Bonfring International Journal of Advances in Image Processing, Vol. 6, No.
3, August 2016
A Survey of MRI Segmentation Techniques for
Brain Tumor Studies
Prajna Udupa and Sarvesh Vishwakarma
Abstract--- Brain tumor is one of the advancing brain
illness among the existing population. The causes of the
condition being non-deterministic, it is found that the survival
rates of people suffering from brain tumor is very less. This
medical condition lacks effective treatment and thus
approaches that enable efficient treatment planning of the
brain tumor is very crucial in the current context. Magnetic
resonance image (MRI) scans are widely used in the diagnosis
and subsequent treatment planning of the brain tumors. While
in most of the cases only tumor regions are segregated from
the MRI scans, segmentation of the tumor along with the
healthy tissues of the brain such as white matter, gray matter
and cerebrospinal fluid enable doctors to study the overall
medical condition of the patient and treat him accordingly.
The overall segmentation procedure includes noise removal,
skull stripping, feature extraction and actual segmentation of
various brain regions. Several methods used for each of these
stages are discussed in this paper. The advantages and
drawbacks of each of them is also highlighted.
Keywords--- Feature Extraction, Noise Removal,
Segmentation, Skull Stripping
I. INTRODUCTION
T HE human brain forms the most vital part of the central
nervous system which is madeup of tissues such as white
matter, gray matter and the cerebrospinal fluid. This is in turn
protected by a layer of membranes and the skull. The different
parts of the human brain are responsible for different functions
of the human biological system. Any damage caused to any of
these parts can affect the functioning of the corresponding
human organ. Brain tumor is one of the most commonly found
ailments of the brain in the present day scenario. Although the
survival rate of people suffering from brain tumors is very
scarce, the medical experts mainly focus on the treatment of
this biological condition that can help elongate the lifespan of
these patients.
Brain tumor is the abnormal growth of cells within the
brain which can be mainly of two types such as malignant and
benign. Malignant tumors are high grade tumors that are
cancerous and spread to the other regions of the brain while
benign tumors are low grade tumors that are non-cancerous
and do not spread to the other regions of the brain [1].
Prajna Udupa, Student, Dept. of CSE, SCEM, Mangalore, India.
E-mail:prajna.mtechscs14@sahyadri.edu.in
Sarvesh Vishwakarma, Professor, Dept. of CSE, SCEM, Mangalore,
India. E-mail:sarvesh.cs@sahyadri.edu.in
DOI: 10.9756/BIJAIP.10467
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The location, size and shape of the tumor can vary in
different individuals and the growth rate of these tumors may
be affected by several unknown factors. Although the causes
of brain tumors is speculative, some of the causes as identified
by researchers include exposure to ionizing radiations,
hereditary factors, subjection to industrial chemicals, other
medical conditions and corresponding medicine intake, body
weight and lack of exercise, smoking and alcohol intake and
so on [2].
People suffering from brain tumors exhibit certain
symptoms as the disease progresses some of which include
headache, vomiting, seizures, fatigue, vision related problems,
difficulty in speaking, impediment of sensation and walking
and feeling unconscious [3]. The diagnosis of these tumors is
usually by medical examination of symptoms along with the
use of medical imaging techniques such as Computed
Tomography (CT) or Magnetic Resonance imaging for the
analysis of the tumor affected brain images. It is then followed
with a biopsy of the sample taken from the tumor affected
brain region that reveals the severity of the tumor [4].
Identification and classification of tumors using traditional
invasive procedures can damage the brain tissues. To avoid
this, non-invasive methods can be used. These methods take
the advantage of widely used magnetic resonance images of
the brain to detect the tumor affected brain regions. The
magnetic resonance images contain different intensities for
different regions or tissues of the brain. In the medical field,
large number of MR images of the brain are generated for
individuals suffering from brain tumors. Manual segmentation
of tumors by experts requires substantial time and is usually
error prone when large number of MR images have to be
examined by them [5], [6]. To ease their work of segmenting
tumors from MR images, automatic tumor segmentation
methods are used. Most of the segmentation algorithms only
segment either the healthy tissues [15]-[18] or tumors [7]-[12]
from these images with a good accuracy. However,
segmentation algorithms that segment both the healthy tissues
along with the tumor affected regions of the brain can help in
efficient medical diagnosis and treatment planning taking into
account all of the other biological conditions of patients.
In this paper, the various methods used for different stages
of the brain MRI segmentation procedure are discussed.
Section 2 presents a survey on these methods. Section 3
highlights the advantages and disadvantages of these methods.
