2015 7th International Conference on Intelligent Human-Machine Systems and Cybernetics
A New Brain MRI Image Segmentation Strategy
Based on K-means Clustering and SVM
Jianwei Liu
School of Automation
Northwestern Polytechnical University
Xi’an, China
xatu07@163.com
Abstract—For the problem of noise and no reference image
during brain magnetic resonance imagery (MRI) image
segmentation, this paper proposes a new strategy to segment
brain MRI image based on K-means clustering algorithm and
support vector machine (SVM).Firstly, the strategy segments
brain MRI image using K-means clustering algorithm to
obtain the initial classification result as the class label,
secondly, the feature vectors of each pixel of brain tissue are
selected as the training samples and test samples, finally, brain
MRI image is segmented by SVM. Experimental results show
that the proposed segmentation strategy obtains better
segmentation effect, especially has a good noise suppression for
brain images with low signal-noise-ratio (SNR).
Keywords-k-means clustering; support vector machine
(SVM); feature extraction;
I. INTRODUCTION
Image segmentation plays an important role in medical
image processing, and is a key technique to analysis,
understand and describe medical images in order to diagnose
curious diseases. At present brain magnetic resonance
imaging (MRI) segmentation has important theoretical and
application value in medical image analysis. Accurate brain
tissue segmentation can improve reliability of brain disease
diagnosis and effectiveness of treatment. But MRI image is
often affected by the noise, gray overlap, partial volume
effect, and the characteristic of different anatomical
structure, the classification of MRI image is a nonlinear
classification problem[1][2][3]. At the same time the number
of brain images samples is limited, therefore, the currently
popular classification method is support vector machine
(SVM) that V. Vapnik and C. Cortes proposed [4]. SVM is a
kind of novel machine learning method, showing better
performance than the Bayesian classifier and neural network
classifier methods, and is regarded as a good alternative of
the traditional learning classification method. Especially
SVM has good generalization performance in the case of
small training samples and high dimension. Because of its
excellent learning performance, SVM has become a hotspot
of machine learning field, and has good application prospect
and benefits to use it for MRI brain image processing
research[5][6][7].
SVM is a supervised classifier, and needs to
segmentation reference image during brain image
978-1-4799-8646-0/15 $31.00 © 2015 IEEE
DOI 10.1109/IHMSC.2015.182
Lei Guo
School of Automation
Northwestern Polytechnical University
Xi’an, China
lguo@ nwpu.edu.cn
segmentation. However, the SVM cannot obtain the category
of the classification data automatically, and selects training
samples according to the reference segmentation image. In
practice, generally there is no segmentation reference image
when brain MRI image is segmented, therefore, selection of
training samples are a problem to be taken into account. In
this paper, in order to implement the unsupervised
classification, all brain image pixels are as the training
samples, which avoids artificial selection of training
samples, and the class label is obtained by K-means
clustering algorithm.
K-means clustering algorithm has been widely used in
medical image processing field because of the characteristics
of simple, fast, unsupervised and good segmentation effect.
The K-means clustering algorithm can divide brain MRI
image into white matter (WM), gray matter (WM) and
cerebrospinal fluid (CSF) and background automatically.
Although K-means clustering algorithm yields good results
for segmenting noise free images without require any manual
intervention, but K-means clustering algorithm is more
sensitive to noise, and it fails to segment images corrupted
by noise and other imaging artifact[8][9].
Therefore this paper proposes a new strategy to segment
brain MRI image based on K-means clustering algorithm and
support vector machine (SVM). Firstly, this paper uses K-
means algorithm to segment brain MRI image to get all
pixels category as the initial class label. Secondly, Good
features which directly affect the segmentation effect are
selected for the SVM classification. Brain MRI image
contains the rich feature information, such as texture, gray
etc. This paper adopts several important feature indexes as
the input vector of SVM, such as gray, mean, variance,
entropy, gradient and mode. These features includes gray
information and spatial structure information of image
pixels, which help to reduce noise. Finally, brain image
segmentation image is obtained by using SVM training
model and predicting brain image pixel category. The
simulation brain MRI image is used for brain tissue
classification, the experimental results show that the
proposed segmentation strategy obtains better segmentation
effect, especially has a good noise suppression for brain
images with low signal-noise-ratio (SNR).
