of synaptic vesicles. Furthermore, neocortical synapses also contain so-called multivesicular bodies,

endosomal organelles containing several vesicles involved in
endocytotic and trafficking functions.
Synaptic boutons are densely packed with synaptic vesicles
ranging from 100 to 2000 synaptic vesicles that are 35 nm
in diameter (Figures 1(a)1(c), 1(e), and 2(b)), representing
and constituting the three functionally defined pools of synaptic vesicles (see succeeding text). A second class of vesicles are
large dense-core vesicles that contain either different neuromodulators (ATP, BDNF, and different neuropeptides such as
NPY, VIP, and CCK) or proteins involved in the buildup of
the presynaptic density, which maintain synapse integrity by
regulating protein ubiquitination and degradation, namely,
Piccolo and Bassoon (Schoch & Gundelfinger, 2006; Waites
et al., 2013).
Release Machinery and Release Probability

at Neocortical Synapses
It is well established that three functionally defined pools of
synaptic vesicles exist: the so-called RRP containing docked
vesicles already fused with the presynaptic membrane
(Figure 1(e) inset), the recycling pool (RP) resembling vesicles
in close vicinity (60200 nm distance) to the presynaptic
density, and the reserve pool. The size of each of these pools
critically determines synaptic efficacy, strength, and plasticity
(Rizzoli & Betz, 2004, 2005). At neocortical synapses, the RRP
and RP are relatively large compared with other CNS synapses,
suggesting a relatively high efficacy and strength in synaptic
transmission as indicated by the release probability. Release of
neurotransmitter at neocortical synapses can occur either from
a single (univesicular) or from multiple vesicles (multivesicular) and in a uni- or multiquantal fashion (Cowan et al., 2003).
However, it is still rather unclear which mode and how many
quanta are released temporarily and spatially and whether
release is frequency-dependent or frequency-independent at a
given synapse. It should be noted that the release machinery is
developmentally regulated; synaptic connections in immature
animals (until postnatal day 15) show higher release probabilities when compared with adult connections although huge
differences between individual neocortical synaptic connections exist, indicating differences in short-term synaptic plasticity, namely, the paired-pulse depression or facilitation
behavior.
Neurotransmitter Receptors at Cortical Synapses

At the PSD, a cocktail of various neurotransmitter receptors
exist that determine and modulate the functional properties of
the synapse (Sudhof, 2012; reviewed by Greger & Esteban,
2007; Hansen, Yuan, & Traynelis, 2007; Rao & Finkbeiner,
2007). The main excitatory (glutamatergic) neurotransmitter
receptors in the neocortex are ionotropic glutamate receptors,
namely, the a-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid (AMPA) (subunits GluR14; Figure 3(a)) and the
N-methyl-D-aspartate (NMDA) (subunits NR1 and NR2A, B, C,
and D; Figure 3(b); Greger & Esteban, 2007; Hansen et al., 2007;
Nusser, 2000; Rao & Finkbeiner, 2007) and kainate receptors
(subunits KA1, KA2, and GluR57; Contractor, Swanson, Sailer,
97
OGorman, & Heinemann, 2000; Schmitz, Mellor, & Nicoll,

2001) that are thought to be predominantly presynaptic. In the
adult neocortex, AMPARs and NMDRs containing synapses represent the majority of glutamatergic synapses although a huge
variability in the subunit composition of both receptors at
PSDs of individual neuronal classes exists (reviewed by Nusser,
2000). In the neocortex, the most abundant subunit of the
AMPARs is GluR2 that regulates the permeability to Ca2 and
other cations, such as sodium and potassium. Functionally,
AMPARs open and close quickly as indicated by their short
kinetics (rapid sensitization and desensitization) and are thus
responsible for the induction and termination of fast synaptic
transmission required to reduce the membrane potential. The
depolarization by AMPAR activation leads to repulsion of the
Mg2 cation in NMDRs, allowing the pore to further open and
pass current, thus resulting in the subsequent activation of
NMDARs. Therefore, AMPARs are believed to be a key receptor
in synaptic transmission and plasticity leading to the concept of
silent synapses that lack AMPARs.
In the adult neocortex, NMDARs are the second prominent
class of glutamatergic neurotransmitter receptors (reviewed by
Greger & Esteban, 2007; Hansen et al., 2007; Rao & Finkbeiner,
2007). Voltage-dependent activation of NMDARs results in the
opening of an ion channel that is nonselective to cations with
an equilibrium potential near 0 mV, namely, Na and small
amounts of Ca2 into the cell and K out of the cell. For the
function of NMDARs, the NR1 subunit is required. The modulation of synaptic transmission and plasticity is governed by
different combinations of NR2A, B, C, and D with NR1. The
actual combinations are region- and layer-specific resulting in
huge differences in synaptic plasticity in individual networks of
the neocortex. Although both AMPARs and NMDARs are colocalized in cortical synapses (Figure 3(c)), it is still rather
unknown which subunit combinations of AMPARs and
NMDARs exist in a given cortical synapse.
Kainate receptors play a role in both the pre- and postsynaptic neurons. In contrast to AMPA and NMDA receptors,
they have a more limited layer-specific distribution in the
neocortex and their function is not well defined.
The most prominent inhibitory neurotransmitter receptors
in the neocortex that respond to the neurotransmitter gaminobutyric acid (GABA) are GABA receptors with three subtypes GABAA (Olsen & Sieghart, 2009), GABAB, and GABAC
(Ulrich & Bettler, 2007). GABAA receptors are ionotropic,
ligand-gated ion channels, whereas GABAB receptors are G
protein-coupled metabotropic receptors. Binding of GABA
molecules on GABAA receptors mainly located at inhibitory,
somatic synapses on both excitatory and inhibitory neurons,
triggers the opening of a chloride ion-selective channel. The
increased chloride (Cl) conductance drives the membrane
potential towards the reversal potential of the Cl ion, which
is about 65 mV in neurons, inhibiting the firing of action
potentials in these neurons. Interestingly, GABA acts excitatory
via GABAA receptors due to a different subunit expression
during prenatal and early postnatal development.
A slow response to GABA is mediated by GABAB receptors
originally defined on the basis of their pharmacological properties. GABAB are thought to be located at inhibitory synapses
terminating on distal and/or proximal dendritic segments of
principal and GABAergic interneurons. Synapses containing
98
the GABAA receptor are found throughout all cortical layers

and are the most abundant receptor subtype, whereas the
layer-specific distribution of synapses containing GABAB
and GABAC receptors has to be investigated in more detail.
While GABAA receptors provide fast and highly efficient inhibition, GABAB receptors have a more long-lasting inhibitory
effect restricted to the dendritic area of activation, although
both receptors are involved in so-called feedforward and feedback inhibition in the neocortex. Thus, GABA receptors are
required to balance excitation and inhibition in individual
cortical networks, for example, the cortical column.
SynapseAstrocyte Interaction in the Neocortex

Glial cells, in particular astrocytes, are the non-neuronal structural element in the neocortex. They are distributed throughout all cortical layers, thereby forming a dense astrocytic
network between neurons. At neocortical synapses, astrocytes
are physical barriers (Figure 1(e) and 1(f)) to neurotransmitter diffusion, thereby preventing spillover of released
neurotransmitter to neighboring synaptic contacts (Danbolt,
2001; Houades, Koulakoff, Ezan, Seif, & Giaume, 2008; Oliet,
Piet, Poulain, & Theodosis, 2004). Glutamate transporters
on astrocytes actively take up glutamate, terminate synaptic
transmission, and speed up the recovery from receptor desensitization. These mechanisms allow the precise spatial and
temporal regulation of the concentration of the glutamate in
the synaptic cleft (Danbolt, 2001; Oliet et al., 2004). Furthermore, astrocytes release gliotransmitters, for example, either
glutamate or GABA (Le Meur, Mendizabal-Zubiaga, Grandes,
& Audinat, 2012), through vesicular exocytosis, which can also
regulate synaptic transmission through the activation of preand postsynaptic receptors. Recently, it has been demonstrated
that astrocytic signaling controls and modulates spike timedependent depression at neocortical L2/3 and L4 synapses
(Min & Nevian, 2012).
In the neocortex and in contrast to larger CNS synapses,
astrocytes not only tightly enwrap the synaptic complex
formed by a presynaptic bouton and its postsynaptic target
structure (a dendrite or spine) but also reach as far as the
synaptic cleft (Figure 1(e) and 1(f)). They are therefore in a
key position for acting as a memory buffer for previous coincident neuronal activity. Hence, they seem to be involved in
modulating synaptic transmission and plasticity of neocortical
synapses (Dallerac, Chever, & Rouach, 2013).
Development of Neocortical Synapses

To date, only a few studies have investigated developing synapses, in particular synapses at early stages of cortical development. In addition, relatively little is known about the synaptic
organization of an early cortical network (but see Anker &
Cragg, 1974; Blue & Parnavelas, 1983a, 1983b; Bourgeois,
Jastreboff, & Rakic, 1989; Cragg, 1972, 1975a, 1975b; Rakic,
Bourgeois, Eckenhoff, Zecevic, & Goldman-Rakic, 1986). Nevertheless, marked structural differences between developmental stages in the rat and mouse neocortex were observed.
Between the first two postnatal weeks, the structural
composition, shape, and size of active zones (transmitter

release sites) as well as the pool of synaptic vesicles underwent considerable changes. Between postnatal days 2 and 4
in rat and mice, only a few synapses were found. The predominant structural elements were dendrodendritic or
dendrosomatic gap junctions. This finding supports the
hypothesis that signal transduction is mediated predominantly by electrical coupling via gap junctions during early
postnatal time. At postnatal day 4, the majority of synapses
were established at dendritic shafts, and spine synapses are
very rarely found. These synapses contain only few releasable synaptic vesicles with no recycling and reserve pool.
The low number of releasable synaptic vesicles underlies
the severe run-down effects (rapid depletion of the releasable pool of synaptic vesicles) and low reliability in synaptic
transmission. With increasing age (postnatal day 10), the
active zone becomes larger with more perforated pre- and
postsynaptic densities although the number of synaptic vesicles could vary substantially between individual synapses.
At postnatal day 20, more spine synapses are generated
followed by a substantial increase in the number of synaptic
vesicles in the RRP, RP, and reserve pools. The results indicate that synapses undergo significant structural and functional changes during their maturation. Whether this pattern
of maturation occurs timely tuned in all cortical layers during cortico- and synaptogenesis is still unknown and has to
be further investigated.

Astrocytes, Oligodendrocytes, and NG2 Glia: Structure and Function;
Language; Evolution of the Cerebral Cortex; Functional and Structural
Diversity of Pyramidal Cells; Functional Connectivity; Somatosensory
Cortex; INTRODUCTION TO SYSTEMS: Network Components;
Neural Networks Underlying Novelty Processing.
References
Anker, R. L., & Cragg, B. G. (1974). Estimation of the number of synapses in a volume
of nervous tissue from counts in thin sections by electron microscopy. Journal of
Neurocytology, 3, 725735.
Blue, M. E., & Parnavelas, J. G. (1983a). The formation and maturation of synapses in
the visual cortex of the rat. I. Qualitative analysis. Journal of Neurocytology, 12,
599616.
Blue, M. E., & Parnavelas, J. G. (1983b). The formation and maturation of synapses in
the visual cortex of the rat. II. Quantitative analysis. Journal of Neurocytology, 12,
697712.
Bourgeois, J. P., Jastreboff, P. J., & Rakic, P. (1989). Synaptogenesis in visual cortex of
normal and preterm monkeys: Evidence for intrinsic regulation of synaptic
overproduction. Proceedings of the National Academy of Sciences of the United
Contractor, A., Swanson, G. T., Sailer, A., OGorman, S., & Heinemann, S. F. (2000).
Identification of the kainate receptor subunits underlying modulation of excitatory
synaptic transmission in the CA3 region of the hippocampus. Journal of
Cowan, W. M., Sudhof, T. C., & Stevens, C. F. (2003). Synapses. Baltimore: John
Hopkins0-8018-7118-2, Paperbacks Edition.
Cragg, B. G. (1972). The development of synapses in cat visual cortex. Investigative
Ophthalmology, 11, 377385.
Cragg, B. G. (1975a). The density of synapses and neurons in normal, mentally
defective ageing human brains. Brain, 98, 8190.

Cragg, B. G. (1975b). The development of synapses in the visual system of the cat.
Dallerac, G., Chever, O., & Rouach, N. (2013). How do astrocytes shape synaptic transmission?
Insights from electrophysiology. Frontiers in Cellular Neuroscience, 7, 159.
Danbolt, N. C. (2001). Glutamate uptake. Progress in Neurobiology, 65, 100105.
Geinisman, Y. (1993). Perforated axospinous synapses with multiple, completely
partitioned transmission zones: Probable structural intermediates in synaptic
plasticity. Hippocampus, 3, 417433.
Geinisman, Y., Detoledo-Morrell, L., & Morrell, F. (1991). Induction of long-term
potentiation is associated with an increase in the number of axospinous synapses
with segmented postsynaptic densities. Brain Research, 566, 7788.
Gibson, J. R., Beierlein, M., & Connors, B. W. (2005). Functional properties of electrical
synapses between inhibitory interneurons of neocortical layer 4. Journal of
Gray, E. G. (1959a). Axo-somatic and axo-dendritic synapses of the cerebral cortex: An
electron microscope study. Journal of Anatomy, 93, 420433.
Gray, E. G. (1959b). Electron microscopy of synaptic contacts on dendrite spines of the
cerebral cortex. Nature, 183, 15921593.
Greger, I. H., & Esteban, J. A. (2007). AMPA receptor biogenesis and trafficking.
Current Opinion in Neurobiology, 17, 289297.
Hansen, K. B., Yuan, H., & Traynelis, S. F. (2007). Structural aspects of AMPA receptor
activation, desensitization and deactivation. Current Opinion in Neurobiology, 17,
281288.
Hormuzdi, S. G., Filippov, M. A., Mitropoulou, G., Monyer, H., & Bruzzone, R. (2004).
Electrical synapses: A dynamic signaling system that shapes the activity of neuronal
networks. Biochimica et Biophysica Acta, 1662, 113137.
Houades, V., Koulakoff, A., Ezan, P., Seif, I., & Giaume, C. (2008). Gap junctionmediated astrocytic networks in the mouse barrel cortex. Journal of Neuroscience,
28, 52075217.
Le Meur, K., Mendizabal-Zubiaga, J., Grandes, P., & Audinat, E. (2012). GABA
release by hippocampal astrocytes. Frontiers in Computational Neuroscience, 6, 59.
Min, R., & Nevian, T. (2012). Astrocyte signaling controls spike timing-dependent
depression at neocortical synapses. Nature Neuroscience, 15, 746753.
Mironov, S. L. (2006). Spontaneous and evoked neuronal activities regulate movements
of single neuronal mitochondria. Synapse, 59, 403411.
Mironov, S. L., & Symonchuk, N. (2006). ER vesicles and mitochondria move and
communicate at synapses. Journal of Cell Science, 119, 49264934.
Nicoletta, N., Fenghua, C., Gregers, W., Maurizio, P., & Randal, N. J. (2013). A new
efficient method for synaptic vesicle quantification reveals differences between
medial prefrontal cortex perforated and non-perforated synapses. Journal of
Comparative Neurology, http://dx.doi.org/10.1002/cne.23482.
99
Nusser, Z. (2000). AMPA and NMDA receptors: Similarities and differences in their
synaptic distribution. Current Opinion in Neurobiology, 10, 337341.
Oliet, S. H., Piet, R., Poulain, D. A., & Theodosis, D. T. (2004). Glial modulation of
synaptic transmission: Insights from the supraoptic nucleus of the hypothalamus.
Glia, 47, 258267.
Olsen, R. W., & Sieghart, W. (2009). GABA A receptors: Subtypes provide diversity of
function and pharmacology. Neuropharmacology, 56, 141148.
Pozzan, T., Magalhaes, P., & Rizzuto, R. (2000). The comeback of mitochondria to
calcium signalling. Cell Calcium, 28, 279283.
Rakic, P., Bourgeois, J. P., Eckenhoff, M. F., Zecevic, N., & Goldman-Rakic, P. S.
(1986). Concurrent overproduction of synapses in diverse regions of the primate
cerebral cortex. Science, 232, 232235.
Rao, V. R., & Finkbeiner, S. (2007). NMDA and AMPA receptors: Old channels, new
tricks. Trends in Neurosciences, 30, 284291.
Rizzoli, S. O., & Betz, W. J. (2004). The structural organization of the readily releasable
pool of synaptic vesicles. Science, 303, 20372039.
Rizzoli, S. O., & Betz, W. J. (2005). Synaptic vesicle pools. Nature Reviews.
Rizzuto, R., Bernardi, P., & Pozzan, T. (2000). Mitochondria as all-round players of the
calcium game. Journal of Physiology, 529, 3747.
Rollenhagen, A., & Lubke, J. H. (2006). The morphology of excitatory central synapses:
From structure to function. Cell and Tissue Research, 326, 221237.
Rollenhagen, A., Satzler, K., Rodriguez, E. P., Jonas, P., Frotscher, M., & Lubke, J. H.R
(2007). Structural determinants of transmission at large hippocampal mossy fiber
synapses. Journal of Neuroscience, 27, 1043410444.
Schmitz, D., Mellor, J., & Nicoll, R. A. (2001). Presynaptic kainate receptor mediation of
frequency facilitation at hippocampal mossy fiber synapses. Science, 291,
19721976.
Schoch, S., & Gundelfinger, E. D. (2006). Molecular organization of the presynaptic
active zone. Cell and Tissue Research, 326, 379391.
Stanley, E. F. (1997). The calcium channel and the organization of the presynaptic
transmitter release face. Trends in Neuroscience, 20, 404409.
Sudhof, T. C. (2012). The presynaptic active zone. Neuron, 75, 1125.
Ulrich, D., & Bettler, B. (2007). GABA(B) receptors: Synaptic functions and mechanisms
of diversity. Current Opinion in Neurobiology, 17, 298303.
Waites, C. L., Leal-Ortiz, S. A., Okerlund, N., Dalke, H., Fejtova, A., Altrock, W. D., et al.
(2013). Bassoon and Piccolo maintain synapse integrity by regulating protein
ubiquitination and degradation. EMBO Journal, 32, 954969.
Zilles, K., Palomero-Gallagher, N., & Schleicher, A. (2004). Transmitter receptors
and functional anatomy of the cerebral cortex. Journal of Anatomy, 205,
417432.
Astrocytes, Oligodendrocytes, and NG2 Glia: Structure and Function

A Verkhratsky, The University of Manchester, Manchester, UK; IKERBASQUE, Basque Foundation for Science, Bilbao,
Spain; University of the Basque Country UPV/EHU, Leioa, Spain
A Butt, University of Portsmouth, Portsmouth, UK
JJ Rodriguez, IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; University of the Basque Country UPV/EHU,
Leioa, Spain
V Parpura, University of Alabama, Birmingham, AL, USA; University of Rijeka, Rijeka, Croatia
Glossary
Oligodendroglia, oligodendrocytes Myelinating cells of

the CNS.
OPC Oligodendroglial precursor cell, precursors of
myelinating oligodendrocytes.
Abbreviations
InsP3R
PNS
TRP
Astroglia, astrocyte Main homeostatic cell of the CNS.

NG2 glia, synantocytes, polydendrocytes Cells of
oligodendroglial lineage evenly distributed through the CNS
and receiving neuronal synaptic inputs; possibly involved in
adult myelination.
ER
CNS
Endoplasmic reticulum
Neuroglia: History, Definition, and Classification

The Birth of the Concept
The concept and term neuroglia was introduced by Virchow
ber
(18211902), in his own commentary to the earlier paper U
das granulierte Ansehen der Wandungen der Gehirnventrikel
(published in 1846 in the journal Allgemeine Zeitschrift fur Psychiatrie; Vol. 3, pp. 242250). In this commentary, Virchow
suggested that the nervous system contains . . .connective substance, which forms in the brain, in the spinal cord, and in the
higher sensory nerves a sort of Nervenkitt (neuroglia), in which
the nervous system elements are embedded. This concept was
made public on 3 April 1858 in the lecture Virchow delivered in
the Charite Hospital in Berlin. For Virchow, the neuroglia was a
typical connective tissue, or the Zwischenmasse in between
tissue. The cellular nature of the neuroglia became apparent
after glial cells were visualized in 1850s and 1860s by Heinrich
Muller, Albert von Kolliker, Max Schulze, Karl Bergmann, and
Otto Deiters. Further advances in studies of neuroglia were
greatly assisted by the introduction of the Golgi black staining
technique.
The term astrocyte (astrn kyt (astron kytos), meaning
star cell) was introduced in 1895 by Michael von Lenhossek to
describe stellate glia; the terms protoplasmic and fibrous glia
were introduced by Andriezen and von Kolliker, respectively.
At the same time, Wilhelm His discovered that the nerve cells
and neuroglia derive from the neuroectoderm.
Two other principal classes of glial cells, the oligodendrocytes and microglia, were discovered by Po del Ro Hortega in
1920s; he also demonstrated that oligodendrocytes are myelinating cells of the central nervous system (CNS), whereas microglia are CNS phagocytes. The NG2 glia were discovered in the
Inositol 1,4,5-trisphosphate receptor

Peripheral nervous system
Transient receptor potential
1980s by William Stallcup and colleagues as cells of oligodendroglial lineage with certain unique features (for history on
neuroglial research, see Kettenmann & Verkhratsky, 2008).
Definition
The common definition of neuroglia has not been generally
established; conceptually, all cells in the nervous system that
are not neurons or vascular cells are considered to be neuroglia
(Kettenmann & Ransom, 2013; Verkhratsky & Butt, 2013).
These cells are highly heterogeneous in their morphology and
physiology and are different in their origins, microglial cells
being of mesodermal descent and all other cells of ectodermal
descent. Nonetheless, all neuroglia have a common function,
which is preservation of the homeostasis of the nervous system. Therefore, the neuroglia can be broadly defined as cells
that maintain homeostasis of the nervous system, represented by
highly heterogeneous cellular populations of different origin,
structure, and function (Verkhratsky & Butt, 2013).
The homeostatic function of neuroglia is executed at many
levels that include body and organ homeostasis (e.g., astrocytes control the emergence and maintenance of the CNS,
peripheral glia are essential for communication between the
CNS and the body, and enteric glia are essential for every aspect
of gastrointestinal function), cellular homeostasis (e.g., stem
astroglia and NG2 glia are the precursors for adult neuro- and
gliogenesis), morphological homeostasis (radial glia provide
the migratory pathways for neural cells in development, astrocytes form the cytoarchitecture of the gray matter, astrocytes
and microglia control synaptogenesis/synaptic pruning, and
myelinating glia maintain the structural integrity of nerves),
molecular homeostasis (regulation of ion, neurotransmitter,
http://dx.doi.org/10.1016/B978-0-12-397025-1.00205-0
101
102
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Astrocytes, Oligodendrocytes, and NG2 Glia: Structure and Function
and neurohormone concentration in the nervous system),

metabolic homeostasis (e.g., astrocytes synthesize glycogen
and may supply neurons with lactate), long-range signaling
homeostasis (by myelination provided by oligodendroglia
and Schwann cells), and defensive homeostasis (represented
by astrogliosis and the activation of microglia in the CNS,
Wallerian degeneration in the CNS and peripheral nervous
system (PNS), and immune reactions of enteric glia).
Classification
Neuroglial cells in the mammalian nervous system are divided
into PNS glia and CNS glia (Figure 1). The glial cells of the PNS
are represented by (i) myelinating Schwann cells that myelinate
peripheral axons, (ii) nonmyelinating Schwann cells that surround multiple nonmyelinating axons, and (iii) perisynaptic
Schwann cells that enwrap peripheral synapses (e.g., neuromuscular junctions). The PNS glial cells, which surround
neurons in peripheral ganglia, are known as satellite glial cells,
and those in the olfactory system are known as olfactory
ensheathing cells. Finally, the PNS includes enteric glia, which
resides in the enteric nervous system. The glia in the CNS is
represented by astrocytes, oligodendrocytes, NG2 glia, and
microglia.
(iii) radial glia, which are bipolar cells with an ovoid cell body
and elongated processes; radial glia are a common feature of
the developing brain, and after its maturation, they disappear
from most brain regions and transform into stellate astrocytes;
(ivv) radial glia-like cells of the retina (Muller glia) and cerebellum (Bergmann glia); (vi) velate astrocytes of the cerebellum;
(viiviii) interlaminar and polarized astrocytes of the primate
cortex; (ix) varicose projection astrocytes, which exist only in the
human brain; (x) tanycytes localized in the periventricular
organs, the hypophysis, and the raphe part of the spinal cord;
(xi) pituicytes of the neurohypophysis; (xii) perivascular
astrocytes; (xiii) marginal astrocytes; and (xivxvi) cells that
line the ventricles or the subretinal space, represented by
ependymocytes, choroid plexus cells, and retinal pigment epithelial
cells. This remarkable morphological heterogeneity is matched
by physiological differences between astrocytes from different brain regions; astroglial cells show different patterns of
expression of neurotransmitter receptors, various types of
transporters, and enzymes (e.g., monoamine oxidase catabolizing dopamine and serotonin and g-aminobutyric acid
(GABA) transaminase catabolizing GABA).
Physiology
Ion distribution and membrane potential
Astroglia
Heterogeneity
Astroglial cells are highly heterogeneous in the morphological appearance and physiological properties (Matyash &
Kettenmann, 2010; Zhang & Barres, 2010). The main types of
astroglia are as follows: (i) protoplasmic astrocytes of the gray
matter of the brain and in the spinal cord; these astrocytes
usually have 510 primary processes with extremely elaborate
branches to form a complex process arborization; (ii) fibrous
astrocytes localized in the white matter of the brain and in
the spinal cord and in the nerve fiber layer of the retina; they
have long (up to 300 mm) processes that run parallel to axons;
The ion content of astroglia differs from neurons in that astroglial cells have substantially higher cytosolic Na (1517 mM
vs. 8 mM in neurons) and Cl (ranging between 30 and
60 mM vs. 10 mM in mature neurons), whereas the concentration of K (120140 mM) and Ca2 (<0.0001 mM) in
astroglia is generally the same as in neurons. These differences
reflect the high activity of Na/K/2Cl cotransporters that
transport 2Cl into the cell in exchange for 1K and 1Na.
As a result, the reversal potential for Cl is 40 mV and the
activation of Cl permeable channels (e.g., GABAA receptors)
triggers Cl efflux and depolarization of astrocytes. Most
mature astrocytes have a strongly negative resting membrane
potential ( 80 to 90 mV), reflecting the predominant
Neuroglia
Ectodermal origin
Mesodermal origin
Microglia

(Macroglia)
Astroglia
Peripheral nervous system
Schwann cells
Non-myelinating
Myelinating
Oligodendroglia
Perisynaptic
Olfactory
ensheathing
NG2 cells
cells
(polydendrocytes)
Figure 1 Classification of neuroglial cells.
Enteric glia
Satellite glial
cells
resting K conductance, which maintains the membrane
potential close to the potassium equilibrium potential (EK).
Ion channels and neurotransmitter receptors

Glial cells express all major types of ion channels, including
K, Na, and Ca2; nonselective channels; and various types
of anion channels (Table 1). In addition, astrocytes express
most if not all known receptors for neurotransmitters,
neurohormones, and neuromodulators (Table 2), which in situ
is tightly regulated by immediate neurochemical environment.
Astrocytes also express high levels of intercellular channels
connexons that form direct intercellular contacts known as gap
junctions, which connect astrocytes into a syncytial structure
both homocellular (astrocytes to astrocyte) and heterocellular
(astrocyte to oligodendrocyte and sometimes to neurons) junctions were identified. Astroglial syncytia (also defined as astroglial syncytial networks; Giaume, Koulakoff, Roux, Holcman, &
Rouach, 2010) are anatomically segregated in different brain
regions. For example, in the somatosensory cortex, astrocytes
are coupled within barrels, but not between the barrels. Similarly, in the olfactory bulb, coupling is confined to astrocytes
within single glomerulus, with little connectivity between
astrocytes from different glomeruli.
Table 1
103
Ion signaling
Astrocytes are electrically silent but are not nonexcitable cells
they use controlled fluctuations of intracellular ion concentrations as their substrate for excitability (Parpura & Verkhratsky,
2012). Moreover, the gap junctional pathway allows propagating
waves of intracellular messengers and ions, which endow astroglia with an intercellular mechanism for long-range signaling.
The best-characterized mechanism for astroglial excitability
is spatiotemporal fluctuations of cytosolic Ca2 concentration,
generally referred to as Ca2 signaling, which are the
best-characterized mechanisms for astroglial excitability
(Verkhratsky, Rodriguez, & Parpura, 2012). Astroglial Ca2
signals are generated primarily by Ca2 release from the endoplasmic reticulum (ER) that acts as a dynamic intracellular
Ca2 store. The ER is capable of accumulating Ca2 ions
through the activity of specific Ca2 pumps of sarco(endo)
plasmic reticulum ATPase type and release Ca2 through ER
Ca2 channels, which, in astroglia, are primarily inositol 1,4,5trisphosphate receptor (InsP3R) type II. The activity of InsP3Rs
in turn is controlled by the second messenger InsP3, which is
produced following the activation of numerous G proteincoupled metabotropic receptors linked to phospholipase C.
In addition, depletion of the ER Ca2 store triggers plasmalemmal Ca2 entry via store-operated Ca2 channels. Changes in
Main types of ion channels in astroglia
Ion channel
Molecular identity
Localization
Main function
Inwardly rectifying
potassium
channels
Kir4.1 (predominant)
Kir2.1, 2.2, 2.3
Kir3.1
Kir6.1, 6.2
Kv1.1, Kv1.2, Kv1.5, and
Kv1.6
Ubiquitous
Maintenance of resting membrane

potential
K buffering
Ubiquitous
Generally unknown; may be involved in

the regulation of proliferation
Kv1.4
Hippocampus; astrocytes in vitro
Unknown
KCa3.1
Cortex
Unknown
Nav1.1, Nav1.2, and

Nav1.3
Spinal cord-cultured astrocytes; only

Nav1.2 were detected in the spinal
cord astrocytes in situ
L- (Cav1.2), N- (Cav2.2),
P/Q- (Cav2.1), R(Cav2.3), and T(Cav3.1)
TRPC1, TRPC4, TRPC5
Astrocytes in vitro; functional

expression in situ remains
controversial
Regulation of differentiation,
proliferation, and migration(?)
Can be upregulated in pathological
conditions
Unknown
Delayed-rectifier
potassium
channels (KD)
Rapidly inactivating
A-type potassium
currents (KA)
Ca2-dependent K
channels
Sodium channels
Calcium channels
Transient receptor
potential (TRP)
channels
Chloride channels
Aquaporins (water
channels)
CLC1, CLC2, CLC3

Volume-regulated
anion channels of
unknown identity
AQP4 (predominant)
AQP9
Region distribution is unknown
Store-operated Ca2 entry
Ubiquitous
Chloride transport; regulation of cell

volume
AQP4 ubiquitous
AQP9 astrocytes in brain stem
and in ependymal cells; tanycytes
in hypothalamus and in subfornical
organ
Water transport
Modified from Verkhratsky, A., & Butt, A. M. (2013). Glial Physiology and Pathophysiology. Chichester: Wiley-Blackwell
104
Table 2
Astroglial receptors to neurotransmitters and neuromodulators
Receptor type
Ionotropic receptors
Glutamate AMPA
receptors
Glutamate NMDA
receptors
GABAA receptors
P2X (ATP)
purinoreceptors
Glycine receptors
Neuronal nicotinic
cholinoceptors
(nAChRs)
Metabotropic receptors
Metabotropic
glutamate receptors
(mGluRs)
GABAB receptors
Adenosine receptors
A1, A2A, A2B, A3
P2Y (ATP)
purinoreceptors
Adrenergic receptors
a1AR, a2AR
b1AR, b1AR
Muscarinic
cholinoceptors
(mAChRs) M1M5
Oxytocin and
vasopressin
receptors
Serotonin receptors
5-HT1A, 5-HT2A, 5HT5A
Angiotensin receptors
AT1, AT2
Bradykinin receptors
B1, B2
Opioid receptors, m, d,
k
Histamine receptors,
H1, H2
Dopamine receptors
D1D5
Properties/physiological effect
Localization in situ
Na/K/Ca2 channels; receptors lacking GluA2 subunit

have some Ca2 permeability (PCa/Pmonovalent 1)
Activation triggers cell depolarization and some Ca2 influx
Na/K/Ca2 channels; astroglial receptors display a weak
Mg2 block and an intermediate Ca2 permeability
(PCa/Pmonovalent 3)
Cl channel
Activation triggers Cl efflux and cell depolarization
Na/K/Ca2 channels
Activation triggers cationic current and cell depolarization
and causes Ca2 entry
Cl channel
Activation triggers Cl efflux and cell depolarization
Na/K/Ca2 channels contain a7 subunit that confers high
Ca2 permeability (PCa/Pmonovalent 6)
Ubiquitous (hippocampus, cortex, cerebellum, and white

matter)
Bergmann glial cells, immature astrocytes
Cortex, spinal cord
Group I (mGluR1,5) controls PLC, InsP3 production, and

Ca2 release from the ER
Group II (mGluR2,3) and group III (mGluR4,6,7) control
the synthesis of adenosine 30 :50 -cyclic monophosphate
(cAMP)
Control PLC, InsP3 production, and Ca2 release from the ER
A1 receptors control PLC, InsP3 production, and Ca2 release
from the ER
A2 receptors increase cAMP
Ubiquitous
Ubiquitous (hippocampus, cortex, cerebellum, optic nerve,

spinal cord, and pituitary gland)
Functional P2X1/5 receptors are present in the cortex
Functional P2X7 receptors are reported in the cortex, in
the hippocampus, and in the retina
Spinal cord
Hippocampus, cultured astrocytes
Hippocampus
Hippocampus, cortex
Ubiquitous
Hippocampus, Bergmann glial cells
Control glial cell proliferation and astrogliosis; b2AR are

upregulated in pathology
Cortex, optic nerve

Hippocampus, amygdala
Control PLC, InsP3 production, and Ca2 release from the

ER; may regulate water channel (aquaporin)
Hypothalamus, other brain regions(?)
Increase in cAMP, energy metabolism
White matter (optic nerve, corpus callosum, and white

matter tracts in the cerebellum and subcortical areas)
?

Inhibition of DNA synthesis, proliferation, and growth and
inhibition of cAMP production
and synthesis of cAMP
Control synthesis of cAMP, InsP3 production, and Ca2
release from the ER
Hippocampus
Hippocampus, cerebellum
Substantia nigra, basal ganglia
Modified from Verkhratsky, A., & Butt, A. M. (2013). Glial Physiology and Pathophysiology. Chichester: Wiley-Blackwell
cytosolic Ca2 activate enzymes/Ca2 sensors that mediate

various cellular responses. Waves of elevated Ca2 can propagate through the astroglial syncytium over long distances,
either by intercellular diffusion of InsP3 or by release of neurotransmitters such as ATP.
An alternative mechanism of astroglial ionic signaling is

based on rapid fluctuations of cytosolic Na concentration
(Kirischuk, Parpura, & Verkhratsky, 2012). These result from
activation of various types of cationic channels (e.g., ionotropic receptors such as AMPA receptors or transient receptor
potential (TRP) channels) or from the activity of Nadependent transporters, most notably glutamate transporters.
Physiological activation of Na fluxes may increase cytosolic
Na concentration by 1020 mM. The transmembrane Na
gradient regulates many homeostatic molecular cascades
expressed in astrocytes, including Na/K ATPase; transporters
for glutamine, glutamate, and GABA; proton and bicarbonate
transporters; and transporters for ascorbic acid, Kir4.1 potassium channels, and glutamine synthetase.
Astroglial Functions
The functions of astrocytes are many and the main functions
are summarized in Table 3. Conceptually, they are responsible
for every possible homeostatic task. In addition, through programs of reactive gliosis, astrocytes act as principal cellular
elements of CNS defense.
Oligodendroglia
Definition
Oligodendrocytes are specialized to form the insulating myelin
sheaths around axons in the CNS (Kettenmann & Ransom, 2013;
Verkhratsky & Butt, 2013). The myelin sheath is a fatty insulating
Table 3
105
layer that provides for the rapid conduction of nerve impulses

and provides for the miniaturization of the vertebrate CNS.
Morphology
Oligodendrocytes are classified into four types according to
morphological appearance. Type I oligodendrocytes are mainly
present in the gray matter and have small rounded somata and
a complex process arborization, with fine branching processes
that myelinate 30 or more small diameter axons with short
internodes. Type II oligodendrocytes are most common in the
white matter and have small somata and parallel arrays of
intermediate length internodes (100250 mm). Type III oligodendrocytes myelinate large diameter axons (e.g., in the medulla
oblongata or the spinal cord funiculi); they are characterized
by larger cell bodies and extend one or more thick primary
processes that rarely branch and myelinate a small number of
axons with long internodes (250500 mm). Type IV oligodendrocytes myelinate a single large diameter axon with a very long
internode (up to 1000 mm in length) and are localized at the
entrance of CNS nerve roots.
In addition, a class of perineuronal oligodendrocytes has
been also identified in gray matter areas where these cells are
directly apposed to neuronal cell bodies. The perineuronal
oligodendrocytes are oval or polygonal cells, functions of
Functions of astrocytes
Development of the CNS

Structural support
Barrier function
Homeostatic function
Metabolic support
Synaptic transmission
Regulation of blood flow

Higher brain functions
Brain defense, neuroprotection, and post-injury

remodeling
Neurogenesis
Neural cell migration and formation of the layered gray matter
Synaptogenesis
Parcellation of the gray matter through the process of tiling
Delineation of the pia mater and vessels by perivascular glia
Formation of neurovascular unit
Regulation of the formation and permeability of bloodbrain and cerebrospinal fluid
brain barriers
Formation of glialvascular interface
Control over extracellular K homeostasis through local and spatial buffering
Control over extracellular pH
Regulation of water transport
Removal of neurotransmitters from the extracellular space
Uptake of glucose; deposition of glycogen
Providing energy substrate lactate to neurons in activity-dependent manner
Regulation of synapse maintenance and assisting in synaptic pruning
Providing glutamate for glutamatergic transmission (through de novo synthesis and
glutamateglutamine shuttle)
Regulating synaptic plasticity
Integrating synaptic fields
Providing humoral regulation of neuronal networks through the secretion of
neurotransmitters and neuromodulators
Regulate local blood supply (functional hyperemia) through the secretion of
vasoconstrictors or vasodilators
Chemoreception regulation of body Na homeostasis
Chemoreception regulation of CO2 and ventilatory behavior
Sleep
Memory and learning
Isomorphic and anisomorphic reactive astrogliosis
Scar formation
Catabolizing ammonia in the brain
Immune responses and secretion of proinflammatory factors (cytokines,
chemokines, and immune modulators)
Reproduced with permission from Verkhratsky, A., & Butt, A. M. (2013). Glial Physiology and Pathophysiology. Chichester: Wiley-Blackwell
106
which remain unknown, that form a concave impression on

the neuron to which they are tightly attached.
Physiology
Voltage-gated ion channels
Oligodendroglial cells express several types of voltage-gated
ion channels:
(i) Outwardly rectifying K channels are represented by the
delayed rectifying K channels, transient A-type K channels, and calcium-activated K channels. All these channels
are expressed mostly in oligodendroglial precursor cells
(OPCs) and are markedly downregulated in mature
oligodendrocytes.
(ii) Inwardly rectifying potassium channels (Kir) are expressed in
high densities in mature oligodendrocytes. They set up a
strongly negative (about 80 mV) resting membrane
potential of these cells.
(iii) Voltage-gated sodium channels (TTX-sensitive Nav) have
been identified in OPCs in vitro and in brain slices. The
expression of Nav channels (type Ia, type IIa1, and type
IIIa) is downregulated in mature myelinating oligodendrocytes, although the transcripts for Nav are identifiable.
The Nav channels can contribute to the differentiation
and migration of OPCs.
(iv) Voltage-operated calcium channels (Cav) of L-type (Cav1.2
and 1.3) and T-type (Cav3.1 and 3.2) are expressed in
OPC and possibly in mature oligodendrocytes. They are
important for the early development, contributing to the
regulation of gene expression, cell proliferation, and cell
migration.
(v) Chloride and acid-sensing ion channels (ASICs) have been
identified in OPCs; the expression of ASIC1a, 2a, and 4
was reported to decrease during differentiation.
(iii) Adenosine purinergic receptors. Adenosine purinergic receptors are involved in the regulation of OPC migration,
proliferation, and differentiation.
(iv) P2X ionotropic purinoceptors. P2X ionotropic purinoceptors
are not well mapped in oligodendroglia, but both OPCs
and mature oligodendrocytes express P2X7 receptors activated by high micromolar ATP concentrations.
(v) P2Y metabotropic purinoceptors. Oligodendrocytes express
multiple P2Y subtypes, although the main receptor may
be P2Y1, which mediates Ca2 signaling and, in OPCs,
stimulates cell migration, inhibits the mitogenic response
to platelet-derived growth factor (PDGF), and promotes
differentiation and cell survival.
(vi) Ionotropic GABAAR. The activation of GABAA receptors in
oligodendrocytes leads to Cl efflux and cell depolarization (because of high intracellular Cl concentration).
The stimulation of GABAAR inhibits proliferation of
OPCs. Similar to other neurotransmitter receptors, expression of GABAAR appears to be downregulated in mature
oligodendrocytes.
(vii) Metabotropic GABAB receptors. Metabotropic GABAB
receptors are expressed by OPCs and stimulate proliferation and migration and are downregulated in myelinating oligodendrocytes.
(viii) Glycine receptors (GlyRs).
(ix) Acetylcholine receptors (AChRs), of which both ionotropic
nicotinic and metabotropic muscarinic varieties were
detected in oligodendrocytes.
(x) Dopamine receptors of D2 and D3 subtypes.
(xi) A variety of receptors to neuromodulators, such as bradykinin
receptors, opioid m and k receptors, cannabinoid CB1 and
CB2 receptors, and adrenaline a1 receptors.
NG2 Glia
Definition
Neurotransmitter receptors
Cells of the oligodendroglial lineage express a wide array of
receptors to neurotransmitters, of which those binding glutamate and ATP appear most abundant, and neurohormones:
(i) Ionotropic glutamate receptors (iGluRs). All three types
(AMPA, kainate, and NMDA) are present in the oligodendrocyte lineage. The Ca2-permeable AMPA receptors
(lacking GluA2 subunit) are mainly expressed in OPCs,
whereas mature cells possess Ca2-impermeable receptors
composed of GluA3 and GluA4 subunits. AMPARs mediate
signaling from neurons to OPCs and are proposed to regulate their differentiation and myelination. Kainate receptors are mainly expressed in mature oligodendrocytes.
NMDA receptors are detected in processes of mature oligodendrocytes where they appear to be triheteromers of
GluN1, GluN2C, and GluN3A/B subunits; this combination confers weak Mg2 block at the resting membrane
potential.
(ii) Metabotropic glutamate receptors (mGluRs). All three groups
of mGluRs have been detected in oligodendroglial cells,
with mGluR5-mediated Ca2 signaling being operative in
OPCs. The expression of mGluRs is downregulated in
mature oligodendrocytes.
NG2 glia are defined by their expression of the chondroitin

sulfate proteoglycan NG2 (cspg4) and as the only glial cell type
that receives direct synaptic input from neurons. NG2 glial are
also known as synantocytes or polydendrocytes (Butt,
Hamilton, Hubbard, Pugh, & Ibrahim, 2005; Nishiyama,
Komitova, Suzuki, & Zhu, 2009) and belong to the oligodendroglial lineage. NG2 glial express PDGFaR and other OPC
markers and generate oligodendrocytes in the developing and
adult CNS. In the adult brain, many NG2 glial do not appear to
be involved in oligodendrocyte generation and may have other
unresolved functions.
Morphology
NG2 glia bear several primary processes; the process-delineated
domains have a certain degree of overlap. In the gray matter,
NG2 glial are distributed as a mosaic, whereas in the white
matter, NG2 glia have an elongated appearance, extending
processes along the axonal axis. NG2 glia constitute 89% of
total cells in the white matter and 23% of total cells in
the gray matter. The ratio of NG2 glia to oligodendrocytes
ranges from 1:1 in the rat hippocampus to 1:10 in the cat
spinal cord.
Physiology
Membrane properties
NG2 glia have a resting membrane potential of around 90 mV
and a membrane resistance of 300 MO, reflecting a high resting
K permeability.
107
thickening of cellular processes and a strong upregulation of

NG2 expression. NG2 glia generate new oligodendrocytes in
the postlesioned period, thus contributing to tissue
regeneration.
Voltage-gated ion channels

NG2 glia express several classes of voltage-gated ion channels
including A-type and delayed-rectifier K channels (with Kv1.3
and Kv1.5 being the most expressed) and inwardly rectifying K
channels, predominantly Kir4.1. The NG2 glia also express TTXsensitive Nav channels and Na spikes can be triggered by
depolarization. Low densities of L-type (Cav1.2 and 1.3) and
T-type (Cav3.1 and 3.2) Ca2 channels have been detected in
NG2 glia, as well as some expression of TRPC1 channels; the
functional relevance of all these channels remains unknown.
Neurotransmitter receptors
NG2 glia are characterized by high expression of AMPA-type
glutamate receptors, with predominant expression of the GluA4
subunit. These AMPARs are activated by neuronal synaptic
input and produce inward currents upon stimulation. NG2
glia are also reported to express low amounts of kainate receptors and a subpopulation of NG2 glia express NMDAR with
weak Mg2 block. NG2 glia have functional GABAA receptors;
GABA-mediated currents reverse at 43 mV, indicating that
NG2 glia maintain a high intracellular Cl concentration. In
addition, NG2 glia may express nAChR, mGluR, a1 adrenergic
receptors, and P2 purinergic receptors, although their functional role is enigmatic.
Functions
Apart from acting as OPC, the functional role for NG2 glia is
unknown. In the adult brain, NG2 glia have been reported to
generate neurons in the piriform cortex, although the majority
of cell fate mapping studies indicate that NG2 glia solely
generate oligodendrocytes at all ages. NG2 glia can also be
reactive and respond to CNS insults by increased proliferation
and morphological remodeling, manifested by shortening and
Acknowledgments
Authors research was supported by Alzheimers Research Trust
(UK) Programme Grant (ART/PG2004A/1) to A. Verkhratsky
and by the National Institutes of Health (the Eunice Kennedy
Shriver National Institute of Child Health and Human Development award HS078678).
References
Butt, A. M., Hamilton, N., Hubbard, P., Pugh, M., & Ibrahim, M. (2005). Synantocytes:
The fifth element. Journal of Anatomy, 207, 695706.
Giaume, C., Koulakoff, A., Roux, L., Holcman, D., & Rouach, N. (2010). Astroglial
networks: A step further in neuroglial and gliovascular interactions. Nature Reviews.
Kettenmann, H., & Ransom, B. R. (Eds.), (2013). Neuroglia. Oxford: Oxford University
Press.
Kettenmann, H., & Verkhratsky, A. (2008). Neuroglia: The 150 years after. Trends in
Neurosciences, 31, 653659.
Kirischuk, S., Parpura, V., & Verkhratsky, A. (2012). Sodium dynamics: Another key to
astroglial excitability? Trends in Neurosciences, 35, 497506.
Matyash, V., & Kettenmann, H. (2010). Heterogeneity in astrocyte morphology and
physiology. Brain Research Reviews, 63, 210.
Nishiyama, A., Komitova, M., Suzuki, R., & Zhu, X. (2009). Polydendrocytes (NG2
cells): Multifunctional cells with lineage plasticity. Nature Reviews. Neuroscience,
10, 922.
Parpura, V., & Verkhratsky, A. (2012). Homeostatic function of astrocytes: Ca2 and
Na signalling. Translational Neuroscience, 3, 334344.
Verkhratsky, A., & Butt, A. M. (2013). Glial physiology and pathophysiology.
Chichester: Wiley-Blackwell.
Verkhratsky, A., Rodriguez, J. J., & Parpura, V. (2012). Calcium signalling in astroglia.
Molecular and Cellular Endocrinology, 353, 4556.
Zhang, Y., & Barres, B. A. (2010). Astrocyte heterogeneity: An underappreciated topic in
neurobiology. Current Opinion in Neurobiology, 20, 588594.
Microglia: Structure and Function

A Verkhratsky, The University of Manchester, Manchester, UK; Basque Foundation for Science, Bilbao, Spain; University
of the Basque Country UPV/EHU, Leioa, Spain
M Noda, Kyushu University, Fukuoka, Japan
V Parpura, University of Alabama, Birmingham, AL, USA; University of Rijeka, Rijeka, Croatia
Glossary
Extraembryonic yolk sac One of the three embryonic

cavities that also include chorion and amnion.
Microglia Innate resident immune cells of the CNS.
Abbreviations
CNS
DAMPs
mGluRs

Danger-associated molecular patterns
Metabotropic glutamate receptors
History and Definition

Microglial cells were described and named by Po del
Ro-Hortega in 19171920. He developed the first microgliaspecific silver carbonate impregnation technique and published detailed description of these cells, which he initially
called garbage collectors, and subsequently coined the term
microglia while proposing to call individual cells microgliocytes (Del Rio-Hortega, 1932). Del Ro-Hortega described all
main properties of microglia including their mesodermal origin, distinct resting phenotype, and ability to undergo complex morphological and functional modifications in response
to brain damage, collectively known as microglial activation
(Del Rio-Hortega, 1932).
Microglial cells are perceived as resident macrophages of
the brain and the spinal cord that define the innate immunity
of the central nervous system (CNS). This broad designation of
microglia seems to be in need of further elaboration, because,
as shall be discussed in the succeeding, microglial cells undergo
specific adaptation to the CNS (CNS environment) and
become a legitimate member of the brain cellular architecture
with numerous physiological functions that far exceed and
complement their immune capabilities.
Developmental Origins
Microglial cells do not share their ontogenetic origins with
other neural cells (neurons and macroglia) of the nervous
system; microglia are of mesodermal origin and the microglial
progenitors derive from the extraembryonic yolk sac being the
primitive c-kit erythromyeloid precursors (Kierdorf et al.,
2013). These precursors enter the CNS during early embryonic
development; for example, in mice, this invasion occurs at
embryonic day 10 (Ginhoux et al., 2010). Whether so
Ramified or resting or surveillant microglia Microglial

phenotype characterized by small soma and long thin
moving processes characteristic for health CNS tissue.
NMDA
PAMPs
TLRs
TNF-a
N-Methyl D-aspartate
Pathogen-associated molecular patterns
Toll-like receptors
Tumor necrosis factor-a
described fountains of microglia (Kershman, 1939) observed

in early postnatal days represent the second wave of invasion
on microglial precursors from the blood or these migrating
microglia derive from precursors already settled in the brain
remains debatable.
Morphology
After entering the CNS, microglial precursors migrate and
disseminate almost homogeneously throughout the parenchyma of the brain and of the spinal cord. In total, microglial
cells account probably for 1015% of all neuroglia, and their
densities are similar in different CNS regions. Migration of
microglial precursors is accompanied by a remarkable morphological and functional metamorphosis: the myeloid
progenitors generally similar to monocytes convert into microglial cells, which acquire neural-like appearance. Differentiated microglial cells have small bodies (45 mm) and several
thin and long processes with characteristic terminal arborization represented by numerous small secondary processes.
This microglial phenotype is generally known as ramified or
resting, although microglial cells are arguably the most restless cells in the nervous system.
Indeed, microglial processes are in continuous motion
(Davalos et al., 2005; Nimmerjahn, Kirchhoff, & Helmchen,
2005), moving through the surrounding CNS tissue at a speed
of 1.5 mm min1. This movement of microglial processes is
accompanied by regular extension/retraction (at 23 mm min1)
of small protrusions. Thus, microglial processes seem to survey
their neighborhood. Microglial processes also define a territorial
domain of a single microglial cell; there is generally little overlap
between microdomains of microglia. Given the speed of
processes movement, the microglial domain could be
completely scanned by these processes within several hours.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00356-0
109
110
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Microglia: Structure and Function
This remarkable motile behavior of mature microglial cells

makes the term of resting microglia somewhat misleading,
and hence, microglial cells in the healthy CNS can be termed
surveillant or ramified microglia.
Physiology
Microglial cells after entering the CNS environment undergo
profound physiological remodeling and acquire receptive
phenotype compatible with the chemical environment. Arguably, ramified microglia is the most receptive cells of the CNS
because they are in possession of multiple receptors to neurotransmitters and neuromodulators as well as immunological
receptors characteristic for myeloid cells (see Figure 1 and
Kettenmann, Hanisch, Noda, & Verkhratsky, 2011; Pocock &
Kettenmann, 2007; Ransohoff & Perry, 2009); the latter ones
include P2X7 purinoceptors, receptors to chemokines and cytokines, and receptors to various tissue mediators such as platelet
activating factor, thrombin, histamine, or bradykinin, all being
critical for triggering various types of immune responses.
Membrane Potential
Most of electrophysiological experiments were performed on
microglial cells in vitro in culture; these experiments consistently reported resting potential 50 mV. Experiments in situ,
in acute brain slices from rat cortex, striatum, and facial
Figure 1 A multitude of receptors expressed in microglia.
nucleus, showed that ramified microglial cells (identified by

fluorescently labeled tomato lectin staining) had high input
resistance and a rather low membrane potential (20 mV,
range 2 mV to 40 mV). In ramified microglia studied in
acute slices from juvenile mice, the resting potential was
around 38 mV, whereas microglia in forebrain slices from
adult mice revealed two subpopulations of cells with resting
potential around between 52 mV and 29 mV, respectively.
Experiments on amoeboid, migrating microglia that can be
found in corpus callosum slices of postnatal rodents, found a
considerable variability in resting membrane potential that
varied between 70 mV and 10 mV (for details, see
Kettenmann et al., 2011).
Ion Channels
Several types of ion channels were described in microglial cells,
especially in culture (see Kettenmann et al., 2011; Noda &
Verkhratsky, 2013 for detailed description and references). It
must be noted that resting microglial cells in situ in brain slices
as a rule have much lower density of voltage-gated currents as
compared with cells in culture. Voltage-gated sodium currents
were described solely on cultured microglial cells from rodents
and humans, although there are numerous contradictory studies that failed to detect any signs of Na channel activity.
Similarly, voltage-gated Ca2 channels were found only in a
single study where small calcium currents were detected
in 30% of cultured cells.

Microglial cells express several types of Ca2-permeable
channels, in particular the channels mediating Ca2 releaseactivated Ca2 current, ICRAC; currents through ICRAC were
detected in cultured microglia and ORAI1 proteins were
found to be mainly responsible. Similarly, microglial cells
express Ca2-permeable channels or transient receptor potential
(TRP) family with predominance of TRPM and TRPV channels,
which could contribute to microglial activation and (TRPV1
channels) induce microglial cell death.
Microglia is in a possession of several types of K channels,
expression of which is generally upregulated upon activation;
ramified microglial cells in situ express very low densities of
potassium channels. In particular, microglial activation is
accompanied by very substantial increase in densities of delayed
rectifier potassium channels mainly of Kv1.2, Kv1.3, and Kv1.5.
Functional activity of Kv channels can be linked to functional
responses of activated microglial such as proliferation or nitric
oxide release. The inward rectifier K channels are markers of
early activation stages of microglial cells; their expression is
rather small in ramified microglial cells in situ; it is significant
in cultured microglia, but it is downregulated by strong activation signals, such as treatment with lipopolysaccharide. Microglial cells were also reported to express Ca2-dependent K
channels (mainly of KCNN4/SK4/KCNN2/SK2 and KCNN3/
SK3 families) and the G protein-activated K channels. Finally,
microglia also express anion/Cl channels, H channels, human
ether-a-go-go-related gene product (HERG)-like K channels, and
Kv7 (KCNQ) channels.
Receptors
Receptors to Neurotransmitters and Neuromodulators
Microglial cells express almost all types of receptors to neurotransmitters and neuromodulators so far found in the nervous
system (Figure 1), including receptors to glutamate, purines,
and GABA. The purinoceptors (adenosine receptors, ionotropic
P2X, and metabotropic P2Y purinoceptors; see Verkhratsky,
Krishtal, & Burnstock, 2009) are, arguably, the most abundant
in microglia. In particular, microglial cells constitutively
express P2X7 receptors that contribute to numerous responses
to neuropathology. The P2X7 receptors are a general feature of
immune cells where they mediate various immune reactions,
including the processing and the release of various cytokines.
Specific properties of P2X7 receptors (which are most likely
associated with their functional relevance) include (i) their
exceptionally low sensitivity to ATP (i.e., receptor needs mM
ATP concentration for activation) and (ii) their ability to form
large transmembrane pores (permeable to molecules with
molecular weight up to 900 Da) upon excessive or long-lasting
stimulation. Thus, the P2X7 receptors are activated in conditions of massive ATP release indicative of neuronal damage
and are linked to immune responses of microglia, being
particular important activators of cytokine release. Incidentally, direct overexpression of P2X7 receptors in microglia is
sufficient to trigger their activation in the in vitro system in the
complete absence of any other exogenous factors (Monif, Reid,
Powell, Smart, & Williams, 2009). Microglia also constitutively
express P2X4 receptors (which are activated by low micromolar
ATP concentrations), which are critically involved in mediating
111
microglial activation in conditions of chronic pain (Inoue &

Tsuda, 2009). In addition, microglia express P2Y2, P2Y6,
P2Y12, and P2Y13 metabotropic purinoceptors, which are
mainly linked to Ca2 signaling. The UTP-sensitive P2Y6 receptors regulate microglial phagocytosis, whereas ADP-preferring
P2Y12 receptors are fundamental for the acute microglial activation including rapid extension of microglial processes, morphological activation, membrane ruffling, and chemotaxis.
Glutamate receptors expressed by microglial cells (Noda &
Verkhratsky, 2013) are represented by all four types of
a-amino-3-hydroxy-5-methyl-isoxazole propionate receptors,
at least three types of kainate receptors, and possibly N-methyl
D-aspartate (NMDA) receptors; the latter were identified only
very recently and seem to be somehow linked to microglial
neurotoxicity (Kaindl et al., 2012). In addition, microglial cells
bear metabotropic glutamate receptors: mGluR5 (group I) linked
to intracellular Ca2 signaling and mGluR2 and 3 (group II)
and mGluR4, 6, and 8 (group III) coupled to adenosine 30 :50
cyclic monophosphate and involved in the regulation of tumor
necrosis factor-a (TNF-a) release and microglial cytotoxicity.
Microglia express GABAB receptors linked to Ca2 signaling and
activation of K conductance, as well as nicotinic acetylcholine
receptors that contain a7 subunit, which confers high Ca2
permeability; other metabotropic receptors identified in microglia include a1A, a2A, b1, and b2 adrenoreceptors, D14 dopamine
receptors, and 5-HT2 serotonin receptors.
Microglial function is also regulated by neuromodulators
and neurohormones. In particular, microglial cells express all
four types of adenosine receptors (which generally suppress
activation process), receptors to bradykinin, ETB endothelin receptors, angiotensin receptors, somatostatin receptors, opioid receptors,
neurotrophin receptors, receptors to thrombin (PAR-1 to PAR-4),
cysteinyl leukotrienes receptors of CysLT1 and CysLT2 types,
Notch-1 receptors, receptors to complement fragments C3a
and C5a, and various receptors to neuropeptides. Microglia
also express various receptors to hormones, such as
glucocorticoid and mineralocorticoid receptors and estrogen
receptor (see Kettenmann et al., 2011, for details).
Immunocompetent Receptors
The immune receptors expressed by microglia are represented
by receptors to chemokines and cytokines and pattern recognition. The latter include (i) lectin-type mannose and b-glucan
receptors; (ii) nucleotide-binding and oligomerization
domain-like receptors; (iii) receptors characterized by an RNA
helicase domain and two caspase-recruitment domains, collectively known now as RIG-I-like receptors (RLR); and (iv) the
Toll-like receptors (TLRs). These TLRs of TLR1 to TLR9 types
are particularly important in the initiation and regulation of
microglial activation in pathological conditions (Aravalli,
Peterson, & Lokensgard, 2007).
Functions or Microglia
Microglial functions are remarkably diverse (Table 1); microglial cells are not only involved in mounting CNS defense
but also critically important for normal development, shaping,
112
Table 1

Diversity of microglial functions
Physiological
CNS development
Neuronal plasticity
Defensive
Recognition of
pathogens
Phagocytosis
Antigen presentation
Immune response
Repair
Pathological
Cytotoxicity
Tumor growth
promotion
Demyelination
Infection
Early synaptogenesis (?)

Phagocyting redundant/postapoptotic neurons
Pruning unwanted/redundant/silent synapses
Secreting trophic factors (e.g., cytokines, growth factors, or neurotrophins)
Monitoring synapses
Regulating synaptic plasticity/connectivity through secretion of cytokines and/or other factors
Secretion of lipoprotein particles for maintenance of cell membranes and synapses
Sensing pathogen-associated molecular patterns (PAMPs) through Toll-like receptors
Recognition of damage through danger-associated molecular patterns through purinoceptors
Ingestion and destruction by digestive enzymes in lysosomes of the following:
(a) Damaged cells, for example, neurons (e.g., neuronophagia or Wallerian degeneration); (b) microorganisms
(e.g., abscess); (c) virally infected cells (e.g., herpes simplex encephalitis); (d) erythrocytes following hemorrhage
Presentation of pathogens (e.g., in bacterial, fungal, viral infections) bound to the major histocompatibility complex (MHC)
for activation of T lymphocytes
Recognition of bound antibody (adaptive immune function)
Secretion of proinflammatory factors, for example, chemokines or interferon-g
Remodeling of extracellular matrix; regulation of stem cell proliferation (e.g., granule cell neurons of hippocampus)
Secretion of glutamate; reactive oxygen species/respiratory burst
Secretion of matrix metalloproteinase
Myelin destruction/phagocytosis in, for example, multiple sclerosis
Viral entry into CNS; hosting of HIV-1; support mycobacteria, including their intracytoplasmic survival (e.g., tuberculosis)
and function of cellular CNS networks (see Kettenmann,

Kirchhoff, & Verkhratsky, 2013, for comprehensive review).
Physiological Functions of Microglia

Microglia can sense neuronal activity by virtue of its multiple
receptors. For monitoring synapses, microglial cells also
employ their motile processes. Namely, it has been shown
that when scanning the CNS tissue, microglial processes frequently establish contacts with synaptic structures (Wake,
Moorhouse, Jinno, Kohsaka, & Nabekura, 2009). Microglial
cells are found to actively modify neuronal connections either
through removing synaptic structures or through releasing
various chemical substances that affect synaptic plasticity. In
particular, microglia are critical for synaptic pruning that
shapes neuronal ensembles during development, and failure
of this function can be responsible for neurodevelopmental
disorders, such as, diseases of autistic spectrum. Removal of
synaptic contacts in developing brain proceeds without microglial activation or changes in microglial territorial domain at
the level of single microglial processes that are seemingly
responsible for this physiological phagocytosis. The physiological synaptic removal can be regulated by CX3R1 fractalkine
receptors and by microglial complement receptors; genetic
removal of both types of receptors results in aberrant synaptic
connectivity (Kettenmann et al., 2013).
Microglial cells regulate synaptic plasticity also through
secretion of neuromodulatory factors. These may include glycine and L-serine acting on neuronal NMDA receptors or brainderived neurotrophic factor that turns inhibitory transmission
in the spinal cord into excitatory through affecting the Cl
distribution. Another neuromodulatory pathway involves
microglial release of TNF-a, which in turn stimulates astrocytes, which subsequently release glutamate and, thus, affect
synaptic activity (Pascual, Ben Achour, Rostaing, Triller, &
Bessis, 2012). Microglial cells can also affect neuronal circuitry
through regulating neurogenesis and through continuous
elimination of redundant neural cells that failed to integrate
into existing networks.
Activation in Pathology
The fundamental function of microglia is to detect the pathology and to produce a defensive response. Microglial activation
forms the backbone for brain immune and defensive responses
to virtually all pathological insults; activated microglia are
indispensable contributors to all neurological diseases (see,
e.g., Perry, Nicoll, & Holmes, 2010).
Molecular signals that trigger microglial activation can be
divided into the ON and OFF signals (see Hanisch & Kettenmann, 2007). Conceptually, the ON signals (which induce
activation) are molecules occurring along with the pathological insult, generally represented by pathogen-associated or
danger-associated molecular patterns (PAMPs or DAMPs,
respectively). The PAMPs are, in essence, pathogens (e.g., fragments of bacteria or viruses), whereas DAMPs are normally
present in the body, but either absent in the brain (e.g., bloodderived factors) or presented by various molecules that appear
in the brain tissue following cellular damage (enzymes) or
appear in an unusually high concentrations (for instance,
ATP massively released following cell damage). The OFF signals (which contain activation) are usually neurotransmitters
(e.g., ACh or adenosine) associated with normal nervous activity of neuroglial circuitry. These molecules are continuously

signaling to microglial cells to prevent their activation; the
removal of OFF signals, however, is indicative of stress and
can initiate activation response. Microglial defensive responses
are also regulated by molecules controlling motility and
phagocytosis; these signals are known as find-me signals that
attract microglial cells to the damaged site and eat-me signals
that label the pathological targets and induce phagocytosis.
Additional signals defined as do not eat me signals, help
signals, and survival signals have been also proposed
(Kierdorf et al., 2013).
Activation of microglia is a complex and multistage
program that results in the appearance of multiple cellular
phenotypes that exert both neuroprotective and neurotoxic
actions (Perry et al., 2010). Fundamentally, microglia activation is a defensive response of the neural tissue and as such it is
indispensable for brain survival and after lesion remodeling.
Microglial activation includes morphological and biochemical
remodeling, which quite often can be reversible, with microglial cells reverting to their ramified phenotype after resolution
of neuropathology. Strong and/or long-lasting insults, however, may trigger an appearance of amoeboid, phagocyting
microglia that can significantly contribute to neurotoxicity.
Conclusions
Microglial cells are fundamental for physiology of the CNS and
are the central elements of nervous tissue defense. Microglial
cells are of myeloid origin; however, after invading the CNS,
they acquire unique morphology and physiology that integrate
them into neural cellular networks. Microglial cells contribute
to normal development of the CNS and are able to influence
synaptic plasticity. In pathology, microglia undergoes complex
program of activation that produces both neuroprotective and
neurotoxic cells, which, by interacting and balancing their
action, define to a large extent the progression and outcome
of neurological diseases.
Acknowledgments
The authors research was supported by the Alzheimers
Research Trust (UK) program grant (ART/PG2004A/1) to AV
and by the National Institutes of Health (The Eunice Kennedy
Shriver National Institute of Child Health and Human Development award HS078678).
113
Competing Financial Interests: The authors declare that they have

no competing financial interests.
References
Aravalli, R. N., Peterson, P. K., & Lokensgard, J. R. (2007). Toll-like receptors in
defense and damage of the central nervous system. Journal of Neuroimmune
Pharmacology, 2, 297312.
Davalos, D., Grutzendler, J., Yang, G., Kim, J. V., Zuo, Y., Jung, S., et al. (2005). ATP
mediates rapid microglial response to local brain injury in vivo. Nature
Del Rio-Hortega, P. (1932). Microglia. In W. Penfield (Ed.), Cytology and cellular
pathology of the nervous system (pp. 482534). New York: Hoeber.
Ginhoux, F., Greter, M., Leboeuf, M., Nandi, S., See, P., Gokhan, S., et al. (2010). Fate
mapping analysis reveals that adult microglia derive from primitive macrophages.
Science, 330, 841845.
Hanisch, U. K., & Kettenmann, H. (2007). Microglia: Active sensor and versatile effector
cells in the normal and pathologic brain. Nature Neuroscience, 10, 13871394.
Inoue, K., & Tsuda, M. (2009). Microglia and neuropathic pain. Glia, 2009(57),
14691479.
Kaindl, A. M., Degos, V., Peineau, S., Gouadon, E., Chhor, V., Loron, G., et al. (2012).
Activation of microglial N-methyl-D-aspartate receptors triggers inflammation and
neuronal cell death in the developing and mature brain. Annals of Neurology, 72,
536549.
Kershman, J. (1939). Genesis of microglia in the human brain. Archives of Neurology
and Psychiatry, 41, 2450.
Kettenmann, H., Hanisch, U. K., Noda, M., & Verkhratsky, A. (2011). Physiology of
microglia. Physiological Reviews, 91, 461553.
Kettenmann, H., Kirchhoff, F., & Verkhratsky, A. (2013). Microglia: New roles for the
synaptic stripper. Neuron, 77, 1018.
Kierdorf, K., Erny, D., Goldmann, T., Sander, V., Schulz, C., Perdiguero, E. G., et al.
(2013). Microglia emerge from erythromyeloid precursors via Pu.1- and Irf8dependent pathways. Nature Neuroscience, 16, 273280.
Monif, M., Reid, C. A., Powell, K. L., Smart, M. L., & Williams, D. A. (2009). The P2X7
receptor drives microglial activation and proliferation: A trophic role for P2X7R pore.
Nimmerjahn, A., Kirchhoff, F., & Helmchen, F. (2005). Resting microglial cells are
highly dynamic surveillants of brain parenchyma in vivo. Science, 308, 13141318.
Noda, M., & Verkhratsky, A. (2013). Physiology of microglia. In H. Kettenmann & B. R.
Ransom (Eds.), Neuroglia (pp. 223237) (3rd ed.). Oxford: Oxford University Press.
Pascual, O., Ben Achour, S., Rostaing, P., Triller, A., & Bessis, A. (2012). Microglia
activation triggers astrocyte-mediated modulation of excitatory neurotransmission.
2012(109), E197E205.
Perry, V. H., Nicoll, J. A., & Holmes, C. (2010). Microglia in neurodegenerative disease.
Nature Reviews. Neurology, 6, 193201.
Pocock, J. M., & Kettenmann, H. (2007). Neurotransmitter receptors on microglia.
Trends in Neurosciences, 30, 527535.
Ransohoff, R. M., & Perry, V. H. (2009). Microglial physiology: Unique stimuli,
specialized responses. Annual Review of Immunology, 27, 119145.
Verkhratsky, A., Krishtal, O. A., & Burnstock, G. (2009). Purinoceptors on neuroglia.
Molecular Neurobiology, 39, 190208.
Wake, H., Moorhouse, A. J., Jinno, S., Kohsaka, S., & Nabekura, J. (2009). Resting
microglia directly monitor the functional state of synapses in vivo and determine the
fate of ischemic terminals. Journal of Neuroscience, 29, 39743980.
Cytoarchitecture and Maps of the Human Cerebral Cortex

Aachen, Germany
K Amunts, Institute of Neuroscience and Medicine (INM-1), Julich, Germany; JARA Julich-Aachen Research Alliance, Aachen,
Germany; University of Dusseldorf, Dusseldorf, Germany
Glossary
Allocortex Part of the cerebral cortex with about six

cytoarchitectonically defined layers (comprises archi- and
paleocortex).
Archicortex Phylogenetically old part of the cerebral cortex
comprises the hippocampal region.
Brodmann area (BA) A cytoarchitectonically defined
cortical region as described by Brodmann (1909).
Gennari stripe Heavily myelinated fibers forming a
horizontal stripe in layer IVB of the primary visual cortex.
Isocortex Part of the cerebral cortex with six
cytoarchitectonically defined layers.
Mesocortex Encompasses the periallocortex and the
proisocortex.
Myeloarchitecture Regionally specific distribution of the
density, length, and course of myelinated fibers in the
cerebral cortex.
This article provides a condensed overview of major aspects of

the cytoarchitecture of the human cerebral cortex with focus on
the isocortex and on those issues which are the anatomical
basis for brain mapping. Thus, many important aspects of
cytoarchitecture cannot be discussed here. A more comprehensive review of the architectonics of the human cerebral cortex
including the anatomy of allocortical areas and connectivity
can be found in Zilles and Amunts (2012).
Cells and Layers of the Cerebral Cortex

Cytoarchitectonic criteria for the parcellation of the cerebral
cortex are not based on a single feature, but take into consideration a set of different morphological aspects, that is, the
number and delineability/visibility of cortical layers, the packing density and size of the cell bodies in the single layers and
averaged over all cortical layers, the occurrence of specialized
cell types, the thickness of the cortical ribbon, and the width of
each layer relative to other layers. This set of criteria was formulated by Korbinian Brodmann, the pioneer of cytoarchitectonics (Brodmann, 1909). Therefore, a single criterion is rarely
enough to define the borders of a cytoarchitectonic area.
Since the early cytoarchitectonic studies, cell body stained
(Nissl or silver stain methods) histological sections were used
which do not allow a detailed analysis of cell types like the Golgi
or modern immunostaining techniques. However, Nissl staining
is easy to apply to human brains even with a longer postmortem
Neocortex Phylogenetically most recent part of the cerebral

cortex (comprises the isocortex).
Paleocortex Phylogenetically old part of the cerebral cortex
comprises the olfactory bulb, (Pre)piriform region, olfactory
tubercle, and septal and periamygdalar regions.
Periallocortex Part of the cerebral cortex between the
allocortex and proisocortex. It comprises the peripaleo- and
periarchicortex.
Periarchicortex Cortical region adjacent to the archicortex
(comprises the entorhinal, perirhinal, retrosplenial,
subgenual areas, and the presubiculum and part of the
cingulate region).
Peripaleocortex Cortical region adjacent to the paleocortex.
Proisocortex Part of the cerebral cortex adjacent to the
isocortex and the periallocortex.
V Myeloarchitectonic area defined by the Vogt-School.
delay and simple immersion fixation. It is also a cheap method

to stain thousands of serial sections through whole, paraffin or
celloidin embedded human brains. The whole brain approach
allows 3D-reconstructions, and using co-registration with MRI
imaging before histology, correction of shrinkage and inevitable
distortions introduced by histological techniques as well as
computation of probability maps (Homke, 2006; Roland &
Zilles, 1994). Thus, 3D models of human brains can be provided
at microscopical resolution in which cytoarchitectonic analyses
can be performed (Amunts, Lepage, Borgeat, et al., 2013). Moreover, such brains can serve as tools for localization of neuroimaging data within a reference space containing cytoarchitectonic
microscopical information (Eickhoff, Stephan, Mohlberg, et al.,
2005; van Essen et al., 2012).
Despite the restrictions regarding cell typing, two major cell
types are generally definable in Nissl stained sections, pyramidal cells and the so-called granular cells. Whereas the triangular
shape of the cell body of pyramidal cells is well recognizable,
the granular cells are not well characterized beyond the statement that they are small in size. von Economo and Koskinas
(1925) emphasized that many granular cells are triangular in
shape and very similar to what can be called a small or very
small pyramidal cell. Other granular cells, however, are clearly
round and of different size. There was an interesting approach
to classify neurononal cell bodies after Golgi impregnation and
deimpregnation followed by Nissl staining (Werner, Hedlich,
& Koglin, 1986; Werner, Hedlich, & Winkelmann, 1985;
Werner, Winkelmann, Koglin, Neser, & Rodewohl, 1989).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00207-4
115
116
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Cytoarchitecture and Maps of the Human Cerebral Cortex
The authors described a set of criteria (relation between

nucleus and cytoplasm, position of cell nucleus, and cell size
and shape) which in most cases enable the identification not
only of pyramidal cells and spiny stellate cells, but also of
bipolar, large and small aspiny, neurogliaform, chandelier,
double bouquet, basket, and Martinotti cells. Unfortunately,
such studies have never been carried out in the human brain,
or corroborated by immunohistochemical studies, although
they potentially provide an interesting perspective for automated image analysis applied to cytoarchitectonic studies.
Based on Nissl stained sections, the mammalian cerebral
cortex can be subdivided into two major parts, that is, isocortex
and allocortex (Vogt, 1910). The isocortex consists of six major
layers and comprises the largest part of the human cortex. The
thickness of the isocortex varies considerably between the different cytoarcitectonic areas (Table 1). In contrast, the allocortex has a laminar pattern ranging from a hardly visible cortical
structure (e.g., induseum griseum, retrobulbar region) to a
highly differentiated cortical organization (e.g., entorhinal
area; Figure 1).
Two regions of the isocortex show a modification of the
inner granular layer IV: the motor cortex (Figure 1) and the
primary visual cortex (Figure 1). The motor cortex (BA4 and
BA6) is defined as being agranular (Brodmann, 1909; Zilles &
Amunts, 2012), although granular cells are found between
layers III and V (Amunts, Schleicher, & Zilles, 1997; GarciaCabezas & Barbas, 2014), because the pyramidal cells of these
layers invade the interface region to such a degree, that a layer
IV is not visible as a clearly separable layer. Unfortunately,
Brodmann (1909) associated the agranular appearance of the
motor cortex with that of frontal limbic areas based on an
evolutionary hypothesis. This however, does not respect the
principal difference in cortical lamination between allocortical
and isocortical regions as described by Sanides (1962) and
Pandya, Seltzer, and Barbas (1988) and recently emphasized
by Garcia-Cabezas and Barbas (2014). The motor cortex must
be seen as a culmination point both in cytoarchitecture and
connectivity (Garcia-Cabezas & Barbas, 2014), whereas the
anterior cingulate region is periallocortex with a principally
different lamination pattern. In contrast to the motor cortex,
the primary visual cortex contains a highly differentiated layer
IV. Three sublayers are visible, layers IVa, IVb, and IVc, which
can be further subdivided into layers IVca and IVcb (Figure 1).
In some regions, layers III, V, and VI can be further subdivided
into IIIa, IIIb, IIIc, Va, Vb, VIa, and VIb, respectively (Figure 1).
Table 1
Thickness (in mm) of isocortical areas and layers in the
human brain.
Layers
Area 4
Area 3
Area 41/42
Area 17
Area 18
IVI
I
II
III
IV
V
VI
3850
200
100
1400
900
1250
1820
220
280
420
280
220
400
2900
260
280
740
450
530
640
1955
246
89
471
653
218
278
2037
272
92
851
148
279
395
Data from von Economo and Koskinas (1925) and Zilles, Armstrong, Schlaug, and
Schleicher (1986).
Principal Subdivisions of the Cerebral Cortex

The isocortex comprises primary sensory areas (somatosensory, auditory, visual, gustatory, and vestibular), higher unimodal sensory areas, multimodal association areas, and motor
areas. Primary sensory areas receive direct unimodal afferents
from the thalamus and are reciprocally connected with higher
order unimodal sensory areas. The latter abut multimodal
association areas which in turn project to other multimodal
areas and/or the motor cortex, including the supplementary
and pre-supplementary motor areas. The isocortex is also
called neocortex because it shows a dramatic increase during
mammalian evolution (Stephan, 1975).
The allocortex comprises the paleo- and archicortex
(Filimonoff, 1947; Stephan, 1975). The paleocortex consists
of the olfactory bulb, retrobulbar region (anterior olfactory
nucleus), olfactory tubercle, (pre)piriform region, and a
minor part of the amygdala (the major part of the amygdala
is noncortical). Since the paleocortex is clearly involved in
olfactory functions, it is also called rhinencephalon. The archicortex is represented by the hippocampal formation (Ammons
horn (CA) with the CA regions, dentate gyrus, and subiculum)
and adjoined by the periarchicortex (see below). Various parts
of the archicortex are often rather loosely termed as cortical
regions of the limbic system.
Cytoarchitecture changes gradually from isocortex to allocortex. The transition zone close to the isocortex is the proisocortex (Sanides, 1962; Vogt & Vogt, 1919), whereas the part
adjoining the allocortex is the periallocortex (Filimonoff,
1947). Both transition zones form the mesocortex (Rose,
1927a). The periallocortex is further subdivided into peripaleocortex (parts of the insular region) and periarchicortex
(entorhinal, perirhinal, presubicular, parasubicular, and parts
of the cingulate cortex; Filimonoff, 1947).
Paleocortex
Here only a brief survey of the cytoarchitectonic characteristics
is given since a detailed description is given in another article
of this volume.
Olfactory bulb. Its laminar structure justifies classification as
a cortical structure. The human olfactory bulb is smaller and
less differentiated than in other primates (Stephan, 1975), but
displays the same basic laminar organization of six layers
including layer 1 which contains the fibers of the olfactory
nerve. The six layers of the olfactory bulb differ fundamentally
from the six isocortical layers by their cell types, internal circuitry, and inputoutput organization.
Retrobulbar region. Unfortunately, it is frequently called
anterior olfactory nucleus, although it is not a subcortical
nucleus, but has a true cortical structure with two layers
(Stephan, 1975). The retrobulbar region is found where the
olfactory tract merges with the hemispheres.
Olfactory tubercle. It is located within the anterior perforate
substance. Its cortical structure is rudimentary, although a
molecular layer is visible, but cells which belong to the ventral
striatum invade the olfactory tubercule. Islands of Calleja can
occasionally be observed in this brain region.
I
II
IIIa
IIIb
IIIc
I
II
IIIa
IIIb
IIIc
IV
IV
V
VIa
VIb
I
II
IIIa
IIIb
IIIc
IV
Va
Vb
I
II
IIIa
IIIb
IV
IIIc
V
VIa
VIa
VIb
VIa
VIb
VIb
I
II
IIIa
III
I
II
IIIa
I
II
III
IIIb
IIIc
III
IV
IV
V
IV
V
VIa
VIb
I
II
VI
V
VI
IVa
IVb
IVca
IVcb
Va
Vb
VIa
VIb
mol
Pre-a
Pre-b
Pre-g
d
Pri-a
Pri-b
Pri-g
(a)
(Continued)
118
Figure 2 Coronal section through the human hippocampus (silver cell body stain). alv alveus, CA1CA4 regions of the Cornu Ammonis; Ent, entorhinal
area; fi, fimbria hippocampi; gr, granular layer of the fascia dentata; LGN, lateral geniculate nucleus; l-m, lacunosum-molecular layer of the Ammons
horn; luc, lucidum layer of the CA3 region; mol, molecular layer of the fascia dentata; mult, multiform layer of the fascia dentata; or, oriens layer of the
Ammons horn; ParS, parasubiculum; ProS, prosubiculum; PrS, presubiculum; pyr, pyramidal layer of the Ammons horn; rad, radiatum layer of the
Ammons horn; Sub, subiculum.
Prepiriform cortex (BA51). It expands between the lateral

olfactory tract and the temporal cortex and has three layers
(Brockhaus, 1940; Pigache, 1970; Rose, 1927a; von Economo
& Koskinas, 1925). In the first layer, the lateral olfactory tract is
found.
Peripaleocortical region of the insular cortex. It constitutes a
transition zone between the prepiriform cortex and the isocortical insular cortex and will be described below in the section
Insular lobe.
Archicortex
The hippocampal formation consists of the Cornu Ammonis
with the regions CA1CA4, the fascia dentata on the dentate
gyrus, and the subiculum. The fascia dentata is composed of an
outer molecular layer underlaid by the thin and extremely cell
dense granular cell layer followed by a multiform layer. The
molecular layer contains the dendrites of the granular cells,
and is a major target of the perforant path from the entorhinal

cortex. In the center of this whole structure, the CA4 region
with pyramidal cells is found. The CA4 region continues into
the CA3, CA2 and finally the large CA1 region. The latter
continues through the prosubiculum into the subiculum,
which is laterally adjoined by the presubiculum, parasubiculum and, finally, the entorhinal cortex. The Cornu Ammonis
has three major layers, a broad pyramidal layer with an oriens
layer below, in which the basal dendrites of the pyramidal cells
are found, and a radiatum and lacunosum-molecular layer
above into which the apical dendrites of the pyramids extend.
In the CA3 region, between the pyramidal and radiatum layers,
a lucidum layer is visible where the mossy fibers terminate.
These fibers are the axons of the granular cells of the fascia
dentata. The axons of the pyramidal cells of the CA3 region
bifurcate and give rise to the Schaffer collaterals which project
to the pyramidal cells of the CA1 region, as well as to axons
leaving the hippocampus via the alveus and the fimbria hippocampi. A cytoarchitectonic overview is given in Figure 2.
Figure 1 Cell body stained sections of areas Fp1, Fp2, BA11, BA4, 3b, 5M, BA20, BA17, Ent.med., Ent.lat., BA25, BA33, and auditory cortex (with
subdivisions). BA4 is the primary motor cortex; BA11 is part of the medial orbitofrontal cortex; BA17 is the primary visual cortex; BA20 is a
cytoarchitectonic region on the inferior temporal gyrus; region Ent. med. and Ent. lat., are medial and lateral parts of the entorhinal cortex, respectively;
Fp1 plus Fp2 (Bludau, Eickhoff, Mohlberg, et al., 2014) are comparable to BA10; Te1.0, 1.2, and 1.3 are cytoarchitectonic subdivisions of the primary
auditory cortex (Morosan, Rademacher, Schleicher, et al., 2001); Te2 (Morosan, Schleicher, Amunts, & Zilles, 2005) is part of BA42, TI1, and TI2 are
cytoarchitectonic subdivisions of the medial belt (BA52); 3b (Geyer, Schleicher, & Zilles, 1999) is part of the primary somatosensory cortex (larger part
of BA3); 5M (Scheperjans, Grefkes, Palomero-Gallagher, Schleicher, & Zilles, 2005; Scheperjans, Hermann, Eickhoff, et al., 2008) is a medial subdivision
of BA5. Roman numerals indicate isocortical layers. For the laminar nomenclature of Ent.med. and Ent.lat., see Braak (1980). White arrows in BA4
indicate giant Betz pyramidal cells. Large black arrows indicate the borders between the core and belt regions of the auditory cortex and between the
medial belt and the insular cortex; small black arrows indicate subdivisions within the core and the medial belt regions. sf, Sylvian fissure; STG, superior
temporal gyrus; and TG, temporal gyrus (Heschl gyrus).
A more detailed review of the anatomy of the hippocampal
region is found in Insausti and Amaral (2012) and of probability maps in Amunts, Kedo, Kindler, et al. (2005).
The retrosplenial cortex consists of areas BA26, BA29, and
BA30. It is not restricted to the region behind the splenium, but
extends along the caudal third of the corpus callosum in the
callosal sulcus. It can be subdivided into a granular and an
agranular part (Rose, 1927b). There is a transition from primitive allocortical to a differentiated isocortical structure when
moving from the supracommissural hippocampus over areas
119
BA26, BA29, and BA30 to isocortical BA23 (Armstrong, Zilles,

Schlaug, & Schleicher, 1986; Vogt, 1985; Zilles, Armstrong,
Schlaug, & Schleicher, et al., 1986). Table 2 provides a comparison of the different parcellations in the literature with the
Brodmann (1909, 1914) parcellation.
The cingulate gyrus contains periarchicortical, proiso- and
isocortical areas. A detailed description of the myeloarchitecture
and comparison with cyto- and receptorarchitectonic maps is
given in another article of this volume. Table 2 provides a
comparison of the different parcellations in the literature.
Table 2
Comparison of various nomenclature systems used in brain maps with the Brodmann (1909, 1914) classification. The nomenclatures of
Brodmann (1909, 1914; BA areas), von Economo and Koskinas (1925), Rose (1927b, 1928), Stephan (1975), Vogt (2009) and the Dusseldorf/Julich
Group (references below) are based on cytoarchitectonic studies. The nomenclature of Vogt (1910) and Vogt and Vogt (1919) is mainly based on
myeloarchitectonic observations, but also includes comparisons with cytoarchitecture. Maps of the Julich/Dusseldorf group are shown in the JuBrain
atlas (www.fz-juelich.de/inm/inm-1/jubrain_cytoviewer) and can be applied by means of the SPM Anatomy Toolbox (www.fz-juelich.de/inm/inm-1/
spm_anatomy_toolbox).
Brodmann
(1909,
1914)
Vogt (1910), Vogt and

Vogt (1919)
von Economo
and Koskinas
(1925)
Rose (1927b, 1928)
Stephan (1975)
Vogt (2009)
Frontal lobe
BA4
BA6
V42, V43
V36V41
FA, FAg
FB
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
Comparability not
clear
Comparability not
clear
V50, V51
V1, V4V9, V10V12
(ventral parts)
Subregio typica
(V17V24, dorsal
part of V12)
FC (?)
n.d.
n.d.
n.d.
4a, 4p
6 (preliminary
delineation)
n.d.
FD (?)
n.d.
n.d.
n.d.
n.d.
FE
FG, FH
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
Fp1, Fp2
n.d.
Rostral parts
of LA1, LA2,
LA3
Area infraradiata
dorsalis (Ird)
24a, 24b, 24c
s24, p24a, p24b,

pv24c, pd24cv,
pd24cd
Subregio medioradiata
(V25-V32)
Caudal parts of
LA1, LA2, LA3
Subregio
infraradiata
communis
(IRBa-d, IRCa-d)
Regio medioradiata
Area medioradiata
(MR)
a24a, a24b,
24c, p24a,
p24b, 24d
BA25
V13, V14
FL, FM
Area subgenualis (Sg)
25
a24a, a24b, 24cv

24cd, p24a,
p24b, p24dv,
p24dd
25a, 25p
BA32
V3, V10V11 (dorsal

parts), V33V35
Subregio extrema
(V15, V16)
FCL, FDL, FEL,

FHL
LB1
n.d.
s32, p32, d32,

32
33, a33, p33
s32, p32, 32
V56, V57
V58, V59 (dorsal part)
V53, V54
V59 (ventral part)
FCBm
FDg
FD
FF
V70
V71, V72 (?)
PC, PCg (?)

PD, PED
(contains
parts of BA2)
PA1
PB1, PB2
PA2, PCg (?)
PE (PEm, Pep),
PED
(contains
parts of BA7)
BA8
BA9
BA10
BA11,
BA12
BA24
BA33
BA44
BA45
BA46
BA47
Parietal lobe
BA1
BA2
BA3
BA5
BA7
V67
V69
V75
V83, V85, V86, V87 (?)
Regio subgenualis
(Sbga, Sbgp)
n.d.
Area infraradiata
ventralis (Irv)
Julich/Dusseldorf
Group
Subregio
infraradiata
ventralis (IRaa-d)
n.d.
n.d.
n.d.
n.d.
33
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
44d, 44v
45a, 45p
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
1
2
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
3a
3b
5L, 5M, 5Ci
7A, 7P, 7PC, hIP3
(Continued)
120
Table 2
(Continued)
Brodmann
(1909,
1914)

Vogt (1919)
von Economo
and Koskinas
(1925)
Rose (1927b, 1928)
Stephan (1975)
Vogt (2009)
BA23
V77V80, V91V96
LC2, LC3
n.d.
n.d.
23d, 23c, d23, v23
BA26
Vl areas except Vl3
LE2
RSga, RSgb (?)
BA29
Vl3
LE1
RSgb (?), RSgg
29 l, 29 m
29 l, 29 m
BA30
Vl areas except Vl3
LD
RSag
30
30
BA31
BA39
BA40
V76, V81, V82, V84

V90
V73V74 (parts), V88,
V89
n.d.
n.d.
n.d.
d31, v31
n.d.
n.d.
BA43
V68, V72 (?), V73V74

(parts)
LC1
PG
Parts of PFop,
PFt, PFcm,
PF, PFm
PFD, parts of
PFop
Area retrosplenialis
granulosa inferior
granulosa superior
agranularis
n.d.
n.d.
n.d.
23d, 23c, d23,

v23
26
n.d.
n.d.
n.d.
31
PGa, PGp
OP 1, OP2, PFop,
PFt, PFcm, PF,
PFm
OP 3, OP 4
OC
OB (OBg,
OBO)
OA (OA1, OA2,
OAm)
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
hOc1
hOc2
n.d.
n.d.
n.d.
hOc3d, hOc3v,
hOc4d, hOc4v,
hOc5 (areas
located within the
region of BA19
and lateral BA37)
and other areas.
Note, that a
homogenous
cytoarchitectonic
or functional area
19 does not exist
Temporal lobe
BA20
n.d.
BA21
n.d.
BA22
n.d.
TE2
TE1
TA1, TA2
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
BA38
BA41
TG, TGA
TC
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
TB
n.d.
n.d.
n.d.
n.d.
n.d.
Te3, Te4 (areas
within BA22)
n.d.
Te1 (Te1.0, Te1.1,
Te1.2)
Te2 (Te2.1, Te2.2)
PH, PHO, PHP,

PHT
n.d.
n.d.
n.d.
Fg1, Fg2 (on the

fusiform gyrus as
parts of medial
PH)
IA1, IA2, IAB,

IB, IBT, IC, ID
Regio insularis
agranularis
(Prpy1, ai4, ai5,
ai7, ai10, ai11)
Regio insularis
propeagranularis
(ai1ai3, ai6, ai7a,
ai8, ai9)
Region insularis
granularis (Ief [I1
and I2], Itf [I3I6,
I9], Itc [I13I16],
Iec [I7, I8,
I10I12, I17I24])
Regio
peripalaeocorticalis
claustralis; other
insular regions not
determined
n.d.
Ig1 and Ig2 (dorsal

part of Vi5), Id1
(Vai6)
Most of the
dysgranular and
agranular areas
not yet
parcellated
Occipital lobe
BA17
Area striata
BA18
Area occipitalis
BA19
BA42
BA37
Insular lobe
Regio
insularis
anterior
and
posterior
Area praeoccipitalis
V38
Area temporalis
transversa interna
Area temporalis
transversa externa
n.d.
Vi1Vi,6 Vai1Vai,4
Vai,6 Vai7
Julich/Dusseldorf
Group
n.d.
(Continued)
Table 2
121
(Continued)
Brodmann
(1909,
1914)

Vogt (1919)
von Economo
and Koskinas
(1925)
n.d.
VTb,1 VTb2
TK
n.d.
n.d.
FMt
Rose (1927b, 1928)
Stephan (1975)
Vogt (2009)
Julich/Dusseldorf
Group
Tuberculum
olfactorium
Regio retrobulbaris
Tuberculum
olfactorium
Regio retrobulbaris
n.d.
n.d.
n.d.
n.d.
References Dusseldorf/Julich Group: Amunts, Schleicher, Burgel, et al. (1999), Amunts, Lenzen, Friederici, et al. (2010), Amunts, Morosan, Hilbig, and Zilles (2012), Amunts,
Schleicher, and Zilles (2004), Amunts, Malikovic, Mohlberg, Schormann, and Zilles (2000), Bludau, Eickhoff, Mohlberg, et al. (2014), Caspers, Zilles, Eickhoff, et al. (2013), Caspers,
Geyer, Schleicher, et al. (2006), Caspers, Eickhoff, Geyer, et al. (2008), Eickhoff, Amunts, Mohlberg, and Zilles (2006), Eickhoff, Schleicher, Zilles, and Amunts (2006), Geyer,
Ledberg, Schleicher, et al. (1996), Geyer, Schleicher, and Zilles (1999), Geyer (2004), Grefkes, Geyer, Schormann, Roland, and Zilles (2001), Kujovic, Zilles, Malikovic, et al. (2013),
Kurth, Eickhoff, Schleicher, et al. (2010), Malikovic, Amunts, Schleicher, et al. (2007), Morosan, Rademacher, Schleicher, et al. (2001), Morosan, Schleicher, Amunts, and Zilles
(2005), Palomero-Gallagher, Mohlberg, Zilles, and Vogt (2008), Palomero-Gallagher, Zilles, Schleicher, and Vogt (2013), Palomero-Gallagher and Zilles (2009), Rottschy, Eickhoff,
Schleicher, et al. (2007), Scheperjans, Grefkes, Palomero-Gallagher, Schleicher, and Zilles (2005), Scheperjans, Hermann, Eickhoff, et al. (2008), Scheperjans, Eickhoff, Homke, et al.
(2008), Scheperjans, Palomero-Gallagher, Grefkes, Schleicher, and Zilles (2005). n.d., not determined; ?, unclear comparability.
Isocortex
Frontal Lobe
The frontal lobe can be subdivided into three major regions:
Motor cortex (including BA4 and BA6) on the anterior wall

of the precentral gyrus and extending rostrally to the precentral gyrus, particularly in its most dorsal aspects. Motor
cortical regions are also found on the mesial cortical surface, extending ventrally into the cingulate sulcus and rostrally near to the level of the genu corporis callosi.
Prefrontal cortex on the dorsolateral, polar, mesial, and
orbital surfaces of the frontal lobe, including BA8, BA9,
BA10, BA11, BA12, BA46, and BA47. The prefrontal region
can be further subdivided into a dorsolateral (BA9, BA10, and
BA46) and a ventro-orbital part (BA11, BA12, and BA47).
The dysgranular to granular BA8 takes an intermediate position between the agranular BA6 and the granular BA9.
Areas of Brocas region including BA44 and BA45.
It must be emphasized, that Brodmanns parcellation

(Figure 3) is helpful for a first insight into cytoarchitectonic
parcellation, but by far not a complete map (Zilles & Amunts,
2010) of the frontal lobe.
Ngowyang (1934) published a more detailed cytoarchitectonic analysis of the frontal lobe (Figure 4). Although he
depicted all frontal areas in this map, a cytoarchitectonic description was only given for the granular and dysgranular prefrontal
areas, and not for the agranular motor and premotor cortex.
Sanides (1962) carried out a combined cyto- and myeloarchitectonic study with a complete mapping of the frontal lobe
(Figure 5). A comparison between both maps shows major
similarities, but also some distinct mismatches regarding the
existence of some areas or subareas, their extent and cytoarchitectonic structure, particularly concerning the classification as
granular, dysgranular, or agranular. Differences in the size of
areas can be explained by intersubject variability, which was
not studied by either author. The identification of an area, or
the lack thereof, may be caused both by the limitations of pure
visual inspection of histological sections combined with intersubject variability of human brains. The characterization of a
given area by the existence and visibility of layer IV (agranular,
dysgranular, and granular) is a frequently used but limited criterion in cytoarchitectonic studies, because it is not an all or none
criterion. It is influenced by subjective estimates of the visibility

of layer IV and the degree of intrusion of pyramidal neurons
from layers III and V into this layer. Apparently, different
observers used different cut off values for that, as can be seen,
e.g., by comparing the classification of areas 41, 49, or 63 in the
maps of Ngowyang (1934) and Sanides (1962, Figures 4 and 5).
Therefore, Vogt and Vogt (1919) and particularly Sanides (1962)
emphasized that the analysis of layer IV must be supplemented
by a careful observation of the relation between layers III and V.
It is important not only to compare the relative width of both
layers, but also the relation of the sizes of the pyramidal cells they
contain. Based on these criteria regarding layers IIIV, Sanides
(1962) further developed a theory of gradation of cytoarchitectonic fields initially suggested by Vogt and Vogt (1919).
Motor cortex. Agranular BA4 of Brodmann (1903a, 1909),
which is the thickest isocortical area (Table 1), represents the
primary motor cortex and contains the giant Betz pyramidal
cells in layer V (Figure 1). The Betz cells differ from other
pyramidal cells not only by their size, but also by their morphology, because they have numerous dendrites originating
from the whole circumference of the cell body (Scheibel &
Scheibel, 1978). Somatosensory area 3a adjoins BA4 in the
fundus of the central sulcus. This border is definable by the
disappearance of Betz cells and the appearance of layer IV in
area 3a (Jones & Porter, 1980). The rostral border of BA4 is
more difficult to define, because the Betz cells do not abruptly
disappear, but taper down in size and single large pyramidal
cells are also found in BA6. BA4 is largely hidden in the central
sulcus, where it covers the anterior wall; only in the most
dorsal parts does BA4 encroach onto the free surface of the
precentral gyrus (Figures 4 and 5). Geyer, Ledberg, Schleicher,
et al. (1996) demonstrated by a combined cyto- and receptorarchitectonic study that BA4 can be subdivided into rostral
caudal areas 4a and 4p, which also differ by function and
connectivity (Binkofski, Fink, Geyer, et al., 2002; Stepniewska,
Preuss, & Kaas, 1993, 2006; Zilles, Schlaug, Geyer, et al., 1996).
Agranular motor area BA6 represents the whole premotor
region, which includes various functionally and connectionally
different areas. This functional heterogeneity reflects a structural
heterogeneity which was already shown by cyto- and myeloarchitectonic studies of Vogt and Vogt (1919), Ngowyang (1934,
Figure 4), Strasburger (1937), and Sanides (1962, Figure 5), as
well as the pigmentoarchitectonic work of Braak (1976, 1980).
122
6
8
7a
7b
9
3,1,2
46
40
39
10
18
45
43
44
41 42
47
11
19
17
22
37
38
21
20
3,1,2
6
8
5
7a
24
23
32
33
7b
26
10
12
34
28
38
29
30
18
17
27
35
25
11
19
31
18
37
19
36
20
Figure 3 Cytoarchitectonic map of the human cerebral cortex. Reproduced from Brodmann, K. (1914). Physiologie des Gehirns. In: P. von Bruns (Ed.),
Neue Deutsche Chirurgie (pp. 85426). Stutgart: Verlag von Ferdinand Enke.
A major subdivision of BA6 is the parcellation of the supplementary motor cortex on the mesial surface of the hemisphere
from the premotor cortex on the lateral surface. But also these
two regions must be further subdivided, as shown by observations in human and nonhuman primates (Barbas & Pandya,
1987; Geyer, Matelli, Luppino, et al., 1998; Geyer, Zilles, Luppino, & Matelli, 2000; Luppino, Matelli, Camarda, & Rizzolatti,
1993; Luppino, Murata, Govoni, & Matelli, 1999; Matelli,
Camarda, Glickstein, & Rizzolatti, 1986; Matelli, Govoni, Galletti, Kutz, & Luppino, 1998; Matelli & Luppino, 1996; Matelli,
Luppino, & Rizzolatti, 1991; Penfield & Welck, 1951; Picard &
Strick, 1996; Rizzolatti, Camarda, Fogassi, et al., 1988; Rizzolatti, Luppino, & Matelli, 1998; Rizzolatti, Fadiga, Gallese, &
Fogassi, 1996; Rizzolatti, Fadiga, Matelli, et al., 1996; Rizzolatti,
Luppino, & Matelli, 1996; Roland & Zilles, 1996; Schubotz,
Anwander, Knosche, von Cramon, & Tittgemeyer, 2010; Tanji,
1994; Vorobiev, Govoni, Rizzolatti, Matelli, & Luppino, 1998;
Wise & Strick, 1984; Zilles, Schlaug, Matelli, et al., 1995; Zilles,
Schlaug, Geyer, et al., 1996). The collaboration between the
Vogts and Foerster (Foerster, 1931, 1936; Vogt & Vogt, 1919,
1926) already led to a subdivision of BA6 into several parts by
architectonic and functional criteria. Posterior area 6aa and an
anterior area 6ab extend over the lateral and mesial surface of
BA6. It was shown, that the mesial part of 6aa coincides with the
location of SMA-proper, and the mesial part of 6ab with preSMA (Zilles, Schlaug, Geyer, et al., 1996). Furthermore, a subdivision of SMA-proper into the putative rostral SMAr and caudal SMAc was proposed (Vorobiev, Govoni, Rizzolatti, Matelli,
& Luppino, et al., 1998). SMA-proper may be comparable with
areas 38l, 39l, and 39z and pre-SMA with areas 36l and 37l of
Sanides (1962, Figure 5(b)). The rostral border of BA6 is difficult
to define, since the adjoining areas BA8, BA9, and BA44 are
dysgranular, and thus, although layer IV is present, sharp borders are not easily detected. A recent receptorarchitectonic study
36 37
47
38b
123
39b 42
48
44
48a
49
50
44a
39b
45
46
51
54
55
52c
52b
39c
43
58
57 56
40
40
53b
59
55
(a)
53c
41
59
52b 53b
50
49
39c
40
43
40
58 57 56
52c
68
41
65
60
(b)
62
63
5
4
53a
61
?
6 7 8 9
8
6
59
52a
64
53a 61
?
53c
51
52b
51
52a
52c
50
68
7 13 14
(c)
39b 42
34
64
insula
70
38a
39a
48
49
65
13 olf
38b
35
66
60
37
36
47
63
62
53b
69
67
36a 37a
Periarchicortex
33
50
3
51
10
10 11
1
(d)
12
11
14
12 13
Figure 4 Cytoarchitectonic map of the human cerebral cortex. (a) Dorsolateral view; (b) ventrolateral view; (c) orbital view; (d) medial view. Dark red
agranular isocortical area (primary motor cortex BA4), light red agranular isocortical areas (premotor cortex BA6), orange dysgranular isocortical areas,
yellow granular isocortical areas, red dotted agranular allocortical areas; olf, olfactory bulb and tract. A small area on the orbital surface (labeled by a
question mark) was not identified by Ngowyang. Modified from Ngowyang, G. (1934). Die Zytoarchitektonik des menschlichen Stirnhirns. National
Research Institute of Psychology, Academia Sinica, 7, 1.
showed that areas are found at the junction of the inferior

frontal sulcus and the precentral sulcus between BA6 and the
Broca region (Amunts, Lenzen, Friederici, et al., 2010), which
were not described in earlier cytoarchitectonic maps. The
homologies of these new areas and hitherto undetected areas
of the human brain with the monkey areas 44 or F5 (Belmalih,
Borra, Contini, et al., 2009) and more specifically F5a (Gerbella,
Belmalih, Borra, Rozzi, & Luppino, 2011) remain to be clarified.
Prefrontal cortex. Petrides and Pandya (1994) and Petrides,
Tomaiuolo, Yeterian, and Pandya (2012) proposed a map of the
human prefrontal cortex which is based on a search on homologies between human and macaque areas. Although their
nomenclature is based on that introduced by Brodmann, the
maps are not directly comparable, particularly in the orbitofrontal region, because here the search for homologies and the modification of Brodmanns system by Walker (1940) introduced
considerable differences. Additionally, Petrides and Pandya
(1994) subdivided BA8 into areas 8Ad, 8Av, and 8B, BA45 into
45A and 45B, and introduced designations like 47/12, 9/46d,
9/46v for areas with transitional cytoarchitectonic features. There
is agreement on the fact that the prefrontal cortex contains a
larger granular than dysgranular part (for more recent work see
Petrides & Pandya, 1999; Preuss & Goldman-Rakic, 1989).
The frontal pole is occupied by BA10 (Bludau, Eickhoff,
Mohlberg, et al., 2014; Brodmann, 1909, 1914; Petrides &
Pandya, 1994). This area and its intersubject variability
38
ce
47
PmZ
48
/48
47
49
44
39/40
45
46
50
40
55/44
51d
FpZ
42
39
37
36
54
Z
FmZ
55
PoZ
43
40/41
53d
52d
56
58
51p
57
52v
41
56/41
59d
59v
53v
65
FoZ
(a)
FmZ
37
36
PmZ
47
39I
FpZ
42dys
Pro/Peri
50z
42
39z
PIZd
47I
50
38I
37I
36I
36I
49 48
ce
39
38
50I
51p
z
2
Pvz
PIZv
Pvl
12
6/1
OmZ
(b)
FpZ
51
2
1
1/
52v
52v 52v/53
PoZ
53v
4
OmZ
61
FoZ
64
60
65
59
62
8
13
olf
63
66
(c)
Figure 5 Cytoarchitectonic map of the human cerebral cortex. (a) Lateral view; (b) medial view; (c) orbital view. Dark red agranular isocortical area
(primary motor cortex BA4), light red agranular isocortical areas (premotor cortex BA6), orange dysgranular isocortical areas, yellow granular isocortical
areas, red dotted agranular allocortical areas. ce, central sulcus; FmZ, frontomotor zone; FoZ, frontopercular zone; FpZ, frontopolar zone; olf, olfactory
bulb and tract; OmZ, orbitomedian zone; PmZ, paramotor zone; PoZ, paropercular zone; Pro/Peri, proiso-periarchicortical region. Modified from
Sanides, F. (1962). Die Architektonik des menschlichen Stirnhirns. Berlin, Gottingen, Heidelberg: Springer Verlag.
Fp1
Fp2
45
44
44
7A
Te1
Te3
V1
V2
hOc5
Fg1
0%
125
100%
Figure 6 Continuous probability maps of frontopolar areas Fp1 (frontal view) and Fp2 (mesial view, cortical ribbon removed; Bludau, Eickhoff, Mohlberg,
et al., 2014), areas BA45 (lateral view) and BA44 (lateral view of left and right hemispheres for comparison of interhemispheric differences) of Brocas speech
region (Amunts, Schleicher, Burgel, et al., 1999), area 7A (left hemisphere only, dorsolateral view) of the superior parietal lobule (Scheperjans, Eickhoff,
Homke, et al., 2008; Scheperjans, Hermann, Eickhoff, et al., 2008), auditory areas Te1 (rostrolateral inflated view; Morosan, Rademacher, Schleicher,
et al., 2001) and Te3 (lateral view; Morosan, Rademacher, Palomero-Gallagher, & Zilles, 2004), primary and secondary visual areas hOc1 (BA17) and hOc2
(BA18) (occipital views; Amunts, Malikovic, Mohlberg, Schormann, & Zilles, et al., 2000), and extrastriate visual areas hOc5 (lateral view, cortical ribbon
removed; Malikovic, Amunts, Schleicher, et al., 2007) and FG1 (basal view; Caspers, Zilles, Eickhoff, et al., 2013). Scale bar encodes overlap probability.
(Figure 6) was recently analyzed with a quantitative microscopical method leading to a subdivision into a medial (Fp2)
and lateral (Fp1) part, with significantly different cytoarchitecture (Bludau, Eickhoff, Mohlberg, et al., 2014). Fp1 has a wider
layer IV and denser layers II and IIIc than Fp2, whereas layer V
is subdivided into Va and Vb in Fp2 but not in Fp1 (Bludau,
Eickhoff, Mohlberg, et al., 2014).
Rajkowska and Goldman-Rakic (1995a) demonstrated
cytoarchitectonic differences between BA9, which is found on
the middle third of the superior frontal gyrus and adjacent
regions of the middle frontal gyrus, and BA46, which is surrounded by BA9 (or areas 9/46d 9/46v of Petrides & Pandya,
1994 on the middle frontal gyrus). Lamina IV is wider and
contains more densely packed cells in BA46 than in BA9, and
BA46 is less myelinated than BA9. This data argues for a
directed architectonic differentiation from BA9 to BA46 as
already described as a gradation stream by Sanides (1962).
Rajkowska and Goldman-Rakic (1995b) also studied the intersubject variability of the areal borders and found lack of correlation between macroscopical landmarks and areal borders.
BA8 belongs to the dysgranular part of the prefrontal cortex,
the paramotor zone PmZ of Sanides (1962, Figure 5), and area
FC of von Economo and Koskinas (1925). The frontal eye field
is located in the posterior part of BA8 (Blanke et al., 2000), that

is, area 8A of Petrides and Pandya (1999), where the superior
frontal sulcus meets the precentral sulcus.
Brocas region. It is found on the inferior frontal gyrus and
comprises dysgranular BA44 in the opercular, and granular
BA45 in the triangular region (Amunts, Schleicher, Burgel,
et al., 1999; Brodmann, 1909, 1914). This region has been a
subject of numerous anatomical studies (Knauer, 1909; Kononowa, 1949; Petrides & Pandya, 1994; Riegele, 1931; Stengel,
1930; Strasburger, 1938; von Economo & Koskinas, 1925)
revealing considerable intersubject variability in cytoarchitecture, extent, and subdivisions (Amunts, Schleicher, Burgel,
et al., 1999; Amunts, Schleicher, & Zilles, 2004; Amunts, Lenzen,
Friederici, et al., 2010; Kononowa, 1935; Figure 6). The quantitative cytoarchitectonic study of Amunts, Schleicher, Burgel,
et al. (1999) provided 3D probabilistic maps of BA44 and
BA45 which show a considerable variation of areal borders
independent of the sulcal pattern. Furthermore, BA44 was
found to be larger on the left than on the right hemisphere of
all ten brains studied. Based on cytoarchitecture and comparative as well as connectional criteria, Petrides and Pandya (1994,
2009) subdivided BA45 into anterior and posterior parts
(45A and 45B, respectively). This subdivision was recently
126
confirmed (i.e., areas 45a and 45p) and enlarged by further

subdivisions of BA44 and the discovery of new areas in the
Broca region using quantitative receptorarchitecture (Amunts,
Lenzen, Friederici, et al., 2010). Architectonic and functional
studies in macaque monkeys (Belmalih, Borra, Contini, et al.,
2009; Nelissen, Luppino, Vanduffel, Rizzolatti, & Orban, 2005)
raised the exciting discussion as to whether human areas 45B/
45p (Amunts, Lenzen, Friederici, et al., 2010; Petrides & Pandya,
1994) and 44v (Amunts, Lenzen, Friederici, et al., 2010) have
evolved from macaque areas 45b or F5.
Parietal Lobe
The postcentral region of the parietal lobe belongs to the
somatosensory cortex, whereas the superior and inferior parietal lobules, separated by the intraparietal sulcus, are parts of
the multimodal association cortex. The most posterior part of
the paracentral lobule and the mesial extent of the superior
parietal lobule, bordered by the subparietal and parietooccipital sulci, constitute the mesial part of this brain region.
For further details see the article regarding the inferior parietal
lobule in this volume, and would only focus here on basic
cytoarchitectonic features and forgotten but still relevant brain
maps of the postcentral and superior parietal regions.
The map of the Russian-School (Sarkissov, Filimonoff,
Kononowa, & Preobrachenskaja, 1955) is very similar to that
of Brodmann (see Zilles & Amunts, 2012) and differs only by
minor details. Brodmann (1909, 1914) found three major areas
on the postcentral gyrus, BA3, BA2, and BA1 in a rostral to
caudal sequence. BA3 must be subdivided into the areas 3a
and 3b by myelo-, cyto-, and receptorarchitectonic as well as
functional criteria (Jones & Porter, 1980; Vogt & Vogt, 1919; von
Economo & Koskinas, 1925; Zilles, Palomero-Gallagher,
Grefkes, et al., 2002). Area 3b, which is one of the thinnest
isocortical areas (Table 1), is characterized by an extremely
dense population of small granular cells throughout layers
IIIV (Figure 1), which led to the term koniocortex. It represents
part of the primary somatosensory cortex, where epicritic sensoric functions are processed. BA1 has a typical six-layered isocortex with large pyramidal cells in deeper layer III and a less
conspicuous layer IV than that of area 3b. The border between
BA1 and BA2 was defined by quantitative cyto- and receptorarchitectonic analyses (Geyer, Schleicher, & Zilles, 1997; Geyer,
Schormann, Mohlberg, & Zilles, 2000; Geyer, Schleicher, &
Zilles, 1999; Grefkes, Geyer, Schormann, Roland, & Zilles,
2001). According to von Economo and Koskinas (1925) and
Grefkes, Geyer, Schormann, Roland, & Zilles, et al., (2001), but
in contrast to Brodmann (1909), BA2 does not extend onto the
mesial hemispheric surface. BA 43 is mainly located on the
operculum Rolandi and encroaches onto the most ventral portion of the postcentral gyrus. It can be best compared with the
recent cytoarchitectonically and functionally defined opercular
regions OP 3 and OP 4 (Eickhoff, Amunts, Mohlberg, & Zilles,
2006; Eickhoff, Schleicher, Zilles, & Amunts, 2006). A comparison of the Brodmann areas on the postcentral gyrus with those
of von Economo and Koskinas (1925) and the myeloarchitectonicaly defined areas of Vogt and Vogt (1919) is given in Table 2.
An extremely detailed map of the human parietal isocortex
containing 46 areas, and even more subdivisions, was published by Gerhardt (1940). Since this map is based on combined cyto- and myeloarchitectonic study of only one
hemisphere, it does not seem meaningful to discuss this map
in detail facing the intersubject variability of human brains.

Schulze (1960) published a cytoarchitectonic map of the inferior parietal lobule based on three brains and confirmed Vogts
(1911) and Batschs (1956) myeloarchitectonic maps of areas
V88V90. Like Batsch, he subdivided each area into several
subareas. A comparison between the maps of Schulze and
Batsch, however, does not provide a match at the subarea
level. This may be caused by the observer dependent delineation procedure used in both studies, and/or by intersubject
variability inherent to the human brain.
The superior parietal lobule comprises BA5, BA7a, and
BA7b of Brodmann (1914, Figure 3). For a comparison with
myeloarchitectonic subdivisions, the map of von Economo
and Koskinas (1925), and recently published probability
maps (Scheperjans, Eickhoff, Homke, et al., 2008; Scheperjans,
Hermann, Eickhoff, et al., 2008; Figure 6), see Table 2. BA5 is
found on the posterior part of the paracentral lobule, the
rostral bank of the callosomarginal sulcus, and continues laterally between the postcentral sulcus and BA7. BA5 shows a
clearly visible layer IV and large pyramidal cells in layer V
(Figure 1). It can be further subdivided into areas 5M, 5L, and
5Ci based on cyto- and receptorarchitecture (Scheperjans, Eickhoff, Homke, et al., 2008; Scheperjans, Grefkes, PalomeroGallagher, Schleicher, & Zilles, 2005; Scheperjans, Hermann,
Eickhoff, et al., 2008). In some parts of BA5, the pyramidal
cells nearly reach the size of Betz cells (von Economo & Koskinas,
1925). BA7a and BA7b are found on the superior parietal lobule
and the precuneus. As in area 5M (Figure 1), a characteristic cell
sparse band can be seen in lower layer V of both subdivisions of
BA7. Based on cyto- and receptorarchitecture, BA7 could be
subdivided into 7PC, 7A, 7P, 7M, and hIP3 (Scheperjans, Eickhoff, Homke, et al., 2008; Scheperjans, Hermann, Eickhoff, et al.,
2008; Scheperjans, Palomero-Gallagher, Grefkes, Schleicher, &
Zilles, 2005). The latter area extends into the intraparietal sulcus.
Temporal Lobe
The temporal lobe comprises auditory and visual, as well as
multimodal association areas. The primary and secondary
auditory areas BA41 and BA42 reach a considerable cortical
thickness (Table 1). The dorsal surface of the superior temporal gyrus is subdivided by the transverse gyrus (or gyri), on
which the primary and secondary auditory cortices are found
(Figure 1), into an anterior and a posterior part. The anterior
part is the planum polare, and the posterior part the planum
temporale, which extends to the end of the lateral (Sylvian)
fissure. The latter contains parts of the Wernicke language
region. The lateral and ventral surfaces of the temporal lobe
are occupied by the medial and inferior temporal, fusiform
(lateral occipito-temporal), and rostral part of the lingual
(medial occipito-temporal) gyri. They contain multimodal
association and visual brain regions. The most medial part of
the temporal comprises periallocortical entorhinal, perirhinal,
parasubicular, and presubicular areas, as well as the hippocampus proper and the small cortical part of the amygdala. The
polar zone of the temporal lobe (BA38) is a multimodal iso- to
proisocortical region and has been included by Mesulam
(1998) in the paralimbic belt.
The most detailed architectonic studies of the temporal
cortex are based on myeloarchitectonic observations. A comparison of the cytoarchitectonic parcellation schemes by
Brodmann (1909), von Economo & Koskinas (1925), and
the Julich/Dusseldorf group is given in Table 2.
Temporopolar region. A recent cytoarchitectonic and immunohistochemical study of the human temporal polar region (Ding,
Van Hoesen, Cassell, & Poremba, 2009) demonstrated that the
agranular perirhinal area BA35 extends into the posterior part of
the polar cortex, and dysgranular area BA36 reaches even more
anteriorly. Granular area TAr and a polysensory granular area
TAp were found anterior to the auditory parabelt area and in the
dorsal bank of the superior temporal sulcus, respectively (Ding,
Van Hoesen, Cassell, & Poremba, 2009). Furthermore, an agranular area TI, which seems to be equivalent to area TI of Beck
(1930), was identified anterior to the limen insulae and the
temporal part of the prepiriform cortex by the presence of olfactory fibers in layer I and the lack of layer IV (Ding, Van Hoesen,
Cassell, & Poremba, 2009). Right at the pole of the polar region,
a dysgranular area TG was observed (Ding, Van Hoesen, Cassell,
& Poremba, 2009). The granular cytoarchitectonic areas TE1 and
TE2 (von Economo & Koskinas, 1925) also reach the temporal
pole region (Ding, Van Hoesen, Cassell, & Poremba, 2009).
A map of the temporopolar region is given in Figure 7.
Auditory cortex. BA41 is found in the lateral fissure
(Figure 6) on the temporal transverse gyrus (Heschl) gyrus,
and has the typical koniocortical structure of primary sensory
areas. It is surrounded caudo-laterally by the secondary auditory BA42, rostrally and laterally by BA22 and BA42, and
medially by BA52. Distinct vertical cell columns (organ
pipes and rain shower formations of von Economo &
Koskinas, 1925) can be seen in BA41 if the section is precisely
vertical to the cortical surface. This is visible in the lateral part
of Te1.0 of Figure 1, whereas the larger medial part has a more
oblique orientation relative to the sectioning plane. The width
of these columns and the intervals between them in auditory
areas are narrower in the right than in the left hemisphere
(Seldon, 1981).
Based on detailed cyto- and receptor architectonic studies, a
parcellation of the human auditory cortex was recently provided
(Clarke & Morosan, 2012; Morosan, Rademacher, Schleicher,
et al., 2001; Morosan, Rademacher, Palomero-Gallagher, &
Zilles, 2004). Notably, the borders of the cytoarchitectonically
defined primary auditory cortex Te1 cannot be defined by macroscopically visible landmarks of the Heschl gyrus, particularly
not at its lateral part (Morosan, Rademacher, Schleicher, et al.,
2001; Rademacher, Morosan, Schormann, et al., 2001). Their
area Te1 (and subdivisions) can be compared with the core
region (BA41), Te2 (and subdivisions) is part of the lateral
belt, and TI (and its subdivisions TI1 and TI2; Figure 1) represents the medial belt, as suggested in a comparison
of anatomical and functional topographies (Moerel, De, & Formisano, 2014). Whereas TI2 is agranular, TI1 shows a transitional appearance between the granular primary auditory cortex
and TI2, with a recognizable layer IV (Figure 1). Therefore, the
TI area of Morosan, Rademacher, Schleicher, et al. (2001) is not
identical with the completely agranular TI area of Beck (1930) as
mentioned above. Subdivisions of a region comparable to TI
were also shown by Rivier and Clarke (1997) and Wallace,
Johnston, and Palmer (2002). For a recent review of the
relation between tonotopic maps and subdivisions of the auditory cortex, see Moerel, De, and Formisano (2014).
BA42 has a less densely packed and narrower layer IV than
BA41. It represents the secondary auditory cortex and the lateral belt. For further details of the cytoarchitecture of the
human auditory cortex, see Amunts, Morosan, Hilbig, and
Zilles (2012).
127
TAr
HG2
TG
HG1
PI
psl GS
TI
GS
psm
In
LI
36 35
U
SG
AG
ss
(a)
7A
TAr
LI
TI
SG
Pir PAC
ss
PACo
Eo
TG
35
rs
Elr EC
cs
36
7A
(b)
rs
35
EC
cs
36
TG
TE
its
(c)
Figure 7 Combined cytoarchitectonic and immunohistochemical map of

the temporal pole region. (a) Dorsal view; (b) mediodorsal view;
(c) medioventral view. AG, ambiens gyrus; cs, collateral sulcus; EC,
entorhinal cortex; Elr, rostrolateral part of the entorhinal cortex; Eo, olfactory
part of the entorhinal cortex; GS, gyri of Schwalbe; HG1 and HG2, Heschl gyri;
In, insula; its, inferior temporal sulcus; LI, limen insulae; PAC, periamygdaloid
cortex; PACo, subarea of periamygdaloid cortex; PI, parainsular cortex; Pir,
prepiriform cortex; psl, lateral temporopolar sulcus; psm, medial
temporopolar sulcus; rs, rhinal sulcus; SG, semilunar gyrus; ss, semiannular
sulcus; TAp, temporal area TAp; TAr, temporal area TAr; TE, temporal
area; TE1 and TE2 of von Economo and Koskinas (1925); TG, temporo-polar
area TG; TI, temporal insular area; U, uncus; 35, area BA35; 36, area BA36.
Gray surfaces indicate parts of the cortex which were removed during
dissection. Modified from Ding, S. L., Van Hoesen, G. W., Cassell, M. D., &
Poremba, A. (2009). Parcellation of human temporal polar cortex:
A combined analysis of multiple cytoarchitectonic, chemoarchitectonic, and
pathological markers. Journal of Comparative Neurology, 514, 595623.
128
Cyto- and receptorarchitectonically defined area Te3

(Morosan, Rademacher, Palomero-Gallagher, & Zilles, 2004;
Morosan, Schleicher, Amunts, & Zilles, 2005; Figure 6), as part
of BA22, is found lateral to BA42 on the lateral surface of the
superior temporal gyrus. Te3 belongs to the functionally
defined parabelt region (Moerel, De, & Formisano, 2014).
Planum temporale. The anatomical term planum temporale is
not equivalent with the functional term Wernicke region,
although parts of the Wernicke region are found on the planum
temporale. The most probable cytoarchitectonic homolog,
which is part of Wernickes region, is the posterior part of
BA22 (Brodmann, 1909), or area Tpt (Galaburda & Sanides,
1980), but Wernickes region is much larger and extends onto
the inferior parietal lobule according to functional and clinical
findings. Area Tpt and the planum temporale are larger in the
left than the right hemisphere (Galaburda, LeMay, Kemper, &
Geschwind, 1978; Galaburda, Sanides, & Geschwind, 1978;
Geschwind & Levitsky, 1968; Jancke & Steinmetz, 1993;
Steinmetz, Rademacher, Huang, et al., 1989). This asymmetry
was interpreted as a larger left auditory association cortex (von
Economo & Horn, 1930).
Lateral and inferotemporal zone. BA20, BA21, BA36, and
BA37 are multimodal association cortices and higher order
visual and auditory cortices (Mesulam, 1998). Only BA36 presents a transitional cytoarchitecture (proisocortex) with an
overall lower cell density than the other areas, which are typical
isocortical regions (e.g., BA20, Figure 1). In the latter areas,
layer III is relatively cell sparse, layer IV is thin, and layer V
is wide.
BA37 is not a homogeneous cytoarchitectonic or functional
cortical area (Nakamura, Kawashima, Sato, et al., 2000). Some
parts are probably multimodal (Mesulam, 1998), others
belong to the visual cortex. BA37 shows cytoarchitectonic characteristics of temporal, parietal, and occipital cortices depending on the actual site under observation. Parts of BA37 on the
fusiform gyrus belong to the ventral stream of the visual cortex
(Mishkin, Ungerleider, & Macko, 1983; Ungerleider & Mishkin, 1982). See paragraph Occipital lobe, in this article.
Occipital Lobe
The occipital lobe houses the visual cortex, but visual areas are
also found in the temporal and parietal lobes. Approximately
half of the human isocortex is occupied by visual areas.
Brodmanns map (1909) shows a tripartition of the occipital lobe into BA17, primary visual area V1, BA18, secondary
visual area V2, andBA19, tertiary visual area (Figure 3).
A similar tripartition was proposed by von Economo and
Koskinas (1925, Table 2), Filimonoff (1932), and Sarkissov
et al. (1955).
The major part of BA17 receives afferents from both eyes
and represents the central part of the visual field at the occipital
pole, whereas the upper visual field is found solely on the
lower bank and the higher visual field on the upper bank of
the calcarine sulcus. The vertical meridian extends along the
border between BA17 and BA18. BA17 shows an extremely
differentiated laminar structure with a prominent, tripartite
layer IV subdivided into sublayers IVac (Figure 1). Layer IVa
receives parvo- and magnocellular afferents and shows a conspicuous immunoreactivity against non-phosphorylated neurofilaments as well as an extracellular proteoglycan distributed
in mesh-like bands which intermingle with dense calbindin

staining (most probably indicating the presence of GABAergic
inhibitory interneurons; Hendry & Carder, 1993; Hof & Morrison, 1995; Preuss & Coleman, 2002; Preuss, Qi, & Kaas,
1999). Layer IVb contains the Gennari stripe, which consists
of myelinated horizontal collaterals of stellate neurons of this
layer, axon collaterals of layer III pyramids and feedback projections from areas V2 and MT/V5, as well as various fibers of
passage. Layer IVc is further subdivided into layers IVca and
IVcb, which receive afferents from the magnocellular and the
parvocellular layers of the lateral geniculate body, respectively.
Layers III and V contain pyramidal cells and numerous smaller
neurons. These small and densely packed granular-like neurons in layer III lead to the classification of BA17 as koniocortex. Layer V has a much lower cell packing density than layer VI.
The border between BA 17 and BA18 is the most easily
recognizable cytoarchitectonic border in the human brain,
because layer IVc, and with it the Gennari stripe, disappear
abruptly at this border. Very large pyramidal cells appear in
layer III at the border region between both areas and are
assigned to BA18. This stripe containing very large pyramids
was defined as area OBg by von Economo and Koskinas
(1925). It is the target of callosal fibers, which connect
equivalent sites of the vertical meridian in both hemispheres
(Clarke & Miklossy, 1990). The cytoarchitectonic maps of
BA17 and BA18 have been revisited using a quantitative,
observer independent cytoarchitectonic approach (Amunts,
Malikovic, Mohlberg, Schorman, & Zilles, 2000). To clearly
indicate the results of studies based on this technique, which
leads to different results compared with the Brodmann map
(Brodmann, 1909, 1914), a nomenclature system was introduced which indicates the species by the letter h, the macroscopic location of the area (in this case Oc for occipital), and a
simple sequence of Arabic numbers (in this case starting from
the primary visual cortex). Thus, BA17 is hOc1 and BA18 is
hOc2, etc. A considerable intersubject variability of hOc1 has
been demonstrated by probability maps (Amunts, Malikovic,
Mohlberg, Schorman, & Zilles, 2000, also see Filimonoff,
1932; hOc1 in Figure 6). Probabilistic surface based maps
of hOc1 and hOc2 (see below) and their relation to sulcal
landmarks were also studied (Fischl, Rajendran, Busa, et al.,
2008). Functional retinotopic studies and comparisons with
the probability maps demonstrated that hOc1 is comparable
with V1 (Abdollahi, Kolster, Glasser, et al., 2014; Georgieva,
Peeters, Kolster, Todd, & Orban, 2009; Wohlschlager, Specht,
Lie, et al., 2005).
V2/BA18 has 1.7 times larger surface than V1/BA17 (Tootell
& Taylor, 1995), and also shows a considerable intersubject
variability (Amunts, Malikovic, Mohlberg, Schorman, & Zilles,
2000; Filimonoff, 1932; hOc2 in Figure 6). Layer III of BA18 is
about 80% thicker and its layer IV nearly 80% thinner than the
respective layers of BA17 (Table 1). Layer III contains larger
pyramidal cells in BA18 than in BA17, and the separation
between layers V and VI is not as obvious in BA18 compared
to BA17. In cytochrome-oxidase (COX) stained sections
(Burkhalter & Bernardo, 1989; Hockfield, Tootell, & Zaremba,
1990), thick COX-positive stripes can be seen in BA18 which
are rich in an extracellular matrix proteoglycan indicative of the
magnocellular pathway in the human brain (Hendry, Hockfield, Jones, & McKay, 1984; Hendry, Jones, Hockfield, &
McKay, 1988; Hockfield, Tootell, & Zaremba, 1990). This
matrix protein is also found in the magnocellular layers of the
lateral geniculate body, in layer IVa of Ba17 (see above), and in
area V5/MT (see below). Functional retinotopic studies and
comparisons with the probability maps demonstrated that
hOc2 is comparable with V2 (Abdollahi, Kolster, Glasser,
et al., 2014; Georgieva, Peeters, Kolster, Todd, & Orban,
2009; Wohlschlager, Specht, Lie, et al., 2005).
Whereas Brodmanns (1903b, 1909) identification of BA17
and BA18 is widely accepted and conforms with areas hOc1
and hOc2, respectively (Amunts, Malikovic, Mohlberg, Schormann, & Zilles, 2000), his concept of BA19 has been rendered
untenable based on current structural (Braak, 1980; Caspers,
Palomero-Gallagher, Caspers, et al., 2013; Caspers, Zilles,
Eickhoff, et al., 2013; Eickhoff, Rottschy, Kujovic, PalomeroGallagher, & Zilles, 2008; Eickhoff, Rottschy, & Zilles, 2007;
Weiner, Golarai, Caspers, et al., 2014; Zilles & Clarke, 1997)
and functional data (Abdollahi, Kolster, Glasser, et al., 2014;
Felleman & van Essen, 1991; Georgieva, Peeters, Kolster, Todd,
& Orban, 2009; Grill-Spector, Golarai, & Gabrieli, 2008; GrillSpector, Kourtzi, & Kanwisher, 2001; Kanwisher & Yovel, 2006;
Kolster, Peeters, & Orban, 2010; Sereno, Lutti, Weiskopf, & Dick,
2013; Tootell & Hadjikhani, 2001; van Essen, Lewis, Drury,
et al., 2001; Watson, Myers, Frackwiak, et al., 1993). Thus, the
use of the term area 19 is no longer justified. A comprehensive
description of the functional parcellation of this brain region is,
however, beyond the scope of the present article. Eighteen extrastriate areas were described based on retinotopic mapping and
fMRI in the human brain (Georgieva, Peeters, Kolster, Todd, &
Orban, 2009; Kolster, Peeters, & Orban, 2010). The functional
nomenclature of the visual cortex is used here, whenever the
comparability between functional and architectonical parcellations is demonstrated or highly probable.
The retinotopically defined area V3 is found immediately
rostral to BA18, mainly on the lateral, but also on the mesial
surface of the occipital lobe (Sereno, Dale, Repas, et al., 1995;
Tootell & Taylor, 1995). The border between BA18 and V3 is
the site of the horizontal meridian of the visual field. A distinct
cytoarchitectonic area hOc3v (Rottschy, Eickhoff, Schleicher,
et al., 2007) was found rostral and lateral to hOc2 in the
collateral sulcus. This area does not have large pyramidal neurons in layers III or V and is weakly myelinated without Baillarger stripes. It also differs by its lighter COX staining from
hOc2 and the rostrally adjoining cortex (Clarke, 1994). Topographically, this area seems to be comparable to the functionally defined area V3v/VP. A second cytoarchitectonic area
hOc3d (Kujovic, Zilles, Malikovic, et al., 2013) is located
dorso-lateral to hOc2 in the region of the superior and transverse occipital sulci. Based on its location and topology hOc3d
is thought to be the putative anatomical substrate of functionally defined area V3d. hOc3v and hOc3d together overlap with
the retinotopically defined area V3 to a considerable degree
(Abdollahi, Kolster, Glasser, et al., 2014; Georgieva, Peeters,
Kolster, Todd, & Orban, 2009; Wilms, Eickhoff, Specht, et al.,
2010). Notably, hOc3v has higher GABAA, M1 and M3 receptor
densities than hOc3d (Eickhoff, Rottschy, Kujovic, PalomeroGallagher, & Zilles, 2008). This indicates an additional receptorarchitectonic subdivision in parallel to the cytoarchitectonic
parcellation within the V3 complex. Thus, hOc3d could be a
part of the dorsal visual stream, whereas hOc3v would belong
to the ventral stream (Ungerleider & Haxby, 1994; Ungerleider
& Mishkin, 1982).
129
Cytoarchitectonic areas hOc4d (Kujovic, Zilles, Malikovic,

et al., 2013) and hOc4v (Rottschy, Eickhoff, Schleicher, et al.,
2007) were identified rostrally to hOc3d and hOc3v, respectively. hOc4v is found in the collateral sulcus and encroaches
onto the fusiform gyrus at more caudal levels. It differs from
hOc3v by a higher overall cell density, larger pyramidal neurons in layer III, and an intense COX staining (Clarke, 1994).
hOc4v overlaps with retinotopically defined areas hV4, VO1,
and phPITv (Abdollahi, Kolster, Glasser, et al., 2014; Wilms,
Eickhoff, Specht, et al., 2010). hOc4d contains larger pyramidal cells in lower layer III, thinner layers V and VI, and a
sharper cortex-white-matter borderline than hOc3d. It overlaps
with retinotopically defined area V3D and, to a lesser degree,
with remaining areas of the V3A complex (Abdollahi, Kolster,
Glasser, et al., 2014; Wilms, Eickhoff, Specht, et al., 2010).
A cortical area activated by moving visual stimuli was found
in the temporo-occipital transition region and interpreted as
the human homolog (Huk & Heeger, 2002; Watson, Myers,
Frackowiak, et al., 1993) of the monkey V5/MT (Zeki, 1974,
1980). The putative anatomical correlate of V5/MT is a small
heavily myelinated area (Clarke & Miklossy, 1990; Deyoe,
Hockfield, Garren, & van Essen, 1990; Tootell & Taylor,
1995) which was not identified in the maps of Brodmann
(1909) or Sarkissov, Filimonoff, Kononowa, and Preobachenskaja (1955), but could correspond to Flechsigs (1920) area 16
or area OAm of von Economo and Koskinas (1925).
A human extrastriate visual area hOc5 was cytoarchitectonically identified (Malikovic, Amunts, Schleicher, et al., 2007;
Figure 6). It has a broad layer III, a high cell density in layer II/
III, and a low density in layer V (Malikovic, Amunts, Schleicher, et al., 2007). A careful analysis of the topographical
relation of this area to the considerably variable sulcal landmarks is provided in this publication. In some cases an inferior
temporal sulcus is separated from the anterior occipital sulcus
and the lateral occipital sulci. In other cases the ascending limb
of the inferior temporal sulcus continues into the anterior
occipital sulcus. In most of the ten analyzed brains, hOc5 was
found in the anterior occipital sulcus (preferentially on its
posterior wall) of 13 out of 20 hemispheres, in the inferior
occipital sulcus in four of 20 hemispheres and in the inferior
lateral occipital sulcus in the remaining three hemispheres
(Malikovic, Amunts, Schleicher, et al., 2007). Similar localizations were reported in a functional imaging study (Dumoulin,
Bittar, Kabani, et al., 2000). The probability maps resulting
from this study show a correlation with functional imaging
data (alternating moving and stationary dot patterns) in a
recent study of human V5/MT (Wilms, Eickhoff, Specht,
et al., 2005). Over 80% of hOc5 was covered by activated
focus, but the activation site was much larger than the
cytoarchitectonically defined area. A considerable match
between the probability map of hOc5 and results of a MEG
study was also found (Barnikol, Amunts, Dammers, et al.,
2006). Since such co-registration studies have a number of
methodical limitations, it remains possible that hOc5 may be
restricted to the retinotopically defined MT and/or pMST
(Abdollahi, Kolster, Glasser, et al., 2014; Georgieva, Peeters,
Kolster, Todd, & Orban, 2009; Huk, Dougherty, & Heeger,
2002; Kolster, Peeters, & Orban, 2010).
Immediately antero-lateral to hOc4v, two cytoarchitectonic
areas, FG1 and FG2, were identified on the posterior fusiform
gyrus (Caspers, Zilles, Eickhoff, et al., 2013). FG1 shows an
130
(1905) identified four areas (BA13BA16) in the insular cortex
of lower primates, but not in the human brain. Here he only
identified a posterior granular and an anterior agranular region
separated by the central sulcus of the insula. Later studies
demonstrated, that this was an oversimplification, the central
sulcus does not coincide with the cytoarchitectonical subdivision of the human insula into granular and agranular regions.
A detailed cytoarchitectonic analysis of the insula was provided
by Rose (1928, Figure 8). In a later study, this map was further
refined by Brockhaus (1940) and the areas were classified as
iso- meso- and allocortical.
Areas ai4, ai5, ai10, ai11, and Prpy1 of Rose (1928) belong
to the agranular allocortical region. Agranular areas ai10, ai11,
and Prpy1 are not visible in Figure 8. Areas i18i24 represent
the isocortical granular region in the posterior part of the insula,
and areas i1i17 the isocortical dysgranular region (Figure 8).
Areas i13 and i22 of Rose (1928) are located within the central
insular sulcus and therefore not depicted in Figure 8. Area ai8 is
also part of the dysgranular isocortex. The mesocortical region,
which includes areas ai1ai3, ai6, ai7, ai7a and further not
shown in Figure 8, is interposed between the dysgranular isocortical and the agranular allocortical regions.
A principal organization scheme of the insula was proposed
by Mesulam and Mufson (1985). Here the (pre)piriform cortex
and agranular allocortical insular areas are surrounded by three
belts of which the first is the mesocortical dysgranular region
which is characterized by an interrupted and inconspicuous
layer IV. It adjoins the orbitofrontal and temporopolar regions.
The second belt is composed of the isocortical dysgranular
inconspicuous separation between layers II and III, a low to

moderate cell density in layer III, and a lower cell density in
layer IV in comparison to neighboring areas of the early visual
cortex. A unique feature of FG1 is the columnar arrangement of
pyramidal cells when compared to surrounding areas. In contrast to FG1, FG2 presents large pyramidal cells in layer IIIc, a
prominent layer IV, and no obvious columnar arrangement
(Caspers, Zilles, Eickhoff, et al., 2013). These areas also differ
in their receptorarchitecture, with significantly higher NMDA,
GABAA, GABAB, muscarinic M3, nicotinic a4/b2 and 5-HT1A
receptor densities in FG2 than FG1 (Caspers, PalomeroGallagher, Caspers, et al., 2013). Probabilistic maps of FG1
(Figure 6) and FG2 were generated and used for a metaanalysis
(Caspers, Zilles, Amunts, et al., 2013). FG1 and FG2 are found
within the object-related visual cortex (Malach, Reppas, Benson, et al., 1995). They are located lateral to the retinotopic
area VO-1 (Arcaro, McMains, Singer, & Kastner, 2009; Brewer,
Liu, Wade, & Wandell, 2005). The position of FG2 can be
compared with that of the functionally defined posterior fusiform face area (Weiner & Grill-Spector, 2010) or visual wordform area (Cohen et al., 2002; Vigneau, Jobard, Mazoyer, &
Tzourio-Mazoyer, 2005).
Insular Lobe
The insular cortex is covered by the frontal and parietal opercula as well as by the temporal lobe. The circular sulcus of Reil
circumscribes the outer border of the insular cortex. It is subdivided by a consistently present central sulcus. Brodmann
BS
BP
brac
CA
cis
BPacl
i1 bra
brp
i10
i7
i3
i8
i4
i18
i11
i2
ai8
i6
ai7
bri
i15
i16
cii
i19
i20
i21
cs
i23
i24
CP
i9
ai7
ai3
ai1 ai2
i14
ai6
ai3
i6
i12
i9
i5
BPacll
i17
prci
ai8
ai6
ai5
ai7
T
ai4
Figure 8 Cytoarchitectonic map of the human insula. Red encodes allocortical agranular areas, blue mesocortical areas, orange isocortical dysgranular
areas, and yellow isocortical granular areas. The identification of iso- meso- and allocortical classification follows Brockhaus (1940). bra, short anterior
insular sulcus; brac, short accessory insular sulcus; BP, first short insular gyrus; BPacI, first accessory short insular gyrus; BPacII, second accessory
short insular gyrus; brp, short posterior insular sulcus; BS, second short insular gyrus; CA, precentral insular gyrus; cii, inferior branch of the circular
sulcus; cis, superior branch of the circular sulcus; CP, postcentral insular gyrus; cs, central insular sulcus; cs, central insular sulcus; bri, short
intermediate insular sulcus; prci, precentral insular sulcus; T, temporal cortex. Modified from Rose, M. (1928). Die Inselrinde des menschen und der
Tiere. Journal fur Psychologie und Neurologie, 37, 467624.
areas and occupies most of the surface of the insular lobe,
extending from anterior parts of the postcentral insular gyrus
over the first and second short insular gyri to the accessory
short insular gyri. The most posterior belt is the granular
region, with a clearly visible layer IV, a subdividable layer III,
and a clear differentiation of layer V from layer VI. The granular
belt is heavily myelinated and has a well discernible outer
stripe of Baillarger. It was recently subdivided using quantitative cytoarchitectonic mapping and functional metaanalysis
into areas Ig1 and Ig2 (Kurth, Eickhoff, Schleicher, et al.,
2010; Kurth, Zilles, Fox, Laird, & Eickhoff, 2010). Ig1 can
probably be compared with the cortical sensory representation
of temperature and pain (Craig, Chen, Bandy, & Reiman, 2000;
Garcia-Larrea, Perchet, Chreach, et al., 2010).
Acknowledgements
This work was supported by the Portfolio Theme Supercomputing and Modeling for the Human Brain of the Helmholtz
Association, Germany.

