INTEGRATION

WAVELET-CURVELET DENOISING
AND POST-SEGMENTATION CORRECTION
WITH FUZZY C-MEANS
FOR MRI BRAIN TUMOR SEGMENTATION
Dian Pratama Putra
P31.2012.01186
Super vi sor
Dr. I ng. Vi ncent Suhart ono
Romi Sat ri a Wahono, M. Eng.

Research Background
The brain tumors have a particularly complicated
structure (Shen et al. 2005), vary greatly in size,
location, shape, internal texture (Resmi 2012),
intensities overlapping with normal brain tissue,
and often an expanding tumor can deflect and
deform nearby brain structures giving an abnormal
geometry also for healthy tissue (Cobzas et al.
2007)
Hence, precise and accurate segmentation of brain
tissue is to be a very challenging problem
Research Background (cont..)
Magnetic Resonance Imaging (MRI) is a popular
method and most widely used in medical imaging
for clinical diagnosis (Balafar et al. 2010)
MRI can be adapted to brain image with
high-contrast, high-spatial resolution and
multi-dimensionality (Sikka et al. 2009)
Segmentation of MRI brain image is
quite complicated, difficult and challenging task
which needs high-speed, high-accuracy and
high-precision (Balafar et al. 2010)

Research Background (cont..)
Fuzzy C-Means (FCM) is a very popular clustering
algorithm (Wang et al. 2013)(Balafar et al. 2011)
and widely applied to medical problems (Li et al.
2011), particularly in the case of brain tumor
segmentation (Gordillo et al. 2013)
FCM is easy to implement, robust to blurring,
applicable to multispectral data and no required
assumptions on the probability density function of
the data (He et al. 2012)
Research Background (cont..)
But, FCM doesnt produce a good result
in noisy and inhomogeneity images
(Hall et al. 1992)
The standard FCM very sensitive to noise (He et
al. 2012)(Zhao et al. 2013),outliers and other
imaging artifacts (Benaichouche et al. 2013)
especially in the presence of intensity noisy and
inhomogeneity in MRI (Qiu et al. 2013)
Research Background (cont..)
Moreover, the result of brain tumor
segmentation by FCM usually is not enough
accurate (Khotanlou et al. 2009) and can
generate some classification errors such as
misclassification pixel (Benaichouche et al.
2013)
Standard FCM for MR image segmentation is
not efficient by itself
Research Background (cont..)
FCM needs a noise reduction method as
pre-segmentation method and a
post-segmentation correction method
to refine the segmented image, improve the
initial results and produce a more accurate
segmentation (Freixenet et al. 2002)
Research Background (cont..)
Wavelet-Transform (WT) and Curvelet-
Transform (CT) is a popular choice noise
reduction method (Starck et al. 2002)(Eklund et
al. 2013)
A combined approach exploiting the advantages
provided by Wavelet-Curvelet Denoising (WCD)
potentially leads to improve performance of
MRI noise reduction
Research Background (cont..)
Meanwhile, to refine the potentially
misclassification pixels, used greedy
algorithm as post-segmentation correction
This approach can reallocate
misclassification pixels to the most
appropriate cluster
Research Background (cont..)
Based on the previous explanation, this
research proposes an integration noise
reduction method by Wavelet-Curvelet
Denoising (WCD) and post-segmentation
correction method by Greedy algorithm with
FCM to improve the MRI brain tumor
segmentation result
Research Problems (RP)
RP1. Fuzzy C-Means (FCM) segmentation
method does not produce a good brain
tumor segmentation result due to the
noisy MRI images
RP2. The result of MRI brain tumor
segmentation by FCM have
misclassification pixels
Research Questions (RQ)
RQ1. How does WCD-based noise reduction method
affect the accuracy of FCM-based MRI brain tumor
segmentation?
RQ2. How does greedy-based algorithm on post-
segmentation correction affect the accuracy of
FCM-based MRI brain tumor segmentation?
RQ3. How does WCD-based noise reduction method
and greedy-based algorithm on post-segmentation
correction affect the accuracy of FCM-based MRI
brain tumor segmentation?


