9.1.2. 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Please note that there is a newer version of this template.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

../../_images/img_nmt1.3_brainmask.axi.png
../../_images/img_nmt1.3_brainmask.cor.png
../../_images/img_nmt1.3_brainmask.sag.png

Skull-stripped NMT with 4-tissue segmentation

../../_images/img_nmt1.3ss_segmentation.axi.png
../../_images/img_nmt1.3ss_segmentation.cor.png
../../_images/img_nmt1.3ss_segmentation.sag.png

Skull-stripped NMT with D99 atlas

../../_images/img_nmt1.3ss_d99atlas.axi.png
../../_images/img_nmt1.3ss_d99atlas.cor.png
../../_images/img_nmt1.3ss_d99atlas.sag.png

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:

    wget 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

../../_images/nmt_v1_afnisuma.png

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:

    wget 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