11.1.1. Macaque Atlas: D99 v2.0 (current)


This page describes the D99 Atlas v2.0: a macaque template and cortical and subcortical atlas, as well as how to download it. The atlas is distributed as a single volume with combined cortical and subcortical areas.

This is a comprehensive, MRI-histology based atlas of the Rhesus macaque monkey brain with segmentation of both cortical and subcortical areas in one 3D volume (see related figure below). We mapped a total of 368 (149 cortical+219 subcortical) regions in this atlas (see suppl Table 1). It is important to note that the 219 parcellated “subcortical” regions also include non-subcortical regions such as the cerebellar cortex and the hippocampal formation. This version 2 of the “D99” template atlas is intended for use as a reference standard for macaque neuroanatomical, functional, and connectional imaging studies involving both cortical and subcortical targets.


You can download and unpack the updated D99 v2.0 atlas and template in any of the following ways:

  • (the AFNI way) copy+paste:

  • (the plain Linux-y terminal way) copy+paste:

    curl -O https://afni.nimh.nih.gov/pub/dist/atlases/macaque/D99_Saleem/D99_v2.0_dist.tgz
    tar -xvf D99_v2.0_dist.tgz
  • (the mouseclick+ way) click here:
    ... and then unpack the zipped directory by either clicking on it or using the above tar command.


D99 related files



symmetric atlas of cortical+subcortial regions


ex vivo MTR D99 volume template


atlas of only right hemisphere


spreadsheet with all 368 segmented areas in the atlas


abbreviations of the 368 areas used in this atlas


useful lists of label combinations


directory of surfaces for right hemisphere

Example images

Top row: This updated D99 digital atlas (version 2.0), now with combined cortical and subcortical segmentation overlaid on the horizontal, sagittal, and coronal D99 ex-vivo MRI template. The cross-hairs in these images show the same location of thalamic subregion VPLc (ventral posterior lateral caudal nucleus) in different planes of sections. Bottom row: The spatial location of segmented subcortical regions on the dorsal and lateral views in 3D. The selected subcortical regions are also indicated with cortical areas in top row. For the segmentation of cortical areas, see below. Abbreviations: 9d-dorsal prefrontal area; SCP-superior cerebellar peduncle; V1-primary visual cortex. Orientation: D-dorsal; V-ventral; R-rostral; C-caudal; L-lateral. Scale bar (10 mm) in the top row applies to sagittal as well as horizontal (axial) and coronal slices.

D99 digital atlas version 2.0 with combined cortical and subcortical segmentation


D99 digital atlas version 2.0 cortical segmentation surfaces


AFNI environment variables

The @Install_D99_macaque command automatically adds AFNI environment variables to use the D99_v2.0 atlas, but these variables can be configured in your ~/.afnirc file in your home directory to take advantage of the D99 atlas for whereami, Show atlas colors and Go to atlas location in the AFNI GUI:

AFNI_SUPP_ATLAS_DIR = directory_where_you_have_installed_D99v2_atlas
AFNI_ATLAS_COLORS = Saleem_D99_v2.0


If you make use of this v2.0 of the D99 atlas, template or accompanying surfaces in your research, please cite this updated 2021 reference:

Saleem KS, Avram AV, Glen D, Yen CC-C, Ye FQ, Komlosh M, Basser PJ (2021). High-resolution mapping and digital atlas of subcortical regions in the macaque monkey based on matched MAP-MRI and histology. Neuroimage 245:118759.

Note that the cortical or subcortical segmentations and area labels in this atlas should not be modified or altered.

For questions, comments and/or suggestions, contact:

Kadharbatcha Saleem (CNRM/HJF/NICHD-NIH)
kadharbatcha.saleem.ctr at usuhs.edu
saleemks at nih.gov
kadsaleem99 at gmail.com
Daniel Glen (NIMH, NIH)
glend at mail.nih.gov