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)

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).

Note

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