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.

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    ABSTRACT: Detection and segmentation of large structures in an image or within a region of interest have received great attention in the medical image processing domains. However, the problem of small pathology detection and segmentation still remains an unresolved challenge due to the small size of these pathologies, their low contrast and variable position, shape and texture. In many contexts, early detection of these pathologies is critical in diagnosis and assessing the outcome of treatment. In this paper, we propose a probabilistic Adaptive Multi-level Conditional Random Fields (AMCRF) with the incorporation of higher order cliques for detecting and segmenting such pathologies. In the first level of our graphical model, a voxel-based CRF is used to identify candidate lesions. In the second level, in order to further remove falsely detected regions, a new CRF is developed that incorporates higher order textural features, which are invariant to rotation and local intensity distortions. At this level, higher order textures are considered together with the voxel-wise cliques to refine boundaries and is therefore adaptive. The proposed algorithm is tested in the context of detecting enhancing Multiple Sclerosis (MS) lesions in brain MRI, where the problem is further complicated as many of the enhancing voxels are associated with normal structures (i.e. blood vessels) or noise in the MRI. The algorithm is trained and tested on large multi-center clinical trials from Relapsing-Remitting MS patients. The effect of several different parameter learning and inference techniques is further investigated. When tested on 120 cases, the proposed method reaches a lesion detection rate of 90%, with very few false positive lesion counts on average, ranging from 0.17 for very small (3-5 voxels) to 0 for very large (50+ voxels) regions. The proposed model is further tested on a very large clinical trial containing 2770 scans where a high sensitivity of 91% with an average false positive count of 0.5 is achieved. Incorporation of contextual information at different scales is also explored. Finally, superior performance is shown upon comparing with Support Vector Machine (SVM), Random Forest and variant of an MRF. Copyright © 2015 Elsevier B.V. All rights reserved.
    No preview · Article · Jul 2015 · Medical image analysis