Proceedings of the 5th International Conference on Smart Systems and Inventive Technology (ICSSIT 2023)
IEEE Xplore Part Number: CFP23P17-ART; ISBN: 978-1-6654-7467-2
Performance Analysis of Ischemic Stroke Lesion
Segmentation in Brain MR Images using Histogram
based Filter Enhanced FCM
2023 5th International Conference on Smart Systems and Inventive Technology (ICSSIT) | 978-1-6654-7467-2/23/$31.00 ©2023 IEEE | DOI: 10.1109/ICSSIT55814.2023.10061114
Senthil Kumar Thiyagarajan1
Electronics and Communication
Engineering
Kalasalingam Academy of Research
and Education
Krishnan Koil,Virudhu Nagar Dt, India
senthilbeece@gmail.com1
Abstract—A medical condition which threatens life by
blocking brain’s blood supplying arteries is called ischemic
stroke. An early and accurate diagnosis of brain stroke is
possible through evaluation of different modalities (DWI,
FLAIR, T1, T2) of medical image format available in Magnetic
Resonance imaging (MRI). Delineation of Stroke lesion from
whole brain MRI, manually by Expert radiologists and
neurologist consumes larger proportion of time and subject to
intra- and inter-observer variation. Hence there is a
demanding need of computer based automated algorithm
which extracts out the stroke lesions from the whole brain MRI
and accelerate the process of early stroke diagnosis. With the
above objective this work proposes Histogram Based Filter
Enhanced Fuzzy C Means that brings in the pro role played by
Histogram (unique Grey level) wise clustering rather than
pixel wise clustering as followed in classical FCM. The
objective function of Histogram based FCM is smoothened
further by filtering through the median filter which
incorporates spatial information into the FCM clustering
technique where local information alone is considered. Above
Changes in classical Fuzzy C Means Clustering technique
through Histogram and median filters provides a greater
improvement with maximum value of 99% accuracy in DWI
and FLAIR 79% Dice in DWI, 98% precision in DWI, 88 %
sensitivity in DWI when compared with available state of art
methods standard FCM, FCM S 1, FCM S 2 and EnFCM.
Keywords— MR Magnetic Resonance; Diffusion Weighted
Imaging (DWI); FCM Fuzzy C Means ; FLuid Attenuated
Inversion Recovery (FLAIR) MRI ; HBFEFCM Histogram
Based Filter Enhanced FCM ; I schemic Stroke Lesion;
Morphological Reconstruction ; MRI Magnetic Resonance
Image ; T1 MRI mode ; T2 MRI mode.
I. INT RODUCT ION
Major contributor around the world for death and
disability is stroke [1]. Stroke is the condition of blood
supply block in arteries of brain leading to deficit in o xygen
supply in cerebrovascular tissue [1][2]. Stroke which occurs
in a larger proportion (around 88% of the total cases ) is
ischemic stroke. Informat ion Ext raction fro m scanned
medical image is greatly supported by advancement in
Co mputer vision and machine learning. Diagnostic medicinal
system needs automated applications in treatment planning,
guidance, disease spread and severity evaluation [5]. A
detailed analysis through acquired brain or neuro image
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Kalpana M urugan2*
Electronics and Communication
Engineering
Kalasalingam Academy of Research
and Education
Krishnan Koil,Virudhu Nagar Dt, India
drmkalpanaece@gmail.com2*
supports stroke lesions detection and predicting the area of
spread of stroke. An early diagnosis of ischemic stroke is
vital for preventing organ disability and death. The
functional impairment of stroke patients is identified through
investigations of stroke lesion’s volume and location [3].
Diffusion and perfusion modes (DWI, FLAIR, T1 and T2)
available in M RI (Magnetic Resonance Imaging) enhances
its performance over CT in stroke region identification [4].
Image segmentation a branch of image processing is used for
separation of an image into groups of identical reg ions based
on similar intensities and other measurable characteristics
[6]. Techniques of Image segmentation includes
thresholding, region growing and clustering [11]. Hypo
Intense signal in DWI and T2 modes are vital for stroke
identification at acute phase while hyper intense signal due to
ischemic stroke attack on T1 Weighted and FLAIR
modalities of M RI helps in the investigation at chronic phase
[7][8][9][10]. Differences in intensity across the different
modality is taken as the key factor for segmentation of stroke
tissue from the whole brain M RI images. The arrangement of
proposed research article includes the following sections I)
Introduction, II) Literature Review, III) Methodology, IV)
Results and Discussion, V)conclusion and References.
II. LIT ERAT URE REVIEW
Neuro Imag ing investigations are vital in understanding the
functions of the brain during stroke attack [10].
Segmentation of stroke infarcted region fro m the whole
brain med ical image through computer aided techniques
reduce diagnosis time. Efficiency of such automated
algorith m is based on its ability to perform seg mentation
without losing the orig inal info rmation available in whole
brain image. A soft segmentation algorithm Fu zzy C Means
helps in preserving the original informat ion available in the
image [11][15]. Standard FCM undergoes a degradation in
segmentation score when the image taken for c lustering
faces attacks fro m noise and intensity variation at different
regions of the image [12]. Standard FCM framework takes
gray level info rmation and not takes spatial informat ion in
to account, this result in efficient segmentation for image
with simp le texture and background while failing at images
of co mplex texture [13]. In order to improve the
segmentation effect spatial information at the locality of the
pixel being clustered by FCM can be added to the objective
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 Proceedings of the 5th International Conference on Smart Systems and Inventive Technology (ICSSIT 2023)
