9.1.3. Macaque template: NMT v2 (current)¶
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.
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
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 |
|---|---|
| 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) |
Download¶
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
Citation/questions¶
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.