Section 4 gives the conclusion to the presented survey.
Bonfring International Journal of Advances in Image Processing, Vol. 6, No. 3, August 2016
II. SURVEY ON MRI SEGMENTATION TECHNIQUES
Segmentation of an image is the task of segregating the
digital image into different fragments or components which
makes the analysis of the image much simpler and easier. The
segmentation process basically identifies boundaries of
various regions within an image and assigns labels to each
pixel in the image based on the similarity characteristics of the
pixels. Typical applications of image segmentation include
medical imaging to locate tumors and pathologies, to plan
surgeries, to measure volume of tissues, to diagnose the
anatomical structures, object detection comprising of face
detection, pedestrian detection, recognition tasks such as face
recognition, fingerprint recognition and so on.
The segmentation process basically includes four
important stages namely Noise Removal, Skull Stripping,
Feature Extraction and Final Segmentation. The noise removal
step helps eliminate pixel variations in the input data. The
skull stripping stage helps extract the desired brain region
from the entire brain MRI. The feature extraction stage helps
extract prominent features for training the segmentation. The
final segmentation stage is used to obtain the segmented image
from the Brain MRI. Each of these stages can be implemented
with a variety of methods which are discussed in the literature
survey.
A. Noise Removal
Noise in images is the variation in illumination or color
information of the images which could be caused by circuit
components of the image capturing device. Noise removal
from Magnetic Resonance images is essential in order to
enhance the image quality and help improve the computational
efficiency of different forms of image processing. The various
segmentation methods available for segmenting the human
brain MRI are highly sensitive to noise, heterogeneous
intensities found in the image and the low contrast between
different regions of the image making image segmentation a
difficult task. Thus removal of noise from these images is very
essential to efficiently segment the brain MRI by overcoming
these challenges.
The Gaussian filter is a simple method used to remove
noise from images and produce a smoothening effect [20]. It
uses a kernel function that has the shape of a bell as a filter
and applies this function to the original image that contains the
noise component within it. Median filters can help remove
impulsive noise from images. They are non-linear in nature
and function by computing the median of the neighborhood
pixels with respect to the pixel of interest [21]. This newly
computed value will be the denoised value for the pixel of
interest.
The Non Local Means method for removing noise from
images computes the value for a particular pixel i by using all
the pixels within a search window that have a similar
neighborhood in comparison to the neighborhood of the pixel I
[22]. Weights are assigned to each of the selected pixels based
on the degree of similarity between the patches of selected
pixel with that of the original pixel i. The value for the pixel i
is then estimated as the weighted average of all the selected
pixels within the selected search window. The Adaptive Non
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Local Means method for noise elimination automatically
selects and reduces the search window size for any given pixel
i based on the count of fit pixels within a search window. The
fit pixels are the pixels for which the computed weight
denoting the similarity index should be above a certain
threshold.
Independent Component Analysis method for noise
removal represents the observed data as an n-dimensional
vector x that contains the pixel information of the image
[23].This data is subjected to pre-processing. Initially the data
is centered by subtracting the data mean from the original data
after which the data is exposed to a whitening process which
aims at removing any of the second-order statistical
dependencies that exist in the original data. Standard Principal
Component Analysis is usually used to perform whitening of
the data which also accomplishes dimensionality reduction of
the data.
The wavelet approach to denoising images comprises of a
basis function called the mother wavelet that has a specific
scale denoting the frequency and a unique translation
representing the time domain for the corresponding signal
[24]. In addition to this any signal f(x) can be denoted using
infinite combinations of a discrete wavelet signal, each
corresponding to different scales and translations. On
convolution of the signal f(x) with the mother wavelet
function, wavelet coefficients for the mother wavelet can be
computed. These coefficients can in turn be used to
reconstruct the original signal f(x). For noise removal of
images using wavelet analysis, the wavelet coefficients are
subjected to thresholding operations at different frequency
values. The coefficients with insignificant energy will be
discarded. This helps to eliminate noise from the signal
without altering the signal.
The Least Mean Square (LMS) adaptive filter makes use
of the coefficient vector W for the signal, the actual input
signal X and the desired signal d [25]. The LMS algorithm
then computes the error signal e from the input signal and the
desired signal as their difference and then by using a specific
step size, it computes the corrected input signal that combines
the error component into it. This method is iterated until the
error signal becomes negligible. The Anisotropic Diffusion
method for removal of noise from MR images is based on the
anisotropic diffusion process [26]. In this process different
regions of the brain enable different amounts of light to be
diffused into them helping to clearly distinguish between
different regions. This method proposed by Perona and Malik
uses the original image and a filter that exploits the local
features of the original image to produce a resultant image.