Auditory Cortex; Cytoarchitectonics, Receptorarchitectonics, and
Network Topology of Language; Functional Organization of the Primary
Visual Cortex; Gustatory System; Gyrification in the Human Brain;
Insular Cortex; Mapping Cingulate Subregions; Myeloarchitecture and
Maps of the Cerebral Cortex; Posterior Parietal Cortex: Structural and
Functional Diversity; Somatosensory Cortex; Sulci as Landmarks; The
Olfactory Cortex; Topographic Layout of Monkey Extrastriate Visual
Cortex; Transmitter Receptor Distribution in the Human Brain;
Vestibular Cortex; Von Economo Neurons.
References
Abdollahi, R. O., Kolster, H., Glasser, M. F., Robinson, E. C., Coalson, T. S., Dierker, D.,
et al. (2014). Correspondences between retinotopic areas and myelin maps in
Amunts, K., Lenzen, M., Friederici, A. D., Schleicher, A., Morosan, P.,
Palomero-Gallagher, N., et al. (2010). Brocas region: Novel organizational
principles and multiple receptor mapping. PLoS Biology, 8, e1000489.
Amunts, K., Lepage, C., Borgeat, L., Mohlberg, H., Dickscheid, T., Rousseau, M. E.,
et al. (2013). BigBrain: An ultrahigh-resolution 3D human brain model. Science,
340, 14721475.
Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000).
Brodmanns areas 17 and 18 brought into stereotaxic space-where and how
variable? NeuroImage, 11, 6684.
Amunts, K., Morosan, P., Hilbig, H., & Zilles, K. (2012). Auditory system. In J. K. Mai &
G. Paxinos (Eds.), The human nervous system (3rd ed., pp. 12701300).
Amsterdam: Academic Press.
Amunts, K., Schleicher, A., & Zilles, K. (1997). Persistence of layer IV in the primary
motor cortex (area 4) of children with cerebral palsy. Journal fur Hirnforschung, 38,
247260.
131
Amunts, K., Schleicher, A., & Zilles, K. (2004). Outstanding language

competence and cytoarchitecture in Brocas speech region. Brain & Language, 89,
346353.
Arcaro, M. J., McMains, S. A., Singer, B. D., & Kastner, S. (2009). Retinotopic
organization of human ventral visual cortex. Journal of Neuroscience, 29,
1063810652.
Armstrong, E., Zilles, K., Schlaug, G., & Schleicher, A. (1986). Comparative aspects of
the primate posterior cingulate cortex. Journal of Comparative Neurology, 253,
539548.
Barbas, H., & Pandya, D. N. (1987). Architecture and frontal cortical connections of the
premotor cortex (area 6) in the rhesus monkey. Journal of Comparative Neurology,
256, 211228.
Barnikol, U. B., Amunts, K., Dammers, J., Mohlberg, H., Fieseler, T., Malikovic, A., et al.
(2006). Pattern reversal visual evoked responses of V1/V2 and V5/MT as revealed
by MEG combined with probabilistic cytoarchitectonic maps. NeuroImage, 31,
86108.
Batsch, E.-G. (1956). Die myeloarchitektonische Untergliederung des Isocortex
parietalis beim Menschen. Journal fur Hirnforschung, 2, 225258.
Beck, E. (1930). Myeloarchitektonik der dorsalen Schlafenlappenrinde beim Menschen.
Belmalih, A., Borra, E., Contini, M., Gerbella, M., Rozzi, S., & Luppino, G. (2009).
Multimodal architectonic subdivision of the rostral part (area F5) of the macaque
ventral premotor cortex. Journal of Comparative Neurology, 512, 183217.
Binkofski, F., Fink, G. R., Geyer, S., Buccino, G., Gruber, O., Shah, N. J., et al. (2002).
Neural activity in human primary motor cortex areas 4a and 4p is modulated
differentially by attention to action. Journal of Neurophysiology, 88, 514519.
Bludau, S., Eickhoff, S. B., Mohlberg, H., Caspers, S., Laird, A. R., Fox, P. T., et al.
(2014). Cytoarchitecture, probability maps and functions of the human frontal pole.
Braak, H. (1976). A primitive gigantopyramidal field buried in the depth of the cingulate
sulcus of the human brain. Brain Research, 109, 219233.
Brewer, A. A., Liu, J., Wade, A. R., & Wandell, B. A. (2005). Visual field maps and stimulus
selectivity in human ventral occipital cortex. Nature Neuroscience, 8, 11021109.
Brockhaus, H. (1940). Die Cyto- und Myeloarchitektonik des Cortex claustralis und des
Claustrum beim Menschen. Journal fur Psychologie und Neurologie, 49, 249348.
Brodmann, K. (1903a). Beitrage zur histologischen Lokalisation der Grosshirnrinde. I.
Die Regio Rolandica. Journal fur Psychologie und Neurologie, 2, 79107.
Brodmann, K. (1903b). Beitrage zur histologischen Lokalisation der Grosshirnrinde. II.
Der Calcarinustyp. Journal fur Psychologie und Neurologie, 2, 133159.
Brodmann, K. (1905). Beitrage zur histologischen Lokalisation der Grosshirnrinde. III.
Die Rindenfelder der niederen Affen. Journal fur Psychologie und Neurologie, 4,
177226.
Brodmann, K. (1909). Vergleichende Lokalisationslehre der Grohirnrinde in ihren
Prinzipien dargestellt auf Grund des Zellbaues. Leipzig: Barth.
Brodmann, K. (1914). Physiologie des Gehirns. In P. von Bruns (Ed.), Neue Deutsche
Chirurgie (pp. 85426). Stutgart: Verlag von Ferdinand Enke.
Burkhalter, A., & Bernardo, K. L. (1989). Organization of corticocortical connections in
human visual cortex. Proceedings of the National academy of Sciences of the United
Caspers, S., Eickhoff, S. B., Geyer, S., Scheperjans, F., Mohlberg, H., Zilles, K., et al.
(2008). The human inferior parietal lobule in stereotaxic space. Brain Structure &
Function, 212, 481495.
Caspers, J., Palomero-Gallagher, N., Caspers, S., Schleicher, A., Amunts, K., &
Zilles, K. (2013). Receptor architecture of visual areas in the face and word-form
recognition region of the posterior fusiform gyrus. Brain Structure & Function.
http://dx.doi.org/10.1007/s00429-013-0646-z.
Caspers, J., Zilles, K., Amunts, K., Laird, A. R., Fox, P. T., & Eickhoff, S. B. (2013).
Functional characterization and differential coactivation patterns of two
cytoarchitectonic visual areas on the human posterior fusiform gyrus. Human Brain
Mapping, 35, 27542767.
Caspers, J., Zilles, K., Eickhoff, S. B., Schleicher, A., Mohlberg, H., & Amunts, K.
(2013). Cytoarchitectonical analysis and probabilistic mapping of two extrastriate
areas of the human posterior fusiform gyrus. Brain Structure & Function, 218,
511526.
Clarke, S. (1994). Modular organization of human extrastriate visual cortex: Evidence
from cytochrome oxidase pattern in normal and macular degeneration cases.
Clarke, S., & Miklossy, J. (1990). Occipital cortex in man: Organization of callosal
connections, related myelo- and cytoarchitecture, and putative boundaries of
functional visual areas. Journal of Comparative Neurology, 298, 188214.
132
Clarke, S., & Morosan, P. (2012). Architecture, connectivity, and transmitter receptors
of human auditory cortex. In D. Poeppel, T. Overath, A. N. Popper, & R. R. Fay
(Eds.), The human auditory cortex (2nd ed., pp. 1138). New York: Springer.
Cohen, L., Lehericy, S., Chochon, F., Lemer, C., Rivaud, S., & Dehaene, S. (2002).
Language-specific tuning of visual cortex? Functional properties of the Visual Word
Form Area. Brain, 125, 10541069.
Craig, A. D., Chen, K., Bandy, D., & Reiman, E. M. (2000). Thermosensory activation of
insular cortex. Nature Neuroscience, 3, 184190.
Deyoe, E. A., Hockfield, S., Garren, H., & van Essen, D. C. (1990). Antibody labeling of
functional subdivisions in visual cortex: Cat-301 immunoreactivity in striate and
extrastriate cortex of the macaque monkey. Visual Neuroscience, 5, 6781.
Ding, S. L., Van Hoesen, G. W., Cassell, M. D., & Poremba, A. (2009). Parcellation of
human temporal polar cortex: A combined analysis of multiple cytoarchitectonic,
chemoarchitectonic, and pathological markers. Journal of Comparative Neurology,
514, 595623.
Dumoulin, S. O., Bittar, R. G., Kabani, N. J., Baker, C. L., Jr., Le, G. G., Bruce, P. G.,
et al. (2000). A new anatomical landmark for reliable identification of human
area V5/MT: A quantitative analysis of sulcal patterning. Cerebral Cortex, 10,
454463.
Eickhoff, S. B., Amunts, K., Mohlberg, H., & Zilles, K. (2006). The human parietal
operculum. II. Stereotaxic maps and correlation with functional imaging results.
Eickhoff, S. B., Rottschy, C., Kujovic, M., Palomero-Gallagher, N., & Zilles, K. (2008).
Organizational principles of human visual cortex revealed by receptor mapping.
Eickhoff, S. B., Rottschy, C., & Zilles, K. (2007). Laminar distribution and codistribution of neurotransmitter receptors in early human visual cortex. Brain
Eickhoff, S. B., Schleicher, A., Zilles, K., & Amunts, K. (2006). The human parietal
operculum. I. Cytoarchitectonic mapping of subdivisions. Cerebral Cortex, 16,
254267.
functional imaging data. NeuroImage, 25, 13251335.
Felleman, D. J., & van Essen, D. C. (1991). Distributed hierarchical processing in the
Filimonoff, I. N. (1932). Uber die Variabilitat der Grohirnrindenstruktur. Mitteilung II
Regio occipitalis beim erwachsenen Menschen. Journal fur Psychologie und
Neurologie, 44, 296.
Filimonoff, I. N. (1947). A rational subdivision of the cerebral cortex. Archives of
Neurology and Psychiatry, 58, 296311.
19731980.
myelogenetischer Grundlage. Leipzig: Thieme.
Foerster, O. (1931). The cerebral cortex in man. Lancet, 218, 309312.
Foerster, O. (1936). The motor cortex in man in the light of Hughlings Jacksons
doctrines. Brain, 59, 135159.
Galaburda, A. M., LeMay, M., Kemper, T. L., & Geschwind, N. (1978). Right-left
asymmetrics in the brain. Science, 199, 852856.
Galaburda, A. M., & Sanides, F. (1980). Cytoarchitectonic organization of the human
auditory cortex. Journal of Comparative Neurology, 190, 597610.
Galaburda, A. M., Sanides, F., & Geschwind, N. (1978). Human brain. Cytoarchitectonic
left-right asymmetries in the temporal speech region. Archives of Neurology, 35,
812817.
Garcia-Cabezas, M. A., & Barbas, H. (2014). Area 4 has layer IV in adult primates.
Garcia-Larrea, L., Perchet, C., Creach, C., Convers, P., Peyron, R., Laurent, B., et al.
(2010). Operculo-insular pain (parasylvian pain): A distinct central pain syndrome.
Brain, 133, 25282539.
Georgieva, S., Peeters, R., Kolster, H., Todd, J. T., & Orban, G. A. (2009). The
processing of three-dimensional shape from disparity in the human brain. Journal
Gerbella, M., Belmalih, A., Borra, E., Rozzi, S., & Luppino, G. (2011). Cortical
connections of the anterior (F5a) subdivision of the macaque ventral premotor area
F5. Brain Structure & Function, 216, 4365.
Gerhardt, E. (1940). Die Cytoarchitektonik des Isocortex parietalis beim Menschen.
Geschwind, N., & Levitsky, W. (1968). Human brain: Left-right asymmetries in temporal
speech region. Science, 161, 186187.
Biology, 174, 189.
Geyer, S., Ledberg, A., Schleicher, A., Kinomura, S., Schormann, T., Burgel, U., et al.
(1996). Two different areas within the primary motor cortex of man. Nature, 382,
805807.
Geyer, S., Matelli, M., Luppino, G., Schleicher, A., Jansen, Y., Palomero-Gallagher, N.,
et al. (1998). Receptor autoradiographic mapping of the mesial motor and
premotor cortex of the macaque monkey. Journal of Comparative Neurology, 397,
231250.
Geyer, S., Schleicher, A., & Zilles, K. (1997). The somatosensory cortex of human:
Cytoarchitecture and regional distributions of receptor-binding sites. NeuroImage,
6, 2745.
Geyer, S., Schleicher, A., & Zilles, K. (1999). Areas 3a, 3b, and 1 of human primary
somatosensory cortex. 1. Microstructural organization and interindividual
Geyer, S., Schormann, T., Mohlberg, H., & Zilles, K. (2000). Areas 3a, 3b, and 1 of
human primary somatosensory cortex. 2. Spatial normalization to standard
anatomical space. NeuroImage, 11, 684696.
Geyer, S., Zilles, K., Luppino, G., & Matelli, M. (2000). Neurofilament protein
distribution in the macaque monkey dorsolateral premotor cortex. European Journal
Grill-Spector, K., Golarai, G., & Gabrieli, J. (2008). Developmental
neuroimaging of the human ventral visual cortex. Trends in Cognitive Sciences, 12,
152162.
Grill-Spector, K., Kourtzi, Z., & Kanwisher, N. (2001). The lateral occipital complex and
its role in object recognition. Vision Research, 41, 14091422.
Hendry, S. H., & Carder, R. K. (1993). Neurochemical compartmentation of monkey and
human visual cortex: Similarities and variations in calbindin immunoreactivity
across species. Visual Neuroscience, 10, 11091120.
Hendry, S. H., Hockfield, S., Jones, E. G., & McKay, R. (1984). Monoclonal antibody
that identifies subsets of neurones in the central visual system of monkey and cat.
Nature, 307, 267269.
Hendry, S. H., Jones, E. G., Hockfield, S., & McKay, R. D. (1988). Neuronal populations
stained with the monoclonal antibody Cat-301 in the mammalian cerebral cortex
and thalamus. Journal of Neuroscience, 8, 518542.
Hockfield, S., Tootell, R. B., & Zaremba, S. (1990). Molecular differences among
neurons reveal an organization of human visual cortex. Proceedings of the National
academy of Sciences of the United States of America, 87, 30273031.
Hof, P. R., & Morrison, J. H. (1995). Neurofilament protein defines regional patterns
of cortical organization in the macaque monkey visual system: A quantitative
immunohistochemical analysis. Journal of Comparative Neurology, 352,
161186.
Homke, L. (2006). A multigrid method for anisotropic PDEs in elastic im age
registration. Numerical Linear Algebra with Applications, 13, 215229.
Huk, A. C., Dougherty, R. F., & Heeger, D. J. (2002). Retinotopy and functional
subdivision of human areas MT and MST. Journal of Neuroscience, 22,
71957205.
Huk, A. C., & Heeger, D. J. (2002). Pattern-motion responses in human visual cortex.
Insausti, R., & Amaral, D. G. (2012). Hippocampal formation. In J. K. Mai & G. Paxinos
(Eds.), The human nervous system (3rd ed., pp. 896942). Amsterdam: Academic
Press.
Jancke, L., & Steinmetz, H. (1993). Auditory lateralization and planum temporale
asymmetry. NeuroReport, 5, 169172.
Jones, E. G., & Porter, R. (1980). What is area 3a? Brain Research Reviews, 2, 143.
Kanwisher, N., & Yovel, G. (2006). The fusiform face area: A cortical region specialized
for the perception of faces. Philosophical Transactions of the Royal Society of
London. Series B: Biological Sciences, 361, 21092128.
Knauer, A. (1909). Die Myeloarchitektonik der Brocaschen Region. Neurologisches
Centralblatt, 28, 12401243.
human middle temporal area MT/V5 and its cortical neighbors. Journal of
Kononowa, E. P. (1935). Structural variability of the cortex cerebri. Inferior frontal gyrus
in adults (Russian). In S. A. Sarkissov & I. N. Filimonoff (Eds.), Annals of the brain
research institute (pp. 49118). Moscow-Leningrad: State Press for Biological and
Medical Literature.
Kononowa, E. P. (1949). The frontal lobe (Russian). In S. A. Sarkissov, I. N. Filimonoff
& N. S. Preobrashenskaya (Eds.), The cytoarchitecture of the human cortex cerebri
(pp. 309343). Moscow: Medgiz.
Kujovic, M., Zilles, K., Malikovic, A., Schleicher, A., Mohlberg, H., Rottschy, C., et al.
(2013). Cytoarchitectonic mapping of the human dorsal extrastriate cortex. Brain
Kurth, F., Eickhoff, S. B., Schleicher, A., Hoemke, L., Zilles, K., & Amunts, K. (2010).
Cytoarchitecture and probabilistic maps of the human posterior insular cortex.
Kurth, F., Zilles, K., Fox, P. T., Laird, A. R., & Eickhoff, S. B. (2010). A link between the
systems: Functional differentiation and integration within the human insula revealed
by meta-analysis. Brain Structure & Function, 214, 519534.
Luppino, G., Matelli, M., Camarda, R., & Rizzolatti, G. (1993). Corticocortical
connections of area F3 (SMA-proper) and area F6 (pre-SMA) in the macaque
Luppino, G., Murata, A., Govoni, P., & Matelli, M. (1999). Largely segregated
parietofrontal connections linking rostral intraparietal cortex (areas AIP and VIP) and
the ventral premotor cortex (areas F5 and F4). Experimental Brain Research, 128,
181187.
Malach, R., Reppas, J. B., Benson, R. R., Kwong, K. K., Jiang, H., Kennedy, W. A., et al.
(1995). Object-related activity revealed by functional magnetic resonance imaging in
human occipital cortex. Proceedings of the National academy of Sciences of the
(2007). Cytoarchitectonic analysis of the human extrastriate cortex in the region of
V5/MT : A probabilistic, stereotaxic map of Area hOc5. Cerebral Cortex, 17,
562574.
Matelli, M., Camarda, R., Glickstein, M., & Rizzolatti, G. (1986). Afferent and efferent
projections of the inferior area 6 in the macaque monkey. Journal of Comparative
Neurology, 251, 281298.
Matelli, M., Govoni, P., Galletti, C., Kutz, D. F., & Luppino, G. (1998). Superior area 6
afferents from the superior parietal lobule in the macaque monkey. Journal of
Matelli, M., & Luppino, G. (1996). Thalamic input to mesial and superior area 6 in the
macaque monkey. Journal of Comparative Neurology, 372, 5987.
Matelli, M., Luppino, G., & Rizzolatti, G. (1991). Architecture of superior and mesial
area 6 and the adjacent cingulate cortex in the macaque monkey. Journal of
Mesulam, M. M. (1998). From sensation to cognition. Brain, 121, 10131052.
Mesulam, M. M., & Mufson, E. J. (1985). The insula of Reil in man and monkey.
Architectonics, connectivity and function. In A. Peters & E. G. Jones (Eds.), Cerebral
cortex (pp. 179226). New York: Plenum.
Mishkin, M., Ungerleider, L. G., & Macko, K. A. (1983). Object and spatial vision: Two
cortical pathways. Trends in Neurosciences, 6, 414417.
Moerel, M., De, M. F., & Formisano, E. (2014). An anatomical and functional
topography of human auditory cortical areas. Frontiers in Neuroscience, 8, 225.
Morosan, P., Rademacher, J., Palomero-Gallagher, N., & Zilles, K. (2004). Anatomical
organization of the human auditory cortex: Cytoarchitecture and transmitter
receptors. In P. Heil, E. Konig, & E. Budinger (Eds.), Auditory cortex Towards a
synthesis of human and animal research (pp. 2750). Mahwah, NJ: Lawrence
Erlbaum.
Morosan, P., Rademacher, J., Schleicher, A., Amunts, K., Schormann, T., & Zilles, K.
(2001). Human primary auditory cortex: Cytoarchitectonic subdivisions and
mapping into a spatial reference system. NeuroImage, 13, 684701.
Morosan, P., Schleicher, A., Amunts, K., & Zilles, K. (2005). Multimodal architectonic
mapping of human superior temporal gyrus. Anatomy and Embryology (Berlin),
210, 401406.
Nakamura, K., Kawashima, R., Sato, N., Nakamura, A., Sugiura, M., Kato, T., et al.
(2000). Functional delineation of the human occipito-temporal areas related to face
and scene processing. A PET study. Brain, 123, 19031912.
Nelissen, K., Luppino, G., Vanduffel, W., Rizzolatti, G., & Orban, G. A. (2005).
Observing others: Multiple action representation in the frontal lobe. Science, 310,
332336.
Ngowyang, G. (1934). Die Zytoarchitektonik des menschlichen Stirnhirns. National
Research Institute of Psychology, Academia Sinica, 7, 1.
Palomero-Gallagher, N., Mohlberg, H., Zilles, K., & Vogt, B. A. (2008). Cytology and
receptor architecture of human anterior cingulate cortex. Journal of Comparative
Neurology, 508, 906926.
Palomero-Gallagher, N., & Zilles, K. (2009). Transmitter receptor systems in cingulate
regions and areas. In B. A. Vogt (Ed.), Cingulate neurobiology & disease, Vol. 1:
Infrastructure, diagnosis, treatment (2nd ed.). Oxford: Oxford University Press.
133
Palomero-Gallagher, N., Zilles, K., Schleicher, A., & Vogt, B. A. (2013). Cyto- and
receptor architecture of area 32 in human and macaque brains. Journal of
Pandya, D. N., Seltzer, B., & Barbas, H. (1988). Input-output organization of the primate
cerebral cortex. In H. D. Steklis & J. Erwin (Eds.), Comparative primate biology
(pp. 3980). New York: Alan R. Liss.
Penfield, W., & Welck, K. (1951). The supplementary motor area of the cerebral cortex; a
clinical and experimental study. AMA Archives of Neurology & Psychiatry, 66,
289317.
Petrides, M., & Pandya, D. N. (1994). Comparative architectonic analysis of the human
and the macaque frontal cortex. In F. Boller, & J. Grafman (Eds.), Handbook of
neuropsychology (pp. 1758). Amsterdam: Elsevier.
Petrides, M., & Pandya, D. N. (1999). Dorsolateral prefrontal cortex: Comparative
cytoarchitectonic analysis in the human and the macaque brain and corticocortical
connection patterns. European Journal of Neuroscience, 11, 10111036.
Petrides, M., & Pandya, D. N. (2009). Distinct parietal and temporal pathways to the
homologues of Brocas area in the monkey. PLoS Biology, 7, e1000170.
Petrides, M., Tomaiuolo, F., Yeterian, E. H., & Pandya, D. N. (2012). The prefrontal
cortex: Comparative architectonic organization in the human and the macaque
monkey brains. Cortex, 48, 4657.
Picard, N., & Strick, P. L. (1996). Motor areas of the medial wall: A review of their
location and functional activation. Cerebral Cortex, 6, 342353.
Pigache, R. M. (1970). The anatomy of "Paleocortex". A critical review. Ergebnisse der
Anatomie und Entwicklungsgeschichte, 43, 62.
Preuss, T. M., & Coleman, G. Q. (2002). Human-specific organization of primary visual
cortex: Alternating compartments of dense cat-301 and calbindin immunoreactivity
in layer 4A. Cerebral Cortex, 12, 671691.
Preuss, T. M., & Goldman-Rakic, P. S. (1989). Connections of the ventral granular
frontal cortex of macaques with perisylvian premotor and somatosensory areas:
Anatomical evidence for somatic representation in primate frontal association
Preuss, T. M., Qi, H., & Kaas, J. H. (1999). Distinctive compartmental organization of
human primary visual cortex. Proceedings of the National academy of Sciences of
Rademacher, J., Morosan, P., Schormann, T., Schleicher, A., Werner, C., Freund, H. J.,
et al. (2001). Probabilistic mapping and volume measurement of human primary
auditory cortex. NeuroImage, 13, 669683.
Rajkowska, G., & Goldman-Rakic, P. S. (1995a). Cytoarchitectonic definition of
prefrontal areas in the normal human cortex: I. Remapping of areas 9 and 46 using
quantitative criteria. Cerebral Cortex, 5, 307322.
Rajkowska, G., & Goldman-Rakic, P. S. (1995b). Cytoarchitectonic definition of
prefrontal areas in the normal human cortex: II. Variability in locations of areas 9 and
46 and relationship to the Talairach Coordinate System. Cerebral Cortex, 5,
323337.
Riegele, L. (1931). Die Cytoarchitektonik der Felder der Brocaschen Regionen. Journal
of Physiology & Neurology, 42, 496514.
Rivier, F., & Clarke, S. (1997). Cytochrome oxidase, acetylcholinesterase, and NADPHdiaphorase staining in human supratemporal and insular cortex: Evidence for
multiple auditory areas. NeuroImage, 6, 288304.
Rizzolatti, G., Camarda, R., Fogassi, L., Gentilucci, M., Luppino, G., & Matelli, M.
(1988). Functional organization of inferior area 6 in the macaque monkey. II.
Area F5 and the control of distal movements. Experimental Brain Research, 71,
491507.
Rizzolatti, G., Fadiga, L., Gallese, V., & Fogassi, L. (1996). Premotor cortex and the
recognition of motor actions. Brain Research. Cognitive Brain Research, 3,
131141.
Rizzolatti, G., Fadiga, L., Matelli, M., Bettinardi, V., Paulesu, E., Perani, D., et al. (1996).
Localization of grasp representations in humans by PET: 1. Observation versus
execution. Experimental Brain Research, 111, 246252.
Rizzolatti, G., Luppino, G., & Matelli, M. (1996). The classic supplementary motor area
is formed by two independent areas. Advances in Neurology, 70, 4556.
Rizzolatti, G., Luppino, G., & Matelli, M. (1998). The organization of the cortical motor
system: New concepts. Electroencephalography and Clinical Neurophysiology, 106,
283296.
Roland, P. E., & Zilles, K. (1994). Brain atlasesA new research tool. Trends in
Roland, P. E., & Zilles, K. (1996). Functions and structures of the motor cortices in
humans. Current Opinion in Neurobiology, 6, 773781.
Rose, M. (1927a). Die sog. Riechrinde beim Menschen und beim Affen. II. Teil
Allocortex bei Tier und Mensch. Journal fur Psychologie und Neurologie, 32,
97160.
134
Rose, M. (1927b). Gyrus limbicus anterior und Regio retrosplenialis (Cortex

holoprotoptychos quinquestratificatus). Vergleichende Architektonik bei Tier und
Mensch. Journal fur Psychologie und Neurologie, 35, 65173.
Rose, M. (1928). Die Inselrinde des menschen und der Tiere. Journal fur Psychologie
Rottschy, C., Eickhoff, S. B., Schleicher, A., Mohlberg, H., Kujovic, M., Zilles, K., et al.
(2007). Ventral visual cortex in humans: Cytoarchitectonic mapping of two
extrastriate areas. Human Brain Mapping, 28, 10451059.
Sanides, F. (1962). Die Architektonik des menschlichen Stirnhirns. Berlin/Gottingen/
Sarkissov, S. A., Filimonoff, I. N., Kononowa, E. P., & Preobrachenskaja, I. S. (1955).
Atlas of the cytoarchitectonics of the human cerebral cortex. Moscow: Medgiz.
Scheibel, M. E., & Scheibel, A. B. (1978). The dendritic structure of the human Betz cell.
In A. A. B. Braxier & H. Pets (Eds.), Architectonics of the cerebral cortex
(pp. 4357). New York: Raven Press.
Scheperjans, F., Eickhoff, S. B., Homke, L., Mohlberg, H., Hermann, K., Amunts, K.,
et al. (2008). Probabilistic maps, morphometry, and variability of cytoarchitectonic
areas in the human superior parietal cortex. Cerebral Cortex, 18, 21412157.
Scheperjans, F., Grefkes, C., Palomero-Gallagher, N., Schleicher, A., & Zilles, K.
(2005). Subdivisions of human parietal area 5 revealed by quantitative receptor
autoradiography: A parietal region between motor, somatosensory and cingulate
cortical areas. NeuroImage, 25, 975992.
Scheperjans, F., Hermann, K., Eickhoff, S. B., Amunts, K., Schleicher, A., & Zilles, K.
(2008). Observer-independent cytoarchitectonic mapping of the human superior
parietal cortex. Cerebral Cortex, 18, 846867.
Scheperjans, F., Palomero-Gallagher, N., Grefkes, C., Schleicher, A., & Zilles, K.
(2005). Transmitter receptors reveal segregation of cortical areas in the human
superior parietal cortex: Relations to visual and somatosensory regions.
Schubotz, R. I., Anwander, A., Knosche, T. R., von Cramon, D. Y., & Tittgemeyer, M.
(2010). Anatomical and functional parcellation of the human lateral premotor cortex.
Schulze, H. A. (1960). Zur individuellen cytoarchitektonischen Gestaltung der linken
und rechten Hemisphare im bereiche des Lobulus parietalis inferior. Journal fur
Hirnforschung, 4, 486517.
Seldon, H. L. (1981). Structure of human auditory cortex. I. Cytoarchitectonics and
dendritic distributions. Brain Research, 229, 277294.
Sereno, M. I., Dale, A. M., Reppas, J. B., Kwong, K. K., Belliveau, J. W., Brady, T. J.,
et al. (1995). Borders of multiple visual areas in humans revealed by functional
surface by combining quantitative T1 with retinotopy. Cerebral Cortex, 23, 22612268.
Steinmetz, H., Rademacher, J., Huang, Y. X., Hefter, H., Zilles, K., Thron, A., et al.
(1989). Cerebral asymmetry: MR planimetry of the human planum temporale.
Journal of Computer Assisted Tomography, 13, 9961005.
Stengel, E. (1930). Morphologische und cytoarchitektonische Studien uber den Bau der
unteren Frontalwindung bei Normalen und Taubstummen. Ihre individuellen und
Seitenunterschiede. Zeitschrift fur die gesamte Neurologie und Psychiatrie, 130,
631677.
Stephan, H. (1975). Allocortex. Berlin: Springer.
Stepniewska, I., Preuss, T. M., & Kaas, J. H. (1993). Architectonics, somatotopic
organization, and ipsilateral cortical connections of the primary motor area (M1) of
owl monkeys. Journal of Comparative Neurology, 330, 238271.
Stepniewska, I., Preuss, T. M., & Kaas, J. H. (2006). Ipsilateral cortical connections of
dorsal and ventral premotor areas in New World owl monkeys. Journal of
Strasburger, E. H. (1937). Die myeloarchitektonische Gliederung des Stirnhirns beim
Menschen und SchimpansenI. Journal fur Psychologie und Neurologie, 47,
460491.
Strasburger, E. H. (1938). Vergleichende myeloarchitektonische Studien an der
erweiterten Brocaschen Region des Menschen. Journal fur Psychologie und
Neurologie, 47(461), 565.
Tanji, J. (1994). The supplementary motor area in the cerebral cortex. Neuroscience
Research, 19, 251268.
Tootell, R. B. H., & Hadjikhani, N. (2001). Where is Dorsal V4 in human visual
cortex? retinotopic, topographic and functional evidence. Cerebral Cortex, 11,
298311.
Tootell, R. B., & Taylor, J. B. (1995). Anatomical evidence for MT and additional cortical
visual areas in humans. Cerebral Cortex, 5, 3955.
Ungerleider, L. G., & Haxby, J. V. (1994). What and where in the human brain. Current
Opinion in Neurobiology, 4, 157165.
Ungerleider, L. G., & Mishkin, M. (1982). Two cortical visual systems. In D. J.

Ingle, M. A. Goodale, & R. J. W. Mansfield (Eds.), Analysis of visual behavior
(pp. 549586). Cambridge: MIT Press.
van Essen, D. C., Lewis, J. W., Drury, H. A., Hadjikhani, N., Tootell, R. B.,
Bakircioglu, M., et al. (2001). Mapping visual cortex in monkeys and humans using
surface-based atlases. Vision Research, 41, 13591378.
van Essen, D. C., Ugurbil, K., Auerbach, E., Barch, D., Behrens, T. E., Bucholz, R., et al.
(2012). The human connectome project: A data acquisition perspective.
Vigneau, M., Jobard, G., Mazoyer, B., & Tzourio-Mazoyer, N. (2005). Word and
non-word reading: What role for the Visual Word Form Area? NeuroImage, 27,
694705.
Vogt, O. (1910). Die myeloarchitektonische Felderung des menschlichen Stirnhirns.
Vogt, O. (1911). Die Myeloarchitektonik des Isocortex parietalis. Journal fur
Vogt, B. A. (1985). Cingulate cortex. In In: A. Peters & E. G. Jones (Eds.), Cerebral
cortex (vol. 4, pp. 89149). New York: Plenum Press.
Vogt, B. A. (2009). Architecture, neurocytology and comparative organization of monkey
and human cingulate cortices. In B. A. Vogt (Ed.), Cingulate neurobiology and
disease pp. 6594. New York: Oxford University Press.
Vogt, C., & Vogt, O. (1926). Die vergleichend-architektonische und die vergleichendreizphysiologische Felderung der Grohirnrinde unter besonderer Berucksichtigung
der menschlichen. Naturwissenschaften, 14, 11901194.
von Economo, C., & Horn, L. (1930). Uber Windungsrelief, Masen und
Rindenarchitektonik der Supratemporalflache, ihre individuellen und
Seitenunterschiede. Z Ges Neur Psychiat, 130, 678755.
von Economo, C., & Koskinas, G. N. (1925). Die Cytoarchitektonik der Hirnrinde des
erwachsenen Menschen. Wien, Berlin: Springer.
Vorobiev, V., Govoni, P., Rizzolatti, G., Matelli, M., & Luppino, G. (1998). Parcellation
of human mesial area 6: Cytoarchitectonic evidence for three separate areas.
Walker, A. E. (1940). A cytoarchitectural study of the prefrontal area of the macaque
Wallace, M. N., Johnston, P. W., & Palmer, A. R. (2002). Histochemical identification of
cortical areas in the auditory region of the human brain. Experimental Brain
Research, 143, 499508.
Watson, J. D., Myers, R., Frackowiak, R. S., Hajnal, J. V., Woods, R. P., Mazziotta, J. C.,
et al. (1993). Area V5 of the human brain: Evidence from a combined study using
positron emission tomography and magnetic resonance imaging. Cerebral Cortex,
3, 7994.
453465.
Weiner, K. S., & Grill-Spector, K. (2010). Sparsely-distributed organization of face
and limb activations in human ventral temporal cortex. NeuroImage, 52,
15591573.
Werner, L., Hedlich, A., & Koglin, A. (1986). Zur Klassifikation der Neuronen im
visuellen Kortex des Meerschweinchens (Cavia porcellus). Eine kombinierte GolgiNissl-Untersuchung unter Einsatz von Deinpragnationstechniken. Journal fur
Werner, L., Hedlich, A., & Winkelmann, E. (1985). Neuronentypen im visuellen Kortex
der Ratte, identifiziert in Nissl- und deinpragnierten Golgi-Praparaten. Journal fur
Werner, L., Winkelmann, E., Koglin, A., Neser, J., & Rodewohl, H. (1989). A Golgi
deimpregnation study of neurons in the rhesus monkey visual cortex (areas 17 and
18). Anatomy and Embryology (Berlin), 180, 583597.
Wilms, M., Eickhoff, S. B., Homke, L., Rottschy, C., Kujovic, M., Amunts, K., et al.
(2010). Comparison of functional and cytoarchitectonic maps of human visual areas
V1, V2, V3d, V3v, and V4(v). NeuroImage, 49, 11711179.
Wilms, M., Eickhoff, S. B., Specht, K., Amunts, K., Shah, N. J., Malikovic, A., et al.
(2005). Human V5/MT : Comparison of functional and cytoarchitectonic data.
Anatomical Embryology (Berlin), 210, 485495.
Wise, S. P., & Strick, P. L. (1984). Anatomical and physiological organization of the
non-primary motor cortex. Trends in Neurosciences, 7, 442446.
Wohlschlager, A. M., Specht, K., Lie, C., Mohlberg, H., Wohlschlager, A., Bente, K.,
et al. (2005). Linking retinotopic fMRI mapping and anatomical probability maps of
human occipital areas V1 and V2. NeuroImage, 26, 7382.
Zeki, S. M. (1974). Functional organization of a visual area in the posterior bank of the
superior temporal sulcus of the rhesus monkey. Journal of Physiology, 236,
549573.
Zeki, S. (1980). The response properties of cells in the middle temporal area (area MT)
of owl monkey visual cortex. Proceedings of the Royal Society of London B:
Zilles, K., & Amunts, K. (2012). Architecture of the cerebral cortex. In J. K. Mai & G.
Paxinos (Eds.), The human nervous system (3rd ed., pp. 836895). Amsterdam:
Academic Press.
Zilles, K., Armstrong, E., Schlaug, G., & Schleicher, A. (1986). Quantitative
cytoarchitectonics of the posterior cingulate cortex in primates. Journal of
135
Zilles, K., & Clarke, S. (1997). Architecture, connectivity, and transmitter receptors of
human extrastriate visual cortex. Comparison with nonhuman primates. Cerebral
Cortex, 12, 673742.
Zilles, K., Palomero-Gallagher, N., Grefkes, C., Scheperjans, F., Boy, C., Amunts, K.,
et al. (2002). Architectonics of the human cerebral cortex and transmitter receptor
fingerprints: Reconciling functional neuroanatomy and neurochemistry. European
Zilles, K., Schlaug, G., Geyer, S., Luppino, G., Matelli, M., Qu, M., et al. (1996).
Anatomy and transmitter receptors of the supplementary motor areas in the human
and nonhuman primate brain. In H. O. Luders (Ed.), Supplementary sensorimotor
area (pp. 2943). Philadelphia: Lippincott-Raven.
Zilles, K., Schlaug, G., Matelli, M., Luppino, G., Schleicher, A., Qu, M., et al. (1995).
Mapping of human and macaque sensorimotor areas by integrating architectonic,
transmitter receptor, MRI and PET data. Journal of Anatomy, 187, 515537.
Myeloarchitecture and Maps of the Cerebral Cortex

Aachen, Germany
Glossary
Allocortex Part of the cerebral cortex with more or less than

six cytoarchitectonically defined layers (comprises archiand paleocortex).
Archicortex Phylogenetically old part of the cerebral cortex
comprises the hippocampal region.
Brodmann area (BA) A cytoarchitectonically defined
cortical region as described by Brodmann (1909).
Gennari stripe Heavily myelinated fibers forming a
horizontal stripe in layer IVB of the primary visual cortex.
Inner stripe of Baillarger Horizontal fibers in the
myeloarchitectonic layer 5b (cytoarchitectonic layer Vb).
Isocortex Part of the cerebral cortex with six
cytoarchitectonically defined layers.
Kaes stripe Horizontal fibers in the myeloarchitectonic
layer 3a1 (cytoarchitectonic layer IIIa).
Mesocortex Encompasses the periallocortex and the
proisocortex.
Myelinated fibers Axons ensheated by myelin containing
lamellae formed by oligodendroglial cells.
Myeloarchitecture Regionally specific distribution of the
density, length and course of myelinated fibers in the
cerebral cortex.
Myeloarchitecture: The Roots of the Concept

The study of the myeloarchitecture of the cerebral cortex started
in the eighteenth century with the detection of a white stripe in
the most caudal part of the occipital lobe in fresh postmortem
human brain tissue by the Italian anatomist Gennari (1782).
Without knowing of this discovery, Vicq dAzyr described this
structure again a few years later (Vicq dAzyr, 1786), as did
Soemmerring (1788) for a third time by mentioning Vicq
dAzyrs work. Later on, this structure was called Gennari- or
Vicq dAzyr-stripe. It is a characteristic myeloarchitectonic
feature restricted to the primary visual cortex in human and
nonhuman primate brains.
Meynert (1868) described radially arranged nerve fiber
bundles between the neuronal somata within the cerebral
cortex, which leave the white matter at nearly right angles. He
also illustrated local differences in the thickness and number of
fibers contained in a fiber bundle, as well as the intrusion
depth of the fibers into the cortex. These findings are the first,
but nonsystematic reports on regional and laminar differences
in fiber architecture of the human cerebral cortex.
Neocortex Phylogenetically most recent part of the cerebral

cortex (comprises the isocortex).
Outer stripe of Baillarger Horizontal fibers in the
myeloarchitectonic layer 4 (cytoarchitectonic layer IV).
Paleocortex Phylogenetically old part of the cerebral
cortex comprises the olfactory bulb, (pre)piriform
region, olfactory tubercle, septal, and periamygdalar
regions.
Periallocortex Part of the cerebral cortex between the
allocortex and proisocortex. It comprises the peripaleo- and
periarchicortex.
Periarchicortex Cortical region adjacent to the archicortex
(comprises the entorhinal, perirhinal, retrosplenial,
subgenual areas and the presubiculum and part of the
cingulate region).
Peripaleocortex Cortical region adjacent to the
paleocortex.
Proisocortex Part of the cerebral cortex adjacent to the
isocortex and the periallocortex.
S Area defined by Sanides based on cyto- and
myeloarchitectonic observations.
V Myeloarchitectonic area defined by the Vogt-School.
Campbell (1905) published a combined cyto- and myeloarchitectonic map of the human brain, in which he described
16 cortical areas. It is the first, though largely incomplete
parcellation scheme. For example, Brocas region is not separated from the premotor cortex, and most of the extrastriate
cortex, the inferior parietal lobule, and medial and inferior
temporal as well as occipito-temporal cortex form one huge
homogeneous conglomerate.
Elliot Smith (1907) examined thin, hand-cut, and
unstained sections through various regions of the human cerebral cortex. He studied the regional variations of the Baillarger
stripes (Figure 1; Baillarger, 1840) caused by the light reflection of the myelinated fibers in those stripes, and proposed a
parcellation of the human cortex into approximately 50 areas
which, he stressed, were sharply delineable. This work can be
seen as a first approach to an exclusively myeloarchitectonic
map of the human cerebral cortex (Figure 2).
Kaes (1907) published an atlas in which he depicted
selected cortical regions from both newborn and adult subjects
using the recently developed Weigert staining technique for
the visualization of myelinated fibers. He defined an outer
http://dx.doi.org/10.1016/B978-0-12-397025-1.00209-8
137
138
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Myeloarchitecture and Maps of the Cerebral Cortex
Cytoarchitecture
I
II
Myeloarchitecture
1
1a
1b
1c
1
2
3a1
3a2
III
Outer
principal
zone
3
3b
4
IV
5a
V
5b
6a1
Inner
principal
zone
VIa
6a2
6
VIb
6b1
6b2
Figure 1 Comparison between cytoarchitectonic and

myeloarchitectonic lamination patterns in the isocortex. The
cytoarchitecture shows the typical six-layered appearance. In this case,
the layers are labeled by Roman numerals. The myeloarchitecture
provides a more differentiated laminar pattern with 13 sublayers
(Vogt & Vogt, 1919; nomenclature after Brodmann, 1914). 1, lamina
tangentialis; 1 , pars supratangentialis (afibrosa); 1a, pars superficialis;
1b, pars intermedia; 1c, pars profunda; 2, lamina dysfibrosa; 3,
lamina suprastriata; 3a, pars superficialis; 3a1, stria KaesBechterewi;
3a2, pars typica laminae suprastriatae; 3b, pars profunda laminae
suprastriatae; 4, stria Baillargeri externa (outer stripe of Baillarger); 5a,
lamina interstriata; 5b, stria Baillargeri interna (inner stripe of Baillarger);
6, lamina infrastriata; 6a1, lamina substriata; 6a2, lamina limitans
externa; 6b1, lamina limitans interna; 6b2, zona corticalis albi gyrorum.
Layers 13 represent the outer principle, and layers 46 the inner
principle zone of Kaes (1907). Modified from Brodmann, K. (1914).
Physiologie des Gehirns. In von Bruns, P. (ed.) Neue Deutsche Chirurgie
(pp. 85426). Stutgart: Verlag von Ferdinand Enke.
principal zone resembling the cytoarchitectonic layers IIII,

and an inner principal zone resembling layers IVVI. Furthermore, he described a more protracted maturation of the outer
compared to the inner principal zone. This is interesting, given
the fact that cortico-cortical connections mainly terminate and
originate in the outer principal zone, whereas projections to
subcortical targets mainly originate from the inner principal
zone. For a more detailed discussion of these early attempts,
see an excellent review by Nieuwenhuys (2013).
It was Oskar and Cecile Vogt together with their collaborators who systematically developed a comprehensive myeloarchitectonic research program. It had the final goal of a
complete map of the human cerebral cortex, which would

not only provide a structure-based myeloarchitectonic parcellation but would integrate this approach together with own
functional observations in monkeys (Vogt & Vogt, 1907,
1919), studies of the neurosurgeon Otfried Foerster in humans
(Foerster, 1931, 1936) and the cytoarchitectonic observations
of Brodmann (1909, 1914) into a multimodal concept of
human brain organization. Despite of huge problems caused
by the consequences of the First World War (see Vogt & Vogt,
1919) and the prosecution by the Nazi regime resulting in the
loss of their research institute in Berlin, Oskar and Cecile Vogt
and their collaborators published a rich amount of data. However, they never succeeded in providing a complete myeloarchitectonic map of the human cerebral cortex. Nieuwenhuys,
Broere, and Cerliani (2014) recently published an interesting
approach to reconstruct a complete myeloarchitectonic map of
the human cerebral cortex based on the various maps of parts
of the brain published by the Vogt-School.
Basic Features of Myeloarchitecture

The term myeloarchitecture was introduced by Oskar Vogt
(1903). Myeloarchitectonic analyses describe the packing density, direction, thickness and length of myelinated nerve fibers
within the cerebral cortex. These fibers mainly take a tangential
or radial direction, and obliquely running fibers are comparatively rare.
Radial fibers can be seen as single fibers of different calibers,
but mostly form bundles. They can be followed up to the
border between the middle and upper third of the third cortical
layer in neocortical areas (euradiate myeloarchitecture;
Table 1). In contrast, they end in deeper layers (infraradiate)
or reach even more superficial layers (supraradiate; Table 1) in
allocortical areas.
Tangential fibers run parallel to the cortical surface
(Figure 1) and differ in their laminar distribution and visibility
between cortical areas. Two major tangential fiber layers are the
outer (in cytoarchitectonic layer IV and myeloarchitectonic
layer 4) and inner (in cytoarchitectonic layer Vb and myeloarchitectonic layer 5b) Baillarger stripes. These stripes can
be more or less clearly visible, or both stripes can be fused
(unitostriate or conjunctostriate; Table 1). Further variations
are listed in Table 1. It is also found, that both stripes are
equally dense (equodensus), or one of them is denser than
the other (externodensior or internodensior; Table 1). An
additional tangential stripe, that is, the KaesBechterew, is
found in upper cytoarchitectonic layer III (myeloarchitectonic
layer 3a1; Figure 1). It is found preferentially in primary and
surrounding unimodal sensory areas. A tangential stripe in
layer 1a is mainly visible in primary sensory areas and the
motor cortex; multimodal association areas do not have such
a conspicuous superficial stripe.
Depending on all these criteria, which have been described
in detail by Vogt and Vogt (1919), myeloarchitectonic brain
mapping was performed. A short summary of the extremely
detailed descriptions of the Vogt-School focused on the most
important criteria is given in Table 1 and illustrated in
Figures 36.
prcB
prcA
pocA
pocB
parsB
frsa
frs
frint
frA
pariA
pariC
peristr
frC
parsA
pariB
fri
B
fri
prfr
frB
139
tempsup
parocc
orb
parstr
tempmed
temppol
str
tempinf
partemp
tempocc
prcB
pocA+B
prcA
frs
frsa
frA
frD
callC
parsB
callA
callB
vh
parsA
parspl
peristr
parstr
prfrB
callD
N.A. suh
prfr
str
pyr
partemp
temppol
pardent
peristr
parstr
Figure 2 Myeloarchitectonic map of the human brain. a, visuo-auditory band; b, visuo-sensory band; callA, area callosa A; callB, area callosa B;
callC, area callosa C; callD, area callosa D; frA, area frontalis A; frB, area frontalis B; frC, area frontalis C; frD, area frontalis D; fri, area frontalis inferior;
friB, area frontalis inferior B (posterior inferior frontal); frint, area frontalis intermedia; frs, area frontalis superior; frsa, area frontalis superior
anterior; N.A., ncl. amygdalae; orb, area orbitalis; pardent, area paradentata; pariA, area parietalis inferior A; pariB, area parietalis inferior B; pariC, area
parietalis inferior C ( area parasylvica); parocc, area parieto-occipitalis; parsA, area parietalis superior posterior (A); parsB, area parietalis superior
anterior (B); parspl, area parasplenialis; parstr, area parastriata; partemp, area paratemporalis; peristr, area peristriata; pocA, area postcentralis A; pocB,
area postcentralis B; prcA, area praecentralis A; prcB, area praecentralis B; prfr, area praefrontalis; prfrB, area praefrontalis B; pyr, area pyriformis;
str, area striata; suh, subiculum hippocampi; tempinf, area temporalis inferior; tempmed, area temporalis medialis; tempocc, area temporo-occipitalis;
temppol, area temporalis polaris; tempsup, area temporalis superior; vh, vesticia hippocampi; X, modification of area postcentralis B (lining the
upper lip of the cingulate sulcus); Y, modification of area postcentralis A (surrounding the lower portion of the central sulcus); Z, modification of area
postcentralis A (infringing onto the Sylvian fissure). Modified from Elliot Smith, G. (1907). A new topographical survey of the human cerebral cortex,
being an account of the distribution of the anatomically distinct cortical areas and their relationship to the cerebral sulci. Journal of Anatomy and
Physiology, 41, 237254.
Myeloarchitecture of Cortical Areas

Myelo- and cytoarchitectonic laminar patterns provide different perspectives of cortical organization (Figure 1). Both features permit a parcellation of the cerebral cortex into numerous
areas and thus allow a microstructurally/microscopically based
brain mapping.
Using cyto- and/or myeloarchitectonic methods, the cerebral
cortex can be divided into two major subdivisions, the isocortex
and the allocortex, based on differences in lamination patterns
(Brodmann, 1909; Vogt, 1903; Vogt & Vogt, 1919). The transition zone between both is constituted by the mesocortex, which
encompasses the periallocortex and the proisocortex
(Brockhaus, 1940; Stephan, 1975). Isocortical ( neocortical)
areas have a six-layered cytoarchitectonic lamination with the
notable exception of the motor cortex, which lacks a clearly
visible layer IV in adult stages. Allocortical areas ( paleo- and
archicortical areas) have more or less than six layers. The isocortex comprises all cortical regions characterized myeloarchitectonically by an euradiate structure (Vogt & Vogt, 1919). The
140
Table 1
Most important terms for myeloarchitectonic descriptions
Presence of Baillarger (layers 4 and 5b) stripes

Astriate
Baillarger stripes cannot be delineated due to the
very high fiber density in layers 5a and 6a1
Occurrence: large parts of the precentral gyrus
Propeastriate
A modification of the astriate type, because of a
slight decrease of the fiber density in layers 5a
and 6a1, that is, the cortex is nearly astriate
Occurrence: parts of the precentral gyrus,
inferior parietal lobule, parts of the superior
temporal gyrus
Propeunistriate
The outer Baillarger stripe is well demarcated,
the inner stripe is less obvious, but better
visible than in the unistriate type, since layer 6a
is less dense than 5b. Fiber density in layer 5a
is slightly lower than in the propeastriate type
Occurrence: dorsal part of the medial frontal
gyrus, parts of transverse and superior
temporal gyri
Bistriate
Both Baillarger stripes clearly detectable because
of lower fiber densities in layers 5b and 6a1
Occurrence: frontal pole, medial frontal gyrus,
parts of the transverse temporal gyrus,
postcentral gyrus, superior parietal lobule,
parts of extrastriate visual cortex
Unistriate
A distinct outer Baillarger stripe is visible, but the
inner stripe cannot be delineated from layer 6
due to high fiber density in sublayer 6a1
Occurrence: superior frontal gyrus, parts of
precentral gyrus, medial orbital region,
anterior cingulate cortex, inferior temporal
gyrus
Unitostriate
Both Baillarger stripes appear to be fused to a
(conjunctostriate)
broad band, due to an increased fiber density
in layer 5a (accompanied by a more or less
prominent thinning of this layer) and a lightly
stained layer 6a
Occurrence: lateral orbital region, posterior
part of the inferior frontal gyrus, parts of
extrastriate visual cortex
Singulostriate
The inner Baillarger stripe is lacking
Occurrence: temporopolar region, primary
visual cortex
Myelin density in Baillarger stripes
Equodensus
Both Baillarger stripes are equally dense
Externodensior
Outer Baillarger stripe denser than inner stripe
Internodensior
Inner Baillarger stripe denser than outer stripe
Intrusion depth of radiate bundles into the cortical ribbon
Euradiate
Radiate bundles reach upper border of layer 3b
Infraradiate
Radiate bundles reach upper border of layer 5b
Supraradiate
Radiate bundles extend into layers 12
Source: Vogt, C., & Vogt, O. (1919). Allgemeinere Ergebnisse unserer Hirnforschung.
Journal fur Psychologie und Neurologie, 25, 279462; Vogt, O. (1910). Die
myeloarchitektonische Felderung des menschlichen Stirnhirns. Journal fur Psychologie
allocortex shows a supraradiate or infraradiate lamination (Vogt

& Vogt, 1919). In the following, Brodmann areas are labeled by
BA followed by Arabic numerals and areas defined by the VogtSchool are labeled by V and/or Arabic numerals.
In this section, we will describe examples of cortical areas
which present typical myeloarchitectonic characteristics
enabling the parcellation of the cerebral cortex and thus
creation of brain maps, as shown in the following section.

Primary motor area BA4/V42 (Figures 3(a) and 4(a)) is astriate, thus lacking discernible inner and outer Baillarger stripes,
as well as a KaesBechterew stripe. This euradiate area has a
very high myelin density, particularly in the granular and
infragranular layers. The density in layer 6 is so high, that the
fibers can be seen as separate structures only in the microscope
with very bright illumination (situation shown for a small part
of layers 5b and 6 in the inset at the left lower corner of
Figure 4(a)). The border between layer VI and the white matter
can only be reliably defined in cytoarchitectonic sections,
where layer VI can be recognized by the typical polymorphic
cell bodies. This makes an automatic segmentation of the
motor cortex in MR images extremely difficult, and frequently
leads to an underestimation of the anatomically correct cortical
thickness, particularly of the primary motor cortex, since the
mostly used MR sequences mainly reflect myelin density.
Primary somatosensory area 3b/V69 (Figures 3(b) and
4(b)) is a typical euradiate isocortical area with two Baillarger
stripes (bistriate), of which the inner stripe is denser than the
outer one (internodensior; Batsch, 1956; Hopf, 1954b). The
bistriate area V67 is located between the primary motor cortex
(V42) and area 3b (V69) and corresponds to area 3a. The border
between V69 and BA1/V70 is clearly visible due mainly to the
appearance of the KaesBechterew stripe in the latter area. V70 is
also bistriate, but both Baillarger stripes are equally dense and
the outer stripe is broader than the inner one (Batsch, 1956;
Hopf, 1954b). The caudally adjoining V71/BA2 differs from
V70 by a denser outer Baillarger stripe (Hopf, 1954b).
The euradiate primary auditory area BA41/Te1
(Figures 3(c) and 4(c)) shows local variations of its myeloarchitectonic structure. The bundles of radial fibers are conspicuously thick in BA41 (region ttr.1 of Hopf (1954a, 1955)).
At some places a fusion of both Baillarger stripes is visible, and
thus leads to a classification as being a unito- or conjunctostriate area (Vogt & Vogt, 1919). A later study demonstrated a
propeuni- to bistriate nature and an internodensior to equodensus structure at other sites within the transverse temporal
gyrus (Hopf, 1954a, 1955). Consistently throughout all subdivisions of Te1, a slight increase of tangential fibers in layer 3a
is visible, resembling the KaesBechterew stripe. The myeloarchitectonic variability within BA41/Te1 seems to reflect
similar cyto- and receptorarchitectonic heterogeneities, which
may indicate functional segregations and eventually tonotopies (Morosan, Rademacher, Palomero-Gallagher, & Zilles,
2004; Morosan et al., 2001). Secondary auditory area BA42/
Te2 (Figure 3(d)) takes an intermediate position between
BA41 and the laterally adjoining area Te3 on the superior
temporal gyrus. Te2 is of the propeuni- to bistriate type
(Hopf, 1954a, 1955). Area Te3 (part of BA22; Figure 3(e))
has a similar myeloarchitecture, but a more bistriate appearance than Te2, with a conspicuous KaesBechterew stripe
(extremostriate; Vogt & Vogt, 1919). A major difference
between the three auditory areas Te1, Te2, and Te3 is the
relation between the thickness of layers 13b and layers 46,
which is relatively smaller in Te1 than in the other two areas,
indicating an increasing space for cortico-cortical connections.
Temporo-polar area BA38 (Figure 3(h)) is a typical singulostriate myeloarchitectonic area because it completely lacks an
inner Baillarger stripe (Hopf, 1954a, 1955).
1
2
3a
1
2
3a
3b
3b
3c
1
2
3a
3a
3a
3b
3b
4
3b
5a
5a
5a
5a
1
2
1
2
5b
5b
5b
5a
5b
5b
6
BA4
V42
(a)
6
BA41
Te1
(c)
3b
V69
(b)
1
2
3a
3b
1
2
BA42
Te2
(d)
BA22
Te3
(e)
1
2
1
2
3a
1
2
3
4
3a
3a
4a
3b
3b
4b
3b
5a
4c
5a
5b
5
5b
5
6
6
BA17
hOc1
(f)
BA18
hOc2
(g)
BA38
temp.pol.
(h)
BA24
V19
(i)
BA29
Vl3
(j)
Figure 3 Drawings of representative iso- and periallocortical areas

showing myelinated fibers and their lamination pattern (modified from
Vogt, C., & Vogt, O. (1919). Allgemeinere Ergebnisse unserer
Hirnforschung. Journal fur Psychologie und Neurologie, 25, 279462).
The cortical thickness of the different areas has been normalized.
Arabic numerals indicate myeloarchitectonic layers (see Figure 1). (a)
Primary motor cortex (BA4/V42), (b) primary somatosensory cortex
(area 3b/V69), (c) primary auditory cortex (BA41/Te1), (d) secondary
auditory cortex (BA42/Te2), (e) superior temporal gyrus (BA22/Te3),
(f) primary visual cortex (BA17/hOc1), (g) secondary visual cortex
(BA18/hOc2), (h) temporal pole (BA38/temp.pol.), (i) anterior cingulate
cortex (BA24/V19), and (j) retrosplenial cortex (BA29/Vl3). BA,
Brodmann areas (Brodmann, 1909); hOc1 and hOc2,
cytoarchitectonically defined human visual areas (Amunts, Malikovic,
Mohlberg, Schormann, & Zilles, 2000); Te1 and Te2,
cytoarchitectonically defined human auditory areas (Morosan et al.,
2001); Te3, cytoarchitectonically defined human unimodal higher
auditory area (part of BA22; Morosan, Schleicher, Amunts, & Zilles,
2005), V, Vogt areas (Vogt & Vogt, 1919).
Primary visual area BA17/hOc1 (Figures 3(f) and 5(a)) is

dominated by the Gennari stripe, that is, the outer Baillarger
stripe. Therefore, Sanides and Vitzthum (1965b) and Braak
(1980) classified BA17 as singulostriate, but an inner Baillarger
stripe was also illustrated in a drawing by Vogt and Vogt (1919),
see Figure 3(f). This latter finding would lead to a characterization of BA17/hOc1 as bistriate and externodensior. Revisiting
141
the original sections from the Vogt Lab (Figure 5(a)), we can
support the definition of Sanides and Vitzthum (1965b) and
Braak (1980) of BA17 as singulostriate area. The secondary
visual area BA18/hOc2 (Figures 3(g) and 5(b)) shows a conjunctostriate myeloarchitecture with a clearly visible Kaes
Bechterew stripe. The border region between BA17/hOc1 and
BA18/hOc2 found considerable interest in the mapping literature (Amunts et al., 2000; Clarke & Miklossy, 1990; Sanides &
Vitzthum, 1965a, 1965b; von Economo & Koskinas, 1925; Zilles
& Clarke, 1997), because it is an example for gradual changes of
cortical architecture at border regions and their functional relevance for brain mapping. It has been shown, that this border
region is a target site of transcallosal fibers and has a peculiar
myeloarchitecture (Figure 5(c) and 5(d)) consisting of a border
tuft (Grenzbuschel; Sanides & Vitzthum, 1965a) and a fringe
area (Randsaum; Sanides & Vitzthum, 1965a). In cytoarchitectonic studies, von Economo and Koskinas (1925) described an
area OBg, which is part of BA18 adjoining the border region, but
probably larger than the border tuft segment (Amunts et al.,
2000). Fiber tracking studies are necessary to solve the question
how cyto- and myeloarchitectonic features correlate with the
distribution of transcallosal fibers.
Regions of the superior (Figure 4(d)) and inferior
(Figure 4(e)) parietal cortex are shown here as examples for
multimodal association areas. On the dorsolateral surface, the
areas of the superior parietal lobule have a bistriate myeloarchitecture, with a slightly wider and denser external Baillarger
stripe compared to the internal stripe (Batsch, 1956; Hopf,
1969; Vogt, 1911). In contrast to the superior parietal region,
the inferior parietal areas have a propeastriate structure
(Table 1) with finer radial fibers and bundles (Batsch, 1956;
Hopf, 1969; Vogt, 1911). Various subregions within both parietal lobules have been delineated on the basis of detailed
myeloarchitectonic features (see in the succeeding text).
Cortex on the lateral surface of the gyrus rectus (Figure 5(f))
is unistriate and the radial fibers stop within layer 3b. This
is an intermediate feature between the classical infra- and euradiate types, called medioradiate by Strasburger (1937). This
reflects the position of the orbital cortex between the proisocortex and the fully differentiated euradiate isocortex.
Figure 3(i) shows a periallocortical region, the anterior
cingulate area BA24/V19. Here, the radial fibers do not reach
the border between layers 3a and 3b, but stop mainly between
layers 5a and 5b. Only a few fibers ascend to the border between
3b and 4. BA24 is, therefore, an infraradiate and unistriate area
with a well recognizable inner Baillarger stripe (Strasburger,
1937). Periallocortical retrosplenial area BA29/Vl3
(Figure 3(j)) is an example of the supraradiate myeloarchitectonic type with a dense stripe of tangential fibers in layer 4.
Notably, a very dense and rather homogeneous agglomeration
of tangential fibers is found in layer 1 of BA29/Vl3, though
without the usual subdivision into sublayers of different fiber
densities typical of isocortical areas. This appearance of layer 1
is a characteristic feature also found in all allocortical regions.
Because of its periallocortical structure, the laminar terminology cannot be directly compared with that of isocortical areas.
Figure 6 shows examples of allocortical regions in the frontal
lobe. Areas V13 and V14a,b are myeloarchitectonic correlates of
areas BA25. They are characterized by the typical supraradiate
structure of the allocortex (clearly visible in V13 and V14a,b)
142
Figure 4 Myelin stained (WeigertKulschitzky method; celloidin embedding) sections through primary motor ((a); BA4), primary somatosensory ((b);
area 3b), primary auditory ((c); Te1), superior (d) and inferior (e) parietal cortex, and gyrus rectus (f) of human brains. Arabic numerals indicate
myeloarchitectonic layers. Original sections form the C & O Vogt Brain Collection, University of Dusseldorf, Germany, are shown. (a), (b), (d), and (e)
come from the right hemisphere of brain A39. (c) is from the right hemisphere of brain A38 and (f) from the left hemisphere of brain A37.
as well as the undifferentiated layer 1 with an increasing myelin

density toward the allocortical core (V14a).
Brain Maps Based on Myeloarchitecture

Frontal Lobe
The first detailed myeloarchitectonic map of the frontal lobe
appeared more than 100 years ago (Vogt, 1910; Figure 7). It
contains 66 mainly euradiate areas which are grouped into six
major regions defined by the visibility of the Baillager stripes,
length and thickness of the radiate fibers.
The first region is unistriate and characterized by thin fibers.
It consists of areas V1V14. Areas V1 and V2 are found on the
orbitofrontal surface, but cannot be clearly assigned to Brodmann areas. Area V3 is part of BA32. Areas V4V9 and the
ventral parts of areas V10V12 are best comparable to the
medial part of the orbitofrontal cortex (Table 2). Areas V13

and V14 resemble the subcallosal area BA25.
The second unistriate infraradiate region consists of areas
V15V32. All these areas, with the exception of V15 and V16,
which correspond to BA33, are subdivisions of BA24. The
dorsal part of area V12 corresponds to the subgenual area s24
(Palomero-Gallagher et al., 2008), and areas V17, V18, V21,
V22, V25, V26, V29, and V30 to pregenual area p24 (PalomeroGallagher et al., 2008). Areas V19, V20, V23, V24, V27, V28,
V31, and V32 are the myeloarchitectonic correlates of the
cytoarchitectonicaly defined midcingulate area 240 (Vogt &
Vogt, 2003).
The third unistriate region of the frontal lobe, with thick
fibers, consists of areas V33V43. Areas V42 and V43 correspond
to the primary motor cortex BA4, which contains the giant Betz
pyramidal cells. Areas V36V41 are parts of the frontomotor
zone of Sanides (1962) and may be comparable to BA6. The
parcellation of BA6 is further supported by cytoarchitectonic
143
Figure 5 Myelin stained (WeigertKulschitzky method; celloidin embedding) sections through the primary (a) and secondary (b) human visual cortex.
(c) and (d) show the border region between hOc1 (BA17) and hOc2 (BA18). Gb, border tuft (Grenzbuschel; Sanides & Vitzthum, 1965a); Rs,
fringe area (Randsaum; Sanides & Vitzthum, 1965a). Arabic numerals indicate myeloarchitectonic layers. Solid arrowheads indicate the border between
primary and secondary visual cortex. Open arrowheads delineate the fringe area and the border tuft region. Original sections form the C & O Vogt
Brain Collection, University of Dusseldorf, Germany, are shown. (a), (b), and (d) are from the right hemisphere of brain A18, and (c) from the
left hemisphere of brain A38.
V13
1
2
3a
3b
4
5a
5b
V12
V14b
V14a
Figure 6 Drawing of representative periallocortical areas showing myelinated fibers and their lamination pattern in a horizontal section through the
subcallosal region. Arabic numerals indicate myeloarchitectonic layers. Modified from Vogt, C., & Vogt, O. (1919). Allgemeinere Ergebnisse unserer
Hirnforschung. Journal fur Psychologie und Neurologie, 25, 279462.
studies of human and macaque brains (Matelli, Luppino,

& Rizzolatti, 1991; Vorobiev, Govoni, Rizzolatti, Matelli, &
Luppino, 1998; Zilles et al., 1996). The mesial prefrontal cortex
rostral to BA4 was subdivided on the basis of architectonic and
stimulation studies (Foerster, 1936; Vogt & Vogt, 1919) into
areas 6aa and 6ab. This finding in the human cortex was further
substantiated by anatomical, connectional, and functional studies in macaque monkeys leading to the concept of a subdivision
of mesial BA6 into a supplementary motor area (SMA proper,
comparable to 6aa) and a presupplementary motor area
144
Figure 7 Myeloarchitectonic map of the human frontal lobe. (a) Lateral view, (b) medial view, (c) dorsal view, and (d) ventral view. Prefrontal
areas rostral to areas V36, V39, and V40 are not shown in the dorsal view. Arabic numbers indicate Vogts myeloarchitectonically defined areas. a,
ascending branch of the lateral fissure; ce, central sulcus; cg, cingulate sulcus; d, diagonal sulcus; h, horizontal branch of the lateral fissure; if, inferior
frontal sulcus; tol, olfactory tuberculum. Modified from Vogt, O. (1910). Die myeloarchitektonische Felderung des menschlichen Stirnhirns.
Table 2
Comparison of various nomenclature systems used in brain mapping with the Brodmann (1909, 1914) classification
Brodmannn
Vogt and Vogt,

Sanides
von Economo and

Koskinas
BA1
BA2
V70
V71, V72 (?)
BA3
BA17
BA18
BA19
V67
V69
V42, V43
V75
V36V41
V83, V85, V86, V87
(?)
Comparability not
clear
Comparability not
clear
V50, V51; S50, S51d,
S51p, S52d, S52v
V1, V4V9, V10V12
(ventral parts)
Area striata
Area occipitalis
Area praeoccipitalis
PC, PCg (?)

PD, PED (contains
parts of BA2)
PA1
PB1, PB2
FA, FAg
PA2, PCg (?)
FB
PE, PED (contains
parts of BA7)
FC (?)
BA20
BA21
n.d.
n.d.
TE2
TE1
BA22
BA23
BA24
n.d.
V77V80, V91V96
V17V32, V12
(dorsal part)
V13, V14
Vl3
Vl areas except Vl3
V76, V81, V82, V84
V3, V33V35,
V10V11 (dorsal
parts)
V15, V16
n.d.
TA1, TA2
LC2, LC3
LA1, LA2, LA3
BA4
BA5
BA6
BA7
BA8
BA9
BA10
BA11, BA12
BA25
BA29
BA30
BA31
BA32
BA33
BA37
BA38
BA39
BA40
BA41
BA42
BA43
BA44
BA45
BA46
145
V38
V90
Parts of V73 and
V74; V88, V89
Area temporalis
transversa interna
Area temporalis
transversa externa
V68; V73V74
(parts), V72 (?)
V56, V57
V58, V59 (dorsal
part); S58, S59d
V53, V54; S53d, S54,
SZ (above s53d in
Figure 8(d))
Nieuwenhuys et al.
Julich/Dusseldorf Group
70
71, 72 (?)
1
2
67
69
42, 43
75
3641
83, 85, 86, 87 (?)
3a
3b
4a, 4p
5L, 5M, 5Ci
6 (preliminary delineation)
7A, 7P, 7PC, hIP3
Comparability not clear
n.d.
FD (?)
n.d.
FE
49 (?), 50 (rostral part),

51, 52 (?)
1, 46, 8, 9, 11 (caudal
part)
BA17
BA18
103119
Fp1, Fp2
FG, FH
OC
OB (OBg, OBO)
OA (OA1, OA2,
OAm)
167, 168
162165, comparability
not clear in the
posterior region of
BA21
136139, 158161
7780, 91-96
12, 1732
n.d.
hOc1
hOc2
hOc3d, hOc3v, hOc4d, hOc4v, hOc5 (areas located
within the region of BA19 and lateral BA37) and other
areas. Note, that a homogenous cytoarchitectonic or
functional area 19 does not exist
n.d.
n.d.
Te3, Te4 (areas within BA22)

23d, 23c, d23, v23
s24, p24a, p24b, pv24c, pd24cv, pd24cd, a24a0 , a24b0 ,
24c0 v 24c0 d, p24a0 , p24b0 , p24dv, p24dd
25a, 25p
29l, 29m
30
31
s32, p32, 320
FL, FM
LE1
LD
LC1
FCL, FDL, FEL, FHL
13, 14
n.d.
n.d.
76, 81, 82, 84
3, 10, 11 (rostral part),
3335 (ventral parts)
LB1
PH, PHO, PHP,
PHT
TG, TGA
PG
Parts of PFop, PFt,
PFcm, PF, PFm
TC
15, 16
33
Fg1, Fg2 (on the fusiform gyrus as parts of medial PH)
120132
90
88, 89
n.d.
PGa, PGp
OP 1, OP2, PFop, PFt, PFcm, PF, PFm
145153
Te1 (Te1.0, Te1.1, Te1.2)
TB
154157
Te2 (Te2.1, Te2.2)
PFD, parts of PFop
68, 72 (?)
OP 3, OP 4
FCBm
FDg
56, 57
58
44d, 44v
45a, 45p
FD
53 (dorsal part)
n.d.
(Continued)
146
Table 2
(Continued)
Brodmannn
BA47
Regio insularis
anterior and
posterior
Vogt and Vogt,

Sanides
von Economo and

Koskinas
S53v, S59v
Vi1Vi6, Vai1Vai4,
Vai6, Vai7
FF
IA1, IA2, IAB, IB,
IBT IC, ID
Nieuwenhuys et al.
Julich/Dusseldorf Group
59
97102
n.d.
Ig1 and Ig2 (dorsal part of Vi5), Id1 (Vai6)
The nomenclatures of Brodmann (1909, 1914; BA areas), von Economo and Koskinas (1925), and the Dusseldorf/Julich Group (references below) are based on cyto- and
receptorarchitectonic studies. The maps of the Julich/Dusseldorf group are shown in the JuBrain atlas (www.fz-juelich.de/inm/inm-1/jubrain_cytoviewer) and can be applied by means
of the SPM Anatomy Toolbox (www.fz-juelich.de/inm/inm-1/spm_anatomy_toolbox). The nomenclature of Vogt (1910) and Vogt and Vogt (1919) (V areas) is based on
myeloarchitectonic, that of Sanides (1962) (S areas) on combined cyto- and myeloarchitectonic observations. The Nieuwenhuys et al. (2014) study is a metaanalysis of the
myeloarchitectonic studies of the Vogt-School. n.d. not determined, ? unclear comparability.
References Dusseldorf/Julich Group: Amunts et al. (1999, 2000, 2010), Amunts, Schleicher, and Zilles (2004), Bludau et al. (2014), Caspers, Zilles, et al. (2013), Caspers et al. (2006,
2008), Eickhoff, Schleicher, Zilles, and Amunts (2006), Eickhoff, Amunts, Mohlberg, and Zilles (2006), Geyer et al. (1996), Geyer, Schleicher, and Zilles (1999), Geyer (2004), Grefkes,
Geyer, Schormann, Roland, and Zilles (2001), Kujovic et al. (2013), Kurth et al. (2010), Malikovic et al. (2007), Morosan et al. (2001, 2005), Palomero-Gallagher, Mohlberg, Zilles,
and Vogt (2008), Palomero-Gallagher and Zilles (2009); Rottschy et al. (2007); Scheperjans, Grefkes, Palomero-Gallagher, Schleicher, and Zilles (2005), Scheperjans, PalomeroGallagher, Grefkes, Schleicher, and Zilles (2005), Scheperjans, Hermann, et al. (2008), Scheperjans, Eickhoff, et al. (2008).
(pre-SMA, comparable to area 6ab; Luppino, Matelli, Camarda,

Gallese, & Rizzolatti, 1991; Matelli et al., 1991; Rizzolatti,
Luppino, & Matelli, 1996). Later this subdivision was demonstrated in the human cortex by cyto- and receptorarchitectonic
studies (Vorobiev et al., 1998; Zilles et al., 1996). Thus, V38 and
V39 on the mesial surface are probably comparable to SMA
proper, whereas V36 and V37 on the mesial surface may be
equivalents of pre-SMA. In conclusion, the myeloarchitectonic
parcellation by Vogt and Vogt (1919) clearly points to a considerable structural differentiation of the motor and premotor
cortex which was missed in the cytoarchitectonic maps of
Brodmann (1909), while von Economo and Koskinas (1925)
were aware of such a differentiation. Areas V33V35 of the third
region are parts of BA32 (Vogt et al., 2013).
The fourth region is propeunistriate and contains areas
V44V50. Most of these areas belong to the paramotor zone
of Sanides (1962). The comparability with the Brodmann and
von Economo and Koskinas schemes is not clear, although
Sanides (1962) defined his areas 54 and 55 as parts of BA9.
The fifth region of Vogt (1910) and Vogt and Vogt (1919) is
bistriate and contains areas V51V56. It is a huge field and a
functionally extremely segregated region in the frontal lobe
which covers parts of BA9, BA10, BA46, and BA44. Sanides
(1962) therefore proposed a new grouping of areas based on
his combined cyto- and myeloarchitectonic studies. On the
lateral surface of the hemisphere, his frontopolar zone containing areas V50, V51, and the small rostral part of V52 (Figure 7),
and his areas S50, S51d, S51p, S52d, S52v, and SZ (between
areas S51d and S51p; Figure 8), is best comparable to BA10.
His paropercular zone encompasses areas V53V55 (Figure 7)
and his areas S53d, S53v, S54, and S55 (Figure 8). Areas S53d
and S54 are best comparable to BA46. The frontoopercular
zone of Sanides (1962) on the lateral surface covers his areas
S56S58, S59d, S59v, and S65 (Figure 8) and includes areas
V56V59 and V65 (Figure 7). Areas V56 and V57 are comparable to BA44, areas V58 and the dorsal portion of V59 to
BA45. Subdivisions of BA44 and BA45 are supported by a
recent receptorarchitectonic study (Amunts et al., 2010) in
which the distribution patterns of multiple transmitter receptors revealed a subdivision of BA44 into areas 44v (comparable
to V56) and 44d (comparable to V57), and of BA45 into 45a

(comparable to the dorsal portion of V59 or to S59d) and 45p
(comparable to V58). Furthermore, the sulcal pattern in the
Broca region (Amunts et al., 1999) shows that the diagonal
sulcus or the ascending branch of the lateral fissure can be the
anterior border of BA44 depending on intersubject variability.
The ventral border of BA45 or area 45a is close to the horizontal branch of the lateral fissure, but can transcend this fissure
ventrally as shown in cyto- and receptorarchitectonic observations (Amunts et al., 1999, 2010; Brodmann, 1909).
The sixth region defined by Vogt (1910) is unitostriate and
contains areas V57V66. As described above, V57, V58, and the
dorsal portion of V59 are parts of Brocas region, whereas the
ventral part of V59 and V60V64 and V66 belong to the lateral
orbital cortex. The ventral parts of V53 and V59 are best comparable to BA47 (Table 2). V65 is located immediately below
the horizontal branch of the lateral fissure on the frontal
operculum. This site has been identified in a receptorarchitectonic study as an opercular area belonging to the Broca region
(Amunts et al., 2010). It is surrounded by areas 45a and BA47.
Sanides (1962, 1964) described large spindle-like neurons
in V66 which are probably the recently widely discussed von
Economo neurons (Allman, Watson, Tetreault, & Hakeem,
2005; Allman et al., 2010; Nimchinsky, Vogt, Morrison, &
Hof, 1995).
A comparison of the myeloarchitectonic maps of the
human frontal lobe by Vogt (1910), Vogt and Vogt (1919),
Strasburger (1937), Hopf (1956), and Sanides (1962) shows
major similarities, but also some discrepancies (Figures 7 and
8). For example, an area 52 is found by Strasburger (1937) and
Sanides (1962) on the orbital surface (Figure 8(g) and 8(h)),
but not by Vogt (1910). Furthermore, Vogt and Sanides show
an area V52 (Figure 7(a)) or S52d (Figure 8(b)) on the lateral
surface, but not Strasburger (Figure 8(a)). An area V34 was
described by Vogt (1910) (Figure 7(a)) and Strasburger (1937)
(Figure 8(e)), but Sanides (1962) did not find a comparable
area (Figure 8(f)). Also the parcellation of the precentral gyrus
differs between the maps of the four authors (Figures 7(a) and
8(a)8(c)). These differences may be caused in part by the
considerable intersubject variability between human brains
147
Figure 8 Comparison between the maps of the human frontal lobe modified after Strasburger (Strasburger, E. H. (1937). Die myeloarchitektonische
Gliederung des Stirnhirns beim Menschen und Schimpansen I. Journal fur Psychologie und Neurologie, 47, 460491; (a) lateral view, (e) medial view,
(g) orbital view), Hopf (Hopf, A. (1956). Uber die Verteilung myeloarchitektonischer Merkmale in der Stirnhirnrinde beim Menschen. Journal fur
148
(e.g., Allman et al., 2010; Amunts et al., 1999; Filimonoff,

1932; Zilles & Amunts, 2010), but also by methodical problems of detecting architectonic differences by pure visual
inspection in serially sectioned human brains, which frequently confront the observer with obliquely sectioned cortical
regions. This latter fact makes the identification of cyto- and
myeloarchitectonic criteria very difficult and can lead to falsepositive and false-negative results. A first approach to an
observer-independent registration of myeloarchitectonic features in the human frontal lobe was published by Hopf
(1968b). He measured the myelin density perpendicularly to
the cortical surface photometrically and could corroborate the
distinct myeloarchitectonic characteristics of the different
regions in the human frontal lobe. However, a critical validation of the detailed parcellation into numerous myeloarchitectonic regions and areas as published by Vogt (1910), Vogt and
Vogt (1919), Strasburger (1937), Hopf (1956), and Sanides
(1962) was technically not possible at the time of this study.
Despite of the differences, a general common perspective of
myeloarchitectonic segregation is recognizable in all four maps
of the human frontal cortex. This has been recently reviewed by
Nieuwenhuys et al. (2014), who proposed a comprehensive
myeloarchitectonic map of the whole human cerebral cortex
based on a composition of the various parcellation schemes
published by the different coworkers of Cecile and Oskar Vogt
and a new effort to reconcile the discrepancies between the
maps by using anatomical landmarks.
Parietal Lobe
The myelin density decreases from the postcentral gyrus to the
more posterior regions of the parietal lobe. Furthermore, the
lowest density of myelinated fibers is found in the inferior
parietal lobule (Hopf & Vitzthum, 1957). This example of a
decrease of myelin density from primary sensory to hierarchically higher multimodal association areas also holds true for
other brain regions like the visual and auditory systems as well
as the prefrontal cortex. Also the density and visibility of the
KaesBechterew stripe as well as the thickness of the radial
fiber bundles decrease considerably from the postcentral
gyrus to the superior and, particularly, the inferior parietal
lobule (Hopf & Vitzthum, 1957).
Two myeloarchitectonic maps of the human parietal cortex
have been published by Vogt (1911) (Figure 9(a)9(c)) and
Batsch (1956) (Figure 9(d)9(f)). The myeloarchitectonic
characteristics of areas V67V73, V75, V79, V81, V83,
V85V87, V89, and V90V92 defined by Batsch (1956), as
well as of several of their subdivisions were confirmed by
photometric measurements (Hopf, 1969, 1970).
The somatosensory region consists of areas V67 (area 3a),

V69 (area 3b), V70 (BA1), and V71 (BA2) in both maps and is
found on the postcentral gyrus. At the most ventral end V72 is
described as a transition area between the somatosensory cortex and the parietal operculum. At the dorsal end a larger area
V75 is depicted in both maps, which is comparable to BA5
(Table 2). Batsch (1956) emphasizes that this area can be
further subdivided into superior and inferior parts
(Figure 9(d) and 9(e)). This has been confirmed by a cytoand receptorarchitectonic study (Scheperjans, Grefkes,
Palomero-Gallagher, Schleicher, & Zilles, 2005) where areas
5M and 5L resemble areas 75sup and 75if of Batsch (1956),
respectively (Figure 9(d)9(f)). Additionally, an area 5Ci was
detected in the cortex around the ascending branch of the
cingulate sulcus, which is also part of area 75sup. The function
of area BA5 is largely unknown, but its architectonical structure
argues for a position higher than the somatosensory cortex of
the postcentral gyrus.
The bistriate areas V83, V85V87 (Hopf & Vitzthum, 1957)
belong to the superior parietal lobule (Figure 9) and can be
compared to BA7. Here again, a more recent cyto- and receptorarchitectonical study revealed a highly differentiated parcellation of BA7 into 7A (comparable to V83), 7P (comparable to
V85), as well as 7PC and hIP3 (comparable to V86 and V87;
Scheperjans, Grefkes, et al., 2005; Scheperjans, PalomeroGallagher, Grefkes, Schleicher & Zilles, 2005; Scheperjans,
Hermann, et al., 2008; Scheperjans, Eickhoff, et al., 2008).
Although a number of intraparietal areas are delineated in
the schematic drawings by Batsch (1956), it is presently not
possible to make a homologization between his myeloarchitectonic areas and existing cytoarchitectonic parcellations
(Choi et al., 2006; Scheperjans, Eickhoff, et al., 2008; Scheperjans, Hermann, et al., 2008) and functional data (Bisley &
Goldberg, 2010; Bremmer, 2011; Grefkes & Fink, 2005; Nieder
& Dehaene, 2009) of this region.
The propeastriate areas V88V90 (Hopf & Vitzthum,
1957) belong to the inferior parietal lobule, where areas
V88 and V89 resemble BA40 and V90 is comparable to
BA39 (Figure 9(a) and 9(b) and 9(d)9(e); Table 2).
Batsch (1956) further subdivided these three myeloarchitectonic areas, indicating a more intense structural differentiation than reflected by the Brodmann and Vogt maps
(Brodmann, 1909; Vogt, 1911). This was also shown by
von Economo (Choi et al., 2006; Scheperjans, Eickhoff,
et al., 2008; Scheperjans, Hermann, et al., 2008) and more
recently by Caspers et al. (Caspers et al., 2006; Caspers
et al., 2008; Caspers, Schleicher, et al., 2013) in cyto- and
receptorarchitectonic observations. PFt and PFop are found
within V88, PF, and PFm are located within V89, and PFcm
resembles parts of V74 and V73 (Caspers et al., 2006),
Hirnforschung, 2, 311333; (c) lateral view, (d) dorsal view), and Sanides (Sanides, F. (1962). Die Architektonik des menschlichen Stirnhirns. Berlin,
Gottingen, Heidelberg: Springer Verlag; (b) lateral view, (f) medial view, (h) orbital view). The maps of Strasburger and Hopf are based on
myeloarchitectonic, and that of Sanides on combined cyto- and myeloarchitectonic observations. Extensive subdivisions by Strasburger (e.g., areas 48
and 48a, etc.) were merged to one larger area (e.g., 48, etc.). Note that the drawing by Strasburger shows a more dorsal aspect of the lateral surface of
the hemisphere, whereas Hopf and Sanides use a perspectives comparable to that of Vogt (1910) (Figure 7). All areas with same numbers in the maps
have been encoded with the same color. Areas identified by just one or two of the authors have been left in gray. A.a, area adolfactoria; Bol, olfactory
bulb; ce, central sulcus; cg, cingulate sulcus; if, inferior frontal sulcus; Pro/Peri, proiso- periallocortical region (not mapped); Pvz and Pvl fields of the
paralimbic zone of Sanides (1962); tol, olfactory tuberculum.
149
Figure 9 Comparison between the myeloarchitectonic maps of the human parietal cortex after Vogt (Vogt, O. (1911). Die Myeloarchitektonik des
Isocortex parietalis. Journal fur Psychologie und Neurologie, 18, 379396; (a) dorsal view, (b) lateral view, (c) medial view) and Batsch (Batsch, E.-G.
(1956). Die myeloarchitektonische Untergliederung des Isocortex parietalis beim Menschen. Journal fur Hirnforschung, 2, 225258; (d) dorsal view, (e)
lateral view, (f) medial view). Arabic numerals indicate myeloarchitectonic areas. Continuous lines surround areas, dashed lines indicate their
subdivisions (only in (d)(f)). All areas with same numbers in the maps of both authors have been encoded with the same color. Subregions in the map
of Batsch are labeled with italic letters or roman numerals. calc, calcarine sulcus; cc, corpus callosum; ce, central sulcus; fissl, lateral fissure; ip,
intraparietal sulcus; p-o, parieto-occipital sulcus; poc, postcentral sulcus; temps, superior temporal sulcus.
which are found on the parietal operculum and therefore

not visible on the maps depicted in Figure 9. Taking the
intersubject variability of cortical areas into consideration,
the maps of Vogt (1911) and Batsch (1956) show a good
match between the larger areas (V67, V69V72, V75, V83,
V85V90), although the latter author presents a much more

detailed parcellation into subareas.
On the medial surface (Figure 9(c) and 9(f)), both authors
included several areas in their map of the parietal cortex
(V76V82, V84, V91V96), which we classify as posterior
150
cingulate areas by their topography and comparison with more

recent cyto- and receptorarchitectonic studies (PalomeroGallagher & Zilles, 2009; Vogt, Vogt, & Laureys, 2006). Areas
V77V79, V93, and V96 are comparable to 23d (Vogt et al.,
2006), that is, the most rostral portion of BA23, which shows a
transitional cytoarchitecture between BA24 and BA23 as
already mentioned by Brodmann (1909). Areas V80, V92,
and V95 could be equivalents of d23, and V91 and V94 of
area v23 (Palomero-Gallagher & Zilles, 2009; Vogt et al.,
2006), whereas V76, V81, V82, and V84 can be compared
with BA31.
Temporal Lobe
The most detailed myeloarchitectonic map of the human temporal lobe presents 60 areas grouped into seven major regions
(Hopf, 1954a, 1955). In a quantitative photometric study
(Hopf, 1968a), the parcellation into these myeloarchitectonic
regions could be confirmed. However, a detailed objective
delineation of the 60 areas was not provided. Thus, we will
here only discuss the mapping of the temporal regions as
shown in Figure 10(a) and 10(c).
Temporopolar region tp (Figure 10(a) and 10(c)), with its
subregions tp.d, tp.l, and tp.m, is characterized by its singulostriate architecture, that is, only one horizontal stripe of
Baillager is visible in layer 4 (Hopf, 1954a). Area tp is comparable to BA38.
The large magnocellular tmag region (Figure 10(b) and
10(c)) with its four subregions is found on the middle and
inferior temporal gyri and is thus comparable to areas BA20
and BA21. Myeloarchitecture of the different subregions and
areas within tmag is uni- to propeastriate and the density of the
inner and outer Baillarger stripes varies from interno- to externodensior depending on the area examined (Hopf, 1954a).
Areas of the tlim region (Figure 10(c)) are found on the
fusiform gyrus. The subregion tlim.o is separated from the
entorhinal area by the collateral sulcus. It has a mixed myeloarchitectonic character depending on the areas, reaching
from singulostriate to propeunistriate and unistriate. The subregion tlim.c is prope- to unistriate, whereas tlim.m is singulostriate. tlim.m is a transition region between the allocortex
and the occipital isocortex (Hopf, 1954a).
The propeunistriate region ttr.1 is found on the (first)
transverse temporal gyrus (Figure 10(a)), and is thus comparable to cytoarchitectonic areas BA41 (Brodmann, 1909) and
Te1 (Morosan et al., 2001). Myeloarchitectonic area ttr.2 has a
similar position as cytoarchitectonic area Te2, and areas tsep
(propeunistriate) and tpartr (propeastriate) on the superior
temporal gyrus as Te3, whereas bistriate area tpari is comparable to TI1 (Morosan et al., 2001).
A myeloarchitectonic map by Beck (1930) with an extreme
parcellation of the supratemporal surface into 79 areas
grouped into seven regions shows, however, a nearly perfect
match with the map of Hopf (1954a) when restricted to the
regional level (Figure 10(a) and 10(d)). The bistriate regions
ttrI, ttrII, ts, and tpar of Beck (1930) resemble areas Te1 (primary auditory), Te2 (secondary auditory), Te3, and TI1, respectively. His singulostriate tp region is comparable to BA38. The
myeloarchitectonic description of ttrIII emphasizes differences
from the typical unimodal sensory structure of ttrI and ttrII,
thus suggesting the classification as a hierarchically higher

temporal cortical area on the posterior part of the dorsal surface of the temporal lobe together with area tpt (Figure 10(d)).
We would like to interpret ttrIII and tpt as possible parts of the
functionally defined Wernicke area.
Occipital Lobe
An early myeloarchitectonic map of the region rostral to BA18
was proposed by Lungwitz (1937). He delineated a total of 17
areas, all of which are euradiate, have a clearly visible Kaes
Bechterew stripe, and are bistriate to conjunctostriate, with a
tendency to a denser external Baillarger stripe (i.e., externodensior). However, a comparison with recent cyto- and receptorarchitectonic maps (Amunts et al., 2000; Caspers, PalomeroGallagher, et al., 2013; Caspers, Zilles, et al., 2013; Eickhoff,
Rottschy, Kujovic, Palomero-Gallagher, & Zilles, 2008; Eickhoff,
Rottschy, & Zilles, 2007; Kujovic et al., 2013; Malikovic et al.,
2007; Rottschy et al., 2007), in vivo magnetic resonance imaging
(MRI) studies of myelin distribution (Glasser & van Essen, 2011)
and functional imaging data (Abdollahi et al., 2014; Ferri,
Kolster, Jastorff, & Orban, 2012; Georgieva, Peeters, Kolster,
Todd, & Orban, 2009; Kolster, Peeters, & Orban, 2010; Sereno,
Lutti, Weiskopf, & Dick, 2013; Wandell, Dumoulin, & Brewer,
2007; Wilms et al., 2010) demonstrates that the parcellation
by Lungwitz (1937) does not match the cyto- or receptorarchitectonic data and cannot be reconciled with functional maps.
Human area MT is the only extrastriate visual area which
can be demonstrated using myelin staining, because of its
extremely high myelin density (Annese, Gazzaniga, & Toga,
2005; Clarke & Miklossy, 1990; Flechsig, 1920; Tootell & Taylor, 1995). It could also be identified by receptor autoradiography in human postmortem brains (Zilles & Clarke, 1997).
The myelin density of distinct retinotopically defined areas
was measured by combining retinotopic and myelin maps
(Abdollahi et al., 2014). It could be demonstrated, that the
myelin density differs significantly between all these retinotopically distinct visual areas. Therefore, a new approach to high
resolution myeloarchitectonic mapping at the microscopic
level seems to be a valuable contribution to fill the gap between
the mesoscopic in vivo studies and cellular observations in the
visual cortex.
Insular Lobe
The most comprehensive myeloarchitectonic study of the insular lobe was published by Brockhaus (1940). He modified an
earlier study by Vogt and Vogt (1911) (Figure 11(a)) and added
own myeloarchitectonic maps of two further brains giving an
impression of intersubject variability (Figure 11(b)11(d)). The
cortex of the insular lobe lies over the claustrum, and is therefore
frequently called claustrocortex. It can be subdivided into isocortical, allocortical, and mesocortical regions.
The isocortical region is the largest part and reaches the
circular sulcus of the insula with the exception of a small
caudodorsal part (T; Figure 11(a), 11(b), and 11(d)), where
the temporal isocortex invades the insular lobe. All areas of the
isocortical part are myeloarchitectonically euradiate. The radial
fiber bundles and the intensity of the Baillarger stripes vary
between the different areas which led to the definition of five
151
Figure 10 Myeloarchitectonic map of the human temporal lobe ((a) dorsal view, (b) lateral view, and (c) medial view; modified from Hopf, A. (1954a).
Die Myeloarchitektonik des Isocortex temporalis beim Menschen. Journal fur Hirnforschung, 1, 208279) and of the dorsal surface (d) of the
temporal lobe (modified from Beck, E. (1930). Myeloarchitektonik der dorsalen Schlafenlappenrinde beim Menschen. Journal fur Psychologie und
Neurologie, 41, 129262). Bold letters code names of regions and subregions, italics of areas. Continuous lines surround the regions, dashed lines
indicate subregional borders, and dotted lines areal borders. Orientations of the maps in panels (a) and (d) are indicated (c, caudal direction; m, medial
direction; l, lateral direction; r, rostral direction). Abbreviations for panels (a)(c): CA, Cornu Ammonis region of the hippocampus; ent, entorhinal
area; mt, mesocortex. The regio temporalis limitans (tlim) is subdivided into caudal (c), medial (m), and oral (o) subregions. tlim.c contains two areas
(e, i), tlim.m two areas (e, i), and tlim.o four areas (a, isf, md, p). The regio temporalis magna (tmag) is subdivided into the caudodorsal (cd),
caudoventral (cv), dorsal (d), and ventral (v) subregions. tmag.cd consists of four areas (lim, if, p, s), tmag.cv of two areas (a, p), tmag.d of five
areas (aif, as, md, p, s), and tmag.v of two areas (as, pif). The regio temporopolaris (tp) is subdivided into the dorsal (d), lateral (l), medial (m), and
152
Figure 11 Myeloarchitectonic maps of the human insular lobe. (a) Modified from Vogt, C. and Vogt, O. (1911). Nouvelle Contribution a` letude de la
myeloarchitecture de lecorce cerebrale. Communication at the XX Congres des Medicins Alienistes et Neurologistes de France et des pays de langue
francaise, Bruxelles, (pp. 311). (b)(d) Modified from Brockhaus, H. (1940). Die Cyto- und Myeloarchitektonik des Cortex claustralis und des Claustrum
beim Menschen. Journal fur Psychologie und Neurologie, 49, 249348. Area ai2 of Vogt and Vogt (1911) comprises areas aio and aic of Brockhaus
(1940). Continuous lines surround areas, dashed lines indicate their subdivisions (only in (c) and (d)). Note interindividual variability by comparing
reconstruction of insular areas in three different brains by Brockhaus (b)(d). Green encodes isocortical areas, blue mesocortical areas, and red
allocortical areas. Dark green areas are cytoarchitectonically defined as granular areas, light green areas are dysgranular regions (Brockhaus, 1940;
Kurth et al., 2010; Vogt & Vogt, 1911). Area i5 in panel (a) is light green with dark green stripes, because it contains both granular and dysgranular
subareas. ai1ai4, ai6ai7 meso- and allocortical insular or temporal areas after Vogt and Vogt (1911), aic and aio allocortical insular areas after
Brockhaus (1940), BP, first short insular gyrus; BS, second short insular gyrus; CA, precentral insular gyrus; CPP, first postcentral insular gyrus; CPS,
second postcentral insular gyrus; cs, central insular sulcus; i1i6, isocortical insular areas after Vogt and Vogt (1911), i1i6 (and subdivisions),
isocortical insular areas after Brockhaus (1940); ibri and ibrm, iso- and mesocortical insular areas (respectively) adjacent to the orbital cortex after
Brockhaus (1940); mi areas (and subdivisions), mesocortical insular areas after Brockhaus (1940); T, temporal cortex; Tp, temporal lobe.
major areas in front (i1i3, i4a, and i4b, with several subareas)
and of seven areas (i5a, i5b, i5c, i5d, i6a, i6b, and i6li, with
several subareas) behind the central sulcus of the insula
(Brockhaus, 1940). Areas ibri and ibrm (Figure 11(c)) are
transition areas between the insular and orbital cortex.
The isocortical region of the insular cortex is by far its
largest part, followed by the mesocortical region. The latter
is found ventrally to the isocortical part and surrounds the
allocortical part of the insular cortex. Isocortical regions are
labeled in green, mesocortical in blue, and allocortical in red

in Figure 11. Most rostrally, the mesocortical insula can
encroach onto the dorsal surface of the temporal lobe
(Figure 11(a)). A broad cytoarchitectonical layer I and a
very weak or nearly absent layer IV is typical of this region.
Von Economo cells are most obvious in area mio (Brockhaus,
1940). In this region the intrusion of radial fibers and the
expression of tangential fiber layers also vary considerably
between the different areas.
ventral (v) subregions. tp.d consists of three areas (e, I, p), tp.l is not further subdivided, tp.m has seven areas (e, i, if, p, pt, Ul, Um), and tp.v two
areas (if, s). The regio temporalis parainsularis (tpari) contains three areas (im, l, m). The regio temporalis paratransversa (tpartr) contains four areas
(a, p, pf, s). The regio temporalis separans (tsep) is subdivided into the lateral (l) and medial (m) subregions. tsep.l contains four areas (a, md, p, pf)
and tsep.m two areas (e, i). The regio temporalis transversa (ttr) is subdivided into the prima caudolateralis (1cl), prima caudomedialis (1cm),
prima orolateralis (1ol), prima oromedialis (1om), and secunda (2) subregions. ttr.1cl is not further subdivided, ttr.1cm has three areas (a, ep, ip),
ttr.1ol three areas (e, I, md), ttr.1om two areas (a, p), and ttr.2 four areas (ae, ai, pe, pi). Abbreviations for panel (d): ent, entorhinal area; Pam,
periamygdalar region; Prpi, prepiriform region; ti, temporal insular region; tp, temporopolar region; tpar, parainsular region; tpt, temporoparietal region;
ttrI, first temporal transversal region; ttrII, second temporal transversal region; ttrIII, third temporal transversal region; ts, supratemporal region.
153
The allocortical insular region is the most central part of the

insular lobe, and abuts the substantia perforata anterior and
the mediodorsal part of the temporal lobe. Notably, the agranular laminar structure of this region differs fundamentally
from that of the iso- and mesocortical insular regions, thus
impairing a comparison of layers between these three regions.
The allocortical insular region contains areas ai2, aio, and aic
(Figure 11(a)). From the myeloarchitectonic point of view
they are characterized by a broad layer 1 and an infraradiate
fiber architecture. Area aio also contains von Economo cells
(Brockhaus, 1940). Areas aic and aio can be clearly delineated
from each other due to the presence of many very thick single
fibers in the former area.
A comparison with the cytoarchitectonic study by Kurth
et al. (2010) confirms that myeloarchitectonic areas i5a and
i6 are dysgranular, whereas areas i5bi5d are granular. The
latter are comparable to the cytoarchitectonic areas Ig1 and
Ig2, whereas areas i6a and i6b probably correspond to
cytoarchitectonic area Id1 (Kurth et al., 2010).
Using T1- and T2-weighted sequences (Wasserthal,

Brechmann, Stadler, Fischl, & Engel, 2014) or T1, T2* and
proton density imaging (De Martino et al., 2014) to visualize
the myelin density in the transverse temporal gyrus in vivo,
the cytoarchitectonically defined primary visual cortex Te1
(Morosan et al., 2001) could be identified, as well as a
neighboring area, probably the medial part of area ttrII (Beck,
1930). Even the subtle cytoarchitectonic differences between
areas Te1.0, Te1.1, and Te1.2 (Morosan et al., 2001) could be
detected in vivo at the single subject level using the 1/T1
sequence (Lutti et al., 2014).
These results open a promising perspective for future comparisons between in vivo imaging of myeloarchitecture using
MRI and ultra-high resolution analysis of myelin and fiber
architecture using histological techniques or polarized light
imaging (Axer, Amunts, et al., 2011; Axer, Grassel, et al., 2011).
MRI: Maps and Lamination Patterns
This work was supported by the Portfolio Theme

Supercomputing and Modeling for the Human Brain of the
Helmholtz Association, Germany.
The above described myeloarchitectonic mapping of the

human cerebral cortex based on microscopic analysis of histological sections is of major interest for the recently evolved
in vivo and postmortem neuroimaging approaches using MRI,
since various sequences or combinations of sequences provide
an enhanced contrast in MR images for myelin. Thus, it is
possible to measure at least the relative myelin density and
the differences between cortical areas (Abdollahi et al., 2014;
Glasser, Goyal, Preuss, Raichle, & van Essen, 2014; Glasser &
van Essen, 2011). The myelin content of cortical areas is not
only a useful tool for mapping, but an important neurobiological aspect of functional and connectional properties, as
already emphasized by Vogt and Vogt (1919). Notably, hierarchically lower cortical regions, for example, primary sensory
areas, have a higher myelin content than hierarchically higher
cortical regions, for example, multimodal association areas
(see Section Parietal Lobe; Glasser et al., 2014; Hopf &
Vitzthum, 1957). Moreover, less myelinated association areas
have a higher aerobic glycolytic activity than heavily myelinated cortical regions (Glasser et al., 2014).
A good match has been found between the myelin maps
based on T1- and T2-weighted MRI (Glasser & van Essen,
2011), cyto- and receptorarchitectonic maps (Amunts et al.,
1999, 2000, 2010; Caspers et al., 2006, 2008; Eickhoff,
Amunts, et al., 2006; Geyer, Schormann, Mohlberg, & Zilles,
2000; Geyer et al., 1996, 1999; Grefkes et al., 2001; Kurth et al.,
2010; Malikovic et al., 2007; Morosan et al., 2001; PalomeroGallagher et al., 2008, 2009; Rottschy et al., 2007; Scheperjans,
Eickhoff, et al., 2008; Vogt et al., 2006; Zilles & Amunts, 2010,
2014), and retinotopic areas (Abdollahi et al., 2014). Myelin
T1mapping was also performed by registration of T*,
2
weighted, T2-weighted, and quantitative T1 or 1/T1 MRI
(Cohen-Adad, 2014; Cohen-Adad et al., 2012; Deistung et al.,
2013; Eickhoff et al., 2005; Geyer, Weiss, Reimann, Lohmann,
& Turner, 2011; Lutti, Dick, Sereno, & Weiskopf, 2014;
Trampel, Ott, & Turner, 2011; Turner, Oros-Peusquens,
Romanzetti, Zilles, & Shah, 2008).
Acknowledgment

Auditory Cortex; Cytoarchitectonics, Receptorarchitectonics, and
Network Topology of Language; Cytoarchitecture and Maps of the
Human Cerebral Cortex; Functional Organization of the Primary Visual
Cortex; Gustatory System; Gyrification in the Human Brain; Insular
Cortex; Mapping Cingulate Subregions; Posterior Parietal Cortex:
Structural and Functional Diversity; Somatosensory Cortex; Sulci as
Landmarks; Topographic Layout of Monkey Extrastriate Visual Cortex;
Transmitter Receptor Distribution in the Human Brain; Vestibular
Cortex; Von Economo Neurons.
References
Abdollahi, R. O., Kolster, H., Glasser, M. F., Robinson, E. C., Coalson, T. S., Dierker, D.,
et al. (2014). Correspondences between retinotopic areas and myelin maps in
Allman, J. M., Tetreault, N. A., Hakeem, A. Y., Manaye, K. F., Semendeferi, K.,
Erwin, J. M., et al. (2010). The von Economo neurons in frontoinsular and anterior
cingulate cortex in great apes and humans. Brain Structure and Function, 214,
495517.
Allman, J. M., Watson, K. K., Tetreault, N. A., & Hakeem, A. Y. (2005). Intuition and
autism: A possible role for Von Economo neurons. Trends in Cognitive Sciences, 9,
367373.
principles and multiple receptor mapping. PLoS Biology, 8.
Brodmanns areas 17 and 18 brought into stereotaxic spaceWhere and how
Amunts, K., Schleicher, A., & Zilles, K. (2004). Outstanding language competence and
cytoarchitecture in Brocas speech region. Brain and Language, 89, 346353.
Annese, J., Gazzaniga, M. S., & Toga, A. W. (2005). Localization of the human cortical
visual area MT based on computer aided histological analysis. Cerebral Cortex, 15,
10441053.
154
Axer, M., Amunts, K., Grassel, D., Palm, C., Dammers, J., Axer, H., et al. (2011). A novel
approach to the human connectome: Ultra-high resolution mapping of fiber tracts in
the brain. NeuroImage, 54, 10911101.
Axer, M., Grassel, D., Kleiner, M., Dammers, J., Dickscheid, T., Reckfort, J., et al.
(2011). High-resolution fiber tract reconstruction in the human brain by means of
three-dimensional polarized light imaging. Frontiers in Neuroinformatics, 5, 34.
Baillarger, J. (1840). Recherches sur la structure de la couche corticale des
circonvolutions du cervau. Memoires de lAcademie royale de Medecine, 8,
149183.
Batsch, E.-G. (1956). Die myeloarchitektonische Untergliederung des Isocortex
Beck, E. (1930). Myeloarchitektonik der dorsalen Schlafenlappenrinde beim Menschen.
Bisley, J. W., & Goldberg, M. E. (2010). Attention, intention, and priority in the parietal
lobe. Annual Review of Neuroscience, 33, 121.
Bludau, S., Eickhoff, S. B., Mohlberg, H., Caspers, S., Laird, A. R., Fox, P. T., et al.
(2014). Cytoarchitecture, probability maps and functions of the human frontal pole.
Bremmer, F. (2011). Multisensory space: From eye-movements to self-motion. The
Journal of Physiology, 589, 815823.
Brockhaus, H. (1940). Die Cyto- und Myeloarchitektonik des Cortex claustralis und des
Claustrum beim Menschen. Journal fur Psychologie und Neurologie, 49, 249348.
Brodmann, K. (1914). Physiologie des Gehirns. In P. von Bruns (Ed.), Neue Deutsche
Chirurgie (pp. 85426). Stutgart: Verlag von Ferdinand Enke.
Campbell, A. W. (1905). Histological studies on the localisation of cerebral function.
Cambridge: Cambridge University Press.
recognition region of the posterior fusiform gyrus. Brain Structure and Function,
http://dx.doi.org/10.1007/s00429-013-0646-z.
areas of the human posterior fusiform gyrus. Brain Structure and Function, 218,
511526.
(2008). The human inferior parietal lobule in stereotaxic space. Brain Structure and
Function, 212, 481495.
Caspers, S., Schleicher, A., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., &
Zilles, K. (2013). Organization of the human inferior parietal lobule based on
receptor architectonics. Cerebral Cortex, 23, 615628.
Choi, H.-J., Amunts, K., Mohlberg, H., Fink, G. R., Schleicher, A., & Zilles, K. (2006).
Cytoarchitectonic mapping of the anterior ventral bank of the intraparietal sulcus in
humans. Journal of Comparative Neurology, 495, 5369.
Clarke, S., & Miklossy, J. (1990). Occipital cortex in man: Organization of callosal
connections, related myelo- and cytoarchitecture, and putative boundaries of
functional visual areas. Journal of Comparative Neurology, 298, 188214.
Cohen-Adad, J. (2014). What can we learn from T2* maps of the cortex? NeuroImage,
93(Pt 2), 189200.
et al. (2012). T2* mapping and B0 orientation-dependence at 7T reveal cyto- and
myeloarchitecture organization of the human cortex. NeuroImage, 60, 10061014.
De Martino, F., Moerel, M., Xu, J., van de Moortele, P. F., Ugurbil, K., Goebel, R., et al.
(2014). High-resolution mapping of myeloarchitecture in vivo: Localization of
auditory areas in the human brain. Cerebral Cortex.
susceptibility mapping (QSM) with magnitude-, phase-, and R2*-imaging at ultrahigh magnetic field strength. NeuroImage, 65, 299314.
Eickhoff, S., Walters, N. B., Schleicher, A., Kril, J., Egan, G. F., Zilles, K., et al. (2005).
High-resolution MRI reflects myeloarchitecture and cytoarchitecture of human
cerebral cortex. Human Brain Mapping, 24, 206215.
Eickhoff, S. B., Amunts, K., Mohlberg, H., & Zilles, K. (2006). The human parietal
operculum. II. Stereotaxic maps and correlation with functional imaging results.
Eickhoff, S. B., Rottschy, C., Kujovic, M., Palomero-Gallagher, N., & Zilles, K. (2008).
Organizational principles of human visual cortex revealed by receptor mapping.
Eickhoff, S. B., Schleicher, A., Zilles, K., & Amunts, K. (2006). The human parietal
operculum. I. Cytoarchitectonic mapping of subdivisions. Cerebral Cortex, 16,
254267.
Elliot Smith, G. (1907). A new topographical survey of the human cerebral cortex,
being an account of the distribution of the anatomically distinct cortical areas and
their relationship to the cerebral sulci. Journal of Anatomy and Physiology, 41,
237254.
Ferri, S., Kolster, H., Jastorff, J., & Orban, G. A. (2012). The overlap of the EBA and the
MT/V5 cluster. NeuroImage, 66C, 412425.
Filimonoff, I. N. (1932). Uber die Variabilitat der Grohirnrindenstruktur. Mitteilung II
Regio occipitalis beim erwachsenen Menschen. Journal fur Psychologie und
Neurologie, 44, 296.
Foerster, O. (1931). The cerebral cortex in man. Lancet, 218, 309312.
Foerster, O. (1936). The motor cortex in man in the light of Hughlings Jacksons
doctrines. Brain, 59, 135159.
Gennari, F. (1782). (Translated in Clarke E and OMalley CD (Eds.), (1996). The human
brain and spinal cord: A historical study illustrated by writings from the antiquity to
the twentieth century (2nd ed.). San Francisco: Norman Publ edn.)De peculiari
structura cerebri nonnulisque ejus morbis. Parma: Ex regio typographeo.
Georgieva, S., Peeters, R., Kolster, H., Todd, J. T., & Orban, G. A. (2009). The
processing of three-dimensional shape from disparity in the human brain. Journal
Biology, 174, 189.
Geyer, S., Ledberg, A., Schleicher, A., Kinomura, S., Schormann, T., Burgel, U., et al.
(1996). Two different areas within the primary motor cortex of man. Nature, 382,
805807.
Geyer, S., Schleicher, A., & Zilles, K. (1999). Areas 3a, 3b, and 1 of human primary
somatosensory cortex. 1. Microstructural organization and interindividual
Geyer, S., Schormann, T., Mohlberg, H., & Zilles, K. (2000). Areas 3a, 3b, and 1 of
human primary somatosensory cortex. 2. Spatial normalization to standard
anatomical space. NeuroImage, 11, 684696.
Glasser, M. F., Goyal, M. S., Preuss, T. M., Raichle, M. E., & van Essen, D. C. (2014).
Trends and properties of human cerebral cortex: Correlations with cortical myelin
content. NeuroImage, 93(Pt 2), 165175.
Glasser, M. F., & van Essen, D. C. (2011). Mapping human cortical areas in vivo based
on myelin content as revealed by T1- and T2-weighted MRI. Journal of
Grefkes, C., & Fink, G. R. (2005). The functional organization of the intraparietal sulcus
in humans and monkeys. Journal of Anatomy, 207, 317.
Hopf, A. (1954a). Die Myeloarchitektonik des Isocortex temporalis beim Menschen.
Journal fur Hirnforschung, 1, 208279.
Hopf, A. (1954b). Zur Frage der Konstanz und Abgrenzbarkeit myeloarchitektonischer
Rindenfelder. Deutsche Zeitschrift fur Nervenheilkunde, 172, 188200.
Hopf, A. (1955). Uber die Verteilung myeloarchitektonischer Merkmale in der
isokortikalen Schlafenlappenrinde beim Menschen. Journal fur Hirnforschung, 2,
3654.
Hopf, A. (1956). Uber die Verteilung myeloarchitektonischer Merkmale in der
Stirnhirnrinde beim Menschen. Journal fur Hirnforschung, 2, 311333.
Hopf, A. (1968a). Photometric studies on the myeloarchitecture of the human temporal
lobe. Journal fur Hirnforschung, 10, 285297.
Hopf, A. (1968b). Registration of the myeloarchitecture of the human frontal lobe with an
extinction method. Journal fur Hirnforschung, 10, 259269.
Hopf, A. (1969). Photometric studies on the myeloarchitecture of the human parietal
lobe. I. Parietal region. Journal fur Hirnforschung, 11, 253265.
lobe. II. Postcentral region. Journal fur Hirnforschung, 12, 135141.
Hopf, A., & Vitzthum, H. (1957). Uber die Verteilung myeloarchitektonische Merkmale
in der Scheitellappenrinde beim Menschen. Journal fur Hirnforschung, 3, 79104.
Kaes, T. (1907). Die Grosshirnrinde des Menschen in ihren Maen und in ihrem
Fasergehalt. Ein gehirnanatomischer Atlas. Erster Teil: Kurven und Tafeln. Zweiter
Teil: Text. Jena: Fischer.
human middle temporal area MT/V5 and its cortical neighbors. Journal of
Kujovic, M., Zilles, K., Malikovic, A., Schleicher, A., Mohlberg, H., Rottschy, C., et al.
(2013). Cytoarchitectonic mapping of the human dorsal extrastriate cortex. Brain
Kurth, F., Eickhoff, S. B., Schleicher, A., Hoemke, L., Zilles, K., & Amunts, K. (2010).
Cytoarchitecture and probabilistic maps of the human posterior insular cortex.
Lungwitz, W. (1937). Zur myeloarchitektonischen Untergliederung der menschlichen
Area praeoccipitalis (Area 19 Brodmann). Journal fur Psychologie und Neurologie,
47, 607637.
Luppino, G., Matelli, M., Camarda, R. M., Gallese, V., & Rizzolatti, G. (1991). Multiple
representations of body movements in mesial area 6 and the adjacent cingulate
cortex: An intracortical microstimulation study in the macaque monkey. Journal of
Lutti, A., Dick, F., Sereno, M. I., & Weiskopf, N. (2014). Using high-resolution
quantitative mapping of R1 as an index of cortical myelination. NeuroImage,
93(Pt 2), 176188.
(2007). Cytoarchitectonic analysis of the human extrastriate cortex in the region of
V5/MT : A probabilistic, stereotaxic map of area hOc5. Cerebral Cortex, 17(3),
562574.
Matelli, M., Luppino, G., & Rizzolatti, G. (1991). Architecture of superior and mesial
area 6 and the adjacent cingulate cortex in the macaque monkey. Journal of
Meynert, T. (1868). Der Bau der Gross-Hirnrinde und seine ortlichen
Verschiedenheiten, nebst einem pathologisch- anatonischem Corollarium.
Vierteljahrsschrift fur Psychiatrie, 88113.
organization of the human auditory cortex: Cytoarchitecture and transmitter
receptors. In P. Heil, E. Konig & E. Budinger (Eds.), Auditory cortex Towards a
synthesis of human and animal research (pp. 2750). Mahwah, NJ: Lawrence
Erlbaum.
mapping of human superior temporal gyrus. Anatomy and Embryology, 210, 401406.
Nieder, A., & Dehaene, S. (2009). Representation of number in the brain. Annual Review
Nieuwenhuys, R. (2013). The myeloarchitectonic studies on the human cerebral cortex
of the Vogt-Vogt school, and their significance for the interpretation of functional
neuroimaging data. Brain Structure and Function, 218, 303352.
Nieuwenhuys, R., Broere, C. A., & Cerliani, L. (2014). A new myeloarchitectonic map of
the human neocortex based on data from the Vogt-Vogt school. Brain Structure and
Function, http://dx.doi.org/10.1007/s00429-014-0806-9.
Nimchinsky, E. A., Vogt, B. A., Morrison, J. H., & Hof, P. R. (1995). Spindle neurons of
the human anterior cingulate cortex. Journal of Comparative Neurology, 355,
2737.
Neurology, 508, 906926.
Palomero-Gallagher, N., Vogt, B. A., Schleicher, A., Mayberg, H. S., Schleicher, A., &
Zilles, K. (2009). Receptor architecture of human cingulate cortex: Evaluation of the
four-region neurobiological model. Human Brain Mapping, 30, 23362355.
regions and areas. In B. A. Vogt (Ed.), Cingulate neurobiology & disease. (2nd ed.).
Infrastructure, diagnosis, treatment (Vol. 1. Oxford: Oxford University Press.
Rizzolatti, G., Luppino, G., & Matelli, M. (1996). The classic supplementary motor area
is formed by two independent areas. In H. O. Luders (Ed.), Supplementary
sensorimotor area (pp. 4556). Philadelphia, PA: Lippincott-Raven.
Rottschy, C., Eickhoff, S. B., Schleicher, A., Mohlberg, H., Kujovic, M., Zilles, K., et al.
(2007). Ventral visual cortex in humans: Cytoarchitectonic mapping of two
extrastriate areas. Human Brain Mapping, 28, 10451059.
Sanides, F. (1962). Die Architektonik des menschlichen Stirnhirns. Berlin, Gottingen,
Heidelberg: Springer Verlag.
Sanides, F. (1964). The cyto-myeloarchitecture of the human frontal lobe and its
relation to phylogenetic differentiation of the cerebral cortex. Journal fur
155
Sanides, F., & Vitzthum, H. (1965a). Die Grenzerscheinungen am Rande

der menschlichen Sehrinde. Deutsche Zeitschrift fur Nervenheilkunde, 187,
708719.
Sanides, F., & Vitzthum, H. (1965b). Zur Architektonik der menschlichen Sehrinde und
den Prinzipien ihrer Entwicklung. Deutsche Zeitschrift fur Nervenheilkunde, 187,
680707.
et al. (2008). Probabilistic maps, morphometry, and variability of
cytoarchitectonic areas in the human superior parietal cortex. Cerebral Cortex, 18,
21412157.
parietal cortex. Cerebral Cortex, 18, 846867.
surface by combining quantitative T1 with retinotopy. Cerebral Cortex, 23,
22612268.
Soemmerring, S. T. (1788). Vom Hirn und Ruckenmark. Mainz: Winkopp und Komp.
Stephan, H. (1975). Allocortex. Berlin: Springer Verlag.
Strasburger, E. H. (1937). Die myeloarchitektonische Gliederung des Stirnhirns beim
Menschen und Schimpansen I. Journal fur Psychologie und Neurologie, 47,
460491.
Tootell, R. B., & Taylor, J. B. (1995). Anatomical evidence for MT and additional cortical
visual areas in humans. Cerebral Cortex, 5, 3955.
Trampel, R., Ott, D. V., & Turner, R. (2011). Do the congenitally blind have a
stria of Gennari? First intracortical insights in vivo. Cerebral Cortex, 21,
20752081.
Turner, R., Oros-Peusquens, A. M., Romanzetti, S., Zilles, K., & Shah, N. J. (2008).
Optimised in vivo visualisation of cortical structures in the human brain at 3T using
IR-TSE. Magnetic Resonance Imaging, 26, 935942.
Vicq dAzyr, F. (1786). Traite danatomie et de physiologie. Paris:
Didot lAine.
Vogt, B. A., Hof, P. R., Zilles, K., Vogt, L. J., Herold, C., & Palomero-Gallagher, N.
(2013). Cingulate area 32 homologies in mouse, rat, macaque and human:
Cytoarchitecture and receptor architecture. Journal of Comparative Neurology, 521,
41894204.
Vogt, B. A., & Vogt, L. (2003). Cytology of human dorsal midcingulate
and supplementary motor cortices. Journal of Chemical Neuroanatomy, 26,
301309.
Vogt, B. A., Vogt, L., & Laureys, S. (2006). Cytology and functionally correlated circuits
of human posterior cingulate areas. NeuroImage, 29, 452466.
Vogt, C., & Vogt, O. (1907). Zur Kenntnis der elektrisch erregbaren
Hirnrindengebiete bei den Saugetieren. Journal fur Psychologie und Neurologie,
25, 279468.
Vogt, C., & Vogt, O. (1911). Nouvelle Contribution a` letude de la
myeloarchitecture de lecorce cerebrale. Communication at the XX Congres des
Medicins Alienistes et Neurologistes de France et des pays de langue francaise.
Bruxelles, pp. 311.
Vogt, O. (1903). Zur anatomischen Gliederung des Cortex cerebri. Journal fur
Vogt, O. (1910). Die myeloarchitektonische Felderung des menschlichen Stirnhirns.
erwachsenen Menschen. Wien, Berlin: Springer.
Vorobiev, V., Govoni, P., Rizzolatti, G., Matelli, M., & Luppino, G. (1998). Parcellation
of human mesial area 6: Cytoarchitectonic evidence for three separate areas.
cortex. Neuron, 56, 366383.
Wasserthal, C., Brechmann, A., Stadler, J., Fischl, B., & Engel, K. (2014). Localizing the
human primary auditory cortex in vivo using structural MRI. NeuroImage, 93(Pt 2),
237251.
156
Zilles, K., & Amunts, A. (2014). Architecture of the cerebral cortex. In J. K. Mai & G.
Paxinos (Eds.), The human nervous system (pp. 836895). (3rd ed.). Amsterdam:
Academis Press.
Zilles, K., & Clarke, S. (1997). Architecture, connectivity, and transmitter receptors of
human extrastriate visual cortex. Comparison with nonhuman primates. Cerebral
Cortex, 12, 673742.
Zilles, K., Schlaug, G., Geyer, S., Luppino, G., Matelli, M., Qu, M., et al. (1996).
Anatomy and transmitter receptors of the supplementary motor areas in the human
and nonhuman primate brain. In H. O. Luders (Ed.), Supplementary sensorimotor
area (pp. 2943). Philadelphia, PA: Lippincott-Raven.
Cortical Surface Morphometry

AC Evans, McGill University, Montreal, QC, Canada
Introduction
Methodology
Structural neuroimaging has undergone a renaissance in

recent years, with the introduction and widespread application
of quantitative techniques for automated extraction of
various morphological metrics. These techniques include
diffusion-based methods (Iturria-Medina, 2013), voxel-based
morphometry (Ashburner & Friston, 2000), volumetric
deformation-based morphometry (Ashburner et al., 1998),
and cortical surface morphometry. The latter approach has
found particular favor, since it provides a series of cortical
metrics that have anatomical meaning, not only most commonly cortical thickness but also metrics of local surface area,
local cortical volume, and various indices of local surface curvature. These metrics are used to capture group differences or
longitudinal changes in cortical anatomy, for example, during
neurodevelopment, learning, or neurodegeneration. These
metrics allow for the exploration of the influence of genetics
or experience on cortical anatomy, long-range coupling of
cortical regions, and brainbehavior relationships in clinical
research and systems neuroscience. The growth of this research
area shows no sign of abating, and in 2013 alone, over 700
publications employed cortical thickness analysis. Figure 1
illustrates its continuing growth for over 20 years.
Despite this widespread adoption, there remain concerns
about the neuroanatomical validity of the most commonly
employed metric, cortical thickness. As will be discussed in
more detail in the succeeding text, the estimation of cortical
thickness depends upon the identification of two boundaries in
3-D MRI data, the pial surface and the boundary between gray
matter (GM) and white matter (WM). This depends upon the
GM/WM contrast in the MRI data, and some authors assert that
MRI-based estimates of cortical thickness do not accurately
reflect the true cytoarchitectural boundaries. While there is
some justification for this position, the situation is arguably
similar to that in functional MRI (fMRI), where the BOLD
signal has been widely used as a surrogate for cerebral blood
flow (CBF). Although the fMRI-based BOLD arises from a
number of sources, including CBF, and is therefore not a direct
measure of CBF, it is nevertheless widely used for functional
imaging in much the same way as cortical thickness is used for
structural imaging, that is, to study group differences, longrange coupling, and brainbehavior analysis. Thus, while
there is a need for further exploration of MRI-based cortical
thickness analysis methods and cross-validation against histological metrics, its applications are likely to continue to expand.
We briefly review here the history, current status, and future
evolution of cortical surface morphometry, from both the
methods themselves and their application in various clinical
research and systems neuroscience applications.
The early evolution of automated cortical surface morphometry

from structural MRI took place in a number of locations simultaneously. The Evans group in Montreal introduced the multisurface ASP technique (Holmes, MacDonald, Sled, Toga, &
Evans, 1996; MacDonald, Avis, & Evans, 1994; MacDonald,
Kabani, Avis, & Evans, 2000), using nested deformable spherical
meshes to fit cortical voxels previously segmented from MRI.
Using a constrained Laplacian model and skeleton-based surface reconstruction, ASP was subsequently extended to CLASP
(Kim et al., 2005; Tohka, Zijdenbos, & Evans, 2004). A singlesurface version of ASP was employed by Thompson, Schwartz,
and Toga (1996) and Thompson et al. (1997) to characterize
cortical surface variability via fluid deformation and coregistration of the extracted pial surfaces from different individuals.
Early work with a deformable mesh was also conducted in St.
Louis (Carman, Drury, & Van Essen, 1995; Van Essen & Drury,
1997; Van Essen et al., 2001) and Frankfurt (BrainVoyager;
Goebel, 1996, 1997, 2012; Kriegeskorte & Goebel, 2001). The
FreeSurfer package (Dale, Fischl, & Sereno, 1999; Fischl, Sereno,
& Dale, 1999), as well as extracting cortical surfaces using a
deformable mesh, also introduced a surface coordinate system
for intersubject comparison. Another widely used approach,
BrainVISA (Mangin, Frouin, Bloch, Regis, & Lopez-Krahe,
1995), employs a more bottom-up approach, similar to marching cubes, fitting triangular facets to presegmented cortical voxels, followed by heuristic operations to smooth the final surface
and correct errors. Lee et al. (2006) conducted a simulationbased comparison of the surface extraction performance of
CLASP, FreeSurfer, and BrainVISA, but, since these algorithms
have undergone continuous development in subsequent years,
direct head-to-head conclusions should be interpreted with caution in 2014. Other validation approaches have also examined
the performance of surface extraction algorithms using real data,
quantifying intersubject reproducibility (Fischl and Dale, 2000),
and comparing the MRI-based estimates of cortical thickness
with postmortem measurements (Kabani, Le Goualher, MacDonald, & Evans, 2001).
Having extracted the surface meshes, it is possible to obtain
morphological metrics at each mesh vertex, such as vertexwise
cortical thickness, area, volume, and curvature, each metric
having various possible mathematical definitions. For
instance, cortical thickness can be defined simply as the distance between linked vertices on inner and outer surfaces or by
curved streamlines, defined by the Laplacian equation (Haidar
& Soul, 2006; Jones, Buchbinder, & Aharon, 2000; Tosun et al.,
2004; Yezzi & Prince, 2003). A subclass of statistical image
analysis has evolved to handle the problem of capturing surface shape change and comparing surface variability across a
http://dx.doi.org/10.1016/B978-0-12-397025-1.00210-4
157
158
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Cortical Surface Morphometry
Cortical thickness publications by year

800
700
600
500
400
300
200
100
1955
1958
1959
1960
1961
1962
1963
1964
1966
1967
1968
1969
1970
1971
1972
1973
1954
1975
1976
1977
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
Figure 1 Number of publications by year identified by cortical thickness in PubMed.
population (Chung, Worsley, Nacewicz, Dalton, & Davidson,

2010, Chung, Robbins, & Evans, 2005).
As cortical thickness analysis has moved into the mainstream, the last decade has seen an explosion of new tools
that use volume-based estimates (Hutton, De Vita, Ashburner,
Deichmann, & Turner, 2008; Scott, Bromiley, Thacker,
Hutchinson, & Jackson, 2009), active surface (Eskildsen &
Ostergaard, 2006, 2007; Han et al., 2004; Tosun et al., 2006),
and registration-based (Das, Avants, Grossman, & Gee, 2009)
approaches. More recently, Dahnke, Yotter, and Gaser (2013)
proposed a volume-based method, projection-based thickness
(PBT), to address the continuing problem of misclassification
errors in the sulci due to the partial volume effect (PVE). This
method does not explicitly fit inner and outer cortical boundaries. Instead, using tissue probability maps as priors, it estimates cortical thickness from the segmented MRI directly. It
emphasizes the importance of the midsurface as a means to
avoid noise, PVE, and topology defects.
With the plethora of available techniques, it is vital to
characterize the performance space of these various tools. Surface morphometry is critically dependent upon the MR image
properties, particularly GM/WM contrast, signal-to-noise ratio,
resolution, and intensity inhomogeneity. Such factors are a
constant scourge of the increasingly prevalent multicenter
studies such as ADNI, NIHPD, and ABIDE where different
scanners are used. Lerch and Evans (2005) used simulated
data to explore the trade-offs in spatial resolution and detection power for different surface-smoothing approaches and
thickness measures. More recently, Pardoe, Abbott, and
Jackson (2013) conducted a similar analysis but using real
data from four ADNI sites. Dahnke et al. (2013) described a
comprehensive platform for validation and comparison of
different surface analysis packages. Han et al. (2006) and
Schnack et al. (2010) had conducted thorough investigations

of the reliability of cortical thickness estimates under the
effects of field strength and scanner manufacturer or model.
Lusebrink, Wollrab, and Speck (2013) compared cortical thickness estimates from 3 to 7 T MRI data, using isotropic voxels of
either 1 or 0.5 mm dimension. They concluded that field
strength by itself did not significantly affect cortical thickness
measurements but the smaller voxels possible at 7 T reduced
thickness values by as much as a third, a consequence of
reduced PVE errors. The acquisition parameters may also vary
with time, affecting the reliability of longitudinal studies.
Wang et al. (2008) reported a stability in global mean cortical
thickness of 2% although one may expect regional stability to
be lower. Wang, Shi, Li, and Shen (2013) proposed a true 4-D
approach with constrained cortical thickness variation that
reduces the impact of machine-related effects at any single
timepoint upon cortical morphometry.
Relationship Between Morphology and Histology

Classical neuroanatomy (Brodmann, 1909; Flechsig, 1920; Vogt
& Vogt, 1919; von Economo & Koskinas, 1925) still informs
much of our modern understanding of functional neuroanatomy. However, these seminal studies were extremely laborintensive and architectonic boundaries were based on a few
subjectively assessed criteria. Modern noninvasive 3-D imaging
techniques hold promise for the recasting of those classical
concepts in strictly quantitative terms. However, the technology
is still evolving and there remain some unanswered questions
regarding the validity and utility of neuroimaging strategies.
Two related and persistent issues in MRI-based cortical morphometry are (i) the extent to which MRI-based estimates of

cortical thickness are concordant with classical neuroanatomy
and (ii) the spatial relationship between sulcal anatomy and
cortical architectonics. These issues take on greater significance
as MR field strength increases and spatial resolution improves,
and it becomes possible to distinguish fine structure of the
cortex in vivo. The simple construct of a homogeneous GM
mantle with a single GM/WM intensity border begins to lose
its meaning at higher resolution. It is well known that the MRI
signal from GM reflects myelin density in T1- and T2*-weighted
images (Glasser, Goyal, Preuss, Raichle, & Van Essen, 2014;
Glasser & Van Essen, 2011; Turner & Geyer, 2014). Cortical
regions with heavy myelin content, such as the primary motor
cortex or area MT in the visual cortex, exhibit lower GM/WM
159
contrast (Van Essen & Glasser, 2014; Figure 2). This lower
intensity gradient has a consequence for surface extraction algorithms, tending to move the GM/WM surface outward and
indicating a thinner cortex. Unless explicitly accounted for in
the cortical thickness algorithm, such spatial variations in myelin content and GM/WM contrast can introduce a spatially
varying cortical thickness where none exists. Such artifacts
force us to consider the underlying architectonic organization
of the human cortex and its relationship to the MRI signal.
T1 maps resemble myelin-stained histology (Geyer, Weiss,
Riemann, Lohmann, & Turner, 2011; Turner & Geyer, 2014),
and myelo- and cytoarchitectural boundaries have been shown
to be similar using a combination of T1-weighted and
Figure 2 Myelin content estimated by taking the voxelwise ratio of T1W (a) to T2W (b) and colorizing (c). (d) Myelin map on the inflated right
hemisphere of the same subject, including heavily myelinated hot spots centered on the area MT (black/white arrow) and in the intraparietal sulcus
(red arrow). Reproduced from Van Essen, D. C., & Glasser, M. F. (2014). In vivo architectonics: A cortico-centric perspective. Neuroimage,
93(Pt 2), 157164.
160
T2-weighted imaging (Glasser & Van Essen, 2011). With such

information, it becomes possible to adjust simple cortical thickness measurements, based on T1-weighted data alone, to
accommodate variations in underlying architectonics.
Higher field strength MRI also gives us new insight into the
architectonics of the human cortex. Most importantly, it allows
us to study the cortex in vivo and noninvasively in 3-D and to
explore the population variability of cortical organization. It is
now routinely possible to image the cortex at 0.5 mm isotropic
resolution at 7 T and identify group differences in cortical
layering (e.g., Augustinack et al., 2005; Trampel, Ott, & Turner,
2011). Such high resolution affords the possibility of segmenting and modeling the laminar surfaces within the cortex (Bazin
et al., 2014; Waehnert et al., 2014). This allows for the creation
of population-averaged T1 maps at different cortical depths to
reveal area-specific myeloarchitecture (Tardif, Dinse, Schafer,
Turner, & Pl, 2013) and, by extension, the architectonic organization of the cortex.
The relationship between sulcal morphology and architectonic boundaries remains a thorny issue. The seminal work of
the Julich group (Zilles & Amunts, 2009, and references
therein) generated probabilistic cyto- and chemoarchitectural
maps of the Brodmann areas that have been incorporated into
public software packages such as statistical parametric mapping (SPM; Eickhoff et al., 2005, 2007). The extent to which
functional neuroanatomy boundaries are predicted by gross
cortical folding remains controversial and has direct impact
upon the practices of functional brain mapping. The use of
coregistered anatomical MRIs to align fMRI images from different subjects implicitly assumes a tight structurefunction
correspondence such that increasing anatomical alignment,
through high-dimensional spatial normalization (warping),
will also increase functional alignment. However, Crivello
et al. (2002) showed that the benefits of image warping were
limited for functional data, because of a weak structure
function correspondence. On the other hand, Auzias et al.
(2011) showed significant improvement in the detection of
functional signals by jointly aligning volumes and cortical
folding patterns. Fischl et al. (2008) demonstrated that there
was indeed some predictive information in sulcal morphology,
particularly for primary Brodmann areas that showed less variability (4 mm) compared with higher-order association
areas (78 mm).
Covariance of Cortical Morphology

The study of functional connectivity with electro- or magnetoencephalography (Stam, Jones, Nolte, Breakspear, & Scheltens,
2007) or fMRI (Biswal et al., 2010) correlation is well established, as is the study of structural connectivity with diffusion
imaging (Iturria-Medina, 2013). However, there is also increasing interest in the use of structural MRI to investigate anatomical
covariance, as described more fully in recent reviews (AlexanderBloch, Giedd, & Bullmore, 2013; Evans, 2013). Lerch et al.
(2006) first demonstrated covariance maps of cortical thickness,
using a seed-based approach to generate vertexwise maps of
cross-sectional covariance. This study was cross-sectional and
more recent studies have examined the correlation of longitudinal rates of change in cortical thickness, or maturational
coupling (Raznahan, Lerch, et al., 2011). Frontotemporal association cortices showed the strongest and most widespread maturational coupling with other cortical areas, while lower-order
sensory cortices showed the least. This work was extended
(Alexander-Bloch, Raznahan, Bullmore, & Giedd, 2013) to
reveal substantial overlap between anatomical, maturational,
and functional networks in the developing brain.
He, Chen, and Evans (2007) adopted an ROI-based
approach to generate a full N N correlation matrix of all
possible region pairs, albeit at lower spatial resolution. Graph
analysis was then used to capture topological indices for these
cortical networks. Chen, He, Rosa-Neto, Germann, and Evans
(2008), Chen, He, Rosa-Neto, Gong, and Evans (2011), and
Chen, Panizzon, et al. (2011) took this further to reveal an
underlying modularity that reflected well-known functional
systems in the young, healthy brain and that was reduced in
the normal aging brain.
It is not yet clear what cellular mechanisms give rise to the
macroscopic cortical thickness correlation observed with MRI.
Gong, He, Chen, and Evans (2012) compared cortical thickness correlation and probabilistic tractography and found that
3540% of thickness correlations converged with a tractography connection. Convergence was mostly found for positive
correlations while almost all of the negative correlations
(>90%) had no corresponding tractography connection. Different mechanisms may therefore underlie positive and negative thickness correlations, the latter not being mediated by a
direct fiber pathway. Also, since both methods suffer from
methodological limitations, the two techniques may be revealing complementary characteristics of a more complete description of brain connectivity.
Genetic Influences upon Cortical Morphology

Considerable progress has been made in the last decade toward
a clearer understanding of the genetic influences on cortical
morphology. However, there are important methodological
factors to consider. Global neuroanatomical measures, such
as brain volume and mean cortical thickness, are highly heritable (Panizzon et al., 2009), and studies of regional heritability must first remove this global component (Schmitt et al.,
2010; Yoon, Perusse, & Evans, 2012), even if this does lead to
lower heritability estimates. It is has also been noted that ROIbased approaches tend to mask heritability at the vertex level
(Eyler et al., 2012), probably a result of genetic boundaries
differing from gross or functional neuroanatomical borders.
Rimol, Hartberg, et al. (2010) and Rimol, Panizzon, et al.
(2010) mapped the heritability of cortical thickness across the
human brain. They identified regionally specific patterns for
specific seed location rather than a single, global genetic factor.
These patterns were consistent with the division between primary and association areas, as well as patterns of brain gene
expression, neuroanatomical connectivity, and brain maturation trajectories. However, no single explanation dominated.
Chen, He, et al. (2011) and Chen, Panizzon, et al. (2011)
explored the genetic component of regional surface area variability in adult twins. They demonstrated a strong anterior-toposterior gradient as well as symmetric patterns of regionalization and subsequently created a human brain atlas based solely
Total surface area (cm2)
Total average thickness (mm)
600
1900
2.8
Cerebral cortical volume (cm3)

650
2000
2.9
161
550
1800
2.7
500
1700
10
15
Age
20
10
15
Age
20
10
15
Age
20
Figure 3 Developmental trajectories of cortical thickness, total surface area, and overall cortical volume. Reproduced from Wierenga, L. M., Langen,
M., Oranje, B. & Durston, S. (2014). Unique developmental trajectories of cortical thickness and surface area. NeuroImage, 87, 120126.
http://www.ncbi.nlm.nih.gov/pubmed/24246495.
on genetic indices (Chen et al., 2012). They recently identified

a dorsalventral genetic gradient in cortical thickness (Chen
et al., 2013) and revealed a dissociation between the organizing principles for cortical surface area and thickness. Surface
area clusters showed great genetic proximity with clusters from
the same lobe, while thickness clusters have close genetic relatedness with clusters that have similar maturational timing.
Other studies have also emphasized the fact that cortical thickness and vertexwise surface area exhibit different genetic influences (Hill et al., 2010; Sanabria-Diaz et al., 2010), and that
studies of regional or vertexwise cortical volume (loosely, the
product of thickness and area) will tend to conflate these two
influences (Panizzon et al., 2009) Figure 3 illustrates the different trajectories of these three cortical metrics during normal
development.
Schmitt et al. (2008) identified genetically mediated frontoparietal and occipital networks of cortical thickness. They also
found (Schmitt et al., 2009) that interhemispheric covariance
in cortical thickness is largely genetically mediated while environmental influence is more intrahemispheric. Conversely, in
a cohort of 8-year-old twins, Yoon, Fahim, Perusse, and Evans
(2010) and Yoon et al. (2012) found genetic environmental
influences to be lateralized, with the language-dominant left
cerebral cortex under stronger genetic control. Intriguingly,
differences in genetic covariance and heritability appear to be
driven by a common genetic factor that influences GM and
WM differently (Schmitt et al., 2010).
The relative influence of genetic and environmental factors
on cortical growth is dynamic and changes with age. Lenroot
et al. (2009) examined age-related differences in the heritability of cortical thickness in a large pediatric sample of twins,
twin siblings, and singletons. The primary sensorimotor cortex,
which develops earlier, showed greater genetic effects earlier in
childhood. Later developing regions within the dorsal prefrontal cortex and temporal lobes showed increasing genetic effects
with maturation. Thus, regions associated with complex cognitive processes such as language, tool use, and executive function are more heritable in adolescents. Joshi et al. (2011)
studied young adult twins to reveal a strong genetic influence
on GM thickness and volume in the frontoparietal regions.
Several regions where cortical structure was correlated with

IQ were shown to be under genetic control. In healthy adolescent twins, however, Yang, Carrey, Bernier, and Macmaster
(2012) and Yang, Joshi, et al. (2012) found that regions with
genetic contributions of > 80% were observed in the prefrontal
cortex, whereas strong unique environmental influences were
found in the parietal association regions. The genetic variance
for thickness in adolescents in the prefrontal regions overlapped with those in the adult sample. However, the unique
environmental effects in the parietal association areas suggest
that these regions are more shaped by experience and could
form targets for early interventions for behavioral disorders.
Applications
There is now a huge literature on clinical and basic applications
of cortical morphometry, in general, and cortical thickness
analysis, in particular, notably in the following areas:
Neurodevelopment: Giedd et al. (1999), Gogtay and
Thompson (2010), Gogtay et al. (2004), Lerch et al. (2006),
Sowell, Thompson, Leonard, et al. (2004), Sowell, Thompson,
and Toga (2004), Thompson et al. (2005), Toga, Thompson,
and Sowell (2006), Raznahan, Lerch, et al. (2011), Raznahan,
Shaw, et al. (2011), Wierenga et al. (2014), Zhou, Lebel, Evans,
and Beaulieu (2013), Lawson, Duda, Avants, Wu, and Farah
(2013), Dennis and Thompson (2013), Khundrakpam et al.
(2013), Alexander-Bloch, Raznahan, et al. (2013), and
Burgaleta, Johnson, Waber, Colom, and Karama (2014).
Gender and aging: Salat et al. (2004), Im et al. (2006, 2008),
Luders, Narr, Thompson, Rex, Jancke, et al. (2006), Luders,
Narr, Thompson, Rex, Woods, et al. (2006), Sowell et al.
(2007), Ecker et al. (2009), Fjell et al. (2009), Lv et al.
(2010), Thambisetty et al. (2010), Chen, Panizzon, et al.
(2011), Chen, He, et al. (2011), Yao, Hu, Liang, Zhao, and
Jackson (2012), Creze et al. (2013), Gautam, Cherbuin,
Sachdev, Wen, and Anstey (2013), and van Velsen et al. (2013).
Cognition and IQ: Giedd et al. (1999), Fjell et al. (2006),
Lerch et al. (2006), Choi et al. (2008), Dickerson et al. (2008),
Andersson, Ystad, Lundervold, and Lundervold (2009),
162
Karama et al. (2009, 2011, 2013), Ziegler et al. (2010), Porter,

Collins, Muetzel, Lim, and Luciana (2011), Burzynska et al.
(2012), Hyatt, Haney-Caron, and Stevens (2012), Schilling
et al. (2012,2013), Walhovd, Tamnes, Ostby, Due-Tonnessen,
and Fjell (2012), Ducharme et al. (2012), and Ameis et al.
(2014).
Alzheimers disease: Thompson et al. (2004), Lerch et al.
(2005, 2008), He, Chen, and Evans (2008), Dickerson et al.
(2009), Julkunen et al. (2010), Kim et al. (2012), McDonald
et al. (2009), Querbes et al. (2009), Reid and Evans (2013),
Ridgway et al. (2012), Sabuncu et al. (2012), Cho, Seong,
Jeong, and Shin (2012), Cho et al. (2013), Hartikainen et al.
(2012), and Eskildsen et al. (2013).
Epilepsy: McDonald et al. (2008), Bernhardt, Chen, He,
Evans, and Bernasconi (2011), and Thesen et al. (2011)
ADHD: Shaw et al. (2006), Makris et al. (2012), Yang,
Carrey, Bernier, and Macmaster (2012), Yang, Joshi, et al.
(2012), Almeida Montes et al. (2013), and McLaughlin et al.
(2013).
Autism: Hardan, Muddasani, Vemulapalli, Keshavan, and
Minshew (2006), Hardan, Libove, Keshavan, Melhem, and
Minshew (2009), Hyde, Samson, Evans, and Mottron (2010),
Jiao et al. (2010), Sato et al. (2013), Doyle-Thomas et al.
(2013), and Ecker et al. (2013).
Depression, OCD, and social anxiety: Jarnum et al. (2011),
Wagner et al. (2012), Ducharme et al. (2013), Mackin et al.
(2013), Truong et al. (2013), and van Eijndhoven et al. (2013).
OCD: Nakamae et al. (2012), Fan et al. (2013), Kim, Jung,
Kim, Jang, and Kwon (2013), Bruhl et al. (2013), and Frick
et al. (2013).
Schizophrenia and psychosis: Kuperberg et al. (2003), Nesvag
et al. (2008), Schultz et al. (2010), Rimol, Hartberg, et al.
(2010), Rimol, Panizzon, et al. (2010), Rimol et al. (2012),
van Haren et al. (2011), Buchy et al. (2012), Vita, De Peri,
Deste, and Sacchetti (2012), and Benetti et al. (2013).
Conclusions
It is apparent that cortical surface morphometry is a booming
industry, with a continuous stream of new methodological
advances and applications in neurology, psychiatry, and developmental neurobiology and cognitive neuroscience. However,
there are also numerous areas where basic assumptions can be
called into question, most notably in the very definition of
cortical thickness, as derived from structural MRI. Such issues
should not be seen as a fundamental flaw in the methodology
but as a caution upon the interpretation of the data. Many
important new insights have arisen from the ability to capture,
noninvasively and automatically, longitudinal and crosssectional measures of cortical morphology at every point on
the brain surface. Some of the concerns regarding the accuracy
of absolute values of cortical thickness are mitigated when one
considers the relative changes inherent in group comparison or
longitudinal studies of cortical morphometry. Of course, such
pragmatic considerations regarding current applications of the
basic techniques do not detract from the drive to improve the
techniques through the use of higher field strength (Fujimoto
et al., 2014; Lusebrink et al., 2013) or novel analytic
approaches to quantify the cortical laminar structures (Tardif
et al., 2013; Turner & Geyer, 2014). The next decade seems
likely to bring a continuing growth of cortical morphometric
methods that are increasingly able to capture the fine structure
of cortical anatomy and revolutionize the painstaking efforts of
the great early twentieth century neuroanatomists.
References
Alexander-Bloch, A., Giedd, J. N., & Bullmore, E. (2013). Imaging structural covariance between human brain regions. Nature Reviews. Neuroscience, 14(5),
322336.
Alexander-Bloch, A., Raznahan, A., Bullmore, E., & Giedd, J. (2013). The convergence
of maturational change and structural covariance in human cortical networks. The
Journal of Neuroscience, 33(7), 28892899. PubMed: 23407947.
Almeida Montes, L. G., Prado Alcantara, H., Martinez Garcia, R. B., De La Torre, L. B.,
Avila Acosta, D., & Duarte, M. G. (2013). Brain cortical thickness in ADHD: Age,
sex, and clinical correlations. Journal of Attention Disorders, 17(8), 641654.
Ameis, S. H., Ducharme, S., Albaugh, M. D., Hudziak, J. J., Botteron, K. N., Lepage, C.,
et al. (2014). Cortical thickness, cortico-amygdalar networks, and externalizing
behaviors in healthy children. Biological Psychiatry, 75(1), 6572.
Andersson, M., Ystad, M., Lundervold, A., & Lundervold, A. J. (2009). Correlations
between measures of executive attention and cortical thickness of left posterior
middle frontal gyrus A dichotic listening study. Behavioral and Brain Functions:
BBF, 5, 41. PubMed: 19796388.
Ashburner, J., & Friston, K. J. (2000). Voxel-based morphometry-the methods.
Ashburner, J., Hutton, C., Frackowiak, R., Johnsrude, I., Price, C., & Friston, K. (1998).
Identifying global anatomical differences: Deformation-based morphometry. Human
Augustinack, J. C., van der Kouwe, A. J., Blackwell, M. L., Salat, D. H., Wiggins, C. J.,
Frosch, M. P., et al. (2005). Detection of entorhinal layer II using 7 Tesla [corrected]
magnetic resonance imaging. Annals of Neurology, 57(4), 489494.
Auzias, G., Colliot, O., Glaune`s, J. A., Perrot, M., Mangin, J.-F., Trouve, A., et al. (2011).
Bazin, P. L., Weiss, M., DInse, J., Schaffer, A., Trampel, R., & Turner, R. (2014). A
computational framework for ultra-high resolution cortical segmentation at 7 T.
Benetti, S., Pettersson-Yeo, W., Hutton, C., Catani, M., Williams, S. C., Allen, P., et al.
(2013). Elucidating neuroanatomical alterations in the at risk mental state and first
episode psychosis: A combined voxel-based morphometry and voxel-based cortical
thickness study. Schizophrenia Research, 150(23), 505511. PubMed: 24084578.
Bernhardt, B. C., Chen, Z., He, Y., Evans, A. C., & Bernasconi, N. (2011). Graphtheoretical analysis reveals disrupted small-world organization of cortical thickness
correlation networks in temporal lobe epilepsy. Cerebral Cortex, 21(9), 21472157.
PubMed: 21330467.
Biswal, B. B., Mennes, M., Zuo, X. N., Gohel, S., Kelly, C., & Smith, S. M. (2010).
Toward discovery science of human brain function. PNAS, 107(10), 47344739.
Prinzipien dargestellt auf Grund des Zellenbaues. Leipzig: Barth.
Bruhl, A. B., Hanggi, J., Baur, V., Rufer, M., Delsignore, A., & Weidt, S. (2013).
Increased cortical thickness in a frontoparietal network in social anxiety disorder.
Human Brain Mapping, 35, 29662977. PubMed: 24039023.
Buchy, L., Ad-Dabbagh, Y., Lepage, C., Malla, A., Joober, R., Evans, A., et al. (2012).
Symptom attribution in first episode psychosis: A cortical thickness study.
Psychiatry Research, 203(1), 613. PubMed: 22917501.
Burgaleta, M., Johnson, W., Waber, D. P., Colom, R., & Karama, S. (2014). Cognitive
ability changes and dynamics of cortical thickness development in healthy children
and adolescents. NeuroImage, 84, 810819. PubMed: 24071525.
Burzynska, A. Z., Nagel, I. E., Preuschhof, C., Gluth, S., Backman, L., Li, S. C., et al.
(2012). Cortical thickness is linked to executive functioning in adulthood and aging.
Human Brain Mapping, 33(7), 16071620. PubMed: 21739526.
Carman, G. J., Drury, H. A., & Van Essen, D. C. (1995). Computational methods for
reconstructing and unfolding the cerebral cortex. Cerebral Cortex, 5(6), 506517.
Chen, C. H., Fiecas, M., Gutierrez, E. D., Panizzon, M. S., Eyler, L. T., Vuoksimaa, E.,
et al. (2013). Genetic topography of brain morphology. Proceedings of the National
Academy of Sciences of the United States of America, 110(42), 1708917094.
PubMed: 24082094.
Chen, C. H., Gutierrez, E. D., Thompson, W., Panizzon, M. S., Jernigan, T. L.,
Eyler, L. T., et al. (2012). Hierarchical genetic organization of human cortical surface
area. Science, 335(6076), 16341636.

