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Brain Tumor Segmentation in Multimodal MRI Using U-Net Layered Structure

Article in Computers, Materials & Continua · December 2022

DOI: 10.32604/cmc.2023.033024

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Computers, Materials & Continua Tech Science Press
DOI: 10.32604/cmc.2023.033024
Article

Brain Tumor Segmentation in Multimodal MRI Using U-Net Layered

Structure
Muhammad Javaid Iqbal1 , Muhammad Waseem Iqbal2 , Muhammad Anwar3, *,
Muhammad Murad Khan4 , Abd Jabar Nazimi5 and Mohammad Nazir Ahmad6

1
Department of Information Technology, The Superior University, Lahore, Pakistan
2
Department of Software Engineering, The Superior University, Lahore, Pakistan
3
Department of Information Sciences, Division of Science and Technology, University of Education, Lahore, Pakistan
4
Department of Computer Science, Government College University, Faisalabad, Pakistan
5
Deptment of Oral and Maxillofacial Surgery, Faculty of Dentistry, Universiti Kebangsaan Malaysia, Kuala Lumpur,
Malaysia
6
Institute of IR4.0, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
*Corresponding Author: Muhammad Anwar. Email: [email protected]
Received: 05 June 2022; Accepted: 22 September 2022

Abstract: The brain tumour is the mass where some tissues become old or
damaged, but they do not die or not leave their space. Mainly brain tumour
masses occur due to malignant masses. These tissues must die so that new
tissues are allowed to be born and take their place. Tumour segmentation
is a complex and time-taking problem due to the tumour’s size, shape, and
appearance variation. Manually finding such masses in the brain by analyzing
Magnetic Resonance Images (MRI) is a crucial task for experts and radiolo-
gists. Radiologists could not work for large volume images simultaneously,
and many errors occurred due to overwhelming image analysis. The main
objective of this research study is the segmentation of tumors in brain MRI
images with the help of digital image processing and deep learning approaches.
This research study proposed an automatic model for tumor segmentation in
MRI images. The proposed model has a few significant steps, which first apply
the pre-processing method for the whole dataset to convert Neuroimaging
Informatics Technology Initiative (NIFTI) volumes into the 3D NumPy
array. In the second step, the proposed model adopts U-Net deep learning
segmentation algorithm with an improved layered structure and sets the
updated parameters. In the third step, the proposed model uses state-of-the-art
Medical Image Computing and Computer-Assisted Intervention (MICCAI)
BRATS 2018 dataset with MRI modalities such as T1, T1Gd, T2, and Fluid-
attenuated inversion recovery (FLAIR). Tumour types in MRI images are
classified according to the tumour masses. Labelling of these masses carried
by state-of-the-art approaches such that the first is enhancing tumour (label
4), edema (label 2), necrotic and non-enhancing tumour core (label 1), and
the remaining region is label 0 such that edema (whole tumour), necrosis and
active. The proposed model is evaluated and gets the Dice Coefficient (DSC)
value for High-grade glioma (HGG) volumes for their test set-a, test set-b, and

This work is licensed under a Creative Commons Attribution 4.0 International License,
which permits unrestricted use, distribution, and reproduction in any medium, provided
the original work is properly cited.
5268 CMC, 2023, vol.74, no.3

test set-c 0.9795, 0.9855 and 0.9793, respectively. DSC value for the Low-grade
glioma (LGG) volumes for the test set is 0.9950, which shows the proposed
model has achieved significant results in segmenting the tumour in MRI using
deep learning approaches. The proposed model is fully automatic that can
implement in clinics where human experts consume maximum time to identify
the tumorous region of the brain MRI. The proposed model can help in a way
it can proceed rapidly by treating the tumor segmentation in MRI.

