Professional Documents
Culture Documents
tkdgus13135@snu.ac.kr
sc_.lee@samsung.com
yun@hufs.ac.kr
Abstract
In this paper, we review and compare three segmentation methods for segmentation
of target organs in medical images, each of which are based on the optimization
of Markov random elds (MRF) and utilize a database of similar images and their
ground truth segmentations to train relevant information. All three methods follow
conventional MRF denitions with unary pixel(voxel)-wise potentials established from
statistical prior knowledge of the training set and binary pixel(voxel)-pairwise potentials
which reward smooth boundaries and high image gradients. The main dierence
between the three methods is the unary potential term dened from the training
data which, specically, are dened by 1) construction of a probabilistic shape model
from aggregation of aligned manual labels, 2) per-patch label fusion by local weighted
averaging of manual labels with weights proportionate to patch appearance similarity,
and 3) a structured patch model which adaptively integrates local shape and appearance
priors and global structure. Experimental evaluation for each method is performed on
the SKI knee MR dataset where performance is measured by segmentation accuracy
and computational time.
Introduction
vi V
(l(vi )) +
vi ,vi
|I(vi ) I(vi )|
,
2
(1)
where l(vi ) is a random variable representing the label of voxel vi in voxel set V
and L is the label variable set of V . (l(vi )) represents the likelihood term which is
dened as the negative log of P (l(vi )), while the exponential function represents the
smoothness term between neighboring nodes (vi , vi ) in neighbor set j . If l(vi ) =
l(vi ), (l(vi ), l(vi )) is set as 0, otherwise, set as 1. I(vi ) is the intensity of voxel vi
and is the average square-distance of intensities between adjacent voxels in V . (1)
is optimized by the -expansion method [4] and L is obtained.
2.1
Deform elds between two volumes can be obtained by image-based non-rigid registration
method. All manual labels in training set are aligned to a target volume V by using
the deform elds. Then, probability maps regarding each label are constructed by
averaging the aligned labels with the same weight. The likelihood term of (1) is
dened as the probability maps in this method. For experiments in this paper, we
used the Drop registration [5], one of the MRF based registration methods, to obtain
the deform elds.
2.2
In this method, a probability of each label for each voxel is computed by using the
patch-based label fusion method [3]. Similar to the global label fusion method in
Sec. 2.1, the aligned manual labels are obtained in the initial step by using the Drop
registration. Details of next steps are listed in following subsections.
Region of interest (ROI) region. ROI region is dened around a target subject
to reduce needless computations in the following steps. To ensure that the target
subject is completely included in the ROI, we enlarge the union of all aligned manual
labels of training data and set this as the ROI.
Subjects and patch selection. First, M closest subjects with the target subject
are chosen from the training data. Similarities between the target subject and the
training subjects are measured as sum of the squared dierence in the ROI. Then,
similar patches are searched in a limited search volume Si for each voxel vi from the
M closest subjects. The similarity between patches is computed as sum of squared
dierence. Based on the patch similarity, weighted voting is conducted on the positions
where structural similarity measure [3] is higher than 0.95.
t=1
(2)
Parameter setting. In the training step, the experiments with various parameter
sets were conducted to some of training data to nd the optimal parameter set. Finally,
we chose the parameter set (M , size of search volume, size of patch) as (10, 7, 9) for
the SKI knee MR data set.
2.3
The structured patch model include corresponding patch sets representing the same
local regions across the training sets and spatial relationships between adjacent patch
sets. In the training step, shape and appearance cues of the corresponding patches
and distances and angles between adjacent patch sets are learned. In the test step,
the training patches of the model are transferred to appropriate positions in a target
volume V by comparing the appearances and the spatial relationships. Finally, the
segmentation is conducted by using the shape and appearance cues of the localized
patches.
V and a reference
volume and normalizing the intensity distribution of V , the structured patches are
localized to V . The patch localization problem is formulated as an energy equation
on Markov random eld (MRF) framework as:
E(v, P) =
(vj |V, Pj ) +
(vj , vj |Pj , Pj ),
(3)
j,j
model is constructed by using the localized classier. Shape and appearance models
are adaptively combined according to the learned model of localized patch on each
local region. Then, the probability maps of local regions are aggregated to a global
probability map. Each voxel can be included in multiple patches on the overlapping
regions between adjacent patches. In this case, probabilities regarding the multiple
patches are averaged to obtain the global probability.
