Hippocampal Segmentation using Mean Shift Algorithm

Guadalupe Desiree Lopez Palafoxa ,Ana Luisa Sosa Ortzb , Oscar Marrufo Melendezc , Orlando
Morales Ballesterosc , Jorge Luis Perez Gonzaleza and Juan Ramon Jimenez Alaniz a
a Neuroimaging
Laboratory, Electrical Engineering Department
Universidad Autonoma Metropolitana Iztapalapa, Mexico City
b Dementia Laboratory, National Institute of Neurology and Neurosurgery, M
exico City
c Neuroimage Department, National Institute of Neurology and Neurosurgery, Mexico City
ABSTRACT
The population is aging as the years pass. There is an increase in life expectancy, but also a decrease in the
quality of life for the presence of chronic degenerative diseases. Processing medical images can identify brain
changes typical of Alzheimers disease (AD) and Mild Cognitive Impairment (MCI) at an early stage. We
propose a new method of segmentation technique using Mean Shift algorithm applying probabilistic maps and
Support Vector Machine with Linear and Radial Basis Kernel for segmentation of the hippocampus on Magnetic
Resonance Images (MRI). The similarity index of DICE for a 8 control subject was calculated obtaining a mean
value of 0.7053 0.0996 using Linear kernel and 0.7275 0.1335 using RBF kernel compared with the manual
segmentation made by radiologist.
Keywords: Hippocampus, Image segmentation, Mean Shift, Support Vector Machine.

1. INTRODUCTION
In the last century, the elderly population has been increasing so fast with profound economic, political and
social consequences. Alzheimers Disease International reports in 2015 that are almost 900 million people aged
60 years and over living worldwide. Rising life expectancy is contributing to rapid increases in this number, and
is associated with increased prevalence of chronic diseases like dementia. Between 2015 and 2050, the number
of older people living in higher income countries is forecast to increase by 56%, compared with 138% in upper
middle income countries, 185% in lower middle income countries, and by 239% (a more than threefold increase)
in low income countries.1 The dementia is a clinical syndrome caused by different disorders that affect cerebral
structures and functions, progressive deterioration of memory, and capacity for independent living2 .1 Dementia
can be a devastating disorder for those who experience it, for their caregivers, their families and society as a
whole, thats why this disorder presents many challenges to health professionals throughout the pathway of care,
from early diagnosis to end of life. The main causes of dementia in older people include Alzheimers Disease
(AD), vascular cognitive impairment (VCI), vascular dementia (VaD) and dementia with Lewy bodies (DLB).3

Alzheimers Disease is a neurodegenerative disorder, which is the most common type of dementia, causing
confusion, memory decline, and loss of cognitive function (Computer-aided classification). It is the most common
cause of dementia and accounts for 50%-75% of all cases with more than 35 million people all over the world.1
Initially the disease affects an individual capability to develop new memories but gradually other complications,
like memory loss, orientation problems, poor judgment, inability to carry out routine tasks, and withdrawal from
social activities.4 Clinical diagnosis of AD is based on a history of progressive and characteristic cognitive decline
and the presence of objective cognitive deficits, includes test like clinical dementia rate (CDR) and minimental
state examination (MMSE). Several neuroimaging techniques have been developed over the past decade, to help
understand the pathophysiology of complex neurological disorders and to provide us with biological indicators
for early diagnosis and response to treatment.5

The Magnetic Resonance Imaging (MRI) has become one of the most used tool for diagnose AD, allows
quantitative estimation of the brain atrophy and identify characteristic patterns of cerebral alterations. The
morphological analysis of the hippocampus has shown that is highly related with disease progress. The atrophy

12th International Symposium on Medical Information Processing and Analysis, edited by Eduardo Romero,
Natasha Lepore, Jorge Brieva, Ignacio Larrabide, Proc. of SPIE Vol. 10160, 101600D
2017 SPIE CCC code: 0277-786X/17/$18 doi: 10.1117/12.2256810

