Received: 12 September 2017

| Revised: 23 December 2017

| Accepted: 31 December 2017
DOI: 10.1002/ima.22267

RESEARCH ARTICLE

Rapid brain tissue segmentation process by modified FCM

algorithm with CUDA enabled GPU machine

T Kalaiselvi | P Sriramakrishnan

Department of Computer Science and

Applications, The Gandhigram Rural
Institute (Deemed to be University),
Gandhigram, Tamil Nadu, India
Correspondence
T Kalaiselvi, Department of Computer
Science and Applications, The
Gandhigram Rural Institute (Deemed to
be University), Gandhigram, Tamil Nadu,
India.
Email: kalaiselvi.gri@ruraluniv.ac.in
Abstract
The proposed work introduces a modified method of fuzzy c means (FCM) algorithm
using bias field correction and partial supervision techniques. The proposed method
is named as bias corrected partial supervision FCM (BCPSFCM). The modified
membership function takes the advantage of available knowledge from labeled pat-
terns with the bias field correction. The experiment is tested on internet brain
segmentation repository with their gold standard. The performance of the method is
compared with three existing methods and 12 state of the art methods using dice coef-
ficient, sensitivity, specificity, and accuracy. Accuracy of the proposed method
reached upto 98%, 98%, and 99% of GM, WM, and CSF segmentation but required
additional computation power from graphics processing unit (GPU). Further parallel
BCPSFCM is proposed with the help of compute unified device architecture enabled
GPU machine and the processing time is reduced up to 49 times than the serial
implementation.

KEYWORDS
bias correction, CUDA, GPU, partial supervision, tissue segmentation

1 | INTRODUCTION
The information technology makes a rapid development in the
medical industry. Technologies are more helpful in the part of
disease identification, inspection of human anatomical struc-
ture, analysis the characteristics of abnormal regions, recon-
struction, registration, and visualization.1 Huge volumes of
data needs to be processed in the medical diagnosis becomes a
painstaking task to the clinicians, who have to manually seg-
mented the data.2 To remove all these difficulties, technologies
helps to quicken the diagnosis process and improve the accu-
racy. In past few decades, computerized methods and algo-
rithms for segmentation, registration, and visualization along
with modern computers are frequently used to assist the doc-
tors in the treatment planning and diagnosis process.
The diagnosis of human being has been significantly
improved after the arrival of magnetic resonance imaging
(MRI) technique.3 MRI provides a cross sectional view of
human anatomy with the soft tissue characteristics. Brain is a
complex organ of human body and connected with the
central nervous system. MRI provides the soft tissue charac-
teristics about the brain structure, tissues, and tumor. In the
brain diagnostic system, brain tissue segmentation is essen-
tial to identify many brain disorders. Segmenting brain tis-
sues into gray matter (GM), white matter (WM), and
cerebrospinal fluid (CSF) helps to identify the neurodegener-
ative diseases like Alzheimer,4 alcoholism,5 bipolar disor-
der,6 Huntington disease,7 multiple Sclerosis,8 and tumors.9
Segmentation is always demand in the field of medical
technologies and further more complicated due to low con-
trast, high noise, intensity non uniformity (INU), and partial
volume effect in MR images. INU or bias field is a low fre-
quency smoothed artifact, which is induced by the radio-
frequency coil in MRI scanner. The bias field introduces the
shading effect in the pixel intensities of same tissue class
vary slowly over the image domain and produce errors with
conventional intensity-based classification. This shading
effect makes a misclassification in the brain tissue segmenta-
tion. Fuzzy clustering is a soft computing technique more
suitable for the brain tissue segmentation and that provides

