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Primatologist: A modular segmentation pipeline for macaque brain morphometry

Balbastre, Y; Rivière, D; Souedet, N; Fischer, C; Hérard, A-S; Williams, S; Vandenberghe, ME; ... Delzescaux, T; + view all (2017) Primatologist: A modular segmentation pipeline for macaque brain morphometry. NeuroImage , 162 pp. 306-321. 10.1016/j.neuroimage.2017.09.007. Green open access

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Abstract

Because they bridge the genetic gap between rodents and humans, non-human primates (NHPs) play a major role in therapy development and evaluation for neurological disorders. However, translational research success from NHPs to patients requires an accurate phenotyping of the models. In patients, magnetic resonance imaging (MRI) combined with automated segmentation methods has offered the unique opportunity to assess in vivo brain morphological changes. Meanwhile, specific challenges caused by brain size and high field contrasts make existing algorithms hard to use routinely in NHPs. To tackle this issue, we propose a complete pipeline, Primatologist, for multi-region segmentation. Tissue segmentation is based on a modular statistical model that includes random field regularization, bias correction and denoising and is optimized by expectation-maximization. To deal with the broad variety of structures with different relaxing times at 7 T, images are segmented into 17 anatomical classes, including subcortical regions. Pre-processing steps insure a good initialization of the parameters and thus the robustness of the pipeline. It is validated on 10 T2-weighted MRIs of healthy macaque brains. Classification scores are compared with those of a non-linear atlas registration, and the impact of each module on classification scores is thoroughly evaluated.

Type: Article
Title: Primatologist: A modular segmentation pipeline for macaque brain morphometry
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.neuroimage.2017.09.007
Publisher version: http://doi.org/10.1016/j.neuroimage.2017.09.007
Language: English
Additional information: © 2017 Elsevier Inc. All rights reserved. This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: Brain, Expectation-maximization, MRI, Macaque, Primatologist, Segmentation
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Imaging Neuroscience
URI: http://discovery.ucl.ac.uk/id/eprint/10034944
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