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 of this region is the first observable characteristic for diagnosis of AD or Mild Cognitive Impairment (MCI)6
however, the segmentation and identification of this region is a qualitative analysis that depends completely on
the experience of the radiologist, also the segmentation in MRI of the hippocampus can take up to two hours
and there is a high intra-operator and inter-operatator variability.7 Automated methods that can reduce the
subjectivity and increase segmentation accuracy, are highly desirable. Atrophy of the hippocampus has also
been related to several other diseases, however this measurement has not been validated how a clinical biomarker
yet. Most algorithms for the segmentation of the hippocampus have used atlas-based and deformable models
techniques. These techniques only may constitute hippocampus segmentation methods, but they are normally
used together and complement one another; alternatively, they are complemented by other techniques such as
classifiers and optimizers, and even basic segmentation techniques such as thresholding.7

MRI segmentation is important in image processing to identify anatomical areas of interest, for this task has
been used the supervised approaches, where intensity values of labeled voxel samples from each tissue must be
provided during the learning phase. In a subsequent classification phase, the unlabeled voxels are classified using
a selected classifier. A clustering technique which does not requires prior information of the numbers of clusters,
and does not restricts their shape of the density distribution is the Mean Shift (MS) procedure. This method
is an iterative technique which estimates the modes of the multivariate distribution of the feature space; the
number of cluster is obtained automatically by finding the centers of the densest regions in the space.8
In order to segment the hippocampus brain structure in a set of MRI studies of healthy subjects, in this
paper we present an algorithm based on a optimal probabilistic atlas together with Mean Shift, Textures and
Support Vector Machine (SVM) methods. Finally our results was contrasted with the manual segmentation by
an expert in neurology. This procedure will be explained in detail in the following sections.

2. MATERIALS AND METHODS

In this section we present the methodology beginning with an extensive explanation of Mean Shift algorithm
which propose is estimate the modes of the multivariate distribution underlying the feature space in order to
attenuate the intensity variations of inhomogeneity regions in MR images. Subsequently the feature extractions
and hippocampus classification based on Support Vector Machine approach are explained.

2.1 Mean Shift Algorithm

The multivariate kernel density estimation with kernel K and window width h is defined by
n
1 X1
f(x) = K (x Xi ) (1)
nhd i=1 h

The kernel function K(x) is a function defined for d-dimensional vectors Xi, i = 1, ..., n that are the given
multivariate data set whose underlying density f is unknown and must be estimated. The kernel is taken to be a
radially symmetric, non-negative function, centered at zero and integrating to one, an example, the multivariate
Epanechnikov that is an optimal kernel for minimize the error at the density estimation function and it is obtained
what is know as mean shift (MS):

1 X
Mh (x) = (Xi x) (2)
nx
Xi Sh (x)

where the size of the region Sh (x) is a function of the bandwidth h and nx is the number of observations Xi
falling within Sh (x).
For multivariate data, a correct choice of bandwidth is a very complex problem. One of the most used method
for local bandwidth adaptation, consider the bandwidth proportional to the inverse of the square root as a first

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 approximation of the local density. The bandwidth h can be varied on each data point h = h(Xi ). For each
point Xi , can be obtained the sample point of density estimator:8
n  
1X 1 x Xi
fsp (x) = K (3)
n i=1 h(Xi )d h(Xi )

And h(Xi ) can be estimated by:

  12

h(Xi ) = h0 (4)
f (Xi )
where h0 represents the fixed bandwidth and is a proportional constant.

2.2 Texture Features

Texture analysis refers to the branch of imaging science that is concerned with the description of characteristic
image properties by textural features. The three principal approaches used in image processing to describe the
texture of a region are statistical, structural and spectral. The texture features provide unique information on the
texture, or spatial variation of pixel, of the region where are applied. Statistical approaches yield characterization
of textures as smooth, coarse and grainy. Structural techniques deal with the arrangement of image primitives,
such as the description of texture based regularly spaced parallel lines. Spectral techniques are based on properties
of the Fourier spectrum.9 One statistical approach in texture description is the variance where P is patched of
dimension (n, m) and is calculated by:

n X
X m
V ariance = Pi,j (i i )2 (5)
i=0 j=0

where i is the mean and the Standard Deviation is the square of the variance.
The entropy and range is defined by

n X
X m
Entropy = Q(i, j)logQ(i, j) (6)
i=1 j=1

n X
X m
Range = max[P (i, j)] min[P (i, j)] (7)
i=1 j=1

These texture features were calculated from the results obtained of the Mean Shift procedure.