Int J Imaging Syst Technol. 2018;1–12. wileyonlinelibrary.com/journal/ima V

C 2018 Wiley Periodicals, Inc. | 1
2 |
more important information from image based on the mem-
bership function.10 This membership function gives the dif-
ferent membership values to each pixel on difference
classes.11
Clustering is a process to identify the hidden structure
from the collection of individual data points (patterns). Par-
tial supervision or semi supervision is introduced by Pedrycz
with fuzzy clustering algorithm.12 This technique is more
helpful in the medical diagnosis field where the clinician
needs help from the machine to identify the hidden data.13
Partial supervision is used to identify the hidden structure of
the image by combining both labeled and unlabeled patterns.
The labeled patterns are a small subset of data, which helps
to cluster the unlabeled patterns and improve the accuracy.
The percent involvement of labeled patterns in terms of
learning processes as shown in Figure 1.
Major problem with the fuzzy clustering technique is its
iterative nature of time consuming process.14 Further, MRI
dataset as a stack of 2D slices requires much time for FCM
computation. GPU computation gives attractive results which
are observed by the researchers, to accelerate various appli-
cations, including medical image analysis.15,16 GPU contains
thousands of scalar processors which are capable to create
large amount of threads to support parallel computation.17
The threads are organized into a hierarchy of grids of thread
blocks can accessed the data from different level of memo-
ries like registers, shared memory and global memory. Com-
pute unified device architecture (CUDA) is a GPU
programming model with the extension of C programming
language developed by NVIDIA Corporation to support par-
allel computation.18
This paper introduces a modified version of FCM algo-
rithm using bias correction and partial supervision techni-
ques. The modified membership function has taking the
advantage of available knowledge taken from labeled pat-
terns with bias field correction. The proposed bias corrected
partial supervision FCM (BCPSFCM) method yields good
segmentation accuracy but still complex in computation.
Since the proposed method in CPU is a time consuming pro-
cess and the GPU based parallel method is proposed and
named as parallel BCPSFCM. The dataset used for testing
the accuracy of the proposed work is gathered from internet
brain segmentation repository (IBSR) with gold standard.
The performance of proposed method is compared with the
three existing methods and 12 state of the art methods using
Dice coefficient (DC), sensitivity, specificity, and accuracy.
The paper is organized as follows: related works of the
proposed work are given in the Section 2; the background of
the proposed work are presented in the Section 3; Section 4
shows the serial and parallel implementation of proposed
BCPSFCM Experimental materials and four evaluation
parameters are discussed in Section 5; Results and analysis
are given in the Section 6; Section 7 concluded the work.
THIRUVENKADAM AND PATHMANABAN
FIGURE 1 The percent of labeled patterns in learning processes
2 | RELATED WORKS
In 2002, Ahmed et al., proposed a bias corrected FCM
(BCFCM) for MR brain image segmentation in the presence
of INU artifact.19 They modified the objective function of
FCM algorithm using spatial neighborhood regularization
term. Al-Taie et al., proposed two variants of BCFCM to
reduce the negative effect of the log transform and over esti-
mation of bias field.20 Adhikari et al., presented a method
named as bias estimated spatial FCM (BESFCM) algorithm
for INU estimation and segmentation of MR images.21 The
new objective function incorporates the spatial information
around the neighborhood of each pixel.
Few partial supervision methods have been proposed in the
applications of remote sensing,22 medical imaging,23 and
image processing.24 Dulyakaran and Rangasanseri developed
geometrical guided FCM (GGFCM) algorithm based on partial
supervision to cluster the multispectral remote sensing image.22
Zhang et al., introduced a new method named as a semi-
supervised kernel-based FCM algorithm called S2KFCM,
which is based on the modified version of kernel based FCM
(KFCM).23 The implementation achieved high accuracy on the
Iris and Wisconsin Breast-Cancer datasets. Pedrycz et al., used
the fuzzy clustering with partial supervision in the analysis and
classification of digital images.24 The experiment is done with
the two collections of images, namely, Columbia object image
library (COIL-20) and a database composed of 2000 outdoor
images. The experiment works with various parameters like
labeling percentage, fuzzification coefficient, number of clus-
ters, and range of noises. Very limited works are proposed for
medical image applications using partial supervision.
Past few decades, several parallel FCM methods have
been proposed for reducing the computation time. Almaz-
rooie et al., implemented a GPU based fuzzy clustering for
brain tissue segmentation.25 The execution time of the
sequential FCM is 519 s for an MRI dataset while the GPU-
based FCM requires only 2.33 s. The algorithm is 245 times
faster than the sequential implementation. Aitali et al., ana-
lyzed a computational complexity of BCFCM algorithm and
proposed a parallel BCFCM (PBCFCM) for medical image
segmentation.26 The method implemented in various GPU’s
and they reduced the computation time upto 52 times than
the serial implementation. Cherradi et al., implemented a par-
allel BCFCM using GPU.27 They reach high computational
THIRUVENKADAM AND PATHMANABAN | 3

gain while using the heterogeneous implementation of CPU For reducing the computational complexity, taking loga-
and GPU. rithm on both side of the Equation 5 and the result is given
in the Equation 6.

3 | BACKGROUND log ðYk Þ5 logðXk Þ1log ðbk Þ (6)

yk 5xk 1 bk (7)
Recent years, lot of methods has been proposed to improve
where, yk is observed log transformed intensity, xk is true log
the performance of FCM algorithm. This section discusses
transformed intensity, and bk is log transformed bias field.
the three existing methods (FCM, BCFCM, and PSFCM)
From the Equation 7, true log transformed intensity cal-
used to develop the proposed BCPSFCM and compared its
culated as xk 5yk 2 bk . Then, substitute the true log trans-
performance.
formed intensity in the standard FCM objective function
(Equation 1) as
3.1 | FCM X
c X
n
2
Jm 5 ik jjyk 2bk 2vi jj
um (8)
The FCM algorithm attempts to partition a finite collection i51 k51
of elements X5fx1 ; x2 ; x3 ; . . . :; xn g into a collection of c
fuzzy clusters with centers V 5 vi , i51; 2; . . . ; c. The parti- Ahmed et al., have added a new term in the objective
tion or membership matrix, U 5 uik , i 51; 2; . . . c; k 5 1; 2; function to make bias correction in the INU affected MR
. . . ; n where uik is a numerical value between 0 and 1 that images.19 That term contains the effect of immediate neigh-
tells the degree to which the element xk belongs to the ith borhoods. Finally, the modified objective function of
cluster. The aim of FCM is to find clusters center that mini- BCFCM is defined as follows:
mize an objective function. X
c X
n
2
The objective function, which is used in FCM is given in JBC 5 ik jjyk 2bk 2vi jj
um
i51 k51
Equation 1.28 !
a X c X n X 2
X
c X
n 1 um jjyr 2br 2vi jj (9)
Jm 5 um Nr i51 k51 ik yr 2Nk
ik dik (1)
i51 k51
where, Nk is the neighboring pixels around the yk , Nr stands
dik 5jjxk 2vi jj2 (2) for cardinality of Nk; and the neighboring effort controlled by
where, m 2 [1, 1] is a weighting exponent that controls the the parameter a.
fuzziness of resulting clusters. The exponential weight m > 1, The modified membership function of BCFCM is given
however, in many applications default value of m52. Eucli- in Equation 10.
dian distance ðdik Þ calculates between the object xk and clus- 1
ters center vi . Minimization of the objective function requires uik 5
Pc D a m21
1 (10)
ik 1Nr gi
to meeting two conditions are given in Equations 3 and 4. j51 Djk 1Nar gj
Pn
uik xk where, Dik 5jjyk 2bk 2vi jj2
vi 5 Pk51
n (3)
m
k51 uik
The cluster centers are calculating using the Equation 11.
Pn  P 
1 u m
ð y 2b Þ1 a
ð y 2b Þ
uik 5
Pc h im21 (4) k51 ik k k Nr yr 2Nk r r
Pn
2
dik vi 5 (11)
l51 dlk ð11aÞ m
k51 uik

