2010 3rd International Congress on Image and Signal Processing (CISP2010)
A Novel Automatic Liver Segmentation Technique
for MR Images
Zhaoxiao Yuan, Yongtian Wang, Jian Yang, Yue Liu
School of Optoelectronics
Beijing Institute of Technology
Beijing, P. R. China
Abstract—This paper presents an automatic liver segmentation
algorithm based on fast marching and improved fuzzy cluster
methods, which can segment liver from abdominal MR images
accurately. The developed method is composed of three major
steps: first, fast marching method and convex hull algorithm are
applied to roughly extract the liver’s boundary and topology,
which provides a basic estimation for the subsequent
calculations; second, an improved fuzzy cluster method,
combining with a multiple cycles processing, is designed to refine
the segmentation result; third, based on the segmented results,
the liver is visualized by Marching Cube method. There are two
major difficulties in MRIs liver segmentation: one is that the
boundaries between liver and adjacent tissues generally have
uniform intensity distributions, which often leads to over
segmentation of the liver; the other is that inner vascular inside
the liver commonly leads to segmentation leakage. In order to
solve these two problems, a prior knowledge based fuzzy cluster
method is proposed. Experiments show that the developed
method is effective and robust for liver segmentation of MR
images.
Keywords- liver segmentation; fast marching; fuzzy cluster;
matching cube
I. INTRODUCTION
Liver disease is one of the most common diseases around
world, which seriously affects the health of human being [1]. In
recent years, as medical imaging technology has developed
profoundly and rapidly, digital image, especially computed
tomography (CT) and magnetic resonance imaging (MRI), has
been widely applied in liver disease diagnosis, liver surgical
planning system and so on. In these applications, the critical
step is to segment liver from digital images accurately and
automatically. Unfortunately, this is a challenging task,
especially in MRIs, because, besides liver, there are various
organs and tissues share the similar intensity distribution,
which make the traditional algorithm based on unitary intensity
impotent to handle this problem. Furthermore, abdominal MRIs
generally have more artifacts affected and a lower gradient
response than CT. In the medical diagnosis, because MRIs
shows the detail information of liver internal structures and
there is no radiation during the process of scan, it holds an
irreplaceable place. As yet, many researchers have developed
various segmentation methods to extract liver in CT images [2-
8]. However, only few of them focus on liver segmentation in
MR images. Sebastian and Gu [9] employed a distance vector
978-1-4244-6516-3/10/$26.00 ©2010 IEEE
transform combining with Fast Marching Method (FMM),
Level Set Method (LSM) to segment liver in MRI in 2005. The
main drawback of this method is that it has not give a satisfying
solution to the leakage and over-segmentation problems. Kan
Cheng et al. [10] proposes statistical methods to get prior
shape, and then introduce LSM and Chan-Vese’s model (CV)
to overcome leakage and over-segmentation. But when the
shape of liver changed due to diseases, the segmentation result
will be affected seriously. Gang Chen et al. [11] adopt a
multiple-initialization and multiple-step LSM method, which
will occur over- and under- segmentation problem on lower
sharp corner regions, and the number of initializations are
difficult to determine.
Analysing the characteristics of MRIs, it is easy to find that
there are two major difficulties for liver segmentation in MR
images: first, the boundaries between liver and adjacent tissues
generally share the uniform intensity distributions, which often
lead to over segmentation of the liver; second, inner vascular
inside the liver commonly leads to segmentation leakage. In
order to solve the mentioned two problems, in this paper, a
prior knowledge based on fuzzy cluster method is proposed.
The explicit description of this method is described in Section
2, which contains three parts. In section 3, the method has been
verified and discussed by presenting and analysing the
segmentation result. Finally, section 4 summarizes this new
method and point out pursuits.
II. THE METHODOLOGY
As mentioned before, liver segmentation from MR images
always suffers the problem of over-segmentation and leakage.
Generally, the main reason of this problem is that abdominal
MRIs have more artifacts affected and a low gradient response,
which cause the contour of liver non-distinct. To handle this
problem, this paper develops a new algorithm combined with
FMM and an improved fuzzy cluster method, which consider
both the structure and intensity factors of liver in MRIs.
A. Overview
Fig. 1 illustrates the overview of the proposed method. It
contains three major steps. The first step is to roughly obtain
the liver’s location and topology by fast marching method,
which provides a primary estimation for the subsequent
calculations. This step also introduces the Convex Hull (CH)
algorithm to smooth the result of FMM. In this step, parallel
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propagation is implemented to complete the algorithm. Second, Similar with the level set method, the fast marching also
an improved fuzzy cluster method, supported by multiple employed an implicit representation for an evolving interface.
cycles processing method, is designed to refine the However, to reduce the calculated quantity, ø contains much
segmentation result. Third, based on the segmented results, the more information. Relatively, the interface at time t is defined
liver is visualized by Marching Cube method. The following as
section describes these three steps in detail. Γ( t ) ={x:φ ( x )= t} , (3)
B. Rough segmentation and embedding function is defined as
This section consists of two parts: rough segmentation by F || ∇φ ||= 1 . (4)
fast marching method and smoothing technique by convex hull
algorithm. Fast marching method was introduced by Sethian Fast marching method uses numerical flux functions to
[12] to increase the computational speed of level set, which discretize the equation above. Additionally, in this case, only
was introduced by Osher and Sethian [13] for capturing one-side differences may be use. So the equation can be
moving fronts. Just as level set, fast marching method is a rewritten as
numerical technique with the idea of interface evolution. It can
handle the problem of changed and complex topologies by Fij2 (( D− xφij )2 + ( D− xφij )2 )=1 , (5)
evolving the interface Γ without having to parameterize the
structure before computation. Considering the advantages, D φ =(φ −φ ) Δx D+ yφij =(φi , j +1−φi , j ) Δy
where − x ij ij i −1, j and . This
here, we employed fast marching method to get the primary equation can be delineated as
structure of liver as a reference for advanced segmentation.
2 2
Essentially, the main idea of level set method is to present 1 1 φi −1, j φi , j +1 φi −1, j φi , j +1 1
( + )φij2 − 2( + )+ + − =0 , (6)
the interface as the zero level set of a higher dimensional Δx 2 Δy 2 Δx2 Δy 2 Δx 2 Δy 2 F
function, such as the signed distance to the interface [14]. The
evolution equation of the level set function is defined as where suppose øi,j-1 and øi+1,j are already determined, while øi,j
is unknow. The speed function, which controls the stop
∂φ ∂t + F || ∇φ ||= 0 , (1) position of evolving process, is defined as follow
where ø is the embedding function and F is the speed function. F ( x , y )=exp( −α |∇Gσ ×I ( x , y )|) , (7)
Through this equation, the motion of the interface Γ(t) is
captured at any time t, which can be presented as follow where α is the gradient constant and Gσ is a Gaussian
convolution filter of standard deviation σ. Here, we implement
Γ ( t ) = {x : φ ( x,t ) = 0} . (2) the narrow-band concept to reduce the complexity from O(N3)
to O(N2) by updating ø only in a narrow band around the curve.
The counter obtained by fast marching method are usually
unsmooth with serration, as Fig.2(a) showed. To refine the
counter, this paper introduces Convex Hull algorithm [15] to
acquire a relative smooth curve. In mathematics, the convex
hull for a set of points X in a real vector space V is the minimal
convex set containing X. For K points x1, x2,…,xK, the Convex
Hull Hconvex(X) is defined as
H ( X ) = {∑ik=1 αi xi | xi∈X , α ∈ R , α ≥ 0,
convex i i , (8)
k
∑i =1 αi = 1, k = 1, 2, ...}