This image is obtained after applying transformations that are
space variant and non-linear in nature.
B. Skull Stripping
The human brain is a vital organ comprising of three main
parts namely the forebrain, the midbrain and the hindbrain. In
the study of brain images, separating these tissues associated
with the brain from that of the non-brain tissues is a crucial
step for processing these brain images. This step is referred to
as skull stripping which helps separate the cerebral tissues
from the other regions like the skull, scalp and the meanings
Bonfring International Journal of Advances in Image Processing, Vol. 6, No. 3, August 2016
that protect the brain. There are various techniques employed
for stripping the skull in image processing.
An elementary method named S3 for brain region
extraction uses a median filter to de-noise the image [27]. It
then computes the mean intensity value twice and uses these
values to eliminate the skull and membrane regions of the
brain. It then produces the binary image using averaged
membrane intensities and applies morphological operations to
get the final skull stripped image. Another method to strip the
skull from brain MR images is by combining thresholding
technique with morphological operations [28]. The cerebral
and non-cerebral tissues are separated from each other by
using a threshold value for the pixel intensity after which the
binary image is generated. This binary image then under goes
morphological operations like erosion, dilation and region
filling to extract the desired brain region.
In the region growing approach, smaller regions of the
brain are determined using some criteria which is previously
defined and then they are combined together to form larger
regions [29].The Brain Extraction Tool method uses an initial
surface model for the brain to which the brain surface present
in the image is overlapped [30]. This involves a deformation
of the initial model to an optimized model by iterative steps
that use a set of local image features. A robust brain extraction
(ROBEX) method for stripping the skull from the brain MR
images uses a discriminative random forest classifier which is
trained to identify the boundary regions of the brain [31]. It
then uses the generative point distribution model to find all the
pixels or points within the boundary region. The graph cuts are
then used to obtain the refined final contour.
Another approach to segment brain tissues from non-brain
tissues is by finding several contour regions within the brain
region extracted from a preliminary segmentation [32].
Starting from an initial contour, it evolves and expands the
curve and repeatedly finds all the pixels within the specified
contour until a final image mask showcasing the brain region
is developed. Hybrid methods constitute a combination of
several techniques used to produce accurate results and thus
enhance the efficiency of skull stripping [27].
C. Feature Extraction
Feature extraction in MR images is usually accomplished
using wavelet transforms. Discrete Wavelet Transform utilizes
a mother wavelet required for the decomposition and then
alters its scaling and translation parameters to generate
wavelet functions from it [34]. This wavelet function is then
used to embed the original input signal onto it to generate the
transformed signal. At each stage of the decomposition, a
down-sampling process is performed to eliminate the
components that do not pass through the filters causing the
decomposed signal to be of smaller length than that of the
original signal. The Stationary Wavelet Transform combines
all the elements that would be selected from multiple
decomposition steps in epsilon-decimated DWT to a single
step [33].The decomposed signal has the same length as that
of the original signal with no elements of the original signal
lost by the decomposition.
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The Edge based method exploits intensity values along the
edges in an image that differ greatly and thus features
extracted using these edge based values can be very useful for
image segmentation [14]. For the edge based intensity values,
first order and second order features are determined and then
used. Appearance based method for feature extraction
combines both first order intensity features and second order
spatial features [13]. First order features are effective if the
contrast of the image is sufficiently good that can help
separate the background from the foreground of the image. In
cases where images are of low contrast, second order spatial
features are used. These second order features are usually
calculated using the co-occurrence matrices of gray intensities.
The Phase Congruency method operates by computing the
local phase and energy values for the image [19]. It is a
frequency dependent technique which computes the Fourier
components for the points in the image and then determines
the points having the same phase values to generate lines,
corners or edges as features.
D. Segmentation
MRI image segmentation is necessary in order to
differentiate between the different regions of the brain from
the MR image scans. In threshold based method, global
thresholding can be used in order to separate the background
of the image from the foreground objects of similar intensity
values when the contrast between the background and
foreground is high [35].In region based methods, a seed value
is chosen either manually or using an automated
seed-determining process that corresponds to the region of
interest [36]. The neighboring pixels of this pixel are then
examined based on some similarity criterion to find the pixels
having similar properties as the seed pixel. Connected regions
are formed using these neighboring pixels and the process is
repeated until no more pixels can be added to the region.
