Regular Paper

Machine Vision and Applications

, Volume 25, Issue 2, pp 301-325

First online:

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

  • Chetan BholeAffiliated withDepartment of Computer Science, University of Rochester
  • , Christopher PalAffiliated withDépartement de génie informatique et génie logiciel, École Polytechnique de Montréal Email author 
  • , David RimAffiliated withDépartement de génie informatique et génie logiciel, École Polytechnique de Montréal
  • , Axel WismüllerAffiliated withDepartments of Imaging Sciences and Biomedical Engineering, University of RochesterDepartment of Radiology, University of Munich

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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.


Segmentation Machine learning Probabilistic graphical models Random fields Adrenal gland Abdomen Graph-cuts