2.3 Support Vector Machine Classification

The Support Vector Machine (SVM) is a supervised learning method that can be used for classification.These
classifiers are linear and attempt to maximize the margin between classes.10 SVM treats the measurements from
a given individual as a single point in a multidimensional space, with the number of dimensions being, in our
application, the number of vertices for the right hippocampus. The classification with SVM, uses a kernel based
supervised learning technique that, when given n training data points x and the corresponding class labels y, then
finds the maximum margin hyperplane separating the two classes by solving a convex optimization problem.11
The purpose is to build a linear discriminant f (x) = w(x) + w0 that classify correctly the data, w is the weights
vector, orthogonal to the decision plane, w0 is the threshold, and (x) is a nonlinear transformation that maps
the input data into a new feature space.12 We used the Mean Shift results to calculated all of the texture propose
and used it as features for the SVM with the template of the hippocampus from LONI.

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 2.4 Data Set and Validation
Data sets for these work were obtained from Alzheimers Disease Neuroimaging Initiative (ADNI) database
(http://adni.loni.usc.edu/). The ADNI was launched in 2003 by the National Institute on Aging (NIA), the Na-
tional Institute of Biomedical Imaging and Bioengineering (NIBIB), the Food and Drug Administration (FDA),
private pharmaceutical companies and non-profit organizations, as one $60 million, 5-year publicprivate part-
nership. The primary goal of ADNI has been to test whether serial magnetic resonance imaging (MRI), positron
emission tomography (PET), other biological markers, and clinical and neuropsychological assessment can be
combined to measure the progression of mild cognitive impairment (MCI) and early Alzheimers Disease (AD).
Determination of sensitive and specific markers of very early AD progression is intended to aid researchers and
clinicians to develop new treatments and monitor their effectiveness, as well as lessen the time and cost of clinical
trials. We used 8 subjects between 60 and 65 years old (4 females and 4 males); all control subjects had MMSE
scores between 24 and 30 (inclusive), a CDR (Clinical Dementia Rating) of zero.
All data were collected on a Skyra 3T scanner (Siemens, Erlangen, Germany) and 64-Ch head coil, using
the sequence T1-weighted magnetization-prepared rapid gradient echo (MPRAGE), transverse images were also
collected for each subject with the following parameters: TR=16.805 ms, TE = 3.16 ms, FA = 9, matrix = 256
x 256, slices = 176, thickness = 1.0 mm and voxel size = 1 x 1 x 1 mm3 . All the processing was made in a Mac
OSX with Matlab R2015a
The propose approach consist in four phases: preprocessing, feature extraction, classification and analysis.
The first phase is a preprocessing and was executed a skull stripping and the spatial normalization of the brain
template T1 of LONI LPBA40, this atlas will have the same dimension of the control subjects, we used Statistical
Parametric Mapping software for this step (http://www.fil.ion.ucl.ac.uk/spm/). We asked a radiologist to make
the manual segmentation of the right hippocampus, this was made in the OSIRIX software.13 The second phase
used was the Mean Shift procedure,8 the results of this part were used to calculate the Range, Variance and
Entropy Textures because the inhomongenity of the image disappear from the MRI. We used the inverse matrix
from the normalization to transform the LPBA40 template of the hippocampus to the same space of the data.
The third phase was worked using SVM with two kernels Linear and RBF(Radial Basis Function) using Matlab-
LIBSVM 3.2 for the implementation. The optimal parameter values of the RBF kernel were determined using
a grid-search and leave-one-out cross validation (LOOCV) on the training set and the values are C = 3.5 and
= 0.06. For reduce the time of processing we made a window analysis taking into account the maximum size
of the window manual segmentation. The classifier was trained with 7 subjects and the classification with one
subject and we made a leave-one out cross validation. During the last phase we calculate the Dice index and
accuracy from each volume. The Dice index measures the overlap coefficient between the two different segmented
volumes, and is calculated as follows:
T
|A B|
Dice = 2 (8)
|A| + |B|

A is the region segmented by the SVM method and B is the region obtained by manual segmentation from
the expert. When no pixel is common to both regions, the Dice is 0. When all the pixels of both regions are
common, the DSC is 1. In the Figure 1 is summarized the process.

