THE IMAGING SCIENCE JOURNAL

2019, VOL. 67, NO. 8, 434–446

https://doi.org/10.1080/13682199.2019.1700875

RESEARCH ARTICLE

Semi-automatic unsupervised MR brain tumour segmentation using a simple

Bayesian Framework
Archana Chaudhari and Jayant Kulkarni
Instrumentation Engineering Department, Vishwakarma Institute of Technology, Pune, Maharashtra, India

ABSTRACT ARTICLE HISTORY

Tumours, one of the pathologies of the brain, are diverse in shape and appearance and overlap Received 17 December 2018
with the normal brain tissues making accurate automatic segmentation a challenge. This work Accepted 25 November 2019
proposes a semi- automatic, unsupervised method for brain tumour segmentation, using
KEYWORDS
magnetic resonance images in a simple Bayesian framework. Pixel is classified as a tumour MRI; Bayes theorem; brain
class by taking into account the knowledge of different brain tissue classes, grey level of tumour; segmentation;
pixels and their neighbourhood. For the Bayesian frame work, the likelihood of the different likelihood; conditional
brain tissue classes is assumed as Gaussian and Gaussian density weights of the pixel probability; prior; posterior
neighbourhood serve as the prior information for accurate tumour segmentation. probability
Experiments conducted on the publically available BRATS database result in an overall
accuracy of 98% for tumour core and 96% for oedema.

Introduction of interest. Segmentation is a process of labelling an

Tumour, one of the pathologies of the brain, is an uncon-
trolled growth of cancer cells. Clinically, tumours are of
different types and have different characteristics. The
primary brain tumours originate in the brain, while the
metastatic brain tumours begin as cancer elsewhere in
the body and spread to the brain. Brain tumours are
further divided as benign and malignant. World Health
Organization classifies the brain tumours into grade I to
IV. Grade I and grade II are benign low-grade brain
tumours; grade III and grade IV are high-grade malignant
brain tumours. Statistical reports show that brain
tumours are the second leading cause of cancer-related
deaths all over the world. Brain tumours are, therefore,
seriously endangering people’s lives and there is an
urgent need for early discovery and action. Clinically,
treatment options for brain tumours include surgery in
most cases, but radiation therapy or chemotherapy can
be used to slow the growth of the tumour. Magnetic res-
onance imaging (MRI) provides good differentiation of
soft tissues and detailed images of the brain. Its non-inva-
sive nature, high contrast, relatively high spatial resol-
ution across the entire field of view and multi-spectral
characteristics make it a popular modality for the brain
tumour diagnosis [1]. The brain is a complex structure
and the brain images contain a lot of information. The
brain consists of different tissues including white
matter (WM), grey matter (GM), cerebrospinal fluid
(CSF), deep brain and sub- cortical structures, brain path-
ologies like tumours and multiple sclerosis lesions. For
diagnostic purpose often only one or two structures are
image into an non–overlapping image, constituting
regions such that all elements of the group have a
common property [2]. Image segmentation consists in
finding a correspondence between radiometric infor-
mation and symbolic labelling [3]. It permits the visualiza-
tion of structure of interest by removing unwanted
information. Segmentation of tumour from the brain
image is the key for diagnosis, surgery and therapy plan-
ning. It also enables structure analysis such as calculation
of the volume of a tumour [4].
Related work
Segmentation techniques can be broadly classified as
pixel classification-based, threshold-based, region-
based and model-based techniques. In thresholding-
based methods, objects are classified using image
intensity either at a global or a local level.
In the specific area of brain tumours, segmentation
consists in separating the different tumour tissues from
the normal brain tissues [5]. Tumours consist of the fol-
lowing regions; tumour cores, which are active tumour
tissues, and swelling oedema and neurotic tissues are sur-
rounding the tumour. The goal of segmentation is to
detect the location and extension of the tumour
regions. Tumours are often diffused with the surrounding
oedema, emerge anywhere in the brain in different
shapes and sizes and extend tentacle-like structures
that make them difficult to segment [6]. Different MRI
modalities produce different types of tissue contrast