Research Objectives (RO)
RO1. To develop an integration of WCD-based noise
reduction method and FCM for improving MRI brain
tumor segmentation accuracy
RO2. To develop an integration of greedy-based algorithm
on post-segmentation correction and FCM for
improving MRI brain tumor segmentation accuracy
RO3. To develop an integration of WCD-based noise
reduction method and greedy-based algorithm on
post-segmentation correction with FCM for improving
MRI brain tumor segmentation accuracy
Relationship between RP, RQ, RO
Research Problem (RP) Research Question (RQ) Research Question (RQ)
RP
1
FCM segmentation method
does not produce a good brain
tumor segmentation result
due to the noisy MRI images
RQ
1
How does WCD-based noise
reduction method affect the
accuracy of FCM-based MRI
brain tumor segmentation?
RO
1
To develop an integration of
WCD-based noise reduction
method and FCM for
improving MRI brain tumor
segmentation accuracy
RP
2
The result of MRI brain tumor
segmentation by FCM have
misclassification pixels
RQ
2
How does greedy-based
algorithm on post-
segmentation correction affect
the accuracy of FCM-based
MRI brain tumor
segmentation?
RO
2
To develop an integration of
greedy-based algorithm on
post-segmentation correction
and FCM for improving MRI
brain tumor segmentation
accuracy
RP1
+
RP2
FCM segmentation method
does not produce a good brain
tumor segmentation result due
to the noisy MRI images, and
the segmented result has
misclassification pixels
RQ
3
How does WCD-based noise
reduction method and
greedy-based algorithm on
post-segmentation correction
affect the accuracy of FCM-
based MRI brain tumor
segmentation?
RO
3
To develop an integration of
WCD-based noise reduction
method and greedy-based
algorithm on post-
segmentation correction with
FCM for improving MRI brain
tumor segmentation accuracy
Research Contributions (RC)
RC1. An integration of WCD-based noise reduction method
and FCM for MRI brain tumor segmentation
(WCD + FCM)
RC2. An integration of FCM and greedy-based algorithm on
post-segmentation correction for MRI brain tumor
segmentation (FCM + G)
RC3. An integration of WCD-based noise reduction method
and greedy-based algorithm on post-segmentation
correction with FCM for MRI brain tumor
segmentation (WCD + FCM + G)
Related Research
1. Sikka et.al (2009) - A Fully Automated Algorithm under
Modified FCM Framework for Improved Brain MR Image
Segmentation
2. Forouzanfar et. al (2010) - Parameter Optimization of
Improved Fuzzy C-means Clustering Algorithm for Brain
MR Image Segmentation
3. Benaichouche et. al. (2013) - Improved Spatial Fuzzy C-
means Clustering for Image Segmentation using PSO
Initialization, Mahalanobis Distance and Post-
segmentation Correction
Related Research (cont..)
Sikka et al. model (2009)

Segmentation
Modified Fuzzy C-Means (MFCM)
Post-segmentation step
NMAC
MRI Brain Dataset
Real : Pancham MRI Center, India
Simulated : BrainWeb and Brainsuite2
Bias
Removal
HUM
Contrast
stretching
HTRCE
Cluster center
estimation
HLPM
Sensitivity (), Specificity ()
and Similarity index ()
Related Research (cont..)
Forouzanfar et al. model (2010)

Paramater optimization
BS (combined GAs + PSO)
Segmentation
Improved Fuzzy C-Means (IFCM)
MRI Brain Dataset
Synthetic : Square image with 4
classes intensity value
Simulated : BrainWeb
Real : IBSR, the Center of
Morphometric Analysis
Under segmentation (UnS),
Over segmentation (OvS),
Incorrect segmentation (InC), and
Similarity index (SI)
Related Research (cont..)
Benaichouche et al. model (2013)

