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INTERNATIONAL JOURNAL OF WISDOM BASED COMPUTING, VOL.

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On Experimenting with Single Subject Multi-Session fMRI Analysis of Human Brain


J. Satheeshkumar, S. Arumugaperumal, R. Rajesh, C. Kesavdas
Abstract Digital image processing has a broad spectrum of applications ranging from robotic vision for industrial automation to image synthesis for cartoon making / fashion design. There are many other applications, such as, remote sensing through satellite and other space crafts, radar and acoustic image processing, image transformation and storage, business applications, robotics and automated inspection of industrial parts. Although there are many other applications, medical imaging is one of the signicant applications, where effective image processing techniques can be applied to identify the difference between normal and abnormal images of various subjects and identifying internal composition or external surface changes of specic portion of human body like brain. Quite a lot of tools are available for analyzing medical imaging especially for analyzing brain images. Statistical Parametric Map (SPM) is one of the effective tool used in medical image processing for identifying defects, diseases and volumetric changes between subjects brain images. This paper highlights importance of SPM and simplied procedural explanation for various modules of SPM. Index Terms SPM, fMRI, Brain Imaging, Statistical Tool.

I. I NTRODUCTION
Image Processing plays a wide role which is clear evidence from the applications of past several decays that includes Image Compression, Diffraction in Image Processing and its application in material science, Signal Processing, Detection and classication of under water mines and mine like objects in sonar imagery, Nondiscrete cellular topologies, Homomorphic processing and its application to Image Enhancement, etc. There are bright chances for the image processing technology, in future, for developing ultimate equivalent machine that would be able to perform visual functions of human beings. According to human being, more than 75 of information received by human is through visuals and various researches are still in progress in this eld. Medical Imaging is one of the fruitful applications of Image Processing for researchers, where various techniques are used to create images of human body (or parts) for clinical purposes in medical science. As a discipline, it is part of biological science and incorporates radiology and neuro science(in wider). It is also considered as part of biomedical engineering, medical physics or medicine depending on the context: Research and Development in the area of
Dr. J. Satheeshkumar (jsathee@rediffmail.com) and Dr. R. Rajesh (kollamrajeshr@ieee.org) are with Dept. of Computer Applications, Bharathiar University, Coimbatore -641 046, India Dr. S. Arumugaperumal is with Dept. of Computer Science, St. Hindu College, Nagercoil, India Dr. C. Kesavdas, Additional Professor, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruavanathapuram, India

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instrumentation, modeling and quantication etc. The need and importance behind the medical imaging is to create the internal image parts of the body without to open it. In ancient days, images were recorded in analog lm by using X-ray technology for diagnosis and treatment. After that, patients(or subjects) with severe diseases were acquired using Computed Tomography [CT], Magnetic Resonance Imaging [MRI] and functional magnetic resonance imaging[fMRI] for analyzing differences between inter subjects (subject based on same factor or modality) or intra subjects (based on different factors). Morphology in computational neuroanatomy is one of the best approaches to identify shape difference between normal and abnormal images. The brain images are one of the interesting research part of medical imaging, where, changes in brain surface, volume reduction due to several factors like, alcoholic effect, brain related diseases, and brain tumors, and variations in internal composition of brain, such as, gray matter, white matter and cerebrospinal uid(CSF) can be effectively identied and analyzed by morphometry methods. The brain is complex parts of the human body, where, enormous neurons in the cortex typically connects 10,000 of nearby neurons in the cortex itself. The target of most of the experiments in neuro imaging is to identify various brain region, whose activation matches perfectly with an aspect of the subjects behavioral task. Once the function of brain area or network area are clearly known, various regions which are responsible for subjects behavior can be possible to judged through online activation measurements. Brain morphology is an emerging eld in clinical neuro science. The Morphometry methods are generally classied into three broad categories, such as, Deformation-Based Morphometry [DBM], TensorBased Morphometry [TBM], Voxel-Based Morphometry [VBM], specically for examining brain shape differences of various subjects by using medical imaging packages. Multiple tools and mathematical methods are on hand for analyzing medical image data for feature enhancement, noise reduction and specically to detect different structures like functional and anatomical pathologic structure of the brain. Due to the increasing performance of the computers and more acquisition of digital image data, the role of enormous mathematical methods in medical image processing has become viable for analyzing images. Statistical parametric mapping shown in the gure 7 is an efcient tool for analyzing cognitive structure of the human brain. This paper is organized as follows. Section II explains data format recognized by SPM and tools used for data conversion. Section III and Section IV deals representation and viewing of an image. Section V deals with the basic modules used in SPM2 software. Section VI concludes the paper.