CONTACT Jayant Kulkarni vitjvk@yahoo.com Instrumentation Engineering Department, Vishwakarma Institute of Technology, 666 Upper Indira
Nagar, Bibvewadi, Pune 411037, Maharashtra, India
© 2019 The Royal Photographic Society

images, thus providing valuable structural information
and enabling the diagnosis and segmentation of
tumours along with their sub-regions [5].
Pixel classification methods proposed in the litera-
ture use pixel features such as grey levels, local
texture or colour to cluster the pixels for MR image seg-
mentation. In clustering, different objects are grouped
into different clusters based on the some appropriate
distance measure between pixels in the feature
space. Fuzzy C means (FCM) and K means are popular
clustering methods proposed for MR image segmenta-
tion. Several variants of the FCM and K means algor-
ithm are proposed for accurate segmentation. FCM
with spatial constraints, which incorporate spatial infor-
mation, are proposed for better segmentation. Other
algorithms, exploiting the neighbouring information
or spatial connection proposed in the literature, can
be found in [7–13]. This research article proposes a
new semi-automatic unsupervised method for seg-
mentation of the tumour core and the surrounding
oedema. The method is based on pixel classification
using a Bayesian framework. It incorporates clustering
and conditional probability along with spatial neigh-
bourhood information. It differs from other clustering
methods in the sense that, along with clustering and
neighbourhood information, the Bayesian analysis is
employed for accurate tumour segmentation. Cluster-
ing methods use a distance measure for pixel classifi-
cation, whereas the proposed method is based on
the posterior probability of the pixel. In the proposed
method pixel is classified as tumour class only when
the posterior probability of the pixel is maximum for
the tumour class. The Gaussian weighted grey levels
of the neighbourhood pixels aid in the pixel classifi-
cation in the form of the prior in a Bayesian framework.
This research article is organized as follows: Section
2 discusses the proposed segmentation method.
Section 3 describes the database along with the evalu-
ation metrics. Section 4 discusses the experimental
work along with the results and Section 5 presents
the conclusion of the research work.
The proposed segmentation method using a
simple Bayesian Framework
In the proposed method K means clustering is used to
quickly produce a primary classification into different
classes, which serve as an initialization step. With the aid
of the primary clusters from K means and Bayesian frame-
work, segmentation of tumour and oedema is achieved.
Tumour segmentation using a simple Bayesian
Framework
Consider the MR image of size, having m rows and n
columns, as represented as F(m, n). Let F(m, n) involve
j pattern classes. The initial classes are decided by the
THE IMAGING SCIENCE JOURNAL 435
K means algorithm. Pixel p(x, y) having coordinates (x,
y) is defined in the image F(m, n) having a grey level
‘g’. For pixel classification in terms of grey levels in an
image, the conditional probability Pk that a pixel p(x,
y) belongs to class j can be represented as
Pk = P( p(x, y) = j; g, F) (1)
The grey levels of a set of 8 neighbourhood pixels of p
(x, y) can be represented as
G [ {gN }
where N = 1, 2, 8. Pixel classification, in terms of neigh-
bourhood grey level information, can be represented
as
Pk = P( p(x, y) = j; g, G) (2)
In the Bayesian framework, the conditional probability
for pixel classified into the jth class can be represented
as
Posterior = Likelihood∗Prior (3)
From Equations (2) and (3),
P(g, G; p(x, y) = j)∗P(j)
P( p(x, y) = j; g, G) = (4)
P (g, G)
where P(g, G; p(x, y) = j) is the likelihood, P(j) rep-
resents the prior and P(g, G) is marginal probability. It
is a normalization factor and is assumed as unity. The
sign ‘*’ denotes multiplication.
According to the Bayesian analysis the pixel p(x, y)
under consideration is said to be classified into the
jth class if its posterior probability is maximum for the
jth class. In other words, the product of the likelihood
and the prior probability for pixel p(x, y) has to be the
maximum for pixel classification in the jth class.
In the proposed method the likelihood of the pixels
belonging to each pattern class is assumed as having a
Gaussian density.
For an n-dimensional case, the Gaussian density of
the vector in the jth pattern class has the following
form
1 −12(x−mj )T Cj−1 (x−mj )
P(x; j) = n n exp (5)
(2p)2 |Cj |2
where each density is specified completely by its mean
vector mj and covariance matrix Cj which are defined as
mj = Ej {x} (6)
Cj = Ej {(x − mj )(x − j)T } (7)
In the Bayesian analysis, the selection of the prior plays
an important role [14]. Considering the probabilities of
each class only as the prior may not lead to an accurate
pixel classification. A need, therefore, arises to embed
