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A SURVEY ON METHODS OF FULLY AUTOMATED MR BRAIN IMAGE

SEGMENTATION

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International Journal of Neural Networks and Applications, 4(1), 2011, pp. 13-18

A SURVEY ON METHODS OF FULLY AUTOMATED MR BRAIN

IMAGE SEGMENTATION
R. Shantha Selva Kumari1 and R. Meena Prakash2
1
Mepco Schlenk Engineering College, Sivakasi, India, E-mail: r_sskp@yahoo.com
2
P. S. R. Engineering College, Sivakasi, India, E-mail: eshwari_2000@rediffmail.com

Abstract: This paper presents a detailed survey on the currently available frame works of automated brain
image segmentation and the methods employed in the frame work for tissue classification, bias field correction
and partial volume effect correction. The frame work of automated MR brain image segmentation can be
broadly divided into model based segmentation frame work , Fuzzy Connectedness segmentation frame
work , Deformable model based frame work and hybrid approaches. The methods employed in the framework
which are discussed here include atlas registration used for initializing the segmentation, thresholding,
Expectation Maximization algorithm for bias field correction, Markov Random Field model for incorporating
contextual information and Artificial Neural Network for clustering.
Keywords: Fuzzy Connectedness, Expectation Maximization, bias field, Markov Random Field, Deformable
model, Artificial Neural Network