IEEE Xplore Part Number: CFP23P17-ART; ISBN: 978-1-6654-7467-2
function of FCM. Based on this idea wide variet ies of
variant in the architecture of standard FCM are continually
being proposed. FCM with spatial constraints (FCM S) [16]
considers intensity variations and hence pixel labels depend
on labels of neighborhood pixels, thus FCM S consumes
more time for co mputations at each iteration when
compared with standard FCM framework [15]. In adaptive
FCM algorith m [14] estimated bias field is used for carrying
out intermediate segmentation and the object ive function
gradually adapts itself during iterative clustering. Chen and
Zhang [16] modify FCM S layout by bringing in average
filtering FCM S1[16] and med ian filtering FCM S2[16] to
include spatial neighborhood properties prior cluster
forming through objective function. Liew A et.al [17]
developed adaptive fuzzy clustering based on spatial
constraint. J.H.Xue et.al. [18] proposed a modified
algorith m for brain segmentation where the effect o f noise is
reduced with the increase in complexity and computation
time. Enhanced FCM (EnFCM) [19] wh ich utilizes
histogram wise computation in cluster format ion provides a
low t ime of co mputation, but results of segmentation are
only comparab le with FCM S [16] as it does not include
spatial neighborhood informat ion. Fro m the above survey
we find FCM framework-based image seg mentation
methods concentrates either on reducing nu mber o f
computations in fuzzy membership calculation, cluster
center computation and objective function min imization or
look in for steps that adapts for including spatial info rmation
into the objective function. Hence, we are in need of a
method that aggregates the above two objectives. Ou r
proposed method Histogram Based Filter Enhanced FCM
(HBFEFCM) introduce the following changes for
enhancement of segmentation scores. i) Morphological
reconstruction of the original M R brain slice which g ives
excellent performance in noise reduction ii) as a
modification in standard FCM segmentation framework
Histogram wise FCM segmentation was used on
morphologically reconstructed image rather than pixel wise
FCM segmentation of the whole brain M RI slice thus
reducing the number of co mputation, besides this a median
filter to smoothen the membership function have been used,
it enhances the membership function and aids in appending
of the spatial features to the innate characters of
membership function which is not available in classical
FCM framework[15]. Median filtering is carried over fu zzy
membership function at the end of all iterat ion or when the
maximu m threshold for clustering have been reached, this
eliminates the computational load on carrying out filtering
over membership function at every step of iteration.
III. M ET HODOLOGY
A. Dataset Description
For this research study on ischemic stroke lesion
segmentation, four modalities of MR Image DWI, FLAIR,
T1 and T2 were taken fro m ISLES Sub Acute Ischemic
Stroke Lesion Seg mentation SISS 2015 [20] dataset with
(28 patients x 4 modes x 154 2D image in a single 3D slice
=)17,248 2D stroke affected image and (28 patients x 154
ground truth per patient =) 4312 ground truth images. The
proposed algorithm and state of art FCM variants taken for
comparison are tested on a sample o f 28x4=112 images (one
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per mode per patient). The number of ground truth images is
28 as it remains same for all four modes taken for each
patient.
B. Preprocessing System using Morphological
Reconstruction
The first step in segmenting stroke infarcted reg ion fro m the
whole brain M RI requires designing of a p reprocessing
system which mit igates the effect of noise and intensity
inhomogeneity in whole brain M RI slice. The proposed
preprocessing unit utilize the idea of morphological
reconstruction which mixes the morphological operation
erosion, reconstruction and compliment in a specified
manner as given in Figure 1 and the output in each step of
morphological reconstruction are shown in Figure 2.
Erosion is one of the fundamental operations in
morphological image processing uses a structuring element
for probing and reducing the shapes contained in the input
image. Reconstruction operation performs morphological
reconstruction of the image marker under the image mask,
and returns the reconstructed image. In this operation
elements of marker are selected in such a manner that it
must be less than or equal to the corresponding elements
of mask. When the values in marker are greater than
corresponding elements in mask, then reconstruction
operation perform clipping the values of marker image to
the mask level befo re start of operation. If the input image to
the complement operation is binary image, zeros become
ones and ones become zeros, while in co mplement operation
of a grayscale or color image, each pixel value is subtracted
fro m the maximu m pixel value, this difference is used as the
pixel value in the output image where dark areas beco me
lighter and light areas become darker.
Performance of proposed preprocessing module is evaluated
by comparing it with mean and median filters. The output
peak signal to noise ratio obtained as aggregated average of
all four modalities of MRI is 23.49% in mean filter 25.26%
in med ian filter and 38.16% in morphological
reconstruction.
Fig. 1. Block diagram of morphological reconstruction unit
Fig. 2. Output at each stage of morphological reconstruction unit
C. Histogram Based Filter Enhanced FCM (HBFEFCM)
In the first step Morphological Reconstruction of the input
whole brain 2D M R image slice (T1, T2, FLAIR, DWI)
were carried out.
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 Proceedings of the 5th International Conference on Smart Systems and Inventive Technology (ICSSIT 2023)
IEEE Xplore Part Number: CFP23P17-ART; ISBN: 978-1-6654-7467-2