more information into the prior such that the posterior
probability is maximized for accurate pixel
436 A. CHAUDHARI AND J. KULKARNI
classification. The information provided by the neigh-
bourhood pixels also contributes to the assignment
of pixels in a particular class. In the proposed
method, the product of the prior probability of the
jth class, along with the sum of all the Gaussian
density weights of eight neighbours of pixel p(x, y)
for the jth class is considered as the prior information.
The pixel p(x, y) under consideration in the proposed
method is classified into the jth class when the
product of Gaussian likelihood of the pixel and the
prior information is maximum for the jth class. Math-
ematically,
Pk = P ( p(x, y) = j; g, G)
= P (g, G; p(x, y) = j)∗ P (j) (8)
In Equation (8), P (g, G; p(x, y) = j) represents the
Gaussian likelihood for pixel p(x, y) and
P (j) represents the prior and is detailed for the pro-
posed method as Equation (8a)
P(j) = p( jth class)∗ SN (gN ∗ P (xN ; j)) (8a)
where p( jth class) represents the probability of the jth
class and it is computed using Equation (5). gN is the
grey level of N neighbourhood pixels and P(xN; j) rep-
resents the Gaussian density weights of the N neigh-
bourhood pixels of p(x, y), computed using Equation
(5).
The Equation (8) is elaborated as
Probability of pixel p(x, y)belonging to jth class =
Gaussian likelihood of pixel p(x, y)
∗(prior probability of jth class)∗(sum of product of
gray levels of eight neighbourhood pixels and
Gaussiandensity weights of eight neighbourhood pixels
around pixel p(x, y))
From Equation (8) it is, therefore, said that for pixel p(x,
y) has to be classified in the jth class the value of Pk as
to be maximum for the jth class. Equation (9) rep-
resents the threshold for pixel classification.
p(x, y) [ ( jth class), for max(Pk = j) (9)
In the proposed method for pixel classification, the
initial clusters in the image are found by using the K
means clustering algorithm. The mean of all the
classes is computed from the clusters. The prior prob-
ability of each class is computed from the initial knowl-
edge of the clusters. The probability of each pixel p(x, y)
in the image F(m, n) for all j classes is computed. Thus
pixel p(x, y) is classified as belonging to the jth class if its
probability is maximum for the jth class. Figure 1 pre-
sents the flow chart of the proposed method.
The proposed method is elaborated in the follwing
steps:
Step 1: Compute the j classes of the input MR image
F(m, n) using K means.
Step 2: In the proposed method the input image is
initialized into j = 5 classes.
Step 3: The mean of each jth class is computed from
the K means. The mean of the jth class is represented as
mj.
Step 4: From the initial clusters the prior probability
of each class p( jth class) is computed as
(number of pixels belonging to j th class)
p( jth class) =
(number of pixels in the image (m ∗ n))
Step 5: Compute the Gaussian likelihood of the pixel p
(x, y) for the jth class using the mean of the jth class
from step 3 and Equation (5).
Step 6: Compute the Gaussian density weights of all
the neighbourhood pixels around p(x, y)
Step 7: Obtain the sum of all the Gaussian density
weights of the neighbours of pixel p(x, y) from Equation
(5) using the term SN (gN ∗ P (xN ; j)) where gN rep-
resent the grey levels of the Nth neighbour of pixel p
(x, y) and P(xN; j) is the Gaussian density weight of
the Nth neighbour of pixel p(x, y). Since the term
involves the product of the grey levels and the Gaus-
sian weights no normalization is needed. Figure 2 rep-
resents the eight neighbours of the pixel p(x, y).
The term in Step 7 can be represented using
Figure 2 as
SN gN ∗ P (xN ; j)
= g1 ∗ P (x − 1, y − 1; j) + g2 ∗ P (x, y − 1; j)
+ g3 ∗ P (x + 1, y − 1; j) + g4 ∗ P (x − 1, y; j)
+ g5 ∗ P (x + 1, y; j) + g6 ∗ P (x − 1, y + 1; j)
+ g7 ∗ P (x, y + 1; j) + g8 ∗ P (x + 1, y + 1; j)
where P is obtained using Equation (5).
Step 8: Obtain the expression of the prior by com-
bining the information from Steps 3, 5 and 6.
Step 9: The probability of the jth class for pixel p(x, y)
can be computed using Equation (8).
Step 10: The pixel p(x, y) is classified in the jth class if
the value of the probability of jth class is maximum.
The algorithm computes the product of the likeli-
hood and the prior for each pixel and each class, and
the pixel classification is done when this product is
maximum for the pixel under consideration for a par-
ticular class.
Results and discussion
The performance evaluation of the proposed method is
tested on MICCAI 2012 and 2013 Challenge database
[15–17]. The training data consist of multi-contrast
MR scans. For each patient, T1, T2, FLAIR, and post-
Gadolinium T1 MR Images are available. Segmentation
evaluation is the task of comparing two segmentations
by measuring the distance or similarity between them,
where one is the segmentation to be evaluated and the
other is the corresponding ground truth segmentation