with the complexity O(nlnn).

Figure 2. The segmentation result of step.

(a) Segmentation result of FMM. (b) Segmentation result of CH.
Figure 1. The overview of the proposed liver segmentation.

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C. Advanced Segmentation Pi, it can be divided into three regions, which is presented by
As shown in Fig. 2, the former algorithm cannot get distance function
satisfactory results, so the further refined calculation is
⎪⎧ D ( x ),if Pi∈(interior of Y∪ Y)
necessary for the liver segmentation. Here we introduce an D=⎨ 1 i , (15)
improved fuzzy cluster method to refine the segmentation ⎪⎩ D2 ( xi ),if Pi∈exterior of Y
result. Clustering is the process of data points into different
where Y is the boundary of the rough segmentation result in
classes, so items with the same property are integrated in a
step 1, and D is a distance function. If the point is inside the
same class. And fuzzy cluster permits data points belong to
captured region and the barycenter of the prior result is defined
more than one cluster with membership grades associated with
as P0 (x0,y0), the distance function D1(x,y) can be defined as
each point to represent the degree belong to the different
clusters. It is often the case that, in the process of fuzzy cluster, D ( x ) = Max ( d ) − d , (16)
the regional characteristics of the data points have been 1 i i0 i0
ignored, which cause the segmentation result devoid of where di0 is the distance between the point Pi and the
integrity property, especially in images where the points are barycenter. If the point is outside of the captured region, it
inherently correlated such as medical images. This paper suggests that the membership grade to liver is low. The further
introduce a improved fuzzy c-means clustering method (FCM) it away from the captured region, the lower the grade is. And
which not only consider the intrinsic value of a single data considering the inaccurate of the former segmentation, the
points, but also take the region information as previous points near the captured boundaries have high uncertainty.
knowledge into account. Considering these properties of points, it requires an S-type
FCM, developed by Bezdek [16], is introduced to classify curve to describe the relationship of distance and
the images into parts, complete a primary geometric belongingness. So D2 is defined as
segmentation. In fuzzy cluster, namely a partition of a set of n
objects into K mutually exclusive clusters, the state of cluster is D ( x ) = − M (1+e− di 0 ) , (17)
2 i
expressed by a n×K matrix U, which is defined as
where M is the upper limit of this function. Here we define a
⎡u11 u1k ⎤ ratio as
⎢ ⎥
U =⎢ ⎥, (9) pi =1− sigmoid ( D ( xi )) , (18)
⎢u uik ⎥⎦
⎣ i1
sigmoid ( x )= M (1−exp( − x ))/(1+ exp( x )) , (19)
where uik represents the membership grade of the i-th object to
the k-th cluster, which must satisfy the following conditions and pi can be normalized as
∑ kK=1uik =1,i =1,2,…,n ; (10) pi '= pi ∑in=1 pi , (20)

