Automated Detection of Glioblastoma Tumor in Brain

Magnetic Imaging Using ANFIS Classifier

P. Thirumurugan,1 D. Ramkumar,2 K. Batri,1,3 D. Sundhara Raja4
1
Department of Electronics and Communication Engineering, PSNA College of Engineering and
Technology, India
2
Department of Electronics and Communication Engineering, Bharat Niketan Engineering
College, Theni, India
3
Department of Electronics and Communication Engineering, PSNA College of Engineering and
Technology, India
4
Department of Electronics and Communication Engineering, SACS MAVMM Engineering
College, India

Received 17 February 2016; revised 9 April 2016; accepted 2 May 2016

ABSTRACT: This article proposes a novel and efficient methodology
for the detection of Glioblastoma tumor in brain MRI images. The pro-
posed method consists of the following stages as preprocessing,
Non-subsampled Contourlet transform (NSCT), feature extraction
and Adaptive neuro fuzzy inference system classification. Euclidean
direction algorithm is used to remove the impulse noise from the
brain image during image acquisition process. NSCT decomposes
the denoised brain image into approximation bands and high fre-
quency bands. The features mean, standard deviation and energy
are computed for the extracted coefficients and given to the input of
the classifier. The classifier classifies the brain MRI image into normal
or Glioblastoma tumor image based on the feature set. The proposed
system achieves 99.8% sensitivity, 99.7% specificity, and 99.8%
accuracy with respect to the ground truth images available in the
dataset. C 2016 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 26,
V
151–156, 2016; Published online in Wiley Online Library (wileyonlinelibrary.-
com). DOI: 10.1002/ima.22169
Key words: contourlet transform; classifier; glioblastoma tumor; fea-
ture extraction
I. INTRODUCTION
Numbers of brain image scanning techniques are available today for
clinical diagnosis as Computer Tomography (CT), Magnetic reso-
nance imaging (MRI), and Positron Emission Tomography etc.
Among the available scanning techniques, MRI is a noninvasive
brain image scanning technique, which clearly shows the soft tissues
of the brain region (Ahmad Chaddad, 2015). It shows the shape, size,
Correspondence to: P. Thirumurugan; e-mail: thirushree12@Yahoo.com
and location of the abnormalities in the brain clearly, which is highly
preferable for many clinical applications. MRI is a sequence of
images, which are categorized into T1-weighted MRI (T1w), T1-
weighted MRI with contrast enhancement (T1wc), T2-weighted MRI
(T2w), and Proton Density-weighted MRI (PDw), Fluid-Attenuated
Inversion Recovery. T1w is an easy annotation method for tumor
analysis, T1wc shows the enhanced border of the brain tumor and
displays the proliferative of the brain tumor region, and T2w shows
the edema region of the brain.
Glioblastoma is a type of tumor in human brain, which can be
clearly visible through MRI image scanning sequences. It is catego-
rized into low grade Glioblastoma and high grade Glioblastoma. The
low grade tumors keep growing for many years and could be consid-
ered as slow invaders of brain safety tissue but the high grade tumors
are incurable with an average life of one year after its revelation (Jun
Kong et al., 2011). It is characterized by abnormal and uncontrolled
cell proliferation, necrosis, and vascular proliferation. The diagnosis of
such tumors requires the analysis of several brain MRI exams, which
attest the tumor invasion. Figure 1.(a) shows the Glioblastoma in T1w
MRI image sequence, Figure 1.(b) shows the Glioblastoma in T1wc
MRI image sequence and Figure 1.(c) show the Glioblastoma in T2w
MRI image sequence.
Due to the availability of large number of brain tumor images in
the clinics, the manual identification of the tumor region is not possible
due to large time consumption and the lack of physician in developing
countries. Hence, there is a need for automatic detection of Glioblas-
toma in a computer aided approach. In this article, the proposed brain
tumor detection method is fully developed in an automated manner
and involves various phases in tumor detection as preprocessing, fea-
tures extraction, classification, and tumor segmentation.

C 2016 Wiley Periodicals, Inc.