Figure 1. Flow chart of the proposed method. (Images reproduced by kind permission of the authors).
[18]. Fenster et al. [19] categorized the requirements of
medical segmentation evaluation into accuracy (the
degree to which the segmentation results agree with
Figure 2. Representation of eight neighbours of pixel p(x, y)
(Images reproduced by kind permission of the authors).
THE IMAGING SCIENCE JOURNAL 437
the ground truth segmentation), the precision as a
measure of repeatability, and the efficiency which is
mostly related to time. Taha et al. give an overview of
the different metrics used for segmentation. For the
proposed method segmentation evaluation is done
using Accuracy, Sensitivity, Specificity, Precision and
Dice Coefficient [18].
The proposed method is compared with the most
basic versions of the KM and FCM algorithm for the
purpose of comparison of distance-based metrics for
pixel classification and probabilistic-based metrics for
pixel classification. The proposed method is compared
with few recent works in the literature.
Results for tumour core and oedema
segmentation
In the proposed method, T1-w contrast-enhanced
images are used to detect tumour core and corre-
sponding FLAIR images from the BRATS database are
used to detect the surrounding oedema. Figure 3
demonstrates the results for BRATS 2012 database
along with ground truth images separately for
tumour core and oedema and segmentation results
438 A. CHAUDHARI AND J. KULKARNI

Figure 3. Segmentation results for BRATS 2012 database. Column First (odd row): T1w contrast-enhanced images. Column first
(even row): corresponding FLAIR images. Column second (odd row) Ground Truth images of Tumour. Column second (even
row) Ground Truth images of oedema. Segmentation results using Column Third: Proposed method. Column Fourth: K means algor-
ithm. Column Fifth: FCM algorithm. (Images reproduced by kind permission of the authors).
 THE IMAGING SCIENCE JOURNAL 439

Figure 4. Segmentation results for the BRATS 2013 database. Column First (odd row): T1w contrast-enhanced images. Column First
(even row): corresponding FLAIR images. Column second (odd row) Ground Truth images of Tumour. Column second (even row):
Ground Truth images of oedema. Segmentation results using Column Third: Proposed method. Column Fourth: K means algorithm.
Column Fifth: FCM algorithm. (Images reproduced by kind permission of the authors).
440 A. CHAUDHARI AND J. KULKARNI

