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 4 th 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. Highlights We 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.

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