Segmentation of Brain MRI Using Active Contour Model
Segmentation of Brain MRI Using Active Contour Model
ABSTRACT: Alzheimer disease is a neurodegenerative disorder that the most affected, but the dementia is striking more and more young
impairs memory, cognitive function, and gradually leads to dementia, people. What constitutes a prime therapeutic challenge is the fact
physical deterioration, loss of independence, and death of the affected that no current treatment can permanently eradicate the disease.
individual. In this context, segmentation of medical images is a very (Aminoff et al, 2007; Bar et al, 2003; Bear et al, 2007; Bollinger et
important technique in the field of image analysis and Computer-
al, 2011; Buckner et al , 2008; Dickerson et al, 2009; Epstein et al,
Assisted Diagnosis. In this article, we introduce a new automatic method
of brain images segmentation based on the Active Contour (AC) model
1999). In fact, it is very important to go through an image processing
to extract the Hippocampus and the Corpus Callosum (CC). Our contri- to detect and locate the affected area. The image segmentation is one
bution is to combine the geometric method with the statistical method of of the techniques that can bring about some crucial information for
the AC. We used the Caselle Level Set and added a learning phase diagnostic assistance. It is defined as the process of partitioning a
to build an average shape and to make the initialization task automatic. digital image into multiple segments or regions.
For the step of contour evolution, we used the principle of Level set The diversity of images, the difficulty of the problems, the
and we added to it the a priori knowledge. Experimental results are researchers varied origins, the evolution of computers, as well as
very promising. V C 2017 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 27,
certain empiricism in the evaluation of results led to the introduction
311, 2017; Published online in Wiley Online Library (wileyonlinelibrary.com). DOI: of a multitude of algorithms. The reliable and accurate segmentation
10.1002/ima.22205
of anatomical volumes whether normal or pathological from imaging
Key words: Alzheimer disease; computer-assisted diagnosis; hippo- systems aims at developing the medical diagnosis because it may
campus; corpus callosum; active contour help studying morphology internal structures, and it may help the
detection and quantification of the lesions. Many segmentation meth-
ods have been proposed for many years for the MRI type of images.
I. INTRODUCTION The automatic brain MRI segmentation is a complex problem from
Alzheimers disease is a neurodegenerative disorder that impairs the point of view of the variability of the human brain in terms of
memory and cognitive function. It is divided into three main phases: images processing acquired by this method. Brain MRI segmentation
the Mild Cognitive Impairment (MCI) stage, the moderate stage, and is an essential basic step that has many applications in neurology
the severe stage. At the mild stage, the person is usually able to think such as quantitative analysis, operational planning, and functional
appropriately, and to make crucial decisions about future; However, imaging. Although very accurate to describe the structures of the
Some negative symptoms are remarkable during this stage such as brain, magnetic resonance images present many difficulties like low
forgetfulness and communication problems, for instance, finding the contrast and inhomogeneity, but their treatment can be achieved
right word or following a conversation. In the moderate stage, there through simple approaches. In this work, we suggest a new automatic
is a further deterioration of mental and physical abilities of the per- method of segmentation based on the Active Contour (AC) model.
son. Memory loss worsens. One can no longer remember his/her per- This article is organized as follows. In the following section, we
sonal history and can no more recognize his/her family and friends. present some related works. In the third section, we present the sug-
In the severe stage, the person is no longer able to remember any- gested method. In the last section, we give some experimental
thing, communicate with anyone, or even take care of oneself. The results, and a discussion.
patient will require a special care day and night. This disease can be
genetic, but that is not the primary cause of degenerative dementia. II. RELATED WORKS
The latest statistics show that there are 12 million patients world-
There are many methods for segmentation of the Brain MRI,
wide. This number keeps growing and the forecast estimates 18 mil-
such as:
lion cases in 2025. In Tunisia, the number is alarming: about 30 000
people are affected, to 1.5 million in the Arab world. The elderly are
A. ASM 1 D Proposed by (Said Taieb et al., 2014). This
Correspondence to: Amira Ben Rabeh; e-mail: [email protected] method proposed by Said Taieb et al. (2014) to extract the
This can be done by examining the variation of homologous char- Sm5 Si (6)
n i51
acteristic points on all forms. If we consider, for example, the first
two lines of the observation matrix, they represent the coordinates of
the first feature point through different forms. By examining the
change in these coordinates and passing from one form to another, The variance, which measures the dispersion of the elementary
one can deduce the path followed by this point and the amplitude of surfaces (Si) relative to the average surface:
variation. However, the problem is that each form is represented by
2
n feature points, each identified by its coordinates (x, y) in the plan. 1X n
Vs5 Si2Sm (7)
Therefore, for a single point, we used 2N variables and for all the n i51
points, we used 2nN variables. To simplify the problem and reduce
the number of variables that describe each shape, the idea is to apply
a principal component analysis (PCA) on the raw data. The standard deviation, which represents the average of all devi-
In practice, the main components are derived from the covariance ations; basic variances compared with the average distance:
matrix associated with the observation matrix. To determine the p
mode of variation of a shape, we can simply compare this shape with r5 Vs (8)
respect to an average computed shape, instead of comparing with all
other forms. This comparison is between the coordinates of points as
Then, we will propose a confidence interval [Sm 2 2r, Sm 1 2r].