Figure 5. Segmentation results for the BRATS-2 database. Column First (odd row): T1w contrast-enhanced images. Column First
(even row): corresponding FLAIR images. Column second (odd row) Ground Truth images of Tumour. Column second (even
row) Ground Truth images of oedema. Segmentation results using Column Third: Proposed method. Column Fourth: K means algor-
ithm. Column Fifth: FCM algorithm. (Images reproduced by kind permission of the authors).
 THE IMAGING SCIENCE JOURNAL 441

Figure 6. Segmentation results for the BRATS-2 synthetic database. Column First (odd row): T1w contrast-enhanced images.
Column First (even row): corresponding FLAIR images. Column second (odd row) Ground Truth images of Tumour. Column
second (even row) Ground Truth images of oedema. Segmentation results using Column Third: Proposed method. Column
Fourth: K means algorithm. Column Fifth: FCM algorithm. (Images reproduced by kind permission of the authors).
 442
Table 1. Evaluation metrics for tumour core segmentation for the BRATS database.
Image Set Accuracy Sensitivity Specificity Precision Dice

A. CHAUDHARI AND J. KULKARNI

PM KM FCM PM KM FCM PM KM FCM PM KM FCM PM KM FCM
12hg3522 0.9898 0.9875 0.9896 0.3399 0.2509 0.5474 0.9995 0.9984 0.9962 0.9100 0.7094 0.6856 0.4949 0.3708 0.6087
12hg3526 0.9912 0.9872 0.9879 0.6166 0.0952 0.5904 0.9959 0.9983 0.9928 0.6556 0.4210 0.5092 0.6355 0.1553 0.5468
12hg3518 0.9934 0.9758 0.9893 0.8568 0.1090 0.6494 0.9972 0.9999 0.9988 0.8952 0.9824 0.9394 0.8756 0.1963 0.7679
12hg3538 0.9741 0.9718 0.9731 0.3566 0.1410 0.3456 0.9926 0.9967 0.9919 0.5935 0.5687 0.5622 0.4455 0.2259 0.4280
13hgg514 0.9964 0.9931 0.9957 0.8718 0.3140 0.6462 0.9976 0.9997 0.9991 0.7828 0.9255 0.8753 0.8249 0.4690 0.7435
13hgg526 0.9961 0.9904 0.9955 0.8779 0.4118 0.8606 0.9978 0.9986 0.9975 0.8516 0.8186 0.8319 0.8646 0.54799 0.8460
13hgg550 0.9953 0.9874 0.9940 0.8582 0.3042 0.7135 0.9978 0.9996 0.9990 0.8765 0.9417 0.9278 0.8673 0.4599 0.8067
13hgg556 0.9871 0.9832 0.9877 0.4329 0.1911 0.4864 0.9976 0.9982 0.9971 0.7764 0.6732 0.7643 0.5559 0.2978 0.5945
2hg686 0.9954 0.9938 0.9950 0.6439 0.3900 0.6656 0.9987 0.9995 0.9981 0.832 0.8811 0.7733 0.7260 0.5407 0.7154
2hg699 0.9936 0.9861 0.9928 0.7727 0.4687 0.8759 0.9991 0.9988 0.9957 0.9552 0.9085 0.8338 0.8543 0.6183 0.8543
2hg705 0.9858 0.9840 0.9860 0.5823 0.2323 0.4382 0.9939 0.9991 0.9970 0.66 0.8404 0.7506 0.6187 0.3640 0.5533
2hg735 0.9712 0.9656 0.9701 0.3954 0.1783 0.3853 0.9954 0.9987 0.9947 0.7852 0.8615 0.7545 0.5259 0.2955 0.5101
hgsyn885 0.9957 0.9916 0.9607 0.8378 0.3391 0.2623 0.9977 0.9998 0.9694 0.8206 0.9580 0.09675 0.8291 0.5009 0.1413
hgsyn903 0.9973 0.9947 0.9977 0.9658 0.5141 0.8826 0.9976 0.9997 0.9989 0.8104 0.9558 0.8972 0.8813 0.6685 0.8898
hgsyn909 0.9923 0.9876 0.9918 0.5570 0.2448 0.5355 0.9995 0.9999 0.9993 0.9551 0.9924 0.9362 0.7036 0.3928 0.6813
hgsyn945 0.9824 0.9737 0.9866 0.4472 0.1659 0.5927 0.9997 0.9999 0.9994 0.9860 0.9855 0.9712 0.6153 0.2840 0.7361
Average 0.9898 0.9846 0.9871 0.6508 0.2719 0.5923 0.9973 0.9991 0.9953 0.8216 0.8390 0.7568 0.7074 0.3992 0.6515