V

Figure 1. (a) Glioblastoma in T1w; (b) Glioblastoma in T1wc; (c)
Glioblastoma in T2w.
This article is organized as, Section II represents various conven-
tional methods for the detection of Glioblastoma in the brain images,
Sections III and IV represents the materials and methods used in this
article to detect and segment the Glioblastoma in the brain, Section
V shows the results and discuss the results of this article with respect
to conventional methods and finally, Section VI depicts the
conclusion.
II. LITERATURE SURVEY
Alexandros Roniotis et al. (2012) investigated to evaluate the model
of Diffusive Glioma. The diffusion–reaction equation (DRE) was
proposed in this work for simulating the spatiotemporal variation of
tumor cell concentration.
Ahmad Chaddad (2015) has used Gaussian Mixture Models to
detect and segment the Glioblastoma in the brain MRI images. The
features like mean, standard deviation (SD) and weight were
extracted from the Glioblastoma brain image and the neural networks
were used to classify the image into normal or Glioblastoma image.
The author achieved average accuracy of 97.05 for T1w images and
91.70% for T2w images.
Jun Kong et al. (2011) proposed a new method to analyze the Glio-
blastoma using The Cancer Genome Atlas technique. The author
investigated a large-scale investigative initiative on glioblastoma and
revealed a significant survival difference between Glioblastoma
patients based on the nuclear morphometry cluster of their tumor. This
observation suggests a potential for predicting patient outcome based
on nuclear morphometry. Most of the conventional systems dealt the
detection and segmentation of brain tumor based on region level fea-
tures, which degraded the accuracy level of the tumor segmentation
and it was not enough for further tumor diagnosis in clinical applica-
tions Lamia Sallemi et al. (2015) developed convivial algorithm for
brain glioblastomas tumor growth modelization. Region of interest
extraction method was used as segmentation technique for segmenting
the abnormal tumor cells in the brain image. A tumor growth estima-
tion model was developed to estimate the severity level of growth of
the tumor cells of the brain image. Reza and Iftekharuddin (2013) pro-
posed fully automated multi-class abnormal brain tissues segmentation
in multimodality brain MRI. A novel texture features such as piece-
wise triangular prism surface area, and textons, along with intensity
difference and regular intensity has have been used in order to charac-
terize different brain tissues. Selvaraj and Dhanasekaran (2015) used
feed forward back propagation neural network to segment the various
tissue regions in the brain.The authors achieved average quality rate
for the segmentation of CSF, WM, and Gray matter were 0.68, 0.98,
and 0.90, respectively. Shantha Kumar and Kumar (2014) proposed
Support vector machine based brain for brain tumor detection and
diagnosis. Texture features were extracted from the segmented abnor-
152 Vol. 26, 151–156 (2016)
mal tissue regions and classified using soft computing techniques. The
authors achieved 99.4% sensitivity, 99.6% specificity, and 99% accu-
racy. Yang et al. (2015) proposed brain tumor segmentation technique
using discrete wavelet transform-based whole-spectral and subspectral
Analysis. The authors achieved 94.8% average tumor segmentation
accuracy. Wang et al. (2009) analyzed growth kinetics Prognostic
using biomathematical model in Glioblastoma revealed investigation.
The growth of Glioblastoma in the brain MRI image was completely
analyzed and the abnormalities in the brain image were diagnosed.
To overcome such limitations, this article proposes a fully com-
puter aided automatic tumor region detection and segmentation
method based on pixel level features which increases the perform-
ance of the tumor segmentation.
III. MATERIALS AND METHODS
A. Materials. In this article, we have used two different dataset
to test our proposed brain tumor segmentation algorithms.
A.1. Cancer Imaging Archive Dataset. A data set of 17 patients
was collected by November 2013 from the publicly available Cancer
Imaging Archive (http://www.cancerimagingarchive.net/) database
for our preliminary study. We excluded patients with incomplete
imaging data set. All of the images had 512*512 pixels acquisition
matrices and were converted into grayscale before further processing.
MRI raw data were filtered to remove noise and standardized by the
linear normalization, followed by multithreshold-based segmentation.
A.2. BRATS Dataset. The data set consits brain images (with
tumor and normal cases) from the BRATS 2012 and BRATS 2013
challenges program, and brain images from the Cancer Imaging
Archive (TCIA) that were prepared as part of BRATS 2014 program
(http://braintumorsegmentation.org/). All the brain images in this
dataset were configured to the identical anatomical template and
interpolated to 1 mm3 voxel resolution. This image dataset consist of
300 high- and low-grade glioma brain tumor cases. This dataset also
contains manually tumor segmented images by expert radiologist.
B. Methods. The Glioblastoma tumor segmentation method is a
crucial task due to the similarity of other tissues with tumor pixels.
The proposed flow of Glioblastoma tumor detection and segmenta-
tion method is depicted in Figure 2. The following steps are involved
in tumor detection as Preprocessing, Nonsubsampled Contourlet
transform (NSCT), Feature extraction, Genetic Algorithm, and
Adaptive neuro fuzzy inference system (ANFIS) classifier. The
Figure 2. Proposed Glioblastoma tumor segmentation methodolo-
gies. [Color figure can be viewed in the online issue, which is avail-
able at wileyonlinelibrary.com.]