Chen, Z. J., He, Y., Rosa-Neto, P., Germann, J., & Evans, A. C. (2008). Revealing
modular architecture of human brain structural networks by using cortical thickness
from MRI. Cerebral Cortex, 18(10), 23742381. PubMed: 18267952.
Chen, Z. J., He, Y., Rosa-Neto, P., Gong, G., & Evans, A. C. (2011). Age-related
alterations in the modular organization of structural cortical network by using
cortical thickness from MRI. NeuroImage, 56(1), 235245. PubMed: 21238595.
Chen, C. H., Panizzon, M. S., Eyler, L. T., Jernigan, T. L., Thompson, W.,
Fennema-Notestine, C., et al. (2011). Genetic influences on cortical regionalization
in the human brain. Neuron, 72(4), 537544. PubMed: 22099457.
Cho, H., Jeon, S., Kang, S. J., Lee, J. M., Lee, J. H., Kim, G. H., et al. (2013).
Longitudinal changes of cortical thickness in early- versus late-onset
Alzheimers disease. Neurobiology of Aging, 34(7) 1921.e91921e15; PubMed:
23391426.
Cho, Y., Seong, J. K., Jeong, Y., & Shin, S. Y. (2012). Individual subject classification
for Alzheimers disease based on incremental learning using a spatial frequency
representation of cortical thickness data. NeuroImage, 59(3), 22172230. PubMed:
22008371.
Choi, Y. Y., Shamosh, N. A., Cho, S. H., DeYoung, C. G., Lee, M. J., Lee, J. M., et al.
(2008). Multiple bases of human intelligence revealed by cortical thickness and
neural activation. The Journal of Neuroscience: The Official Journal of the Society
for Neuroscience, 28(41), 1032310329. PubMed: 18842891.
Chung, M. K., Robbins, S., & Evans, A. C. (2005). Unified statistical approach to
cortical thickness analysis. Information Processing in Medical Imaging:
Proceedings of the . . . Conference, 19, 627638. PubMed: 17354731.
Chung, M. K., Worsley, K. J., Nacewicz, B. M., Dalton, K. M., & Davidson, R. J. (2010).
General multivariate linear modeling of surface shapes using SurfStat. NeuroImage,
53(2), 491505.
Creze, M., Versheure, L., Besson, P., Sauvage, C., Leclerc, X., & Jissendi-Tchofo, P.
(2013). Age- and gender-related regional variations of human brain cortical
thickness, complexity, and gradient in the third decade. Human Brain Mapping, 35,
28172835. PubMed: 24142374.
Crivello, F., Schormann, T., Tzourio-Mazoyer, N., Roland, P. E., Zilles, K., &
Mazoyer, B. M. (2002). Comparison of spatial normalization procedures and their
impact on functional maps. Human Brain Mapping, 16(4), 228250.
Dahnke, R., Yotter, R. A., & Gaser, C. (2013). Cortical thickness and central surface
estimation. NeuroImage, 65, 336348. PubMed: 23041529.
Segmentation and surface reconstruction. NeuroImage, 9(2), 179194. PubMed:
9931268.
Das, S. R., Avants, B. B., Grossman, M., & Gee, J. C. (2009). Registration
based cortical thickness measurement. NeuroImage, 45(3), 867879. PubMed:
19150502.
Dennis, E. L., & Thompson, P. M. (2013). Typical and atypical brain development: A
review of neuroimaging studies. Dialogues in Clinical Neuroscience, 15(3),
359384. PubMed: 24174907.
Dickerson, B. C., Feczko, E., Augustinack, J. C., Pacheco, J., Morris, J. C., Fischl, B.,
et al. (2009). Differential effects of aging and Alzheimers disease on medial
temporal lobe cortical thickness and surface area. Neurobiology of Aging, 30(3),
432440. PubMed: 17869384.
Dickerson, B. C., Fenstermacher, E., Salat, D. H., Wolk, D. A., Maguire, R. P.,
Desikan, R., et al. (2008). Detection of cortical thickness correlates of cognitive
performance: Reliability across MRI scan sessions, scanners, and field strengths.
NeuroImage, 39(1), 1018. PubMed: 17942325.
Doyle-Thomas, K. A., Duerden, E. G., Taylor, M. J., Lerch, J. P., Soorya, L. V.,
Wang, A. T., et al. (2013). Effects of age and symptomatology on cortical thickness
in autism spectrum disorders. Research in Autism Spectrum Disorders, 7(1),
141150. PubMed: 23678367.
Ducharme, S., Albaugh, M. D., Hudziak, J. J., Botteron, K. N., Nguyen, T. V., &
Truong, C. (2013). Anxious/depressed symptoms are linked to right ventromedial
prefrontal cortical thickness maturation in healthy children and young adults.
Cerebral Cortex, 24, 29412950. PubMed: 23749874.
Ducharme, S., Hudziak, J. J., Botteron, K. N., Albaugh, M. D., Nguyen, T. V., &
Karama, S. (2012). Decreased regional cortical thickness and thinning rate are
associated with inattention symptoms in healthy children. Journal of the American
Academy of Child and Adolescent Psychiatry, 51(1), 1827. PubMed: 22176936
e12.
Ecker, C., Ginestet, C., Feng, Y., Johnston, P., Lombardo, M. V., Lai, M. C., et al.
(2013). Brain surface anatomy in adults with autism: the relationship between
surface area, cortical thickness, and autistic symptoms. JAMA Psychiatry, 70(1),
5970. PubMed: 23404046.
Ecker, C., Stahl, D., Daly, E., Johnston, P., Thomson, A., & Murphy, D. G. (2009). Is
there a common underlying mechanism for age-related decline in cortical
thickness? Neuroreport, 20(13), 11551160. PubMed: 19690502.
163
Eickhoff, S. B., Paus, T., Caspers, S., Grosbras, M. H., Evans, A. C., Zilles, K., et al.
(2007). Assignment of functional activations to probabilistic cytoarchitectonic areas
revisited. NeuroImage, 36(3), 511521.
Eickhoff, S. B., Stephan, K. E., Mohlberg, H., Grefkes, C., Fink, G. R., & Amunts, K.
functional imaging data. NeuroImage, 25, 13251335 http://www2.fz-juelich.de/
inm/inm-1/spm_anatomy_toolbox.
Eskildsen, S. F., Coupe, P., Garca-Lorenzo, D., Fonov, V., Pruessner, J. C.,
Collins, D. L., et al. (2013). Prediction of Alzheimers disease in subjects with mild
cognitive impairment from the ADNI cohort using patterns of cortical thinning.
Eskildsen, S. F., & Ostergaard, L. R. (2006). Active surface approach for extraction of
the human cerebral cortex from MRI. Medical Image Computing and ComputerAssisted Intervention, 4191, 823830 Eds: Larsen R, Nielsen M, Sporring J.
Eskildsen, S. F., & Ostergaard, L. R. (2007). Quantitative comparison of two cortical
surface extraction methods using MRI phantoms. Medical Image Computing and
Computer-Assisted Intervention, 4791, 409416 Eds: Ayache N, Ourselin S,
Maeder A.
Evans, A. C. (2013). Networks of anatomical covariance. NeuroImage, 80, 489504.
Eyler, L. T., Chen, C. H., Panizzon, M. S., Fennema-Notestine, C., Neale, M. C., Jak, A.,
et al. (2012). A comparison of heritability maps of cortical surface area and
thickness and the influence of adjustment for whole brain measures: A magnetic
resonance imaging twin study. Twin Research and Human Genetics, 15(3),
304314. PubMed: 22856366.
Fan, Q., Palaniyappan, L., Tan, L., Wang, J., Wang, X., Li, C., et al. (2013). Surface
anatomical profile of the cerebral cortex in obsessive-compulsive disorder: A study
of cortical thickness, folding and surface area. Psychological Medicine, 43(5),
10811091. PubMed: 22935427.
Fischl, B., & Dale, A. M. (2000). Measuring the thickness of the human cerebral cortex
from magnetic resonance images. Proceedings of the National Academy of Sciences
of the United States of America, 97(20), 1105011055. PubMed: 10984517.
19731980.
Fischl, B., Sereno, M. I., & Dale, A. M. (1999). Cortical surface-based analysis. II:
Inflation, flattening, and a surface-based coordinate system. NeuroImage, 9(2),
195207. PubMed: 9931269.
Fjell, A. M., Walhovd, K. B., Reinvang, I., Lundervold, A., Salat, D., Quinn, B. T., et al.
(2006). Selective increase of cortical thickness in high-performing elderly
Structural indices of optimal cognitive aging. NeuroImage, 29(3), 984994.
PubMed: 16176876.
Fjell, A. M., Westlye, L. T., Amlien, I., Espeseth, T., Reinvang, I., Raz, N., et al. (2009).
High consistency of regional cortical thinning in aging across multiple samples.
Cerebral Cortex, 19(9), 20012012. PubMed: 19150922.
Frick, A., Howner, K., Fischer, H., Eskildsen, S. F., Kristiansson, M., & Furmark, T.
(2013). Cortical thickness alterations in social anxiety disorder. Neuroscience
Letters, 536, 5255. PubMed: 23328446.
Fujimoto, K., Polimeni, J. R., van der Kouwe, A. J., Reuter, M., Kober, T., Benner, T.,
et al. (2014). Quantitative comparison of cortical surface reconstructions from
MP2RAGE and multi-echo MPRAGE data at 3 and 7 T. NeuroImage, 90, 6073.
Gautam, P., Cherbuin, N., Sachdev, P. S., Wen, W., & Anstey, K. J. (2013). Sex
differences in cortical thickness in middle aged and early old-aged adults:
Personality and total health through life study. Neuroradiology, 55(6), 697707.
PubMed: 23468177.
Geyer, S., Weiss, M., Riemann, K., Lohmann, G., & Turner, R. (2011). Microstructural
Giedd, J. N., Blumenthal, J., Jeffries, N. O., Castellanos, F. X., Liu, H., Zijdenbos, A. P.,
MRI study. Nature Neuroscience, 2(10), 861863.
Glasser, M. F., Goyal, M. S., Preuss, T. M., Raichle, M. E., & Van Essen, D. C. (2014).
Trends and properties of human cerebral cortex: Correlation with cortical myelin
content. NeuroImage, 93, 165175.
Glasser, M. F., & Van Essen, D. C. (2011). Mapping human cortical areas in vivo based
on myelin content as revealed by T1- and T2-weighted MRI. The Journal of
Neuroscience, 31(32), 1159711616.
Goebel, R. (1996). BrainVoyager: A program for analyzing and visualizing functional
and structural magnetic resonance datasets. NeuroImage, 3, S604.
Goebel, R. (1997). BrainVoyager 2.0: From 2D to 3D fMRI analysis and visualization.
NeuroImage, 5, S635.
164
Goebel, R. (2012). BrainVoyager Past, present, future. NeuroImage, 62(2),

748756.
United States of America, 101(21), 81748179. PubMed: 15148381.
Gogtay, N., & Thompson, P. M. (2010). Mapping gray matter development: Implications
for typical development and vulnerability to psychopathology. Brain and Cognition,
72(1), 615. PubMed: 19796863.
Gong, G., He, Y., Chen, Z. J., & Evans, A. C. (2012). Convergence and divergence of
thickness correlations with diffusion connections across the human cerebral cortex.
Haidar, H., & Soul, J. S. (2006). Measurement of cortical thickness in 3D brain MRI
data: Validation of the Laplacian method. Journal of Neuroimaging: Official
Journal of the American Society of Neuroimaging, 16(2), 146153. PubMed:
16629737.
Han, X., Jovicich, J., Salat, D., van der Kouwe, A., Quinn, B., Czanner, S., et al. (2006).
Reliability of MRI-derived measurements of human cerebral cortical thickness: The
effects of field strength, scanner upgrade and manufacturer. NeuroImage, 32(1),
180194. PubMed: 16651008.
Han, X., Pham, D., Tosun, D., Rettmann, M., Xu, C., & Prince, J. (2004). CRUISE:
Cortical reconstruction using implicit surface evolution. NeuroImage, 23(3),
9971012.
Hardan, A. Y., Libove, R. A., Keshavan, M. S., Melhem, N. M., & Minshew, N. J. (2009).
A preliminary longitudinal magnetic resonance imaging study of brain volume and
cortical thickness in autism. Biological Psychiatry, 66(4), 320326. PubMed:
19520362.
Hardan, A. Y., Muddasani, S., Vemulapalli, M., Keshavan, M. S., & Minshew, N. J.
(2006). An MRI study of increased cortical thickness in autism. The American
Journal of Psychiatry, 163(7), 12901292. PubMed: 16816240.
Hartikainen, P., Rasanen, J., Julkunen, V., Niskanen, E., Hallikainen, M., Kivipelto, M.,
et al. (2012). Cortical thickness in frontotemporal dementia, mild cognitive
impairment, and Alzheimers disease. Journal of Alzheimers disease: JAD, 30(4),
857874. PubMed: 22466003.
He, Y., Chen, Z. J., & Evans, A. C. (2007). Small-world anatomical networks in the
human brain revealed by cortical thickness from MRI. Cerebral Cortex, 17(10),
24072419. PubMed: 17204824.
He, Y., Chen, Z., & Evans, A. (2008). Structural insights into aberrant topological
patterns of large-scale cortical networks in Alzheimers disease. The Journal of
Neuroscience: The Official Journal of the Society for Neuroscience, 28(18),
47564766. PubMed: 18448652.
Hill, J., Inder, T., Neil, J., Dierker, D., Harwell, J., & Van Essen, D. C. (2010). Similar
patterns of cortical expansion during human development and evolution. PNAS
USA, 107, 1313513140.
Holmes, C. J., MacDonald, D., Sled, J. G., Toga, A. W., & Evans, A. C. (1996). Cortical
peeling: CSF/grey/white matter boundaries visualized by nesting isosurfaces.
Proceedings Visualization in Biomedical Computing, 4, 99104.
Hutton, C., De Vita, E., Ashburner, J., Deichmann, R., & Turner, R. (2008). Voxel-based
cortical thickness measurements in MRI. NeuroImage, 40, 17011710.
Hyatt, C. J., Haney-Caron, E., & Stevens, M. C. (2012). Cortical thickness and folding
deficits in conduct-disordered adolescents. Biological psychiatry, 72(3), 207214.
PubMed: 22209639.
Hyde, K. L., Samson, F., Evans, A. C., & Mottron, L. (2010). Neuroanatomical
differences in brain areas implicated in perceptual and other core features of autism
revealed by cortical thickness analysis and voxel-based morphometry. Human Brain
Mapping, 31(4), 556566. PubMed: 19790171.
Im, K., Lee, J. M., Lee, J., Shin, Y. W., Kim, I. Y., Kwon, J. S., et al. (2006). Gender
difference analysis of cortical thickness in healthy young adults with surface-based
methods. NeuroImage, 31(1), 3138. PubMed: 16426865.
Im, K., Lee, J. M., Lyttelton, O., Kim, S. H., Evans, A. C., & Kim, S. I. (2008). Brain size
and cortical structure in the adult human brain. Cerebral Cortex, 18(9), 21812191.
PubMed: 18234686.
Iturria-Medina, Y. (2013). Brain anatomical networks on the prediction of abnormal
brain states. Brain Connectivity, 3(1), 121.
Jarnum, H., Eskildsen, S. F., Steffensen, E. G., Lundbye-Christensen, S.,
Simonsen, C. W., Thomsen, I. S., et al. (2011). Longitudinal MRI study of cortical
thickness, perfusion, and metabolite levels in major depressive disorder. Acta
Psychiatrica Scandinavica, 124(6), 435446. PubMed: 21923809.
Jiao, Y., Chen, R., Ke, X., Chu, K., Lu, Z., & Herskovits, E. H. (2010). Predictive models
of autism spectrum disorder based on brain regional cortical thickness.
Jones, S. E., Buchbinder, B. R., & Aharon, I. (2000). Three-dimensional mapping of
cortical thickness using Laplaces equation. Human Brain Mapping, 11, 1232.
Joshi, A. A., Lepore, N., Joshi, S. H., Lee, A. D., Barysheva, M., Stein, J. L., et al. (2011).
The contribution of genes to cortical thickness and volume. Neuroreport, 22(3),
101105. PubMed: 21233781.
Julkunen, V., Niskanen, E., Koikkalainen, J., Herukka, S. K., Pihlajamaki, M.,
Hallikainen, M., et al. (2010). Differences in cortical thickness in healthy controls,
subjects with mild cognitive impairment, and Alzheimers disease patients: A
longitudinal study. Journal of Alzheimers disease: JAD, 21(4), 11411151.
PubMed: 21504134.
Kabani, N., Le Goualher, G., MacDonald, D., & Evans, A. C. (2001). Measurement of
cortical thickness using an automated 3-D algorithm: A validation study.
Karama, S., Ad-Dabbagh, Y., Haier, R., Deary, I., Lyttleton, O., Lepage, C., et al. (2009).
Positive association between cognitive ability and cortical thickness in a
representative US sample of healthy 6 to 18 year-olds. Intelligence, 37(2), 145155.
PubMed: 20161325.
Karama, S., Bastin, M. E., Murray, C., Royle, N. A., Penke, L., & Munoz Maniega, S.
(2013). Childhood cognitive ability accounts for associations between
cognitive ability and brain cortical thickness in old age. Molecular Psychiatry, 19,
555559. PubMed: 23732878.
Karama, S., Colom, R., Johnson, W., Deary, I. J., Haier, R., Waber, D. P., et al. (2011).
Cortical thickness correlates of specific cognitive performance accounted for by the
general factor of intelligence in healthy children aged 6 to 18. NeuroImage, 55(4),
14431453. PubMed: 21241809.
Khundrakpam, B. S., Reid, A., Brauer, J., Carbonell, F., Lewis, J., Ameis, S., et al.
(2013). Developmental changes in organization of structural brain networks.
Cerebral Cortex, 23(9), 20722085. PubMed: 22784607.
Kim, G. H., Jeon, S., Seo, S. W., Kim, M. J., Kim, J. H., Roh, J. H., et al. (2012).
Topography of cortical thinning areas associated with hippocampal atrophy (HA) in
patients with Alzheimers disease (AD). Archives of Gerontology and Geriatrics,
54(2), e122e129.
Kim, S. G., Jung, W. H., Kim, S. N., Jang, J. H., & Kwon, J. S. (2013). Disparity
between dorsal and ventral networks in patients with obsessive-compulsive
disorder: Evidence revealed by graph theoretical analysis based on
cortical thickness from MRI. Frontiers in Human Neuroscience, 7, 302. PubMed:
23840184.
Kim, J. S., Singh, V., Lee, J. K., Lerch, J., Ad-Dabbagh, Y., MacDonald, D., et al.
(2005). Automated 3-D extraction and evaluation of the inner and outer cortical
surfaces using a Laplacian map and partial volume effect classification. NeuroImage,
27(1), 210221. PubMed: 15896981.
Kriegeskorte, N., & Goebel, R. (2001). An efficient algorithm for topologically correct
segmentation of the cortical sheet in anatomical MR volumes. NeuroImage, 14(2),
329346.
Kuperberg, G. R., Broome, M. R., McGuire, P. K., David, A. S., Eddy, M., Ozawa, F., et al.
(2003). Regionally localized thinning of the cerebral cortex in schizophrenia.
Archives of General Psychiatry, 60(9), 878888. PubMed: 12963669.
Lawson, G. M., Duda, J. T., Avants, B. B., Wu, J., & Farah, M. J. (2013). Associations
between childrens socioeconomic status and prefrontal cortical thickness.
Developmental Science, 16(5), 641652. PubMed: 24033570.
Lee, J. K., Lee, J. M., Kim, J. S., Kim, I. Y., Evans, A. C., & Kim, S. I. (2006). A novel
quantitative cross-validation of different cortical surface reconstruction algorithms
using MRI phantom. NeuroImage, 31(2), 572584.
Lenroot, R. K., Schmitt, J. E., Ordaz, S. J., Wallace, G. L., Neale, M. C., Lerch, J. P., et al.
(2009). Differences in genetic and environmental influences on the human cerebral
cortex associated with development during childhood and adolescence. Human
Lerch, J. P., & Evans, A. C. (2005). Cortical thickness analysis examined through power
analysis and a population simulation. NeuroImage, 24(1), 163173. PubMed:
15588607.
Lerch, J. P., Pruessner, J., Zijdenbos, A. P., Collins, D. L., Teipel, S. J., Hampel, H.,
et al. (2008). Automated cortical thickness measurements from MRI can accurately
separate Alzheimers patients from normal elderly controls. Neurobiology of Aging,
29(1), 2330. PubMed: 17097767.
Lerch, J. P., Pruessner, J. C., Zijdenbos, A., Hampel, H., Teipel, S. J., & Evans, A. C.
(2005). Focal decline of cortical thickness in Alzheimers disease identified by
computational neuroanatomy. Cerebral Cortex, 15(7), 9951001. PubMed:
15537673.
Lerch, J. P., Worsley, K., Shaw, W. P., Greenstein, D. K., Lenroot, R. K., Giedd, J., et al.
(2006). Mapping anatomical correlations across cerebral cortex (MACACC)
using cortical thickness from MRI. NeuroImage, 31(3), 9931003. PubMed:
16624590.
Luders, E., Narr, K. L., Thompson, P. M., Rex, D. E., Jancke, L., & Toga, A. W. (2006).
Hemispheric asymmetries in cortical thickness. Cerebral Cortex, 16(8), 12321238.
PubMed: 16267139.

Luders, E., Narr, K. L., Thompson, P. M., Rex, D. E., Woods, R. P., Deluca, H., et al.
(2006). Gender effects on cortical thickness and the influence of scaling. Human
Brain Mapping, 27(4), 314324. PubMed: 16124013.
Lusebrink, F., Wollrab, A., & Speck, O. (2013). Cortical thickness determination of the
human brain using high resolution 3 T and 7 T MRI data. NeuroImage, 70,
122131. PubMed: 23261638.
Lv, B., Li, J., He, H., Li, M., Zhao, M., Ai, L., et al. (2010). Gender consistency and
difference in healthy adults revealed by cortical thickness. NeuroImage, 53(2),
373382. PubMed: 20493267.
MacDonald, D., Avis, D., & Evans, A. C. (1994). Multiple surface identification
and matching in magnetic resonance imaging. Proceedings of SPIE, 2359,
160169.
MacDonald, D., Kabani, N., Avis, D., & Evans, A. C. (2000). Automated 3-D extraction of
inner and outer surfaces of cerebral cortex from MRI. NeuroImage, 12(3), 340356.
PubMed: 10944416.
Mackin, R. S., Tosun, D., Mueller, S. G., Lee, J. Y., Insel, P., Schuff, N., et al. (2013).
Patterns of reduced cortical thickness in late-life depression and relationship to
psychotherapeutic response. The American Journal of Geriatric Psychiatry: Official
Journal of the American Association for Geriatric Psychiatry, 21(8), 794802.
PubMed: 23567394.
Makris, N., Seidman, L. J., Brown, A., Valera, E. M., Kaiser, J. R., Petty, C. R., et al.
(2012). Further understanding of the comorbidity between attention-deficit/
hyperactivity disorder and bipolar disorder in adults: An MRI study of cortical
thickness. Psychiatry Research, 202(1), 111. PubMed: 22640688.
Mangin, J.-F., Frouin, V., Bloch, I., Regis, J., & Lopez-Krahe, J. (1995). From 3D MR
images to structural representations of the cortex topography using topology
preserving deformations. Journal of Mathematical Imaging and Vision, 5(4),
297318.
McDonald, C. R., Hagler, D. J., Jr., Ahmadi, M. E., Tecoma, E., Iragui, V.,
Gharapetian, L., et al. (2008). Regional neocortical thinning in mesial temporal lobe
epilepsy. Epilepsia, 49(5), 794803. PubMed: 18266751.
McDonald, C. R., McEvoy, L. K., Gharapetian, L., Fennema-Notestine, C.,
Hagler, D. J., Jr., Holland, D., et al. (2009). Regional rates of neocortical atrophy
from normal aging to early Alzheimer disease. Neurology, 73(6), 457465.
PubMed: 19667321.
McLaughlin, K. A., Sheridan, M. A., Winter, W., Fox, N. A., Zeanah, C. H., &
Nelson, C. A. (2013). Widespread reductions in cortical thickness following severe
early-life deprivation: A neurodevelopmental pathway to attention-deficit/
hyperactivity disorder. Biological Psychiatry, 76, 629638. PubMed: 24090797.
Nakamae, T., Narumoto, J., Sakai, Y., Nishida, S., Yamada, K., Kubota, M., et al. (2012).
Reduced cortical thickness in non-medicated patients with obsessive-compulsive
disorder. Progress in Neuro-Psychopharmacology & Biological Psychiatry, 37(1),
9095. PubMed: 22251565.
Nesvag, R., Lawyer, G., Varnas, K., Fjell, A. M., Walhovd, K. B., Frigessi, A., et al.
(2008). Regional thinning of the cerebral cortex in schizophrenia: Effects of
diagnosis, age and antipsychotic medication. Schizophrenia Research, 98(13),
1628. PubMed: 17933495.
Panizzon, M. S., Fennema-Notestine, C., Eyler, L. T., Jernigan, T. L., Prom-Wormley, E.,
Neale, M., et al. (2009). Distinct genetic influences on cortical surface area and
cortical thickness. Cerebral Cortex, 19(11), 27282735. PubMed: 19299253.
Pardoe, H. R., Abbott, D. F., & Jackson, G. D. (2013). Sample size estimates for wellpowered cross-sectional cortical thickness studies. Human Brain Mapping, 34(11),
30003009. PubMed: 22807270.
Porter, J. N., Collins, P. F., Muetzel, R. L., Lim, K. O., & Luciana, M. (2011).
Associations between cortical thickness and verbal fluency in childhood,
adolescence, and young adulthood. NeuroImage, 55(4), 18651877. PubMed:
21255662.
Querbes, O., Aubry, F., Pariente, J., Lotterie, J. A., Demonet, J. F., Duret, V., et al.
(2009). Early diagnosis of Alzheimers disease using cortical thickness: impact of
cognitive reserve. Brain: A Journal of Neurology, 132(Pt 8), 20362047. PubMed:
19439419.
Raznahan, A., Lerch, J. P., Lee, N., Greenstein, D., Wallace, G. L., Stockman, M., et al.
(2011). Patterns of coordinated anatomical change in human cortical development:
A longitudinal neuroimaging study of maturational coupling. Neuron, 72, 873884.
Raznahan, A., Shaw, P., Lalonde, F., Stockman, M., Wallace, G. L., Greenstein, D., et al.
(2011). How does your cortex grow? The Journal of Neuroscience, 31(19),
71747177. PubMed: 21562281.
Reid, A. T., & Evans, A. C. (2013). Structural networks in Alzheimers disease. European
Neuropsychopharmacology: The Journal of the European College of
Neuropsychopharmacology, 23(1), 6377. PubMed: 23294972.
Ridgway, G. R., Lehmann, M., Barnes, J., Rohrer, J. D., Warren, J. D., Crutch, S. J., et al.
(2012). Early-onset Alzheimer disease clinical variants: multivariate analyses of
cortical thickness. Neurology, 79(1), 8084. PubMed: 22722624.
165
Rimol, L. M., Hartberg, C. B., Nesvag, R., Fennema-Notestine, C., Hagler, D. J., Jr.,
Pung, C. J., et al. (2010). Cortical thickness and subcortical volumes in
schizophrenia and bipolar disorder. Biological Psychiatry, 68(1), 4150. PubMed:
20609836.
Rimol, L. M., Nesvag, R., Hagler, D. J., Jr., Bergmann, O., Fennema-Notestine, C.,
Hartberg, C. B., et al. (2012). Cortical volume, surface area, and thickness in
schizophrenia and bipolar disorder. Biological Psychiatry, 71(6), 552560.
PubMed: 22281121.
Rimol, L. M., Panizzon, M. S., Fennema-Notestine, C., Eyler, L. T., Fischl, B.,
Franz, C. E., et al. (2010). Cortical thickness is influenced by regionally specific
genetic factors. Biological Psychiatry, 67(5), 493499. PubMed: 19963208.
Sabuncu, M. R., Buckner, R. L., Smoller, J. W., Lee, P. H., Fischl, B., & Sperling, R. A.
(2012). The association between a polygenic Alzheimer score and cortical thickness
in clinically normal subjects. Cerebral Cortex, 22(11), 26532661. PubMed:
22169231.
Salat, D. H., Buckner, R. L., Snyder, A. Z., Greve, D. N., Desikan, R. S., Busa, E., et al.
(2004). Thinning of the cerebral cortex in aging. Cerebral Cortex, 14(7), 721730.
PubMed: 15054051.
Sanabria-Diaz, G., Melie-Garca, L., Iturria-Medina, Y., Aleman-Gomez, Y.,
Hernandez-Gonzalez, G., Valdes-Urrutia, L., et al. (2010). Surface area and cortical
thickness descriptors reveal different attributes of the structural human brain
networks. NeuroImage, 50, 14971510.
Sato, J. R., Hoexter, M. Q., Oliveira, P. P., Jr., Brammer, M. J., Murphy, D., & Ecker, C.
(2013). Inter-regional cortical thickness correlations are associated with autistic
symptoms: A machine-learning approach. Journal of Psychiatric Research, 47(4),
453459. PubMed: 23260170.
Schilling, C., Kuhn, S., Paus, T., Romanowski, A., Banaschewski, T., Barbot, A., et al.
(2013). Cortical thickness of superior frontal cortex predicts impulsiveness and
perceptual reasoning in adolescence. Molecular Psychiatry, 18(5), 624630.
PubMed: 22665261.
Schilling, C., Kuhn, S., Romanowski, A., Schubert, F., Kathmann, N., & Gallinat, J.
(2012). Cortical thickness correlates with impulsiveness in healthy adults.
Schmitt, J. E., Lenroot, R., Ordaz, S. E., Wallace, G. L., Lerch, J. P., Evans, A. C., et al.
(2009). Variance decomposition of MRI-based covariance maps using geneticallyinformative samples and structural equation modeling. NeuroImage, 47(1), 5664.
Schmitt, J. E., Lenroot, R. K., Wallace, G. L., Ordaz, S., Taylor, K. N., Kabani, N., et al.
(2008). Identification of genetically mediated cortical networks: A multivariate study
of pediatric twins and siblings. Cerebral Cortex, 18, 17371747.
Schmitt, J. E., Wallace, G. L., Lenroot, R. K., Ordaz, S. E., Greenstein, D., Clasen, L.,
et al. (2010). A twin study of intracerebral volumetric relationships. Behavior
Genetics, 40, 114124.
Schnack, H. G., van Haren, N. E., Brouwer, R. M., van Baal, G. C., Picchioni, M.,
Weisbrod, M., et al. (2010). Mapping reliability in multicenter MRI: Voxel-based
morphometry and cortical thickness. Human Brain Mapping, 12, 19671982.
Schultz, C. C., Koch, K., Wagner, G., Roebel, M., Nenadic, I., Schachtzabel, C., et al.
(2010). Complex pattern of cortical thinning in schizophrenia: Results from an
automated surface based analysis of cortical thickness. Psychiatry Research, 182(2),
134140. PubMed: 20418074.
Scott, M. L., Bromiley, P. A., Thacker, N. A., Hutchinson, C. E., & Jackson, A. (2009). A
fast, model-independent method for cerebral cortical thickness estimation using
MRI. Medical Image Analysis, 13(2), 269285. PubMed: 19068276.
Shaw, P., Lerch, J., Greenstein, D., Sharp, W., Clasen, L., Evans, A., et al. (2006).
Longitudinal mapping of cortical thickness and clinical outcome in children and
adolescents with attention-deficit/hyperactivity disorder. Archives of General
Psychiatry, 63(5), 540549. PubMed: 16651511.
Sowell, E. R., Peterson, B. S., Kan, E., Woods, R. P., Yoshii, J., Bansal, R., et al. (2007).
Sex differences in cortical thickness mapped in 176 healthy individuals
between 7 and 87 years of age. Cerebral Cortex, 17(7), 15501560. PubMed:
16945978.
children. The Journal of Neuroscience: The Official Journal of the Society for
Neuroscience, 24(38), 82238231.
Sowell, E. R., Thompson, P. M., & Toga, A. W. (2004). Mapping changes in the human
cortex throughout the span of life. The Neuroscientist: A Review Journal Bringing
Neurobiology, Neurology and Psychiatry, 10(4), 372392.
Stam, C., Jones, B., Nolte, G., Breakspear, M., & Scheltens, P. (2007). Small-world
networks and functional connectivity in Alzheimers disease. Cerebral Cortex, 17,
9299.
Tardif, C. L., Dinse, J., Schafer, A., Turner, R., & Pl, B. (2013). Multi-modal surfacebased alignment of cortical areas using intra-cortical T1 contrast. In L. Shen, T.
Liu, P. T. Yap, H. Huang, D. Shen & C. F. Westin (Eds.), Multimodal brain image
166
analysis 2013 (pp. 222232). Switzerland: Springer International Publishing LNCS

8159.
Thambisetty, M., Wan, J., Carass, A., An, Y., Prince, J. L., & Resnick, S. M. (2010).
Longitudinal changes in cortical thickness associated with normal aging.
Thesen, T., Quinn, B. T., Carlson, C., Devinsky, O., DuBois, J., McDonald, C. R., et al.
(2011). Detection of epileptogenic cortical malformations with surface-based MRI
morphometry. PLoS One, 6(2), e16430. PubMed: 21326599.
Thompson, P. M., Hayashi, K. M., Sowell, E. R., Gogtay, N., Giedd, J. N.,
Rapoport, J. L., et al. (2004). Mapping cortical change in Alzheimers disease, brain
development, and schizophrenia. NeuroImage, 23(Suppl. 1), S2S18. PubMed:
15501091.
Thompson, P. M., MacDonald, D., Mega, M. S., Holmes, C. J., Evans, A. C., &
Toga, A. W. (1997). Detection and mapping of abnormal brain structure with a
probabilistic atlas of cortical surfaces. Journal of Computer Assisted Tomography,
21(4), 567581.
Thompson, P. M., Schwartz, C., & Toga, A. W. (1996). High-resolution random mesh
algorithms for creating a probabilistic 3D surface atlas of the human brain.
Thompson, P. M., Sowell, E. R., Gogtay, N., Giedd, J. N., Vidal, C. N., Hayashi, K. M.,
et al. (2005). Structural MRI and brain development. International Review of
Neurobiology, 67, 285323. PubMed: 16291026.
Toga, A. W., Thompson, P. M., & Sowell, E. R. (2006). Mapping brain maturation.
Trends in Neurosciences, 29(3), 148159. PubMed: 16472876.
Tohka, J., Zijdenbos, A. P., & Evans, A. C. (2004). Fast and robust parameter estimation
for statistical partial volume models in brain MRI. NeuroImage, 23(1), 8497.
Tosun, D., Rettmann, M. E., Han, X., Tao, X., Xu, C., Resnick, S. M., et al. (2004).
Cortical surface segmentation and mapping. NeuroImage, 23(Suppl. 1),
S108S118. PubMed: 15501080.
Tosun, D., Rettmann, M. E., Naiman, D. Q., Resnick, S. M., Kraut, M. A., & Prince, J.
(2006). Cortical reconstruction using implicit surface evolution: Accuracy and
precision analysis. NeuroImage, 29(3), 838852.
Trampel, R., Ott, D. V.M, & Turner, R. (2011). Do the congenitally blind
have a Stria Gennari? First intracortical insights in vivo. Cerebral Cortex, 21,
20752081.
Truong, W., Minuzzi, L., Soares, C. N., Frey, B. N., Evans, A. C., Macqueen, G. M., et al.
(2013). Changes in cortical thickness across the lifespan in major depressive
disorder. Psychiatry Research, 214(3), 204211. PubMed: 24099630.
Turner, R., & Geyer, S. (2014). Comparing like with like: The power of knowing where
you are. Brain Connectivity, 4, 547557. PubMed: 24999746.
van Eijndhoven, P., van Wingen, G., Katzenbauer, M., Groen, W., Tepest, R.,
Fernandez, G., et al. (2013). Paralimbic cortical thickness in first-episode
depression: Evidence for trait-related differences in mood regulation. The American
Journal of Psychiatry, 170(12), 14771486. PubMed: 23929204.
Van Essen, D. C., & Drury, H. A. (1997). Structural and functional analyses of human
cerebral cortex using a surface-based atlas. The Journal of Neuroscience, 17,
70797102.
Van Essen, D. C., Drury, H. A., Dickson, J., Harwell, J., Hanlon, D., & Anderson, C. H.
(2001). An integrated software suite for surface-based analysis of cerebral cortex.
Journal of the American Medical Informatics Association, 8, 443459.
Van Essen, D. C., & Glasser, M. F. (2014). In vivo architectonics: A cortico-centric
perspective. NeuroImage, 93(Pt 2), 157164.
van Haren, N. E., Schnack, H. G., Cahn, W., van den Heuvel, M. P., Lepage, C.,
Collins, L., et al. (2011). Changes in cortical thickness during the course of illness
in schizophrenia. Archives of General Psychiatry, 68(9), 871880. PubMed:
21893656.
van Velsen, E. F., Vernooij, M. W., Vrooman, H. A., van der Lugt, A., Breteler, M. M.,
Hofman, A., et al. (2013). Brain cortical thickness in the general elderly population:
The Rotterdam Scan Study. Neuroscience Letters, 550, 189194. PubMed:
23831346.
Vita, A., De Peri, L., Deste, G., & Sacchetti, E. (2012). Progressive loss of cortical gray
matter in schizophrenia: A meta-analysis and meta-regression of longitudinal MRI
studies. Translational Psychiatry, 2, e190. PubMed: 23168990.
Vogt, C., & Vogt, O. (1919). Allgemeinere ergebnisse unserer hirnforschung. Journal
Erwachsenen Menschen. Berlin: Springer.
Waehnert, M. D., Dinse, J., Weiss, M., Streicher, M. N., Waehnert, P., Geyer, S., et al.
(2014). Anatomically-motivated modelling of cortical laminae. NeuroImage, 93,
210220.
Wagner, G., Schultz, C. C., Koch, K., Schachtzabel, C., Sauer, H., & Schlosser, R. G.
(2012). Prefrontal cortical thickness in depressed patients with high-risk for suicidal
behavior. Journal of Psychiatric Research, 46(11), 14491455. PubMed:
22868048.
Walhovd, K. B., Tamnes, C. K., Ostby, Y., Due-Tonnessen, P., & Fjell, A. M. (2012).
Normal variation in behavioral adjustment relates to regional differences in cortical
thickness in children. European Child & Adolescent Psychiatry, 21(3), 133140.
PubMed: 22302474.
Wang, X., Bauer, W., Chiaia, N., Dennis, M., Gerken, M., Hummel, J., et al. (2008).
Longitudinal MRI evaluations of human global cortical thickness over minutes to
weeks. Neuroscience Letters, 441(2), 145148. PubMed: 18603368.
Wang, L., Shi, F., Li, G., & Shen, D. (2013). 4D segmentation of brain MR images with
constrained cortical thickness variation. PLoS One, 8(7), e64207. PubMed:
23843934.
Wierenga, L. M., Langen, M., Oranje, B., & Durston, S. (2014). Unique developmental
trajectories of cortical thickness and surface area. NeuroImage, 87, 120126.
PubMed: 24246495.
Yang, X. R., Carrey, N., Bernier, D., & Macmaster, F. P. (2012). Cortical thickness in
young treatment-naive children with ADHD. Journal of Attention Disorders. http://
dx.doi.org/10.1177/1087054712455501 PubMed: 22912507.
Yang, Y., Joshi, A. A., Joshi, S. H., Baker, L. A., Narr, K. L., Raine, A., et al. (2012).
Genetic and environmental influences on cortical thickness among 14-year-old
twins. Neuroreport, 23(12), 702706. PubMed: 22713927.
Yao, Z., Hu, B., Liang, C., Zhao, L., & Jackson, M. (2012). A longitudinal study of
atrophy in amnestic mild cognitive impairment and normal aging revealed by
cortical thickness. PLoS One, 7(11), e48973. PubMed: 23133666.
Yezzi, A. J., & Prince, J. L. (2003). An Eulerian PDE approach for computing tissue
thickness. IEEE Transactions on Medical Imaging, 22, 10.
Yoon, U., Fahim, C., Perusse, D., & Evans, A. C. (2010). Lateralized genetic and
environmental influences on human brain morphology of 8-year old pediatric twins.
NeuroImage, 53(3), 11171125.
Yoon, U., Perusse, D., & Evans, A. C. (2012). Mapping genetic and environmental
influences on cortical surface area of pediatric twins. Neuroscience, 220, 169178.
Zhou, D., Lebel, C., Evans, A., & Beaulieu, C. (2013). Cortical thickness
asymmetry from childhood to older adulthood. NeuroImage, 83, 6674. PubMed:
23827331.
Ziegler, D. A., Piguet, O., Salat, D. H., Prince, K., Connally, E., & Corkin, S. (2010).
Cognition in healthy aging is related to regional white matter integrity, but
not cortical thickness. Neurobiology of Aging, 31(11), 19121926. PubMed:
19091444.
Zilles, K., & Amunts, K. (2009). Receptor mapping: Architecture of the human cerebral
cortex. Current Opinion in Neurology, 22, 331339.
Embryonic and Fetal Development of the Human Cerebral Cortex

I Kostovic and M Judas, Croatian Institute for Brain Research, Zagreb, Croatia
Glossary
represents the neocortical primordium before the

appearance of the cortical plate; thus, the term marginal
zone should be used only after the formation of the cortical
plate (Bystron et al., 2008). However, it should be noted that
Wilhelm His (His, 1904), when describing what is presently
called preplate (his Mantelschicht or mantle layer) already
distinguished its inner (deep) cellular part and outer
noncellular part (Randschleier or marginal veil) and
proposed that the CP will form within the inner part of the
mantle layer.
Proliferative zones Periventricular (ventricular zone (VZ)
and subventricular zone (SVZ)) transient fetal zones in
which progenitor neuroepithelial cells undergo successive
mitotic divisions (proliferation) to form all future cortical
neurons and glial cells.
Prosencephalon The forebrain that is the most rostral of
three primary cerebral vesicles, which gives rise to paired
secondary endbrain (telencephalic) vesicles that is the future
cerebral hemispheres and to the diencephalon.
Subplate Transient fetal zone, first described in the human
brain as a major site of early synaptogenesis (Kostovic &
Molliver, 1974) and in the fetal rhesus monkey brain as the
waiting compartment for growing cortical afferents (Rakic,
1977). It is most developed in the human brain (Kostovic &
Rakic, 1990), commonly recognized as crucial for proper
cortical development (Kanold & Luhmann, 2010), as a
missing link in brain injury of the premature infant (Volpe,
1996) and pivotal for evo-devo interpretations of the human
brain evolution (Judas, Sedmak, & Kostovic, 2013; Kostovic
& Rakic, 1990). For a comprehensive historical review, see
Judas, Sedmak, and Pletikos (2010a).
Telencephalon Paired secondary cerebral vesicles
(endbrain) or future cerebral hemispheres, which in the
midline remain connected by the telencephalon impar,
lamina terminalis, and the commissural plate.
Abbreviations
PP
P-SP
SP
SPr
SVZ
VZ
WM
Embryonic and fetal zones Transient laminar architectonic

compartments of the cerebral (telencephalic) wall, as
defined by Boulder Committee (1970) and its revisited
version (Bystron et al., 2008). These are (from ventricular to
pial surface) the ventricular zone (VZ), subventricular zone
(SVZ), intermediate zone (IZ), subplate zone (SP), cortical
plate (CP), and marginal zone (MZ).
Fetal white matter A common term encompassing
growing afferent and efferent cortical pathways, which in
early fetal and midfetal periods are represented by two main
components: (1) the intermediate zone (its main part) and
(2) some bundles within the subventricular zone and welldefined periventricular bundles such as the corpus callosum,
anterior commissure, and internal capsule. During the last
trimester, the fetal white matter gradually replaces transient
proliferative zones and the subplate, so that in the early
postnatal brain, the white matter finally stretches from the
superficial cerebral cortex to the ventricular ependyma.
Interstitial white matter neurons Interstitial neurons of the
adult subcortical (gyral) white matter are postnatal
remnants of fetal subplate neurons, as initially
demonstrated by Kostovic and Rakic (1980). For a detailed
review, see Judas, Sedmak, Pletikos, and Jovanov-Milosevic
(2010b).
Neocortical anlage The embryonic and fetal primordium of
the future cerebral cortex, which in early embryo consists of
the preplate, but after the formation of the cortical plate
(7th8th PCW) encompasses three transient fetal zones:
marginal zone (MZ), cortical plate (CP), and subplate (SP).
Neuroepithelium Proliferating neuroepithelial cells that
make up the neural plate and neural tube.
Preplate According to a recent consensus (Bystron et al.,
2008), the term preplate replaced older concepts of the
pallial anlage (Rickmann et al., 1977) and the primordial
plexiform layer (Marin-Padilla, 1978). The preplate
CP
CX
ECM
IZ
MZ
PCW
Cortical plate
Cerebral cortex
Extracellular matrix
Intermediate zone
Marginal zone
Postconceptional weeks
The cerebral cortex originates from the wall of the prosencephalon, which develops during the fourth postconceptional week
(PCW; His, 1904; ORahilly & Muller, 2006). The first step in
complex morphogenesis and histogenesis of the cerebral cortex
Preplate
Presubplate
Subplate zone
Subplate remnant
Subventricular zone
Ventricular zone
White matter
is the formation of two lateral evaginations of the prosencephalon, that is, the formation of telencephalic (endbrain)
vesicles, which differentiate into dorsal thin neuroepithelial
wall (pallium) and thickened basal portion (subpallium).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00193-7
167
168
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Embryonic and Fetal Development of the Human Cerebral Cortex
During the fifth PCW, paired telencephalic vesicles form the

future cerebral hemispheres and remain connected in the midline by the telencephalon impar (the region of future lamina
terminalis and the commissural plate). The future ventricular
system develops from cavities of these hemispheric vesicles,
while the pallium represents the anlage of the cerebral neocortex. Further changes in shape and macroscopic structure of the
fetal cerebral (telencephalic) wall may be followed in vivo or
in utero by means of ultrasound or magnetic resonance imaging
(Kostovic, Judas, Rados, & Hrabac, 2002; Prayer et al., 2006).
However, the developmental analysis of fine microstructural
changes and cellular events, which enable the formation of
areal, laminar, columnar, and neuronal network organization
of the cerebral cortex, requires the application of histological
and molecular biology methods on the postmortem human
tissue, in combination with experimental studies in animal
models (Molnar et al., 2006).
Histogenetic Cellular Events

There are many cellular (histogenetic) events involved in corticogenesis: neuronal proliferation and migration, specification
of morphological and molecular neuronal phenotypes (growth
of dendrites, dendritic spines, and axons), cytoarchitectonic
aggregation of specific neuronal populations, establishment
of neuronal circuitry and connectivity (growth of axon pathways and synaptogenesis), elimination of exuberant connectivity elements (pruning of axons, elimination of overproduced
spines and synapses, and developmental cell death), proliferation and differentiation of glial cell types, and myelination.
The formation of neuronal circuitry begins already in the early
fetal period, undergoes a series of transient patterns of organization, and displays plasticity during the entire lifespan
(Figure 1). While all histogenetic events contribute to the formation of transient and/or permanent neuronal circuitry in a
significantly overlapping manner, their intensity varies or may
be even limited to a certain developmental period (Figure 1).
Thus, the functional organization of the brain and the mode of
its interaction with environmental factors and influences also
vary in different developmental periods. Therefore, certain
developmental periods may be described as sensitive/critical
periods characterized by increased vulnerability for adverse
intrinsic and extrinsic pathogenetic influences.
The proper number of cortical neurons is produced by
mitotic divisions (proliferation) of progenitor neuroepithelial
cells within two proliferative zones (ventricular zone (VZ) and
subventricular zone (SVZ)) aptly described as the factories of the
cortex (Bystron, Blakemore, & Rakic, 2008). In the VZ, progenitor cells divide asynchronously; during the DNA replication
phase, their nuclei move away from the VZ surface and then
move back to undergo another mitotic cycle (Rakic, 1988).
During the early embryonic period, progenitor neuroepithelial
cells span the entire thickness of the cerebral wall and undergo
symmetrical divisions, thus doubling the progenitor pool by
each cycle of mitosis. The onset of corticogenesis is marked by
the beginning of asymmetrical progenitor divisions, which give
rise to young postmitotic neurons and glial cells. Radial glial cells
are generated early and serve not only as radial guides for migration of principal (pyramidal) neurons (http://rakiclab.med.yale.
edu/research/index.aspx) but also as neural stem cells (Bystron
et al., 2008; Fishell & Kriegstein, 2003). Neurons are also being
produced in subsequently formed SVZ (Figure 2), which is
Figure 1 Developmental periods of occurrence and intensity of main neurogenetic events in cortical histogenesis. Note the predominance of
proliferation and migration during the first trimester, growth of axons and dendrites during the second and third trimesters, and prolonged postnatal
synaptogenesis, myelination, and neurochemical maturation.
169
Figure 2 Sequential development of transient laminar compartments in the neocortical cerebral wall from early embryonic (a) to late fetal period (g)
when six-layered pattern and subplate remnant coexist. Proliferative zones (ventricular zone,VZ and subventricular zone, and SVZ) shown in green; early
synaptic and postmitotic layers with postmigratory neurons (preplate, PP; subplate zone, SP; marginal zone, and MZ) shown in blue; connectivity layer
with postmigratory neurons (cortical plate, CP) shown in gray; axon strata (fetal white matter) shown in red; progenitor cells green, early-differentiating
neurons of MZ and SP blue, CP neurons and migratory neurons black, and glia brown.
especially developed in the primate brain. Finally, some neurons

of the hippocampal archicortex are also being produced in situ,
within the dentate gyrus. In comparison with rodents, the primates and humans display significantly greater number of
mitotic cycles in proliferative zones, which may explain why
they have significantly larger brains and more cortical areas
(Rakic, 1995).
A salient feature of cortical development is that all neurons
are being generated in proliferative periventricular zones and
then have to undergo long neuronal migration to reach their
final (subpial) destination in the future cerebral cortex (Rakic,
1972). Young postmitotic migratory neurons are bipolar and
travel along radial glial guides to reach the cortical plate in
which they form radial ontogenetic columns (Rakic, 1988,
1995). While principal (pyramidal) cortical neurons migrate
radially from the pallial VZ, cortical interneurons originating
from subpallial proliferative zones or the SVZ predominantly
follow tangential routes of migration (Bystron et al., 2008).
Cortical neurons are generated in the inside-out pattern, meaning that later-generated neurons settle in progressively more
superficial cortical layers (Bystron et al., 2008; Rakic, 1988,
1995). However, there is significant exception to that insideout neurogenetic sequence: the earliest-generated and cogenerated cortical cells are CajalRetzius cells of the marginal
zone (MZ) and some subplate neurons (Allendoerfer & Shatz,
1994), but it should be noted that neurons are also continuously added to both MZ and subplate zone (SP) during the
subsequent fetal period (Bystron et al., 2008).
Molecular specification of cerebral cortical neurons is commonly divided in two major processes: the areal specification
and the specification of subsets of cortical neurons. According
to the protomap hypothesis (Rakic, 1988, 1995), areal and
laminar position and the cellular phenotype of cortical neurons are specified at the time of their last (asymmetrical) division in proliferative zones. The areal position is specified by
signaling molecules secreted from several patterning centers,
such as the commissural plate and the cortical hem (OLeary,
Chou, & Sahara, 2007). Members of the Fgf family are secreted
from the commissural plate and involved in the specification
of anteriorposterior axis, while members of the Wnt and Bmp
families are secreted from cortical hem and involved in the
specification of posteromedial cortical areas including the hippocampus. Furthermore, the sonic hedgehog is expressed in
the ventral telencephalon and hypothalamus and important
for the specification of the basal telencephalon and subpallium. Other signaling molecules are secreted from the antihem
located between the paleocortical and striatal primordia
(Mallamaci, 2011). These signaling molecules function
through dose-dependent activation of various transcriptional
factors in VZ and SVZ neuronal progenitors, which, combined
with gradient expression of other signaling molecules, creates a
multitude of possible outcomes (Mallamaci, 2011; OLeary
et al., 2007). The specification of subsets of cortical neurons
is regulated by a wealth of recently described genes (Bayatti
et al., 2008; Kwan, Sestan, & Anton, 2012; Mallamaci, 2011;
Molyneaux, Arlotta, Menezes, & Macklis, 2007; Wang
170
et al., 2010). The specification of neurotransmitter phenotype

is important for functioning of neurons and synapses.
Fetal neurons may transiently express neurotransmitters, and
these transmitters may change their functional role during
development for example, the role of GABA shifts from
excitatory to inhibitory.
The aggregation of postmigratory neurons in different
cytoarchitectonic compartments represents a basic property of
brain development. Some postmigratory neurons aggregate in
the telencephalic basal ganglia and nuclei, while cortical neurons aggregate in transient or permanent fetal zones, cortical
layers, and modular compartments.
The differentiation of neuronal morphological phenotype
involves the development of characteristic dendritic and axonal
arborizations and dendritic spines and begins as soon as neurons settle within the cortical plate (Mrzljak, Uylings, Kostovic,
& Van Eden, 1988). However, this is a protracted process, which
in association cortical areas continues well into the third year of
postnatal life (Petanjek, Judas, Kostovic, & Uylings, 2008).
The differentiation of main cortical neuronal circuitry elements (axons, synapses, dendrites, and dendritic spines)
begins early and is typically characterized by initial overproduction of circuitry elements. However, the construction of
neuronal circuits is a very protracted process, which undergoes
a series of reorganizational events and reaches its adultlike
organization during the third decade of postnatal life. For
example, ingrowth and outgrowth of cortical axonal pathways
occur during the fetal and perinatal periods (Figure 4). On the
other hand, the elimination of overproduced synapses and
dendritic spines continues until the young adult age
(Petanjek et al., 2011).
Glial cell types, such as astrocytes and oligodendrocytes, are
being generated from progenitor neuroepithelial cells (Bystron
et al., 2008; Jakovcevski, Filipovic, Mo, Rakic, & Zecevic, 2009).
For example, radial glial cells gradually transform into astrocytes (Schmechel & Rakic, 1979). However, microglial cells are
presumably of nonneuronal (nonneuroepithelial) origin and
invade the cerebral wall quite early (Monnier et al., 2007,
Monnier, Evrard, Gressens, & Verney, 2006; Verney, Monnier,
Fallet-Bianco, & Gressens, 2010). Myelination begins in primary cortical areas shortly before the birth, whereas the intracortical myelination is a late postnatal event.
Developmental Phases of Corticogenesis, Sequential

Development of Transient Cellular Compartments
(Zones), and Dynamics of Histogenetic Events
The aforementioned developmental cellular processes unfold
in the spatially defined framework of transient laminar compartments, that is, embryonic and fetal zones (Bystron et al.,
2008), which can be delineated and defined by means of
various histological and in vivo imaging techniques. While the
basic cellular events in the telencephalon are similar to those in
other parts of the central nervous system, the subsequent
phases of cortical development display unique laminar compartments (Bystron et al., 2008).
Before the 6th PCW, the cerebral wall consists of pseudostratified proliferative neuroepithelium forming the VZ
(Boulder Committee, 1970; Bystron et al., 2008). The first
lamination appears between the 6th PCW and 7th PCW,

when the first postmitotic neurons migrate from the VZ
towards the pial surface of the cerebral vesicle. These first
neurons with their processes form the preplate (PP; Figure 2;
Meyer, 2007; Meyer, Schaaps, Moreau, & Goffinet, 2000). The
PP is the fountainhead for several classes of transient neurons,
such as fetal CajalRetzius cells and early-generated subplate
cells. The PP cells communicate via nonsynaptic junctions,
while the early PP fibers represent the axons of PP neurons
(Bystron et al., 2008). The PP was classically described as the
mantle layer, Mantelschicht (His, 1904), and subsequently
described as the pallial anlage (Rickmann, Chronwall, &
Wolff, 1977) or the primordial plexiform layer (Marin-Padilla,
1978). In addition to these two cellular zones (VZ and PP),
there is a thin and cell-free neuroepithelial marginal veil,
Randschleier (His, 1904), just below the pial surface. During
the seventh PCW, another proliferative zone is formed the
SVZ (Bystron et al., 2008). At that time, the medial (limbic)
pallium, or cortical hem, is slightly curved and contains
enlarged plexiform PP, that is, the MZ of classical terminology.
This represents the anlage of the hippocampal region (see
other relevant chapters in this encyclopedia).
The onset of the fetal period (8th14th PCW) is characterized by the formation of the cortical plate (CP) (Figure 2) as a
compact and cell-dense layer composed of cell bodies and
proximal dendrites of postmigratory cortical neurons vertically
aligned in ontogenetic columns (Rakic, 1988). The CP initially
appears in mediolateral pallial region and remains here significantly thicker than in the medial pallium. According to the
radial unit hypothesis (Rakic, 1988, 1995), cortical neurons
are generated in proliferative units of the VZ, migrate along
radial glial guides, and settle in vertical ontogenetic columns
within the CP (http://rakiclab.med.yale.edu/research/index.
aspx). After the formation of the CP, the neocortical anlage
consists of three zones: MZ with CajalRetzius cells (above the
CP), the CP, and the thin plexiform presubplate (P-SP) layer
(Figure 2) (below the CP) (Kostovic & Rakic, 1990); the presubplate is also described as the subplate intermediate zone
(IZ; Bystron et al., 2008). Below the neocortical anlage, there is
the IZ (Figure 2) rich in fibers and migratory cells, followed by
the SVZ and VZ. Axons of the IZ represent afferent fibers
originating from monoaminergic brain stem nuclei and cholinergic basal forebrain nuclei, thalamocortical afferents, and
efferent axons from CP and subplate cells.
The archicortical hippocampus develops in the medial
(limbic) end of the pallium, where the CP formation is
delayed; the archicortical CP appears at the 12th PCW and
remains thinner and less compact than the neocortical CP
(Kostovic, Seress, Mrzljak, & Judas, 1989). The main cytoarchitectonic landmarks of the archicortex are its curved shape and
significant enlargement of its MZ. In the basal paleocortical
(subpallial) cerebral cortex, the CP is not developed.
This period is dominated by three dynamic events: (1)
intense proliferation in VZ and SVZ, (2) the presence of massive waves of migratory neurons in the IZ, and (3) the development of the first synapses (at the 8th PCW), which appear
both above the CP (in the MZ) and below it (in the fibrillar
presubplate), but not within the CP (see Figure 2, blue zones).
This early bilaminar synaptogenesis (Molliver, Kostovic, & Van
der Loos, 1973) enables the formation of transient and
endogenous neuronal circuitry, which is nonsensory-driven
and experience-independent. However, it is generally accepted
that such early spontaneous neural activity plays an important
role in the developmental shaping of neuronal circuitry
(Allendoerfer & Shatz, 1994; Kanold & Luhmann, 2010;
Kostovic & Judas, 2010).
Between the 12th and 14th PCW, the deep portion of the
neocortical CP becomes loosely organized and transforms into a
(a)
171
new, synapse-rich, and prominent SP (Kostovic & Rakic, 1980).

This process is incomplete in the hippocampal and ventral cingulate cortex. The dramatic expansion of the human SP reflects
its voluminous extracellular matrix (up to 70% of subplate volume; this enhances MRI delineation of the SP) and rich axonal
content and suggests the addition of new neurons.
Midfetal period (15th23rd PCW) is characterized by typical fetal pattern of transient lamination (Figure 3). The main
(b)
(c)
1 = Ventricular zone (germinal matrix)

2 = Periventricular fiber rich zone
3 = Subventricular cellular zone
4 = Intermediate zone (fetal white matter)
5 = Subplate zone
6 = Cortical plate
7 = Marginal zone
(d)
(e)
1 2 3
(f)
(g)
(h)
(i)
Figure 3 Transient midfetal pattern of cerebral wall lamination as revealed by histological (a), histochemical (c), and T1-weighted MRI (b) of the
in vitro human fetal brain. Arrowheads indicate the border between the intermediate zone (fetal white matter) and the subplate (the thickest cortical
compartment). Reproduced with permission from Kostovic, I., Judas, M., Rados, M., & Hrabac, P. (2002). Laminar organization of the human
fetal cerebrum revealed by histochemical markers and magnetic resonance imaging. Cerebral Cortex, 12, 536544.
172
change is large expansions of SP, which is much thicker than

CP (Bystron et al., 2008; Kostovic & Rakic, 1990). The neocortical anlage consists of the MZ, CP, and SP. The SP is composed
of transient and permanent types of postmigratory, earlydifferentiating neurons, migratory neurons, glia, and growing
axons. It is the site of intensive synaptogenesis and the most
important connectivity compartment of the fetal cortex, essential for sequential ingrowth of cortical afferents. Thus, the SP
contains a massive amount of waiting thalamocortical and
other afferents (Allendoerfer & Shatz, 1994; Kostovic & Judas,
2007, 2010; Kostovic & Rakic, 1990; Zecevic & Verney, 1995).
In contrast to the lateral (neocortical) pallium, the medial
(limbic) pallium displays a narrow SP but thickened MZ and
thinner, S-curved hippocampal CP. In contrast to that in
rodents, primate and human hippocampal formation develops
ventrally, in the prospective temporal lobe. The cingulate
cortex (above the corpus callosum) and the entorhinal cortex

(adjacent to hippocampus) display transitional (mesocortical)
features: MZ is thicker than in the neocortex but thinner than
in the archicortex. Notably, the hippocampus and cingulate
cortex develop faster than the neocortex (Hevner & Kinney,
1996) and display cytoarchitectonic areal parcellation already
at the 15th PCW (Kostovic, Petanjek, & Judas, 1993, Kostovic
et al., 1989). Major dynamic cellular events are proliferation
and migration of predominantly association neurons for upper
cortical layers. There is sequential growth of axons through
subplate (Figure 4) as well as intense synaptogenesis between
the thalamocortical axons and subplate neurons.
The late fetal period roughly corresponds to the second half
of gestation and is quite prolonged (4 months!) in the human
brain. The first part of the late fetal period (third trimester,
24th32nd PCW) corresponds to clinically important period
Figure 4 Development of cortical axon pathways in the human fetus. Analysis of sequential development using different histochemical markers and
diffuse tensor MRI techniques can reveal nuclei of origin, pathway selection, waiting with synaptic engagement in the subplate, and ingrowth into
the cortical plate. (a) 10th, 5th PCW, (b) 20th PCW, (c) 23rd PCW, and (d) 28th PCW.
173
I
II
FI
III
FII
FI
FIII
FII
IV
FIII
MZ
FIV
FIV
FV
FV
CP
VI
FVI
FVI
MZ
CP
SP
CP
MZ
CP
SPU
SPP
SPL
SP
SP
WM
IZ
IZ
IZ
SP
SP
MZ
IZ
WM
SV
V
10.5 w
13.5 w
17 w
1925 w
2629 w
3234 w
Newborn
Figure 5 Composite drawing of differentiating neurons stained with Golgi method in the human prenatal prefrontal cortex. Note early differentiation of
subplate and marginal zone neurons and acceleration of dendritic development of cortical pyramidal neurons during the last trimester of gestation.
Reproduced with permission from Mrzljak, L., Uylings, H. B. M., Kostovic, I., & Van Eden, C. G. (1988). Prenatal development of neurons in
the human prefrontal cortex: I. A qualitative Golgi study. Journal of Comparative Neurology, 271, 355386.
of prematurely born infants. This phase of cortical development is characterized by several new features: the onset of
gyrification, the peak of subplate development (which receives
new contingents of growing callosal and associative pathways),
the onset of lamination within the CP that reflects the
ingrowth of thalamocortical fibers, and dendritic maturation
of pyramidal neurons (Figure 5). Clinically and functionally,
the most relevant event is the appearance of thalamocortical
synapses within the CP (Kostovic & Judas, 2007, 2010;
Molliver et al., 1973), which are the substrate for early-evoked
potentials and cortical responses to pain stimuli. During establishment of permanent thalamocortical synapses, some thalamic axons retain transient contact with subplate neurons
(Allendoerfer & Shatz, 1994). Thus, there is prolonged coexistence of transient and permanent circuitry in the developing human neocortex (Kostovic & Judas, 2007). In the
hippocampus, there is rapid differentiation of pyramidal neurons with intensive synaptogenesis along their apical dendrites.
During this period, there is a gradual cessation of neuronal
proliferation and migration, with gradual disappearance of the
VZ and SVZ. Both astrocytes and oligodendrocytes are being
produced in large numbers, while initial areal differentiation
enables distinction between primary and associative cortical
areas (Kostovic & Rakic, 1984, 1990).
During the second part of the late fetal period (33rd PCW
onward), three major events are the transformation of fetal
zones, the change in MRI properties (due to gradual reduction
of extracellular matrix and isotropy changes caused by axonal
rearrangements), and expansive growth of the white matter.
Cortical white matter predominantly increases due to abundance and intense growth of corticocortical pathways. Within
the neocortex, a six-layered basic pattern of lamination is
clearly observed, concomitantly with the formation of secondary gyri and sulci and initial development of hemispheric
asymmetry. There is gradual resolution of the SP, especially at

the bottom of cortical sulci (Figure 2).
The production of new neurons is over, except in the hippocampal dentate gyrus. The myelination continues in primary
motor and somatosensory cortices and begins in the associative parietal cortex. This phase is functionally characterized by
the establishment of behavioral states and sleep/wake pattern,
the EEG synchronization, evoked potentials, and event-related
potentials. Current fMRI studies also revealed the existence of
resting-state activity and development of cortical hubs. While
MRI clearly reveals the existence of long associative pathways,
their functional organization in the fetus remains unknown.
At term (37th40th PCW), the cerebral cortex remains
immature and displays the presence of subplate remnant with
numerous interstitial neurons within the gyral white matter
(Judas, Sedmak, Pletikos, & Jovanov-Milosevic, 2010; Kostovic
et al., 2012). Associative pyramidal neurons still have relatively
few dendritic spines, and cortical interneurons are not well
developed; granular layer 4 is still present in future agranular
motor cortex. The GABA begins to function as inhibitory neurotransmitter already before birth. Functional studies reveal
that active neuronal circuitry exists not only in primary motor
and sensory cortical areas but also in cortical regions representing emotional and social brain.
The data on fetal cortical development are significant for a
number of reasons. First, detailed knowledge on normal cortical development is required for understanding the functional
development of the human cerebral cortex and relevant gene
environment interactions. Second, it is very important to recognize the existence of early functional development of human
fetal brain. The first cortical synapses appear already at the 8th
PCW, and this early fetal cortical activity is endogenous and
spontaneous. In contrast, cortical activity in very preterm
infants may be evoked by external stimuli, including pain.
174
While we do not know when memory functions begin to

develop, it is noteworthy that hippocampal and entorhinal
areas are among the first to differentiate, already during midgestation. Third, this early differentiation of cortical circuitry
(especially hippocampal and cingulate limbic areas) represents
the prospective substrate for default and resting-state activity.
The development of complex cortical circuitry (especially
corticocortical connections) represents the basis for the establishment of connectome (see related chapters). Finally, the
data on normal cortical development are essential for studying
developmental origin of neurological and cognitive disorders
and for the interpretation of neurological phenomena
observed in utero (fetal neurology) or in vivo (in prematurely
born infants).

Neurons; Cortical Surface Morphometry; Cytoarchitectonics,
Cytoarchitecture and Maps of the Human Cerebral Cortex; Development
of the Basal Ganglia and the Basal Forebrain; Evolution of the Cerebral
Cortex; Fetal and Postnatal Development of the Cortex: MRI and
Genetics; Functional and Structural Diversity of Pyramidal Cells;
Functional Connectivity; Genoarchitectonic Brain Maps; Gyrification in
the Human Brain; Myeloarchitecture and Maps of the Cerebral Cortex;
Quantitative Data and Scaling Rules of the Cerebral Cortex; Synaptic
Organization of the Cerebral Cortex; The Resting-State Physiology of
the Human Cerebral Cortex; INTRODUCTION TO CLINICAL BRAIN
MAPPING: Developmental Brain Atlases; INTRODUCTION TO
METHODS AND MODELING: Cortical Thickness Mapping; GraphTheoretical Analysis of Brain Networks; Integrative Computational
Neurogenetic Modeling; Lesion Segmentation; Methodological Issues
in fMRI Functional Connectivity and Network Analysis.
References
Allendoerfer, K. L., & Shatz, C. J. (1994). The subplate, a transient neocortical structure:
Its role in the development of connections between thalamus and cortex. Annual
Bayatti, N., Moss, J. A., Sun, L., Ambrose, P., Ward, J. F., Lindsay, S., et al. (2008). A
molecular neuroanatomical study of the developing human neocortex from 8 to 17
postconceptional weeks revealing the early differentiation of the subplate and
subventricular zone. Cerebral Cortex, 18, 15361548.
Bystron, I., Blakemore, C., & Rakic, P. (2008). Development of human cerebral cortex:
Boulder Committee revisited. Nature Reviews Neuroscience, 9, 110122.
Boulder Committee. (1970). Embryonic vertebrate central nervous system: Revised
terminology. Anatomical Record, 166, 257262.
Fishell, G., & Kriegstein, A. R. (2003). Neurons from radial glia: The
consequences of asymmetric inheritance. Current Opinion in Neurobiology, 13, 3441.
Hevner, R. F., & Kinney, H. C. (1996). Reciprocal entorhinal-hippocampal connections
established by human fetal midgestation. Journal of Comparative Neurology, 372,
384394.
His, W. (1904). Die Entwickelung des menschlichen Gehirns wahrend der ersten
Monate. Leipzig: Hirzel.
Jakovcevski, I., Filipovic, R., Mo, Z., Rakic, S., & Zecevic, N. (2009). Oligodendrocyte
development and the onset of myelination in the human fetal brain. Frontiers in
Judas, M., Sedmak, G., & Kostovic, I. (2013). The significance of the subplate for
evolution and developmental plasticity of the human brain. Frontiers in Human
Judas, M., Sedmak, G., & Pletikos, M. (2010). Early history of subplate and interstitial
neurons: From Theodor Meynert (1867) to the discovery of the subplate zone
(1974). Journal of Anatomy, 217, 344367.
Judas, M., Sedmak, G., Pletikos, M., & Jovanov-Milosevic, N. (2010). Populations of
subplate and interstitial neurons in fetal and adult human telencephalon. Journal of
Anatomy, 217, 381399.
Kanold, P. O., & Luhmann, H. J. (2010). The subplate and early cortical circuits. Annual
Kostovic, I., Jovanov-Milosevic, N., Rados, M., Sedmak, G., Benjak, V.,
Kostovic-Srzentic, M., et al. (2012). Perinatal and early postnatal reorganization of
the subplate and related cellular compartments in the human cerebral wall as
revealed by histological and MRI approaches. Brain Structure and Function. http://
dx.doi.org/10.1007/s00429-012-0496-0490.
Kostovic, I., & Judas, M. (2007). Transient patterns of cortical lamination during
prenatal life: Do they have implications for treatment? Neuroscience and
Biobehavioral Reviews, 31, 11571168.
Kostovic, I., & Judas, M. (2010). The development of the subplate and
thalamocortical connections in the human foetal brain. Acta Paediatrica, 99,
11191127.
Kostovic, I., Judas, M., Rados, M., & Hrabac, P. (2002). Laminar organization of the
human fetal cerebrum revealed by histochemical markers and magnetic resonance
imaging. Cerebral Cortex, 12, 536544.
Kostovic, I., & Molliver, M. E. (1974). A new interpretation of the laminar development
of cerebral cortex: Synaptogenesis in different layers of neopallium in the human
fetus. Anatomical Record, 178, 395.
Kostovic, I., Petanjek, Z., & Judas, M. (1993). Early areal differentiation of the human
cerebral cortex: Entorhinal area. Hippocampus, 3, 447458.
Kostovic, I., & Rakic, P. (1980). Cytology and time of origin of interstitial neurons in the
white matter in infant and adult human and monkey telencephalon. Journal of
Neurocytology, 9, 219242.
Kostovic, I., & Rakic, P. (1984). Development of prestriate visual projections in the
monkey and human fetal cerebrum revealed by transient cholinesterase staining.
the visual and somatosensory cortex of the macaque monkey and human brain.
Kostovic, I., Seress, L., Mrzljak, L., & Judas, M. (1989). Early onset of synapse
formation in the human hippocampus: A correlation with Nissl-Golgi architectonics
in 15- and 16.5-week-old fetuses. Neuroscience, 30, 105116.
Kwan, K. Y., Sestan, N., & Anton, E. S. (2012). Transcriptional co-regulation of
neuronal migration and laminar identity in the neocortex. Development, 139,
15351546.
Mallamaci, A. (2011). Molecular bases of cortico-cerebral regionalization. Progress in
Marin-Padilla, M. (1978). Dual origin of the mammalian neocortex and evolution of the
cortical plate. Anatomy and Embryology, 152, 109126.
Meyer, G. (2007). Genetic control of neuronal migrations in human cortical
development. Advances in Anatomy Embryology and Cell Biology, 189, 1111.
Meyer, G., Schaaps, J. P., Moreau, L., & Goffinet, A. M. (2000). Embryonic and early
fetal development of the human neocortex. Journal of Neuroscience, 20,
18581868.
Molliver, M. E., Kostovic, I., & Van der Loos, H. (1973). The development of synapses
in cerebral cortex of the human fetus. Brain Research, 50, 403407.
Molnar, Z., Metin, C., Stoykova, A., Tarabykin, V., Price, D. J., Francis, F., et al. (2006).
Comparative aspects of cerebral cortical development. European Journal of
Molyneaux, B. J., Arlotta, P., Menezes, J. R. L., & Macklis, J. D. (2007). Neuronal
subtype specification in the cerebral cortex. Nature Reviews Neuroscience, 8,
427437.
Monnier, A., Adle-Biassette, H., Delezoide, A. L., Evrard, P., Gressens, P., & Verney, C.
(2007). Entry and distribution of microglial cells in human embryonic and fetal
cerebral cortex. Journal of Neuropathology and Experimental Neurology, 66,
372382.
Monnier, A., Evrard, P., Gressens, P., & Verney, C. (2006). Distribution and
differentiation of microglia in the human encephalon during the first two trimesters
of gestation. Journal of Comparative Neurology, 499, 565582.
Mrzljak, L., Uylings, H. B. M., Kostovic, I., & Van Eden, C. G. (1988). Prenatal
development of neurons in the human prefrontal cortex: I. A qualitative Golgi study.
OLeary, D. D., Chou, S. J., & Sahara, S. (2007). Area patterning of the mammalian
ORahilly, R., & Muller, F. (2006). The embryonic human brain. An atlas of
developmental stages (3rd ed.). New York: Wiley-Liss.
Petanjek, Z., Judas, M., Kostovic, I., & Uylings, H. B. M. (2008). Life-span alterations of
basal dendritic trees of pyramidal neurons in the human prefrontal cortex: A layerspecific pattern. Cerebral Cortex, 18, 915929.
Petanjek, Z., Judas, M., Simic, G., Rasin, M. R., Uylings, H. B., Rakic, P., et al. (2011).
Extraordinary neoteny of synaptic spines in the human prefrontal cortex.
108, 1328113286.
Prayer, D., Kasprian, C., Krampl, E., Ulm, B., Witzani, L., Prayer, L., et al. (2006). MRI of
normal fetal brain development. European Journal of Radiology, 57, 199216.
Rakic, P. (1972). Mode of cell migration to the superficial layers of fetal monkey
neocortex. Journal of Comparative Neurology, 145, 6184.
Rakic, P. (1977). Prenatal development of the visual system in the rhesus monkey.
Philosophical Transactions of the Royal Society of London, Series B, 278, 245260.
Rakic, P. (1988). Specification of cerebral cortical areas. Science, 241, 170176.
Rakic, P. (1995). A small step for the cell: A giant leap for mankind A
hypothesis of neocortical expansion during evolution. Trends in Neurosciences, 18,
383388.
175
Rickmann, M., Chronwall, B. M., & Wolff, J. R. (1977). On the development of nonpyramidal neurons and axons outside the cortical plate: The early marginal zone as a
pallial anlage. Anatomy and Embryology, 151, 285307.
Schmechel, D. E., & Rakic, P. (1979). A Golgi study of radial glia cells in developing
monkey telencephalon: Morphogenesis and transformation into astrocytes. Anatomy
and Embryology, 156, 115152.
Verney, C., Monnier, A., Fallet-Bianco, C., & Gressens, P. (2010). Early microglial
colonization of the human forebrain and possible involvement in periventricular
white-matter injury of preterm infants. Journal of Anatomy, 217, 436448.
Volpe, J. J. (1996). Subplate neurons missing link in brain injury of the premature
infant? Pediatrics, 97, 112113.
Wang, W. Z., Hoerder-Suabedissen, A., Oeschger, F. M., Bayatti, N., Ipes, B. K.,
Lindsay, S., et al. (2010). Subplate in the developing cortex of mouse and human.
Journal of Anatomy, 217, 368380.
Zecevic, N., & Verney, C. (1995). Development of catecholamine neurons in human
embryos and fetuses, with special emphasis on the innervation of the cerebral
Cytoarchitectonics, Receptorarchitectonics, and Network Topology of Language

M Catani, NatBrainLab, Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry PO50 Kings College
London, London, United Kingdom
Glossary
Cytoarchitectonics the post-mortem analysis of the cellular

distribution in the grey matter that permits the subdivision
of the cortex into distinct areas or fields.
Receptorarchitectonics the study of the receptor
distribution in the grey matter that defines the unique
receptorial fingerprint of each cortical area.
Language development in humans occurred as a direct consequence of the functional specialization of cortical areas located
in the temporal (i.e., Wernickes region) and frontal lobes (i.e.,
Brocas region) of the left hemisphere. These areas are primarily dedicated to language and for this reason are identified as
core language regions. Other more bilaterally distributed cortical areas connect to these left-lateralized core regions and
form an extended language network. In this article, we aim
to introduce the reader to current approaches used to map the
main language areas as defined by cytoarchitectonics, receptorarchitectonics, and their networks as defined by in vivo diffusion tractography. Although our approach is fundamentally
anatomical, we refer to possible functional correlates and associated symptoms whenever possible.
Core Language Regions

Methods and theoretical approaches to anatomically based
definitions of Brocas region have changed throughout the
history of its study, resulting in the proposal of many different
parcellation schemes (for a review, see Amunts & Zilles, 2012).
On the surface, Brocas region corresponds to the pars opercularis and pars triangularis of the inferior frontal gyrus.
Cytoarchitectonically, the pars opercularis and pars triangularis are largely occupied by areas 44 and 45, respectively.
Their most distinct feature is the presence of very large pyramidal cells in deep layer III. These two areas differ from each
other for the thickness of layer IV, well developed in area 45
but thinner and invaded by pyramidal cells from neighboring
layers III and V in area 44. Layer IV is known to process, among
others, input from the thalamus.
Probabilistic cytoarchitectonic maps of areas 44 and 45
have been generated using quantitative and statistical criteria
for delineating their borders (Figure 1(a); Amunts et al.,
1999). These maps reveal important anatomical features of
Brocas region. Intersubject variability of the overall surface
and extent of these two areas is evident in the healthy human
brain (Amunts et al., 2004). In addition, a large portion of
these two areas is buried in the depths of the sulci, which
Tractography MRI-based method that uses diffusion

imaging of water molecule to reconstruct the trajectories of
white matter connections.
prevents any possibility of predicting their exact extent and

location solely on the basis of the surface anatomy of the
inferior frontal gyrus (Figure 1(a)), which is in itself highly
variable among people (Ono, Kubik, & Abernathey, 1990).
One advantage of probabilistic maps is that they offer a
quantitative approach to cortical localization in patients with
brain lesions and in functional activation studies (see www.
jubrain.fz-juelich.de; Amunts et al., 2004; Fischl et al., 2007).
For example, it has been shown that the maximum probability
map for area 44 is more likely to overlap with activations
generated by tasks involving syntactic processing (Friederici &
Kotz, 2003) and lexical decision (Heim, Eickhoff, Ischebeck, &
Amunts, 2007), whereas area 45 is more involved in semantic
tasks (Amunts et al., 2004). The cytoarchitectonic maps can
also be used as seed regions to study the structural and functional connectivities of language networks (Heim, Eickhoff, &
Amunts, 2011). These are only a few applications of many. An
important aspect to consider is that functional activations often
do not correspond to the cytoarchitectonic subdivision of
Brocas region into two areas when language-related activations
are superimposed on probabilistic maps. Indeed, often, activations overlap only in part with these areas and extend to other
neighboring areas (Indefrey et al., 2001). Several reasons may
explain the lack of an exact correspondence between functional
activations and cytoarchitectonic maps, including methodological shortcomings of both techniques, which may limit our
ability to capture the complex segregation of Brocas region.
The application of novel receptorarchitectonic analysis to
cortical areas (Zilles & Amunts, 2009) shows that Brocas region
is indeed more complex than previously assumed. Amunts et al.
(2010) analyzed the receptor distribution of different neurotransmitter systems (glutamate, GABA, serotonin, and acetylcholine) in serial sections of the posterior frontal cortex. The receptor
analysis showed that not only do areas 44 and 45 differ in their
receptor distribution profile, but also each area can be further
subdivided into multiple areas (Figure 1(b)). These subareas
show a similar receptorarchitectonic pattern to areas 44 and 45,
which arguably suggests their involvement in language-related
processes. Interestingly, ventral area 6 has a pattern that is more
similar to areas 44 and 45 than to area 47, which suggests a more
http://dx.doi.org/10.1016/B978-0-12-397025-1.00211-6
177
178
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Cyto-/Receptor-architectonics & Network Topology
Figure 1 Cortical mapping of Brocas region based on postmortem cytoarchitectonic and receptorarchitectonic analyses. (a) Top, surface view of the
probabilistic maps for Brodmanns area 44 (BA 44) and Brodmanns area 45 (BA 45) derived from quantitative cytoarchitectonic measurements of
ten individual brains. The probabilistic maps are intended to quantify the interindividual variability of the areas that compose Brocas region, where hot
tones correspond to a high anatomical overlap and cold tones to higher variability. This interindividual variability can be appreciated in the bottom
panel, where the left and right maps for BA 44 (red) and BA 45 (yellow) are reported for two representative brains. Note, for example, the difference in the
leftright asymmetry of BA 44 and BA 45. In addition, the borders of the two areas are not always well identified by the main sulci of this region:
inferior frontal sulcus (IFS), horizontal ramus of the lateral fissure (HRLF), ascending ramus of the lateral fissure (ARLF), precentral sulcus (PrCS),
diagonal sulcus (DS). (The data are from Amunts et al., 2004.) (b) Further segregation of Brocas region based on neurotransmitter receptor distribution.
This analysis can reveal unique characteristics of subregions that may share similar cytoarchitectonic morphology. Areas 44v and op8, for
example, have a similar density of GABAA or alternately GABAA receptors but different density of cholinergic muscarinic receptors M1.
distant structural and possibly functional relatedness between

areas of the same gyrus (i.e., areas 44, 45, and 47 are parts of the
inferior frontal gyrus) and between areas lying in different gyri
(areas 44 and 45 in the inferior frontal gyrus and area 6 in the
precentral gyrus; Figure 2).
The anatomical correlates of Wernickes region are more
ambiguously defined than those of Brocas region. In its modern definition, Wernickes region occupies the posterior aspect
of the superior temporal gyrus and part of the middle temporal
gyrus and is involved in multiple aspects of language processing (Binder et al., 2000; Hickok & Poeppel, 2007). Cytoarchitectonically, Wernickes region includes areas 22 and 42 and
part of area 37 (Aboitiz & Garcia, 1997), with further segmentations identified using probabilistic cytoarchitectonic and
receptorarchitectonic mappings. The superior temporal gyrus,
for example, is occupied by three distinct areas (Figure 3). Area
Te1, the primary auditory cortex, occupies a large portion of
the Heschl gyrus (Morosan et al., 2001). Area Te2 is partially
located on the most lateral aspect of the Heschl gyrus and on
the opercular surface of the superior temporal gyrus, whereas

area Te3 occupies approximately the posterior two-thirds of the
free surface of the superior temporal gyrus (Morosan,
Schleicher, Amunts, & Zilles, 2005) and differs from its neighboring areas for the prominent size and high density of pyramidal neurons in layer IIIc and a high cellular density in layer
V. With respect to receptor architecture, Te3 is characterized by
a low density of muscarinic M2 receptors (Morosan et al.,
2005). Te3 comprises further subdivisions (Rivier & Clarke,
1997; Wallace, Johnston, & Palmer, 2002) that have some
correspondence with findings from functional activation studies (Friederici & Kotz, 2003).
Mesgarani, Cheung, Johnson, and Chang (2014) had
recently shown that the superior temporal gyrus responds
selectivity to distinct phonetic features of spoken language
and contains the acousticphonetic representation of speech.
In their comment to this paper, Grodzinsky and Nelken (2014)
emphasized that speech representation in the experiment was
dominated by abstract and linguistically defined features.
179
Figure 2 The cluster tree illustrates similarities between frontal areas based on their receptor distribution profile. Modified from Amunts, K., Lenzen,
M., Friederici, A. D., Schleicher, A., Morosan, P., Palomero-Gallagher, N., et al. (2010). Brocas region: Novel organizational principles and multiple
receptor mapping. PLoS Biology, 8, e1000489.
#1
#2
#3
#4
#5
#1 #2 #3 #4 #5
Te1
Te2
Te3
Te1.0
(b)
(c)
Te2
Te1.1
Te2
(e)
(d)
Te3
(a)
TI
Te4
(f)
Figure 3 The cytoarchitectonic of the language areas in the superior temporal region. Morosan, P., Schleicher, A., Amunts, K., & Zilles, K. (2005).
Multimodal architectonic mapping of human superior temporal gyrus. Anatomy and Embryology, 210, 401406.
180

action monitoring, distinguishing self from others actions,
and low-level aspects of mentalizing (Lombardo et al., 2010;
Yoshida, Saito, Iriki, & Isoda, 2011). The anterior insula is
highly connected to the frontal operculum and Brocas region
(Catani et al., 2012; Cerliani et al., 2012) and is often activated
in language production tasks (Dronkers, 1996). In the ventral
occipitotemporal region, the visual word form area is specialized for processing written strings (Cohen et al., 2000).
Finally, the anterior temporal lobe, which includes area 38
and anterior portions of areas 20, 21, 22, and 36, has been
recognized as an important language hub involved in semantic
processing (Catani et al., 2013; Mesulam et al., 2013).
Other Cortical Regions

In addition to Brocas and Wernickes regions, other cortical
areas are relevant to speech and language. Geschwinds region
in the inferior parietal lobule involves area 40 in the supramarginal gyrus and area 39 in the angular gyrus (Catani, Jones, &
Ffytche, 2005). A more recent parcellation of this region into
seven cytoarchitectonic areas has been proposed, with five
subdivisions covering area 40 and two subdivisions covering
area 39 (Caspers et al., 2006). Of the five anterior subdivisions,
the three most anterior ones show a receptor architecture similar to that of area 44 in the frontal lobe (Caspers et al., 2013).
Geschwinds region is part of an extended network that links
core language regions to areas involved in memory, semantic
knowledge, and social cognition (Binder, Desai, Graves, &
Conant, 2009; Jacquemot & Scott, 2006; Meyer, Obleser,
Anwander, & Friederici, 2012; Vilberg & Rugg, 2008).
In the mesial aspect of the superior frontal gyrus, area 6
and, in part, posterior areas 8 and 32 form an important
language region that participates in planning, initiation, and
monitoring of speech (Paulesu, Frith, & Frackowiak, 1993;
Penfield & Roberts, 1959). This region, which corresponds to
the anterior cingulate cortex and presupplementary motor area
(preSMA), has also been characterized using modern cytoarchitectonic or receptorarchitectonic mapping in the human and
macaque brains (Geyer et al., 1998; Palomero-Gallagher,
Mohlberg, Zilles, & Vogt, 2008). The preSMA is involved in
Subcortical Structures
Cortical language areas form complex networks with the thalamus, basal ganglia, and cerebellum (Cappa & Vallar, 1992;
Schmahmann & Pandya, 2008; Catani & Thiebaut de Schotten,
2012). Damage to these subcortical structures can manifest with
either isolated aphasia or language deficits that are part of more
complex neurological syndromes. Anatomical and clinical studies suggest that these cortico-subcortical networks are segregated
(Figure 4). Brocas region and the preSMA, for example, receive
their main afferents from the anterior thalamus (i.e., ventral
anterior nucleus). Stuttering and reduced spontaneous speech
have been described in association with damage of the ventral
4
5
3-
1-
6
46
10
44
40
45
11
43
47
38
41
42
21
39
19
22
18
17
37
20
MD
IN
VLp
LD
LP
VA
Mid
VLa
VLm
CM
VPl
Pul
VPm
VPi
LGN
MGN
Figure 4 Thalamocortical connections of the language areas. A: Anterior group; LGN: lateral geniculate nucleus; LP: lateroposterior; MD: mediodorsal;
MGN: medial geniculate nucleus; Mid: midline group; Pul: pulvinar; VA: ventral anterior; VLa: ventral lateral anterior; VPi: ventral posterior
inferior; VPl: ventral posterior lateral; VPm: ventral posterior medial; VLp: ventral lateral posterior. Modified from Catani, M., & Thiebaut de Schotten, M.
(2012). Atlas of human brain connections. Oxford, UK: Oxford University Press.

anterior nucleus or its connections to language frontal areas
(Watkins, Smith, Davis, & Howell, 2008). Wernickes and
Geschwinds regions receive projections primarily from the pulvinar and the lateral posterior nuclei, respectively. Reduced
comprehension is more commonly associated with lesions to
these posterior thalamic nuclei (Cappa & Vallar, 1992).
Pure lesions of the thalamus do not conform to classical
neurological taxonomy of aphasia syndromes, and a precise
clinicalanatomical correlation is often difficult to perform in
these patients since lesions are often large and involve multiple
thalamic nuclei and surrounding white matter (Cappa &
Vallar, 1992). In general, repetition deficits are rare and comprehension deficits of mild intensity. Severe writing difficulties
and semantic paraphasias are relatively more common.
The striatum composed of the caudate and putamen is
another important relay station of the cortico-subcortical
loops. Stimulation of the striatum is associated with involuntary
language production, while lesions more frequently cause nonfluent speech (Crosson, 1992). In bilinguals, the left caudate has
an important role in language switch (Crinion et al., 2006).
The cerebellum receives cortical afferents from language
areas through the pontine nuclei and projects to the same
areas via the thalamus. In patients with cerebellar lesions,
verbal fluency can be impaired to the point of telegraphic
speech or mutism, but true aphasic disorders are rare. Anomia,
agrammatic speech, and abnormal prosody (i.e., high-pitched,
hypophonic whining) have been also reported in these
patients (Schmahmann & Pandya, 2008).
181
has been studied in humans with postmortem blunt dissections and more extensively with diffusion imaging tractography (Figure 5(a)).
The arcuate fasciculus is a dorsal perisylvian association tract
connecting Wernickes, Geschwinds, and Brocas regions.
Within the arcuate fasciculus, two parallel pathways have been
distinguished: the medial, direct pathway connecting Wernickes
region with Brocas region (i.e., the arcuate fasciculus sensu stricto
or long segment) and the indirect pathway, consisting of an
anterior segment that links Brocas region to Geschwinds region
and a posterior segment between Geschwinds and Wernickes
regions (Catani et al., 2005). Lopez-Barroso et al. (2013) showed
that performance in word learning correlates with microstructural properties and strength of functional connectivity of the
direct connections between Brocas and Wernickes regions. This
study demonstrates that our ability to learn new words relies on
an efficient and fast communication between auditory temporal
and motor frontal regions. Schulze, Vargha-Khadem, and
Mishkin (2012) suggested that the absence of these connections
in nonhuman primates might explain our unique ability to learn
new words. The long segment is also important for syntactic
processing (Tyler et al., 2011; Wilson et al., 2011) and word
repetition (Parker Jones et al., 2014). Within the indirect pathway, the anterior and posterior segments have different roles in
reading (Thiebaut de Schotten, Cohen, Amemiya, Braga, &
Dehaene, 2014), phonological and semantic processing (Binder
et al., 2009; Newhart et al., 2012), verbal working memory
(Jacquemot & Scott, 2006), and pragmatic interpretation
(Hagoort, 2013).
Language areas of the temporal and frontal lobes are also
interconnected by a set of ventral longitudinal tracts (Catani &
Mesulam, 2008). The inferior longitudinal fasciculus carries
visual information from occipital and posterior temporal
White Matter Pathways

Language areas are reciprocally connected through a complex
system of association and commissural tracts whose anatomy
Brocas
region
Anterior
temporal
lobe
Arcuate fasciculus (long segment)
Frontal aslant tract
Arcuate fasciculus (anterior segment)
Uncinate fasciculus
Arcuate fasciculus (posterior segment)
Inferior longitudinal fasciculus
Wernickes
region
Geschwinds
region
Visual word
form area
Inferior fronto-occipital fasciculus
(a)
(b)
Figure 5 Language networks visualized with diffusion tractography. (a) Association pathways of the left hemisphere connecting the main language
regions. (b) Density of callosal cortical projections based on diffusion imaging. Hot tones indicate higher degree of transcallosal connections.
Note the reduced interhemispheric connectivity for most of the language regions.
182
areas to the anterior temporal lobe (Catani, Jones, Donato, &

Ffytche, 2003) and plays an important role in visual object
recognition, reading, and linking object representations to
their lexical labels. The uncinate fasciculus connects the anterior temporal lobe to the orbitofrontal region and part of the
inferior frontal gyrus and may play an important role in lexical
retrieval, semantic associations, and naming (Catani et al.,
2013). The uncinate fasciculus is severely damaged in those
patients with the semantic variant of primary progressive aphasia (Catani et al., 2013). The inferior fronto-occipital fasciculus
provides direct connections between occipital (and perhaps
the posterior temporal cortex) and frontal cortices in the
human brain (Forkel et al., 2012). The relevance of this fasciculus to reading, writing, and other aspects of language remains
to be established (Duffau et al., 2005; Forkel et al., 2012).
The frontal aslant tract is a newly described pathway connecting Brocas region with medial frontal areas including the
preSMA and cingulate cortex (Catani et al., 2012; Lawes et al.,
2008). Medial regions of the frontal lobe facilitate speech initiation through direct connection to the pars opercularis and pars
triangularis of the inferior frontal gyrus. Patients with lesions to
these areas present with various degrees of speech impairment
from a total inability to initiate speech (i.e., mutism) to mild
altered fluency (Catani et al., 2012; Naeser, Palumbo, HelmEstabrooks, Stiassny-Eder, & Albert, 1989). The frontal aslant
tract is damaged in patients with the nonfluent/agrammatic
form of primary progressive aphasia (Catani et al., 2013).
The frontal operculum is connected to the insula through a
system of short U-shaped fronto-insular tracts (Catani et al.,
2012; Cerliani et al., 2012). Direct insular inputs to Brocas
region from the insula provide visceral and emotional information for speech output modulation according to internal
states. Lesions to these insular connections may result in
motor aprosodia (e.g., flat intonation) and apraxia of speech
(Dronkers, 1996).
In addition to the earlier tracts, data from axonal tracing
studies in the monkey have suggested the existence of additional pathways, including the middle longitudinal fasciculus
(Seltzer & Pandya, 1984) and the extreme capsule tract
(Schmahmann & Pandya, 2006). The exact role of these tracts
in humans remains to be demonstrated.
Interhemispheric Asymmetry and Gender Differences

Lateralization of language functions and underlying structural
asymmetry are characteristic features of human brain organization. Several hypotheses have been proposed in the past to
explain language lateralization. One of these proposals suggests that evolutionary pressures guiding brain size and lateralization of specialized language areas are accompanied by
reduced interhemispheric connectivity and greater intrahemispheric connectivity (Aboitiz, Scheibel, Fisher, & Zaidel, 1992).
Thus, by being connected through less transcallosal fibers or
fibers of smaller and slower-conducting diameter, specialized
areas reduce unnecessary cross talk and maintain separate
parallel processing systems through association tracts (i.e.,
arcuate fasciculus; Doron & Gazzaniga, 2008). Indeed, diffusion tractography in humans reveals that language areas show
reduced transcallosal connections compared with nonlanguage regions (Figure 5(b)).

Cytoarchitectonic asymmetry, although already present in
one-year-old infants, becomes progressively more evident
throughout childhood (Amunts, Schleicher, Ditterich, & Zilles,
2003). In adults, leftward asymmetry has been reported for
Brocas region using cytoarchitectonic analysis (Brodmann
area 44 in the pars opercularis) (Amunts et al., 1999; Uylings,
Jacobsen, Zilles, & Amunts, 2006). Significant leftward asymmetry in the volume of the pars opercularis has also been
reported based on in vivo MRI-based measurements (Keller
et al., 2007). Gray matter concentration differences in the
posterior part of the inferior frontal gyrus (pars opercularis)
have been found to correlate with language dominance
assessed by the sodium amytal procedure (Dorsaint-Pierre
et al., 2006). Asymmetry has also been observed for receptor
architecture. A larger concentration of cholinergic M2 receptors
has been found in left areas 44v and 44d compared with the
right counterparts. Other receptors show no interhemispheric
differences (Amunts et al., 2010). Structural asymmetry at the
microstructural level has been reported for other regions of
the temporal lobe, including areas 42 and 22 (Buxhoeveden,
Switala, Litaker, Roy, & Casanova, 2001; Galaburda, Sanides, &
Geschwind, 1978; Hutsler & Galuske, 2003; Jacobs, Schall, &
Scheibel, 1993).
Leftright asymmetries have been investigated with respect
to the underlying white matter (Catani et al., 2007, 2012;
Lopez-Barroso et al., 2013; Nijhuis, van Cappellen van Walsum,
& Norris, 2013). An extreme degree of leftward lateralization
of the long segment of the arcuate fasciculus has been reported
in 60% of the normal population (Figure 6(a); Catani et al.,
2007). The remaining 40% of the population show either a
mild leftward lateralization (20%) or a bilateral, symmetrical
pattern (20%). Overall, females are more likely to have a bilateral pattern compared with males (Figure 6(b)). The degree
of lateralization of the long segment has important clinical
implications. Forkel et al. (2014) showed that patients with
aphasia are more likely to recover normal language at 6 months
if at the time of the stroke they have a larger volume of the long
segment in the right unaffected hemisphere (Figure 6(c)). The
frontal aslant tract, although left-lateralized in most people,
shows a more bilateral pattern compared with the arcuate
fasciculus, which could explain the prompt recovery of speech
functions in those patients with unilateral damage of this tract
(Catani et al., 2012).
Conclusion
In this article, we suggest an anatomical language model
encompassing a core and an extended language network. The
core network includes the arcuate fasciculus connecting Brocas
and Wernickes regions. This network is left-lateralized in most
human brains. In addition, an extended network provides
access to social, emotional, and attentional inputs necessary
for successful language performances. One unique feature of
language as cognitive process is the extraordinary ability to
access, process, and bind together information derived from
memory and sensorial perception to create and convey
18
183
85%
Females
Number. of subjects
14
Group 1 (~60%)
Strong left lateralization
Males
10
40%
30%
30%
10%
5%
0
Group 2
Group 3
Group 1
Lateralization pattern
(b)
Group 2 (~20%)
Bilateral, left lateralization
(a)
Group 3 (~20%)
Bilateral, symmetrical
Aphasia quotient (AQ) six months

post-stroke
100
90
80
70
10
(c)
5
0
5
10
Right long segment (index size)
Figure 6 The distribution of the pattern of lateralization of the long segment in (a) three groups and (b) differences in lateralization between genders.
Modified from Catani, M., Allin, M. P., Husain, M., Pugliese, L., Mesulam, M. M., Murray, R. M., et al. (2007). Symmetries in human brain
language pathways correlate with verbal recall. Proceedings of the National Academy of Sciences of the United States of America, 104, 1716317168.
(c) Recovery of language 6 months after stroke is correlated with the volume of the right long segment. Reproduced from Forkel, S. J.,
Thiebaut de Schotten, M., DellAcqua, F., Kalra, L., Murphy, D., Williams, S., et al. (2014). Right arcuate fasciculus volume predicts recovery from
left stroke aphasia. Brain (in press).
messages. Perhaps, this ability derives from the development of

a unique pattern of connections that typifies human brains. A
precise correspondence between contemporary neurocognitive
models of language (e.g., Hagoort, 2013; Hickok & Poeppel,
2007; Jeon & Friederici, 2013), functional activation, and
anatomically defined characteristics of cortical areas and connecting pathways remains a challenging task in contemporary
brain mapping.
Acknowledgments
We would like to thank Valentina Bambini, Stephanie Forkel,
and other members of the Neuroanatomy and Tractography
Laboratory (www.natbrainlab.com), the Institute of Neuroscience and Medicine of the Research Center Julich, and C. and O.
Vogt Institute for Brain Research of the Heinrich Heine University Dusseldorf for their helpful comments on the
manuscript. Michel Thiebaut de Schotten kindly provided the

data set for Figure 5.
References
Aboitiz, F., & Garcia, G. L. (1997). The evolutionary origin of language areas in the
human brain. A neuroanatomical perspective. Brain Research Reviews, 25,
381396.
Aboitiz, F., Scheibel, A. B., Fisher, R. S., & Zaidel, E. (1992). Fiber composition of the
human corpus callosum. Brain Research, 598, 143153.
principles and multiple receptor mapping. PLoS Biology, 8, e1000489.
Amunts, K., Schleicher, A., Burgel, U., Mohlberg, H., Uylings, H. B. M., & Zilles, K.
(1999). Brocas region revisited: Cytoarchitecture and intersubject variability. The
Amunts, K., Schleicher, A., Ditterich, A., & Zilles, K. (2003). Brocas region:
Cytoarchitectonic asymmetry and developmental changes. The Journal of
184
Amunts, K., Weiss, P. H., Mohlberg, H., Pieperhoff, P., Eickhoff, S., Gurd, J., et al.
(2004). Analysis of the neural mechanisms underlying verbal fluency in
cytoarchitectonically defined stereotaxic space The role of Brodmanns areas 44
and 45. NeuroImage, 22, 4256.
Amunts, K., & Zilles, K. (2012). Architecture and organizational principles of Brocas
region. Trends in Cognitive Sciences, 16, 418426.
Binder, J. R., Desai, R. H., Graves, W. W., & Conant, L. L. (2009). Where is the semantic
system? A critical review and meta-analysis of 120 functional neuroimaging studies.
Binder, J. R., Frost, J. A., Hammeke, T. A., Bellgowan, P. S.F, Springer, J. A.,
Kaufman, J. N., et al. (2000). Human temporal lobe activation by speech and
nonspeech sounds. Cerebral Cortex, 10, 512528.
Buxhoeveden, D. P., Switala, A. E., Litaker, M., Roy, E., & Casanova, M. F. (2001).
Lateralization of minicolumns in human planum temporale is absent in nonhuman
primate cortex. Brain, Behavior and Evolution, 57(6), 349358.
Cappa, S. F., & Vallar, G. (1992). Neuropsychological disorders after subcortical
lesions: Implications for neural models of language and spatial attention. In G.
Valla, S. F. Cappa, & C.-W. Wallesch (Eds.), Neuropsychological disorders
associated with subcortical lesions (pp. 741). New York, NY: Oxford University
Press.
Catani, M., Allin, M. P., Husain, M., Pugliese, L., Mesulam, M. M., Murray, R. M., et al.
(2007). Symmetries in human brain language pathways correlate with verbal recall.
104, 1716317168.
Catani, M., Dellacqua, F., Vergani, F., Malik, F., Hodge, H., Roy, P., et al. (2012). Short
frontal lobe connections of the human brain. Cortex, 48, 273291.
Catani, M., Jones, D. K., Donato, R., & Ffytche, D. H. (2003). Occipito-temporal
connections in the human brain. Brain, 126, 20932107.
Catani, M., Jones, D. K., & Ffytche, D. H. (2005). Perisylvian language networks of the
human brain. Annals of Neurology, 57, 816.
Catani, M., & Mesulam, M. (2008). The arcuate fasciculus and the disconnection theme
in language and aphasia: History and current state. Cortex, 44, 953961.
Catani, M., Mesulam, M. M., Jakobsen, E., Malik, F., Martersteck, A., & Wieneke, C.
(2013). A novel frontal pathway underlies verbal fluency in primary progressive
aphasia. Brain, 37, 17241737.
Catani, M., & Thiebaut de Schotten, M. (2012). Atlas of human brain connections.
Oxford, UK: Oxford University Press.
Cerliani, L., Thomas, R. M., Jbabdi, S., Siero, J. C., Nanetti, L., & Crippa, A. (2012).
Probabilistic tractography recovers a rostrocaudal trajectory of connectivity
variability in the human insular cortex. Human Brain Mapping, 33, 20052034.
Cohen, L., Dehaene, S., Naccache, L., Lehericy, S., Dehaene-Lambertz, G.,
Henaff, M. A., et al. (2000). The visual word form area: Spatial and temporal
characterization of an initial stage of reading in normal subjects and posterior splitbrain patients. Brain, 123, 291307.
Crinion, J., Turner, R., Grogan, A., Hanakawa, T., Noppeney, U., & Devlin, J. T. (2006).
Language control in the bilingual brain. Science, 9, 15371540.
Crosson, B. (1992). Subcortical functions in language: A working model. Brain and
Language, 25, 257292.
Doron, K. W., & Gazzaniga, M. S. (2008). Neuroimaging techniques offer new
perspectives on callosal transfer and interhemispheric communication. Cortex, 44,
10231029.
Dorsaint-Pierre, R., Penhune, V. B., Watkins, K. E., Neelin, P., Lerch, J. P., Bouffard, M.,
et al. (2006). Asymmetries of the planum temporale and Heschls gyrus:
Relationship to language lateralization. Brain, 129(Pt. 5), 11641176.
Dronkers, N. F. (1996). A new brain region for coordinating speech articulation. Nature,
384, 159161.
Duffau, H., Gatignol, P., Mandonnet, E., Peruzzi, P., Tzourio-Mazoyer, N., & Capelle, L.
(2005). New insights into the anatomo-functional connectivity of the
semantic system: A study using cortico-subcortical electrostimulations. Brain, 128,
797810.
Fischl, B., Rajendran, N., Busa, E., Augustinack, J., Hinds, O., & Yeo, B. T. T. (2007).
19731980.
Forkel, S. J., DellAcqua, F., Thiebaut de Schotten, M., Kalra, L., Murphy, D., Williams,
S., & Catani, M. (2014). Right arcuate fasciculus volume predicts recovery from left
stroke aphasia. Brain, 137, 20272039.
Forkel, S. J., Thiebaut de Schotten, M., Kawadler, J. M., Dellacqua, F., Danek, A., &
Catani, M. (2012). The anatomy of fronto-occipital connections from early blunt
dissections to contemporary tractography. Cortex, 56, 7384.
Friederici, A. D., & Kotz, S. A. (2003). The brain basis of syntactic processes: Functional
imaging and lesions studies. NeuroImage, 20(Suppl. 1), S8S17.
Galaburda, A. M., Sanides, F., & Geschwind, N. (1978). Human brain. Cytoarchitectonic
left-right asymmetries in the temporal speech region. Archives of Neurology, 35,
812817.
Geyer, S., Matelli, M., Luppino, G., Schleicher, A., Jansen, Y., Palomero-Gallagher, N.,
et al. (1998). Receptor autoradiographic mapping of the mesial motor and premotor
cortex of the macaque monkey. The Journal of Comparative Neurology, 397, 231250.
Grodzinsky, Y., & Nelken, I. (2014). Neuroscience: The neural code that makes us
human. Science, 343, 978979.
Hagoort, P. (2013). MUC (memory, unification, control) and beyond. Frontiers in
Psychology, 416, 113.
Heim, S., Eickhoff, S. B., & Amunts, K. (2011). Different roles of cytoarchitectonic BA 44
and BA 45 in phonological and semantic verbal fluency as revealed by dynamic
causal modelling. NeuroImage, 48, 616624.
Heim, S., Eickhoff, S. B., Ischebeck, A. K., & Amunts, K. (2007). Modality-independent
involvement of the left BA 44 during lexical decision making. Brain Structure &
Function, 212, 95106.
Hickok, G., & Poeppel, D. (2007). The cortical organization of speech processing.
Hutsler, J., & Galuske, R. A. W. (2003). Hemispheric asymmetries in cerebral cortical
networks. Trends in Neurosciences, 26(8), 429435.
Indefrey, P., Brown, C. M., Hellwig, F., Amunts, K., Herzog, H., Seitz, R. J., et al. (2001).
A neural correlate of syntactic encoding during speech production. Proceedings
59335936.
Jacobs, B., Schall, M., & Scheibel, A. B. (1993). A quantitative dendritic analysis of
Wernickes area in humans. II. Gender, hemispheric, and environmental factors. The
Jacquemot, C., & Scott, S. K. (2006). What is the relationship between phonological
short-term memory and speech processing? Trends in Cognitive Sciences, 10,
480486.
Jeon, H. A., & Friederici, A. D. (2013). Two principles of organization in the prefrontal
cortex are cognitive hierarchy and degree of automaticity. Nature Communications,
4, 2041.
Keller, S. S., Highley, J. R., Garcia Finana, M., Sluming, V., Rezaie, R., & Roberts, N.
(2007). Sulcal variability, stereological measurement and asymmetry of Brocas area
on MR images. Journal of Anatomy, 211, 534555.
Lawes, I. N., Barrick, T. R., Murugam, V., Spierings, N., Evans, D. R., Song, M., et al.
(2008). Atlas-based segmentation of white matter tracts of the human brain using
diffusion tensor tractography and comparison with classical dissection.
Lombardo, M. V., Chakrabarti, B., Bullmore, E. T., Wheelright, S. J., Sadek, S. A.,
Suckling, J., et al. (2010). Shared neural circuits for mentalizing about the self and
others. Journal of Cognitive Neuroscience, 22, 16231635.
Lopez-Barroso, D., Catani, M., Ripollesa, P., DellAcqua, F., Rodrguez-Fornells, A., &
de Diego-Balaguera, R. (2013). Word learning is mediated by the left arcuate
fasciculus. Proceedings of the National Academy of Sciences of the United States of
America, 110, 1316813173.
Mesgarani, N., Cheung, G., Johnson, K., & Chang, E. F. (2014). Phonetic feature
encoding in human superior temporal gyrus. Science, 343, 10061010.
Mesulam, M. M., Wieneke, C., Hurley, R., Rademaker, A., Thompson, C. K.,
Weintraub, S., et al. (2013). Words and objects at the tip of the left temporal lobe in
primary progressive aphasia. Brain, 136, 601618.
Meyer, L., Obleser, J., Anwander, A., & Friederici, A. D. (2012). Linking ordering in
Brocas area to storage in left temporo-parietal regions: The case of sentence
processing. NeuroImage, 62, 19871998.
(2001). Human primary auditory cortex: Cytoarchitectonic subdivision and mapping
into a spatial reference system. NeuroImage, 13, 684701.
mapping of human superior temporal gyrus. Anatomy and Embryology, 210,
401406.
Naeser, M. A., Palumbo, C. L., Helm-Estabrooks, N., Stiassny-Eder, D., & Albert, M.
(1989). Severe nonfluency in aphasia. Role of the medial subcallosal fasciculus and
other white matter pathways in recovery of spontaneous speech. Brain, 112, 138.
Newhart, M., Trupe, L. A., Gomez, Y., Cloutman, J., Molitoris, J. J., & Davis, C. (2012).
Asyntactic comprehension, working memory, and acute ischemia in Brocas area
versus angular gyrus. Cortex, 48, 12881297.

Nijhuis, E. H., van Cappellen van Walsum, A. M., & Norris, D. G. (2013). Topographic
hub maps of the human structural neocortical network. PLoS One, 8, e65511.
Ono, M., Kubik, S., & Abernathey, C. D. (1990). Atlas of the cerebral sulci. Stuttgart: Thieme.
Palomero-Gallagher, N., Mohlberg, H., Zilles, K., & Vogt, B. J. (2008). Cytology and
receptor architecture of human anterior cingulate cortex. The Journal of Comparative
Neurology, 508, 906926.
Parker Jones, O., Prejawa, S., Hope, T. M., Oberhuber, M., Seghier, M. L., Leff, A. P.,
et al. (2014). Sensory-to-motor integration during auditory repetition: A combined
fMRI and lesion study. Frontiers in Human Neuroscience, 8, 24.
Paulesu, E., Frith, C. D., & Frackowiak, R. S. J. (1993). The neural correlates of the
verbal component of working memory. Nature, 362, 342345.
Penfield, W., & Roberts, L. (1959). Speech and brain mechanisms. Princeton, NJ:
Princeton University Press.
Rivier, F., & Clarke, S. (1997). Cytochrome oxidase, acetyl-cholinesterase, and NADPHdiaphorase staining in human supratemporal and insular cortex: Evidence for
multiple auditory areas. NeuroImage, 6, 288304.
Schmahmann, J., & Pandya, D. N. (2006). Fiber pathways of the brain. New York, NY:
Oxford University Press.
Schmahmann, J. D., & Pandya, D. N. (2008). Disconnection syndromes of basal
ganglia, thalamus, and cerebrocerebellar systems. Cortex, 44, 10371066.
Schulze, K., Vargha-Khadem, F., & Mishkin, M. (2012). Test of a motor theory of longterm auditory memory. Proceedings of the National Academy of Sciences of the
Seltzer, B., & Pandya, D. N. (1984). Further observations on parieto-temporal
connections in the rhesus monkey. Experimental Brain Research, 55, 301312.
185
Thiebaut de Schotten, M., Cohen, L., Amemiya, E., Braga, L. W., & Dehaene, S. (2014).
Learning to read improves the structure of the arcuate fasciculus. Cerebral Cortex,
24, 989995.
Tyler, L. K., Marslen-Wilson, W. D., Randall, B., Wright, P., Devereux, B. J., Zhuang, J.,
et al. (2011). Left inferior frontal cortex and syntax: Function, structure and
behaviour in patients with left hemisphere damage. Brain, 134, 415431.
Uylings, H. B. M., Jacobsen, A. M., Zilles, K., & Amunts, K. (2006). Left-right
asymmetry in volume and number of neurons in adult Brocas area. Cortex, 42,
652658.
Vilberg, K. L., & Rugg, M. D. (2008). Memory retrieval and the parietal cortex: A
review of evidence from a dual-process perspective. Neuropsychologia, 46,
17871799.
Wallace, M. N., Johnston, P. W., & Palmer, A. R. (2002). Histochemical identification of
cortical areas in the auditory region of the human brain. Experimental Brain
Research, 143, 499508.
Watkins, K. E., Smith, S. M., Davis, S., & Howell, P. (2008). Structural and
functional abnormalities of the motor system in developmental stuttering. Brain,
131, 5059.
Wilson, S. M., Galantucci, S., Tartaglia, M. C., Rising, K., Patterson, D. K., &
Henry, M. L. (2011). Syntactic processing depends on dorsal language tracts.
Neuron, 72, 397403.
Yoshida, K., Saito, N., Iriki, A., & Isoda, M. (2011). Representation of others action by
neurons in monkey medial frontal cortex. Current Biology, 21, 249253.
SB Eickhoff and VI Muller, Research Centre Julich, Julich, Germany; HHU Dusseldorf, Dusseldorf, Germany
Glossary
Network-based functional connectivity analysis Analysis

to delineate functional connectivity within an a prioridefined network of regions.
Resting-state functional connectivity Time series
correlation in BOLD fMRI data acquired during the absence
of an externally purported task.
Brain Organization and the Different Aspects

of Connectivity
The human brain is organized along two fundamental principles, functional segregation and functional integration
(Friston, 2002). Here, functional segregation refers to the fact
that the brain, in particular, the cerebral cortex, is not a
homogeneous entity but can be subdivided into regionally
distinct modules. Such modules, for example, cortical areas
or subcortical nuclei, may be defined based on microstructural
properties such as cyto-, myelo-, or receptor architecture,
resulting in anatomical brain maps detailing the structural
heterogeneity of the cerebral cortex. Additionally, functional
criteria, that is, response properties as investigated by functional neuroimaging approaches such as fMRI, likewise suggest
a regional specialization for the processing of specific stimuli
or the performance of particular cognitive operations. Structural and functional mapping approaches thus emphasize the
segregation of gray matter into distinct modules that are distinguished from each other in terms of microanatomy and
response characteristics. The concept of functional integration,
on the other hand, highlights that no brain region is by itself
sufficient to perform a particular cognitive, sensory, or motor
process. Rather, all of these mental capacities or functions in
the psychological sense have to rely on a dynamic interplay
and exchange of information between different regions
(Friston, 2002). Furthermore, a particular cortical area may
be engaged by many different cognitive tasks; that is, there is
no one-to-one mapping between brain regions and mental
functions. From a conceptual point of view, it has thus been
argued that the recruitment and dynamics within distributed
brain networks are the most important foundation for the
implementation of mental operations. However, it should be
noted that functional integration and segregation are not necessarily in contrast, but rather complement each other, as
functional integration can be conceptualized as the interaction
between specialized regions, each performing a distinct computational subprocess (Eickhoff & Grefkes, 2011; Friston,
2002).
Nevertheless, in recent years, there has been a substantial
shift in our concepts of the brain organization and the neurobiology of higher mental operations away from a mainly
localizing approach toward a view that stresses the role of
Seed-based functional connectivity analysis Analysis to

delineate functional connectivity of one (or more) seed
region with the rest of the brain.
Task-based functional connectivity Above chance coactivations of brain regions across a large set of different
neuroimaging studies.
networks and thus brain connectivity in understanding mental

functions.
In spite of the now pivotal role of connectivity analyses in
functional systems neuroscience, the concept of brain connectivity in itself has remained somewhat enigmatic. Most importantly, there is no such thing as the connectivity of a particular
brain area. Rather, several conceptually different aspects of
brain connectivity may be distinguished. Among them, a
major, natural dividing line is that between anatomical
connectivity and functional connectivity. The former
represents the hard-wired connections between different
brain areas formed by fiber tracts containing multiple individual axons, that is, a structural property of the brain. Evidently,
such structural connections are a necessary prerequisite for any
interaction between different parts of the brain but not in
themselves sufficient to characterize these interactions giving
rise to cognitive functions (Friston, 2011). Anatomical or structural connectivity, as investigated at the axonal level in nonhuman primates using invasive tracing approaches or
approximated in vivo by means of diffusion-weighted imaging,
thus represents the scaffold on which any transfer of information may take place but does not reflect the coupling and
dynamic interactions between different parts of the brain. In
contrast to structural connectivity, functional connectivity in a
broader sense thus denotes the interactions between regional
activity and hence the dynamic within the respective networks.
Within this broad category that may be used to summarize any
functional relationships between different parts of the brain
independently of the anatomical connections by which they
are implemented, two different concepts may be distinguished.
One is effective connectivity, which denotes the influence that
one node within a particular neuronal system exerts over
another (Friston, 1994) and hence comes closest to the intuitive notion of functional interactions. It assesses the directed,
either excitatory or inhibitory, effects that one particular area
causes in another remote one. Given the fact that such interactions are rarely static, effective connectivity is usually considered in a dynamic, that is, time- and often context-dependent
manner. Since such causal influences may not be directly measured using todays neuroimaging techniques, investigating
effective connectivity usually depends on models of functional
interactions that estimate the influences between brain regions
based on dependencies, temporal precedence, and other
http://dx.doi.org/10.1016/B978-0-12-397025-1.00212-8
187
188
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Functional Connectivity
aspects. The other aspect in the description of functional interactions in the brain networks that is also the most widely
employed approach to the investigation of brain connectivity
at the moment is functional connectivity in the more confined
sense.
Functional Connectivity: Definition and Conceptual

Implications
Functional connectivity is defined as the temporal coincidence
of spatially distant neurophysiological events (Friston, 1994).
That is, two regions are considered to show functional connectivity if there is a statistical relationship between the measures
of activity recorded for them. The notion behind this connectivity approach is that areas are presumed to be coupled or are
components of the same network if their functional behavior is
consistently correlated with each other. In contrast to effective
connectivity analyses, which rest on numerous assumptions
regarding both the underlying neurobiology and the model
chosen to estimate it, functional connectivity represents a
much more direct approach to the analysis of functional
networks. In particular, it concurs with the intuitive notion
that when two things happen together, these two things should
be related to each other. By relying very little on a priori
assumptions, functional connectivity analysis thus rather
reflects a straightforward, observational measure of functional
relationships. This definition, however, already clearly reveals
two key aspects that need to be considered when dealing with
functional connectivity analyses.
The first is the important caveat that functional connectivity
per se is purely correlative in nature. As just noted, two regions
show functional connectivity, if increased activity in one region
is associated above chance with activity in another. As always
with correlations, however, this does not imply any causal
relationship or even any sort of direct connection between
these two regions. Correlated activity in two regions may, for
example, be mediated via additional structures relaying information from the first area to the second. Such relay processes
could moreover be transmitted through cascades of several
intermediates or via corticalsubcortical loops involving, for
example, the basal ganglia or the cerebellum. In such cases,
activity in one area may represent the ultimate drive of activity
in the other even in the absence of a structural connection, that
is, fibers running between the two areas. Strong functional
connectivity may hence be observed even if structural connections are weak or absent, although in most cases, these two
aspects of brain connectivity show at least some level of convergence (Eickhoff et al., 2010). Furthermore, it is also possible
that a third area induces correlated activation between regions
that actually do not have any form of direct interaction. Therefore, functional connectivity may be driven by an external
source inducing concurrent activity in both areas. An example
of such situation would be the feedforward of stimulus-driven
activity in early sensory areas that is forwarded to parietal
sensory areas for perceptual analysis and, in parallel, to premotor cortex for response preparation. Even if both would be
implemented in completely segregated streams, this scenario
would lead to correlated activity changes in higher sensory
areas and motor regions, that is, functional connectivity
between them. Thus, functional connectivity may be observed

even between regions that are not functionally interacting with
each other due to effects of the experimental setup. A similar
consideration also holds for structured noise or confounds,
such as motion or physiological effects (Birn, 2012; Duncan
& Northoff, 2013). If their influence is not removed from the
data or accommodated in the analysis, spurious correlations
will arise. It follows that while functional connectivity investigations themselves require much less elaborate modeling and a
priori assumptions than most approaches to effective connectivity analyses, they at the same time are much more susceptible to biological and technical confounds that may influence
the noise spectrum of the data and induce spurious correlations that may be mistaken as functional interactions. Consequently, as will be detailed in the succeeding text, removing or
accounting for potential confounds has become a major aspect
not only of development but also of conjecture, in particular,
with respect to resting-state functional connectivity analyses.
Secondly, it should be remarked that the notion of functional
connectivity may pertain to any form of neurophysiological
events. That is, any above-chance coincidence of brain activity
signals recorded in different parts of the brain may be considered
as evidence for coupling between them, which may be direct,
indirect, or spurious, and hence functional connectivity. Restingstate analyses, that is, time-series correlations in BOLD fMRI data
acquired in a task-free state, may thus be used to assess functional
connectivity in the brain. However, it must be remembered that
functional connectivity represents a much broader concept that
may not be equated with such resting-state analyses. Rather,
functional connectivity may, for example, also be realized as
correlated spiking patterns or field potentials. This application
of functional connectivity analysis is commonly found in
electrophysiological experiments in nonhuman species, where
direct recordings of individual cells or multiunit activity may be
correlated among different recording sites (Aertsen, Erb, & Palm,
1994; Gerstein & Perkel, 1969). In humans, it may also be
applied to direct recordings during deep brain stimulation by
correlating electrophysiological recordings from the implanted
electrodes between different sites or contacts or by correlating
them with cortical signals as measured, for example, by magnetoencephalography (MEG) or electroencephalography (EEG)
(e.g., Hohlefeld et al., 2013; Lourens et al., 2013). Another
non-fMRI application of functional connectivity analyses is the
delineation of correlations or more precisely coherence between
EEG sensors, which due to the high temporal resolution of EEG
may be computed as broadband correlations or specific for
particular frequency bands. In these instances, functional connectivity analyses indicate coherent oscillations, that is, neuronal
mass activity, between different regions of the brain reflecting
synchronous activity (Ruchkin, 2005). In terms of fMRI data,
functional connectivity may be investigated on measurements
that are obtained while the subject is passively lying in the
scanner (resting state) or on fMRI data recorded during a particular task (e.g., Ebisch et al., 2013). Finally, the analysis of the
coactivation patterns across many different task-based fMRI
experiments can likewise be used to investigate functional connectivity in the brain (Eickhoff et al., 2010). In such analyses, the
individual experiments represent the units of observation, and
the analysis aims at identifying the above-chance coincidence of
reported activations across different experiments. In summary,

functional connectivity may thus be assessed using various data
modalities and analysis approaches, rendering it a broad concept
rather than a particular method.
Functional Connectivity in fMRI

The currently most widely applied strategy for the examination
of functional connectivity is based on the assessment of correlated signal changes in fMRI time series. In this approach, the
functional connectivity between two locations of the brain is
estimated by the (linear) correlation coefficient between their
fMRI time series. The idea underlying functional connectivity
MRI thus confines to the fundamental concept of functional
connectivity analyses, that is, coincidence of signals between
different brain areas as outlined in the preceding text. The
popularity of functional connectivity MRI data then stems
from the fact that, given the richness of fMRI data, which
usually consists of several hundred time points of wholebrain voxel-wise data, this approach has the perspective to
yield information on functional connectivity across the entire
brain at the level of individual subjects.
Functional Connectivity in fMRI Data on Specific Experimental

Paradigms
Analyses of functional connectivity by the correlation of
regional BOLD signal intensities may be performed on fMRI
time series obtained during the performance of experimental
paradigms, that is, while subjects are engaged in a particular
cognitive or perceptual experiment. In these cases, however,
the major predicament is the immanent presence of taskdriven correlations. That is, all those regions that are activated
by the particular experimental condition at hand will necessarily show functional connectivity due to common stimulusevoked modulations. Importantly, these effects may not easily
be discarded as spurious or trivial. Rather, the common recruitment by a particular condition in fact follows precisely the idea
of functional connectivity as the coincidence of neurophysiological events. Nevertheless, it is often regarded as not adding
substantial new information above the observation of jointly
activated regions in a conventional fMRI analysis. However,
functional connectivity analysis by correlation of voxel- or
region-wise fMRI time series obtained during the performance
of an experimental paradigm that entails multiple conditions
may provide insight into how closely different regions interact
during the assessed experimental condition and how this coupling may change as a function of the condition at hand. In the
context of more complex experiments consisting of multiple
contextual sets, functional connectivity describes to which
degree two regions are commonly corecruited and hence
presumably coupled. When performed across the entire time
series, that is, across all conditions, the correlation of regional
fMRI signals may thus be regarded as a measure of the overall
functional connectivity between the regions at hand across the
entire experimental setting.
If, however, functional connectivity measures are computed
separately for a condition, task- or context-specific differences
may be assessed. For example, assuming an experiment with
two conditions presented in a block design, the correlation
189
between the local BOLD time series of two regions may be

computed independently for those blocks where one or the
other condition was present and then contrasted with each
other. While representing an easy window into paradigmrelated changes in interregional coupling, these approaches
have become largely obsolete today. In particular, one of the
key problems associated with computing functional connectivity during the performance of experimental paradigms is the
delay and dispersion of task-related neuronal activity by the
hemodynamic response function. Consequently, time-series
correlation estimated from those scans taken during the presence of the respective experimental condition may not reflect
the functional coupling during its performance. Rather, functional connectivity during that particular condition would be
observable later (but with potentially variable delay between
regions) in the time series. These problems posed by hemodynamic coupling render condition-specific functional connectivity problematic outside of cases in which very long,
for example, minutes, blocks are employed for each
condition. Consequently, the assessment of condition- and
context-specific effects in fMRI time series obtained during
experimental paradigms is now primarily the domain of analyses, in which both the presence of each particular condition
of context and the hemodynamic response are explicitly
modeled. Effective connectivity models such as dynamic
causal modeling or Granger causality mapping (Goebel, Roebroeck, Kim, & Formisano, 2003) have thus by now largely
superseded functional connectivity analyses as the method of
choice to investigate connectivity during the performance of
experimental paradigms. One of the key advantages of these
effective connectivity models over straight time-series correlations is that they investigate context-specific influences between
different brain regions while explicitly accommodating the
delay of condition-related fMRI changes caused by the hemodynamic response function. In other words, if the timing of experimental manipulations is known, which is the case in fMRI data
obtained during the performance of an experimental paradigm,
effective connectivity models represent a substantially more
specific approach to investigating context-dependent couplings
than the analysis of functional connectivity.
Functional Connectivity in Resting-State fMRI Data

In contrast to connectivity analyses in the context of experimental paradigms, where the timing is known, the situation is
completely different, if there are no experimentally controlled
manipulations, that is, when the timing of the underlying
mental activity is unknown. In this case, functional connectivity analyses by fMRI time-series correlations thus represent the
main avenue toward analyzing the interactions between
different brain regions. Therefore, the currently most widely
used application of functional connectivity analysis pertains to
the assessment of resting-state fMRI data. In such acquisitions,
fMRI images are obtained using the same BOLD-sensitive
sequences as in fMRI activation studies, usually with a time
of repetition (TR) of 23 s, for about 510 min. Importantly,
and in contrast to classical fMRI approaches using experimental paradigms, the subjects are lying in the scanner without
being challenged by a particular task. That is, resting-state fMRI
is based on BOLD time series consisting of several hundreds of
190
individual BOLD-sensitive images that are obtained while the

subjects do not perform any externally purported task but are
rather instructed to let their mind wander and not think about
anything specific. It should be self-evident that the content and
timing in the flow of thought are individual and hence different for each subject as they are not externally triggered.
Consequently, no predefined time points are available, which
would allow modeling of the associated hemodynamic
response; that is, there is no condition- or context-related
activity. Likewise, any methods for effective connectivity
modeling, which also depend on an experimental input function describing the relevant timing of events, are not applicable
in a straightforward manner.
The beginning of resting-state functional connectivity analyses thus mainly goes back to positron emission tomography
(PET) studies more than a decade ago, which showed that
metabolic activity at rest was not random but rather seemed
to have a discernible structure. In particular, it was observed
that local fludeoxyglucose (FDG)-activity counts of different,
distant brain regions were significantly correlated across subjects (Horwitz, Duara, & Rapoport, 1984; Moeller, Strother,
Sidtis, & Rottenberg, 1987). In other words, these studies indicated that spatially structured patterns of functional connectivity are accessible in the unstructured task-free state. In a
seminar paper, Biswal, Yetkin, Haughton, and Hyde (1995)
then showed in an individual subject that by testing for regions
whose resting-state time series are significantly correlated with
that of the primary motor cortex, they could identify many core
regions of the brains motor network. This paper thus revealed
that meaningful functional connectivity may be inferred from
single-subject fMRI images acquired in a task-free state by the
analysis of time-series correlations. In the following, restingstate fMRI has risen to remarkable popularity due to the combination of several key properties. First of all, it poses very low
demands on subjects compliance, given that these do not need
to complete any paradigm and consequently do not have to
execute an experiment with a sufficient performance. Rather,
all that is required is to remain still in the scanner for
510 min, which makes these acquisitions well suited for
larger cohorts of subjects that would otherwise feature a high
dropout rate, for example, clinical populations or children.
Resting-state fMRI thus represents an approach, which allows
most insights into the functional organization of the brain
requiring least participation by the subjects. Additionally,
multiple analyses are possible on the same data, as it is not
constrained by task-specific effects. Functional connectivity
analysis is therefore a procedure that is not dependent on
knowing the timing of mental operations and that reduces
the (subject-specific) time-series information to parametric
information about the strength of interactions, which may
additionally be aggregated across subjects. Consequently,
resting-state functional connectivity analysis has become an
important approach in basic and clinical neuroscience.
In parallel to its growing popularity and importance, there
has been an increasing awareness and discussion on potential
confounding effects in resting-state functional connectivity
analyses. In particular, it has been noted that the raw fMRI
signal time courses are noisy due to scanner artifacts, motioninduced effects, and physiological sources such as cardiac and
respiratory cycles (Birn, 2012; Duncan & Northoff, 2013).
While some of this noise is unstructured and hence only

increases unexplained variance in the data, other sources of
noise represent systematic confounds that may induce spurious correlations between the time courses of different brain
regions. For example, let us assume changes in the global
fMRI signal, be it due to scanner drifts or physiological effects
that affect all voxels in the same manner. If these global
signal changes over time are large enough, relative to the
region-specific changes in BOLD activity that reflect the signal
of interest, the correlation between pairs of regions will be
close to perfect. Given the potential dominance of this effect
over the relatively subtle functionally relevant fluctuations of
the regional BOLD signal, there is a danger that global signal
changes may strongly influence the overall level of functional
connectivity as estimated from a subjects fMRI time series.
Several approaches to deal with this problem have been
proposed (Murphy, Birn, & Bandettini, 2013). In a very simplistic approach, one could just extract the time series of a
sphere placed in the ventricles and/or the deep white matter
to represent the global signal change, following the logic that
these will not contain regionally specific patterns of activity
changes. These time courses may then be entered as regressors
of no interest in a general linear model (GLM) or removed
from the regional time series of interest prior to the correlation analysis. Alternatively, the time courses for global gray
and white matter and cerebrospinal fluid may be computed
by averaging across all voxels in that particular tissue class,
reducing the influence of any subjective placement of the
reference time series. In this context, however, it remains
debated whether the mean gray-matter signal should actually
be removed as it may reflect meaningful neurobiological
information. Moreover, as another alternative approach, the
mean signal time course may also be computed in a wholebrain mask, that is, averaged across the entire image. While
all of these approaches are useful to remove spurious (positive) correlations from the data, it has been a matter of
conjecture and argument whether global signal removal in
itself may actually induce an artificial anticorrelation structure
in the data, that is, replace spuriously high correlations with
potentially likewise spurious anticorrelations (Murphy, Birn,
Handwerker, Jones, & Bandettini, 2009).
Besides these issues related to global signal changes, which
affect the whole brain similarly, it is still a matter of debate how
best to remove the effects of noise that is related to head
motion and cardiovascular and respiratory effects. Importantly, however, in contrast to global signal changes, these
effects may be specific to a particular type of connection, a
particular direction, or a particular group of subjects. As one
example, it has been shown that head motion may lead to an
apparent increase in local functional connectivity, while the
connectivity between more distant regions becomes attenuated
(Satterthwaite et al., 2013). Likewise, cardiorespiratory effects
do not affect the entire brain in the same fashion but seem to
have a regional preponderance, for example, near the brainstem (Dagli, Ingeholm, & Haxby, 1999). While a complete
coverage of the various approaches and aspects of correcting
for physiological confounds in resting-state imaging is well
beyond the scope of this overview and at the same time these
methods are still rapidly evolving, they can be roughly divided
into two classes (Murphy et al., 2013). Some approaches make

use of recorded (heartbeat and respiration) or estimated (head
motion) time courses detailing these confounds, which are
then used to remove the influence of the confounding factors
in a model-based fashion. Other approaches are based on datadriven decomposition of the data using, for example, principle
or independent component analyses (ICA). In these, either a
certain set of dominant components in the data, reflecting
global signal and systematic sources of variation, are blindly
subtracted or components that have spatiotemporal characteristics incompatible with neurobiological activity are identified
and removed from the data. Finally, it needs to be considered
that due to the noise spectrum of fMRI data and the fact that
the hemodynamic response function acts as a low-pass filter,
correlations in BOLD signal that are indicative of functional
connectivity between neuronal processes in different regions
are predominantly present in a particular frequency range,
usually assumed to be located between 0.01 and 0.1 Hz (Fox
& Raichle, 2007; Greicius, Krasnow, Reiss, & Menon, 2003). In
order to focus the analyses on these neurobiologically meaningful frequencies, temporal band-pass filtering is usually
applied.
In summary, there is thus an important need to reduce both
global and biased spurious correlations by multiple processing
steps such as spatial and temporal filtering and removal of
signal contributions from motion, physiological noise, and
global signal fluctuations before meaningful functional connectivity may be estimated from task-free data.
There is also an ongoing debate on the physiological basis
of BOLD signal correlations in the absence of an externally
purported task. For example, it has been suggested that these
fluctuations are driven by intrinsic activity events constrained
by anatomical connections between the respective areas (Fox &
Raichle, 2007). In this concept, resting-state functional connectivity may thus be regarded to be largely a reflection of the
anatomical connectivity between different brain regions in the
absence of an external task. Supporting this view, simulation
studies show that one may generate patterns similar to restingstate fluctuations by injecting stochastic activity in structural
networks defined by anatomical connectivity information
(Honey, Kotter, Breakspear, & Sporns, 2007). On the other
hand, some patterns of functional resting-state connectivity
exist, which cannot be explained by known, direct anatomical
connections. As noted in the preceding text, indirect connections, cascades, or loops could mediate these indirect effects,
and hence, functional dynamics may extend well beyond
known, major fiber connections. However, it remains unresolved what drives these interactions in a physiological sense,
that is, why there should be stochastic fluctuations of sufficient
magnitude to propagate along anatomical connections. In particular, it would be unlikely that stochastic activity changes
having an emergent structure due to the anatomical connectivity architecture should be present without a psychological
correlate.
This predicament has motivated a modified view on the
psychophysiology of the resting-state networks, which deempathizes the resting aspect. Rather, it is assumed that the
brain is never at rest (Buckner & Vincent, 2007) as there is
always a large amount of ongoing activity composed of a vast
variety of mental functions, even when a subject is lying still in
the scanner. These range from bodily perception and
191
somatosensation to memories and reflections, emotions and

feelings, and explicit cognitive reasoning and planning including inner speech. That is, when lying in an MRI scanner without a specific paradigm to focus on, we are not thus resting but
rather performing all sorts of mental operations in succession
or parallel. The correlation in the MR signal time course
between two regions should thus reflect the degree to which
these jointly participate in the various networks engaged in the
absence of an externally preset task. Resting-state activity
would hence consist of a, more or less random, sampling of
all the different task-related networks that the brain is capable
of, with a certain preponderance for introspective and interpersonal aspects (Schilbach et al., 2012). This view not only
presents a plausible explanation for the apparent presence of
networks resembling those seen in task-based fMRI but also
reconciles the psychological experience of rest with the
hypothesis of coordinated stochastic fluctuations in brain
activity. In particular, while these fluctuation would look random to the outside observer as the activity change in a particular region follows no specifiable temporal pattern, these
would not be generated stochastically but rather reflect the
ongoing, unconstrained train of thought of the subject. It has
thus been proposed to avoid the term resting state in favor of
task-free functional connectivity or functional connectivity in
the absence of an external structured task set (Buckner &
Vincent, 2007; Schilbach et al., 2012), given that rest may not
be an adequate term to describe the ongoing mental operations
during mind wandering or unconstrained, endogenously controlled cognition in an fMRI scanner.
Task-Based Functional Connectivity and Coactivations

