Brain Tumor Segmentation and 3D Visualization

using Fluid Vector Flow

K.Muthu Kumar,B.Tech.,(M.Tech)
Department of computer science and engg
Student, PSN College of Engineering
conferancemuthu@gmail.com

Abstract Medical Imaging is
perceived to designate the set of
techniques that noninvasively produce
images of the internal aspect of the body.
MRI is more suitable for imaging the
brain due to its ability of discriminating
soft tissues with no side effects. Manual
segmentation of brain tumors by medical
practitioners is a time consuming task and
has inability to assist in accurate
diagnosis. Several automatic methods
have been developed to overcome these
issues. Tumors doesnt exhibit any shape
and causes deformations of nearby
structures of the brain. Active contour
models play a vital role in accurately
delineating the boundary of the tumor.
Several active contour models such as
traditional snake, Gradient Vector Flow,
Boundary Vector Flow, Magnetostatic
Active Contour models, Fluid Vector
Flow are in existence of which Fluid
Vector Flow addresses problems of
insufficient capture range and poor
convergence for concavities faced by the
other models. Fluid vector flow is
insensitive to initialization that make it
attractive one for segmenting brain
tumor. Fluid Vector Flow is utilized for
segmentation of two dimensional brain
tumor MR images to extract the tumor
and that tumor can be projected into the
three dimensional plane to analyze the
depth of the tumor.

Keywords Active contour
models, brain tumor, snakes, vector
flow, projection.



I. Introduction

Medical imaging is a technique and
process used to create images of the
human body for clinical purposes such as
medical procedures seeking to reveal,
diagnose or examine disease. Medical
Science incorporates the study of normal
anatomy and physiology. In the clinical
context, medical imaging is generally
equated to radiology or clinical imaging
and the medical practitioner responsible
for interpreting the images is a radiologist.
As a field of scientific investigation,
medical imaging constitutes a sub-
discipline of biomedical engineering,
medical physics or medicine depending on
the context. Research and development in
the area of instrumentation, image
acquisition, modeling and quantification
are usually the preserve of biomedical
engineering, medical physics and computer
science. [1]
Medical imaging constitutes
various modalities to create images of
t he human body such as X-RAY,
Comput ed Tomography (CT), Magnetic
Resonance Imaging (MRI), and
Ultrasound. X-RAY, invented by Winhelm
in 1895 is the oldest source of
electromagnetic radiation used for
imaging having wavelength in the range of
0.01 to 10 nanometers. It emits high
radiation to create images of the human
body thereby causing side effects such as
cancer and eye cataract. Then Computed
Tomography (CT) came into existence.
CT scan utilizes X-ray to produce two
dimensional images of the structures in the
thin section of the body. CT produces a
volume of data which can be manipulated
through a process known as windowing, in
order to demonstrate various bodily
structures based on their ability to block
the X-ray beam. Although most common
in medicine, CT is also used in other
fields, such as nondestructive materials
testing. Since it has a greater ionizing
radiation dose burden, repeated scans must
be limited to avoid health effects.
Active Contour Models or Snakes are
effective tools for segmentation. There are
two types of active contour models,
parametric and level set active contour
models. Parametric active contour models
are able to extract a single object and are
often faster than level set models.
Parametric snakes have two weaknesses;
the capture range is limited and inability
to capture acute concave shapes. Level set
active contour models are able to capture
multiple objects and complex geometries
and are slower than parametric methods.
In the presence of noise level set snakes
capture multiple false objects. In the
existing work parametric active contour
models such as Gradient Vector Flow
(GVF), Boundary Vector Flow (BVF) and
Fluid Vector Flow (FVF) and level set
active contour models such as
Magnetostatic Active Contour model
(MAC) were used for extracting the
boundary of the brain tumor but these
models differ by their capture range and
their ability to capture acute concavities.
FVF demonstrated improvements over
other techniques with its large capture
range and better convergence for
concavities. It is proposed to utilize Fluid
Vector Flow for extracting the tumor in
brain MR image and projection of
extracted tumor into the three dimensional
space i.e. 3D visualization to analyze the
depth of the tumor.

