RT Journal Article
SR Electronic
T1 A comprehensive macaque fMRI pipeline and hierarchical atlas
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.08.05.237818
DO 10.1101/2020.08.05.237818
A1 Benjamin Jung
A1 Paul A. Taylor
A1 Jakob Seidlitz
A1 Caleb Sponheim
A1 Pierce Perkins
A1 Leslie G. Ungerleider
A1 Daniel Glen
A1 Adam Messinger
YR 2020
UL http://biorxiv.org/content/early/2020/08/06/2020.08.05.237818.abstract
AB Functional neuroimaging research in the non-human primate (NHP) has been advancing at a remarkable rate. The increase in available data establishes a need for robust analysis pipelines designed for NHP neuroimaging and accompanying template spaces to standardize the localization of neuroimaging results. Our group recently developed the NIMH Macaque Template (NMT), a high-resolution population average anatomical template and associated neuroimaging resources, providing researchers with a standard space for macaque neuroimaging (Seidlitz, Sponheim et al., 2018). Here, we release NMT v2, which includes both symmetric and asymmetric templates in stereotaxic orientation, with improvements in spatial contrast, processing efficiency, and segmentation. We also introduce the Cortical Hierarchy Atlas of the Rhesus Macaque (CHARM), a hierarchical parcellation of the macaque cerebral cortex with varying degrees of detail. These tools have been integrated into the neuroimaging analysis software AFNI (Cox, 1996) to provide a comprehensive and robust pipeline for fMRI processing, visualization and analysis of NHP data. AFNI’s new @animal_warper program can be used to efficiently align anatomical scans to the NMT v2 space, and afni_proc.py integrates these results with full fMRI processing using macaque-specific parameters: from motion correction through regression modeling. Taken together, the NMT v2 and AFNI represent an all-in-one package for macaque functional neuroimaging analysis, as demonstrated with available demos for both task and resting state fMRI.HighlightsThe NMT v2, a stereotaxically aligned symmetric macaque template, is introduced.A new atlas (CHARM), defined on NMT v2, parcellates the cortex at six spatial scales.AFNI’s @animal_warper aligns and maps data between monkey anatomicals and templates.AFNI’s afni_proc.py facilitates monkey fMRI analysis with automated scripting and QC.Demos of macaque task and resting state fMRI analysis with these tools are provided.Competing Interest StatementThe authors have declared no competing interest.