Table 2. Evaluation metrics for oedema segmentation for the BRATS database.
Image Set Accuracy Sensitivity Specificity Precision Dice
PM KM FCM PM KM FCM PM KM FCM PM KM FCM PM KM FCM
12hg3520 0.9771 0.9823 0.9714 0.7161 0.2624 0.0000 0.9807 0.9921 0.9847 0.3357 0.3120 0.0000 0.4571 0.2850 0.1465
12hg3524 0.9855 0.9740 0.9848 0.8330 0.4051 0.7812 0.9923 0.9993 0.9939 0.8278 0.9623 0.8498 0.8304 0.5702 0.8141
12hg3516 0.9502 0.9574 0.9449 0.4449 0.2246 0.9286 0.9728 0.9901 0.9456 0.4221 0.5034 0.4328 0.4332 0.3106 0.5904
12hg3536 0.9474 0.9459 0.9421 0.4696 0.2838 0.5807 0.9830 0.9952 0.9691 0.6724 0.8154 0.5830 0.5530 0.4210 0.5818
13hgg512 0.9839 0.9737 0.9698 0.6029 0.3696 0.5725 0.9907 0.9846 0.9770 0.5399 0.3018 0.3097 0.5697 0.3323 0.4019
13hgg524 0.9797 0.9835 0.9833 0.7962 0.5372 0.6677 0.9860 0.9991 0.9943 0.6651 0.9524 0.8037 0.7248 0.6869 0.7294
13hgg548 0.9759 0.9857 0.9184 0.5702 0.3814 0.1837 0.9815 0.9941 0.9286 0.2980 0.4694 0.0343 0.3914 0.4208 0.0578
13hgg545 0.9607 0.9588 0.9592 0.5585 0.3095 0.5035 0.9796 0.9893 0.9806 0.5620 0.5761 0.5495 0.5602 0.4026 0.5255
2hg684 0.9764 0.9630 0.9754 0.8804 0.3149 0.7275 0.9803 0.9888 0.9852 0.6394 0.5279 0.6618 0.7408 0.3945 0.6931
2hg697 0.9528 0.9545 0.9517 0.7194 0.4659 0.6867 0.9708 0.9922 0.9722 0.6559 0.8225 0.6559 0.6861 0.5948 0.6710
2hg703 0.9791 0.9702 0.9676 0.2308 0.0935 0.0136 0.9937 0.9873 0.9863 0.4169 0.1263 0.0190 0.2971 0.1075 0.0158
2hg733 0.9683 0.9696 0.9715 0.6681 0.3719 0.5845 0.9832 0.9992 0.9906 0.6624 0.9573 0.7554 0.6652 0.5356 0.6590
hgsyn883 0.9530 0.9685 0.9637 0.1588 0.5755 0.3833 0.9785 0.9812 0.9824 0.1918 0.4954 0.4116 0.1738 0.5324 0.3970
hgsyn901 0.9479 0.9685 0.9837 0.3116 0.5382 0.6273 0.9727 0.9853 0.9976 0.3080 0.5872 0.9092 0.3098 0.5617 0.7424
hgsyn907 0.9871 0.9755 0.9890 0.5395 0.5645 0.6600 0.9986 0.9860 0.9974 0.9070 0.5099 0.8687 0.6766 0.5358 0.7501
hgsyn943 0.9810 0.9686 0.9841 0.3135 0.6013 0.4466 0.9984 0.9782 0.9982 0.8408 0.4190 0.8643 0.4568 0.4938 0.5889
Average 0.9691 0.9687 0.9663 0.5508 0.3937 0.5217 0.9839 0.9901 0.9802 0.5591 0.5836 0.5443 0.5329 0.4491 0.5228
 THE IMAGING SCIENCE JOURNAL 443