The notion that functional connectivity can be computed in
the absence of an external structured task set easily leads to the
complementary aspect of task-dependent functional connectivity, which is the correlation of neurophysiological responses
during the performance of externally purported experimental
tasks. As noted in the preceding text, functional connectivity
may be inferred from correlation analysis between fMRI time
series from different brain regions during the performance of a
particular task. In this case, however, functional connectivity
analysis is limited to the task at hand or more precisely to
the particular experimental implementation of a given task.
While such an approach may reveal new insight into the functional network underlying that particular experimental paradigm, it does not allow, however, answering the core question
about task-based functional connectivity: Which other regions
does a particular area in question work with? Or in other
words, if a particular area is activated, which other brain
regions are then more likely to be coactivated than it would
be expected by chance? In order to answer this question comprehensively, task-based functional connectivity analysis needs
to be performed across a large number of different tasks and
implementations. Moreover, ideally, such data-driven definition of task-interacting brain networks should cover a broad
range of functional domains in order to reveal associations
between regions beyond a particular mental function. That is,
the key question for task-based functional connectivity may
not be resolved by the investigation of interactions during a
192
particular experimental setup but can only be addressed by

investigating above-chance coactivations between different
parts of the brain across a large set of functional neuroimaging
studies.
The possibility of actually implementing this idea has
emerged from the advent of large-scale databases on functional
neuroimaging results. Such resources, like the BrainMap
(http://brainmap.org), the SumsDB (http://sumsdb.wustl.
edu/sums/index.jsp), and Neurosynth (http://neurosynth.
org) databases, have been developed in parallel to the growth
of the functional neuroimaging field in order to keep up with
the vast amount of fMRI findings published each year. In
addition to these, several other database projects have been
present over the course of the last decade, including the initially successful but ultimately short-lived fMRIDC (Van Horn
et al., 2001), the European NeuroGenerator project (Roland
et al., 2001), and many smaller initiatives, often representing
the work of a single individual. It turned out that storage of raw
neuroimaging data or even full statistical parametric maps
seems impossible at the moment for several reasons. These
range from the amount of storage space needed; to the reluctance of many researchers to make their data, collected with
great investment of time and resources, freely available; to
problems in backfilling older experiments. Consequently, all
of the current approaches listed in the preceding text have been
developed as coordinate-based databases. That is, they usually
contain, for each included study, the location of the local
maxima reported for each particular contrast (which may be
retrieved from the published paper without any help from the
original authors) and associated meta-data describing the
experimental design, that is, the neuropsychological context
of the experiment and the aspects that are to be isolated by
the respective contrast. They thus make use of the high standardization of neuroimaging data, reported as tables of maxima coordinates and in particular of the ubiquitous adherence
to standard coordinate systems such as the Montreal Neurological Institute (MNI) system. Importantly, the assembled
data in these databases now allow testing for significant convergence of reported findings on a particular task, that is, topicbased meta-analyses. Rather, the results reported across all
different kinds of tasks and experiments may be readily compared with each other and integrated with respect to the spatial
location of significant neural activity. Neuroimaging databases
thus provide the aforementioned broad pool of neuroimaging
data across many different mental states that is needed to assess
functional connectivity in terms of above-chance coactivation
probabilities between different areas. Databases of several
thousands of fMRI studies thus enable us to ask if two regions
in the brain are more likely to show coactivation than one
would expect by chance, that is, if there is a coincidence of
reported activity in these two regions across many different
experiments. In practice, task-based functional connectivity of
a given region is established by retrieving all experiments from
a database that feature at least one focus of activation within
this region of interest. Coordinate-based meta-analysis is then
performed over all activation foci reported in these experiments in order to test for significant convergence. As the experiments entered into such an analysis are selected based on the
presence of an activation in a given seed region, any significant
convergence of coordinates outside that seed would reflect
above-chance coactivation (Eickhoff et al., 2010). Importantly,

such meta-analytic connectivity modeling (MACM) does not differentiate between different experimental paradigms or other
factors, but rather is solely based on the likelihood of observing
activation in a target region (or voxel). Consequently, it avoids
any a priori bias based on potentially premature taxonomic
considerations but represents a completely data-driven
approach to the identification of functionally interacting
brain networks during the performance of activation experiments. It is also of note that MACM, in spite of all its differences to the currently much more popular resting-state
functional connectivity analysis, exactly follows the definition
of functional connectivity by testing for coincidences of neurophysiological events. More precisely, MACM tests for the
coincidence (joint reporting within a given contrast) of taskevoked activation in different brain regions (representing the
neurophysiological events). Importantly, it has to be noted
that MACM in particular differs from other functional connectivity measures such as not only resting-state connectivity but
also, for example, MEG/EEG coherence, with regard to timescales. While other approaches are based on temporal dynamics in individual subjects, in task-based functional connectivity
analysis via coactivation mapping, the unit of observation is
not a specific point in an acquired time series but rather a
particular neuroimaging experiment (cf. Jakobs et al., 2012
for a more detailed discussion of the conceptual commonalities and differences). Also, connectivity is not being estimated
for a given subject but in a pool of many different experiments,
each involving multiple subjects. Thus, task-based (MACM)
functional connectivity is not expressed as coherent fluctuation
across time but rather as coherent activation across
experiments.
Compared to resting-state functional connectivity analysis,
MACM holds advantages and disadvantages. Probably, the
biggest drawback of MACM is, as mentioned in the preceding
text, that it is per definition not applicable to individual subjects. Consequently, there is no straightforward approach
to integrate information from MACM task-based functional
connectivity with measures of performance and establish
brainbehavior relationships. Therefore, MACM findings may
primarily serve as priors for future studies investigating functional or structural connectivity in a set of new subjects. MACM
may thus be particularly useful as an independent, hypothesisforming approach that may then be tested using, for example,
resting-state functional connectivity or fiber tract analysis from
diffusion-weighted imaging. In turn, compared with task-free
functional connectivity measures, MACM task-based functional connectivity analysis features two distinct advantages.
First, MACM delineates networks that are conjointly recruited
by a broad range of tasks and should hence reflect robust, that
is, meaningful patterns of coordinated activity in response to
an external challenge. Second, the MACM approach can also be
used to investigate what kinds of experiments yield
coactivation between two regions (Muller et al., 2013).
While, as noted in the preceding text, MACM does not allow
any inference on brainbehavior relationships, as it is not
suitable for individual subject analysis, it thus allows establishing a link between functional connectivity and particular mental operations. In other words, MACM does not provide an
answer to the question, how does connectivity in a particular

network relate to performance but instead provide inference
on the mental operations, which recruit that particular connection, that is, functional inference. Evidently, these two aspects
are highly complementary on each other, and together, they
may allow a comprehensive inference on what kind of tasks
recruit a given connection and how its strength relates to
individual measures of performance. The complementarity
between MACM and resting-state functional connectivity
analysis, however, expands beyond this aspect. In contrast to
resting-state functional connectivity, MACM analyses are based
on task-related neural activity and therefore reflect functional
connectivity in response to external challenges and largely miss
spontaneous networks related to self-initiated behavior and
thought. Thus, MACM (based on published activation coordinates for various neuropsychological tasks across many papers)
and resting-state correlations (based on BOLD time series of
individual subjects in the absence of an external task) are based
on two completely independent sources of data, each of which
not only provides insight into brain network organization in a
different mental state but most likely also holds its own pattern
of confounds and noise.
A comprehensive assessment of the functional connectivity patterns of a particular seed region may thus consist of
performing a meta-analysis both identifying significant
coactivation in all experiments activating that seed region
(MACM) and identifying all voxels in the brain whose time
series in a task-free state (resting state) shows significant
correlation with the reference time course extracted from
that seed (Muller et al., 2013). In a comparison of both
functional connectivity maps, two situations may arise.
Either, regions are congruently implicated as being functionally connected with the seed in both analyses. Such convergent evidence across fundamentally different states (presence
and absence of tasks) may be regarded as a very strong indication of a functional coupling with the seed. A mismatch
between both analyses in turn must always carefully be examined for the potential effects of confounds and noise, which
should be quite different across these two approaches and
result in different spurious functional connectivity findings.
On the other hand, however, strong but nonmatching evidence obtained from both analyses may also relate to the
fundamental differences between the two states (Jakobs
et al., 2012). In particular, it is well conceivable that a given
brain region interacts with a particular set of areas (related,
e.g., to planning and internal goals) during spontaneous, selfinitiated mental operations and with another distinct set of
areas (related, e.g., to sensory processing) during the performance of externally presented experimental paradigms. Both
convergence and divergence of results may hence contribute
to our understanding of functionally connected networks in
the brain. In addition and as noted in the preceding text, they
may provide complementary information on the kind of tasks
corecruiting two functionally connected areas and the relationship with interindividual variability of neurocognitive
measures, respectively. While there has yet been little to no
research along these lines, the prospect of differentiating
internally and externally driven functional connectivity networks and their relation to a broad range of cognitive paradigms and individual performance measures may hold an
important potential for understanding the physiology of the
193
two main states of brain function, reaction to the external

world and reflection on our inner states.
How to Analyze FC: Seed Correlations

A very straightforward approach to functional connectivity
analysis, independently of the actual data modality at hand,
for example, resting-state fMRI time series or databases of
activation experiments for coactivation mapping, is to perform
seed region correlation. These analyses are founded on one or
more a priori defined regions of interest (seeds), whose functional connectivity pattern is then delineated across the rest of
the brain. In particular, seed-based functional connectivity
analyses first involve extracting the signal of interest from the
seed region, that is, the identification of the neurophysiological events for that region whose connectivity is to be examined.
In time series-based approaches, such as resting-state fMRI, this
involves the extraction of a characteristic time series (usually
the first eigenvariate) for the seed region, which then represents
the signal of interest. Subsequently, the local time series of all
other locations of the brain (typically all voxels in a 3-D
dataset, although regional or sensor-space measures are likewise possible) are compared with this seed time series. As
noted previously, one of the main problems associated with
time series-based functional connectivity analyses is spurious
correlations introduced by structured noise or confounds in
the data that may influence the observed relationship between
the assessed signal time series and hence bias the results. Thus,
confounding effects must be removed either using knowledge
on these confounds in an explicit mode or by data-driven
denoising (cf. the preceding text) from the time series of the
seed and those of all other locations. Functional connectivity
between the seed and each other location may then be quantified and statistically tested based on these denoised data
using bivariate approaches, in particular linear correlation
coefficients, which in most cases are subsequently transformed
into Fisher Z-scores for standardization. Alternatively, functional connectivity may be assessed by setting up and estimating a GLM for each location in the brain in which the time
series of the seed represents the explanatory variable of interest,
while the confounds are added as covariates of no interest. In
either case, single-subject estimates of functional connectivity
with the seed for each location of the brain are then subjected
to a second-level analysis testing for the consistency of effects
across subjects.
Task-based functional connectivity by meta-analytic connectivity modeling, in turn, takes a slightly different approach.
First, all experiments (in a database) that feature at least one
focus of activation in the seed region are identified. Here, the
search may be restricted to specific kinds of studies, for
example, only to studies on healthy subjects. All coordinates
reported in the respective experiments are then extracted. Next,
quantitative coordinate-based meta-analysis is conducted in
order to test for convergence of reported coactivation in those
experiments by, for example, using the activation likelihood
estimation algorithm. Evidently, as experiments were defined
by the activation within the seed region, all experiments
included in the analysis feature at least one focus of activation
in that region. In turn, the seed will always show the highest
194
(a) Resting-state FC
(b) Task-based FC
Figure 1 Example of seed-based functional connectivity analyses: based on a functionally defined seed in the hand area of the left primary motor
cortex (blue), functional connectivity was delineated by resting-state (a) and task-based functional connectivity analyses (b). Both analyses are
thresholded at the same level of significance (p < 0.05, corrected for multiple comparisons). Note that using of the same seed region and threshold, both
approaches to functional connectivity show a fundamentally similar motor-related network. Yet, several divergences between both approaches are
also apparent, indicating that resting-state and task-based functional connectivity analyses provide complementary information.
convergence of activity. Significant convergence of the reported

foci outside the seed in turn indicates above-chance
coactivation and hence task-based functional connectivity.
Importantly, in spite of the different analytic approach investigating convergence of spatially sparse signals rather than
computing the correlation of spatially continuous data,
MACM has the same localizing properties with resting-state
functional connectivity analyses. Consequently, both may be
applied to the same seed region in order to delineate its functional connectivity pattern in two complementary approaches
using completely independent datasets and reflecting coupling
in different mental states. This is illustrated in Figure 1 showing seed-based functional connectivity mapping using restingstate and meta-analytic connectivity analyses seeded in the
hand area of the left primary motor cortex.
The main advantage of seed-based functional connectivity
analysis is that it represents an approach toward functional
network mapping by delineating those regions in the brain
showing functional connectivity with the seed. Importantly,
these approaches are thus spatially localizing; that is, they
provide information about where in the brain functional connectivity with the seed is found. They perform this spatial
inference, however, in an indirect fashion. Rather than using
an explicit spatial model and performing a statistical inference
on the model parameters pertaining to spatial locations, the
functional connectivity with the seed is analyzed and statistically tested independently for each location (voxel) in the
brain. By plotting those locations at which the respective test
became significant, following correction for multiple comparisons, the spatial pattern of regions showing functional
connectivity is then recovered. This approach is thus analogous
to the standard approach in task-based fMRI analysis in which
regions of significant activation are identified by plotting those
locations where the inference using a GLM-based mass-
univariate approach became significant. Moreover, seedbased analyses may also be used to localize regions showing
significant differences in functional connectivity with the
regions of interest. In the context of resting-state functional
connectivity, such contrasts may, for example, be used to identify regions, which show a significant difference in functional
connectivity with the seed between patients and controls, that
is, regions that show a disease-dependent dys-connectivity with
that seed. In task-based functional connectivity analyses, coactivation patterns with a seed between different tasks and
behavioral domains may be compared. That is, additional
contextual filters may be applied when identifying those experiments in the database that feature activation within the seed
and the ensuing whole-brain coactivation patterns may then be
compared. This allows, for example, identifying those regions,
which show significantly more consistent coactivation with the
seed in cognitive tasks as compared with motor tasks.
Thus, there are various applications for seed-based functional connectivity analyses based on resting-state fMRI or
analyses of coactivations, which may be applied independently
but can also be combined. In particular, when performed for
more several, conceptually related, seed regions of interest,
such analyses may represent a powerful approach to the delineation of functional networks interacting (differentially) with a
set of a priori defined regions. In this case, the seed regions
would in turn provide the functional context for the interpretation of the observed connectivity patterns.
On the downside, it must be acknowledged that the results
of seed-based functional connectivity analyses strongly depend
on the precise localization of the seed. Consequently, the
quantitative definition of the seed, that is, the operationalization of the scientific question by a binary mask, is crucial to the
entire endeavor. As an example, suppose one wants to investigate the functional connectivity of the hand area within the

primary motor cortex. In this case, the seed region could be
drawn by the investigator using anatomical landmarks (hand
knob), but it could also be based on a significant cluster of
activation in a previous fMRI experiment of hand movements
or a significant cluster of convergence in a meta-analysis of
such tasks. In either of these cases, the next question would
be if the seed is defined by an a priori defined functional cluster
or a sphere around the local maxima coordinate and/or additionally masked by an anatomical mask of the primary motor
cortex, constructed either from macroanatomy (posterior wall
of the precentral gyrus) or from probabilistic cytoarchitectonic
maps (e.g., areas 4a and 4p). All of these approaches, and
potentially many more, could be considered valid representations of the hand area of the primary motor cortex, even
though they most likely will differ notably in their precise
location and extent and consequently also in their functional
connectivity pattern. The seed definition hence provides an
important initial constraint and potential bias in these kinds
of functional connectivity analyses.
As an unrelated but likewise important consideration, seedbased functional connectivity analyses may become difficult to
manage if the number of seeds grows, as each individual seed
will result in at least one whole-brain connectivity map, with
additional statistical maps coming from contrast or conjunction analyses of different populations or task settings. In
particular, if the effects for the different seeds do not overlap,
such analyses may easily end up without a clearly interpretable
result. Moreover, while the choice of the seed may provide a
functional context for the interpretation of functional connectivity or dys-connectivity maps, it must be considered that the
ensuing interpretation often requires a (potentially overly simplified) one-to-one mapping between a spatial location and an
associated mental process. In particular, the interpretation of
the established functional connectivity map or the regions
showing abnormal connectivity in a patient sample will often
be focused on a particular functional context that was associated with the seed when planning the respective study. Often,
however, a region of the brain may be associated with several
different functional properties, rendering the (subjective)
reverse inference and focus on one functional aspect open to
potential bias.
The final drawback worth mentioning is that seed-based
functional connectivity analyses may be particularly sensitive
to the influence of confounds, in particular those that have a
spatial structure. One example for such spatially structured
confounds in resting-state functional connectivity analyses
may be the heterogeneous effects of motion on short- versus
long-range connections strengths, where the former are accentuated and the latter reduced (Satterthwaite et al., 2013). If
moreover motion is also not homogeneously or randomly
present in two different samples, for example, in patients
versus controls, a contrast of seed-based functional connectivity measures between the two groups would reveal a significant
difference in long-range connections with weaker connectivity
shown for the group that had shown more motion. In taskbased (MACM) functional connectivity, the unequal sampling
of the entire brain by experimental tasks, that is, the fact that a
lot of experiments use a similar (visual) input, mental operation, and (hand) motor output structure and hence show in
particular frequent activation in the visual, parietal, and
195
posterior frontal cortices but rather infrequently report regions

like the middle temporal gyrus, may likewise be considered a
spatially structured confound.
How to Analyze FC: Network Analysis

Another approach that is less focused on localization is the
investigation of functional connectivity within an a priori
defined network of regions. In this kind of analysis, included
regions may be considered as the nodes of the ensuing brain
network, whereas the estimated functional connectivity would
represent the edges between these (Behrens & Sporns, 2012).
Independent of the use of resting-state fMRI time series or taskbased connectivity modeling (MACM), a network-based analysis
of functional connectivity in a predefined network first always
involves the extraction of the signal of interest from each of the a
priori defined regions. In resting-state functional connectivity
analyses, the most common approach would be to compute
the characteristic time series for each region, for example, the
mean or first eigenvariate of all voxels that are part of the respective region. Secondly, these signals need to be processed, for
example, by removing variance that can be explained by global
signals or physiological confounds. Following this preprocessing, a vector representing the signal (time series) of the neurobiological feature of interest will be obtained for each of the a
priori defined regions. From these, the cross correlation between
the individual regions then readily assembles a functional connectivity matrix. That is, the similarity in the signal vector is
computed between each pair of regions or nodes, usually by
means of Fisher Z-transformed linear correlation coefficients.
The full set of values for all pairs or regions then represents the
functional connectivity within the assessed network. Each edge
in the resulting network is characterized by a single value and
would be computed for each subject individually. These values,
one per connection, that is, pair of regions, and the subject may
then be subjected to various kinds of follow-up analyses. In
contrast, in task-based coactivation analyses, the signal would
usually be provided by a vector detailing the involvement of a
region in all experiments stored in the employed database. That
is, a vector will be obtained for every region of the network,
containing for every experiment of the database the information
if the respective region is reported or not. In a next step, in most
cases, noninformative aspects such as experiments that activate
none of the predefined regions will be removed. Then, the similarity of the vectors will be computed for all pairs of regions in
the respective network, which again will result in a single value
for every edge of the network. These values that would represent
the likelihood of coactivation potentially corrected for overall
biases in activation probability may then again be used for
follow-up analyses. For example, the functional resting-state
connectivity along each edge may be compared between two
groups of subjects such as patients and controls. Likewise,
when phenotypic measures of the subjects are available, the
individual, subject-specific strength of the functional connectivity along each connection may be correlated with the behavioral
covariate of interest. This thus allows investigating the relationship between the connectivity in a predefined network and the
respective phenotype (see Figure 2 for an example).
196
Resting-state FC
Functional connectivity
(a)
Action_Execution
Action_Execution_
Speech
0.4
0.3
0.2
0.1
0
2
3
4
Likelihood ratio
Finger tapping
-0.1
Recitation/repetition
-0.2
Flexion/extension
-0.3
(b)
Task-based FC
35
40
45
50 55 60 65 70
Finger tapping score
75
80
85
0
(c)
4
6
Likelihood ratio
Figure 2 Example of network-based functional connectivity analyses investigating a specific network: In this case, functional connectivity was
investigated in a motor network identified in a previous fMRI study (a). By using resting-state functional connectivity analyses, the connectivity strength
between each pair of nodes was computed and then subsequently related to behavioral measurements. This analysis revealed a significant positive
correlation between functional connectivity between the left cerebellum and right basal ganglia and the interindividual variability of performance in a
finger-tapping test (b). In contrast, by using task-based coactivation analysis and functional decoding using the BrainMap database, it could be shown
that coactivation of the left cerebellum with the right basal ganglia was significantly associated to experiments related to action execution and to tasks
like finger tapping, recitation/repetition, and flexion/extension (c). The integration of task-based and resting-state functional connectivity analyses thus
allows both functional decoding of mental operations associated with a particular connection and its relation to interindividual differences in phenotype.
In particular, in larger networks covering multiple individual regions, this approach may likewise become localizing by
testing which connections within the examined network show
a relationship to a neurocognitive measure of interest or a
difference between patients and controls. These kinds of
analyses may thus be seen as an extension of the localizing
framework for seed-based functional connectivity analyses or
brainbehavior correlations using other imaging modalities to
the network level. Finally, the properties of individual nodes or
the entire network may be summarized using network measures derived from graph theory such as the average degree, the
average shortest path length, and the presence of hubs. These
graph theoretical analyses, although outside the scope of this
overview, have the appeal that they allow the characterization
of complex networks or the role of individual nodes within
these by a few characteristic numbers. They come, however,
with the downside that these measures are usually fairly
abstract, making them at time difficult to interpret in a neurobiological sense. Moreover, they also represent a highly
reduced characterization of usually complex connectivity
patterns.
Similarly, as in seed-based analyses, how to set up the regions
of interest, that is, the nodes making up the investigated network,
has an important influence on the ensuing functional connectivity measures and any follow-up analyses. Evidently, these
regions of interest may be assembled in many different ways,
reflecting different ideas and goals for the functional connectivity
network analysis. Broadly, however, the various approaches and

definition of networks should fall into two classes, one referring
to whole-brain networks and the other to specific (functional)
networks not covering the entire brain. In the former, the entire
brain is subdivided into regions of interest (see Figure 3(a) for an
example), which can be performed by a number of different
ways, with the most prevalent being a subdivision based on
(macro)anatomical atlases or a geometric division into parcels
of roughly equal size (Behrens & Sporns, 2012). Alternatively,
the parcels may also be estimated from the data itself, for example, by spatially constrained ward clustering to identify patches
that feature a homogeneous (resting-state) functional connectivity pattern (Behrens & Sporns, 2012). Independently of the
method used to define these regions, if the investigated nodes
cover the entire brain, the ensuing network will evidently also
represent the complete brain-wide functional connectivity pattern or functional connectome (Sporns, Tononi, & Kotter, 2005).
While analyses of the full functional connectome have received
much attention recently, it needs to be cautioned that this does
not represent a singular, well-defined property of a particular
individual, but may rather depend on the way the brain is
divided into separate regions, the preprocessing steps, and the
confound removal, among other factors. One of the major
advantages of connectome-style analysis is the fact that it does
not rely on a priori hypotheses outside of the assumptions going
into the definition of the individual regions. It thus allows the
investigation of all functional connections and the localization
197
200
400
600
800
1000
1200
1400
1600
(a)
(b)
200 400 600 800 1000 1200 1400 1600
Figure 3 Example of a network-based, connectome-style functional connectivity analysis covering the entire brain. The whole brain was subdivided
into 1600 equally sized regions of interests (a). Resting-state functional connectivity was then determined by correlating all 1600 nodes with each
other resulting in a full connectivity matrix for the entire brain (b).
of those interactions that, for example, differ between two populations or that relate to a particular phenotype. This advantage,
however, comes with a potentially severe multiple comparison
problem. For example, at a granularity of 1000 regions of interest
(which would be equivalent to each cortical region covering
roughly 23 cm2 of cortex, i.e., probably more than an individual functional module), any statistical inference on the ensuing
functional connectome would need to deal correcting for almost
half a million parallel tests. Increasing the granularity in order to
arrive at more specific coverage of functional units substantially
worsens the problem as the number of parallel tests increases to
the second degree with the number of regions. Conversely,
reducing the number of regions ameliorates the multiple comparison problem but in turn dramatically reduces the specificity
of any findings. In particular, it may be argued that these larger
regions, which would result from a parcellation of lower granularity, would contain multiple functional modules, each showing a potentially specific pattern of functional connectivity.
Averaging across these may thus obscure relevant features in
the functional connectome. In other words, choosing a finegrained parcellation with the extreme case of considering
each voxel individually will allow a more specific analysis
and localization of effects but comes at a rapidly increasing
multiple comparison problem. In turn, choosing a broader parcellation will lead to less problems in statistical inference but
entails lower specificity and probably also validity of the findings. This predicament has more recently started an interest in
the use of multivariate pattern-analysis approaches for the investigation of connectome data (e.g., Sripada et al., 2013). These
avoid the problem of multiple independent tests but rather use
the entire pattern of functional connectivity measures, that is, the
strengths along all edges of the whole-brain network, to identify
patterns that are predictive of, for example, clinical classifications
(health vs. disease) or phenotypic variables such as cognitive
performance. Referring the reader to the respective section on
pattern analyses for further details, we would thus summarize
that network-based analyses in which the regions of interest
cover the entire brain have the intriguing potential of characterizing the entire functional connectome but are still faced with
open questions on how to parcel the brain into distinct regions

and challenged by the necessary trade-off between specificity and
validity on one hand and data reduction on the other.
Alternatively and falling into the other class of network
definition (those not covering the entire brain), the investigated
regions may also represent a set of brain locations that are
considered to form a functional network based on information
other than functional connectivity, for example, a previous fMRI
study or a meta-analysis of activation findings. As an example,
the regions of interest for a network-based analysis of functional
connectivity of the motor system may be defined by those brain
areas, which are involved in hand movements. This would
restrict the analysis to a particular functional system and thus
increase the interpretability of findings. In contrast to the investigation of the full functional connectome, such analyses may be
regarded as hypothesis-driven investigations of functional connectivity in which the definition of the network represents the
operationalization of the neurobiological hypothesis. In the
case of the motor system and as shown in Figure 2, this approach
would, for example, allow to assess whether interindividual
differences in the functional connectivity between different
cortical and subcortical motor areas are related to phenotypic
differences in motor behavior. Such hypothesis-driven approach
obviously has the main advantage that the analysis is focused
on those regions that have a functional relevance to the behavior at hand. In addition to better interpretability, those analyses
also avoid incidental findings in other parts of the brain that
may be driven by residual confounding effects or represent false
positives. At the same time, such functional definition will, in
most cases, keep the number of regions and hence the multiple
comparison problem limited. This in turn increases the sensitivity of the analysis, as less severe correction is required. Using
a priori knowledge on a functional system of interest in order to
investigate functional connectivity within that system has thus
two main advantages: the obtained findings are functionally
more specific and also more sensitive due to a lower number of
parallel comparisons. In turn, one potential disadvantage is
(again) the dependency on the exact definition of the seeds.
As detailed in the preceding text in the section on seed-based
198
functional connectivity, there is no general standard for this

definition, which represents the operationalization of the neurobiological hypothesis, that is, the investigated system, into a
set of regions of interest. Rather, the same neurobiological
entity, for example, the motor system, may be parameterized
into a set of regions or nodes by many different approaches,
which most likely will have an influence on the obtained network measures. In other words, whereas the functional connectivity analyses in a priori defined network should represent a
largely, though not completely, unbiased approach, the definition of the respective nodes is potentially much more open to
bias. A second potential drawback that is shared with all
hypothesis-driven analysis approaches is the fact that such
investigations are blind to effects outside the hypothesized
network. As connectivity is only assessed between an a priori
defined set of regions, even the most substantial or relevant
influence of an outside region, that is, one that was not part of
the predefined set of nodes, will be missed. Consequently, the
validity of network-based approaches focusing on a particular
functional system is crucially determined by both the completeness of the a priori network model and the quality by which
the chosen regions of interest reflect the relevant nodes. There
is, however, a justified hope that the recent emergence of
meta-analytic approaches, which have by now already resulted
in robust definitions of several cognitive systems, may provide a
solution to these problems. In particular, defining the nodes of
functional brain networks by those regions that show convergent
evidence for functional involvement in a specific neurobiological system, computing the functional connectivity between these
network nodes, and relating the interindividual differences in
functional connectivity strength to phenotypic measures that
probe the respective neurobiological system at the behavioral
level may represent a promising approach to bridging functional
localization, connectivity, and behavior.
How to Analyze FC: Independent Component Analysis

As can be inferred from the preceding text, functional connectivity analyses may be performed by different approaches, such
as correlations on time series from resting-state fMRI data and
task-driven coactivations across a large number of functional
neuroimaging experiments. Beyond that, the different analysis
methods for functional connectivity also show a continuum
ranging from strongly hypothesis-driven approaches (networkbased analyses in confined a priori defined sets of nodes), to
analyses that investigate the whole-brain connectivity of one or
a few predefined regions of interest (seed-based analyses), to
those that investigate the functional connectivity between any
pair of a large set of regions covering the entire brain
(connectome-style analyses). All of these approaches, however,
rely on some a priori definition of brain regions or nodes. ICA
in turn represents an alternative, completely data-driven
approach to functional connectivity analysis. The key idea
behind ICA is to separate a signal provided by a time series
(or a large set of findings from previous neuroimaging studies)
into a set of mutually independent and associated time
courses. In other words, ICA identifies sets of voxels or regions
that cofluctuate across time (in resting-state or task-based fMRI
data) or that are coactivated across experiments. Each
component thus represents a system of regions that show

functional connectivity with each other (see Figure 4 for an
example of a component derived by ICA). In this context, it is
interesting to note that the ICA decomposition of resting-state
fMRI time series and the BrainMap database have yielded
highly convergent sets of components, indicating that a similar
decomposition into functional systems may be achieved by
applying it to data across many tasks and experiments and
resting-state data (Smith et al., 2009). In itself, however, ICA
is a purely decomposing approach, which only enables the
identification of mutually independent sets of regions of high
within-component functional connectivity. By using dualregression approaches though, subject-specific versions of the
spatial maps determined at the group level and their associated
time series may be computed. Statistical analysis may then be
sought by testing for differences in the expression of a particular component at each voxel between two groups or be related
to a particular phenotype. The ensuing results, which are specific for a given component and consist of voxels in which
there is, for example, a significant group difference, have sometimes been mislabeled as differences in functional connectivity
within region A. However, there is obviously no connectivity
within a region. These results thus denote a difference in the
functional coupling between the identified set of voxels and
the rest of the component. That is, a significant group difference in the analysis of a specific component reveals that the
ensuing voxels are more or less tightly integrated into that
component in one group of subjects compared with the other.
While the technical details of ICA, in particular with respect
to its application toward resting-state fMRI data, are detailed in
a separate part of this book, some advantages and drawbacks of
ICA-based analyses relative to the other functional connectivity
approaches should be considered. Evidently, a main strength
of ICA-based functional connectivity analyses is that it is a
completely data-driven approach that does not require any a
priori choice of regions or network nodes. Rather, not only the
components themselves but also their number may be estimated from the data at hand, resulting in an unbiased definition of functional connectivity networks. Moreover, by
decomposing the entire dataset, the different estimated components provide the possibility of investigating multiple functional systems at once. They thus represent a middle road
between the two classes of network-based functional connectivity approaches outlined in the preceding text. While being
much more complete than a priori networks covering a particular functional system, they provide a data-driven grouping
into such systems of coherent connectivity that is not intrinsically given by connectome analyses. Finally, ICAs have been
shown to be highly robust, not only across different experimental states such as task and rest (Smith et al., 2009) but also
across subjects. In particular, the identification of many common components is possible even on the level of individual
subjects (Zuo et al., 2010).
There are, however, also several drawbacks that need to be
considered in the context of ICA to assess functional connectivity. One of them is the direct flip side of one of the main
strengths, namely, the completely data-driven approach lacking any a priori knowledge. While this property is advantageous when investigating the functional organization of the
human brain without any constraints, it does also have
199
Figure 4 Example of a component derived by independent component analyses using resting-state fMRI data. Here, the color scale indicates how
strongly each voxel is associated with this particular component (thresholded at p > .5 for displaying purposes). Using dual regression, subject-specific
versions of this group-level spatial map and their associated time series may be computed and subsequently subjected to statistical inference
testing for differences across subjects or groups in the expression of that particular component at each voxel.
limitations. In particular, as the components are estimated

from the data, they do not represent a standardized test set
that may be employed to probe functional connectivity in a
specific prespecified network. This makes it difficult to directly
compare findings across studies or populations. Moreover,
conventional ICAs usually focus on the assessment of
between-group effects of brainbehavior correlations within
each component, that is, test whether a set of voxels are more
strongly or weakly integrated into the respective component
and, if so, where these voxels are more strongly or weakly
integrated. Once estimated, the identified components thus
represent rather strong constraints on the statistical analysis
of the data. For example, it is easy to test if a voxel in the
primary motor cortex is more or less integrated into the ICA
component representing the motor system in a group of
patients, and the findings should be well interpretable. In
contrast, a change in the integration of this voxel with a different component, for example, the visual system, is technically
equally feasible but may be much more difficult to interpret as
that particular voxel is not per se significantly associated with
the respective component.
Finally, given a considerable degree of consistency between
datasets, ICA studies have presented converging evidence for the
existence of several distinct components (i.e., functional networks) in fMRI datasets obtained during a task-free, resting
state. Moreover, as noted in the preceding text, most of these
resting-state networks closely resemble networks that are
commonly engaged in task-based fMRI studies (Smith et al.,
2009). This has led to the intuitive but still not fully validated
notion that virtually, any functional system in the brain is
discernible by ICA decomposition. It has also contributed to
the now widely established functional labeling of these components as dorsal attention network, visual network, auditory
network, sensorimotor network, central-executive network,
core network, and so on. While intuitive and certainly convenient in reporting ICA findings, these labels are unfortunately
primarily an example of largely subjective reverse inference. Just
because a component looks spatially similar to a set of regions
that have been found in task-based fMRI studies does not yet
implicate that these networks are associated with the respective
cognitive function. Moreover, one needs to consider that, due to
the simplicity and consequent recent popularity of ICA-based

resting-state functional connectivity analyses, many of these
labels have become associated with sets of connotations that
may have become somewhat detached from task-based cognitive psychology. Terms like saliency network and default mode
network may provide useful vehicles to denoting a particular
spatial component consisting of the bilateral anterior insula and
the midcingulate cortex/SMA and a bilateral posterior inferior
parietal and anterior and posterior midline network, respectively. They have, however, evolved to carry functional connotations that may or may not be valid and in any case hinder an
unbiased investigation into their functional roles.
Summary and Conceptual Considerations

Understanding the organization of the human brain will necessarily be a multimodal endeavor that requires the consideration of both the regional specialization (using structural and
functional brain mapping) and the integration between
specialized regions, that is, the integrated analysis of structure,
function, and connectivity. In this context, functional connectivity analyses should hold a crucial position as they may
provide a bridge between structural connectivity, representing
the scaffold of fiber connections between remote brain regions,
and functional specialization as revealed by the pattern of taskrelated activity. Investigating functional connectivity allows the
delineation of interacting networks and the amount of functional coupling between the respective regions in a robust
fashion using rather limited assumptions. It must be acknowledged, though, that functional connectivity is per se a correlative approach, which entails several important caveats.
Probably, the most important implication from this correlative
nature is the consideration that functional connectivity
between two regions does not imply any direct interaction
between them. Rather, several different routes such as relays
or loops may realize not only the required coincidence of
neurophysiological events but also the common influences
by the third region. Moreover, given the straightforward but
rather nondiscriminative nature of functional connectivity
analyses, they may be particularly sensitive to confounding
200
factors, that is, aspects other than the effects of interest, which
affect the correlation structure in the data. Keeping these
caveats in mind, however, functional connectivity analyses
have a unique role in multimodal brain mapping that is complementary to functional and structural mapping and anatomical connectivity analyses.
It must also be noted that functional connectivity represents
a very broad concept that comprises multiple different possible
analysis approaches. These range from hypothesis-driven
investigations of interregional coupling among a set of predefined regions, usually from a particular functional system; to
seed-based analyses testing for regions showing significant
functional connectivity with that particular seed; to connectome analyses investigating the full functional connectivity
pattern between a large set of regions covering the entire
brain; to finally ICAs decomposing the signal in a completely
data-driven fashion. Moreover, functional connectivity estimated on resting-state fMRI time series represents not only
the most widely used approach but also the probably most
feasible method to obtain functional network information in
larger or less compliant cohorts of subjects. In the spectrum of
functional connectivity modalities, however, it only represents
one possible aspect. In turn, investigation of task-based coactivation patterns and cross correlation analyses of MEG/
EEG time series may provide valuable and most important
complementary information in functional interactions during
a different mental state, that is, the performance of externally
structured tasks, and at a higher temporal resolution, respectively. In this context, one important question for further
research is the relationship between different aspects of functional connectivity and their relation to measures of structural
connectivity and functional specialization.

Myeloarchitecture and Maps of the Cerebral Cortex; Transmitter
Receptor Distribution in the Human Brain; INTRODUCTION TO
METHODS AND MODELING: BrainMap Database as a Resource for
Computational Modeling; Dynamic Causal Models for fMRI; Effective
Connectivity; Graph-Theoretical Analysis of Brain Networks; MetaAnalyses in Functional Neuroimaging; Multi-voxel Pattern Analysis;
Resting-State Functional Connectivity.
References
Aertsen, A., Erb, B., & Palm, G. (1994). Dynamics of functional coupling in the cerebral
cortex: An attempt at a model-based interpretation. Physica D, 75, 103128.
Behrens, T. E., & Sporns, O. (2012). Human connectomics. Current Opinion in
Birn, R. M. (2012). The role of physiological noise in resting-state functional
connectivity. NeuroImage, 62, 864870.
Buckner, R. L., & Vincent, J. L. (2007). Unrest at rest: Default activity and spontaneous
network correlations. NeuroImage, 37, 10911096 discussion 10971099.
Dagli, M. S., Ingeholm, J. E., & Haxby, J. V. (1999). Localization of cardiac-induced
signal change in fMRI. NeuroImage, 9, 407415.
Duncan, N. W., & Northoff, G. (2013). Overview of potential procedural and participantrelated confounds for neuroimaging of the resting state. Journal of Psychiatry and
Ebisch, S. J., Mantini, D., Romanelli, R., Tommasi, M., Perrucci, M. G., Romani, G. L.,
et al. (2013). Long-range functional interactions of anterior insula and medial frontal
cortex are differently modulated by visuospatial and inductive reasoning tasks.
Eickhoff, S. B., & Grefkes, C. (2011). Approaches for the integrated analysis of structure,
function and connectivity of the human brain. Clinical EEG and Neuroscience, 42,
107121.
Eickhoff, S. B., Jbabdi, S., Caspers, S., Laird, A. R., Fox, P. T., Zilles, K., et al. (2010).
Anatomical and functional connectivity of cytoarchitectonic areas within the human
parietal operculum. Journal of Neuroscience, 30, 64096421.
Fox, M. D., & Raichle, M. E. (2007). Spontaneous fluctuations in brain activity observed
with functional magnetic resonance imaging. Nature Reviews. Neuroscience, 8,
700711.
Friston, K. (1994). Functional and effective connectivity in neuroimaging: A synthesis.
Friston, K. (2002). Beyond phrenology: What can neuroimaging tell us about distributed
circuitry? Annual Review of Neuroscience, 25, 221250.
Friston, K. J. (2011). Functional and effective connectivity: A review. Brain Connectivity,
1, 1336.
Gerstein, G. L., & Perkel, D. H. (1969). Simultaneously recorded trains of action
potentials: Analysis and functional interpretation. Science, 164, 828830.
Goebel, R., Roebroeck, A., Kim, D. S., & Formisano, E. (2003). Investigating directed
cortical interactions in time-resolved fMRI data using vector autoregressive
modeling and Granger causality mapping. Magnetic Resonance Imaging, 21,
12511261.
Greicius, M. D., Krasnow, B., Reiss, A. L., & Menon, V. (2003). Functional connectivity
in the resting brain: A network analysis of the default mode hypothesis.
100, 253258.
Hohlefeld, F. U., Huchzermeyer, C., Huebl, J., Schneider, G. H., Nolte, G., Brucke, C.,
et al. (2013). Functional and effective connectivity in subthalamic local field
potential recordings of patients with Parkinsons disease. Neuroscience, 250C,
320332.
Honey, C. J., Kotter, R., Breakspear, M., & Sporns, O. (2007). Network structure of
1024010245.
Horwitz, B., Duara, R., & Rapoport, S. I. (1984). Intercorrelations of glucose
metabolic rates between brain regions: Application to healthy males in a state of
reduced sensory input. Journal of Cerebral Blood Flow and Metabolism, 4,
484499.
Jakobs, O., Langner, R., Caspers, S., Roski, C., Cieslik, E. C., Zilles, K., et al. (2012).
Across-study and within-subject functional connectivity of a right temporo-parietal
junction subregion involved in stimulus-context integration. NeuroImage, 60,
23892398.
Lourens, M. A., Meijer, H. G., Contarino, M. F., Van Den Munckhof, P.,
Schuurman, P. R., Van Gils, S. A., et al. (2013). Functional neuronal activity and
connectivity within the subthalamic nucleus in Parkinsons disease. Clinical
Moeller, J. R., Strother, S. C., Sidtis, J. J., & Rottenberg, D. A. (1987). Scaled subprofile
model: A statistical approach to the analysis of functional patterns in positron
emission tomographic data. Journal of Cerebral Blood Flow and Metabolism, 7,
649658.
Muller, V. I., Cieslik, E. C., Laird, A. R., Fox, P. T., & Eickhoff, S. B. (2013). Dysregulated
left inferior parietal activity in schizophrenia and depression: Functional connectivity
and characterization. Frontiers in Human Neuroscience, 7, 268.
Murphy, K., Birn, R. M., & Bandettini, P. A. (2013). Resting-state fMRI confounds and
cleanup. NeuroImage, 80, 349359.
Murphy, K., Birn, R. M., Handwerker, D. A., Jones, T. B., & Bandettini, P. A. (2009). The
impact of global signal regression on resting state correlations: Are anti-correlated
networks introduced? NeuroImage, 44, 893905.
Roland, P., Svensson, G., Lindeberg, T., Risch, T., Baumann, P., Dehmel, A., et al.
(2001). A database generator for human brain imaging. Trends in Neurosciences,
24, 562564.
Ruchkin, D. (2005). EEG coherence. International Journal of Psychophysiology, 57,
8385.
Satterthwaite, T. D., Elliott, M. A., Gerraty, R. T., Ruparel, K., Loughead, J., Calkins, M. E.,
et al. (2013). An improved framework for confound regression and filtering for control
of motion artifact in the preprocessing of resting-state functional connectivity data.
Schilbach, L., Bzdok, D., Timmermans, B., Fox, P. T., Laird, A. R., Vogeley, K., et al.
(2012). Introspective minds: Using ALE meta-analyses to study commonalities in
the neural correlates of emotional processing, social and unconstrained cognition.
PLoS One, 7, e30920.

America, 106, 1304013045.
Sporns, O., Tononi, G., & Kotter, R. (2005). The human connectome: A structural
description of the human brain. PLoS Computational Biology, 1, e42.
Sripada, C. S., Kessler, D., Welsh, R., Angstadt, M., Liberzon, I., Phan, K. L., et al.
(2013). Distributed effects of methylphenidate on the network structure of the resting
brain: A connectomic pattern classification analysis. NeuroImage, 81, 213221.
201
Van Horn, J. D., Grethe, J. S., Kostelec, P., Woodward, J. B., Aslam, J. A., Rus, D., et al.
(2001). The functional magnetic resonance imaging data center (fMRIDC): The
challenges and rewards of large-scale databasing of neuroimaging studies.
Philosophical Transactions of the Royal Society of London. Series B: Biological
Sciences, 356, 13231339.
Zuo, X. N., Kelly, C., Adelstein, J. S., Klein, D. F., Castellanos, F. X., & Milham, M. P.
(2010). Reliable intrinsic connectivity networks: Testretest evaluation using ICA
and dual regression approach. NeuroImage, 49, 21632177.
The Resting-State Physiology of the Human Cerebral Cortex

D Bzdok and SB Eickhoff, Institut fur Neurowissenschaften und Medizin (INM-1), Julich, Germany
Glossary
Default-mode network A resting-state connectivity-derived

network that was initially proposed to be consistently
decreasing neural activity during experimental paradigms
requiring stimulus-guided behavior. It is now believed to be
mostly, but not exclusively, active in the absence of external
stimulation.
Intrinsic connectivity network (ICN) Analogous to restingstate networks (RSNs), coherent spatiotemporal coupling in
blood oxygen level-dependent (BOLD) fluctuations with
emphasis on consistency across task-related and taskunrelated brain states.
Introduction
Without focus on an explicit task, the brain is not at rest. Rather,
the brain is continuously metabolizing large quantities of oxygen
and glucose energy from the cerebral blood vessels to fuel general
maintenance and ongoing neural communication. The baseline
brain metabolism is subject to surprisingly little modulations due
to the cognitive load necessary to process environmental challenges. Such basic properties of oxygen and glucose consumption
will be introduced in the first half of this article and discussed
with respect to their relation to vasculature and neural activity. In
the second half of this article, we will detail three metabolismrelated aspects of brain physiology that are frequently intermingled but clearly distinct. These are the functional connectivity
(i.e., a class of methodological approaches), resting-state (RS)
correlations (i.e., a particular methodological approach), and
default-mode network (DMN; i.e., a neural network with coherent RS fluctuations). In particular, functional connectivity can be
defined as temporal correlations between spatially distant neurophysiological events (Friston, Frith, Fletcher, Liddle, &
Frackowiak, 1996). It is believed to quantify the statistical relationship of the functional interaction between brain regions.
One example of functional connectivity is RS connectivity. RS
connectivity measures functional coupling between distant
brain regions by correlation between time series of the metabolic
fluctuations outside of an experimental context. RS connectivity,
in turn, led to the discovery of several robust resting-state
networks (RSNs), including the DMN. The latter is widely held
to reflect ongoing random thought in the absence of structured
environmental challenges. We will elaborate these aspects of
brain physiology along the lines of metabolism, the RS signal,
ensuing RS connectivity and thus derivable neural networks.
Metabolic Properties of Brain Physiology

Vascular Mechanisms
Although the brain makes up only 2% of the body weight, it
receives 11% of the cardiac output. Fluctuations in cerebral
Resting-state connectivity Coherent temporal coupling in

spatially distant resting-state BOLD fluctuations used to
measure functional coupling between brain regions.
Resting-state network Coherent spatiotemporal coupling
in resting-state BOLD fluctuations yields a set of robust
neural networks.
Resting-state signal Fluctuations in physiological signals
recorded in the absence of externally structured
experimental settings that are reflected in voxels time
courses. These signals are thought to have neuronal,
metabolic, cardiac, and respiratory origins.
blood flow depend on further factors, including arterial

blood pressure, cognitive states (e.g., sleep), age, and pharmacological influence (e.g., sedatives). In general, the anatomy of
local capillary networks and the functional brain architecture
have an intimate relationship (Cox, Woolsey, & Rovainen,
1993). Importantly, this explains why highly vascularized cortical areas (e.g., primary sensory areas and the speech-related
Brocas and Wernickes areas) have a higher baseline probability to be observed in neuroimaging studies (Harrison, Harel,
Panesar, & Mount, 2002).
Blood demand and blood supply generally work in
concert in the human brain. In the example of task-induced
metabolic consumption, the onset of vibratory stimulation of
participants hand entails regional accumulation of metabolic
equivalents that cause regional blood flow increase (cf.
neurovascular coupling in the succeeding text) in the contralateral somatosensory cortex (Fox & Raichle, 1986). On
a microanatomical scale, local increases in neural activation
entail privileged local blood supply at the expense of
immediately neighboring neuronal populations (i.e.,
vascular-steal phenomenon). On a macroanatomical scale,
however, regional increases in brain activity due to recruitment of a particular cognitive process induce regional blood
flow changes of only a few percent. The regional changes in
blood flow accompanied by cognitive phenomena are thus
not measurable as changes in total blood flow to the brain,
although the brains hemodynamic reserve permits doubling
the blood influx.
Cerebral autoregulation, finally, refers to the physiological
mechanisms of blood vessels that keep the blood flow constant
across a range of blood pressure levels (50170 mmHg). This
physiological response occurs at fast and slow timescales.
Dynamic cerebral autoregulation maintains a constant blood
flow following transient blood pressure changes within seconds. Static cerebral autoregulation reflects adjustments to
enduring blood pressure changes (e.g., chronic hypertension).
Conceptually, cerebral blood flow appears to be governed by
prediction, rather than measurement, of energy consumption
(Logothetis & Wandell, 2004).
http://dx.doi.org/10.1016/B978-0-12-397025-1.00213-X
203
204
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | The Resting-State Physiology of the Human Cerebral Cortex
Neurovascular Coupling
The neuroscientist is typically interested in neural activity,
which was suggested to induce regional blood flow changes
already in the nineteenth century (Roy & Sherrington, 1890).
Physiologically, neurovascular coupling describes the brain
vasculatures time-lagged dilation response to locally increasing metabolic products. This is directly observable using water
or butanol positron emission tomography and indirectly using
functional magnetic resonance imaging (fMRI) as the BOLD
(blood oxygen level-dependent) signal (Figure 1). The BOLD
signal is caused by local changes in blood oxygenation, that is,
the oxyhemoglobin to deoxyhemoglobin ratio (red blood cells
carrying vs. not carrying oxygen) (Logothetis & Wandell, 2004;
Ogawa, Lee, Kay, & Tank, 1990). It exhibits an initial dip after
the onset of neural activity increase that is attributed to the fast
local increase in deoxyhemoglobin. The ensuing hyperperfusion and the thus generated (relative) hyperoxygenation (cf.
next paragraph) then dictate the BOLD signal shape (hemodynamic response function). It is variable across the brain regions
of an identical organism, across organisms, and probably
across different tasks. Neural activation is finally followed by
reinhibition of blood flow observable as an undershoot at the
end of the BOLD signal (Logothetis, Pauls, Augath, Trinath, &
Oeltermann, 2001).
Comparing neural activity and corresponding BOLD signals, the BOLD signal is at least one order of magnitude noisier, scales roughly linearly with neural activity, and is better
predicted by local field potentials than multiunit spiking activity. The BOLD signal is possibly more associated with input to
and processing in a local neuronal population rather than its
output. There is thus no clear-cut quantitative relation between
the spike rate of neuronal populations and the ensuing BOLD
response. Rather, the BOLD signal reflects a mixture of transient spikes and continuous membrane potentials (Logothetis
& Wandell, 2004).
Relation Between Blood Flow and Oxygen Supply

Despite the brains small size, relative to the body, it consumes
20% of total oxygen (Clark & Sokoloff, 1999). The cerebral
metabolic rate is often expressed as oxygen consumption. The
resting brain is characterized by a globally similar oxygen
3.0
Open
Closed
Open
Closed
Open
Closed
extraction function (OEF) across brain regions. This indicates

a tightly coupled baseline relationship between blood flow and
oxygen utilization (Figure 2). This is remarkable given considerable regional differences in these hemodynamic (i.e., blood
flow) and metabolic (i.e., oxygen) variables across different
gray matter regions as well as between the gray matter and
white matter.
In fact, blood flow and glucose consumption change in
parallel, while oxygen consumption is likewise closely related
but may regionally decouple from the former (Raichle et al.,
2001). This relative independence of blood flow and oxygen
consumption is associated with regional changes in neural
activity. It drives the BOLD signal, the physiological basis for
fMRI technology. An increased neural activity may thus be
viewed as a transient regional decrease in the OEF. More specifically, oxygen delivery increases more than the oxygen utilization. That is, neural activity increases are characterized by an
increase of blood flow without a concurrent increase of oxygen
consumption (Gusnard, Akbudak, Shulman, & Raichle, 2001),
that is, the OEF is decreased relatively, transiently, and locally
when brain regions increase neural activity.
Energy Consumption
The baseline energy demand of the human brain is very high
and almost exclusively covered by the consumption of glucose.
Glucose metabolism in turn is tightly coupled with oxygen
metabolism. However, 10% of the overall glucose is consumed
in anaerobic pathways.
On a microscale, as much as 50% of baseline energy consumption is explained by the physiology of ongoing synaptic
transmission, including neurotransmitter recycling, as well as
maintenance and restoration of electrochemical membrane
potentials (Attwell & Laughlin, 2001). Such synaptic activity
is closely coupled with glucose uptake and oxygen consumption. The metabolic increase due to neural activity is primarily
located in the nerve terminals rather than cell bodies of neurons. This implies intra- and interneuronal housekeeping functions as particularly important in the human brains resting
functionality. In contrast to this baseline consumption, environmental events evoke increased energy costs of only less than
5%. Importantly, however, most neuroimaging investigations
focus on these (minor) metabolic changes due to external
Open
Closed
% BOLD change
2.5
2.0
1.5
Open
Closed
0.5
0
0.5
1
0
50
100
150
200
250
Times (s)
Figure 1 Left: Depicts the unaveraged blood oxygen level-dependent (BOLD) time course (in magenta) in a part of the primary visual cortex. BOLD
time series were recorded during a task that asked participants to open and close their eyes. The blue lines indicate this paradigm. Right: Result of
contrast analysis between trials with open and closed eyes by subtraction between both conditions. Taken from Fox, D. F., & Raichle, M.E., (2007).
Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging. Nature Reviews. Neuroscience, 8, 700711, Figure 1.
205
Metabolic and circulatory consequences of deactivation and activation

Deactivation
Activation
CBF
CBV
CMRO2
OEF
Hgb-O2
BOLD
()
0
(+) ()
0
Percentage change from baseline
(+)
Figure 2 The relationship between metabolic and circulatory changes in brain areas with increasing (activation) or decreasing (deactivation) neural
activity. CBF cerebral blood flow, CBV cerebral blood volume, CMRO2 cerebral metabolic rate for oxygen, OEF oxygen extraction function,
HgbO2 hemoglobin carrying oxygen, BOLD blood oxygen level-dependent signal. Taken from Raichle, M. E., MacLeod, A. M., Snyder, A. Z., Powers,
W. J., Gusnard, D. A., & Shulman, G. L., (2001). A default mode of brain function. Proceedings of the National Academy of Sciences of the United
States of America, 98, 676682, Figure 3.
stimulation, rather than the majority of metabolic demands

due to biochemical maintenance of neuronal architecture.
On a macroscale, the metabolic baseline turnover is not
equally distributed across the brain. The metabolic demands
are variable across brain regions and (to a smaller extent)
across time. The highest metabolic consumption locates, first,
to the posterior cingulate cortex extending into the adjacent
retrosplenial cortex and precuneus and, second, to the medial
prefrontal cortex extending into the anterior cingulate cortex
(Raichle et al., 2001; Reivich et al., 1979).
Taken together, the biggest fraction of the various brain
signals do not correlate with a particular behavior, stimulus,
or experimental task. The constant blood flow, oxygen intake,
and energy consumption are highly linked. These partially
uncouple in a task setting, but the relative change is very small.
RS Signals
In the absence of task (i.e., during mind wandering), interneuronal communication continues. This is suggested by physiological fluctuations in resting brains that contribute to the
fluctuations of the BOLD signal as measured by fMRI. More
specifically, the RS signal follows a 1/f distribution with
increasing power at lower frequencies. Such signal properties
were also consistently observed in EEG (electroencephalogram), magnetoencephalography, local field potentials, and
human behavioral measurements (Fox & Raichle, 2007).
Low-frequency fluctuations resembling the (fMRI) RS signal
have furthermore been observed in a number of physiological
measurements, including oxygen availability, cytochrome oxidase activity, and blood flow and volume. Physiologically
interrelated mechanisms might thus contribute to ongoing
neural computation reflected by the RS (BOLD) signal.
Importantly, the (small) amplitude of the RS signal is modulated by transient psychological states (e.g., arousal, attention,
and alertness) as well as cardiac and respiratory influences.

Indeed, the decomposability of the RS signal into independent
components suggests a set of distinct influences rather than one
coherent signal pattern (Fukunaga et al., 2006). More specifically, evidence exists in favor of a neuron-, metabolism-,
vasculature-, and oxygen-driven genesis of the RS signal. A neuronal origin of RS fluctuations is suggested by correlation
between fluctuations in fMRI data and in electrophysiological
EEG data of the alpha rhythm (812 Hz) (Goldman, Stern,
Engel, & Cohen, 2002). A metabolic origin is conceivable given
that metabolic oscillations, indexed by (oxygen metabolizing)
cytochrome oxidase measured by near-infrared spectroscopy,
occur spontaneously without external stimulation (Obrig et al.,
2000). A vascularrespiratory origin is suggested by covariance
between variabilities in fMRI data and arterial carbon dioxide,
known to potently dilate vessels (Birn, Diamond, Smith, &
Bandettini, 2006; Wise, Ide, Poulin, & Tracey, 2004). Additionally, Fourier transformation of RS signals typically exhibits peaks
at the heart and respiratory frequencies.
To date, the stratification of the physiological factors underlying the RS signal is poorly understood. It is, however,
commonly agreed that the variability in the RS signal arises
from both physiological factors and the organisms mental
operations.
RS Connectivity
Correlation analysis can detect temporal coincidence in spontaneous, slow fluctuations (0.010.1 Hz) in fMRI signals. This is
taken as a measure of RS connectivity between topographically
distant parts of the brain. Faster frequencies, not apparent in
(intrinsically low-pass-filtered) BOLD signals, in turn are predominantly associated with cardiac and respiratory sources. RS
connectivity is task-unconstrained by probing participants that
lie in the scanner without following a defined experimental task.
206
Instead, participants are instructed to think of nothing in particular, let their minds go, and leave their eyes open/closed or
look at a fixation cross. During mind wandering, humans mentally shift between various heterogeneous types of thoughts,
memories, and predictions. This is why RS connectivity is
believed to reflect the repertoire of cognitive operations that
the human brain can perform (Smith et al., 2009; but see
Mennes, Kelly, Colcombe, Castellanos, & Milham, 2013).
The most commonly used methodological approach to
measure RS connectivity is seed correlation with a predefined
region of interest. In fact, the feasibility of exploiting BOLD
signals to investigate spatially distributed networks was first
demonstrated by seeding from the primary motor cortex
(Biswal, Yetkin, Haughton, & Hyde, 1995). Time series of a
motor seed, obtained from a finger-tapping task, were temporally correlated with the rest of the brain. This yielded a distributed network of motor-related brain regions within and
across hemispheres (Figure 3). As the BOLD signal contains
both neuronal and nonneuronal components (cf. the preceding text), several nonneuronal contributions are typically
removed from the correlation maps (Satterthwaite et al.,
2013). This hypothesis-driven approach has successfully recovered many robust neural networks related to visual, auditory,
episodic memory, language, and dorsal attention systems.
Independent component analysis (ICA) is the other most
common form of RS analysis. ICA decomposes multivariate
neuroimaging data into a set of discrete fluctuation patterns
coherently correlated across time and space. It is a more datadriven approach than seed correlation. Without a priori region,
ICA can simultaneously extract several networks while separating out nonneuronal variance from movements, ventricles,
white matter, and respiratory and cardiac cycles (Beckmann,
DeLuca, Devlin, & Smith, 2005). Despite their differences, ICA
and seed correlation generate functional networks that are
highly comparable.
RS connectivity is modulated by age, experience, and disease
as well as conscious, cognitive, and emotional states. A comprehensive testretest reliability study on RS connectivity (Shehzad
et al., 2009) concluded that (i) statistically significant
correlations at group level were more reliable than nonsignificant ones, (ii) significant positive correlations were more
reliable than significant negative ones, and (iii) regions within a
neural networks were more reliably correlated with each other
than with other brain regions. Moreover, the more reliably a
voxel is positively correlated with a given network, the more
reliably it is negatively correlated with voxels from other networks. A comprehensive description of RS connectivity should
therefore comprise positive and negative correlations. Despite
initial skepticism, RS connectivity results were repeatedly shown
to be consistent across participants, brain scans, time points,
and other factors (e.g., eyes open vs. closed).
In sum, seed correlation and ICA studies thus showed that
RS connectivity reflects robust functional relationships
between brain regions.
Resting-State Networks
Observed RS connectivity patterns led to the discovery of the
coherent spatiotemporal fluctuations termed resting-state networks (RSNs). Notably, there are probably not a deterministic
number of RSNs in the brain as they are decomposable up to
single-region networks. The individual RSNs exhibit BOLD
signal variability that typically revolves around 23%
(Damoiseaux et al., 2006). High BOLD signal variability even
tends to coincide with high spatiotemporal consistency of
RSN. Structural connectivity by fiber bundles does constrain
but not exhaustively determine functional connectivity in RSN,
as evidenced by empirical measurements and computational
modeling (Honey et al., 2009).
Relation of RSN Fluctuations and Task-Evoked Responses

The properties of RSN are related to human behavior during
task and at rest. On the one hand, task-related measurement of
functional coupling between regions of a particular (e.g., language) network usually follows behavioral performance. On
the other hand, task-unrelated measurement of functional
Figure 3 Left: Task-evoked BOLD response during left and right finger movement in functional magnetic resonance imaging. Right: Resting-state
connectivity of a seed region in the motor cortex. a/b bilateral primary motor cortex, c Brodmanns area 6, d extension of the primary sensorimotor
cortex, e premotor area. Taken from Biswal, B., Yetkin, F. Z., Haughton, V. M., & Hyde, J. S., (1995). Functional connectivity in the motor cortex
of resting human brain using echo-planar MRI. Magnetic Resonance in Medicine, 34, 537541, Figure 3.
coupling between regions of a particular network often also
allows prediction of the extent of neural response during corresponding behavioral performance. Indeed, several authors
speculate that the continuous fluctuations in known networks
might reflect the brains tracking and prediction of environmental events to adaptively optimize future behavioral
responses (Binder et al., 1999). Within and outside of experimental settings, activity in RSN thus seems to relate to psychological processes. Interestingly, experimentally imposed
cognitive sets modulate connectivity within RSN such that
negative RS correlations are more strongly modulated than
positive RS correlations. This continuation and modulation
of RS fluctuations during experimentally controlled brain
states complicates the interpretation of neuroimaging findings.
In a seminal study (Smith et al., 2009), ICA was applied
individually to large quantities of task-constrained and taskunconstrained fMRI data to maximize intranetwork homogeneity and between-network heterogeneity. These two separate
decompositions of brain signals into networks yielded largely
homologues network pairs, including sensorimotor, visual,
auditory, executive control, saliency, and dorsal attention networks (Figure 4). The authors concluded that an identical
repertoire of neural networks is underlying functional brain
architecture in active and resting brain states. These were hence
more generally called intrinsic connectivity networks.
Brain regions simultaneously increasing neural activity
in response to a given external stimulus or task increase correlation between each other and decrease correlation with
207
other regions, and the same seems true in the absence of an

explicit task.
The Default-Mode Network

The probably best-known RSN is DMN (Gusnard & Raichle,
2001) that was discovered with and mainly characterized by RS
connectivity. The DMN was initially proposed to be exclusive
in decreasing neural activity consistently during experimental
paradigms requiring stimulus-guided behavior. This RSN was
therefore proposed to reflect the neural correlates underlying
unfocussed everyday mind wandering (Schacter, Addis, &
Buckner, 2007). This, in turn, would suggest a close correspondence between the physiological and psychological baselines
of the human brain (Schilbach, Eickhoff, Rotarska-Jagiela,
Fink, & Vogeley, 2008). It was later even argued that this
network is systematically anticorrelated with brain regions
more active during task performance (Fox et al., 2005). This
was recently challenged by repeated reports of brain regions
exhibiting both task-constrained and task-unconstrained
increases in neural activity (Buckner, Andrews-Hanna, &
Schacter, 2008). More specifically, the DMN is now known to
consistently increase neural activity during a small set of complex cognitive tasks, including social cognition, autobiographical recall, and spatial navigation (Bzdok et al., 2013; Spreng,
Mar, & Kim, 2009). Task-, RS-, and meta-analysis-informed
research on the DMN thus corroborated that this particular
network consistently decreases activity during externally
Figure 4 Ten matched pairs of networks independently derived from independent component analysis of task-unrelated resting-state data from
36 subjects (resting-state network, RSN) and task-related coordinates from neuroimaging contrasts from the BrainMap database (BM). The networks
were paired automatically using spatial cross correlation. Taken from Smith, S. M., Fox, P. T., Miller, K. L., Glahn, D. C., Fox, P. M., Mackay, C. E.,
et al. (2009). Correspondence of the brains functional architecture during activation and rest. Proceedings of the National Academy of Sciences
of the United States of America, 106, 1304013045, Figure 1.
208
focussed mental tasks and typically increases activity during a

small set of internally focussed mental tasks.
Computational Studies
Theoretical studies based on computational modeling of RSN
dynamics also contributed several implications (Deco, Jirsa, &
McIntosh, 2011): (i) Different models of fast and slow oscillations can explain empirically observed spatiotemporal RSN
behavior, without being mutually exclusive. That is, there are
different conceivable ways for RSN nodes to functionally cooperate. (ii) The configuration of RSN is a function of assessed time
window over which network dynamics are measured. Assessment of long time windows yields strong similarity with
known anatomical connectivity patterns. Assessment of short
time windows yields nodes of RSN that transiently form new
functional networks. (iii) Incorporation of stochastic (i.e., noisy)
and deterministic (i.e., constant) elements into RSN dynamics
yields transient oscillatory features provided that the deterministic framework is critical (i.e., instable). That is, an optimal
amount of randomness appears necessary to drive RSN dynamics
in the absence of external stimulation (Faisal, Selen, & Wolpert,
2008). Computational modeling approaches thus highlight correspondence between measures of time and space, anatomical
connectivity between nodes, and sources of randomness as key
factors that orchestrate the physiology of RSN.
Conclusion
A set of fluctuating yet robust brain networks that span several
spatial and temporal scales determine functional brain architecture across rest and task. These brain networks are tightly
coupled with brain oxygen and glucose metabolism as well as
continuous mental operations. Neuroimaging studies using
seed correlation and ICA recovered well-known neural networks and evidenced their relation to behavioral performance.
They might be the physiological instantiation of a human
beings mental repertoire.

Anatomical MRI for Human Brain Morphometry; Functional MRI
Dynamics; Molecular fMRI; INTRODUCTION TO ANATOMY AND
PHYSIOLOGY: Functional Connectivity; INTRODUCTION TO
CLINICAL BRAIN MAPPING: Imaging as Means to Study
Cerebrovascular Pathophysiology; INTRODUCTION TO METHODS
AND MODELING: Resting-State Functional Connectivity;
INTRODUCTION TO SYSTEMS: Large-Scale Functional Brain
Organization.
References
Attwell, D., & Laughlin, S. B. (2001). An energy budget for signaling in the grey matter
of the brain. Journal of Cerebral Blood Flow and Metabolism, 21, 11331145.
Beckmann, C. F., DeLuca, M., Devlin, J. T., & Smith, S. M. (2005). Investigations into
resting-state connectivity using independent component analysis. Philosophical
10011013.
Binder, J. R., Frost, J. A., Hammeke, T. A., Bellgowan, P. S., Rao, S. M., & Cox, R. W.
(1999). Conceptual processing during the conscious resting state: A functional MRI
study. Journal of Cognitive Neuroscience, 11, 8093.
Birn, R. M., Diamond, J. B., Smith, M. A., & Bandettini, P. A. (2006). Separating
respiratory-variation-related fluctuations from neuronal-activity-related fluctuations
in fMRI. NeuroImage, 31, 15361548.
Buckner, R. L., Andrews-Hanna, J. R., & Schacter, D. L. (2008). The brains default
network: Anatomy, function, and relevance to disease. The Annals of the New York
Bzdok, D., Langner, R., Schilbach, L., Jakobs, O., Roski, C., Caspers, S., et al. (2013).
Characterization of the temporo-parietal junction by combining data-driven
parcellation, complementary connectivity analyses, and functional decoding.
Clark, D. D., & Sokoloff, L. (1999). Basic neurochemistry. In G. J. Siegel, B. W.
Agranoff, R. W. Albers, S. K. Fisher, & M. D. Uhler (Eds.), Molecular, cellular and
medical aspects (pp. 637670). Philadelphia, PA: Lippincott-Raven.
Cox, S. B., Woolsey, T. A., & Rovainen, C. M. (1993). Localized dynamic changes in
cortical blood flow with whisker stimulation corresponds to matched vascular and
neuronal architecture of rat barrels. Journal of Cerebral Blood Flow and Metabolism,
13, 899913.
Damoiseaux, J. S., Rombouts, S. A., Barkhof, F., Scheltens, P., Stam, C. J.,
Smith, S. M., et al. (2006). Consistent resting-state networks across healthy
America, 103, 1384813853.
Deco, G., Jirsa, V. K., & McIntosh, A. R. (2011). Emerging concepts for the dynamical
organization of resting-state activity in the brain. Nature Reviews. Neuroscience, 12,
4356.
Faisal, A. A., Selen, L. P., & Wolpert, D. M. (2008). Noise in the nervous system. Nature
Reviews. Neuroscience, 9, 292303.
Fox, P. T., & Raichle, M. E. (1986). Focal physiological uncoupling of cerebral blood
flow and oxidative metabolism during somatosensory stimulation in human
America, 83, 11401144.
Fox, D. F., & Raichle, M. E. (2007). Spontaneous fluctuations in brain activity observed
with functional magnetic resonance imaging. Nature Reviews. Neuroscience, 8,
700711.
Fox, M. D., Snyder, A. Z., Vincent, J. L., Corbetta, M., Van Essen, D. C., & Raichle, M. E.
(2005). The human brain is intrinsically organized into dynamic, anticorrelated
functional networks. Proceedings of the National Academy of Sciences of the United
Friston, K. J., Frith, C. D., Fletcher, P., Liddle, P. F., & Frackowiak, R. S. (1996).
Functional topography: Multidimensional scaling and functional connectivity in the
brain. Cerebral Cortex, 6, 156164.
Fukunaga, M., Horovitz, S. G., van Gelderen, P., de Zwart, J., Jansma, J.,
Ikonomidou, V., et al. (2006). Large-amplitude, spatially correlated fluctuations in
BOLD fMRI signals during extended rest and early sleep stages. Magnetic
Goldman, R. I., Stern, J. M., Engel, J., Jr., & Cohen, M. S. (2002). Simultaneous EEG
and fMRI of the alpha rhythm. Neuroreport, 13, 24872492.
Gusnard, D. A., Akbudak, E., Shulman, G. L., & Raichle, M. E. (2001). Medial prefrontal
cortex and self-referential mental activity: Relation to a default mode of brain
function. Proceedings of the National Academy of Sciences of the United States of
America, 98, 42594264.
Gusnard, D. A., & Raichle, M. E. (2001). Searching for a baseline: Functional imaging
and the resting human brain. Nature Reviews. Neuroscience, 2, 685694.
Harrison, R. V., Harel, N., Panesar, J., & Mount, R. J. (2002). Blood capillary
distribution correlates with hemodynamic-based functional imaging in cerebral
Honey, C. J., Sporns, O., Cammoun, L., Gigandet, X., Thiran, J. P., Meuli, R., et al.
(2009). Predicting human resting-state functional connectivity from structural
connectivity. Proceedings of the National Academy of Sciences of the United States
of America, 106, 20352040.
Neurophysiological investigation of the basis of the fMRI signal. Nature, 412,
150157.
Logothetis, N. K., & Wandell, B. A. (2004). Interpreting the BOLD signal. Annual Review
Mennes, M., Kelly, C., Colcombe, S., Castellanos, F. X., & Milham, M. P. (2013). The
extrinsic and intrinsic functional architectures of the human brain are not equivalent.
Obrig, H., Neufang, M., Wenzel, R., Kohl, M., Steinbrink, J., Einhaupl, K., et al. (2000).
Spontaneous low frequency oscillations of cerebral hemodynamics and metabolism
in human adults. NeuroImage, 12, 623639.
Raichle, M. E. (2008). Loss of resting interhemispheric functional connectivity
after complete section of the corpus callosum. Journal of Neuroscience, 28,
64536458.
Raichle, M. E., MacLeod, A. M., Snyder, A. Z., Powers, W. J., Gusnard, D. A., &
Shulman, G. L. (2001). A default mode of brain function. Proceedings of
676682.
Reivich, M., Kuhl, D., Wolf, A., Greenberg, J., Phelps, M., Ido, T., et al. (1979). The
[18F]fluorodeoxyglucose method for the measurement of local cerebral glucose
utilization in man. Circulation Research, 44, 127137.
Roy, C. S., & Sherrington, C. S. (1890). On the regulation of the blood supply of the
brain. Journal of Physiology, 11, 85108.
Satterthwaite, T. D., Elliott, M. A., Gerraty, R. T., Ruparel, K., Loughead, J.,
Calkins, M. E., et al. (2013). An improved framework for confound regression and
filtering for control of motion artifact in the preprocessing of resting-state functional
connectivity data. NeuroImage, 64, 240256.
209
Schacter, D. L., Addis, D. R., & Buckner, R. L. (2007). Remembering the past to imagine
the future: The prospective brain. Nature Reviews. Neuroscience, 8, 657661.
Schilbach, L., Eickhoff, S. B., Rotarska-Jagiela, A., Fink, G. R., & Vogeley, K. (2008).
Minds at rest? Social cognition as the default mode of cognizing and its putative
relationship to the "default system" of the brain. Consciousness and Cognition, 17,
457467.
Shehzad, Z., Kelly, A. M., Reiss, P. T., Gee, D. G., Gotimer, K., Uddin, L. Q., et al.
(2009). The resting brain: Unconstrained yet reliable. Cerebral Cortex, 19,
22092229.
America, 106, 1304013045.
Spreng, R. N., Mar, R. A., & Kim, A. S. (2009). The common neural basis of
autobiographical memory, prospection, navigation, theory of mind, and the default
mode: A quantitative meta-analysis. Journal of Cognitive Neuroscience, 21, 489510.
Wise, R. G., Ide, K., Poulin, M. J., & Tracey, I. (2004). Resting fluctuations in arterial
carbon dioxide induce significant low frequency variations in BOLD signal.
Genoarchitectonic Brain Maps

L Puelles, University of Murcia, Murcia, Spain; Instituto Murciano de Investigacion Biosanitaria [IMIB], Murcia, Spain
Introduction
Adult and developing brain structure has been variously studied
in the past, giving rise to cytoarchitectonic, myeloarchitectonic,
glioarchitectonic, and chemoarchitectonic brain maps. A powerful variant of chemical neuroanatomy recently named
genoarchitectony (Ferran et al., 2009; Puelles & Ferran, 2012)
resulted from the possibility to map gene expression in terms of
specific cytoplasmic mRNA content with in situ hybridization
(ISH) procedures. In the standard case, an mRNA probe is
produced whose nucleotide sequence is complementary to a
targeted sector of mRNA transcript sequence; the target sequence
is selected to be highly characteristic of a specific gene, using
in silico genomic sequence analysis. The probe is tagged with an
epitope that allows subsequent visualization and is applied to
fixed tissue (sections or whole mounts) under reaction conditions that favor its specific hybridization to the target mRNA
molecules in the cellular cytoplasm. The protocol ensures by
diverse washing steps that the reaction product remains
restricted to those cells that expressed the gene of interest at
the moment of fixation. Various degrees of signal intensity are
obtained, depending on the number of copies of the specific
mRNA transcript and the reaction conditions. The expression of
a gene may be stable over time, eventually providing a molecular marker for the cell type, if the expression is selective (at least
regionally), or may be transient, when associated to a transient
developmental stage or a mature nonconstitutive (occasional)
cell function. It is possible to perform double or triple ISH
reaction against different gene sequences (Lauter, Soll, &
Hauptman, 2011), as well as complementing the ISH with an
immunochemical reaction.
Since translation of mRNA into protein largely occurs in the
cell body, the ISH reaction mainly visualizes neuronal or glial
somata. Exceptionally, some neurons with large quantities of
transcripts may transport them into their axons, leading to
axonal labeling (this applies likewise for radial glial cell processes). A needed note of caution is that the presence of a
specific mRNA transcript in the cytoplasm of a cell does not
necessarily imply that the corresponding protein is being produced, though that is often the case (in critical cases, appropriate controls are required). On the other hand, ISH may allow
us to identify the cellular sources of transported or secreted
proteins that accumulate in a particular neuropile, but are not
detectable in cell bodies, due to low concentration.
ISH reaction provides a very discriminative dissection tool
for the study of brain structure and function, due to the existence of thousands of genes in the genome and their variable
expression patterns in specific cells at particular periods of
prenatal or postnatal life. This approach provides direct access
to the molecular phenotype of even previously unknown cell
types as it evolves dynamically over ontogenetic time. Genes
coding for transcription factors are crucial for the understanding of differentiative developmental processes and related
functional genetic networks. While in many cases the new

genoarchitectonic data merely enrich previous description of
neuroanatomical structure obtained by other means, in some
cases, they highlight apparent inconsistencies with conventional concepts, particularly as regards the developmental
(vs. arbitrary or conventional) definition of boundaries and
the resulting ascription of neuronal populations to given brain
regions (and causal environments). Such cases suggest the
need to reexamine the relevant neuromorphological issues
and eventually propose alternative concepts.
Offering fruitful interaction with other research methods,
genoarchitectonic analysis of the brain is a modern approach
that is promoting significant advance in neuroanatomical
knowledge, by virtue of the high resolutive power of ISH,
potent molecular discrimination (among thousands of gene
markers), and the importance of genes in the chain of molecular causes of brain structure and function.
Developmental Genoarchitectonic Brain Maps

Mappings of gene expression at neural plate stages are peculiar
in that many of the observed expression domains are highly
dynamic, that is, the limits and overall position of the cell
fields expressing a gene change in position over short periods
of time (this is best appreciated by comparing the expression
fields with fate maps). This dynamism reflects the existence of
transient specification states that are subject to modulating
(inducing or repressing) influences from neighboring areas.
Sometimes, the changes are due to nonequal antagonistic
effects occurring across a molecular boundary (when two
genes expressed in adjacent fields directly or indirectly inhibit
each others expression). The strongest effect leads to displacement of the molecular boundary to a locus where the two
antagonistic forces equilibrate.
A good example is provided by the antagonism between the
early neural genes Otx2 and Gbx2 (Figure 1). At early neural plate
stages, Otx2 expression dominates practically the whole neural
territory, excepting a small domain in the prospective spinal cord,
where Gbx2 expression first emerges. Gbx2 activity indirectly
downregulates Otx2 across the mutual transverse boundary,
overpowering the lesser capacity of Otx2 to downregulate it, thus
forcing the reduction of the latters expression domain rostralward
and increasing correspondingly its own domain. Over the following hours, the Otx2/Gbx2 limit results displaced rostralward across
the spinal cord and hindbrain regions and finally becomes stabilized at the prospective midbrainhindbrain boundary. This
molecular boundary then remains invariant during the rest of
development and is still detectable in the adult. Other instances
of transient antagonism between alternative molecular specification states are known that also lead to final equilibrium states at
specific boundaries; such mechanisms may act across the anteroposterior (AP) or dorsoventral (DV) dimensions of the neural
http://dx.doi.org/10.1016/B978-0-12-397025-1.00214-1
211
212
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Genoarchitectonic Brain Maps
Early
Intermediate
Later (fixed)
pros
Otx2
Otx2
Otx2
mes
Gbx2
hb
Gbx2
sc
Gbx2
Dynamic
Dynamic
Equilibrium
Figure 1 Three schemata illustrate early dynamic changes in the respective expression domains of the transcriptor factor genes Otx2 and Gbx2 at
the neural plate stages. Antagonistic interaction at the boundary of these two territories is transiently won by Gbx2, so that its domain results
expanded and that of Otx2 simultaneously contracts. Eventually, an equilibrium is reached at the midbrainhindbrain boundary. This is a common early
mechanism for establishing regional boundaries but seems limited to stages in which the distances are small. pros, prosencephalon; mes,
mesencephalon; hb, hindbrain; sc, spinal cord.
primordium (e.g., roof-derived dorsalizers against floor-derived

ventralizers, establishing at the equilibrium point the alarbasal
boundary).
In other cases of dynamic pattern changes, a transient temporospatial gradient of a secreted diffusible morphogen is
established across the neural wall, usually starting from a linear
neuroepithelial source identified as a secondary organizer, where
the morphogen concentration is maximal. This provides what
amounts to positional molecular information relative to the
signal source and the potential opposed sink (end of the
gradient or border with inhibitory or antagonistic surround).
An example is provided by the double gradient of FGF8 that is
produced by the activity of the isthmic secondary organizer
(IOrg; Figure 2). Such a signaling mechanism is generally noninstructive, being used by the neuroepithelial cells of the relevant substrate to select in a steplike pattern alternative gene
transcriptional states depending on their sensitivity to the local
strengths of the gradiental signals, which results from the
specification states they started with.
As a consequence of such molecular regionalization, different sectors of the brain wall result progressively differentially
specified, and stable boundaries increase in number (Figure 2,
bottom panel). Each delimited neuroepithelial domain initiates and develops further along time a characteristic molecular
profile (set of active/inactive developmental genes), which ulteriorly conditions the details of subsequent differential structural development via regionally independent control of
proliferation, neurogenesis/gliogenesis, differentiation, and
axonal navigation/synaptogenesis. Early patterning thus essentially occurs during the phase of molecular specification of
early neuroepithelial progenitor domains, and this conditions
the developmental course and fate of their neuronal derivatives
within the resulting radial histogenetic areas (this transfers the

early pattern in the ventricular zone to the mantle zone, where
further subdivision or migratory intermixing of regions is possible). One result of such early molecular regionalization is
that neural development is heterochronic (different timetables
in different places), so that late patterning effects may still
proceed in one area as neurogenesis and differentiation already
begin in neighboring areas. Each progenitor domain is held to
produce a specific neuronal type or a temporal sequence of
types. Structural diversification is later elaborated beyond the
production of distinct cell types in each histogenetic area by
secondary emergence of differential adhesive and/or migratory
cellular properties, leading to interactions of the diverse neuronal and glial derivatives within the mantle zone, deployment
of various radial or tangential migratory phenomena, and the
aggregation of definitive nuclei and cell layers. Axonal navigation and resultant synaptogenesis occur in parallel, guided
likewise by the molecular heterogeneity of the mantle layer
of the regionalized brain wall and its intrinsic radial glial
framework.
This glimpse into how adult anatomical boundaries emerge
via molecular patterning effects suggests that all natural
boundaries in the brain probably represent robust equilibrium
states across a linear limit. Most brain boundaries arise in
response to patterning mechanisms oriented along either the
AP or DV dimensions of the neural primordium. Therefore,
they are topologically orthogonal to each other, constituting
the framework of longitudinal zones (floor, basal, alar, and
roof plates and their diverse microzonal subdivisions) intercrossed with a set of transverse interneuromeric boundaries.
The morphogenetic bending of the neural tube (mainly at the
cephalic and cervical flexures), the evagination of the eye,
IOrg (source of FGF8)

Mes
Rostral
hindbrain
r2
Alar
Basal
SC
TG
IC
InC
Plsth
Isthmus
CbVermis
r1
CbHem
r2
Flocculus
Alar
Basal
Figure 2 Schematic illustration of the gradiental field mechanism
generated by the isthmic organizer (IOrg), a typical example of a
secondary organizer. The upper panel shows that initially, the morphogen
FGF8 is secreted by the IOrg and spreads gradientally both rostrally
and caudally, within a given spatial range, the signal becoming less
abundant the more distant from the source (red line). The bottom
panel illustrates the reaction of the relevant midbrain and hindbrain
territories. They become regionalized in a steplike fashion into diverse
anteroposterior subdivisions characterized by differential molecular
identities and correlative structural differences. The general fates are
identified. The dashed line in r1 marks its internal subdivision into
rostral and caudal parts. CbVermis, vermis of cerebellum; CbHem,
hemisphere of cerebellum; IC, inferior colliculus; InC, intercollicular area;
IOrg, isthmic organizer; r1, rhombomere 1; r2, rhombomere 2; SC,
superior colliculus; TG, tectal gray.
telencephalic and cerebellar formations, and the massive

growth of the thalamus and the pons cause various topographic distortions tending to obscure the primary framework
of orthogonal natural limits. Genoarchitectonic studies often
are able to identify gene expression patterns that relate to the
cryptic schema of primary regionalization.
Developmentally fixed molecular boundaries thus represent natural limits that usually are strongly conserved over
evolutionary time, due to natural selection of relevant genomic
canalization, redundant gene pathways, or other sorts of morphogenetic buffering (Waddington, 1940, 1975). Ideally, we
are interested in defining all brain boundaries in terms of such
primary (neuroepithelial) or secondary (neuronal) natural
limits; thus tracing back to early patterning causes the complexities of adult structure. In practice, however, we deal with a
number of neuroanatomical boundaries that were first defined
by scholastic authority or convention among peers in historical
213
periods in which available causal molecular knowledge was

nearly nonexistent. Sometimes we already have strong molecular evidence against some of these traditional limits or
anatomical conceptions, but, as would be expected, the established view is slow to pass into obsoleteness. The dogmatic
weight of tradition also bears on widespread misconceptions
about the definition of the AP and DV dimensions of the adult
brain, notably the neural length axis. These are concepts that
are eminently susceptible of a natural molecular causal definition, with obvious advantages in terms of explanatory power. It
is therefore convenient to examine the implications of modern
genoarchitectonic data on these general issues, since they may
fail to support long-held anatomical beliefs. On the other
hand, continued credit given to traditional boundaries unsupported by modern molecular data clearly handicaps scientific
progress, at least by blinding the believer to alternative interpretations of data and better planning of experiments.
As a consequence of the new molecular scenario, the field of
neuroanatomy is moving away from the columnar brain model,
which has dominated the field for the last 100 years (Herrick,
1910; Kuhlenbeck, 1927, 1973; Swanson, 2012). This popular
paradigm has not stood the test of developmental gene patterns, many of which do not agree in topography, mutual
relationships, or causal correlations with the predictions of
this model (e.g., it is no longer possible to imagine the hypothalamus as a ventral part of the diencephalon; see Puelles,
Martinez-de-la-Torre, Bardet, & Rubenstein, 2012). In retrospect, the columnar model was originally proposed in order
to accommodate apparent functional brain subdivisions
implicit in the diverse motor and sensitive components of the
cranial and spinal nerves and their related neuronal columns
in the brain stem that Herrick (1910) attempted to extrapolate
into the forebrain. Unfortunately, he could not attend to any
developmental regional patterning phenomena because they
were unknown at the time.
In contrast, interest has increased recently in the prosomeric
brain model (Figures 3(a), 3(b) and 4; Puelles, 2013; Puelles,
Harrison, Paxinos, & Watson, 2013; Puelles, Martnez, Martnezde-la-Torre, & Rubenstein, 2004; Puelles et al., 2012; Puelles,
Martnez-de-la-Torre, Paxinos, Watson, & Martnez, 2007;
Puelles & Rubenstein, 1993, 2003), which represents a corrected
and expanded version of older neuromeric paradigms. This sort
of model includes causally, molecularly, and fate-defined transverse developmental units (neuromeres) forming a series along
the AP axis as well as orthogonally intersecting longitudinal
zones distributed along the DV dimension; in this model, the
neural axis is explicitly defined by keeping track of the cephalic
and cervical axial flexures of the neural tube and the causal
inductive relationship of the neural tube with the axial mesoderm. The prosomeric axis ends in the hypothalamus, whereas
the columnar axis was postulated to end in the telencephalon
(there is now substantial experimental and evolutionary evidence that the telencephalic vesicles are secondary outgrowths
emerging dorsally from the primordial alar hypothalamic
region). The structural framework of brain regions emphasized
by the prosomeric model presently seems massively consistent
with known gene patterns and patterning mechanisms across all
vertebrates (e.g., Figure 3(a) and 3(b)).
The forebrain, midbrain, and hindbrain brain parts are thus
visualized as divided into transverse units known as segments
214
(a)
Tbr1
Otp/Sim1
Dl5
Gb2
Pa3/Pa7
Pallium
E
ch
Hb
Pallial A
Subpall. A
St
ALON
EPH
NC TH
IE
p2
ZL
PTh p3 ZI
Pa
Subpallium
Septal
roofplate
PRM
PB
RTu
hp1
SPa
POA hp2
ac
VMH
AH
AB
(b)
m2
RP
alarbasal limit
FP
Cephalic
STh
Rt
Dg
m1
ita nigra
tan
bs
Su
PThE
Pal
MES
PT
p1
PHy flexure
THy
RM
Mam
PM
Tu
Arc
Limit of median
acroterminal
region
NHy
Eye SCH
Figure 3 Panel (a) illustrates an example of a developmental genoarchitectonic ISH mapping (the gen Enc1; blue signal), which is counterstained by
immunohistochemistry of calbindin (brown signal); note that both labels complement each other in regional distribution, emphasizing various
anteroposterior and dorsoventral limits. The sagittal section is of an E12,5 mouse embryo, and the forebrain (the telencephalon, hypothalamus, and
diencephalon, as defined in the prosomeric model; see (b)), midbrain, and rostral hindbrain enter into the frame. The major anatomical regions are
identified, aiming for comparison with the bottom panel. Panel (b) shows the prosomeric model for this area of the brain, illustrating the length axis as
revealed by the roof and floor plates (both in gray) and the alarbasal boundary (red line); the zona limitans interthalamica singularity (ZL; zli
marked by Enc1 in (a)) represents another secondary organizer the middiencephalic one which is important for prethalamic and thalamic patterning.
Note also the dorsoventral continuity of the telencephalon and the hypothalamus and the more caudally placed diencephalon (extending between
thicker black borders marked by arrows) and mesencephalon. Various gene expression patterns appear color-coded (see upper right corner); obviously,
the Enc1 pattern shown in (a) does not underline all details contemplated on the model, but is visibly consistent with it on the whole.
or neuromeres (5 prosomeres, 2 mesomeres, and 12 rhombomeres, respectively). This subdivision into transverse units is
fundamentally metameric, insofar as neuromeres share their
primary DV structure (floor, basal, alar, and roof plates).
Adult Genoarchitectonic Brain Maps

The discrete regional expression of many gene patterns, interpretable within the prosomeric model of brain structure, opens
a vast scenario of possibilities for genoarchitectonic brain
maps (Hawrylycz et al., 2011; Thompson et al., 2014; see the
Allen Developing Mouse Brain Atlas; developingmouse.brainmap.org).
On one hand, some of the transcription factors and other

markers that originally characterized the appearance of
anatomical boundaries during early developmental stages
maintain identical or directly related adult patterns of expression, so that many adult neuroanatomical boundaries can be
delineated by genoarchitectonic evidence. The discriminative
power offered by ISH of gene expression is clearly above that of
standard cytoarchitecture, since it reaches cellular levels of
resolution, and often also improves over histochemical or
immunohistochemical delimitation. The latter approaches
nevertheless represent excellent counterstains for the ISH
(Figure 3(a)).
Various public databases presently offer for inspection and
downloading extensive collections of gene expression patterns
215
Figure 4 This image corresponds to one of the sections used for the P56 reference atlas of the Allen Developing Mouse Brain Atlas and illustrates how
a sagittal section through the adult mouse brain would start to be interpreted using the prosomeric model (only the alarbasal border and the
interprosomeric limits are delineated), in order to map any gene expression studied in this database at this section level.
in the developing and/or adult mouse brain (also other species, including man and some nonmammals). These important
data sets are often correlated with anatomical reference atlases
(caution needs to be recommended in their use, due to the
persistence of the obsolete columnar brain model; so far, only
the Allen Institute for Brain Science offers the prosomeric
model in its developmental atlas (Figure 4), though not consistently in all its atlases; it is important that the user develops
his or her own interpretive criteria, preferably keeping in mind
relevant developmental data, and does not blindly confide in
the authority of experts that leave developmental advances
aside). There is also very useful data-mining software associated to these repositories, which allow searching the databases
in various ways, including relative position, coexpression, and
time dynamics. In this way, it has been possible to identify
layer-specific gene markers in the cerebral cortex and investigate fine molecular subdivisions in many regions of the brain.
Unfortunately, some of the early developmental expression
patterns fade out during the postnatal period. Specific studies
are then needed to determine which are the new relevant
genoarchitectonic markers at these sites, in order to retrace
the cryptic boundary. These are normally represented by differentiation markers of the boundary-related neurons or glia or
by genes that control differential aspects of the local adult
functional molecular phenotype. Fate-mapping results and
transgenic analysis of the progeny of given molecularly defined
progenitor domains serve to corroborate such analyses.
Genes coding for neurotransmitter- and peptide-characteristic
markers can be efficiently mapped genoarchitectonically, as well
as those coding for the rich variety of transporters, channels, and
receptors, plus the cascades of intermediate messengers and regulators of biochemical events at the cell membrane, cytoplasmic
matrix and organelles, or the cell nucleus. Markers associated to
connective cells, meninges, blood vessels and blood-derived cells,
melanocytes, glial cell types, tanycytes, and various circumventricular organs can be used as well in genoarchitectonic mappings.
Finally, genoarchitectonic maps allow nowadays the development of transgenic tools by which injected substances can be
precisely targeted to molecularly defined brain areas, so that the
projections of given neurons can be specifically studied. These
are just some examples of many other technical breakthroughs
that are emerging as genoarchitectonic maps develop their scientific potential. Application of these maps to clinical issues is still
in its infancy, though some correlations are starting to appear.
For instance, interventional radiological neurosurgeons are finding that sectors of the cerebral cortex that were originally delimited genoarchitectonically in embryos seem relevant to
understand the characteristic spatial distributions of arteriovenous malformations they need to treat surgically in their patients.

Development of the Diencephalon; Myeloarchitecture and Maps of the
Cerebral Cortex; Transmitter Receptor Distribution in the Human Brain;
INTRODUCTION TO METHODS AND MODELING: Integrative
Computational Neurogenetic Modeling; Modeling Brain Growth and
Development; Tissue Classification; Topological Inference.
References
Ferran, J. L., Dutra de Oliveira, E., Sanchez-Arrones, L., Sandoval, J. E.,
Martnez-de-la-Torre, M., & Puelles, L. (2009). Genoarchitectonic analysis of
regional histogenesis in the chicken pretectum. The Journal of Comparative
Neurology, 517, 405451.
Hawrylycz, M., Baldock, R. A., Burger, A., Hashikawa, T., Johnson, G. A., Martone, M.,
et al. (2011). Digital atlasing and standardization in the mouse brain. PLoS
Computational Biology, 7(2), e1001065.
216
Herrick, C. J. (1910). The morphology of the forebrain in amphibia and reptilia.

Kuhlenbeck, H. (1927). Vorlesungen uber das Zentralnervensystem der Wirbeltiere.
Jena: Gustav Fischer.
Kuhlenbeck, H. (1973). The central nervous system of vertebrates, Vol. 3, part II: Overall
morphological pattern. Basel: Karger.
Lauter, G., Soll, I., & Hauptman, G. (2011). Multicolor fluorescent in situ hybridization
to define abutting and overlapping gene expression in the embryonic zebrafish
brain. Neural Development, 6, 10.
Puelles, L. (2013). Plan of the developing vertebrate nervous system relating
embryology to the adult nervous system (prosomere model, overview of brain
organization). In: J. L. R. Rubenstein & P. Rakic (Eds.), Comprehensive
developmental neuroscience: Patterning and cell type specification in the
developing CNS and PNS (pp. 187209). Amsterdam: Academic Press.
Puelles, L., & Ferran, J. L. (2012). Concept of genoarchitecture and its genomic
fundament. Frontiers in Neuroanatomy 6, 47. http://dx.doi.org/10.3389/
fnana.2012.00047. eCollection 2012.
Puelles, L., Harrison, M., Paxinos, G., & Watson, C. (2013). A developmental ontology
for the mammalian brain based on the prosomeric model. Trends in Neuroscience,
36, 570578.
Puelles, L., Martnez, S., Martnez-de-la-Torre, M., & Rubenstein, J. L. R. (2004).
Gene maps and related histogenetic domains in the forebrain and midbrain.
In G. Paxinos (Ed.), The rat nervous system (3rd ed., pp.325). San Diego, CA:
Academic Press.
Puelles, L., Martinez-de-la-Torre, M., Bardet, S., & Rubenstein, J. L. R. (2012).
Hypothalamus. In C. Watson, G. Paxinos & L. Puelles (Eds.), The mouse nervous
system (pp. 221312). London: Academic Press/Elsevier, Chapter 8.
Puelles, L., Martnez-de-la-Torre, M., Paxinos, G., Watson, C., & Martnez, S. (2007). The
chick brain in stereotaxic coordinates: An Atlas featuring neuromeric subdivisions and
mammalian homologies. San Diego, CA: Elsevier/Academic Press.
Puelles, L., & Rubenstein, J. L. R. (1993). Expression patterns of homeobox and other
putative regulatory genes in the embryonic mouse forebrain suggest a neuromeric
organization. Trends in Neurosciences, 16, 472479.
Puelles, L., & Rubenstein, J. L. R. (2003). Forebrain gene expression domains and the
evolving prosomeric model. Trends in Neurosciences, 26, 469476.
Swanson, L. W. (2012). Brain architecture: Understanding the basic plan (2nd ed.).
Thompson, C. L., Ng, L., Menon, V., Martinez, S., Lee, C.-K., Glattfelder, K., et al.
(2015). A high resolution spatiotemporal atlas of gene expression of the C57Bl/6J
developing mouse brain. Neuron, 83, 309323.
Waddington, C. H. (1940). Organisers and genes. Cambridge: Cambridge University
Press.
Waddington, C. H. (1975). The evolution of an evolutionist. Edinburgh: Edinburgh
University Press, pp. 99102.
Basal Ganglia
A Wree, University Medical Center Rostock, Rostock, Germany
O Schmitt, University Medical Center Rostock, Rostock, Germany
Glossary
Aspiny neurons Is a population which is subdivided into

4 populations of interneurons. The cholinergic
subpopulation (aspiny type II neurons). GABAergic
parvalbumin expressing interneurons. GABAergic nitric
oxide synthase and somatostatin expressing interneurons.
GABAergic calretinin expressing interneurons.
Caudate-Putamen A complex of the nuclues caudatus and
the putamen which exists in laboratory rats and mice.
Direct pathway Striatum ! SNr/GPi ! Thalamus.
Hyperdirect pathway Motor cortex ! STN ! GPi !
Thalamus.
Abbreviations
AChE
ChAT
DARPP-32
DR1
DR2
GPe
GPi
MSN
nc
Acetylcholine esterase
Choline acetyl transferase
DA- and cAMP-regulated phosphoprotein
32 kDa
D1 dopamine receptor
D2 dopamine receptor
Globus pallidus pars externa (external
segment)
Globus pallidus pars interna (internal
segment)
Medium spiny neuron of Str
Nucleus
Introduction
As early as 1664, the anatomist Thomas Willis separated a
subcortical region from the lateral ventricle and thalamus and
named it the corpus striatum (Willis, 1664, p. 167; Figure 1).
Later on, Parent (1986) introduced the term basal ganglia
for the corpus striatum and further subcortical nuclear regions.
According to structural, functional, chemoarchitectonic, and
hodologic properties, the basal ganglia include the corpus
striatum (the caudate nucleus and putamen, often also termed
as the neostriatum), nucleus accumbens (part of the ventral
striatum), globus pallidus (external and internal segments),
nucleus subthalamicus, and substantia nigra pars compacta
(SNc) and pars reticulata (some publications also include the
amygdaloid body and the claustrum). The basal ganglia, which
are massively influenced by widespread cortical afferents,
process and modulate motivated and goal-directed behaviors,
as their circuits project back primarily to the motor cortex
(Alexander & Crutscher, 1990; Alexander, DeLong, & Strick,
1986). With regard to the processing of motor signals, the
Indirect pathway Striatum ! GPe ! STN! GPi !

Thalamus.
Matrix Acetylcholine esterase rich regions within the
striatum.
Medium spiny neurons Consists of two populations. The
direct pathway population expresses the excitatory
dopamine 1 receptor, substance P and dynorphin. The
indirect pathway population expresses the inhibitory
dopamine 2 receptor and enkephalin.
Neostriatum Nucleus caudatus and putamen.
Striosome (Patch) Acetylcholine esterase poor regions
within the striatum.
NC
NOS
P
PAN
PD
PPN
PV
Str
SNc
SNr
STN
TAN
VTA
Caudate nucleus
Nitric oxide synthase
Putamen
Phasically active neuron
Parkinsons disease
Pedunculopontine nucleus
Parvalbumin
Striatum
Substnatia nigra pars compacta
Substnatia nigra pars reticulata
Subthalamic nucleus
Tonically active neuron
Ventral tegmental area
integration of special thalamic nuclei and cortical regions

(i.e., the agranular lateral cortex) into the basal ganglia network is mandatory. Thus, various basal ganglia circuits (basal
ganglia thalamocortical circuits) can be separated as functional
entities: motor, oculomotor, dorsolateral prefrontal, lateral
orbitofrontal, and anterior cingular basal ganglia circuits or
loops, originally described in the rhesus monkey by
Alexander et al. (1986). However, basal ganglia circuits represent only a small amount of known connections involving the
basal ganglia. Numerous ipsilateral and contralateral intrinsic
connections, as well as extrinsic inputs and outputs to and
from regions outside the basal ganglia, are known.
The striatum can be divided into a larger dorsal and a smaller
ventral part. The ventral striatum (also termed as the paleostriatum) is distinguished by its partially different anatomy and
function. The ventral striatum includes the nucleus accumbens
(divided to inner core and outer shell), the most rostroventral
portions of the caudate and putamen, and the striatal cells of the
olfactory tubercle and the anterior perforated substance (Heimer
et al., 1999). The ventral basal ganglia consist of the ventral
http://dx.doi.org/10.1016/B978-0-12-397025-1.00215-3
217
218
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Basal Ganglia
Figure 1 Cover page of the book Cerebri Anatome of Thomas Willis and the first published illustration of the corpus striatum (A) on page 167. The
legend to A says the following: Corpus striatum in medio discissum, ut illius stria medullares appareant.
striatum or nucleus accumbens; the ventral pallidum, which is

the ventral and medial extremes of the external and internal
pallidal segments; and the ventral tegmental area (VTA), which
is a medial continuation of the dorsal SNc (Fudge & Haber,
2002). The ventral basal ganglia are primarily associated with
cognitive and limbic functions and play a key role in cognitive
and emotional behaviors, including learning and memory,
reward, reinforcement, addictive behavior, and habit formation.
Accordingly, the ventral striatum is the only basal ganglia territory that receives subcortical input from the amygdala and the
hippocampus (Fudge, Kunishio, Walsh, Richard, & Haber,
2002; Haber, Lynd-Balta, & Mitchell, 1993).
Although historically the basal ganglia were primarily
known for their executive motor functions as obviously seen
in neurodegenerative diseases (Parkinsons disease (PD) and
Huntingtons chorea), it became clear that the basal ganglia
were also involved in motor planning and in sensorimotor
integration (DeLong & Georgopoulos, 1991; Marsden, 1984).
More recent studies also speak of an involvement of the basal
ganglia in associative, cognitive, and limbic functions (Aron,
Poldrack, & Wise, 2009) and also in autonomic functions via
the hypothalamic system. The basal ganglia are therefore
involved in all processes that result in goal-directed behaviors
through movements including motivation, emotions,
cognition, and learning (Boraud, Bezard, Bioulac, & Gross,
2002). Noteworthy, this complexity is mirrored by the respective symptoms in neurodegenerative diseases (Kliem &
Wichmann, 2009; Nelson & Kreitzer, 2014).
Most studies on the neuroanatomy and neurophysiology of
the basal ganglia were done in rats and mice and some in
primates. This article tries to focus on primates and humans,

with rodent studies included when necessary.
Topography of the Basal Ganglia

The striatum is divided by the internal capsule into the caudate
nucleus and putamen. The caudate nucleus lies medial to the
internal capsule, while the putamen is located lateral to it (Mai,
Paxinos, & Voss, 2008; Nieuwenhuys, Voogd, & van Huijzen,
2008) (Figure 1). During embryological growth of descending
cortical fiber bundles through the striatum, some bridges of
gray matter still remain, and as a result, the two parts of the
striatum are not completely separated (caudolenticular gray
bridges) (Figure 2).
The caudate nucleus consists of an anterosuperior massive
head, a narrower body (corpus) at the level of the interventricular foramen and the thalamus, and a C-shaped tail (Latin
cauda), which without clear border to the corpus tapers rostrally and merges with its extremity (anterior tip) the amygdaloid body. The head and the body of the caudate lie adjacent to
the lateral floor of the anterior cornu and central part of the
lateral ventricle. The tail of the caudate continues adjacent to
the surface of the C-shaped ventricle, which follows into the
roof of its inferior cornu (Figure 1). Separated by the internal
capsule, the caudate nucleus curves around the putamen. At
the anterior extension, which is at the level of the anterior
perforated substance, the head of the caudate nucleus fuses
with the putamen.
219
Figure 2 The basal ganglia are shown in histological sections of a human brain dataset of Amunts et al. (2013) in neuroVIISAS (Schmitt & Eipert, 2012)
(http://neuroviisas.med.uni-rostock.de/neuroviisas.html). (a) A frontal section through the human brain depicting the rostral part of the striatum
with NCc and P, both incompletely separated by the internal capsule leaving caudolenticular gray bridges. Further details of the basal ganglia more
rostral than the level of (a) are given in (b) and details of the basal ganglia more caudal in (ce). ACb, accumbens nucleus; CGB, caudolenticular gray
bridges; GPe, globus pallidus pars externa; GPi, globus pallidus pars interna; IC, internal capsule; NCc, caput nuclei caudati (head); NCcp, corpus
nuclei caudati (body); NCcd, cauda nuclei caudati (tail); P, putamen; SN, substantia nigra pars compacta and pars reticulata; STN, subthalamic nucleus;
VL, ventrolateral thalamic nucleus; MD, mediodorsal thalamic nucleus.
The so-called lentiform nucleus consists of the putamen

and the medially situated globus pallidus. The term lentiform
nucleus is indelible, although not very useful. Here, two structures are put together that have different embryological origins
(the putamen from the telencephalic anlage and globus pallidus from the diencephalic anlage) and different cellular
compositions.
In frontal or horizontal sections, the lentiform nucleus lies
laterally to the internal capsule and appears like a cone of an
onion with three shells: (1) a darker outer zone (putamen)
followed medially by (2) the lighter tinted globus pallidus, first
by the external pallidal segment and then by the internal
pallidal segment, with the external and internal segments
separated by (3) a narrow lamina medullaris medialis (internal

medullary lamina). The lamina medullaris lateralis is found
between the putamen and the external pallidal segment.
The subthalamic nucleus (STN) and the substantia nigra
can be considered as intrinsic nuclei of the basal ganglia.
The substantia nigra is part of the tegmentum of the midbrain, extending throughout its whole length, and is divided
into a compact part and a reticular part. The compact part,
which can be seen already with the naked eye in transverse
sections of the mesencephalon, is composed of medium-sized
mostly pigmented (neuromelanin) multipolar neurons. Ventral to the compact part is the reticular part. The reticular part
contains smaller mostly unpigmented neurons and is limited
220
by a blurred border to the crus cerebri where processes of the

gray matter extend between and intermingle with the descending fibers of the adjacent cerebral peduncle. The reticular part
extends more rostrally than the compact part into the subthalamic region where it lies close to the internal segment of the
globus pallidus (both structurally similar and both nuclei containing a significant amount of iron and GABAergic projection
neurons having comparable efferences).
The STN as part of the diencephalon is a small lentil-like
gray matter lying dorsal and medial to the substantia nigra with
a partial rostrocaudal overlap of the nuclei. The STN is recognized in fixed brain sections by its light brown color and
demarcated by the fasciculus lenticularis (superior), the zona
incerta (posteroinferior), and the crus posterior of the internal
capsule (anterolateral, separating it from the medial aspect of
the globus pallidus).
Cytoarchitecture of the Basal Ganglia

The various basal ganglia nuclei contain numerous cell types
that are divided into two general groups: projection neurons
and interneurons.
Striatum: Cell Types and Intrinsic Organization

In cresyl violet-stained sections, the number of small to medium
striatal neurons per hemisphere averaged in 100 million for
males and 105 million for females. For the large striatal cells
(most probable cholinergic interneurons), the respective means
were 670 000 in males and 570 000 in females (Schroder, Hopf,
Lange, & Thorner, 1975). More specifically, in the human
putamen, 80 million neurons per hemisphere were estimated
stereologically (Schmitt, Eggers, & Haug, 1995).
The principal neuron of the striatum is the medium-sized
densely spiny neuron (medium spiny neuron, MSN) (DiFiglia,
Aronin, & Martin, 1982; DiFiglia, Pasik, & Pasik, 1976). This
projection neuron accounts for about 75% of striatal neurons
in man and is characterized by a perikaryon diameter of about
1020 mm with 47 radiating dendrites, which are densely
packed with 10 00015 000 spines per neuron, contacted at
their heads by corticostriatal afferents mostly from cortical
layer 5 pyramidal neurons of practically all cortical areas (however with very different densities). Other inputs are derived
from the thalamus (associated with sensory, motor,
association, and limbic systems; intralaminar nuclei; and specific thalamic nuclei) (Galvan & Smith, 2011; Gerfen & Wilson,
1996; McFarland & Haber, 2000; Sidibe & Smith, 1996; Smith
et al., 2009, 2014), the brain stem (dopaminergic from the
SNc, serotonergic from the dorsal and medial nuclei raphe, and
noradrenergic from locus coeruleus), and cholinergic striatal
interneurons and from local collaterals of other MSNs (Haber
& Gdowki, 2004). GABA is the main transmitter of MSNs,
which express striatal signaling protein DA- and cAMPregulated phosphoprotein 32 kDa (DARPP-32). MSNs are subdivided into two major subpopulations of approximately
equal number based on their neurochemical content, main
projection region, and pattern of axonal collateralization
(Bolam, Brown, Moss, & Magill, 2009; Cepeda et al., 2008).
One subpopulation gives rise to efferents forming the direct
pathway, which preferentially project to the output nuclei of

the basal ganglia, the globus pallidus pars interna (GPi), and
the substantia nigra pars reticulata (SNr) (but also send a few
collaterals to the globus pallidus pars externa (GPe) and SNc)
(Figures 3 and 4). They selectively express substance P, dynorphin, and D1 dopamine receptors (Haber & Watson, 1985).
The axons of the second subpopulation form the indirect
pathway. They project to the GPe and co-contain enkephalin
and express D2 dopamine receptors (Figure 5). Both populations also exhibit local axon collaterals, targeting mainly onto
other MSNs and interneurons (Smith, Bevan, Shink, & Bolam,
1998). Not only mostly spine necks but also dendrites of the
MSNs are targeted by the dopaminergic axons from the SNc
that densely innervate the striatum (Bateup et al., 2010; Gerfen
& Surmeier, 2011; Wilson, 2004).
In monkeys, MSNs are phasically active neurons (PANs).
Phasically active neurons have a very low spontaneous discharge rate (0.51 spike s1) but a relatively high phasic firing
rate associated with behavioral tasks, such as movements,
preparation for movements, and the performance of learned
tasks.
The remaining about 25% neurons of the striatum are
aspiny interneurons (Kawaguchi, 1997; Kawaguchi, Wilson,
Augood, & Emson, 1995). At least four populations of interneurons exist, with three of them being GABAergic
interneurons and one being cholinergic. The large cholinergic
interneurons (aspiny type II neurons, diameter 2035 mm,
choline acetyltransferase (ChAT)-immunoreactive) only
account for about 1% of all striatal neurons. Those interneurons have 314 long and frequently branching dendrites that
cover a large field of 700800 mm in diameter and exhibit an
extensive axonal field (DiFiglia & Carey, 1986). It is hypothesized that cholinergic interneurons play an important role in
integrating inputs between functional and compartmental
regions of the striatum (Holt, Graybiel, & Saper, 1997; Holt,
Hersh, & Saper, 1996; Pisani, Bernadi, Ding, & Surmeier,
2007). Such a connectivity suggests an interaction of functionally intertwined regulatory system (Calabresi, Picconi, Tozzi,
Ghiglieri, & Di Filippo, 2014). These interneurons receive
input from the cortex, thalamus, and MSNs and in turn innervate MSNs at their cell bodies and proximal dendrites. As they
are also heavily innervated by dopaminergic terminals from
the SNc and express D2 receptors, they play a key role in
parkinsonism (Figure 5). In PD, massively reduced dopaminergic input is followed by an increased firing rate and release
of acetylcholine, which in turn stimulates MSNs.
The striatum additionally contains three types of relative
small- to medium-sized (perikaryal diameter 1025 mm)
GABAergic interneurons: (1) parvalbumin (PV)-positive
interneurons (fast-spiking), (2) nitric oxide synthase (NOS)/
somatostatin-expressing interneurons, and (3) calretininexpressing interneurons (Bernacer, Prensa, & Gimenez-Amaya,
2012). The 25 profusely branched primary dendrites receive
major inputs from the cortex, the specific and unspecific thalamic nuclei, and dopaminergic input from the SNc (in the rat
also from GPe neurons); they give inhibitory input to the MSNs
(for review, see Holt et al., 1997).
In primates and in humans, but not in rodents, a significant
number of small (812 mm) dopaminergic neurons exist at the
dorsal, lateral, and ventral borders of the caudate and
Striatum
SNr
Primary
motoric
cortex
Medium spiny neurons

Excitatory
D1 receptors
Thalamus
Ventral nuclei
Ventrolateral nc.
Ventromedial nc.
SNc
STN
Medium spiny neurons
Secondary
motoric
cortex
Intralaminary nuclei
Parafascicular nc.
Central medial nc.
Central lateral nc.
Direct pathway
GPi
Motoric
corticostriatal
output
221
Indirect pathway
GPe
Inhibitory
D2 receptors
Hyperdirect pathway
Figure 3 Summary of the so-called motor basal ganglia pathways in a simplified block diagram of the principal connections. The nuclei of the basal
ganglia, the striatum, the external segment of the globus pallidus (GPe), the internal segment of the globus pallidus (GPi), the substantia nigra pars
reticulata (SNr), the substantia nigra pars compacta (SNc), and the subthalamic nucleus (STN) are shown in their main connections with the motor
cortex and thalamus. The two major inputs to the striatum come from the cortex and the thalamus (intralaminar nuclei and ventral nuclei). The SNr
and GPi built up the output nuclei of the basal ganglia, projecting as part of the loop to thalamic nuclei. Dopaminergic neurons of the SNc are reciprocally
connected to the striatum (other SNc efferents are not depicted in this scheme) and modulate cortical and thalamic information flow through the
striatum. In the direct pathway, the information flow leads to a disinhibition of thalamus. The indirect pathway from the striatum through the GPe and
STN to GPi/SNr results in a reduced disinhibition and a reduced thalamic stimulation of the motor cortex and the striatum. The STN also receives
cortical input, forming the hyperdirect pathway. The arrows indicate the direction of the projection and the principal transmitters used by the respective
projection neurons: green, glutamatergic; red, GABAergic; yellow, dopaminergic. GPe, globus pallidus pars externa; GPi, globus pallidus pars
interna; nc, nucleus; SNc, substantia nigra pars compacta; SNr, substantia nigra pars reticulata; STN, subthalamic nucleus.
putamen. Little is known about this cell type as it is not found

in rat and mouse. The same holds true for the very few dopaminergic neurons in human striata (Bernacer et al., 2012).
Specific histochemical features of the striatum are the
clusterings of neurons (cell islands) and discontinuities of
the neuropil, which can be observed by analyzing histochemical distribution of acetylcholine esterase (AChE) reactivity (Yeterian & Pandya, 1998). AChE-poor striatal regions
(striosomes, or patches) are embedded in a densely stained
AChE matrix. Moreover, striosomes have dense opiate receptor.
Interneurons and especially their dendrites cross the borders
between striosomes and matrix. The functional significance of
this compartmental organization including partly different
input/output characteristics is still not resolved.
Pallidal Complex: Cell Types and Intrinsic Organization

The pale impression of the globus pallidus in macroscopic
sections is based on the low perikaryal density, the elaborated
dendritic fields of large projection neurons, and the abundant
myelinated striatopallidal axons.
In humans, the average total number of GPe neurons is
calculated in the range of 11.46 million, while the number
of the GPi is in the range of 310 000350 000 (Thorner, Lange,
& Hopf, 1975). The morphology of neurons in the globus
pallidus is rather uniform. The main cell type of the globus

pallidus is a relatively large GABAergic neuron (perikaryal
diameter 2060 mm) with triangular or polygonal cell body
giving rise to thick, sparsely spined, poorly branching dendrites
(Braak & Braak, 1982). The dendrites can cover a field up to
2 mm in their principal plane, and their very distal portions
form complex dendritic endings. Dendrites of the large pallidal
neurons form a disklike territory oriented perpendicular to
incoming striatal fibers. Thus, a large pallidal neuron is innervated by a group of striatopallidal afferents (compare neuronal
numbers of striatum and GP). Myelinated striatal axons give
off thin unmyelinated collaterals forming symmetrical synapses with pallidal neurons. In the GPe, these axons and terminals are immunoreactive for encephalin, in the GPi for
substance P. Besides striatal afferents, GP neurons receive
input from the STN and from axon collaterals of other pallidal
neurons.
GPe neurons project to the topographically related territories of the STN via the subthalamic fasciculus and the SNr
(and the SNc and striatum, at least in the rat) (Sato, Lavallee,
Levesque, & Parent, 2000) (Figures 35).
GPi neurons project to various thalamic nuclei depending
on the functional source of striatal input: Somatosensoryrelated striatal input is transferred to the ventrolateral thalamic
nucleus (oral part), input from association areas of the
222
AGI
GPe
Str
GPi
STN
SNc
SNr
Figure 4 Much of the intrinsic connectivity of the basal ganglia has been
revealed in the laboratory rat as shown in the wiring diagram. Many
reciprocal connections are described in publications applying anterograde
and retrograde tract tracing methods. These data were collected and
represented in this overview diagram using neuroVIISAS (Schmitt &
Eipert, 2012). AGl, agranular lateral cortex (M1); GPe, globus pallidus pars
externa; GPi, globus pallidus pars interna; SNc, substantia nigra pars
compacta; SNr, substantia nigra pars reticulata; STN, subthalamic nucleus;
Str, striatum; T, thalamus.
striatum is transferred to the ventroanterior (parvocellular

part) and mediodorsal thalamic nucleus, and limbic striatal
input is transferred to the mediodorsal thalamic nucleus and
the lateral habenula (Baron, Sidibe, DeLong, & Smith, 2001;
Goldman-Rakic & Porrino, 1985). On the way to the thalamic
relay nuclei, GPi fibers also give off collaterals that innervate
the intralaminar nuclei (centromedian and parafascicular
nuclei) (Sidibe, Pare, & Smith, 2002). Projections of GPi also
go to tegmental structures involved in locomotion and posture
control (parvocellular reticular formation and the pedunculopontine nucleus (PPN)).
For the understanding of the microcircuitry, it is important
to know that the GABAergic large pallidal neurons are tonically
active cells, that is, having a high resting discharge.
Additional to the majority of neurons (large projecting
neurons), presumably interneurons, were found, one type
called microneuron and the other type medium-sized. All
these neurons are GABAergic, coexpressing either the calciumbinding protein parvalbumin or calbindin. Their role in the
microcircuitry is not fully understood at present.
Subthalamic Nucleus: Cell Types and Intrinsic Organization

In humans, the average total number of STN neurons is calculated in the range of 560 000870 000 (Lange, Thorner, &
Hopf, 1976). The STN mainly consists of multipolar,
pyramidal, or round perikarya (diameter about 3040 mm)
that extend their 48 dendrites in the principal plane of the
nucleus. Their dendrites have few to many spines, are
extensively branched, and cover large fields of the nucleus.

Their axons emerge from the soma and mostly bifurcate: One
axon collateral ascends to the globus pallidus, and the other
axon collateral descends to SNr (Sato, Parent, Levesque, &
Parent, 2000). The STN neurons employ glutamate as transmitter (Figure 5).
The STN receives major inhibitory input from the GPe
(Figure 5). These projections terminate in a functionally topographic manner. Two other important inputs to the STN are
derived from the cortex (the motor, premotor, and prefrontal
cortices; these projections are also topographically organized
and forming the hyperdirect pathway) and the intralaminar
thalamic nuclei (Nambu, 2009; Nambu, Tokuno, & Takada,
2002; Nambu et al., 2000). The corticosubthalamic and the
thalamosubthalamic axon terminals are glutamatergic and
form asymmetrical synapses with small-diameter dendrites.
Further input to STN neurons derives from dopamine neurons
of the SNc (the loss of inhibitory dopaminergic action via D2
receptors in PD patients in the STN could account for its
hyperactivity), serotonergic neurons from the dorsal raphe
nucleus, and cholinergic inputs of the PPN.
The main excitatory outputs of the STN go to the SNr and
GPi. Few and individual STN neurons innervate nerve cells in
the GPe, the PPN, and the SNc.
The STN neurons show a relatively high resting discharge
rate that can be modulated by inhibitory afferents mainly from
the GPe and excitatory inputs from the cortex and the intralaminar thalamic nuclei (Wichmann, Bergman, & DeLong,
1994). Those neurons have a very powerful and critical role
for the activity in basal ganglia output neurons (GPi and SNr).
This is clinically important for understanding deep brain stimulation given to this nucleus.
Substantia Nigra: Cell Types and Intrinsic Organization

The substantia nigra is subdivided on the basis of cytoarchitectonic and neurochemical criteria into the compact part (SNc)
and the reticular part (SNr). Moreover, inside the SNc, there are
three further subnuclei (see later in text). However, in humans, a
clear border between compact part and reticular part does not
exist because of the invasion of tyrosine hydroxylaseimmunoreactive neurons into the SNr (Olszewski & Baxter,
1982). In healthy humans, the average total number of pigmented neurons in the SNc is calculated in the range of
300 000550 000, while counts of nonpigmented neurons in
the SNr range 260 000280 000 (Hardman et al., 2002).
Substantia nigra pars reticulata (SNr)

Neurons of the SNr resemble those of the principal neurons of
the GPi: medium to large multipolar neuron (mean diameter
about 25 mm) with long, thick infrequently branching, aspiny
dendrites, which are almost completely covered with synaptic
contacts. These neurons use the transmitter GABA and lack
melanin. The connections of the SNr are also similar to those
of the GPi. SNr afferents originate mainly from the MSNs
(direct pathway), and the STN (indirect pathway) (Figures 3
and 5). The efferences of SNr neurons also resemble those
of the GPi, but do not exactly connect to the same subnuclei:
the nigrothalamic projections terminate (more rostrally than
the pallidothalamic projections) at the magnocellular part
223
Glut
AGI
DPW
GABA
DR1
ACh
Str
DR2
GABA
IPW
DR2
Glut
GABA
DA
GABA
Thalamus
GPi/SNr
SNc
GPe
Glut
STN
Figure 5 Neurotransmitters and dopamine receptors of the main projection neurons forming the direct (DPW) and indirect (IPW) pathways through
the basal ganglia. The arrows indicate the direction of the projection and the principal transmitters used by the respective projection neurons: green,
glutamatergic; red, GABAergic; yellow, dopaminergic; blue, cholinergic. ACh, acetylcholine; AGl, agranular lateral cortex (the primary motor cortex); DA,
dopamine; DR1, dopamine receptor 1; DR2, dopamine receptor 2; GABA, g-aminobutyric acid; Glut, glutamate; GPe, globus pallidus pars externa;
GPi, globus pallidus pars interna; SNc, substantia nigra pars compacta; SNr, substantia nigra pars reticulata; STN, subthalamic nucleus; Str, striatum.
of the ventroanterior nucleus (VAmc), the medial part of the

ventrolateral nucleus (VLm), and the paralaminar part of the
medial dorsal nucleus (MDpl) of the thalamus. These thalamic
nuclei project to the prefrontal cortex, frontal eye field, and
supplementary eye field, forming the prefrontal and oculomotor
loops. In contrast to the GPi, the SNr projects to the superior
colliculus (control of eye movements) (Hikosaka, Nakamura, &
Nakahara, 2006; Hikosaka & Wurtz, 1983). It is assumed that
the segregation of GPi and SNr resembles two main functions:
The SNr is involved in movements of the eyes, head, and neck,
and the GPi is involved in limb and axial movements, the latter
also called skeletal movements (Hikosaka, 2009).
Substantia nigra pars compacta

Besides a few small GABAergic neurons, most of the SNc neurons are dopaminergic (tyrosine hydroxylase-immunoreactive)
and melanin-rich. The melanin content increases and the number of neurons slightly decreases with normal age. The SNc is
divided into a (1) dorsal group, (2) a large densocellular
region, and (3) a ventral group exhibiting cell columns. Dopaminergic neurons of the densocellular region and ventral
group (often summarized as ventral tier) are much more
vulnerable in PD than those of the dorsal group and the
dopaminergic neurons of the VTA situated medial to the
SNc (the latter summarized as dorsal tier). This holds also
true for the N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine
(MPTP)-induced toxicity. The dorsal tier neurons express calbindin. The ventral tier neurons are calbindin-negative and
have high levels of neuromelanin, and their dendrites are
oriented ventrally and horizontally and occupy major portions of the pars reticulata. Furthermore, they express high
levels of dopamine transporter and D2 receptor mRNAs.
The relatively large multipolar SNc neurons (diameter
about 2545 mm) not only have long and spine-poor dendrites
mainly situated in the SNc but also extend into the SNr (Yelnik,
Francois, Percheron, & Heyner, 1987). They receive dense synaptic input from the striatal MSNs (GABA), the GPe (GABA),
the STN (glutamate), the PPN (acetylcholine), and dorsal
raphe nuclei (serotonin) (Figures 3 and 5). Axons leave the
SNc and mainly project to the striatum and via collaterals also
to GPe and STN and colliculus superior (Hedreen & DeLong,
1991). However, a dendritic release of dopamine is shown to
influence via D2 autoreceptors neighboring dopaminergic SNc
neurons. In the striatum, the axons of the SNc neurons ramify
massively giving rise to about 300 000 symmetrical synapses
that are located predominantly at the neck of various spines of
many MSNs in a topographic fashion.
Ventral tegmental area

Neurons found in the VTA resemble those of the dorsal tier of
SNc. VTA neurons primarily innervate the ventral striatum.
Basic Circuitry of Basal Ganglia

The roles of the basal ganglia are complex and include (1)
focused selection of intended movements (selection, initiation, inhibition, and termination) that have been learned by
repetition and training (writing, speech, eye movements, trunk
224
movements, mastication, vocalization, and habits); (2) learning, acquisition, and adjustment of new behaviors; and (3)
development of habits depending on reinforcement. The
basal ganglia can act in a very efficient way to select an appropriate action in a particular context (Hikosaka, 2009). Moreover, the basal ganglia also contribute to a wide range of
cognitive functions that drive behaviors. These functions
include learning, memory, skill, planning, switching, sequencing, timing, and the processing of rewards and other feedback.
The basal ganglia are parts of circuits or loops involved in
the chain cortexbasal gangliathalamuscortex; the basal
ganglia can be functionally grouped into four categories: (1)
input nuclei, the striatum and STN receiving cortical inputs;
(2) output nuclei, GPi and SNr projecting to the thalamus and
the brain stem; (3) connecting nucleus, GPe connecting the
input nuclei to the output nuclei; and (4) modulatory nucleus,
SNc modulating the activity of the basal ganglia (Figure 6).
Generally, the striatum as the input nucleus receives excitatory glutamatergic input from the cerebral cortex. Striatal projection neurons innervate the output nuclei, GPi/SNr, via two
different pathways: (1) the direct pathway (MSN with GABA,
substance P, and dynorphin project directly to the GPi/SNr) and
(2) the indirect pathway (MSN with GABA and enkephalin
project indirectly and polysynaptically to the GPi/SNr via the
Motoric, sensorimotoric
GPe and STN) (Albin, Young, & Penney, 1989; Anderson, 2009;
Baev et al., 2002; Kravitz, Tye, & Kreitzer, 2012).
Excitation of striatal neurons through the direct
monosynaptic pathway has inhibitory effects on GPi/SNr neurons. As GPi/SNr neurons are inhibited by the MSNs GABA,
they themselves release fewer GABA at their thalamic
terminals, thus allowing the thalamic nuclei project to cortical
areas and thereby increasing the excitatory influence on the
cortex. The behavioral results of this direct chain are locomotor
activation and movements. Excitatory signals of the striatal
neurons through the indirect pathway have excitatory effects
on GPi/SNr neurons because both striato-GPe and GPe-STN
projections are inhibitory (net effect is in a disinhibition of
GPi/SNr neurons) and STNGPi/SNr projections are excitatory. Subsequently, increased activity of GPi/SNr neurons
leads to increased GABA release in thalamic nuclei, the latter
leading to decreased thalamocortical excitatory projections. At
the end, this effect results in a reduction of locomotor activity
and movement.
Excitation from the cerebral cortex, additional to the basal
ganglia circuitry, is forwarded directly and with fast conduction
velocity to the STN in a somatotopically organized manner.
The STN can therefore also be considered an input nucleus of
the basal ganglia, forming a third pathway, the hyperdirect
Associative, cognitive
Limbic
Motor cortex
Oculomotor
cortex
Dorsolateral
prefrontal cortex
Orbital + medial
prefrontal cortex
Anterior
cingular cortex
Putamen
Central lateral
caput and corpus
nc. caudati
Dorsolateral
caput nc. caudati
Ventromedial
caput nc. caudati
Ventral striatum
vl GPi
cdm GPi
Idm GPi
mdm GPi
cl SNR
vl SNR
rl SNR
rm SNR
rd SNR
pm MDmc
rl GPi
VP
VLo
I VAmc
VApc
m VAmc
VLm
MDpl
MDpc
MDmc
CMm
CMm
PFc
PFc
PFa
Eye movements
Working memory,
strategic planing
Reward based
behaviors,
motivation
Emotions,
drug addiction
Execution of wanted
motor behavior,
habits
Figure 6 Functional segregation of direct pathways through the basal ganglia (modified after Alexander et al., 1986). The circuit motor/sensorimotor,
associative/cognitive, or limbic territories of specific regions of the cerebral cortex, the striatum, the pallidum pars interna, the substantia nigra pars
reticulata, and the specific and intralaminar nuclei are involved. cdm GPi, caudal dorsomedial globus pallidus pars interna; cl GPi, caudolateral globus
pallidus pars interna; cl SNr, caudolateral substantia nigra pars reticulata; CMl, central median nucleus lateral part; CMm, central median nucleus
medial part; ldm GPi, lateral dorsomedial globus pallidus pars interna; MDmc, mediodorsal thalamic nucleus magnocellular part; MDpc, mediodorsal
thalamic nucleus parvocellular part; MDpl, mediodorsal thalamic nucleus paralaminar part; mdm GPi, medial dorsomedial globus pallidus pars
interna; nc, nucleus; PFa, parafascicular nucleus anterior part; PFc, parafascicular nucleus caudal part; pm MDmc posteromedial mediodorsal thalamic
nucleus magnocellular part; rd SNr: rostrodorsal substantia nigra pars reticulata; rm SNr, rostromedial substantia nigra pars reticulata; rl GPi,
rostrolateral globus pallidus pars interna; l VAmc, lateral ventroanterior thalamic nucleus magnocellular part; m VAmc medial ventroanterior thalamic
nucleus magnocellular part; VApc, ventroanterior thalamic nucleus parvocellular part; vl GPi, ventrolateral globus pallidus pars interna; VLm,
ventrolateral thalamic nucleus medial part; VLo, ventrolateral thalamic nucleus oral part; vl SNr, ventrolateral substantia nigra pars reticulata; VP, ventral
pallidum. http://neuroviisas.med.uni-rostock.de/neuroviisas.html.

pathway. Here, the STN neurons receiving cortical input project monosynaptically to the GPi/SNr.
The output nuclei of the basal ganglia, the GABAergic GPi/
SNr neurons, have high resting discharge rates (40100 Hz)
that underlie a tonic inhibition of neurons in the target regions
of the basal ganglia under resting conditions. Increased activity
of striatal afferents to these neurons leads to a reduction in
their firing rate and hence reduced inhibition (i.e., disinhibition) of their targets. This disinhibition is generally considered
to be a key factor in the way basal ganglia influence behavior.
The behavioral result of this neuronal chain is locomotor
activation/movements.
Striatal dopamine release from SNc projection neurons
differentially modulates MSNs in the direct and indirect pathway (at least when the classical circuitry model is concerned;
however, see Calabresi et al. (2014) for a more refined view).
Dopamine excites striatal neurons through dopamine D1
receptors in the direct pathway, whereas it inhibits striatal
neurons in the indirect pathway through dopamine D2 receptors. The consequences of this DA modulation are massive. DA
release in the striatum results in (1) the enhancement of the
positive feedback loop to the cortex through the direct pathway
and (2) the inhibition of the negative feedback to the cortex
through the indirect pathway.
Although the concept of direct and indirect pathway is sound
in many aspects, recent data speak against two completely separated pathways (Calabresi et al., 2014; Kravitz et al., 2012). There
are many additional intrinsic and extrinsic connections of the
various basal ganglia nuclei (Parent, 1990; Parent & Hazrati,
1993; Schmitt & Eipert, 2012) (Figure 4), and it is easily assumed
that two such pairs of neuronal connection chains cannot fully
explain the basal ganglia role in the development of coordinated
goal-directed complex behaviors (Redgrave et al., 2010).
While surely simplified and actually under debate, various
aspects of locomotor activation/movements can be related to
different loops or circuits as firstly pointed out by Alexander
et al. (1986). There is a morphological and functional topography from cortical connections to the striatum, from the striatum to the pallidum/SNr, from these output structures to the
thalamus, and, finally, back to cortex. These multiple parallel,
segregated but at the same time partially overlapping, and
functionally distinct loops thus involve respective cortical
areas, corresponding parts of the basal ganglia, and corresponding thalamic nuclei and circle back to the cortex. However, it
should be kept in mind that most behaviors probably require
cycling through multiple loops as an integrative process.
Generally, (1) motor, (2) oculomotor, (3) dorsolateral prefrontal, (4) orbital and medial prefrontal, and (5) anterior cingular basal ganglia circuits or loops are distinguished (Figure 6).
Others summarize motor and oculomotor loops as sensorimotoric loop, dorsolateral prefrontal and orbital and medial prefrontal loops as associative and cognitive loop, and the anterior
cingular basal ganglia loop as limbic and motivational loop.
The motor loop controls movement execution of limbs and
axial movements, that is, the premotor areas involved in different aspects of motor planning and the motor cortex involved in
the execution of those plans. The loop goes from the motor
cortices (the primary motor cortex (M1), supplementary motor
area (SMA), cingulate motor area, caudal part (CMAc), and
caudal premotor cortex (PM)), to the somatomotor territories
of the basal ganglia (caudoventral putamen, ventrolateral
225
GPe/GPi, and dorsal STN each territory with somatotopic

organization), finally to the VL of the thalamus back to the
original cortices (Wiesendanger & Wiesendanger, 1985)
(Figure 6).
The oculomotor loop controls eye movements. The loop
goes from frontal eye field and supplementary eye field, to the
central-lateral part of the head and body of the caudate
nucleus, to the ventral part of the GPe, to the ventral part of
the STN, to the dorsolateral part of the SNr, finally to the VAmc
and MDpl back to the originating cortices (Figure 6). Other
SNr projections reach the superior colliculus.
The dorsolateral prefrontal loop is involved in working
memory, shifting, and strategic planning of behaviors, that is,
involved in higher cognitive processes or the so-called executive
functions (Groenewegen & Uylings, 2010; Petrides & Pandya,
1999; Rolls, 2000). The dorsolateral prefrontal cortex projects to
the head of the caudate nucleus that projects to the respective
ldm GPi and rl SNr, both projecting to the parvocellular parts of
the ventroanterior and mediodorsal nuclei. These nuclei send
efferents to the dorsolateral prefrontal cortex (Figure 6).
The orbital and medial prefrontal loop is involved in/
linked with the development of reward-based behaviors and
partly resembles the dorsolateral prefrontal loop with respect
to the related chain partners. Both circuits were therefore
summed up as related to cognition and associative behavior.
The anterior cingular loop is involved in the limbic system,
in emotion, motivation, and drug addiction (Koob & Nestler,
1997). Starting from the anterior cingulate cortex, it goes to the
ventral striatum, to the ventral pallidum and rostrolateral GPi
and rostrodorsal SNr, further to the mediodorsal nucleus (pm
MDmc) (and lateral habenular nucleus), and finally back to
the anterior cingulate cortex (Figure 6).
Diseases with symptoms related to disturbances in the basal
ganglia are frequent. Especially in PD and in Huntingtons
disease although motor symptoms are most obvious the
basal ganglia contribute to a wide range of altered cognitive
functions. Thus, symptoms include shortcomings in associationand motivation-driven tasks as learning, memory, skills, planning, switching, sequencing, timing, and processing of rewards
(Albin et al., 1989; Baev et al., 2002; Marsden, 1984; Nelson &
Kreitzer, 2014).