unique grey level number of columns (L)

H= ( )    Minimu m value obtained by differentiating the objective
Where - orig inal 2D image of d ifferent M RI modalities function with respect to
∑
extracted fro m 3D t rain ing and testing images given in (7)
ISLES 2015 dataset normalized using gaussian distribution. ∑ ∑

- Morphological Reconstruction operation using

closing operators Above calculations fro m (1) to (7) are carried out
H-image output obtained after morphological on each iteration. The algorithm is stopped either at
maximu m nu mber of iteration (t=i) or ( )( )
Reconstruction operation
Histogram (Gray levels vs number of pixels at each gray ( ) ( )< τ when the difference in membership function
level) of the morphologically reconstructed image is at present and previous iteration is less than the min imu m
calculated and fed to mod ified object ive function evaluator error threshold of objective function(τ). After the final
which is also fed with Nu mber of clusters(C), fu zzy iteration or on reaching the min imu m error threshold
membership exponent(m), number of iterat ions(i), minimu m objective the membership function is filtered with median
error threshold of objective function(τ) to close before all filter to add local or neighbouring features to the
iteration. membership ship function. A block diagram indicat ing the
∑ ∑ ‖ ‖ + (2) algorith mic steps as discussed above is given in the Figure
3
- Modified Objective Function
m- fuzzy membership’s weighing exponent which provides
proportion of fuzziness in classification results
H-image obtained by morphological operation
- Grey level in morphologically reconstructed image
- Fu zzy membership at Histogram’s Gray level L when
it belongs to cluster K
L-Gray Level
k-cluster
c-total number of clusters
-center of Kth cluster
Fig. 3. Block diagram of HBFEFCM
∑ (3)
P-Total nu mber o f pixels in the morphologically IV. RESULTS AND DISCUSSION
reconstructed image H
Co mparison of segmentation result through Histogram
- Nu mber of p ixels in the morphologically reconstructed
Based Filter Enhanced FCM (HBFEFCM) algorith m and
image H with Gray level L
ground truth given in isles 2015 [20] dataset gives one class
N-total nu mber of Histogram’s Gray level L in the
of pixel as given below
morphologically reconstructed image H
True Positive (TP) - Nu mber of ground truth’s stroke
Value of L varies from 1 to N
lesion correctly segmented in image cluster output of
- Fuzzy factor introduced to bring changes in the
HBFEFCM algorithm as stroke lesions
standard Histogram wise framed FCM is as given below
True Negative (TN) - Nu mber of ground truth’s non-
(∑ ) (4)
stroke lesion correctly segmented in image cluster output of
Where - Multip licat ive constant used for finding the HBFEFCM algorithm as non-stroke lesions.
cluster’s centre and membership function. They are
False Positive (FP) - Nu mber of ground truth’s stroke
obtained as minima value calculat ions fro m differentiat ion
lesion wrongly segmented in image cluster output of
of modified objective function with respect to the cluster
HBFEFCM algorithm as non-stroke lesion pixel
‘s centre and membership function.
∑ ∑ ‖ ‖ (∑ ) False Negative (FN) - Nu mber o f ground truth’s non-
stroke lesion in image cluster output of HBFEFCM
(5)
The final equation fo r the Fu zzy Membership matrix algorithm wrongly segmented as stroke lesion.
consisting of membership function and cluster Centre can be With above four categories of segmented pixel class, the
obtained by minimizing the derivative of objective function following segmentation scores were measured.
with respect to and Minimu m value obtained by i) Accuracy is the percent of pixels that are classified
correctly.
differentiating modified ob jective function in (5) with
respect to gives solution of membership mat rix as given
in equation below.
ii) True Positive Rate (TPR) (or) Recall rate (or)
‖ ‖
Sensitivity: sensitivity gives the proportion of
∑ ‖ ‖ correctly identified true positive by HBFEFCM.
(6)
gives the fuzzy membership partition matrix for each
cluster with Cluster number of rows(K) and number o f Increase in TPR increases the accuracy of lesion

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detection. Segmentation result of HBFEFCM gives the fo llo wing

iii) DICE or F-measure: Intersection between ground
truth and segmented clusters are given at each
pixel by DICE or F-Measure.
iv) Positive Pred ictive Value (PPV) (or) Precision
Rate: Precision indicates the proportion of true
positives among the combined sum of true and
false positives, a higher value of precision shows
the true presence of stroke lesion in given MRI
slice.
Figure 4 shows the segmentation result with original M RI
mode and ground truth for each mode.
maximu m values, 99% accuracy in DW I and FLAIR, 88%
sensitivity in DWI, 79%of DICE in DWI mode, 98% o f
precision in DW I (fro m Table 1). Seg mentation of stroke
infarct with available FCM based state of art methods FCM
[15], FCM S1 [16], FCM S2 [16], EnFCM [ 19] are
performed and the segmentation scores thus evaluated for
each method is co mpared against our proposed method
HBFEFCM . segmentation scores of the proposed method
compared against state of art methods [15,16,19] are
provided in bold caption under each tabulation fro m Table II
to Table VI. It is very clear fro m the co mparison of
segmentation scores against state of art FCM variants our
proposed method outperforms state of art methods using
FCM variants [15][16][19] o f segmentation. It is clear fro m
runtime score (Table VI, Figure 10) p ixel wise clustering
performed in FCM [15], FCM S1 [16] and FCM S2[16]
requires a larger co mputation time where FCM S1 and FCM
S2 co mputation time exceeds FCM as they adopt mean and
med ian filtering operation on the input image at each
iteration of clustering. The algorith m EnFCM [19] and our
proposed method HBFEFCM requires lesser computation
time as they perform h istogram wise clustering, a s maller
increase in co mputation time in HBFEFCM over EnFCM
[19] is due to the median filtering operation performed over
the fuzzy membership function to include spatial
informat ion at the end of all iterat ions or reaching the
minimum threshold.

TABLE II. ACCURACY OF HBFEFCM COMPARED AGAINST STATE OF

ART
METH
ODS Method FLAIR DWI T1 T2
Fig. 4. Original MRI slice, Ground truth, Segmented Cluster in a) DWI b) FCM 0.9497 0.9493 0.8837 0.8908
FLAIR c) T1 d) T2 FCM S1 0.9529 0.9694 0.9037 0.9127
FCM S2 0.9530 0.9694 0.9151 0.9325
segmentation scores of HBFEFCM for each MRI modality EnFCM 0.9636 0.9755 0.9164 0.9330
are given in Table 1 and Figure 5. HBFEFCM 0.9866 0.9897 0.9375 0.9570