for KM and FCM algorithms. Figures 4–6 demonstrate Table 3. Comparison of the proposed method with recent
the segmentation results for tumour core and methods for tumour core segmentation from the BRATS
oedema with high-grade Glioma for BRATS 2013, database (T1c images).
Methods Accuracy Sensitivity Specificity Dice Coefficient
BRATS 2 and BRATS 2 synthetic images. Since K
PSO 0 .9397 0 .9796 0 .8268 0 .9316
means and Fuzzy C means method are classical pixel PCA 0.9374 0.9807 0.8271 0 .9316
classification methods, hence the proposed method is SE-LS 0.9413 0 .9815 0 .8277 0 .9408
compared with the K means and Fuzzy C means PM 0.9898 0.6508 0.9839 0.7074
SE-TLBO 0 .9459 0 .9923 0 .9025 0 .8762
method. Tables 1 and 2 present the comparison of CNN Not computed 0.79 0.79 0.79
the evaluation metrics for the proposed method (PM)
with ground truth, KM and FCM algorithms for
tumour core and oedema segmentation, respectively. neural network (CNN). Except sensitivity the exper-
The proposed method is also compared with other imental results of the proposed method are compar-
recent tumour segmentation methods in the literature. able with the recent supervised methods in the
Table 3 presents the comparison of the proposed literature.
method with recent methods in the literature for Table 4 summarizes the average computation time
tumour core segmentation on the BRATS database. for the proposed method along with K means and
The average segmentation accuracy using the pro- Fuzzy C-means algorithms for one slice of the BRATS
posed method for tumour core is observed as 98% database. The computation time thus depends on the
and it is comparable with K means and FCM algorithms. algorithm complexity and also on the processor. It
Sensitivity, which refers to the ability to detect the can be minimized using fast processors.
tumour core or oedema correctly, is observed to be
around 65% but better than K means and FCM algor-
ithms. One of the reasons for this is clustering Results using the proposed method without the
methods depend on the Euclidean distance between use of neighbourhood information as the prior
pixels for classification, but the proposed method In the Bayesian framework, the likelihood of the tissue
implements conditional probability along with neigh- class, the prior knowledge of the tissue class along with
bourhood information for pixel classification. Specifi- spatial neighbourhood information are used to esti-
city is related to the ability to correctly detect healthy mate the pixels belonging to a certain tissue class.
tissues and is observed to be around 99% and is com- Figure 7 represents the pixel profile of the segmented
parable with KM and FCM algorithms. Precision is a image with the use of 8 neighbours as the priors and
measure of repeatability, and its efficiency is around without the use of 8 neighbours as the priors. Exper-
82%. The average Dice coefficient, which is a measure iments for the same are conducted on images from
of overlap between segmentation and ground truth, BRATS 2012 and BRATS 2013 high-grade and low-
is observed to be 70% and is better than KM and grade Glioma database, respectively. The pixel profile
FCM algorithms. and the visual perception of the segmented images
In the case of oedema segmentation the average with and without neighbourhood pixels further vali-
segmentation accuracy using the proposed method is date the effectiveness of the spatial neighbourhood
observed as 96% and is comparable with K means information as the prior.
and FCM algorithms. The average sensitivity is
observed to be 55% and is better than K means and
FCM algorithms. The average specificity and precision Segmentation results on real brain tumour
is observed to be 98% and 55%, respectively. The images from Radiopaedia
average Dice coefficient is observed to be 53% and is
better than the K means and FCM algorithms. Since To test the effectiveness of the proposed method
the probability of each pixel for each class is computed experiments are conducted on real MR Brain images
the computation time of the proposed method is containing tumour from Radiopaedia [20]. Figure 8
greater than the K means and the Fuzzy C-means shows segmentation results on axial T1-w and FLAIR
algorithms. images having Gliosarcoma. Figure 8(b) shows the
Table 3 represents the evaluation metrics for the skull stripped image for T1-w images. Skull stripping
proposed method using T1-weighted contrast- is a pre-processing step before image segmentation
enhanced images (T1-c) from the BRATS database for to remove the skull. Many different methods are
tumour core segmentation with the following recent
supervised methods: Particle swam optimization Table 4. The average computation time required for the
using Markov random field (PSO), Principal component proposed segmentation method for the BRATS database.
Analysis (PCA), Shannon Entropy and Level Set (SE-LS), Time required for(sec) Proposed method K means Fuzzy C-means
Shannon entropy-based teaching learning-based Tumour segmentation 85.55 0.297 32.44
Oedema segmentation 88.32 0.310 33.56
optimization (SE-TLBO) and a two-input convolutional
444 A. CHAUDHARI AND J. KULKARNI