Keywords: Brain tumour segmentation; magnetic resonance images

modalities; dice coefficient; low-grade glioma; U-Net

1 Introduction
The abnormal growth of cells or masses in the body is known as a tumour. These masses, known
as brain tumours, build in the brain or other body organs. According to the “National Cancer Institute
(NCI)” [1], normal cells in the human body grow and later become old and must die in due time. After
that, new cells take their place when the body needs them. But when cancer occurs in the body organ,
this process disturbs badly. After time passes, these cells should die, but they remain alive; they divide
and spread into the body’s other tissues. This process of division and spreading continues, making a
tumour shape mass. Tumours are of two general types: one is a malignant tumor, and the second is
a benign tumor. Malignant tumor divides and can spread to different positions in the body to make
new tumor cells [2].
This spreading of tumour cells happens through the blood or lymph system. On the other hand, a
benign tumour does not divide and spread. Although benign tumours can easily be removed from the
body, malignant tumors create trouble. This research study is essential and challenging because many
people suffer from this disease and die because of a late diagnosis. Most of the time, experts take time
to identify whether a patient has a tumor and, if it has, where it is located in the brain. This problem
occurs because of the manual system. Nowadays, the technology works in every field of study and
performs very healthy tasks. Especially in the biomedical imaging domain, computer science works to
contribute value to complex problems [3].
MRI is an imaging technology primarily used in neurology and neurosurgery [4]. This imaging
technology allows viewing the brain, spinal cord, and anatomy of vascular tissues. The main advantage
of this technology is that it provides a 3D view of the concerned area or location. For instance, the
brain can be seen as axial, sagittal, and coronal views. Axial view means to see the brain from the top
or bottom, sagittal view means to see the brain from the left or right, and coronal view means to see
the brain from the backside of the head or front. MRI has four different modalities T1, T1C, T2, and
FLAIR sequences [5]. Each sequence has a particular purpose, but the most frequently used are T1,
T1C, T2, and FLAIR. A brain structure containing a tumour such as an edema or necrosis could be
easily segmented. In brain structure, including tumors. But routinely, the FLAIR imaging sequence is
used as a standard MRI sequence to detect the tumour tissues in the brain images. The main challenge
is segmenting the brain’s tumorous region after examining the MRI images. For this purpose, there
are three different segmentation ways: the first is a manual method, the second is a semi-automatic
method, and the last is a fully automatic method. In the manual mode, the neurology and neurosurgery
experts manually view and analyze the brain MRI, then highlight the tumour area if they find it. In
the second method of tumorous segmentation, the human expert and the computing software are
involved. The human expert gives the input to the system, and the software process the information,
CMC, 2023, vol.74, no.3 5269

then returns the results to the human expert. However, this method is not too good because, for every
expert, output results will be varied based on their experience or analysis.
The fully automatic method [6] means no involvement of a human expert. The automated system
works itself without taking the manual inputs to initialize. Some image processing and machine
learning algorithms work in the system that segments the image and then classifies the brain’s normal
vs. tumorous cells. This method’s main challenge is handling the brain tumor’s different sizes, shapes,
and irregular boundaries in MRI.

1.1 Problem Statement

The proposed model addresses the complex challenge of accurate brain tumor segmentation. This
research study addressed the tumour’s size, shape and variation. It also focused on identifying the
irregular tumour boundaries in brain MRI images [7]. There is a need to address the large volume
dataset for training and to deploy the model on real-time implementations. A big challenge is to address
the irregular boundary variation of the brain tumor in MRI.

1.2 Motivation of the Study

The proposed research model in this study is automatic brain tumor segmentation. This proposed
model introduces the pre-processing techniques that help to identify the tumor size, shape and
appearance from the brain MRI images [8]. This research study suggested a deep learning model
named U-Net with improved layered structure and updated parameters with their values for tumour
segmentation in the state-of-the-art BRATS 2018 [5] training dataset. This research study’s challenge
is accurately segmenting tumor regions from MRI. The proposed model will accurately address the
tumour’s size, shape and appearance [9]. It also identifies the tumour boundaries from brain MRIs.
The main focus is brain tumour segmentation using MRIs in the early stages [10].
The rest of the paper is divided into different sections. Section 2 discusses the existing techniques,
Section 3 elaborates on the dataset, Section 4 focuses on the proposed methodology, and Section 5
discusses the evaluated results. The conclusion and future work are discussed at the end of the paper.

2 Literature Review
The best solution is the need for any real-time problem such that accurate tumor segmentation
is the need of time. Early detection and finding the precise area of the tumour is still a crucial
problem. Various techniques were already worked on and proposed with existing methods [11]. But
there are research gaps in tumour segmentation, such that an early diagnosis, accurate tumour area
segmentation, the size, and shape of the tumour variations, and how one can accurately segment
out in multiple slices. It proposed an automatic method for brain tumor segmentation using MRI
[12]. They used a superpixel-based method for image segmentation and manually extracted features,
i.e., statistical, texture, fractal and curvature. A randomized classifier was applied to classify between
normal and abnormal superpixels. The proposed model was evaluated using the BRATS 2017 dataset
with the FLAIR sequence. The main objective of the proposed system was to identify the tumorous
images and segment the tumorous area. DSC value got 0.88 with test samples.
A classification method took FLAIR images as input and classified the results into tumor and
non-tumour slices [13]. This research study used a superpixel-based segmentation approach to divide
the image into small patches. The proposed research study extracted statistical, texture and fractal
features from the MRI. In the end, this research study applied three different classifiers, Support Vector
5270 CMC, 2023, vol.74, no.3