Figure 3. 9 3 9 window split into 8 directions, each direction is
noted as Direction1 to Direction 8 and center pixel is considered for
noise inspection. [Color figure can be viewed in the online issue,
which is available at wileyonlinelibrary.com.]
classifier classifies the brain T1wc MRI image sequence into either
Glioblastoma or normal image. The mathematical morphological
operations are now applied on the Glioblastoma image to segment
the tumor region for further clinical diagnosis.
IV. PROPOSED METHODOLOGY
A. Preprocessing. Brain MRI images are affected by impulse
noises during the image acquisition process. Preprocessing is used to
detect and remove the noises from the MRI brain image. The pro-
posed noise reduction algorithm includes two steps, dividing the fil-
tering window into eight equal directions and finding of the
Euclidean direction. The Euclidean direction is the direction with
more identical pixels. The proposed algorithm for noise reduction is
explained as:
Step 1: The medical image, which is to be denoised is first split
into m 3 n pixel blocks as shown in Figure 3. These blocks should
not be over lapped with other. In this work, we split the noisy image
of size 9 3 9 sub blocks.
Step 2: Initially first sub-block (of size 9 3 9) is divided into
eight orthogonal direction patterns such as 308 each and each orthog-
onal directional pattern consists of 9 pixels.
Figure 5. Illustration of NSCT transform: (a) Three stage pyramid decomposition; (b) Sub bands on 2D-frequency plane.
Figure 4. (a) Source brain image; (b) denoised brain image.
Step 3: Remove the current pixel from the selected orthogonal
direction pattern and hence it gives eight pixels in each eight
directions.
Step 4: The orthogonal direction patterns are sorted in ascending
order and then from these sorted values, remove the lowest and high-
est vector patterns.
This sorted vector contains both minimum and maximum value
pixels. Similarly, all corresponding minimum and maximum value in
each orthogonal vector patterns are determined and their minimum
and maximum values are noted.
Step 5: Find the SD for eight orthogonal sorted direction patterns.
hX i
SDn 5Sqrt ðx2xn Þ2 =N
where, “N” represents the number of pixels in each direction and n
varies from 1 to 8. Xn is the pixels in a each direction and x is the
center pixel.
Step 6: Find the minimum of these SDs and the corresponding
direction is considered as the Euclidean direction and it is given as,
 
