A Hybrid Segmentation Method using MRF and GVF Snakes

Alexander Rukletsov*, Reinhard Mnner Institute for Computational Medicine, University of Heidelberg, Mannheim, Germany
ABSTRACT
In this paper a hybrid method for segmentation of 2-D medical images of human organs is proposed. To capture object's global properties the Markov random fields (MRFs) are involved. The result of the MRF segmentation is used to recalculate gradient vector flow based snake external forces in a further snake progression step. A MRF MAP solution is estimated using the MMD algorithm. To reduce the computation time, MRF estimation is restricted only to sites, where the state uncertainty is higher than some threshold value. Tests on MR slices and ultrasound images of the left ventricle of the human heart are reported. Keywords: Medical image segmentation, Markov random fields, active contour models, gradient vector flow.

1. INTRODUCTION
Image segmentation is one of the most important tasks in computer vision. The role of segmentation algorithms in contemporary medical applications steadily increases due to their relevance in diagnostics, surgical procedures, image understanding. Though a wide variety of segmentation techniques has been proposed in the last decades, there is no general algorithm that can be successfully applied in medical imaging in general case due to specific shapes of anatomical objects and properties of imaging techniques like MRI, CT and ultrasound (US). In this paper a problem of segmentation of a single closed anatomical object from MRI or US images using a seed contour is considered. A survey on classical image segmentation approaches can be found in [1]. A more recent review, focusing mainly on segmentation of medical B-mode ultrasound images, both 2-D and 3-D, is given in [2]. Most of the segmentation methods used in medical imaging can be divided into two classes: region-based and edge-based. Common examples of region-based methods are classical region growing [3], Mumford-Shah models [4], [14] and MRF-based algorithms [5], [6], [7]. Deformable models are among the most widely used edge-base methods [8]. Active contour models, or snakes were proposed in [9]. They were revisited and modified by other authors, thus leading to the improvements of the snake algorithm, such as Balloon snakes [10], gradient vector flow (GVF) snakes [11], and to the rise of new classes of deformable models (geometric [12] and geodesic [13], [14] active contours). Despite the fact that the techniques mentioned above are well-known and widely used, they have some drawbacks. For instance, the edge-based methods usually tend to over-smooth boundaries and are sensitive to noise, while the region-based methods can generate holes inside the target objects and the boundaries obtained from these methods rarely resemble shapes of anatomical structures. However, various image segmentation approaches coupling MRF and deformable models have been presented in the literature. In [15] a graphical model theory is used to integrate MRF and active contours. Similar approaches, but for 3-D case are described in [16], [17]. Available texture information can be exploited in some cases (e.g. see [18], [19]) to detect textured regions more precisely. In [20] a hybrid approach to the segmentation of the human liver from CT scans is reported. A MRF model is used there to determine an initial liver boundary, which is then refined using the GVF snake. In this paper a hybrid method for segmenting boundaries of human organs from 2-D MR slices and US images is proposed. A snake model gives the ability to produce a smooth, closed contour of natural shape, resembling anatomical structures, such as human organs. A MRF model contributes noise robustness, as well as facilitates capturing image properties. To combine these two models a MRF maximum a posteriori (MAP) solution is used in each iteration to recalculate the snake dynamic external forces. The GVF field is calculated before each snake progression step in order to extend the capture range of the external forces.