Machine (SVM), AdaBoost and Random Forest (RF), to classify the superpixels whether they are
tumorous or not. After comparing these three classifiers, this research study found RF performs better
and has a precision value of 5% greater than other classifiers. The BRATS 2012 dataset was used as a
test sample to evaluate the proposed model.
A new model for the extraction of brain tumors was introduced [14]. In this method, brain MRI
images with FLAIR sequence were used for the model training. After image acquisition, the tumour
was enhanced in the images. After segmenting the tumour, the marker-based watershed segmentation
method was used to extract shape, texture and point features. This model used the chi-square approach
to select 70% of high-priority features at the feature selection step. For classification, this model passed
these features to the SVM machine learning classifier, which classified the images as tumorous and
non-tumorous. The proposed method was trained and tested upon three different datasets, such as
Harvard, BRATS-2013 and privately collected data. The accuracy values were calculated of these
datasets Harward, BRATS-2013 and Private 98.17%, 98.88% and 98.50%, respectively.
The focus was on finding the tumor region and whether it was a benign or malignant tumor [15].
The process followed these steps: first pre-processing images to remove noise. Second segmentation
to find the area of interest, the third features extraction, and the fourth classification using a
Neural Network. The results of the proposed model were 93.33% accuracy, 96.6% specificity, 93.33%
sensitivity and precision, with 94.44% this model claimed that this model performs better than the
AdaBoost that classifies the images into three types (Normal image, benign image, and malignant
image) with accuracy 89.90%. In addition, 60 MRI images were privately collected to train and test
the proposed model.
The fully-automated multi-parametric method [16], segmented brain tumours, In the experimental
setup, the first step was pre-processing like skull stripping, noise removal and enhancing the image
dataset. For segmentation, applied super pixel-based segmentation was based on spatial and intensity-
based distances. After that, extract features on the different paradigms like first-order statistical-based
features, texton features based on the histogram and fractal features. The next step performed feature
selection and normalization by using PCA for feature selection and ICA for feature normalization
because ICA was the most efficient for selecting the significant features. And then, to apply SMOTE
for class balancing, MICCAI BRATS 2012 dataset was used to evaluate the model, and DSC was
obtained 0.91 for this dataset.
The work was explained [17], which was proposed for brain segmentation, detecting tumorous
areas and evaluating the efficacy of statistical features over Gabor features. This research study claimed
that this comparison was made the first time. The algorithm used mutual information from two
hemispheres of the brain. When an image slice with a tumour was found, it was segmented to delineate
the tumor area. The proposed algorithm took fewer computing powers than the others. This research
study trained and tested the model over the BRATS-2013 standard dataset.
Another study [18] was proposed the technique to diagnose the abnormalities in the MRI using
a computer-aided diagnosis approach. The research aimed to develop a robust system that accurately
identifies MRI images and brain-related disease MRI. Also, tumor types were detected, which the
proposed model. The proposed system used Gabor texture and statistical feature extraction techniques.
The SVM classifier was used for the classification and the whole system was trained on the brain Atlas-
Harvard medical school dataset. The accuracy achieved up to 90.6%, proving the system outcome.
Further, in another study, [19,20] the segmentation method was discussed based on the confidence
region detection in the MRI. The crucial problem discussed in this study was the variation of the tumor
in MRI slices due to variations in intensities and spatial. The proposed technique of confidence region
CMC, 2023, vol.74, no.3 5271

and contour detection was provided to detect the tumorous area in MRI. The proposed model gives
the best solution for tumorous region detection in MRI.
A method proposed by Anwar et al. [21] classifies normal and abnormal images and the volume
of detected tumors. First, the proposed applied pre-processing techniques enhance the image intensity.
Then k-means and Fuzzy C-Means clustering algorithms are used to generate clusters of images.
Features are extracted from the clustered images and passed to the SVM classifier that categorizes
the images as normal or abnormal. Next, the abnormal images are segmented through Active contour
by level set (ACLS). Finally, intensity adjustment and the tumor area and volume were computed from
the abnormal images. The tested dataset consists of 40 slices collected privately.
It was proposed that the automated brain tumor segmentation model can accurately find the
tumor segments in brain MRI. This research study used a superpixel-based approach to segment the
tumourous region in the MRI. First, different features were extracted, like statistical, curvature, tax
to taxation, gabbor, and SIFT, to create the feature vector for the model training. Then, machine
Learorithms were used to train the model using SVM, Decision tree and KNN to classify the abnormal
and normal superpixels. A significant contribution was introducing the class balancing algorithm for
the unbalanced feature vector and training the BRATS 2017 whole dataset and superpixel approach
to identify the tumorous regions in MRI images. The proposed model outperformed as compared to
the other state-of-the-art methods. The proposed model obtained 0.85 DSC and 0.82 DSC values in
HGG and LGG test volumes, respectively [7].
Reviewing various already implemented techniques showed some crucial challenges, such as
accurate segmentation in MRI and detection of the tumour’s contour, size and shape. Early detection
for tumour segmentation and to segment the tumorous area is a crucial problem that still needs to be
resolved. Based on the previous techniques, the proposed model suggests the solution for the automatic
brain tumor segmentation using U-Net improved layered structure on the state-of-the-art BRATS
2018 dataset.