The rest of this paper is organized as follows. In the next
section segmentation strategy is introduced. Section 3
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presents experimental results and discussion. Finally, the This paper adopts support vector machine (SVM)
paper is summarized in section 4. package - LIBSVM, which was developed by Dr. Chih-
JenLin from Taiwan University, and has characteristics of
II. SEGMENTATION STRATEGY simple, fast, effective and general [10].
A. K-means Clustering Algorithm C. Feature Selection
K-means algorithm is a classical algorithm to solve the Segmentation result depends on features extraction to a
clustering problem proposed by MacQueen in 1967, and is large extent, in addition to the choice of the classifier. At
also a simple and efficient clustering algorithm. It can make present the common features include local gray statistical
the minimum square distance between all point in clustering features and local texture features, such as mean, median,
domain and the cluster center [8][9]. contrast, correlation, entropy, angular second moment
K-means algorithm classifies a sample set X (x1, x2, ···, xn) (ASM), and variance, etc. Let f denotes brain MRI image. i
into k clusters with the aim at minimizing an objective and j represents row and column of the image respectively.
function, where n is the number of samples and Ci represents Let f ' represents neighborhood image of the current pixel,
1 whose size is s x s, s is odd [6]. This paper adopts several
the clustering center, C = ¦ x , i =1, 2, ···, k, Ni is the
i main features as follows:
N i x∈xi
(1) Gray (I)
sample number of the ith cluster xi. The objective function J
is given as: I = f (i, j ) (2)
k n 2 (2) Mean ()
J = ¦¦ x (ji ) − Ci (1) 1 s−1 s−1 ಫ
i =1 j =1 μ= ¦¦ f (i, j )
s 2 i=0 j =0
(3)
2
(i )
Where, x j − Ci is a distance measure between a data (3) Standard deviation (Std)
s −1 s −1
1
point xj and the cluster center Ci, the Euclidean distance is
adopted as the distance measure in this paper. Therefore, the
Std =
s2
¦¦ ( f ಬ (i, j ) − μ )
i = 0 j =0
2
(4)
K-means algorithm is an iterative clustering algorithm that (4) Entropy (E)
finds a correct classification result which minimizes the sum L −1
squared error. The K-means algorithm is described as
follows:
E = −¦ pi log 2 pi (5)
i =0
(1) Initialize cluster centroids Ci with k random samples;
Where, E is the neighborhood image local entropy, pi is
(2) Assign each sample point xj to the nearest cluster
the ratio between the number of pixels, whose gray values
center.
are equal, and the total number of pixels in the image.
1 (5) Gradient (G)
(3) Recalculating each clustering center: C = ¦x, i
i
N i x∈xi
=1, 2, ···, k ; G (i, j ) = ( f (i + 1, j ) − f (i , j )) 2 + ( f (i , j + 1) − f (i , j )) 2 (6)
(4) Repeat steps (2) and (3) until Ci no longer changes.
B. SVM (6) Mode (M)
Mode represents the most frequency pixel gray value of
Brain MRI image classification is a small sample the neighborhood image.
learning problems, but the small sample learning exists lots
of problems such as over learning, lack of learning, which M (i, j ) = max{ frequency{ f ' (i, j )}} (7)
increases the difficulty of brain image classification. Support Then the above features are as the input vector of SVM.
vector machine (SVM) method adopts the structural risk Because the extracted features can have a lot of differences
minimization instead of the traditional empirical risk in values, especially ignoring small value features which
minimization, which not only obtains good classification contributed to the classification, the features normalization is
ability in the small sample, nonlinear and high dimensional very important. This paper uses the following formula to
space, but also has better extension. SVM is based on normalize features:
statistical learning theory of VC dimension (Vapnik - V
Chervonenk dimension) and structural risk minimization V= (8)
max(V )
principle. According to the limited sample information SVM
finds the best compromise between the complexity of the Here, V represents feature vector, max (V) represents
model and the learning ability, in order to get the best maximum value of V. After normalization, the feature values
generalization capability classification method [7]. are limited in the range of [0, 1].
Therefore, this paper uses SVM method to segment brain D. Brain MRI Image Segmentation Step Based on K-means
MRI images. and SVM
(1) Read brain MRI images for segmentation.

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 (2) Using K-means algorithm to segment brain MRI
image into four categories (WM, GM, CSF, background) as
the initial class label.