The bias estimation ðbk Þ during iteration is calculated

using the Equation 12.
3.2 | BCFCM Pc
um
ik vi
MRI scanner produces the output image ðY Þ that contains the bk 5 yk 2 Pi51
c m (12)
u
i51 ik
true tissue intensities ðX Þ with the intensity inhomogeneity
(b). Therefore, output image with n pixels can be defined in
the form of 3.3 | PSFCM
Yk 5Xk :bk ; k51; 2; . . . :; n (5) A prior knowledge about the belongingness of the same
th
where, Yk is observed intensity at the k pixel of the output objects may be useful in the clustering process. Partial super-
image, Xk is true tissue intensity of the k th pixel and bk is vision forms an intermediate framework that takes advantage
intensity inhomogeneity or bias field of the k th pixel. of clustering mechanisms and in case of labeled patterns
4 | THIRUVENKADAM AND PATHMANABAN

accommodates the knowledge about the labels in guiding the The objective function is minimized by updating the
process of unsupervised learning. Available knowledge of membership matrix U5uik in the following way.
small portion of the labeled patterns or data points signifi-   Pc 
1 11 d 12bk l51 flk
cantly improves the results of clustering process. Labeled uik 5 Pc 1dbk fik (16)
l51 dik =dlk
11d 2 2
pattern is less but accurate and unlabeled pattern is not accu-
rate whereas their amount is huge. The label and unlabeled
pattern handled by the boolean vector as defined as follows.
4 | PROPOSED METHOD
b5½bk ; k51; 2; . . . ; n (13)
where, The proposed BCPSFCM is a modified version of BCFCM
( and PSFCM. This method is developed for brain tissue seg-
1 if xk is labeled mentation, which takes the advantage of available knowledge
bk 5 (14)
0 otherwise from the known labeled patterns in the input image. The
automatic bias estimation and correction are added during
Membership values of labeled pattern arranged in the the clustering process ðuik Þ. The method is robustness against
form of matrix F5½Fik ; where i51; 2; . . . ; c; k51; 2; . . . ; n: the INU and available knowledge effectively used with the
The objective function of the partial supervision defined labeled patterns to improve the segmentation accuracy. Block
as diagram of the proposed BCPSFCM as shown in Figure 2.
X
c X
n X
c X
n The method is divided into three phases. First phase
Jps 5 um 2
ik dik 1 d ðuik 2fik bk Þm dik2 (15) works with the preprocessing steps like brain portion extrac-
i51 k51 i51 k51
tion and region of interest (ROI) selection. Then the algo-
where, d (d  0) denotes a scaling factor which maintains a rithm automatically checks the availability of GPU-CUDA.
balance between label and unlabeled patterns. If the availability is failed, control of execution moved into

FIGURE 2 The block diagram of the proposed BCPSFCM [Color figure can be viewed at wileyonlinelibrary.com]
THIRUVENKADAM AND PATHMANABAN | 5

F I G U R E 3 Preprocessing of the proposed method. A, Sample T1 weighted coronal image. B, Brain portion extraction using BEM2D. C, ROI selec-
tion. D, ROI extraction

the second phase. Second phase contains initialization and
clustering process of BCPSFCM in CPU. Phase three is exe-
cuted only if the device contains GPU and that supports the
CUDA programming. The methodology of the proposed
work is briefly explained in this section.
4.1 | Phase 1: Preprocessing
The proposed method takes the input of MR images from
IBSR repository, which contains 20 T1-weighted volumes.
The removal of non brain portion (scalp, skull, eyes, neck,
and fat) is important from MRI human head scans which
help to improve the accuracy and speed of the medical diag-
nosis process. The brain extraction is done by our own
method named as two dimensional approach of brain extrac-
tion method (BEM2D).29 In this method, an adaptive inten-
sity thresholding is used to obtain the binary image. The run
length scheme is used to get the rough brain mask and largest
connected component helps to reach the brain portion. The
method yields high segmentation accuracy than brain

FIGURE 4 The block diagram of the Parallel BCPSFCM [Color figure can be viewed at wileyonlinelibrary.com]
6 | THIRUVENKADAM AND PATHMANABAN

