MR brain image segmentation by growing

hierarchical SOM and probability clustering

(BMU) for the input vector xi are adjacent units [5]:
te =

A. Ortiz, J.M. Gorriz, J. Ramrez and D. Salas-Gonzalez

Introduction: Magnetic resonance imaging (MRI) provides valuable

clinical information regarding tissue distribution on the brain for diagnosing brain disorders such as schizophrenia or Alzheimers disease.
Segmentation consists in partitioning an image into its constituent
parts. Thus, segmentation of a brain MRI provides different regions corresponding to different tissues. Then, having separated the different
regions, it is possible to perform a quantitative evaluation of the distribution of the tissues on the brain. However, the difference among the
amount of pixels corresponding to each tissue makes the segmentation
process difcult to be accurate. On the other hand, the evaluation of
the different tissues found on a brain MRI is usually done through
visual ratings performed by experts and other subjective steps, which
are time consuming and prone to error.
A fully computer-aided segmentation system for the automatic segmentation of brain magnetic resonance (MR) images is presented in
this Letter. Hence, the segmentation process has been split into two
phases. The rst step consists in extracting the more discriminant features from the MRI in order to maximise the classier performance.
The second phase uses a classier to gure out the different tissues
present on the MRI. For the classication task, previous approaches
are based on the intensity values of the whole brain image (histogrambased methods) [1], clustering techniques such as K-means [2] or
classic self-organising maps [3]. In this work we use a classier based
on growing hierarchical self-organising maps (GHSOM). The main
advantage of this classier is the ability to discover the inherent hierarchy of the data. Moreover, we use a probabilistic model over each
map for labelling the neurons. The result is a fully unsupervised segmentation tool which does not need to use any a priori information to
segment brain images.
Feature extraction and selection: In the rst stage, rst order and
second order as well as moment and scale invariants are extracted
from the image using overlapped 2D windows. These features are computed by using the extracted windows as independent 2D images. Then,
the intensity feature corresponds to the central pixel on each window.
Second-order features are computed from the grey level co-occurrence
matrix (GLCM) [4]. Moreover, moment and scale invariants provide
independence with the orientation and the size of an image. Once the
features on each window are calculated, a feature vector is stored and
associated to the central pixel on the window. The features are normalised by subtracting the mean and dividing by the standard deviation in
order to avoid one feature being more important than others for the classier. The resultant matrix comprises the input space of the classier.
Nevertheless, a feature selection stage is necessary in order to supply
the classier with the more discriminant ones. This is accomplished by
multiobjective optimisation, which maximises the goodness of the classier. Let xi = (x1 , x2 , . . . , xn ) be the data vector belonging to the unit
Cj , and xk the kth feature computed. Then, two error measurements
can be performed for an SOM classier. The rst evaluates the
average distance from the input vectors to the prototypes v
 m . This is
the quantisation error and is dened for a map unit m as

v
 m xi 
(1)
qem =
xi [Cj

On the other hand, the topological error for a map with N neurons
measures the topology preservation. This measurement uses the u(xi )
function which is 1 if the rst and the second best matching unit

(2)

Note that making qe and te as low as possible, the classier will perform
better. Then, multiobjective optimisation is accomplished in order to
minimise both measurements at the same time. This is done by composing a tness function as
Fqtp = (0.5 qe + 0.5 te )

(3)

for the BMU path p. This BMU is computed for a map m as

j 
Um (xi ) = arg min xi v

(4)

The BMU path calculation is shown in Fig. 1. Thus, only the features
that result in more discriminants for the classier are stored in a new
feature vector.
1.0
0.9
Tanimoto's performance

A fully automatic tool to assist the segmentation of brain magnetic resonance images (MRI) is presented. Thus, the gured out regions can be
evaluated for the diagnosis of brain disorders. The main problem to be
handled consists in discovering different regions on the image without
using a priori information. The new approach consists in hybridising
multiobjective optimisation for feature selection with a growing hierarchical self-organising map (GHSOM) classier and a probability
clustering method. The segmentation results yield average overlap
metric values of 0.32, 0.75 and 0.69 for white matter, grey matter
and cerebrospinal uid, respectively, over the Internet Brain
Segmentation Repository database. These results mean an improvement over the values reached by other existing techniques.

N
1
u(xi )
N i=1

manual

0.8
0.7
0.6
0.5

WM

0.4

GM

0.3
0.2
0.1
0
RLGHSOM CGMM

marro

tskm

mlc

map

fuzzy

bmap

amap

Fig. 1 Averaged Tanimotos coefcient comparison calculated over set of 20

real brain scans from IBSR repository
Results for grey matter (GM) and white matter (WM)
Manual segmentation results correspond to four brains averaged over two experts