(3) Extracting the SVM training samples. In this paper, in
order to implement the unsupervised classification, all brain
image pixels are as the training samples and test samples,
which avoids artificial selection of training samples.
(4) Extracting features of samples, features of samples
are: gray, mean, variance, entropy, gradient and mode. Each
sample point corresponding to six image features and one
class label constitutes each pixel feature vector as training
samples to train SVM after normalization processing. Using
the same way, each sample point corresponding to six image
Figure 1. Simulation brain MRI Figure 2. Reference segmentaion
features constitutes each pixel feature vector as test samples image image
after normalization processing.
(5) Training samples from (4) and gets a SVM classifier,
namely the classification model, here this paper uses
Gaussian radial basis kernel function.
(6) Classifying the test samples from (4) by using
classification model from (5) to obtain segmentation image.
III. EXPERIMENTAL RESULTS
In order to verify the validity of the proposed strategy,
simulated brain MRI images are segmented by the proposed
strategy and K-means algorithm respectively. In order to
quantify the evaluation segmentation effect, this paper adopts
the Jaccard similarity (JS) coefficient analyze and compare
the segmentation result quantitatively [11], which is defined Figure 3. Segmentation results Figure 4. Segmentation results
as follows: by K-means algorithm by this strategy

V k ∩ VTk
J k ( S , T ) = Sk (9) TABLE I. THE EVALUATION OF BRAIN TISSUE SEGMENTATION
VS ∪ VTk Noise level Tissue K-means algorithm The proposed strategy
Where, VTk is the ground truth of class k, and VSk is the WM 0.8996 0.9086
segmental results, k represents brain tissue classification. The
ratio is between 0 and 1, the greater the value is, the better 5% GM 0.8074 0.8126
segmentation results get. CSF 0.7653 0.7343
The experimental data comes from brain MRI data of WM 0.8624 0.8928
McGill Montreal University Neurology Institute
(http://www.bic.mni.mcgill.ca/brainweb). The website 7% GM 0.7491 0.7914
provides a lot of MRI simulated brain data with a variety of CSF 0.7228 0.7330
slice thicknesses, noise levels, and levels of intensity non- WM 0.8122 0.8702
uniformity. The simulated brain MRI image database is often
9% GM 0.6721 0.7619
used as the gold standard for image segmentation. The size
of experiment data is 181 x 217 x 181, and its spatial CSF 0.6671 0.7300
resolution is 1 mm isotropic. The experiment adopts T1-
weighted data with 40% intensity non-uniformity and noise IV. CONCLUSION
level 5%, 7%, 9%. Here, 40% intensity non-uniformity and
In this paper, a new strategy to segment brain MRI image
noise level 9% T1-weighted simulated brain MRI image data
based on K-means clustering algorithm and support vector
as an example shows the segmentation results. Fig.1 is the
machine (SVM) was proposed for noise brain image
input image data, Fig.2 is reference segmentation image,
segmentation without reference image. Firstly, the class label
Fig.3 is segmentation result by K-means algorithm, and Fig.4
was obtained using K-means clustering algorithm, secondly,
segmentation results by the proposed segmentation strategy.
the feature vectors of each pixel of brain tissue are selected
Table I gives evaluation of brain tissue segmentation
as the training samples and test samples, finally, brain MRI
results of WM, GM, and CSF in terms of Jaccard Similarity
image is segmented by SVM. Experimental results showed
Coefficients for the simulated brain MRI images with
the proposed strategy obtained better segmentation effect,
different noise. As can be seen from Table I, the proposed
especially for the low SNR brain MRI images.
strategy obtains better segmentation accuracy than K-means
algorithm even at low SNR brain images.

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 ACKNOWLEDGMENT [6] H.X. Xu, Y. Li, G.X Zhu, X. Zhang and J.W. Tian, “Segmentation of
Magnetic Resonance Brain Tissues Image Based on Support Vector
This work is fully supported by a grant from the National Machines,” Journal of Image and Graphics, vol. 10, Oct. 2005, pp.
Natural Science Foundation of China (Project 1275-1280, doi:10.3969/j.issn.1006-8961.2005.10.012. ( in Chinese )
No.61273362). [7] H. Liu, K. Wang, and D. Liu, “Segmentation of Magnetic Resonance
Brain Tissues Image Based on Support Vector Machines and Level
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