I. INTRODUCTION II. MRI SEGMENTATION CONCEPT

Magnetic resonance imaging (MRI) is a non-
invasive imaging technique since no ionizing
radiation is employed. It gives three dimensional
(3D) information about the human soft tissue
anatomy [1]. Magnetic Resonance Images of the
brain are highly significant in the treatment of brain
diseases such as Multiple Sclerosis, Schizophrenia,
epilepsy and others. Segmentation of brain tissues
into white matter, gray matter and cerebrospinal
fluid plays a crucial rule in diagnosis of the brain
disorders. For example, quantification of white
matter lesions is needed for the treatment of
multiple sclerosis. Volumetric analysis of the
different tissue classes is crucial for the treatment
of Schizophrenia and epilepsy. Manual
segmentation is time consuming and prone to
significant intra- and inter- observer variability
thereby reducing the precision of the analysis of the
segmentation. Therefore, fully automatic, highly
accurate, and robust tissue segmentation technique
is an invaluable tool for treatment of
neurodegenerative diseases. In this paper, we
review the state of the art technologies in the
automatic segmentation of MR brain images and
provide a scope for future research work in this
area.
A. MRI Principles
MRI is based on the principles of Nuclear Magnetic
Resonance (NMR). Nuclei with an even number of
protons and neutrons have no net spin or angular
momentum while nuclei with an odd number of
protons and neutrons possess a net spin. The
nucleus of hydrogen atom is made up of only a
single proton and possesses a net spin. The
hydrogen atoms are abundant in the fat and water
content of human body. An angular moment occurs
due to the net spin of the nucleus around its axis.
Due to the rotating proton, a current loop is also
created which results in magnetic field. Due to this
magnetic field and the angular moment, the proton
exhibits a magnetic dipole moment parallel to the
rotation axis. Under normal condition, the magnetic
dipole moments are randomly oriented and hence
the net magnetic field will be zero. When placed in
a magnetic field, the proton with its magnetic dipole
moment is subjected to precession around the field
axis. The frequency of this precession is called the
Larmor frequency and is directly proportional to
the strength of the magnetic field i.e., vo = γBo where
Bo is the main magnetic field strength and γ is called
gyro magnetic ratio whose value is 42.56 MHz/
Tesla. The application of a magnetic field Bo would
create a net equilibrium magnetization Mo per cubic
14
centimeter which is aligned to the Bo field. Mo is
very much weaker than Bo and hence not directly
observable. By perturbing Mo away from Bo field
axis with an appropriate RF pulse having a
frequency equal to larmor frequency, a longitudinal
magnetization component M L and a transverse
magnetization component MT is produced. When
the RF pulse is turned off, the longitudinal
magnetization component ML recovers to M0 with
a relaxation time T 1 and the transverse
magnetization component MT de phases and decays
to zero with a relaxation time T2 . During relaxation,
the protons lose energy by emitting their own RF
signal with the amplitude proportional to MT. This
signal is called Free Induction Decay(FID) response
signal. The FID response signal is measured by an
RF coil placed around the object being imaged. In
Magnetic Resonance Imaging, linear gradient field
is employed to get spatial information, Three tissue
parameters decide the quantitative description of
the MR signal: the proton density which determines
Mo and the relaxation times T1 and T2. The RF pulse
is repeated at a predetermined rate called repetition
time, TR. The time between which the RF pulse is
applied and the response signal is measured is the
echo delay time TE. With proper selection of TR and
TE, the MR image can be made to contrast different
tissue types.
B. Problems Associated with MR Brain Image
Segmentation
Partial Volume effects are the most commonly
occurring artefacts in MR brain images where
multiple tissue types contribute to a single pixel,
resulting in a blurring of intensity across
boundaries. PVA (Partial Volume Averaging)
artefacts occur due the limited resolution of the
imaging device and due to this, fine anatomical
structures are lost in the image. Partial volume
effects in MRI can be overcome by soft segmentation
that allows regions or classes to overlap.
Membership functions are defined for soft
segmentation as
0 ≤ mk(j) ≤ 1 for all j, k (1)
Σmk(j)=1 for k = 1,...K and for all j (2)
The value of a membership function mk(j) can
be interpreted as the contribution of class k to
location j. Therefore, if the membership values are
greater than zero for two or more classes, they are
overlapping. Membership functions can be derived
by fuzzy clustering and classifier algorithms. Soft
International Journal of Neural Networks and Applications
segmentations can be converted to hard
segmentations by assigning a pixel to its class with
highest membership value.
Another difficulty associated with the
segmentation of brain images is the intensity in-
homogeneity artefact. The INU (Intensity Non
Uniformity) artefact arises due to in- homogeneity
in the magnetic field, and exists as an unwanted
low frequency bias term modulating the signal. This
causes a shading effect to appear over the image.
Methods that simultaneously segment the image
and estimate the in-homogeneity give good results
than the methods that employ pre filtering
operation which removes the in-homogeneity
before actual segmentation.
All MR images are affected by random noise.
The noise comes from the stray currents in the
detector coil due to the fluctuating magnetic fields
arising from random ionic currents in the body, or
the thermal fluctuations in the detector coil itself.
This may cause errors in tissue segmentation.
C. The MRI Tissue Segmentation Problem
An image can be modeled as the union of c
homogeneous regions
Ak, A = Uk=1,..c (3)
where each homogeneous region is specified by
Ak(x, y) = pk+nk (4)
where p k represents signal intensity and n k
represents additive, zero mean random noise
component.
Figure (1) represents the MR brain image
segmentation into WM,GM and CSF.
The image formation process in MRI can be
modelled as
s(x) = o(x)b(x) + n(x) (5)
where s(x) is the measured MR signal, o(x) is the
true signal emitted by the tissue, b(x) is the
unknown smoothly varying bias field, and n(x) is
an additive noise assumed to be independent of
b(x). Accurate segmentation of an MR image thus
requires an accurate estimation of the unknown bias
field b(x) and removing this bias field from the
measured MR signal prior to or during
segmentation. Using the estimated b(x), the log
transformed true signal can be recovered as,
log o(x) = log s(x) – log b(x) (6)
A Survey on Methods of Fully Automated MR Brain Image Segmentation
Figure 1: WM,GM,CSF Segmentation of T1 Weighted Image
(a) Input Image (b)White Matter (c) Gray Matter
(d) CSF
III. METHODS
In this section, we present a review of different
approaches for fully automated MR brain image
segmentation under three frame works, namely
model based segmentation framework, deformable
model based segmentation framework and fuzzy
connectedness segmentation framework. The
implementation and significance of each method is
analyzed.
A. Model Based Segmentation Framework
In the model based segmentation framework, the
MR signal is modelled as a realization of a random
process with a parametric probability distributions
that is corrected by a smooth polynomial in-
homogeneity or bias field. [2][3][4]. The hidden
segmentation z is modelled as the realization of a
random process with some probability density
