Subcortical Atlas of the Rhesus Macaque (SARM) for Magnetic Resonance Imaging

Abstract

Digitized neuroanatomical atlases are crucial for localizing brain structures and analyzing functional networks identified by magnetic resonance imaging (MRI). To aid in MRI data analysis, we have created a comprehensive parcellation of the rhesus macaque subcortex using a high-resolution ex vivo structural imaging scan. The structural scan and its parcellation were warped to the updated 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 subcortical parcellation and nomenclature reflect those of the 4th edition of the Rhesus Monkey Brain in Stereotaxic Coordinates (RMBSC4; Paxinos et al., in preparation). The SARM features six parcellation levels, arranged hierarchically from fine regions-of-interest (ROIs) to broader composite regions, suited for fMRI studies. As a test, we ran a functional localizer for the dorsal lateral geniculate (DLG) nucleus in three macaques and found significant fMRI activation in this atlas region. The SARM has been made openly available to the neuroimaging community and can easily be used with common MR data processing software, such as AFNI, where the atlas can be embedded into the software alongside cortical macaque atlases.HighlightsWe present the Subcortical Atlas of the Rhesus Macaque (SARM).SARM provides a neuroanatomical reference frame for neuroimaging analysis.The entire subcortex is mapped, including the thalamus, basal ganglia, and brainstem.ROIs are grouped hierarchically, making SARM useful at multiple spatial resolutions.SARM is in the NMT v2 template space and complements the CHARM atlas for the cortex.

Effective connectivity and spatial selectivity-dependent fMRI changes elicited by microstimulation of pulvinar and LIP

“…Note that dPul(a) label in each animal does not imply that these sites were in the anterior (sometimes called oral) pulvinar, which is located further anterior than the majority of our dPul(a) sites, as can be seen in the NMT v2 SARM atlas space ( Figure S2 ). In monkey B, however, both dPul(a) and dPul stimulation sites were by ∼1.5-2 mm more anterior than in monkey C in the normalized atlas space, and extended into anterior pulvinar according to the SARM atlas (Hartig et al, 2020).…”

“…The coronal template outlines were adapted from http://braininfo.rprc.washington.edu/PrimateBrainMaps/atlas/Mapindex.html, also available at https://scalablebrainatlas.incf.org/macaque/DB09 (Wu et al, 2000). For all analyses we utilized the recent SARM atlas in NMT v2 template space that uses anterior, medial, lateral and inferior delineation (APul, MPul, LPul, IPul) (Hartig et al, 2020; Jung et al, 2021). Since various atlases and research papers adopt different pulvinar nomenclature and abbreviations (e.g.…”

“…To facilitate the comparability between the results in two individual animals, and to promote standardization for data sharing, we utilized recently published NMT v2 template and associated hierarchical cortical CHARM and subcortical SARM atlases (Hartig et al, 2020; Jung et al, 2021; Seidlitz et al, 2018). As compared to the AC-PC space with the anterior commissure (AC) as an origin, NMT v2 is in a stereotaxic space, with the origin at the intersection of the midsagittal plane and the interaural line.…”

Brainwide mesoscale functional networks revealed by focal infrared neural stimulation of the amygdala

“…All structural and functional images were co-registered to the digital version of rhesus monkey atlas with AFNI command 3dAllineate and 3dNwarpApply. We used D99 digital atlas (version 1.2b) (Reveley et al, 2016) for cortical segmentation, and SARM digital atlas (Hartig et al, 2020) for subcortical segmentation. The alignment was then manually examined according to an MR-histology atlas (Saleem and Logothetis, 2012), as well as www.brainmaps.org for subcortical and brainstem sites, annotations of brain regions were then assigned to all voxels in the brain.…”