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 Manual Segmentation
Processing
Mean Shift
Mode Class

Preprocessing
Skull Stripping
Texture Analysis Phase 3
Entropy Range

Classification
(
Supported Vector Machine
Std

Normalization
J

110 Hippocampus Template

Validation

Phase 1
7 J
Dice Index

Phase 2 Phase 4

Figure 1: Detail of the proposed approach. The approach is divided in four phases: Phase 1 is the image
preprocessing, Phase 2 is the processing of the image that includes Mean Shift procedure, Texture Features
and Hippocampus template, Phase 3 is the classification that use the results of the Phase 2 and Phase 4 is the
validation of the propose approach.

3. RESULTS AND DISCUSSION

In this section the results of the approach along with a validation of segmentation and classification methods
are presented. Qualitative results can be observed in Figure 2; on the right side (Figure 2b) an example of the
segmentation of the hippocampus made by an expert in axial section is shown. On the other hand, in Figure 2a
the result of automatic segmentation of the hippocampus in the same plane is shown. Qualitatively it can be
noted that the automatic results are acceptable compared with manual segmentation.

(a) (b)
Figure 2: Segmentation of the right hippocampus for the same slice. a) Automatic segmentation by SVM b)
Manual segmentation by an expert

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 Moreover, a quantitative evaluation of the results is obtained by calculating the index rate DICE between
SVM classification and manual segmentation. Table 1 shows the results of this quantitative evaluation. In
columns 2 and 3 the results of DICE index are observed for the automatic method vs manual segmentation;
column 2 corresponds to the results obtained by linear kernel SVM (0.7053 0.0996) and column 3 the results
obtained by RBF kernel SVM (0.7275 0.1335). We observed that the RBF has substantially best results
compared with the linear kernel. This is believed to be due to the nonlinear characteristics of used distribution.
We observed that the RBF has best results compared with the linear kernel.
Others authors report similar index values of the hippocampus segmentation using probabilistic atlas; Kwak14
reported a Dice index of 0.72 0.04, Tong15 reported a Dice index of 0.88 and Platero16 reported a Dice index
of 0.76 0.05 from different databases and segmentation methods. These authors used a probabilistic map to
perform their segmentation of the hippocampus. However, our method has an advantage because few features
for classification are used and we believe that can be easily extrapolated for segmentation of the olfactory bulb,
brain structure that is essential in the evaluation and monitoring of Alzheimers Disease.

Table 1: Dice Index evaluation

Subject Dice with Linear Kernel Dice with RBF Kernel

1 0.8286 0.9406
2 0.5149 0.5013
3 0.6472 0.6189
4 0.7800 0.8034
5 0.6408 0.6577
6 0.7557 0.7837
7 0.7483 0.7786
8 0.7266 0.7357

4. CONCLUSIONS
In this paper is presented a new algorithm for hippocampus segmentation on MR images. The proposed method
begins by incorporating the mean shift algorithm for the purpose of homogenize the variations of intensity caused
by the inhomogeneity of the field. Subsequently, a classification step is carried out using, mean shift, probabilistic
atlas, texture, and intensity information accompanied by a pattern recognition strategy based on SVM. The
results show that the proposed method is competitive compared with other targeting methods reported in the
literature, however we believe that this method can be easily extrapolated to the segmentation of the olfactory
bulb, essential for monitoring, evaluation and diagnosis of Alzheimers Disease.
In the future work, the proposed method will be used for the segmentation of the olfactory bulb in patients
with Alzheimers Disease, Mild Cognitive Impairment and Control subject from the National Institute of Neu-
rology and Neurosurgery and subsequent comparison of the differences between the volumes of the hippocampus
and the olfactory bulb.

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