function f(z/Φ z ) that is parameterized by the
parameter set Φ z. z has generated the observed
intensities y with probability density function
f(y/z, Φy) parameterized by Φy. Estimation of the
segmentation z is straightforward once the model
parameters Φ ={Φ y , Φ z} are known. Both the
segmentation and the model parameters can be
estimated simultaneously by interleaving the
segmentation with estimation of model parameters.
15
The intensity of a voxel belonging to class k is
normally distributed around a mean µ k , with
variance σ2 grouped in θk ={µk, σ2}. The overall
model parameters is indicated by Φy = {θ1, …. θk, C}
where C denote the set of bias field parameters. The
bias field in MR is modelled as a multiplicative
effect. Hence it is worked on log-transformed
intensities, which makes the bias additive. Thus,
three steps are involved in this frame work,
classification of voxels, estimation of the normal
distributions and estimation of the bias field. The
Expectation Maximization algorithm is used to
estimate the maximum likelihood (ML) parameters
Ö by iteratively estimating the hidden data z based
on the current parameter estimation Φ and
recalculating Φ that maximizes the likelihood of the
complete data.
The independent model explained above
classifies the voxels based on their intensity only.
This yields acceptable segmentation results as long
as the different classes are well separated in
intensity feature space. But in brain tissues, voxels
surrounding the brain show an MR intensity that is
very similar to brain tissue. This results in erroneous
classifications of small regions surrounding the
brain as gray matter or white matter. Hence spatial
and anatomical constraints are incorporated by
introducing the Markov Random Field. The
difference lies that in the independent model each
voxel had the same a priori probability to belong
to class k, whereas now this probability depends
on the classification of the neighbouring voxels.
The prior classification is derived from a digital
brain atlas that contains spatially varying prior
probability maps for the location of white matter,
gray matter and CSF. The use of atlas avoids
interactive user intervention to initialize the
algorithm and make the method fully automated.
B. Deformable Model based Segmentation
Framework
Deformable models are model-based techniques for
delineating region boundaries by using closed
parametric curves or surfaces that deform under the
influence of internal and external forces[5].To
delineate an object boundary in an image, a closed
curve or surface must first be placed near the
desired boundary and then allowed to undergo an
iterative relaxation process. Internal forces are
computed from within the curve or surface to keep
it smooth throughout the deformation. External
16
forces are usually derived from the image to drive
the curve or surface toward the desired feature of
interest. The main advantages of deformable
models are their ability to directly generate closed
parametric curves or surfaces from images and their
incorporation of a smoothness constraint that
provides robustness to noise and spurious edges.
A disadvantage is that they require manual
interaction to place an initial model and choose
appropriate parameters. Deformable models may
be parametric deformable models or Level set
deformable models and are classified as geometric
active contours, gradient based level set active
contours, Geodesic Active contours depending
upon the method for contour extraction. A detailed
survey is found in [10].
In [7], a three stage method is employed to
segment images. The first stage, Segment Head, uses
intensity histogram analysis to remove background
noise and provide a head mask defining the head.
The second stage Generate Initial Mask produces a
mask that approximately identifies the intracranial
boundary. A head image is filtered using a
nonlinear anisotropic diffusion filter, to identify
regions corresponding to brain. The nonlinear
anisotropic diffusion effectively counters RF in-
homogeneity by smoothing the brain regions and
by reducing the intensity of the narrow non brain
regions such as the scalp. With the initial brain mask
as seed, the third step, Generate Final Brain Mask,
locates the intracranial boundary using an active
contour algorithm. The active contour model
algorithm consistently tracks the edge of the brain,
even in the presence of partial volume effects. This
method effectively provides fully automatic
intracranial boundary detection algorithm which
can be used for studies of Multiple Sclerosis Lesions.
The points in the contour iteratively approach the
intracranial boundary through the solution of an
energy minimization problem.
M3DLS algorithm[11], a multiphase 3D Level
Set Algorithm utilizes a multi phase extension of
the region based deformable model based on the
Mumford-Shah functional by iteratively deforming
two closed curves separating four regions. An
automated MR brain tissue segmentation that
integrates both geometric and statistical image
features into edge-based deformable model
formulation is employed [8]. The advantage of this
method is the stabilization of the active contour. In
this approach, first the Gaussian Mixture EM
parameters are estimated such that each mixture
International Journal of Neural Networks and Applications
distribution represents one single class. Based on
these estimated distributions, the normalized
posterior probability of each voxel is calculated. The
hybrid geometric-statistical feature is derived by
combining both the voxel statistics and the image
gradient information. To initialize the active
contour, a voxel threshold is introduced. The hybrid
feature and the contour initialization are
determined individually for each tissue to be
segmented and each contour is then propagated
independently.
C. Fuzzy Connectedness Segmentation
Framework
The fuzzy connectedness (FC) works on voxel basis
and therefore can better segment objects with
irregular or complex shapes and hence better suited
for brain MRI. The FC method takes simultaneously
into consideration the degree of space adjacency,
degree of intensity adjacency, and degree of
intensity gradient adjacency between two voxels.
In the fully automated method of brain image
segmentation proposed in [12], four steps are
included. In Atlas registration, [18] the pre
segmented atlas is registered onto the MRI through
a rigid registration method. In FC Segmentation, with
the registered atlas as initial segmentation , the brain
tissues are segmented. The prior information of
tissues are specified which include (1) the intensity
probability distribution (2) the intensity difference
probability distribution (IDPD) (3) initial seeds. In
PABIC correction, the INU artefacts are estimated
and corrected. The PABIC (Parametric Bias Field
Correction) method employs Gaussian components
decomposition algorithm for decomposing the
intensity histogram of tissue into number of
Gaussian components and choosing the one with
the largest amplitude to represent the tissue. Then
Re-FC Segmentation is done by taking the PABIC
corrected MRI as the subject and the FC-segmented
MRI as the initial segmentation.
Fuzzy clustering algorithm requires a priori
knowledge about the number of clusters, nature
of data, clustering criteria and so on. Histogram
of MR images may be used to determine the
number of clusters but they fail for diseased cases.
In [14] Artificial Neural Network (ANN) is
employed to find out the exact number of clusters
and FCM algorithm is used in the next stage for
segmentation. Neural Networks have the ability
of doing parallel operation and they simulate
biological learning.
A Survey on Methods of Fully Automated MR Brain Image Segmentation 17