3 Materials and Methods

The proposed model has some most important points that were discussed in the study and
implemented during the development and research work. The primary purpose is brain tumor
segmentation using deep learning techniques and finding the accurate tumor from the MRI. In
addition, the following steps are performed during the research and development.

3.1 Dataset
There are various open-source datasets for the brain tumor segmentation challenge in which the
most common use nowadays is MICCAI BRATS. The proposed model has collected a multimodal
MRI dataset for brain tumor segmentation from BRATS 2018 challenge [22]. This dataset has some
specifications, i.e., it has only an axial view, and four sequences are discussed below in detail. And
some of the essential points about the BRATS 2018 dataset are discussed here.
All the given volumes in the BRATS 2018 are available in the form of neuroimages named NifTI
(.nii.gz), which have different modalities like T1, T2, T1Gd and FLAIR. However, various available
techniques use only the FLAIR sequence for experimental analysis because it is more visible spatial.
The BRATS dataset already defined their three labels in their research paper [5] published in the
Institute of electrical and electronics engineers (IEEE). The labels are like enhancing tumour labelled 4,
5272 CMC, 2023, vol.74, no.3

edema labelled 2, Necrotic tumour, and the tumour which is non-enhancing core labelled one and
labelled 0 for the remaining regions.
After performing pre-processing, distributed the dataset and converted it into the same structural
format. As all the data was skull stripped, this converted it into the (1 mm3 ) resolution, the same for
all the datasets. All the BRATS 2018 datasets contain two main folders named HGG, which have
210 volumes (patients) of data. And the other is LGG which has only 75 volumes of patient data.
Each volume has an MRI scan of the specific patient; the folders or volumes have four modalities,
as mentioned above. There is also a ground truth for each volume inside, and in volume one NifTI
file consists of four modalities and one ground truth for each modality. There are various solutions
to read and convert the NifTI (.nii.xx) files into the array named 3D NumPy. Because all the volumes
have NifTI files, it isn’t easy to compute as it is in the format.

3.2 Data Preprocessing

Pre-processing requires a few steps, which are mentioned in detail to prepare the dataset for
the proposed model. Without pre-processing, it could not get the optimum results. There are some
necessary steps that this study followed are mentioned below:
Step-01: The dataset obtained from the BRATS 2018 was already skull stripped, collected all the
MRI scans for each patient, and then combined them. The purpose is to make them NumPy array
and the size for the array mentioned in the form of (N, S, N1, N1, X), where these annotations are:
N = Number of HGG/LGG datasets or volumes
N1 = Total 2D slices from the MRI 3D each volume
X = Number of modalities or sequences
So, all the pre-processing is held using the Google Collaboratory, which provides free Graphics
processing unit (GPU) and Tensor Processing Unit (TPU) services to compute a large amount of data.
Due to RAM availability and fast computation used and handled very accurately.
Step-02: In this step, this model handles the HGG and LGG volumes one by one. The purpose
is to get the 3-D volume given in the example (N, 155, 240, 240, 4). HGG has a total of 210 patients
or volumes dataset, and LGG has 75 patients or volumes. There is a need to distribute HGG volumes
into three equal parts like N = 70, which makes 210 for the three HGG sets and makes three sets
named data11.npy for the first set containing N = 70, the second was data12.npy which has N = 70,
and the last was data13.npy also has N = 70. LGG has only N = 75, which is only one set and named
data2.npy. As all the volumes have ground truths, it was gt11, gt12, and gt13 for the HGG volumes
and gt2 for the LGG volumes.
Step-03: In this step, pre-processed all the given data separately. Observing the slices, they do not
show the tumor area, so it decides to remove the unnecessary slices from the volumes at the start and
end of the volume. This model used only slices from 30 to 120 for all the data files. The final shape is
extracted like (N1, 240, 240, 4). Also, the same shape was extracted for the ground truths. As for the
HGG volume, the value for N1 was 90 × 70 = 5600, and for the LGG volumes, the N1 was 90 × 75
= 6750.
Step-04: The final and experimental dimension is the optimum value (N1, 192, 192, 4), and we use
this shape for all the data files.
CMC, 2023, vol.74, no.3 5273

Step-05: The last pre-processing step divides the data into three forms: the first is for training
with 60%, the second is for validation with 20%, and the last is testing with a 20% ratio. Then the final
prepared dataset is used for the model for training and testing purposes.

3.3 Proposed Model

This model proposes the deep learning approach using U-Net (CNN algorithm) for the semantic
segmentation problem with its improved layer structure and tuned parameters. The detailed picture
for the proposed model is shown in Fig. 1. In the proposed model, all the steps are discussed and
performed during the execution. First, arrange the dataset and apply the pre-processing steps to make
the data usable for the model.

