Template and atlas zoo

Brainana supports multiple NHP templates and atlases for registration and parcellation. The overview below summarizes the template and atlas options available in the pipeline.

Overview of template and atlas zoo options.

Template zoo

Download: template_zoo/template

The following templates can be used as output_space (e.g. in Command-line arguments or in the configuration). Choose a template and/or resolution (e.g. NMT2Sym:res-05) via the configuration generator or a config YAML.

  • NMT2Sym (doi) — NMT v2 symmetric template.

    • Multiple resolutions are available (e.g. res-025, res-05, res-1).

    • NMT2Sym:res-05 is the Brainana default.

  • NMT2Asym (doi) — NMT v2 asymmetric (left/right preserved) template.

  • MEBRAINS (doi)

  • Yerkes19 (doi)

  • D99 (doi)

Custom template

Instead of a bundled template name, output_space also accepts a path to your own template image. Pass an absolute path to a .nii / .nii.gz file (via --output_space or template.output_space in a config YAML). Outputs then use the fixed BIDS space label template (e.g. *_space-template_*), and the resolved path is recorded in each derivative’s JSON sidecar and in dataset_description.json (TemplateSource.Custom: true).

# Local run
./run_brainana.sh run main.nf \
    --bids_dir /path/to/bids --output_dir /path/to/out \
    --output_space /path/to/my_template.nii.gz

# Docker: mount the template into the container and pass the in-container path
docker run --rm \
    -v /path/to/bids:/input -v /path/to/out:/output \
    -v /path/to/my_template.nii.gz:/template.nii.gz \
    liuxingyu987/brainana:<version> /input /output --output_space /template.nii.gz

The path must exist and end in .nii/.nii.gz — otherwise the run aborts immediately with an error (there is no silent fallback). A custom template has no bundled atlases, so atlas-based outputs are skipped for the template space.

Atlas zoo

Download: template_zoo/atlas

  • ARM1–ARM6 (doi) — Combined hierarchical macaque brain atlas.

    • ARM merges CHARM for cortical regions and SARM for subcortical regions.

    • Six levels of parcellation granularity are available (1 = coarsest, 6 = finest).

    • Brainana performs individual ARM2 parcellations for T1w data.

  • D99

    • Saleem, K.S. & Logothetis, N.K. A combined MRI and histology atlas of the rhesus monkey brain. San Diego, CA: Academic Press, 2007.

  • Retinotopy (doi) — Group-average polar angle and eccentricity maps for mapping visual field representations (e.g. V1, V2, V3).

  • Other atlases * See the download directory above for the full list and references.

Note

FreeSurfer-format surfaces and atlases for NMT2Sym, NMT2Asym, and MEBRAINS are available at macaque_template_surfaces.