D. Other Methods Table I

Overview of MR Brain Image Segmentation
Water shed segmentation method is a popular Frameworks
method which may be used for MRI segmentation.
But the drawback here is over segmentation. Hence Segmentation Advantages Limitations Supportive
Frame methods
in [17] merging process for the over segmentation
work employed
is done using Fuzzy C Means Clustering algorithm
following the water shed segmentation. K Nearest Model Based The method The method Markov
Neighbour (KNN) classifier is employed to partition (2,3,4) overcomes requires Random Field
the regions that needed re-segmentation. Hybrid the drawback initialization is employed
of spectral of the to incorporate
approaches of level set method with fuzzy overlap of classifica- contextual
segmentation and level set method with atlas based MR intensities tion information.
segmentation show better segmentation results [15, of different process. Atlas
16]. tisse classes initialization
which is is done.
IV. DISCUSSIONS AND FUTURE predominant
in intensity-
CHALLENGES based
Automated segmentation of MR brain images is a methods.
supportive tool for the doctors in the diagnosis of Deformable The method Segmenta- Hybrid
brain diseases such as schizophrenia, Alzheimer’s Model yields a nice tion result geometric-
disease, epilepsy etc., The problem of segmenting MR Based (7,10) representation relies on the statistical
Brain image into White Matter, Gray Matter and CSF of the tissues initial feature is
has been addressed using various approaches. and bound- contour derived for
Manual intervention is required in many of these aries. It also placement. each tissue to
simplifies be segmented.
methods. The foremost requirement is fully
optimization.
automated method without any external
intervention. The main challenges in MR brain image Fuzzy Conn- The method The method Atlas
segmentation are Partial Volume Effect, Intensity In ectedness provides tends to be Registration
(12,14) reduced affected by is used for
homogeneity artefact and random noise. Most
Computa- Intensity initialization
segmentation methods need initialization for which tional Non- and PABIC
atlas registration with known set of labels can be complexity Uniformity method is
prescribed. From the survey, it is observed that each and better artifact. adapted to
method is having its own advantages and drawbacks suited for correct the
as listed out in the table. The future scope lies in complex brain INU artifacts.
combining the various methods leading to hybrid structures.
approach which adapts the advantages of each Hybrid Combines the Computa- Based on the
method involved and overcoming the drawbacks. Approach advantage of tional requirements,
(15,16,17) each method Complexity the above said
Future research should also focus on the
involved is involved. supportive
computation time, reduction in complexity and methods may
accuracy of the segmentation results. be employed.

V. CONCLUSION
In this paper, the various existing methods for fully
automated MR brain image segmentation have been
meticulously analyzed and a detailed survey report
has been given. Based on the study, it is observed
that the most applicable methods for MR brain
image segmentation can be listed under three
categories –model based statistical approach,
deformable model based method and fuzzy
connectedness segmentation. A serious discussion
has also been made of the hybrid approach
employing combination of several methods. This
paper is based on the number of research articles
published in the previous decade. The references
cited in bibliography provide a good
comprehension of current trends and future scope
in fully automated MR Brain Image Segmentation.
The further research focuses in construction of
hybrid methods which acquire advantages of each
method and at the same time reducing the
computational complexity, improving the accuracy
and avoiding the human intervention.
 18
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International Journal of Neural Networks and Applications
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