Due to optimization for the human brain, most common skullstripping/brain-extraction methods achieve insufficient results for non-human brains, which then require further manual intervention. Making use of the available brain-extraction from a template/atlas, this approach implements brain-extraction through reversal (rigid- and non-rigid) deformation of a template-derived mask.

-time-saving and straightforward (with various optional parameters for further optimization)
-multi-step registration (2- or 3-step) for improved registration to low resolution datasets
-robust FSL (FLIRT, FNIRT) or ANTs (SyN) registration frameworks
-compatible with T1-/T2-weighted datasets

Please cite: atlasBREX: Automated template-derived brain extraction in animal MRI
Scientific Reports, volume 9, Article number: 12219 (2019)
DOI: 10.1038/s41598-019-48489-3