Development of the Basal Ganglia and the Basal Forebrain; Functional
Connectivity; Motor Cortex; Thalamus: Anatomy; Transmitter Receptor
Distribution in the Human Brain; INTRODUCTION TO CLINICAL
BRAIN MAPPING: Huntingtons Disease for Brain Mapping: An
Encyclopedic Reference; The Anatomy of Parkinsonian Disorders;
INTRODUCTION TO COGNITIVE NEUROSCIENCE: Motor
Decision-Making; INTRODUCTION TO SYSTEMS: Bimanual
Coordination; Neural Correlates of Motor Deficits in Young Patients
with Traumatic Brain Injury; Neural Networks Underlying Novelty
Processing; Oculomotor System; Reward; Visuomotor Integration;
Working Memory.
References
Albin, R. L., Young, A. B., & Penney, J. B. (1989). The functional anatomy of basal
ganglia disorders. Trends in Neurosciences, 12(10), 366375.
226
Alexander, G. E., & Crutscher, M. D. (1990). Functional architecture of basal ganglia

circuits: Neural substrates of parallel processing. Trends in Neurosciences, 13,
266271.
Alexander, G. E., DeLong, M. R., & Strick, P. L. (1986). Parallel organization of
functionally segregated circuits linking basal ganglia and cortex. Annual Review of
Amunts, K., Lepage, C., Borgeat, L., Mohlberg, H., Dickscheid, T., Rousseau, M.E., et al.
(2013). BigBrain: An ultrahigh-resolution 3D human brain model. Science,
340(6139), 14721475.
Anderson, M. E. (2009). Basal ganglia: Motor functions. In M. D. Binder, N. Hirokawa &
U. Windhorst (Eds.), Encyclopedia of neuroscience (pp. 105110). Berlin: Springer.
Aron, A. R., Poldrack, R. A., & Wise, S. P. (2009). Cognition: Basal ganglia role. In
M. D. Binder, N. Hirokawa & U. Windhorst (Eds.), Encyclopedia of neuroscience
(pp. 10691077). Berlin: Springer.
Baev, K. V., Greene, K. A., Marciano, F. F., Samanta, J. E., Shetter, A. G., Smith, K. A.,
et al. (2002). Physiology and pathophysiology of cortico-basal gangliathalamocortical loops: Theoretical and practical aspects. Progress in NeuroPsychopharmacology & Biological Psychiatry, 26, 771804.
Baron, M. S., Sidibe, M., DeLong, M. R., & Smith, Y. (2001). Course of motor and
associative pallido-thalamic projections in monkeys. Journal of Comparative
Neurology, 429, 490501.
Bateup, H. S., Santinib, E., Shenc, W., Birnbaumd, S., Valjentb, E., Surmeierc, D. J.,
et al. (2010). Distinct subclasses of medium spiny neurons differentially regulate
striatal motor behaviors. Proceedings of the National Academy of Sciences of the
Bernacer, J., Prensa, L., & Gimenez-Amaya, J. M. (2012). Distribution of GABAergic
interneurons and dopaminergic cells in the functional territories of the human
striatum. PLoS One, 7(1), e30504.
Bolam, J. P., Brown, M. T., Moss, J., & Magill, P. J. (2009). Basal ganglia: Internal
organization. In M. D. Binder, N. Hirokawa & U. Windhorst (Eds.), Encyclopedia of
neuroscience (pp. 97104). Berlin: Springer.
Boraud, T., Bezard, E., Bioulac, B., & Gross, C. E. (2002). From single extracellular unit
recording in experimental and human parkinsonism to the development of a
functional concept of the role played by the basal ganglia in motor control. Progress
in Neurobiology, 66, 205283.
Braak, H., & Braak, E. (1982). Neuronal types in the striatum of man. Cell and Tissue
Research, 227, 319342.
Calabresi, P., Picconi, B., Tozzi, A., Ghiglieri, V., & Di Filippo, M. (2014). Direct and
indirect pathways of basal ganglia: A critical reappraisal. Nature Neuroscience, 17,
10221030.
Cepeda, C., Andre, V. M., Yamazaki, I., Wu, N., Kleiman-Weiner, M., & Levine, M. S.
(2008). Differential electrophysiological properties of dopamine D1 and D2
receptor-containing striatal medium-sized spiny neurons. European Journal of
DeLong, M. R., & Georgopoulos, A. P. (1991). Motor functions of basal ganglia. In
M. R. DeLong (Ed.), The nervous system II (pp. 10171061). Handbook of
physiologyOxford: Oxford University Press.
DiFiglia, M., Aronin, N., & Martin, J. B. (1982). Light and electron microscopic
localization of immunoreactive leu-enkephalin in the monkey basal ganglia. The
DiFiglia, M., & Carey, J. (1986). Large neurons in the primate neostriatum examined
with the combined Golgi-electron microscopic method. Journal of Comparative
DiFiglia, M., Pasik, P., & Pasik, T. (1976). A Golgi study of neuronal types in the
neostriatum of monkeys. Brain Research, 114, 245256.
Fudge, J. L., & Haber, S. N. (2002). Defining the caudal ventral striatum in primates:
Cellular and histochemical features. The Journal of Neuroscience, 22, 1007810082.
Fudge, J. L., Kunishio, K., Walsh, C., Richard, D., & Haber, S. N. (2002). Amygdaloid
projections to ventromedial striatal subterritories in the primate. The Journal of
Galvan, A., & Smith, Y. (2011). The primate thalamostriatal system: Anatomical
organization, functional roles and possible involvement in Parkinsons disease.
Basal Ganglia, 1, 179189.
Gerfen, C. R., & Surmeier, D. J. (2011). Modulation of striatal projection systems by
dopamine. Annual Review of Neuroscience, 34, 441466.
Gerfen, C. R., & Wilson, C. J. (1996). The basal ganglia. In L. W. Swanson, A. Bjorklund
& T. Hokfelt (Eds.), Integrated systems of the CNS (Part III) (pp. 371468). Oxford:
Elsevier.
Goldman-Rakic, P. S., & Porrino, L. J. (1985). The primate mediodorsal (MD) nucleus and
its projection to the frontal lobe. Journal of Comparative Neurology, 242, 535560.
Groenewegen, H., & Uylings, H. B.M (2010). Organization of prefrontal-striatal
connections. In H. Steiner, Y. Kuei & K. T. Tseng (Eds.), Handbook of basal ganglia:
Structure and function (pp. 353365). Oxford: Elsevier.
Haber, S. N., & Gdowki, M. J. (2004). The basal ganglia. In G. Paxinos & J. K. Mai
(Eds.), The human nervous system (pp. 676738). (2nd ed.). Amsterdam: Elsevier.
Haber, S. N., Lynd-Balta, E., & Mitchell, S. J. (1993). The organization of the
descending ventral pallidal projections in the monkey. Journal of Comparative
Neurology, 329, 111129.
Haber, S. N., & Watson, S. J. (1985). The comparative distribution of enkephalin,
dynorphin and substance P in the human globus pallidus and basal forebrain. The
Hardman, C. D., Henderson, J. M., Finkelstein, D. I., Horne, M. K., Paxinos, G., &
Halliday, G. M. (2002). Comparison of the basal ganglia in rats, marmosets,
macaques, baboons, and humans: Volume and neuronal number for the output,
internal relay, and striatal modulating nuclei. Journal of Comparative Neurology,
445, 238255.
Hedreen, J. C., & DeLong, M. R. (1991). Organization of striatopallidal, striatonigral,
and nigrostriatal projections in the Macaque. Journal of Comparative Neurology,
304, 569595.
Heimer, L., De Olmos, J. S., Alheid, G. F., Person, J., Sakamoto, N., Shinoda, K., et al.
(1999). The human basal forebrain. Part II. In F. E. Bloom, A. Bjorklund & T. Hokfelt
(Eds.), Handbook of chemical neuroanatomy (pp. 57226). Amsterdam: Elsevier.
Hikosaka, O. (2009). Basal ganglia and oculomotor control. In M. D. Binder, N.
Hirokawa & U. Windhorst (Eds.), Encyclopedia of neuroscience (pp. 5361). Berlin:
Springer.
Hikosaka, O., Nakamura, K., & Nakahara, H. (2006). Basal ganglia orient eyes to reward.
Hikosaka, O., & Wurtz, R. H. (1983). Visual and oculomotor functions of monkey
substantia nigra pars reticulata. IV. Relation of substantia nigra to superior
colliculus. Journal of Neurophysiology, 49, 12851301.
Holt, D. J., Graybiel, A. M., & Saper, C. B. (1997). Neurochemical architecture of the
human striatum. Journal of Comparative Neurology, 384, 125.
Holt, D. J., Hersh, L. B., & Saper, C. B. (1996). Cholinergic innervation in the human
striatum: A three-compartment model. The Journal of Neuroscience, 74, 6787.
Kawaguchi, Y. (1997). Neostriatal cell subtypes and their functional roles. Neuroscience
Research, 27, 18.
Kawaguchi, Y., Wilson, C. J., Augood, S. J., & Emson, P. C. (1995). Striatal
interneurones: Chemical, physiological and morphological characterization. Trends
in Neurosciences, 18, 527535.
Kliem, M. A., & Wichmann, T. (2009). Basal ganglia: Functional models of normal and
disease states. In M. D. Binder, N. Hirokawa & U. Windhorst (Eds.), Encyclopedia of
neuroscience (pp. 8792). Berlin: Springer.
Koob, G. F., & Nestler, E. J. (1997). The neurobiology of drug addiction. The Journal of
Neuropsychiatry and Clinical Neurosciences, 9, 482497.
Kravitz, A. V., Tye, L. D., & Kreitzer, A. C. (2012). Distinct roles for direct and indirect
pathway striatal neurons in reinforcement. Nature Neuroscience, 15, 816818.
Lange, H., Thorner, G., & Hopf, A. (1976). Morphometric-statistical structure analysis of
human striatum, pallidum and nucleus subthalamicus. III. Nucleus subthalamicus.
Journal fur Hirnforschung, 17, 3141 (Article in German).
Mai, J., Paxinos, G., & Voss, T. (2008). Atlas of the human brain (3rd ed.). San Diego:
Academic Press.
Marsden, C. D. (1984). Function of the basal ganglia as revealed by cognitive and motor
disorders in Parkinsons disease. Canadian Journal of Neurological Sciences, 11,
129135.
McFarland, N. R., & Haber, S. N. (2000). Convergent inputs from thalamic motor nuclei
and frontal cortical areas to the dorsal striatum in the primate. The Journal of
Nambu, A. (2009). Basal ganglia: Physiological circuits. In M. D. Binder, N. Hirokawa &
U. Windhorst (Eds.), Encyclopedia of neuroscience (pp. 111117). Berlin: Springer.
Nambu, A., Tokuno, H., Hamada, I., Kita, H., Imanishi, M., Akazawa, T., et al. (2000).
Excitatory cortical inputs to pallidal neurons via the subthalamic nucleus in the
monkey. Journal of Neurophysiology, 84, 289300.
Nambu, A., Tokuno, H., & Takada, M. (2002). Functional significance of the
cortico-subthalamo-pallidal hyperdirect pathway. Neuroscience Research, 43,
111117.
Nelson, A. B., & Kreitzer, A. C. (2014). Reassessing models of basal ganglia function
and dysfunction. Annual Review of Neuroscience, 37, 117135.
Nieuwenhuys, R., Voogd, J., & van Huijzen, C. (2008). The human central nervous
system (4th ed.). Berlin: Springer.
Olszewski, J., & Baxter, D. (1982). Cytoarchitecture of the human brain stem (2nd ed.).
Basel: Karger.
Parent, A. (1986). Comparative neurobiology of the basal ganglia. New York: Wiley.
Parent, A. (1990). Extrinsic connections of the basal ganglia. Trends in Neurosciences,
13, 254258.
Parent, A., & Hazrati, L. N. (1993). Anatomical aspects of information processing in
primate basal ganglia. Trends in Neurosciences, 16, 111115.

Petrides, M., & Pandya, D. N. (1999). Dorsolateral prefrontal cortex: Comparative
cytoarchitectonic analysis in the human and the macaque brain and corticocortical
connection patterns. European Journal of Neuroscience, 11, 10111036.
Pisani, A., Bernadi, G., Ding, J., & Surmeier, D. J. (2007). Re-emergence of striatal
cholinergic interneurons in movement disorders. Trends in Neurosciences, 30,
545553.
Redgrave, P., Rodriguez, M., Smith, Y., Rodriguez-Oroz, M. C., Lehericy, S.,
Bergman, H., et al. (2010). Goal-directed and habitual control in the basal ganglia:
Implications for Parkinsons disease. Nature Reviews. Neuroscience, 11, 760772.
Rolls, E. T. (2000). The orbitofrontal cortex and reward. Cerebral Cortex, 10, 284294.
Sato, F., Lavallee, P., Levesque, M., & Parent, A. (2000). Single-axon tracing study of
neurons of the external segment of the globus pallidus in primate. Journal of
Sato, F., Parent, M., Levesque, M., & Parent, A. (2000). Axonal branching pattern of
neurons of the subthalamic nucleus in primates. The Journal of Comparative
Neurology, 424, 142152.
Schmitt, O., Eggers, R., & Haug, H. (1995). Quantitative investigations into the
histostructural nature of the human putamen. I. Staining, cell classification and
morphometry. Annals of Anatomy, 177, 243250.
Schmitt, O., & Eipert, P. (2012). NeuroVIISAS: Approaching multiscale simulation of the
rat connectome. Neuroinformatics, 10, 243267.
Schroder, K. F., Hopf, A., Lange, H., & Thorner, G. (1975). Morphometrical-statistical
structure analysis of human striatum, pallidum and subthalamic nucleus. Journal fur
Hirnforschung, 16, 333350 (Article in German).
Sidibe, M., Pare, J. F., & Smith, Y. (2002). Nigral and pallidal inputs to functionally
segregated thalamostriatal neurons in the centromedian/parafascicular
intralaminar nuclear complex in monkey. The Journal of Comparative Neurology,
447, 286299.
Sidibe, M., & Smith, Y. (1996). Differential synaptic innervation of striatofugal neurones
projecting to the internal or external segments of the globus pallidus by thalamic
afferents in the squirrel monkey. The Journal of Comparative Neurology, 365,
445465.
Smith, Y., Bevan, M. D., Shink, E., & Bolam, J. P. (1998). Microcircuitry of the direct
and indirect pathways of the basal ganglia. The Journal of Neuroscience, 86,
353387.
Smith, Y., Galvan, A., Ellender, T. J., Doig, N., Villalba, R. M., Huerta-Ocampo, I., et al.
(2014). The thalamostriatal system in normal and diseased states. Frontiers in
Systems Neuroscience, 8, 5.
Smith, Y., Raju, D., Nanda, B., Pare, J. F., Galvan, A., & Wichmann, T. (2009). The
thalamostriatal systems: Anatomical and functional organization in normal and
parkinsonian states. Brain Research Bulletin, 78, 6068.
227
Thorner, G., Lange, H., & Hopf, A. (1975). Morphometrical-statistical structure analysis
of human striatum, pallidus and subthalamic nucleus. II. Globus pallidus. Journal
fur Hirnforschung, 16, 401413 (Article in German).
Wichmann, T., Bergman, H., & DeLong, M. R. (1994). The primate subthalamic
nucleus. I. Functional properties in intact animals. Journal of Neurophysiology, 72,
494506.
Wiesendanger, R., & Wiesendanger, M. (1985). The thalamic connections with medial
area 6 (supplementary motor cortex) in the monkey (Macaca fascicularis).
Willis, T. (1664). Cerebri anatome: cui accessit nervorum descriptio et usus. Amsterdam.
Wilson, C. J. (2004). Basal ganglia. In G. M. Shepherd (Ed.), The synaptic organization
of the brain (pp. 361413). (5th ed.). New York: Oxford University Press.
Yelnik, J., Francois, C., Percheron, G., & Heyner, S. (1987). Golgi study of the primate
substantia nigra. I. Quantitative morphology and typology of nigral neurons. Journal
Yeterian, E. H., & Pandya, D. N. (1998). Corticostriatal connections of the superior
temporal region in rhesus monkeys. Journal of Comparative Neurology, 399,
384402.
Relevant Websites
http://bigbrain.cbrain.mcgill.ca The BigBrain LORIS Database of the Montreal
Neurological Institute and the Forschungszentrum Julich.
http://www.thehumanbrain.info/about_us.php The human brain info is a web based
interactive knowledge and atlas system of the Atlas of the human brain from Mai,
Voss and Paxinos.
http://www.loni.usc.edu/ The Laboratory of Neuro Imaging (LONI) offers challenging
tools for brain atlases and differents sets of imaging data.
http://de.slideshare.net/ananthatiger/anatomy-of-basal-ganglia This extensice slide
show provides a good overview of the basalganglia.
http://neuroscience.uth.tmc.edu/s3/chapter04.html The electronic textbook for
neurosciences contains a chapter of the Basal Ganglia with many structural and
functional details.
http://neuroviisas.med.uni-rostock.de/neuroviisas.html NeuroVIISAS is generic
framework for the integration of digital atlases, connectomes and population
simulations. It has a database on its webpage for querying all known connections of
the rat nervous system.
http://homepage.psy.utexas.edu/HomePage/Class/Psy394U/Hayhoe/
IntroSensoryMotorSystems/week7/Ch43.pdf This very informative web resource
about the basal ganglia has been build by Mahlon De Long.
Thalamus: Anatomy
MT Herrero, University of Murcia, Murcia, Spain
R Insausti, University Castilla La Mancha, Albacete, Spain
C Estrada, University of Murcia, Murcia, Spain
Glossary
function is thought to be the faithful transmission of the

spike message relayed by thalamic cells to postsynaptic
structures.
Thalamic modulators Thalamic afferents that target distal
dendrites and influence spike transmission by adjusting the
cellular and synaptic mechanisms underlying spike
generation.
Thalamic nucleus The intersection of a thalamocortical
source space with one territory.
Thalamic region A gross topographical division
corresponding to the nuclei included on it. The dorsal
thalamus has two regions: the allothalamic and the
isothalamic regions.
Thalamic space (this term is not in use nowadays) The
source space was the thalamic space where neurons project
to a given cortical target, and then, the thalamic nucleus was
defined as the intersection of a thalamocortical space with
one territory.
Thalamic territory The cerebral space filled by afferent
endings from one source (when having a distinct
topography in a region, a given territory makes a
subregion).
Tonic mode When the neurons respond to depolarization
and hyperpolarization.
Abbreviations
Anterior nuclear complex
AM Anteromedial nucleus (anterior group)

AV Anteroventral nucleus (anterior group)
LD Laterodorsal nucleus (anterior group)
Medialmidline group
Pt
PV
Re
Allothalamic region It is divided into (i) the

paraventricular area or midline nuclei, (ii) the center
medianparafascicular complex (isolated by a continuous
capsule), and (iii) the intralaminar nuclei within the lamina
medialis.
Burst mode also called oscillatory mode Neurons have an
intrinsic rhythmicity and are tonically hyperpolarized.
External medullary lamina Bundle of myelinated nerve
fibers laterally around the dorsal thalamus that separates the
ventral and lateral thalamus from the subthalamic nucleus
and the reticular nucleus.
Internal medullary lamina (IML) Y-shaped bundle of
myelinated nerve fibers that course through the thalamus
along its rostrocaudal axis.
Isothalamic region It constitutes the bulk of the thalamus.
The IML divides the principal thalamic nuclei into two
major parts: a medial group on one side and a ventrolateral
group on the other side. The anterior part of the IML splits
into two lamellae and surrounds the anterior group of
thalamic nuclei.
Situs Topographical locations that may or may not
correspond to cytoarchitectonic subdivisions.
Thalamic drivers Thalamic afferents that target proximal
dendrites with relatively large synaptic boutons, and its
AD
Anterodorsal nucleus (anterior group)
MDmc
MDpc
Mediodorsal nucleus, magnocellular (midline

group)
Mediodorsal nucleus, parvocellular (midline
group)
Lateral group
LP
VA
VL
VM
Lateral posterior nucleus (lateral dorsal group)

Ventral anterior nucleus (lateral ventral group)
Ventral lateral nucleus (lateral ventral group)
Ventral medial nucleus (lateral ventral group)
VP
VPL
VPM
VPpo
VPI
Paratenial nucleus (midline group)

Paraventricular nucleus (midline group)
Nucleus reuniens (midline group)
Ventral posterior nucleus (lateral ventral group)

Ventral posterolateral nucleus
Ventral posteromedial nucleus
Ventral posterior nucleus
Ventral posterior inferior nucleus
http://dx.doi.org/10.1016/B978-0-12-397025-1.00216-5
229
230
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Thalamus: Anatomy
Intralaminar group
CL
CM
Central lateral nucleus (intralaminar group

anterior/rostral)
Centromedian nucleus (intralaminar group
posterior/caudal)
PCn
Pf
Paracentral nucleus (intralaminar group anterior/

rostral)
Parafascicular nucleus (intralaminar group
posterior/caudal)
Posterior group
PM
Metathalamus
MGN Medial geniculate nucleus (metathalamus)

RN
Reticular nucleus
Pul
LGN
Pulvinar inferior/medial nucleus (posterior group)
Pulvinar complex (posterior group)
Lateral geniculate nucleus (metathalamus)
The Thalamus
The diencephalon, which forms the central core of the brain, is
at the dorsal end of the brain stem. Inside the diencephalon,
the dorsal thalamus (just called the thalamus) is its largest
component; however, the human thalamus is small when
compared to the rest of the encephalon (Tuohy et al., 2004).
The thalamus is a midline bilateral structure with two symmetrical halves separated by the third ventricle but connected by
the interthalamic adhesion (massa intermedia), a flattened gray
band (Morel, 2007). Then, the medial surface of the thalamus
corresponds to the upper part of the lateral wall of the third
ventricle. From a radiological point of view, thalamic segmentation defines the anterior boundary of the thalamus as the first
slice caudal to the anterior commissure: at rostral slices, the
thalamus starts behind the columnae fornicis and the mammillary bodies, and at the caudal slices, the thalamus is the region
below the fornix. The geniculate nuclei (both medial and
lateral) were included in the outline at levels where the lateral
geniculate nucleus (LGN) was attached to the corpus of the
thalamus and not separated from it by a white matter tract.
Ventrally, the thalamus is located close to the hypothalamus
and the mesencephalon. The hypothalamus lies ventral to the
thalamus and is more anteriorly situated relative to the
thalamus; therefore, in coronal sections, the mammillary bodies (the caudal part of the hypothalamus) are at the same plane
of section compared with the anterior complex of the thalamus. At all levels, the thalamus is bordered medially by the
third ventricle, dorsally by the lateral ventricles, and laterally
by the internal capsule on both sides (Figure 1(a) and 1(b)).
The thalamus has an average volume of around 9 cm3 in males
and 8 cm3 in females being around 5.7 cm in length, 2.5 cm in
height, and about 2 cm in width. It has been estimated that
there are about 10 million thalamic neurons in each
hemisphere.
The thalamus, the major relay to the cerebral cortex, is not
only the part of the nervous system where sensory inputs
(except olfaction) can be modulated but also the relay for
limbic pathways and cerebellar and basal ganglia inputs to
the cerebral cortex (Zhang et al., 2010). Moreover, the
thalamus is also implicated in numerous systems and functions as in alertness, arousal, memory, and the ability to
accomplish tasks of fast information processing. The thalamus dispenses specific alerting or engagement response to the
different domains of function to which it contributes. With
the exception of the reticular nucleus (RN), the other nuclei
of the thalamus project to the cerebral cortex and receive
reciprocal connections from the same cortical areas that in
turn can modulate the thalamic functions filtering its thalamic inputs.
Ontogeny of the Thalamus

The ontogeny of the nervous system can be envisioned as a
tube (neural tube) that results from the closure of a furrow
that is formed in the dorsal part of the embryo (neuroectoderm). The furrow, once closed to form a tube, dilates into
several cerebral vesicles, which will derive in the main divisions of the central nervous system. The correspondence
between neural tube vesicles and fully developed central nervous system is as follows: the telencephalon (the cerebral
cortex), diencephalon (the thalamus and hypothalamus), mesencephalon (the mesencephalon), and rhombencephalon (the
cerebellum, pons, and medulla). The remainder of the neural
tube becomes the spinal cord. The diencephalic vesicle separates into a dorsal and a ventral part by the thalamohypothalamic sulcus. The classical partition of the
diencephalon corresponded to Herricks columnar model;
however, the new prosomeric model (Puelles & Rubinstein,
1993) indicates that the rostral forebrain (including the telencephalon and hypothalamus) represents a complex protosegment not divided into prosomeres, whereas the caudal
forebrain is divided into three prosomeres (P1, P2, and P3)
and the thalamus corresponds to P2 (Figure 1(c)). The caudal
population of thalamic progenitors in P2 gives rise to all
thalamic nuclei that relay sensory information from the
periphery to primary sensory regions of the neocortex via
thalamocortical axons (Vue, Aaker, Taniguchi, et al., 2007).
231
(a)
(b)
(c)
Figure 1 The thalamus is an oval-shaped region located in the center of the brain. (a) Coronal cross section of the brain showing the thalamic medial
surface that forms part of the lateral wall of the third ventricle (III) and is usually connected to the opposite thalamus by the gray matter
interthalamic connection (interthalamic adhesion) and the thalamic lateral limits, the internal capsule, and the caudate nucleus; please note the lateral
border of the superior surface of the thalamus is limited by the stria terminalis (gray) and overlying thalamostriate vein (blue), which separate
thalamic nuclei from the body of the caudate nucleus. Additionally, the external medullary lamina, white matter, separates the main body of the thalamus
Continued
232
Anatomical General Topography and Thalamic Nuclei

The thalamus differentiates into a series of neuronal groups
that can be classified according to a number of landmarks that
determine their relative position in the thalamus (see Table 1
for a classical description). The principal terms in the nomenclature are the anteroposterior, mediolateral, and dorsoventral
subdivisions, but, in fact, there are three types of thalamic
nuclei in relation to its function: specific, nonspecific, and
association nuclei. However, as the specific partitions of the
different nuclei and territories differ from author to author to
name the thalamic nuclei, there nomenclature is still very
confusing. In general, there has been a rigid conception of
the thalamic nucleus combining cytoarchitectonic techniques, comparative anatomy, and cortical connections (with
underexploitation of subcortical afferents), and it has been
established according to rational and historically grounded
rules.
In this article, we basically follow the terminology of Hirai
and Jones (1989) that is important in relation to functional
studies, but we include as well other terms used in the literature. From a morphological point of view, the thalamus is
divided into three regions (anterior, lateral, and medial) that
are anatomically defined by a Y-shaped bundle of myelinated
nerve fibers termed the internal medullary lamina (IML) that
courses through the thalamus along its rostrocaudal axis
(Figure 2). The anterior pole of the thalamus is between the
arms of the rostral part of the IML, and it is made up of the
anterior nuclear (AN) complex, of which the anterodorsal
(AD), anteromedial (AM), and the anteroventral (AV) nuclei
are the most representative. Thalamic nuclei medially located
to the IML receive the name of midline thalamic nuclei and
include the mediodorsal nucleus (or dorsal medial nucleus)
(MD) with two subnuclei (magno- and parvocellular, medial
and laterally located, respectively) and the midline structures
(the paratenial, paraventricular, nucleus reuniens, and rhomboid, beneath the wall of the third ventricle). The nuclei external to the IML form a lateral group of neuronal ensembles
bounded by the RN of the thalamus (a thin shell of neurons
covering the entire lateral aspect of the thalamus and separated
from the thalamus by the external medullary lamina, EML).
The lateral group is subdivided into ventral and dorsal tiers,
each of which contains different subnuclei. The lateral ventral
tier contains the ventral anterior (VA), the ventral lateral (VL),
the ventral medial (VM), and the ventral posterior (VP) nuclei.
This last one is divided into the ventral posterolateral (VPL)
nuclei and ventral posteromedial (VPM) and the ventral posterior (VPpo) and ventral posterior inferior (VPI) nuclei. The
lateral dorsal (LD) tier contains, from rostral to caudal, the LD
nucleus (included in the anterior group), the lateral posterior

(LP) nucleus, and, finally, the thalamus thickens and expands
posteriorly to constitute the pulvinar complex (Pul) (also considered as posterior thalamus, and it is only well represented in
human and nonhuman primates). The metathalamus is
located at the posterior part of the pulvinar with two distinct
groups forming the relay for hearing (the medial geniculate
nucleus, MGN) and vision (LGN). Furthermore, within the
IML are the intralaminar nuclei, among those being rostrally
the central lateral (CL) and paracentral nuclei (PCn) and caudally the centromedian (CM) and parafascicular (Pf) nuclei
(Figure 2). Further subdivisions are recognized, in particular
in the human thalamus. Thus, the thalamus contains no less
than 40 different nuclei, some of which can be related to
specific sensory inputs, while others are more related to other
functional systems such as the limbic system or the reticular
formation (Krauth et al., 2010).
General Topography from the Functional Point of View

Every nucleus in the dorsal thalamus receives subcortical
inputs and projects to the cerebral cortex. Ramon y Cajal was
the first to demonstrate thalamocortical fibers, their terminations in the cortex, and the feedback provided by corticothalamic fibers (Ramon y Cajal, 1900, 1903). Thalamic nuclei also
project to the amygdala, the hippocampal formation, the striatum, and other basal telencephalic areas. In relation to these
functional projections, thalamic nuclei could be divided into
those that project to the cerebral cortex and those that project
to the cortex and striatum (as the intralaminar nuclei) (Jones,
2007). Moreover, those projecting to the cortex include (i) the
specific sensory relay nuclei (the VP, the medial geniculate, and
the lateral geniculate nuclei) projecting to the layer IV of its
corresponding cortical area (and with both afferents and efferents topographically organized) and (ii) the thalamic nuclei
projecting upon several cortical areas in a diffuse manner,
whose projections end in one or more of several layers (mainly
layers I and VI). However, from a general functional point of
view, the thalamic nuclei can be grouped in six functional
classes (Schmahmann & Pandya, 2008): (i) the RN, (ii) the
specific sensory nuclei, (iii) the effector nuclei, (iv) the limbic
nuclei, (v) the intralaminar nuclei, and (vi) associative nuclei.
(i) The reticular nucleus (RN) (situs perithalamicus) was
described by Kolliker as the Gitterkern or lattice nucleus
(because of the fibrous latticework characteristic of the
area) (Kolliker, 1896). The RN surrounds much of the
thalamus like an eggshell and can be divided into different
sectors topographically connected with different thalamic
Figure 1 Contd from the reticular nucleus. (b) Sagittal section showing the rostral limits, the anterior commissure (AC), and the caudal limits, the
posterior commissure (PC). It can be noted that dorsally, the thalamus is bounded by the fornix (and subarachnoid space in the form of the transverse
cerebral fissure) and ventrally is limited by the hypothalamic sulcus (HS, sulcus of Monro) of the third ventricle (this sulcus in the lateral wall of third
ventricle extends from the upper end of midbrain aqueduct posteriorly to the interventricular foramen anteriorly). (c) Cartoon of the prosomeric
model showing the three prosomeres part of the caudal forebrain, being P2 (in gray) the segment origin of the thalamus (modified from Epstein, 2012).
AC, anterior commissure; CC, corpus callosum; Cd, caudate nucleus; cDi, caudal diencephalon; CM, centromedian nucleus; HS, hypothalamic
sulcus; Hyp, hypothalamus; IA, interthalamic adhesion; IC, internal capsule; LP, lateral posterior nucleus; LV, lateral ventricle; MD, mediodorsal nucleus;
Mes, mesencephalon; Met, metencephalon; PC, posterior commissure; Pf, parafascicular nucleus; RN, reticular nucleus; ST, stria terminalis; Tel,
telencephalon; Th, thalamus; TSV, thalamostriate vein; VPL, ventral posterior lateral nucleus; VPM, ventral posteromedial nucleus; III, third ventricle.
Note: The interthalamic adhesion (mediodorsal neurons) is found in 7080% of humans and its anteroposterior diameter is about 1 cm in length.

Table 1
233
Diencephalic elements in hierarchical order

Abbreviations
Comments
I. Diencephalic nonthalamic elements

I.A. Perithalamus, PTh (ventral thalamus, thalamus ventralis)
i. Nucleus perithalamicus
PTh
Situs perithalamicus
PTh
N. reticular, RN
Situs incertus
PTh ZI
Zona incerta, Zi
Situs pregeniculatus
PTh Pr
N. pregeniculatus or prepeduncularis
I.B. Epithalamus, Hb
Hb
Habenula, Hb
i. Nucleus habenulae lateralis
HbL (Hlmc)
ii. Nucleus habenulae medialis
HbM (Hlpc)
II. Thalamus, Th (dorsal thalamus)
II.A. Allothalamus (neuronal types different from those of the isothalamus)
i. Regio paraventricularis (paramediana)
E
Midline nuclei interthalamic adhesion (massa intermedia)
ii. Regio centralis
C
Center medianparafascicular complex
Nucleus centralis medius
CMe
N. centromedian, CM
Nucleus centralis parafascicularis
CPf
N. parafascicular, Pf
Nucleus centralis paralateralis
CPl
iii. Regio intralaminaris
Il
Intralaminar nuclei (in true sense of term)
Nucleus intralaminaris oralis
Ilo
N. paracentral, PCn
Nucleus intralaminaris caudalis
Ilc
N. centralis lateral, CL
Nucleus intralaminaris posterior
Ilp
N. posterioris, ILa
iv. Nucleus limitans
Li
II.B. Isothalamus (made up of bushy thalamocortical projection neurons microneurons)
II.B.1. (Superregio) regio superior
S
Nucleus anterior
A
N. anterior principalis (anteroventral, AV anteromedial, AM)
Nucleus anterodorsalis
AD
N. anterior accesorius, Aa (anterodorsal, AD)
Nucleus superficialis
S
N. laterodorsal, LD
II.B.2. Superregio medioposterior
i. Regio medialis
M
Main part of the mediodorsal nucleus, MD
Nucleus medialis (in human)
M
Nucleus medialis medialis
MM
N. MD magnocellular, MDmc
Nucleus medialis lateralis
ML
N. MD parvocelular, MDpc
ii. Regio posterior
P
Main part of the pulvinar, Pul
Nucleus posterior
Situs medialis
PuM
N. pulvinar medial (inferior), PM
Situs lateralis
PuL
N. pulvinar lateral, PL
Situs oralis
PuO
N. pulvinar oral, PO
Situs oralis dorsalis
PuOD
N. lateral posterior, LP
II.B.3. Superregio basalis
i. Regio basalis
B
Nucleus suprageniculatus
Spinothalamic fibers
ii. Regio Intergeniculata
Ig
Nucleus intergeniculatus
Tectal thalamus
II.B.4. Superregio inferolateralis
Sensory and motor thalamus
i. Regio lateralis
L
Lateral mass paralaminar areas of the MD
Sensorimotor thalamus
a. Motor thalamus
a.1. Subregio oralis
LO
Nigral and pallidal thalamusa
Nucleus lateralis oralis
LO
N. ventral anterior, VA (VOL DO)
Situs principales
LOl
VOL (VOe, VLo)
Situs dorsalis
LOd
DO (DOe, VA dorsolateral)
Situs ventralis
LOv
VOV (VLm, lateral)b
a.2. Subregio dorsalis
LR
Nigral and pallidal thalamusa
Nucleus lateralis rostralis
LR
N. ventral medial, VM (VOM LPo)
Situs polaris
LRPo
Situs perifascicularis
LRmc
Situs ventralis medialis
LRpm
Situs paralaminaris rostralis
PlO
Nucleus lateralis rostralis pars medialis
LRM
Nigral and amygdalar thalamus
a.3. Subregio intermedia
LI
Cerebellar thalamus
Nucleus lateralis intermedius lateralis
LIL
N. ventral lateral, VL
(Continued)
234
Table 1

(Continued)
Nucleus lateralis intermedius mediodorsalis

Situs ventralis medialis
Situs dorsalis
Situs postremus
Situs paralaminaris intermedius
b. Sensorial thalamus
b.1. Subregio caudalis
Nucleus ventralis caudalis lateralis
Nucleus ventralis caudalis medialis
b.2 Subregio arcuata
Nucleus lateralis arcuatus
ii. Regio geniculata

Nucleus geniculatus medialis
Nucleus geniculatus lateralis
Abbreviations
Comments
LIM
LIMm
LIMd
LIMps
pIl
N. ventralis intermedius (Vim) Dl

Vimc
Dl
LCL
LCM
LArc
G
Gm
Gl
Lemniscal thalamus
N. ventral posterolateral, VPL
N. ventral posteromedial, VPM
Gustatory thalamus
Spinothalamic thalamus
N. ventral posterior inferior, VPI
N. ventral posterior, VPpo
Auditory thalamus, MGN
Visual thalamus, LGN
The dorsal thalamus (II) is divided into allo- (II.A) and isothalamus (II.B).
a
There is no polar subdivision without lower afferents in front of the pallidal and nigral territories and thus no reason for isolating a nucleus lateralis polaris or a polar VA (Percheron
et al., 1996).
b
Nucleus lateralis oralis, situs ventralis (LOv) nucleus ventralis oralis posterior, Vop (Hassler, 1959) nucleus ventral lateral ventral (Hirai & Jones, 1989). Pallidal connections.
c
Nucleus lateralis intermedius mediodorsalis, situs ventralis medialis (LIMm) N. ventralis intermedius (Vim) (Hassler, 1959) nucleus ventral lateral posterior (ventral part) (Hirai &
Jones, 1989). Cerebellar connections.
Source: Modified with permission from Herrero, M. T., Barcia, C., Navarro, & J. M. (2002). Functional anatomy of thalamus and basal ganglia. Childs Nervous System, 18, 386404;
previously modified from Percheron, G., Francois, C., Talbi. B., Yelnik, J., & Fenelon, G. (1996). The primate motor thalamus. Brain Research Reviews, 22, 93181.
nuclei and with different functions (arousal, hearing, emotional, movement, sight or touch). The RN is the only
thalamic nucleus that does not project to the cerebral cortex but in this nucleus blend afferents from cortical areas,
from the globus pallidus, and from dorsal thalamic nuclei.
In fact, most inputs to other thalamic nuclei are collaterals
of fibers passing through this nucleus modulating the flow
of information from other nuclei to the cortex. Its neurons
are GABAergic (inhibitory) and contribute to the synchrony and rhythms of thalamic activity with a relevant
importance in consciousness, sleep, and epilepsy. These
GABAergic cells are innervated by collateral branches of
thalamocortical and corticothalamic fibers (with connectivity with both the thalamic nuclei and its associated
cortical area) (Jones, 2002a, 2002b).
(ii) The specific sensory thalamic nuclei include the ventroposterior nuclei (lateral, medial, and inferior; VPL, VPM, and
VPI, respectively) and the geniculate nuclei (medial and
lateral; MGN and LGN, respectively). The topographical
organization of the afferents to the somatosensory thalamic nuclei is contralateral (however, some nuclei have
both contralateral and ipsilateral connections (as the gustatory system, Iannilli, Singh, Schuster, Gerber, &
Hummel, 2012)). The ventroposterior nuclei receive topographically organized projections from the dorsal column
(medial lemniscus) and the spinothalamic and the trigeminothalamic tracts: VPL nucleus controls body and
limbs, and VPM nucleus the head, neck, and gustatory
relays. VPL and VPM nuclei are somatotopically interconnected with primary unimodal somatosensory parietal
cortices (Figures 2 and 3, Table 2). The gustatory
information, which is important in taste detection and

recognition, is controlled by the parvicellular/paucicellular part of the medial tip of the VPM nucleus, close to the
midline. VPI nucleus concentrates spinothalamic tract
afferents instead of dorsal columnmedial lemniscus
ones. The spinothalamic relay for pain and temperature
sensation in humans terminates in the posterior portion of
the VPM (VPpo) nucleus, and lesions to this area would be
the neural substrate for thalamic pain syndromes (Craig,
2003). VPI and VPpo nuclei are important regions for
discriminative processing and perception of painful stimuli. The somatosensory thalamus has anteroposteriorly
oriented rods with a somatotopic distribution. Each rod
(a compilations of neurons) relays sensory information to
one specific cortical column. It have been described two
types of rods: nociceptive and non-nociceptive (Apkarian,
Shi, Bruggemann, & Airapetian, 2000). The MGN can be
divided into three main subdivisions, the ventral, dorsal,
and medial (Bartlett, 2013). The MGN has a role in both
elementary audition and higher-level auditory processing;
it receives projections from the inferior colliculus and
sends its axons to the primary and association auditory
temporal cortices (Figures 2 and 3, Table 2). The LGN
comprises six histologically distinct layers that receive
organized and topographic projections from the retina
(retinotopic mapping) as well as from visual cortical
areas. Optic tract axons originating in the contralateral
nasal retina innervate layers 1, 4, and 6 of the LGN, and
axons from ipsilateral temporal retina innervate layers 2,
3, and 5 (Chen, Zhu, Thulborn, & Ugurbil, 1999). LGN
neurons send its axons topographically to the primary and
235
L
V
AN
RN
MD
IM
VA
IA
LD
LP
VL
Pu
l
VP
EM
LGN
Rostral
MGN
Middle
Caudal
LP
LD
A (R)
P (C)
Coronal plane
AD
RN
RN
RN
VPL
CL
VA
CL
MD
Pt
Pul
MD
PV PCn
CM
VL
CM
VM
Re
Pf
VPM
Pf
MTT
VL
MGN
LGN
Middle
Ventral
Dorsal
VA
Axial plane
RN
MD
VL
Sagittal plane
Pt
VP
CM
VA
VL
LP
PV
VP
VPM
CL
MD
VP
Pf
CM
MG Pul
N
LGN
RN
LD
VL
CL
Pv
Medial
RN
VA
MD
VPM
AD
AV
Re
D
Pul
Pul
Middle
Lateral
LD
LP
AD
MD
AV
Pt
VA
Re
VA
Pul
VL
Pf
VP
Pul
VL
MG
CM
VP
LG
Figure 2 At the top: Divisions of the thalamus. Nuclei: yellow, anterior group; blue, lateral group; purple, posterior group; green, midline group; orange,
intralaminar group. Underneath: anatomy and subdivisions of the thalamus nuclei analyzed by means of coronal, axial, and sagittal planes.
Continued
236
MC
C
PMC
SS
PC
PFC
POC
AC
VC
TC
A
L
M
P
V
AN
RN
IA
M
IM
VA
SMA
MC
LD
SSC
LP
VL
CC
PFC
Pu
l
VP
RS
EM
POC
LGN
MGN
VC
TC
Figure 3 Topography of projections of the thalamic nuclei. (a) Cerebral cortex, lateral view of the right hemisphere; (b) cerebral cortex, sagittal view of
the left hemisphere; (c) thalamic nuclei. Please see the code of colors similar in the left thalamic nuclei and its corresponding cortical areas (Behrens
et al., 2003). A, anterior; AC, auditory cortex; AN, anterior nuclear complex; CC, cingulate cortex; D, dorsal; EML, external medullary lamina; IA,
interthalamic adhesion; IML, internal medullary lamina; L, lateral; LD, laterodorsal nucleus; LGN, lateral geniculate nucleus; LP, lateral posterior nucleus;
M, medial; MC, motor cortex; MD, mediodorsal nucleus; MGN, medial geniculate nucleus; PC, parietal cortex; PFC, prefrontal cortex; PMC, premotor
cortex; P, posterior; POC, parieto-occipital cortex; Pul, pulvinar complex; RN, reticular nucleus; RS, retrospenial cortex; SMA, supplementary motor
area; SSC, somatosensory cortex; TC, temporal cortex; V, ventral; VA, ventral anterior nucleus; VC, visual cortex; VL, ventral lateral nucleus; VP, ventral
posterior nucleus.
secondary occipital visual cortices (Schneider, Richter, &

Kastner, 2004; Figure 2, Table 2).
(iii) The thalamic effector nuclei are the motor nuclei, which
include the VA, the VM, and the VL nuclei, which are
covering the entire anterior part of the lateral region of the
thalamus. The motor thalamus is the center of integration
of networks and not just a relay of information to the
cortex; then, these nuclei underlie the ability to modulate
behaviors concerning movement and aspects of language
(Haber & Calzavara, 2009). The thalamic effector nuclei
receive neuronal afferents from the basal ganglia (the substantia nigra pars reticulata and medial globus pallidus by
the thalamic fasciculus) and from the cerebellum (by the
dentatorubrothalamic tract); then, the named motor
thalamus is made up of three topographically distinct territories: nigral, pallidal, and cerebellar. The thalamic cerebellar territory is located caudally in front of the somesthetic
ventral posterior nucleus. These nuclei are implicated in the
control of movement because they are strategically located
between motor areas of the cerebral cortex and motorrelated subcortical structures, such as the cerebellum and
basal ganglia; in fact, these nuclei are a part of the segregated
but integrated cortico striatalthalamocortical loops (the
functional entities for motor and sensory processes as well
as for higher cognitive functions like cognitive and emotional processes, which also include the dorsomedial,
intralaminar, and anterior thalamic nuclei) (Figure 3;
Metzger et al., 2013).
Figure 2 Contd A, anterior; AD, anterodorsal nucleus; AV, anteroventral nucleus; C, caudal; CL, central lateral nucleus; CM, centromedian nucleus;
D, dorsal; EML, external medullary lamina; IA, interthalamic adhesion; IML, internal medullary lamina; L, lateral; LD, laterodorsal nucleus; LGN, lateral
geniculate nucleus; LP, lateral posterior nucleus; M, medial; MD, mediodorsal nucleus; MGN, medial geniculate nucleus; MTT, mammillothalamic tract;
P, posterior; PCn, paracentral nucleus; Pf, parafascicular nucleus; Pt, paratenial nucleus; Pul, pulvinar complex; PV, paraventricular nucleus; R, rostral;
Re, nucleus reuniens; RN, reticular nucleus; V, ventral; VA, ventral anterior nucleus; VL, ventral lateral nucleus; VM, ventral medial nucleus; VP, ventral
posterior nucleus; VPL, ventral posterior lateral nucleus; VPM, ventral posteromedial nucleus.

Table 2
237
Afferent and efferent projections of the thalamic nuclei
Nucleus
Anterior nuclear complex
Anterodorsal, anteromedial, and
anteroventral nuclei
Laterodorsal nucleus
Medialmidline group
Lateral group
Lateral posterior nucleus
Ventral anterior nucleus
Ventral lateral nucleus
Ventral posterolateral nucleus
Ventral posteromedial nucleus
Intralaminar nuclei
Posterior group pulvinar complex
Metathalamus
Medial geniculate nucleus
Lateral geniculate nucleus
Reticular nucleus
Afferents
Efferents
Mammillary complex (from hippocampus)

Cingulate cortex
Cingulate cortex
Prefrontal cortex
Amygdala, olfactory cortex
Basal ganglia
Medial and lateral prefrontal cortices

Orbitofrontal cortex
Posterior cingulate cortex Posterior parietal region

Extrastriate occipital areas
Posterior cingulate cortex

Extrastriate occipital cortices
Posterior parietal cortex
Premotor cortical cortex
Dorsolateral prefrontal cortex
Substantia nigra pars reticulata and medial globus

pallidus
Premotor cortex
Deep cerebellar nuclei
Motor cortex, premotor cortex, supplementary motor area
Lemniscus medialis (body and limbs)

Lemniscus medialis and trigeminal lemniscus
(head, neck, and gustatory relays)
Spinothalamic relays (pain)
Somatosensory cortex
Spinal cord, periaqueductal gray matter, reticular

formation, cerebellum
Anterior: cortical area of eye movement

Posterior: striatum
Superior colliculus
Secondary somatosensory cortices
Hippocampal formation; parahippocampal, prefrontal,

cingular, posterior parietal temporal, and occipital
cortices
Insula
Inferior colliculus
Retina (optic tract)
Auditory temporal cortex

Visual occipital cortex
Thalamocortical projections
Corticothalamic projections
Globus pallidus
Dorsal thalamic nuclei
Thalamic nuclei
The VA nucleus has two parts: (i) the magnocellular

part, VAmc, which receives nigral inputs, and (ii) the
parvocellular part, VApc, which receives neuronal projections from the internal globus pallidus. The VA
nucleus has a role in the initiation and planning of
movement, having reciprocal interconnections with
dorsal premotor cortical areas and with the caudal
dorsolateral prefrontal cortex (DLPFC); also, it receives
nonreciprocal afferents from medial prefrontal areas
(Figures 2 and 3, Table 2).
The VM nucleus, receiving afferents from the substantia
nigra pars reticulata, is a point of convergence for several
components of the extrapyramidal motor system. The
nigrothalamic projection is topographic: medial and
lateral areas of the pars reticulata connect to medial
and lateral parts of the VM nucleus, respectively. The
medial VM nucleus projects to the medial prefrontal
cortex, and the lateral VM nucleus projects to the lateral
prefrontal cortex, which is sensorimotor (Figures 2
and 3, Table 2). The function of the medial VM
nucleus is engaged in behavioral inhibition, while
the function of the lateral VM nucleus is related to

motoric slowing or loss of motivational attention.
The VL nucleus sends neuronal output to the frontal
primary motor cortex (M1) and premotor cortex and
supplementary motor area (SMA) (Figures 2 and 3,
Table 2). It can be distinguish two sectors: (a) The VP
one is related to the motor cortex and helps to the
coordination and planning of movement, playing a
role in the learning of movement (its lesion causes
ataxia); and (b) the dorsal sector projects to the
posterior parietal cortex, to the prefrontal cortex, and
to the superior temporal cortex. The dorsal sector of the
VL nucleus is related with articulation of words and
language and the encoding and retrieval of verbal and
nonverbal information. The nucleus ventralis oralis posterior (Vop) receives the main output from motor
regions of medial globus pallidus, sending projections
to the SMA and DLPFC and then to M1
(Figures 2 and 3, Table 2). The nucleus ventralis intermedius, Vim (ventral LP nucleus), receives afferents
from the contralateral cerebellum and is the main
238
surgery target for treating tremor (Hyam, Owen, Kringelbach, et al., 2012; Schatelbrand & Bailey, 1959).
(iv) The thalamic limbic nuclei (Although nowadays the concept
of limbic system (related to emotion and memory) is
diffuse and variable, it was initially related to the cortex
that surrounds the thalamus, the grand lobe limbique of
Broca and the Papezs circuit. This circuit starts in the subiculum of the hippocampal formation projecting (fimbriafornix system) to the hypothalamic mammillary
complex that projects (mammillothalamic tract) to the
AN complex of the thalamus that sends its projections to
the cingulate cortex.) related to the limbic system (limbic
system used in its broadest sense) are located at the anterior
half part of the thalamus: the rostral pole with the AN
complex, the LD nucleus, and the magnocellular part of
the dorsomedial nucleus. Its function in general is related
with memory, learning, mood, emotional experiences, and
motivation (Child & Benarroch, 2012). The anterior complex is made up of the AD, AM, and AV nuclei and the LD
nucleus, which is considered a caudal extension of the
anterior complex. This group receives the projection from
the mammillary complex, being the AD nucleus the
nucleus that receives bilateral projections, while the projections to the AM and AV nuclei are only ipsilateral. It has
been established that it is only the posterior cingulate
cortex that receives afferents from the AN complex and
the LD of the thalamus, while anterior cingulate cortex
does receive afferents from the midline thalamic nuclei.
The anterior complex is reciprocally connected with the
hippocampal formation (memory-related functions)
through the mammillary nuclei. The mammillary nuclei
receive the postcommissural fornix and project to the AN
complex through the mammillothalamic tract. Other functional activities of the AN complex are related to the prefrontal cortex, with which it has extensive connections, as
well with parts of the cingulate cortex (The anterior cingulate cortex receives afferents as well from the MD thalamic
nucleus. In fact, there are two functional components
in the cingulate cortex: an anterior cingulate cortex territory under the dependence of the magnocellular part of
the MD nucleus and a posterior cingulate cortex dependent on the thalamic AN complex.) (Figures 2 and 3,
Table 2).
(v) The intralaminar thalamic nuclei can be classified into an
anterior and a posterior group. The anterior includes the
PCn and CL nuclei. The posterior group is integrated by
the CM and the Pf nuclei. The last two nuclei are the most
representative of the group and are related mainly to the
striatum and basal ganglia being the CM nucleus implicated in motor functions and the Pf nucleus in emotional
and cognitive circuits/loops. The intralaminar nuclei
have reciprocal connections with cortical areas and
receive afferents from the spinal cord, the brain stem,
and the cerebellum. In fact, the midline nuclei receive
nonspecific projections from the periaqueductal gray matter processing the motivational and affective components
of pain. Moreover, due to its cortical connections, the
intralaminar nuclei can form important hubs in frontal,
parietal, and temporal networks (Saalman, 2014; Figures 2 and 3, Table 2): (a) The anterior intralaminar
nuclei (PCn and CL nuclei) are part of the oculomotor
thalamus acting during spontaneous eye movements and

are active in arousal regulation probably synchronizing
ensembles of cortical neurons in different circuits; and
(b) the posterior intralaminar (CM and Pf) nuclei
showed preferential connectivity with subcortical structures (with the exception of the anterior insula) and
provided information about behaviorally relevant sensory events to the striatum and, therefore, can modulate
cortical synchrony by direct inputs to the cortex or
through thalamostriatal inputs to corticothalamocortical
loops (Figure 3).
(vi) The associative thalamic nuclei are those nuclei that have no
peripheral afferents, have no links with the primary
sensorimotor cortices, but are strongly interconnected
with cortical association regions. The associative nuclei
are the MD nucleus, the LP nucleus, and the Pul.
The mediodorsal nucleus (MD). Its size in humans is
much larger relative to the nonhuman primate and
constitutes an easy target for volumetric and functional studies (Mitchell & Chakraborty, 2013). It presents well-defined connections with the lateral,
orbital, and medial prefrontal cortex in nonhuman
primates as well as in humans. The territories projecting to the prefrontal cortex form adjacent bands running in a dorsolateral to ventromedial direction. The
magnocellular division (MDmc), which is the most
medially located band, is connected with the medial
frontal and orbitofrontal cortices and functionally
included in the limbic territories (Figures 2 and 3,
Table 2); the adjacent, parvocellular band (MDpc) is
related to the dorsolateral frontal cortex, and the most
lateral band (paralaminar) is specifically related to the
frontal eye fields. MD function is important for the
understanding of different symptoms of thalamic
syndromes. The nucleus reuniens provides afferents to
the entorhinal cortex and is reciprocally connected with
the prefrontal cortex. Other heterogeneous midline
nuclei (corresponding to the allothalamus, regio paraventricularis) are the paratenial, paraventricular, paracentral, and rhomboidal nuclei. Therefore, a great
number of small volume individual nuclei are concentrated in a small extension of brain tissue; for instance,
midline infarcts of the thalamus usually damage several
nuclei, thus making it difficult to assign specific function to particular nuclei.
The lateral posterior (LP) nucleus is interconnected
with the posterior cingulate cortex, the posterior parietal region, the lateral and dorsal extrastriate occipital
areas, and the parahippocampal region. Being able to
integrate multimodal sensory information, it is engaged
in goal direction reaching, spatial functions, and conceptual and analytical thinking.
The pulvinar complex (Pul) is the most conspicuous
part of the thalamus. It presents extensive connections
with the hippocampal formation; the parahippocampal, prefrontal, cingular, posterior parietal, and temporal cortices; and the insula. These connections sustain
various functions such as memory, attention, spatial
neglect, and visuospatial information. The anterior
extension of the nucleus named anterior pulvinar
nucleus (nucleus pulvinar oralis, PO) has been pointed

as one important part of the brain related to the appreciation of the pain. It is interconnected with the secondary somatosensory cortical as well as with cortical
association areas in the inferior parietal region
(Figures 2 and 3, Table 2). The lateral pulvinar (PL) is
specially linked with the posterior parietal region, with
the superior temporal cortex, and with dorsal extrastriate occipital areas, playing a role in the integration
of somatosensory, auditory, and visual information.
The inferior/medial pulvinar (PM) nucleus group lies
medial to the medial geniculate nucleus and it is interconnected with temporal and occipital areas concerned
with visuomotor responses as visual motion and visual
discrimination.
Thalamic Neurons and Afferents: Neurotransmitters,

Neuromodulators, and Function
Thalamic nuclei have the ability to filter signals, and to do so,
each thalamic projection neuron has an intrinsic rhythmicity.
All are in one of two basic physiological states: tonic mode and
burst mode. In tonic mode, thalamic neurons respond to
depolarization and hyperpolarization. In burst mode, thalamic
neurons are tonically hyperpolarized (for instance, during
sleep) and do not communicate specific information. But if a
novel stimulus is presented (by afferent fibers), the immediate
change of the physiological mode (from burst to tonic) can
alert the cortical areas. These changes are possible because
thalamic relay neurons (in all thalamic nuclei and in all species) have a symmetrical, bushy dendritic field (originally
described by Kolliker, 1890) (Jones, 2009). These neurons are
excitatory having glutamate as neurotransmitter (with the
exception of the RN in which projection neurons are all
GABAergic). There are two classes of relay cells: calbindinand parvalbumin-positive cells. The parvalbumin neurons are
topographically concentrated in certain nuclei, and the calbindin ones define a matrix in the whole thalamus and project
diffusely to the cortex. This fact provides a substrate for binding
together activities of multiple cortical areas that receive focused
input from single thalamic nuclei. Moreover, in all thalamic
nuclei exist many inhibitory (GABAergic and peptidergic)
interneurons, and its function is very important in controlling
the transmission of signals through the thalamus.
In general, thalamic afferents can be divided into drivers
and modulators (Varela, 2014). Thalamic drivers target proximal dendrites with relatively large synaptic boutons, and its
function is thought to be the faithful transmission of the spike
message relayed by thalamic cells to postsynaptic structures.
Thalamic modulators target distal dendrites and influence
spike transmission by adjusting the cellular and synaptic mechanisms underlying spike generation. Then, they are thought to
fine-tune the message relayed by thalamic cells and control its
probability of transmission. Thalamic modulators are heterogeneous in regard to their origin, the neurotransmitter they
use, and the effect on thalamic cells. The activity of thalamic
nuclei is changed by thalamic modulators as cholinergic, serotonergic, dopaminergic, and noradrenergic afferents from the
brain stem; histaminergic afferents from the hypothalamus;
and glutamatergic afferents from the cortical areas. Corticothalamic fibers interact with RN cells and relay cells through
glutamatergic receptors (NMDA, AMPA, and metabotropic).
239
The presence of specific and diffuse corticothalamic projections may serve to promote coherent activity of large populations of cortical and thalamic neurons in perception, attention,
and conscious awareness (Jones, 2002a). Additionally, thalamic nuclei receive inhibitory projections from the RN. The
interactions between RN cells and relay cells are mediated by
GABAergic inhibitory receptors (GABA-A and GABA-B). There
are intrinsic thalamic circuitries (generated and maintained by
corticothalamic projections) that interact with GABAergic cells
of the RN and glutamatergic relay cells. These intrinsic circuits
underlie rhythmic activities of neurons in the thalamo
corticothalamic network (associated with changes in the conscious state). Electrical synapses are a major feature of the
inhibitory circuitry in the thalamocortical system, mainly in
the RN. The interaction between inhibitory neurons can induce
rhythmic action potentials that are synchronized within a millisecond precision, being the substrate of temporal and spatial
coordination of the complex neural activity in the thalamocortical projections (The electrical synapses are active in the inhibitory circuitry of the thalamocortical system. Electrical synapses
have gap junction channels interconnecting neurons. Gap
junction channels (made of specific proteins connexins)
allow ionic current and small organic molecules to pass
directly between cells, usually with symmetrical ease
(Cruikshank, Landisman, Mancilla, & Connors, 2005).
Glutamatergic afferents from cortical layer VI

3050% of the pyramidal cells in layer VI of cortical areas
project to the thalamus with a high degree of topographic
precision. This is a very important afferent because layer VI
neurons receive input from all cortical layers and its information could serve to integrate processed cortical information
with the direct input from the thalamus.
Cholinergic afferents
Cholinergic systems have been broadly involved in state regulation (sleepwake cycle and attention) and may contribute to
state-dependent changes in information routing in the neocortex; brain stem cholinergic inputs can modulate cortical activity through the thalamus. Cholinergic neurons projecting to
the thalamus have collaterals to more than one thalamic
nucleus as well as to other nonthalamic regions. The main
sources of cholinergic innervation are the laterodorsal tegmental nucleus (LDTN) and the pedunculopontine tegmental
nucleus (PPN). The MD, LP, VA, ventral lateral, LD, and posterior nuclei receive fibers from the LDTN and the intralaminar
nuclei, and the CL nuclei receive afferent fibers bilaterally from
the PPN. The CM nucleus receives from both cholinergic areas.
Additionally, the PPN projects both to the LGN and to the
superior colliculus.
Serotonin innervation
Serotonergic projections from medial and lateral divisions of
the midbrain are implicated in the control of the sleepwake
cycle as well as in emotional disorders like depression. In the
thalamus, serotonergic afferents target preferentially the midline, anterior, and intralaminar nuclei (which are strongly
interconnected with cortical executive areas), where they have
heterogeneous effects on membrane potential and could evoke
changes in firing mode throughout the sleepwake cycle.
240
Noradrenaline (and galanin) projections
Thalamic Arterial Supply
Noradrenergic afferents come from the locus coeruleus (LC).

The LP nucleus, the Pul, and the somatosensory thalamus are
densely innervated by the LC. Thalamic noradrenaline modulation is important in executive and motor disorders as well as
in sensory responses.
Dopaminergic modulation
The thalamus does not receive strong dopaminergic innervation from the substantia nigra, but it gets dopamine afferents from the ventral tegmental area, the hypothalamus, the
zona incerta, the periaqueductal gray, and the lateral parabrachial nucleus. The densest projections are to the midline
thalamus, and the lowest densities are found in sensory firstorder nuclei. Dopaminergic terminals are often near thalamic terminals at their targets (e.g., the neocortex and
striatum); this means that at least some of the thalamic
dopaminergic modulation may occur at the terminal site
rather than at the soma.
Histamine
The histaminergic projection arises from the hypothalamic
tuberomammillary neurons (which are only active during
wakefulness and their degree of activation correlates with alertness levels). This modulator can be involved in attentional
levels and in the regulation of general changes of activity across
states of vigilance through the sleepwake cycle. Histaminergic
presynaptic receptors (H3 and H4) could be important in the
modulation of thalamostriatal terminals.
AN
IA
RN
D
IM
VA
MD
LD
VA
One of the main sources of information about thalamic functions is due to diseases of the cerebrovascular system, comparing the clinical symptoms with the location of the lesion on
in vivo neuroimaging or on pathological examination of the
brain (Schmahmann, 2003). The symptoms can reveal the
functional and behavioral roles of different thalamic nuclei,
but it is exceptional to have clean lesions (the infarcts usually
affect to vascular territories, which are not specific of single
nuclei) (Schmahmann & Pandya, 2008). In fact, vascular
lesions involve larger regions implicating few anatomical
nuclei; however, the functions of one (or more) region(s)
depending on the personal variation of the vascular anatomy
of each individual frequently prevail. The thalamic arteries vary
between individuals (the number of arteries and its position,
the origin, or the nuclei supplied by each branch). For instance,
the tuberothalamic artery is absent in approximately one-third
of the population (its territory is supplied by the paramedian
artery). Thalamic infarction or hemorrhage of each of the
different arterial territories develop the main four thalamic
vascular syndromes: (i) the tuberothalamic artery, which is a
branch of the carotid artery; (ii) the paramedian artery, which
is branch of the basilar artery; (iii) the inferolateral artery,
which is a branch of the posterior cerebral artery; and (iv) the
posterior choroidal artery, which is a branch of the mesencephalic artery (the mesencephalic artery is the P1 region of the
posterior cerebral artery) (Figure 4). For more details about the
vascular supply of thalamic nuclei and the main clinical features after focal thalamic infarctions, please see Tables 3 and 4
(modified from Schmahmann & Pandya, 2008).
P
V
VL
LP
VL
MD
Pu
VP
VP
EM
LGN
MGN
9
2
Pul
2
4
6 Tuberothalamic artery
7 Paramedian artery
8 Posterior choroidal artery
9 Inferolateral artery
Figure 4 Thalamic vascularization. A, anterior; AN, anterior nuclear complex; D, dorsal; EML, external medullary lamina; IA, interthalamic adhesion;
IML, internal medullary lamina; L, lateral; LD, laterodorsal nucleus; LGN, lateral geniculate nucleus; LP, lateral posterior nucleus; M, medial; MD,
mediodorsal nucleus; MGN, medial geniculate nucleus; P, posterior; Pul, pulvinar complex; V, ventral; VA, ventral anterior nucleus; VL, ventral lateral
nucleus; VP, ventral posterior nucleus. The tuberothalamic artery (6, in yellow) is a branch of the carotid artery (1); the paramedian artery (7, in green) is
a branch of the basilar artery (2); the posterior choroidal artery (8, in purple) is a branch of the mesencephalic artery (3) (the P1 region of the posterior
cerebral artery); the inferolateral artery (9, in blue) is a branch of the posterior cerebral artery (4). The posterior communicant artery (5) is located
between the carotid and the basilar arteries. Modified from Schmahmann, J. D., & Pandya, D. N. (2008). Disconnection syndromes of basal ganglia,
thalamus, and cerebrocerebellar systems. Cortex, 44, 10371066.
Table 3
Thalamic arterial supply
Thalamic arterial supply

Inferolateral artery
Principal
inferolateral
branch
Four major
thalamic arteries
Tuberothalamic
artery
Paramedian
artery
Nuclei irrigated
RN
AD, AM, AV
MD (ventral
pole)
IL
VA, VL
(rostral pole)
IML (ventral)
VAP
MTT
MD, PV
CL, CM, Pf
VPM
LD
Pul
(ventromedial)
Tracts irrigated
VP
VL (ventral part)
Posterior choroidal artery
Medial
branch
Inferolateral
pulvinar branches
Lateral
branches
Medial
branches
MGN
LD
Pul (rostral and
lateral)
LGN
LD
LP
Pul
(inferolateral)
MGN
CM, Pf
Pul
IML (dorsal)
AD, anterodorsal nucleus; AM, anteromedial nucleus; AV, anteroventral nucleus; CL, central lateral nucleus; CM, centromedian nucleus; IL, intralaminar nuclei; IML, internal medullary
lamina; LD, laterodorsal nucleus; LGN, lateral geniculate nucleus; LP, lateral posterior nucleus; MD, mediodorsal nucleus; MGN, medial geniculate nucleus; MTT, mammillothalamic
tract; Pf, parafascicular nucleus; Pul, pulvinar complex; PV, paraventricular nucleus; RN, reticular nucleus; VA, ventral anterior nucleus; VAP, ventral amygdalofugal pathway; VL,
ventral lateral nucleus; VP, ventral posterior nucleus; VPM, ventral posteromedial nucleus. The tuberothalamic artery is a branch of the carotid artery; the paramedian artery is a branch
of the basilar artery; the inferolateral artery is a branch of the posterior cerebral artery; the posterior choroidal artery is a branch of the mesencephalic artery (the P1 region of the
posterior cerebral artery).
Source: Modified from Schmahmann, J. D., & Pandya, D. N. (2008). Disconnection syndromes of basal ganglia, thalamus, and cerebrocerebellar systems. Cortex, 44, 10371066.
Table 4
Clinical features of focal infarction
Artery and territory

Tuberothalamic
artery
Paramedian artery
Inferolateral artery
Clinical features of focal infarction

RN
AD, AM, AV
MD (ventral pole)
IL
VA, VL (rostral pole)
Tracts irrigated
MD, PV
CL, CM, Pf
VPM
LD
Pul (ventromedial)
Tracts irrigated
Principal inferolateral
branch
IML
VAP
MTT
IML
VP complex
VA, VL, VM
Medial branch
Inferolateral pulvinar
branches
Posterior choroidal
artery
Lateral branches
Medial branches
MGN
Pul (rostral and
lateral)
LD
Pul (inferolateral),
LGN
LD, LP
Pul, MGN
CM, Pf
Confusion, memory, emotion, behavior

Executive failure, acalculia, apraxia
Fluctuating arousal and orientation
Impaired learning, memory, autobiographical memory
Personality changes, perseveration, apathy, abulia
Superimposition of temporally unrelated information
True to hemisphere:
Language ! if VL involved on left side
Hemispatial neglect ! if right-sided involved
Confusion, memory, language, behavior
Altered social skills and personality (including apathy, aggression,
and agitation)
Decreased arousal (coma vigil if bilateral)
Impaired learning and memory, confabulation, temporal
disorientation
Poor autobiographical memory
True to hemisphere:
Aphasia ! if left-sided
Spatial deficits ! if right-sided
Variable elements of a triad: hemisensory loss, hemiataxia, and
hemiparesis
Sensory loss (variable extent, all modalities)
Hemiataxia, hemiparesis, dystonia, tremor
Postlesion pain syndrome (DejerineRoussy) ! if right hemisphere
predominant
Auditory consequences
Behavioral impairment
Visual field loss (hemianopsia and quadrantanopsia)
Aphasia
Memory impairment
Variable sensory loss
Weakness
AD, anterodorsal nucleus; AM, anteromedial nucleus; AV, anteroventral nucleus; CL, central lateral nucleus; CM, centromedian nucleus; IL, intralaminar nuclei; IML, internal medullary
lamina; LD, laterodorsal nucleus; LGN, lateral geniculate nucleus; LP, lateral posterior nucleus; MD, mediodorsal nucleus; MGN, medial geniculate nucleus; MTT, mamilothalamic
tract; Pf, parafascicular nucleus; Pul, pulvinar complex; PV, paraventricular nucleus; RN, reticular nucleus; VA, ventral anterior nucleus; VAP, ventral amygdalofugal pathway; VL,
ventral lateral nucleus; VP, ventral posterior nucleus; VPM, ventral posteromedial nucleus.
Source: Modified from Schmahmann, J. D., & Pandya, D. N. (2008). Disconnection syndromes of basal ganglia, thalamus, and cerebrocerebellar systems. Cortex, 44, 10371066.
242
The thalamus not only relays peripheral information but also

plays a central role in cortical function. The role of thalamic
neurons is more complex than just sending information to the
cortical areas; the thalamic nuclei, with complex cell and circuit
properties, have dynamic roles controlling the flow of all
information, allowing the target cortical areas to be updated at
all time. The role of the RN is essential on this because inputs
coming, for example, to the MD nucleus from the periphery, or
from intrinsic brain structures, excite relay neurons; the collaterals
of these neurons cortically projecting axons excite the RN cells
projecting back to the same nucleus, thus forming an inhibitory
feedback connection to the relay cells. Additionally, fibers returning to the thalamus from the cortical area to which the MD
nucleus projects excite, by collaterals, cells in the same sector of
the RN, and its projection cells into the MD nucleus provide an
inhibitory feedforward to the relay cells. This bidirectional circuitry holds the key to understanding certain aspects of the capacity of the cortex to induce and/or maintain thalamocortical
synchrony (Jones, 2002b). However, we still do not know the
diverse thalamic circuitries and how those control the information
flowing to the cortex. In the last years, with the new in vivo techniques, novel thalamic functions have been described, but this is
just the tip of the iceberg, and we are far from understanding the
complex role of all these small but very important thalamic nuclei.
Acknowledgments
This article is supported by the University of Murcia (Campus
Mare Nostrum) and Spanish Center for Networked Biomedical
Research on Neurodegenerative Diseases (CIBERNED) (CB05/
05/505) to MTH and by grant BFU 2009-14705 of the Ministry
of Economy and Competitiveness and Junta de Comunidades
de Castilla-La Mancha to RI. The invaluable assistance of Juani
Alegra (Maqueta2, Murcia) to MTH through her drawings is
gratefully acknowledged.
References
Apkarian, A. V., Shi, T., Bruggemann, J., & Airapetian, L. R. (2000). Segregation of
nociceptive and non-nociceptive networks in the squirrel monkey somatosensory
thalamus. Journal of Neurophysiology, 84, 484494.
Bartlett, E. L. (2013). The organization and physiology of the auditory thalamus and its
role in processing acoustic features important for speech perception. Brain and
Language, 126, 2948.
Behrens, T. E.J, Johansen-Berg, H., Woolrich, M. W., et al. (2003). Non-invasive
mapping of connections between human thalamus and cortex using diffusion
imaging. Nature Neuroscience, 6, 750757.
Chen, W., Zhu, X. H., Thulborn, K. R., & Ugurbil, K. (1999). Retinotopic mapping of
lateral geniculate nucleus in humans using functional magnetic resonance imaging.
96, 24302434.
Child, N. D., & Benarroch, E. E. (2013). Anterior nucleus of the thalamus: Functional
organization and clinical implications. Neurology, 81, 18691876.
Craig, A. D. (2003). Pain mechanisms: Labelled lines versus convergence in central
processing. Annual Review of Neuroscience, 26, 130.
Cruikshank, S. J., Landisman, C. E., Mancilla, J. G., & Connors, B. W. (2005).
Connexon connexions in the thalamocortical system. Progress in Brain Research,
149, 4157.
Epstein, D. J. (2012). Regulation of thalamic development by sonic hedgehog. Frontiers in
Neuroscience, 6, 57. http://dx.doi.org/10.3389/fnins.2012.00057 (eCollection 2012).
Haber, S., & Calzavara, R. (2009). The cortico-basal ganglia integrative network: The
role of the thalamus. Brain Research Bulletin, 78, 6974.
Hassler, R. (1959). Anatomy of the thalamus. In G. Schaltenbrand, & P. Bailey (Eds.),
Introduction to stereotaxis with an atlas of the human brain. Stuttgart: Thieme.
Herrero, M. T., Barcia, C., & Navarro, J. M. (2002). Functional anatomy of thalamus and
basal ganglia. Childs Nervous System, 18, 386404.
Hirai, T., & Jones, E. G. (1989). A new parcellation of the human thalamus on the basis
of histochemical staining. Brain Research Reviews, 14, 134.
Hyam, J. A., Owen, S. L., Kringelbach, M. L., et al. (2012). Contrasting connectivity of
the ventralis intermedius and ventralis oralis posterior nuclei of the motor thalamus
demonstrated by probabilistic tractography. Neurosurgery, 70, 162169.
Iannilli, E., Singh, P. B., Schuster, B., Gerber, J., & Hummel, T. (2012). Taste laterality
studied by means of umami and salt stimuli: An fMRI study. NeuroImage, 60,
426435.
Jones, E. G. (2002a). Progress thalamic organization and function after Cajal. Progress
in Brain Research, 136, 333357.
Jones, E. G. (2002b). Thalamic circuitry and thalamocortical synchrony. Philosophical
16591673.
Jones, E. G. (2007). The thalamus (2nd ed.). Cambridge, UK: Cambridge University
Press.
Jones, E. G. (2009). Synchrony in the interconnected circuitry of the thalamus and
cerebral cortex. Annals of the New York Academy of Sciences, 1157, 1023.
Kolliker, A. (1896). (6th ed.). Handbuch der Gewebelehre des Menschen.
Nervensysteme des Menschen und der Thiere (Vol. 2, p. 95). Leipzig: Engelman.
Krauth, A., Blanc, R., Poveda, A., et al., (2010). A mean three-dimensional atlas of the human
thalamus: Generation from multiple histological data. NeuroImage, 49, 20532062.
Metzger, C. D., van der Werf, Y. D., & Walter, M. (2013). Functional mapping of
thalamic nuclei and their integration into cortico-striatal-thalamo-cortical loops via
ultra-high resolution imaging-from animal anatomy to in vivo imaging in humans.
Frontiers in Neuroscience, 7, 24.
Mitchell, A. S., & Chakraborty, S. (2013). What does the mediodorsal thalamus do?
Frontiers in Systems Neuroscience, 7, 37.
Morel, A. (2007). Stereotactic atlas of the human thalamus and basal ganglia. New York:
Informa Healthcare Inc.
Percheron, G., Francois, C., Talbi, B., Yelnik, J., & Fenelon, G. (1996). The primate
motor thalamus. Brain Research Reviews, 22, 93181.
Puelles, L., & Rubinstein, J. L. (1993). Expression patterns of homeobox and other
putative regulatory genes in the embryonic mouse forebrain suggest a neuromeric
organization. Trends in Neurosciences, 16, 472479.
Ramon y Cajal, S. (1903). Plan de estructura del talamo optico. Madrid: Congreso
Medico Internacional.
Ramon y Cajal, S. (1900). Cajal: Contribucion al estudio de la va sensitiva central y de
la estructura del talamo optico. (Con cuatro grabados.) Revista trimestral
micrografica, tomo V.
Saalman, Y. B. (2014). Intralaminar and medial thalamic influence on cortical
synchrony, information transmission and cognition. Frontiers in Systems
Schatelbrand, G., & Bailey, P. (1959). Introduction to stereotaxis with an atlas of the
human brain. Stuttgart: Thieme.
Schmahmann, J. D. (2003). Vascular syndromes of the thalamus. Stroke, 34,
22642278.
Schmahmann, J. D., & Pandya, D. N. (2008). Disconnection syndromes of basal
ganglia, thalamus, and cerebrocerebellar systems. Cortex, 44, 10371066.
Schneider, K. A., Richter, M. C., & Kastner, S. (2004). Retinotopic organization and
functional subdivisions of the human lateral geniculate nucleus: A high-resolution
functional magnetic resonance imaging study. Journal of Neuroscience, 24,
89758985.
Tuohy, E., Leahy, C., Dockery, P., et al. (2004). P1: An anatomical and MRI study of the
human thalamus. Journal of Anatomy, 205, 527.
Varela, C. (2014). Thalamic neuromodulation and its implications for executive
networks. Frontiers in Neural Circuits, 8, 69. http://dx.doi.org/10.3389/
fncir.2014.00069.
Vue, T. Y., Aaker, J., Taniguchi, A., et al. (2007). Characterization of progenitor domains
in the developing mouse thalamus. Journal of Comparative Neurology, 505, 7391.
Zhang, D., Snyder, A. Z., Shimony, J. S., et al. (2010). Non-invasive functional and
structural connectivity mapping of the human thalamocortical system. Cerebral
Cortex, 20, 11871194.
Relevant Websites
http://blog.susannereiterer.eu/wp-content/uploads/2013/01/06Mang_et-al-ThalamusSeg_MRM2011.pdf Thalamus Segmentation Based on the Local Diffusion
Direction: A Group Study.
http://www.princeton.edu/~napl/research.htm University of Princeton NAPL.
http://users.umassmed.edu/charlene.baron/pdfs/AxialMRI_Atlas08oe.pdf UMass
Medical School Mind Brain Behavior 1.
Cerebellum: Anatomy and Physiology

F Sultan, HIH for Clinical Brain Research, Tuebingen, Germany
Abbreviations
CF
DCN
IO
MF
PC
PF
Climbing fiber
Deep cerebellar nuclei
Inferior olive
Anatomy
Cerebellum: Basic Structural Organization
The cerebellum is present in nearly all vertebrates and
undergoes a remarkable expansion in the mammalian and
avian orders. The cerebellum of mammals is composed of a
strongly folded cerebellar cortex that covers the white matter
and the deep cerebellar nuclei (DCN). The cerebellar cortex
consists of three layers: the granule cell layer, the molecular
layer, and, in between these two, the Purkinje cells (PCs)
arranged in a two-dimensional array. The cerebellar cortex
receives two kinds of afferents, the mossy fiber (MF) and
climbing fiber (CF), which mediate a wide variety of vestibular,
somatosensory, visual, and auditory sensory modalities, as
well as tectal and cerebral cortical afferents. MFs contact the
granule cells that send their axons to the molecular layer where
they make T-shaped ramifications, the so-called parallel fibers
(PFs). These PFs are very thin and unmyelinated and form
excitatory synapses on their postsynaptic targets. They contact
the dendritic trees of the PCs and of the inhibitory interneurons of the molecular layer (the so-called basket and stellate
cells) up to a distance of 23 mm from the site of bifurcation.
The myelinated CFs, all of which have their origin in the
inferior olive (IO), contact the PCs directly. The PCs mediate
the sole output of the cerebellar cortex by projecting to the
DCN and to the vestibular nuclei.
Unlike in the cerebral cortex, there are few obvious structural differences among different regions of the cerebellar
cortex. Moreover, in comparison with the cerebral cortex,
the cerebellar cortex stands out through its well-defined geometric texture. The parallel arrangement of the folds of the
cerebellum, with the folds all running in a laterolateral
direction, is readily apparent macroscopically. The PFs all
run along the folds. They constitute one-half of the orthogonal cerebellar lattice, while the dendritic trees of the PCs and
the dendrites and axons of the basket and stellate cells provide
the other. The latter all ramify only in the direction perpendicular to the folds.
The majority of the cell types in the cerebellum are inhibitory. However, the granule cells with their PF axons are the
most numerous cells in the cerebellum and are excitatory. The
excitatory pyramidal cells in the cerebral cortex form contacts
with each other, whereas the granule cells do not. In fact, the
division of the cerebellar cortex into two major layers (the
granular and molecular layers) appears to have the important
consequence of keeping the granule cell dendrites and their
Mossy fiber
Purkinje cell
Parallel fiber
axons separate, that is, retaining the dendrites in the granule

cell layer and the axons in the molecular layer, thereby preventing them from making synapses among themselves.
Nomenclature and Macroscopic Anatomy of the Cerebellum

Unlike the unique cerebellar microcircuit, which shows a
marked degree of similarity within different regions of the
cerebellum and within different species, there are intriguing
differences in the relative size of the cerebellar lobes in different species. Careful dissection in mammals reveals a singular
chain within the anterior region (lobus anterior), which splits
within the posterior lobe into three ends (the hemispheres and
the posterior vermis).
Early ontogenetic studies delineated three parts within the
cerebellum: a middle part (vermal, connected to the middle
cerebellar nuclei), an intermediate part (connected to the two
interposed nuclei), and a lateral part (connected to the lateral
nuclei, dentate nucleus in apes and humans). This parasagittal
organization was later shown by Jan Voogd to have a much
finer structure (Voogd, 1969). The three parts could be further
delineated into much finer zones, known as the longitudinal
zones.
Several different procedures are used for naming the lobes
and lobules of the mammalian cerebellum. The nomenclatures
are illustrated in Figure 1(a) and 1(b) and were based on
comparative studies of the mammalian cerebellum by the
Dutch anatomist Lodewijk Bolk (Bolk, 1906) and later by
Larsells study of the birds cerebellum (Larsell, 1948).
In mammals, the hemispheres exhibit two regions where
the folial chain expands more than at the corresponding vermal site (Figure 1(b)). This leads to the formation of two loops
in the folial chain. The first loop includes the lobules of crus I
and crus II, while the second loop is in the region of the
paraflocculus. The two loops are separated by the paramedian
lobe, which remains in close proximity to the vermal region
(lobule VIII). The vermal lobules are numbered IX according
to Larsells studies. On the basis of the assumption that the
vermal and hemispheric lobules correspond in numbers, the
latter are equivalently numbered with roman numerals with an
H prefix.
One marked feature of the mammalian cerebellar cortex is
its extensive anteroposterior length (Figure 1(c) and 1(d)).
The extensive folding within the cerebellum is the result of
having to accommodate a larger sheet of tissue.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00218-9
243
244
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Cerebellum: Anatomy and Physiology
Anterior lobe
Anterior lob.
A X B C 1 C 2 C3 D 1 Y D 2
I
II/III
Crus I
IV/V
VI
Lob. simplex
Lob. simplex
VIIA
Crus II
VIIB
Paramedian lob. VIII

10 cm
30 cm
Dorsal parafloc.
XI
Ventral parafloc.
Crus I
X
Flocculus
(b)
(c)
Vent.
Floc. parafloc.
Paramed.
Dors.
parafloc. lob.
Crus II
(a)
(d)
Figure 1 Introduction to the cerebellar anatomy. (a) Drawing of the dorsal view of the human cerebellum. Modified from Riley, H. A. (1928).
The mammalian cerebellum. Archives of Neurology & Psychiatry, 20, 8951034. The cerebellum is slightly stretched to enable the different lobules to
be more easily distinguished. In (b), the correspondence of the human lobes and lobules to that of the cats cerebellum is shown. Modified
from Glickstein, M., Sultan, F., & Voogd, J. (2009). Functional localization in the cerebellum. Cortex, 47, 5980. The cats cerebellum is now
stretched semiquantitatively. The right-hand side of (b) shows the longitudinal zones (A, X, B, C13, D12, and Y) according to Voogd and Bigare (1980).
(b) Within the vermis (middle folial chain), the lobule numbering IX according to Larsell (1948) is shown. The quantitative extent of the
unfolded cat (c) and the human cerebellum (d) is shown. The silhouette-like maps were obtained by connecting the ends of the most prominent folia.
The scale in between corresponds to 10 cm for the cat and 30 cm for the human cerebellum. Modified from Sultan, F., & Braitenberg, V. (1993).
Shapes and sizes of different mammalian cerebella. A study in quantitative comparative neuroanatomy. Journal fur Hirnforschung, 34, 7992.

Cerebellar Afferents
The cerebellar cortex receives its information via two distinct
afferents: the MF and CF. They differ markedly in their synaptic
anatomy and physiology and in their source and site of termination. The CFs originate solely from the neurons of IO and
constitute a direct pathway that terminates on the PC dendrites. They also provide collaterals to the cerebellar nuclei.
MFs comprise the major input to the cerebellum. By contrast, the MFs make contacts with granular and Golgi cells and
form an indirect pathway that terminate in the granular layer.
The CFs contact approximately 10 PCs (Shinoda, Sugihara,
Wu, & Sugiuchi, 2000) in a 1:1 fashion (an adult PC receives
input from one CF only; Eccles, Ito, & Szentagothai, 1967;
Rossi, Wiklund, Van Der Want, & Strata, 1989). The MFs
bifurcate to terminate in about 100200 enlarged presynaptic
islands called rosettes, thereby contacting about 20004000
granule cell dendrites (Palkovits, Magyar, & Szentagothai,
1972; Shinoda et al., 2000). Via the PFs, one MF could
therefore ultimately reach out to several thousand PCs. In
addition to visual and vestibular information, MFs convey
information from auditory, proprioceptive, and exteroceptive
somatosensory receptors; for a review, see Voogd (2004). MFs
convey information from vestibular, proprioceptive, and
exteroceptive receptors. In mammals, the largest number of
MFs conveys information from the cerebral cortex
(Glickstein, Sultan, & Voogd, 2011).
The MFs convey information by rate coding in a veridical
manner and with up to several hundreds of spikes per second
(Gibson, Horn, & Pong, 2004), thereby conveying information
about position, direction, and velocity of body parts or external
stimuli (tactile, proprioceptive, vestibular, visual, and auditory). By contrast, the CFs have a much lower firing frequency
(average of 0.21 Hz) and have been proposed to signal the
occurrence of an unexpected event (Gellman, Gibson, & Houk,
1985) or to resynchronize or reset PCs (Murphy & Sabah,
1971); for a review, see Gibson et al. (2004).
Cerebellar modules
The cerebellar cortex shows no obvious differences between its
various areas. Analysis of its connections and chemoarchitecture reveal, however, that the PCs are arranged in a series of
precisely organized zones (Voogd, 1969) with different histochemical properties (Hawkes & Leclerc, 1987). The zonal organization of the cerebellar output system is the basis of the
modular organization of the cerebellum. The zones are a series
of stripes oriented perpendicularly to the folia and fissures. The
functional nature of the zones is determined by the output of
their target nuclei (for a review, see Glickstein et al., 2011).
The longitudinal or parasagittal zones were originally
defined by mapping both the anatomical connectivity
(Voogd, 1969) and the electrophysiological receptive field
responses (Oscarsson, 1969) following somatosensory stimulation. Oscarsson and colleagues showed that the longitudinal
zones in the cat were 1 mm wide (along the PF axis) and
100 mm long. An even finer parcellation into microzones
with 200 mm width was also shown (Oscarsson, 1979). PCs
within such a zone project to a defined region of the cerebellar
output structures, the DCN and vestibular nuclei. Neurons
within the IO nucleus are organized in subgroups that project
245
their axons as CFs to PCs that are restricted within a longitudinal zone. The IO neurons also innervate subgroups of the DCN
and vestibular nuclei via axon collaterals. These subgroups
then receive input from the same PCs. These connected subgroups of neurons in the IOPCDCN and IODCN paths
join to constitute a module. Oscarsson proposed that these
modules are the operational units of the cerebellum
(Oscarsson, 1979). The importance of these zones was reinforced by the fact that they were found in a number of animals.
In various animal species (birds and mammals), very similar pattern can be observed in several regions within the
cerebellum (notably the regions at the rostral and caudal
ends, that is, the lobus anterior and the floccularnodular
parts). Careful mapping of the sensory receptive fields divulged
that longitudinal zones can be divided even further into what
are known as microzones.
Based on the molecular gene expression found in PCs, it
was possible to unveil a concept similar to that of longitudinal/
sagittal zones. The first molecule to be studied in depth was
Zebrin II (metabolic aldolase C), which was discovered by
Hawkes and Leclerc (1987) in PCs and surrounding glia. Subsets of PC positive for the epitope alternate with negative
stripes. Like the zones, the stripes are distributed symmetrically
across the midline. Later studies showed that the Zebrin stripes
do not show the full complexity of heterogeneous molecular
markers in PCs, since even finer bands can be detected within
Zebrin bands (see Apps & Hawkes, 2009 for review). The way
in which the strips are organized is reminiscent of the microzonal organization. They are similar in both size
(100300 mm wide) and number (several hundred stripes
in mice and rats). Each stripe is estimated to have several
hundred PCs (total number of PCs in rats 3 105).
Cerebellar Nuclei and Cerebellar Output

All of the output of the cerebellar cortex converges onto the
DCN and parts of the vestibular nuclei. These nuclei then
mediate the cerebellar output to the red nucleus, parts of the
thalamus, the reticular formation, the IO, the vestibular nuclei,
and other brainstem centers. The DCN can be delineated into
several nuclei, which have different inputoutput and cytological characteristics. All DCN subregions contain GABAergic
and glutamatergic cells (Batini, Compoint, Buisseret-Delmas,
Daniel, & Guegan, 1992). The glutamatergic neurons constitute a rather homogeneous population of large projection
neurons, which send their axons to the ventrolateral thalamus
(Sakai, Inase, & Tanji, 1996), the red nucleus (Kennedy,
Gibson, & Houk, 1986), the vestibular nuclei (Walberg,
Pompeiano, Brodal, & Jansen, 1962), and various other brain
stem nuclei. The GABAergic cells can be separated into at least
two distinct groups: the larger one projects to the IO (Angaut &
Sotelo, 1987), while the neurons of the smaller group very
probably do not project to targets outside the DCN. For
unknown reasons, a substantial portion of the GABAergic neurons in the DNC seem to coexpress the inhibitory transmitter
glycine (Chen & Hillman, 1993).
Based on classical descriptions, four cerebellar nuclei are
generally distinguished: the medial (NM, fastigial), posterior
interposed (NIP, globose), anterior interposed (NIA,
emboliform), and lateral (NL, dentate) nuclei. A further cell
246
cluster, the interstitial cell groups, is located between the fastigial and posterior interposed nuclei.
The differentiation of subregions within the DCN is intimately linked to the parcellation of the connected cerebellar
cortex and IO. Using aldolase C labeling, the DCN can be
further distinguished into ten regions. In an elaborate study,
multiple small tracer injections into the IO revealed clustering
of the IODCN collaterals (collaterals of the CF), demarking
well-delineated subregions in the DCN (Figure 2). The extent
of the IO collaterals in the DCN was limited to a radius of
about 100150 mm. A careful analysis by Sugihara and
Shinoda (2007) showed that these numerous clusters could
be classified into five classes on the basis of the origin of the
respective olivary axons, the connection to the cerebellar

cortex and their targets. The neurons of groups I, II, and V
are usually located within the aldolase C-positive staining
region and the remainder within the unstained region of the
DCN. Sugihara and Shinoda also linked the classes via their
output connections to vestibular, collicular, and other
somatosensory functions. In a recent pharmacological deactivation study in the cats IO, Gibson and colleagues (Horn,
Pong, & Gibson, 2010) observed behavioral motor deficits
following the inactivation of different modules. They
observed unique and complex deficits that affected the forelimb coordination in either a reach-to-grasp or locomotive
tasks, depending on which modules were affected. This is
Group
Cerebellar
cortex
aldolase C
Cerebellar
cortex zones
I
(green)
Mesodiencephalic
IIa
(cyan and blue)
Vestibular
IIa
(cyan and blue)
Collicular
III
(yellow and orange)
Somatosensory,
Vestibular,
Mesodiencephalic
IV
(pink and red)
Somatosensory
V (gray)
Visual
Caudodorsal view
(b)
(a)
(c)
Figure 2 Cerebellar zones. Mapping of the topography of the olivocortical and olivonuclear projections together with aldolase C immunostaining. In the
work by Sugihara and Shinoda (2007), five groups were distinguished and mapped onto the unfolded cerebellar cortex of a rat (a). (b) and (c) show
the 3-D scheme and two views of the left DCN (b: ventral portions; c: dorsocaudal view). The zones defined by aldolase C are marked by numerals
with / signs, denoting aldolase C-positive and aldolase C-negative stained regions. The convention is that the numbering ascends from the most
medial stripe. This plot is the summary of a large number of experiments, tracing the olivocerebellar, olivonuclear, and corticonuclear projections. The
correspondence of this nomenclature with Voogds zones (Figure 1(b)) is shown in the table. The table also denotes the afferent types received by
the corresponding olivary regions and the color coding. The arrows represent a finer topographic correspondence within each group between the areas
in the cortex and the nuclei. Reproduced from Sugihara, I., Fujita, H., Na, J., Quy, P. N., Li, B.-Y., & Ikeda, D. (2009). Projection of reconstructed
single purkinje cell axons in relation to the cortical and nuclear aldolase C compartments of the rat cerebellum. The Journal of Comparative Neurology,
512, 282304, with permission of John Wiley & Sons, Inc.

one of the first studies to experimentally confirm the relationship between a specific function and the cerebellar zones/
modules.
Scaling of the Cerebellum: Evidence for Prominent

Irregularities Embedded in Marked Regularities
Despite the fact that its surface is comparable to the surface of
one cerebral hemisphere (Sultan, 2002), the cerebellum in
mammals occupies only 1020% of the total brain volume.
The surface of the cerebellum increases simultaneously with
the increase in the surface of the cerebral cortex. The discrepancy between volume and surface between the two cortices is
due to the fact that in mammals, the white matter of the
cerebral cortex increases with brain size from 15% to 75%,
while the cerebellar volume remains constant. Despite this
lower contribution to brain volume, with regard to numbers,
cerebellar neurons actually comprise the majority of neurons
in the brain (6080% of all neurons from mouse to human).
This discrepancy is due to two factors. The first factor is the
high density of cerebellar neurons (i.e., the granule cells),
which is about 10 times higher than the density of neurons
in the cerebral cortex and which remains remarkably constant
in the brains of different sizes. By contrast, in the cerebral
cortex of most larger brains, neuron density decreases. This is
due to the second factor: the increase in the axonal volume
leading to white matter increase and neuron density decrease
in the gray matter (for a review, see Schuz & Sultan, 2009).
The scaling of the brains, as is observed in different-sized
animals with different-sized brains, shows a remarkable regularity and points to rules that provide clues to the underlying
functional network architecture (Braitenberg, 2001). Equally
important is a departure from a regular scaling, which is
observed in the especially large-brained mammals (primates
and cetaceans). The cerebellum is ideal for seeking such deviations from the rule, due to its otherwise strict modular
composition.
Variations in Cerebellar Shape Within Mammals

Unlike the surprisingly extensive anteroposterior extension of
the unfolded cerebellum, the mediolateral extension provides
a different observation. The cerebellar width (unfolded
laterolateral extension) does not vary considerably between
mammals, which is in full agreement with the longitudinal
zone organization in mammals (Sultan & Braitenberg, 1993).
The few exceptions in which we observe changes in width are
therefore worth mentioning. In humans (as in all apes), in
marine mammals, and possibly even in elephants, there is a
substantial increase in cerebellar width (Figure 3), indicating a
change in the pattern of longitudinal zones or microzonal
pattern. In apes and humans, this is most clearly observed in
crus I and crus II of the hemispheres. The cerebellar hemispheres are connected to parts of the DCN, known as the
dentate nucleus. This nucleus reveals a unique expansion,
beginning in monkeys (Matano & Hirasaki, 1997) and continuing through apes to the human dentate nucleus. The longitudinal zone that increases in width is known as the D-zone
(see Figure 1(b)). The enlargement of the cerebellum in
247
Elephant
Chimpanzee
Manatee
Kangaroo
Rhesus
Flying fox
Rabbit
Porpoise
Rat
Cat
Bear
Cow
Figure 3 Comparative anatomy of the cerebellum. Mapping different

lobules and lobes in the cerebellum of mammals. These somewhat
stretched cerebellums (only right half shown) were devised by Riley
(1928) and have been colored to ease the distinction of the different
lobes. In contrast to the hemispheric chain, the vermal folial chain
continues into the posterior vermis (green) and the nodulus (yellow);
from the anterior end (pointing rightward in the figure), the anterior lobe
is colored in red, followed by the lobus simplex (cyan), crus I and crus II
(blue), the paramedian lobe (orange), the dorsal paraflocculus (violet),
and the ventral paraflocculus and flocculus (yellow).
primates has long fueled the theory that the cerebellum is

involved in higher cognitive nonsensorimotor functions.
The human dentate is one of the two folded nuclei of the
brain, the other being the pars principalis of the IO, which has,
interestingly enough, strong connections with the dentate
nucleus. It is not clear why these two nuclei are folded. At
any rate, this feature seems to be peculiar to humans and the
great apes, since other mammals with large cerebella, such the
cetaceans, exhibit more globular nuclei.
The primate and hominid dentate is traditionally divided
into an evolutionary older dorsal half and a newer ventral half
(Dum, Li, & Strick, 2002; Leiner, Leiner, & Dow, 1993;
Schmahmann & Caplan, 2006). One popular model assumes
that this division reflects the emergence of a cerebellofrontal
projection and the enhancement of specifically human cognitive functions mediated by the prefrontal cortex such as language. The morphological differentiation was based on the
thicker (macrogyric) folds in the ventral part with smaller
neurons and thinner (microgyric) folds in the dorsal part of
the nucleus (summarized by Dow, 1942). Quantification of
the dentate thickness validates this approach in the macaque
monkey. However, this is much less evident in the human
dentate (see Figure 4). The human dentate model reveals that
the majority of the folds run in a course perpendicular to the
248
Prosimian-type
Simian-type
Hominoid-type
Log dentate volume (mm3)
103
Human
Baboon
Gibbon
Spider monkey
Rhesus monkey
102
101
Primates/lsq: y=1.04x +0.0015;r^2=0.98; n=45
100
100
101
(a)
102
Log brain weigth (g)
103
dors
ant
post
vent
(b)
(d)
lat
med
5 mm
(c)
1
0.5
0
(e)
5 mm
Figure 4 Comparative DCN. Regularities and irregularities are evident in the scaling of the cerebellar dentate nucleus. In (a), data from the study of
Macleod, Zilles, Schleicher, Rilling, and Gibson (2003) are shown (Glickstein et al., 2011). Plotted is the dentate volume versus brain volume for
primates on a double-logarithmic plot. A proportional increase in the volume of both can be observed (slope of regression line of 1.04). Different primate
suborders are denoted with different symbols. The gibbon is the first ape that shows a highly folded dentate, although the volume of its dentate is
comparable to other monkeys of similar size. (be) Surface reconstructions of the dentate nucleus of the macaque (b and c) and of the human (d and e).
Overlaid on the surfaces is the thickness of the lamina at the respective site color-coded with white depicting thicker regions (see color bar). Clearly, a
thicker macrogyric part can be discerned in the ventrolateral region of the macaque. This is not the case in the human dentate. Scale bars: 5 mm.
folds of the cerebellar cortex and parallel to the parasagittal

microzones of the cerebellum (Voogd & Glickstein, 1998).
The major change in the hemispheres of the ape cerebellum
is an increase in width (Sultan & Braitenberg, 1993). The
marked transition from the monkey to human dentate is first
observed in Gibbons (see Glickstein, Sultan, & Voogd, 2009 for
a review). Gibbons are the evolutionarily earliest apes that we
know of that already had a dentate that differed from that of
monkeys. Gibbons excel in a suspensory locomotion-type
called brachiation, long thought to be the primate specialization leading to the emergence of bipedalism and later to the
emergence of human typical manipulative skills (Gebo, 1996
for review). Interestingly enough, fMRI studies have also
shown that the human dentate nucleus is activated in manipulative tasks (Dimitrova et al., 2006; Gao et al., 1996).
The specialization of the primate cerebellum becomes particularly evident when compared to marine mammals (see
Figure 4). In cetaceans (whales and dolphins) and pinnipeds
(seals), the second loop containing the dorsal and ventral
paraflocculus is much larger. The huge size of the paraflocculus
is due to an expanded (width and length) C2 zone and an
extremely expanded nucleus interpositus posterior, as opposed
to the primate D2-dentate expansion in width and length. This
differential expansion in these very encephalized animals is an
excellent example of specialized brain architecture and refutes
the theory that regular brain scaling underlays large brains. In

view of the connected and coenlarged auditory structures (see
Oelschlager, 2008), a role of the cerebellum in the enhanced
auditory capabilities of marine mammals becomes more than
mere speculation.

Evolution of the Cerebral Cortex; The Brain Stem; INTRODUCTION
TO SYSTEMS: Neural Correlates of Motor Deficits in Young Patients
with Traumatic Brain Injury.
References
Angaut, P., & Sotelo, C. (1987). The dentato-olivary projection in the rat as a
presumptive gabaergic link in the olivocerebelloolivary loop An ultrastructuralstudy. Neuroscience Letters, 83, 227231.
Apps, R., & Hawkes, R. (2009). Cerebellar cortical organization: A one-map hypothesis.
Batini, C., Compoint, C., Buisseret-Delmas, C., Daniel, H., & Guegan, M. (1992).
Cerebellar nuclei and the nucleocortical projections in the rat: Retrograde tracing
coupled to GABA and glutamate immunohistochemistry. Journal of Comparative
Bolk, L. (1906). Das Cerebellum der Saugetiere. Jena: Gustav Fischer Verlag.
Braitenberg, V. (2001). Brain size and number of neurons: An exercise in synthetic
neuroanatomy. Journal of Computational Neuroscience, 10, 7177.
Chen, S., & Hillman, D. E. (1993). Colocalization of neurotransmitters in the deep
cerebellar nuclei. Journal of Neurocytology, 22, 8191.
Dimitrova, A., De Greiff, A., Schoch, B., Gerwig, M., Frings, M., Gizewski, E. R., et al.
(2006). Activation of cerebellar nuclei comparing finger, foot and tongue
movements as revealed by fMRI. Brain Research Bulletin, 71, 233241.
Dow, R. S. (1942). The evolution and anatomy of the cerebellum. Biological Reviews of
the Cambridge Philosophical Society, 17, 179220.
Dum, R. P., Li, C., & Strick, P. L. (2002). Motor and nonmotor domains in the monkey
dentate. Annals of the New York Academy of Sciences, 978, 289301.
Eccles, J. C., Ito, M., & Szentagothai, J. (1967). The cerebellum as a neuronal machine.
Berlin: Springer-Verlag.
Gao, J. H., Parsons, L. M., Bower, J. M., Xiong, J., Li, J., & Fox, P. T. (1996).
Cerebellum implicated in sensory acquisition and discrimination rather than motor
control. Science, 272, 545547.
Gebo, D. L. (1996). Climbing, brachiation, and terrestrial quadrupedalism: Historical
precursors of hominid bipedalism. American Journal of Physical Anthropology,
101, 5592.
Gellman, R., Gibson, A. R., & Houk, J. C. (1985). Inferior olivary neurons in the awake
cat: Detection of contact and passive body displacement. Journal of
Gibson, A. R., Horn, K. M., & Pong, M. (2004). Activation of climbing fibers.
Cerebellum, 3, 212221.
Glickstein, M., Sultan, F., & Voogd, J. (2009). Functional localization in the cerebellum.
Cortex, 47, 5980.
Glickstein, M., Sultan, F., & Voogd, J. (2011). Functional localization in the cerebellum.
Cortex, 47, 5980.
Hawkes, R., & Leclerc, N. (1987). Antigenic map of the rat cerebellar cortex: The
distribution of parasagittal bands as revealed by monoclonal anti-Purkinje cell
antibody mabQ113. Journal of Comparative Neurology, 256, 2941.
Horn, K. M., Pong, M., & Gibson, A. R. (2010). Functional relations of cerebellar
modules of the cat. Journal of Neuroscience, 30, 94119423.
Kennedy, P. R., Gibson, A. R., & Houk, J. C. (1986). Functional and anatomic
differentiation between parvicellular and magnocellular regions of red nucleus in the
monkey. Brain Research, 364, 124136.
Larsell, O. (1948). The development and subdivisions of the cerebellum of birds.
249
Leiner, H. C., Leiner, A. L., & Dow, R. S. (1993). Cognitive and language functions of
the human cerebellum. Trends in Neurosciences, 16, 444447.
Macleod, C. E., Zilles, K., Schleicher, A., Rilling, J. K., & Gibson, K. R. (2003).
Expansion of the neocerebellum in Hominoidea. Journal of Human Evolution, 44,
401429.
Matano, S., & Hirasaki, E. (1997). Volumetric comparisons in the cerebellar complex of
anthropoids, with special reference to locomotor types. American Journal of
Physical Anthropology, 103, 173183.
Murphy, J. T., & Sabah, N. H. (1971). Cerebellar Purkinje cell responses to afferent
inputs. I. Climbing fiber activation. Brain Research, 25, 449467.
Oelschlager, H. H.A (2008). The dolphin brainA challenge for synthetic
neurobiology. Brain Research Bulletin, 75, 450459.
Oscarsson, O. (1969). The sagittal organization of the cerebellar anterior lobe as
revealed by the projection patterns of the climbing fiber system. In S. R. Llin (Ed.),
Neurobiology of cerebellar evolution and development. Chicago, IL: American
Medical Association.
Oscarsson, O. (1979). Functional units of the cerebellum Sagittal zones and
microzones. Trends in Neurosciences, 2, 143145.
Palkovits, M., Magyar, P., & Szentagothai, J. (1972). Quantitative histological analysis
of the cerebellar cortex in the cat. IV. Mossy fiber-Purkinje cell numerical transfer.
Riley, H. A. (1928). The mammalian cerebellum. Archives of Neurology & Psychiatry,
20, 8951034.
Rossi, F., Wiklund, L., Van Der Want, J. J. L., & Strata, P. (1989). Climbing fibre
plasticity in the cerebellum of the adult rat. European Journal of Neuroscience, 1,
543547.
Sakai, S. T., Inase, M., & Tanji, J. (1996). Comparison of cerebellothalamic
and pallidothalamic projections in the monkey (macaca-fuscata) A
double anterograde labeling study. Journal of Comparative Neurology, 368,
215228.
Schmahmann, J. D., & Caplan, D. (2006). Cognition, emotion and the cerebellum.
Brain, 129, 290292.
Schuz, A., & Sultan, F. (2009). Brain connectivity and brain size. In In: L. R. Squire
(Ed.), New Encyclopedia of neuroscience (vol. 2. Oxford: Academic Press.
Shinoda, Y., Sugihara, I., Wu, H. S., & Sugiuchi, Y. (2000). The entire trajectory of
single climbing and mossy fibers in the cerebellar nuclei and cortex. Progress in
Sugihara, I., Fujita, H., Na, J., Quy, P. N., Li, B.-Y., & Ikeda, D. (2009). Projection of
reconstructed single purkinje cell axons in relation to the cortical and nuclear
aldolase C compartments of the rat cerebellum. The Journal of Comparative
Neurology, 512, 282304.
Sugihara, I., & Shinoda, Y. (2007). Molecular, topographic, and functional organization
of the cerebellar nuclei: Analysis by three-dimensional mapping of the
olivonuclear projection and aldolase C labeling. Journal of Neuroscience, 27,
96969710.
Sultan, F. (2002). Analysis of mammalian brain architecture. Nature, 415,
133134.
Sultan, F., & Braitenberg, V. (1993). Shapes and sizes of different mammalian cerebella.
A study in quantitative comparative neuroanatomy. Journal fur Hirnforschung, 34,
7992.
Voogd, J. (1969). The importance of fiber connections in the comparative anatomy of
the mammalian cerebellum. In S. R. Llin (Ed.), Neurobiology of cerebellar evolution
and development. Chicago, IL: American Medical Association.
Voogd, J. (2004). Cerebellum and precerebellar nuclei. In G. Paxinos & J. K. May
(Eds.), The human nervous system. Amsterdam: Elsevier.
Voogd, J., & Bigare, F. (1980). Topographical distribution of olivary and corticonuclear fibers in the cerebellum: A review. In J. Courville (Ed.), The inferior olivary
nucleus: Anatomy and physiology. New York: Raven Press.
Voogd, J., & Glickstein, M. (1998). The anatomy of the cerebellum. Trends in
Walberg, F., Pompeiano, O., Brodal, A., & Jansen, J. (1962). The fastigiovestibular
projection in the cat. An experimental study with silver impregnation methods.
The Brain Stem

C Watson, Curtin University, Perth, Australia; Neuroscience Research Australia, Sydney, Australia
J Ullmann, University of Queensland, Brisbane, Australia
Glossary
Axial hindbrain The cylindrical part of the hindbrain that

lies between the midbrain and spinal cord; the axial
hindbrain includes the mature isthmus and 11
rhombomeres.
Diffusion weighted imaging A form of MRI based on the
diffusion of water molecules in a voxel.
Genetic fate mapping The use of site-specific recombinases
combined with reporter alleles to demonstrate the postnatal
anatomical location of transient regions of gene expression
during development.
Genetic inducible fate mapping The use of an inducible
form of Cre expression that can be limited to a short
time period during development, which can be
achieved by triggering the expression of a modified
estrogen receptor (ER) by administration of the drug
tamoxifen.
Introduction
The brain stem joins the forebrain to the spinal cord. It consists
of the midbrain and the hindbrain. The cerebellum is an
outgrowth of the rostral hindbrain and technically should be
included as part of the hindbrain. However, it is not considered
in most texts to be an integral part of the brain stem, and in this
book, it will be dealt with in a separate article. We have found
that the best way to deal with this semantic problem is to use
the term axial hindbrain to distinguish the cylindrical parts of
the hindbrain from the cerebellar outgrowth.
The discovery of gene targeting in mice (Capecchi, 1989,
2005) has opened a new era of brain anatomy, in which
patterns of developmental gene expression can be used to
define the true relationships and subdivisions of parts of the
brain. These new revelations have had a major impact on
concepts relating to the midbrain and hindbrain. The most
important of these changes are
the realization that the ventral surface of the midbrain is

restricted to the region of emergence of the oculomotor
nerve;
the discovery that the substantia nigra and ventral tegmental area extend from the isthmus to the rostral
diencephalon;
the recognition that the isthmus is a complete segment of
the hindbrain, separating the midbrain from the
rhombomeres;
the identification of 11 rhombomeric segments in the
hindbrain;
the need to abandon the terms pons and medulla as
regional designators in the hindbrain (these terms derive
Intersectional fate mapping The combined use of two

different site-specific recombinases (Flp and Cre) to define a
specific functional population (such serotonergic neurons)
within a specific rostro-caudal location (e.g. within a
particular rhombomere).
Isthmus A discrete segment of the hindbrain that lies
between the midbrain and the first rhombomere.
Mesomere A segment of the midbrain defined by gene
expression; there are two mesomeres, the rostral one being
much larger than the caudal.
Proton density Concentration of hydrogen ions within a
sample of tissue.
Rhombomere A discrete segment of the hindbrain defined
by gene expression and demonstrating lineage restriction
during development; there are 11 rhombomeres.
T1 Spin-lattice or longitudinal relaxation in MRI.
T2 Spinspin or transverse relaxation in MRI.
from the enormous size of the basilar pons in humans and

their application to most other mammals is a cause of
widespread confusion).
This article will explain the need for brain maps to adopt a new
conceptual view of the brain stem and will outline key issues in
mapping the brain stem.
Current Maps of the Mammalian Brain Stem

The past 30 years have seen the publication of an extensive
series of histological brain atlases that have mapped the brain
stem of a range of mammals. The development of these new
atlases followed the discovery of the monoamine neuron
groups in the brain stem and the development of a range of
immunohistochemical markers in the 1970s. The new atlases
provide an unprecedented display of accurate anatomical
detail and, in most cases, offer stereotaxic coordinates as well.
The most cited of these are the atlases of the Paxinos group,
covering the rat (Paxinos & Watson, 1982, 1986, 1997, 1998,
2005, 2007), mouse (Franklin & Paxinos, 2007; Paxinos &
Franklin, 2013), rhesus monkey (Paxinos, Huang, Petrides, &
Toga, 2009), marmoset monkey (Paxinos, Watson, Petrides,
Rosa, & Tokuno, 2012), and human (Paxinos & Huang, 1995;
Paxinos, Huang, Sengul, & Watson, 2012; Paxinos, Watson,
Petrides, Rosa, & Tokuno, 2012). Collectively, this family of
atlases provides the main anatomical platform for mammalian
brain research around the world, and the rat atlas alone has
been cited more than 60 000 times. In addition to these standard atlases, this group has prepared chemoarchitectonic
atlases of rat and mouse (Paxinos, Watson, Carrive, Kirkcaldie,
http://dx.doi.org/10.1016/B978-0-12-397025-1.00219-0
251
252
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | The Brain Stem
& Ashwell, 2009; Watson & Paxinos, 2010) and atlases of the
developing brain of rat and mouse (Ashwell & Paxinos, 2008;
Paxinos, Halliday, Watson, Koutcherov, & Wang, 2007). A
notable feature of the Paxinos family of atlases is that they all
use the same nomenclature and abbreviations, mutatis
mutandis.
Outside of this family of atlases, some other notable works
have appeared the rat brain atlases of Swanson (2003) and
Kruger, Saporta, and Swanson (1995); the Allen Mouse Brain
Atlas (Dong, 2008); and the hamster brain atlas of Morin and
Wood (2001). Of these, the first three use the nomenclature of
Swanson (2003), but the Morin and Wood atlas uses the
nomenclature of Paxinos and Watson (1982).
ventral surface of the midbrain is the emerging root of the

oculomotor nerve. The main error resulting from this misunderstanding is the inclusion in the midbrain of many structures
that are either diencephalic or isthmic. These include the diencephalic and isthmic parts of the substantia nigra and ventral
tegmental area, the trochlear nucleus (isthmus), and the interpeduncular nucleus (isthmus and first rhombomere) (Puelles
et al., 2012).
Gene expression patterns indicate that the midbrain has two
rostrocaudal segments a larger rostral area called mesomere 1
and a much smaller preisthmic segment called mesomere 2
(Puelles et al., 2012) (Figure 1).
The Isthmus
The Midbrain
The midbrain (mesencephalon) joins the diencephalon to the
hindbrain. During development, the neuraxis undergoes a
sharp bend in the region of the midbrain, which distorts the
adult anatomy of the midbrain (Puelles, Puelles, & Watson,
2012). This bend, called the cephalic flexure, causes the midbrain to assume a pronounced wedge shape in the sagittal
plane in all vertebrate brains (Figure 1). The result of this
distortion is that the ventral surface is very compressed, and
the dorsal surface is expanded, the latter forming the four
colliculi in the mammalian brain. The significance of the compression of the ventral surface is not generally appreciated, but
it has important implications for understanding the anatomy
of the midbrain in all mammals. The only reliable mark of true
The isthmus seems to be a forgotten part of the mammalian

brain. Most researchers and textbook writers either ignore its
existence entirely or mistakenly lump it with the caudal
mesencephalon (e.g., Brodal, 2010). The isthmus is in fact
the most rostral part of the hindbrain (marked by Gbx2 expression), not a caudal part of the mesencephalon (which shares
Otx2 expression with the forebrain) (Hidalgo-Sanchez, Millet,
Simeone, & Alvarado-Mallart, 1999; Millet, Bloch-Gallego,
Simeone, & Alvarado-Mallart, 1996). In common with the
adjacent rhombomeres of the hindbrain, the isthmus contains
serotoninergic raphe neurons (which the mesencephalon does
not) (Aitken & Tork, 1988) and contributes to the formation of
the cerebellum (which the mesencephalon does not) (Eddison,
Toole, Bell, & Wingate, 2004).
Pallium
Roof
plate
Pretectum
Diencephalon
Telencephalon
p1
p2
Striatum
Substantia
nigra
STh
Terminal
hypothalamus
Eye
Basilar
pons
r1
r2
r3
r4
in
Preoptic
area
Cerebellum
is
a
br
nd
Peduncular
hypothalamus
Dg
m2
Hi
Cephalic
flexure
p3
Pallidum
Midbrain
m1
Cervical
flexure
r11
Spinal
cord
Figure 1 A diagram of a sagittal view of a developing brain showing the subdivisions of the brain stem and the adjacent forebrain. The diagram shows
the boundaries of the diencephalic prosomeres (p3, p2, and p1), the mesomeres of the midbrain (m1 and m2), and the isthmus (is) and
rhombomeres of the hindbrain (only r1, r2, r3, r4, and r11 are labeled). The subthalamic nucleus (STh) and the mammillary area of the
hypothalamus (MB) are labeled, as are the subdivisions of the telencephalon (Dg, diagonal domain). The diagram is based on an original prepared
by Professor Luis Puelles (Puelles et al., 2012). Note the fact that the pontine nuclei (basilar pons) are restricted to the ventral parts of r3 and r4.

The isthmus of the mammalian brain should be recognized
as a distinct segment of the brain, separating the mesencephalon from the first rhombomere (Watson, 2012). The signature
components of the isthmus are the trochlear nucleus (Vaage,
1973), the caudal linear nucleus, and the parabigeminal
nucleus (Hidalgo-Sanchez, Millet, Bloch-Gallego, & AlvaradoMallart, 2005; Watson, 2012). A surprising finding is that the
caudal part of the substantia nigra and the ventral tegmental
253
area develop as an outgrowth of the ventral part of the isthmus

in the rat (Marchand & Poirier, 1983). The isthmic nature of
the caudal substantia and nigra and ventral tegmental area is
confirmed by the expression of fgf8 in these two areas an
fgf8-Cre lineage (Watson, 2010). The relationship of the isthmus to the midbrain can be appreciated in Figure 2, in which
the isthmic territory is labeled in a diagram of a sagittal section
of the rat brain.
Pineal
gland
Cerebral cortex
um Hippocampus
3V
u mac
ST
Preoptic
area
och
Fourth ventricle
4N
Fourth ventricle
3N
p3
Pa
Olfactory
tubercle
m (p1)
a lli
Diencephalon
Pretectu
Su
bp
Thalamus (p2)
ix
Septum
For n
Olfactory
bulb
Cerebellum
Periaqueductal
gray
Mesenceph
alon
pus
Cor
Inferior
colliculus
(auditory)
Superior
colliculus
(visual)
os
call
hm
Ist
scp
r1
r2
Hypothalamus
r3
VMH
Pituitary
gland
Basilar
pontine
nuclei
Rhombencephalon
r4
r5
r6
r7
Pyramidal tract
r8
r9
r10
r11
Pyramidal
decussation
Figure 2 This shows a sagittal section of an adult rat brain accompanied by a diagram that identifies some major features of the midbrain
(mesencephalon) and hindbrain (isthmus and rhombencephalon). Note the severe restriction of the ventral surface of the midbrain, due to the cephalic
flexure. The boundary between the oculomotor nucleus (3N) and the trochlear nucleus (4N) represents the junction of midbrain and isthmus. The
superior cerebellar peduncle (scp) and the 11 rhombomeres (r1r11) are labeled. In noting that the pontine nuclei are ventral components of
rhombomeres 3 and 4, it must be remembered that the rostral interrhombomeric boundaries are very oblique, sloping from dorsal to ventral at about 45
to the vertical. The prosomeres of the diencephalon (p1p3) are labeled. Other structures labeled include the paraventricular and ventromedial nuclei of
the hypothalamus (Pa and VMH), the optic chiasm (och), the anterior commissure (ac), and the bed nucleus of the stria terminalis (ST).
254
The Problem of the Pons

In human neuroanatomy textbooks, the hindbrain has traditionally been divided into a rostral half, the pons, and a caudal
half, the medulla oblongata (e.g., Brodal, 2010). These subdivisions were named on account of the appearance of the
massive pontine crossing in the human brain. Unfortunately,
this subdivision does not reflect developmental subdivisions
and so has become the source of much confusion in comparative studies. Studies of gene expression in mammalian rhombomeres show that the pontine nuclei arise in the rhombic lip
in rhombomeres 67 and migrate to their final position in the
ventral part of r3 and r4 (Farago, Awatramani, & Dymecki,
2006) (Figures 1 and 2). However, the basilar pons becomes
massively enlarged in primates and the pontine swelling
appears to extend from the midbrain to the level of the inferior
olive in the human. In animals with a modest pontine crossing, like the mouse, the pons remains in the ventral part of r3
and r4. The variation in size of the external bulge of the pons
makes it inappropriate to use this feature as a topographic
descriptor to subdivide the hindbrain.
The Rhombomeres
The rhombomeres are transverse developmental units of the
embryonic hindbrain (Figure 1). The rostral rhombomeres
(r1r6) are initially marked by transverse constrictions in the
neural tube wall in the early embryo (Nieuwenhuys, 1998;
Orr, 1887; Vaage, 1973; von Kupffer, 1906), but these constrictions disappear after the early embryonic period. The caudal
rhombomeres (r8r11) are not separated by overt constrictions
in the developing hindbrain (Cambronero & Puelles, 2000). The
boundaries and contents of the rhombomeres in the avian brain
have been delineated by fate mapping and by studies of hox gene
expression (Cambronero & Puelles, 2000; Marin, Aroca, &
Puelles, 2008; Marn & Puelles, 1995). A detailed presentation
of the boundaries and contents of rhombomeres is found in the
atlas of the chicken brain of Puelles, Martinez-de-la-Torre,
Paxinos, Watson, and Martinez (2007). A number of studies
have now shown that the rhombomeric boundaries and rhombomere contents in the mouse are essentially the same as found
in the chick (Aroca & Puelles, 2005; Farago et al., 2006; Jensen
et al., 2008; Pasqualetti, Diaz, Renaud, Rijlii, & Glover, 2007).
However, Lumsden and Krumlauf, who are pioneers in the field
of gene expression in the rhombomeres (Krumlauf, 1994; Lumsden & Keynes, 1989; Lumsden & Krumlauf, 1996), have in recent
publications consistently ignored Puelles contention that there
are 11 rhombomeres and not 8 as previously thought. In recent
review articles, Lumsden, Krumlauf, and their colleagues did not
discuss or even cite any of the relevant Puelles hindbrain studies
of the past 20 years (Kiecker & Lumsden, 2005; Tumpel,
Wiedemann, & Krumlauf, 2009). Even if Puelles is subsequently
proven to be wrong, his work has appeared in major journals
and deserves consideration. In our opinion, this type of covert
censorship has no place in modern science.
A Guide to Recognizing the Isthmus and Individual

Rhombomeres in Sections of the Mammalian Brain
Because the terms isthmus and rhombomere are not yet commonly used in textbooks, we have prepared a list of some of the
landmarks by which these segmental structures can be recognized. Our knowledge of the segmental position of these structures is based chiefly on extensive studies in the chick
(Cambronero & Puelles, 2000; Marin et al., 2008; Marin &
Puelles, 1995; Puelles et al., 2007), but the same segmental
pattern is clearly present in the mouse (Farago et al., 2006;
Jensen et al., 2008; Watson, 2010):
Isthmus trochlear nucleus, parabigeminal nucleus, rostral

part of cerebellar vermis, and decussation of superior cerebellar peduncle
Rhombomere 1 locus coeruleus, caudal interpeduncular
nucleus, cerebellar hemisphere, and caudal cerebellar
vermis
Rhombomere 2 main part of motor trigeminal nucleus
Rhombomere 3 rostral pontine nuclei
Rhombomere 4 caudal pontine nuclei and exit of the
facial nerve
Rhombomere 5 abducens nucleus, superior olive, trapezoid body, and genu of facial nerve
Rhombomere 6 facial nucleus
Rhombomere 7 compact part of nucleus ambiguus
Rhombomere 8 rostral part of inferior olive and subcompact part of nucleus ambiguus
Rhombomere 9 middle part of inferior olive, loose part of
nucleus ambiguus, and caudal pole of interpolar spinal
trigeminal nucleus
Rhombomere 10 caudal part of inferior olive, nucleus
retroambiguus, and rostral pole of caudal spinal trigeminal
nucleus
Rhombomere 11 pyramidal decussation
Twenty-First Century Methods for Mapping

the Brain Stem
During the 1980s, the use of histochemical markers (notably
acetylcholinesterase) and immunohistochemical markers
(such as tyrosine hydroxylase and calcium binding proteins)
fueled rapid development of accurate maps of the brain stem.
The chemoarchitectonic atlas of the rat brain prepared by the
Paxinos group is a significant product of these developments.
This atlas of the brain stem (Paxinos, Carrive, Wang, & Wang,
1999) is based on a rotation of eight markers applied to
about 250 consecutive sections of the brain stem. This publication therefore represents a unique archive that has the
capacity to add value to any project that attempts to map of
the brain stem. A revised version of the rat chemoarchitectonic atlas was published in 2009 (Paxinos, Watson, Carrive,
Kirkcaldie, & Ashwell, 2009). The advantage of histochemical
and immunohistochemical markers is that they are relatively
cheap and easy to use, and yet they provide important additional information to assist the interpretation of Nissl-stained
sections.
The next phase in brain stem mapping techniques began in
the 1990s and has flourished in the first decade of the twentyfirst century. This phase saw the introduction of three important new mapping technologies the use of gene expression
libraries, site-specific recombinases, and high-resolution magnetic resonance (MR) imaging.
255
reference atlas (Dong, 2008) and a number of very sophisticated (and robust) search engines. One example is the AGEA
tool, which can be used to pick out a single brain region (such
as the inferior olive) and ask what genes are selectively
expressed there. The availability of the Allen gene expression
atlas means that any scientist can access ISH data at no cost. In
addition to the adult brain gene expression atlas, the Allen site
also offers a series of atlases of the developing mouse brain
(Allen Developing Mouse Brain Atlas: http://mouse.brainmap.org) showing the expression of a subset of genes with
ISH at different developmental stages. An example of such a
preparation is seen in Figure 3, in which the raphe serotonergic
Gene Expression in the Brain Stem

In situ hybridization (ISH) methods to demonstrate gene
expression have been available since the early 1980s, but
most studies were focused on only one or two genes. This
situation has been revolutionized by the development of
open access libraries of gene expression in the mouse brain,
the most comprehensive of which is that in the Allen Institute
for Brain Science Web site. The Allen Mouse Brain Atlas (http://
mouse.brain-map.org) makes available photographic series of
ISH preparations representing about 26 000 genes. These
image sets are supported by an electronic version of the Allen
DR
mes
mes
is
PMnR
ROb
r4
RMg
RPa
DR
mes
MnR
is
PnR
r4
ROb
RPa
Figure 3 Photographs of two sagittal sections of an E18.5 mouse brain showing the expression of the serotonin solute carrier 6a4 (Slc6a4) in the
raphe nuclei as revealed by in situ hybridization. The upper image is from a midline section, and the lower image is from a section just lateral to the
midline. The location of serotoninergic (5HT) neurons in the raphe nuclei is clearly shown (DR, dorsal raphe; PMnR, paramedian raphe; RMg,
raphe magnus; RPa, raphe pallidus; ROb, raphe obscures). Note that 5HT neurons are confined to the hindbrain, with the exception of a few that
migrate into the caudal midbrain (mes) from the isthmus (is). Note also that rhombomere 4 (r4) does not contain any 5HT neurons. These images
are taken with permission from the Allen Developing Mouse Brain Atlas created by the Allen Institute for Brain Science (Allen Mouse Brain Atlas
(Internet). Seattle (WA): Allen Institute for Brain Science) 2009. Available from http://mouse.brain-map.org.
256
neurons are labeled through the expression of the serotonin

solute carrier slc6a4 in an E18.5 mouse brain.
Genetic Fate Mapping Using Site-Specific Recombinases

The first genetic fate mapping made use of the site-specific
recombinases (Cre or Flp) combined with reporter alleles
(Dymecki & Tomasiewicz, 1998; Tvrdik & Capecchi, 2012;
Zinyk, Mercer, Harris, Anderson, & Joyner, 1998). The special
feature of site-specific recombinases is that the reporter genes
continue to be expressed throughout development, even though
the initial period of expression of the gene of interest has finished (Dymecki, 1996; Dymecki & Kim, 2007). The most widely
used reporter allele is Rosa26 (Soriano, 1999), but another
valuable reporter is the Tau-loxP-STOP-loxP-mGFP-nLacZ allele
(Hippenmeyer et al., 2005). The latter reporter contains two
reporter proteins one to label the nucleus (lacZ) and another
to label neuronal processes (myristoylated GFP) in postmitotic
neurons. Figure 4 shows the expression of Phox2b in a sagittal
section of a newborn mouse brain from a Cre lineage labeled
with LacZ. In this section, the branchial motor nuclei (motor
trigeminal, facial, and ambiguus) are strongly labeled, as is the
rostral part of the nucleus of the solitary tract.
Genetic Inducible Fate Mapping Using CreER

One of the useful features of Cre and Flp recombinases is that
they label all cells that express a particular gene at all stages from
the development to the mature brain (Joyner & Sudarov, 2012).

For some purposes, the cumulative fate map produced in this
way is ideal. However, this cumulative map cannot reveal the
separate subpopulations that are labeled at different times during development. A method to overcome this disadvantage has
been invented, making use of an inducible form of Cre expression that can be limited to a short period during development
(about 24 h). The most widely used form of inducible Cre uses a
modified estrogen receptor that can be triggered into expression
by administration of the drug tamoxifen (Joyner & Zervas, 2006;
Joyner & Sudarov, 2012; Machold & Fishell, 2005). CreER lineages can thus be used to select gene expression on a day-by-day
basis. Joyner has called this method genetic inducible fate mapping (Joyner & Zervas, 2006). An example of the value of
inducible fate mapping is shown in Figure 5, in which the
time of origin of a specific population of Atoh1 expressing
cells from the rhombic lip can be distinguished.
Combined Use of Cre and Flp: Intersectional Genetic Fate

Mapping
By combining the effect of Flp and Cre recombinases in the
same animal, only the cells that express the gene linked to each
of the two recombinases will be labeled. This sophisticated
development of the site-specific recombinase technique has
been pioneered by the Susan Dymecki group at Harvard. The
technique enables two different selection techniques to be
applied simultaneously. In this way, the presence of a gene-
4b
Cb
pc
3N
4N
Sol
5N
Sol
IP
Amb
7N
r2
Pn
(a)
(b)
Figure 4 (a) An image of a thick sagittal slice about 1.5 mm from the midline of the brain stem of a mouse from a Phox2b-cre-LacZ lineage, stained to
show the presence of LacZ. Phox2b is chiefly expressed in the brachial motor, visceral motor, and visceral sensory neurons. The neurons of
branchial motor nuclei (motor trigeminal, 5N; facial, 7N; and ambiguus, Amb) are clearly labeled, whereas the hypoglossal motor neurons are not. The
rostral part of the solitary nucleus complex is also strongly labeled. (b) A thick sagittal slice from the same brain as shown in (a), but very close to
the midline. As anticipated, the visceral sensory nucleus (the solitary nucleus, Sol) is strongly labeled. The ventral border of the staining in Sol contains a
line of vagal motor neurons, but they are hard to distinguish at this magnification. Two interesting features can be noted: Firstly, the oculomotor
(3N) and trochlear (4N) motor neurons are labeled; secondly, a band of neuropil staining nicely marks out the territory of the second rhombomere (r2).
The expression in 3N and 4N is at first surprising, since they are traditionally classified as somatic motor, but the expression of Phox2b confirms a
long-standing suspicion by evolutionary biologists that these two nuclei were originally branchial motor supplying the most rostral gill muscles in
very early vertebrates. The significance of Phox2b expression in r2 is not clear, but it provides a fortuitous demonstration of the extent of the r2
segment. It shows incidentally that r2 is interposed between the pontine nuclei (Pn), which are in r3 and r4, and the interpeduncular nuclei (IP), which
are in r1 and the isthmus. The cerebellum (Cb) and the posterior commissure (pc) are labeled for reference. The images in (a) and (b) were kindly
supplied by Dr. Petr Tvrdik of the Mario Capecchi Laboratory at the University of Utah.
Figure 5 A pair of images to show the value of the CreER approach in

the study of early brain development. A comparison of all Atoh1 lineages
at E14.5 (Atoh1-LacZ) with those that expressed Atoh1 at E10.5 (Atoh1CreERT2 with LacZ reporter, tamoxifen (Tm) administered at E10.5)
reveals that deep cerebellar neurons (DNs) are an early-born Atoh1
population, whereas granule cell precursors located in the external
granule layer (EGL) are specified later. These unpublished images were
kindly supplied by Dr Rob Machold of the New York University School
of Medicine. The images are based on data on aspects rhombic lip
development previously reported by Machold and Fishell (2005).
0.00 mm
producing serotoninergic cell can be linked to another that is

expressed in one or more rhombomeres. This results in labeling of a particular population of serotoninergic cells that
develop from a particular rostrocaudal location (Jensen et al.,
2008). This technique, called intersectional genetic fate mapping, has been very effectively used in a number of studies of
hindbrain development (Awatramani, Soriano, Rodriguez,
Mai, & Dymecki, 2006; Farago et al., 2006; Jensen et al.,
2008). A further elaboration of this approach is to add the
dimension of time by combining it with the CreER method;
this can enable the further selection of a subpopulation according to which day the cells were generated.
MRI: High-Resolution Magnetic Imaging of the

Brain Stem
The new generation MR scanners have added an additional
dimension to brain mapping: they can acquire three-
-1.88 mm
V1
SuG
257
SuVe
PDTg
6N
IP
7n
6n
ml
RIP
Pn
ml
-2.92 mm
-1.40 mm
Crus1
Crus2
Med
4n
me5
PM
scp
Cop
SpVe
Pr
mlf
5N
Pr5
RtTg
VCA
Sp5I
ROb
LSO
Sol
Amb
Tz
Figure 6 A group of four coronal MR images of the brain stem from an image set derived from an average of MR of the brains of 18 C57BL/6J mice.
Each section is identified in the top left of the image with the distance from the interaural plane of the corresponding section in the mouse brain atlas of
Paxinos and Franklin (2013). A number of different fiber bundles, nuclei, and cortical areas are identified. The contrast in the images is very favorable and
the averaging of 18 brains has reduced noise to a very low level. Some small nuclei (such as the abducens nucleus (6N), the nucleus of the trapezoid
body (Tz), the reticulotegmental nucleus, the posterodorsal tegmental nucleus, the nucleus raphe interpositus (RIP), the nucleus raphes obscurus
(ROb), and the nucleus ambiguus (Amb)) and small fiber bundles (such as the mesencephalic trigeminal tract (me5), the trochlear nerve (4n), and the
abducens nerve (6n)) are relatively easy to distinguish. Some larger nuclei, such as the interpeduncular nucleus (IP), the lateral superior olive (LSO), the
pontine nuclei (Pn), the medial cerebellar nucleus (Med), the superior vestibular nucleus (SuVe), the principal trigeminal sensory nucleus (Pr5), the
trigeminal motor nucleus (5N), the ventral cochlear nucleus anterior part (VCA), the nucleus prepositus (Pr), the solitary nucleus (Sol), the spinal
vestibular nucleus (SpVe), and the spinal trigeminal nucleus interpolar part (Sp5I), display characteristic contrast areas with sharp borders. Major fiber
bundles (such as the medial lemniscus (ml), superior cerebellar peduncle (scp), the facial nerve (7n), and the medial longitudinal fasciculus (mlf)) stand
out well against their surrounds. The primary visual cortex (V1), the superficial gray layer of the superior colliculus (SuG), and a number of cerebellar
lobules (Crus 1, Crus 2, the paramedian lobule (PM), and the copula (Cop)) are labeled for reference.
258
dimensional data sets, can be used with live animals, and can
repeat scans over time in order to track the development of
changes in the brain. The first reports of the use of these methods
in the 1990s defined the boundaries of only a limited number
of structures in the brain, but since 2005, much more detailed
MR atlases of rodent brains have been published (Johnson,
Calabrese, Badea, Paxinos, & Watson, 2012; Ullmann et al.,
2012).
The enhanced characterization of brain anatomy with MRI is
the result of advances in three different areas. First, improvements in MRI scanners, coils, and acquisition sequences have
resulted in the acquisition of very high-resolution and highcontrast data sets. Numerous facilities around the world now
work with magnets with field strengths greater than 16 T, and
when combined with specially built solenoid or cryogen-cooled
coils, data sets can be acquired with resolutions of 30 mm3 or
better (Ullmann et al., 2012; Ullmann, Cowin, Kurniawan, &
Collin, 2010). Additionally, a multitude of acquisition
sequences (such as T1, T2, proton density, and diffusion tensor
imaging) can be derived from a single data set, and this has led
to the creation of detailed multidimensional atlases of the central nervous system (Johnson et al., 2010).
Second, the development of contrast agents for both
in vivo and ex vivo imaging has facilitated the identification
of a greater number of structures. Gadolinium-based compounds, which transiently bind to the hydrogen protons in
water, reduce relaxation times (Weinmann, Brasch, Press, &
Wesbey, 1984) and produce contrast that closely parallels the
cell density found in the brains. Areas with high cell density
appear hyperintense while regions with low cell density
appear hypointense. More recently, additional contrast agents
have also shown great promise; these include Luxol fast
blue (Blackwell, Farrar, Fischl, & Rosen, 2009), chromium
(Watanabe, Tammer, Boretius, Frahm, & Michaelis, 2006),
and manganese, a calcium analog that can be transported
along voltage-gated calcium channels to assess neuronal function and highlight specific brain areas that are active (Pautler
& Koretsky, 2002).
Third, improvements in registration algorithms, in combination with greater access to powerful computer clusters,
enable registration of an ever-increasing number of data sets
and the creation of more detailed probabilistic atlases. While
initial rodent atlases were based on an individual animal,
todays modern brain atlas can be made up of data sets
from a large number of brains, which greatly improves the
contrast-to-noise ratio. Moreover, the registration can now be
based on a recursive nonlinear hierarchical fitting strategy
with a robust averaging process that places a lower weight
on data that are greater than two standard deviations from
the current model (Fonov et al., 2011). This iterative process
requires the use of powerful computer clusters that were
previously not available. The result is the production of digital brain atlas that represents the average normalized intensity and shape of a population, a high contrast-to-noise ratio,
and a very high level of anatomical structural detail.
The combination of these three developments has produced very detailed MRI-based atlases of the rodent brain.
The Australian Mouse Brain Mapping Consortium, based in
the University of Queensland, has made use of a 16.4 T scanner
and averaging techniques to produce very high-resolution
images of mouse brains. The images of the brain stem shown
here are taken from a minimum deformation model made up

of the ex vivo scans of brains from 18 mice. The clarity of the
images is outstanding, and the individual coronal images stand
up well against low-power photographs of Nissl-stained sections of the mouse brain (Paxinos & Franklin, 2013). As would
be expected, the myelinated fiber bundles are sharply defined,
but many nuclei are also clearly visible as distinct pale areas.
Examples are the nucleus ambiguus, the abducens nucleus, the
nucleus raphes obscurus, and the reticulotegmental nucleus
(Figure 6).
Johnson et al. (2012) from Duke University had also shown
that a high-quality set of rat brain MR images can be registered
with the images from a standard rat brain atlas (Paxinos &
Watson, 2007) to enable automated segmentation of the MR
images if required.

Anatomical MRI for Human Brain Morphometry; INTRODUCTION TO
ANATOMY AND PHYSIOLOGY: Genoarchitectonic Brain Maps.
References
Aitken, A. R., & Tork, I. (1988). Early development of serotonin-containing neurons and
pathways as seen in wholemount preparations of the fetal rat brain. Journal of
Aroca, P., & Puelles, L. (2005). Postulated boundaries and differential fate in the
developing rostral hindbrain. Brain Research Reviews, 49, 179190.
Ashwell, K. W.S, & Paxinos, G. (2008). Atlas of the developing rat nervous system (3rd
ed.). San Diego: Elsevier Academic Press.
Awatramani, R., Soriano, P., Rodriguez, C., Mai, J. J., & Dymecki, S. M. (2006). Cryptic
boundaries in roof plate and choroid plexus identified by intersectional gene
activation. Nature Genetics, 35, 7075.
Badea, A., Ali-Sharief, A. A., & Johnson, G. A. (2007). Morphometric analysis of the
C57BL/6J mouse brain. NeuroImage, 37, 683693.
Blackwell, M. L., Farrar, C. T., Fischl, B., & Rosen, B. R. (2009). Target-specific contrast
agents for magnetic resonance microscopy. NeuroImage, 46, 382393.
Branda, C. S., & Dymecki, S. M. (2004). Talking about a revolution: The impact of
site-specific recombinases on genetic analyses in mice. Developmental Cell, 6,
728.
Brodal, P. (2010). The central nervous system (4th ed.). New York: Oxford University
Press.
Cambronero, F., & Puelles, L. (2000). Rostrocaudal nuclear relationships in the avian
medulla oblongata: Fate-map with quail-chick chimeras. Journal of Comparative
Neurology, 427, 522545.
Capecchi, M. R. (1989). The new mouse genetics: Altering the genome by gene
targeting. Trends in Genetics, 5, 7076.
Capecchi, M. R. (2005). Essay: gene targeting in mice: Functional analysis of the
mammalian genome for the twenty-first century. Nature Reviews. Genetics, 6, 507512.
Dong, H. W. (2008). The Allen reference atlas: A digital color brain atlas of the C57BL/
6J mouse. Hobeken, NJ: John Wiley and Sons Inc.
Dymecki, S. M. (1996). Flp recombinase promotes site-specific DNA recombination in
embryonic stem cells and transgenic mice. Proceedings of the National Academy of
Science, 93, 61916196.
Dymecki, S. M., & Kim, J. C. (2007). Molecular neuroanatomys "Three Gs": A primer.
Neuron, 54, 1734.
Dymecki, S. M., & Tomasiewicz, H. (1998). Using Flp-recombinase to characterize
expansion of Wnt1-expressing neural progenitors in the mouse. Developmental
Biology, 201, 5765.
Eddison, M., Toole, L., Bell, E., & Wingate, R. J.T (2004). Segmental identity and
cerebellar granule cell induction in rhombomere 1. BMC Biology, 2, 14. http://dx.
doi.org/10.1186/1741-7007-2-14.
Farago, A. F., Awatramani, R. B., & Dymecki, S. M. (2006). Assembly of the brainstem
cochlear nuclear complex is revealed by intersectional and subtractive genetic fate
maps. Neuron, 50, 205218.
Fonov, V., Evans, A. C., Botteron, K., Almli, C. R., McKinstry, R. C., & Collins, D. L.

Franklin, K. B.J, & Paxinos, G. (2007). The mouse brain in stereotaxic coordinates
(3rd ed.). San Diego: Elsevier Academic Press.
Hidalgo-Sanchez, M., Millet, S., Bloch-Gallego, E., & Alvarado-Mallart, R.-M. (2005).
Specification of the meso-isthmo-cerebellar region: The Otx2/Gbx2 boundary. Brain
Research Reviews, 49, 134149.
Hidalgo-Sanchez, M., Millet, S., Simeone, A., & Alvarado-Mallart, R.-M. (1999).
Comparative analysis of Otx2, Gbx2, Pax2, Fgf8, and Wnt1 gene expressions during
the formation of the midbrain/hindbrain domain. Mechanisms of Development, 80,
175178.
Hippenmeyer, S., Vrieseling, E., Sigrist, M., Portmann, T., Laengle, C., Ladle, D. R.,
et al. (2005). A developmental switch in the response of DRG neurons to ETS
transcription factor signaling. PLoS Biology, 3, e159. http://dx.doi.org/10.1371/
journal.pbio.0030159.
Jensen, P., Farago, A., Awatramani, R., Scott, M., Deneris, E., & Dymecki, S. (2008).
Redefining the serotonergic system by genetic lineage. Nature Neuroscience, 11,
417419.
Johnson, G. A., Badea, A., Brandenburg, J., Cofer, G., Fubara, B., Liu, S., et al. (2010).
Waxholm space: An image-based reference for coordinating mouse brain research.
Johnson, G. A., Calabrese, E., Badea, A., Paxinos, G., & Watson, C. (2012). A
multidimensional magnetic resonance histology atlas of the Wistar rat brain.
Joyner, A., & Sudarov, A. (2012). Genetic neuroanatomy. In C. Watson, G. Paxinos & L.
Puelles (Eds.), The mouse nervous system. San Diego: Elsevier Academic Press.
Joyner, A. L., & Zervas, M. (2006). Genetic inducible fate mapping in mouse:
Establishing genetic lineages and defining genetic neuroanatomy in the nervous
system. Developmental Dynamics, 235, 23762385.
Kiecker, C., & Lumsden, A. (2005). Compartments and their boundaries in vertebrate
brain development. Nature Reviews. Neuroscience, 6, 553564.
Kruger, L., Saporta, S., & Swanson, L. W. (1995). Photographic atlas of the rat brain:
The cell and fiber architecture illustrated in three planes with stereotaxic
coordinates. Cambridge: Cambridge University Press.
Krumlauf, R. (1994). Hox genes in vertebrate development. Cell, 78, 191201.
Lumsden, A., & Keynes, R. (1989). Segmental patterns of neuronal development in the
chick hindbrain. Nature, 337, 424428.
Lumsden, A., & Krumlauf, R. (1996). Patterning the vertebrate neuraxis. Science, 274,
11091115.
Machold, R., & Fishell, G. (2005). Math1 is expressed in temporally discrete pools of
cerebellar rhomic-lip neural progenitors. Neuron, 48, 1724.
Marchand, R., & Poirier, L. J. (1983). Isthmic origin of neurons of the rat substantia
nigra. Neuroscience, 9, 373381.
Marin, F., Aroca, P., & Puelles, L. (2008). Hox gene colinear expression in the avian
medulla oblongata is correlated with pseudorhombomeric domains. Developmental
Biology, 323, 230247.
Marn, F., & Puelles, L. (1995). Morphological fate of rhombomeres in quail/chick
chimeras: A segmental analysis of hindbrain nuclei. European Journal of
Millet, S., Bloch-Gallego, E., Simeone, A., & Alvarado-Mallart, R. M. (1996). The caudal
limit of Otx2 gene expression as a marker for the midbrain/hindbrain boundary: A
study using in situ hybridization and chick/quail homotopic grafts. Development,
122, 37853797.
Morin, L. P., & Wood, R. I. (2001). A stereotaxic atlas of the golden hamster brain. San
Diego: Academic Press.
Nieuwenhuys, R. (1998). Morphogenesis and general structure. In: R. Nieuwenhuys,
H. J. Donkelaar & C. Nicholson (Eds.), The central nervous system of vertebrates
(vol. 1, p. 222). Berlin: Springer.
Orr, H. J. (1887). Contribution to the embryology of the lizard. Journal of Morphology,
1, 311372.
Pasqualetti, M., Diaz, C., Renaud, J.-S., Rijlii, F. M., & Glover, J. C. (2007). Fatemapping the mammalian hindbrain: Segmental origins of vestibular projection
neurons assessed using rhombomere-specific hoxa2 enhancer elements in the
mouse embryo. Journal of Neuroscience, 27, 96709681.
Pautler, R. G., & Koretsky, A. P. (2002). Tracing odor-induced activation in the olfactory
bulbs of mice using manganese-enhanced magnetic resonance imaging.
Paxinos, G., Carrive, P., Wang, H., & Wang, P.-Y. (1999). Chemoarchitectonic atlas of
the rat brainstem. San Diego: Academic Press.
Paxinos, G., & Franklin, K. B.J (2013). The mouse brain in stereotaxic coordinates
(4th ed.). San Diego: Elsevier Academic Press.
259
Paxinos, G., Halliday, G., Watson, C., Koutcherov, Y., & Wang, H. Q. (2007). Atlas of the
developing mouse brain at E17.5, P0, and P6. San Diego: Elsevier Academic Press.
Paxinos, G., & Huang, X. F. (1995). Atlas of the human brainstem. San Diego: Academic
Press.
Paxinos, G., Huang, X.-F., Petrides, M., & Toga, A. W. (2009). The rhesus monkey brain
in stereotaxic coordinates (2nd ed.). San Diego: Elsevier Academic Press.
Paxinos, G., Huang, X.-F., Sengul, G., & Watson, C. (2012). Organization of human
brainstem. In J. K. Mai & G. Paxinos (Eds.), The human nervous system (3rd ed.).
San Diego: Elsevier Academic Press.
Paxinos, G., & Watson, C. (1982). The rat brain in stereotaxic coordinates. Sydney:
Academic Press.
Paxinos, G., & Watson, C. (1986). The rat brain in stereotaxic coordinates (2nd ed.).
Sydney: Academic Press.
Paxinos, G., & Watson, C. (1997). The rat brain in stereotaxic coordinates (3rd ed.). San
Diego: Academic Press.
Paxinos, G., & Watson, C. (1998). The rat brain in stereotaxic coordinates
Comprehensive (4th ed.). San Diego: Academic Press.
Paxinos, G., & Watson, C. (2005). The rat brain in stereotaxic coordinates: The new
coronal set (5th ed.). San Diego: Elsevier Academic Press.
Paxinos, G., & Watson, C. (2007). The rat brain in stereotaxic coordinates (6th ed.). San
Diego: Elsevier Academic Press.
Paxinos, G., Watson, C., Carrive, P., Kirkcaldie, M., & Ashwell, K. (2009).
Chemoarchitectonic atlas of the rat brain (2nd ed.). San Diego: Elsevier Academic Press.
Paxinos, G., Watson, C., Petrides, M., Rosa, M., & Tokuno, H. (2012). The marmoset
brain in stereotaxic coordinates. San Diego: Elsevier Academic Press.
Puelles, L., Martinez-de-la-Torre, M., Paxinos, G., Watson, C., & Martinez, S. (2007).
The chick brain in stereotaxic coordinates: An atlas featuring neuromeres and
mammalian homologies. San Diego: Elsevier Academic Press.
Puelles, E., Puelles, L., & Watson, C. (2012). Midbrain. In C. Watson, G. Paxinos & L.
Puelles (Eds.), The mouse nervous system (pp. 337359). San Diego: Elsevier
Academic Press (Chapter 10).
Puelles, L., & Watson, C. (2012). Diencephalon. In C. Watson, G. Paxinos & L. Puelles
(Eds.), The mouse nervous system (pp. 331336). San Diego: Elsevier Academic
Press (Chapter 9).
Soriano, P. (1999). Generalized lacZ expression with the ROSA26 Cre reporter strain.
Nature Genetics, 21, 7071.
Swanson, L. W. (2003). Brain maps III: The structure of the rat brain (3rd ed.). San
Tumpel, S., Wiedemann, L. M., & Krumlauf, R. (2009). Hox genes and segmentation of
the vertebrate hindbrain. In: O. Pourquie (Ed.), Hox genes. Current topics in
developmental biologyvol. 88. San Diego: Academic Press.
Tvrdik, P., & Capecchi, M. R. (2012). Gene targeting. In C. Watson, G. Paxinos & L.
Puelles (Eds.), The mouse nervous system. San Diego: Elsevier Academic Press.
Ullmann, J. F.P, Cowin, G., Kurniawan, N. D., & Collin, S. P. (2010). A threedimensional digital atlas of the zebrafish brain. NeuroImage, 51, 7682.
Ullmann, J. F., Keller, M. D., Watson, C., Janke, A. L., Kurniawan, N. D., Yang, Z., et al.
(2012). Segmentation of the C57BL/6J mouse cerebellum in magnetic resonance
images. NeuroImage, 62, 14081414.
Vaage, S. (1973). The histogenesis of the isthmic nuclei in chick embryos (Gallus
domesticus). 1. A morphological study. Zeitschrift fur Anatomie und
Entwicklungsgeschichte, 142, 283314.
von Kupffer, C. (1906). Die Morphogenie des Central Nervensystems. In O. Hertwig
(Ed.), Handbuch der vergleichenden Entwicklungslehre der Wirbeltiere. Jena:
Gustav Fischer Bd 2 Teil 3.
Watanabe, T., Tammer, R., Boretius, S., Frahm, J., & Michaelis, T. (2006). Chromium
(VI) as a novel MRI contrast agent for cerebral white matter: Preliminary results in
mouse brain in vivo. Magnetic Resonance in Medicine, 56, 16.
Watson, C. (2010). The presumptive isthmic region in a mouse as defined by fgf8
expression. Brain, Behavior and Evolution, 75, 315.
Watson, C. (2012). Hindbrain. In C. Watson, G. Paxinos & L. Puelles (Eds.), The mouse
nervous system (pp. 397422). San Diego: Elsevier Academic Press (Chapter 12).
Watson, C., & Paxinos, G. (2010). Chemoarchitectonic atlas of the mouse brain. San
Weinmann, H.-J., Brasch, R. C., Press, W.-R., & Wesbey, G. E. (1984). Characteristics
of gadolinium-DTPA complex: A potential NMR contrast agent. American Journal of
Roentgenology, 142, 619624.
Zinyk, D., Mercer, E. H., Harris, E., Anderson, D. J., & Joyner, A. L. (1998). Fate
mapping of the mouse midbrainhindbrain constriction using a site-specific
recombination system. Current Biology, 8, 665668.
Transmitter Receptor Distribution in the Human Brain

Aachen, Germany
Glossary
BA38 Temporal pole.

