.. _nh_macaque_template_nmtv2: **Macaque template: NMT v2 (current)** ======================================================== .. contents:: :local: .. highlight:: none 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 :ref:`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: .. list-table:: :header-rows: 1 :widths: 20 80 :stub-columns: 0 * - 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): .. list-table:: :header-rows: 1 :widths: 20 80 :stub-columns: 0 * - 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 ----------------------------------- .. list-table:: :header-rows: 1 :widths: 100 * - Full NMT with brainmask * - .. image:: media/nmt_v2.0/img_nmt2.0sym_brainmask.axi.png * - .. image:: media/nmt_v2.0/img_nmt2.0sym_brainmask.cor.png * - .. image:: media/nmt_v2.0/img_nmt2.0sym_brainmask.sag.png | .. list-table:: :header-rows: 1 :widths: 100 * - Skull-stripped NMT with 5-tissue segmentation * - .. image:: media/nmt_v2.0/img_nmt2.0symss_segmentation.axi.png * - .. image:: media/nmt_v2.0/img_nmt2.0symss_segmentation.cor.png * - .. image:: media/nmt_v2.0/img_nmt2.0symss_segmentation.sag.png | .. list-table:: :header-rows: 1 :widths: 100 * - Skull-stripped NMT with the CHARM (level 2) * - .. image:: media/nmt_v2.0/img_nmt2.0symss_charmL2.axi.png * - .. image:: media/nmt_v2.0/img_nmt2.0symss_charmL2.cor.png * - .. image:: media/nmt_v2.0/img_nmt2.0symss_charmL2.sag.png | .. list-table:: :header-rows: 1 :widths: 100 * - Skull-stripped NMT with the CHARM (level 5) * - .. image:: media/nmt_v2.0/img_nmt2.0symss_charmL5.axi.png * - .. image:: media/nmt_v2.0/img_nmt2.0symss_charmL5.cor.png * - .. image:: media/nmt_v2.0/img_nmt2.0symss_charmL5.sag.png *The script used to make these images with ``@chauffeur_afni`` is available here:* :download:`do_view_nmt_v2.0_sym.tcsh `. .. _nh_macaque_template_nmtv2_sym_dl: 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**:: curl -O 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. .. _nh_macaque_template_nmtv2_asym_dl: 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**:: curl -O 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**