T A BL E 1 Details of IBSR20 dataset

Volume Dataset First Last Total number

no name Gender Age slice slice of slices

1 1_24 Female 35 21 63 65

2 2_4 Female 34 1 65 65

3 4_8 Female 29 7 67 61

4 5_8 Female 20 1 60 60

5 6_10 Male 22 1 63 63

6 7_8 Male 29 1 60 60

7 8_4 Male 27 1 63 63

8 11_3 Male 28 1 63 63

9 12_3 Male 38 1 63 63

10 13_3 Male 32 1 63 63

11 15_3 Male 31 1 60 60

12 16_3 Female 36 1 60 60

13 17_3 Female 29 1 63 63

14 100_23 Female 23 1 63 63

15 110_3 Male 25 0 63 64

16 111_2 Male 27 0 63 64

17 112_2 Male 32 1 63 63

18 191_3 Female 32 1 63 63

19 202_3 Female 28 1 63 63

20 205_3 Female 24 1 63 63

extraction tool, brain surface extractor, and model-based
level sets. The sample MR image from IBSR volume and
their corresponding skull stripped image are shown in Figure
3A,B, respectively. The slice selection is used to select the
image one by one until reach the last slice in the volume and
clearly given in Figure 2.
Normally MR brain image has more number of back-
ground pixels where nuclear magnetic resonance signal is void.
This makes the clustering process more time consumable and
inaccurate. Therefore, this ROI extraction is an automatic pro-
cess, which helps to concentrate the clustering process in the
tissue region alone. This reduces the more number of back-
ground data points in the clustering process. The ROI bound-
ary selection and ROI extraction are shown in Figure 3C,D.
4.2 | Phase 2: BCPSFCM
Second phase will be executed if the device does not meet
the requirement of parallel computation. The second phase of
the proposed method starts with the initialization of the
BCPSFCM. Generally four major regions are available in
MR images and that provides the good contrast between GM
(dark gray) and WM (light gray) tissues, CSF is void and
black intensity which is similar to background region there-
fore the initialization of number of clusters c53: The most
difficult challenge among these segmentation is different tis-
sue regions usually overlap to each other.
The proposed method initializes the labeled patterns
from image using advantage of available knowledge. From
the Figure 3D, the image having less number of back-
ground data points which is clearly known cluster with the
CSF region. Likewise high intensity pixels come under the
WM tissue. The background pixel and high intensity pixel
are marked as labeled patterns, which are less but accurate
and useful to guide the clustering process of huge unla-
beled patterns.
The label and unlabeled pattern handled by the boolean
vector as
THIRUVENKADAM AND PATHMANABAN | 7

F I G U R E 5 Qualitative analysis by various methods on sample image. GM is shown in green, WM in blue, CSF in red. A, Sample image. B, Gold
standard. C, FCM. D, BCFCM. E, PSFCM. F, BCPSFCM [Color figure can be viewed at wileyonlinelibrary.com]

b5½bk ; k51; 2; . . . ; n (17) The clustering process of BCPSFCM is based on updat-

ing values of membership function, clusters center and bias
where,
( field estimation. From Equations 19–21 are calculated during
1; If xk is labeled pattern the iteration process. The modified membership function of
bk 5 (18) BCPSFCM is defined as:
0; otherwise unlabeled pattern
2 3
 Pc 
Membership values of labeled pattern initializes in the 1 6 11d 12b k l51 lk 7
f
4 1 51dbk fik
Pc Dik 1Nar gi m21
form of matrix F5½Fik ; where i51; 2; . . . ; c; k51; 2; . . . ; n: uik 5 (19)
11d
Membership function ðuik Þ and clusters center ðvi Þ are initial- j51 Djk 1Nar gj
izes in the random manner.
The clusters center is defined as follows,

Pn  P  P 
n 2
k51 um
ik ðyk 2bk Þ1 Nar yr 2Nk ðyr 2br Þ 1 k51 uik 1dbk ðuik 2fik Þ xk
m
vi 5  Pn   m  (20)
2
2 ð11aÞ k51 uik 1 uik 1dbk ðuik 2fik Þ
m

4.3 | Phase 3: Parallel BCPSFCM

The bias estimation is calculated based on
Pc The phase 3 is executed when the device status succeeds
um
ik vi
bk 5 yk 2 Pi51c m (21) with the availability of GPU-CUDA. Block diagram of the
u
i51 ik parallel BCPSFCM as shown in Figure 4. Proposed parallel
P
where, Dik 5jjyk 2bk 2vi jj2 and gi 5 yr 2Nk jjyr 2br 2vi jj2 . algorithm in the form of CPU and GPU code are imple-
Generally d is a propositional to the rate of n=lp. Here, lp mented using Microsoft VC11 and CUDA 7.0 libraries.
stands for number of labeled patterns. CPU computation starts with initialization of parameters and
The termination criteria can be used for convergence if allocates the necessary memory on GPU. Then transfer all
cluster centers no longer moved in the successive iterations the required data from CPU to allotted GPU memory. For
and defined as the data parallelization, the method uses two kernels with
thread per pixel. CPU starts the execution of the kernel-1
sumðabsðvi 2v i ÞÞ < E (22)
then control moves to GPU. Kernel-1 calculates the modified
where, vi , v i are new and old cluster center values, E is the membership function as given in the Equation 19. The num-
termination condition between 0 and 1. ber of threads equal to number of pixels in the image. Every
8 | THIRUVENKADAM AND PATHMANABAN

T A BL E 2 Quantitative analysis in the form of DC value of pro-

posed method

Average DC
Volume name GM WM CSF

1 0.88 0.81 0.18

2 0.83 0.76 0.11

3 0.80 0.74 0.52

4 0.81 0.79 0.55

5 0.80 0.76 0.28

F I G U R E 6 DC graph of the proposed BCPSFCM segmentation
6 0.85 0.84 0.29
results on IBSR20 dataset [Color figure can be viewed at wileyonlineli-
7 0.82 0.81 0.35 brary.com]

