9.1.1. Macaque template: NMT v2 (current)

Overview

Here we present the NIMH Macaque Template (NMT), version 2.0. This is a group template from 31 macaques with surfaces and a 5-class tissue segmentation.

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

Be sure to also check out the accompanying CHARM (Cortical Hierarchy Atlas of the Rhesus Macaque) dataset, described here.

Contents

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

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_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

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_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.

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


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

supplemental_CHARM/

the CHARM atlas levels as individual volumetric files

supplemental_masks/

masks of “other” things (cerebellum, ventricles, L-R hemispheres)


Example images

Full NMT with brainmask

../../_images/img_nmt2.0sym_brainmask.axi.png
../../_images/img_nmt2.0sym_brainmask.cor.png
../../_images/img_nmt2.0sym_brainmask.sag.png

Skull-stripped NMT with 5-tissue segmentation

../../_images/img_nmt2.0symss_segmentation.axi.png
../../_images/img_nmt2.0symss_segmentation.cor.png
../../_images/img_nmt2.0symss_segmentation.sag.png

Skull-stripped NMT with the CHARM (level 2)

../../_images/img_nmt2.0symss_charmL2.axi1.png
../../_images/img_nmt2.0symss_charmL2.cor1.png
../../_images/img_nmt2.0symss_charmL2.sag1.png

Skull-stripped NMT with the CHARM (level 5)

../../_images/img_nmt2.0symss_charmL5.axi1.png
../../_images/img_nmt2.0symss_charmL5.cor1.png
../../_images/img_nmt2.0symss_charmL5.sag1.png

The script used to make these images with ``@chauffeur_afni`` is available here: do_view_nmt_v2.0_sym.tcsh.

Download symmetric NMT v2 datasets

You can download and unpack the symmetric variant/form of the NMT v2 in any of the following ways:

  • (the AFNI way) copy+paste:

    @Install_NMT -nmt_ver 2.0 -sym sym
    
  • (the plain Linux-y terminal way) copy+paste:

    wget https://afni.nimh.nih.gov/pub/dist/atlases/macaque/nmt/NMT_v2.0_sym.tgz
    tar -xvf NMT_v2.0_sym.tgz
    
  • (the mouseclick+ way) click on this link,
    ... and then unpack the zipped directory by either clicking on it or using the above tar command.

Download asymmetric NMT v2 datasets

You can download and unpack the asymmetric variant/form of the NMT v2 in any of the following ways:

  • (the AFNI way) copy+paste:

    @Install_NMT -nmt_ver 2.0 -sym asym
    
  • (the Linux-y terminal way) copy+paste:

    wget https://afni.nimh.nih.gov/pub/dist/atlases/macaque/nmt/NMT_v2.0_asym.tgz
    tar -xvf NMT_v2.0_asym.tgz
    
  • (the mouseclick+ way) click on this link,
    ... and then unpack the zipped directory by either clicking on it or using the above tar command.

Citation/questions

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

Jung B, Taylor PA, Seidlitz PA, Sponheim C, Glen DR, Messinger A (2020). “A Comprehensive Macaque FMRI Pipeline and Hierarchical Atlas.” NeuroImage, submitted.
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.
For questions, comments and/or suggestions, contact:
Adam.Messinger @ nih.gov
benjamin.jung @ nih.gov
glend @ mail.nih.gov