Pixel classification
PSO Algorithm
Segmentation
IFCM with Mahalanobis Distance
Pixel re-classification
Greedy Algorithm
Optimal segmentation accuracy
(SA)
MRI Brain Dataset
Synthetic: Images containing different
numbers of clusters, types
and noises levels
Simulated: BrainWeb
Summary of State-of-the-art
on MRI Brain Segmentation
Model
Method
Dataset Evaluation Results
Pre-processing Segmentation
Post-
processing
Sikka
et al.
(2009)
Bias Removal: HUM,
Contrast stretching:
HTRCE and Cluster
center estimation:
HLPM
Segmentation
using MFCM
Post-
processing
using NMAC
MRI Real: Pancham
MRI Center, India
MRI Simulated:
BrainWeb &
Brainsuite2
Sensitivity (),
Specificity ()
and Similarity
index ()
WM: = 0.91913;
= 0.97687;
= 0.93453
GM: = 0.90833;
= 0.95201; = 0.88426
Forou-
zanfar
et al.
(2010)
Parameter
optimization using
combined GA and
PSO
Segmentation
using IFCM
________ MRI Synthetic: Square
image
MRI Simulated:
Brainweb
MRI Real: IBSR
Under-seg,
Over-seg,
Incorrect-seg,
and Similarity
index
Simulated: UnS 0.27 %;
OvS 3.1 %; InC 0.44 %
Real: UnS 4.2800 %; OvS
20.0522 %; InC 7.1315 %;
SI 92.8685 %
Benaich
ouche
et al.
(2013)
Pixel classification:
PSO
Segmentation
using IFCM with
Mahalanobis
distance
Post-
processing
correction
using Greedy
Algorithm
MRI Synthetic: MRI
image with different
clusters numbers,
types, noises levels
MRI Simulated:
BrainWeb
Optimal
segmentation
accuracy (SA)
SA MRI = 93.80 %
SA synthetic =
93.11 % (Gaussian),
95.17 % (Uniform), 91.69
% (Salt & Pepper)
Theoretical Framework
Wavelet and Curvelet Transform
Image Segmentation
Fuzzy C-means (FCM) Clustering
Post-segmentation Correction
Theoretical Framework (cont..)
Wavelet and Curvelet Transform
Wavelet and Curvelet transform is used primarily for
smoothing, noise reduction and lossy compression
Wavelets are mathematical functions that
decompose data into different frequency
components that can be studied with a resolution
matched to their scale
Curvelet decompose the image into a set of wavelet
bands and analyze each band by local ridgelet
transform with different block size for each scale
level

Theoretical Framework (cont..)
Wavelet-based denoising technique
includes the following steps:
1. Transform the original image into wavelet domain
and acquire the wavelet coefficients
2. Process the wavelet coefficients. Typically involves
thresholding the wavelet coefficients to minimize
the contribution of noise in the wavelet domain
3. Take inverse wavelet transform on the processed
coefficients to produce the denoised image
Theoretical Framework (cont..)
Curvelet-based denoising technique includes
the following steps:
1. Compute all thresholds for curvelets
2. Compute norm of curvelets
3. Apply curvelet transform to noisy image
4. Apply hard thresholding to the curvelet
coefficients
5. Apply inverse curvelet transform to the result
of step (4)

Theoretical Framework (cont..)
Wavelet-Curvelet Combined Approach
Wavelets do not restore long edges with high
fidelity
Curvelets are challenged with small features
Wavelet-Curvelet Denoising (WCD) combined
approach exploiting the advantages provided
potentially leads to improve MRI noise reduction
performance
Theoretical Framework (cont..)
Image Segmentation
The principal goal of the segmentation process
is to partition an image into regions (also called
classes or subsets) that are homogeneous with
respect to one or more characteristics, property
or features
Theoretical Framework (cont..)
MRI Segmentation
In the specific case of MRI brain tumors,
segmentation consists of separating the
different tumor tissues such as solid or active
tumor, edema, and necrosis, from normal brain
tissues, such as gray matter (GM), white matter
(WM) and cerebrospinal fluid (CSF)
Theoretical Framework (cont..)
Fuzzy C-means (FCM) Clustering
FCM clustering is a very popular clustering algorithm
and widely applied to medical problems, particularly
in the case of brain tumor segmentation
The number of clusters is normally passed as an
input parameter
FCM uses an Euclidean distance measure to assign
fuzzy memberships to data element for clustering the
data
Theoretical Framework (cont..)
Post-segmentation Correction
The segmentation algorithm can generate some
classification errors that need to be corrected in
order to refine the segmentation
These errors lead to false contours, local
deformations in the natural contours and stray
pixels in the homogeneous areas of the image
Theoretical Framework (cont..)
Post-segmentation Correction
Steps of potentially misclassification pixels correction:
1. Detection of these pixels in the segmented image by
extracting all pixels that do not have the same label in
their 33 neighborhood (

)
2. Reclassification of these extracted pixels using local
information in a 55 neighborhood (

) of each
extracted pixel in the original image by minimizing
homogeneous criterion
Research Framework
INDICATORS MEASUREMENTS PROPOSED METHOD OBJECTIVE
Sensitivity
( )
Specificity
( )
Segmentation
Accuracy
( SA )
Dataset
NITRC and NA-MIC
MRI Brain image
Pre-processing
Processing
FUZZY C-MEANS
Post-processing
GREEDY ALGORITHM
MODEL ACCURACY
c
WAVELET-CURVELET
DENOISING
Research Design
1. Data collection
2. Initial data processing
1) Image acquisition
2) Ground truth image Processing
3. Proposed model
4. Experiment
5. Evaluation
Data Collection
Initial Data Processing
Proposed Model
Experiment
Evaluation
1. Data Collection
Stack of MRI human brain image
Data set downloaded from :
1. Neuroimaging Informatics Tools and Resources
Clearinghouse (NITRC)
2. National Alliance for Medical Image Computing
(NA-MIC)
2. Initial Data Processing
Performing data acquisition in image
processing is always the initial step through
the workflow sequence, because without an
image, no processing is possible
Initial data processing divided into:
1) Image Acquisition
2) Ground Truth image processing