* Corresponding author, e-mail address: alexander.rukletsov@ziti.uni-heidelberg.de

Fourth International Conference on Digital Image Processing (ICDIP 2012), edited by Mohamed Othman, Sukumar Senthilkumar, Xie Yi, Proc. of SPIE Vol. 8334, 833414 2012 SPIE CCC code: 0277-786X/12/$18 doi: 10.1117/12.946104 Proc. of SPIE Vol. 8334 833414-1 Downloaded From: http://spiedigitallibrary.org/ on 12/11/2012 Terms of Use: http://spiedl.org/terms

2. METHOD DESCRIPTION
The goal of the proposed method is to extract a smooth, closed boundary of human organs in reasonable time using a seed contour inside the target object. The method can be interpreted as a GVF snake with non-standard dynamic external forces. A traditional snake is a contour c(s ) , where s [0, 1] is the snake parameter. Let i , 1 i n be an image pixel and d i be its brightness. As the snake deforms external forces are recomputed using a MRF model and the GVF field. A configuration of the MRF depends on d i and on the current position of the contour c(s ) . The result of the MRF configuration estimation is used to build the GVF field which acts as the external energy of the snake. The segmentation result is obtained after some number of iterations, when the contour evolutions converge to some final contour.

2.1

MRF model

Markov random fields [22] came from probability theory and are used in computer vision due to several reasons. One of them is that MRF models allow to extract quantitative characteristics from prior constraints and contextual information. The implemented MRF model is based on the work [15] and applied here to segment a target object using a standard smoothness prior and some guess about the object boundary. This guess is obtained from the current contour position which is changed during the snake evolution. A recomputation of the GVF field is based on the result of the MRF MAP estimation. Consider a lattice with n sites. The size of the lattice is equal to the size of the input 2-D image. For each site i a state value xi L is assigned. L is a set of region labels, L =1{(if the site i belongs to the object) , 0 (if the site i belongs to the background)}. Denote image intensities by D and lattice configuration by X . For xi the first order Ising neighbourhood system [22] is used (systems of higher order significantly slow the computation while giving small benefit). Since X is a joint random variable and the Markov property for X is satisfied, the model forms a random field.
The MAP criterion can be used to find the labeling X that represents a segmentation of the target object. The posterior probability can be computed according to the Bayes rule ( P (D ) is constant and therefore can be ignored):

P ( X | D ) P(D | X )P( X ) .

(1) (2)

A solution of the segmentation problem is then the MAP estimate of the MRF model:
X = arg max P ( X | D ) .
x

The relationship between image pixels and the random field state (image likelihood term) can be represented as a Gaussian over intensity:
P (d i | xi ) = 1 2 i2

(d i i )2 2 i2

(3)

where is a weighting coefficient, Z is a normalizing constant, i and i are the brightness mean and variance of the region corresponding to the value xi . They are updated during each iteration using X configuration. The prior probability consists of two terms. First is the standard smoothness prior:
Ps (xi ) =
(xi ,x j ) 1 , e Z jNi

(4)

where N i is the Ising neighbourhood of the site i , is a weighting coefficient and (x, y ) is the Kronecker delta, i.e. (xi , x j )= 1 if xi = x j ; (xi , x j )= 0 if xi x j . To penalize the sites which are far from the contour position, the second part of the prior probability, a contour proximity constraint similar to one in [15] is introduced. Since the segmentation result is obtained from the snake position and the MRF model is used to tune the snake performance in the vicinity of the contour, only sites near the contour should be considered. The farther from the contour the site is, the more likely it belongs either to the object or to the background. This dependency between the contour position c(s ) and the state

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xi is defined as follows:

1+ e Pc (xi = background ) = 1 Pc (xi = object ) ,

Pc (xi = object ) =

dist (i,c (s ))

(5)

with
dist (i,c(s )) = sign(i,c(s )) min pos (i ) c(s ) ,
s

(6)

where sign(i, c(s )) = 1 if pixel i is inside c(s ) and sign(i, c(s )) = 1 otherwise; pos(i ) stands for image coordinates of site i and controls the uncertainty of the state xi depending on its distance from the contour. Now the a posteriori distribution of the proposed MRF model can be derived:
i

P ( X | D ) (P(d i | xi ) Ps (xi ) Pc (xi )) .

(7)

To approximate the MAP estimation the Modified Metropolis Dynamics (MMD) algorithm [21] was used. The MAP estimation gives the object region, whose boundary is used to compute the snake external forces.

