atlasBREX: Automated template-derived brain extraction in animal MRI

Johannes Lohmeier, Takaaki Kaneko, Bernd Hamm, Marcus R. Makowski, Hideyuki Okano

Research output: Contribution to journalArticlepeer-review

17 Citations (Scopus)


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 (

Original languageEnglish
Article number12219
JournalScientific reports
Issue number1
Publication statusPublished - 2019 Dec 1

ASJC Scopus subject areas

  • General


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