Macaque atlas: the SARM
Creators: name: Hartig, Renée
name: Glen, Daniel
name: Jung, Benjamin
name: Logothetis, Nikos K.
name: Paxinos, George
name: Garza-Villarreal, Eduardo A.
name: Messinger, Adam
name: Evrard, Henry C.
Publisher: name: Zenodo
Year: 2020
Subjects: segmentation
fMRI
brainstem
non-human primates
nhp
anatomy
cerebellum
thalamus
subcortical
atlas

description: <strong>Macaque atlas: the SARM</strong> <strong>Overview</strong> 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: Macaque template: NMT v2 (current). <strong>Contents</strong> 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 <em>ex vivo structural </em>imaging and histological data. The structural scan was warped to the NIMH Macaque Template (NMT v2), an <em>in vivo</em> 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, field-of-view, 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, whereby SARM Level 1 is volume "[0]" and Level 6 is volume "[5]". The distribution also includes a binary SARM mask file. The download includes a CSV table file of the hierarchically-organized ROI labels. This can be viewed as a simple text file or within any spreadsheet software, such as Microsoft Excel. <strong>Download</strong> The SARM can be downloaded directly here, and it is also distributed as part of the NMT v2 download. For each form/variant of the NMT, there is a matching SARM dataset, as well. To download and unpack the datasets, please see the instructions… … here for the <strong>symmetric</strong> from: Download symmetric NMT v2 datasets … here for the <strong>asymmetric</strong> from: Download asymmetric NMT v2 datasets Additional supplemental files (including the original <em>ex vivo </em>anatomical scan, brain mask, subcortical parcellation, label file, transformation scripts to compute the nonlinear registration of the individual G12 to the NMTv2 and related artifact masks) may also be downloaded here. <strong>Citation/questions</strong> 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). “Magnetic Resonance Imaging Atlas of the Rhesus Macaque Subcortex.” 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 egarza@comunidad.unam.mx
description: Preprint: https://www.biorxiv.org/content/10.1101/2020.09.16.300053v1
description: {"references": ["Hartig R, Glen D, Jung B, Logothetis NK, Paxinos G, Garza-Villarreal EA, Messinger A, Evrard C (2020). \"Magnetic Resonance Imaging Atlas of the Rhesus Macaque Subcortex.\" NeuroImage, submitted."]}