2.2

Snake forces

The energy of the contour controls the snake movement and consists of the internal energy term (independent to input data, it does not allow the contour to stretch and bend too much) and the external energy term (usually a function of image intensity, edges, etc):
E (c ) = Eint (c )+ Eext (c ) = 1 (s ) |c' (s )|2 + 2 (s ) |c' ' (s )|2 ds + ext (s )Eext (c ) ,
0 1

(8)

where 1 (s ) and 2 (s ) control the tension and rigidity of the contour respectively, Eext (c ) is the energy potential derived from the input data, it pulls the snake towards the structures of interest and ext (s ) is its weighting coefficient. The farther the real boundary is, the worse is the convergence of the snake with the traditional gradient-based external forces. To address this problem and to extend snake's capture range, the GVF external force can be used [11]. In this paper the GVF field is recomputed in every iteration from a binary edge map obtained from the MRF solution.

2.3

Algorithm description

The proposed method operates iteratively. The input of the algorithm is a closed contour or a single point lying inside the target object. This input is used to initialize the GVF snake. The iteration starts with the construction of the MRF model. The result of the MRF MAP solution estimated by the MMD algorithm is used to recalculate the GVF field. The iteration ends with the snake progression step minimizing the total energy of the snake (internal and external, based on the GVF field). Unlike in common snake-based models, the initial seed contour does not need to be close to the real boundary because of the properties of the GVF field and the MRF model involved.

3. IMPLEMENTATION ISSUES AND RESULTS

The prior probabilities (5) and can be used to significantly speed up the MRF minimization process. The uncertainty of the site's state xi reaches its maximum on the contour and decreases with distance from the contour. Thus, the sites for which Pc (xi ) is higher than some threshold value 0 (in this work 0 = 0.999 was defined), may be excluded from the MRF minimization algorithm. The site labels are therefore estimated in a narrow band area around the contour and accepted without computation outside this area (see figure 1).

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Figure 1. The states of the sites outside the band are derived without computation. The white area represents the object, the black one is the background, the curve C is the current contour position. All sites in the dashed shadowed area are labeled as the background, in dotted as the object, controls the band width and is close to 0. The sequential algorithm was implemented in MATLAB and tested on a 3 GHz AMD quad-core computer. One complete iteration (which includes 20-30 MMD iterations, 400 GVF iterations and one snake progression step) for a 180 180 image took from 5 to 30 seconds, depending on the contour length. The coefficients of the terms in the MRF model can be estimated during minimization by the EM algorithm, but can be set to constant values for certain image types. Snake weights were chosen constant: 1 (s ) = 0.5 , 2 (s ) = 0.2 , ext (s ) = 2 . The segmentation results of the proposed and the GVF snake methods applied on three images of the left ventricle of the human heart are shown in figure 2 (MRI; top row: Siemens Sonata, 1.72 mm/pixel; bottom row: [15]) and figure 3 (US, Philips iE 33). The initial contour in figure 3 is obtained using a coarse preprocessing step.

Figure 2. Contour evolution on MR images of the left ventricle of the human heart. Proposed method: initial contour (a), 15th iteration (b). The GVF snake: 15th iteration (c), 200th iteration (d).

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Figure 3. Contour evolution on a US image of the left ventricle of the human heart. Proposed method: initial contour (a), 15th iteration (b). The GVF snake: 15th iteration (c), 200th iteration (d).

4. CONCLUSION
In this paper a hybrid method for medical image segmentation that implements snake and MRF models is proposed. The snake model allows to generate smooth, natural contours, while MRF contributes the ability to capture global properties. As shown by the experiments, the proposed approach is able to produce visually correct results in reasonable time. The algorithm converges fast to a solution and outperforms the GVF snake algorithm. The proposed method can be easily generalized and used for 3-D images. Among the future improvements an automatic estimator of all algorithm parameters for various image types can be mentioned. Additional information, such as texture, may be exploited to improve the quality of the segmentation.