8 0.87 0.84 0.42

9 0.89 0.81 0.49 5 | MATERIALS AND

EVALUATION PARAMETERS
10 0.90 0.84 0.23

11 0.79 0.76 0.58 The method used 20 normal T1 datasets that are obtained
from the IBSR with gold standard images, which is created
12 0.79 0.74 0.45
by center for morphometric analysis at Massachusetts general
13 0.81 0.79 0.37 hospital.30 The details of IBSR20 dataset are given in the
Table 1. Each dataset has 60 slices with 256 3 256 size
14 0.90 0.86 0.33
and 1 3 1 3 3 mm3 slice thickness. Among the 20 subjects,
15 0.85 0.80 0.21 10 subjects are from male and female respectively. The
16 0.86 0.84 0.32

17 0.82 0.79 0.27 TA B L E 3 Average DC (mean 6 standard deviation) values of

existing and proposed methods
18 0.80 0.78 0.25

Method Method Average DC

19 0.86 0.82 0.51
no. name GM WM CSF
20 0.87 0.86 0.56
1 ANN 0.69 6 0.09 0.77 6 0.14 0.15 6 0.06
Average 0.84 0.80 0.37
2 FAST 0.68 6 0.06 0.79 6 0.10 0.13 6 0.04
Deviation 0.03 0.03 0.14
3 FANTASM 0.70 6 0.10 0.77 6 0.14 0.15 6 0.06

4 FFCM 0.69 6 0.03 0.80 6 0.04 0.11 6 0.03

thread calculates the membership degree of each pixel for all 5 FSL FAST 0.77 6 0.09 0.75 6 0.05 –
the clusters. Then threads calculate the new clusters center
based on the Equation 20 but the final summation operations 6 GMM 0.77 6 0.09 0.74 6 0.02 0.25 6 0.12
are not included. Summation operation makes the computation 7 HLSSVM 0.76 6 0.02 0.76 6 0.04 –
infeasible in GPU. Resultant data alone transfers to the CPU
8 HHLSSVM 0.78 6 0.03 0.78 6 0.03 –
for summation operation and calculate new cluster centers.
New centers transfer back to the GPU and start the 9 KM 0.67 6 0.14 0.78 6 0.05 0.13 6 0.10
kernel-2 execution for bias field estimation. After kernel-2
10 KNN 0.64 6 0.09 0.80 6 0.06 0.13 6 0.04
completion, the control returns back to the CPU. The process
will be repeated until reach the termination condition. After 11 PVC 0.66 6 0.11 0.63 6 0.23 0.13 6 0.05
the termination, membership values of all pixels transfer
12 SPM 0.76 6 0.06 0.80 6 0.04 0.17 6 0.07
from GPU to CPU and release the GPU memory. Finally,
defuzzification process helps to obtain the segmented tissue 13 BCPSFCM 0.84 6 0.03 0.80 6 0.03 0.37 6 0.14
region of the MR image.
THIRUVENKADAM AND PATHMANABAN | 9

T A BL E 4 Evaluation parameters of existing and proposed The evaluation metrics sensitivity, specificity, and accu-
methods racy determine the strength of the method proposed. Sensi-
tivity relates to the testing ability of correctly identified
Evaluation Tissue
parameters type FCM BCFCM PSFCM BCPSFCM tissue regions. Specificity computes the percentage of non
tissue regions correctly detected. Accuracy is the proportion
DC GM 0.79 0.79 0.80 0.84 of true results and gives percentage of how much tissue and
WM 0.73 0.76 0.79 0.80 non tissue region exactly detected. All the evaluation param-
CSF 0.27 0.27 0.28 0.37
eters mentioned above was reaches its best value at one and
Sensitivity GM 0.68 0.71 0.77 0.78 worst score at zero. The evaluation parameters are defined
WM 0.87 0.88 0.93 0.94 as:
CSF 0.34 0.34 0.40 0.42 TP
Sensitivity5 (24)
Specificity GM 0.98 0.99 0.99 0.99
TP1FN
WM 0.97 0.98 0.98 0.98
TN
Specificity5 (25)
CSF 0.99 0.99 0.99 0.99 TN1FP
TP1TN
Accuracy GM 0.96 0.96 0.97 0.97 Accuracy5 (26)
TP1TN1FP1 FN
WM 0.96 0.97 0.98 0.98
CSF 0.99 0.99 0.99 0.99
6 | RESULTS AND DISCUSSION

subject’s age lies between 20 and 38. The dataset named as
2, 3, 4, 5, 11, 12, and 13 are low contrast scans and affected
by INU artifact.
There are four evaluation parameters used to determine
the performance of the proposed method. The parameters are
DC, sensitivity, specificity, and accuracy. DC is used to eval-
uating the accuracy of the proposed work for segmenting the
GM, WM, and CSF regions on IBSR20 dataset and com-
puted as31:
2TP
DCðA; BÞ5
FP12TP1FN
where, True positive (TP) and True negative (TN) are
count of pixels correctly segmented as tissue and non tis-
sue regions. False positive (FP) and False negative (FN)
are number of pixels falsely identified as tissue and non
tissue regions. DC value zero means complete disagree-
ment and one for complete agreement with the gold stand-
ard image. High value of DC is accepted by the medical
community.
The experiments are performed in CPU with 1.73 GHz Intel
I3 processor, 2 GB RAM, and Windows 7 operating system.
The parallel BCPSFCM are developed using CUDA in NVI-
DIA QUADRO K5000 GPU donated by the NVIDIA Cor-
poration with the configurations of 1.4 GHz processor, 8
multiprocessors, 1536 streaming cores, 4GB of GDDR5, and
173GB/s memory bandwidth.
The segmentation results of the proposed and existing
methods on sample image are shown in Figure 5. The seg-
mented regions GM, WM, and CSF are represented by
green, blue, and red colors, respectively. The qualitative
(23)
analysis is done by comparing the results with the available
gold standard image given in Figure 5B. The results of pro-
posed BCPSFCM have high similarity with the gold standard
image, which are marked by circles in Figure 5F. The yellow
circle denotes the efficiency of the proposed method in CSF
region detection along with interhemispheric fissure whereas
all the exiting methods missed the regions. The black circle
refers the additional efficiency of the proposed method in
GM and WM segmentation. The qualitative analysis showed