II. DATA F ORMAT


High resolution MR-scanner will be usually used to scan the subjects (or patients) brain image. Two possible categories of data can be acquired from the scanner such as, structural data and functional data. The Structural data are usually high-resolution images with higher number of slices, where as the functional

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Fig. 1.

Dicom Viewer: used to view the DICOM format images

Fig. 2.

Mriconverter : used to convert Dicom images to Analyse format

images are low resolution images with less number of slices. The functional data represent information about brain motor activation area for various functionalities. The output obtained from scanner can be of different kind of format like, Digital Image Compression (DICOM), NIFTY, etc. DICOM format is one of the familiar outcome of most of the scanners. Software tools like DICOM viewer shown in the gure 1is used to view the dicom images. Since SPM recognize the data in analyze format [*.ing and *.hdr pair], format converting software is needed which convert source format to analyze data format. Most popular softwares such as, MriCro shown in the gure 2 and MriConverter are used to convert the Dicom images to analize format. Mriconverter is one of the best tool used to create .img and .hdr pair for every source image in DICOM representation. These images are collectively referred as digital images, where the header (.hdr les) portion contains information about raw data including various characteristics of raw image and raw data (.img les) contains numbers, which are used to represent color or gray scale value of every position in the image.

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Fig. 3. Slice: Two-dimensional representation of an image, Volume: Collection of slices forms threedimensional representation of images.

III. I MAGE R EPRESENTATION


Image can be represented either by pixel or by voxel. Picture Elements (Pixels) are used to represent two-dimensional images; where as three-dimensional images are represented by voxels (Volume elements). Pixel is a single point in a 2D image. The number of pixels in an image is referred as resolution. Like wise, voxel is a unit of graphic information that denes a point in a three dimensional space, in which, each of the coordinate is dened in terms of its position, color and density. Collection of pixels forms two dimensional image or slice where as collection of slices forms three dimensional representation of images called volume shown in the gure 3. Medical professionals and researchers are using images represented by voxels and three dimensional software to view X-Ray, Cathode Tube Scans, Magnetic Resonance Imaging and Functional MRI, and to effectively analyze the interior part of the body from outside.

IV. V IEWING AN IMAGE


Images in analyze format (.img and .hdr pair) can be viewed by using an option Display in spm tool. Three different kind of images can be given by display option, such as, coronal, sagital and axial view shown in the gures 4, 5 and 6 respectively.

V. M ODULES OF SPM2 - A V IEW


Now a days various tools are available for analyzing medical images especially for brain related issues. Statistical parametric mapping (SPM) is one of the effective, exible and freely available tool which works with the support of MATLAB for analyzing brain images (with different modalities like PET, MRI and fMRI etc). SPM is developed by the welcome department imaging neuroscience, a department of institute of the neurology and University college London. Various versions of SPM are SMP 94, SPM version1, SPM2, SPM2b and the latest version is SPM 5. This paper enlighten step by step explanation of SPM2 shown in gure 7, which helps the beginners for their better understanding of the software. SPM was developed with the support of MATLAB functions, Scripts, data les

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Fig. 4.

Coronal view of the subjects brain

Fig. 5.

Sagital view of the subjects brain

and precompiled C routines. MATLAB is an engineering mathematics package produced by MathWork, Natick, USA, in which, either MATLAB 6.0 or other versions are needed for executing SPM version 2. The functional modules used for analyzing brain images using SPM are Image realign, coregistering an image, normalization, smoothing an image, segmentation and nding statistical inference of the image. 5.1. Image Realignment Image realignment is the process of adjusting or rearranging images based on some reference image for avoiding movement related artifact in source images. SPM2 uses least square approach and 6-parameter rigid body transformation during image realignment process [1], [2], [3]. The choice of selecting a reference image plays a vital role where, spm uses rst slice of the rst volume as reference image. First slice of remaining volumes other than rst will be realigned based on rst slice of rst volume; remaining slices of every volume are realigned based on rst slice of corresponding volume. The slice should be chosen in such a way that it should minimize realignment error and there by compromising with the fact that the error cannot be completely avoided. Hence a proper selection will be either slice or slice, which will realign the slice in the middle of the volume better than the slice in the

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Fig. 6.