The rest of this paper is organized
as follows. In Section II, related work is
described. Section III introduces
segmentation and projection of tumor.
Discussions are presented in Section IV,
the study of conclusion in Section V.
II. RELATED WORK
Soft Computing techniques such as
fuzzy logic and neural networks have been
used for segmentation of brain tumor.
Segmentation of brain tumor using HSOM
(Hierarchical Self Organizing Map), an
unsupervised clustering technique maps
high dimensional inputs to one or two
dimensional discrete lattice of neuron units
[2]. HSOM method aids physicians in
tumor diagnosis and monitoring. Another
segmentation technique which is an
extension to traditional Fuzzy C-Means
(FCM) clustering algorithm which
considers two influential factors: feature
difference between neighboring pixels and
the relative locations of neighboring pixels
in the image [4].
FCM, by considering those factors
greatly restrained the influence of noise.
Fuzzy algorithms for Learning Vector
Quantization (FALVQ), an unsupervised
learning process discriminated normal
tissues and abnormalities of the brain by
partitioning the set of feature vectors
obtained from an MR image into a
relatively small number of clusters [6].
Yan Zhu and Hong Yan proposed an
optimization framework for detection of
tumor boundaries using a Hopfield
neural network [8]. The tumor boundary
was detected in consecutive slices in such
a way to extensively making use of the
aspect of connectivity to speed up the
process. Since a tumor doesnt have
accurate shapes, detection of tumor
boundary is a difficult task. Active
Contour Models play a vital role in
accurately capturing the boundary of the
tumor. One such is the traditional snakes
or active contours. They are nothing but
curves defined within an image domain
that can move under the influence of
internal forces coming from within the
curve itself and external forces computed
from the image data [5], [7]. There are two
key difficulties with snakes. First, the
initial contour must, in general, be close to
the true boundary or else it will likely
converge to the wrong result.
The second problem is that active
contours have difficulties progressing
into boundary concavities. Then a new
class of external forces for active contour
models that addresses both problems
called Gradient Vector Flow (GVF) [9]
emerged. It diffuses the edge information
from the object contour to its
neighborhood. Particular advantages of
the GVF snake over a traditional snake
are its insensitivity to initialization and its
ability to move into boundary concavities.
Its initializations can be inside, outside, or
across the objects boundary and it does
not need prior knowledge about whether
to shrink or expand toward the boundary.
Then a new external force which is
generated by a novel interpolation scheme
which reduced the computational
requirement significantly called Boundary
Vector Flow (BVF) [10] came into
existence. It has improved the capture
range and concave object extraction
capability than Gradient Vector Flow.
BVF provided large downward force thus
reducing the evolution steps required to
converge to the object. Magnetostatic
Active Contour model (MAC) utilized
bidirectional force field with the ability of
dynamically updating itself while the
contour evolves [3]. MAC being a level
set active contour model may capture
multiple false objects in the presence of
noise. S. Lobregt described a new
technique called discrete dynamic contour
model [7] for defining contours in 2D
images.
It consists of a set of
connected vertices as the initial model
and undergoes deformations to extract the
boundary of the object. It incorporated
elegant solutions to shrinking and
clustering problems. Tao Wang
developed a new concept called Fluid
Vector Flow (FVF) [1] for addressing the
problems of limited capture range and
poor convergence for concavities. FVF is
insensitive to initialization by taking
advantage of the boundary map generated
from the image. The capture range of FVF
extends to the whole image because the
vector flow energy spreads around the
entire image.
Figure-1 Proposed system flow diagram
III .Proposed Method
The Objective is to segment the
brain tumor using Fluid Vector Flow
(FVF) and three dimensional visualization
of tumor. The contour evolves to capture
the target object i.e. the brain tumor. The
methods used are preprocessing, binary
boundary map generation, vector flow
initialization, FVF and Depth Analysis.
Fig.1 shows the flow diagram of the
proposed method which starts with
smoothing the input image using a
Gaussian smoothing filter and edge
finding using a gradient operator. Then
binary boundary map is generated, and
vector flow is initiated, and FVF is
computed iteratively until the object i.e.
the tumor is extracted. Then the extracted
tumor is projected onto the three
dimensional plane for analyzing the depth
or volume of the tumor

A. Preprocessing
Gaussian Filter: A Gaussian filter
[34] is a filter whose impulse response is a
Gaussian function. Gaussian filters are
created to shun overshoot of step function
input while reducing the rise and fall time.
Gaussian filter has the minimum possible
group delay. In mathematical terms, a
Gaussian filter changes the input signal by
convolution with a Gaussian function and
this change is also called as Weierstrass
transform. The input image undergoes
smoothing using Gaussian smoothing filter
for elimination of noise. Gaussian filter is
a linear spatial filter which is used for
reducing the high frequency components
of an image as a result it smooths the
edges of the input image. Gaussian
Smoothing is performed by convolving the
input image with the Gaussian function i.e.

( , )* ( , ) G x y I x y
o


2 2
2
2
2
1
( , )
2
x y
G x y e
o
o
to
+

=

Where I(x, y) is the input image, G

(x, y)
is Gaussian smoothing filter with standard
deviation , x and y are the spatial
coordinates, and * is the convolution
operator.
Gradient operator is then applied to the
smoothened image to find edges in the
image which have been suppressed by the
Gaussian filter i.e.
( ( , )* ( , )) G x y I x y
o
V
Where is the gradient operator which
calculates the directional changes in
intensity values.