Figure 1: Proposed model methodology

5274 CMC, 2023, vol.74, no.3

Then apply the U-Net algorithm in which convolution, pooling, and final segmented results
are achieved from the start of the input layer. The detailed picture shows in Fig. 1 how the U-
net model worked for the semantic segmentation in the brain tumor segmentation process. This
model was developed and inspired by the study of semantic segmentation [23] and apply it to the
brain tumor segmentation problem using U-Net for this problem. The U-Net model has various
convolution operations on each layer, improving the tumor segmentation in MRI. The U-Net model
[24] is convolutional network architecture used for fast and precise image segmentation, specifically
in medical imaging. It has a multi-channel feature map, and the number of channels is usually shown
on top of the architecture. The x-y size shows the box’s lower-left edge, and some boxes show the
feature maps. And the arrows denote the different operations. Most of the already existing techniques
use Fully convolutional neural networks (FCNN) [25] and various using Recurrent neural network
(RNN) [26] models for tumour segmentation in MRI using the different types of datasets.
Fig. 1 illustrates the proposed U-Net architecture for tumor segmentation with their improved
layered network. The proposed model suggested a Dynamic convolutional layer (DCL) which helps
to improve the training in the U-Net algorithm. This additional layer convolves with 1 × 1 convolution
in the U-Net model. Lower branch, the number of channels will be changed due to the 1 × 1
convolution, and in the upper branch, these channels will also be changed on the feature maps. The
1 × 1 convolution will also sum up the 1 × 1 convolution branch with the stack for the 1 × 1
convolution [27]. This layered approach helps smooth the computation and gets every minor change
in the slice so the tumour area can be identified after the computation.
The U-net has multiple applications, as it is used for pattern recognition, image segmentation, and
computer vision. In this proposed model, update the existing U-Net and add more layers to get the
best outcome. As discussed in the results section, the proposed model is evaluated using the BRATS
2018 dataset and obtained optimum DSC values for the HGG and LGG volumes. At the end of the
proposed model, use an evaluation measure to identify the model performance.

4 Results and Discussion

As discussed in the previous section for the proposed model and this section, we discuss the results
obtained. The obtained results from the proposed model are reasonable. See the resulting images
shown in Figs. 2 and 3. The proposed model is evaluated both for HGG and LGG volumes. The
pictorial results view for the HGG and LGG volumes are shown in Figs. 2 and 3, respectively.

4.1 Results for HGG Volumes

HGG volumes evaluated using test images and results are shown in Fig. 2 and for a few samples
to show the model’s accuracy. Fig. 2 is shown (a) the actual slice for the test set-01, (b) the segmented
image for the test set-01, and (c) the ground truth for the test set-01 slice. Whereas (d) HGG test set-02
actual slice, (e) segmented image from test set-02, and (f) ground truth for the test set-02 slice. The
proposed model was evaluated using a that took a few sample slices from the dataset to test the model.
Therefore, a few visible results obtained after evaluation are shown in Fig. 2. Both HGG and LGG
volume test datasets were used to evaluate the proposed model. The BRATS 2018 dataset was labeled
data from an experienced radiologist, and the visual results showed the best performance as seen in
the ground truths.
Fig. 3 shows the HGG volume test set-03 pictorial results in which (a) HGG test set-03 is for an
actual slice, (b) segmented image, and (c) ground truth for the given slice.
CMC, 2023, vol.74, no.3 5275

Figure 2: HGG Volumes where (a) hgg test set-01 slice, (b) segmented image set-01, (c) ground truth
image test set-01, (d) hgg test set-02 slice, (e) segmented image test set-02, (f) ground truth image test
set-02

Figure 3: HGG Volume where (a) HGG test set-03 Slice, (b) segmented image test set-03, (c) ground
truth image test set-03

4.2 Results for LGG Volumes

Results obtained to evaluate the LGG volumes test set are shown in Fig. 4. Which shows (a) the
LGG test set actual slice, (b) segmented image obtained from the slice, (c) ground truth, and whereas
shows other sample slice results in (d) test set actual slice, (e) segmented image and (f) ground truth
for the second slice.

4.3 Evaluated Results

DSC & DSC loss functions are commonly used to check the model’s accuracy. DSC is used
primarily for medical imaging analysis and to evaluate the models for medical imaging. The DSC
formula is shown in Eq. (1), given below.
Dice Coefficient = (2|X ∩ Y|)/(|X| + |Y|) (1)
5276 CMC, 2023, vol.74, no.3

Figure 4: LGG Volumes for (a) test set-01 Slice, (b) segmented image test set, (c) ground truth image
test set, whereas another slice (d) LGG test set slice, (e) segmented image test set, (f) ground truth
image test set

Here are cardinalities for the two sets represented by |X| and |Y| in which the east set shows their
elements [28]. Applying this equation can get the overlap values for the resulting image with the ground
truth images. Which gives us the values the images overlap with each other.