In the classification method, the training data is used to
generate manual segmentation which is then used as a
reference for automatic segmentation of the new input data
[37]. This method requires the image to be segmented to
contain distinct features that are quantifiable that allows
correct labeling of image pixels by the training data. The
clustering algorithm is trained to learn on its own from the
available data to deduce the segmentation [38]. Clustering
methods do require an initial segmentation to identify the
different classes in an image and they are highly sensitive to
this initial segmentation.
Parametric and Geometric deformable models combine the
prior knowledge related to the location, size and shape of
different structures with the constraints learnt from the image
data to deform the original model that then produces the
segmented model of the brain MRI [39].K-Nearest Neighbors
method can be used to segment the MR image by classifying
each pixel using an integer value k that determines the number
of neighboring pixels to be examined, a Euclidean distance to
determine the k closest neighbors and a set of labeled
examples for some training data [41].
Bonfring International Journal of Advances in Image Processing, Vol. 6, No. 3, August 2016
Bayesian approach makes use of a supervised and
parametric approach [42]. In this method, using the training
dataset, the data and its associated classes are identified for
which the probability values are also computed. For each new
data that arrives, the posterior probability is computed using
the Bayes rule along with the prior probability computed for
the training set to determine the class with maximum posterior
probability. This is the class assigned to the data. Statistical
model based approaches can be used for image segmentation
[43]. Markov random field models spatial interactions among
the neighboring pixels of an image. It is a statistical model that
is used in combination with other segmentation algorithms
that helps to place pixels with similar properties other than
pixel intensities into one group.
Artificial Neural Network based approach can be
implemented as a classifier where the weights for the ANN are
determined using the training data and then use these weights
to segment the new data [44]. It can also be implemented as a
clustering method or a deformable model. The numerous
interconnections between the neural network nodes helps
model the spatial interactions among the image pixels. Atlas
guided approaches for brain MRI segmentation make use of a
standard template or atlas that is generated using the
anatomical information from images which require
segmentation [45]. This atlas is then used as a reference to
segment new images taken as input. This approach performs
an atlas warping where it finds a one-to-one mapping from the
previously segmented atlas image to the target image to be
segmented. Use of hybrid approaches to segment the brain
MR images produces more efficient results by overcoming the
drawbacks of either of the approaches [46].
III. ANALYSIS OF EXISTING METHODS
The various methods used for the different stages of brain
MRI segmentation have their own benefits and drawbacks
which are discussed in this section.
A. Noise Removal
Although Gaussian filters are easy to implement, they
result in generation of blurred images that fail to highlight the
edges from the other brain regions in MR images. Median
filters are simple in nature and help preserve the edge
information and produce efficient smoothening of images. The
searching of pixels within the search window employed by the
Non Local Means method is an exhaustive process which
increases the computational complexity and results in no
refinement of performance measure.
Wavelet analysis helps to eliminate noise for the signals
that could be discontinuous in both time and frequency
domain. The LMS method for noise elimination enjoys
simplicity in both hardware and software implementations. It
was found to be robust and helped achieve a good
performance measure with only concise information about the
actual input signals and the desired signals. The choice of the
step size and the length of the filter used can affect the
performance of the method. The Anisotropic Diffusion
method of noise elimination facilitates smoothening of image
regions that preserve continuity in the images while
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eliminating the smoothening effect across image boundaries
thus helping to highlight the different brain regions.
B. Skull Stripping
The S3 method adaptively computes the threshold value
making it more robust. Although it outperforms the other
methods like BET, BSE and ROBEX, it will suffer efficiency
if used with low contrast images or highly noisy images due to
erroneous threshold values computed. Although thresholding
combined with morphological method is simple and efficient,
it fails to clearly differentiate between the brain and non-brain
regions of same intensity values. In order to attain higher
accuracy in skull stripping using this method, the threshold
value selection plays a major role. The performance of the
region growing approach depends on the seed value selected
for the brain and non-brain regions either manually or using
any algorithm.
The Brain Extraction Tool method is known for its speed
and eliminates any kind of registration or preprocessing. A
potential drawback could be over estimation of the brain
surface and sensitivity to noise resulting in inaccurate
stripping [31]. The ROBEX method fails to generate sharp and
accurate brain regions, especially if the brain comprises of
highly convoluted regions [27]. It requires more time for
computation as compared with its counterpart methods.
Another drawback is to standardize the image intensity values
in order to produce more accurate final segmentation.