Figure 7. Pixel profile of the segmented image with the use of 8 neighbours as the priors and without the use of 8 neighbours as
the priors for the images from the BRATS 2012 and 2013 database. (a) T1w contrast-enhanced image with high-grade Glioma (b)
synthetic T2w image with high-grade glioma (c) FLAIR image with low-grade Glioma (d)–(f) Segmented image using 8 neighbours
as the priors. (g)–(i) Pixel profile using 8 neighbours as prior. (j)–(l) Segmented image without 8 neighbours as the priors. (m)–(o)
Pixel profile without 8 neighbours as the prior. (Images reproduced by kind permission of the authors).

proposed in the literature for skull stripping [21,22]. In the results of segmentation using the proposed
the proposed work skull stripping is carried out using method and (d) and (e) demonstrate the segmented
morphological operations. Figure 8(c) demonstrates images using KM and FCM algorithms for T1-w

Figure 8. Results of the proposed segmentation method on axial images with Gliosarcoma from Radiopaedia. (a) T1-w image
enhancing tumour core (b) skull stripped T1-w image. Tumour segmented images using (c) Proposed method (d) K means algor-
ithm (e) Fuzzy C means algorithm. (f) FLAIR image enhancing oedema (g) skull stripped FLAIR image. Oedema-segmented images
using (h) Proposed method (i) K means algorithm (j) Fuzzy C means algorithm. (Images reproduced by kind permission of the
authors).
images. T1-w image is used to segment the tumour
core and the FLAIR image is used to segment the sur-
rounding oedema.
Conclusions
This article presented a semi-automatic method for the
segmentation of tumour core and the surrounding
oedema using a simple Bayesian framework. Gaussian
likelihood of the tissue class, the prior knowledge of
the tissue class and Gaussian-weighted spatial neigh-
bourhood information are used to classify the pixels
belonging to tumour and oedema class. The pixel is
classified as tumour or oedema when its posterior prob-
ability is maximum for the tumour class. Experiments
conducted on the publicly available BRATS database
result in an average segmentation accuracy of 98%
and 96% for tumour core and oedema, respectively.
Comparison of the proposed method with other pixel
classification-based clustering methods demonstrates
encouraging performance in most of the cases. The pro-
posed method based on probability metrics demon-
strates encouraging results when compared to other
pixel classification distance-based metrics.
Disclosure statement
No potential conflict of interest was reported by the authors.
Notes on contributors
Archana Chaudhari received the B.E. and M. Tech. degrees
from Savitribai Phule Pune University, Pune, India. She is cur-
rently working as Assistant Professor in Instrumentation
THE IMAGING SCIENCE JOURNAL 445
Engineering Department at Vishwakarma Institute of Tech-
nology, affiliated to Savitribai Phule Pune University. Her
main areas of interest are Signal and Image processing,
Pattern Recognition, Biomedical Image Analysis and
Machine Learning.
Jayant Kulkarni received the B.E., M.E., and Ph.D. degrees
from Marathwada University, India. He is currently working
as Professor in Instrumentation Engineering Department at
Vishwakarma Institute of Technology, affiliated to Savitribai
Phule Pune University. His main areas of interest are Signal
and Image processing, Pattern Recognition, Machine Learn-
ing, Image Surveillance applications.
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