uik ∈[0,1],i =1,2,…, n;k =1,2,…, K . (11) So Jm can be rewritten as

The target function of FCM is defined as
2
J = ∑ kK=1 ∑in=1(uik )m ||βi − xk || = ∑ kK=1 ∑in=1(uik )m D ( xi , β k ) ,
m As a common knowledge, MR images offer a wide range of
= ∑ kK=1 ∑in=1(uik )m dik 2 ,i < m≤∞
where m is weighting exponent controlling the fuzziness, D(·)
is a distance metric between the data vector xk and the
prototype vector βi, and dik denotes D(·). The aim of FCM is to
find minimized Jm by optimized a pair of (uik*, βi*). uik* and βi*
can be calculated by
* multiple cycles processing employed Gaussian filter with
* = 1 K ( dik )1 ( m −1) ,1≤i≤ K ;1≤k ≤n; ,
uik ∑ j =1
*
dij
βi* =∑ nk =1(uik
* )m x k * m
∑ nk =1(uik ) ,1≤i ≤ K .
The result of the first step have already roughly indicated
the location of liver in MR images, which can be seen as the
previous knowledge in fuzzy cluster method, for it contains the
information about structure and topology. Let Pi define an
arbitrary points in image I, which can be presented in Cartesian
coordinate system as (xi,yi). According to the position of point
2
J m = ∑ kK=1∑in=1 pi '(uik )m ||βi − xk || . (21)
(12)
intensity, which, on one hand, represent more details of
structures, on the other hand, weaken the integrity of the whole
structure. These details are useful in diagnoses, but seriously
impact the accuracy of segmentation. For example, the inner
vascular inside the liver commonly leads to leakage, for the
method automatically considered the vascular wall as the
boundary of liver. So it is necessary to introduce a method to
decrease these details ensuring the quality of segmentation. The
(13)
multiple parameters to keep a balance between detail and
integer, where the Gaussian filter is defined as
(14) Gσ =σ ( −1/2) exp( − ( x 2 + y 2 )/4σ ) . (22)
The image after Gaussian filter I’ is defined as
I '( x , y ) =∇Gσ ∗I0 ( x , y ) . (23)
σ is a variable parameter, which is defined as
σ =ΔSi ,i +1 αΔSi −1,i , (24)

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where ∆Si,i+1 is the area difference between the i-th and (i+1)-th
segmentation result. The initial Gaussian σ is the largest one,
which ensures every pixel related with more points to reduce
the detail of MR image. The stop condition of this multiple
cycles processing is ∆σ<ε. At last, this paper introduces
erosion, dilation and gauss smooth as post treatment to refine
the result.

D. Visualization
Visualization has already played an important role in
medical diagnostics, which illustrate the patient’s condition and
pathology clearly and directly. This section employed a
surface-oriented visualization method—Marching Cubes to
illustrate the structure of liver. Marching cubes is published by
Figure 3. Other experiment results.
Lorensen and Cline [17] in 1987. The basic principle of
marching cubes is to subdivide the 2D or 3D space into small (a) Result of MR images. (b) Result of CT (the left column shows the original
cubes, and each cube matches to a precalculated array of 28 slice and reference results given by experts, the middle column shows the
result of FMM, and the right column shows the final result).
polygon configurations replacing the original cubes with
regular polygons. Considering reflections and rotations, it can
be summarized to 15 types of unique cases [18]. In this paper, A. Volumetric Overlap Error (VOE)
the segmentation result is treated as a volumetric data. Volumetric Overlap Error is defined as