The contour method thus facilitates to strip the skull
efficiently by being able to produce genuine results in less
time. It is also found to be insensitive to noise that is spread
randomly over the image due to the curvature term not
permitting it in the evolving curve. This method was found to
perform well for both normal and tumor affected brain MR
images. It is found to be accurate and robust to all inputs. But
it fails for extremely noisy and low contrast datasets.
C. Feature Extraction
Although DWT can be used to extract features from MR
images, they exhibit the translation variance problem which
makes them unfavorable. SWT overcomes the translation
variance problem of DWT.SWT can also be used to
accomplish enhanced noise removal when compared with
DWT along with edge detection as it preserves all the features
of the original input. It is also found that DWT can be applied
only to images with a size equal to a power of 2 whereas SWT
allows application to images of random size values[33].
Since the Edge based method depends on edge intensities,
it performs poorly for noisy image and requires removal of
noise for efficient performance. The texture based features
used in Appearance based method are insensitive to intensity
values and help to efficiently segment the images. The Phase
Congruency method is insensitive to intensity variations as it
does not determine the edges based on intensity values.
Bonfring International Journal of Advances in Image Processing, Vol. 6, No. 3, August 2016
D. Segmentation
Threshold based methods can fail for low contrast images.
The region based method of segmentation is simple and
effective in accurately segmenting regions of similar
properties without being computation intensive. At the
boundary of two different tissue classes, this method fails to
correctly classify the image pixels as belonging to one of these
two tissue classes due to the partial volume effect that blurs
the intensity of pixels in this region. These methods require
appropriate selection of the seed point in order to identify a
region of interest. It is also sensitive to noise and thus can
result in holes to be present in the segmented image or cause
disconnected regions to be developed [36].
The classification method can be applied to images with
multiple classes. This approach requires manual intervention
to obtain the training data serving as a potential drawback. It
does not perform any spatial modeling and thus is sensitive to
heterogeneous intensities. It is also found that using separate
training set for each possible image to be segmented is a
tedious job and using a limited training set to segment large
number of input images can result in inaccurate segmentation
results [37]. Clustering methods are sensitive to noise and
intensity in homogeneities as they do not model spatial
interactions. But absence of spatial modeling has helped in
producing faster computation results [38].
The constant propagation of contours in parametric
deformable model approach can result in inaccurate
segmentation when faced with missing boundary parts by not
being able to identify homogeneous regions of interest [39].To
overcome this problem, Geometric deformable models are
used. They require placing an initial contour at the center of
the region boundary for the region of interest and then
generating successive active contours using a level-set
function to obtain the final contour for the region of interest.
This method poses difficulties in the practical implementation
as most of the segmentation methods are not capable of
dealing with objects having regularity in their shapes [40].
The K-Nearest Neighbor method is simple and easy to
implement and turns out to be effective when implemented
with efficient noise reduction methods. This approach can
result in reduced performance with large trainingset as the
performance is directly proportional to the size of the training
set and requires iterating over the entire set. It also requires
only limited features as input since classification needs to be
done for each and every pixel. It is sensitive to noise and
inhomogeneous intensities due to absence of spatial filtering.
Repeated iterations to improve the classification result can
make the method slow. It is not favorable for MRI tumor
segmentation when the training set has some of the under-
represented classes [41].
The Bayesian approach considers tumor and edema to
follow a normal distribution which is not true. It also fails
when the brain comprises of large deformations. But this
method was found to be computationally efficient and
produced faster segmentation results [42].Since the statistical
model approach supports spatial modeling, it is found to be
insensitive to noise and heterogeneous intensities. Because of
the spatial modeling, this method is computation intensive.
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Selection of parameters that control the strength of spatial
interaction is difficult. A very high initialization of parameter
values can result in loss of structural information producing
over smoothed segmentation results [43].
Due to the highly parallel nature of processing in Artificial
Neural Network based approaches, they can turn out to be
very fast and efficient. But since they are usually implemented
on standard serial computer, the computational advantage is
reduced [44].A combination of linear and non-linear
transformations are used for the mapping in atlas guided
approach. This approach thus enables efficient labeling of the
target image using the atlas. Accurate segmentation of
complex structures is difficult due to variations in anatomical
structures over different subjects of a diverse population [45].
IV. CONCLUSION
MRI image segmentation is one of the active areas of
research requiring high focus. This survey paper focused on
the various methods available to accomplish the different
stages of the segmentation process. It also presented each of
their benefits and drawbacks. With each of these methods
having their own advantages and disadvantages, it is essential
to develop efficient segmentation algorithms that can combine
these methods to result in efficient and effective segmentation
results.
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