CIVET-Macaque: An automated pipeline for MRI-based cortical surface generation and cortical thickness in macaques

The MNI CIVET pipeline for automated extraction of cortical surfaces and evaluation of cortical thickness from in-vivo human MRI has been extended for processing macaque brains. Processing is performed based on the NIMH Macaque Template (NMT), as the reference template, with the anatomical parcellation of the surface following the D99 and CHARM atlases. The modifications needed to adapt CIVET to the macaque brain are detailed. Results have been obtained using CIVET-macaque to process the anatomical scans of the 31 macaques used to generate the NMT and another 95 macaques from the PRIME-DE initiative. It is anticipated that the open usage of CIVET-macaque will promote collaborative efforts in data collection and processing, sharing, and automated analyses from which the non-human primate brain imaging field will advance.

Automated summary

The MNI CIVET pipeline has been extended to process macaque brains using the NMT template and D99, CHARM atlases for anatomical parcellation. Processing of anatomical scans of approximately 126 macaques using CIVET-macaque is expected to promote collaborative efforts and advance the field of non-human primate brain imaging.