III. EXPERIMENTS 100(1−( I seg ∩ I std ) ( I seg ∩ I std )) , (25)

The proposed segmentation method has been applied to
series of abdominal MR images with size of 512×512×48,
which are obtained from Chinese PLA General Hospital,
Beijing. The relevant parameters of the images are as follow:
slice thickness 5.0 mm, repetition time 4.456, echo time 2.16,
magnetic field strength 15000, and flip angle 12º.
Fig. 3(a) shows the segmentation’s results of MRI, in which
the data is from a patient with liver atrophy. The boundary of
FMM, shown in the middle column, is obviously blurry and
incorrect. And the right column of Fig. 3(a) shows the result of
the new method, which modifies and optimizes the original
result of FMM successfully. In order to verify the effectiveness
and robustness of the developed method, as presented in
Fig.3(b), it has also been applied to CT. Comparatively, CT has
a narrow range of intensity and high intensity response, which
in some degree decreases the fault rate, even under the original
fast marching method. However, the boundary is still serrate
and inaccurate, as shown in the middle column of Fig. 3(b).
The segmentation result of the developed method, shown in the
right column of Fig. 3(b), has greatly improved. Fig. 4 shows
the volume structure of liver in 3D space.
To evaluate the quality of segmentation result given by the
new method, this paper employs the empirical discrepancy
approach with three error measures introduced in [19]. The
automatic extracted boundaries are compared with reference
results generated by expert manually labeled in the original MR
images by white line in Fig. 3. Let Iseg represents the set of
voxels of segmentation result, and Istd represents the set of
voxels of reference result. And the result is shown in Table I.
which represents the ratio between intersection and union of
the segmentation result and standard data. The result is close to
0 if these two data are similar, and 100 if they are completely
different.
B. Relative Volume Difference (RVD)
The RVD between the segmentation result Iseg and
reference standard Istd given by expert is expressed as
100(|I seg − I std | I std ) . (26)
Different from VOE, the relative volume difference does not
directly represent that Istd and Iseg are identical or overlap, but to
reveal the trend to over-segmentation or leakage by combining
with other critical standard.
C. Root Mean Square Symmetric Surface Distance
(RMSSSD)
Root mean square symmetric surface distance, expressed as
follow, is a judge criterion based on surface distances,
RMSSSD ( I ,I ) = 1 |S ( I seg ) + S ( I std )|
seg std
(27)
× ∑ S ∈S ( I d 2 ( S seg , S ( I seg ))+ ∑ S ∈S ( I ) d 2 ( S std , S ( I std ))
seg seg ) std std
where S(·) is the set of surface voxels, and d(·,·) is defined as
the minimized Euclidean distance from sseg to the volume
surface. If the segmentation result is identical to the reference
model, then RMSSSD tends to 0. Constructively, if they are not
matched precisely, the punish value will be greater.

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Figure 4. Liver visualization in 3D space.
TABLE I. PERFORMANCE METRICS (%) OF THE PROPOSED LIVER
SEGMENTATION
VOE RVD RMSSSD
Data 1 6.7 3.9 2.3
Data 2 6.8 3.8 2.1
Data 3 7.0 4.3 3.1
Table I shows the segmentation performance evaluation
results of the three data sets presented before. It can be
observed that the results of developed method are close to the
reference boundaries given by experts. As mentioned before,
data 1 and 2 are captured from patients with liver atrophy. This
verified that the developed method can been applied on both
normal and atrophic livers. Moreover, the performance score of
data 3 presents that the method can also be applied on CT.
IV. CONCLUSIONS
This paper introduces an automatic liver segmentation
method which can segment liver from MR images, even if the
liver is atrophic with unconventional structure. It is based on an
improved multiple cycles fuzzy cluster algorithm, which
classes items according to intensity and prior knowledge. The
effectiveness of this method has already been testified by series
of 3D abdominal MR images, where the results show that the
developed method has the potential to segment liver
parenchyma accurately from 3D medical images with low
gradient responses on the boundaries. The problem of over-
segmentation and leakage has, in some degree, been solved.
Furthermore, it can also be applied on CT, which broadens the
application scope of the developed method.
In the future, we will make further effort on accelerating the
speed of the whole algorithm with parallel computation, and
also we will focus on increasing the robustness of the method
to make it adapt to multiple modalities.
ACKNOWLEDGMENT
The authors would like to thank Dr. Tong Lu of the PLA
Hospital, Beijing for providing the data sets used in the
experiments. This work was supported in part by the National
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Basic Research Program of China (2010CB732505), in part by
National Science Foundation Program of China (60902103)
and in part by the Innovation Team Development Program of
the Chinese Ministry of Education (IRT0606).
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