5. REFERENCES
[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] Pal, N. R. and Pal, S. K., A review on image segmentation techniques, Pattern Recognition 26(9), 12771294 (1993). Noble, J. A. and Boukerroui, D., Ultrasound Image Segmentation: A Survey, IEEE Transactions on Medical Imaging 25(8), 9871010 (2006). Gonzalez, R. C. and Woods, R. E., [Digital Image Processing], 2nd Edition, Prentice Hall, (2002). Mumford, D. and Shah, J., Optimal Approximations by Piecewise Smooth Functions and Associated Variational Problems, Communications on Pure and Applied Mathematics 42, 577685 (1989). Katartzis, A., Sahli, H., Cornells, J., Costaridou, L. and Panayiotakis, G., A MRF-Based Approach for the Measurement of Skin Thickness in Mammography, Medical image analysis methods, chapter 8, CRC Press, (2005). Hlindzich, D. and Kryvanos, A., A Three-Dimensional Segmentation Approach for Automatic Human Heart Modelling, AITTH, 4953 (2008). Ouadfel, S. and Batouche, M., MRF-based image segmentation using Ant Colony System, Electronic Letters on Computer Vision and Image Analysis 2(2), 1224 (2003). Tsechpenakis, G., Deformable Model-Based Medical Image Segmentation, Multi Modality State-of-the-Art Medical Image Segmentation and Registration Methodologies, 1, 3367 (2011). Kass M., Witkin, A. and Terzopoulos, D., Snakes: Active contour models, International Journal of Computer Vision 1(4), 321 331 (1988). Cohen, L. D., On Active Contour Models and Balloons, Computer Vision, Graphics and Image Processing: Image Understanding, 53(2), (1991). Xu, C. and Prince, J. L., Snakes, Shapes, and Gradient Vector Flow, IEEE Transactions on Image Processing 7(3), 359369 (1998). Caselles, V., Catt, F., Coll, T. and Dibos, F., A geometric model for active contours in image processing, Numerische. Mathematik 66, 131 (1993). Caselles, V., Kimmel, R. and Sapiro, G., Geodesic Active Contours, International Journal of Computer Vision 22(1), 6779 (1997). Aubert, G. and Kornprobst, P., [Mathematical Problems in Image Processing: Partial Differential Equations and the Calculus of Variations], 2nd Edition, Springer, (2006). Huang, R., Pavlovic, V. and Metaxas, D. N., A Graphical Model Framework for Coupling MRFs and Deformable Models, IEEE Conference on CVPR, (2004).

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[16] Huang, R., Pavlovic, V. and Metaxas, D., A tightly coupled region-shape framework for 3D medical image segmentation, IEEE Int. Symposium on Biomedical Imaging, (2006). [17] Chen, T. and Metaxas, D., Integration of Gibbs Prior Models and Deformable Models for 3D Medical Image Segmentation, International Conference on Pattern Recognition 1, 719722 (2002). [18] Huang, X., Qian, Z., Huang, R. and Metaxas, D., Deformable-model based Textured Object Segmentation. International Conference on Energy Minimization Methods in CVPR, (2005). [19] Mahmoodi, S. and Gunn, S., Snake based Unsupervised Texture Segmentation using Gaussian Markov Random Fields Models, IEEE International Conference on Image Processing, 3414 417 (2011). [20] Alomari, R. S., Kompalli, S. and Chaudhary, V., Segmentation of the liver from abdominal CT using Markov Random Field model and GVF snakes, International Conference on Complex, Intelligent and Software Intensive Systems, 293298 (2008). [21] Berthod, M., Kato, Z., Yu, S. and Zerubia, J., Bayesian image classification using Markov random fields, Image and Vision Computing 14, 285296 (1996). [22] Kindermann, R. and Snell, J. L., [Markov random fields and their applications], American Mathematical Society, (1980).

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