3
Experimental Results
data set [7] was released for the bone and cartilage segmentation challenge in
MICCAI 2010 (http://www.ski10.org). MR images were acquired in the sagittal plane
with a pixel spacing of 0.4 0.4 mm2 and a slice distance of 1 mm with varying image
sizes. Since ground truth labels of the test set were not opened, we selected sub
samples, ten subjects for training and eight subjects for testing, from the training set
for in this experiments. All experiments was done by C++ on a PC with 2.93 GHz
Intel Core i7 CPU, NVIDIA Geforce GTX 480, and 16GB of RAM.
We measured the segmentation accuracy as the Dice Similarity Coecient (DSC).
DSC represents the ratio of overlapping volume to the average of the two volumes as
R |
DSC(S, R) = |2|SS|+|
, where S represents the voxels of the segmentation result and
R|
R represents that of the reference segmentation.
SKI
Idx
1
2
3
4
5
6
7
8
avg
GP
0.923
0.917
0.871
0.947
0.946
0.937
0.926
0.945
0.927
Femur
LF
0.960
0.929
0.942
0.962
0.976
0.964
0.956
0.967
0.957
SPM
0.952
0.956
0.942
0.925
0.970
0.974
0.966
0.951
0.954
GP
0.923
0.896
0.922
0.930
0.964
0.911
0.927
0.917
0.924
Tibia
LF
0.968
0.936
0.951
0.973
0.983
0.970
0.961
0.972
0.964
SPM
0.969
0.975
0.981
0.972
0.982
0.976
0.955
0.973
0.973
GP
0.381
0.453
0.483
0.404
0.654
0.523
0.412
0.500
0.476
Carti(F)
LF
SPM
0.722
0.665
0.300
0.692
0.693
0.744
0.600
0.524
0.741
0.698
0.696
0.621
0.651
0.654
0.692
0.618
0.637
0.652
GP
0.170
0.153
0.414
0.133
0.558
0.180
0.199
0.157
0.245
Carti(T)
LF
0.598
0.202
0.600
0.403
0.710
0.583
0.621
0.570
0.536
Conclusion
We came up with the performances of bone and cartilage segmentation for three
MRF-based segmentation methods based on the global shape prior, the label fusion,
and the structured patch model. LF and SPM methods outperformed GP method in
terms of the segmentation accuracy, while GP and SPM methods outperformed LF
method in terms of the computational time.
References
[1] van der Lijn, F. and den Heijer, T. and Breteler, M. M. and Niessen, W.
J. Hippocampus segmentation in MR images using atlas registration, voxel
classication, and graph cuts. NeuroImage, 2008. V.43. P.708-720.
[2] Lotjonen, J. M. and Wolz, R. and Koikkalainen, J. R. and Thurfjell, L. and
Waldemar, G. and Soininen, H. and Rueckert, D. Fast and robust multi-atlas
segmentation of brain magnetic resonance images. NeuroImage, 2010. V.49(3).
P.2352-2365.
[3] Pierrick Coupe and Jose V. Manjon and Vladimir Fonov and Jens Pruessner and
Montserrat Robles and D. Louis Collins. Patch-based segmentation using expert
priors: Application to hippocampus and ventricle segmentation. NeuroImage,
2011, V.54(2). P.940-954
SPM
0.528
0.480
0.589
0.343
0.529
0.515
0.445
0.462
0.486
[4] Vladimir Kolmogorov and Ramin Zabih, What energy functions can be
minimized via graph cuts?. IEEE Transactions on Pattern Analysis and Machine
Intelligence, 2004. V.26(2), P.147-159
[5] Glocker, B. and Komodakis, N. and Tziritas, G. and Navab, N. and Paragios,
N. Dense image registration through MRFs and ecient linear programming.
IEEE Transactions on Pattern Analysis and Machine Intelligence, 2008. V.12.
P.731-741.
[6] Park, S. and Yun, I. and Lee, S. Data-driven Segmentation Method based on
Structured Patch Model for Medical Images. IPMI, 2013.
[7] Tobias Heimann and Bryan J. Morrison and Martin A. Styner and Marc
Niethammer and Simon K. Wareld, Segmentation of Knee Images: A Grand
Challenge. In Proc. MICCAI, 2010.