characteristics compared with counterparts in average shape. The
For each iteration, we calculate the surface of the area. If the
deviation of the ith shape with respect to the average shape may be
surface is lower than the lower limit of the interval, we stop the
defined by the expression:
evolution of the curve.
dxi5xi1 ; yi1 ; xi2 ; yi2 ; . . . ; xin ; yin 2x1 ; y1 ; x2 ; y2 ; . . . ; xn ; yn 5xi2x A.3. Priori Knowledge of Standard Deviation. Each image is
(2) recorded by the variation of the studied area.
We integrate the prior variance. We search the average, the
XN
When x5 N1 xi, the average computed shape from the learning variance, and the standard deviation of the variance of form.
i51
base aligned.
Vars 5 Var1; Var2; . . . ; Varn (9)
Automatic initialization of the average shape Our first contribu-
tion is to overcome the stage of manual initialization. In this way: Constructing a vector contains all the variations of the areas of the
0 1
X1Y1 0 1 hippocampus of the samples of the base.
B C p1 The average change in interest structures:
B X2Y2 C B
B C B p2 C C
B C
B.........C B C
1X n
B C B C
B C B
B . . . :: C
C
Varm5
n i51
Vari (10)
M5B C
B . . . . . . . . . C5B C (3)
B C B
B . . . :: C
C
B.........C B C
B C B The variance, which measures the dispersion of elementary varia-
B C @ . . . :: C
A
B XNYN C tions (Si) relative to the average variation.
@ A
pN
1X n
Vvar5 Vari2Varm2 (11)
N 5 n*Nech n i51
n: number of points that have the outline of an image.
Nech: number of samples The greater the variance is, the more heterogeneous the appropriate
The M matrix is of dimension N * 2 area (hippocampus) is. The standard deviation, which represents the
Through this matrix, the average position is determined by: average of all deviations basic variances compared with the average
distance.
1X N
Posm5 pi (4) p
N i51
r5 Vvar (12)
A.2. Priori Knowledge of the Surface. Each image is recorded Then, we will propose a confidence interval [Varm 2 2r, Varm 1
by the surface of the studied form by using Eq. (5): 2r].
The goal is to derive a compact formulation describing the per-
X
nbl X
nbc
Si5 Xij (5) mitted variance. In fact, from Vars, we can calculate the parametric
i51 j51 statistics. The basic idea is if there is a level change out of range, it
offers the inverse of the curve. The curve evolves internally instead
Xij: the pixel is in the iem row and column jem. of the convergence towards the outer neighbor pixels.
During evolution, all forms represented by the curves can be defined 2bmax i bi bmax i ; i5 1 . . . t (18)
by:
The final outline, describing the shape of the target object, must
fx; y=/x; y; t50g (15) belong to this space. In the localization process, the evolution of the
initial curve (which is usually the average shape) is done through a
With this implicit representation, this model provides an opportunity strategy using local intensity of the image. This development can be
to change the topology, and thus the detection of multiple contours done in the space of predefined authorized deformations.
from a single initial curve. However, the numerical implementation The ASM tenders ability to integrate a strong knowledge very
of the 1 level function is very time-consuming. Indeed, the evalua- effectively prior shape on the structures of interest. It is based on sta-
tion of 1 involves estimating local features (normal curvature) at tistical models of shape structures designed to guide the segmenta-
any point of the image. Several other similar models, using an tion step. This reduces solutions space and always lead to correct
implicit representation of the curve and adopting geometric con- forms (Andreopoulos et al., 2008; Aymeric et al., 2005; Babalola et
straints for evolution have been proposed. This implicit representa- al., 2009; Bascle et al., 1994).
tion explains all the success of this class of geometric models. B.4. Fusion of the Two Models. In the learning step, we used
Indeed, the theoretical results have shown the existence and the the principle of the Statistical model; we used n patterns and we
uniqueness of the solution, which depends on few parameters. determined the average shape and the average position. In addition,
we calculated the two confidence intervals to integrate the priori Body We launch the initial curve.
knowledge. For each iteration, calculating the surface and the variation:
For the evolution of the curve, we used the principle of the geo- If the surface is higher than the upper limit of the interval:
metric model: evolution of the curve based on neighbored pixels.
