atlasBREX

atlasBREX performs automated template-derived brain extraction from animal magnetic resonance imaging (MRI) to enable accurate whole-brain segmentation across species (macaques, marmosets, rodents) and to mitigate effects of extracranial tissues and field inhomogeneities.

Key Features:

• Template-Derived Approach: Utilizes a generic template-derived methodology with anatomical templates to guide brain extraction for macaques, marmosets, and rodents.
• Versatility Across Protocols: Supports multiple MRI protocols, including T1-weighted and T2-weighted imaging.
• Rigid and Non-Rigid Deformation: Applies both rigid and non-rigid deformation based on unbiased anatomical atlas building with a priori estimates derived from the study cohort and an initial approximate brain extraction.

Scientific Applications:

• Animal neuroimaging preprocessing: Provides accurate skull-stripping and whole-brain masks for macaque, marmoset, and rodent MRI datasets.
• Downstream anatomical analyses: Enables image registration and morphometric assessments by delivering consistent whole-brain segmentation.

Methodology:

The method propagates an anatomical template to individual subjects in reverse order and applies rigid and non-rigid deformation informed by unbiased anatomical atlas building with a priori estimates derived from the study cohort and an initial approximate brain extraction.