atlasBREX: Automated template-derived brain extraction in animal MRI

Abstract We proposed a generic template-derived approach for (semi-) automated brain extraction in animal MRI studies and evaluated our implementation with different animal models (macaque, marmoset, rodent) and MRI protocols (T1, T2). While conventional MR-neuroimaging studies perform brain extract...

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Autores principales:	Johannes Lohmeier, Takaaki Kaneko, Bernd Hamm, Marcus R. Makowski, Hideyuki Okano
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/104a6aa34add4fe0832aaabd14a7c175
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spelling	oai:doaj.org-article:104a6aa34add4fe0832aaabd14a7c1752021-12-02T16:08:43ZatlasBREX: Automated template-derived brain extraction in animal MRI10.1038/s41598-019-48489-32045-2322https://doaj.org/article/104a6aa34add4fe0832aaabd14a7c1752019-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-48489-3https://doaj.org/toc/2045-2322Abstract We proposed a generic template-derived approach for (semi-) automated brain extraction in animal MRI studies and evaluated our implementation with different animal models (macaque, marmoset, rodent) and MRI protocols (T1, T2). While conventional MR-neuroimaging studies perform brain extraction as an initial step priming subsequent image-registration from subject to template, our proposed approach propagates an anatomical template to (whole-head) individual subjects in reverse order, which is challenging due to the surrounding extracranial tissue, greater differences in contrast pattern and larger areas with field inhomogeneity. As a novel approach, the herein introduced brain extraction algorithm derives whole-brain segmentation using rigid and non-rigid deformation based on unbiased anatomical atlas building with a priori estimates from study-cohort and an initial approximate brain extraction. We evaluated our proposed method in comparison to several other technical approaches including “Marker based watershed scalper”, “Brain-Extraction-Tool”, “3dSkullStrip”, “Primatologist-Toolbox”, “Rapid Automatic Tissue Segmentation” and “Robust automatic rodent brain extraction using 3D pulse-coupled neural networks” with manual skull-stripping as reference standard. ABX demonstrated best performance with accurate (≥92%) and consistent results throughout datasets and across species, age and MRI protocols. ABX was made available to the public with documentation, templates and sample material (https://www.github.com/jlohmeier/atlasBREX).Johannes LohmeierTakaaki KanekoBernd HammMarcus R. MakowskiHideyuki OkanoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-9 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Johannes Lohmeier Takaaki Kaneko Bernd Hamm Marcus R. Makowski Hideyuki Okano atlasBREX: Automated template-derived brain extraction in animal MRI
description	Abstract We proposed a generic template-derived approach for (semi-) automated brain extraction in animal MRI studies and evaluated our implementation with different animal models (macaque, marmoset, rodent) and MRI protocols (T1, T2). While conventional MR-neuroimaging studies perform brain extraction as an initial step priming subsequent image-registration from subject to template, our proposed approach propagates an anatomical template to (whole-head) individual subjects in reverse order, which is challenging due to the surrounding extracranial tissue, greater differences in contrast pattern and larger areas with field inhomogeneity. As a novel approach, the herein introduced brain extraction algorithm derives whole-brain segmentation using rigid and non-rigid deformation based on unbiased anatomical atlas building with a priori estimates from study-cohort and an initial approximate brain extraction. We evaluated our proposed method in comparison to several other technical approaches including “Marker based watershed scalper”, “Brain-Extraction-Tool”, “3dSkullStrip”, “Primatologist-Toolbox”, “Rapid Automatic Tissue Segmentation” and “Robust automatic rodent brain extraction using 3D pulse-coupled neural networks” with manual skull-stripping as reference standard. ABX demonstrated best performance with accurate (≥92%) and consistent results throughout datasets and across species, age and MRI protocols. ABX was made available to the public with documentation, templates and sample material (https://www.github.com/jlohmeier/atlasBREX).
format	article
author	Johannes Lohmeier Takaaki Kaneko Bernd Hamm Marcus R. Makowski Hideyuki Okano
author_facet	Johannes Lohmeier Takaaki Kaneko Bernd Hamm Marcus R. Makowski Hideyuki Okano
author_sort	Johannes Lohmeier
title	atlasBREX: Automated template-derived brain extraction in animal MRI
title_short	atlasBREX: Automated template-derived brain extraction in animal MRI
title_full	atlasBREX: Automated template-derived brain extraction in animal MRI
title_fullStr	atlasBREX: Automated template-derived brain extraction in animal MRI
title_full_unstemmed	atlasBREX: Automated template-derived brain extraction in animal MRI
title_sort	atlasbrex: automated template-derived brain extraction in animal mri
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/104a6aa34add4fe0832aaabd14a7c175
work_keys_str_mv	AT johanneslohmeier atlasbrexautomatedtemplatederivedbrainextractioninanimalmri AT takaakikaneko atlasbrexautomatedtemplatederivedbrainextractioninanimalmri AT berndhamm atlasbrexautomatedtemplatederivedbrainextractioninanimalmri AT marcusrmakowski atlasbrexautomatedtemplatederivedbrainextractioninanimalmri AT hideyukiokano atlasbrexautomatedtemplatederivedbrainextractioninanimalmri
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atlasBREX: Automated template-derived brain extraction in animal MRI

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