BA39 Posterior part of the inferior parietal cortex.
BA4 Primary motor cortex.
BA40 Anterior part of the inferior parietal cortex.
BA41 Primary auditory cortex.
BA42 Secondary auditory cortex.
BA44 Posterior part of Brocas region.
BA45 Anterior part of Brocas region.
BA46 Prefrontal area.
BA47 Lateral prefrontal orbital area.
BA5 Anterior part of the superior parietal lobule.
BA6 Premotor cortex.
BA7 Posterior part of the superior parietal lobule.
BA8, 9 Prefrontal cortical areas.
CA1-3 Regions of the cornu ammonis (CA) of the
hippocampus.
Infragranular layers Layers V to VI of the cerebral cortex.
Ionotropic receptor This receptor builds an ion channel
and consists of several subunits and exerts fast effects.
Metabotropic receptor This receptor acts via second
messenger systems and exerts slow effects.
Supragranular layers Layers IIII of the cerebral cortex.
Abbreviations
ChAT
DG
GABA
GAD
Ncl
NMDA
QNB
(Inner)granular layer Layer IV of the cerebral cortex.

3b Primary somatosensory cortex.
BA1, 2 Somatosensory cortex.
BA10 Polar prefrontal area.
BA11, 12 Medial orbital prefrontal areas.
BA17 Primary visual cortex (V1, area striata).
BA18 Secondary visual cortex (V2).
BA19 Region of the early extrastriate visual cortex.
BA20 Brodmanns area on the inferior temporal gyrus.
BA21 Brodmanns area on the medial temporal gyrus.
BA22 Brodmanns area on the superior temporal gyrus.
BA23 Periallocortical part of the posterior cingulate cortex.
BA24 Periallocortical part of the anterior cingulate cortex.
BA25 Subcallosal cingulate cortex.
BA29, 30 Retrosplenial areas.
BA31 (Pro)isocortical part of the posterior cingulate cortex.
BA32 (Pro)isocortical part of the anterior cingulate cortex.
BA34 Dorsal part of the entorhinal area.
BA35 Perirhinal area.
BA36 Ectorhinal area (parahippocampal gyrus).
BA37 Occipitotemporal cortex.
5-HT
AMPA
BA
BZ
CA
Serotonin
a-Amino-3-hydroxy-5-methyl-4isoxazolepropionic acid
Brodmanns area
Benzodiazepine binding site of the GABAA
receptor
Cornu ammonis
Transmitter Receptors and Brain Mapping

Each transmitter can bind to several receptor types and elicit
fast (via ionotropic receptors) or slow (via metabotropic receptor) changes of the membrane potential. The human brain
expresses numerous excitatory, inhibitory, and modulatory
receptors. Multiple receptor types are present in the cell membrane of each single neuron. In the cerebral cortex, receptors of
the classical transmitter systems are found in all regions, but
not at the same density (expression levels). Thus, quantitative
analysis of the regional distribution of receptor densities can be
used for brain mapping.
Choline acetyltransferase
Dentate gyrus
g-Amino-butyric acid
Glutamate decarboxylase
Nucleus
N-Methyl-D-aspartate
Quinuclidinyl benzilate
In vivo demonstration of receptors can be performed with

positron emission tomography (PET) or single photon emission tomography (SPECT). Whereas both methods are clinically important, several restrictions must be considered in
brain mapping. The spatial resolution of these techniques
does not enable the detection of differences in laminar expression patterns of receptors. Furthermore, the number of highly
specific ligands available for visualization of different receptors
is limited and not more than one or two receptor types can be
visualized in a single subject for safety reasons.
In vitro demonstration of receptors at very high resolution
(from light microscopy to confocal laser and electron
http://dx.doi.org/10.1016/B978-0-12-397025-1.00221-9
261
262
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Transmitter Receptor Distribution in the Human Brain
microscopy) has been performed (e.g., Gonzalez-Albo &

DeFelipe, 2000; Nusser et al., 1998). In this case, the spatial
scale is restricted to a few synapses but provides detailed information about single and multiple receptor localizations at
synaptic and extrasynaptic sites. However, this approach is
difficult to apply to normal healthy human tissue because it
requires extremely short postmortem times and does not allow
mapping of large brain regions or complete hemispheres.
A method that provides a bridge between the mesoscale
of PET and SPECT and the ultra-high-resolution scale of electron microscopy is receptor binding studies using quantitative
in vitro receptor autoradiography (Zilles, Schleicher, PalomeroGallagher, & Amunts, 2002). Although these studies do not
provide single-cell resolution and identification of ionotropic
receptor subunits, they enable mapping at a spatial resolution
between 1 and 20 mm (depending on the actual technique)
and coverage of complete sections through the whole human
brain. Furthermore, visualization of binding sites reveals native
receptor complexes, which are functionally relevant. Since
numerous specific ligands are available for nearly all receptor
types, it is possible to visualize multiple receptors in alternating
serial sections of a single brain and, thus, to study the balance
between multiple receptor types in a given brain region or
cortical layer. This approach also enables absolute quantification in fmol/mg protein, which is necessary to detect the
intersubject, regional, and laminar differences, since most
receptors are expressed in all brain regions but at different
levels. Therefore, this article focuses on receptor binding studies in the human brain during the last three decades and provides future perspectives on brain mapping based on the
multireceptor analysis of functional systems.
Regional Distribution of Transmitter Receptors

in the Human Cerebral Cortex
In this paragraph, we provide an overview of the vast literature
in Figure 1. For a comprehensive reference of receptor data, see
figure legends. Some studies localize receptor data by anatomical descriptions of gyri, nuclei, or hippocampal regions or
using Brodmanns scheme (Brodmann, 1909). Our group measured the receptor data in cytoarchitectonically defined brain
regions by comparison with immediately adjacent cell bodystained sections (Zilles, Schleicher, Palomero-Gallagher, &
Amunts, 2002). This latter approach provides a considerably
more detailed analysis of the regional differences in receptor
densities. As examples, Figure 2 shows the absolute regional
and laminar densities of various receptor binding sites in the
human occipital cortex, and Figure 3 depicts the relative distribution of GABAA, M2, and a2 receptors in the primary motor
(BA4), somatosensory (area 3b), and auditory (BA41, Te1)
cortices together with the immediately surrounding regions.
In order to compare the data from different sources, it was
necessary to summarize the results of major receptor types as
color-coded maps based on a modified scheme of Brodmanns
map (see lower right edge of Figure 1). These schematic drawings include data not only of numerous cortical areas but also
of the amygdala, basal ganglia, and diencephalon. Since binding techniques and quantification methods vary between studies, relative values are given by the color codes for each receptor
type separately (see legend to Figure 1).
The highest absolute densities of receptor binding sites

(fmol/mg protein) are found for the different ionotropic and
metabotropic GABA and glutamate receptors in the cerebral
cortex compared to the different cholinergic, dopaminergic,
adrenergic, and serotonergic receptor subtypes (Figure 2).
The following are a few examples of extreme values and their
regional and intersubject variation in a sample of 69 human
hemispheres (own unpublished data): The mGluR2/3 receptors occur at a density of 5202 846 fmol mg 1 protein in the
part of BA32 located rostral to the genu of the corpus callosum
and of 2034 564 fmol mg 1 protein in BA29. The benzodiazepine binding sites of the GABAA receptor are found at
3321 381 fmol mg 1 protein in BA29 and 1548 273
fmol mg 1 protein in a dorsal extrastriate visual area. In contrast, the nicotinic a4/b2 receptor binding sites reach 87 40
fmol mg 1 protein in BA29 and 36 29 fmol mg 1 protein in
BA36, and the dopamine D1 receptors, 136 55 fmol mg 1
protein in the anterior part of BA4 and 55 28 fmol mg 1
protein in the anterior part of BA4.
Glutamate Receptors
AMPA receptors reach highest densities in BA47, posterior part
of BA39, BA24, and BA25. Lowest values are found in the
motor, visual, auditory, somatosensory, and parahippocampal
cortices. In the hippocampus, AMPA receptors reach highest
densities in the pyramidal layer of the CA1 region of the cornu
ammonis (CA) and the molecular layer of the dentate gyrus
(DG), intermediate levels in CA2 and CA3, and lowest values
in the subiculum.
NMDA receptors show a rather homogeneous distribution
throughout the cortex, with somewhat higher densities in BA9,
BA45, BA47, and BA25. Lowest densities were described in
BA4, area 3b, BA41, BA42, BA24, and BA32. The frontal cortex
only reaches 50% of the NMDA receptor density of CA1 and
the DG of the hippocampus. NMDA receptors are found at
highest densities in CA1 and the DG, at intermediate levels in
the entorhinal cortex, and at lower levels in CA2/3 and the
subiculum.
Kainate receptors present highest densities in BA9, BA46,
BA47, BA7, the middle and inferior temporal gyri, BA24, and
the parahippocampal cortex. Lowest densities are found in
primary sensory areas 3b, BA17, and BA41, as well as in BA42
and the primary motor cortex. In the hippocampus, by far,
highest kainate receptor densities are found in CA3 (the stratum lucidum and pyramidal layer) and the hilus of the DG,
whereas densities in CA1, the subiculum, the presubiculum,
and the entorhinal cortex are lower.
Comparison between receptor subtypes. In all neocortical
areas, NMDA receptors occur at much higher densities than
kainate receptors (Amunts et al., 2010; Caspers et al., 2013;
Dean et al., 2001; Jansen, Faull, & Dragunow, 1989;
Palomero-Gallagher et al., 2009; Zavitsanou, Ward, & Huang,
2002; Zilles, Bacha-Trams, Palomero-Gallagher, Amunts, &
Friederici, 2014). The primary motor, somatosensory, auditory,
and visual cortices, as well as the anterior cingulate and superior
parietal association cortices, show higher absolute AMPA than
kainate densities, whereas both receptors have comparable
densities in the middle frontal gyrus (Jansen et al., 1989; Zavitsanou et al., 2002).
AMPA
NMDA
Kainate
GABAA
M1
M2
Nicotinic 4/2
263
5-HT1A
5-HT2
D1
D2
8
3,2,1
4
5
9
46
40
10 45 44 43 41 42
47
22
11
21
38
20
Map
8
9
39
18
19
17
37
10 32
12
11
3,2,1
5
24
23 31
19
AB C
18
D EFG RSP
17
25 27
19
18
34 35
28 36
37
38
20
FG1, FG2
Figure 1 Schematic maps of the regional distribution of glutamatergic AMPA (3H-AMPA or 3H-CNQX), NMDA (3H-MK801) and kainate (3H-kainate),
GABAergic GABAA (3H-muscimol, 3H-flunitrazepam, or 3H-flumazenil), cholinergic M1 (3H-pirenzepine), M2 (3H-oxotremorine-M or 3H-AF-DX384) and
a4/b2 (3H-epibatidine, 3H-nicotine, or 5-[125I]-A-85380), adrenergic a1 (3H-prazosin) and a2 (3H-UK 14,304, 3H-RX 821002, or 125I-iodoclonidine),
serotonergic 5-HT1A (3H-8-OH-DPAT or 3H-WAY-100635) and 5-HT2 (3H-ketanserin), and dopaminergic D1 (3H-SCH 23390) and D2 (125I-epidepride,
3
H-spiroperidol, 3H-raclopride, or 125I-NCQ 298 in the presence of raclopride) receptor binding sites in the human brain. The densities are given as
relative values for each receptor type. Red codes high density; green, intermediate density; and blue, low density. Gray indicates regions for which no
data are available. Dotted blue regions in the temporal lobe indicate minimally higher D2 receptor densities. The anatomical localization is based on
Brodmanns map (Brodmann, 1909) in most of the papers and shown in the lower right part of the figure. Arabic numbers, Brodmanns areas; A,
caudateputamen; B, globus pallidus; C, diencephalon; D, amygdala; E, CA1 region of the hippocampus; F, CA2/3 region of the hippocampus; G, the
dentate gyrus; RSP, retrosplenial areas. References for glutamate receptors: Ball et al. (1994), Caspers, Schleicher, et al. (2013), Caspers,
Palomero-Gallagher, et al. (2013), Court et al. (1993), Dean et al. (2001), Dewar, Graham, and McCulloch (1990), Dure et al. (1991), Eickhoff et al.
(2007), Gao et al. (2000), Ibrahim et al. (2000), Jansen et al. (1989), Kornhuber et al. (1989), Kravitz, Gaisler-Salomon, and Biegon (2013),
Meador-Woodruff, Davis, and Haroutunian (2001), Meoni et al. (1998), Morosan, Rademacher, Palomero-Gallagher, and Zilles (2004), Noga and Wang
(2002), Palomero-Gallagher et al. (2009), Palomero-Gallagher and Zilles (2009), Perry et al. (1993), Scarr, Pavey, Sundram, MacKinnon, and Dean
(2003), Scheperjans, Palomero-Gallagher, Grefkes, Schleicher, and Zilles (2005), Tremblay, Represa, and Ben-Ari (1985), Villares and Stavale (2001),
(Continued)
264
AMPA
NMDA
Kainate
mGlu2/3
GABAA
700
950
800
6200
2000
40
50
60
200
150
M1
M2
M3
Nicotinic 4/2
1000
350
1500
200
100
15
500
5-HT1A
5-HT2
D1
450
1250
700
600
120
30
50
100
Nicotinic 4/2 (detail)
Figure 2 Coronal sections showing the absolute densities of AMPA (3H-AMPA), NMDA (3H-MK801), kainate (3H-kainate), mGlu2/3 (3H-LY 341,495),
GABAA (3H-muscimol), muscarinic M1 (3H-pirenzepine), muscarinic M2 (3H-oxotremorine-M), muscarinic M3 (3H-4-DAMP), nicotinic a4/b2
(3H-epibatidine), a1 (3H-prazosin), a2 (3H-UK 14,304), 5-HT1A (3H-8-OH-DPAT), 5-HT2 (3H-ketanserin), and D1 (3H-SCH 23390) receptor binding sites in
the human occipital lobe. Distribution of nicotinic a4/b2 receptors in the primary visual cortex is shown at a higher magnification. Arrow points at
the nicotinic a4/b2 receptor-rich layer IVc; arrowheads mark the borders between BA17 and BA18.
Figure 1Contd Villegas, Estruch, Mengod, and Cortes (2011), Zavitsanou et al. (2002), Zilles (2005), Zilles and Amunts (2009), Zilles et al. (2014),
and Zilles, Schleicher, Palomero-Gallagher, and Amunts (2002). References for GABA receptors: Caspers, Palomero-Gallagher, et al. (2013), Caspers,
Schleicher, et al. (2013), Dean et al. (2001), Eickhoff et al. (2007), Morosan et al. (2004), Nishino et al. (1988), Palomero-Gallagher et al. (2009),
Palomero-Gallagher and Zilles (2009), Perry et al. (1993), Scheperjans, Palomero-Gallagher, Grefkes, Schleicher, and Zilles (2005), Zezula et al. (1988),
Zilles (2005), and Zilles et al. (2014). References for acetylcholine receptors: Araujo et al. (1988), Caspers, Palomero-Gallagher, et al. (2013), Caspers,
Schleicher, et al. (2013), Cortes et al. (1986), Cortes, Probst, and Palacios (1987), Cortes and Palacios (1986), Court et al. (1993), Court et al. (1997),
Crook, Tomaskovic-Crook, Copolov, and Dean (2000), Crook, Tomaskovic-Crook, Copolov, and Dean (2001), Eickhoff et al. (2007), Lin et al. (1986),
Lowenstein et al. (1990), Marutle et al. (2001), Matsumoto et al. (2005), Morosan et al. (2004), Nastuk and Graybiel (1988), Palomero-Gallagher et al.
(2009), Palomero-Gallagher and Zilles (2009), Perry, Court, Johnson, Piggott, and Perry (1992), Perry et al. (1993), Piggott et al. (2002), Piggott
et al. (2003), Pimlott et al. (2004), Rodriguez-Puertas et al. (1997), Scheperjans, Palomero-Gallagher, Grefkes, Schleicher, and Zilles (2005), Sihver,
Gillberg, and Nordberg (1998), Vanderheyden et al. (1990), Zilles (2005), and Zilles et al. (2014). References for noradrenalin receptors: Aldrich et al.
(1994), Caspers, Palomero-Gallagher, et al. (2013), Caspers, Schleicher, et al. (2013), De Vos, Vauquelin, De, De Backer, and Van (1992), Eickhoff
et al. (2007), Gross-Isseroff, Dillon, Fieldust, and Biegon (1990), Gross-Isseroff et al. (2000), Morosan et al. (2004), Palomero-Gallagher et al.
(2009), Palomero-Gallagher and Zilles (2009), Pazos et al. (1988), Scheperjans, Palomero-Gallagher, Grefkes, Schleicher, and Zilles (2005), Zilles,
Schleicher, Palomero-Gallagher, and Amunts (2002), and Zilles et al. (2014). References for serotonin receptors: Burnet et al. (1997), Caspers,
Palomero-Gallagher, et al. (2013), Caspers, Schleicher, et al. (2013), Cross and Slater (1989), Dean et al. (2001), Eickhoff et al. (2007), Gross-Isseroff,
Salama, Israeli, and Biegon (1990a), Hall et al. (1997), Hoyer et al. (1986a); Hoyer, Pazos, Probst, and Palacios (1986b), Matsumoto et al. (2005),
Morosan et al. (2004), Palacios et al. (1988), Palomero-Gallagher et al. (2009), Palomero-Gallagher and Zilles (2009); Pazos et al. (1987a,1987b),
Perry et al. (1993), Scheperjans, Palomero-Gallagher, Grefkes, Schleicher, and Zilles (2005), and Zilles et al. (2014). References for dopamine receptors:
Caspers, Palomero-Gallagher, et al. (2013), Caspers, Schleicher, et al. (2013), De Keyser et al. (1988), Eickhoff et al. (2007), Joyce et al. (1991),
Kessler et al. (1993), Kohler et al. (1991), Palacios et al. (1988), Palomero-Gallagher et al. (2009), Palomero-Gallagher and Zilles (2009), Rieck, Ansari,
Whetsell, Deutch, and Kessler (2004), Scheperjans, Palomero-Gallagher, Grefkes, Schleicher, and Zilles (2005), Sun et al. (2012), and Zilles
et al. (2014).
GABAA
cs
1
Te1
2
3a
3b
M2
cs
1
Te1
3a
3b
cs
1
Te1
3a
2
3b
Low
High
Figure 3 Sections showing the relative density distribution of GABAA,

muscarinic M2, and adrenergic a2 receptor binding sites in the human
primary motor (BA4), somatosensory (area 3b), and auditory (BA41,
Te1) cortices. Area 3a (Jones & Porter, 1980) is part of the
somatosensory cortex with features both of the motor and primary
somatosensory cortices.
GABA Receptors
The GABAA receptor shows a relatively homogeneous distribution throughout the cortex, with highest densities in BA17 and
fusiform areas FG1 and FG2 (Caspers, Zilles, et al., 2013) and
lowest densities in BA46, BA4, BA41, and BA42. The primary
auditory and somatosensory cortices also have slightly higher
GABAA receptor densities than the surrounding secondary
areas, but their values do not reach the high density of the
primary visual cortex. The latter value is due to the exceptionally high density in layers IIIVcb (Zezula, Cortes, Probst, &
Palacios, 1988; Zilles, Palomero-Gallagher, & Schleicher, 2004;
Zilles & Schleicher, 1993). In the hippocampus, GABAA receptor binding sites reach highest densities in the CA1 pyramidal
and lacunosum molecular layers, in the molecular layer of the
DG, and in the presubiculum and lowest concentrations in the
hilus, CA3, and subiculum.
265
information on the regional distribution between neocortical

areas. No major differences were found between BA8, BA9,
BA10, and BA46, which have similar densities to most parts
of the postcentral gyrus, superior parietal lobule, extrastriate
visual cortex, superior and inferior temporal gyri, and BA23
and BA31. Lowest densities were found in BA4, BA6, area 3b of
the postcentral gyrus, BA24, BA25, BA32, retrosplenial areas,
and areas FG1 and FG2. Highest densities were measured in
BA17, middle temporal gyrus, BA47, BA5, and the anterior part
of BA39. The hippocampus has, together with the lateral prefrontal, parietal, and extrastriate visual cortices, an intermediate M1 receptor density, which is clearly higher than in the
thalamus. Relatively high densities are found in CA1 and the
DG, followed by the other hippocampal regions.
When analyzing M2 receptor (3H-oxotremorine-M binding)
distribution patterns, the most conspicuous finding is the very
high density in the primary somatosensory, visual, and auditory areas (Figure 2), indicating an important role of this
receptor in the signal processing of thalamocortical input
(Zilles & Amunts, 2010). The secondary sensory areas have
lower M2 receptor densities, thus allowing a distinct mapping
of primary and secondary cortices. Very high densities were
also seen in BA31, the retrosplenial cortex, fusiform areas FG1
and FG2, and BA7. Lowest M2 receptor densities are found in
BA4, the posterior part of BA39, BA9, BA44, and BA47. The M2
receptors are higher in the CA13 regions and the entorhinal
area, particularly in its deeper layers, compared to most neocortical areas. The DG contains slightly lower M2 receptor
densities than the CA.
The nicotinic a4/b2 receptor binding sites are expressed at
low densities throughout the cortex, with slightly higher values
in the motor, early visual, primary auditory and somatosensory, retrosplenial, and entorhinal cortices, as well as in BA23
and BA31. Interestingly, compared to the surrounding secondary sensory cortices, the primary sensory cortices show a
lamina-specific maximum in layer IV (Figure 2). A similar
situation is observed in the premotor and primary motor cortices, with a maximum in deeper layer III (Zilles & Amunts,
2009; Zilles et al., 2004). Highest nicotinic a4/b2 receptor
densities are found in the middle layer of the entorhinal area,
the parvocellular islands of the subiculum, and the stratum
lacunosum-moleculare of the CA. Lowest densities occur in the
pyramidal layers of the CA and the hilus of the DG.
Comparison between receptor subtypes. Muscarinic binding sites are considerably higher in the cerebral cortex than
nicotinic binding sites (Court et al., 1997; Lange, Wells, Jenner,
& Marsden, 1993; Palomero-Gallagher & Zilles, 2009; Zilles
et al., 2014). A comparison of M1 versus M2 receptors shows a
higher density of the former type throughout the human cortex
(Amunts et al., 2010; Caspers, Schleicher, et al., 2013; Eickhoff,
Rottschy, & Zilles, 2007; Lange et al., 1993; PalomeroGallagher et al., 2009; Piggott et al., 2002; Zilles et al., 2014).
Noradrenaline Receptors
Acetylcholine Receptors
Although earlier studies reported M1 receptor data from hemispheric lobes (Araujo, Lapchak, Robitaille, Gauthier, &
Quirion, 1988; Rodriguez-Puertas, Pascual, Vilaro, & Pazos,
1997), this gross parcellation does not provide sufficient
The a1 adrenoceptors are found at intermediate densities in

most cortical areas. Somewhat lower densities are reported for
BA17, area 3b, BA41, BA42, BA4, lateral and medial orbital
cortices, and retrosplenial areas. Highest densities are seen in
all cingulate areas (BA23, BA24, BA25, BA31, and BA32), BA9,
266
BA46, BA7, and posterior part of BA39. In the hippocampus,

a1 adrenoceptor densities are considerably higher in the DG and
CA3 than in CA1, CA2, or the subicular complex (Gross-Isseroff,
Dillon, Fieldust, & Biegon, 1990; Zilles, 2005).
The a2 receptors (full agonist 3HUK 14, 304 or antagonist
3
HRX 821002 binding) reach highest densities in BA46,
BA44, BA24, BA7, primary visual, somatosensory, and primary
and secondary auditory cortices. Lowest densities are found in
BA4, BA47, and BA39. The very high density in the primary
sensory areas enables their clear mapping. In contrast, a2
receptor density visualized by the partial agonist binding
(125I-iodoclonidine) was found to be lower in the postcentral
than in the precentral gyrus (Gross-Isseroff, Weizman, Fieldust,
Israeli, & Biegon, 2000). Intermediate a2 adrenoceptor densities are described throughout the hippocampal regions, with
somewhat higher values in the lacunosum-moleculare layer of
CA1 and CA2.
The b1 adrenoceptors are present at highest densities in the
motor and temporal cortices, at intermediate values in the
hippocampus and prefrontal and parietal cortices, and at lowest values in the occipital cortex (De Paermentier, Cheetham,
Crompton, & Horton, 1989; Pazos, Probst, & Palacios, 1985).
Comparison between receptor subtypes. a1 Adrenoceptor
binding site densities are generally higher in neocortical areas
than a2 adrenoceptor densities, with the notable exception of
primary sensory areas (Eickhoff et al., 2007; Scheperjans,
Palomero-Gallagher, Grefkes, Schleicher, & Zilles, 2005; Zilles
et al., 2014). In the frontal cortex, b adrenoceptors are present
in lower densities than a2 receptors (Sastre, Guimon, & GarciaSevilla, 2001).
Serotonin Receptors
The 5-HT1A receptor densities in BA6, BA9, BA10, BA11, BA46,
BA24, and BA32 are comparable to those of most other cortical
areas. The primary motor, visual, and somatosensory areas and
the primary and secondary auditory areas, the language areas
BA44 and BA45, and BA47 and retrosplenial areas present
lower 5-HT1A receptor densities. BA25 stands out by a considerably higher 5-HT1A receptor density. Notably, the hippocampus and the entorhinal cortex present, together with BA25, the
highest 5-HT1A receptor densities. In the hippocampus, they
reach the highest value in CA1 and much lower densities in
CA3. The density is slightly lower in the subiculum than in
CA1, but higher than in the entorhinal cortex when averaged
over all cortical layers. Notably, the anterior part of the entorhinal cortex can be clearly delineated from the medial and
posterior parts by a conspicuous decrease of 5-HT1A receptor
densities in the deeper layers from a very high level in the
anterior part to a low level in the medial and posterior parts,
whereas the density remains comparable in the more superficial layers of all parts of the entorhinal cortex (Pazos, Probst, &
Palacios, 1987a).
Highest 5-HT2 densities are found in BA9, BA10, BA11,
BA44, BA45, BA46, BA24, BA25, BA31, BA32, retrosplenial
areas, and the entorhinal cortex. The primary motor cortex
has the lowest density of all areas in the frontal lobe. Low
densities were also found in the extrastriate visual areas; in
the superior, middle, and inferior temporal gyri; and in the
parahippocampal gyrus. The primary visual, primary and secondary auditory, and primary somatosensory cortices present
slightly higher 5-HT2 receptor densities than surrounding

areas. The hippocampus shows lower 5-HT2 receptor densities
than frontal, cingulate, and parietal areas. Within the hippocampus, some authors (Dewar, Graham, & McCulloch, 1990;
Gross-Isseroff, Salama, Israeli & Biegon, 1990b; Matsumoto,
Inoue, Iwazaki, Pavey, & Dean, 2005) described higher 5-HT2
receptor densities in the DG than in the CA (pyramidal layer),
but other authors (Hoyer, Pazos, Probst, & Palacios, 1986a;
Pazos, Probst, & Palacios, 1987b) reported the opposite relation. All authors agree that the subiculum exhibits the lowest
5-HT2 receptor density of all hippocampal regions.
Serotonin 5-HT3 receptors occur at very low densities
in most neocortical regions and reach somewhat higher densities in the prefrontal cortex and hippocampus (Marazziti
et al., 2001).
The density of the 5-HT4 receptor in the temporal cortex is
similar to that in the hippocampus and amygdala, but clearly
lower than in the caudate (Reynolds et al., 1995).
No major differences are found between the different hippocampal regions and layers regarding 5-HT7 receptor densities (Martin-Cora & Pazos, 2004).
Comparison between receptor subtypes. The 5-HT1A receptor densities in prefrontal and anterior cingulate areas BA9,
BA10, BA45, BA46, and BA24 are considerably lower than 5HT2 receptor densities (Burnet, Eastwood, & Harrison, 1997;
Dean et al., 2001; Palomero-Gallagher & Zilles, 2009; Pazos
et al., 1987a).
Dopamine Receptors
The D1 receptors occur with low density throughout all neocortical areas. Slightly higher densities are found in BA7, BA17,
BA24, BA25, BA39, BA40, BA46, FG1, and FG2. The overall D1
receptor density is very low in the hippocampus. The relatively
highest density is found in the pyramidal layer of CA1, with
very low values in the DG.
The D2 receptors are around the limit of detection. In the
temporal cortex, minimally higher D2 values were reported.
The overall D2 receptor density is low in the hippocampus.
Highest values are found in the radiatum layer of CA3 and the
hilus of the DG; intermediate densities, in the subiculum and
presubiculum; and lowest densities, in the entorhinal cortex,
parasubiculum, and other regions and layers of the hippocampus (Joyce, Janowsky, & Neve, 1991; Kohler et al., 1991).
Comparison between receptor subtypes. D2 receptors occur
by 25 times lower values than D1 receptors in the cerebral
cortex; in the hippocampus, this difference is not so conspicuous (De Keyser et al., 1988; Palacios, Camps, Cortes, &
Probst, 1988).
Regional Distribution of Transmitter Receptors in the

Human Amygdala, Basal Ganglia, Diencephalon,
and Cerebellum
Amygdala
The amygdala is a cytoarchitectonically heterogeneous structure
with subregions of different cellular compositions, connectivities, and functions (Amunts et al., 2005; De Olmos, 2004;
Figure 1). This heterogeneity is reflected by a comparable diversity of receptor distribution patterns, not only between receptors
but also regarding the regional density of a given receptor subtype. To the best of our knowledge, a comprehensive study of
the subregional receptor expression is presently not available.
The mean AMPA, NMDA, and kainate receptor densities are
below the level of values reported for the hippocampus. The
lateral and basal nuclei contain comparable AMPA and kainate
receptor densities (Graebenitz et al., 2011; Noga & Wang,
2002). Within the lateral nucleus, NMDA receptors show the
highest densities, followed by kainate and AMPA receptors
(Graebenitz et al., 2011).
Mean GABAA receptor densities in the amygdala are comparable to those found in CA1. Highest densities are found in
the lateral nucleus and much lower densities in the basal and
basolateral nuclei (Graebenitz et al., 2011; Zezula et al., 1988).
The M1 receptor density of the amygdala is similar to that
of CA1 and the dentate. It differs only slightly between the
basal, basolateral, and lateral nuclei (Cortes, Probst, Tobler, &
Palacios, 1986; Graebenitz et al., 2011). The M2 receptor density in the lateral nucleus reaches an intermediate level between
the total hippocampal region and the neocortex. However,
the basolateral nucleus shows a clearly higher density than the
lateral nucleus (Graebenitz et al., 2011). Nicotinic a4/b2 receptor
densities are very low and are similar between the lateral and
basolateral nuclei (Graebenitz et al., 2011; Zilles, Schleicher,
Palomero-Gallagher, & Amunts, 2002).
The overall a1 adrenoceptor density in the amygdala is
comparable to that of the cerebral cortex. Slightly lower values
are found in the basal and basolateral nuclei than in the lateral
nucleus (Aldrich et al., 1994; Graebenitz et al., 2011). The a1
adrenoceptor density of the amygdala is considerably higher
than the a2 density. The a2 adrenoceptors are considerably
lower in the amygdala compared to the cerebral cortex and
reach slightly higher values in the basal and basolateral nuclei
than in the lateral nucleus (Aldrich et al., 1994; Graebenitz
et al., 2011). The b1 adrenoceptor density is considerably lower
than in the basal ganglia and slightly lower compared to the
neocortex (De Paermentier et al., 1989).
The amygdala contains a very low mean 5-HT1A receptor
density. Lowest values are found in the lateral, basolateral, and
basal accessory nuclei. The granular and cortical nuclei as well
as the transitory zone exhibit higher densities (Graebenitz
et al., 2011; Hall et al., 1997; Pazos et al., 1987a). The 5-HT2
receptor densities are also very low in the amygdala but higher
than the 5-HT1A receptor densities, with highest values in the
lateral and basolateral nuclei (Graebenitz et al., 2011; Pazos
et al., 1987b). 5-HT3 receptors reach intermediate densities in
the amygdala, slightly higher than in the hippocampus, but
clearly lower compared to the striatum (Marazziti et al., 2001).
The D1 receptor of the amygdala reaches the level of the
anterior cingulate and posterior parietal cortices and a five
times higher density than D2 receptors in the amygdala. The
D1 receptor density is slightly higher in the basolateral than in
the lateral nucleus (Graebenitz et al., 2011). The D2 receptor
density is very low but approximately three times higher than
in the neocortex.
Basal Ganglia
The basal ganglia comprise various subcortical nuclei, each of
which has a distinct cytological and neurochemical organization
(Haber & Gdowski, 2004). They are strongly interconnected
267
with the cortex and thalamus and are associated with motor,
cognitive, and emotional functions (Figure 1).
AMPA receptor densities in the caudateputamen are
comparable to those measured in the frontal cortex, whereas
NMDA and kainate receptor densities only reach approximately half of the cortical values. The densities of all three
receptor types are considerably higher in the caudateputamen
than in the globus pallidus or the subthalamic nucleus (Ball,
Shaw, Ince, & Johnson, 1994; Meoni, Mugnaini, Bunnemann,
Trist, & Bowery, 1998; Villares & Stavale, 2001). Slightly lower
AMPA and NMDA values are found in the caudateputamen
than in the ncl. accumbens; they do not differ in their kainate
receptor densities (Meador-Woodruff, Hogg, & Smith, 2001).
AMPA and NMDA receptors seem to be higher concentrated in
the matrix than in the striosomes, whereas kainate receptors
show the reverse distribution (Dure, Young, & Penney, 1991).
GABAA receptor densities in the caudateputamen only
reach 40% of the values measured in the motor cortex but are
approximately 50% higher than in the globus pallidus, particularly its medial part, or the subthalamic nucleus (Nishino,
Fujiwara, Noguchi-Kuno, & Tanaka, 1988; Zezula et al., 1988).
Interestingly, an increasing rostrocaudal gradient in GABAA
receptor density was found in the caudateputamen, though
not in the globus pallidus.
The density of cholinergic muscarinic M1 receptors in the
caudateputamen is approximately twice that of the frontal,
inferior parietal, and extrastriate visual cortices and considerably higher than in the globus pallidus and subthalamic
nucleus, but slightly lower than in the ncl. accumbens. Within
the caudateputamen, contradictory results have been
reported regarding the association of M1 receptors with the
striosomematrix segregation. Whereas Lowenstein, Joyce,
Coyle, and Marshall (1990) reported higher M1 receptor density in the matrix, Nastuk and Graybiel (1988) assigned higher
M1 receptor densities to the striosome compartment.
M2 receptor densities in the caudateputamen are approximately twice those of BA20, BA21, BA22, and BA36 and four
times higher than in BA24. They are also significantly higher in
the caudateputamen than in the globus pallidus (Piggott
et al., 2002, 2003). M2 receptors are homogeneously distributed
throughout the matrix and striosomes (Nastuk & Graybiel,
1988). A comparison between the densities of M1 and M2
receptors shows a more than two times higher density of M1
receptors in the caudateputamen (Rodriguez-Puertas et al.,
1997). Nicotinic a4/b2 receptor densities are very low in the
caudateputamen and comparable to those of the hippocampus
and neocortex (Lange et al., 1993). Nevertheless, they are by
three times higher in the caudateputamen than in the globus
pallidus (Nordberg, Alafuzoff, & Winblad, 1992).
The a1 adrenoceptor density in the caudateputamen is
approximately a third of that in the middle temporal gyrus.
In the medial part of the globus pallidus, a1 densities are
similar to those of the caudateputamen; in the lateral part,
lower densities are found (Aldrich et al., 1994). The a2 adrenoceptor density in the caudateputamen is approximately
half of that measured in the superior, middle, or temporal
gyri and only reaches 25% of values found in the superior
frontal gyrus. In the globus pallidus, a2 adrenoceptors only
reach one-third of the density of the caudateputamen
(Aldrich et al., 1994). Considerably higher b adrenoceptor
densities are found in the caudateputamen (with highest
268
densities in striosomes), the ncl. accumbens, and the lateral

part of the globus pallidus than in the neocortex (De
Paermentier et al., 1989; Pazos et al., 1985).
The density of 5-HT1A receptors in the basal ganglia only
reaches a tenth of the values in the frontal cortex, whereas 5HT2 densities in the caudateputamen are similar to those
found in frontal cortical areas. The caudateputamen and ncl.
accumbens present comparable 5-HT2 receptor densities,
which are clearly higher than in the globus pallidus (GrossIsseroff, Salama, Israeli, & Biegon, 1990b; Pazos et al., 1987b).
Notably, 5-HT2 receptor densities of the caudate decline from
rostral to caudal levels and are higher in the caudate than in the
putamen at rostral levels (Gross-Isseroff, Salama, Israeli, &
Biegon, 1990b). The basal ganglia have 5-HT3 receptor densities more than twofold higher as found in the amygdala and
hippocampus (Marazziti et al., 2001). The 5-HT4 receptor
densities in the caudateputamen are comparable to those
found in the lateral part of the globus pallidus but considerably
higher than those found in its medial part or in the cortex
(Reynolds et al., 1995). The serotonin 5-HT7 receptors reach
the second highest densities in the caudateputamen and ncl.
accumbens when compared to other brain regions (MartinCora & Pazos, 2004).
The density of D1 and D2 receptors in the basal ganglia is
considerably higher than in the neocortex or hippocampus.
Caudateputamen and ncl. accumbens contain comparable D1
and D2 receptor densities, which are higher than in the globus
pallidus (Sun, Xu, Cairns, Perlmutter, & Mach, 2012). Notably,
the lateral and medial parts of the globus pallidus differ in their
D1 receptor density by nearly five times, with a lower value in
the lateral part (Palacios et al., 1988). Furthermore, D2 receptor
densities seem to be higher in the rostral compared to the
caudal part of the caudateputamen (Joyce et al., 1991). The
D2 receptor density is two times higher in the striosomes
compared to the matrix of the caudateputamen (Joyce,
Sapp, & Marshall, 1986). The D3 receptors reach considerably
higher densities in the ncl. accumbens than in the caudate
putamen, whereas the globus pallidus again shows lowest
receptor densities (Sun et al., 2012).
Diencephalon
The diencephalon consists of numerous nuclei with different
cellular structures and connectivities (Jones, 2007). It relays
sensory and motor information between brain regions and
controls many autonomic and limbic functions (Percheron,
2004; Saper, 2004; Figure 1). A detailed description of the
receptor expression in the different nuclei is far beyond the
scope of this article. Therefore, we focus here on mean values of
the thalamus, with some examples of selected nuclei.
On average, the densities of AMPA, NMDA, and kainate
receptors are low compared to the hippocampus and some
cortical regions. Only the NMDA receptors reach intermediate
densities, as most cortical areas. The limbic anterior thalamic
nucleus presents intermediate to high NMDA and low kainate
receptor densities (Ball et al., 1994). The AMPA and NMDA
receptors reach lowest values in the reticular nucleus (Ibrahim
et al., 2000), which receives input from the whole cortex and
projects to numerous thalamic nuclei. Somewhat higher
NMDA receptor densities are found in the medial geniculate
body (Meoni et al., 1998). Highest kainate receptor densities

are seen in the limbic anterior and dorsomedial thalamic
nuclei (Ibrahim et al., 2000).
GABAA receptor densities in the thalamus reach values similar to the cortex. Highest densities are found in the limbic
median nuclei and lowest in the pulvinar (Zezula et al.,
1988). The corpus geniculatum laterale has values comparable
to those in the neocortex, whereas the corpus geniculatum
mediale reaches approximately 50% (Zezula et al., 1988). In
the hypothalamus, highest GABAA receptor densities are found
in the mammillary bodies (Palacios, Probst, & Mengod, 1992;
Zezula et al., 1988).
On average, cholinergic muscarinic M1 receptor density of
the thalamus is lower than in the cortex and reaches only
approximately 10% of that of the caudateputamen. The
mean M2 receptor density in the thalamus is comparable to
most cortical regions and double of that of the M1 receptors in
the thalamus (Piggott et al., 2002). Nicotinic a4/b2 receptors
averaged over the whole thalamus are denser than in the cortex
and hippocampus. Highest densities are seen in the lateral
geniculate body and in the limbic anteroprincipal thalamic
nucleus (Court et al., 1997; Pimlott et al., 2004).
Mean thalamic a1 adrenoceptor density is comparable to
most neocortical regions. It shows highest densities in the
limbic anterior thalamic nucleus (Gross-Isseroff, Dillon, Fieldust, & Biegon, 1990). The b1 adrenoceptor densities in the
thalamus and hypothalamus are considerably lower than in
the basal ganglia and slightly lower compared to the neocortex
(De Paermentier et al., 1989).
Mean thalamic 5-HT1A receptor densities are much lower
than in most cortical regions. Highest densities are found in the
paraventricular and parts of the intralaminar nuclei (Pazos
et al., 1987a), which are targets of the ascending reticular
activating system and serotonergic afferents from the raphe
nuclei. On average, 5-HT2 receptors occur at higher densities
than the 5-HT1A receptors in the thalamus. The 5-HT2 densities
are higher in the thalamus than in the hippocampus. Highest
densities are found in the mammillary body (Gross-Isseroff,
Salama, Israeli, & Biegon, 1990b; Pazos et al., 1987b). The
5-HT7 receptor density is very low in all thalamic nuclei, with
the notable exception of the centromedial nucleus, which
reaches the highest density of all measured brain regions
(Martin-Cora & Pazos, 2004).
Very low D1 and D2 receptor densities are found in the
thalamus (Piggott et al., 2007; Sun et al., 2012). They are
comparable to those of the hippocampus and most cortical
regions but clearly lower than in the caudateputamen. In
contrast, D3 receptors reach levels comparable to those found
in the caudateputamen (Sun et al., 2012).
Cerebellum
The AMPA receptor density of the cerebellar cortex is similar to
that of the occipital neocortex, but the NMDA and kainate
values are higher (compare Figures 2 and 4). Within the cerebellar cortex, AMPA densities are higher in the molecular than
in the granular layer, and the opposite holds true for kainate
and NMDA receptors (Dewar, Chalmers, Shand, Graham, &
McCulloch, 1990; Jansen, Dragunow, Faull, & Leslie, 1991;
Jansen, Faull, & Dragunow, 1990; Makowiec, Albin, Cha,
AMPA
1500
GABAA
250
7000
NMDA
500
Kainate
3500
250
2200
mGlu2/3
10000
GABAB
500
5500
M3
200
750
150
1000
D1
200
400
269
Map
M2
50
250
nic 4/2
15
500
25
1200
5-HT2
5-HT1A
30
400
50
300
1000
150
Figure 4 Sections showing AMPA, NMDA, kainate, mGlu2/3, GABAA, GABAB, muscarinic M2, muscarinic M3, nicotinic a4/b2, a1, a2, 5-HT1A, 5-HT2,
and D1 receptor binding sites in the human cerebellum. 1: Molecular layer of the cerebellar cortex; 2: granular layer of the cerebellar cortex; 3: ncl.
dentatus; 4: white matter of the cerebellum. Muscarinic M1 receptors are not shown because their density in the cerebellum is below the detection level.
Young, & Gilman, 1990). The dentate nucleus contains similar

NMDA, but considerably lower AMPA and kainate receptor
densities compared to the cerebellar cortex. The metabotropic
mGlu2/3 receptors of the cerebellar cortex reach higher
values than those in the occipital neocortex (compare Figures 2
and 4). The granular layer contains a higher density than the
molecular layer, and the dentate nucleus is below the detection
level.
The GABAA receptor densities are similar in the cerebral and
cerebellar cortices. Similar densities are found in the molecular
and granular cell layers and much lower values in the dentate
nucleus (Albin & Gilman, 1990; Albin, Price, Sakurai, Penney,
& Young, 1991; Whitehouse, Muramoto, Troncoso, &
Kanazawa, 1986; Zezula et al., 1988). The agonist binding
(3H-muscimol) of the GABAA receptor shows a higher density
in the granular than in the molecular layer (Schmitz, Reichelt,
Walkowiak, Richards, & Hebebrand, 1988; Whitehouse et al.,
1986; also see Figure 4). The opposite relation between both
layers is found for the GABAB receptor (Albin & Gilman, 1990,
also see Figure 4). In the case of the GABAB receptor, the
dentate nucleus can be detected, though at a low density.
The cholinergic muscarinic M1 receptor density is around
the detection level of receptor autoradiography (Lin, Olson,
Okazaki, & Richelson, 1986; Piggott et al., 2002) and, therefore, not shown in Figure 4. The M2 receptor density is much
lower in the cerebellar than in the cerebral cortex, with slightly
higher values in the molecular than in the granular layer of the
cerebellum (Piggott et al., 2002). The dentate nucleus is not
detectable. The M3 receptors of the cerebellar cortex and dentate nucleus show similar densities but lower values than in the
occipital lobe (compare Figures 2 and 4). Nicotinic a4/b2
receptor densities are higher in cerebellar than in the cerebral
cortex and higher in the molecular than in the granular cell
layer of the cerebellum. The dentate nucleus takes an intermediate position between the values of both layers (Court et al.,
1997; Pimlott et al., 2004).
270
The a1 adrenoceptor densities of the cerebellar cortex

are higher than those of the occipital cortex and the dentate
nucleus is clearly recognizable. The a2 adrenoceptor densities
of the cerebellar cortex are lower than those of BA17, but
slightly higher than those of extrastriate areas (compare
Figures 2 and 4). The molecular layer shows a higher value
than the granular layer. The density on the dentate nucleus is
very low. The b2 adrenoceptors reach only half of the density
as found in the hippocampus but show similar densities
to those measured in the thalamus and hypothalamus
(De Paermentier et al., 1989).
Very low 5-HT1A receptor densities are found in the cerebellar cortex and dentate nucleus (Hall et al., 1997), which
are considerably lower than the values found in the superficial
layers of the cerebral cortex (compare Figures 2 and 4).
Cerebellar 5-HT2 receptor densities are comparable to those
of the occipital neocortex. They show lowest values in the
molecular layer and highest in the dentate nucleus (Pazos
et al., 1987b).
Neither D1 nor D2 receptors could be demonstrated by De
Keyser et al. (1988), but in our material, higher D1 receptor
densities in the cerebellar and dentate nucleus than in the
occipital cortex are found (compare Figures 2 and 4), particularly in the molecular layer (Palacios et al., 1988). Very low
densities of D2 receptors are described, with somewhat higher
values in the granular than molecular layer of the cerebellar
cortex (Palacios et al., 1988).
Laminar Distribution of Transmitter Receptors

in the Human Neocortex
The six-layered laminar structure of the neocortex is an anatomical feature of its connectional organization. The supragranular layers IIII are mainly sources and targets of
intrahemispheric and interhemispheric connections, granular
layer IV is a major target of the thalamocortical input, whereas
the infragranular layers VVI send their output mainly to subcortical targets. Since most of the synaptic contacts occur at the
dendritic trees, and the dendrites of layer V pyramids extend up
to the most superficial layers, preferential localizations of synaptic contacts or receptor densities in a cortical layer cannot
simply be assigned to the cells in this layer. This cell-specific
assignment can only be solved by immunohistochemical
methods using laser scanning microscopy or electron microscopy. Nevertheless, receptor autoradiography provides laminar
specific data on receptor concentrations, which bridge the gap
between mesoscopic, microscopic, and ultra-high-resolution
scales. Moreover, the laminar pattern is an important feature
for delineation of cortical areas based on receptor expression
levels.
Under this perspective, we see a segregation of the receptor
subtypes described here into three groups: one group shows
highest densities in the superficial, mostly supragranular, layers,
a second group in the infragranular layers, and a third group in
layer IV and/or layer III, which also receives thalamocortical
input.
Group 1 (Figure 5): highest densities in the supragranular
layers are found for AMPA, NMDA, GABAA, M1, M3, a1, a2, and
5-HT1A receptors. Nicotinic a4/b2 receptors show highest
densities in the supragranular layers III (together with layer

IV) of BA32. The D2 receptor reaches not only highest densities
in layers III but also very high densities in layers VVI of the
temporal neocortex.
Group 2 (Figure 5): highest densities in the infragranular
layers are found for the kainate, 5-HT7, D1 (only layer V), and
D2 (all other neocortical areas) receptors. The M2 receptor
shows highest densities in layer V of the prefrontal cortex.
Group 3 (Figure 5): highest densities in the granular layer
and/or in layer III are found for GABAA (together with layer II),
M2 (in area 44d of Brocas region), nicotinic a4/b2 (in lower
layer III of BA4 and layer IV of BA32), b1 (layer III), and 5-HT2
(layer III) receptors.
Therefore, we suggest that the group 2 receptors mainly
influence the cortical output, whereas the group 3 receptors
play an important role in the processing of the thalamocortical
input. The group 1 receptors, however, can be localized on
both input and output neurons.
Development and Aging

During adult stages, NMDA receptor densities decrease with
increasing age in prefrontal area BA9 and in the caudate
putamen and ncl. accumbens (Hellstrom-Lindahl & Court,
2000; Villares & Stavale, 2001). During fetal development,
AMPA receptors of the whole hippocampal region reach a
transitory maximum around the 20th gestational week,
which declines by 30% by the end of the 26th gestational
week (Lee & Choi, 1992). A similar time course was seen for
the NMDA and kainate receptors, with an even stronger decline
after the 22nd week (Lee & Choi, 1992). Kainate receptor
densities decrease in CA3 and the molecular layer of the DG
between birth and adult stages (Represa, Tremblay, Schoevart,
& Ben-Ari, 1986).
The development of GABAA receptors in the cerebral and
cerebellar cortices exhibits a considerable heterochrony.
Whereas in the cerebral cortex these receptors attain adult
values approximately 5 months after birth, in the cerebellum,
only 10% of the adult value was reached at birth, and these
densities continued increasing after the fifth postnatal month
(Brooksbank, Atkinson, & Balazs, 1981). Interestingly, the
activity of GAD, a presynaptic marker, developed somewhat
more slowly on the cerebral cortex than that of the GABAA
receptors, whereas GAD reached adult values by the fifth postnatal month in the cerebellar cortex (Brooksbank et al., 1981).
Since the GABAA receptors were demonstrated by the agonistic
binding sites (3H-muscimol binding), not all GABAA receptors
may be demonstrated in this study. In a following study, it
was shown that the BZ binding sites of the GABAA receptor
develop more rapidly in the cerebellum and less rapidly in the
cerebral cortex (Brooksbank, Atkinson, & Balazs, 1982). Additionally, the concentration of GABA in both brain regions
increased more rapidly than that of GAD (Brooksbank et al.,
1982). Taken together, both studies provide information
concerning a concerted development of both the transmitter
and the GABAA receptor during fetal and early postnatal
developments.
No decline was found in the frontal cortex for all cholinergic muscarinic receptor subtypes together (3H-QNB binding)
AMPA
I
II
III
IV
V
VI
NMDA
I
II
III
IV
V
VI
M2
I PF 44d
II
III
IV
V
VI
1
I
II
III
IV
V
VI
5-HT2
I
II
III
IV
V
VI
I
II
III
IV
V
VI
I
II
III
IV
V
VI
1
5-HT1A
D1
I
II
III
IV
V
VI
32
I
II
III
IV
V
VI
I
II
III
IV
V
VI
5-HT7
I
II
III
IV
V
VI
4/2
M3
2
I
II
III
IV
V
VI
GABAA
I
II
III
IV
V
VI
I
II
III
IV
V
VI
I
II
III
IV
V
VI
M1
Kainate
D2
I
II
III
IV
V
VI
271
between 20th gestational week and adult stages

(Bar-Peled et al., 1991), though their densities diminish significantly during aging (Rinne, 1987). Interestingly, in CA1, muscarinic receptors (3H-QNB binding) show a discrete though
significant decline between 20th gestational week and adult
stages (Bar-Peled, Israeli, et al., 1991; Court et al., 1997), and
there is a significant reduction of the binding to all muscarinic
receptors during aging (Rinne, 1987). Furthermore, a dramatic
reduction of muscarinic receptor density (all subtypes
together) was found in the putamen and globus pallidus
between 24th gestational week and adult stages (Bar-Peled,
Israeli, et al., 1991). There is also a significant reduction of all
muscarinic receptors in the caudateputamen during aging
(Rinne, 1987). Nicotinic a4/b2 receptors decline between fetal
and early postnatal stages in all subregions of the hippocampus, whereas the a7 nicotinic receptors do not show clear
differences between fetal and adult stages in binding densities,
with the notable exception of CA1, where a sharp decline was
described between fetal and neonatal stages (Court et al.,
1997). During adult stages, nicotinic receptors also decrease
with increasing age in the entorhinal cortex, DG, and prefrontal area BA9 (Court et al., 1997; Hellstrom-Lindahl & Court,
2000). In the caudateputamen, this age-related decrease of
nicotinic receptors was found only after the age of 70 years
(Hellstrom-Lindahl & Court, 2000). The age-related decrease
Figure 5 Laminar distribution of glutamatergic AMPA, NMDA, and

kainate; GABAergic GABAA; cholinergic M1, M2, and M3 (3H-4-DAMP) and
a4/b2; adrenergic a1, a2, and b1 (125I-cyanopindolol); serotonergic 5HT1A, 5-HT2, and 5-HT7 (3H-mesulergine); and dopaminergic D1 and D2
receptor binding sites in the human neocortex. Ligands used as specified
in Figure 1. The densities are given as relative values for each receptor
type. Red indicates high density; green, intermediate density; and blue,
low density. The laminar distribution of muscarinic M2 receptors is
shown for the inferior parietal cortex (area PF; Caspers et al., 2006) and
the dorsal part of area 44 in Brocas region (area 44d; Amunts et al.,
2010) because of considerable differences in laminar patterns between
cortical regions. For the same reasons, we show the laminar distribution
of nicotinic a4/b2 receptors in the primary motor cortex (BA4) and
anterior cingulate area 32 (Palomero-Gallagher, Zilles, Schleicher, &
Vogt, 2013) and of dopaminergic D2 receptors (Joyce et al., 1991) in the
temporal cortex (T) and the other neocortical areas (N). Receptors for
glutamate: Amunts et al. (2010), Carlson, Penney, and Young (1993),
Caspers, Palomero-Gallagher, et al. (2013), Caspers, Schleicher, et al.
(2013), Eickhoff et al. (2007), Jansen et al. (1989), Meador-Woodruff,
Davis, and Haroutunian (2001), Palomero-Gallagher and Zilles (2009),
Scheperjans, Grefkes, Palomero-Gallagher, Schleicher, and Zilles (2005),
Shaw and Ince (1994), Zavitsanou et al. (2002), Zilles et al. (2002), Zilles,
Schleicher, Palomero-Gallagher, and Amunts (2002), Zilles et al. (2004),
Zilles et al. (2014), and Zilles and Amunts (2010). Receptors for GABA:
Amunts et al. (2010), Carlson et al. (1993), Caspers, Palomero-Gallagher,
et al. (2013), Caspers, Schleicher, et al. (2013), Deng and Huang (2006),
Eickhoff et al. (2007), Morosan et al. (2004), Palomero-Gallagher and
Zilles (2009), Scheperjans, Grefkes, Palomero-Gallagher, Schleicher, and
Zilles (2005), Scheperjans, Palomero-Gallagher, Grefkes, Schleicher, and
Zilles (2005), Vogt, Sikes, and Vogt (1990), Zezula et al. (1988), Zilles,
Palomero-Gallagher, et al. (2002), Zilles, Schleicher, PalomeroGallagher, and Amunts (2002), Zilles et al. (2004), Zilles et al. (2014), and
Zilles and Amunts (2009). Receptors for acetylcholine: Amunts et al.
(2010), Caspers, Palomero-Gallagher, et al. (2013), Caspers, Schleicher,
et al. (2013), Cortes and Palacios (1986), Eickhoff et al. (2007), Morosan
et al. (2004), Palomero-Gallagher and Zilles (2009), Rodriguez-Puertas
et al. (1997), Scheperjans, Grefkes, Palomero-Gallagher, Schleicher, and
Zilles (2005), Scheperjans, Palomero-Gallagher, Grefkes, Schleicher, and
Zilles (2005), Sihver et al. (1998), Vogt et al. (1990), Vogt, Crino, and
Volicer (1991), Zilles, Palomero-Gallagher, et al. (2002), Zilles,
Schleicher, Palomero-Gallagher, and Amunts (2002), Zilles, Eickhoff, and
Palomero-Gallagher (2003), Zilles et al. (2004), Zilles et al. (2014), Zilles
and Amunts (2009), and Zilles and Amunts (2010). Receptors for
noradrenaline: Amunts et al. (2010), Caspers, Palomero-Gallagher, et al.
(2013), Caspers, Schleicher, et al. (2013), Eickhoff et al. (2007), Morosan
et al. (2004), Palomero-Gallagher and Zilles (2009), Pazos et al. (1988),
Scheperjans, Grefkes, Palomero-Gallagher, Schleicher, and Zilles (2005),
Scheperjans, Palomero-Gallagher, Grefkes, Schleicher, and Zilles (2005),
Vogt et al. (1991), Zilles, Palomero-Gallagher, et al. (2002), Zilles,
Schleicher, Palomero-Gallagher, and Amunts (2002), Zilles et al. (2014),
and Zilles and Amunts (2010). Receptors for serotonin: Caspers,
Palomero-Gallagher, et al. (2013), Caspers, Schleicher, et al. (2013),
Dean et al. (2001), Dewar, Graham, and McCulloch (1990), Dillon, GrossIsseroff, Israeli, and Biegon (1991), Eickhoff et al. (2007), Hall et al.
(1997), Hoyer et al. (1986b), Martin-Cora and Pazos (2004), Morosan
et al. (2004), Palomero-Gallagher and Zilles (2009), Pazos et al.
(1987a,1987b), Scheperjans, Grefkes, Palomero-Gallagher, Schleicher,
and Zilles (2005), Scheperjans, Palomero-Gallagher, Grefkes, Schleicher,
and Zilles (2005), Vogt et al. (1990), Zilles, Schleicher, PalomeroGallagher, and Amunts (2002), Zilles et al. (2004), and Zilles et al. (2014).
Receptors for dopamine: Caspers, Palomero-Gallagher, et al. (2013),
Caspers, Schleicher, et al. (2013), Dawson, McCabe, Stensaas, and
Wamsley (1987), Eickhoff et al. (2007), Joyce et al. (1991), PalomeroGallagher and Zilles (2009), Scheperjans, Grefkes, Palomero-Gallagher,
Schleicher, and Zilles (2005), Zilles, Schleicher, Palomero-Gallagher, and
Amunts (2002), and Zilles et al. (2014).
272
of nicotinic a4/b2 receptors demonstrated by binding studies is

supported by studies of messenger RNA expression in the
human frontal cortex, hippocampus, and putamen (Tohgi,
Utsugisawa, Yoshimura, Nagane, & Mihara, 1998a,1998b).
A considerable reduction (about 50%) of a2 adrenoceptors
occurs during aging (age range 1581 years) in the superior
frontal gyrus and the anterior cingulate cortex, as well as in the
postcentral gyrus and the hippocampus, whereas no reduction
was found in other cortical areas (Gross-Isseroff et al., 2000).
The 5-HT1A receptors reach a transient maximum in density
during mid-gestation, which is 34 times higher than the adult
value in the frontal cortex and 35 times higher than the adult
value in the pyramidal layer of CA and the granular layer of the
DG (Bar-Peled et al., 1991). The 5-HT2 receptor shows an agedependent decline between 17 and 100 years of age, both in
the frontal cortex and the hippocampus (Marcusson, Morgan,
Winblad, & Finch, 1984).
During postnatal development, D1 receptor densities in the
caudateputamen decline between birth and the sixtieth
decade (Montague, Lawler, Mailman, & Gilmore, 1999). If
higher ages are included, the density of D1 receptors no longer
changes in the caudateputamen, globus pallidus, or substantia nigra during aging, whereas the D2 receptors in the
caudateputamen show a significant decline (Morgan et al.,
1987; Rinne, 1987). A significant decrease of the striatal dopamine uptake sites between birth and the ninetieth decade
matches with these receptor changes (Zelnik, Angel, Paul, &
Kleinman, 1986).
Receptors and Functional Systems

A single receptor type can characterize the borders of a functionally and cytoarchitectonically defined cortical region.
Prominent examples are the M2 receptor and the delineation
of the BA17, area 3b, and BA41 from the surrounding cortical
areas or the identification of the mossy fiber region by kainate
receptors. However, in many cases, the simultaneous evaluation of the expression patterns of multiple receptors in cortical
regions provides novel criteria and delineations that cannot be
achieved by a single receptor analysis. These multireceptor
expression patterns are characteristic fingerprints of each cortical area, which allow a detailed mapping of the human cerebral cortex (Amunts et al., 2010; Eickhoff et al., 2007;
Palomero-Gallagher & Zilles, 2009; Zilles & Amunts, 2010).
A further analysis of receptor fingerprints shows that cortical regions that belong to a larger functional system are more
similar than the fingerprints of areas that belong to other
neural systems. It has been shown that receptor fingerprints
in the cingulate cortex reveal a subdivision into four regions
differentially involved in emotional processing, mediation of
motor and cognitive processes via premotor planning with
motivational characteristics, spatial orientation, memory, and
visuospatial functions (Palomero-Gallagher et al., 2009).
It has also been shown that the fingerprints of BA44 and
BA45 are more similar to each other than to the ventral premotor cortex or the ventrally adjacent BA47, which is often
interpreted as part of Brocas region (Amunts et al., 2010). In a
following analysis of many functionally identified language
and nonlanguage regions, the receptor fingerprints identified
a complex system of language-related areas in the left hemisphere that consists of the four subdivisions of BA44 and BA45,
BA47, an hitherto unidentified area in the inferior frontal
sulcus close to its junction with the precentral sulcus, the
secondary auditory area BA42, and a region in the posterior
part of the superior temporal gyrus and sulcus (Zilles et al.,
2014). The fingerprints of the areas in this functional system
clearly differ from those of primary sensory cortical areas,
multimodal areas of the inferior and superior parietal lobules,
higher extrastriate visual areas, BA32, and the primary motor
cortex. A separate analysis of the fingerprints of the right and
left hemispheres revealed a notable interhemispheric
difference.
A fingerprint analysis of the different areas of the inferior
parietal lobule in comparison with motor, auditory, somatosensory, and visual areas and BA44 demonstrated a very close
relation between BA39 and the extrastriate area V3v (Caspers,
Schleicher, et al., 2013), thus supporting the notion that at
least the posterior part of BA39 (i.e., area PGp) is a hub in the
ventrodorsal visual stream (Pisella, Binkofski, Lasek, Toni, &
Rossetti, 2006).
The hierarchical cluster analysis of the receptor fingerprints
of fusiform areas FG1 and FG2 (Caspers, Palomero-Gallagher,
et al., 2013) argues for their position between the ventral visual
stream (Ungerleider & Haxby, 1994) and multimodal association areas of the inferior parietal lobule (Caspers et al., 2006;
Wu et al., 2009). FG1 and FG2 are involved in the processing of
visual objects (Grill-Spector, Kourtzi, & Kanwisher, 2001;
Malach, Levy, & Hasson, 2002) but differ from the early visual
areas of the ventral stream (Orban, van Essen, & Vanduffel,
2004; Sereno et al., 1995; Wilms et al., 2010). A principal
component analysis shows that all visual areas are separated
from nearly all other cortical areas studied, but FG1 and FG2
segregate from early visual areas, thus indicating their close
association with multimodal association areas of the inferior
parietal lobule (Caspers, Palomero-Gallagher, et al., 2013).
Therefore, the mapping using multiple receptor expressions
(receptor fingerprints) not only is an excellent approach to
cortical parcellation on the basis of its neurochemical
organization but also provides insight into principles of
structural and functional connectivities as well as systemic
organization.
Acknowledgments
This work was supported by the portfolio theme Supercomputing and Modeling for the Human Brain of the Helmholtz
Association, Germany.

Amygdala; Basal Ganglia; Cerebellum: Anatomy and Physiology;
Cortical GABAergic Neurons; Cytoarchitectonics,
Cytoarchitecture and Maps of the Human Cerebral Cortex; Embryonic
Postnatal Development of the Cortex: MRI and Genetics; Gyrification in
the Human Brain; Sulci as Landmarks; Thalamus: Anatomy.
References
Albin, R. L., & Gilman, S. (1990). Autoradiographic localization of inhibitory and
excitatory amino acid neurotransmitter receptors in human normal and
olivopontocerebellar atrophy cerebellar cortex. Brain Research, 522, 3745.
Albin, R. L., Price, R. H., Sakurai, S. Y., Penney, J. B., & Young, A. B. (1991). Excitatory
and inhibitory amino acid binding sites in human dentate nucleus. Brain Research,
560, 350353.
Aldrich, M. S., Prokopowicz, G., Ockert, K., Hollingsworth, Z., Penney, J. B., & Albin, R. L.
(1994). Neurochemical studies of human narcolepsy: Alpha-adrenergic receptor
autoradiography of human narcoleptic brain and brainstem. Sleep, 17, 598608.
principles and multiple receptor mapping. PLoS Biology, 8, .
Araujo, D. M., Lapchak, P. A., Robitaille, Y., Gauthier, S., & Quirion, R. (1988).
Differential alteration of various cholinergic markers in cortical and subcortical
regions of human brain in Alzheimers disease. Journal of Neurochemistry, 50,
19141923.
Ball, E. F., Shaw, P. J., Ince, P. G., & Johnson, M. (1994). The distribution of excitatory
amino acid receptors in the normal human midbrain and basal ganglia with
implications for Parkinsons disease: A quantitative autoradiographic study using [3H]
MK-801, [3H]glycine, [3H]CNQX and [3H]kainate. Brain Research, 658, 209218.
Bar-Peled, O., Gross-Isseroff, R., Ben-Hur, H., Hoskins, I., Groner, Y., & Biegon, A.
(1991). Fetal human brain exhibits a prenatal peak in the density of serotonin 5HT1A receptors. Neuroscience Letters, 127, 173176.
Bar-Peled, O., Israeli, M., Ben-Hur, H., Hoskins, I., Groner, Y., & Biegon, A. (1991).
Developmental pattern of muscarinic receptors in normal and Downs syndrome
fetal brain An autoradiographic study. Neuroscience Letters, 133, 154158.
Brooksbank, B. W., Atkinson, D. J., & Balazs, R. (1981). Biochemical development of
the human brain. II. Some parameters of the GABA-ergic system. Developmental
Brooksbank, B. W., Atkinson, D. J., & Balazs, R. (1982). Biochemical development of
the human brain. III. Benzodiazepine receptors, free gamma-aminobutyrate (GABA)
and other amino acids. Journal of Neuroscience Research, 8, 581594.
Burnet, P. W., Eastwood, S. L., & Harrison, P. J. (1997). [3H]WAY-100635 for 5-HT1A
receptor autoradiography in human brain: A comparison with [3H]8-OH-DPAT and
demonstration of increased binding in the frontal cortex in schizophrenia.
Neurochemistry International, 30, 565574.
Carlson, M. D., Penney, J. B., Jr., & Young, A. B. (1993). NMDA, AMPA, and
benzodiazepine binding site changes in Alzheimers disease visual cortex.
Neurobiology of Aging, 14, 343352.
recognition region of the posterior fusiform gyrus. Brain Structure and Function.
http://dx.doi.org/10.1007/s00429-013-0646-z.
areas of the human posterior fusiform gyrus. Brain Structure and Function, 218,
511526.
Cortes, R., & Palacios, J. M. (1986). Muscarinic cholinergic receptor subtypes in
the rat brain. I. Quantitative autoradiographic studies. Brain Research, 362,
227238.
Cortes, R., Probst, A., & Palacios, J. M. (1987). Quantitative light microscopic
autoradiographic localization of cholinergic muscarinic receptors in the human
brain: Forebrain. Neuroscience, 20, 65107.
Cortes, R., Probst, A., Tobler, H. J., & Palacios, J. M. (1986). Muscarinic cholinergic
receptor subtypes in the human brain. II. Quantitative autoradiographic studies.
Court, J. A., Lloyd, S., Johnson, M., Griffiths, M., Birdsall, N. J., Piggott, M. A., et al.
(1997). Nicotinic and muscarinic cholinergic receptor binding in the human
273
hippocampal formation during development and aging. Brain Research.

Developmental Brain Research, 101, 93105.
Court, J. A., Perry, E. K., Johnson, M., Piggott, M. A., Kerwin, J. A., Perry, R. H., et al.
(1993). Regional patterns of cholinergic and glutamate activity in the developing
and aging human brain. Brain Research. Developmental Brain Research, 74, 7382.
Crook, J. M., Tomaskovic-Crook, E., Copolov, D. L., & Dean, B. (2000). Decreased
muscarinic receptor binding in subjects with schizophrenia: A study of the human
hippocampal formation. Biological Psychiatry, 48, 381388.
Crook, J. M., Tomaskovic-Crook, E., Copolov, D. L., & Dean, B. (2001). Low
muscarinic receptor binding in prefrontal cortex from subjects with schizophrenia: A
study of Brodmanns areas 8, 9, 10, and 46 and the effects of neuroleptic drug
treatment. The American Journal of Psychiatry, 158, 918925.
Cross, A. J., & Slater, P. (1989). High affinity serotonin binding sites in human brain: A
comparison of cerebral cortex and basal ganglia. Journal of Neural Transmission,
76, 211219.
Dawson, T. M., McCabe, R. T., Stensaas, S. S., & Wamsley, J. K. (1987).
Autoradiographic evidence of [3H]SCH 23390 binding sites in human prefrontal
cortex (Brodmanns area 9). Journal of Neurochemistry, 49, 789796.
De Keyser, J., Claeys, A., De Backer, J. P., Ebinger, G., Roels, F., & Vauquelin, G.
(1988). Autoradiographic localization of D1 and D2 dopamine receptors in the
human brain. Neuroscience Letters, 91, 142147.
De Olmos, J. S. (2004). Amygdala. In G. Paxinos, & J. K. Mai (Eds.), The Human
Nervous System (2nd ed., pp. 739868). Amsterdam: Elsevier.
De Paermentier, F., Cheetham, S. C., Crompton, M. R., & Horton, R. W. (1989). Betaadrenoceptors in human brain labelled with [3H]dihydroalprenolol and [3H]CGP
12177. European Journal of Pharmacology, 167, 397405.
De Vos, H., Vauquelin, G., De, K. J., De Backer, J. P., & Van, L. I. (1992). Regional
distribution of a2A- and a2B-adrenoceptor subtypes in postmortem human brain.
Journal of Neurochemistry, 58, 15551560.
Dean, B., Pavey, G., McLeod, M., Opeskin, K., Keks, N., & Copolov, D. (2001). A change
in the density of [3H]flumazenil, but not [3H]muscimol binding, in Brodmanns Area 9
from subjects with bipolar disorder. Journal of Affective Disorders, 66, 147158.
Deng, C., & Huang, X. F. (2006). Increased density of GABAA receptors in the superior
temporal gyrus in schizophrenia. Experimental Brain Research, 168, 587590.
Dewar, D., Chalmers, D. T., Shand, A., Graham, D. I., & McCulloch, J. (1990). Selective
reduction of quisqualate (AMPA) receptors in Alzheimer cerebellum. Annals of
Dewar, D., Graham, D. I., & McCulloch, J. (1990). 5 HT2 receptors in dementia of
Alzheimer type: A quantitative autoradiographic study of frontal cortex and
hippocampus. Journal of Neural Transmission. Parkinsons Disease and Dementia
Section, 2, 129137.
Dillon, K. A., Gross-Isseroff, R., Israeli, M., & Biegon, A. (1991). Autoradiographic
analysis of serotonin 5-HT1A receptor binding in the human brain postmortem:
Effects of age and alcohol. Brain Research, 554, 5664.
Dure, L. S., Young, A. B., & Penney, J. B. (1991). Excitatory amino acid binding sites in
the caudate nucleus and frontal cortex of Huntingtons disease. Annals of
Gao, X. M., Sakai, K., Roberts, R. C., Conley, R. R., Dean, B., & Tamminga, C. A. (2000).
Ionotropic glutamate receptors and expression of N-methyl-D-aspartate receptor
subunits in subregions of human hippocampus: Effects of schizophrenia. The
American Journal of Psychiatry, 157, 11411149.
Gonzalez-Albo, M. C., & DeFelipe, J. (2000). Colocalization of glutamate ionotropic
receptor subunits in the human temporal neocortex. Cerebral Cortex, 10, 621631.
Graebenitz, S., Kedo, O., Speckmann, E. J., Gorji, A., Panneck, H., Hans, V., et al.
(2011). Interictal-like network activity and receptor expression in the epileptic
human lateral amygdala. Brain, 134, 29292947.
Grill-Spector, K., Kourtzi, Z., & Kanwisher, N. (2001). The lateral occipital complex and
its role in object recognition. Vision Research, 41, 14091422.
Gross-Isseroff, R., Dillon, K. A., Fieldust, S. J., & Biegon, A. (1990). Autoradiographic
analysis of a1-noradrenergic receptors in the human brain postmortem. Effect of
suicide. Archives of General Psychiatry, 47, 10491053.
Gross-Isseroff, R., Salama, D., Israeli, M., & Biegon, A. (1990a). Autoradiographic
analysis of age-dependent changes in serotonin 5-HT2 receptors of the human brain
postmortem. Brain Research, 519, 223227.
Gross-Isseroff, R., Salama, D., Israeli, M., & Biegon, A. (1990b). Autoradiographic
analysis of [3H]ketanserin binding in the human brain postmortem: Effect of suicide.
Gross-Isseroff, R., Weizman, A., Fieldust, S. J., Israeli, M., & Biegon, A. (2000).
Unaltered a2-noradrenergic/imidazoline receptors in suicide victims: A postmortem
274
brain autoradiographic analysis. European Neuropsychopharmacology, 10,

265271.
Haber, S. N., & Gdowski, M. J. (2004). The basal ganglia. In G. Paxinos & J. K. Mai
(Eds.), The human nervous system (2nd ed., pp. 676738). Amsterdam: Elsevier.
Hall, H., Lundkvist, C., Halldin, C., Farde, L., Pike, V. W., McCarron, J. A., Fletcher, A.,
Cliffe, I. A., Barf, T., Wikstrom, H., & Sedvall, G. (1997). Autoradiographic
localization of 5-HT1A receptors in the post-mortem human brain using [3H]WAY100635 and [11C]way-100635. Brain Research, 745, 96108.
Hellstrom-Lindahl, E., & Court, J. A. (2000). Nicotinic acetylcholine receptors during
prenatal development and brain pathology in human aging. Behavioural Brain
Research, 113, 159168.
Hoyer, D., Pazos, A., Probst, A., & Palacios, J. M. (1986a). Serotonin receptors in the
human brain: II. Characterization and autoradiographic localization of 5-HT1C and 5HT2 recognition sites. Brain Research, 376, 97107.
Hoyer, D., Pazos, A., Probst, A., & Palacios, J. M. (1986b). Serotonin receptors in the
human brain: I. Characterization and autoradiographic localization of 5-HT1A
recognition sites. Apparent absence of 5-HT1B recognition sites. Brain Research,
376, 8586.
Ibrahim, H. M., Hogg, A. J., Jr., Healy, D. J., Haroutunian, V., Davis, K. L., &
Meador-Woodruff, J. H. (2000). Ionotropic glutamate receptor binding and subunit
mRNA expression in thalamic nuclei in schizophrenia. The American Journal of
Psychiatry, 157, 18111823.
Jansen, K. L., Dragunow, M., Faull, R. L., & Leslie, R. A. (1991). Autoradiographic
visualisation of [3H]DTG binding to sigma receptors, [3H]TCP binding sites, and L[3H]glutamate binding to NMDA receptors in human cerebellum. Neuroscience
Letters, 125, 143146.
Jansen, K. L., Faull, R. L.M, & Dragunow, M. (1989). Excitatory amino acid receptors in
the human cerebral cortex: A quantitative autoradiographic study comparing the
distributions of TCP, [3H]glycine, L-[3H]-glutamate, [3H]AMPA and [3H]kainic acid
binding sites. Neuroscience, 32, 587607.
Jansen, K. L., Faull, R. L., & Dragunow, M. (1990). NMDA and kainic acid receptors
have a complementary distribution to AMPA receptors in the human cerebellum.
Jones, E. G. (2007). The thalamus (2nd ed.). Cambridge: Cambridge Press.
Jones, E. G., & Porter, R. (1980). What is area 3a? Brain Research Reviews, 2, 143.
Joyce, J. N., Janowsky, A., & Neve, K. A. (1991). Characterization and distribution of [125I]
epidepride binding to dopamine D2 receptors in basal ganglia and cortex of human
brain. Journal of Pharmacol and Experimental Therapeutics, 257, 12531263.
Joyce, J. N., Sapp, D. W., & Marshall, J. F. (1986). Human striatal dopamine receptors
are organized in compartments. Proceedings of the National academy of Sciences of
Kessler, R. M., Whetsell, W. O., Ansari, M. S., Votaw, J. R., de, P. T., Clanton, J. A., et al.
(1993). Identification of extrastriatal dopamine D2 receptors in post mortem human
brain with [125I]epidepride. Brain Research, 609, 237243.
Kohler, C., Ericson, H., Hogberg, T., Halldin, C., & Chan-Palay, V. (1991). Dopamine D2
receptors in the rat, monkey and the post-mortem human hippocampus. An
autoradiographic study using the novel D2-selective ligand 125I-NCQ 298.
Neuroscience Letters, 125, 1214.
Kornhuber, J., Mack-Burkhardt, F., Riederer, P., Hebenstreit, G. F., Reynolds, G. P.,
Andrews, H. B., et al. (1989). [3H]MK-801 binding sites in postmortem brain
regions of schizophrenic patients. Journal of Neural Transmission, 77, 231236.
Kravitz, E., Gaisler-Salomon, I., & Biegon, A. (2013). Hippocampal glutamate NMDA
receptor loss tracks progression in Alzheimers disease: Quantitative
autoradiography in postmortem human brain. PLoS One, 8, e81244.
Lange, K. W., Wells, F. R., Jenner, P., & Marsden, C. D. (1993). Altered muscarinic and
nicotinic receptor densities in cortical and subcortical brain regions in Parkinsons
disease. Journal of Neurochemistry, 60, 197203.
Lee, H., & Choi, B. H. (1992). Density and distribution of excitatory amino acid
receptors in the developing human fetal brain: A quantitative autoradiographic
study. Experimental Neurology, 118, 284290.
Lin, S. C., Olson, K. C., Okazaki, H., & Richelson, E. (1986). Studies on muscarinic
binding sites in human brain identified with [3H]pirenzepine. Journal of
Neurochemistry, 46, 274279.
Lowenstein, P. R., Joyce, J. N., Coyle, J. T., & Marshall, J. F. (1990). Striosomal
organization of cholinergic and dopaminergic uptake sites and cholinergic M1
receptors in the adult human striatum: A quantitative receptor autoradiographic
study. Brain Research, 510, 122126.
Makowiec, R. L., Albin, R. L., Cha, J. H., Young, A. B., & Gilman, S. (1990). Two types
of quisqualate receptors are decreased in human olivopontocerebellar atrophy
cerebellar cortex. Brain Research, 523, 309312.
Malach, R., Levy, I., & Hasson, U. (2002). The topography of high-order human object
areas. Trends in Cognitive Sciences, 6, 176184.
Marazziti, D., Betti, L., Giannaccini, G., Rossi, A., Masala, I., Baroni, S., et al. (2001).
Distribution of [3H]GR65630 binding in human brain postmortem. Neurochemical
Research, 26, 187190.
Marcusson, J. O., Morgan, D. G., Winblad, B., & Finch, C. E. (1984). Serotonin-2
binding sites in human frontal cortex and hippocampus. Selective loss of S-2A sites
with age. Brain Research, 311, 5156.
Martin-Cora, F. J., & Pazos, A. (2004). Autoradiographic distribution of 5-HT7
receptors in the human brain using [3H]mesulergine: Comparison to other
mammalian species. British Journal of Pharmacology, 141, 92104.
Marutle, A., Zhang, X., Court, J., Piggott, M., Johnson, M., Perry, R., Perry, E., &
Nordberg, A. (2001). Laminar distribution of nicotinic receptor subtypes in cortical
regions in schizophrenia. Journal of Chemical Neuroanatomy, 22, 115126.
Matsumoto, I., Inoue, Y., Iwazaki, T., Pavey, G., & Dean, B. (2005). 5-HT2A and
muscarinic receptors in schizophrenia: A postmortem study. Neuroscience Letters,
379, 164168.
Meador-Woodruff, J. H., Davis, K. L., & Haroutunian, V. (2001). Abnormal kainate
receptor expression in prefrontal cortex in schizophrenia.
Meador-Woodruff, J. H., Hogg, A. J., Jr., & Smith, R. E. (2001). Striatal ionotropic
glutamate receptor expression in schizophrenia, bipolar disorder, and major
depressive disorder. Brain Research Bulletin, 55, 631640.
Meoni, P., Mugnaini, M., Bunnemann, B. H., Trist, D. G., & Bowery, N. G. (1998). [3H]
MK-801 binding and the mRNA for the NMDAR1 subunit of the NMDA receptor are
differentially distributed in human and rat forebrain. Brain Research. Molecular
Montague, D. M., Lawler, C. P., Mailman, R. B., & Gilmore, J. H. (1999). Developmental
regulation of the dopamine D1 receptor in human caudate and putamen.
Morgan, D. G., Marcusson, J. O., Nyberg, P., Wester, P., Winblad, B., Gordon, M. N.,
et al. (1987). Divergent changes in D-1 and D-2 dopamine binding sites in human
brain during aging. Neurobiology of Aging, 8, 195201.
organization of the human auditory cortex: Cytoarchitecture and transmitter receptors.
In P. Heil, E. Konig & E. Budinger (Eds.), Auditory cortex Towards a synthesis of
human and animal research (pp. 2750). Mahwah, NJ: Lawrence Erlbaum.
Nastuk, M. A., & Graybiel, A. M. (1988). Autoradiographic localization and biochemical
characteristics of M1 and M2 muscarinic binding sites in the striatum of the cat,
monkey, and human. Journal of Neuroscience, 8, 10521062.
Nishino, N., Fujiwara, H., Noguchi-Kuno, S. A., & Tanaka, C. (1988). GABAA receptor
but not muscarinic receptor density was decreased in the brain of patients with
Parkinsons disease. Japanese Journal of Pharmacology, 48, 331339.
Noga, J. T., & Wang, H. (2002). Further postmortem autoradiographic studies of AMPA
receptor binding in schizophrenia. Synapse, 45, 250258.
Nordberg, A., Alafuzoff, I., & Winblad, B. (1992). Nicotinic and muscarinic subtypes in
the human brain: Changes with aging and dementia. Journal of Neuroscience
Research, 31, 103111.
Nusser, Z., Lujan, R., Laube, G., Roberts, J. D., Molnar, E., & Somogyi, P. (1998). Cell
type and pathway dependence of synaptic AMPA receptor number and variability in
the hippocampus. Neuron, 21, 545559.
Orban, G. A., van Essen, D. C., & Vanduffel, W. (2004). Comparative mapping of higher
visual areas in monkeys and humans. Trends in Cognitive Sciences, 8, 315324.
Palacios, J. M., Camps, M., Cortes, R., & Probst, A. (1988). Mapping dopamine receptors
in the human brain. Journal of Neural Transmission, Supplement, 27, 227235.
Palacios, J. M., Probst, A., & Mengod, G. (1992). Receptor localization in the human
hypothalamus. Progress in Brain Research, 93, 5768.
Palomero-Gallagher, N., Vogt, B. A., Schleicher, A., Mayberg, H. S., Schleicher, A., &
Zilles, K. (2009). Receptor architecture of human cingulate cortex: Evaluation of the
four-region neurobiological model. Human Brain Mapping, 30, 23362355.
regions and areas. In B. A. Vogt (Ed.), Infrastructure, diagnosis, treatment (2nd ed.).
Cingulate neurobiology and disease (vol. 1). Oxford: Oxford University Press.
Palomero-Gallagher, N., Zilles, K., Schleicher, A., & Vogt, B. A. (2013). Cyto- and
receptor architecture of area 32 in human and macaque brains. Journal of
Pazos, A., Gonzalez, A. M., Pascual, J., Meana, J. J., Barturen, F., & Garca-Sevilla, J. A.
(1988). a2-adrenoceptors in human forebrain: Autoradiographic visualization and
biochemical parameters using the agonist [3H]UK-14304. Brain Research, 475,
361365.
Pazos, A., Probst, A., & Palacios, J. M. (1985). Beta-adrenoceptor subtypes in the
human brain: Autoradiographic localization. Brain Research, 358, 324328.
Pazos, A., Probst, A., & Palacios, J. M. (1987a). Serotonin receptors in the human brain.
III. Autoradiographic mapping of serotonin-1 receptors. Neuroscience, 21, 97122.
Pazos, A., Probst, A., & Palacios, J. M. (1987b). Serotonin receptors in the human
brain. IV. Autoradiographic mapping of serotonin-2 receptors. Neuroscience, 21,
123139.
Percheron, G. (2004). Thalamus. In G. Paxinos & J. K. Mai (Eds.), The human nervous
system (2nd ed., pp. 592675). Amsterdam: Elsevier.
Perry, E. K., Court, J. A., Johnson, M., Piggott, M. A., & Perry, R. H. (1992).
Autoradiographic distribution of [3H]nicotine binding in human cortex: Relative
abundance in subicular complex. Journal of Chemical Neuroanatomy, 5, 399405.
Perry, E. K., Court, J. A., Johnson, M., Smith, C. J., James, V., Cheng, A. V., et al.
(1993). Autoradiographic comparison of cholinergic and other transmitter receptors
in the normal human hippocampus. Hippocampus, 3, 307315.
Piggott, M. A., Ballard, C. G., Dickinson, H. O., McKeith, I. G., Perry, R. H., &
Perry, E. K. (2007). Thalamic D2 receptors in dementia with Lewy bodies,
Parkinsons disease, and Parkinsons disease dementia. International Journal of
Piggott, M. A., Owens, J., OBrien, J., Colloby, S., Fenwick, J., Wyper, D., Jaros, E., et al.
(2003). Muscarinic receptors in basal ganglia in dementia with Lewy bodies,
Parkinsons disease and Alzheimers disease. Journal of Chemical Neuroanatomy,
25, 161173.
Piggott, M., Owens, J., OBrien, J., Paling, S., Wyper, D., Fenwick, J., et al. (2002).
Comparative distribution of binding of the muscarinic receptor ligands pirenzepine,
AF-DX 384, (R, R)-I-QNB and (R, S)-I-QNB to human brain. Journal of Chemical
Pimlott, S. L., Piggott, M., Owens, J., Greally, E., Court, J. A., Jaros, E., et al. (2004).
Nicotinic acetylcholine receptor distribution in Alzheimers disease, dementia with
Lewy bodies, Parkinsons disease, and vascular dementia: In vitro binding study
using 5-[125I]-A-85380. Neuropsychopharmacology, 29, 108116.
Pisella, L., Binkofski, F., Lasek, K., Toni, I., & Rossetti, Y. (2006). No doubledissociation between optic ataxia and visual agnosia: Multiple sub-streams for
multiple visuo-manual integrations. Neuropsychologia, 44, 27342748.
Represa, A., Tremblay, E., Schoevart, D., & Ben-Ari, Y. (1986). Development of high affinity
kainate binding sites in human and rat hippocampi. Brain Research, 384, 170174.
Reynolds, G. P., Mason, S. L., Meldrum, A., De, K. S., Parnes, H., Eglen, R. M., et al.
(1995). 5-Hydroxytryptamine (5-HT)4 receptors in post mortem human brain tissue:
Distribution, pharmacology and effects of neurodegenerative diseases. British
Journal of Pharmacology, 114, 993998.
Rieck, R. W., Ansari, M. S., Whetsell, W. O., Jr., Deutch, A. Y., & Kessler, R. M. (2004).
Distribution of dopamine D2-like receptors in the human thalamus:
Autoradiographic and PET studies. Neuropsychopharmacology, 29, 362372.
Rinne, J. O. (1987). Muscarinic and dopaminergic receptors in the aging human brain.
Rodriguez-Puertas, R., Pascual, J., Vilaro, M. T., & Pazos, A. (1997). Autoradiographic
distribution of M1, M2, M3, and M4 muscarinic receptor subtypes in Alzheimers
disease. Synapse, 26, 341350.
Saper, C. B. (2004). Hypothalamus. In G. Paxinos & J. K. Mai (Eds.), The human
nervous system (2nd ed., pp. 513550). Amsterdam: Elsevier.
Sastre, M., Guimon, J., & Garcia-Sevilla, J. A. (2001). Relationships between beta- and
alpha2-adrenoceptors and G coupling proteins in the human brain: Effects of age
and suicide. Brain Research, 898, 242255.
Scarr, E., Pavey, G., Sundram, S., MacKinnon, A., & Dean, B. (2003). Decreased
hippocampal NMDA, but not kainate or AMPA receptors in bipolar disorder. Bipolar
Disorders, 5, 257264.
Schmitz, E., Reichelt, R., Walkowiak, W., Richards, J. G., & Hebebrand, J. (1988). A
comparative phylogenetic study of the distribution of cerebellar GABAA/benzodiazepine
receptors using radioligands and monoclonal antibodies. Brain Research, 473, 314320.
Shaw, P. J., & Ince, P. G. (1994). A quantitative autoradiographic study of [3H]kainate
binding sites in the normal human spinal cord, brainstem and motor cortex. Brain
Sihver, W., Gillberg, P. G., & Nordberg, A. (1998). Laminar distribution of nicotinic
receptor subtypes in human cerebral cortex as determined by [3H](-)nicotine, [3H]
cytisine and [3H]epibatidine in vitro autoradiography. Neuroscience, 85, 11211133.
275
Sun, J., Xu, J., Cairns, N. J., Perlmutter, J. S., & Mach, R. H. (2012). Dopamine D1, D2,
D3 receptors, vesicular monoamine transporter type-2 (VMAT2) and dopamine
transporter (DAT) densities in aged human brain. PLoS One, 7, e49483.
Tohgi, H., Utsugisawa, K., Yoshimura, M., Nagane, Y., & Mihara, M. (1998a). Agerelated changes in nicotinic acetylcholine receptor subunits a4 and b2 messenger
RNA expression in postmortem human frontal cortex and hippocampus.
Neuroscience Letters, 245, 139142.
Tohgi, H., Utsugisawa, K., Yoshimura, M., Nagane, Y., & Mihara, M. (1998b).
Alterations with aging and ischemia in nicotinic acetylcholine receptor subunits a4
and b2 messenger RNA expression in postmortem human putamen. Implications for
susceptibility to parkinsonism. Brain Research, 791, 186190.
Tremblay, E., Represa, A., & Ben-Ari, Y. (1985). Autoradiographic localization of kainic
acid binding sites in the human hippocampus. Brain Research, 343, 378382.
Vanderheyden, P., Gies, J. P., Ebinger, G., De, K. J., Landry, Y., & Vauquelin, G. (1990).
Human M1-, M2- and M3-muscarinic cholinergic receptors: Binding characteristics
of agonists and antagonists. Journal of Neurological Sciences, 97, 6780.
Villares, J. C., & Stavale, J. N. (2001). Age-related changes in the N-methyl-D-aspartate
receptor binding sites within the human basal ganglia. Experimental Neurology,
171, 391404.
Villegas, E., Estruch, R., Mengod, G., & Cortes, R. (2011). NMDA receptors in frontal
cortex and hippocampus of alcohol consumers. Addiction Biology, 16, 163165.
Vogt, B. A., Crino, P. B., & Volicer, L. (1991). Laminar alterations in g-aminobutyric
acidA, muscarinic, and b adrenoceptors and neuron degeneration in cingulate cortex
in Alzheimers disease. Journal of Neurochemistry, 57, 282290.
Vogt, B. A., Sikes, R. W., & Vogt, L. J. (1990). Anterior cingulate cortex and the medial
pain system. In B. Kolb & R. C. Tees (Eds.), The cerebral cortex of the rat
(pp. 313344). Cambridge, MA: MIT.
Whitehouse, P. J., Muramoto, O., Troncoso, J. C., & Kanazawa, I. (1986).
Neurotransmitter receptors in olivopontocerebellar atrophy: An autoradiographic
study. Neurology, 36, 193197.
Wu, S. S., Chang, T. T., Majid, A., Caspers, S., Eickhoff, S. B., & Menon, V. (2009).
Functional heterogeneity of inferior parietal cortex during mathematical cognition
assessed with cytoarchitectonic probability maps. Cerebral Cortex, 19, 29302945.
Zavitsanou, K., Ward, P. B., & Huang, X. F. (2002). Selective alterations in ionotropic
glutamate receptors in the anterior cingulate cortex in schizophrenia.
Zelnik, N., Angel, I., Paul, S. M., & Kleinman, J. E. (1986). Decreased density of human
striatal dopamine uptake sites with age. European Journal of Pharmacology, 126,
175176.
Zezula, J., Cortes, R., Probst, A., & Palacios, J. M. (1988). Benzodiazepine receptor
sites in the human brain: Autoradiographic mapping. Neuroscience, 25, 771795.
Zilles, K. (2005). Evolution of the human brain and comparative cyto- and receptor
architecture. In S. Dehaene, J. R. Duhamel, M. D. Hauser & G. Rizzolatti (Eds.),
From monkey brain to human brain (pp. 4156). Cambridge: MIT Press.
Zilles, K., & Amunts, K. (2010). Centenary of Brodmanns map Conception and fate.
Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D.
(2014). Common molecular basis of the sentence comprehension network revealed
by neurotransmitter receptor fingerprints. Cortex, 63, 7989.
Zilles, K., Eickhoff, S. B., & Palomero-Gallagher, N. (2003). The human parietal cortex: A
novel approach to its architectonic mapping. Advances in Neurology, 93, 121.
Zilles, K., Palomero-Gallagher, N., Grefkes, C., Scheperjans, F., Boy, C., Amunts, K., &
Schleicher, A. (2002). Architectonics of the human cerebral cortex and transmitter
receptor fingerprints: Reconciling functional neuroanatomy and neurochemistry.
European Neuropsychopharmacology, 12, 587599.
Zilles, K., Palomero-Gallagher, N., & Schleicher, A. (2004). Transmitter receptors
and functional anatomy of the cerebral cortex. Journal of Anatomy, 205, 417432.
Zilles, K., & Schleicher, A. (1993). Cyto- and myeloarchitecture of human visual cortex
and the periodical GABAA receptor distribution. In B. Gulyas, D. Ottoson & P. E.
Roland (Eds.), Functional organisation of the human visual cortex (pp. 111121).
Oxford: Pergamon Press.
Zilles, K., Schleicher, A., Palomero-Gallagher, N., & Amunts, K. (2002). Quantitative
analysis of cyto- and receptor architecture of the human brain. In A. W. Toga & J. C.
Mazziotta (Eds.), Brain mapping the methods (2nd ed., pp. 573602). Amsterdam:
Elsevier.
Motor Cortex
E Borra, M Gerbella, S Rozzi, and G Luppino, Universita` di Parma, Parma, Italy
Abbreviations
CB
DLPF
Calcium-binding protein calbindin

Dorsolateral prefrontal cortex
Introduction
The primate frontal lobe hosts two large regions: a rostral one
involved in cognitive functions, designated as prefrontal cortex,
and a caudal one the motor cortex mostly devoted to motor
functions. This article will be mostly focused on the description
of the main anatomical and functional organizational principles of the motor cortex. Specifically, we will show that the
primate motor cortex hosts a multiplicity of architectonically
distinct areas displaying specific cortical and subcortical connections underpinning a parallel processing of different aspects
of motor control. Though most of the available information
presented here derives from studies in nonhuman primates,
state-of-the-art anatomical and functional mapping techniques
suggest that similar organizational principles also exist in
humans.
Architectonic Heterogeneity of the Motor Cortex

In the primate brain, the motor cortex is architectonically
characterized by the lack of an evident layer IV and is thus
also referred to as agranular frontal cortex.
Although the motor cortex was classically subdivided by
Brodmann (1909) in two large cytoarchitectonic areas, the
caudally located area 4 and the rostrally located area 6, several
subsequent studies described different architectonic entities
within area 6 (see, e.g., Geyer, Matelli, Luppino, & Zilles,
2000). However, the large variability among the various parcellations in terms of size, extent, and topography of cortical
areas has been used in the past as an argument against the
possibility that architectonic maps could provide a reliable
anatomical framework of reference for the description of the
functional properties of the various parts of the motor cortex.
Over the last 20 years, to overcome these problems, we have
adopted a multimodal architectonic approach based on the
combination of classic architectonic techniques with newer,
mostly chemoarchitectonic, ones. Chemoarchitectonic techniques can reveal regional differences in the distribution of
specific neuronal subpopulations. In particular, the immunostaining of nonphosphorylated epitopes on the neurofilament
protein triplet with the monoclonal antibody SMI-32 (Hof &
Morrison, 1995) allows the identification of a subpopulation
of pyramidal projection neurons, possibly giving information
on specific aspects of the output components of the cortex.
Furthermore, the immunolabeling for calcium-binding
IPL
SPL
VLPF
Inferior parietal lobule

Superior parietal lobule
Ventrolateral prefrontal cortex
proteins, in particular calbindin (CB), reveals cell populations

mostly represented by inhibitory interneurons (see Hof et al.,
1999), thus showing differences in the organization of the
local cortical circuitry. This multimodal architectonic approach
has proved to be extremely useful for a more reliable and
objective assessment of architectonic borders in the motor
cortex (see, e.g., Belmalih et al., 2007) and resulted in the
map shown in Figure 1. In this parcellation scheme, area F1
roughly corresponds to area 4 (primary motor cortex), whereas
each of the three main sectors of the Brodmann area 6 (mesial,
dorsal, and ventral area 6), consists of caudal and rostral premotor subdivisions.
In this map, each identified area has been defined based on
several architectonic distinguishing features, which have been
described in previous studies to which the reader is referred
(see Belmalih et al., 2007). Furthermore, some architectonic
features shared by different areas can be used for identifying
three different rostrocaudal architectonic domains. The caudalmost domain, corresponding to F1, is characterized by low cell
density, poor lamination, and a very prominent layer V with
giant pyramidal cells arranged in multiple rows. In SMI-32
immunostaining, giant pyramidal cells are very evident, while
in CB immunostaining there is dense population of CBimmunopositive cells, confined to layer II and the uppermost
layer III. Rostral to F1, a caudal premotor domain is formed by
the medial area F3, the dorsal premotor area F2, and the ventral
premotor areas F4, F5p, and F5c. Increase in cell density in
layer III, decrease of large layer V pyramids, and increase in
layer III SMI-32 immunopositive pyramids and in layer II and
upper III CB-immunopositive cells are common features of
caudal premotor areas that characterize them with respect to
F1. More rostrally, the rostral premotor domain is formed
by areas F6, F7, and F5a. A prominent, non-sublaminated
layer V, the presence of granular cells indicative of an incipient
layer IV, marked decrease in density of SMI-32 immunopositive pyramids, and strong increase in CB-immunopositive cells
and neuropil characterize these areas with respect to the caudal
premotor ones (Figure 2). In the next sections, we will show
how these architectonic features define different sets of areas
sharing some general connectional and functional properties.
Thus, neurochemical architectonic features can be informative
not only of the location and extent of a given architectonic area
but also of its possible assignment to a given functional
domain. Accordingly, a multimodal architectonic approach
could be very useful for the definition of functionally distinct
areas or domains in the human motor cortex.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00222-0
277
278
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Motor Cortex
Figure 1 Three-dimensional reconstructions of an illustrative monkey cerebral hemisphere, showing a map of the architectonic areas of the motor
cortex and the multiplicity of body representations. The reconstruction on the right is shown from a rostrolateral view in which the posterior bank
of the arcuate sulcus was exposed with dissection along its fundus. The small hemisphere below shows with a darker color, the brain sector removed
to expose the postarcuate bank. CgS, cingulate sulcus; CS, central sulcus; IAS, inferior arcuate sulcus; IPS, intraparietal sulcus; LF, lateral fissure;
LuS, lunate sulcus; PS, principal sulcus; SAS, superior arcuate sulcus.
Classes of Motor Areas and General Pattern of Cortical

Connectivity
Descending Motor Projections from the Motor Cortex

and Parallel Control of Motor Execution
Over the years, the proposed map shown in Figure 1 has been
validated by converging evidence showing that each of these
architectonic subdivisions is functionally and connectionally
distinct, thus fulfilling all the criteria generally accepted for the
definition of a cortical area (see Van Essen, 1985).
Accordingly, the organization of the macaque motor cortex
is much more complex than previously thought and appears as
a mosaic of several distinct areas that contains a multiplicity of
body movement representations (Figure 1). There is clear evidence for a similar general organization also in the human
motor cortex (Fink, Frackowiak, Pietrzyk, & Passingham,
1997). This complex organizational picture raised the question
of which could be the possible role played in motor control by
each area.
A crucial contribution in addressing this issue has been
provided by hodological studies. Specifically, tract tracing
experiments unraveling each motor areas anatomical connections with other cortical areas or subcortical structures showed
up to be crucial for the functional interpretation of each areas
role in motor control. Taken together, this body of evidence first
showed that each frontal motor area has a specific pattern of
anatomical connections. Furthermore, based on their general
pattern of cortical and subcortical connectivity, the various
premotor areas can be grouped into two major groups
(Rizzolatti & Luppino, 2001) corresponding to the areas of
the caudal and the rostral premotor domains, respectively.
As a whole, the motor cortex is a source of different descending

motor pathways providing it with an access to brain stem and
spinal motor centers. In primates, particularly well studied has
been the corticospinal tract, because of its relevance in the control of skilled actions, which is one major hallmark of primate
evolution (see, e.g., Lemon, 2008). The origin of the corticospinal tract has been studied in great detail by Strick and coworkers
(e.g., He, Dum, & Strick, 1993, 1995). These data showed that
corticospinal projections originate not only from the primary
motor area but also from all the various caudal premotor areas.
These projections are somatotopically organized: hindlimb and
forelimb cortical motor fields are the sources of projections to
the lumbar and cervical spinal cord, respectively, while face/
mouth fields are the sources of corticobulbar projections
(Morecraft, Louie, Herrick, & Stilwell-Morecraft, 2001). Both
the primary and the caudal premotor areas mostly project to
the intermediate zone of the spinal cord. However, F1 is also a
source of monosynaptic projections to spinal motor neurons
(see, e.g., Lemon, 2008). These last projections are peculiar to
the primates and are considered the neural substrate for the
ability of making skilled hand actions. Accordingly, F1 is considered the final common pathway, at the cortical level, at least
for controlling this type of movements. Indeed, in line with this
view, all the caudal premotor areas display somatotopically
organized connections with F1. However, the existence of corticospinal projections from these areas indicates that they could be
279
d
CS
SAS PS
IPS
CS
IAS
1 mm
F1
F2
F7
8b
(a)
CS
F1
F2
F7
8b
(b)
CS
SAS
IPS
PS
IAS
F5c
CS
PS
IAS
F4
F1
F5p
F5a
(c)
F1
CS
F4
F5c
IAS
PS
F5p
(d)
F5a
Figure 2 Chemoarchitectonic features of the different rostrocaudal motor domains and the transition between the agranular and the granular
frontal cortices. (a) and (c): Low-power photomicrographs of two SMI-32-immunostained parasagittal sections shown in a medial to lateral order,
respectively. (b) and (d): Low-power photomicrographs of two CB immunostained parasagittal sections shown in a medial to lateral order,
respectively. The top view of the hemispheres in (a) and (c) shows approximately the dorsolateral level where the pair of sections in (a) and (b) and that
in (c) and (d) were taken, respectively. Arrows on the photomicrographs indicate the location of cytoarchitectonic borders reported from adjacent
Nissl-stained sections. Scale bar in (a) applies to all the photomicrographs. Abbreviations as in Figure 1.
involved in the generation and control of movements not only

through F1 but also in parallel with it. The exact role of the
corticospinal projections from the caudal premotor areas in
motor control is still poorly understood, but there is evidence
that these projections play an important role in the functional
recovery observed after lesions of the primary motor cortex in
primates. This appears to be the case, for example, for the
recovery of manual dexterity observed after primary motor cortex

lesions (Murata et al., 2008). Indeed, after post-lesion-intensive
motor training, it has been shown that the hand motor field
of F5p, which is a source of corticospinal projections (Borra,
Belmalih, Gerbella, Rozzi, & Luppino, 2010), undergoes to plastic changes and shows recovery-related increases in activity
(Dancause et al., 2006; Nishimura et al., 2007).
280
Differently from the caudal premotor areas, the rostral ones

do not project to the spinal cord. However, these areas, as well
as the caudal premotor areas, are sources of projections to
the reticular formation (Keizer & Kuypers, 1989) and other
brain stem structures, such as the superior colliculus (Borra,
Gerbella, Rozzi, Tonelli, & Luppino, 2012). These projections
represent a further neural substrate for a parallel control of
motor execution. In this context, the rostral premotor areas
can be involved in the generation of motor behavior only
indirectly, through their subcortical relays or their connections
with the caudal premotor areas.
Cortical Connectivity of the Motor Cortex and Parallel

Control of Action Selection and Organization
Cortical afferents to the frontal motor areas originate mostly
from the parietal and the prefrontal cortex (see Rizzolatti &
Luppino, 2001).
The strong and reciprocal connections with the parietal
cortex are a major source of input to the motor areas, and
this is especially true for F1 and the caudal premotor areas.
Recent functional evidence indicates that, similar to the motor
cortex, also the posterior parietal cortex is formed by a mosaic
of independent areas, located in the parietal operculum and in
the inferior parietal lobule (IPL) and in the superior parietal
lobule (SPL), each of which deals with specific aspects of
sensory visual and/or somatosensory information and
with the control of specific effectors (see, e.g., Rizzolatti,
Luppino, & Matelli, 1998). Studies on the organization of the
parietofrontal connections have shown that motor and parietal
areas are connected with each other in a very specific way. Each
motor area is reciprocally connected to a specific set of parietal
areas. Typically, within such a set of parietal areas connected to
a given motor area, some display much denser connections
(predominant connections). Therefore, within the general
framework of parietofrontal connections, it is possible to identify a series of largely segregated anatomical circuits formed by
parietal and motor areas linked by predominant connections.
In general, these circuits link SPL with dorsal and mesial premotor areas and IPL with ventral premotor areas. Functional
evidence, when available, indicates that parietal and frontal
areas forming each of these circuits share common functional
properties. Therefore, the functional correlate of this anatomical organization is that each of these circuits is more specifically involved into particular aspects of sensorimotor
transformations that rely on a full integration of sensory and
motor signals at both the parietal and motor levels. These
processes result in the generation of potential motor acts (see
succeeding text). Accordingly, the parietofrontal circuits have
been considered the functional units of the cortical motor
system (Rizzolatti et al., 1998).
Recent evidence has shown that parietofrontal visuomotor
circuits, which are targets of the dorsal visual stream, can be
grouped into two major substreams: a dorsodorsal one, linking
the SPL with the dorsal premotor cortex, and a ventrodorsal
one, linking the IPL with the ventral premotor cortex
(Rizzolatti & Matelli, 2003). This distinction is based on data
showing that (a) the dorsal visual stream inputs to the SPL and
the IPL mostly originate from distinct extrastriate visual areas,
that is, area V6 and MT, respectively, and (b) the IPL, but not
the SPL, is connected also to temporal polymodal areas or
inferotemporal areas located at the highest levels of the ventral
visual stream. It has been then proposed that while the dorsodorsal stream is involved in visuomotor transformation for
online control of movement, the ventrodorsal stream is
involved in motor control based also on perceptual processes
and is crucial in mediating motor cognitive functions. A similar
organizational model has been proposed by Jeannerod and
Jacob (2005) for the human parietal cortex.
A further major source of input to the motor cortex is the
lateral prefrontal cortex. This cortex is a functionally heterogeneous region essential for different aspects of executive functions, that is, optimizing behavioral performance when
cognitive processes are required (Tanji & Hoshi, 2008). Prefrontal projections to the motor cortex are primarily directed to the
rostral premotor areas (see Gerbella, Belmalih, Borra, Rozzi, &
Luppino, 2011, and Rizzolatti & Luppino, 2001). Specifically,
the dorsal part of the lateral prefrontal cortex (DLPF) projects to
F7, the ventral (VLPF) part projects to F5a, whereas both DLPF
and VLPF project to F6. These projections could play a role in
the selection of the appropriate potential actions, generated as
the result of sensorimotor transformations, based on abstract
rules, memorized information, and behavioral goals. This process could be at the basis of the transformation of potential
actions into actual actions.
Cortical Motor Networks

It is largely accepted today in neuroscience that cortical functions are not confined to individual areas, but result from the
specific contribution of several different areas linked together
by cortical connections and forming functionally specialized
networks. This is true also for cortical control of voluntary
movements. Indeed, it is clear today that the various premotor
areas are nodes of functionally specialized networks involving
areas located in different cortical regions and underpinning
different aspects of action selection and organization.
One paradigmatic example of functionally specialized
motor network is the lateral grasping network, recently
described based on functional and connectional data, and
involved in selecting and controlling goal-directed hand
actions (Figure 3). In this network, the hand field of F5p
represents the gateway for the access of signals related to specific
potential hand motor acts to the primary motor cortex (Borra
et al., 2010). The selection of motor acts represented in F5p
relies on information both from the posterior parietal areas and
from F5a, which integrates parietal and prefrontal information
(Gerbella et al., 2011). In the parietal component of the network, AIP contributes to visuomotor transformations for grasping, that is, the generation of potential hand motor acts based
on object properties. This process mostly relies on visual information reaching AIP from the dorsal and the ventral visual
stream areas, related to object intrinsic properties and to object
identity, respectively (Borra et al., 2008). Furthermore, PFG
contributes to encode the motor goal of sequential actions
281
References
IPS
SAS
F1
AIP
PS
PFG
CS
F5p
IAS
F5a
46vc
12r
SII
LF
STS
Figure 3 Summary view of the cortical connections of the lateral

grasping network. Abbreviations as in Figure 1.
(see Fogassi & Luppino, 2005), and SII contributes with information related to haptic coding of objects (Fitzgerald, Lane,
Thakur, & Hsiao, 2004). In the prefrontal component of the
network, area 12r contributes to the exploitation of nonspatial
memory-based or working memory information related to
object properties (e.g., weight, center of mass, fragility, and
texture) or identity, for controlling object-oriented actions
(Borra, Gerbella, Rozzi, & Luppino, 2011). Finally, area 46vc
contributes to selecting and monitoring hand actions based on
behavioral goals and behavioral guiding rules, in order to organize motor acts in intentional action sequences (Gerbella,
Borra, Tonelli, Rozzi, & Luppino, 2013).
Concluding Remarks
The data reviewed in the preceding text show that a multidisciplinary approach based on multimodal architectonic,
functional, and connectional techniques has been crucial for
obtaining a modern view of the organizational principles of
the nonhuman primate motor cortex. The much lower resolution of the connectional and functional techniques currently
available for studies in humans still preclude a detailed
description of the organization of the human motor cortex.
However, tractographic studies showing general connectional
features of different premotor regions similar to those observed
in macaques (e.g., Schubotz, Anwander, Knosche, Von
Cramon, & Tittgemeyer, 2010) and functional imaging studies
showing topographical and functional homologies (e.g.,
Bremmer et al., 2001; Cavina-Pratesi et al., 2010) in the organization of the nonhuman primate and human motor and
parietal cortex confirm the eminent role of monkey studies
for the investigation of human cortical functions.

Cognition; Posterior Parietal Cortex: Structural and Functional
Diversity; INTRODUCTION TO SYSTEMS: Visuomotor Integration.
Belmalih, A., Borra, E., Contini, M., Gerbella, M., Rozzi, S., & Luppino, G. (2007).
A multiarchitectonic approach for the definition of functionally distinct areas and
domains in the monkey frontal lobe. Journal of Anatomy, 211, 199211.
Borra, E., Belmalih, A., Calzavara, R., Gerbella, M., Murata, A., Rozzi, S., et al. (2008).
Cortical connections of the macaque anterior intraparietal (AIP) area. Cerebral
Cortex, 18, 10941111.
Borra, E., Belmalih, A., Gerbella, M., Rozzi, S., & Luppino, G. (2010). Projections of the
hand field of the macaque ventral premotor area F5 to the brainstem and spinal cord.
Borra, E., Gerbella, M., Rozzi, S., & Luppino, G. (2011). Anatomical evidence for the
involvement of the macaque ventrolateral prefrontal area 12r in controlling goaldirected actions. Journal of Neuroscience, 31, 1235112363.
Borra, E., Gerbella, M., Rozzi, S., Tonelli, S., & Luppino, G. (2014). Projections to the
superior colliculus from inferior parietal, ventral premotor, and ventrolateral
prefrontal areas involved in controlling goal-directed hand actions in the macaque.
Bremmer, F., Schlack, A., Shah, N. J., Zafiris, O., Kubischik, M., Hoffmann, K.-P., et al.
(2001). Polymodal motion processing in posterior parietal and premotor cortex: A
human fMRI study strongly implies equivalencies between humans and monkeys.
Neuron, 29, 287296.
Brodmann, K. (1909). Vergleichende Lokalisationslehre der Groshirnrinde. Leipzig:
Barth (Reprinted 1925).
Cavina-Pratesi, C., Monaco, S., Fattori, P., Galletti, C., Mcadam, T. D., Quinlan, D. J.,
et al. (2010). Functional magnetic resonance imaging reveals the neural substrates
of arm transport and grip formation in reach-to-grasp actions in humans. The
Dancause, N., Barbay, S., Frost, S. B., Zoubina, E. V., Plautz, E. J., Mahnken, J. D., et al.
(2006). Effects of small ischemic lesions in the primary motor cortex on
neurophysiological organization in ventral premotor cortex. Journal of
Fink, G. R., Frackowiak, R. S. J., Pietrzyk, U., & Passingham, R. E. (1997). Multiple
nonprimary motor areas in the human cortex. Journal of Neurophysiology, 77,
21642174.
Fitzgerald, P. J., Lane, J. W., Thakur, P. H., & Hsiao, S. S. (2004). Receptive field
properties of the macaque second somatosensory cortex: Evidence for multiple
functional representations. Journal of Neuroscience, 24, 1119311204.
Fogassi, L., & Luppino, G. (2005). Motor functions of the parietal lobe. Current Opinion
in Neurobiology, 15, 626631.
Gerbella, M., Belmalih, A., Borra, E., Rozzi, S., & Luppino, G. (2011). Cortical
connections of the anterior (F5a) subdivision of the macaque ventral premotor area
F5. Brain Structure and Function, 216, 4365.
Gerbella, M., Borra, E., Tonelli, S., Rozzi, S., & Luppino, G. (2013). Connectional
heterogeneity of the ventral part of the macaque area 46. Cerebral Cortex, 23, 967987.
Geyer, S., Matelli, M., Luppino, G., & Zilles, K. (2000). Functional neuroanatomy of the
primate isocortical motor system. Anatomy and Embryology, 202, 443474.
He, S. Q., Dum, R. P., & Strick, P. L. (1993). Topographic organization of corticospinal
projections from the frontal lobe: Motor areas on the lateral surface of the
hemisphere. Journal of Neuroscience, 13, 952980.
He, S. Q., Dum, R. P., & Strick, P. L. (1995). Topographic organization of corticospinal
projections from the frontal lobe: Motor areas on the medial surface of the
hemisphere. Journal of Neuroscience, 15, 32843306.
Hof, P. R., Glezer, I. I., Conde, F., Flagg, R. A., Rubin, M. B., Nimchinsky, E. A., et al.
(1999). Cellular distribution of the calcium-binding proteins parvalbumin,
calbindin, and calretinin in the neocortex of mammals: Phylogenetic and
developmental patterns. Journal of Chemical Neuroanatomy, 16, 77.
Hof, P. R., & Morrison, J. H. (1995). Neurofilament protein defines regional patterns of
cortical organization in the macaque monkey visual system: A quantitative
immunohistochemical analysis. Journal of Comparative Neurology, 352, 161186.
Jeannerod, M., & Jacob, P. (2005). Visual cognition: A new look at the two-visual
system model. Neuropsychologia, 43, 301312.
Keizer, K., & Kuypers, H. G. J. M. (1989). Distribution of corticospinal neurons with
collaterals to the lower brain stem reticular formation in monkey (Macaca
fascicularis). Experimental Brain Research, 74, 311318.
Lemon, R. N. (2008). Descending pathways in motor control. Annual Review of
Morecraft, R. J., Louie, J. L., Herrick, J. L., & Stilwell-Morecraft, K. S. (2001). Cortical
innervation of the facial nucleus in the non-human primate: A new interpretation of
the effects of stroke and related subtotal brain trauma on the muscles of facial
expression. Brain, 124, 176208.
282
Murata, Y., Higo, N., Oishi, T., Yamashita, A., Matsuda, K., Hayashi, M., et al. (2008).
Effects of motor training on the recovery of manual dexterity after primary motor
cortex lesion in macaque monkeys. Journal of Neurophysiology, 99, 773786.
Nishimura, Y., Onoe, H., Morichika, Y., Perfiliev, S., Tsukada, H., & Isa, T. (2007).
Time-dependent central compensatory mechanisms of finger dexterity after spinal
cord injury. Science, 318, 11501155.
Rizzolatti, G., & Luppino, G. (2001). The cortical motor system. Neuron, 31, 889901.
Rizzolatti, G., Luppino, G., & Matelli, M. (1998). The organization of the cortical motor
system: New concepts. Electroencephalography and Clinical Neurophysiology, 106,
283296.
Rizzolatti, G., & Matelli, M. (2003). Two different streams form the dorsal visual system:
Anatomy and functions. Experimental Brain Research, 153, 146157.
Schubotz, R. I., Anwander, A., Knosche, T. R., Von Cramon, D. Y., & Tittgemeyer, M.
(2010). Anatomical and functional parcellation of the human lateral premotor cortex.
Tanji, J., & Hoshi, E. (2008). Role of the lateral prefrontal cortex in executive behavioral
control. Physiological Reviews, 88, 3757.
Van Essen, D. C. (1985). Functional organization of primate visual cortex. In E. G.
Jones, & A. Peters (Eds.), Cerebral cortex. New York: Plenum Press.
Somatosensory Cortex
JH Kaas, Vanderbilt University, Nashville, TN, USA
Glossary
Barrel A collection of neurons in primary somatosensory

cortex that looks something like a barrel and represents a
single mystacial sensory whisker on the face. The rows of
barrels that represent the rows of mystacial vibrissae make
up the cortical barrel field.
Cortex Short for neocortex, a thick sheet of six layers that
caps the forebrain of all mammals and makes up 80% of the
human brain.
Cortical area Cortex is divided into a number of regions

called areas that are structurally specialized to process certain
inputs and provide altered outputs. Cortical areas were
considered to be the organs of the brain. The subcortical
equivalent is called a nucleus.
Introduction
Receptors and Peripheral Nerve Afferents
The brains of all vertebrates have somatosensory systems that

process information from receptors in the skin and body in
order to guide motor behavior and avoid damage. Mammals
have a thick neocortex of six layers that evolved from something like the small, thin dorsal cortex of reptiles, and this
dorsal cortex likely had some somatosensory input from the
thalamus. However, all mammals have a more complex region
of somatosensory cortex that is subdivided into four or five
cortical areas that are differently specialized for processing
somatosensory inputs. These inputs come from receptors in
the skin that respond to touch, vibration, tissue damage, or
temperature change, as well as deeper receptors in muscles and
joints that signal movement and limb position. The receptor
information is conducted by afferent sensory axons in peripheral nerves to the spinal cord and brain stem where they
activate neurons that participate in reflexes and neurons that
conduct sensory information to the contralateral somatosensory thalamus. The activated thalamic neurons in turn project
to areas of somatosensory cortex. Somatosensory cortex
includes a primary area, S1; belt-like somatosensory areas
along the rostral and caudal borders of S1; and one or two
areas lateral to S1, the second somatosensory area, S2, and the
parietal ventral somatosensory area, PV (see Figure 1). Most
mammals also have separate motor areas rostral to somatosensory cortex that receive inputs from somatosensory cortex and
use this information to guide motor cortex outputs that
produce behavior. S1 of other mammals corresponds to area
3b of primates. An early anatomist, Brodmann, divided anterior somatosensory cortex into four areas currently known
more by their numbers than their original names. Area 3b is
bordered rostrally by area 3a and caudally by area 1. Area 1 is
bordered by area 2. Other areas involved in somatosensory
processing in primates include S2 and PV of other mammals,
other areas of the cortex of the lateral sulcus, and areas or
subdivisions of posterior parietal cortex, a region that is greatly
expanded in primates.
Primary somatosensory cortex (S1) is activated by touch and

pressure on the glabrous skin and the movement of hairs on
the hairy skin. Almost all mammals have specialized receptors
(Abraira & Ginty, 2013) around the base of the long whiskers
or vibrissae that are used to detect objects at a short distance
from the body. These long vibrissae are usually most densely
distributed on the side of the face and lower jaw, but they also
occur above the eye, on the wrist, and on other locations on the
body (Brecht, Preilowski, & Merzenich, 1997). Such sensory
vibrissae are variable in number and location across species,
but they have received the most attention in rats and mice as
the long mystacial vibrissae are individually represented in S1,
as well as in the ventroposterior (VP) nucleus and trigeminal
nuclei of the brain stem. In S1, the collection of neurons best
activated by a single whisker is visible in several different stains
of brain sections. This collection of neurons for an individual
whisker has been given the colorful name the cortical barrel.
The part of S1 with rows of barrels corresponding to rows of
whiskers is called the barrel field. These mystacial whiskers
detect and help identify objects near the face and mouth.
Shorter hairs on the upper and lower jaws are more finely
spaced and they provide more details about objects that may
be identified as food (Brecht et al., 1997).
Other peripheral nerve afferents subserving touch are associated with morphologically specialized receptor cells in the
skin. These specialized receptors allow afferent types to code
different features of touch and provide different types of information to the brain (Abraira & Ginty, 2013). The Merkel cells
mediate the responses of the slowly adapting type 1 afferents
(SA-I) that signal a maintained touch on the skin or displacement of a hair. Type two slowly adapting afferents (SA-II)
signal skin deformations, pressure on teeth, and tendon stretch
during movement. Type I rapidly adapting afferents (RA-I),
from receptors in hair follicles and skin, signal changes in
skin contact and surface texture. The highly specialized
Pacinian corpuscles for rapidly adapting type II afferents
http://dx.doi.org/10.1016/B978-0-12-397025-1.00223-2
283
284
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Somatosensory Cortex
ot
Foo
M2
M1
CS
Visual
Dys.
Pa
w
Olfactory
bulb
V1
S1
Pa
Fo
Face and
S1
vibrissae
Face
p
Li
5 mm
Upper
lip
Face
Face
PV
Li m b s
S2
Li m b s
R hin a l s
Aud
ulcu
Figure 1 A dorsolateral view of a rat brain showing the locations of somatosensory areas. These areas include the primary area, S1 of granular cortex,
which contains a representation of the touch receptors of the contralateral body surface. S1 is disrupted rostrally by dysgranular (Dys) cortex that
forms another representation of the contralateral body but of deep receptors in muscles and joints. Two smaller representations lateral to S1 are
somatotopically organized and respond to touch: the second somatosensory area (S2) and the parietal ventral somatosensory area (PV). A narrow
band of cortex caudal to S1, the caudal somatosensory area (CS), gets inputs from S1. Somatosensory areas provide inputs to primary motor
cortex (M1) and secondary motor cortex (M2, premotor cortex). Primary visual cortex (V1) and auditory cortex (Aud) are shown for reference.
(SA-II) are deeper in the skin and are very sensitive to vibration.
SA-II afferents might, for example, detect the vibrations that
travel through the ground that are made by an approaching
predator. Other afferents signal tissue damage (pain), temperature, and poorly localized touch.
The Brain Stem and Spinal Cord Targets

Different classes of afferents have different targets in the spinal
cord and brain stem (Abraira & Ginty, 2013). The slowly adapting and rapidly adapting (SA and RA) afferents from the lower
body enter the spinal cord and form the two branches. One
branch ascends to the dorsal column pathway of the spinal
cord to the dorsal column nuclei at the junction of the spinal
cord with the brain stem, the cuneate nucleus for the forelimb
and adjoining trunk, and the gracile nucleus for the hind limb
and adjoining trunk. The other branch of the afferent axon
terminates in the dorsal horn of the spinal cord where it activates
neurons that function locally or project to the dorsal column
nuclei. Afferents from the head, face, and mouth project to
components of the trigeminal complex in the brain stem. The
principal trigeminal nucleus receives SA and RA tactile afferents,
including those from the long facial whiskers.
The Thalamic Targets

The gracile, cuneate, and principal trigeminal nuclei of the brain
stem and upper spinal cord all project to the ventroposterior (VP)
nucleus of the contralateral somatosensory thalamus (Kaas,
2012). The principal nucleus of the trigeminal complex projects
to the VP medial (VPM) division, and the cuneate and gracile
nuclei project to medial and lateral subnuclei of the VP lateral
(VPL) division. Thus, VP contains a systematic representation of
the SA and RA receptors of the body from medial (tail and hind
limb) to lateral (teeth and tongue) in the nucleus. As a complication, neurons from the representation of teeth and tongue also
project ipsilaterally to VPM in most mammals. Thus, VPM has
separate representations of contralateral and ipsilateral teeth and
tongue. This may be important since the teeth and tongue on
both sides of the mouth function closely together. In some
rodents, especially in rats and mice, isolated groups of neurons
in VP are best activated by the movement of a single mystacial
vibrissa. Each cell group, called a barreloid in VP (van der Loos,
1976), projects to a matching cortical barrel in S1.
Afferents from muscles and joints that provide position
sense (proprioception) terminate in other nuclei in the upper
spinal cord and brain stem and activate neurons that also
project to the contralateral somatosensory thalamus. These
proprioceptive inputs terminate dorsal to VP in the ventroposterior superior (VPS) nucleus in primates and rostrodorsal cap
to VP in rats, cats, and probably most mammals (Francis, Xu, &
Chapin, 2008; Kaas, 2008). Other afferents related to pain,
temperature, and touch activate spinal cord and brain stem
neurons that cross to the opposite side of the spinal cord
ascend to the somatosensory thalamus in the spinothalamic
tract and its equivalent in the brain stem. Some of these
spinothalamic axons terminate in the ventroposterior inferior
(VPI) nucleus just under VP in primates or a similar region
capping caudoventral VP in other mammals. Other spinothalamic axons terminate in other parts of the somatosensory
thalamus, including a nucleus, that is part of a pain network,
and parts of the posterior nuclear complex. All these thalamic
nuclei receive other inputs, including feedback connections
from somatosensory cortex, and they generally contain a
mixture of about 75% excitatory neurons that project to cortex
and 25% inhibitory neurons that suppress ongoing activity in
the nucleus and help constrict the receptive fields of thalamic
neurons. However, in VP, rats and mice replace inhibitory
neurons in VP with inhibitory inputs from the thalamic reticular nucleus.
Somatosensory Cortex of Anterior Parietal Cortex

All mammals have at least four or five major divisions or areas
of somatosensory cortex (Figure 1). The main division, the
primary somatosensory area (S1), is characterized by dense
inputs from VP to layer 4, layer 4 that is packed with small
neurons, a somatotopic organization from tail to tongue in a
mediolateral direction across cortex, and neurons throughout
that respond to touch in ways that reflect the SA and RS tactile
afferents (Kaas, 1983, 2012). In primates, the architectonic
area 3b of Brodmann corresponds to S1 (although the term
S1 continues to be used in humans to refer to four architectonic areas of Brodmann, areas 3a, 3b, 1, and 2; see in the
succeeding text). S1 is now often referred to as area 3b in
nonprimate mammals in addition to primates. Layer 4 neurons in S1 may be grouped in clusters separated by narrow
septa of fewer and smaller neurons, such as in the barrel field
of mice and rats, with a barrel of neurons for each facial
whisker, but also elsewhere in S1 for each digit and pad of
the palm and toe of the hind foot (Dawson & Killackey, 1987).
Such septa also separate the representations of individual
digits, and other body parts, in S1 of some primate species.
The dense clusters of neurons receive the activating inputs from
VP, while the septal neurons have other thalamic connections,
connections with the neuron packed clusters, and connections
with other structures, including S1 of the opposite cerebral
hemisphere. Thus, S1 has two functionally different divisions,
the neuron-dense cluster regions that make up most of S1 and
the narrow septal regions that have more integrative functions
(Kim & Ebner, 1999). In addition, quite locally, within a single
digit representation, for example, the relay of RA and SA inputs
from VP to S1 terminates in small, separate territories in layer 4
in primates and possibly some other mammals (Kaas, 2012).
This separation suggests that it is important to preserve the SA
and RA types of information all the way to S1. Together, the
classes of modular subdivisions of S1 contribute separate representations of different inputs at the local level. Yet, at the
global level, S1 contains an overall systematic representation of
the contralateral body and both contralateral and ipsilateral
teeth and tongue, from the tail to the tongue in a mediolateral
pattern across cortex (Dawson & Killackey, 1987; Kaas, 2012;
Remple, Henry, & Catania, 2003).
Neurons in S1 respond to touch or pressure on a limited
portion of the skin called the excitatory receptive field of a
neuron. Layer 4 neurons have direct thalamic input and the
smallest and simplest receptive fields. The receptive fields
largely reflect the response characteristics of the SA or RA
inputs from VP. These responses are modified by connections
between neurons in S1, including those from inhibitory neurons within S1, inputs from thalamic nuclei other than VP, and
the so-called feedback connections from other somatosensory
areas, including S1 and other areas of the other cerebral hemisphere. Because neurons in layer 3 above layer 4, and layers 5
and 6 below layer 4, have more of these other connections,
these neurons have larger and more complex receptive fields.
For example, neurons may be excited by touch in only one
small part of the hand, the excitatory receptive field, but that
response may be increased or reduced by touch on other parts
of the hand or even the other hand in monkeys (Reed, Qi, &
Kaas, 2011). Neurons in the barrel field of rats are even
285
selective for the movements of the activating facial whisker in

particular directions.
Besides differing somewhat in response properties, neurons
in different layers of S1 have different connections. Layer 4
neurons project to other layers in S1 and other layers also
connect with each other. In addition, layer 6 neurons provide
feedback connections to VP, and layer 5 neurons project to
subcortical to structures. Layer 3 cells provide most of the outputs to other cortical areas, and these connections help identify
other areas of cortex that are predominantly somatosensory in
function.
One of these additional somatosensory areas in primates is
area 3a just rostral to S1 (area 3b). Area 3a has a less developed
layer 4 than area 3b and has other characteristics that suggest
that it is somewhat motor as well as sensory in function. The
thalamic input to area 3a is proprioceptive and this information from the VPS is important in guiding motor behavior.
Neurons in area 3a also respond to touch, and this depends
on inputs from area 3b. Outputs of area 3a include those to
motor cortex, M1, and to premotor neurons in the brain stem
and spinal cord, providing further evidence for the proposed
motor functions of area 3a. An area 3a has also been recognized in cats and other carnivores, but area 3a, as such, has not
been commonly recognized in other mammals. Yet, in rats and
mice, the cortex along the rostral border of S1, called dysgranular cortex (Figure 1) because of its less well-developed layer
of small granular neurons, has the histological appearance
and location relative to granular S1 of area 3a of primates.
Often, this dysgranular cortex is included with granular S1 in
the cortical region called S1, but dysgranular cortex is a separate cortical area that has proprioceptive input from the thalamus, from the head of VP, and dysgranular cortex has other
connections that are very much like those of area 3a of primates. Overall, the evidence suggests that an area 3a or dysgranular area exists in all or most mammals.
Just caudal to S1, a narrow strip of cortex with input from
S1 has been found in all studied mammals. The connections
from S1 to this caudal somatosensory strip, CS, are to adjacent
locations, providing evidence that this caudal strip contains a
tail to tongue representation from medial to lateral in cortex, as
in S1. Typically, this caudal strip of cortex is unresponsive or
poorly responsive to touch in anesthetized mammals, so little
is known about neuron response properties, or the detailed
organization of the representation. This cortex is in the location of area 1 of primates (Kaas, 1983, 2012), which contains
neurons that respond well to touch, with receptive fields that
are only slightly larger than those in area 3b (S1). Microelectrode recordings indicate that area 1 contains a systematic
representation of the contralateral skin that is a mirror reversal
of the somatotopy in area 3b. The region of area 1 is not very
responsive to touch or other somatosensory stimuli in anesthetized prosimian primates or in anesthetized marmoset
monkeys. Given the connections from S1 (area 3b) to this
caudal cortex across mammalian taxa, and the various responsiveness of area 1 in primates, it seems likely that area 1 is
homologous to CS (Figure 1). Thus, CS might be labeled area 1
in all mammals.
In primates, area 1 depends on projections from area 3b to
layer 4 of area 1 for responsiveness to touch, although layer 3
of area 1 receives projections from the VP (3) (Kaas, 2012).
286
Area 1 neurons are RA and appear to reflect RA receptor

activity. Some area 1 neurons code for direction of movement
of touch on the skin, and many are sensitive to the orientation
of a bar press on the skin. Thus, area 1 has the characteristics
expected for a higher-order somatosensory area that further
processes inputs from area 3b.
In rodents, and a number of other mammals, a narrow strip
of cortex caudal to CS is regarded as posterior parietal cortex. In
anthropoid primates (monkeys, apes, and humans), cortex in
this location was called area 2 by Brodmann. Area 2, a strip of
cortex about the width of area 1 immediately caudal to area 1,
contains neurons responsive to touch, sometimes on both
hands, and area 2 neurons are especially responsive during
tactile stimulation as a result of limb movements. The inputs
to area 2 include those from area 3b and area 1, hereby providing information about skin contact, and from the VPS
nucleus of the somatosensory thalamus. VPS provides information about body movements that activate muscle spindle
and joint receptors. Thus, area 2 neurons combine information
about skin contact locations with information about body
movement and position. Area 2 of one hemisphere is densely
connected with area 2 of the other hemisphere, so that information from two sides of the body, especially the two hands,
can be combined. These sensory inputs allow area 2 to be
important in finger coordination and discriminations of object
shapes by touch. Area 2 provides somatosensory information
to other regions of somatosensory cortex and to premotor
cortex in the frontal lobe. The representation of the body in
area 2 roughly parallels that of area 1 but is more complex.
Somatosensory Cortex of Lateral Parietal Cortex

Cortex lateral and slightly caudal to S1 responds to tactile
stimuli in all mammals. A representation of the complete
contralateral body was found when cortex lateral to S1 was
explored with surface electrodes, and this region was termed
the second somatosensory area, S2. When the S2 region was
explored in more detail with microelectrodes, it was discovered
that the S2 region contains two systematic representations of
the body, at least in most mammals (Krubitzer, Campi, &
Cooke, 2011; Remple et al., 2003). The name S2 was retained
for the more dorsal of the two representations, while the more
ventral representation was called the parietal ventral somatosensory area, PV (Figure 1). Both S2 and PV have neurons that
respond well to touch, although with larger receptive fields
than those for neurons in S1. Major inputs to S2 and PV are
from S1 (and area 3a, 1, and 2 in primates) and directly from
the ventral posterior nucleus, VP, and from the VPI nucleus.
Parts of S2 and PV respond to auditory stimuli. Outputs of S2
and PV are to other somatosensory areas, including posterior
parietal cortex, and to motor and premotor cortices. Functional
differences between S2 and PV are likely, but not yet
understood.
In primates, S2 and PV are buried in cortex of the upper
bank of the lateral fissure, where there is evidence of several
often poorly understood somatosensory areas, including a
region that appears to be especially involved in the perception
of pain (Kaas, 2012).
Posterior Parietal Cortex

In most mammals, posterior parietal cortex forms a narrow strip
between the anterior parietal somatosensory cortex and cortex
that is clearly visual. This narrow strip appears to be multisensory, with somatosensory, visual, and possibly auditory cortex
connections, as well as connections with frontal cortex. In primates, posterior parietal cortex is a greatly expanded region. This
expanded region is most likely specialized for planning and
guiding movements based on sensory inputs (Kaas, 2012; Kaas,
Gharbawie, & Stepniewska, 2011). The more rostral half of this
region, involved in grasping and manipulation of objects,
receives mainly somatosensory inputs, including those from
area 2, S2, PV, and other somatosensory areas of the insula and
lateral sulcus. The caudal half of the posterior parietal cortex,
involved in reaching, is dominated by visual inputs. Other parts
of posterior parietal cortex are involved in eye and head movements to view objects of interest, self-defensive movements of
the head and arm, and the bringing of food to the mouth. In
humans, posterior parietal cortex is activated during the use of
tools. Posterior parietal subregions project differently to motor
and premotor cortices, including the frontal eye field.