4.3.1 Model Loss Graph

The graph for the DSC loss is shown in Fig. 5, in which the training and validation datasets model
loss is shown. DSC training and validation datasets decrease as the number of epochs increases. At
the start of the epochs, the DSC values were maximum, and as the number of epochs increased, the
dice values went down. It means the proposed model is best and gives good results.

Figure 5: Model loss graph for training and validations data with DSC and epoch

4.3.2 Model Score Graph

The model score graph in Fig. 6 shows the DSC value against the training and validation datasets.
The DSC values are going best by increasing the number of epochs. The graph is very clear about the
CMC, 2023, vol.74, no.3 5277

model’s accuracy and can say it is very near to the actual results [29]. Increasing the number of epochs
is going to increase the DSC values.

Figure 6: Model score graph for the training and validations data with DSC and epoch

The proposed model outperformed the brain tumor segmentation in the state-of-the-art dataset
BRATS 2018. The DSC values for the HGG and LGG volumes test sets are shown in Table 1. Divide
the dataset for training, validation, and testing. The testing sets are used here to check the model’s
accuracy and get outperformed results, as shown in Table 1.

Table 1: Evaluation results using the test dataset

Test samples Test sets DSC values
1 HGG volumes set-a 0.9795
2 HGG volumes set-b 0.9855
3 HGG volumes set-c 0.9793
4 LGG volumes set 0.9950

After performing various experiments, this model got the best value for DSC for both HGG and
LGG volumes. The HGG and LGG volumes used for the testing had max DSC values of 0.9855 and
0.9950, respectively. These are proofs of the proposed model.

4.4 Comparison with State-of-the-art Techniques

The proposed model was compared with state-of-the-art techniques. Under the same circum-
stances and dataset used for these techniques, it evaluates the proposed model using MICCAI BRATS
dataset as a whole and the results as shown in Table 2. DSC values are clearly shown and compared.
The proposed model has better values than the state-of-the-art techniques. The proposed model was
compared with DSC values [30], strategies applied in the state-of-the-art methods in the given papers,
and dataset volumes were used for the model evaluation.
The problem statement points have been resolved to develop the proposed model, and the
challenge of getting the three-label tumours from the MRI has been performed with the best DSC
values for HGG and LGG volumes.
5278 CMC, 2023, vol.74, no.3

Table 2: Results comparison of the proposed model with state-of-the-art techniques

No. State-of-the-art techniques DSC values
1 Mohammad A. Naser [30] 0.92
2 Chandan Ganesh [31] 0.86
3 Proposed Model 0.99

The proposed model can accurately determine the size and structure of the tumor in MRI. The
DSC values in Tables 1, 2, and pictorial results Figs. 2–4 show that the proposed model outperforms
the BRATS dataset.
The proposed model outperformed brain tumor segmentation. This model used the state-of-the-
art dataset BRATS 2018. Some pre-processing steps are performed, passing the prepared dataset to
the deep learning model for segmentation [31]. DSC value is better after applying it to the test dataset.
The accurate tumour can be seen according to the problem statement shown in Figs. 2 and 3. The test
data results for the proposed model are shown in Table 1. All the three labels for the tumour can be
seen in Figs. 2 and 3 against the ground truths.
The proposed model fulfilled all the mentioned requirements in the problem statement and
challenge to solve the tumor segmentation in the brain MRI. It can use various other datasets like
BRATS or other real-time datasets to improve the model scalability in future work. Therefore, it is
concluded that the proposed model fulfils the requirements as it performs automatically for many
datasets. It can segment out accurately the tumour size as given in the ground truths. The DSC values
show that the proposed model has the best results with the maximum value obtained by test sets.

4.5 Major Contribution

The proposed model targets significant challenges such as tumor size, shape area, and tumor
appearance in MRI images. This research study suggested the model with a deep learning approach
improved ‘layers’ network U-Net algorithm. First, apply primary pre-processing techniques to utilize
the large volume dataset. The proposed model adds Dynamic Convolution Layers in the improved U-
Net algorithm for segmentation and classification. The proposed model was evaluated using BRATS
2018 training for the whole dataset. The proposed model outperforms the HGG and LGG volumes
and has shown results in statistics and visuals.