Tissue classication by GHSOM: A GHSOM-based model is used to

classify the computed feature vectors. GHSOM [6] is a hierarchical
SOM model, which has the ability to build an SOM hierarchy. The
depth of the created hierarchy and the breadth of the generated maps
are adapted to the input data to keep the quantisation error of each
map unit below a dened threshold. Moreover, the breadth limit of
each map and the hierarchy depth can be limited by two parameters t1
and t2 , respectively. After the training process, each discovered class
is labelled. However, some map units may remain unlabelled if they
do not correspond to any BMU for the input data (i.e. the GHSOM is
oversized). We can take advantage of this by applying a majorityvoting scheme for labelling the unlabelled units on each map when
new data is presented to the GHSOM. This is accomplished by using
a 2D-Gaussian kernel s centred on the BMU unit u of width 1, dening
the neighbourhood of an unlabelled BMU. Thus, the probability of successfully labelling an unlabelled BMU is dened as
Pl =

Ms(u,1)
(u)
1

(5)

Then, the unlabelled BMU is labelled with the most occurring label
inside the Gaussian kernel. As a result, new clusters are dened on
each hierarchy level.
Experiments: The experiments were performed over the images provided by the Internet Brain Segmentation Repository (IBSR) database
[7]. This database is widely used in the literature for evaluating the segmentation algorithms since it also provides manually segmented
volumes. On the other hand, the results shown in the IBSR website
are referred to the average of 20 coronal brain scans. Initially, the
256 256 64-voxel IBSR brain images are split by using overlapped
windows of 7 7 pixels on each 2D slice. Then, features from each
image slice are extracted and each of the coronal, axial and sagittal
slices are segmented separately. After that, we compute an n m 3
matrix containing the features of the three slices, where n is the
number of extracted windows, and m is the number of features selected
by multiobjective optimisation. Then, the Jaccard/Tanimoto coefcient
[7] averaged over 20 coronal brain scans is calculated. Fig. 1 shows the
average overlap metric (averaged Jaccard/Tanimoto index) obtained by
using our segmentation method with the probability-based labelling for
white matter (WM), grey matter (GM) and cerebrospinal uid (CSF) calculated over a set of 20 real coronal brain scans from the IBSR. Fig. 2
shows the segmentation results guring out the WM, GM and CSF

ELECTRONICS LETTERS 12th May 2011 Vol. 47 No. 10

for coronal, axial and sagittal planes, and the ground truth provided by
the IBSR database. Fig. 2 shows the comparison between an image segmented by our algorithm and the ground truth from the IBSR database
[7].
axial plane, RLGHSOM segmented

coronal plane, RLGHSOM segmented

sagital plane, RLGHSOM segmented

axial plane, ground truth

coronal plane, ground truth

sagital plane, ground truth

Fig. 2 Segmentation example for three planes, coronal, axial and sagittal, of
image 100_23, slice 128, 30, 66 from IBSR database
White segment corresponds to white matter (WM), light grey to grey matter (GM)
and dark grey to cerebrospinal uid (CSF)

average overlap

Fig. 3 provides a comparison among average overlap metric data for

the segmentation algorithms shown on the IBSR website and the results
from our algorithm (RLGHSOM). These results are calculated over the
20 real coronal brain scans. As shown in Fig. 3, our results clearly outperform the results obtained by the algorithms published on the IBSR
web page [7] as well as other algorithms such as CGMM [8], especially
for CSF and GM tissues.
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0

RLGHSOM
CGMM
marro
tskm
mlc
map
fuzzy
CSF

GM

WM

Fig. 3 Average overlap metric calculated over 20 real brain scans from IBSR
repository
Results for CSF (cerebrospinal uid), GM (grey matter) and WM (white matter)
Dashed line corresponds to authors algorithm (RLGHSOM)

Conclusions: A computer-aided segmentation tool for guring out the

three basic tissues on an MRI brain image in an unsupervised way is presented. The system was developed by performing feature extraction and
selection using multiobjective optimisation, which reduces the feature
space. Then, the most important features feed a classier based on

GHSOM, which has the ability to discover hierarchical relationships

among the data. A probability-based labelling model is used over each
map on the GHSOM, which improves the performance of the classier.
As a result, an accurate method for labelling the classier units is
obtained. Thus, our approach reaches 1, 0.32, 0.75 and 0.69 average
overlap metric for background (BCK), WM, GM and CSF, respectively,
for the IBSR database volumes. These values clearly outperform the
results obtained by other segmentation algorithms taken from the
IBSR website. Moreover, the average overlap metric comparison
shown in Fig. 3 makes clear that the segmentation method based on
GHSOM presented in this Letter outperforms the results obtained by
other segmentation, especially for CSF and GM tissues.
Acknowledgments: This work was partly supported by the Spanish
Government under the PETRI DENCLASES (PET2006-0253),
TEC2008-02113, NAPOLEON (TEC2007-68030-C02-01) projects
and the Consejera de Innovacion, Ciencia y Empresa (Junta de
Andaluca, Spain) under the Excellence Project (TIC-02566).
# The Institution of Engineering and Technology 2011
1 February 2011
doi: 10.1049/el.2011.0322
One or more of the Figures in this Letter are available in colour online.
A. Ortiz (Departamento de Ingeniera de Comunicaciones, Universidad
de Malaga, Spain)
E-mail: aortiz@ic.uma.es
J.M. Gorriz, J. Ramrez and D. Salas-Gonzalez (Departamento Teora
de la Senal, Telematica y Comunicaciones, Universidad Granada,
Spain)
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