A fast stochastic framework for automatic MR brain images segmentation

Marwa Ismail, Ahmed Soliman, Mohammed Ghazal, Andrew E Switala, Georgy Gimel’farb, Gregory N Barnes, Ashraf Khalil and Ayman El-Baz

PLOS ONE, 2017, vol. 12, issue 11, 1-24

Abstract: This paper introduces a new framework for the segmentation of different brain structures (white matter, gray matter, and cerebrospinal fluid) from 3D MR brain images at different life stages. The proposed segmentation framework is based on a shape prior built using a subset of co-aligned training images that is adapted during the segmentation process based on first- and second-order visual appearance characteristics of MR images. These characteristics are described using voxel-wise image intensities and their spatial interaction features. To more accurately model the empirical grey level distribution of the brain signals, we use a linear combination of discrete Gaussians (LCDG) model having positive and negative components. To accurately account for the large inhomogeneity in infant MRIs, a higher-order Markov-Gibbs Random Field (MGRF) spatial interaction model that integrates third- and fourth- order families with a traditional second-order model is proposed. The proposed approach was tested and evaluated on 102 3D MR brain scans using three metrics: the Dice coefficient, the 95-percentile modified Hausdorff distance, and the absolute brain volume difference. Experimental results show better segmentation of MR brain images compared to current open source segmentation tools.

Date: 2017
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0187391

DOI: 10.1371/journal.pone.0187391

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