9.1.4. Macaque atlas: the SARM

Overview

Here we present the Subcortical Atlas of the Rhesus Macaque (SARM).

This atlas is defined in the coordinates/space of the NMT v2 template, described here:

Contents

Digitized anatomical atlases are crucial for examining brain structure and the functional networks identified by magnetic resonance imaging (MRI). To aid in MRI data analysis, we created a complete parcellation of the rhesus macaque subcortex using high-resolution ex vivo structural imaging and histological data. The structural scan was warped to the NIMH Macaque Template (NMT v2), an in vivo population template, where the parcellation was refined to produce the Subcortical Atlas of the Rhesus Macaque (SARM). The NMT v2 has several forms and variants (based on symmetry/asymmetry, FOV and voxel size), and for each of these there is an accompanying SARM.

Using an updated version of the Rhesus Monkey Brain in Stereotaxic Coordinates (Paxinos et al., 2009; Paxinos et al., in preparation) for guidance, the SARM features 6 parcellation levels, arranged hierarchically from fine regions-of-interest (ROIs) to broader composite regions, suited for fMRI studies.

The SARM is distributed as a single dataset with six sub-volumes. Note that for the purpose of using AFNI sub-brick selectors, SARM Level 1 is volume “[0]” and Level 6 is volume “[5]”, because AFNI (like Python and C) use zero-base counting.

Note that the NMT v2.0 download also includes a CSV table file of the ROI labels, hierarchically organized. This can be viewed as a simple text file or within any spreadsheet software, such as shown in the following image.

Example images

The following images were made using the symmetric NMT v2 template (with “standard” spatial resolution = 0.25 mm, and FOV for the SARM atlas) and accompanying SARM.

NMT underlay with the SARM (level 1) overlaid

../../_images/img_nmt2.0symss_sarmL1.axi.png
../../_images/img_nmt2.0symss_sarmL1.cor.png
../../_images/img_nmt2.0symss_sarmL1.sag.png

NMT underlay with the SARM (level 2) overlaid

../../_images/img_nmt2.0symss_sarmL2.axi.png
../../_images/img_nmt2.0symss_sarmL2.cor.png
../../_images/img_nmt2.0symss_sarmL2.sag.png

NMT underlay with the SARM (level 3) overlaid

../../_images/img_nmt2.0symss_sarmL3.axi.png
../../_images/img_nmt2.0symss_sarmL3.cor.png
../../_images/img_nmt2.0symss_sarmL3.sag.png

NMT underlay with the SARM (level 4) overlaid

../../_images/img_nmt2.0symss_sarmL4.axi.png
../../_images/img_nmt2.0symss_sarmL4.cor.png
../../_images/img_nmt2.0symss_sarmL4.sag.png

NMT underlay with the SARM (level 5) overlaid

../../_images/img_nmt2.0symss_sarmL5.axi.png
../../_images/img_nmt2.0symss_sarmL5.cor.png
../../_images/img_nmt2.0symss_sarmL5.sag.png

NMT underlay with the SARM (level 6) overlaid

../../_images/img_nmt2.0symss_sarmL6.axi.png
../../_images/img_nmt2.0symss_sarmL6.cor.png
../../_images/img_nmt2.0symss_sarmL6.sag.png

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

Download

The SARM is distributed as part of the NMT v2 download using @Install_NMT (See the instructions for the NMT installation below).

The SARM atlas is available only in the symmetric NMT space.

To download and unpack the datasets together with the NMT template and atlases, please see these instructions...

You may download the SARM datasets separately, from the AFNI website using the links below. * (the plain Linux-y terminal way) copy+paste:

wget https://afni.nimh.nih.gov/pub/dist/atlases/macaque/SARM/SARM.tgz
tar -xvf SARM.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.

AFNI environment variables

The @Install_NMT script automatically adds AFNI environment variables to use the SARM atlas, but these can beThese variables can be configured in your .afnirc file in your home directory to take advantage of the SARM atlas for “whereami”, “Show atlas colors” and “Go to atlas location” in the AFNI GUI:

AFNI_SUPP_ATLAS_DIR = directory_where_you_have_installed_atlas/SARM
AFNI_ATLAS_COLORS = SARM
AFNI_WHEREAMI_DEC_PLACES = 2

Citation/questions

If you make use of the SARM in your research, please cite:

Hartig R, Glen D, Jung B, Logothetis NK, Paxinos G, Garza-Villarreal EA, Messinger A, Evrard C (2020). “Subcortical Atlas of the Rhesus Macaque (SARM) for Magnetic Resonance Imaging.” NeuroImage, submitted.
For questions, comments and/or suggestions, contact:
henry.evrard @ tuebingen.mpg.de
renee.hartig @ tuebingen.mpg.de
adam.messinger @ nih.gov
glend @ mail.nih.gov