Columns of the Mammalian Cortex; Cytoarchitecture and Maps of the
Human Cerebral Cortex; Evolution of the Cerebral Cortex; Motor
Cortex;Posterior Parietal Cortex: Structural and Functional Diversity.
References
Abraira, V. E., & Ginty, D. D. (2013). The sensory neurons of touch. Neuron, 79,
618639.
Brecht, M., Preilowski, B., & Merzenich, M. M. (1997). Functional architecture of the
mystacial vibrissae. Behavioural Brain Research, 84, 8197.
Dawson, D. R., & Killackey, H. P. (1987). The organization and mutability of the forepaw
and hindpaw representations in the somatosensory cortex of the neonatal rat.
Francis, J. T., Xu, S., & Chapin, J. K. (2008). Proprioceptive and cutaneous
representations in the rat ventral posterolateral thalamus. Journal of
Kaas, J. H. (1983). What, if anything, is SI? The organization of first somatosensory
area of cortex. Physiological Reviews, 63, 206231.
Kaas, J.H. (2008). The somatosensory thalamus and associated pathways. The senses:
A comprehensive reference London: Elsevier.
Kaas, J. H. (2012). Somatosensory system. In J. K. Mai & G. Paxinos (Eds.), In The
human nervous system (3rd ed.). London: Elsevier.
Kaas, J. H., Gharbawie, O. A., & Stepniewska, I. (2011). The organization and evolution
of dorsal stream multisensory motor pathways in primates. Frontiers in
Kim, U., & Ebner, F. F. (1999). Barrels and septa: Separate circuits in rat barrel field
Krubitzer, L., Campi, K. L., & Cooke, D. F. (2011). All rodents are not the same: A
modern synthesis of cortical organization. Brain, Behavior and Evolution, 78,
5193.
Reed, J. L., Qi, H. X., & Kaas, J. H. (2011). Spatiotemporal properties of neuron
response suppression in owl monkey primary somatosensory cortex when stimuli
are presented to both hands. Journal of Neuroscience, 31, 35893601.
Remple, M. S., Henry, E. C., & Catania, K. C. (2003). Organization of
somatosensory cortex in the laboratory rat (Rattus norvegicus): Evidence for two
lateral areas joined at the representation of the teeth. Journal of Comparative
Neurology, 467, 105118.
van der Loos, H. (1976). Barreloids in mouse somatosensory thalamus. Neuroscience
Letters, 2, 16.
Functional Organization of the Primary Visual Cortex

R Goebel, Maastricht University, Maastricht, The Netherlands
Introduction
The primary visual cortex is commonly known as area V1, or
area 17 according to Brodmann (Brodmann, 1909), or area OC
according to von Economo (von Economo & Koskinas, 1925).
The primary visual cortex is the first cortical area in which the
visual information converge after their initial separate processing in the retina and subcortical nuclei, in particular lateral
geniculate nucleus (LGN) and superior colliculus. It is believed
that the unity of the information needed for a complete reconstruction for the visual world is still preserved in this first
cortical processing stage of the visual pathway. Beyond area
V1, different features of the visual world are processed in
separate cortical areas in a massively parallel manner
(Felleman & Van Essen, 1991; Ungerleider & Haxby, 1994).
While most of our knowledge about the structure and function
of V1 originate from studies in nonhuman primates, in particular that of old-world monkeys (Felleman & Van Essen, 1991),
the basic scaffold of the functional architecture in humans is
generally assumed to be homologous to that of other primates.
Anatomy and Lamination

Already in 1776 Gennari (1782) isolated V1 (without knowing
about its visual nature) from the rest of cortex based on an
observable line (stria of Gennari), which is a 300-mm-thick
horizontal band of myelinated fibers within layer IV
(see below) that is visible to the naked eye in cadaver brain
sections. The Gennari line is the reason why primary visual
cortex is also known as striate cortex and the rest of the visual
cortex as extrastriate cortex. In recent years it has become possible to visualize the stripe of Gennari in the human brain using
in vivo 7 T TSE anatomical MRI (Trampel et al., 2011). In
humans, much of area V1 lies on the medial surface of the
respective hemispheres, surrounding the calcarine fissure in
the occipital lobe (Brodmann, 1909; Zilles, 1990). Rostrally
and posterolaterally area V1 is bordered by the lunate and
inferior occipital sulci, respectively. In adult macaque monkeys,
1 mm3 of V1 tissue contains approximately 4700 neurons, 2900
microglia, 3400 oligodendrocytes, and 49 000 astrocytes
(OKusky & Colonnier, 1982). The total number of neurons in
human V1 has been estimated at around 140 million in each
hemisphere (Leuba & Kraftsik, 1994). The primary visual cortex
consists of a wide variety of cells (Lund, 1988; Peters & Jones,
1984). Traditionally, the cells in V1 have been classified into two
morphologically and functionally distinct types: excitatory pyramidal cells and a wide variety of nonpyramidal cells (Peters &
Jones, 1984). The axons of pyramidal cells provide the feedforward and feedback projections to the other cortical areas and
subcortical structures, respectively (Lund, 1988). The axons of
nonpyramidal cells are confined within primary visual cortex.
Like other cortical areas, V1 consists of a laminated sheet of

cells that are arranged into six main layers (most dorsal layer 1
through most ventral layer 6) with the entire thickness from pia
to the white matter being about 2 mm (OKusky & Colonnier,
1982). In fact, primate striate cortex has been subdivided more
fine-grained than most cortical areas into 11 identifiable laminar divisions (1, 2, 3, 4A, 4B, 4Ca, 4Cb, 5A, 5B, 6A, and 6B).
The laminated anatomical segregation and the unique pattern
of connectivity between the laminae throughout V1 suggest a
division of computational labor between the different laminae
(Hubel & Wiesel, 1972; Lund, 1988). Layer 4, which receives
most visual input from the LGN, is further divided into four
layers, labeled 4A, 4B, 4Ca, and 4Cb. While there is a great
variability of cell types, its density, and the pattern of connectivity from layer to layer, the layering, cell types, and feedforward/feedback connections across different cortical areas
on the other hand are reported to be surprisingly similar
(Rockel, Hiorns, & Powell, 1980). This in turn gave rise to the
notion of a canonical circuitry performing fundamentally
similar computation across all neocortical areas, including V1
(Douglas, Martin, & Whitteridge, 1989). Using high-resolution
functional magnetic resonance imaging (fMRI) it has become
possible to roughly distinguish functional signals from cortical
layers providing new opportunities to separate bottom-up
from top-down influences in V1 (see section Mapping Orientation Columns and Cortical Layers with ultrahigh field fMRI).
Retinotopic Mapping with fMRI

One of the early exciting applications of fMRI was retinotopic
mapping that worked remarkably well on 1.5 T scanners with
the gradient echo (GE) echo planar imaging MR pulse
sequence. Using appropriate visual stimuli to map eccentricity
and polar angle, the early visual areas can be charted in individual human brains (Sereno et al., 1995). This is possible
because the mapping from the retina to the primary visual
cortex is topographic, that is, neighboring regions in one area
(retina) project to neighboring regions in another area (primary visual cortex). This transformation preserves the qualitative spatial relations of the retina but also reveals systematic
scaling effects, that is, there is much more cortical tissue
devoted for foveal regions as compared to peripheral regions
of the visual field. This cortical magnification (M scaling) can
be expressed as millimeters of cortical surface per degree of
visual angle and varies by a factor of approximately 100
between the foveal and peripheral representation of the primary visual cortex of primates (Daniel & Whitteridge, 1961).
A successful delineation of the early visual areas with fMRI
exploits the fact that successive visual areas alternate with a
mirror or non-mirror representation of the visual field. Multiple horizontal and vertical meridian representations across the
visual cortex, thus, indicate the transitions between early visual
http://dx.doi.org/10.1016/B978-0-12-397025-1.00224-4
287
288
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Functional Organization of the Primary Visual Cortex
areas. Using traveling-wave (phase-encoded) visual stimuli

(expanding ring and rotating wedge), fMRI studies have successfully revealed multiple meridian representations arranged
in approximately parallel bands along the flattened cortical
surface (Sereno et al., 1995) separating early visual areas.
FMRI-based retinotopic mapping has quickly become an
important tool to noninvasively define the borders of V1 and
other early visual areas (e.g., Goebel, Khorram-Sefat, Muckli,
Hacker, & Singer, 1998; Goebel, Muckli, Zanella, Singer, &
Stoerig, 2001; Tootell, Dale, Sereno, & Malach, 1996; Wandell,
Dumoulin, & Brewer, 2007). Since there is significant variability in the size, location, and shape of V1, the area boundaries
need to be mapped in each individual subject.
More recently, an alternative technique has been proposed
that uses a model-driven approach to estimate neuronal population receptive fields (pRFs) as the basis to create visual field
maps (Dumoulin & Wandell, 2008). This approach estimates a
model of the pRF for voxels in visual cortex that best explains
measured voxel time courses evoked by the stimulus sequence
presented during one or more functional runs. The visual stimuli may be the same as used in conventional retinotopic experiments (rings and wedges) but also other stimuli can be used
(e.g., bars at different positions and orientation). The pRF
method not only produces more accurate visual field maps
than the conventional phase-encoded approach (Dumoulin &
Wandell, 2008), it also enables estimation of additional neuronal quantities such as the size of pRFs. It is thus, an important
method for clinical applications, for example, to reveal abnormal visual field maps in various diseases such as macular degeneration or atypical retinocortical projections (Haak et al., 2013).
The standard pRF model (Dumoulin & Wandell, 2008) that is
used to predict fMRI data is specified as a Gaussian with three free
parameters, the position x0 and y0 of the pRF as well as its
standard deviation (size) s. These parameters are defined in
stimulus space (degrees of visual angle) making it easy to interpret
resulting maps. Note that the pRF approach is not limited to the
(standard) Gaussian model, that is, other models can be
employed that may estimate, for example, models with noncircular receptive fields (Senden, Reithler, Gijsen, & Goebel,
2014) or without a priori assumptions about a specific pRF
shape (Lee, Papanikolaou, Logothetis, Smirnakis, & Keliris,
2013; Zimmermann, Senden, De Martino, & Goebel, 2014). For
the standard Gaussian model, the three parameters define the
position and extent of a two-dimensional Gaussian function g:

2
2
gx, y e
xx0
yy0
2s2
A predicted time course can be generated for a specific

model by calculating the overlap of a specified receptive field
with the presented visual stimulus sequence at each time point.
This will generate a positive response at times when a presented
stimulus falls within the models receptive field. Note that an
alternative receptive field located at another location will produce a different time course since the stimulus sequence will
usually overlap with the other models receptive field at different moments of time. Further note that a model with a larger
receptive field size will be influenced by stimuli that are further
away from the pRF centre than an alternative model with a
smaller receptive field size even if the center of the two models
is located at the same position in the visual field. If rich visual
stimulus sequences are used, each model will, thus, produce a
unique predicted time course. The predicted time courses from

different pRF models can be compared with the measured time
course of a specific voxel (or vertex on a cortex mesh representation). In order to allow a proper comparison of a model time
course with a measured voxel time course, model time courses
need to be convolved with a (standard or empirically derived)
hemodynamic impulse response function. The pRF model that
generates a predicted time course that best explains the variance of a voxels time course will be selected as the pRF model
for that voxel. Note that conventional eccentricity and polar
angle values can be easily derived for each voxel (or vertex) by
converting the position parameters x0 and y0 of the best fitting
pRF model to a corresponding eccentricity value ecc and polar
angle value a:
q
ecc x20 y02 a tan 1 y0 =x0
Figure 1 shows eccentricity and polar angle maps obtained
from a pRF retinotopic mapping fMRI study on selected anatomical slices as well as on folded and inflated cortex meshes of
the right hemisphere. The horizontal and vertical half-meridians
of the polar angle map (Figure 1(d)) are used to functionally
delineate the extent of V1 separating it from V2. These boundaries can be calculated explicitly using the field sign technique
(Sereno et al., 1995), which integrates the polar and eccentricity
map to determine whether a position on a surface representation belongs to a mirror or nonmirror representation of the
visual field by comparing the local eccentricity gradient with
the local polar angle gradient. This method assigns a mirror
image field sign (1) for all points within V1 while points in
V2 will get a non-mirrored field sign (1); points in V3 will
again get a mirror image field sign (1) and so on. The first
contiguous mirror field sign map around the calcarine sulcus
demarcates the extent of V1 (limited in the posterioranterior
eccentricity direction by the extent of the used stimulus display).
The representation of the V1 horizontal meridian (dotted line in
Figure 1(d)) is contained within the calcarine sulcus. The upper
(dorsal) bank of V1 contains the lower visual field representation (bluegreen colors), and the lower (ventral) bank contains
the upper visual field representation (blueyellow colors) of the
contralateral visual hemifield. The border between V1 and dorsal V2 (V2d) is identified by the first vertical meridian representation of the lower visual field in the polar angle map (or field
sign map). Similarly, the border between V1 and ventral V2
(V2v) is identified by the first vertical meridian representation
of the upper visual field. Figure 1(d) shows two exemplary fitted
pRF models for two locations in V1. The model in the upper
inset is located close to the horizontal meridian (x 4.9 ,
y 1.4 ) with a pRF size of 0.8 while the model in the lower
inset is located close to the vertical meridian (x 0.3 ,
y 0.9 ) with a pRF size of 0.4 . Note that the estimated pRF
size increases with eccentricity, that is, the first model with an
eccentricity of 5.1 has a pRF size which is twice as large as that
of the second model with an eccentricity of 0.95 of visual angle.
Mapping Orientation Columns and Cortical Layers with

Ultrahigh Field fMRI
It was discovered early on that the neurons in V1 are spatially
organized according to their receptive field properties (Hubel
Calcarine sulcus
289
Fitted pRF
model
Calcarine sulcus
x = 4.9
y = 1.4
s = 0.8
Occipital lobe
V2d
(a)
V1
Calcarine sulcus
V2v
VP
10.0
hV4
HM
x = 0.3
y = 0.9
s = 0.4
0.0
(b)
Eccentricity
(c)
Polar angle
(d)
Fitted pRF
model
Figure 1 Topography of primary visual cortex and surrounding areas in a single subject revealed by retinotopic mapping analysis based on the
population receptive field (pRF) method. (a) Eccentricity values in the range from 0 to 10 of visual angle (see color bar in (b)) were calculated from the
estimated pRF x and y location of visually responsive voxels and visualized on a selected mid-sagittal (left) and coronal slice (right). (b) The same
eccentricity map visualized on a view of the medial bank of a folded cortex mesh of the right hemisphere (anterior is to the left, posterior is to the right).
(c) While a 3D rendering of a folded 3D mesh as in (b) better reveals the topographic layout of the eccentricity map than 2D slices as in (a), the full
topographic layout of V1 is only revealed on inflated (or fully flattened) cortex meshes. (d) Polar angle values, calculated from the same estimated
pRF location values, can be used to demarcate the extent of V1 and surrounding areas by identifying the horizontal and vertical (half-)meridians. The
lower left visual field quadrant is mapped to the upper bank of the calcarine sulcus demarcated by the left horizontal meridian (dotted line labeled
HM) and the vertical half-meridian of the lower visual field. The upper left visual field quadrant is mapped to the lower bank of the calcarine sulcus
demarcated again by the left horizontal meridian and the vertical meridian of the upper visual field. Fitted pRF models are shown in insets for two
exemplary locations within V1 (for details see text).
& Wiesel, 1969). If one inserts a recording electrode vertically

into the cortical plate, the measured receptive field properties
of the neurons from pia to the white matter will be similar to
each other. Thus the primary visual cortex is parceled into
narrow columns of cells sharing similar receptive field properties. Such clusters of iso-receptive field properties are called
cortical columns (Hubel & Wiesel, 1977). Cortical columns
represent one of the most ubiquitous organizing principles of
the cortex and the possibility to reveal its functional organization in various cortical areas has been limited to animal studies
using single or multiunit recordings (Hubel & Wiesel, 1968)
and optical imaging (Malonek & Grinvald, 1996). In recent
years, however, it has become possible to map the columnarlevel functional organization in primary visual cortex using
ultrahigh field (UHF) fMRI. With a functional resolution of
500 mm in-plane at 7 T, orientation columns could be revealed
in the human primary visual cortex (Yacoub, Harel, & Ugurbil,
2008). While earlier fMRI studies have reported ocular dominance columns (ODCs) in the human cortex (e.g., Cheng,
Waggoner, & Tanaka, 2001; Yacoub, Shmuel, Logothetis, &
Ugurbil, 2007), the fMRI study by Yacoub et al. (2008) is the
first that revealed orientation columns (as well as ODCs)
within human primary visual cortex at a level of detail that
was previously only achievable with invasive optical imaging
studies. The study exploited the high signal-to-noise ratio of
ultrahigh magnetic field (7 T) MRI scanners that allowed
measuring with submillimeter resolution (voxel size:
0.5 mm 0.5 mm 3.0 mm). Furthermore, a spin echo (SE)

BOLD sequence was used in order to minimize the effects
of nonspecific large vessels, especially surface veins, that dominate the signal when using conventional GE BOLD sequences
(Norris, 2012; Yacoub et al., 2007). Because of technical constraints related to the SE sequence, only a single slice in selected
individuals with a straight calcarine sulcus could be used,
a limitation that has been resolved using the 3D GRASE
(gradient and SE) sequence (Feinberg, Harel, Ramanna, Ugurbil, & Yacoub, 2008) in more recent columnar mapping
studies (Zimmermann et al., 2011). The stimuli were presented
in a phase-encoded manner, that is, a continuous display
of whole-field orientations was presented. The colors (red
bluegreenyellowred) in Figure 2(b) indicate the calculated
phase at the stimulus frequency, which denotes the preferred
stimulus orientation of a given voxel. As in optical imaging
(Bonhoeffer & Grinvald, 1991), a total set of orientations (forming a hyper column) appears repeatedly across primary visual
cortex with pinwheels at points of singularity where multiple
orientation preferences converge.
The high spatial resolution of UHF fMRI also provides the
capability to resolve, in a coarse manner, the cortical laminar
structure of V1 and other human cortical areas establishing an
experimental link to cortical microcircuits (Douglas & Martin,
2007; Douglas et al., 1989). Each radially organized circuit
stretches over the cortical layers and organizes feedforward
and feedback outputs and inputs in discrete layers. Specifically,
290
Scalebar = 0.5 mm
(a)
2p
0
(b)
Phase
Figure 2 Ocular dominance and orientation columns in human visual

cortex. a) Red and blue represent voxels that demonstrated preference to
right and left eye stimulation, respectively. b) Depicts the orientation
preference maps from the same cortical areas as their corresponding
ODC maps in a). ODC borders are marked with solid black lines on both
the ODC and orientation maps. (Color bar for orientation map b) :
calculated phase at the stimulus frequency; scale bar: 0.5 mm.). Figure
reprinted with permission from fMRI at High Magnetic Field: Spatial
Resolution Limits and Applications (Volume 1).
bottom-up sensory input arrives primarily at layer IV (granular

layer). In contrast, superficial layers IIII are dominated by topdown projections while the infragranular layers VVI mainly
project back to subcortical structures (Logothetis, 2008). Using
UHF fMRI and a layer modeling technique (Waehnert et al.,
2014; Zimmermann et al., 2011), activity can be sampled at
different depth levels (De Martino et al., 2013; Koopmans,
Barth, Orzada, & Norris, 2011; Olman et al., 2012;
Zimmermann et al., 2014). The currently achievable spatial
resolution is sufficient to distinguish about three cortical
depth levels that roughly correspond to upper layers (backward
connections), middle layers (forward connections), and lower
layers. High spatial resolution fMRI has thus the potential to
reveal different calculations in different layers (Olman et al.,
2012) as well as to reveal causal direction information flow
from laminar response profiles complementing other effective
connectivity approaches that are based on temporal information (Bastos et al., 2012; Roebroeck & Goebel, 2014).
A Crucial Role of V1 in Theories of Perception

Although most of the midbrain projections directly reach primary visual cortex (V1) they form only a small proportion of
the synaptic input in V1 (up to only 5%, Douglas & Martin,
2007). Area V1 is therefore likely involved in many other
cognitive processes such as perceptual organization and visual
attention that are based on lateral and top-down influences. In
recent years, increasing neuroimaging evidence has been accumulated that confirms the crucial role of V1 for perception
demonstrating information feedback of color, shape, and
even auditory information from non-retinal sources to primary
visual cortex (e.g., Bannert & Bartels, 2013; Kok & de Lange,
2014; Smith & Muckli, 2010; Vetter, Smith, & Muckli, 2014).
This neuroimaging data is compatible with the predictive coding theory that assumes that early sensory areas are prepared
with a predictive model for the external incoming information
through cortical feedback from higher cognitive areas (Bastos
et al., 2012; Mumford, 1992; Rao & Ballard, 1999). More
specifically, top-down predictions are generated and sent
downwards to early visual areas in order to enable comparison
of sensory hypotheses (reflecting the expected state of the
world) with incoming bottom-up sensory information. This
comparison results in a prediction error that is used to update
the higher-level representations reducing prediction error at
lower levels in the next round. With its possibility to separate
responses in cortical layers, UHF fMRI will likely play an
important role in the future to link processing in different
layers of the canonical microcircuit to the predictive coding
theory (Bastos et al., 2012). More generally, fMRI at the mesoscopic level of cortical columns and layers will further elucidate
the role of V1 in perception, attention, and visual awareness
(Lamme, Super, Landman, Roelfsema, & Spekreijse, 2000;
Tong, 2003).
Acknowledgments
Supported by the European Research Council (ERC) under
European Unions Seventh Framework Program FP7/
20072013/ERC Grant Agreement Number 269853.

Functional MRI Dynamics; High-Field Acquisition; High-Speed, HighResolution Acquisitions; MRI and fMRI Optimizations and Applications;
and Spatial Resolution of fMRI; INTRODUCTION TO ANATOMY
AND PHYSIOLOGY: Columns of the Mammalian Cortex;
INTRODUCTION TO COGNITIVE NEUROSCIENCE: Prediction and
Expectation; INTRODUCTION TO METHODS AND MODELING:
Computational Modeling of Responses in Human Visual Cortex.
References
Bannert, M. M., & Bartels, A. (2013). Decoding the yellow of a gray banana. Current
Biology, 23, 22682272.
Bastos, A. M., Usrey, W. M., Adams, R. A., Mangun, G. R., Fries, P., & Friston, K. J.
(2012). Canonical microcircuits for predictive coding. Neuron, 76, 695711.
Bonhoeffer, T., & Grinvald, A. (1991). Iso-orientation domains in cat visual cortex are
arranged in pinwheel-like patterns. Nature, 353, 429431.
Brodmann, K. (1909). Vergleichende Lokalisationslehre der Grosshirnrinde. Leipzip:
Johann Ambrosius Barth.
revealed by high-field functional magnetic resonance imaging. Neuron, 32,
359374.
Daniel, P. M., & Whitteridge, D. (1961). The representation of the visual field on the
cerebral cortex in monkeys. Journal of Physiology, 159, 203221.
De Martino, F., Zimmermann, J., Muckli, L., Ugurbil, K., Yacoub, E., & Goebel, R.
(2013). Cortical depth dependent functional responses in humans at 7 T: improved
specificity with 3D GRASE. PloS One, 8, e60514.
Douglas, R. J., & Martin, K. A.C (2007). Mapping the matrix: The ways of neocortex.
Neuron, 56, 226238.
Douglas, R. J., Martin, K. A. C., & Whitteridge, D. (1989). A canonical microcircuit for
neocortex. Neural Computation, 1, 480488.
Dumoulin, S. O., & Wandell, B. A. (2008). Population receptive field estimates in human
visual cortex. NeuroImage, 39, 647660.
Feinberg, D., Harel, N., Ramanna, S., Ugurbil, K., & Yacoub, E. (2008). Submillimeter
single-shot 3D GRASE with inner volume selection for T2-weighted fMRI
applications at 7 Tesla. Proceedings of the International Society for Magnetic
Gennari, F. (1782). De peculiari structura cerebri nonnulisque ejus morbis. Parma
(Italy): Ex Regio.
Goebel, R., Khorram-Sefat, D., Muckli, L., Hacker, H., & Singer, W. (1998). The
constructive nature of vision: Direct evidence from functional magnetic resonance
imaging studies of apparent motion and motion imagery. The European Journal of
Goebel, R., Muckli, L., Zanella, F. E., Singer, W., & Stoerig, P. (2001). Sustained
extrastriate cortical activation without visual awareness revealed by fMRI studies of
hemianopic patients. Vision Research, 41, 14591474.
Haak, K. V., Langers, D. R., Renken, R., van Dijk, P., Borgstein, J., & Cornelissen, F. W.
(2013). Abnormal visual field maps in human cortex: A mini-review and a case
report. Cortex, 56C, 1425.
Hubel, D. H., & Wiesel, T. N. (1968). Receptive fields and functional architecture of
monkey striate cortex. The Journal of Physiology, 195, 215243.
Hubel, D. H., & Wiesel, T. N. (1969). Anatomical demonstration of columns in the
monkey striate cortex. Nature, 221, 747750.
Hubel, D. H., & Wiesel, T. N. (1972). Laminar and columnar distribution of geniculocortical fibers in the macaque monkey. The Journal of Comparative Neurology, 146,
421450.
Hubel, D. H., & Wiesel, T. N. (1977). Ferrier lecture. Functional architecture of macaque
monkey visual cortex. Proceedings of the Royal Society of London. Series B:
Kok, P., & de Lange, F. P. (2014). Shape perception simultaneously up- and
downregulates neural activity in the primary visual cortex. Current Biology, 24,
15311535.
Koopmans, P. J., Barth, M., Orzada, S., & Norris, D. G. (2011). Multi-echo fMRI of the
cortical laminae in humans at 7 T. NeuroImage, 56, 12761285.
Lamme, V. A. F., Super, H., Landman, R., Roelfsema, P. R., & Spekreijse, H. (2000). The
role of primary visual cortex (V1) in visual awareness. Vision Research, 40,
15071521.
Lee, S., Papanikolaou, A., Logothetis, N. K., Smirnakis, S. M., & Keliris, G. A. (2013). A
new method for estimating population receptive field topography in visual cortex.
Leuba, G., & Kraftsik, R. (1994). Changes in volume, surface estimate,
three-dimentional shape and total number of neurons of the human primary
visual cortex from midgestation until old age. Anatomy and Embryology, 190,
351366.
Logothetis, N. K. (2008). What we can do and what we cannot do with fMRI. Nature,
453, 869878.
Lund, J. S. (1988). Anatomical organization of macaque striate visual cortex. Annual
Mumford, D. (1992). On the computational architecture of the neocortex. II. The role of
cortico-cortical loops. Biological Cybernetics, 66, 241251.
Norris, D. G. (2012). Spin-echo fMRI: The poor relation? NeuroImage, 62,
11091115.
291
OKusky, J., & Colonnier, M. (1982). A laminar analysis of the number of neurons, glia,
and synapses in the visual cortex (area 17) of adult macaque monkeys. The Journal
Olman, C., Harel, N., Feinberg, D. A., He, S., Zhang, P., et al. (2012). Layer-specific
fMRI reflect different neuronal computations at different depths in human V1. PloS
One, 7, e32536.
Peters, A., & Jones, E. G. (1984). Classification of cortical neurons. In A. Peters, & E. G.
Jones (Eds.), Cerebral cortex (pp. 107121). New York: Plenum.
Rao, R. P., & Ballard, D. H. (1999). Predictive coding in the visual cortex: A functional
interpretation of some extra-classical receptive-field effects. Nature Neuroscience, 2,
7987.
Rockel, A. J., Hiorns, R. W., & Powell, T. P.S (1980). The basic uniformity in structure
of the neocortex. Brain, 103, 221244.
Roebroeck, A., & Goebel, R. (2014). Computational causal modeling of high-resolution
functional MRI data. In M. S. Gazzaniga (Ed.), The cognitive neurosciences V.
Senden, M., Reithler, J., Gijsen, S., & Goebel, R. (2014). Evaluating population
receptive field estimation frameworks in terms of robustness and reproducibility.
PLoS One, 9, e114054.
Smith, F. W., & Muckli, L. (2010). Nonstimulated early visual areas carry information
about surrounding context. Proceedings of the National Academy of Sciences of the
Tong, F. (2003). Primary visual cortex and visual awareness. Nature Reviews.
Tootell, R. B., Dale, A. M., Sereno, M. I., & Malach, R. (1996). New images from human
visual cortex. Trends in Neurosciences, 19, 481489.
Trampel, R., Ott, D. V. M., & Turner, R. (2011). Do the congenitally blind have a stria of
Gennari? First intracortical insights in vivo. Cerebral Cortex, 21, 20752081.
Vetter, P., Smith, F. W., & Muckli, L. (2014). Decoding sound and imagery content in
early visual cortex. Current Biology, 24, 12561262.
erwachsenen Menschen. Vienna: Springer Verlag.
Waehnert, M. D., Dinse, J., Weiss, M., Streicher, M. N., Waehnert, P., Geyer, S., et al.
(2014). Anatomically motivated modeling of cortical laminae. NeuroImage, 93,
210220.
America, 105, 1060710612.
Yacoub, E., Shmuel, A., Logothetis, N., & Ugurbil, K. (2007). Robust detection of ocular
dominance columns in humans using Hahn Spin Echo BOLD functional MRI at 7
Tesla. NeuroImage, 37, 11611177.
Zilles, K. (1990). Cortex. In G. Paxinos (Ed.), The human nervous system
(pp. 757802). San Diego, CA: Academic Press.
Zimmermann, J., Goebel, R., De Martino, F., van de Moortele, P. F., Feinberg, D.,
Adriany, G., et al. (2011). Mapping the organization of axis of motion selective
features in human area MT using high-field fMRI. PloS One, 6, e28716.
Zimmermann, J., Senden, M., De Martino, F., & Goebel, R. (2014). Cortical depth
dependent connective population receptive fields at sub-millimeter resolution.
Submitted.
Topographic Layout of Monkey Extrastriate Visual Cortex

W Vanduffel, KU Leuven Medical School, Leuven, Belgium; Harvard Medical School, Boston, MA, USA; Massachusetts General
Hospital, Charlestown, MA, USA
Q Zhu, KU Leuven Medical School, Leuven, Belgium
Abbreviations
AD
AF
AL
AM
antSTS
DP
fMRI
FST
HM
IT
LPP
LVF
LVM
MF
midSTS
ML
mPPA
mRSC
MSTv
Anterior dorsal face patch
Anterior fundus face patch
Anterior lateral face patch
Anterior medial face patch
Anterior STS body patch
Dorsal prelunate area
Functional magnetic resonance
imaging
Fundus of superior temporal area
Horizontal meridian
Inferior temporal cortex
Lateral place patch
Lower visual field
Lower vertical meridian
Middle fundus face patch
Middle STS body patch
Middle lateral face patch
Monkey homologue of PPA
Monkey homologue of RSC
Topographic Organization of Macaque

Occipitotemporal Visual Cortex
Primates rely heavily on vision for interaction with the environment that, in monkeys, is interpreted by more than 30
visual areas covering almost half of the cerebral cortex
(Felleman & Van Essen, 1991; Kaas, 1997). The defining
features of these parcellations are based on cyto- and myeloarchitectonics, function and topography, and anatomical
connectivity. Despite several decades of research in dozens of
laboratories, however, the precise number and borders of these
visual areas remain a matter of debate fueled largely by inconsistencies arising from the difficulty of interpolating data across
hundreds of subjects and experiments. Only for a decade or so
has functional imaging in nonhuman primates allowed us to
obtain detailed topographic information in a noninvasive
manner across the entire brains of individual, living subjects
to reveal accurate maps that avoid interpolation issues.
Retinotopic Organization of Occipitotemporal Cortex

The early retinotopic mapping data obtained in monkeys have
confirmed the existence of alternating representations of vertical meridian (VM) and horizontal meridian (HM) between
V1V2, V2V3, and V3V4 (Brewer, Press, Logothetis, & Wandell, 2002; Fize et al., 2003; Vanduffel et al., 2001, 2002). An
HM also defines the anterior border of V4 (Figure 1). Each
of these areas contains a representation of the entire
Medial superior temporal area, ventral

part
MT
Middle temporal area
mTOS
Monkey homologue of TOS
MVPA
Multivoxel pattern analysis
OTd
Dorsal occipitotemporal area
PITd
Posterior inferotemporal dorsal area
PITv
Posterior inferotemporal ventral area
PL
Posterior lateral face patch
PPA
Parahippocampal place area
pPL
Posterior PL face patch
RSC
Retrosplenial cortex
STP
Superior temporal polysensory area
STS
TEO
Temporaloccipital visual area
TOS
Transverse occipital sulcus
UVF
Upper visual field
UVM
Upper vertical meridian
V1, V2, V3, and V4 Visual areas 14
VM
Vertical meridian
contralateral hemifield, with segregated upper and lower quadrants (the so-called split-field representations) in ventral and
dorsal portions of the occipital cortex, respectively. Besides a
foveal and lower field representation in the ventral cortex,
possibly corresponding to architectonic area TEO, these original fMRI mapping studies yielded little evidence for visual field
maps anterior to ventral V4.
Within the visual hierarchy, area V3A is the first region
located exclusively in the dorsal visual cortex containing a
representation of both the upper and lower quadrants surrounded by a VM (complete hemifield). This area is located
on the anectant gyrus and its foveal representation is separated
from the central foveal confluence of areas V1V4. However,
unlike these latter areas, area V3A remains difficult to identify
consistently in all subjects.
A more recent high-resolution retinotopic mapping study
(Kolster et al., 2009) revealed that MT and its immediate
neighbors are organized as a visual field map cluster with a
shared foveal representation surrounded by a semicircular
array of isoeccentricity contours (Figure 1). The existence of
such field map clusters was first described by Wandell, Brewer,
and Dougherty (2005) who proposed it as a general organizational principle with which the extrastriate cortex groups areas
sharing similar functionalities. The shared foveal representation is distinct from the central foveal confluence of V1V4 and
is located in the posterior bank of the STS. Areas MT, MSTv,
and FST each contains a complete contralateral visual field,
while in the original study, only the upper quadrant was
http://dx.doi.org/10.1016/B978-0-12-397025-1.00225-6
293
294
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Topographic Layout of Monkey Extrastriate Visual Cortex
Figure 1 Biologically relevant phase-encoded stimuli and retinotopic organization of the macaque occipitotemporal cortex. Color code and line
conventions: see insets. Stars indicate the positions of the central visual field representations. Green line indicates the eccentricity ridge around the MT
cluster. A, anterior; D, dorsal; RH, right hemisphere. Modified from Janssens, T., Zhu, Q., Popivanov, I. D., & Vanduffel, W. (2014). Probabilistic
and single-subject retinotopic maps reveal the topographic organization of face patches in the macaque cortex. The Journal of Neuroscience,
with permission.
consistently observed in V4t. Another full hemifield ventral to

the MT cluster was identified with a foveal representation
distinct from that of the MT cluster, which we assigned to
PITd, in accordance with Felleman and Van Essen (1991).
Recent retinotopic mapping studies by Kolster, Janssens,
Orban, and Vanduffel (2014) and Janssens, Zhu, Popivanov,
and Vanduffel (2014) used checkerboard and dynamic,
biologically relevant, phase-encoded stimuli, respectively, to
focus on the cortex anterior to V4 and below the MT cluster.
Both studies showed clear evidence of a split hemifield anterior
to the HM of V4, with a contralateral lower (LVF) and upper
visual field (UVF) rostral to dorsal and ventral V4, respectively.
This definition of V4A fits exactly its previous descriptions that,
nonetheless, have yet to win general acceptance (Pigarev,
Nothdurft, & Kastner, 2002; Stepniewska, Collins, & Kaas,

2005; Zeki, 1971). Rostral to V4A and distinct from the MT
cluster, three additional hemifields were found. The first, OTd,
is located between V4A and V4t of the MT cluster. The feature
distinguishing OTd from V4t is a region of higher eccentricity
representations along their common border. To make this
distinction, we assume that regions with low-eccentricity representations and sharing the same polar angle values, but
which are separated from each other by a band of higher
eccentricities, must belong to two different field maps. OTd
shares an LVM with V4A and a UVM with PITd. The latter area
extends more rostrally to an LVM that bordered, at least partially, a more caudoventral field map, PITv. The latter area
shares a UVM with ventral V4A, more caudally. The Janssens
et al. (2014) study showed that V4A, PITd, PITv, and OTd
shared a common foveal representation, distinct from the central foveal confluence (of V1V4) or the MT cluster (V4t, MT,
MSTv, and FST) (Figure 1). Hence, in the monkey occipitotemporal cortex, at least three separate visual field map clusters
can be identified, indicating an evolutionarily preserved and
fundamental organizational principle of the primate visual
cortex (Kolster et al., 2009). As Wandell et al. (2005) proposed,
such clustering may be the most efficient manner of minimizing neural distances between processing modules that require
strong functional interactions. The Janssens et al. (2014) study
also hinted at other regions anterior to the MT and PIT clusters
showing foveal biases. These regions, located in the anterior
bank of the STS (corresponding to STP) and in the middle
temporal gyrus, do not necessarily overlap with regions showing face selectivity, as postulated for the human visual cortex
(Hasson, Levy, Behrmann, Hendler, & Malach, 2002).
Relationship Between Retinotopy and Clustering of

Object-Category Selectivity in Occipitotemporal Cortex
Specific pathologies suggest that the ventral cortex possesses a
modular organization for processing specific objects (e.g., faces
in the case of prosopagnosia) or visual features (e.g., color
in the case of achromatopsia). Corroborating fMRI results
(Epstein & Kanwisher, 1998; Kanwisher, McDermott, &
Chun, 1997; Schwarzlose, Baker, & Kanwisher, 2005) showed
that clustered regions in the human occipitotemporal cortex
indeed preferentially processed specific object classes. This is
particularly the case for faces, bodies, and places. In the succeeding text, we summarize the locations of these categoryselective patches in the monkey and discuss their relationship
to the retinotopic organization of the occipitotemporal cortex.
Faces
Several groups have shown a set of cortical regions that are
preferentially activated by faces compared to nonface objects
(Pinsk et al., 2009; Popivanov, Jastorff, Vanduffel, & Vogels,
2012; Tsao, Freiwald, Tootell, & Livingstone, 2006). Initial
reports defined six such patches: PL, ML, MF, AL, AF, and AD
(with P posterior, M medial, A anterior, L lateral,
F fundus, and D dorsal) (Figure 2). The AF described by
Tsao et al. (2008) likely corresponds to a combination of AF
and AD (Pinsk et al., 2009).
In addition, using concurrent microstimulation and fMRI,
Tsaos group showed that the face patches in the monkey
extrastriate cortex formed an interconnected functional network (Moeller, Freiwald, & Tsao, 2008). Quite surprisingly,
when using dynamic facial expressions, Zhu et al. (2012)
observed an additional face-responsive region lateral to the
face patches (Figure 2).
Although significant progress has been made in understanding the neuronal response characteristics of monkey
face patches (Freiwald & Tsao, 2010; Freiwald et al., 2009;
Hadj-Bouziane et al., 2008; Issa & DiCarlo, 2012; Pinsk et al.,
2009; Tsao et al., 2006), little is known about their topographic
organizations. Relating face patches to retinotopic areas, however, has implications for the neural computations they
295
perform (Freiwald & Tsao, 2010; Halgren et al., 1999). A face

patch within the retinotopic cortex supposedly processes relatively low-level information specific to the location of faces (or
face components) in the visual field. On the other hand,
higher-level processing requiring invariant facial information
is difficult to reconcile with a rigid retinotopic organization.
Processes involved in face identification are thus assumed to
depend on the integration of information converging at higher
levels of the visual system.
Recently, Janssens et al. (2014) described the relationship
between the face patches and the topographic organization of
the extrastriate cortex. They showed that PL is located within
retinotopic area PITd, while ML shows a consistent foveal bias.
In contrast, MF, anterior temporal, and prefrontal monkey face
patches are not retinotopically organized. These authors also
showed evidence for additional, smaller face patches in the
occipital cortex, one posterior to PL within retinotopic area
V4t (pPL, posterior PL) and a second immediately anterior to
MF (aMF) (Figure 2). Additional patches have been reported in
the ventral cortex (Janssens et al., 2014; Ku, Tolias, Logothetis,
& Goense, 2011) but await confirmation in future studies.
Bodies
A number of imaging studies have also shown occipitotemporal areas responding more strongly to images of bodies
and body parts than to faces and other object categories (Bell,
Hadj-Bouziane, Frihauf, Tootell, & Ungerleider, 2009; Bell
et al., 2011; Pinsk et al., 2009; Pinsk, Moore, Richter, Gross,
& Kastner, 2005; Popivanov et al., 2012; Popivanov, Jastorff,
Vanduffel, & Vogels, 2014; Tsao, Freiwald, Knutsen, Mandeville, & Tootell, 2003). These body-selective patches are located
adjacent to the middle and anterior face patches (Popivanov
et al., 2012): The midSTS patch lies between the ML and MF
face patches, while parts of the antSTS patch abut AL medially
and AF more laterally (Figure 2). As with most face patches, the
body patches are located within the nonretinotopic cortex,
except for the most posterior part of the midSTS patch. Interestingly, within the body patches, multivoxel pattern analysis
(MVPA) primarily differentiated between faces and other
object classes (including bodies) instead of the expected distinction between animate and inanimate objects (Popivanov
et al., 2012).
Scenes
Alongside face and body patches, fMRI has also revealed evidence for three specialized scene-processing modules in the
human visual cortex: the parahippocampal place area (PPA),
transverse occipital sulcus (TOS), and retrosplenial cortex
(RSC). In the monkey, Tootells group described sceneselective regions in the dorsal occipital cortex: mTOS in a
region partially overlapping V3A, V4d, or DP; mRSC on the
medial wall near peripheral V1; and mPPA lying lateral to the
ML face patch (Nasr et al., 2011). Kornblith et al. (2013) also
described a scene patch located more lateroventrally within the
OTS, which they call the lateral place patch (LPP) and which
may correspond to mPPA (Figure 2).
Other recent monkey fMRI studies revealed an interesting
pattern of color-selective patches that were paired with the face
296
Figure 2 Clustering of object-category selectivity in the macaque occipitotemporal cortex. Regions (colored area) and coordinates (filled circle)
are displayed on F99 right hemisphere flattened surface. Face, body, and place patches. Modified with permission from Janssens, T., Zhu, Q., Popivanov,
I. D., & Vanduffel, W. (2014). Probabilistic and single-subject retinotopic maps reveal the topographic organization of face patches in the macaque
cortex. The Journal of Neuroscience; Popivanov, I. D., Jastorff, J., Vanduffel, W., & Vogels, R. (2012). Stimulus representations in body-selective
regions of the macaque cortex assessed with event-related fMRI. Neuroimage, 63(2), 723741; Nasr, S., Liu, N., Devaney, K. J., Yue, X., Rajimehr, R.,
Ungerleider, L. G., et al. (2011). Scene-selective cortical regions in human and nonhuman primates. Journal of Neuroscience, 31(39), 1377113785.
AM, mRSC, and LPP: coordinates from Tsao, Schweers, Moeller, and Freiwald (2008); Nasr et al. (2011); and Kornblith, Cheng, Ohayon, and Tsao
(2013). Regions sensitive to motion (beyond the MT cluster) and emotional expressions: from Nelissen, Vanduffel, and Orban (2006) and Zhu et al.
(2012). Coordinates of color-sensitive regions, from Lafer-Sousa and Conway (2013). Retinotopic areas: probabilistic map from Janssens et al. (2014).
Line and symbol (star) conventions as Figure 1. LuS, lunate sulcus; IOS, inferior occipital sulcus; STS, superior temporal sulcus; OTS, occipitotemporal
sulcus; IPS, intraparietal sulcus.
patches (Lafer-Sousa & Conway, 2013; Figure 2). Another

intriguing recent finding showed that intensive training with
artificial symbols resulted in the emergence of categoryselective patches near one of the face patches (Srihasam,
Mandeville, Morocz, Sullivan, & Livingstone, 2012). Hence,
in the nature-versus-nurture debate concerning the formation
of category-selective regions, it appears that both experience
(Srihasam et al., 2012) and genetics, as evidenced by remarkably stable patterns across individuals, are coexisting driving
forces. When the category-selective data obtained in several
research groups (Figure 2) are combined, a striking pattern
emerges whereby multiple processing clusters (supermodules,
each containing patches selective for several object categories)
are repeated several times along the caudorostral axis of IT. In a

manner similar to the visual field map clusters in the retinotopic cortex, this may constitute a general organizational principle in the nonretinotopic cortex through which wiring
distances are minimized across modules sharing a particular
type of functionality (which has yet to be defined).
We predict that imaging capabilities will continue to improve
using, for example, advanced implanted phased array coils
(Janssens et al., 2012) or by moving to superhigh-field scanners
(>7 T) and different imaging contrasts. Such methodological
advances may vastly increase the spatial and temporal resolution
of fMRI up to columnar and laminar levels. Furthermore, it will
become imperative to obtain multiple, independent lines of
evidence, such as combined retinotopic, functional, connectional, and possibly detailed anatomical (e.g., myelin density)
information, in formulating conclusions about specific parcellation schemes (Janssens, Arsenault, Polimeni, & Vanduffel, 2013)
or homologies across species. Hence, in vivo imaging technology
in concert with ex vivo histological tools will further advance our
view concerning the topographic layout of the monkey visual
cortex, providing vital clues to the organizational principles that
triggered its onto- and phylogenetic development. All this information will prove critical to our understanding of the workings
of the human brain.
Acknowledgments
This work received support from Inter-University Attraction
Pole 7/21, Programme Financing PFV/10/008, Impulsfinanciering Zware Apparatuur and Hercules funding of the KU
Leuven, and Fonds Wetenschappelijk OnderzoekVlaanderen
G0A5613N, G043912N, G062208N10, G059309N10,
G083111N10, and K714811N. QZ is postdoctoral fellow of
FWO Vlaanderen. The Martinos Center for Biomedical Imaging
is supported by the National Center for Research Resources
grant P41RR14075. The authors declare that they have no
competing financial interests.

Evolution of the Cerebral Cortex; Functional Organization of the
Primary Visual Cortex; INTRODUCTION TO SOCIAL COGNITIVE
NEUROSCIENCE: Body Perception; Face Perception: Extracting
Social Information from Faces: The Role of Static and Dynamic Face
Information; INTRODUCTION TO SYSTEMS: Face Perception;
Large-Scale Functional Brain Organization; Motion Perception; Primate
Color Vision.
References
Bell, A. H., Hadj-Bouziane, F., Frihauf, J. B., Tootell, R. B., & Ungerleider, L. G. (2009).
Object representations in the temporal cortex of monkeys and humans as revealed
by functional magnetic resonance imaging. Journal of Neurophysiology, 101(2),
688700.
Bell, A. H., Malecek, N. J., Morin, E. L., Hadj-Bouziane, F., Tootell, R. B., &
Ungerleider, L. G. (2011). Relationship between functional magnetic resonance
imaging-identified regions and neuronal category selectivity. Journal of
Neuroscience, 31(34), 1222912240.
Brewer, A. A., Press, W. A., Logothetis, N. K., & Wandell, B. A. (2002). Visual areas in
macaque cortex measured using functional magnetic resonance imaging. Journal of
Neuroscience, 22(23), 1041610426.
Epstein, R., & Kanwisher, N. (1998). A cortical representation of the local visual
environment. Nature, 392(6676), 598601.
Fize, D., Vanduffel, W., Nelissen, K., Denys, K., Chef dHotel, C., Faugeras, O., et al.
(2003). The retinotopic organization of primate dorsal V4 and surrounding areas: A
functional magnetic resonance imaging study in awake monkeys. Journal of
Neuroscience, 23(19), 73957406.
Freiwald, W. A., & Tsao, D. Y. (2010). Functional compartmentalization and viewpoint
generalization within the macaque face-processing system. Science, 330, 845851.
Freiwald, W. A., Tsao, D. Y., & Livingstone, M. S. (2009). A face feature space in the
macaque temporal lobe. Nature Neuroscience, 12, 11871196.
Hadj-Bouziane, F., Bell, A. H., Knusten, T. A., Ungerleider, L. G., & Tootell, R. B. (2008).
Perception of emotional expressions is independent of face selectivity in monkey
297
inferior temporal cortex. Proceedings of the National Academy of Sciences, 105,

55915596.
Halgren, E., Dale, A. M., Sereno, M. I., Tootell, R. B., Marinkovic, K., & Rosen, B. R.
(1999). Location of human face-selective cortex with respect to retinotopic areas.
Issa, E. B., & DiCarlo, J. J. (2012). Precedence of the eye region in neural processing of
faces. The Journal of Neuroscience, 32, 1666616682.
Hasson, U., Levy, I., Behrmann, M., Hendler, T., & Malach, R. (2002). Eccentricity bias
as an organizing principle for human high-order object areas. Neuron, 34(3),
479490 (accessed April 1925).
Janssens, T., Arsenault, J., Polimeni, J. R., & Vanduffel, W. (2013). Definition of the
macaque posterior parietal regions using MRI-based measures of retinotopy,
connectivity, myelination, and function. sfn abstract 64.04/GG12.
Janssens, T., Keil, B., Farivar, R., McNab, J. A., Polimeni, J. R., Gerits, A., et al. (2012).
An implanted 8-channel array coil for high-resolution macaque MRI at 3 T.
NeuroImage, 62(3), 15291536.
Janssens, T., Zhu, Q., Popivanov, I. D., & Vanduffel, W. (2014). Probabilistic and
single-subject retinotopic maps reveal the topographic organization of face patches
in the macaque cortex. The Journal of Neuroscience, 34(31), 1015610167.
Kaas, J. H. (1997). Theories of visual cortex organization in primates. Cerebral Cortex,
12, 91125.
Kanwisher, N., McDermott, J., & Chun, M. M. (1997). The fusiform face area: A module
in human extrastriate cortex specialized for face perception. The Journal of
Neuroscience, 17(11), 43024311.
Kolster, H., Janssens, T., Orban, G. A., & Vanduffel, W. (2014). The retinotopic
organization of macaque occipitotemporal cortex anterior to V4 and caudo-ventral to
the MT cluster. Journal of Neuroscience, 34(31), 1016810191.
Kolster, H., Mandeville, J. B., Arsenault, J. T., Ekstrom, L. B., Wald, L. L., &
Vanduffel, W. (2009). Visual field map clusters in macaque extrastriate visual cortex.
Kornblith, S., Cheng, X., Ohayon, S., & Tsao, D. Y. (2013). A network for scene
processing in the macaque temporal lobe. Neuron, 79(4), 766781.
Ku, S. P., Tolias, A. S., Logothetis, N. K., & Goense, J. (2011). fMRI of the faceprocessing network in the ventral temporal lobe of awake and anesthetized
macaques. Neuron, 70(2), 352362.
Lafer-Sousa, R., & Conway, B. R. (2013). Parallel, multi-stage processing of colors,
faces and shapes in macaque inferior temporal cortex. Nature Neuroscience, 16(12),
18701878.
Moeller, S., Freiwald, W. A., & Tsao, D. Y. (2008). Patches with links: A unified system
for processing faces in the macaque temporal lobe. Science, 320(5881), 13551359.
Nasr, S., Liu, N., Devaney, K. J., Yue, X., Rajimehr, R., Ungerleider, L. G., et al. (2011).
Scene-selective cortical regions in human and nonhuman primates. Journal of
Neuroscience, 31(39), 1377113785.
Nelissen, K., Vanduffel, W., & Orban, G. A. (2006). Charting the lower superior temporal
region, a new motion-sensitive region in monkey superior temporal sulcus. Journal
of Neuroscience, 26(22), 59295947.
Pigarev, I. N., Nothdurft, H. C., & Kastner, S. (2002). Neurons with radial receptive fields
in monkey area V4A: Evidence of a subdivision of prelunate gyrus based on
neuronal response properties. Experimental Brain Research, 145(2), 199206.
Pinsk, M. A., Arcaro, M., Weiner, K. S., Kalkus, J. F., Inati, S. J., Gross, C. G., et al.
(2009). Neural representations of faces and body parts in macaque and human
cortex: A comparative fMRI study. Journal of Neurophysiology, 101(5), 25812600.
Pinsk, M. A., Moore, T., Richter, M. C., Gross, C. G., & Kastner, S. (2005). Methods for
functional magnetic resonance imaging in normal and lesioned behaving monkeys.
Journal of Neuroscience Methods, 143(2), 179195.
Popivanov, I. D., Jastorff, J., Vanduffel, W., & Vogels, R. (2012). Stimulus
representations in body-selective regions of the macaque cortex assessed with
event-related fMRI. NeuroImage, 63(2), 723741.
Popivanov, I. D., Jastorff, J., Vanduffel, W., & Vogels, R. (2014). Heterogeneous singleunit selectivity in an fMRI-defined body-selective patch. Journal of Neuroscience,
34(1), 95111.
Schwarzlose, R. F., Baker, C. I., & Kanwisher, N. (2005). Separate face and body selectivity
on the fusiform gyrus. The Journal of Neuroscience, 25(47), 1105511059.
Srihasam, K., Mandeville, J. B., Morocz, I. A., Sullivan, K. J., & Livingstone, M. S.
(2012). Behavioral and anatomical consequences of early versus late symbol
training in macaques. Neuron, 73(3), 608619.
Stepniewska, I., Collins, C. E., & Kaas, J. H. (2005). Reappraisal of DL/V4 boundaries
based on connectivity patterns of dorsolateral visual cortex in macaques. Cerebral
Cortex, 15(6), 809822.
Tsao, D. Y., Freiwald, W. A., Knutsen, T. A., Mandeville, J. B., & Tootell, R. B. (2003).
Faces and objects in macaque cerebral cortex. Nature Neuroscience, 6(9), 989995.
Tsao, D. Y., Freiwald, W. A., Tootell, R. B., & Livingstone, M. S. (2006). A cortical
region consisting entirely of face-selective cells. Science, 311(5761), 670674.
298
Tsao, D. Y., Schweers, N., Moeller, S., & Freiwald, W. A. (2008). Patches of faceselective cortex in the macaque frontal lobe. Nature Neuroscience, 11(8), 877879.
Vanduffel, W., Fize, D., Mandeville, J. B., Nelissen, K., Van Hecke, P., Rosen, B. R., et al.
(2001). Visual motion processing investigated using contrast agent-enhanced fMRI
in awake behaving monkeys. Neuron, 32(4), 565577.
Vanduffel, W., Fize, D., Peuskens, H., Denys, K., Sunaert, S., Todd, J. T., et al. (2002).
Extracting the third dimension from motion: Differences in human and monkey
intraparietal cortex. Science, 298, 413415.
Wandell, B. A., Brewer, A. A., & Dougherty, R. F. (2005). Visual field map clusters in
human cortex. Philosophical Transactions of the Royal Society of London, Series B:
Biological Sciences, 360(1456), 693707.
Zeki, S. M. (1971). Convergent input from the striate cortex (area 17) to the cortex of the
superior temporal sulcus in the rhesus monkey. Brain Research, 28(2), 338340.
Zhu, Q., Nelissen, K., Van den Stock, J. V., De Winter, F. L., Pauwels, K., de Gelder, B.,
et al. (2012). Dissimilar processing of emotional facial expressions in human and
monkey temporal cortex. NeuroImage, 66C, 402411.
Auditory Cortex
JP Rauschecker, Georgetown University, Washington, DC, USA
Subdivisions of Auditory Cortex

As has been established on the basis of cytoarchitectonics
(Pandya & Sanides, 1972), the auditory region in the superior
temporal cortex of the macaque consists of a core with a
koniocortical appearance (including areas A1 and R), which
is surrounded by a belt. The cytoarchitecture is matched
by distinct histochemical differences (Hackett, 2011; Jones,
Dellanna, Molinari, Rausell, & Hashikawa, 1995; Kaas &
Hackett, 2000) that make the core stand out by dark staining
compared to the belt (with intermediate staining) and another
zone termed parabelt (PB) with very light staining (Hackett,
Stepniewska, & Kaas, 1998; Morel, Garraghty, & Kaas, 1993)
(Figure 1). In humans, cytoarchitectonic criteria have also
been used to identify primary auditory cortex (Morosan et al.,
2001). Functional imaging studies in both humans and monkeys confirm the subdivision of auditory cortex into core, belt,
and PB and reveal further that auditory-responsive regions exist
also in the premotor and prefrontal cortices, inferior parietal
cortex, and cerebellum (Figure 1) (Chevillet, Riesenhuber, &
Rauschecker, 2011; Petkov, Kayser, Augath, & Logothetis,
2006; Poremba et al., 2003).
Early Parallel Processing in the Auditory Cortex

Parallel processing streams in the auditory cortex of rhesus
monkeys start as early as the core areas: Area A1 and the rostral
auditory area (R) are both primary-like areas with neurons
sharply tuned for frequency and tonotopic maps that are
mirror-symmetric to each other. Combined lesion and tracer
studies (Rauschecker, Tian, Pons, & Mishkin, 1997) have
shown that both areas receive input from the principal relay
nucleus of the auditory thalamus, the ventral part of the medial
geniculate nucleus (MGv). By contrast, the caudomedial area
(CM), another area on the supratemporal plane of the
macaque, receives input only from the medial and dorsal subnuclei of the medial geniculate (MGd and MGm). Therefore,
lesions of A1 lead to unresponsiveness of neurons in CM to
tonal stimulation, but not of neurons in area R, which receives
parallel input from MGv.
Selectivity for Band-Passed Noise and Frequency

Sweeps in the Auditory Belt
Areas of the lateral belt (LB) were characterized later
(Rauschecker, Tian, & Hauser, 1995), when it was demonstrated that LB neurons showed an enhanced response to
band-passed noise (BPN) compared to pure tones (Figure 2
(a) and 2(b)). This demonstrated the ability of LB neurons to
integrate over a finite frequency spectrum in a facilitatory
manner. By comparison, this integrative ability is largely

absent in A1 neurons.
The finding of robust auditory responses to BPN stimuli in
LB permitted systematic mapping of that region. BPN bursts
have a clearly defined center frequency and a defined bandwidth. Mapping of the LB along the rostrocaudal dimension
reveals a smooth gradient for best center frequency with two
reversals (Rauschecker & Tian, 2004; Rauschecker et al., 1995).
This means that the LB comprises three cochleotopically organized areas, which were termed the anterolateral, middle lateral, and caudolateral areas (AL, ML, and CL; Figure 2(c)).
LB neurons integrate over frequency in a rather specific way,
which produces the best response at a specific best
bandwidth. The same was later found for the medial belt
(Kusmierek & Rauschecker, 2009).
Neurons with selectivity for the center frequency and bandwidth of BPN bursts could participate in the decoding of
communication sounds, which contain many instances of
BPN bursts in a variety of species (Wang, 2000), including
humans.
Similarly, communication sounds in most species contain
changes in frequency over time (FM sweeps), also sometimes
referred to as chirps or glides. Neurons in the LB are highly
selective for both FM rate and direction (Tian & Rauschecker,
2004): >90% of LB neurons respond to FM stimuli in at least
one direction, but even more striking is the selectivity of LB
neurons for FM rate. Such neurons would be ideal candidates
for the extraction of communication sound features, such as
formant transitions in human speech.
In its functional role, area AL can be likened to visual area
V4, which contains neurons selective for the size of visual
objects (Desimone & Schein, 1987) and plays a pivotal role
in the ventral visual what stream.
Selectivity for Species-Specific Calls

Neurons in the LB have also been tested directly with whole
monkey calls (MC) or components thereof. As expected, MC
stimuli elicited more vigorous responses in LB than pure tones.
MC stimuli were also generally more effective than BPN bursts
but not necessarily more so than FM sweeps, which often
remained the best stimuli.
To quantify MC selectivity in different LB areas, a MC preference index was established in one study (Tian, Reser, Durham,
Kustov, & Rauschecker, 2001). The LB areas differed in their
degree of MC selectivity, as quantified on this basis: Area AL had
the greatest percentage of highly selective neurons, followed by
ML, whereas CL had the smallest percentage of highly selective
neurons. Comparison of MC selectivity showed AL to be more
selective than both ML and CL (p 0.0006 and p 0.0287,
respectively, MannWhitney U-test). This difference was also
http://dx.doi.org/10.1016/B978-0-12-397025-1.00226-8
299
10
+2
+8 +14 +20 +26 +32 +38
ce
ip
ip
ai
ip
la
la
orm
tmp
oi
PG
LC
la
TA
ts
OA
ip
ci
PG
ts
as
TA
ts
tma
TE
oi
10
Auditory
ts
ca
ca
tmp
TH
OB
Auditory and visual
TE
TF
+2
ot
Visual
FC
FD
as
ce
ci
ci
LA
ip
ce
PF
IB
(a)
TF
ts
rh
TG
tma
TE
FD
p
ci
la
FD
p
ai
FDv
la
TA
A
FD
p
FCD
IB
+14
as
ci
LA
ai
la
TE
TH
FD
FBA
TA
ts
+8
ci
LA
+20
rh
TGv
TGd
FF
FL
orm
+26
FDv
FL
+32
FDv
FL
+38
ts
(b)
Figure 1 Auditory cortex defined by functional mapping with 2-deoxyglucose (2-DG) and by histochemical markers in the rhesus monkey. (a)
Schematic summary of cortical areas related to the processing of auditory, auditory plus visual, and visual stimuli (red, pink, and gray areas,
respectively), based on a comparison of the present results with those obtained in an earlier 2-DG visual experiment. Standard coronal sections through
the right hemisphere are at levels indicated by the vertical lines on the lateral surface view (upper left). Numerals refer to number of millimeters
anterior () or posterior () to the interaural plane. Boundaries were determined by visual inspection followed by quantitative examination of the
autoradiographs for the individual cases, and the boundary positions were averaged across the cases within each study. Cortical abbreviations are the
cytoarchitectonic designations of Bonin and Bailey. Sulcal abbreviations: ai, inferior limb of arcuate; as, superior limb of arcuate; ca, calcarine; ce,
central; ci, cingulate; ip, intraparietal; l, lunate; la, lateral; oi, inferior occipital; orm, medial orbital; ot, occipitotemporal; p, principal; rh, rhinal; tma,
anterior middle temporal; tmp, posterior middle temporal; and ts, superior temporal. (Reproduced from Poremba, A., Saunders, R. C., Crane, A. M.,
Cook, M., Sokoloff, L., & Mishkin, M. (2003). Functional mapping of the primate auditory system. Science, 299, 568572.) (b) Brain sections were cut
parallel to the surface of artificially flattened cortex and processed for parvalbumin. A large, dark oval corresponding to the core auditory area I (AI) is
apparent. The rostral core area (R) is also apparent as a dark oval, whereas the rostrotemporal area (RT) is most visible in (b). In (b), note also
slight differences in the darkness of the caudomedial (CM), caudolateral (CL), middle lateral (ML), and anterolateral (AL) areas of the auditory belt. Dots
outline these areas, as well as the lip of the lateral sulcus (LS). An arrowhead marks the diamidino yellow injection site. Scale bar 5 mm.
Reproduced from Hackett, T. A., Stepniewska, I., & Kaas, J. H. (1998). Subdivisions of auditory cortex and ipsilateral cortical connections of the parabelt
auditory cortex in macaque monkeys. Journal of Comparative Neurology, 394, 475495.
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Auditory Cortex
1/3 octave
1/2 octave
1 octave
10
5
0
2 octaves
White noise (WN)
BP Firing rate (spikes per second)
Frequency (kHz)
Pure tone (PT)
301
500
300
200
100
70
AL (n = 31)
ML (n = 89)
CL (n = 16)
p < 0.0001
50
30
20
20 30
A (V) 0
0 100 200 300 400
(a)
50 70 100
200 300 500
PT Firing rate (spikes per second)

(b)
Time (ms)
CS
Is
sts
NCR
8
0.4
6.5
0.35
20
12.5
CL
0.6
10
2
3
1.2
ML
0.35
11
0.8
M
AL
(c)
C
L
Figure 2 Lateral belt areas of the rhesus monkey auditory cortex. The use of band-passed noise bursts (a) leads to significant enhancement of the
response in lateral belt areas (b). This allows mapping of LB areas and reveals a cochleotopic map with two reversals. The three areas were
termed anterolateral (AL), middle lateral (ML), and caudolateral (CL) areas. Reproduced from Rauschecker, J. P., Tian, B., & Hauser, M. (1995).
Processing of complex sounds in the macaque nonprimary auditory cortex. Science, 268, 111114.
highly significant when all three areas were compared together

(p 0.0026, KruskalWallis, df 2).
Spatial tuning in neurons of the LB shows the opposite areal
distribution the highest selectivity is found in CL and lowest
in AL. This has led to the hypothesis that AL and CL, which lie
on opposite ends of the LB along its rostrocaudal extent, form
the beginning of two pathways for the processing of auditory
object and space information (Rauschecker & Tian, 2000; Tian
et al., 2001). Selectivity along the anteroventral stream
increases further towards more anterior locations (Kikuchi,
Horwitz, & Mishkin, 2010; Kikuchi, Horwitz, Mishkin, &
Rauschecker, 2014). This trend extends all the way to the
temporal pole, which is auditorily activated in the macaque
and shows a hemispheric difference for species-specific communication sounds (Poremba et al., 2004).
Auditory Belt Projections to the Prefrontal Cortex

An anatomical study in rhesus monkeys, combined with physiological mapping of LB areas, has demonstrated the existence of
largely separate pathways originating in the LB and projecting to
different target regions in the prefrontal cortex (Romanski et al.,
1999) (see Figure 3). In this study, three different fluorescent
tracers were injected into matched frequency regions of the three
LB areas after these had been physiologically mapped. Injections
into area AL produced label in ventrolateral and orbital regions
of prefrontal cortex, whereas CL injections led to labeling of the
dorsolateral prefrontal cortex (DLPFC). The latter is known for
its involvement in spatial working memory, whereas the former
regions are assumed to participate in object working memory
(Goldman-Rakic, 1996).
302
PFC
8a,46
PP
LIP VIP
10,12
Where
Tpt, TPJ
CPB
PP
46d 8a
46v
CL
CM
MGd
CPB
ML
AL
A1
RPB
Ts1/Ts2
MGv
RPB
What
Parabelt
AL
Belt
Core
Cortex
Thalamus
Ts1/Ts2
Figure 3 Schematic diagram of dual auditory cortical pathways in primates representing auditory object/pattern (what) processing in an anteroventral
projection and auditory space (where) processing in a posterodorsal projection (modified and expanded from Rauschecker, J. P. & Tian, B. (2000).
Mechanisms and streams for processing of what and where in auditory cortex. Proceedings of the National Academy of Sciences of the United States of
America, 97, 1180011806). The projections of the posterodorsal stream are highlighted in solid lines; participating cortical areas are marked with oblique
lines. The anteroventral pathway is shown in dashed lines. Areas that are not uniquely participating in either pathway are shown in dark blocks (primary auditory
cortex, A1) or stippled (middle lateral belt area, ML). Prefrontal connections of the LB are also shown directly on a lateral view of a rhesus monkey brain.
(Reproduced from Romanski, L. M., Tian, B., Fritz, J., Mishkin, M., Goldman-Rakic, P. S., & Rauschecker, J. P. (1999). Dual streams of auditory afferents target
multiple domains in the primate prefrontal cortex. Nature Neuroscience, 2, 11311136.) Abbreviations: MGd, medial geniculate nucleus; dorsal division; MGv,
medial geniculate nucleus, ventral division; CM, caudomedial area; R, rostral area; CL, caudolateral area; CPB, caudal parabelt area; RPB, rostral parabelt area;
Tpt, temporoparietal area; TPJ, temporoparietal junction; PP, posterior parietal cortex; LIP, lateral intraparietal area; VIP, ventral intraparietal area; Ts1, Ts2,
rostral temporal areas of Pandya & Sanides (1972); PFC, prefrontal cortex. Brodmann areas are abbreviated with their respective numbers.
(a)
0.03
0.00
(b)
(c)
Figure 4 Meta-analysis of speech sound representations in the human brain. Results of neuroimaging studies are shown with foci meeting inclusion criteria
for ALE-statistic maps for regions of significant concordance (p < 103). Analyses show an anterior progression with phoneme-length studies showing the
greatest concordance in the left mid-STG ((a); nexp 14), word-length studies showing the greatest concordance in the left anterior STG ((b); nexp 16), and
phrase-length analyses showing the greatest concordance in the left anterior STS ((c); nexp 19). nexp denotes the number of experiments (i.e., the number of
contrasts from independent samples) contributing to each analysis. Reproduced from DeWitt, I. & Rauschecker, J. P. (2012). Phoneme and word recognition
in the auditory ventral stream. Proceedings of the National Academy of Sciences of the United States of America, 109, E505E514.

These projection patterns conform to the physiological
response properties found in the aforementioned study of Tian
et al. (2001), which assigned superior selectivity for auditory
patterns and space to areas AL and CL, respectively. The studies
by Tian et al. (2001) and Romanski et al. (1999), therefore, form
the cornerstones of the theory according to which dualprocessing streams in nonprimary auditory cortex underlie the
perception of auditory objects and auditory space (Rauschecker
& Tian, 2000): according to the tracer results, the anteroventral
pathway originates from area AL of the LB. Recent physiological
data indicate, however, that this pathway may have its origin
already in (the rostral auditory core) area R (Kusmierek, Ortiz, &
Rauschecker, 2012). The anteroventral stream projects further
from AL via the rostral superior temporal gyrus (STG) and
superior temporal sulcus (STS) into the ventrolateral prefrontal
cortex (VLPFC) and forms the main substrate for auditory pattern recognition and object identification. An auditory domain
is found in the VLPFC, in which neurons show responses to
complex, nonspatial sounds, including animal and human
vocalizations (Cohen et al., 2009; Romanski & GoldmanRakic, 2002). By contrast, another pathway projecting caudodorsally into the posterior parietal cortex and DLPFC is thought
to be involved in auditory spatial processing.
Human Imaging Studies

Human neuroimaging studies have confirmed the organization
of auditory cortex into core and belt areas by using the same
types of stimuli as in the monkey studies (Chevillet et al., 2011;
Wessinger et al., 2001). A core region, robustly activated by
pure-tone stimuli, is found along Heschls gyrus. This puretone responsive region in human auditory cortex is surrounded
by belt regions both medially and laterally, which are activated
preferentially by BPN bursts, corresponding to results in nonhuman primates (Kusmierek & Rauschecker, 2009; Rauschecker
et al., 1995). Finally, a region activated by vowel sounds was
identified more anterolaterally (Chevillet et al., 2011).
Various findings from human neuroimaging strongly support
the dual-stream hypothesis of auditory processing: AL areas of
the superior temporal cortex are activated by intelligible speech
(Binder, Liebenthal, Possing, Medler, & Ward, 2004; Scott,
Blank, Rosen, & Wise, 2000) or speech-like sounds (Alain,
Arnott, Hevenor, Graham, & Grady, 2001; Binder et al., 2000;
Maeder et al., 2001), whereas caudal belt and PB areas (projecting up dorsally into posterior parietal cortex) are activated by
auditory spatial tasks. Some of the areas in anterior human STG
do seem to represent species-specific sounds, whereas others may
encode more general auditory object information (Leaver &
Rauschecker, 2010; Zatorre, Bouffard, & Belin, 2004).
Thus, it becomes increasingly clear that behaviorally relevant auditory patterns or objects are discriminated in an
anterior auditory what stream. With regard to speech, it had
long been assumed that these processes are located posteriorly
in a region called the planum temporale or Wernickes area.
These views were largely based on human stroke studies performed more than a century ago (Galaburda, Sanides, &
Geschwind, 1978) (see reviews by DeWitt & Rauschecker,
2013; Rauschecker & Scott, 2009). By contrast, a recent metaanalysis of human speech processing reviewing over 100
303
IFG / vPMC
dPMC
Pre-SMA
z = 61
z = 47
z = 16
z = 3
Figure 5 Brain areas active during anticipatory imagery of familiar

music. Stimuli consists of the final seconds of familiar or unfamiliar tracks
from a compact disk (CD), followed by 8 s of silence. During the silence
following familiar tracks from their favorite CD (anticipatory silence (AS)
following familiar music (FM)), subjects (Ss) reported experiencing
anticipatory imagery for each subsequent track. Stimuli presented during
unfamiliar trials consisted of music that the Ss had never heard before
(unfamiliar music (UM)). Thus, during this condition, Ss could not
anticipate the onset of the following track (nonanticipatory silence (NS)).
While in the MRI scanner, subjects were instructed to attend to the
stimulus being presented and to imagine, but not vocalize, the subsequent
melody where appropriate. Activated brain regions were found in frontal
and premotor regions, including the inferior frontal gyrus (IFG) and
superior frontal gyrus (SFG), presupplementary motor area (pre-SMA),
and dorsal premotor cortex (dPMC) and ventral premotor cortex (vPMC).
Reproduced from Leaver, A., Van Lare, J. E., Zielinski, B. A., Halpern, A., &
Rauschecker, J. P. (2009). Brain activation during anticipation of sound
sequences. Journal of Neuroscience, 29, 24772485.
neuroimaging studies of phoneme, word, and phrase recognition confirms an anterior rather than posterior location of the
Wernickes area (DeWitt & Rauschecker, 2012) (Figure 4).
Given the role of the posterior ST in auditory spatial processing mentioned in the preceding text, the question arises what
if any role this region is playing in speech processing. An
answer is provided by human imaging data that implicate the
auditory dorsal stream in audiomotor integration and control,
including the processing of sequences (Figure 5) (Leaver et al.,
2009; Rauschecker, 2011; Rauschecker & Scott, 2009). It
appears that the dorsal stream creates an interface between
sensory and motor networks and performs a matching operation between predicted outcomes and actual events. While the
computational algorithms in the brain are far from clear, they
must resemble the internal forward models that have revolutionized thinking in motor control and robotics (Kawato,
1999; Wolpert, Ghahramani, & Jordan, 1995).

Anatomy and Physiology of the Mirror Neuron System; Cell Types in
the Cerebral Cortex: An Overview from the Rat Vibrissal Cortex;
Cortical Surface Morphometry; Cytoarchitectonics,
Cytoarchitecture and Maps of the Human Cerebral Cortex; Embryonic
and Fetal Development of the Human Cerebral Cortex; Evolution of the
Cerebral Cortex; Fetal and Postnatal Development of the Cortex: MRI
and Genetics; Functional and Structural Diversity of Pyramidal Cells;
304
Functional Connectivity; Functional Organization of the Primary Visual

Cortex; Lateral and Dorsomedial Prefrontal Cortex and the Control of
Cognition; Quantitative Data and Scaling Rules of the Cerebral Cortex;
Somatosensory Cortex; Sulci as Landmarks; Synaptic Organization of
the Cerebral Cortex; Thalamus: Anatomy; The Brain Stem; The RestingState Physiology of the Human Cerebral Cortex; Topographic Layout of
Monkey Extrastriate Visual Cortex; INTRODUCTION TO CLINICAL
BRAIN MAPPING: Disorders of Audition; Disorders of Language;
Language; INTRODUCTION TO COGNITIVE NEUROSCIENCE:
Bilingualism; Music; Semantic Processing; Speech Perception; Speech
Production; Syntax in the Brain; The Neurobiology of Sign Language;
INTRODUCTION TO SOCIAL COGNITIVE NEUROSCIENCE:
Action Perception and the Decoding of Complex Behavior; DualProcess Theories in Social Cognitive Neuroscience; The Use of Brain
Imaging to Investigate the Human Mirror Neuron System;
INTRODUCTION TO SYSTEMS: Grammar and Syntax; Hubs and
Pathways; Large-Scale Functional Brain Organization; Network
Components; Somatosensory Processing; Speech Sounds.
References
Alain, C., Arnott, S. R., Hevenor, S., Graham, S., & Grady, C. L. (2001). What and
where in the human auditory system. Proceedings of the National Academy of
Binder, J. R., Frost, J. A., Hammeke, T. A., Bellgowan, P. S., Springer, J. A.,
Kaufman, J. N., et al. (2000). Human temporal lobe activation by speech and
nonspeech sounds. Cerebral Cortex, 10, 512528.
Binder, J. R., Liebenthal, E., Possing, E. T., Medler, D. A., & Ward, B. D. (2004). Neural
correlates of sensory and decision processes in auditory object identification.
Chevillet, M., Riesenhuber, M., & Rauschecker, J. P. (2011). Functional correlates of
the anterolateral processing hierarchy in human auditory cortex. Journal of
Cohen, Y. E., Russ, B. E., Davis, S. J., Baker, A. E., Ackelson, A. L., & Nitecki, R. (2009).
A functional role for the ventrolateral prefrontal cortex in non-spatial auditory
cognition. Proceedings of the National Academy of Sciences of the United States of
America, 106, 2004520050.
Desimone, R., & Schein, S. J. (1987). Visual properties of neurons in area V4 of the
macaque: Sensitivity to stimulus form. Journal of Neurophysiology, 57, 835868.
DeWitt, I., & Rauschecker, J. P. (2012). Phoneme and word recognition in the auditory
ventral stream. Proceedings of the National Academy of Sciences of the United
States of America, 109, E505E514.
DeWitt, I., & Rauschecker, J. P. (2013). Wernickes area revisited: Parallel streams and
word processing. Brain and Language, 127, 181191.
Galaburda, A. M., Sanides, F., & Geschwind, N. (1978). Human brain. Cytoarchitectonic leftright asymmetries in the temporal speech region. Archives of Neurology, 35, 812817.
Goldman-Rakic, P. S. (1996). The prefrontal landscape: Implications of functional
architecture for understanding human mentation and the central executive.
Philosophical Transactions of the Royal Society of London, Series B: Biological
Sciences, 351, 14451453.
Hackett, T. A. (2011). Information flow in the auditory cortical network. Hearing
Research, 271, 133146.
Hackett, T. A., Stepniewska, I., & Kaas, J. H. (1998). Subdivisions of auditory cortex and
ipsilateral cortical connections of the parabelt auditory cortex in macaque monkeys.
Jones, E. G., Dellanna, M. E., Molinari, M., Rausell, E., & Hashikawa, T. (1995).
Subdivisions of macaque monkey auditory cortex revealed by calcium-binding
protein immunoreactivity. Journal of Comparative Neurology, 362, 153170.
Kaas, J. H., & Hackett, T. A. (2000). Subdivisions of auditory cortex and processing
streams in primates. Proceedings of the National Academy of Sciences of the United
Kawato, M. (1999). Internal models for motor control and trajectory planning. Current
Kikuchi, Y., Horwitz, B., & Mishkin, M. (2010). Hierarchical auditory processing
directed rostrally along the monkeys supratemporal plane. Journal of Neuroscience,
30, 1302113030.
Kikuchi, Y., Horwitz, B., Mishkin, M., & Rauschecker, J. P. (2014). Processing of
harmonics in the lateral belt of macaque auditory cortex. Frontiers in Neuroscience,
8, 204.
Kusmierek, P., Ortiz, M., & Rauschecker, J. P. (2012). Sound-identity processing in
early areas of the auditory ventral stream in the macaque. Journal of
Kusmierek, P., & Rauschecker, J. P. (2009). Functional specialization of medial auditory
belt cortex in the alert rhesus monkey. Journal of Neurophysiology, 102,
16061622.
Leaver, A. M., & Rauschecker, J. P. (2010). Cortical representation of natural complex
sounds: Effects of acoustic features and auditory object category. Journal of
Leaver, A., Van Lare, J. E., Zielinski, B. A., Halpern, A., & Rauschecker, J. P. (2009).
Brain activation during anticipation of sound sequences. Journal of Neuroscience,
29, 24772485.
Maeder, P. P., Meuli, R. A., Adriani, M., Bellmann, A., Fornari, E., Thiran, J. P., et al.
(2001). Distinct pathways involved in sound recognition and localization: A human
fMRI study. NeuroImage, 14, 802816.
Morel, A., Garraghty, P. E., & Kaas, J. H. (1993). Tonotopic organization, architectonic
fields, and connections of auditory cortex in macaque monkeys. Journal of
Pandya, D. N., & Sanides, F. (1972). Architectonic parcellation of the temporal
operculum in rhesus monkey and its projection pattern. Zeitschrift fur Anatomie und
Entwicklungsgeschichte, 139, 127161.
Petkov, C. I., Kayser, C., Augath, M., & Logothetis, N. K. (2006). Functional imaging
reveals numerous fields in the monkey auditory cortex. PLoS Biology, 4, e215.
Poremba, A., Malloy, M., Saunders, R. C., Carson, R. E., Herscovitch, P., & Mishkin, M.
(2004). Species-specific calls evoke asymmetric activity in the monkeys temporal
poles. Nature, 427, 448451.
Poremba, A., Saunders, R. C., Crane, A. M., Cook, M., Sokoloff, L., & Mishkin, M.
(2003). Functional mapping of the primate auditory system. Science, 299,
568572.
Rauschecker, J. P. (2011). An expanded role for the dorsal auditory pathway in
sensorimotor integration and control. Hearing Research, 271, 1625.
Rauschecker, J. P., & Scott, S. K. (2009). Maps and streams in the auditory cortex:
Nonhuman primates illuminate human speech processing. Nature Neuroscience,
12, 718724.
Rauschecker, J. P., & Tian, B. (2000). Mechanisms and streams for processing of what
and where in auditory cortex. Proceedings of the National Academy of Sciences of
Rauschecker, J. P., & Tian, B. (2004). Processing of band-passed noise in the lateral
auditory belt cortex of the rhesus monkey. Journal of Neurophysiology, 91,
25782589.
Rauschecker, J. P., Tian, B., & Hauser, M. (1995). Processing of complex sounds in the
macaque nonprimary auditory cortex. Science, 268, 111114.
Rauschecker, J. P., Tian, B., Pons, T., & Mishkin, M. (1997). Serial and parallel
processing in rhesus monkey auditory cortex. Journal of Comparative Neurology,
382, 89103.
Romanski, L. M., & Goldman-Rakic, P. S. (2002). An auditory domain in primate
prefrontal cortex. Nature Neuroscience, 5, 1516.
Romanski, L. M., Tian, B., Fritz, J., Mishkin, M., Goldman-Rakic, P. S., &
Rauschecker, J. P. (1999). Dual streams of auditory afferents target multiple
domains in the primate prefrontal cortex. Nature Neuroscience, 2, 11311136.
Scott, S. K., Blank, C. C., Rosen, S., & Wise, R. J. S. (2000). Identification of a pathway
for intelligible speech in the left temporal lobe. Brain, 123, 24002406.
Tian, B., & Rauschecker, J. P. (2004). Processing of frequency-modulated sounds in
the lateral auditory belt cortex of the rhesus monkey. Journal of Neurophysiology,
92, 29933013.
Tian, B., Reser, D., Durham, A., Kustov, A., & Rauschecker, J. P. (2001). Functional
specialization in rhesus monkey auditory cortex. Science, 292, 290293.
Wang, X. (2000). On cortical coding of vocal communication sounds in primates.
97, 1184311849.
Wessinger, C. M., Vanmeter, J., Tian, B., Van Lare, J., Pekar, J., & Rauschecker, J. P.
(2001). Hierarchical organization of the human auditory cortex revealed by
functional magnetic resonance imaging. Journal of Cognitive Neuroscience, 13, 17.
Wolpert, D. M., Ghahramani, Z., & Jordan, M. I. (1995). An internal model for
sensorimotor integration. Science, 269, 18801882.
Zatorre, R. J., Bouffard, M., & Belin, P. (2004). Sensitivity to auditory object features in
human temporal neocortex. Journal of Neuroscience, 24, 36373642.
Vestibular Cortex
C Lopez, Centre National de la Recherche Scientifique (CNRS), Marseille, France; Aix Marseille Universite, Marseille, France
The peripheral vestibular organs are located in the inner ears

and contain two categories of mechanosensitive receptor cells
encoding three-dimensional (3D) head rotations (in the semicircular canals) and translations (in the otolith organs). Receptors in the otolith organs also encode the Earths gravitational
pull, thus providing crucial information about head orientation with respect to gravity. While the contributions of vestibular signals to postural and oculomotor control have been
extensively described (Goldberg et al., 2012), vestibular signals
have only recently been implicated in a growing number of
cognitive and perceptual functions. These functions include
spatial navigation and memory, vertical perception, internal
models of gravity, bodily awareness, and self-consciousness
(Barra et al., 2010; Blanke, 2012; Brandt et al., 2005; Ferre`
et al., 2013; Indovina et al., 2005; Lacquaniti et al., 2013;
Lopez et al., 2008; Mast et al., 2014; Smith, 1997) and are
subtended by neural pathways running from the peripheral
vestibular organs to the vestibular nuclei, thalamus, and cerebral cortex. In the present article, we summarize the current
understanding of the cortical areas receiving vestibular signals,
focusing on the human vestibular cortex (for reviews
about animal vestibular cortex, see Berthoz, 1996; Brandt &
Dieterich, 1999; Fukushima, 1997; Guldin & Grusser, 1998;
Lopez & Blanke, 2011).
Methods to Stimulate Vestibular Receptors in

Neuroimaging Studies
As compared to the wealth of knowledge ascertained about the
primary sensory cortices, data about the human vestibular cortex
are relatively sparse, essentially due to technical difficulties to
provide adequate vestibular stimulation during neuroimaging
recordings. It should be noted that noninvasive investigations of
cortical vestibular processing are technically challenging because
common neuroimaging techniques (fMRI, PET, and magnetoencephalography) preclude head movements and thus the application of natural and physiological vestibular stimulations (angular
and linear head accelerations). Electroencephalography and functional near-infrared spectroscopy can be applied during physical
body movements, but to date have not provided precise information about the location of the human vestibular cortex (Hood &
Kayan, 1985; Karim et al., 2013). Accordingly, stimulation techniques apart from physical body motion have been applied to
artificially stimulate the peripheral vestibular apparatus as early
as the 1980s (Tuohimaa et al., 1983). Three main types of
stimulation have been used (see Figure 1) (review in Lopez
et al., 2012):
Caloric vestibular stimulation (CVS). During CVS, warm or

cold water (or air) is injected in the external auditory canal.
The thermal energy is transmitted to the inner ear and
creates convective motion in the endolymphatic fluid filling the semicircular canals. Depending on the temperature
used, the ensuing motion of the endolymphatic fluid

activates/inactivates mechanosensitive hair cells located
in the crista ampullaris, which generates a sensation that
the head is spinning.
Galvanic vestibular stimulation (GVS). GVS consists of applying a percutaneous current through electrodes placed on
the skin covering the mastoid processes. The current modulates the level of hyperpolarization of the vestibular neuroepithelia, increasing the firing rate in the vestibular
afferents to the side of the cathode and decreasing it to the
side of the anode. GVS stimulates all otolithic and semicircular canal afferents, thus providing more complex sensations of motion than CVS (Fitzpatrick & Day, 2004).
Auditory stimulation. High-intensity clicks at 120 dB as well
as short tone bursts at the frequency of 500 Hz (applied at
102 dB for 10 ms) have been used to stimulate vestibular
receptors. These auditory stimuli mainly activate the neural
pathways originating at the otolithic receptors.
Main Cortical Vestibular Areas

At least ten separate cortical areas responding to vestibular stimulation have been identified in animals using physical vestibular
stimulation or electrical stimulation of the vestibular nerve, and
similar vestibular areas have been showed in humans using the
stimulation methods described in the previous section (see
Figure 2). Vestibular areas identified using CVS, GVS, and auditory stimulation are primarily located in the depth of the lateral
sulcus and in the perisylvian cortex that is, in the posterior
insula, parietal operculum, and temporoparietal junction and
are also distributed in the primary somatosensory cortex, posterior parietal cortex (intraparietal sulcus), frontal cortex, extrastriate cortex, cingulate cortex, and hippocampus. Altogether,
these areas constitute the vestibular cortex, which is a highly
distributed network of multisensory areas (Akbarian et al., 1993;
Grusser et al., 1994; Guldin & Grusser, 1998; Lopez & Blanke,
2011). We describe in the succeeding text the main vestibular
cortical areas.
Parietoinsular Vestibular Cortex

Human neuroimaging data and animal electrophysiological
data converge on the crucial role played by a region located
at the most posterior part of the lateral sulcus in vestibular
processing, an area referred to as the parietoinsular vestibular
cortex (PIVC) in the literature (Figure 2(a)).
The PIVC was originally described by Grusser and colleagues in a series of electrophysiological and anatomical studies conducted in Old World and New World monkeys
(Akbarian et al., 1993, 1994; Grusser et al., 1982, 1990a,
1990b; Guldin et al., 1992, 1993; Guldin & Grusser, 1998).
In Java monkeys, these authors identified neurons responding
http://dx.doi.org/10.1016/B978-0-12-397025-1.00227-X
305
306
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Vestibular Cortex
Caloric vestibular
stimulation (CVS)
Galvanic vestibular
stimulation (GVS)
Injection of cold (0, 4, 10, and 20 C)

or warm (44 C) water or gas into the
external auditory canal.
Application of a percutaneous
current through an anode and a
cathode placed on the opposite
mastoid processes.
Presentation of 102 dB clicks (1 ms

long, at 1 Hz) or short tone bursts
(10 ms long, 500 Hz, at 3 Hz)
through headphones.
P
P
VN
A
H
VN
A
H
U
S
U
S
Air-conducted sounds
preferentially activate saccular
receptors.
Firing rate increases in the

ipsilateral afferents to the cathodal
electrode.
(b)
VN
Warm water increases firing rate

in the afferents of the horizontal
semicircular canals.
(a)
Sounds
(saccular stimulation)
(c)
Figure 1 Methods to stimulate the vestibular receptors in neuroimaging studies. (a) Caloric vestibular stimulation, (b) galvanic vestibular
stimulation, and (c) auditory stimulation are the three main methods used to artificially stimulate the peripheral vestibular organs without physical
head movements. A, H, P: anterior, horizontal, and posterior semicircular canals; S: saccule; U: utricle; VN: vestibular nerve. Reprinted from Lopez, C.,
Blanke, O., & Mast, F. W. (2012). The vestibular cortex in the human brain revealed by coordinate-based activation likelihood estimation metaanalysis. Neuroscience, 212, page 161, Copyright (2012), with permission from Elsevier.
to natural vestibular stimulation (whole-body rotations) in the

parietal operculum, posterior insula, and retroinsular region
(Grusser et al., 1990a). Projection of vestibular-responding
neurons on cytoarchitectonic maps of the lateral sulcus and
insula suggests that the PIVC is mainly located in the retroinsular area (Ri) and granular insular cortex (Ig) in Java monkeys (Grusser et al., 1990a), while studies in squirrel monkeys
revealed that PIVC neurons are mostly located in the Ri, especially in its internal part (Guldin et al., 1992). More recent
investigations into the rhesus monkeys PIVC showed that
responses to animal translations and rotations were mostly
located in the cytoarchitectonic area Ri and at the junction
between the secondary somatosensory cortex, Ri, and Ig
(Chen et al., 2010; Liu et al., 2011).
Several arguments have been advanced to support the idea
that the PIVC is a core area underpinning cortical vestibular
processing: (1) Injections of tracers into the PIVC revealed that
it is strongly interconnected with multiple vestibular areas,
including the primary and secondary somatosensory cortices
and the premotor and posterior parietal cortices (Guldin &
Grusser, 1998); (2) the PIVC sends monosynaptic projections
to the vestibular nuclei, controlling vestibular information
processing in the brainstem (Guldin et al., 1993); and (3) the
PIVC is a multisensory region for coding head-in-space
motion based on vestibular, visual motion, and somesthetic

signals (Grusser et al., 1990b; Shinder & Newlands, 2014).
Because the PIVC has been identified in three species of Old
World and New World monkeys, it is very likely that a human
homologue of the monkey PIVC exists.
During the last twenty years, human neuroimaging studies
have endeavored to identify the human PIVC, but its exact
location is still debated (Lopez & Blanke, 2011). The majority
of fMRI, PET, and magnetoencephalography studies showed
that CVS, GVS, and auditory stimulation activate the posterior
and anterior insula, the parietal operculum, and the temporoparietal junction including the superior temporal gyrus and
inferior parietal lobule (Figures 2(b) and 3) (Bense et al.,
2001; Bottini et al., 1994; Bucher et al., 1998; Della-Justina
et al., 2014; Deutschlander et al., 2002; Dieterich et al., 2003;
Eickhoff et al., 2006; Emri et al., 2003; Fasold et al., 2002;
Hegemann et al., 2003; Indovina et al., 2005; Janzen et al.,
2008; Marcelli et al., 2009; Schlindwein et al., 2008; Tuohimaa
et al., 1983; Vitte et al., 1996; Wang et al., 2008; zu Eulenburg
et al., 2013). All these regions located in the depth of, or
around, the lateral sulcus could be the human equivalent of
the monkey PIVC.
Two recent coordinate-based activation likelihood estimation meta-analyses aimed at better defining the location of the
3aNv
3aHv
2v
VIP MIP
307
6
Periarcuate cortex
7
Intra.
VPS
PIVC
te
al
p.
ter
La
tem
p.
Su
ua
Arc
al
nt r
Ce
MST
Hippocampus
(a)
Posterior insula,
parietal operculum,
and temporoparietal junction
PIVC

area 7, VIP, MIP
areas 2v, 3av
213
4
40
Premotor cortex
area 6v, FEF
39
9
22
19
42
44
46
41
18
45
22
10
17
47
37
11
38
21
20
MT/MST
Anterior insula
312
6
Cingulate gyrus
Vestibular
cingulate
9
region
10
Precuneus
31
23
24
GVS
23
19
30
29
33
18
32
11
12
35
17
18
38
36
28
CVS
Bottini et al., 1994
Vitte et al., 1996
Suzuki et al., 2001
Fasold et al., 2002
et al., 2002
Dieterich et al., 2003
Emri et al., 2003
Hegemann et al., 2003
Indovina et al., 2005
Wang et al., 2008
Marcelli et al., 2009
zu Eulenburg et al., 2013
37
Lobel et al., 1998

Bucher et al., 1998
Bense et al., 2001
Fink et al., 2003
Stephan et al., 2005
Eickhoff et al., 2006
Smith et al., 2012
Della-Justina et al., 2013
19
Sounds
Hippocampus and
parahippocampal gyrus
20
Miyamoto et al., 2007

Schlindwein et al., 2008
Janzen et al., 2008
(b)
Figure 2 Main vestibular areas identified in the monkey and human cerebral cortex. (a) Vestibular areas identified in monkeys include areas 2v, 6v, 7,
and 3av. 3aHv, 3a-hand-vestibular region; 3aNv, 3a-neck-vestibular region; MIP, medial intraparietal area; MST, medial superior temporal area; PIVC,
parietoinsular vestibular cortex; VIP, ventral intraparietal area; VPS, visual posterior sylvian area. Major sulci shown are the arcuate sulcus (arcuate),
central sulcus (central), lateral sulcus (lateral), intraparietal sulcus (intra.), and superior temporal sulcus (sup. temp.). (b) Schematic representation
of vestibular activations revealed by human neuroimaging studies during caloric vestibular stimulation (CVS, red symbols), galvanic vestibular
stimulation (GVS, green symbols), and auditory stimulation (blue symbols). Vestibular areas assumed to be homologous to vestibular areas identified
in animals are indicated in bold letters. FEF, frontal eye fields. Adapted from Lopez, C., & Blanke, O. (2011). The thalamocortical vestibular system
in animals and humans. Brain Research Reviews, 67, page 129, Copyright (2011), with permission from Elsevier.
308
CVS
GVS
Sounds
Figure 3 Meta-analytic definition of the human vestibular cortex.

Summary of vestibular activations identified by coordinate-based
activation likelihood estimation meta-analyses for caloric vestibular
stimulation (CVS; 9 studies), galvanic vestibular stimulation (GVS; 4
studies), and auditory stimulation (3 studies). Activations are plotted
irrespective of the side of the stimulation. Reprinted from Lopez, C.,
Blanke, O., & Mast, F. W. (2012). The vestibular cortex in the human
brain revealed by coordinate-based activation likelihood estimation metaanalysis. Neuroscience, 212, 166, Copyright (2012), with permission
from Elsevier.
core vestibular cortex by calculating common brain activations

evoked by various stimulation methods. Regions responding
to CVS, GVS, and auditory stimulation were all localized in the
lateral sulcus and the adjacent perisylvian cortex (Figure 3).
Lopez et al. (2012) calculated the overlap between these activations and found that only one small area in the retroinsular
region was activated by all three methods of vestibular stimulation, suggesting that it could be part of the human PIVC
(Figure 4(a)). Two other regions of convergence were located
in the parietal operculum and the posterior insula, which
could also form parts of the PIVC. This finding is corroborated
by intracranial stimulations in epileptic patients showing that
vestibular responses can also be evoked during stimulation of
the posterior insula (Isnard et al., 2004; Mazzola et al., 2014).
Using a similar coordinate-based meta-analytic approach of
the vestibular cortex, zu Eulenburg et al. (2012) proposed
that the cytoarchitectonic area OP2 within the parietal operculum may be the human PIVC. Indeed, this region was not only
one of the brain regions showing significant convergence of
activations across several brain imaging studies, but was also
functionally connected with all other vestibular regions identified by the meta-analysis (Figure 4(b)). In conclusion, the
human area OP2, posterior insula, and retroinsular region may
be homologous to the monkey PIVC, originally found at the
junction between these three areas at the posterior end of the

lateral sulcus (Guldin & Grusser, 1998).
Of note, in humans as in monkeys, the PIVC is strongly
multisensory: The posterior insula and parietal operculum
integrate vestibular, tactile, interoceptive, and nociceptive signals and hence constitute an important role in bodily awareness and cognition (Baumgartner et al., 2010; Bottini et al.,
2001; Craig, 2002; Mazzola et al., 2012; zu Eulenburg et al.,
2013). There are so far only few explorations of the PIVC
functions in humans. For example, it has been shown that
this region is involved in predicting the influence of gravitational acceleration on visual motion of objects (e.g., estimating
the time of collision of a ball that is falling down; Indovina
et al, 2005). Another function of the PIVC related to the
perception of gravity is to elaborate a sense of the vertical and
of which way is up (Barra et al., 2010; Brandt et al., 1994), two
perceptual functions that are crucial to maintain the bipedal
and erected human posture. Implications of the PIVC in the
highest aspects of bodily awareness and self-consciousness
have recently been proposed as damage to this region can
impair the sense of unity between the self and the body (inducing out-of-body experiences and apparent reduplications of the
self) and alter the sense of body ownership (Blanke, 2012;
Heydrich & Blanke, 2013; Lopez et al., 2008).
Primary Somatosensory Cortex

Functional neuroimaging studies showed that CVS and GVS
activate the anterior part of the intraparietal sulcus, close to the
postcentral gyrus (Fasold et al., 2002; Lobel et al., 1998; Suzuki
et al., 2001). This region is probably homologous to area 2v, a
vestibular area identified in the monkeys primary somatosensory cortex (Schwarz et al., 1973; Schwarz & Fredrickson,
1971). Vestibular-evoked potentials have been recorded in
area 2v during electrical stimulations of the vestibular nerve,
posterior to the somatosensory representations of the hand
and mouth.
Human neuroimaging studies have also revealed activations in the primary somatosensory cortex in a region that
could be equivalent to area 3aHv (3a-hand-vestibular region)
and area 3aNv (3a-neck-vestibular region) originally
described in monkeys (Bottini et al., 1994; Emri et al., 2003;
Fasold et al., 2002). While area 3aHv is in the somatosensory
dkvist et al., 1974), area
representation of the hand and arm (O
3aNv is in the representation of the neck and the trunk (Guldin
& Grusser, 1998). A functional significance of vestibular projections to the primary somatosensory cortex could be to precisely code the position of the body segments in space through
multisensory convergence and to achieve a better postural
control. Vestibulo-somesthetic convergence in the somatosensory cortex may also account for the influence of CVS, GVS,
and vestibular diseases on tactile and proprioceptive perceptions (Ferre` et al., 2013; Lopez, 2013).
Posterior Parietal Cortex

Functional neuroimaging studies showed that CVS and GVS
activate the posterior part of the intraparietal sulcus, indicating
that a vestibular region exists in the human intraparietal sulcus
that is distinct from area 2v located more anteriorly in the
III
Ri
II
III IV OP2
Ri
IV
OP2
III
309
II
I
cis
CVS and GVS
CVS and sounds
GVS and sounds
CVS and GVS and sounds
(a)
(b)
Figure 4 Human parietoinsular vestibular cortex. (a) Core vestibular cortex in the posterior end of the lateral sulcus identified with coordinate-based
activation likelihood estimation meta-analysis. Spatial overlap between activations related to CVS, GVS, and sounds. Regions in yellow, magenta,
and cyan show spatial overlap between two techniques to stimulate the peripheral vestibular organs. The white area shows the spatial overlap
between three techniques of vestibular stimulation (i.e., caloric vestibular stimulation (CVS), galvanic vestibular stimulation (GVS), and auditory
stimulation). I, II, III: short insular gyri (anterior insula); IV and V: long insular gyri (posterior insula); cis: central insular sulcus; H: Heschls gyrus; Ri:
retroinsular cortex; OP: parietal operculum. Reprinted from Lopez, C., Blanke, O., & Mast, F. W. (2012). The vestibular cortex in the human brain
revealed by coordinate-based activation likelihood estimation meta-analysis. Neuroscience, 212, Page 168, Copyright (2012), with permission from
Elsevier. (b) Functional connectivity of the PIVC. Cytoarchitectonic area OP2 was used as a seeding point to analyze the PIVC functional
connectivity (resting state). The PIVC is functionally connected with the bilateral perisylvian cortex, inferior parietal cortex, primary motor and
somatosensory cortex, area 6, and V5. Reprinted from zu Eulenburg, P., Caspers, S., Roski, C., & Eickhoff, S. B. (2012). Meta-analytical definition and
functional connectivity of the human vestibular cortex. NeuroImage, 60(1), 166, with permission from Elsevier.
somatosensory cortex (Fasold et al., 2002; Lobel et al., 1998;

Suzuki et al., 2001). This intraparietal region is activated by
both otolithic (auditory clicks) and semicircular canal (CVS)
stimulations, suggesting a canalarotolithic convergence in
this region (Miyamoto et al., 2007; Suzuki et al., 2001).
These findings are in line with animal electrophysiological
data showing vestibular-responding neurons in two multisensory areas located in the fundus of the intraparietal sulcus: the
ventral intraparietal area (VIP) and medial intraparietal area
(Bremmer et al., 2002; Chen et al., 2011a, 2011b; Klam & Graf,
2006; Schlack et al., 2005). Most of the electrophysiological
studies in monkeys have been conducted in area VIP, a multimodal area representing 3D body rotations and translations by
combining vestibular and optic flow signals (Chen et al.,
2011b). VIP receives visual inputs from the middle temporal
(MT) area and the medial superior temporal (MST) area and is
strongly interconnected with the motor cortex and PIVC. VIP
neurons also respond to tactile and vestibular stimuli
(Bremmer et al., 2002) and are another important candidate
for multimodal coding of self-motion and for selfconsciousness (Blanke, 2012). Finally, we would like to note
that CVS also activates Brodmann area 7 in both the lateral
superior parietal cortex (Vitte et al., 1996) and precuneus
(Suzuki et al., 2001; Figure 2(b)).
motor cortex and premotor cortex (Bense et al., 2001; Emri

et al., 2003; Fasold et al., 2002; Lobel et al., 1998; Miyamoto
et al., 2007), presumably in relation to the vestibular control of
motor, postural, and oculomotor functions. The supplementary motor area, located in the medial surface of the frontal
cortex, was also activated during CVS and GVS (Della-Justina
et al., 2014; Smith et al., 2012; Wang et al., 2008). Additional
vestibular activations in the dorsolateral prefrontal cortex, as
well as in the middle/superior frontal gyri, may be related to
vestibular processing in the frontal eye fields (FEF) (Bense
et al., 2001; Dieterich et al., 2003; Miyamoto et al., 2007;
Stephan et al., 2005). There is evidence of cortical control of
saccades, smooth-pursuit eye movements, and vestibular nystagmus by the FEF. Studies in animals are in line with neuroimaging studies in humans as they also revealed vestibular
projections to the primary motor cortex and premotor cortex
(area 6; see Figure 2(a)) (Ebata et al., 2004; Fukushima &
Kaneko, 1995; Fukushima et al., 2006; Sugiuchi et al., 2005).
Other electrophysiological studies conducted in monkeys
reported activations more anteriorly in the periarcuate cortex
(Ebata et al., 2004). The functional implications of vestibular
projections to the arcuate cortex and dorsomedial frontal cortex, which coincide with the FEF and the supplementary eye
fields, are the control of saccades and smooth-pursuit eye
movements (Fukushima et al., 2000).
Frontal Cortex
Neuroimaging data showed that both CVS and GVS activate
several regions of the lateral and medial frontal lobes (Figure 2
(b)). Vestibular activations were mainly found in the primary
Extrastriate Visual Cortex

Human neuroimaging studies revealed that the MT gyrus and
neighboring regions in the ventral visual stream are activated
310
by GVS (Bense et al., 2001; Smith et al., 2012; Stephan et al.,

2005) and CVS (Wang et al., 2008). These activations overlap
with the location of the MT/MST complex, which is sensitive to
visual motion. A recent study by Smith et al. (2012) used
functional localizers to differentiate between MST and MT
and showed that only MST was strongly activated by GVS,
whereas MT was not. Activations were found only in the anterior portion of MST, indicating that MST contains at least two
subregions, one that receives vestibular signals and another
that does not. This finding is corroborated by electrophysiological data in monkeys showing that the dorsal portion of
MST (MSTd) contains neurons responding to natural vestibular stimulation and optic flow (Bremmer et al., 1999; Chen
et al., 2008; Gu et al., 2008, 2007; Takahashi et al., 2007).
Thus, the anterior portion of MST found activated during GVS
could be the human homologue of MSTd.
Cingulate Cortex
Vestibular activations have often been reported in the cingulate
cortex, in both its anterior part (Brodmann areas 24/32) and
posterior part (area 23) (Bense et al., 2001; Bottini et al., 1994;
Della-Justina et al., 2014; Dieterich et al., 2003; Fasold et al.,
2002; Miyamoto et al., 2007). Activations of the caudal part of
the anterior cingulate cortex were also evident from a metaanalysis of vestibular activations (Lopez et al., 2012). This
portion of the anterior cingulate cortex has been involved in
motor control (i.e., cingulate motor area) and attention. Cingulate activations reported in humans may be located in a
region homologue to the vestibular cingulate region described
in monkeys (Guldin & Grusser, 1998). Tracer studies showed
that the vestibular cingulate region is connected with the PIVC
and somatosensory area 3a, but there is so far no direct recording of vestibular-responsive neurons in this region.
Hippocampus
Functional MRI studies revealed that CVS activates the hippocampus, the subiculum, and the parahippocampal gyrus (BA
36) (Suzuki et al., 2001; Vitte et al., 1996). These data suggest
vestibular processing in the human hippocampus in relation
with spatial navigation and memory (Brandt et al., 2005). This
finding is in agreement with electrophysiological recordings in
macaque monkeys showing that hippocampal neurons
respond to passive whole-body displacements (OMara et al.,
1994). Further studies demonstrated that the activity of place
cells and head direction cells is strongly dependent on vestibular signals (Smith, 1997) since, for example, experimental
inactivation of the peripheral vestibular system deteriorates
the place and direction selectivity of hippocampal neurons
(Stackman et al., 2002).
Conclusions
Neuroimaging data obtained over the last two decades have
identified a highly distributed vestibular cortical network centered on the PIVC and perisylvian cortex. Yet, neuroimaging
studies used only artificial vestibular stimulations (CVS, GVS,
and auditory stimulation) that have no physiological
equivalent. Future neuroimaging studies should endeavor to

develop more natural methods to stimulate vestibular receptors to achieve a better mapping of the human vestibular
cortex.
Acknowledgments
The research leading to these results has received funding from
the People Programme (Marie Curie Actions) of the European
Unions Seventh Framework Programme (FP7/20072013)
under REA grant agreement number 333607 (BODILYSELF,
vestibular and multisensory investigations of bodily self-consciousness). We thank Steven Gale for correcting this paper.

Insular Cortex; Motor Cortex; Posterior Parietal Cortex: Structural and
Functional Diversity; Somatosensory Cortex; INTRODUCTION TO
METHODS AND MODELING: Meta-Analyses in Functional
Neuroimaging; INTRODUCTION TO SYSTEMS: Autonomic Control;
Oculomotor System; Somatosensory Processing.
References
Akbarian, S., Grusser, O. J., & Guldin, W. O. (1993). Corticofugal projections to the
vestibular nuclei in squirrel monkeys: Further evidence of multiple cortical
vestibular fields. The Journal of Comparative Neurology, 332, 89104.
Akbarian, S., Grusser, O. J., & Guldin, W. O. (1994). Corticofugal connections between
the cerebral cortex and brainstem vestibular nuclei in the macaque monkey. The
Barra, J., et al. (2010). Humans use internal models to construct and update a sense of
verticality. Brain, 133, 35523563.
Baumgartner, U., et al. (2010). Multiple somatotopic representations of heat and
mechanical pain in the operculo-insular cortex: A high-resolution fMRI study.
Bense, S., et al. (2001). Multisensory cortical signal increases and decreases during
vestibular galvanic stimulation (fMRI). Journal of Neurophysiology, 85, 886899.
Berthoz, A. (1996). How does the cerebral cortex process and utilize vestibular signals?
In R. H. Baloh & G. M. Halmagyi (Eds.), Disorders of the vestibular system
(pp. 113125). New York: Oxford University Press.
Blanke, O. (2012). Multisensory brain mechanisms of bodily self-consciousness.
Bottini, G., et al. (1994). Identification of the central vestibular projections in man: A
positron emission tomography activation study. Experimental Brain Research, 99,
164169.
Bottini, G., et al. (2001). Cerebral representations for egocentric space: Functionalanatomical evidence from caloric vestibular stimulation and neck vibration. Brain,
124, 11821196.
Brandt, T., & Dieterich, M. (1999). The vestibular cortex. Its locations, functions, and
disorders. Annals of the New York Academy of Sciences, 871, 293312.
Brandt, T., Dieterich, M., & Danek, A. (1994). Vestibular cortex lesions affect the
perception of verticality. Annals of Neurology, 35, 403412.
Brandt, T., et al. (2005). Vestibular loss causes hippocampal atrophy and impaired
spatial memory in humans. Brain, 128, 27322741.
Bremmer, F., et al. (1999). Linear vestibular self-motion signals in monkey medial
superior temporal area. Annals of the New York Academy of Sciences, 871,
272281.
Bremmer, F., et al. (2002). Visual-vestibular interactive responses in the macaque
ventral intraparietal area (VIP). The European Journal of Neuroscience, 16,
15691586.
Bucher, S. F., et al. (1998). Cerebral functional magnetic resonance imaging of
vestibular, auditory, and nociceptive areas during galvanic stimulation. Annals of

Chen, A., DeAngelis, G. C., & Angelaki, D. E. (2010). Macaque parieto-insular
vestibular cortex: Responses to self-motion and optic flow. The Journal of
Chen, A., DeAngelis, G. C., & Angelaki, D. E. (2011a). A comparison of vestibular
spatiotemporal tuning in macaque parietoinsular vestibular cortex, ventral
intraparietal area, and medial superior temporal area. The Journal of Neuroscience,
31(8), 30823094.
Chen, A., DeAngelis, G. C., & Angelaki, D. E. (2011b). Representation of vestibular and
visual cues to self-motion in ventral intraparietal cortex. The Journal of
Neuroscience, 31(33), 1203612052.
Chen, A., et al. (2008). Clustering of self-motion selectivity and visual response
properties in macaque area MSTd. Journal of Neurophysiology, 100, 26692683.
Craig, A. D. (2002). How do you feel? Interoception: The sense of the physiological
condition of the body. Nature Reviews. Neuroscience, 3, 655666.
Della-Justina, H. M., et al. (2014). Galvanic vestibular stimulator for fMRI studies.
Revista Brasileira de Engenharia Biomedica, 30(1), 7082.
Deutschlander, A., et al. (2002). Sensory system interactions during simultaneous
vestibular and visual stimulation in PET. Human Brain Mapping, 16, 92103.
Dieterich, M., et al. (2003). Dominance for vestibular cortical function in the nondominant hemisphere. Cerebral Cortex, 13, 9941007.
Ebata, S., et al. (2004). Vestibular projection to the periarcuate cortex in the monkey.
Neuroscience Research, 49, 5568.
Eickhoff, S. B., et al. (2006). Identifying human parieto-insular vestibular cortex using
fMRI and cytoarchitectonic mapping. Human Brain Mapping, 27, 611621.
Emri, M., et al. (2003). Cortical projection of peripheral vestibular signaling. Journal of
Fasold, O., et al. (2002). Human vestibular cortex as identified with caloric stimulation
in functional magnetic resonance imaging. NeuroImage, 17, 13841393.
Ferre`, E. R., et al. (2013). The balance of feelings: Vestibular modulation of bodily
sensations. Cortex, 49(3), 748758.
Fitzpatrick, R. C., & Day, B. L. (2004). Probing the human vestibular system with
galvanic stimulation. Journal of Applied Physiology, 96, 23012316.
Fukushima, K. (1997). Corticovestibular interactions: Anatomy, electrophysiology, and
functional considerations. Experimental Brain Research, 117, 116.
Fukushima, K., & Kaneko, C. R. (1995). Vestibular integrators in the oculomotor
system. Neuroscience Research, 22, 249258.
Fukushima, K., et al. (2000). Activity of smooth pursuit-related neurons in the monkey
periarcuate cortex during pursuit and passive whole-body rotation. Journal of
Fukushima, J., et al. (2006). The vestibular-related frontal cortex and its role in smoothpursuit eye movements and vestibular-pursuit interactions. Journal of Vestibular
Research, 16, 122.
Goldberg, J. M., et al. (2012). The vestibular system: A sixth sense. New York: Oxford
University Press.
Grusser, O. J., Pause, M., & Schreiter, U. (1982). Neural responses in the parietoinsular vestibular cortex of alert Java Monkey (Macaca fascicularis). In
Physiological and pathological aspects of eye movements (pp. 251270). The
Hague, Boston, London: Jung.
Grusser, O. J., Pause, M., & Schreiter, U. (1990a). Localization and responses of
neurones in the parieto-insular vestibular cortex of awake monkeys (Macaca
fascicularis). The Journal of Physiology, 430, 537557.
Grusser, O. J., Pause, M., & Schreiter, U. (1990b). Vestibular neurones in the parietoinsular cortex of monkeys (Macaca fascicularis): Visual and neck receptor
responses. The Journal of Physiology, 430, 559583.
Grusser, O. J., et al. (1994). Comparative physiological and anatomical studies of the
primate vestibular cortex. In B. Albowitz et al. (Eds.), Structural and functional
organization of the neocortex (pp. 358371). Berlin: Springer-Verlag.
Gu, Y., Angelaki, D. E., & Deangelis, G. C. (2008). Neural correlates of multisensory cue
integration in macaque MSTd. Nature Neuroscience, 11, 12011210.
Gu, Y., DeAngelis, G. C., & Angelaki, D. E. (2007). A functional link between area MSTd
and heading perception based on vestibular signals. Nature Neuroscience, 10,
10381047.
Guldin, W. O., Akbarian, S., & Grusser, O. J. (1992). Cortico-cortical connections and
cytoarchitectonics of the primate vestibular cortex: A study in squirrel monkeys
(Saimiri sciureus). The Journal of Comparative Neurology, 326, 375401.
Guldin, W. O., & Grusser, O. J. (1998). Is there a vestibular cortex? Trends in
Guldin, W. O., Mirring, S., & Grusser, O. J. (1993). Connections from the neocortex to
the vestibular brain stem nuclei in the common marmoset. Neuroreport, 5,
113116.
Hegemann, S., et al. (2003). Magnetoencephalography during optokinetic and
vestibular activation of the posterior insula. Annals of the New York Academy of
Sciences, 1004, 457464.
311
Heydrich, L., & Blanke, O. (2013). Distinct illusory own-body perceptions

caused by damage to posterior insula and extrastriate cortex. Brain, 136(Pt 3),
790803.
Hood, J. D., & Kayan, A. (1985). Observations upon the evoked responses to natural
vestibular stimulation. Electroencephalography and Clinical Neurophysiology, 62,
266276.
Indovina, I., et al. (2005). Representation of visual gravitational motion in the human
vestibular cortex. Science, 308, 416419.
Isnard, J., et al. (2004). Clinical manifestations of insular lobe seizures: A stereoelectroencephalographic study. Epilepsia, 45, 10791090.
Janzen, J., et al. (2008). Neural correlates of hemispheric dominance and ipsilaterality
within the vestibular system. NeuroImage, 42, 15081518.
Karim, H., et al. (2013). Functional brain imaging of multi-sensory vestibular
processing during computerized dynamic posturography using near-infrared
spectroscopy. NeuroImage, 74, 318325.
Klam, F., & Graf, W. (2006). Discrimination between active and passive head
movements by macaque ventral and medial intraparietal cortex neurons. The Journal
Lacquaniti, F., et al. (2013). Visual gravitational motion and the vestibular system in
humans. Frontiers in Integrative Neuroscience, 7, 101.
Liu, S., Dickman, J. D., & Angelaki, D. E. (2011). Response dynamics and tilt versus
translation discrimination in parietoinsular vestibular cortex. Cerebral Cortex, 21,
563573.
Lobel, E., et al. (1998). Functional MRI of galvanic vestibular stimulation. Journal of
Lopez, C. (2013). A neuroscientific account of how vestibular disorders impair bodily
self-consciousness. Frontiers in Integrative Neuroscience, 7, 91.
Lopez, C., & Blanke, O. (2011). The thalamocortical vestibular system in animals and
humans. Brain Research Reviews, 67, 119146.
Lopez, C., Blanke, O., & Mast, F. W. (2012). The vestibular cortex in the human brain
revealed by coordinate-based activation likelihood estimation meta-analysis.
Lopez, C., Halje, P., & Blanke, O. (2008). Body ownership and embodiment: Vestibular
and multisensory mechanisms. Neurophysiologie Clinique, 38, 149161.
Marcelli, V., et al. (2009). Spatio-temporal pattern of vestibular information
processing after brief caloric stimulation. European Journal of Radiology, 70,
312316.
Mast, F. W., et al. (2014). Spatial cognition, body representation and affective
processes: The role of vestibular information beyond ocular reflexes and control of
posture. Frontiers in Integrative Neuroscience, 8, 44.
Mazzola, L., et al. (2012). Spatial segregation of somato-sensory and pain activations in
the human operculo-insular cortex. NeuroImage, 60(1), 409418.
Mazzola, L., Lopez, C., Faillenot, I, Chouchou, F., Mauguie`re, F., & Isnard, J. (2014).
Vestibular responses to direct stimulation of the human insular cortex. Annals of
Neurology, 76(4), 609619.
Miyamoto, T., et al. (2007). Saccular stimulation of the human cortex: A functional
magnetic resonance imaging study. Neuroscience Letters, 423, 6872.
OMara, S. M., et al. (1994). Neurons responding to whole-body motion in the primate
hippocampus. The Journal of Neuroscience, 14, 65116523.
Odkvist, L. M., et al. (1974). Projection of the vestibular nerve to the area 3a arm field
in the squirrel monkey (Saimiri sciureus). Experimental Brain Research, 21,
97105.
Schlack, A., et al. (2005). Multisensory space representations in the macaque ventral
intraparietal area. The Journal of Neuroscience, 25, 46164625.
Schlindwein, P., et al. (2008). Cortical representation of saccular vestibular stimulation:
VEMPs in fMRI. NeuroImage, 39, 1931.
Schwarz, D. W.F, Deecke, L., & Fredrickson, J. M. (1973). Cortical projection of group I
muscle afferents to areas 2, 3a, and the vestibular field in the rhesus monkey.
Schwarz, D. W.F, & Fredrickson, J. M. (1971). Rhesus monkey vestibular cortex: A
bimodal primary projection field. Science, 172, 280281.
Shinder, M. E., & Newlands, S. D. (2014). Sensory convergence in the parieto-insular
vestibular cortex. Journal of Neurophysiology, 111, 24452464.
Smith, P. F. (1997). Vestibular-hippocampal interactions. Hippocampus, 7, 465471.
Smith, A. T., Wall, M. B., & Thilo, K. V. (2012). Vestibular inputs to human motionsensitive visual cortex. Cerebral Cortex, 22(5), 10681077.
Stackman, R. W., Clark, A. S., & Taube, J. S. (2002). Hippocampal spatial
representations require vestibular input. Hippocampus, 12, 291303.
Stephan, T., et al. (2005). Functional MRI of galvanic vestibular stimulation with
alternating currents at different frequencies. NeuroImage, 26, 721732.
Sugiuchi, Y., et al. (2005). Vestibular cortical area in the periarcuate cortex: Its afferent
and efferent projections. The Annals of the New York Academy of Sciences, 1039,
111123.
312
Suzuki, M., et al. (2001). Cortical and subcortical vestibular response to caloric
stimulation detected by functional magnetic resonance imaging. Brain Research.
Cognitive Brain Research, 12, 441449.
Takahashi, K., et al. (2007). Multimodal coding of three-dimensional rotation and
translation in area MSTd: Comparison of visual and vestibular selectivity. The
Tuohimaa, P., et al. (1983). Studies of vestibular cortical areas with short-living 15O2
isotopes. ORL: Journal for Oto-Rhino-Laryngology and Its Related Specialties, 45,
315321.
Vitte, E., et al. (1996). Activation of the hippocampal formation by vestibular stimulation:
A functional magnetic resonance imaging study. Experimental Brain Research, 112,
523526.
Wang, Z., et al. (2008). Why cold water delays the onset of vestibular vertigo An
functional MRI study. European Journal of Radiology, 67(3), 459465.
Zu Eulenburg, P., et al. (2012). Meta-analytical definition and functional connectivity of
the human vestibular cortex. NeuroImage, 60(1), 162169.
Zu Eulenburg, P., et al. (2013). Interoceptive and multimodal functions of the operculoinsular cortex: Tactile, nociceptive and vestibular representations. NeuroImage, 83,
7586.
Gustatory System
TC Pritchard, The Pennsylvania State University College of Medicine, Hershey, PA, USA
Introduction
Animals meet their energy needs for healthy development and
growth by ingesting food. In the wild, where the line between
food and nonfood items is often blurred and survival hangs in
the balance, animals must distinguish safe and nutritious
foods from toxic and potentially lethal substances. The gustatory system plays a key role in this process. The elaborate
process of taste perception begins when chemicals released
from foods and beverages bind to taste buds receptors that
line the oral cavity. After this information is transmitted to
the brain, neural circuitry located in the caudal hindbrain
makes a swift decision to either accept (swallow) or reject
(expectorate) the substance. Reflexive orofacial movements
complete the task of acceptance or rejection. Other brainstem
circuits manage autonomic reflexes that release saliva, gastric
enzymes, and insulin during ingestion. The forebrain completes the sensory analysis of taste quality and then uses this
highly processed gustatory information to support more complex taste-guided behaviors. These motivated behaviors are
shaped by multisensory input, including feedback from the
internal milieu regarding the long- and short-term nutritional
needs of the animal. This article describes the organization of
the gustatory system from its humble beginning as an array of
chemoreceptors in the mouth to its participation in sophisticated reward-based behaviors in the cerebral cortex. This article
emphasizes the gustatory system of nonhuman primates,
which represents the best model available for the taste system
of humans.
Taste Bud Distribution and Innervation

Taste perception begins when aqueous-based chemicals stimulate the taste buds located in the oral cavity. Taste buds are
small, goblet-shaped structures that contain a dozen or more
receptor, sustentacular (support), and basal (stem) cells
(Figure 1). The sustentacular cells provide tropic support for
the taste receptor cells, which succumb to the harsh environment of the oral cavity every 1014 days. New taste receptor
cells develop from the basal cells that line the perimeter of the
taste bud. The apical tip of each taste receptor cell is capped by
numerous microvilli which protrude into the oral cavity
through a small pore. Taste transduction takes place when
food/beverage-derived molecules bind to the receptor proteins
or pass through the ion channels that line the microvillar
membrane. The epithelial surfaces of the soft palate, epiglottis,
uvula, larynx, and upper esophagus are also studded with the
pores of the underlying taste buds. Because the extralingual
taste buds help protect the airway, they do not contribute to
the conscious perception of taste.
Taste buds on the tongue are embedded within papillae
that are located on the anterior, lateral, and posterior parts of
its dorsal and lateral surfaces. Fungiform papillae are

mushroom-shaped structures located on the anterior twothirds of the tongue. On average, each fungiform papilla contains approximately six taste buds whose microvilli access the
oral cavity through their respective taste pores. The foliate
papillae, by comparison, are a series of epithelial folds along
the lateral margins of the tongue near the palatoglossal arch.
Because the taste pores are within the walls of the foliate clefts,
sapid stimuli must enter these trenches to reach the taste receptors. The foliates location inboard of the molars enables the
mechanical action of chewing to force fluid into the clefts and
down to the taste pores. The circumvallate papillae consist of
711 circular, squat plugs arranged as a chevron across the
midline of the posterior tongue. Taste buds are embedded
within the papillar and epithelial walls of the trench that
surrounds each circumvallate papilla. Abrasion of the posterior
tongue against the hard palate during mastication opens the
trench and directs fluids to the taste buds.
Lingual and extralingual taste buds are innervated by the
facial, glossopharyngeal, and vagus nerves. Taste receptors on
the anterior two-thirds of the tongue, part of the soft palate,
and the anterior foliate papillae are innervated by two
branches of the facial nerve: chorda tympani and greater superficial petrosal. Taste buds on the posterior third of the tongue,
the posterior foliate papillae, part of the soft palate, and the
epiglottis, uvula, and pharynx are supplied by the glossopharyngeal nerve and possibly the vagus nerve. Neural innervation
of the larynx is provided by the vagus nerve.
The Central Nervous System

Medulla and Pons
In all mammalian species studied to date, including humans,
gustatory information is conveyed to the nucleus of the solitary
tract (NST) in the medulla by the facial, glossopharyngeal, and
vagus nerves. The NST consists of rostral gustatory and caudal
visceral divisions. Axons of the facial nerve terminate in the
rostral NST, immediately anterior to the terminal zone of the
glossopharyngeal nerve. The vagus nerve, whose small taste
contingent is vastly outnumbered by sensory axons originating
in the thoracic, abdominal, and pelvic viscera, terminates in
the caudal half of the NST. Because axons of the facial, glossopharyngeal, and vagus nerves terminate in the NST from anterior to posterior, the spatial organization of taste within the
NST resembles that of the tongue. Electrophysiological recordings in animals have confirmed that neurons in the rostral NST
respond to sapid stimulation of the anterior tongue and soft
palate while more caudal areas of the NST are activated by
gustatory stimulation of the posterior tongue. Although there
is some interspecies variation in the anatomical organization
of the NST, these differences are minor (Pritchard, 2012).
Given the strength of the comparative literature, it is safe to
http://dx.doi.org/10.1016/B978-0-12-397025-1.00228-1
313
314
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Gustatory System
say that the anatomical organization of the gustatory system is

highly conserved as far centrally as the NST of the medulla. For
this reason, it was unexpected to find significant differences in
the efferent projections of the NST in primate and subprimate
species (Figure 2).
In rats, hamsters, mice, and cats, neurons in both the rostral
gustatory and caudal visceral regions of the NST project to the
pontine parabrachial nucleus (PBN) via the central tegmental
tract (CTT). The PBN is an oval-shaped band of neurons that
frames the brachium conjunctivum as it courses through the
rostrodorsal pons. Not surprisingly, numerous electrophysiological studies have demonstrated that neurons in the PBN
respond to sapid stimulation of the tongue. Tracing experiments have shown that taste neurons in the PBN of these
species project to a group of neurons that form the medial tip
of the ventroposteromedial (VPM) nucleus of the thalamus.
Because these neurons are small, this area is known as the
parvicellular division of VPM or VPMpc. The thalamus is
such an important relay for ascending sensory information,
every sensory system that projects to the neocortex passes
through a region of the thalamus dedicated to that sensory
modality.
In primates, axons originating from the neurons in the
caudal, visceral part of the NST enter the CTT and terminate
in the ipsilateral PBN. Electrophysiological studies have confirmed that PBN neurons respond to visceral and nociceptive
stimulation. Although the ascending projections from the rostral, gustatory pole of the NST also ascend through the CTT,
they bypass the PBN and terminate in the ipsilateral thalamic
relay, VPMpc (Beckstead, Morse, & Norgren, 1980). Consistent
with the anatomical data, there is no electrophysiological evidence that PBN neurons respond to gustatory stimulation, but
this issue should be investigated more thoroughly. Given its
role as a visceral relay, it is not surprising that neurons in the
PBN project to limbic/autonomic nuclei such as the hypothalamus, the amygdala, and the bed nucleus of the stria terminalis
rather than VPMpc. In summary, the NST and VPMpc both
have gustatory and visceral subdivisions in subprimate species,
but in nonhuman primates and presumably humans, the PBN
is strictly a visceral relay. The presence of a direct NST-VPMpc
projection in nonhuman primates represents a significant species difference, the implication of which is not understood.
The projection from the NST to VPMpc in nonhuman primates ascends ipsilaterally. A number of studies have examined
the brainstem taste pathways in patients who have had cardiovascular accidents or sustained focal damage from multiple
sclerosis. Lesion variability and the close proximity of the
PBN, the CTT, and the medial lemniscus have compromised
many of these studies and made interpretation of these data
difficult. The challenge for these investigators has been to
determine whether the damaged area includes the PBN itself,
the afferent or efferent projections of the PBN, or the ascending
axons from NST neurons that bypass the PBN en route to the
thalamus. At present, the weight of evidence supports an ipsilateral trajectory for the ascending taste pathway in humans.
Thalamus
Figure 1 Diagram of a mammalian taste bud (lateral view).
Rodent
Primate
OFC
As described earlier, anatomical tract-tracing and electrophysiological experiments have demonstrated that the mammalian
relay for taste in the thalamus is located immediately medial to
the representation of oral touch and temperature. The significant interspecies differences in the ascending taste pathway
between primate and non-primate species in the caudal brainstem have had no impact on the location of the thalamic taste
area. Although the same nucleus serves as the thalamic relay in
all mammalian species, there is no universally accepted name.
In nonhuman primates, it is called VPMpc. The clinical literature places the thalamic taste relay in the homologous region
in humans.
Insula
VPMpc
Ventral forebrain
PBN
Facial
Glossopharyngeal
Vagus
NST
Figure 2 Schematic diagram of the taste circuitry of the rodent and
primate.
Cortex
Investigators using anatomical techniques have shown that
neurons in the thalamic gustatory relay, VPMpc, project to a
small crescent of cortex in the rostral insula and adjacent inner
operculum (Pritchard, Hamilton, Morse, & Norgren, 1986).
Electrophysiological experiments in several species have
confirmed that the insularopercular cortex contains tasteresponsive neurons. Although several older studies placed
primary taste cortex in humans near the cortical somatosensory
representation of the oral cavity at the foot of the postcentral
gyrus, these findings have been refuted by more recent reports.
The most authoritative study, to date, describes a series of

patients who had sustained a brain injury, including several
with damage to the anterior insula (Motta, 1959). One patient
reported a profound hypogeusia (taste weakness) on the right
side of the tongue after a hunting accident in which single
pellet of lead shot compromised the circulation to the rostral
insula on the right side. These and other studies in humans and
nonhuman primates demonstrate that taste information does
not cross during its ascent from tongue to cortex. After gustatory information reaches primary taste cortex, it is distributed
to the ventral and posterior insulae. Projections to the language
areas of the left hemisphere provide the basis for identification
of taste quality. For identification of taste quality following
sapid stimulation of the right side of the tongue, the information crosses to the left hemisphere after passing through primary taste cortex (Figure 3).
The basic blueprint for sensory processing is that the analysis performed by primary sensory cortex is elaborated upon,
sequentially, by secondary and tertiary sensory cortices. Using
anatomical data as a guide, the higher order taste cortices are
located in the ventral insula, the adjacent agranular insular
cortices, and the caudal orbitofrontal cortex (OFC), which
forms the ventral surface of the frontal lobe. Although the
interleaved nature of the cortical circuitry in these areas
makes it difficult to describe the point-to-point progression
of taste information through these areas, it is clear that the
taste signal gradually leaves areas traditionally defined as sensory cortex and enters association cortices more closely aligned
with emotion, reward, and executive action.
Cortical Processing of Taste Information

Modern noninvasive imaging techniques such as functional
magnetic resonance imaging (fMRI), positron emission
tomography (PET), and magnetoencephalography (MEG)
have ushered in a new and exciting era of brain exploration.
These techniques permit investigators to visualize human brain
anatomy in exquisite detail, and in some cases, measure brain
function while subjects learn a skill or perform a task. Most
Frontal lobe
Inner operculum
Insula
Temporal lobe
Figure 3 Schematic diagram of a coronal section of a monkey brain at

the anteriorposterior level of the rostral insula. The insert on the right
shows the grainy distribution of terminal label within primary taste
cortex following a tracer injection in the thalamic taste nucleus, VPMpc.
The dense label at the junction between the dorsal insula and the
inner operculum has been called the gustatory macula, or focal
point for cortical taste processing. Tracer spread ventrally and laterally
into the body of the insula and inner operculum, respectively,
indicates that these areas receive direct but lighter projections from the
thalamus. The lack of terminal label in the ventral insula means that
taste neurons located there are outside the classically defined boundary
of primary taste cortex.
315
scientists who have used these imaging techniques to examine

the gustatory system have emphasized cortical function. Collectively, these studies have blurred the line between sensory
processing of taste and the site where sensory information
serves taste-guided behavior. For example, the insula, besides
serving as primary taste cortex, is heavily invested in perception
of positive and negative emotional states, especially facial
expressions related to ingestive behavior. The insula is particularly responsive to facial expressions that signal disgust. Sensitivity to facial expressions of disgust may be a protective
mechanism that builds upon the well-established ability of
the gustatory brainstem to protect us from poisonous and
toxic substances. The case of a patient who suddenly stopped
smoking tobacco after suffering an insular stroke suggests that
this area also plays a role in addictive behavior.
Noninvasive imaging methodology also has been used to
investigate how taste contributes to the higher order functions
associated with the frontal lobe such as personality, memory,
emotion, social inhibition, and planning and execution of
behavior. In the realm of taste, some areas of the OFC have
been implicated in flavor perception and reward comparison.
Flavor and taste are distinct sensations that the lay public
often uses interchangeably but incorrectly to describe the sensations associated with food. Taste is the percept that originates
solely from the taste buds in the oral cavity, and for this reason,
taste perception is limited in scope to a few basic qualities such
as salty, sweet, sour, and bitter, and perhaps two or three others
like fat and glutamate. Flavor, on the other hand, is an emergent sensation consisting of taste, smell, temperature, touch,
and even nociceptive information. This sensory syncytium
creates the perceptual richness we normally associate with
foods and beverages. Although taste and touch are closely
affiliated in many parts of the brain, convergence of olfactory
and gustatory information occurs for the first time in the OFC.
Some neurons in the OFC respond to coincident stimulation
of these independent sensory modalities. For this reason, some
have speculated that flavor perception takes place in the OFC.
The OFC also plays a key role in reward-guided behavior.
Life requires that choices be made; some are bad, some are
good, and some are better. The OFC sorts through the available
choices by comparing their respective rewards or by considering the costs and benefits of each. Both electrophysiological
studies in animals and noninvasive images studies in humans
have shown that neural activity in parts of the caudal OFC
reflects the available reward options. These rewards may
involve positive and negative gustatory reinforcers such as
food or secondary reinforcers such as money. The OFC, by
weighing the reward value linked to the different choices,
helps us choose the behavior that leads to the best outcome
(Hosokawa et al., 2007). In life, the calculus is often complicated. Sometimes the choice is between two behaviors that
have different reward probabilities and payoffs. Consider
poker. When should a player attempt to draw an inside
straight? A statistician may say never, but in reality a poker
player may consider multiple factors including the size of the
pot, and whether s/he has been winning or is desperate for a
win. Gambling paradigms (not necessarily poker) are ideal for
laboratory testing because the stakes, the odds, and the outcomes can be precisely calculated. If the experimenter changes
the rules of the game, normal subjects will adjust their strategy
316
in order to maximize their return. Patients with damage to the

OFC, however, often make poor choices. If they do develop a
winning strategy, they struggle to adjust when the rules of the
game change. Outside of the laboratory, these are the folks
who make poor personal and professional decisions because
they do not weigh the costs, the benefits, the odds of winning,
and possible fluctuating reward values. In life, fluctuating
reward values are the rule rather than the exception. For example, the value of a food reward varies according to the subjects
hunger status. When a person drinks fruit juice to the point of
satiety, that juice, but not other beverages, loses its value as a
reinforcer. This phenomenon, called sensory-specific satiety, is
observed at the neuronal level in the OFC and illustrates that
reward is not a static commodity. One of the main functions of
the OFC is to maximize reward attainment by promoting
sound decision-making.
Summary
The multistep process of gustatory perception begins when
sapid stimuli bind to taste receptors located on the microvilli
of the taste buds that protrude into the oral cavity. Primary
afferent fibers that synapse on the taste receptor cells project to
neurons located in the rostral half of the NST in the medulla. In
rodents, taste information is relayed from the NST to the PBN,
which in turn, projects to VPMpc. In nonhuman primates and
presumably humans, the ascending projections from the NST
bypass the PBN. Gustatory neurons in VPMpc project to the
rostrodorsal insula and inner operculum, which serves as primary taste cortex. Neurons in primary taste cortex project to
secondary cortical areas in the ventral and agranular insulae.
Projections arising from these secondary taste areas to the OFC
may provide the anatomical basis for perception of flavor as
well as the role that taste information plays in reward evaluation and goal-seeking behavior.
Taste Processing in the Hypothalamus and Amygdala

The gustatory system guides feeding behavior through its projections to the hypothalamus and the amygdala. In rodents,
gustatory projections to the hypothalamus and amygdala arise
from the PBN; in monkeys and presumably humans, the routes
are less certain but they appear to originate in the insula. The
hypothalamus and the amygdala, rather than contributing to
sensory coding per se, are more heavily invested in feeding
behavior, broadly defined.
Hypothalamic neurons that respond to the gustatory,
olfactory, and visual attributes of food are in close proximity
to cells that respond to fluctuating blood glucose levels. Their
proximity to one another enables the hypothalamus to monitor
the chemosensory nature of food in the context of the animals
internal milieu, in general, and their hunger/satiety status, in
particular. Not surprisingly, the activity of some hypothalamic
neurons is modulated by the animals level of hunger/satiety.
The amygdala also monitors the internal and external
worlds so that need-driven behaviors, such as feeding, are
managed in the context of emotional and motivational states.
Through its connections with other areas of the limbic system
and the OFC, the amygdala contributes to the emotive aspects
of taste and feeding.

Development of the Diencephalon; Insular Cortex; The Olfactory
Cortex; INTRODUCTION TO COGNITIVE NEUROSCIENCE:
Neuroimaging of Economic Decision-Making; Reward Processing;
Value Representation; INTRODUCTION TO SYSTEMS: Functional
Brain Imaging of Human Olfaction; Reward; Taste, Flavor, and
Appetite.
References
Beckstead, R. M., Morse, J. R., & Norgren, R. (1980). The nucleus of the solitary tract in
the monkey: Projections to the thalamus and brain stem nuclei. Journal of
Hosokawa, T., Kato, K., Inoue, M., & Mikami, A. (2007). Neurons in the macaque
orbitofrontal cortex code relative preference of both rewarding and aversive
outcomes. Neuroscience Research, 57, 434445.
Motta, G. (1959). I centri corticali del gusto. Bulletino delle Scienze Mediche, 131,
480493.
Pritchard, T. C. (2012). Gustatory system. In G. Paxinos & J. Mai (Eds.), The human
nervous system (pp. 11871218). (3rd ed.). New York: Elsevier.
Pritchard, T. C., Hamilton, R. B., Morse, J. R., & Norgren, R. (1986). Projections from
thalamic gustatory and lingual areas in the monkey, Macaca fascicularis. Journal of
Posterior Parietal Cortex: Structural and Functional Diversity

S Caspers, Institute of Neuroscience and Medicine (INM-1), Julich, Germany
Glossary
PEm Magnocellularis subregion of superior parietal area

PE in von Economo and Koskinas (1925).
PEp Parvocellularis subregion of superior parietal area PE
in von Economo and Koskinas (1925).
PEg Gigantopyramidalis subregion of superior parietal
area PE in von Economo and Koskinas (1925).
PF Inferior parietal area PF on supramarginal gyrus (rostral
main inferior parietal area in von Economo and
Koskinas (1925)).
PFcm Inferior parietal area PFcm on supramarginal gyrus
(columnata magnocellularis subregion of PF in von
Economo and Koskinas (1925)).
PFm Inferior parietal area PFm on supramarginal gyrus
(magnocellularis subregion of PF in von Economo and
Koskinas (1925)).
PFop Inferior parietal area PFop (opercular subregion of
PF in von Economo and Koskinas (1925)).
PFt Inferior parietal area PFt (tenuicorticalis subregion of
PF in von Economo and Koskinas (1925)).
PG Caudal main inferior parietal area in von Economo and
Koskinas (1925).
PGa Inferior parietal area PG anterior.
PGp Inferior parietal area PG posterior.
Abbreviations
hIP2
hIP3
IPL
IPS
PPC
SLF
SPL
V3d
V5
5Ci Superior parietal area 5 around cingulate sulcus.

5L Superior parietal area 5 lateral.
5M Superior parietal area 5 medial.
7A Superior parietal area 7 anterior.
7M Superior parietal area 7 medial.
7P Superior parietal area 7 posterior.
7PC Superior parietal area 7 postero-caudal.
75inf Rostral superior parietal area 75 inferior in
Batsch (1956).
75scm Superior parietal area 75 in cingulate sulcus in
Gerhardt (1940).
75sup Rostral superior parietal area 75 superior in
Batsch (1956).
PA2 Area on the paracentral lobule and adjacent rostral
superior parietal lobule in von Economo and
Koskinas (1925).
PDE Transition area between postcentral sulcus and rostral
superior parietal lobule in von Economo and
Koskinas (1925).
PE Caudal main superior parietal lobule area in von
Economo and Koskinas (1925).
5-HT1A
5-HT2
AF
AMPA
BA
CBP
GABA
hIP1
5-Hydroxytryptamine (serotonin) receptor 1A

5-Hydroxytryptamine (serotonin) receptor 2
Arcuate fasciculus
a-amino-3-hydroxy-5-methyl-4isoxazolepropionic acid (glutamate) receptor
Brodmann area
Connectivity-based parcellation
g-aminobutyric acid
Human intraparietal area 1
Microstructural Parcellation and Features

The posterior parietal cortex (PPC) covers the posterior aspect
of the parietal lobe, caudal to the postcentral sulcus. It can be
subdivided into the inferior (IPL) and the superior parietal
lobule (SPL), which are separated by the intraparietal sulcus
(IPS). The gyral and sulcal patterns show considerable interindividual variability as they develop late during ontogeny (Ono,
Kubik, & Abernathey, 1990; Rademacher, Caviness, Steinmetz, &
Galaburda, 1993). Since macroanatomical landmarks are sparse
in PPC, a functionally informative parcellation needs to be based
on microstructural features as a structural basis for the concept
of functional segregation (Friston, 2002; Tononi, Sporns, &
Edelman, 1994).