F I G U R E 7 Bias correction on sample image using BCPSFCM. A, Sample image. B, Bias estimated image. C, Bias corrected image. D, Segmented
image [Color figure can be viewed at wileyonlinelibrary.com]
10 | THIRUVENKADAM AND PATHMANABAN

that the proposed method yielded more appropriate segmen- TA B L E 6 Space and Time complexities of the existing and pro-
tation than the existing methods. posed methods
Quantitative analysis in the form of DC value by the pro-
Method Space Time
posed method is given in Table 2 and shown in Figure 6. name complexity complexity
BCPSFCM yielded high segmentation accuracy for GM and
WM regions. The graph is shown that the accuracy of GM FCM O ðnd1ncÞ O ðnc2 diÞ
and WM are fallen in the artifact datasets (2, 3, 4, 5, 11, 12, BCFCM O ðnd1ncÞ O ðnc2 diÞ
and 13). The GM and WM segmentation are given 84% and
80% of DC values with the gold standard, respectively. WM PSFCM O ðnd1nc1lÞ O ðnciÞ
segmentation is provided low DC than the GM due to artifact BCPSFCM O ðnd1nc1lÞ O ðnciÞ
made direct impact on the WM tissues.32 From the study,
most of the methods were not considered CSF segmentation
results of CSF segmentation is combined with the GM
and produced lower accuracy than the GM and WM on
region.
IBSR datasets.32–35
Four evaluation parameters on proposed method are
The segmentation accuracy in terms of DC value of pro-
computed and compared with three existing methods and are
posed and twelve state of an art methods on IBSR20 dataset
given in Table 4. The proposed method achieved higher DC
are given in the Table 3. The 12 state of the art methods are
value than existing methods. Sensitivity and specificity
gathered from Valverde et al.,32 and Kasiri et al.36 They are
showed the efficiency of the method to segment the tissue
artificial neural network (ANN), FMRIB’s automated seg-
and non tissue (background) regions. In brain tissue segmen-
mentation tool (FAST), fuzzy and noise tolerant adaptive
tation, sensitivity is more essential than the specificity. The
segmentation method (FANTASM), fast FCM (FFCM),
BCPSFCM gave high sensitivity results in all the tissue seg-
FMRIB software library (FSL FAST), Gaussian mixture
mentation. In the Table 4, specificity means all the method
model (GMM), hierarchical least-square support vector
effectively detects the background region, which is void
machine (HLSSVM), hybrid hierarchical LSSVM
black pixels in the image. Accuracy of the method is
(HHSSVM), K-means (KM), K-nearest neighbor (KNN),
achieved upto 98%, 98%, and 99% of GM, WM, and CSF
partial volume classifier (PVC), and statistical parametric
segmentation.
mapping (SPM).
The bias estimation and correction by the proposed
The results are given in the form of mean (l) followed
BCPSFCM on sample image as shown in the Figure 7. INU
by the plus or minus (6) standard deviation (r). Here, high
affected image and the corresponding bias estimated image as
l value denotes the high segmentation accuracy and low r
shown in Figure 7A,B. The bias corrected and segmented
value denotes the method stabling in the dataset. The pro-
image results as shown in Figure 7C,D. The bias estimation
posed method provided high segmentation accuracy and low
function helps to estimate the bias field during iteration and
r than state of art methods in GM and WM segmentation.
make the correction in the next iteration. The experimental
The proposed method yielded high accuracy on the CSF seg-
results with the artifact and non artifact datasets are given in the
mentation than other methods. All methods have very low
Table 5. Seven artifact datasets yielded average segmentation
value of CSF segmentation and some methods ignore them
accuracy and thirteen non artifact dataset gave high values. The
due to divergences on the classification of SCSF with respect
table showed that the proposed method is given high accuracy
to gold standard.32 The CSF is very small portion in the brain
than existing methods on both artifact and non artifact datasets.
scans and having very close intensities with GM and thus the
Space and time complexities are given in terms of big-
Oh notation in the Table 6 using the number of data
points ðnÞ, dimension of the data points ðd Þ, number of clus-
T A BL E 5 Experimental results of artifact and non artifact datasets
on IBSR20
ters ðcÞ, and number of labeled patterns ðlÞ.37 Here space and

Average DC TA B L E 7 Processing time of existing and proposed methods

Artifact dataset Nonartifact dataset Method Processing time
Method name GM WM CSF GM WM CSF name (seconds/dataset)

