9.1.3. Macaque template: NMT v2 (current)


Here we present the NIMH Macaque Template (NMT), version 1.2 and 1.3. This is a group template from 31 macaques with surfaces and GM/WM/CSF segmentations.

The NMT v2 is the most current version of this dataset.

Please see also the accompanying CHARM (Cortical Hierarchy Atlas of the Rhesus Macaque. !!!! add link


There are both symmetric and asymmetric “variants” for the NMT v2.

Additionally, for each variant there are sets of data with different spatial resolution and FOV:

  • the “standard” NMT has 0.25 mm isotropic voxels and a “brain-focused” FOV,
  • the “low-res” NMT has 0.5 mm isotropic voxels and a “brain-focused” FOV,
  • the “full-head” NMT has 0.25 mm isotropic voxels and a larger FOV, encompassing more non-brain material.

An example of the contents in the download of the symmetric NMT v2 (which is essentially mirrored in the asymmetric version) is provided here:

NMT v2 contents Description
CustomAtlases.niml atlas description text file for AFNI
NMT_changelog.txt text file of changes and updates to the distributed datasets
NMT_v2.0_sym/ directory of the “standard” NMT files (i.e., standard spatial resolution of 0.25 mm iso voxels and brain-focused FOV)
NMT_v2.0_sym_05mm/ directory of the “low-res” NMT files (0.5 mm iso voxels; lower spatial resolution but still useful, if not preferred, for some analysis cases like in standard FMRI processing)
NMT_v2.0_sym_env.csh script to set AFNI environment variables for AFNI to use atlases and make AFNI more monkey friendly. Note: running this script will change your default atlases for whereami functionality, so if you also do human studies, be aware that you might have to change some environment settings again later.
NMT_v2.0_sym_fh/ directory of the “full head” NMT files (i.e., 0.25 mm iso voxels but a larger FOV, more non-brain material), which may be useful for some alignment cases
NMT_v2.0_sym_surfaces/ directory of GIFTI surfaces of many of the tissue/segmentation regions
supplemental_CHARM/ directory of tables of CHARM ROI index/label definitions and more
supplemental_D99/ directory of a table of D99 ROI index/label definitions
supplemental_Paxinos/ directory of a table of Paxinos ROI index/label definitions

An example of the contents of the “standard” NMT directory NMT_v2.0_sym/, above are as follows (within similar sets of data in the “low-res” and “full-head” directories):

NMT_v2.0_sym/ contents Description
CHARM_in_NMT_v2.0_sym.nii.gz hierarchical atlas (6 levels) in NMT v2 space
D99_atlas_in_NMT_v2.0_sym.nii.gz D99 atlas in NMT v2 space
NMT_v2.0_sym_brainmask.nii.gz binary brain mask (including cerebellum)
NMT_v2.0_sym_GM_cortical_mask.nii.gz binary mask of cortical GM
NMT_v2.0_sym.nii.gz the NMT v2 template, with non-brain material surrounding
NMT_v2.0_sym_segmentation.nii.gz tissue segmentation of the whole brain
NMT_v2.0_sym_SS.nii.gz the NMT itself, skullstripped, not stirred
Paxinos_atlas_in_NMT_v2.0_sym.nii.gz Paxinos atlas in NMT v2 space
supplemental_CHARM/ the CHARM atlas levels as individual volumetric files
supplemental_masks/ masks of “other” things (cerebellum, ventricles, L-R hemispheres)


To download and unpack the datasts to your present working directory, copy+paste …

  • … this for the symmetric variant:

    @Install_NMT -nmt_ver 2.0 -sym sym
  • … this for the asymmetric variant:

    @Install_NMT -nmt_ver 2.0 -sym asym


If you make use of the NMT v2 template or accompanying data in your research, please cite:

Seidlitz J, Sponheim C, Glen DR, Ye FQ, Saleem KS, Leopold DA, Ungerleider L, Messinger A (2018). “A Population MRI Brain Template and Analysis Tools for the Macaque.” NeuroImage 170: 121–31. https://doi.org/10.1016/j.neuroimage.2017.04.063.

Jung B, Taylor PA, Seidlitz PA, Sponheim C, Glen DR, Messinger A (2020). “A Comprehensive Macaque FMRI Pipeline and Hierarchical Atlas.” NeuroImage, submitted.

For questions, comments and/or suggestions, contact: