Subject-Specific Sparse Dictionary Learning for Atlas-Based Brain MRI Segmentation

• Published in: IEEE journal of biomedical and health informatics Vol. 19; no. 5; pp. 1598 - 1609
• Main Authors: Roy, Snehashis, Qing He, Sweeney, Elizabeth, Carass, Aaron, Reich, Daniel S., Prince, Jerry L., Pham, Dzung L.
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.09.2015
• Subjects: Adult; Aged; Algorithms; Biomedical imaging; brain; Brain - pathology; Brain modeling; Dictionaries; dictionary; Female; histogram matching; Humans; Hydrocephalus, Normal Pressure - pathology; Image Processing, Computer-Assisted - methods; Image segmentation; Lesions; Machine Learning; magnetic resonance imaging (MRI); Magnetic Resonance Imaging - methods; Male; Manuals; Middle Aged; Multiple Sclerosis - pathology; patches; segmentation; sparsity; Training data; Young Adult; magnetic resonance imaging (MRI); Brain; dictionary; histogram matching; patches; segmentation; sparsity
• DOI: 10.1109/JBHI.2015.2439242
• ISSN: 2168-2194

Quantitative measurements from segmentations of human brain magnetic resonance (MR) images provide important biomarkers for normal aging and disease progression. In this paper, we propose a patch-based tissue classification method from MR images that uses a sparse dictionary learning approach and atlas priors. Training data for the method consists of an atlas MR image, prior information maps depicting where different tissues are expected to be located, and a hard segmentation. Unlike most atlas-based classification methods that require deformable registration of the atlas priors to the subject, only affine registration is required between the subject and training atlas. A subject-specific patch dictionary is created by learning relevant patches from the atlas. Then the subject patches are modeled as sparse combinations of learned atlas patches leading to tissue memberships at each voxel. The combination of prior information in an example-based framework enables us to distinguish tissues having similar intensities but different spatial locations. We demonstrate the efficacy of the approach on the application of whole-brain tissue segmentation in subjects with healthy anatomy and normal pressure hydrocephalus, as well as lesion segmentation in multiple sclerosis patients. For each application, quantitative comparisons are made against publicly available state-of-the art approaches.