atlasBREX: Automated template-derived brain extraction in animal MRI

Lohmeier J, Kaneko T, Hamm B, Makowski MR, Okano H (2019)

Publication Type: Journal article

Publication year: 2019

Journal

Scientific Reports Nature Publishing Group: Open Access Journals - Option B

Book Volume: 9

Article Number: 12219

Journal Issue: 1

DOI: 10.1038/s41598-019-48489-3

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).

Involved external institutions

Charité - Universitätsmedizin Berlin DE Germany (DE) Riken Institute of Physical and Chemical Research / 理化学研究所 JP Japan (JP)

How to cite

APA:

Lohmeier, J., Kaneko, T., Hamm, B., Makowski, M.R., & Okano, H. (2019). atlasBREX: Automated template-derived brain extraction in animal MRI. Scientific Reports, 9(1). https://doi.org/10.1038/s41598-019-48489-3

MLA:

Lohmeier, Johannes, et al. "atlasBREX: Automated template-derived brain extraction in animal MRI." Scientific Reports 9.1 (2019).

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