9.1.4. 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Please note that there is a newer version of this template.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).
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 |
Download¶
To download and unpack the datasts to your present working directory, copy+paste:
@Install_NMT -nmt_ver 1.3
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.
NMT v1.2¶
| A SUMA view of the NMT v1.2. |
|---|
|
Download¶
To download and unpack the datasts to your present working directory, copy+paste:
@Install_NMT -nmt_ver 1.2
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.