Axial view of the subjects brain

Fig. 7.

Modules of SPM2 software

ends of the volumes. Table I and Table II shows that error range can be reduced signicantly by considering slice as reference image in realignment phase [10], [12]. 5.2. Coregister This option is used to register or realign source image based on target image so as to apply same transformation to all images even though different images are considered for analysis. For example, structural MR images can be realigned based on PET images and PET images can be realigned based on MR image series. The registration used in this tool is based on information theory [4], [5], [6]. The gure 8 shows translation error in x, y and z direction the gure 9 shows rotation error in pitch, roll and yaw respectively. 5.3. Normalization Spatial normalization is the process of mapping PET, MRI and fMRI images with some reference image [1], [7] for reducing residual errors between source and target images. This phase determines optimum 12-parameter afn transformation.

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TABLE I R ANGE OF T RANSLATION E RROR IN R EALIGNMENT P HASE Reference Image Position Direction X Range Y Range Z Range First Slice Min Max -0.0733 , 0 0.0733 0 , 0.1076 0.1076 -0.0259 , 0.0860 0.1119

Min Max -0.0661 , 0 0.0661 0 , 0.0961 0.0961 -0.0126 , 0.0363 0.0489

Min Max -0.0638 , 0 0.0638 0 , 0.0937 0.0937 -0.0066 , 0.0644 0.0710

TABLE II R ANGE OF ROTATION E RROR IN R EALIGNMENT P HASE


Reference Image Position Direction Pitch Range Roll Range Yaw Range First Slice Min Max -7.3229 , 10 X 0.001732 -0.0012 , 0 0.0012 -7.9452 , 3.1750 X 11.1202 X

Min Max -4.0372 , 1.1699 X 5.2071 X -1.6528 , 2.3070 X 3.9598 X -7.3184 , 3.1214 X 10.4398 X

Min Max -7.5952 , 1.4748 X 9.0700 X -5.0159 , 2.3205 X 7.3394 X -7.4274 , 4.0697 X 11.4971 X

0.1 x translation y translation z translation

0.08

0.06

0.04

0.02

mm
0 0.02 0.04 0.06 0.08

10

20

30

40

50 image

60

70

80

90

100

Fig. 8.

Translation error in x, y and z direction

x 10

pitch roll yaw 2

mm

10

20

30

40

50 image

60

70

80

90

100

Fig. 9.

Rotation error in pitch, roll and yaw

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Fig. 10. Reference Images used to map with source image: MNI Template image (left), Single subject T1 mean image (right)

Fig. 11. Complexities in normalization. Images before normalization(left) and Images after normalization(right)

The normalization can be broadly classied as label-based techniques and nonlabel based techniques. Similar features (labels) in the image and template can be identied by label-based approach, where as, spatial transformation that minimizes some index of the difference between an object and a template image can be analyzed by non-label based approaches. An advantage using spatially normalized images is that the motor activation area for different functionalities can be analyzed accurately based on set of meaningful coordinates with in standard space [8]. In a study about single subjects brain, the mapping process of subject image with pre dened template (MNI created based on considering 13 subjects high resolution MR images) as shown in the gure 10is not suggestible during image analysis. When the mean image is used for mapping, there may be higher possibilities of variation between object and reference image as shown in the gure 11. Because of stretching and shrinking based on template, there may be higher chances of losing data or signicant shift in motor activation area. 5.4. Smoothing Smoothing is a kind of enhancing an image for accurately analyzing target image. Isotropic Gaussian kernel can be used for smoothing images to analyze the differences between groups and local volume of various tissues (such as, gray matter and white matter) can be calculated from the smoothed images based on intensity value of pixel or voxel value of an image. In general, the process of smoothing will decrease the image resolution and increase the signal to noise

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Fig. 12. Source image in left represent before normalization and smoothing and target image in right represent normalized and smoothed image

Fig. 13.

