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Templates and Atlases (data-others/atlas)
Templates and atlases for human and animal brains distributed through the Fiber Data Hub, including the Common Hierarchical Atlas (CHA) cross-species gray-matter parcellation spanning rodents, nonhuman primates, and humans.
- Related Hub documentation: HCP-1065 templates · Tractography atlas & T2R connectome
- Quality control & download: QC results · Download guide
- Secondary direct assets: GitHub Releases ↗
Overview
The Common Hierarchical Atlas (CHA) provides a unified anatomical framework for cortical and subcortical gray-matter parcellation across multiple species using species-specific minimal deformation templates (MDTs) aligned to the AC-PC axis (except for the human ICBM152 reference).
- Primary species: Human, Rhesus macaque, Marmoset, and Mouse (with Rat coverage via MRI-based alignment from mouse).
- File naming: Species atlas volumes are distributed as
<species>_CHA.nii.gz.
Hierarchical Levels
- Level 0 — Tissue Compartments: Gray matter (GM), White matter (WM), Deep gray matter (DGM), Cerebellum (CBL), and Cerebrospinal fluid (CSF).
- Level 1 — Macro-Regions: Frontal (FRO), Parietal (PAR), Temporal (TEM), Occipital (OCC), Insular (INS), Cingulate (CIN), Olfactory (OLF), Basal ganglia (BG), and Thalamic / hypothalamic system (THL).
- Level 2 — Subdivisions: 26 Level-2 regions in primates and 21 Level-2 regions in rodents (with Parietal lobe and Caudoputamen undivided in rodents). Claustrum, substantia nigra, and subthalamic nuclei are excluded where cross-species MRI boundaries are not reliably separable.
Species Reference Templates & Source Atlases
- Human: ICBM152 Nonlinear Asymmetrical 2009a template (cross-referenced with FreeSurferSeg and Brodmann areas)
- Rhesus macaque: MDT generated from PRIME-DE T1-weighted MRI (cross-referenced with CIVM and Inia19 / NeuroMaps)
- Marmoset: Brain/MINDS / MBM-derived reference with AC-centered coordinate adjustment (cross-referenced with Brain/MINDS, MBM, and Paxinos atlases)
- Mouse: High-resolution diffusion MRI MDT (cross-referenced with Allen Brain Atlas)
- Rat: MDT generated from ex vivo diffusion MRI aligned to the common framework