diropt 5min SD1; SD2; SD3; SD4; SD5; SD6; SD7; SD8; (1)
Step 7: Determine the similarity factor “S” between the current pixel
(xct) under process and the pixels in the optimum direction. The
value of “S” can expressed by,
Vol. 26, 151–156 (2016) 153
Table I. Sub bands of NSCT transform.
Step 12: Denoised Pixel is finally computed as the summation of
Sub-band 1 Sub-band 2 Sub-band 3 Sub-band 4 Sub-band 5 product of density weight function of the surrounding neighbor pix-
0.2097 0.4480 19.0948 82.3034 122.9 els and it is represented as Figure 4
20.0227 0.6547 26.9038 2228.8247 192.7 X
20.2625 21.7866 13.7429 132.0185 189.3 Denoised Pixel5 Fcdf 3 xi (7)
20.3382 0.3505 241.3273 232.2940 191.6
20.1991 4.2280 39.5494 16.45930 210.1
0.04577 1.9822 224.5147 22.62494 188.0
0.2094 22.9696 4.6387 15.51267 189.2
0.1662 22.6102 0.9153 222.0866 174.7 B. NSCT Transform. It is a multiscale and multidirectional
20.0541 0.1168 3.8932 0.6617 186.5 transform, which has two stages as Non-Subsampled Pyramid (NSP)
20.2846 21.0808 20.5481 29.7698 192.6 and Non-Subsampled Directional filter bank (NSDFB). The decom-
position of the NSP leads to the formation of low frequency and high
  frequency components of the input image at each level of the decom-
X diropt2xct position stage. The property of NSP is obtained by NSFB structure,
S5 abs (2)
255 which is similar to that of Laplacian pyramid, which is achieved by
using the nonsubsampled filter banks.
Step 8: Set the threshold T and verify whether the current pixel under The decomposition of NSCT is illustrated in Figure 5. The
process is either noisy xnoisy or an original pixel xorig. denoised brain image is applied to the NSCT transform, which
( decomposes the image into low frequency components (Low pass
xorig ; if S 2 T; f0  T  k23g sub band), high frequency components (Band pass sub band image).
xout 5 (3)
xnoisy ; else This also leads to the formation of multiscale decomposition of the
brain image. Each layer of the low pass sub band image decomposes
The noisy pixel is immediately omitted after detection and it is not the levels and thus generates the coefficients.
carried over in further steps and “k” represents the denoising window Let “r” be the level of decomposition;
size. Here, “k” is considered as 9. Number of sub bands (Ns) of the NSCT transform is given as,
Step 9: Apply density weighted filter over the pixels, which were
detected as noisy pixels and its surrounding pixels. Ns 5 2r 11 (8)
Step 10: Determine Euclidean weight 1 and 2 of the noisy pixel
as If the level of decomposition is 2, then 5 sub bands are produced.
Among the 5 sub-bands, the number of detailed or high frequency
X
Ed15 Xi (4) sub-bands are 4 and the number of approximation sub-band is 1.
Each sub-band has the size of the denoised brain image and Table I
shows the values of sub-bands.
where “i” represents the neighboring pixels of noisy pixel to be
denoised.

1X C. Feature Extraction. Features are the characteristics of the

Euclidean weight 2 5 Ed25 ðxi2Ed1Þ (5)
n image and it is categorized into generic and individual feature set.
Generic features are the common features and it is not able to clas-
where “n” represents the histogram count of the noisy pixel to be sify the objects. Individual features are unique and differentiates the
denoised. various objects in the image. Feature extraction plays an important
Step 11: Compute density weight function as role in the classification of the brain MRI image into normal or Glio-
ðxi2Ed1Þ2  blastoma tumor image. The following features are extracted from
Fcdf 5e Ed2 (6) coefficients of each sub-band and it is described as,

Figure 6. (a) Source brain image; (b) ground truth Tumor segmented image. (c). Tumor region segmentation by proposed method. [Color figure
can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

154 Vol. 26, 151–156 (2016)

Figure 7. (a) Source brain images; (b) Ground truth images; (c) Proposed tumor segmentation results; (d) Conventional tumor segmentation
results (Shanthakumar and Ganesh kumar). [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

P used in this article for classification of brain MRI image. The input
Approximation band coefficients 1
P layer of the ANFIS classifier is constructed with number of neurons,
High frequency band coefficients which is equal to the size of the extracted features. The hidden layer
Mean5 (9)
Number of decomposition levels with different number of neurons is tested and finally four hidden
layers is configured for obtaining the optimal classification rate. In
  this article, four hidden layers and each hidden layer with 20 neurons
1
SD5  stdApproximation band2coefficients 1 stdhigh2frequency band2coefficients are configured. The output layer consist a single neuron and thus pro-
n
duces a single binary output 0 (Normal image) or 1 (Glioblastoma
(10)
X
r tumor image).
Energy5 jDi;j j2 ; j51; . . . n (11)
i51 E. Morphological Operations. Once the Glioblastoma tumor
image is detected using the ANFIS classifier, Morphological opera-
where, “r” represents the number of sub-bands in NSCT transform. tions are used to segment the tumor region in the brain MRI image.
“Di;j ’’ represents the extracted coefficients. These features are given The Morphological opening and closing are the two functions of
as input to the classifier to classify the brain MRI image into either morphological operations.
normal or Glioblastoma tumor image. The two basic operations, dilation and erosion, are further com-
bined into more complex sequences, namely, opening and closing.
D. ANFIS Classifier Design. A multilayer ANFIS classifier Opening consists of an erosion followed by a dilation and is used in
consists of an input layer, three hidden layers and an output layer, is the elimination of pixels in regions that are too small to contain the
structuring element. The structuring element probes the image look-
Table II. Performance evaluation of brain tumor segmentation. ing for small objects to filter them out of the image. Morphological
Glioblastoma Image opening is given by,
Sequence Se (%) Sp (%) Acc (%)
A8B5ðAhBÞ丣B (12)
1 92.5 92.9 99.1
2 97.6 98.3 98.5
3 89.1 96.8 96.7 Table III. Performance comparison of proposed method (Cancer Imaging
4 98.2 99.6 99.1 Archive Dataset).
5 97.6 99.7 98.9
Sensitivity Specificity Accuracy
6 94.9 98.9 99.2
Methodology (%) (%) (%)
7 99.1 97.1 97.9
8 98.9 99.8 98.9 Proposed work 99.8 99.7 99.8
9 97.1 95.9 99.4 Ahmad Chaddad (2015) – – 97.05
10 92.3 99.5 99.1 Selvaraj and Dhanasekaran (2015) – 75 83.00
Average 95.7 97.8 98.6 Shanthakumar and Ganesh kumar (2014) 99.4 99.6 99.5