4.6 Limitation of the Model

The proposed model suggested the solution for accurate brain tumor segmentation in MRI.
BRATS 2018 challenge open-source dataset used for the evaluation of proposed performance.
The improved layered architecture of the deep learning U-Net model outperformed the dynamic
convolutional layers able to identify the tumourous region in the MRI. The accurate size of the tumor
in MRI was detected during tumor segmentation, and the tumor’s shape was determined according
to the manual annotation of the ground truth images by experienced radiologists. In real-time, the
proposed model can segment the tumor in MRI for large volume patients.
CMC, 2023, vol.74, no.3 5279

5 Conclusion
Accurately brain tumor segmentation for the MRI in which different features effects differently
the segmentation results. The proposed model was developed to compute the large volume of the
MRI dataset and accurately segment it. This proposed model applied some pre-processing techniques
to store and process a large amount of data. This model used the U-Net with additional layers, giving
the MRI high-dimension outputs. Furthermore, the Dice Coefficient values show that the proposed
system has excellent results with maximum values obtained from the test datasets. The purpose was
to accurately address the tumor’s localization and segment the tumorous area. Compared with the
already developed techniques, the approach segments the tumorous area with excellent dice values.
The proposed system suggested a solution by introducing pre-processing methods for a large volume
of data.
Pre-processing steps were performed to make the NumPy array for further data processing. The
proposed model used the BRATS 2018 dataset for evaluation. Accurate tumor segmentation can be
seen in Figs. 2 and 3. These figures represent segmented tumor results for the HGG volumes. Fig. 4
the visual effects for the LGG volumes. The test data results for the proposed model in dice values
are shown in Table 1. Dice values were obtained using the BRATS 2018 dataset, which shows the best
results for HGG and LGG volumes. This proposed model outperformed as compared to the state-of-
the-art methods for brain tumor segmentation.

Acknowledgement: The authors, therefore, gratefully acknowledge the authors technical and financial
support.

Funding Statement: The authors received no funding for this research.

Conflicts of Interest: The authors declare they have no conflicts of interest to report regarding the
present study.

References
[1] O. Tandel, G. S. Biswas, M. Kakde, O. G. Tiwari, A. Suri et al., “A review on a deep learning perspective
in brain cancer classification,” Cancers, vol. 11, no. 1, pp. 111, 2019.
[2] D. Burgo, L. Saenz, R. M. Hernández, G. Orive and J. L. Pedraz, “Nanotherapeutic approaches for brain
cancer management,” Nanomedicine Nanotechnology Biology and Medicine, vol. 10, no. 5, pp. 905–919,
2014.
[3] M. Anwar, F. Masud, R. A. Butt, S. M. Idrus, M. N. Ahmad et al., “Traffic priority-aware medical data
dissemination scheme for IoT based WBASN healthcare applications,” Computers, Materials & Continua,
vol. 71, no. 3, pp. 4443–4456, 2022.
[4] T. Arti, S. Shilpa and P. Millie, “Brain tumor segmentation and classification from magnetic resonance
images review of selected methods from 2014 to 2019,” Pattern Recognition Letters, vol. 131, no. 1, pp.
244–260, 2020.
[5] B. H. Menze, A. Jakab, S. Bauer, K. Farahani, J. Kirby et al., “The multimodal brain tumor image
segmentation benchmark (brats),” IEEE Transactions on Medical Imaging, vol. 34, no. 10, pp. 1993–2024,
2015.
[6] R. Saouli, M. Akil and R. Kachouri, “Fully automatic brain tumor segmentation using end-to-end
incremental deep neural networks in MRI images,” Computer Methods and Programs in Biomedicine, vol.
166, no. 1, pp. 39–49, 2018.
[7] F. Shaffer and J. P. Ginsberg, “An overview of heart rate variability metrics and norms,” Frontiers in Public
Health, vol. 5, no. 1, pp. 1–17, 2017.
5280 CMC, 2023, vol.74, no.3