TABLE I. SEGMENTATION SCORES OF HISTOGRAMS BASED FILTER

Recall
MO DES Accuracy Rate DICE Precision
DWI 0.986642 0.850584 0.796821 0.95500
FLAIR 0.989723 0.884774 0.775125 0.98421
T1 0.937505 0.379862 0.536145 0.515193
T2 0.956957 0.697875 0.632623 0.62002
ENHANCED FCM ALGORITHM (HBFEFCM)

Fig. 6. Accuracy of HBFEFCM compared against state of art method (*

proposed method)

TABLE III. RECALL RATE OF HBFEFCM COMPARED AGAINST STATE

OF ART METHODS

Method FLAIR DWI T1 T2

FCM 0.7389 0.8289 0.3263 0.6203
FCM S1 0.7560 0.8422 0.3303 0.6484
FCM S2 0.7541 0.8402 0.3536 0.6563
Fig. 5. Segmentation scores of Histogram based filter enhanced FCM EnFCM 0.7827 0.8698 0.3647 0.6736
(HBFEFCM) HBFEFCM 0.8506 0.8848 0.3799 0.6979

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HBFEFCM 0.1515 0.1218 0.1303 0.1868

Fig. 7. Recall Rate of HBFEFCM compared against state of art methods Fig. 10. Run time (in seconds) of HBFEFCM compared against state of art
(* proposed method) methods (* proposed method)

TABLE IV. DICE SCORE OF HBFEFCM COMPARED AGAINST STATE The results of segmentation using conventional FCM
OF ART METHODS
variants and proposed HBFEFCM as indicated in Table II to
Me thod FLAIR DWI T1 T2 VI, Figure 6 to 9 shows supportive and progressive
FCM 0.4511 0.5214 0.3463 0.4113 performance wh ile segmenting stroke infarct region fro m
FCM S1 0.6801 0.6921 0.3913 0.4584 FLAIR and DW I modes while T1 and T2 modes lag in
FCM S2 0.6612 0.6713 0.3651 0.4413 segmentation task due to following reasons. The T1 mode’s
EnFCM 0.7123 0.7342 0.4251 0.5613 pixel in outer cortex are hypo intense nature where the
HBFEFCM 0.7751 0.7968 0.5361 0.6326 stroke infarct p ixels are also hypo intense hence the outer
cortex reg ion are also segmented along with stroke lesions.
In T2 mode the pixels at inner white matter are hyper
intense as in match with hyper intense stroke lesions hence
the inner wh ite matter region is segmented along with stroke
lesions. Hence alternative method wh ich overco me the
above two drawbacks can be carried out in future.

V. CONCLUSION
A modified clustering-based segmentation technique to
segment ischemic stroke lesion fro m mu lti-mode MRI
image wh ich brings a change in standard framework o f
Fig. 8. DICE score of HBFEFCM compared against state of art methods clustering technique FCM by adopting histogram wise
(* proposed Method)
cluster formation and objective function min imization was
TABLE V. P RECISION SCORE OF HBFEFCM COMPARED AGAINST developed. This decreases the computational load and
STATE OF ART METHODS increases the speed of segmentation via clusters.
Me thod FLAIR DWI T1 T2 Morphological Reconstruction prior to HFBEFCM supports
FCM 0.9000 0.9301 0.2842 0.5242 in eliminating noises of different kinds and provides
FCM S1 0.9100 0.9502 0.3010 0.5300 improved noise performance. Median filter wh ich filters the
FCM S2 0.9210 0.9511 0.3601 0.5350 fuzzy membership function at the end of all iterat ion or
EnFCM 0.9300 0.9600 0.4100 0.5610 reaching the threshold have helped in including the spatial
HBFEFCM 0.9550 0.9842 0.5152 0.6200
features for support of efficient segmentation. Results of
segmentation gives better segmentation metric scores with
99% accuracy in DW I and FLAIR, 88% sensitivity in DWI,
79%o f DICE in DWI mode, 98% o f precision in DWI
against standard state of art techniques. Segmentation lags
in T1, T2 modes of M RI image, optimization in selection o f
FCM para meters are the future works that can be appended
in enhancing further the perfo rmance of our proposed
HBFEFCM algorithm.

Fig. 9. Precision score of HBFEFCM compared against state of art REFERENCES

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