11.1.3. Macaque template: NMT v1 (older)

Overview

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.

Please note that there is a newer version of this template. See this page: Macaque template: NMT v2 (current).

Note

NMT v1.* and NMT v2 are not compatible. They do not overlay, and they define different spaces. Please see Jung et al. (2020) for more details about their different properties.

NMT v1.3

Contents

NMT v1.3 contents	Description
CustomAtlases.niml	atlas description text file for AFNI
D99_atlas_1.2a_al2NMT.nii.gz	D99 atlas in NMT v1.3 space
NMT_brainmask.nii.gz	binary brain mask (including cerebellum)
NMT_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_GM_cortical_mask.nii.gz	binary mask of cortical GM
NMT_GM_cortical_mask_withWM.nii.gz	map of cortical GM and WM
NMT.nii.gz	the NMT itself, including non-brain material
NMT_segmentation_4class.nii.gz	map of tissue segmentation, cortex and cerebellum
NMT_SS.nii.gz	the NMT itself, skullstripped
NMT_subject_align	a script used to perform affine and nonlinear alignments of an anatomical volume to the NMT using AFNI commands. Note: In the NMT v2, this script has been replaced with the AFNI command @animal_warper
NMT_subject_morph	a script that uses ANTs to perform template-based morphometrics of a native scan. Requires outputs from NMT_subject_align. Note: we do not recommend use of this script, as the new CIVET-macaque pipeline conducts automated surface-based morphometrics in the NMT space.
NMT_subject_pipeline	a wrapper script that performs NMT_subject_align, NMT_subject_process and NMT_subject_morph using a single command!
NMT_subject_process	a script used to perform template-based skullstripping and segmentation in the native space of a subject using AFNI and ANTs commands. Requires outputs from NMT_subject_align. Note: In the NMT v2, template-based skullstripping is performed by the AFNI command @animal_warper
processing_masks/	directory of tissue and segmentation volumes
quick_view.csh	example script to quickly view surfaces and volumes in suma and afni
README.md	go ahead, I dare you to read it
supplemental_D99/	directory of a table of D99 ROI index/label definitions
supplemental_masks/	directory of NIFTI volumes of “other” structures (vasculature, cerebellum, LR brainmask, olfactory bulb)
surfaces/	directory of GIFTI surfaces of many of the tissue/segmentation regions

Example images

Full NMT with brainmask

Skull-stripped NMT with 4-tissue segmentation

Skull-stripped NMT with D99 atlas

The script used to make these images with ``@chauffeur_afni`` is here: do_view_nmt_v1.3.tcsh

Download

You can download and unpack the datasets in any of the following ways:

• (the AFNI way) copy+paste:

  @Install_NMT -nmt_ver 1.3
  

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

  curl -O https://afni.nimh.nih.gov/pub/dist/atlases/macaque/nmt/NMT_v1.3.tgz
  tar -xvf NMT_v1.3.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 v1.3 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:

Adam.Messinger @ nih.gov

benjamin.jung @ nih.gov

glend @ mail.nih.gov

NMT v1.2

Contents

The following volumetric, surface and supplementary datasets are available as part of the download, but at present we would recommend using one of the more modern versions of the NMT for most applications.

NMT v1.2 list of contents

atlases/	blood_vasculature.gii	cerebellum.gii
index.html	lh.GM.gii	lh.GM.inflated.surf.gii
lh.mid.gii	lh.mid.inflated.surf.gii	lh.WM.gii
lh.WM.inflated.surf.gii	NMT_blood_vasculature_mask.nii.gz	NMT_both.spec
NMT_brainmask.nii.gz	NMT_cerebellum_mask.nii.gz	NMT.fullhead.nii.gz
NMT_GM_cortical_mask.nii.gz	NMT.nii.gz	NMT_olfactory_bulb_mask.nii.gz
NMT_segmentation_4class.nii.gz	NMT_segmentation_CSF.nii.gz	NMT_segmentation_GM.gz
NMT_segmentation_WM.gz	NMT_SS.nii.gz	NMT_subject_align.csh
NMT_subject_morph	NMT_subject_process	README.md
rh.GM.gii	rh.GM.inflated.surf.gii	rh.mid.gii
rh.mid.inflated.surf.gii	rh.WM.gii	rh.WM.inflated.surf.gii
volumetric_transformations/

A SUMA view of some of the data in the NMT v1.2

Download

You can download and unpack the datasets in any of the following ways:

• (the AFNI way) copy+paste:

  @Install_NMT -nmt_ver 1.2
  

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

  curl -O https://afni.nimh.nih.gov/pub/dist/atlases/macaque/nmt/NMT_v1.2.tgz
  tar -xvf NMT_v1.2.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 v1.2 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.

For questions, comments and/or suggestions, contact:

Adam.Messinger @ nih.gov

Jakob.Seidlitz @ nih.gov

glend @ mail.nih.gov