Paradigm design using boxcar.

ratio as shown in the gure 12. SPM uses Gaussian curve and Full Width Half Maximum criterion for smoothing images. 5.5. Basic Models This option is used to congure design matrix, data specication, data format etc., where various design types can be selected (like one sample test, two sample test, one way anova etc). Design matrix constitute experimental parameters, type of hypothesis testing and hemodynamic function used for analysis. Design specication is a type of matrix where each scan having respective row and each column having specic effect or stimulus function. Interscan interval is the time needed to scan whole brain once or for one volume. This time can be obtained from scanner parameters as shown in the gure 1. Vector of onset is another parameter which can be calculated from Boxcar method as as shown in the gure 13. Experiments are generally designed based on the combination of rest and stimulus activation. Figure 13 shows that, the experiment started with 10 scans (3.58 sec) of rest followed by 10 scans (3.58 sec) of lip movement. Five cycles of rest-lip movement completes the experiment obtaining 100 volumes of data. 5.6. Statistical Analysis Many techniques have been proposed for statistically analyzing fMRI data, and a variety of these are in general use. The aim of such analysis is to produce an image identifying the regions, which show signicant signal change in response

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Fig. 14. Glass Brain. The motor activation region of the lip movement is visible as dark gray clusters in the glass brain

to the task. For a given image and general linear model, the estimate function of SPM congure model parameters, variance of parameter and smoothness of residual elds. The model can be represented through design matrix. The basic model at any voxel is of the form Y = X * B + e where, Y - Design matrix X - Data Matrix B - parameters (unknown) and e - Residual error Some times confounds are necessary to represent model. This can represent by modifying above formula as follows K * Y = K * X * B + K * e , where K represent any matrix (eg. convolution matrix). 5.7. Visualization of output The result section is used to characterize results of statistical analysis. Once parameter estimation is over, the next step is to dene the contrast. The Contrast designer window will help to dene t-contrast, f-contrast or both for further analysis. Figure 14 shows the T-map which gives the maximum intensity projection on the so called glass brain [9]. Fields signicantly activated by stimuli(lipmotion) obtained after t-test (p-values are adjusted for search volume) are shown in Table III. Orthogonal sections of the threshold statistic image overlaid on high resolution weighted structural image is shown in gure 15, where the coloured regions show the activations due to lip movement. Figure 16 shows the 3-D view of activation regions for lip-movement [11], [13].

VI. C ONCLUSION
This paper help researchers for understanding statistical parametric mapping software and visualizing cognitive functionality of complex human brain structure. Statistical Parametric Mapping(SPM) is one of the best tool for nding statistical inferences and to extract information from three dimensional structure of human brain.

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Fig. 15. Overlay of ltered SPM on a structural image. The coloured regions show the activations due to lip movement

Fig. 16.

Three Dimensional view of activation regions for lip-movement

TABLE III F IELDS SIGNIFICANTLY ACTIVATED BY LIP - MOTION OBTAINED AFTER T- TEST ( P - VALUES ARE ADJUSTED
FOR SEARCH VOLUME )

set-level p 0.591 c 10

Cluster-level

voxel-level

x, y, z T 8.07 5.59 6.08 3.87 3.43 5.30 7.01 5.18 5.56 3.72 3.32 4.94

mm

0.000 0.001

180 70

0.000 0.000

0.011 ...............

42

0.001

0.000 0.003 0.000 0.838 0.997 0.012

0.000 0.000 0.000 0.017 0.052 0.000

0.000 0.000 0.000 0.000 0.000 0.000

55 43 -47 -51 -43 51

-16 -16 -12 -27 -31 8

26 45 23 11 15 -4

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ACKNOWLEDGEMENT The rst author is thankful for the support received from Sri Chandrasekarendra Saraswathi Viswa Mahavidyalaya University, Kanchipuram, India. The rst and second authors are thankful to the University Grants Commission(UGC) for their project funding support towards successful completion of the work. The rst two authors are thankful to all staff members of the School of Computer Science and Engineering, Bharathiar University for their support.

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