3D segmentation of abdominal CT imagery with graphical models, conditional random fields and learning

Machine Vision and Applications (Impact Factor: 1.35). 02/2014; 25(2). DOI: 10.1007/s00138-013-0497-x


Probabilistic graphical models have had a tremendous impact in machine learning and approaches based on energy function minimization via techniques such as graph cuts are now widely used in image segmentation. However, the free parameters in energy function-based segmentation techniques are often set by hand or using heuristic techniques. In this paper, we explore parameter learning in detail. We show how probabilistic graphical models can be used for segmentation problems to illustrate Markov random fields (MRFs), their discriminative counterparts conditional random fields (CRFs) as well as kernel CRFs. We discuss the relationships between energy function formulations, MRFs, CRFs, hybrids based on graphical models and their relationships to key techniques for inference and learning. We then explore a series of novel 3D graphical models and present a series of detailed experiments comparing and contrasting different approaches for the complete volumetric segmentation of multiple organs within computed tomography imagery of the abdominal region. Further, we show how these modeling techniques can be combined with state of the art image features based on histograms of oriented gradients to increase segmentation performance. We explore a wide variety of modeling choices, discuss the importance and relationships between inference and learning techniques and present experiments using different levels of user interaction. We go on to explore a novel approach to the challenging and important problem of adrenal gland segmentation. We present a 3D CRF formulation and compare with a novel 3D sparse kernel CRF approach we call a relevance vector random field. The method yields state of the art performance and avoids the need to discretize or cluster input features. We believe our work is the first to provide quantitative comparisons between traditional MRFs with edge-modulated interaction potentials and CRFs for multi-organ abdominal segmentation and the first to explore the 3D adrenal gland segmentation problem. Finally, along with this paper we provide the labeled data used for our experiments to the community.

29 Reads
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: . The solution of binary classification problems using support vector machines (SVMs) is well developed, but multi-class problems with more than two classes have typically been solved by combining independently produced binary classifiers. We propose a formulation of the SVM that enables a multi-class pattern recognition problem to be solved in a single optimisation. We also propose a similar generalization of linear programming machines. We report experiments using bench-mark datasets in which ...
    ESANN 1999, 7th European Symposium on Artificial Neural Networks, Bruges, Belgium, April 21-23, 1999, Proceedings; 01/1999
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: We compare two recently proposed frameworks for combining generative and discriminative probabilistic classifiers and apply them to semi-supervised classification. In both cases we explore the tradeoff between maximizing a discriminative likelihood of labeled data and a generative likelihood of labeled and unlabeled data. While prominent semi-supervised learning methods assume low density regions between classes or are subject to generative modeling assumptions, we conjecture that hybrid generative/discriminative methods allow semi-supervised learning in the presence of strongly overlapping classes and reduce the risk of modeling structure in the unlabeled data that is irrelevant for the specific classification task of interest. We apply both hybrid approaches within naively structured Markov random field models and provide a thorough empirical comparison with two well-known semi-supervised learning methods on six text classification tasks. A semi-supervised hybrid generative/discriminative method provides the best accuracy in 75% of the experiments, and the multi-conditional learning hybrid approach achieves the highest overall mean accuracy across all tasks.
    Proceedings of the 13th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, San Jose, California, USA, August 12-15, 2007; 08/2007
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: There have been significant efforts to build a probabilistic atlas of the brain and to use it for many common applications, such as segmentation and registration. Though the work related to brain atlases can be applied to nonbrain organs, less attention has been paid to actually building an atlas for organs other than the brain. Motivated by the automatic identification of normal organs for applications in radiation therapy treatment planning, we present a method to construct a probabilistic atlas of an abdomen consisting of four organs (i.e., liver, kidneys, and spinal cord). Using 32 noncontrast abdominal computed tomography (CT) scans, 31 were mapped onto one individual scan using thin plate spline as the warping transform and mutual information (MI) as the similarity measure. Except for an initial coarse placement of four control points by the operators, the MI-based registration was automatic. Additionally, the four organs in each of the 32 CT data sets were manually segmented. The manual segmentations were warped onto the "standard" patient space using the same transform computed from their gray scale CT data set and a probabilistic atlas was calculated. Then, the atlas was used to aid the segmentation of low-contrast organs in an additional 20 CT data sets not included in the atlas. By incorporating the atlas information into the Bayesian framework, segmentation results clearly showed improvements over a standard unsupervised segmentation method.
    IEEE Transactions on Medical Imaging 05/2003; 22(4):483-92. DOI:10.1109/TMI.2003.809139 · 3.39 Impact Factor
Show more