3. Image Acquisition
Data set still in raw form and cannot be used
directly
The raw data files have the extension *.IMG
and *.NRRD (Nearly Raw Raster Data)
Additional tools to perform data-acquisition:
a) 3D-Slicer from National Institutes Health (NIH)
b) 3D-Doctor from Able Software Corporation


Ground Truth Image Processing
Decomposing method (ground truth) used to
measure accuracy degree of medical image
segmentation results objectively
Ground truth made manually segmentation
using image processing application or
hand-labeled by people

4. Proposed Model
Putras model
(2014)

Noise reduction
Wavelet-Curvelet Denoi sing
(WCD)
Segmentation
Fuzzy C-Means (FCM)
Pixel re-classification
Greedy Algorithm
MRI Brain Dataset
Simulated : NA-MIC
Real : NITRC
Segmentation accuracy (SA),
Sensitivity (),
Specificity ()
Compared Model
Model
Method
Dataset Evaluation Results
Pre-processing
Segmen-
tation
Post-
processing
Sikka
et al.
(2009)
Bias Removal: HUM,
Contrast stretching:
HTRCE and Cluster center
estimation: HLPM
Segmentation
using MFCM
Post-
processing
using NMAC
MRI Real: Pancham MRI
Center, India
MRI Simulated: BrainWeb &
Brainsuite2
Sensitivity (),
Specificity ()
and Similarity
index ()
WM: = 0.91913; = 0.97687; =
0.93453
GM: = 0.90833; = 0.95201; =
0.88426
Forou-
zanfar
et al.
(2010)
Parameter optimization
using combined GA and
PSO
Segmentation
using IFCM
________ MRI Synthetic: Square
image
MRI Simulated: Brainweb
MRI Real: IBSR
Under-seg, Over
seg, Incorrect-
seg, and
Similarity index
Simulated: UnS 0.27%; OvS 3.1%;
InC 0.44%
Real: UnS 4.2800%; OvS 20.0522
%; InC 7.1315%; SI 92.8685%
Benaich
ouche
et al.
(2013)
Pixel classification: PSO Segment-ation
using IFCM
with
Mahalanobis
distance
Post-process-
ing correction
using Greedy
Algorithm
MRI Synthetic: MRI image
with different clusters
numbers, types, noises
levels
MRI Simulated: BrainWeb
Optimal
segmentation
accuracy (SA)
SA MRI = 93.80 %
SA synthetic = 93.11% (Gaussian),
95.17% (Uniform), 91.69% (Salt &
Pepper)
Putra
(2014)

Noise reduction using
Wavelet-Curvelet
Denoising (WCD)
Segmen-
tation using
Fuzzy C-
Means
(FCM)
Post-
segmentatio
n correction
using
Greedy
Algorithm
MRI Real:
NITRC
MRI Simulated:
NA-MIC
Segmentation
Accuracy (SA),
Sensitivity (),
Specificity ()

?
5. Experiment
Experiment performance using MATLAB ver.R2013a
Segmentation MRI brain tumor experiment divide:
1. Only using FCM segmentation method (FCM)
2. Using FCM plus WCD-based noise reduction method
(WCD + FCM)
3. Using FCM plus Greedy-based algorithm on post-
processing (FCM + Greedy)
4. Using FCM plus WCD-based noise reduction method
and Greedy-based algorithm on post-processing
(WCD + FCM +Greedy)

Evaluation
Quantitative evaluation performance analysis is
based on three figures of merit:
1. Segmentation accuracy () =
+
+ + +

2. Sensitivity () =

+

3. Specificity () =

+

Research Schedule
No Activity
2014, January 2014, February 2014, March
1 2 3 4 1 2 3 4 1 2 3 4
1 Study of Literature
2 Initial Data Processing
3 Designing Proposed Model
4 Experiment and Result
5 Evaluation
6 Thesis Writing
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Questions ?
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FOR YOUR ATTENTION