FCM 0.74 0.69 0.29 0.83 0.76 0.26 FCM 33

BCFCM 0.75 0.72 0.29 0.83 0.79 0.24 BCFCM 1492

PSFCM 0.76 0.72 0.30 0.84 0.81 0.26 PSFCM 1671

BCPSFCM 0.80 0.76 0.41 0.86 0.82 0.34 BCPSFCM 1996

THIRUVENKADAM AND PATHMANABAN
T A BL E 8 Processing time of serial and parallel implementation of
BCPSFCM
Processing time
Device Platform (seconds/dataset)
MATLAB 1996
CPU
C Programming 363
GPU CUDA 41
time complexity estimation exact only with the assumptions.
The average processing time taken by all the methods is
given in Table 7. FCM is an iterative method taken more
time to find the optimal results. From our experimental test,
traditional FCM has taken around 33 s/dataset. BCFCM has
taken 1492 s/dataset to estimate, correct, and segment the tis-
sues because it includes additional computation for bias esti-
mation and correction. Similarly, PSFCM used labeled
patterns that need additional computation and thus process-
ing time around 1671 s/dataset. Proposed BCPSFCM yielded
high segmentation accuracy but also takes the processing
time nearly 1996 s/dataset. These results are shown that the
proposed method required additional computational power
from GPU.
Processing time of proposed method implemented in var-
ious platforms are given in Table 8. The proposed
BCPSFCM implemented in MATLAB is computationally
expensive. Therefore, BCPSFCM is implemented in C lan-
guage and the processing time is shown in Table 8. The C
implementation helps to convert into CUDA code for parallel
implementation. Table 8 shows that the C implementation is
nearly 5 times faster than the MATLAB implementation.
The parallel implementation is 9 folds speedup than the C
implementation and 49 times faster than the MATLAB
implementation. Time calculation made after the I/O opera-
tions, which show the processing time more clearly.
7 | CONCLUSION
The proposed work aimed to segment the brain tissues with
bias correction and labeled patterns. The method is compared
with three existing methods and 12 state of the art methods.
The method yielded high Dice value of GM and WM seg-
mentation upto 84% and 80%, respectively. Accuracy of the
method is achieved upto 98%, 98%, and 99% of GM, WM,
and CSF segmentation. The proposed method is given high
accuracy than others and the computationally expensive. The
computational problem is overcome by the parallel
BCPSFCM method with the support of GPU – CUDA
model. Thread per pixel is used to reduce the computational
time upto 49 times than the serial implementation.
| 11
AC K NO WLE DG M E NT
The authors gratefully acknowledge the support of NVI-
DIA Corporation Private Ltd., USA with the donation of
the QUADRO K5000 GPU used for this research. The
authors wish to thank all the reviewers and associate editor
for their fruitful comments and suggestions for significant
improvement of the manuscript.
O RC ID
Kalaiselvi T http://orcid.org/0000-0002-0197-2077
RE FER EN CE S
[1] Chen YT. Medical Image Segmentation using Independent Com-
ponent Analysis-Based Kernelized Fuzzy c-Means Clustering.
Hindawi Math Problems Eng. 2017;2017:1–21. CrossRef]
[10.1155/2017/5892039]
[2] Despotovic I, Goossens B, Philips W. MRI Segmentation of the
Human Brain: Challenges Methods and Applications. Comput
Math Methods Med. 2015;2015:1–23.
[3] Dahab DA, Ghoniemy SSA, Selim GMI. Automated brain tumor
detection and identification using image processing and probabil-
istic neural network techniques. Int J Image Process Vis Com-
mun. 2012;1:1–8.
[4] Zhang J, Gao Y, Gao Y, Munsell BC, Shen D. Detecting ana-
tomical landmarks for fast Alzheimer’s disease diagnosis. IEEE
Trans Med Imaging 2016;35:2524–2533.
[5] Cosa A, Canals S, Valles-Lluch A, Moratal D. Unsupervised
segmentation of brain regions with similar microstructural prop-
erties: Application to alcoholism. Conference Proceedings on
IEEE Engineering and Medicine and Biology Society. 2013;
1053–1056.
[6] Bansal R, Hao X, Peterson BS. Segmenting and validating brain
tissue definitions in the presence of varying tissue contrast.
Magn Reson Imaging 2017;35:98–116.
[7] Coppen EM, van der Grond J, Hafkemeijer A, Rombouts SA,
Roos RA. Early grey matter changes in structural covariance net-
works in Huntington’s disease, Neuroimage 2016;12:806–814.
[8] Roura E, Oliver A, Cabezas M, Valverde S, Pareto D, Vilanova
 Llado X. A toolbox for multi-
JC, Ramio-Torrenta L, Rovira A,
ple sclerosis lesion segmentation. Neuroradiology 2015;57:
1031–1043.
[9] Kalaiselvi T, Nagaraja P. Fully automatic method for segmenta-
tion of brain tumor from multimodal magnetic resonance images
using wavelet transformation and clustering technique. Int J
Imaging Syst Technol. 2016;26:305–314.
