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

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. HighlightsO_LIWe present the Subcortical Atlas of the Rhesus Macaque (SARM). C_LIO_LISARM provides a neuroanatomical reference frame for neuroimaging analysis. C_LIO_LIThe entire subcortex is mapped, including the thalamus, basal ganglia, and brainstem. C_LIO_LIROIs are grouped hierarchically, making SARM useful at multiple spatial resolutions. C_LIO_LISARM is in the NMT v2 template space and complements the CHARM atlas for the cortex. C_LI