Inferior parietal lobule
Intraparietal sulcus
Superior longitudinal fasciculus
Superior parietal lobule
Visual area 3, dorsal part
Visual area 5
Cytoarchitectonic Characteristics and Maps

Brodmann (1909) subdivided the PPC into four areas: areas 5
and 7 on the SPL and areas 40 and 39 on the IPL. These
bipartitions were also identified by Smith (1907). No parcellation of the IPS was provided, although sometimes the ventral
wall is assigned to the IPL and the dorsal wall to the SPL. von
Economo and Koskinas (1925) extended this parcellation
scheme by showing that the two main areas on the IPL and
the SPL, respectively, do not feature a homogeneous
architecture but are rather organized in subfields with modifications to the general cytoarchitectonic characteristics. Thus,
the IPL was subdivided into the two major areas PF and PG
with the subfields PFt, PFop, PFcm, and PFm, whereas the SPL
http://dx.doi.org/10.1016/B978-0-12-397025-1.00229-3
317
318
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Posterior Parietal Cortex: Structural and Functional Diversity
was parcellated into the two major areas PA2 and PE with the
subfields PEm, PEp, and PEg. Furthermore, von Economo and
Koskinas (1925) provided a separate area within the IPS and the
adjacent postcentral sulcus, termed PED. Gerhardt (1940) identified several subdivisions within the IPL (74, 88, 89, 90)
and the SPL (75, 75scm, 83, 84, 85, 86, 87), which mainly
follow the myeloarchitectonic subdivisions found by Vogt
and Vogt (1919).
Recent studies provided new 3D maps of PPC areas within
a common reference space (Figure 1) as part of the JuBrain
Cytoarchitectonic Atlas (Zilles & Amunts, 2010), which is
based on observer-independent delineations in ten human

postmortem brains (Schleicher et al., 2005).
Caspers et al. (2006, 2008) presented maps of seven cytoarchitectonically distinct areas within the IPL, five of which are located
on the supramarginal gyrus (PFop, PFt, PF, PFm, PFcm) and
approximately cover the range of Brodmann area (BA) 40 and
two of which are located on the angular gyrus (PGa, PGp),
covering BA 39. The SPL was also subdivided into seven distinct
areas, three of which (5L, 5M, 5Ci) were located in the region
of BA 5 and four of which (7PC, 7P, 7A, 7M) were located
in BA 7 (Scheperjans, Eickhoff, et al., 2008; Scheperjans,
Figure 1 Cytoarchitectonic maps of the human PPC. (a) Map of Brodmann (1914) and (b) map of von Economo and Koskinas (1925) (SPL highlighted
in green, IPL highlighted in blue). (c) Maps of the JuBrain Cytoarchitectonic Atlas, according to: IPL Caspers et al. (2006, 2008); SPL Scheperjans,
Eickhoff, et al. (2008), Scheperjans, Hermann, et al. (2008); IPS Choi et al. (2006), Scheperjans, Eickhoff, et al. (2008), Scheperjans, Hermann,
et al. (2008). Top row: left, right, and dorsal views on PPC (pial surface reconstruction); bottom row: left dorsal and right dorsal view (white matter
interface reconstruction for visualization of IPS areas). Color coding according to legend within the figure. IPL, inferior parietal lobule; IPS,
intraparietal sulcus; SPL, superior parietal lobule.
Hermann, et al., 2008). For the IPS, three cytoarchitectonic maps
are available up till now that cover the anterior portion: areas
hIP1, hIP2 (Choi et al., 2006), and hIP3 (Scheperjans, Eickhoff,
et al., 2008; Scheperjans, Hermann, et al., 2008), which are
assumed to be the human homologues of macaque areas
anterior intraparietal area (AIP), ventral intraparietal area (VIP),
and medial intraparietal area (MIP), respectively (Grefkes &
Fink, 2005).
All these areas differ in their cytoarchitectonic characteristics, making each area a distinct microstructurally defined
entity (for overview: Caspers, Amunts, & Zilles, 2012). Overall,
all PPC areas have a generally well-developed layer IV and a
pronounced layer III. But the areas within each part of PPC,
that is, IPL, SPL, and IPS, share some common features which
distinguish them from areas of the other parts. The areas of the
SPL have much bigger pyramidal cells in lower layer III and
layer V as compared to the IPS and the IPL. While in the SPL
and the IPL, the major part of the cortex is covered by supragranular layers, pushing the infragranular layers to the lower
third, they are more equally proportioned in the IPS areas.
Layer III is cell denser and the layering is less pronounced in
the SPL and the IPL as compared to the IPS.
Myeloarchitecture
Myeloarchitectonical studies revealed a similar variety of PPC
parcellations (for a recent review: Nieuwenhuys, 2013).
Flechsig (1920) mainly corroborated the cytoarchitectonic parcellation of Brodmann (1909) by defining two areas (22, 29)
in the SPL but three areas (26, 37, 42) in the IPL. The most
detailed myeloarchitectonic map of the PPC was provided by
Vogt (1911) and Vogt and Vogt (1919). They identified four
areas in the IPL (74, 88, 89, 90) and six in the SPL (75, 83, 84,
85, 86, 87). This parcellation was later largely corroborated by
Batsch (1956) who additionally added some subdivisions, for
example, of area 75 into areas 75inf and 75sup. The extent of
some areas differed slightly from that of Vogt and Vogt (1919).
Hopf and Vitzthum (1957) and Hopf (1969) found similar
minor deviations from these maps, but in general postulated a
comparably complex myeloarchitecture within PPC.
Receptorarchitecture
The receptor architecture of the PPC areas reflects the neurochemical architecture as the basis for their involvement in different functional systems (Zilles & Amunts, 2009). Based on the
receptor architecture, the same seven IPL areas as identified
cytoarchitectonically were found (Caspers et al., 2013). Additionally, similarity analyses of the receptor distributions in these
areas revealed a functionally meaningful tripartition of the IPL,
consisting of a rostral (areas PFop, PFt, PFcm), a middle (areas
PF, PFm), and a caudal group (areas PGa, PGp). Within the SPL,
differences in receptor distribution were found according to the
seven SPL areas (Scheperjans, Grefkes, Palomero-Gallagher,
Schleicher, & Zilles, 2005; Scheperjans, Palomero-Gallagher,
Grefkes, Schleicher, & Zilles, 2005). Further analyses showed
that the rostral areas of the BA 5 region were more similar to
each other than to the areas of the caudal BA 7 region.
While there are distinct differences between the PPC areas,
there are also some similarities in receptor distribution. The
319
rostral PPC areas (both the IPL and the SPL) have a similar
receptor distribution as somatosensory cortex, whereas the
caudal PPC areas are more similar to extrastriate visual areas.
At the protein level, this difference between the rostral and
the caudal PPC is accompanied by an increase in receptor
concentration of the glutamatergic AMPA, the GABAergic
GABAA, and the cholinergic nicotinic receptors and a mirrored
decrease in concentration of the serotoninergic 5-HT1A and
5-HT2 receptors.
Connectivity Patterns
In order to understand the role of the PPC areas within the
brain, their connections to other brain areas and their involvement in different functional brain networks need to be considered. Based on detailed anatomical maps of the PPC areas, the
structural and functional connectivity patterns provide information about the basis for their functional integration.
Structural Connectivity
With the advent of diffusion MR imaging to study structural
connectivity in humans in vivo (Le Bihan & Johansen-Berg,
2011), novel insight into the human brains fiber architecture
was gained, so far mainly deduced from tracer studies in
macaques.
Using connectivity-based parcellation (CBP) based on the
structural connectivity information to other areas of the brain,
different parts of the PPC were parcellated into areas with
distinct structural connectivity. CBP of the IPL revealed five
subregions with distinct connectivity profiles (Mars et al.,
2011; Wang et al., 2012), which were in good agreement with
the cytoarchitectonically delineated areas PFop, PFt, PFm, PGa,
and PGp (see Section Microstructural Parcellation and Features). Another study identified three subregions within the
IPL, a rostral, a middle, and a caudal one (Ruschel et al.,
2013), which is in line with the three main areas of the macaque
IPL (Gregoriou, Borra, Matelli, & Luppino, 2006) as well as with
insights from receptorarchitecture which demonstrated such a
functionally relevant tripartition of the human IPL (see Section
Microstructural Parcellation and Features). CBP of the lateral
SPL and the adjacent IPS distinguished five regions with distinct
connectivity profiles (Mars et al., 2011), which corresponded
to cytoarchitectonic areas 7A, 7PC, 5L, and hIP3 (see Section
Microstructural Parcellation and Features). Another study
identified three subregions on the mesial part of the SPL
(Zhang et al., 2013), which corresponded to cytoarchitectonic
areas 5L/5M, 7A, and 7M/7P (see Section Microstructural Parcellation and Features).
The fiber architecture of the PPC is dominated by two major
fiber bundles. The arcuate fasciculus (AF) is the main connection pathway of the IPL to the inferior frontal gyrus, mainly to
Brocas area, and the adjacent premotor cortex, and to the
posterior temporal cortex (Catani, Jones, & ffytche, 2005).
The superior longitudinal fasciculus (SLF) with its three parts
(I, II, III) connects all aspects of the PPC with areas of the
frontal lobe (Thiebaut de Schotten et al., 2011). The AF is
often deemed part of the SLF III (Martino et al., 2013). But
there is evidence that the AF is lateralized to the left, while the
320
SLF III (and II) is lateralized to the right hemisphere which is

thought to reflect the dominance of the language network in
the left and the visuospatial network in the right hemisphere
(see Section Functional Segregation; Parker et al., 2005;
Powell et al., 2006; Thiebaut de Schotten et al., 2011).
Via these fiber pathways, all IPL areas are strongly connected to inferior frontal and posterior temporal areas. Additionally, while the rostral IPL (areas PFt, PF) is mainly
connected with premotor, motor, primary, and secondary
somatosensory cortex and rostral SPL, this pattern shifts to
connections to middle and superior frontal cortex, middle
and caudal SPL, posterior insula, anterior parts of middle and
inferior temporal cortex, and lateral occipital cortex when
moving over middle (area PFm) to caudal IPL (areas PGa,
PGp) (Caspers et al., 2011). This is well in line with observations in macaques derived by means of tracer studies (Cavada
& Goldman-Rakic, 1989; Petrides & Pandya, 2009).
Rushworth, Behrens, and Johansen-Berg (2006) found strong
connections of the rostral IPL with the SLF III, of the caudal IPL
with the parahippocampal gyrus, and of the SPL with the
superior colliculus. The mesial parts of the SPL exhibited strong
connections with the postcentral gyrus, the rostral IPL, and the
thalamus (areas 5L/5M), additionally with the putamen and
pallidum (mesial part of area 7A), and with the mesial and
lateral occipital cortex (areas 7P/7M) (Zhang et al., 2013).
Tracer studies in macaques report additional connections
with primary motor and lateral and mesial premotor areas,
middle frontal gyrus, secondary somatosensory cortex, and
posterior temporal cortex (Caminiti, Ferraina, & Johnson,
1996; Cavada & Goldman-Rakic, 1989). Posterior IPS is
strongly connected to extrastriate visual areas of the dorsal
stream, particularly area V3d, and to the superior temporal
gyrus, whereas more anterior IPS regions exhibit stronger connectivity to motor, premotor, and prefrontal cortex, including
the frontal eye field (Bray, Arnold, Iaria, & MacQueen, 2013;
Greenberg et al., 2012).
Besides the efforts to functionally decode the role of different
PPC areas or their involvement in specific functional brain
networks (see Section Functional Segregation), studying
the resting-state functional connectivity allows identifying
frequently occurring functional correlations between different
brain areas in a task-free state of the brain (Fox &
Raichle, 2007).
In a whole-brain CBP study based on resting-state data, the
PPC was involved in four different networks (Yeo et al., 2011):
a rostral IPL network interacting with caudal inferior frontal
cortex, frontal operculum, supplementary motor, and posterior temporal cortex; a caudal IPL network interacting with
rostral inferior frontal, medial prefrontal, posterior cingulate,
and anterior temporal cortex, which correlates with the default
mode network; an IPS network interacting with lateral prefrontal and posterior inferior temporal cortex; and an SPL network
interacting with dorsal premotor and lateral temporo-occipital
cortex. In a more fine-grained parcellation of the cortex into 17
networks, the parcellation of the PPC followed the main line of
the coarser segregation, adding subparcellations particularly
within the IPL.
Another study showed that the caudal IPL is furthermore

functionally connected with the parahippocampal gyrus while
the middle IPL interacts with the anterior prefrontal cortex
(Mars et al., 2011). The latter finding needs to be stressed
since such connection patterns are not only observed in
macaques but are also revealed by structural connectivity analyses in humans (Caspers et al., 2011), favoring the view that
these connections evolved in humans, potentially coinciding
with the evolution of a larger prefrontal cortex. Posterior lateral
SPL and the adjacent medial wall of the IPS were connected to
area V5. Anterior SPL and adjacent IPS were strongly connected
to the frontal eye field and dorsal premotor cortex. Uddin et al.
(2010) additionally demonstrated that caudal IPL and IPS
areas PGa, PGp, and hIP3 were strongly correlated with lateral
occipital cortex, whereas anterior IPS area hIP2 had additional
functional connectivity with the insula, midcingulate cortex,
and putamen.
Functional Segregation
Action Processing and Apraxia
Different PPC areas contribute, together with motor, premotor,
and prefrontal areas, to the planning and control of actions,
including the choice of the appropriate action set as well as
distinguishing between different goals or targets of an action
(Rowe & Siebner, 2012). Rostral IPL and adjacent IPS are
involved in the perception of observed actions and play a
role in imitating an action (Caspers, Zilles, Laird & Eickhoff,
2010; Molenberghs, Cunnington & Mattingley, 2012), being
responsible for mapping an observed action onto ones own
motor system and thus providing the parietal nodes of the
human mirror neuron system (Cattaneo & Rizzolatti, 2009;
Iacoboni & Mazziotta, 2007). Taken together, this ability helps
to interpret observed actions, which is essential in everyday
social interactions (Ocampo & Kritikos, 2011).
Areas of the lateral aspect of the superior parietal cortex and
adjacent IPS, on the other hand, are mainly involved in visuomotor coordination regarding planning and choosing the
appropriate action for reaching a given target. These areas
also enable the identification of the relevant objects needed
for the action (Culham & Valyear, 2006; Iacoboni, 2006; Lindner, Iyer, Kagan, & Andersen, 2010).
Lesions to these rostral PPC areas particularly within the left
hemisphere, for example, due to stroke of the middle cerebral
artery, typically lead to different forms of apraxia, such as
motor or tactile, keeping subjects from knowing the correct
program for performing an action or using a tool (Freund,
2003; Goldenberg, 2009; Rushworth, Johansen-Berg, Gobel, &
Devlin, 2003).
Visuospatial and Nonspatial Attention and Neglect

Visuospatial attention and reorientation in space also involve
different PPC areas, which are mainly located in the middle
parts of the IPL, the IPS, and the SPL of the right hemisphere.
These functions are tightly linked with the visuomotor integration system, with partially overlapping recruitment of the PPC
areas, but also include spatial working memory processes.
All visuospatial functions can be mainly attributed to the
sequel of the dorsal visual stream with its different subsystems
(Krawitz, Saleem, Baker, & Mishkin, 2011). Hereby, a dorsal
system involving the middle IPS and the adjacent SPL maintains attention, while a ventral system involving the middle
aspect of the IPL and the temporo-parietal junction contributes
to attention reorientation (Corbetta, Patel, & Shulman, 2008).
The functional right hemispheric lateralization is supported by
respective structural connectivity, that is, the lateralization of
the SLF II is associated with visuospatial performance
(Thiebaut de Schotten et al., 2011).
Disruption of these frontoparietal attention networks is
largely associated with neglect, that is, the missing attention
to one part of space or to certain features, particularly after
right hemisphere lesions since attention to both hemispaces
largely depends on the right hemisphere (Mesulam, 1999). In
accordance with the two main attention systems, spatial
neglect mainly occurs after lesions to the PPC areas of the
dorsal attention network, while lesions to the ventral system
mainly accompany nonspatial neglect (Corbetta & Shulman,
2011; Ptak & Schnider, 2011).
Language (Geschwinds Area) and Aphasia

With regard to language functions, the left angular gyrus,
which within the language network is also known as housing
Geschwinds area (Geschwind, 1970), was associated with
semantic processing, such as deriving the meaning of words
and understanding sentences. It is assumed that the angular
gyrus is mainly responsible for semantic retrieval (Vigneau
et al., 2006), related to the working memory load of the task.
A similar role has been attributed to ventral aspects of the
rostral IPL at the transition from the lateral surface into the
depth of the Sylvian fissure due to increased working memory
load if syntactic or semantic complexity is enhanced (Price,
2000, 2012). Furthermore, a shift from rostral to caudal IPL
areas regarding the analysis of language was assumed, with
rostral areas dedicated to sounds, middle areas to words,
and caudal areas to the meaning of sentences (Shalom &
Poeppel, 2008).
If the angular gyrus and thus mainly Geschwinds language
region or the underlying white matter are destroyed, sensory
and conduction types of aphasia occur (Ardila, 2010;
Dronkers, Wilkins, Van Valin, & Redfern, 2004).
Cognitive Functions (Arithmetics, Reasoning, Memory)

The PPC areas are also involved in numerous other cognitive
functions. Here, three of them shall be mentioned, namely,
arithmetics, reasoning, and memory functions.
Number processing as well as arithmetic operations is
mainly supported by posterior IPS and adjacent SPL and IPL
areas. Hereby, basic number processing as some kind of general number sense relies on posterior IPS areas bilaterally,
which is thought to reflect the semantic content of number
quantity and allows assigning numbers to certain spatial
positions (Nieder & Dehaene, 2009). In addition to the
IPS, surrounding areas of the caudal SPL and IPL become
more involved during arithmetical operations, particularly
if task demands are increased (Arsalidou & Taylor, 2011;
Dehaene, 2009).
321
Moral reasoning is supported by activation of the angular

gyrus, in which the angular gyrus together with the medial
prefrontal and posterior cingulate cortex decode the moral
content of a given situation (Raine & Yang, 2006). But the
angular gyrus is also involved in general reasoning relevant to
problem solving as well as memory retrieval (Seghier, 2013).
Together with the precuneus, that is, medial SPL, the angular
gyrus is furthermore involved in prospective memory functions
(Burgess, Gonen-Yaacovi, & Volle, 2011) as well as selfperception and generation of internal thoughts (Cavanna &
Trimble, 2006), which is also reflected by the involvement of
these two PPC regions in the default mode network
(Smallwood, Brown, Baird, & Schooler, 2012).
Relating Structure and Function in the PPC

The structural and connectional features of the PPC areas
support the functional roles, which are ascribed to them. The
growing research on network architecture and connectivity has
led to a deeper understanding about the relationship between
the structural and functional composition of the PPC, which is
supported by respective network partners particularly in the
frontal lobe. While rostral PPC areas are mainly involved in
higher somatosensory and motor functions, including action
processing, middle and caudal PPC areas could be associated
with different forms of visual processing, including visuospatial attention. All these functions are well supported by the
involvement of PPC areas in different networks, in which the
PPC areas might provide preparatory analysis steps for execution within the frontal lobe. Additionally, the PPC is also
involved in cognitive functions, for example, self-insight or
moral reasoning, for which the network partners were also
identified, but the role of the PPC is less well understood.

Anatomy and Physiology of the Mirror Neuron System;
Cytoarchitecture and Maps of the Human Cerebral Cortex;
Myeloarchitecture and Maps of the Cerebral Cortex; Myeloarchitecture
and Maps of the Cerebral Cortex; Transmitter Receptor Distribution in
the Human Brain; INTRODUCTION TO CLINICAL BRAIN
MAPPING: Disorders of Language; Language; INTRODUCTION TO
COGNITIVE NEUROSCIENCE: Numerosity; Semantic Processing;
INTRODUCTION TO METHODS AND MODELING: Fiber Tracking
with DWI; INTRODUCTION TO SOCIAL COGNITIVE
NEUROSCIENCE: A Neural Network for Moral Decision Making; The
Use of Brain Imaging to Investigate the Human Mirror Neuron System;
INTRODUCTION TO SYSTEMS: Action Understanding; Cortical
Action Representations; Salience Network; Visuospatial Attention.
References
Ardila, A. (2010). A review of conduction aphasia. Current Neurology and Neuroscience
Reports, 10(6), 499503.
Arsalidou, M., & Taylor, M. J. (2011). Is 2 2 4? Meta-analyses of brain areas
needed for numbers and calculations. NeuroImage, 54(3), 23822393.
322
Batsch, E. G. (1956). Die myeloarchitektonische Untergliederung des Isocortex

Bray, S., Arnold, A. E. G. F., Iaria, G., & MacQueen, G. (2013). Structural connectivity of
visuotopic intraparietal sulcus. NeuroImage, 82, 137145. http://dx.doi.org/
10.1016/j.neuroimage.2013.05.080.
Brodmann, K. (1909). Vergleichende Lokalisationslehre der Grosshirnrinde. Leipzig:
Barth.
Brodmann, K. (1914) Zweiter Abschnitt: Physiologie des Gehirns. In Von Bruns P (Ed.)
Neue Deutsche Chirurgie, 11. Band: Allgemeine Chirurgie der Gehirnkrankheiten.
I. Teil (pp. 87426). Stuttgart: Verlag von Ferdinand Enke.
Burgess, P. W., Gonen-Yaacovi, G., & Volle, E. (2011). Functional neuroimaging
studies of prospective memory: What have we learnt so far? Neuropsychologia,
49(8), 22462257.
Caminiti, R., Ferraina, S., & Johnson, P. B. (1996). The sources of visual information to
the primate frontal lobe: A novel role for the superior parietal lobule. Cerebral
Cortex, 6, 319328.
Caspers, S., Amunts, K., & Zilles, K. (2012). Posterior parietal cortex: Multimodal
association cortex. In J. H. Mai, & G. Paxinos (Eds.), The human nervous system
(pp. 10271045). (3rd ed.). San Diego, CA: Academic Press.
(2008). The human inferior parietal lobule in stereotaxic space. Brain Structure and
Function, 212(6), 481495.
Caspers, S., Eickhoff, S. B., Rick, T., von Kapri, A., Kuhlen, T., Huang, R., et al. (2011).
Probabilistic fibre tract analysis of cytoarchitectonically defined human inferior
parietal lobule areas reveals similarities to macaques. NeuroImage, 58, 362380.
Caspers, S., Zilles, K., Laird, A. R., & Eickhoff, S. B. (2010). ALE meta-analysis of action
observation and imitation in the human brain. NeuroImage, 50, 11481167.
Catani, M., Jones, D. K., & ffytche, D. (2005). Perisylvian language networks of the
human brain. Annals of Neurology, 57, 816.
Cattaneo, L., & Rizzolatti, G. (2009). The mirror neuron system. Annals of Neurology,
66(5), 557560.
Cavada, C., & Goldman-Rakic, P. S. (1989). Posterior parietal cortex in rhesus monkey:
I. Parcellation of areas based on distinctive limbic and sensory corticocortical
connections. Journal of Comparative Neurology, 287, 393421.
Cavanna, A. E., & Trimble, M. R. (2006). The precuneus: A review of its functional
anatomy and behavioural correlates. Brain, 129(3), 564583.
Choi, H. J., Zilles, K., Mohlberg, H., Schleicher, A., Fink, G. R., Armstrong, E., et al.
(2006). Cytoarchitectonic identification and probabilistic mapping of two distinct
areas within the anterior ventral bank of the human intraparietal sulcus. Journal of
Corbetta, M., Patel, G., & Shulman, G. L. (2008). The reorienting system of the human
brain: From environment to theory of mind. Neuron, 58(3), 306324.
Corbetta, M., & Shulman, G. L. (2011). Spatial neglect and attention networks. Annual
Culham, J. C., & Valyear, K. F. (2006). Human parietal cortex in action. Current Opinion
in Neurobiology, 16(2), 205212.
Dehaene, S. (2009). Origins of mathematical intuitions: The case of arithmetic. Annals
of the New York Academy of Sciences, 1156, 232259.
Dronkers, N. F., Wilkins, D. P., Van Valin, R. D., Jr., Redfern, B. B., & Jaeger, J. J.
(2004). Lesion analysis of the brain areas involved in language comprehension.
Cognition, 92(12), 145177.
Fox, P. T., & Raichle, M. E. (2007). Spontaneous fluctuations in brain activity observed
700711.
Freund, H. J. (2003). Somatosensory and motor disturbances in patients with parietal
lobe lesions. Advances in Neurology, 93, 179193.
Friston, K. J. (2002). Beyond phrenology: What can neuroimaging tell us about
distributed circuitry? Annual Review of Neuroscience, 25, 221250.
Gerhardt, E. (1940). Die Cytoarchitektonik des Isocortex parietalis beim Menschen.
Journal of Psychology and Neurology, 49, 367419.
Geschwind, N. (1970). The organization of language and the brain. Science, 170,
940944.
Goldenberg, G. (2009). Apraxia and the parietal lobes. Neuropsychologia, 47(6),
14491459.
Greenberg, A. S., Verstynen, T., Chiu, Y. C., Yantis, S., Schneider, W., & Behrmann, M.
(2012). Visuotopic cortical connectivity underlying attention revealed with whitematter tractography. Journal of Neuroscience, 32, 27732782.
Grefkes, C., & Fink, G. R. (2005). The functional organization of the intraparietal sulcus
in humans and monkeys. Journal of Anatomy, 207(1), 317.
Gregoriou, G. G., Borra, E., Matelli, M., & Luppino, G. (2006). Architectonic
organization of the inferior parietal convexity of the macaque monkey. Journal of
lobe. I. Parietal region. Journal fur Hirnforschung, 11(4), 253265.
Hopf, A., & Vitzthum, H. G. (1957). Uber die Verteilung myeloarchitektonischer
Merkmale in der Scheitellappenrinde beim Menschen. Journal fur Hirnforschung,
3(23), 79104.
Iacoboni, M. (2006). Visuo-motor integration and control in the human posterior cortex:
Evidence from TMS and fMRI. Neuropsychologia, 44(13), 26912699.
Iacoboni, M., & Mazziotta, J. C. (2007). Mirror neuron system: Basic findings and
clinical applications. Annals of Neurology, 62(3), 213218.
Krawitz, D. J., Saleem, K. S., Baker, C. I., & Mishkin, M. (2011). A new neural framework
for visuospatial processing. Nature Reviews Neuroscience, 12(4), 217230.
Le Bihan, D., & Johansen-Berg, H. (2011). Diffusion MRI at 25: Exploring brain tissue
structure and function. NeuroImage, 61(2), 324341.
Lindner, A., Iyer, A., Kagan, I., & Andersen, R. A. (2010). Human posterior parietal
cortex plans where to reach and what to avoid. Journal of Neuroscience, 30(35),
1171511725.
Mars, R. B., Jbabdi, S., Sallet, J., OReilly, J. X., Croxson, P. L., Olivier, E., et al. (2011).
Diffusion-weighted imaging tractography-based parcellation of the human parietal
cortex and comparison with human and macaque resting-state functional
connectivity. Journal of Neuroscience, 31(11), 40874100.
Martino, J., De Witt Hamer, P. C., Berger, M. S., Lawton, M. T., Arnold, C. M.,
de Lucas, E. M., et al. (2013). Analysis of the subcomponents and
cortical terminations of the perisylvian superior longitudinal fasciculus: A fiber
dissection and DTI tractography study. Brain Structure and Function, 218,
105121.
Mesulam, M. M. (1999). Spatial attention and neglect: Parietal, frontal and cingulate
contributions to the mental representation and attentional targeting of salient
extrapersonal events. Philosophical Transactions of the Royal Society, B: Biological
Sciences, 354(1387), 13251346.
Molenberghs, P., Cunnington, R., & Mattingley, J. B. (2012). Brain regions with mirror
properties: a meta-analysis of 125 human fMRI studies. Neuroscience &
Biobehavioral Reviews, 36, 341349.
Nieder, A., & Dehaene, S. (2009). Representation of number in the brain. Annual Review
Nieuwenhuys, R. (2013). The myeloarchitectonic studies on the human cerebral cortex
of the Vogt-Vogt school, and their significance for the interpretation of functional
neuroimaging data. Brain Structure and Function, 218, 303352.
Ocampo, B., & Kritikos, A. (2011). Interpreting actions: The goal behind mirror neuron
function. Brain Research Reviews, 67(12), 260267.
Ono, M., Kubik, S., & Abernathey, C. D. (1990). Atlas of the cerebral sulci. Stuttgart:
Thieme.
Parker, G. J. M., Luzzi, S., Alexander, D. C., Wheeler-Kingshott, C. A. M.,
Ciccarelli, O., & Ralph, M. A. L. (2005). Lateralization of ventral and dorsal auditorylanguage pathways in the human brain. NeuroImage, 24, 656666.
Petrides, M., & Pandya, D. N. (2009). Distinct parietal and temporal pathways to the
homologues of Brocas area in the monkey. PLoS Biology, 7(8), e1000170.
Powell, H. W., Parker, G. J., Alexander, D. C., Symms, M. R., Boulby, P. A.,
Wheeler-Kingshott, C. A., et al. (2006). Hemispheric asymmetries in languagerelated pathways: A combined functional MRI and tractography study. NeuroImage,
32(1), 388399.
Price, C. J. (2000). The anatomy of language: Contributions from functional
neuroimaging. Journal of Anatomy, 197(3), 335359.
Price, C. J. (2012). A review and synthesis of the first 20 years of PET and fMRI studies
of heard speech, spoken language and reading. NeuroImage, 62(2), 816847.
Ptak, R., & Schnider, A. (2011). The attention network of the human brain: Relating
structural damage associated with spatial neglect to functional imaging correlates of
spatial attention. Neuropsychologia, 49(11), 30633070.
Rademacher, J., Caviness, J., Steinmetz, H., & Galaburda, A. M. (1993). Topographical
variation of the human primary cortices: Implications for neuroimaging, brain
mapping, and neurobiology. Cerebral Cortex, 3, 313329.
Raine, A., & Yang, Y. (2006). Neural foundations to moral reasoning and antisocial
behavior. Social Cognitive and Affective Neuroscience, 1(3), 203213.
Rowe, J. B., & Siebner, H. R. (2012). The motor system and its disorders. NeuroImage,
61(2), 464477.
Ruschel, M., Knosche, T. R., Friederici, A. D., Turner, R., Geyer, S., & Anwander, A.
(2013). Connectivity architecture and subdivisions of the human inferior parietal
cortex revealed by diffusion MRI. Cerebral Cortex, 24(9), 24362448. http://dx.doi.
org/10.1093/cercor/bht098.
Rushworth, M. F. S., Behrens, T. E. J., & Johansen-Berg, H. (2006). Connection
patterns distinguish 3 regions of human parietal cortex. Cerebral Cortex, 16,
14181430.
Rushworth, M. F., Johansen-Berg, H., Gobel, S. M., & Devlin, J. T. (2003). The left
parietal and premotor cortices: Motor attention and selection. NeuroImage,
20(Suppl. 1), S89S100.
et al. (2008). Probabilistic maps, morphometry, and variability of
cytoarchitectonic areas in the human superior parietal cortex. Cerebral Cortex,
18(9), 21412157.
autoradiography: A parietal region between motor, somatosensory, and cingulate
cortical areas. NeuroImage, 25(3), 975992.
parietal cortex. Cerebral Cortex, 18(4), 846867.
NeuroImage, 28(2), 362379.
Schleicher, A., Palomero-Gallagher, N., Morosan, P., Eickhoff, S. B., Kowalski, T.,
de Vos, K., et al. (2005). Quantitative architectural analysis: A new approach to
cortical mapping. Anatomy and Embryology, 210(56), 373386.
Seghier, M. L. (2013). The angular gyrus: Multiple functions and multiple subdivisions.
The Neuroscientist, 19(1), 4361.
Shalom, D. B., & Poeppel, D. (2008). Functional anatomic models of language:
Assembling the pieces. The Neuroscientist, 14, 119127.
Smallwood, J., Brown, K., Baird, B., & Schooler, J. W. (2012). Cooperation between the
default mode network and the fronto-parietal network in the production of an internal
train of thought. Brain Research, 1428, 6070.
323
Smith, G. E. (1907). A new topographical survey of the human cerebral cortex, being an
account of the distribution of the anatomically distinct cortical areas and their
relationship to the cerebral sulci. Journal of Anatomy, 41, 237254.
Thiebaut de Schotten, M., DellAcqua, F., Forkel, S. J., Simmons, A., Vergani, F.,
Murphy, D. G. M., et al. (2011). A lateralized brain network for visuospatial attention.
Nature Neuroscience, 14(10), 12451246.
Tononi, G., Sporns, O., & Edelman, G. M. (1994). A measure for brain complexity:
Relating functional segregation and integration in the nervous system. Proceedings
of the National Academy of Sciences of the United States of America, 91(11),
50335037.
Uddin, L. Q., Supekar, K., Amin, H., Rykhlevskaia, E., Nguyen, D. A., Greicius, M. D.,
et al. (2010). Dissociable connectivity within human angular gyrus and intraparietal
sulcus: Evidence from functional and structural connectivity. Cerebral Cortex, 20,
26362646.
Vigneau, M., Beaucousin, V., Herve, P. Y., Duffau, H., Crivello, F., Houde, O., et al.
(2006). Meta-analyzing left hemisphere language areas: Phonology, semantics, and
sentence processing. NeuroImage, 30(4), 14141432.
von Economo, K., & Koskinas, G. (1925). Die Cytoarchitektonik der Hirnrinde des
erwachsenen Menschen. Wien: Springer.
Wang, J., Fan, L., Zhang, Y., Liu, Y., Jiang, D., Zhang, Y., et al. (2012). Tractography-based
parcellation of the human left inferior parietal lobule. NeuroImage, 63(2), 641652.
Yeo, B. T., Krienen, F. M., Sepulcre, J., Sabuncu, M. R., Lashkari, D., Hollinshead, M.,
Zhang, Y., Fan, L., Zhang, Y., Wang, J., Zhu, M., Zhang, Y., et al. (2013). Connectivitybased parcellation of the human posteromedial cortex. Cerebral Cortex, 24(3),
719727. http://dx.doi.org/10.1093/cercor/bhs353.
cortex. Current Opinion in Neurology, 22(4), 331339.
Zilles, K., & Amunts, K. (2010). Centenary of Brodmanns map Conception and fate.
Mapping Cingulate Subregions

BA Vogt, Cingulum NeuroSciences Institute, Manlius, NY, USA; Institute of Neuroscience and Medicine (INM-1), Julich,
Germany; Boston University School of Medicine, Boston, MA, USA
Glossary
NeuN Neuron-specific nuclear binding protein; antibody

for neurons without coreacting with glial or vascular
elements.
Perisplenial A general area around the splenium of the
corpus callosum.
SMI32 Antibody to intermediate neurofilament proteins.
Abbreviations
pMCC
RSC
sACC
Spls
vPCC
Nomenclature
CML Caudomedial lobule of vPCC.

Dysgranular Variable thickness layer IV where layer IIIc and
Va pyramids may abut.
ECG External cingulate gyrus formed by area 32.
Granular A well-defined layer IV.
aMCC
CG
cgs
dPCC
pACC
Anterior midcingulate cortex

Cingulate gyrus
Cingulate sulcus
Dorsal posterior cingulate cortex
Perigenual anterior cingulate cortex
Vogt and Vogt (1919) published the most thorough map of

areas on the human medial surface. There was, however, little
histological documentation of the area features, and it has yet
to be fully appreciated. Figure 1 shows this masterpiece and
points to many correlations with current findings: The red
asterisks emphasize nine divisions of area 32 and the numbers
(with arrows) refer to the following:
(1) There are two vertical and one horizontally oriented division of area 25.
(2) There are four longitudinally oriented areas (starting at
the corpus callosum) we refer to as areas 33, 24a, 24b,
and 24c.
(3) There is a significant vertical border above the rostrum of
the corpus callosum, which is the border between the
anterior cingulate cortex (ACC) and the midcingulate
cortex (MCC).
(4) There are four subdivisions of the anterior MCC (a330 ,
a24a0 , a24b0 , and a24c0 ), and the parenthesis emphasizes
the posterior MCC and its divisions.
(5) There is a continuation of motor cortex that emerges on
the medial surface (primitive gigantopyramidal field,
Braak, 1976; and area 24d, Luppino, Matelli, Camarda,
Gallese, & Rizzolatti, 1991). The marginal ramus (mr) of
the cingulate sulcus (cgs) was opened for their area 75
(part of area 23c).
(6) Area 23d forms the rostral, dysgranular part of dorsal
posterior cingulate cortex (dPCC).
Posterior midcingulate cortex

Retrosplenial cortex; areas 29 and 30.
Subgenual anterior cingulate cortex
Splenial sulci
Ventral posterior cingulate cortex
The prime designates areas in midcingulate cortex
(7) Divisions of dPCC including areas d23a and d23b.

(8) The retrosplenial areas on the ventral bank of the
cingulate gyrus (CG).
(9) Ventral PCC.
(10) The ventral area 31 caudal to area 23.
Thus, the essential organization of cingulate cortex was known
by the Vogts early in the twentieth century, and although human
functional imaging has yet to resolve these elegant observations,
this remains the challenge for the coming decades.
Obviously, Brodmanns (1909) map reflected broad strokes
rather than precise histology. Whereas Brodmann identified
four areas in ACC (areas 25, 33, 32, and 24), the Vogts identified 41 areas and our current map designates 21 areas. The
cytoarchitecture is so different in parts of Brodmanns areas 24
and 32 that they cannot be considered the same area or even
part of the same region. Importantly, no investigator has ever
activated Brodmanns entire ACC in a functional imaging study
meaning that it does not have a single underlying function,
and the importance of this fact has yet to be fully appreciated;
Brodmanns ACC is not a structure/function region.
Beyond cytoarchitectural differentiations of ACC and MCC
(see the succeeding text), ligand binding autoradiography
is a valuable adjunct to cytoarchitectural studies (PalomeroGallagher, Mohlberg, Zilles, & Vogt, 2008; PalomeroGallagher, Schleicher, Zilles, & Vogt, 2013; Palomero-Gallagher,
Vogt, Mayberg, Schleicher, & Zilles, 2009) and provides an elegant demonstration that Brodmanns ACC is not uniform.
http://dx.doi.org/10.1016/B978-0-12-397025-1.00230-X
325
326
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Mapping Cingulate Subregions
67 69
71
38
47
67
42
37
36
35
70
69
39
71
48
mr
ECG
cgs
34
49
30
24
20
23
19
18
50
29
22
2.
4.
3.
71
39 I
79
96
93
83 I
83
75
75 112
80
77
96 78
75
71
5.
28
27
CG
26
33
32
31
82
spls
6. 95
92
85
7.
81
91
85 I
cas
25
84
8.
21 17
pcgs
51
15
94
76
14
1
10
11
12
13
1.
10.
9.
Figure 1 Vogt and Vogts (1919) map of areas on the medial surface (two images in their Figure 51 merged). The red highlights were added as an aid
to interpreting this work in the context of recent findings. The most important are the horizontal divisions within the cingulate gyrus (2), the border
between ACC and MCC (3), the nine divisions of area 32 (asterisks), the two parts of MCC (4), the border between aMCC and pMCC (parenthesis marking
pMCC), and an extension of motor cortex into the cingulate sulcus (5). cas, callosal sulcus; CG, cingulate gyrus; cgs, cingulate sulcus; ECG,
external cingulate gyrus; mr, marginal ramus of the cgs; spls, splenial sulci.
Figure 2 shows his ACC divided into anterior and posterior parts
(at pointer) (arrows show coronal section positions). Sections in
Figure 2(b) are autoradiographs for two of the 15 receptors that
were chosen because an asymmetry index showed them to be
statistically different (Palomero-Gallagher et al., 2009). Clearly,
GABAA receptors are quite low in anterior area 24, while they are
extremely high in layers IIII of posterior area 24. In contrast,
-amino-3-hydroxy-5-methyl-4 isoxazole-proprionic acid receptors are very high in layers IV in anterior area 24 but extremely
low in posterior area 24. A polar plot of 15 receptors (Figure
2(c)) is of binding throughout the entire area, and receptors that
are significantly different in each subregion are noted with asterisks. Eight of the 15 neurotransmitter receptors differed significantly in the two divisions. Thus, the anterior and posterior parts
of Brodmanns ACC are qualitatively different in their neurochemistry and connections.
Although the midcingulate concept arose from a cytoarchitectural study (Vogt Nimchinsky, Vogt, & Hof, 1995), this and
other neurobiological differences have emerged including
functional imaging (Palomero-Gallagher et al., 2008, 2009;
Vogt, 2009a, 2009b; Vogt & Palomero-Gallagher, 2012; Vogt,
Vogt, & Laureys, 2006; Yu et al., 2011) to support the hypothesis that MCC differs qualitatively from ACC. Thus, MCC is not
a division of ACC, and studies that subdivide ACC into dorsal,
rostral, ventral, or caudal are employing Brodmanns centuryold view without reference to substantial recent observations.
They also overlook the predictive nature of the eight-subregion
model. Following on this issue, it is often said that the name
for a subregion is simply a matter of consensus. Ernst Mach
stated, to name is to classify, to establish ideal affiliations

analogous relationships between little known phenomena,
and to identify the general idea or principle wherein they lie
latent (Cajal, 1999). In fact, MCC represents more than a
name; it represents a fundamentally different model of cingulate organization based on numerous neurobiological observations that reflect the general principle wherein the
fundamental organization of cingulate cortex lies latent. Since
this new model cannot be verified with a single imaging
method, it is a conceptual perspective based on cytoarchitecture, receptor binding, and functional studies.
Finally, the first principle of neuroanatomy is that every
major structural difference predicts an important functional
difference. Embedded in every cytoarchitectural study is the
fact that projections arise from neurons of different sizes in
each layer. For example, we identified the structural differences between ACC and MCC (Vogt et al., 1995). Bush, Luu,
and Posner (2000) later performed a meta-analysis of the
affective and cognitive divisions, and this border matched
the cytoarchitectural border (Figure 3(a)). Areas and layers
will ultimately be the foci of functional studies; however, this
will require higher-resolution imaging. Although we are now
transitioning from the regional to the subregional level of
analysis, future studies will resolve individual areal and laminar functions. Thus, the cytology of areas and layers must be
considered, particularly because networks are composed of
neurons in particular layers and future network models will
be devised around neuronal architecture rather than area
activity.
Brodmanns
anterior
cingulate cortex
24
32
BA24
2923
25
(a)
GABAA
427
2105
AMPA
345
Anterior
(b)
Polar plot
Posterior
AMPA
2500
D1
Kainate
2000
5-HT2
NMDA
1500
1000
5-HT1A
GABAA
500
0
a2
GABA
a1
BZ
N
M1
M
(c)
M2
Figure 2 Assessment of 15 neurotransmitter receptors in the anterior and posterior parts of Brodmanns area 24. (a) Map of his anterior cingulate
region with a pointer separating its two parts used in the analysis. (b) Coronal sections for two receptors through each part show a radical difference
in the laminar patterns of binding. (c) Polar plots for anterior (red line SD) and posterior (green line SD) with asterisks emphasizing the
receptors that are statistically significant. The null hypothesis was rejected, and these findings validate the midcingulate concept; that is, caudal ACC is
not a part of ACC. Modified from Palomero-Gallagher et al. (2009) Receptor architecture of human cingulate cortex: insights into the four-region
neurobiological model. Human Brain Mapping 30: 23362355.
70
70
60
50
40
30
20
10
Cognitive
task
Emotional
task
60
50
pMCC
40
Cognitive
division
30
aMCC
100
20
10
pACC
cc
50
0
10
20
Affective
division
sACC
30
(a)
(b)
Figure 3 (a) Meta-analysis of Bush et al. (2000) showing activity in the affective and cognitive divisions of cingulate cortex. The black arrow marks the
border between pACC and aMCC. (b) Correlations of resting glucose metabolism seeded in area s32 showing the functional independence and
border between ACC and MCC.
328
Subregional Cytoarchitecture
Cingulate Flat Map
A complete flat map of cingulate areas (Vogt, 2009b) is in

Figure 4(a). The Talairach and Tournoux (1988) coordinate
system is overlayed on the map, and overlaying these two
systems is an approximation as the latter coordinates are for a
brain that is not characteristic of most, individual areas have a
high degree of variability, and their landmarks and proportional grid system are inconsistent (Amunts, Malikovic,
Mohlberg, Schormann, & Zilles, 2000; Grachev et al., 1999;
Li, Freeman, Tran-Dinh, & Morris, 2003; Nowinski, 2001). Our
flat map was derived from a healthy control GPC who was an
80-year-old, right-handed, white male who died from pneumonia and retroperitoneal hemorrhage. There was no evidence
of neurological or psychiatric disorders, and the brain had an
unremarkable postmortem histology. The left hemisphere is
used throughout this article but is flipped for coregistration to

some findings.
Flat map construction begins with histological sections
(Figure 4(b)) onto which the midcortical layer is drawn. The
apices and fundi of each gyrus and sulcus, respectively, are
marked and the distances between each pair determined
(Figure 4(c)). These lines are flattened (Figure 4(d)) and
their intersection distance retained along the corpus callosum.
The sulci are opened rostral and caudal to the corpus callosum
(double arrows; Figure 4(a)). The largest sulci have been
exposed and filled with a uniform gray to show sulcal areas:
paracingulate sulcus (pcgs), cgs, splenial sulci (spls), and callosal sulcus (cas). The splenium was rotated ventrally at the
small dotted line to expose the retrosplenial cortex (RSC), and
the length of the corpus callosum is shown with a red double
arrow. The external cingulate gyrus (ECG) and CG are also
noted. Since this is a flat map, the Talairach and Tournoux
(d)
(a)
4
5
X
Apex
3
4
cgs
Apex
X
Fundus
Fundus
Apex
(b)
X
1
cc
(c)
1
X
Figure 4 (a) Flat map of cingulate areas with the coordinates from Talairach and Tournoux (1988). The flattening orientations are shown with double
arrows over the genu and behind the splenium of the corpus callosum. As the splenium was rotated ventrally to expose the ventral bank of the cgs
to show areas 29 and 30, the actual length of the corpus callosum is shown with the red double arrow. (b) A histological section with the midcortical
layer marked. (c) The latter line is broken into segments and measured. (d) The segments are flattened and used to derive the flat map.

coordinates are not accurate for all of the cingulate cortex, and
red arrows on the coordinate scales alert to where they are
useful and where they are not due to opening of the sulci.
They are useful in the y-axis at 4.3 to 6.7 cm and in the
z-axis between 1.3 and 1.5. Since the cgs is maintained
intact but is exposed and extended dorsally, z-axis coordinates
between 1.5 and 4.5 are only accurate for the CG surface.
Activation sites are coregistered to this map using the dorsal
apex of the corpus callosum and cgs as landmarks.
Subgenual and Perigenual ACC

James (1884) proposed that emotion is dependent on peripheral autonomic feedback. This association is made in ACC,
which stores emotional (valenced) memories of objects and
events and has autonomic afferent and regulatory functions.
The subgenual ACC (sACC) projects to visceral regulatory
nuclei including the central nucleus of the amygdala, parabrachial nucleus, and lateral hypothalamus (review Vogt & Vogt,
2009). Bancaud and Talairach (1992) made a critical distinction between ACC and MCC; the most frequent response to
medial cortex electrical stimulation was intense or overwhelming fear including one individual who reported the feeling that
death was imminent. Stimulation of ACC evoked the report,
I was afraid and my heart started to beat, whereas stimulation of MCC evoked the report, I felt something, as though
329
I was going to leave. The former report is one of pure fear,

while the latter is early premotor planning with motivational
features. Electrical stimulation of areas 25 and 24 evokes
changes in respiratory and cardiac rates and blood pressure,
mydriasis, piloerection, and facial flushing (Escobedo,
Fernandez-Guardiola, & Solis, 1973; Pool, 1954) and gastrointestinal responses included nausea, vomiting, epigastric sensation,
salivation, or bowel or bladder evacuation (Meyer, McElhaney,
Martin, & McGraw, 1973; Pool & Ransohoff, 1949). Also, blood
flow is elevated in sACC when healthy women recall sad experiences (George et al., 1995; Mayberg et al., 1999) and when subjects evaluate emotional faces (George et al., 1993).
Cingulate gyral surface cytoarchitecture in ACC and MCC is
shown in Figure 5 with pairs of sections for neuron-specific
nuclear binding protein (NeuN antibody) and intermediate
neurofilament proteins (SMI32 antibody). The sACC is composed of areas 25, s33, s24, and s32, while the perigenual ACC
(pACC) includes areas p33, p24ac, and p32 (PalomeroGallagher et al., 2008). Figure 5(e) shows that area 25 has a
rudimentary architecture with external (layers IIIII) and internal (VVI) pyramidal layers that have little differentiation,
while areas 24 and 32 have differentiated layers III and Va
and a dysgranular layer IV in the latter. The lack of layer V
differentiation in area 25 is particularly notable with the SMI32
section, since neurofilament proteins are expressed by large
projection neurons.
p24b
p24a
(c)
a24b
(b)
(a)
(d)
(e)
25
(f)
24b
Figure 5 Cytoarchitecture of the gyral surface in ACC and MCC including sampling sites for pairs of NeuN and SMI32 images (a). The blue dashed
arrow emphasizes the substantial expression of intermediate neurofilament proteins in layer III of area p24b0 compared with those in area p24a0 .
Scale bar, 1 mm.
330
Laminar differentiation is shown in Figure 5 from ventral

to caudal cingulate areas. Area 24b layer III (Figure 5(f)) is
differentiated from layer II, although layer II is quite broad and
layers VaVI are more apparent than in area 25. Layer III in area
24b has some large pyramids expressing neurofilament proteins, although they are fewer than in area 25. The number
of these latter neurons is greatly reduced in layer III of areas
a24b0 and p24b0 , while in area p24b0 , they emerge again as
the trend to very large pyramids in layer IIIc asserts itself
throughout PCC.
There are four divisions of area 32 (Palomero-Gallagher
et al., 2008) with cytoarchitecture and ligand binding differences (Figure 6). The key cytoarchitectural difference occurs in
layer III where there is a progressive shift in the largest pyramids in layer IIIab in area s32 to the deep part of layer IIIc in
Area 32:
location and
architecture
area 320 . There is also a progressive reduction in neuron densities in layers Va and Vb. The fingerprints of ligand binding for
the mean of all layers (Figure 6(b)) and the laminar binding
patterns for benzodiazepine (BZ) (Figure 6(c)) and GABAB
(Figure 6(d)) receptors are shown. The BZ binding is most
dense in layers IIIIV of area s32, and it is progressively lower
in areas p32, d32, and 320 . Although a similar trend occurs
for GABAB binding, that for area d32 is higher than that for
area p32.
Anterior and Posterior MCC

Brodmann (1909) realized the need for a structure between
ACC and RSC in rodents where he placed area 23; however, he
recognized that it did not have a layer IV as in primates. In fact,
III ab
III c
IV
Va
Vb
200 mm
(a)
s32
BZ
IIIc
IV
Va
Vb
NMDA
VI
GABA A
(c)
727
1409
2091
2773
GABAB
M3 M2 M1
BZ
I/II
s32
(b)
32
I/II
AMPA Kainate
5HT1A
a2b
a1
N
d32
IIIab
Fingerprint
layer III
3000
2500
D1 2000
5HT2 1500
1000
p32
IIIab
p32
IIIc
d32
IV
Va
32
Vb
VI
GABA
436
1145
1855
2564
(d)
Figure 6 (a) Location of each sample site and associated cytoarchitecture of four divisions of area 32. The red arrows draw attention to the progressive
shift in the largest neurons in layer IIIab of area s32 to layer IIIc in area 320 . (b) Fingerprint of binding for 15 receptors in layer III with arrows
emphasizing significant differences in GABAB and benzodiazepine (BZ) binding. (c) Laminar profiles in binding showing the highest BZ mainly in layers III
and IV and progressive reduction in binding from area s32 to area 320 . GABAB binding is more concentrated in layers II and IIIab and undergoes
significant changes with area s32 having the broadest distribution of receptors and area 320 the fewest. The laminar differences in binding confirm
cytoarchitectural findings of four divisions of area 32. Reproduced from Vogt, B. A., & Palomero-Gallagher, N. (2012). Cingulate cortex. In: G. Paxinos &
J. K. Mai (Eds.), The human nervous system (3rd ed.). (pp. 943987). Academic Press, Chapter 25.

this is MCC in rodents (Vogt & Paxinos, 2014). Thus, along
with the Vogt and Vogts (1919) map of areas on the medial
surface (Figure 1), MCC was already emerging at the beginning
of the twentieth century. One strategy for identifying the ACC/
MCC border is with correlations among clusters of voxels in
basal glucose metabolism, and Figure 3(b) shows a statistical
parametric map for 153 healthy subjects. The correlation was
seeded in area s32 and correlated clusters were identified (Vogt,
2009a). The entire ACC has significant correlations with area
s32 and suggests that the histological ACC operates as a metabolic unit rather than the broader anterior cingulate construct
of Brodmann. Also, ACC and MCC have significantly different
levels of basal glucose metabolism and support their independent functionality.
The MCC is composed of anterior and posterior divisions
(aMCC and pMCC) (Vogt Berger, & Derbyshire, 2003). The
two premotor areas in the cgs have large layer Vb neurons in
aMCC and pMCC with unique cytoarchitectures, and the gyral
surface shows differences that parallel those in the sulcus. For
example, areas a24b0 (Figure 5(d)) and p24b0 (Figure 5(b))
distinguish aMCC and pMCC. Although layer III appears similar in both areas with NeuN, the latter has robust expression of
neurofilament proteins by large layer III pyramids, there is a
substantial increase in the breadth of layers V and VI, and layer
VI neurons are smaller than in the former area.
A very important study by Enriquez-Geppert et al. (2013)
functionally differentiated aMCC and pMCC. They showed
that conflict manipulated by congruency of flanking stimuli
relative to a target (congruent vs. incongruent) and motor
inhibition by a within-trial response change of the initiated
response (keep response vs. stop-change) was associated with
two principal components: High conflict on incongruent trials
activated pMCC (PC1) and stop-change trials modulated
aMCC (PC2). This is a critical validation of the dichotomy of
MCC structure and function and provides tests for patients that
have a selective impairment in one of these two subregions, for
example, disruption of glucose metabolism in pMCC in posttraumatic stress disorder (Shin et al., 2009).
Cingulate Premotor Areas

Electrical stimulation of MCC evokes complex and contextdependent gestures such as touching, kneading, rubbing or
pressing the fingers or hands together, and lip puckering or
sucking (Meyer et al., 1973; Talairach et al., 1973). These
movements are often adapted to the environment and can be
modified by sensory stimuli and resisted. The concept of
attention-for-action proposed by Posner, Peterson, Fox, and
Raichle (1988) provided an early premotor orientation for
MCC function. These areas contain neurons with premotor
discharge properties (Shima et al., 1991) coded according to
the changing reward properties of particular behaviors (Shima
& Tanji, 1998), and human imaging shows altered blood flow
during sequences of complex finger apposition movements
(Kwan, Crawley, Mikulis, & Davis, 2000).
Braak (1976) played a critical role in introducing the modern era of cingulate neurobiology when he reported the primitive gigantopyramidal field in the caudal cgs with pigment
architecture. This field was subsequently termed area 24d in
331
monkeys by Luppino et al. (1991). Figure 7(e) and 7(f) shows

the key features of this area including a pigment architecture
preparation kindly provided by Heiko Braak (Figure 7(f) PA).
Spinal projections were first shown by Biber, Kneisley, and
LaVail (1978) and Nudo and Masterton (1990), and area 24d
has a neuron dense layer Va and sparse layer Vb, the latter of
which contains large corticospinal projection neurons visible
with NeuN and SMI32.
Figure 7 also shows area p24c0 in comparison with area 24d
and gyral surface areas p24a0 and p24b0 . Area p24c0 has very
dense and broad layers Va and Vb compared with all areas at
this level. As is the case for area a240 , p24b0 has a broader layer
IIIc than p24a0 with pyramids that are larger and express substantially more neurofilament proteins. Large neurons in layer
Vb of area p24b0 are smaller than those in p24c0 (red asterisks;
Figure 7(d)).
The border between the two premotor cortices is rostral to
the vertical plane at the anterior commissure, and this cortex is
composed of five areas: areas 24c and a24c0 form the rostral
cingulate premotor area and areas p24c0 , 24d, and 23c form the
caudal cingulate premotor area. These are premotor rather than
motor areas for a number of reasons: (1) Although they have
spinal projections, compared to motor and supplementary
motor cortices, the projections are only about one-quarter as
dense; (2) they are involved in more than motor functions
including anticipation of performing a task long before an
overt action and other cognitive functions (Kirsch et al.,
2003; Murtha, Chertkow, Beauregard, Dixon, & Evans, 1996);
and (3) area 24c0 has a particularly high level of dopamine-1
receptors (Figure 8) suggesting that it has a role beyond motor
function such as coding the reward value of stimuli and
contexts.
Palomero-Gallagher and Zilles (2009) published a thorough assessment of the cingulate subregional, areal, and laminar distributions of binding for 15 neurotransmitter receptors.
Figure 8 provides sulcal binding for four ligands derived from
this work and NeuN for comparison. The cytology shows that
layer Vb in all of the premotor areas has some large pyramids as
predicted from the distribution of corticospinal projection
neurons. The largest, however, are in areas a24c0 , p24c0 (not
shown), and 24d. The following observations are of particular
note: (1) Kainate receptors are most dense in layers V and VI,
while AMPA and NMDA receptors are mainly in layers IIII/IV
in area 23c. The corticospinal neurons themselves are likely
under heavy regulation by kainate receptors, although their
apical dendrites in the superficial layers participate in other
glutamatergic functions. (2) Kainate receptors undergo a progressive diminution in density from rostral to caudal premotor
areas. (3) NMDA receptor densities are approximately equivalent as are GABAA receptor densities except for area 24d. This is
a common feature, therefore, for all of the premotor areas. The
fact that area 24d is under weak inhibitory control may have
significant functional consequences. (4) Area 24c0 has the
highest density of dopamine-1 receptors suggesting its involvement in coding the reward value of stimuli and contexts. Thus,
the cingulate premotor areas share many similarities in terms
of neuron composition and transmitter receptor binding.
Finally, area 23c is unique as it has a layer IV and relatively
the highest superficial layer GABAA regulation and the lowest
density of deep-layer kainate receptors.
332
(a)
(b)
p24c
(f)
p24b
(e)
area 24d
p33
p24a
(c) p24a
p24b
p24c
(d) X1.5
Figure 7 The cingulate premotor areas and adjacent areas on the gyral surface. (a) Sampling sites (different orientations due to a change in the
plane of section). (b) Section through area p240 . (c) Higher magnification of three p240 areas and (d) magnification of sections in (c) by 1.5. The red
asterisks in layer Vb emphasize the largest neurons in area p24c0 compared with those in area p24b0 . (e) Section through area 24d. (f) Three
preparations of area 24d including pigment architecture (PA) originally used by Heiko Braak to identify this area. These three photographs provide a
means of extrapolating from the PA to NeuN and SMI32 preparations. Scale bar, 100 mm.
Dorsal and Ventral Posterior Cingulate Cortex

Dorsal PCC (dPCC) is involved in topographic and topokinetic memory, that is, orientation of the body in space. Olson,
Musil, and Goldberg (1993, 1996) proposed that it is involved
in large visual scene assessment, part of which is subserved by
the orbital position of the eye and that the orbital position
signal is used to generate a map of the head and body in space.
Mental navigation along memorized routes elevates blood
flow in PCC (Berthoz, 1997; Ghaem et al., 1997; Maguire,
Frith, Burgiss, Donnett, & OKeefe, 1998), and topographic
disorientation is produced by right-hemisphere, perisplenial
lesions (Takahashi, Kawamura, Shiota, Kasahata, & Hirayama,

1997). In contrast, the ventral PCC (vPCC) evaluates the emotional and nonemotional contents of sensory objects and contexts in terms of self-relevance (Johnson et al., 2002; Phan,
Wager, Taylor, & Liberzon, 2002), it is activated to a greater
extent by familiar places than objects (Sugiura, Shah, Zilles, &
Fink, 2005), and it receives input from the ventral visual stream
(Vogt et al., 2006). The elegant study by Sugiura et al. showed
that vPCC has particularly high activity during exposure to
familiar places over objects and dPCC is most active during
presentation of familiar objects. Coactivation of RSC along
Kainate
AMPA
NMDA
GABAA
333
D1
24c
a24c
24d
23c
Figure 8 Sulcal area cytology with matched receptor binding from Palomero-Gallagher and Zilles (2009): area 24c in ACC, areas a24c0 and 24d in MCC,
and area 23c in dPCC. The lines on each cytoarchitectural area mark the border between layers IIIc and Va, and on the left magnified sections, it is
between layers Va and Vb. Of particular note is that layer Vb neurons are largest in areas a24c0 and 24d, kainate binding is highest in layer V of area 24c
and progressively decreases in caudal areas, AMPA receptors are mainly in superficial layers and decrease caudally, and dopamine-1 receptors are
at highest levels in area a24c0 and quite low in other areas. Scale bars, 500 mm; autoradiograph scale for relative comparisons.
with dPCC suggests that reciprocal connections among these

regions (Vogt & Pandya, 1987) have important functional
consequences. Thus, vPCC determines self-relevance via connections with sACC where long-term memories of valenced
events are stored and RSC where self-referenced episodic memories are stored. Such coding is then directed to MCC for
skeletomotor system output. In contrast, dPCC has a closer
link with MCC and appears to be associated with sensorimotor
orientation in space and rapid adjustments to visuospatial
needs in the context of the dorsal multisensory stream (Vogt
et al., 2006).
The PCC is composed of areas 23 and 31, and its two-part
parcellation is based on primate cytology (Vogt Vogt, Farber, &
Bush, 2005, 2006), monkey connections (Shibata & Yukie,
2003, 2009), human functional imaging (Vogt et al., 2006),
and multireceptor binding (Palomero-Gallagher et al., 2009).
The monkey vPCC was recognized by Goldman-Rakic, Selemon, and Schwartz (1984) as the caudomedial lobule (CML)
with heavy frontal connections, and later, its intracingulate
connections with sACC were reported (Vogt & Pandya,
1987). Further, Shibata and Yukie (2003) showed differential
thalamic afferents with dPCC receiving unique inputs from the
mediodorsal, central lateral, ventral anterior, and lateral nuclei.
Figure 9 compares a pair of sections dorsal to the splenium (b)
and caudal to it (e). The latter location is the CML (Figure
9(e)), which is an extension of the posterior cingulate gyrus
and is composed of ventral area 23 (Vogt et al., 2006).
Figure 9(b) (NeuN) shows the indusium griseum (IG) and
subicular rudiment (Sub) forming the fasciolar gyrus above the
corpus callosum. Ectosplenial area 26 is the first part of the

ventral bank of the CG, is transitional to area 29, and is composed mainly of an external pyramidal layer. Area d23b has less
densely packed layer II neurons, smaller pyramids in layer IIIc,
thin layer Va, and a relatively sparse layer Vb in comparison
with v23b (Figure 9(e); CML). Intermediate neurofilament
proteins are expressed by large pyramids in layers III and Va
and are more extensive in v23b than in d23b (Vogt et al.,
2006). Also, SMI32-labeled pyramids in layer Va of area d23b
are sparse in comparison with those in area v23b. Area 23c, in
contrast, has a thin layer IV and a very dense layer Va, and layer
IIIc is composed of larger neurons. The thickness of layers IIIV
in area 23c is significantly greater than that of layers VVI (layer
Va marked with red asterisk in Figure 9(b) and layer III in
Figure 9(c)). Finally, ventral area 31 (v31) (Figure 9(e)) has a
more pronounced layer II, quite large layer IIIc pyramids, a
broad layer IV, a thick layer Va, and a less dense layer Vb than
area 23c. Area 31 has the thickest layer IV of any cingulate area.
RSC and the Perisplenial Location

Human imaging has been plagued by mislocalizing RSC due
mainly to Talairach and Tournouxs (1988) interpretation of
Brodmanns map. While the latter map implied that RSC is in
the cas, the former authors extended areas 29 and 30 onto the
gyral surface caudal to the splenium. We analyzed this issue in
detail (Vogt Vogt, Perl, & Hof, 2001) and found no support for
it. A number of studies report small retrosplenial strokes (e.g.,
Takahashi et al., 1997) where the stroke not only is limited to
334
NeuN
SMI32
d23b
d23b
d23a
(a)
Area d23b
23c
23c
d23a
CML
(b)
v31
(c)
(d)
Area v23b
Area 30
v23b
v23a
36
(e)
(f)
(g)
Figure 9 Histology of posterior cingulate and retrosplenial cortices. (a) Medial surface with section orientations. The asterisk marks a splenial sulcus
(spls) branch that extends to the callosal sulcus (cas). (b) dPCC just caudal to dysgranular area 23d. The asterisk emphasizes the layer Va border
between areas d23b and 23c, and the square is the position of area 30 enlargement in (g) and (c) matched SMI32 section to (b), with the border of layer
III marked with an asterisk between areas d23b and 23c and an arrow showing area d23b enlarged in (d). (e) Caudomedial lobule (CML; NeuN) with
a box for the cortex enlarged for (f) v23b. (f, g) show the cytoarchitecture of the surface cortex on the CML and area 30 in the callosal sulcus. The key
point is that area 30 does not extend onto the caudal surface of the cingulate gyrus as shown in the Talairach and Tournoux (1988) atlas. Instead,
areas 29 and 30 are buried in the caudal end of the cas around the splenium of the corpus callosum (sCC). CG, cingulate gyrus; cgs, cingulate sulcus;
ECG, external cingulate gyrus; IG, indusium griseum; mr, marginal ramus of the cgs; pcgs, paracingulate sulcus; pos, parieto-occipital sulcus; Sub,
dorsal subicular rudiment. All scale bars are 1 mm.
RSC but also involves area 23 and part of area 31; white matter
damage assures that the resulting symptoms are not solely due
to damage to areas 29 and 30. This literature also blurs the
relationship between the retrosplenial location around the
splenium and RSC defined cytoarchitecturally. To avoid this
ongoing confusion, we suggest the term perisplenial when
referring to a general location around the splenium and reserving the word retrosplenial for cytoarchitectonically defined
areas 29 and 30. In the few instances where there is adequate
spatial resolution to locate RSC (Sugiura et al., 2005),
retrosplenial is a valid term.
Area 30 (Figure 9(g)) has a wide layer II from which layer
IIIab pyramids are poorly differentiated compared with that in
area v23b. Layer IIIc is clearly present but layer IV is dysgranular; that is, it is variable in thickness and pyramids in layers IIIc
and Va often intermingle. Layer Va is not as broad and neuron
dense as layer VI in area v23b and is substantially more elaborated than in area 30. These many differences assert the claim
that area 30 is not present on the caudal cingulate gyral surface.
Area 30, however, is also located in the cas around the splenium (Figure 9(e), sCC) where it is flanked by area 29m.
Magnetic Resonance Imaging: Subregions

and Connections
Although cytoarchitecturally defined areas and subregions
should serve as the basis of functional and connection studies,
there is an alternative approach. Torta and Cauda (2011)

divided cingulate cortex into 12 equally spaced regions of
interest (ROIs) for a meta-analytic coactivation analysis. The
12 ROIs were associated with different combinations of activity
including reward, attention, pain discrimination, emotion,
language, action execution, memory, semantic discrimination,
and episodic recall. Findings such as the role of ROI 8/area d23
(dPCC) in motor functions including action execution and
finger tapping are well known (Vogt & Sikes, 2009), and
there was a lack of precision of imaging outcomes based on
task design and vague definition of behavior and emotion that
reflect reward-related or pain-related activations. Further,
attention may underlie most of the tasks but is identified as a
unique function in one part of cingulate cortex. Thus, conclusions from a study that explicitly overlooked anatomical organization did not expand understanding of cingulate functions,
and this non-structure/function approach emphasizes the
importance of beginning with the cytoarchitectural map rather
than the opposite.
Diffusion Tensor Imaging Tractography

One of the best studies of human cingulate connections with
MR diffusion tensor imaging (DTI) is that of Beckmann,
Johansen-Berg, and Rushworth (2009). They determined cingulate connectivity with an algorithm to search for regional
variations in the probabilistic connectivity profiles of all cingulate voxels with the rest of the brain; nine subregions

emerged. The probabilities of a connection between cingulate
cortex and 11 predefined ROIs were also calculated, and cingulate voxels with a high probability of connection with the
different targets formed separate clusters (Figure 10(a)). An
explicit attempt was made to relate the connection clusters to
cytoarchitectural entities, but note the following: Although #1
was in sACC, #2 is split between this subregion and pACC;
although #3 is restricted to pACC, it does not differentiate areas
24 and 32; #4 is in aMCC and #6 in pMCC; however, #5 and
#7 extend throughout MCC and #8/#9 engages the entire PCC.
Thus, these clusters have some correlation with subregions but
do not designate cytoarchitectural areas because cingulate connections do not respect cytoarchitectural borders.
Figure 11 shows five of the connections and findings for
similar areas in the monkey. While it is not expected that
human and monkey connections have an exact correspondence, there should be some broad similarities. The amygdala
cluster is in sACC, and while the central nucleus of the amygdala does project to sACC (Chiba, Kayahara, & Nakano, 2001),
the lateral and accessory basal nuclei have extensive projections throughout ACC and aMCC. Although the hippocampus
has limited cingulate connections, parahippocampal cortex
has robust, widely distributed, and reciprocal connections
with most of the CG. Clusters 1, 2, and 79 reflect this fact to
some extent, although monkey connections predict a very
robust projection that should include all 9 clusters. The ventral
335
stratum identified mainly sACC and a small extension to area

33 along the cas. Again, this appears to be but a part of a much
larger projection for this region and the dorsal striatum.
Finally, clusters 12 and 57 were associated with the parietal
ROI, and this reflects to some extent the connection shown in
monkeys. Thus, some critical connectivity in the human cingulate cortex has been identified. From the outset, however, we
know that connections are not limited to single areas or subregions. Thus, cytoarchitecturally defined ROIs would be a
better method for analyzing cingulate connectivity and functions. Indeed, Yu et al. (2011) evaluated the cingulate subregional model with resting-state functional connectivity and
supported unique contributions of each subregion in different
cortical networks.
Parcellation with Landmarks

Figure 11(b) shows the outcome of a study by Destrieux et al.
(2010). They performed a computer-assisted hand parcellation
to classify each vertex as sulcal or gyral and then subparcelled
the cortex into 74 labels per hemisphere. Twelve datasets were
used to develop rules and algorithms that produced labels
consistent with anatomical rules and automated computational parcellation. This approach localized six cingulate
ROIs; ROI 32 incorporated area 25 but not the remainder of
sACC; six was in pACC, seven in aMCC, eight in pMCC, nine in
Figure 10 Medial surfaces from MRI studies. In all instances, the subregional borders are marked with arrows, and the external edge of the cingulate
cortex is marked with red dots. Red arrows in (b) and (d) emphasize mismatches between the boundary of cingulate cortex and the maps, and red
parentheses emphasize where area 32 should be located in the maps. (a) Beckmann et al. (2009), (b) Destrieux, Fischl, Dale, and Halgren (2010), (c, d)
Craddock, James, Holtzheimer, Hu, and Mayberg (2012) for 50 and 1000 specified ROIs, respectively, (e) left and (f) right hemispheres from Yeo,
Krienen, Sepulcre, et al. (2011).
336
Amygdala
CS
M
AB
LB
RS
Lat
Hippocampal cortex
CS
CC
RS
RS
RhS
Ventral striatum
CS
CS
CC
CC
Dorsal striatum
CS
CS
CC
CC
Parietal cortex
IPS
CS
CC
STS
Figure 11 Comparison of human connections shown by Beckmann et al. (2009) and those for monkey; striatal monkey connections from Kunishio and
Haber (1994) and all others from Vogt and Pandya (1987).
dPCC, and ten in vPCC. Area 32 on the ECG was not part of
pACC or aMCC (red brackets), and part of dPCC was not
included with ROI 9 (red arrow). Thus, this cingulate model
is close in many ways to the cytoarchitectural observations and
could be modified to accommodate these few shortcomings.
Local Connections
Craddock et al. (2012) used a data-driven method to generate
an ROI atlas by parceling whole-brain resting-state functional
MRI (fMRI) data into spatially coherent regions of homogeneous functional connectivity. ROI size and hence the number
of ROIs in a parcellation had the greatest impact on their
suitability for functional connectivity analysis. Figure 11

shows the outcome of specifying either 50 (c) or 1000 (d)
ROIs. There is some correspondence in the 50 ROI map to
the six cingulate subregions in the rostrocaudal (y-axis) plane,
but there is no relationship to areas in the dorsoventral (z-axis)
as the ROIs clearly extend beyond cingulate cortex and do not
identify area 32 of the ECG. These investigators state that
parcellation results containing higher numbers of ROIs (e.g.,
1000) most accurately represent functional connectivity patterns at the voxel scale and are preferable when interpretability
can be sacrificed for accuracy. Although ROIs in the cingulate
cortex reflect some cytoarchitectural boundaries, they still do
not identify area 32 of the ECG (red parenthesis) nor are they

accurate in the dorsal part of dPCC (red arrows). Thus, this
method identifies some relationships with boundaries set by
cytoarchitectural analyses; however, they are not exact and may
be viewed as confirmation of cytoarchitectural studies to the
extent that there are functional connectivity patterns supporting the rostrocaudal distribution of subregions.
Network Connections
Yeo et al. (2011) published a study of resting-state
functional connectivity using surface-based alignment, and
Figure 11(e) and 11(f) shows their results. The most striking
correspondences of these connections with the cytoarchitectural
map are in sACC, pACC, and dPCC, which were uniquely identified, and the differentiation of aMCC and pMCC. Sites of
discordance include the failure to identify area 32, the premotor
areas in aMCC, RSC is combined with PCC and heterogeneity in
vPCC. Of course, these are functional networks that do not
necessarily require concordance with cytoarchitectural observations, although it is a concern that area 32 does not stand out as
having unique connectivities.
Yu et al. (2011) evaluated resting-state functional connectivity of each cingulate subregion from a network perspective;
each subregion was integrated in predescribed functional networks and showed anticorrelated resting-state fluctuations.
The sACC and pACC were involved in an affective network
and anticorrelated with the sensorimotor and cognitive networks, while the pACC also correlated with the default-mode
network and anticorrelated with the visual network. The aMCC
was correlated with the cognitive and sensorimotor networks
and anticorrelated with the visual, affective, and default-mode
networks, whereas the pMCC correlated with the sensorimotor
network and anticorrelated with the cognitive and visual networks. The dPCC and vPCC involved in the default-mode
network and anticorrelated with the sensorimotor, cognitive,
337
and visual networks, and RSC was mainly correlated with the
PCC and thalamus. Based on this hypothesis-driven approach,
they confirmed the subregional analysis in terms of functional
neuroanatomy.
Correlations as Connections and Neuropathology

The premise of basal glucose metabolism or resting fMRI correlations is that regions with similar levels of activity at rest are
more likely to discharge together and engage in common
information transfers than regions with substantially different
levels of resting activity. Also, if direct connections have been
demonstrated between a pair of areas in the monkey, there is a
high probability that such sharing will occur. For example,
seeding of basal glucose metabolism was used to evaluate
correlations of dPCC and vPCC to determine circuits that
differentiate these two subregions identified anatomically
(Vogt et al., 2006). A major problem identifying connections
arises when they are assessed in disease states. When new
connections are found with seeding/correlation studies, does
this mean that there has been sprouting to form a new monosynaptic connection or has the disease itself altered metabolism and blood flow in a way that generates a new correlation
when a new connection has not grown?
Mainero, Boshyan, and Hadjikhani (2011) used restingstate fMRI to compare the functional connectivity between the
periaqueductal gray (PAG) and areas involved in nociception
and somatic sensation in subjects with migraine and healthy
controls when the former were pain-free (Figure 12(c)). They
showed stronger connectivity between the PAG and nociceptive and somatosensory areas in migraineurs. From a medial
surface perspective, however, it appears that pACC and aMCC
have a similar level of PAG correlations. Also, there are extensive correlations in PCC and parietal and visual cortices
that have little or nothing to do with pain (Figure 12(c2)).
(a)
24b
24c
24b
32
24a
24c
(c) 1
24b
24a
32
10 m
(b)
25
25
(c) 2
Figure 12 (a) Topographic projections to the periaqueductal gray (Dujardin & Jrgens, 2005; labeled neurons observed in all cases). Distribution
of PAG projection neurons in layer V of ACC (An, Bandler, Ongur, & Price, 1998). (c1) Correlations of fMRI voxels with PAG resting state in healthy
controls and (c2) PAG correlations in migraineurs (Mainero et al., 2011). The vast majority of PAG correlations in the migraine state do not represent
PAG connections.
338
Moreover, the PAG only receives rostral cortical afferents, which

are not reciprocal. Figure 12 shows cortical PAG afferents topographically (a) and by their layer of origin (b) in the monkey.
The following points are of note: (a) although PCC has limited
projections to the PAG, no correlations are in the control cases;
(b) projections from ACC and aMCC are massive, while the
correlations are weak in the rostral part of aMCC and nonexistent caudally; (c) correlations observed in the migraineurs
in PCC and parietal and visual cortices do not represent connections. It appears that bouts of cortical spreading depression
experienced during migraine have altered blood flow that
reflects basal levels normally seen in the PAG; however, the
correlations likely do not represent connections.
In conclusion, although the connectivity study of Yu et al.
(2011) confirmed unique interactions of cingulate subregions
with predetermined networks, DTI tractography shows only
weak connectivity of cingulate cortex. Since afferents never
terminate in a single area and efferents to a particular site do
not arise from single areas, strict correlations between cytology
and connections cannot be expected. Indeed, area 320 is one of
the more interesting areas from a functional perspective in its
role in feedback-mediated decision making (Bush, 2009), yet
none of the connection studies identifies area 320 as a unique
area. Also, low-density projections are not observed (e.g.,
amygdala projections to PCC; Buckwalter, Schumann, & Van
Hoesen, 2008), and cingulate sulci cannot be used to guide
locating areas. Where connections are particularly dense and
concentrated, like those between the mammillary bodies and
anterior thalamic nuclei, DTI provides a more compelling
picture of connectivity; however, such studies provide limited
information when applied to cingulate cortex itself (Granzieraa
et al., 2011).
The cingulate subregional model based on cytoarchitecture
and receptor binding evolved in tandem with functional imaging to produce a relatively coherent perspective on cingulate
organization. The purpose of the subregional model, however,
is not to simply provide labels and a descriptive framework,
but to understand structure/function units and a context for
predicting the role of cingulate subregions in complex cortical
networks.

Functional Connectivity; Quantitative Data and Scaling Rules of the
Cerebral Cortex; Sulci as Landmarks; Von Economo Neurons;
INTRODUCTION TO CLINICAL BRAIN MAPPING: Depression;
Emotion and Stress; Pain Syndromes; INTRODUCTION TO
COGNITIVE NEUROSCIENCE: Interactions between Attention and
Emotion; Value Representation; INTRODUCTION TO METHODS
AND MODELING: Diffusion Tensor Imaging; Tract Clustering,
Labeling, and Quantitative Analysis; INTRODUCTION TO SOCIAL
COGNITIVE NEUROSCIENCE: Emotion Perception and Elicitation;
Emotion Regulation; Empathy; How the Brain Feels the Hurt of
Heartbreak: Examining the Neurobiological Overlap Between Social and
Physical Pain; Mentalizing; INTRODUCTION TO SYSTEMS: Cortical
Action Representations; Emotion; Hubs and Pathways; Large-Scale
Functional Brain Organization; Neural Networks Underlying Novelty
Processing; Pain: Acute and Chronic; Reward.
References
Brodmanns areas 17 and 18 brought into stereotaxic space Where and how
An, X., Bandler, R., Ongur, D., & Price, J. L. (1998). Prefrontal cortical projections to
longitudinal columns in the midbrain periaqueductal gray in macaque monkeys.
Bancaud, J., & Talairach, J. (1992). Clinical semiology of frontal lobe seizures.
Advances in Neurology, 57, 358.
Beckmann, M., Johansen-Berg, H., & Rushworth, M. F. S. (2009). Connectivity-based
parcellation of human cingulate cortex and its relation to functional specialization.
Berthoz, A. (1997). Parietal and hippocampal contribution to topokinetic and
topographic memory. Philosophical Transactions of the Royal Society, B: Biological
Sciences, 352, 14371448.
Biber, M. P., Kneisley, L. W., & LaVail, J. H. (1978). Cortical neurons projecting to the
cervical and lumbar enlargements of the spinal cord in young and adult rhesus
monkeys. Experimental Neurology, 59, 492508.
Braak, H. (1976). A primitive gigantopyramidal field buried in the depth of the cingulate
sulcus of the human brain. Brain Research, 109, 219233.
Brodmann, K. (1909). Vergleichende lokalisationslehre der grosshirnrinde in ihren
prinzipien dargestellt auf grund des zellenbaues. Leipzig: Barth.
Buckwalter, J. A., Schumann, C. M., & Van Hoesen, G. W. (2008). Evidence for direct
projections from the basal nucleus of the amygdala to retrosplenial cortex in the
Macaque monkey. Experimental Brain Research, 186, 4757.
Bush, G. (2009). Dorsal anterior midcingulate cortex: Roles in normal cognition and
disruption in attention-deficit/hyperactivity disorder. In B. A. Vogt (Ed.), Cingulate
neurobiology and disease (pp. 245274). London: Oxford University Press.
Bush, G., Luu, P., & Posner, M. I. (2000). Cognitive and emotional influences in
anterior cingulate cortex. Trends in Cognitive Sciences, 4, 215222.
Cajal, R. Y. (1999). Advice for a young investigator. Cambridge, MA: MIT Press,
translated by Swanson, N. and Swanson, L. W.
Chiba, T., Kayahara, T., & Nakano, K. (2001). Efferent projections of infralimbic and
prelimbic areas of the medial prefrontal cortex in the Japanese monkey, Macaca
fuscata. Brain Research, 888, 83101.
Craddock, R. C., James, G. A., Holtzheimer, P. E., III, Hu, X. P., & Mayberg, H. S.
(2012). A whole brain fMRI atlas generated via spatially constrained spectral
clustering. Human Brain Mapping, 33, 19141928.
Destrieux, C., Fischl, B., Dale, A., & Halgren, E. (2010). Automatic parcellation of
NeuroImage, 53, 115. http://dx.doi.org/10.1016/j.neuroimage.2010.06.010.
Dujardin, E., & Jrgens, U. (2005). Afferents of vocalization-controlling periaqueductal
regions in the squirrel monkey. Brain Research, 1034, 114131.
Enriquez-Geppert, S., Eichele, T., Specht, K., Kugel, H., Pantev, C., & Huster, R. J.
(2013). Functional parcellation of the inferior frontal and midcingulate
cortices in a Flanker-stop-change paradigm. Human Brain Mapping, 34(7),
15011514.
Escobedo, F., Fernandez-Guardiola, A., & Solis, G. (1973). Chronic stimulation of the
cingulum in humans with behavior disorders. In L.V. Laitinen & K. E. Livingston
(Eds.), Surgical approaches in psychiatry (pp. 6568). Lancaster (UK), Baltimore:
MTP.
George, M. S., Ketter, T. A., Gill, D. S., Haxby, J., Ungerleider, L. G., Herscovitch, P.,
et al. (1993). Brain regions involved in recognizing facial emotion or identity: An
oxygen-15 PET study. Journal of Neuropsychiatry and Clinical Neurosciences, 5,
384394.
George, M. S., Ketter, T. A., Parekh, P. I., Horwitz, B., Herscovitch, P., & Post, R. M.
(1995). Brain activity during transient sadness and happiness in healthy women.
The American Journal of Psychiatry, 152, 341351.
Ghaem, O., Mellet, E., Crivello, F., Tzourio, N., Mazoyer, B., Berthoz, A., et al. (1997).
Mental navigation along memorized routes activates the hippocampus, precuneus,
and insula. NeuroReport, 8, 739744.
Goldman-Rakic, P. S., Selemon, L. D., & Schwartz, M. L. (1984). Dual pathways
connecting the dorsolateral prefrontal cortex with the hippocampal
formation and parahippocampal cortex in the rhesus monkey. Neuroscience, 12,
719743.
Grachev, I. D., Berdichevsky, D., Rauch, S. L., Heckers, S., Kennedy, D. N.,
Caviness, V. S., et al. (1999). A method for assessing the accuracy of intersubject
registration of the human brain using anatomic landmarks. NeuroImage, 9,
250268.
Granzieraa, C., Hadjikhanif, N., Arzyc, S., Seeckd, M., Meulib, R., & Kruegere, G.
(2011). In-vivo magnetic resonance imaging of the structural core of the Papez
circuit in humans. NeuroReport, 22, 227231.

Habas, C. (2010). Functional connectivity of the human rostral and caudal cingulate
motor areas in the brain resting state at 3 T. Neuroradiology, 52, 4759.
James, W. (1884). What is emotion? Mind, 9, 188205.
Johnson, S. C., Baxter, L. C., Wilder, L. S., Pipe, J. G., Heiserman, J. E., &
Prigatano, G. P. (2002). Neural correlates of self-reflection. Brain, 125, 18081814.
Kirsch, P., Schienle, A., Stark, R., Sammer, G., Blecker, C., Walter, B., et al. (2003).
Anticipation of reward in a nonaversive differential conditioning paradigm and the
brain reward system: An event-related fMRI study. NeuroImage, 20, 10861095.
Kunishio, K., & Haber, S. N. (1994). Primate cingulostriatal projection: Limbic striatal
versus sensorimotor striatal input. Journal of Comparative Neurology, 350, 337356.
Kwan, C. L., Crawley, A. P., Mikulis, D. J., & Davis, K. D. (2000). An fMRI study of the
anterior cingulate cortex and surrounding medial wall activations evoked by noxious
cutaneous heat and cold stimuli. Pain, 85, 359374.
Li, D. F., Freeman, A. W., Tran-Dinh, H., & Morris, J. G. (2003). A Cartesian coordinate
system for human cerebral cortex. Journal of Neuroscience Methods, 125, 137145.
Luppino, G., Matelli, M., Camarda, R. M., Gallese, V., & Rizzolatti, G. (1991). Multiple
representations of body movements in mesial area 6 and the adjacent cingulate
cortex: An intracortical microstimulation study in the macaque monkey. Journal of
Maguire, E. A., Frith, C. D., Burgiss, N., Donnett, J. G., & OKeefe, J. (1998). Knowing
where things are: Parahippocampal involvement in encoding object locations in
virtual large-scale space. Journal of Cognitive Neuroscience, 10, 6176.
Mainero, C., Boshyan, J., & Hadjikhani, N. (2011). Altered functional magnetic
resonance imaging resting-state connectivity in periaqueductal gray networks in
migraine. Annals of Neurology, 70, 838845.
Mayberg, H. S., Liotti, M., Brannan, S. K., McGinnis, S., Mahurin, R. K., Jerabek, P. A.,
et al. (1999). Reciprocal limbic-cortical function and negative mood: Converging
PET findings in depression and normal sadness. The American Journal of
Meyer, G., McElhaney, M., Martin, W., & McGraw, C. P. (1973). Stereotactic
cingulotomy with results of acute stimulation and serial psychological testing. In
L. V. Laitinen & K. E. Livingston (Eds.), Surgical approaches in psychiatry
(pp. 3958). Lancaster (UK), Baltimore: MTP.
Murtha, S., Chertkow, H., Beauregard, M., Dixon, R., & Evans, A. (1996). Anticipation
causes increased blood flow to the anterior cingulate cortex. Human Brain Mapping,
4, 103112.
Nowinski, W. L. (2001). Modified Talairach landmarks. Acta Neurochirurgica, 143,
10451057.
Nudo, R. J., & Masterton, R. B. (1990). Descending pathways to the spinal cord, III:
Sites of origin of the corticospinal tract. Journal of Comparative Neurology, 296,
559583.
Olson, C. R., Musil, S. Y., & Goldberg, M. E. (1993). Posterior cingulate cortex and
visuospatial cognition: Properties of single neurons in the behaving monkey. In
B. A. Vogt & M. Gabriel (Eds.), Neurobiology of cingulate cortex and limbic
thalamus. Boston: Birkhauser.
Olson, C. R., Musil, S. Y., & Goldberg, M. E. (1996). Single neurons in posterior
cingulate cortex of behaving macaque: Eye movement signals. Journal of
Neurology, 508, 906926.
Palomero-Gallagher, N., Schleicher, A., Zilles, K., & Vogt, B. A. (2013). Differentiation
of monkey area 32 and human comparative analysis. Journal of Comparative
Neurology, 521, 32723286.
Palomero-Gallagher, N., Vogt, B. A., Mayberg, H. S., Schleicher, A., & Zilles, K. (2009).
Receptor architecture of human cingulate cortex: Evaluation of the four region
neurobiological model. Human Brain Mapping, 30, 23362355.
regions and areas. In B. A. Vogt (Ed.), Cingulate neurobiology and disease
(pp. 3163). London: Oxford University Press.
Phan, K. L., Wager, T., Taylor, S. F., & Liberzon, I. (2002). Functional neuroanatomy of
emotion: A meta-analysis of emotion activation studies in PET and fMRI.
Pool, J. L. (1954). The visceral brain of man. Journal of Neurosurgery, 11, 4563.
Pool, J. L., & Ransohoff, J. (1949). Autonomic effects on stimulating rostral portion of
cingulate gyri in man. Journal of Neurophysiology, 12, 385392.
Posner, M. I., Peterson, S. E., Fox, P. T., & Raichle, M. E. (1988). Localization of
cognitive operations in the human brain. Science, 240, 16271631.
339
Shibata, H., & Yukie, M. (2003). Differential thalamic connections of the posteroventral
and dorsal posterior cingulate gyrus in the monkey. European Journal of
Shibata, H., & Yukie, M. (2009). Temporocingulate interactions in the monkey. In B. A.
Vogt (Ed.), Cingulate neurobiology and disease (pp. 145162). London: Oxford
University Press.
Shima, K., Aya, K., Mushiake, H., Inase, M., Aizawa, H., & Tanji, J. (1991). Two
movement-related foci in the primate cingulate cortex observed in signal-triggered
and self-paced forelimb movements. Journal of Neurophysiology, 65, 188202.
Shima, K., & Tanji, J. (1998). Role for cingulate motor area cells in voluntary movement
selection based on reward. Science, 282, 13351338.
Shin, L. M., Lasko, N. B., Macklin, M. L., Karpf, R. D., Milad, M. R., Orr, S. P., et al.
(2009). Resting metabolic activity in the cingulate cortex and vulnerability to
posttraumatic stress disorder. Archives of General Psychiatry, 66, 10991107.
Sugiura, M., Shah, N. J., Zilles, K., & Fink, G. R. (2005). Cortical representations of
personally familiar objects and places: Functional organization of the human
posterior cingulate cortex. Journal of Cognitive Neuroscience, 17, 116.
Takahashi, N., Kawamura, M., Shiota, J., Kasahata, N., & Hirayama, K. (1997). Pure
topographic disorientation due to right retrosplenial lesion. Neurology, 49,
464469.
Talairach, J., Bancaud, J., Geier, S., Bordas-Ferrer, M., Bonis, A., & Szikla, G. (1973).
The cingulate gyrus and human behavior. Electroencephalography and Clinical
Talairach, J., & Tournoux, P. (1988). Co-planar stereotaxic atlas of the human brain.
Stuttgart and New York: Georg Thieme.
Torta, D. M., & Cauda, F. (2011). Different functions in the cingulate cortex, a metaanalytic connectivity modeling study. NeuroImage, 56, 21572172.
Vogt, B. A. (2009a). Regions and subregions of the cingulate cortex. In B. A. Vogt (Ed.),
Cingulate neurobiology and disease (pp. 330). London: Oxford University Press.
Vogt, B. A. (2009b). Architecture, neurocytology and comparative organization of
monkey and human cingulate cortices. In B. A. Vogt (Ed.), Cingulate neurobiology
and disease (pp. 6593). London: Oxford University Press.
Vogt, B. A., & Palomero-Gallagher, N. (2012). Cingulate cortex. In G. Paxinos & J. K.
Mai (Eds.), The human nervous system (pp. 943987) (3rd ed.). Amsterdam:
Academic Press (Chapter 25).
Vogt, B. A., & Pandya, D. N. (1987). Cingulate cortex of rhesus monkey. II. Cortical
afferents. Journal of Comparative Neurology, 262, 271289.
Vogt, B. A., & Paxinos, G. (2014). Cytoarchitecture of mouse and rat cingulate cortex
with human homologies. Brain Structure and Function, 219, 185192. http://dx.
doi.org/10.1007/s00429-012-0493-3.
Vogt, B. A., & Sikes, R. W. (2009). Cingulate nociceptive circuitry and roles in pain
processing: The cingulate premotor pain model. In B. A. Vogt (Ed.), Cingulate
neurobiology and disease (pp. 312338). London: Oxford University Press.
Vogt, C., & Vogts, O. (1919). Allegemeine ergebnisse unserer hirnforschung. Journal
Vogt, B. A., & Vogt, L. J. (2009). Opioids, placebos and descending control of pain and
stress systems. In B. A. Vogt (Ed.), Cingulate neurobiology and disease (pp. 339
364). London: Oxford University Press.
Vogt, B. A., Berger, G. R., & Derbyshire, S. W. J. (2003). Structural and functional
dichotomy of human midcingulate cortex. European Journal of Neuroscience, 18,
31343144.
Vogt, B. A., Vogt, L. J., & Laureys, S. (2006). Cytology and functionally correlated
circuits of posterior cingulate areas. NeuroImage, 29, 452466.
Vogt, B. A., Nimchinsky, E. A., Vogt, L. J., & Hof, P. R. (1995). Human cingulate cortex:
Surface features, flat maps, and cytoarchitecture. Journal of Comparative Neurology,
359, 490506.
Vogt, B. A., Vogt, L., Farber, N. B., & Bush, G. (2005). Architecture and
neurocytology of the monkey cingulate gyrus. Journal of Comparative Neurology,
485, 218239.
Vogt, B. A., Vogt, L. J., Perl, D. P., & Hof, P. R. (2001). Cytology of human caudomedial
cingulate, retrosplenial, and caudal parahippocampal cortices. Journal of
Yeo, B. T.T, Krienen, F. M., Sepulcre, J., Sabuncu, M. R., Lashkari, D., Hollinshead, M.,
Yu, C., Zhou, Y., Liu, Y., Jiang, T., Dong, H., Zhang, Y., et al. (2011). Functional
segregation of the human cingulate cortex is confirmed by functional connectivity
based neuroanatomical parcellation. NeuroImage, 54, 25712581.
Amygdala
D Yilmazer-Hanke, Creighton University, Omaha, NE, USA
Glossary
Allocortex (noun), allocortical (adjective) The allocortex

is a cortex that is different from the typically six-layered
isocortex.
Ammons horn sclerosis (also hippocampal
sclerosis) Loss of pyramidal neurons in the hippocampal
sector CA1 (Sommers sector) combined with glial scar
formation that is often associated with some damage to
other hippocampal sectors.
Beta-amyloid deposits Extracellular accumulation of
amyloid-beta peptides that form deposits associated with
neural toxicity and inflammation.
Commissure White matter tract that connects the right and
left sides of the central nervous system.
Cytoarchitecture Architecture of a brain region based on
neuronal cell types including their morphology and
locations.
Deja` vu Just knowing or the perception that something is
familiar, often resulting from a simplex partial seizure (focal
seizure without loss of consciousness).
Downstream connection Efferent connection of a brain
region to another brain region, which controls the function
of the latter region based on the hierarchical organization of
the brain.
Epigastric aura Simplex partial seizure (focal seizure
without loss of consciousness) with epigastric symptoms
like sensation or discomfort arising in the abdominal region.
Homology (noun), homologous (adjective) Similarity of
structures based on evolutionarily or developmentally
common origin.
Ictal An event that occurs during a seizure.
Interictal An event that occurs between seizures.
Isocortex (noun), isocortical (adjective) Six-layered cortex
typically found in the mammalian telencephalon.
Lewy bodies Round intracellular inclusions often with a
halo found in Parkinsons disease and related disorders that
contain abnormal aggregates of ubiquitylated proteins,
mainly of alpha-synuclein.
The amygdala (from the Greek word amygdala pl. amygdalae)

is a nuclear complex located in the medial temporal lobe of
the brain (Figure 1). As a high-order limbic brain region,
it controls attention, motivation, autonomic functions, and
emotional recognition, learning, and memory. Due to its
involvement in various emotional and neurological disorders,
the amygdala has further attracted considerable attention from
clinicians and researchers.
The amygdaloid complex was first discovered in the beginning of the nineteenth century by Burdach (181922). Meynert
(1867) and Kolliker (1886) gave a more detailed description of
this brain region, but Volsch (190610) provided the most
Lewy neurites Neurites with elongated inclusion containing

the same material found in Lewy bodies.
Limbic brain regions Brain regions that form an arc at the
medial surface of each cerebral hemisphere.
Lipofuscin Autofluorescent granules with brown-yellowish
appearance in histological sections that accumulate in longliving cells, which correspond to lipid-containing residues in
lysosomes.
Magnocellular Large-celled, composed of large cells.
Neurite Neuronal cell processes of undefined origin that
could be axonal or dendritic.
Neurofibrillary tangles Intracellular accumulation of the
insoluble form of hyperphosphorylated protein tau.
Nuclear complex A brain region that is composed of a
conglomeration of miscellaneous nuclei.
Ontogenesis (noun), ontogenetic (adjective) The
development of an individual organism from
embryogenesis through adulthood until aging.
Pallium (noun), pallial (adjective) Cortex or cortical.
Parvicellular (also parvocellular) Small-celled, composed
of small cells.
Periallocortex (noun), periallocortical (adjective) The
periallocortex is a transitory cortex interposed between the
allocortex and isocortex.
Perisomatic Around the soma (cell body).
Phylogenesis (noun), phylogenetic (adjective) The
evolutionary development of species.
Piriform Pear-shaped.
Sublenticular Below the lenticular nucleus (a name for the
putamen and globus pallidus together, although these two
nuclei are anatomically and functionally different).
Subpallium (noun), subpallial (adjective) Subcortical
region (below the cortex).
Topography (distinguish from topology) Description of
the spatial relationship of anatomical structures in a certain
region.
Topology The spatial organization of distant parts of a
structure in relationship to each other.
comprehensive delineation of individual nuclei of the mammalian amygdala. Johnston (1923) included observations in
marsupials, reptiles, and amphibians into his considerations
and adapted the delineation of amygdalar nuclei to the modern nomenclature, which is still used today with some
variation.
Recent classifications of the amygdala often distinguish
three major nuclear groups that are anatomically, functionally,
developmentally, and evolutionarily distinct: (i) the deeply
located basolateral group, which develops from the claustroamygdaloid complex and shows coordinated expansion along
with the evolutionarily newer neocortical sensory association
http://dx.doi.org/10.1016/B978-0-12-397025-1.00232-3
341
342
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | Amygdala
Figure 1 Oblique view to the brain showing ventral (basal) and medial
parts of the temporal and frontal lobes and midline structures. The
amygdala expands laterally where it is deeply hidden in the medial
temporal lobe. It reaches the surface of the medial temporal lobe at the
semilunar gyrus (SLG), which is separated from the parahippocampal
gyrus (PHG) by the semiannular sulcus (sas). AS, anterior perforating
substance; CrC, crus cerebri; cs, collateral sulcus; FuG, fusiform
gyrus; III. V, the 3rd ventricle; IRc, infundibular recess; MB, mammillary
body; OCh, optic chiasm; Olf, olfactory; OT, optic tract; PHG,
parahippocampal gyrus; rs, rhinal sulcus; sas, semiannular sulcus; SLG,
semilunar gyrus; SN, substantia nigra; SRc, supraoptic recess; TPol,
pole of the temporal lobe. Black pin fixes the OCh at the base of the frontal
lobe. Bar 1 cm.
areas and related allocortical/periallocortical regions; (ii) a

phylogenetically old and layered superficial cortex-like region at
the medial surface of the amygdala that is linked to the olfactory system; and (iii) the centromedial group of the amygdala
with a subcortical-like cytoarchitecture and downstream connections for the regulation of species-specific behaviors like
fear, fighting, defense, feeding, and reproduction. The term
extended amygdala refers to nuclei with homology to the centromedial group, which are located in the basal forebrain or are
embedded in the stria terminalis, a fiber tract extending to the
main body of the amygdala.
Topography
In mammals, large portions of the amygdala proper are surrounded by temporal cortical areas. In primates, the amygdala
is encircled anteriorly by the piriform cortex and ventrally by
the entorhinal cortex. This is in marked contrast to rodents, in
which the piriform cortex lies ventrally and the entorhinal
cortex is localized posteriorly, indicating an anterior rotation
of primate mesiotemporal structures. In many mammalian
species, the hippocampus head is interposed between the
amygdala and the respective cortex at caudal levels. Laterally,
the inferior limb of the external capsule separates the basolateral group of the amygdala from the claustrum and endopiriform nucleus. The superficial cortex-like region and the medial
nucleus (Me) assigned to the centromedial group occupy the
medial surface of the amygdala. The central nucleus (Ce), also
located in the latter group, lies in the angle between the Me and
basolateral group. Dorsally, the Me and Ce are surrounded by
various basal forebrain structures. The cortical fiber systems
connecting the amygdala with other brain areas run in the
external capsule and subamygdaloid white matter. The ventral
amygdalofugal pathway and stria terminalis connect the amygdala

to subcortical areas (Figure 2).
The lateral (LA), basolateral (BL, also basal), and basomedial
(BM, also accessory basal) nuclei forming the basolateral nuclear
group are separated by medullary laminae. The BL and
BM have magnocellular and parvicellular subnuclei, and caudal portions of all three nuclei reach the lateral ventricle. In
primates, a paralaminar nucleus was also described. In the
cortex-like superficial region, a nucleus of the olfactory tract
(NLOT) and a cortical amygdaloid nucleus (Co) are distinguished. The Co has rostral (anterior) and caudal (posterior)
parts recognizable in many mammals. In the centromedial
group, the Me forms a crescent shape around the fundus of
the entorhinal sulcus neighboring ventrally the Co. The rodent
and hamster Me is composed of at least three divisions, named
the anterior, posteroventral, and posterodorsal subnuclei.
In the Ce, medial, lateral, and lateral capsular subnuclei
were recognized. Groups of intercalated nuclei (ICN) that
belong to the centromedial group are interspersed between
the basolateral group and Ce/Me. In addition, the amygdaloid
body has several transition areas with neighboring regions
including the amygdalapiriform, amygdalarentorhinal
(parahippocampalamygdaloid), amygdalarhippocampal,
amygdalarclaustral, and amygdalarstriatal areas.
The extended amygdala consists of distant forebrain nuclei
that are not located within the amygdaloid body itself, but are
connected to it through cell bridges. The anterior cell bridge is
formed by the sublenticular extended amygdala (SLEA) and
interstitial nucleus of the posterior limb of the anterior
commissure localized in the substantia innominata and also
includes the anterior amygdaloid area. These cell groups share
similarities with neurons in specific subnuclei of the centromedial group and radiate into the corresponding (sub)nuclei
of the Ce and Me. The posterior cell bridge is formed by the bed
nucleus of the stria terminalis (BST). The main portion of
the BST is localized between the lateral septum and caudate
putamen complex. However, additional cell groups of the BST
embedded in the stria terminalis form a column, which courses
along the wall of the lateral ventricle and blends into the
amygdala from posteriorly.
Architecture
The cell types found in the basolateral group are comparable to
the cerebral cortex, but nuclei in this group do not occupy the
brain surface. Instead, they form a subcortical nuclear mass
similar to the claustrum. Like in the cortex, approximately
7090% of neurons in the basolateral group constitute glutamatergic spiny modified pyramidal and stellate projection
neurons. These neurons do not show a recognizable pattern
in their orientation within individual amygdalar nuclei, compatible with a nuclear rather than cortical organization. The
remaining neurons consist of a heterogeneous population of
nonpyramidal spine-sparse interneurons with various sizes
and shapes that are mostly GABAergic and classically coexpress
a variety of neuropeptides such as neuropeptide Y, somatostatin, vasoactive intestinal peptide, and cholecystokinin.
Projection neurons and interneurons have common electrophysiological properties with their cortical counterparts.
343
Figure 2 Coronal myelin sections through the middle third of the main body of the amygdala at the z-coordinate 5.4 mm. Acp, anterior commissure
posterior limb; AG, ambient gyrus; al, ansa lenticularis; BC, basal nucleus of Meynert; BL, basolateral amygdaloid nucleus (also basal nucleus); i,
intermediate part; mg, magnocellular part; pvl, lateral parvicellular part; pvm, medial parvicellular part; BM, basomedial amygdaloid nucleus (also
accessory basal nucleus); mg, magnocellular part; pv, parvicellular part; vm, ventromedial part; CeL, central amygdaloid nucleus lateral part; CeM,
central amygdaloid nucleus medial part; Cl, claustrum; en, entorhinal sulcus; Ent, entorhinal cortex; Epn, endopiriform nucleus; icm, intermediate
caudomedial fiber masses; ICN, intercalated nuclei; ilf, inferior longitudinal fasciculus (also inferior limb of the external capsule); La, lateral amygdaloid
nucleus; DM, dorsomedial part; L, lateral part; VM, ventromedial part; li, intermediate amygdalar medullary lamina; ll, lateral amygdalar medullary
lamina; lm, medial amygdalar medullary lamina; MeP, medial amygdaloid nucleus posterior part; ot, optic tract; PHA, parahippocampalamygdaloid
area; PL, paralaminar amygdaloid nucleus; Pu, putamen; sas, semiannular sulcus (also semiannular fissure or amygdaloid fissure); SLEA, sublenticular
extended amygdala; SLG, semilunar gyrus; SO, supraoptic nucleus; unc, uncinate fasciculus; unn, uncal notch; VCo, ventral cortical nucleus; Ri,
rostral inferior part; Rs, rostral superior part. Adapted from Yilmazer-Hanke et al. (2012a) and the Atlas of the Human Brain, Plate 26 in Mai et al. (2007),
with permission from Academic Press.
The superficial cortex-like region harboring the Co and

NLOT resembles in many ways primitive olfactory cortical
areas such as the (pre)piriform (primary olfactory) cortex.
The neuronal cell types in this region match those in the
basolateral group, although dendritic branching of pyramidal
neurons is less complex than in the deep nuclei. Golgi studies
in various mammals show that the apical dendrites of pyramidal neurons, which are located in the outer and deep cellular
layers of the Co, extend into the superficial molecular layer.
Some parts of this amygdalar region were called periamygdaloid cortex, because its three-layered structure and the pattern
of its intense anatomical connections to olfactory cortical and
subcortical areas parallel an olfactory cortical organization.
However, there are also some differences in the ontogenetic
development of the Co in comparison with the cerebral cortex,
because, contrary to the cortex, it develops in an outside-in
fashion. In addition, some subfields are poorly laminated, and
therefore, the term cortical amygdaloid nucleus (Co) has
persisted along with the term periamygdaloid cortex in the
amygdalar nomenclature.
The nuclei of the centromedial group possess GABAergic
and peptidergic long-distance projection neurons that target
the hypothalamus and/or brain stem. The laterally located
nuclei, namely, the ICN and lateral/lateral capsular Ce, contain
striatal-type medium-sized spiny neurons with extensive dendritic branching. In contrast, neurons in the Me and medial Ce
contain ovoid or fusiform perikarya and sparsely branched

dendritic trees with fewer spines. So far, interneurons were
only reported in the Ce and ICN. Consistent with the concept
of extended amygdala, the morphology of neurons in the
lateral extended amygdala resembles neurons in the ICN and
lateral/lateral capsular Ce, whereas neurons of the medial
extended amygdala show a larger similarity to neurons of the
medial Ce and Me.
Development
The cortex-like cytoarchitecture in the basolateral nuclear
group and superficial cortex-like amygdala suggests a common
origin of neuronal cell types in both regions. Developmental
studies show that neurons in these two regions are derived
from specific pools of telencephalic progenitor neurons. Both
amygdalar regions are populated by excitatory pyramidal neurons displaying various pallial markers during development
(e.g., Emx2 and Tbr1) and by interneurons migrating from
the medial or caudal ganglionic eminences.
The centromedial nuclei located in the amygdala proper
contain neurons that originate mostly from subpallial telencephalic regions. Because neurons in the extended amygdala
show morphological, histochemical, neurochemical, and connectional similarities to neurons in the centromedial group,
344
neurons in corresponding parts may have a similar developmental origin. Indeed, the majority of neurons that migrate to
the Me and medial nuclei of the BST and SLEA originate from
the telencephalic anterior peduncular and preoptic areas. Furthermore, the Ce, ICN, lateral BST, and lateral SLEA all contain
neurons expressing markers of the lateral ganglionic eminence
(striatal primordium). Yet, the lateral BST may have a different
developmental origin than the rest of this group, because
in-wandering cells predominantly originate from the medial
ganglionic eminence (pallidal primordium) rather than the
striatum, at least at early developmental stages.
Connections
The basolateral group and cortex-like superficial region are the
sensory input stations of the amygdala. Olfactory inputs predominate in the Co and NLOT, but intra-amygdalar and insular afferents are other significant sources of information. In
contrast, the basolateral group receives converging multimodal
cortical and subcortical sensory afferents, which is the basis for
associative learning. These afferents arise from high-order
visual, acoustic, somatosensory, gustatory, and viscerosensory
cortical areas and the posterior thalamus. Both regions also
have extensive connections with fronto-temporo-insular cortical areas. Connections to the entorhinalhippocampal system
contribute to the integration of emotional and contextual/
cognitive information, whereas direct and indirect projections
(through ventral striato-pallidal regions and mediodorsal thalamic nuclei) to medial prefrontal areas are important for
motivation, goal-directed behavior, and decision-making.
The centromedial nuclei are characterized by prominent
downstream projections. The Me is a heterogeneous and sexually dimorphic nucleus that is mainly driven by olfactory stimuli and modulates food intake, sexual behavior, and defensive
responses through projections to hypothalamic areas. The Ce
controls fear responses and autonomic reactions through projections to various hypothalamic and brain stem regions. Both
nuclei are also involved in the regulation of hormonal homeostasis. Evolutionarily, the superficially located Me is often
regarded as an anatomical and functional continuum with
the Co, a primitive layered superficial amygdalar region associated with the olfactory system, because the two regions coevolved independently in various species known to
communicate with olfactory signals. This is in stark contrast
to the Ce that serves as a striatal-like viscero- and somatomotor
output center of the basolateral group, which is driven by
multimodal but nonolfactory stimuli. Nevertheless, a considerable portion of the Me and Co lack connections with olfactory areas in primates, suggesting an adaptation to more
complex social behaviors. Recent behavioral data in rodents
further indicate that distinct subregions of the BST are involved
in similar behaviors and functions like the Ce and Me.
Role in Emotional Behavior and Learning and Memory

The amygdala plays an essential role in the regulation of emotional responses and species-specific behaviors. The integration
of multimodal external and internal stimuli allows the
amygdala to fulfill these multiple functions. In functional

studies, only 47% of amygdalar neurons respond to different
types of unimodal stimuli (visual, acoustic, somatosensory,
and gustatory), but this changes rapidly when more complex
stimuli are presented. The amygdala engages heavily when
individuals are exposed to food; to stimuli that are novel or
have cognitive significance; to faces, especially if they are
loaded with emotions; or to rewarding or punishing reinforcers. Imaging studies further documented lateralization of
amygdalar activity in humans and amygdalar involvement in
declarative (conscious) learning and sound processing including tinnitus. Species differences in amygdalar chemoarchitecture were shown for the expression of peptides and transmitter
receptors, but their impact on behavior is less clear.
Without doubt, the amygdala is critical for the acquisition,
recall, consolidation, reconsolidation, and extinction of
implicit (unconscious) forms of emotional learning, which
are best characterized in Pavlovian (classical) conditioning
paradigms. In rodents, synchronous oscillation of amygdalar
neurons in concert with cortical brains areas during emotional
learning and recall is thought to promote synaptic plasticity.
Emotional memory is stored at neocortical sites, but synaptic
plasticity also occurs in the amygdala and related brain areas.
In the classical fear circuit, the La acts as the sensory input
station for the converging neutral stimulus (NS) and aversive
unconditioned stimulus (US) during learning of conditioned
responses. Through associative learning, the NS is transformed
into a conditioned stimulus that elicits the fear response in the
absence of the US. The information processed in the basolateral group is relayed to the Ce and ICN for the induction and
inhibition of the conditioned fear response, respectively
(Figure 3(a)). In instrumental learning, where unpleasant
stimuli can be avoided through decision-making, as well as in
reward processing and motivation-related behavior, the connections of the BL to the prefrontal cortex are essential (Figure
3(b)). Amygdalarinsular pathways are important in taste conditioning and for gustatory memory formation. The connections of the Ce to the cholinergic basal forebrain nuclei are vital
for attentional processes related to emotional learning.
Amygdalar Pathology in Disorders

Amygdalar dysfunction can lead to a variety of emotional
disorders. Among those, anxiety disorders such as generalized
anxiety disorder, panic disorder, post-traumatic stress disorder,
obsessivecompulsive disorder, and social phobia become
increasingly common. The involvement of the amygdala in
stress regulation may be related to alterations found in depression and bipolar disorder and also withdrawal-associated
symptoms in addiction. In addition, the amygdala seems to
contribute to deficits in social behavior found in autism spectrum disorders and schizophrenia.
Amygdalar damage is well documented in mesial temporal
lobe epilepsy, and the removal of the amygdala has been
incorporated in standard surgical procedures aimed at treating
intractable epilepsy. Neuronal loss, astrogliosis, and perineuronal satellitosis are more severe in cases with Ammons horn
sclerosis. A loss of perisomatic inhibition and alterations in
peptidergic interneurons were reported. Patients often suffer
MEDIAL PREFRONTAL
CORTEX
MEDIAL PREFRONTAL
CORTEX
tion
tinc
r ex
Fea
CS+US
La
ICN
BL
HIPPOCAMPAL
FORMATION
CA1
CA3
GP/SNr, Th
dStr
vP, mdTh
Acb
vStr
DG Sub
Stimuli La
ith
kw
ac tual
b
n
ed ex
Fe Cont matio
r
o
Inf
Motor
Output
STRIATUM
Complex
Ce
FRONTAL ASSOCIATION
AND MOTOR AREAS
dIFron
M1
IL
AC
ENTORHINAL
CORTEX
345
ICN
Ce
BL
AMYGDALA
AMYGDALA
SNc
Conditioned
Fear
(a)
VTA
DOPAMINERGIC NUCLEI
(b)
Figure 3 Brain circuits involved in two commonly studied forms of behavioral conditioning. (a) In Pavlovian (classical) fear-conditioning, the
conditioned stimulus (CS) and unconditioned stimulus (US) that are paired in time converge on the lateral amygdala (La) leading to associative learning.
The information processed within the La is relayed through indirect intra-amygdalar pathways (via BL, BM and ICN) to the central nucleus (Ce), which
induces a reflexive fear response through its projections to hypothalamic and brain stem regions, for example, cessation of behavior (freezing), increase
in startle response, and autonomic changes in heart rate, blood pressure, body temperature, sweating, and electric skin resistance. Feedback from
hippocampal circuits to the amygdala provides contextual information, and the medial prefrontal cortex can inhibit the fear response. (b) In instrumental
conditioning, the stimuli reaching the amygdala are more complex and the individual is required to make a choice (decision-making) that results in a
complex motor behavior like pressing a lever. The activation of the ventral striato-pallidal system directed towards the medial prefrontal cortex and the
coactivation of frontal association areas are needed to eventually generate the motor response together with dorsal striatal loops and cerebellar loops
(not shown). AC, anterior cingulate cortex; Acb, accumbens nucleus; BL, basolateral (basal) amygdaloid nucleus; Ce, central amygdaloid nucleus;
dlFron, dorsolateral frontal cortex; dStr, dorsal striatum; GP, globus pallidus; ICN, intercalated nuclei; IL, infralimbic cortex; La, lateral amygdaloid
nucleus; M1, primary motor cortex; mdTh, mediodorsal thalamic nucleus; SNc, substantia nigra pars compacta; SNr, substantia nigra pars reticulata;
Th, thalamus; VP, ventral pallidum; vStr, ventral striatum; VTA, ventral tegmental area.
from ictal and interictal fear and symptoms like deja` vu or

epigastric auras.
The amygdala shows Alzheimer-related neurofibrillary tangles and beta-amyloid deposits early during the course of the
disease. However, the basolateral group and cortical nuclei
with pallial origin are more severely affected than the centromedial group derived from subpallial neurons. Alzheimerrelated changes in the amygdala may be associated with
depression and deficits in emotional memory seen at early
disease stages.
In Parkinsons disease, alpha-synuclein containing Lewy
bodies and Lewy neurites are found mainly in ventral portions of the basolateral group and cortical nuclei, but the Ce
is also severely affected. Amygdalar pathology in Parkinsons
disease may contribute to visuospatial and olfactory deficits
and autonomic dysfunction commonly found in Parkinsons
patients.
Patients with UrbachWiethe disease, a genetic disorder
leading to bilateral calcification of the amygdala, show deficits in episodic autobiographical memory. Additional symptoms like hypersexuality, hyperphagia/hyperorality, and
visual agnosia are seen in KluverBucy syndrome resulting
from bilateral anterior temporal lobe damage that includes

the amygdala. An involvement of the amygdala in Huntingtons disease and neuronal ceroid lipofuscinosis was also
observed.

Cognition; INTRODUCTION TO CLINICAL BRAIN MAPPING:
Alzheimers Disease; Huntingtons Disease for Brain Mapping: An
Encyclopedic Reference; Schizophrenia; Temporal Lobe Epilepsy; The
Anatomy of Parkinsonian Disorders.
References
Aggleton, J. P. (1992). The amygdala: Neurobiological aspects of emotion, memory and
mental dysfunction. New York: Wiley-Liss.
Aggleton, J. P. (2000). The amygdala: A functional analysis. New York: Oxford
University Press.
de Olmos, J. (2004). Amygdala. In G. Paxinos & J. Mai (Eds.), The human nervous
system (pp. 739868). (2nd ed.). San Diego, CA: Academic Press.
346
Mai, J. K., Paxinos, G., & Voss, T. (2007). Atlas of the Human Brain. San Diego, CA:
Academic Press.
Shinnick-Gallagher, P., Pitkanen, A., Shekhar, A., & Cahill, L. (2009). The amygdala in
brain function: Basic and clinical approaches. New York: New York Academy of
Sciences.
Whalen, P. J., & Phelps, E. A. (2008). The human amygdala. New York: Guilford
Publications.
Yilmazer-Hanke, D. (2012a). Amygdala. In J. K. Mai & G. Paxinos (Eds.), The human
nervous system (pp. 759834). (3rd ed.). London: Academic Press (Elsevier Ltd).
Yilmazer-Hanke, D. M. (2012b). Insights into the amygdala: Structure, function and

implications for disorders. Hauppauge, NY: Nova Science Publishers.
Relevant Websites
www.alz.org ALZ.
www.nimh.nih.gov/health/topics/anxiety-disorders NIH.
www.parkinson.org Parkinson.
The Olfactory Cortex

TJ van Hartevelt and ML Kringelbach, Aarhus University, Aarhus, Denmark; University of Oxford, Oxford, UK
Introduction
Olfaction, or as it is more commonly known, the sense of
smell, is of great importance for species survival in terms of
both reproduction and food selection, especially when taken
together with the sense of taste (gustation). Taste and smell are
so closely linked that when people talk about, for example, the
flavor of food, they in fact talk about this multimodal experience. Studies on, among others, single-cell organisms indicate
that the combined chemical sense of taste and smell is possibly
the oldest of the senses and the most universally employed
(Hoover, 2010; Kovacs, 2004).
Humans and other animals rely strongly on olfaction to
locate and identify food sources. Most animals also rely heavily
on olfaction for mate selection and to identify their offspring.
Further evidence for the importance of olfaction can be found
in the size of the olfactory organ and system in a vast majority
of species. For example, dogs have about 100 times more
olfactory receptor cells compared to humans.
It has been argued that compared to other animals, humans
depend less on olfactory functions and more on other senses
such as vision and hearing (Jacobs, 2009). Evidence does exist
however for how we rely heavily on our sense of smell to
identify spoiled or toxic food, or our ability to identify sources
of potential danger. The function of olfaction with regard to
food selection is not limited to identifying potential dangerous
food sources. Deficits in olfactory function can sometimes lead
to malnutrition (Warner, Peabody, Flattery, & Tinklenberg,
1986). The lack of olfaction is a strong predictor of anhedonia,
the lack of pleasure in eating or smelling and tasting food, and
as such may contribute to the malnutrition.
In addition to the function of smell in food selection,
olfaction is also important in sex. Although humans do not
use olfaction for mate selection to the extent other animals do,
olfaction is still related to sex drive. Studies using smell for
attractiveness ratings show that men and women are susceptible to pheromones and rate the opposite sex as more or less
attractive depending on their hormonal state and the hormonal state of the opposite sex (Mostafa, Khouly, & Hassan,
2012). Smells from family members are readily identified as
such (and generally rated as less attractive), which may indicate
a mechanism to select genetically different partners and avoid
inbreeding. Mothers are able to recognize the smell of their
newborn babies (and vice versa) after prior exposure of as little
as 1 h (Porter, 1998).
Furthermore, olfactory dysfunction is associated with apathy, depression, and a lower quality of life (Cramer, Friedman,
& Amick, 2010; Smeets et al., 2009). These observations combined with the fact that olfactory neurons project directly to the
amygdala and hippocampus without a thalamic relay suggests
a prominent role for olfaction in mediating hedonic experience. Taken together, the weight of the evidence shows that
olfaction is a very important sensory system in humans which
needs to be fully functioning to support not only our survival

but very much our sense of well-being in general.
This article outlines the human olfactory system and pathways from the olfactory epithelium to the olfactory cortices.
This is primarily based on experimental work in other animals
and in particular using new evidence from functional imaging
studies in humans.
The Olfactory System

Similar to other sensory systems, olfactory information must
be transmitted from peripheral structures (the olfactory epithelium) to more central structures (the olfactory bulb and olfactory cortices), integrated to detect and discriminate specific
stimuli, and then transferred to other parts of the brain in
order to reach sensory awareness and affect behavior. The
olfactory system is different from the other sensory systems in
three fundamental ways.
First, as mentioned before, olfaction is the only sensory
modality that is directly connected into the cerebral hemisphere (in a sense, the telencephalon developed in relation to
olfactory input). Possibly because of this phylogenetic relationship, olfactory sensory activity is transferred directly from the
olfactory bulb to the olfactory cortex, without a thalamic relay.
Secondly, the neural integration and analysis of olfactory stimuli may not involve a topographic organization beyond the
olfactory bulb. Olfactory stimuli are not intrinsically ordered
along spatial axes, like vision and somatic sensation, or along a
frequency axis, like audition.
Thirdly, olfactory receptor neurons exhibit significant turnover throughout life. Olfactory neurons have a short life span
averaging 3060 days. They are constantly replaced by
mitotic division of the basal stem cell population in the olfactory epithelium. The olfactory receptors are the only neurons
that are inserted in the surface epithelium of the body and are,
therefore, directly exposed to the environment. It is likely that
this makes them more vulnerable to insult and necessitates
their regenerative capacity.
Humans are generally considered microsmatic, with a
poorly developed olfactory system compared to that of
macrosmatic mammals. Indeed, the structure and lamination
of the olfactory bulb and primary olfactory cortex (POC) are
not as well-defined in humans as in rodents. Furthermore, the
olfactory structures certainly do not make up as large a fraction
of the forebrain in humans as in, for example, rats. However,
almost all of the major olfactory structures found in rats are
also present in humans, and in absolute terms the human
structures are far from rudimentary. The volume of the olfactory bulb in a young adult human is reported to be 5060 mm3
(per side) (Turetsky et al., 2000), while it is only 1520 mm3 in
rats (Hinds & Mcnelly, 1977). Similarly, the primary olfactory
cortical areas such as the anterior olfactory nucleus (AON),
http://dx.doi.org/10.1016/B978-0-12-397025-1.00235-9
347
348
INTRODUCTION TO ANATOMY AND PHYSIOLOGY | The Olfactory Cortex
piriform cortex, and periamygdaloid cortex (PAC) are readily

recognizable around the junction of the frontal and temporal
lobes of human brains. What is more, humans are able to
discriminate between odors differing by only one carbon
atom (Laska & Teubner, 1999).
The vomeronasal organ is another interesting difference
between humans and other animals. Although some
researchers have argued that humans do not possess a vomeronasal organ, this structure has in fact been found in humans
(Jacob et al., 2000). However, further evidence suggests that
this system is no longer an active or functioning system in
humans (Frasnelli, Lundstrom, Boyle, Katsarkas, & JonesGotman, 2011; Mast & Samuelsen, 2009).
Olfactory Bulb
In most primates, including humans, the olfactory bulb is pulled
forward from its point of attachment to the cerebral hemisphere,
remaining connected by a relatively long olfactory stalk or
peduncle. The olfactory bulb in young adult humans is
5060 mm3 (per side) (Turetsky et al., 2000). The intrinsic structural features of the human olfactory bulb are similar to those in
other species, but they are somewhat less sharply defined. The
olfactory bulb has a concentric laminar structure with distinct
neuronal somata and synaptic neuropil separated into layers.
Although our understanding of the synaptic organization of the
olfactory bulb depends on observations made in rats and other
animals (Mori, Nagao, & Yoshihara, 1999), it is very likely that
the human bulb has the same basic organization (see Figure 1).
In humans, 8000 glomeruli and 40 000 mitral cells have
been counted in young adults (Meisami, Mikhail, Baim, &
Bhatnagar, 1998). There is a progressive decrease with age in
(a)
the number and structural integrity of the glomeruli, and in the

thickness of the glomerular/periglomerular layer (Bhatnagar,
Kennedy, Baron, & Greenberg, 1987; Meisami et al., 1998). In
olfactory bulbs from very old individuals (>90 years old)
< 30% of the glomeruli and mitral cells were recognized.
Together with the degeneration of the olfactory epithelium
mentioned earlier, this presumably is related to the decline in
olfactory function with age.
Primary Olfactory Cortex

Cortical Structure and Projections of the Olfactory Bulb
The axons of mitral and tufted cells run through the granule cell
layer and emerge from the caudolateral aspect of the olfactory
bulb to form the lateral olfactory tract (LOT). This tract forms
the bulk of the olfactory peduncle in humans and other primates. The LOT can be visualized readily in human brain sections stained for fibers or myelin. It runs just deep to the pial
surface, from the olfactory peduncle onto the posterior ventral
surface of the frontal lobe and then laterally around the junction
between the frontal and temporal lobes (the limen insulae) and
onto the anteromedial part of the temporal lobe (see Figure 2).
Most of the primary olfactory cortical (POC) areas have a relatively simple structure, with a broad plexiform layer composed
of dendrites of neurons in deeper layers (I), a well defined,
compact layer of pyramidal-like cell somata (II), and a deeper
layer(s) of pyramidal and nonpyramidal cells (III and higher).
Anterior Olfactory Nucleus

The AON is the most rostral of the tertiary olfactory structures.
In primates, including humans, there is a bulbar part of this
(b)
Figure 1 Olfactory epithelium and olfactory bulb. (a) The location of the olfactory epithelium inside the nasal cavity, the connections to the olfactory
bulb, and the location of and connections from the olfactory bulb to primary olfactory cortices. (b) The connections from the olfactory epithelium
entering the olfactory bulb through the cribriform plate. The organization of the glomerular and mitral layer is clearly indicated. Reproduced from
van Hartevelt, T. J., Kringelbach, M. L. (2012). The olfactory system. In: Mai, J. K., Paxinos, G. (Eds.), The human nervous system (pp. 12191238).
3rd ed. San Diego: Academic Press.
349
(a)
(b)
Figure 2 The olfactory bulb, lateral olfactory tract, and primary olfactory cortices. (a) The cut line along the temporal lobe to make the
underlying olfactory areas visible. (b) The olfactory bulb (OB), projecting through the lateral olfactory tract (LOT) to the anterior olfactory nucleus (AON),
the olfactory tubercle (OTUB), both anterior and posterior piriform cortices (APC and PPC, respectively), and the entorhinal cortex (EC). Reproduced
from Gottfried, J. A. (2010). Central mechanisms of odour object perception. Nature Review Neuroscience, 11, 628641.
nucleus located in the rostral part of the olfactory peduncle,

including several groups of pyramidal-like cells in the caudolateral part of the olfactory bulb. As in other olfactory cortical
areas, axons of the mitral and tufted cells synapse on the distal
segments of dendrites that extend into the plexiform layer
around the neuron clusters. More caudal medial and lateral
subdivisions of the AON are situated on either side of the LOT
where it joins the orbitofrontal cortex, at the posterior end of
the olfactory peduncle.
Additionally, olfactory perception is influenced by alternating air intake through the nostrils. Recently, Kikuta et al. (2010)
found that rodents can localize the source of an odor by comparing the inputs to the left and right nostril. This is achieved by
neurons in the AON pars externa, which showed different
response levels to ipsi- versus contranostril odor stimulation. A
recent study in humans has shown a similar ability and also
shows that odor object localization leads to activation of parietal
structures (the classical dorsal stream; Frasnelli et al., 2012).
Olfactory Tubercle
More caudally on the ventral surface of the frontal lobe, the LOT
runs at the junction of the olfactory tubercle (OTUB), medially,
and the piriform cortex, dorsal and laterally (Figure 3). The
OTUB is a prominent structure in rodents and birds with a
well-developed laminar structure similar to that in other olfactory cortical areas. It is much less distinct in primates, but still
has a laminar arrangement of cell bodies and afferent fibers.
Both in humans and nonhuman primates the OTUB is less
readily identifiable due to the small size of the basal forebrain
bulge, which houses the OTUB (Wesson & Wilson, 2011). In
human imaging studies the OTUB has been identified between
the uncus and the medial forebrain bundle. Furthermore,
besides the direct inputs from the olfactory bulb, the OTUB
also receives minor input from the olfactory amygdala

(Martinez-Marcos, 2009).
Piriform Cortex
The piriform cortex is the largest and most distinctive primary
olfactory cortical area. The piriform cortex is situated deep and
lateral to the LOT, from the caudolateral aspect of the frontal
lobe, around the limen insulae, to the rostral dorsomedial
aspect of the temporal lobe (Figure 2). The piriform cortex is
characterized by a densely packed layer II composed of moderately large pyramidal cell somata, and a less dense layer III of
slightly larger pyramidal cells and other neurons. Layer II is
found throughout the piriform cortex but layer III is only well
developed in the caudal part of the cortex.
Evidence from anatomical, physiological, and functional
differences suggests that the piriform cortex can actually be
divided into two different sections, the anterior piriform cortex
(APC) and the posterior piriform cortex (PPC) (Gottfried,
2010). However, input from the olfactory bulb does not
appear to exhibit spatial patterning across the piriform cortex.
Additionally, contrary to the olfactory bulb, the piriform cortex
has not been shown to have a spatial organization.
Anterior Cortical Nucleus of the Amygdala and PAC

Caudal and lateral to the piriform cortex the axons from the
olfactory bulb continue into several small areas on the medial
surface of the amygdala. The anterior cortical amygdaloid
nucleus is directly caudal to the piriform cortex and is characterized by a relatively loosely packed layer II and even more
diffuse layer III. The PAC is a larger area located ventrolateral to
the piriform cortex. It is markedly heterogeneous, and in
Signal change (%)
350
0.8
0.4
0
0.4
0
APC
(a)
8 12 16 20 24 26
Time (s)
8 12 16 20 24 26
Time (s)
Signal change (%)
PPC
0.8
0.4
0
0.4
0.8
0
8 12 16 20 24 26
Time (s)
Different group
Same group
Signal change (%)
(b)
8 12 16 20 24 26
Time (s)
Different quality
Similar quality
0.8
0.6
0.4
0.2
0
0.2
(c)
1
0
1
2
Subjective pleasantness of smell
Figure 3 Olfactory processing in humans measured with neuroimaging. A dissociation has been found between the anterior and posterior parts of
the piriform cortex with the anterior part encoding the difference between group of odors but not their perceptual quality, while the posterior part encodes
perceptual quality but not between group of odors (Gottfried, 2010). (a) Specifically, the presentation of odorants from the same functional group leads
to significantly reduced activity in the APC (circled in red), as shown in the leftmost plot, while the rightmost graph shows no significant differences
for perceptual quality. (b) This is different from the presentation of odorants containing similar perceptual qualities which leads to reduced activity in the
posterior piriform cortex (circled in red). Here, the leftmost plot shows no effect for functional group, while the rightmost graph shows a significant
difference between perceptual qualities. Following this perceptual processing, the affective valence is processed in the orbitofrontal cortex. (c) Region of
the medial orbitofrontal (circled in white) and medial prefrontal cortices correlate significantly with the subjective pleasantness ratings of odors, as
demonstrated by the correlation between signal change and pleasantness ratings (shown on the right). Reproduced from Rolls, E. T., Kringelbach, M. L. &
De Araujo, I. E. T. (2003). Different representations of pleasant and unpleasant odours in the human brain. European Journal of Neuroscience, 18, 695703.
monkeys and humans can be divided into five subdivisions,

PACO, PAC1, PAC2, PAC3, and PACS, based on architectonic
differences (Carmichael, Clugnet, & Price, 1994). All but the
most caudal of these (PACS) receive input from the olfactory
bulb in monkeys, although the layer of axons is thick only in
PACO, and is quite thin in PAC1, PAC2, and PAC3.
& Van Groen, 1984; Price, 1973). In monkeys, however, the

olfactory bulb input is limited to a small olfactory zone at the
rostral edge of the entorhinal cortex (Amaral, Insausti, & Cowan,
1987; Carmichael et al., 1994). Even in this region, the olfactory
projection is relatively slight, both in density, and in the thickness of the superficial lamina in layer I in which the fibers end.
Rostral, Olfactory Entorhinal Cortex
Centrifugal Projections to the Olfactory Bulb
In rodents and carnivores, a large fraction of the entorhinal

cortex receives fibers directly from the olfactory bulb (Boeijinga
All of the olfactory cortical areas except the OTUB send fibers
back to the olfactory bulb (Carmichael et al., 1994). These

fibers arise from cells in layers II and III of the cortex and end
primarily in the granule cell layer of the olfactory bulb. The
projection from the AON and (in monkeys) the anterior part of
the piriform cortex is bilateral, with fibers crossing in the
anterior commissure.
Olfactory Projections beyond the POC

Olfactory information is transmitted from the POC to several
other parts of the forebrain, including the orbitofrontal cortex,
amygdala, hippocampus, ventral striatum, hypothalamus, and
mediodorsal thalamus (Carmichael et al., 1994), areas that are
associated with affective learning and memory. Although these
connections have been best studied in rodents, there is also
some experimental data from monkeys, and functional imaging studies have recently provided data on humans.
Human Imaging of Olfactory Sensory Activity

Several studies have used functional imaging methods to identify the human cortical areas activated by olfactory stimuli
(Zald & Pardo, 2000). Odorant-induced responses were first
obtained in the region of primary cortex by Zatorre, JonesGotman, Evans, and Meyer (1992) and have been confirmed
by subsequent reports from the same research group (Dade,
Jones Gotman, Zatorre, & Evans, 1998; Small, Jones-Gotman,
Zatorre, Petrides, & Evans, 1997). Other studies however have
failed to find substantial activation of primary olfactory areas
(e.g., Sobel et al., 1998; Yousem et al., 1997; Zald & Pardo,
1997). Several factors may explain the inconsistency. Technical
factors such as the susceptability artifact related to nearby
bone and air sinuses make it difficult to image this region
with fMRI. Neuronal responses to odorants in the piriform
cortex are also rapidly adapting and may be coded for by
temporal or spatial patterns of activity instead of response
amplitude. Further, sniff-related activity may mask odorantrelated activity (Sobel et al., 1998). When these are taken into
account, odorant-related activation can be visualized in the
POC (Sobel et al., 2000).
Olfactory-related activity has consistently been detected in
the orbitofrontal cortex (Rolls et al., 2003; Royet et al., 2001;
Small et al., 1997; Sobel et al., 2000; Zald & Pardo, 1997;
Zatorre et al., 1992). All of these studies found an area of
activation in the central orbitofrontal cortex, in some cases
through the rostral to caudal extent (Sobel et al., 2000). It
has also been demonstrated that there was a correlation
between the subjective pleasantness ratings of the odors with
activity of a medial region of the rostral orbitofrontal cortex.
In contrast, a correlation between the subjective unpleasantness ratings of odors was found in regions of the left and
more lateral orbitofrontal cortex (Anderson et al., 2003; Rolls
et al., 2003).
It is not yet possible to identify these areas in terms of the
architectonic subdivisions of the orbitofrontal cortex, but they
appear to correspond to the orbitofrontal network defined in
monkeys (Carmichael & Price, 1996). Zald and Pardo (1997)
also identified an area in the lateral orbitofrontal/anterior
insular cortex with activity following stimulation with aversive
351
odors; the region of the amygdala was also activated to the

same odors.
Imaging studies have shown activation in the piriform cortex during olfactory learning and memory tasks as well as
olfactory tasks related to motivational and cognitive states.
This indicates a higher or more elaborate function of the piriform cortex than solely the function of a relay to olfactory
cortical areas beyond the POC (Gottfried, 2010).
A more recent fMRI study has found activity in the central
posterior orbitofrontal cortex related to the detection of discrepant olfactory events (Sabri, Radnovich, Li, & Kareken,
2005). Although this study also found activation in the subgenual cingulate cortex, this activity may be attributed to selective attention. These areas were only activated if there was no
attention paid to the olfactory stimuli. However, when attention was being paid to the olfactory stimulation, activation was
found in a small part of the right and lateral OFC region.
The OFC has been shown to be activated during a multitude
of tasks, ranging from odor discrimination learning to multisensory integration. In addition, patients with orbitofrontal
lesions (e.g., head trauma) have difficulties with odor identification, memory, and discrimination while having little difficulties with odor detection. More specifically, a case study
showed that an injury in the right OFC led to anosmia while
activation in the left OFC and bilateral piriform cortex still
allowed for odor-evoked autonomic responses to unpleasant
smells. This lateralization of olfactory functioning finds support from an early PET study by Zatorre et al. (1992), who
found greater activation in right OFC compared to the contralateral homologous OFC after odorant stimulation.
Meanwhile, olfaction areas in the temporal lobes were symmetrically active. Although some have suggested that the right
OFC is necessary for conscious olfactory processing (Li et al.,
2010), lesion studies in patients with medically refractory epilepsy showed a similar impairment on all olfactory tasks after
unilateral temporal lobectomy, leaving detection thresholds
intact (Eskenazi, Cain, Novelly, & Friend, 1983). This would
seem to indicate a more complex system with regard to olfactory tasks.
In favor of a lateralization of olfactory function is an MRI
study measuring gray matter loss using voxel-based morphometry in people suffering from anosmia (Bitter et al., 2010). This
study showed a greater atrophy on the right side. This controlled study furthermore showed that anosmia leads to
reduced gray matter in the anterior cingulate cortex, the middle
cingulate cortex, the dorsolateral prefrontal cortex, the subcallosal gyrus, and the NAcc. Further analysis in this study showed
volume loss in the right piriform cortex, the right insular
cortex, and the right OFC. Direct comparison of these results
with fMRI data from the same participants showed an overlap
of areas activated in healthy participants with gray matter loss
areas in anosmic participants.
It has long been thought that orthonasal and retronasal
olfactory stimulation is similar to each other. Reported activation in piriform cortex, insula, OFC, hippocampus, and entorhinal cortex after retronasal stimulation by Cerf-Ducastel and
Murphy (2001) contributed to this belief, as the reported areas
are similar to those active after orthonasal olfactory stimulation. No direct comparisons were made, however, between the
two different types of olfactory stimulation. More recently it
352
has been found that there are fundamental differences in both

odor perception as well as neural activation. According to
Small, Gerber, Mak, and Hummel (2005), the insula, opercula,
thalamus, hippocampus, amygdala/piriform, and caudolateral
OFC show greater activation after orthonasal stimulation
whereas the perigenual cingulate, posterior cingulate, medial
OFC, and superior temporal gyrus extending into the temporal
operculum show greater activation after retronasal olfactory
stimulation. A very important note is that this difference was
only found in food-related odors. Nonfood odors did not
result in a similar dissociation.
This finding supports one of the first theories of orthonasal
versus retronasal differences coined by Rozin (1982), stating
that there are different behavioral consequences depending on
the two types of information. In short, orthonasal stimulation
represents information from odor sources in the environment
ranging from animals to plants to fire. Retronasal stimulation
signals information from odor sources in the oral cavity, which
is generally an object that has been previously selected as food.
Olfaction as a Multimodal System

Food selection is one of the most important functions of olfaction, and there is close connection between olfaction and gustation. Ultrasound imaging has shown that retronasal stimulation
(compared with orthonasal stimulation) increases the speed
of swallowing (Welge-Lussen, Ebnother, Wolfensberger, &
Hummel, 2009). However, only food-related odors were used
in this study, so whether this is specifically related to food intake
or also to nonfood-related odors requires further investigation.
The central orbitofrontal cortical region that responds to
odorants also is active by taste stimuli (Small et al., 1999). This
corresponds well with the anatomical evidence in monkeys
that corticocortical interconnections within the orbitofrontal
cortex relate olfactory and gustatory systems. The responses to
simultaneous, matched taste and olfactory stimuli appear to be
quantitatively different from both unimodal stimuli alone,
suggesting that flavor is not a simple convergence of its component senses (Small et al., 1997). As suggested by recordings
in monkeys (see earlier discussion), the olfaction- and tasterelated responses in the orbitofrontal cortex also depend on
hedonic properties of the stimuli. For example, fMRI responses
to food-related olfactory stimuli show specific decreases after
feeding to satiety with that food (ODoherty et al., 2000). Also,
in addition to areas with activity following either olfactory
stimulation or taste stimulation, such as parts of the orbitofrontal cortex, amygdala, insular cortex, and anterior cingulate
cortex, some parts of the orbitofrontal cortex are active only
when both taste and olfactory stimuli were combined (De
Araujo, Rolls, Kringelbach, Mcglone, & Phillips, 2003).
Taken together, the evidence indicates that the orbitofrontal
cortex must be considered as a key node in the brain networks
available for the analysis of food and food-related stimuli.
More generally, it has been proposed that the orbitofrontal
cortex plays a central role for the analysis of reward and
hedonic processing (Kringelbach, 2005; see Figure 4).
This view is further supported by how olfactory dysfunction
has been shown to influence malnutrition (Lafreniere & Mann,
2009; Mesholam, Moberg, Mahr, & Doty, 1998). Both
Parkinsons disease and Alzheimers disease are accompanied
by malnutrition and weight loss without clear evidence for

changes in metabolism (Korczyn & Gurevich, 2009; Warner
et al., 1986). Also, the loss of smell (and taste) in elderly is
believed to negatively influence appetite and pleasure of food
intake, which in turn lead to malnutrition.
Besides the gustatory system, the trigeminal system also
plays a prominent role in olfaction. The free nerve endings of
the trigeminal nerve are stimulated by a majority of odorants.
Additionally, the trigeminal nerve is also stimulated by odorless vapors such as carbon dioxide, which induces a sensation
of pain (Hummel, Mohammadian, Marchl, Kobal, & Lotsch,
2003; Kobal, 1985). The stimulation of the trigeminal system
by odorants is known to influence the perception of odorants.
Animal studies have shown that, whereas trigeminal stimuli
have an inhibitory effect on olfactory afferent nerves, blockage
of trigeminal activity enhances activity in, for example, the
olfactory bulb (Brand, 2006; Stone, Williams, & Carregal,
1968). It is furthermore believed that pungency, as tested
with carbon dioxide, can diminish or suppress certain odors.
However, olfactory sensitivity for both purely olfactory as well
as olfactory/trigeminal odorants increases after previous trigeminal stimulation. The effect of trigeminal activity on olfactory perception is believed to be both central as well as
peripheral, for example, interaction may take place in parts of
the thalamus and fibers of the trigeminal nerve innervate the
olfactory epithelium (Brand, 2006).
Contrary to the olfactory system, the trigeminal system has
a limited amount of sensations (e.g., pain, temperature,
humidity) compared to the vast amount of odors detected by
the olfactory system and is more involved in protective reflexes
than the olfactory system. So, although most odorants stimulate both systems, they are separate systems and can indeed be
affected separately, for example, most patients with Parkinsons disease suffer from olfactory dysfunction while the trigeminal system appears to be unaffected (Barz et al., 1997).
Olfactory Dysfunction and Anhedonia

There is a vast amount of literature on olfactory dysfunction,
ranging from nasal fractures and head trauma to toxic exposure, depression, and neurodegenerative disorders. Head
trauma can cause olfactory dysfunction by severing the neurons from the olfactory epithelium to the olfactory bulb
through the cribriform plate, where scar tissue is subsequently
blocking the growth of new neurons. Olfactory dysfunction
due to neurodegenerative disorders could perhaps tell us
more about the nature of the olfactory system. Although the
literature on olfactory dysfunction in, for example, Parkinsons
disease or Alzheimer disease kept growing steadily for the past
30 years, the exact underlying mechanisms for olfactory dysfunction in these disorders is still largely unknown (Doty,
2007; Hawkes, 2003; Murphy, Cerf-Ducastel, CalhounHaney, Gilbert, & Ferdon, 2005). Whereas both apathy and
olfactory dysfunction are commo

Brain Mapping An Encyclopedic Reference (-PUNISHER-)

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Brain Mapping An Encyclopedic Reference (-PUNISHER-)

Uploaded by

Copyright:

Available Formats

BRAIN MAPPING

This page intentionally left blank

AMSTERDAM BOSTON HEIDELBERG LONDON

Academic Press is an imprint of Elsevier

Publisher: Lisa Tickner

This page intentionally left blank

VOLUME 1 TABLE OF CONTENTS

INTRODUCTION TO ACQUISITION METHODS

Anatomical MRI for Human Brain Morphometry

A van der Kouwe and B Fischl

Obtaining Quantitative Information from fMRI

G Bruce Pike and RD Hoge

Contrast Agents in Functional Magnetic Resonance Imaging

AR Hoy and AL Alexander

Basic Principles of Electroencephalography

D Millett, P Coutin-Churchman, and JM Stern

Functional MRI Dynamics

Evolution of Instrumentation for Functional Magnetic Resonance Imaging

JA de Zwart and JH Duyn

High-Speed, High-Resolution Acquisitions

LL Wald and JR Polimeni

Basic Principles of Magnetoencephalography

R Hari, L Parkkonen, and M Hamalainen

A Hai and A Jasanoff

Pulse Sequence Dependence of the fMRI Signal

P Jezzard and PJ Koopmans

Volume 1 Table of Contents

Functional Near-Infrared Spectroscopy

RJ Cooper and DA Boas

Perfusion Imaging with Arterial Spin Labeling MRI

Positron Emission Tomography and Neuroreceptor Mapping In Vivo

R Lanzenberger and A Hahn

Susceptibility-Weighted Imaging and Quantitative Susceptibility Mapping

E Mark Haacke, JR Reichenbach, and Y Wang

Temporal Resolution and Spatial Resolution of fMRI

MRI and fMRI Optimizations and Applications

PA Ciris and R Todd Constable

fMRI at High Magnetic Field: Spatial Resolution Limits and Applications

E Yacoub, K Ugurbil, and N Harel

INTRODUCTION TO METHODS AND MODELING

Computerized Tomography Reconstruction Methods

Pharmacokinetic Modeling of Dynamic PET

Q Guo and RN Gunn

Optical Image Reconstruction

S Arridge and RJ Cooper

Image Reconstruction in MRI

L Ying and Z-P Liang

Artifacts in Functional MRI and How to Mitigate Them

L Hernandez-Garcia and M Muckley

Diffusion Tensor Imaging

Probability Distribution Functions in Diffusion MRI

Y Rathi and C-F Westin

Q-Space Modeling in Diffusion-Weighted MRI

I Aganj, G Sapiro, and N Harel

Fiber Tracking with DWI

J-D Tournier and S Mori

Tract Clustering, Labeling, and Quantitative Analysis

Tissue Microstructure Imaging with Diffusion MRI

G Nedjati-Gilani and DC Alexander

Tissue Properties from Quantitative MRI

Intensity Nonuniformity Correction

Nonlinear Registration Via Displacement Fields

J Modersitzki, S Heldmann, and N Papenberg