Inverse the changing curvature. (To ensure that the outline
We combined the two models, the geometric and the statistical to
does not converge to other areas that appear to be consistent
integrate the priori knowledge to the geometric model, and therefore,
the segmentation method will be automatic. The objective of the two with the area studied) and stop the evolution of the curve.
models fusion is to improve the segmentation quality. The curve can If the surface is in the range of trust:
converge towards other homogeneous areas with the studied area.
Integrating the priori knowledge of the surface, we can improve the The daily evolution is kept.
limit. The curve can converge towards other inhomogeneous areas If the variation exceeds the upper range of the confidence
with the studied area via integrating the priori knowledge of the vari- interval:
ation. We can improve the limit of the segmentation.
Basic algorithm Once the learning phase is done, we get two con- A reverse development is provided, the curve changes internal-
fidence intervals: For each iteration, we extract the area studied (Hip- ly instead of converging toward the outer neighbor pixels.
pocampus or the Corpus Callosum, CC) from contour. Then, we Output We find the final curve and we extract the correct area.
calculate the surface. If the surface is included in the interval, we fol-
low the daily evolution, otherwise if the surface exceeds the upper
IV. EXPERIMENTAL RESULTS
bound, the evolution stops. We calculate the variation of the studied
area. If the variation exceeds the upper limit, the daily changes are We are interested to extract the two areas: Hippocampus and Corpus
reversed, so the curve evolves internally instead of converging Callusm. We used three subjects: normal, suffering from Alz-
toward the outer neighbor pixels. heimers disease in the early stage and another in an advanced stage.
Using the constraint of the variation to improve the limit by the We used the two sections frontal and sagittal for any subjects. We
figures below: the contour may include the hippocampus more areas segmented the hippocampus of the three subjects by four methods:
surrounding it and that are not homogeneous with the desired area. parametric model (snake; Charmi et al., 2008), static model (ASM;
Through the confidence interval of variation and a priori knowledge, Cootes and Taylor, 1994), geometric model (Level Set; Caselles
these limitations can be overcome (Fig. 2). et al., 1997) and the fourth method is our proposed method Modify
The constraint of the surface is used to improve the limit by the Level set which is a combination between the static and geometric
figures below: the contour may include the hippocampus more areas models. We show the results in the figure below (Fig. 4).
surrounding it and that are homogeneous with the desired area. Using our method Modify Level Set, we can calculate some fea-
Through the surface of confidence interval and a priori knowledge, tures of geometries such as surface, perimeter, and standard devia-
these limitations can be overcome (Fig. 3). tion. We present in the table below the measurement of the features
The algorithm in below presents the principle of our method: for the two parts of hippocampus (Tables I and II).
Input After the step of the training:
A.1. EXTRACTION OF THE CC
We determine the two confidence intervals of the Surface and We segmented the CC of the three subjects by four methods (Fig. 5).
the variation. In reviewing the results: for lines 3, 4, and 5, we note that the
We determine the average shape and the initial curve. curve migrates to similar intensity regions and sometimes not. For
Hippocampus L Hippocampus R
Surface Perimeter Standard Deviation Surface Perimeter Standard Deviation
Subject 1 1039 174.61 7 1425 170 8.3
Subject 2 1019 166 14 1267 160 17
Subject 3 902 155 17 1111 151 18.7
Figure 5. Results segmentation corpus callosum. The six lines present in order: initial image, image manually segmented, the result using the
snake method (parametric model), the result using the ASM method (statistical model), the result using the method Level Set (geometric model),
the result using the Modify Level Set method (geometric model 1 Statistics). Column 1 shows a normal subject, column 2 about Alzheimer (primary
stage) and the third column corresponds to an Alzheimers subject (advanced stage). [Color figure can be viewed at wileyonlinelibrary.com]