Vol. 26, 151–156 (2016) 155

Table IV. Performance comparison of proposed method (BRATS Dataset).
Sensitivity Specificity Accuracy
Methodology (%) (%) (%)
Proposed work 99.6 98.12 99.1
Bo Song et al. (2016) 97.87 95.1 – sition process. NSCT decomposes the denoised brain image into
Guang Yang et al. (2015) 91.29 – 94.8
Closing consists of a dilation followed by erosion and is used in fill-
ing up holes and small gaps in the image. Closing and opening will
generate different results even though both consist of erosion and
dilation.
A8B5ðA丣BÞB (13)
The morphologically closed image is morphologically multiplied
with the source brain MRI image to segment the tumor region alone.
Figure 6.(a) shows the original source brain image, Figure 6.(b)
shows the ground truth tumor segmentation image and Figure 6.(c)
shows the Tumor region segmentation by proposed method Figure 7.
V. RESULTS AND DISCUSSION
To validate the effectiveness of the proposed Glioblastoma tumor
detection in brain MRI image, the following parameters are used.
 Sensitivity ½Se5TP=ðTP1FNÞ (14)
 Specificity ½Sp5TN=ðTN1FPÞ (15)
 Accuracy ½Acc5 ðTP1TNÞ=ðTP1FN1TN1FPÞ (16)
These parameters are evaluated for a set of images available in
publicly accessible dataset and listed in Table II, where, TP denotes
true positive, FP denotes false positive, FN is false negative, and TN
is true negative. True Positive refers to the correctly identified tumor
pixels, True Negative refers to the wrongly identified tumor pixels,
False Positive refers to the correctly identified nontumor pixels and
False Negative refers to the wrongly identified nontumor pixels.
Table II shows the performance evaluation of Glioblastoma brain
tumor segmentation. The proposed system achieves 95.7% sensitiv-
ity, 97.8% specificity, and 98.6% accuracy with respect to the ground
truth images available in the dataset. Table III shows the perform-
ance comparisons of the proposed method with conventional meth-
odologies as Ahmad Chaddad (2015), Selvaraj and Dhanasekaran
(2015), and Shanthakumar and Ganesh kumar (2014) on Cancer
Imaging Archive Dataset. Table IV shows the performance compari-
sons of the proposed method with conventional methodologies as Bo
Song et al. (2016), and Guang Yang et al. (2015), on BRATS
Dataset.
The MATLAB R2014 is used for the simulation purpose and the
proposed system is analyzed using Intel Pentium Core 2 Duo proces-
sor with 2GB internal RAM. The proposed methodology takes 10 s
to classify the given test image into either normal or tumor image.
156 Vol. 26, 151–156 (2016)
VI. CONCLUSION
In this article, Glioblastoma tumor in brain MRI image is detected
using ANFIS classifier. Euclidean direction algorithm is used to
remove the impulse noise from the brain image during image acqui-
approximation bands and high frequency bands. The features mean,
SD and energy are computed for the extracted coefficients and given
to the input of the ANFIS classifier. The proposed methodology
achieves 99.8% sensitivity, 99.7% specificity, and 99.8% accuracy.
The results are compared with conventional methodologies for Glio-
blastoma tumor detection and segmentation.
ACKNOWLEDGMENTS
The authors would like to thank their friends and colleagues for
their constant help and support throughout the study and to obtain
the results.
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