[8] C. Hao, Q. Zhiguang, D. Yi, T. Lan and Q. Zhen, “Brain tumor segmentation with deep convolutional
symmetric neural network,” Neurocomputing, vol. 392, no. 1, pp. 305–313, 2020.
[9] L. T. Car, A. Soong, B. M. Kyaw, K. L. Chua, N. L. Beer et al., “Health professions digital education on
clinical practice guidelines: A systematic review by digital health education collaboration,” BMC Medicine,
vol. 17, no. 1, pp. 1–16, 2019.
[10] A. H. Majid, M. Anwar and M. W. Ashraf, “Classified structures and cryptanalysis of Wg-7, Wg-8 and
Wg-16 stream ciphers,” Technical Journal, vol. 23, no. 2, pp. 50–55, 2018.
[11] M. Mehmood, E. Ayub, F. Ahmad, M. Alruwaili, Z. A. Alrowaili et al., “Machine learning enabled early
detection of breast cancer by structural analysis of mammograms,” Computers, Materials and Continua,
vol. 67, no. 1, pp. 641–657, 2021.
[12] S. Mohammadreza, G. Yang, T. Lambrou, N. Allinson, T. L. Jones et al., “Automated brain tumour
detection and segmentation using superpixel-based extremely randomized trees in flair MRI,” International
Journal of Computer Assisted Radiology and Surgery, vol. 12, no. 2, pp. 183–203, 2017.
[13] Z. U. Rehman, S. S. Naqvi, T. M. Khan, M. A. Khan and T. Bashir, “Fully automated multi-parametric
brain tumour segmentation using superpixel based classification,” Expert Systems with Applications, vol.
118, no. 1, pp. 598–613, 2019.
[14] M. Malik, M. W. Iqbal, S. K. Shahzad, M. T. Mushtaq, M. R. Naqvi et al., “Determination of COVID-19
patients using machine learning algorithms,” Intelligent Automation and Soft Computing, vol. 31, no. 1, pp.
207–222, 2022.
[15] M. A. khan, L. U. Ikram, A. Rehman, M. Ishaq, M. Sharif et al., “Brain tumor detection and classification
a framework of marker-based watershed algorithm and multilevel priority features selection,” Microscopy
Research and Technique, vol. 82, no. 6, pp. 909–922, 2019.
[16] H. Byale, G. M. Lingaraju and S. Sivasubramanian, “Automatic segmentation and classification of brain
tumor using machine learning techniques,” International Journal of Applied Engineering Research, vol. 13,
no. 14, pp. 11686–11692, 2018.
[17] Z. U. Rehman, S. S. Naqvi, T. M. Khan, M. A. Khan and T. Bashir, “Fully automated multi-parametric
brain tumour segmentation using superpixel based classification,” Expert Systems with Applications, vol.
118, no. 1, pp. 598–613, 2019.
[18] N. Nooshin, K. Miroslav and Nabizadeh, “Brain tumors detection and segmentation in mr images gabor
wavelet vs. statistical features,” Computers and Electrical Engineering, vol. 45, no. 1, pp. 286–301, 2017.
[19] E. Arif, S. K. Shahzad, R. Mustafa, M. A. Jaffar and M. W. Iqbal, “Deep neural networks for gun detection
in public surveillance,” Intelligent Automation and Soft Computing, vol. 32, no. 2, pp. 909–922, 2022.
[20] P. G. Rajan and C. Sundar, “Brain tumor detection and segmentation by intensity adjustment,” Journal of
Medical Systems, vol. 43, no. 8, pp. 1–3, 2019.
[21] M. Anwar, A. H. Abdullah, A. Altameem, K. N. Qureshi, F. Masud et al., “Green communication for
wireless body area networks: Energy aware link efficient routing approach,” Sensors, vol. 18, no. 10, pp.
3237, 2018.
[22] K. Ejaz, M. S. Rahim, U. I. Bajwa, H. Chaudhry, A. Rehman et al., “Hybrid segmentation method with
confidence region detection for tumor identification,” IEEE Access, vol. 9, no. 1, pp. 35256–35278, 2020.
[23] M. Ghaffari, A. Sowmya and R. Oliver, “Automated brain tumor segmentation using multimodal brain
scans a survey based on models submitted to the brats 2012–2018 challenges,” IEEE Reviews in Biomedical
Engineering, vol. 13, no. 1, pp. 156–168, 2019.
[24] D. Ahmed, M. W. Iqbal, S. K. Shahzad, M. R. Naqvi and F. Muneer, “Smart health architecture integration
model,” in Proc. 1st Int. Conf. on Healthcare Computing Systems and Technologies (CHEST), Birjand, Iran,
pp. 1–7, 2019.
[25] M. Anwar, A. H. Abdullah, R. R. Saedudin, F. Masud and F. Ullah, “CAMP: Congestion avoidance and
mitigation protocol for wireless body area networks,” International Journal of Integrated Engineering, vol.
10, no. 6, pp. 59–65, 2018.
[26] X. Liu, Z. Deng and Y. Yang, “Recent progress in semantic image segmentation,” Artificial Intelligence
Review, vol. 52, no. 2, pp. 1089–1106, 2019.
 CMC, 2023, vol.74, no.3 5281

[27] Z. X. Zhao, Y. Wu, G. Song, Z. Li, Y. Zhang et al., “A deep learning model integrating FCNNs and CRFs
for brain tumor segmentation,” Medical Image Analysis, vol. 43, no. 1, pp. 98–111, 2018.
[28] M. Anwar, A. H. Abdullah, K. N. Qureshi and A. H. Majid, “Wireless body area networks for healthcare
applications: An overview,” Telkomnika, vol. 15, no. 3, pp. 1088–1095, 2017.
[29] T. Magadza and S. Viriri, “Deep learning for brain tumor segmentation: A survey of state-of-the-art,”
Journal of Imaging, vol. 7, no. 2, pp. 119, 2021.
[30] M. A. Naser and M. J. Deen, “Brain tumor segmentation and grading of lower-grade glioma using deep
learning in MRI images,” Computers in Biology and Medicine, vol. 121, no. 1, pp. 103758, 2020.
[31] C. G. B. Yogananda, B. R. Shah, M. V. Jahromi, S. S. Nalawade, G. K. Murugesan et al., “A fully automated
deep learning network for brain tumor segmentation,” Tomography, vol. 6, no. 1, pp. 186–193, 2020.

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