B. Binary Boundary Map Generation
The boundary map is defined as
( , ) ( ( , )* ( , )) MB x y G x y I x y
o
=V
Where G

(x, y) is the Gaussian

smoothing filter with standard deviation
, * is the convolution operator, and is
the gradient operator. The normalized
boundary map is defined as

( , ) min( ( , ))
( , )
max( ( , ) min( ( , ))
B B
NB
B B
M x y M x y
M x y
M x y M x y

( , ) 1 ( , )
0
BB NM
M x y if M x y T
else
= >


The choice of suitable threshold value
varies depending on the intensity
distribution and contrast associated with
the set of i mages bei ng anal yzed. For
t he brai n MR i mages a threshold of
0.1 is used to achieve object continuity
and for extracting the low intensity region.
The extracted boundary provides an
envelope to ensure that final convergence
is not out of bound.
C. Vector Flow I nitialization

The contour must be initialized to initialize
the external force field. The initial contour
can be inside, outside or overlapping the
target objects. FVF is insensitive to
initialization by taking advantage of the
binary boundary map. Contour C can be
represented as
( ) ( ) 0,1,..... 1
i i
c i x y i P ={ , } e| |
Where P is the number of points on the
contour. An external energy function is
defined as
( , ) ( cos , sin )
e x y
E x y f f _ o u o u = + + -----
----------------------------------- (8)
When M
BB
(x, y) = 0 , E
e
(x,y) holds the
first value in (8), otherwise holds zero.
Where is a normalization operator, =
1 (controls the inward or outward
direction when the contour is outside or
inside),
( ) ( ( , ))
x y
f f I x y _
,
= V and [ , 2 ] o u t e

D. FVF Computation and Contour
Extraction
A trace method is applied to the binary
boundary map to get a list of control
points. The control points are used to
generate the external force fields. FVF has
directional and gradient forces. The
directional force attracts the evolving
contour toward the control points even for
control points in a concave region. When
the contour is close to the object, the
gradient force fits the contour onto the
object. One control point is sequentially
selected and this point flows freely along
the o b j e c t b o u n d a r y a n d
g e n e r a t e s e x t e r n a l f o r c e f i e l d
dynamically. A parameter is used to
manage the selection of control point. The
method selects 1 out of control points to
achieve better time efficiency. Once the
control point moves to its new location it
generates new external force field for
further evolution of contour until
convergence is achieved. FVF computation
is iteratively performed to extract the
tumor.

Figure -2
Comparision of the segmenting image



E. Volumetric Projection and Depth
Analysis
Volumetric projection of brain
tumor is needed for diagnostic application
such as analyzing the depth of the tumor.
The extracted tumor enclosed by the
contour can be projected on to the three
dimensional plane (i.e. x, y, z plane). Mesh
is used for three dimensional visualization
or projection of t u mo r . Three
Di me n s i o n a l mode l i ng a l s o
k n o wn a s meshing is the process of
developing a mathematical representation
of any three dimensional surfaces or
object. To perform meshing, a grid must
be set up in X and Y directions and then
create a two dimensional grid of
coordinate[x, y] with mesh-grid. It
generates x and y arrays for three
dimensional projection. As a result of
this projection the tumor is visualized in
three dimensions i.e. length, breadth and
depth. Depending upon the gray variations
of the projected tumor the depth of the
tumor is analyzed. This projection
method requires considerable interactive
guidance for satisfactory results since it is
sensitive to image noise and pseudo edges
which are common problems in medical
images. Compared to traditional methods
the model based segmentation i.e. Fluid
vector flow aids in accurate projection and
analysis of depth of tumor.
TABLE -1
Comparative results on segmented images (%)
ACTIVE
CONTOUR
MODELS
Segmentation validation
Correct
detection
Pc (%)
False
detection Pf
(%)
BVF 65.67 6.48
MAC 78.53 9.34
FVF 87.38 4.79

Discussion
This paper presented an active
contour model based approach for
automatic segmentation of tumor in brain
MRI images and three dimensional
visualization to analyze the depth of the
tumor. Since MRI is the best modality
for imaging the brain which is
composed of soft tissues, this method
utilizes two dimensional brain MR images.
Compared to traditional segmentation
methods active contour models aids in
efficient segmentation of tumor. There are
several active contour models such as
Gradient vector flow, Boundary vector
flow and Magnetostatic active contour
models. All these models have difficulties
regarding capture range and convergence.
Since Fluid Vector Flow model has the
ability of capturing the entire object i.e. the
tumor and acute convergence into
boundary concavities. Since segmentation
aids in diagnosing the area of the tumor,
volumetric projection is performed to
visualize the depth of the tumor. Since
manual segmentation of tumors by
physicians is a time consuming
task, this segmentation method with
projection is time preserving and also
provides accurate diagnosis.

V. CONCLUSIONS
A parametric Fluid Vector Flow (FVF)
active contour model is utilized for
automatic segmentation of tumor in brain
MR images and the segmented tumor is
visualized in three dimensions for depth
analysis. Since a tumor doesnt exhibits
any prior shape, delineating the tumor
accurately is a difficult task. FVF is
utilized for segmentation because it can
deform in all directions for capturing the
tumor. It also addresses the issues of
limited capture range and the inability to
extract complex contours with acute
concavities.Segmentation aids in
visualization of area of tumor. Volumetric
projection is proposed to analyze the third
dimension i.e. the volume or depth o f the
tumor. This automatic method for brain
tumor segmentation and three dimensional
visualization will help physicians in
accurate diagnosis.

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