[10] Dunn JC. A fuzzy relative of the ISODATA process and its use
in detecting compact well-separated clusters. J Cybern. 1973;3:
32–57.
[11] Sucharitha M, Geetha KP. Brain tissue segmentation using fuzzy
clustering techniques. Technol Health Care 2015;23:571–580.
[12] Pedrycz W, Waletzky J. Fuzzy clustering with partial supervi-
sion. IEEE Trans Syst Man Cybern. 1997;27:787–795.
[13] Bouchachia A, Pedrycz W. Data clustering with partial supervi-
sion. Data Min Knowl Disc 2006;12:47–78.
12 | THIRUVENKADAM
[14] Al-Ayyoub M, Abu-Dalo AM, Jararweh Y, Jarrah M, Sa’d MA. A
GPU-based Implementations of the Fuzzy C-means Algorithms for
Medical Image Segmentation. J Supercomputing 2015;71:3149–3162.
[15] Kalaiselvi T, Sriramakrishnan P, Somasundaram K. Survey of
using GPU CUDA programming model in medical image analy-
sis. Inform Med Unlocked 2017;9:133–144.
[16] Pratx G, Xing L. GPU computing in medical physics: A review.
Med Phys 2011;38:2685–2697.
[17] Kirk DB, Hwu WW. Programming Massively Parallel Processor:
A Hands-on Approach. 2nd ed. Burlington, MA: Elsevier, 2012.
[18] CUDA C Programming Guide. PG-02829-001_v8.0. NVIDIA
Corporation. Tech. Report, June 2017.
[19] Ahmed MN, Yamany SM, Mohamed N, Farag AA, Moriarty T. A
modified fuzzy C-means algorithm for bias field estimation and seg-
mentation of MRI data. IEEE Trans Med Imaging. 2002;21:193–199.
[20] Al-Taie A, Hahn HK, Linsen L. Improve bias-corrected fuzzy C
means segmentation of brain MRI data. Int J Hybrid Inf Tech-
nol. 2014;7:65–84.
[21] Adhikari SK, Sing JK, Basu DK. Bias Field Estimation and Seg-
mentation of MRI Images using a Spatial Fuzzy C Means Algo-
rithm. 2nd International Conference on Control, Instrumentation,
Energy and Communication (CIEC). 2016.
[22] Dulyakaran P, Rangasanseri Y. Fuzzy C-Means Clustering using
Spatial Information with Application to Remote Sensing. 22nd
Asian Conference on Remote Sensing. 2001.
[23] Zhang D, Tan K, Chen S. Semi-supervised Kernel-Based Fuzzy
C-Means. Int Conf Neural Inf Process. 2004;1229–1234.
[24] Pedrycz W, Amato A, Lecce VD, Piuri V. Fuzzy clustering with
partial supervision in organization and classification of digital
images. IEEE Trans Fuzzy Syst. 2008;16:1008–1026.
[25] Almazrooie M, Vadiveloo M, Abdullah R. GPU based Fuzzy C-
Means Clustering Algorithm for Image Segmentation. 2016;1–
13:arXiv:1601.00072.
[26] Aitali N, Cherradi B, El A, Bouattane O, Youssfi M. Parallel imple-
mentation of bias field correction fuzzy C-means algorithm for
image segmentation. Int J Adv Comput Sci Appl. 2016;7:375–383.
[27] Cherradi B, Ali NA, Abbassi AE, Bouattane O, Youssfi M.
CPU and GPU Behaviour Modelling Versus Sequential and Par-
allel Bias Field Correction Fuzzy C-means Algorithm Implemen-
tations. Contemp Eng Sci. 2017;10:423–438.
AND PATHMANABAN
[28] Bezdek JC. Pattern Recognition with Fuzzy Objective Function
Algorithms. New York: Plenum Press; 1981:1–256.
[29] Somasundaram K, Kalaiselvi T. Automatic Brain Extraction
Methods for T1 Magnetic Resonance Images using Region
Labeling and Morphological Operations. Comput Biol Med.
2011;41:716–725.
[30] Internet Brain Segmentation Repository, Center for Morphomet-
ric Analysis at Massachusetts General Hospital. Available at:
http://www.cma.mgh.harvard.edu/ibsr/index.html. Accessed
August 2017.
[31] Dice LR. Measures of the Amount of Ecologic Association
between Species. Ecology 1945;26:297–302.
[32] Valverde S, Oliver A, Cabezas M, Roura E, Llado X. Compari-
son of 10 brain tissue segmentation methods using revisited
IBSR annotations. J Magn Reson Imaging 2015;41:93–101.
[33] Tohka J, Dinov ID, Shattuck DW, Toga AW. Brain MRI tissue
classification based on local Markov random fields. Magn Reson
Imaging 2010;28:557–573.
[34] Wels M, Zheng Y, Huber M, Hornegger J, Comaniciu D. A dis-
criminative model-constrained EM approach to 3D MRI brain
tissue classification and intensity non-uniformity correction. Phys
Med Biol. 2011;56:3269–3300.
[35] Tian G, Xia Y, Zhang Y, Feng D. Hybrid genetic and variational
expectation-maximization algorithm for Gaussian-mixture-model
based brain MR image segmentation. IEEE Trans Inf Technol
Biomed. 2011;15:373–380.
[36] Kasiri K, Kazemi K, Dehghani MJ, Helfroush MS. A hybrid
hierarchical approach for brain tissue segmentation by combining
brain atlas and least square support vector machine. J Med Sig-
nals Sens. 2013;3:232–243.
[37] Bouchachia A, Pedrycz W. Fuzzy c-means algorithms for very
large data. IEEE Trans Fuzzy Syst. 2012;20:1130–1146.
How to cite this article: Kalaiselvi T, Sriramakrishnan
P. Rapid brain tissue segmentation process by modified
FCM algorithm with CUDA enabled GPU machine. Int
J Imaging Syst Technol. 2018;00:1–12. https://doi.org/
10.1002/ima.22267