CIVET-Chimp: An automated pipeline for MRI-based cortical surface extraction in chimpanzees

The MNI CIVET pipeline for automated extraction of cortical surfaces and evaluation of cortical thickness from in vivo human magnetic resonance imaging has recently been extended to process macaque brains and, following this work, has since been broadened to process chimpanzee (Pan troglodytes) brains. The pipeline uses the NCBR (National Chimpanzee Brain Resource) 3 T dataset, the largest high-resolution chimpanzee magnetic resonance imaging collection, and processing is performed in a derived standardized MNI-like NCBR reference space. An average population surface, constructed from the cortical surfaces of the individual NCBR subjects, serves as the basis for surface-based registration for group comparisons and ROI-based analyses, with integrated Davi130 and Brainnetome parcellations. A surface-based transformation is provided for mapping common human average surfaces (MNI152 and fsavg) to the MNI-NCBR chimpanzee average surface to facilitate inter-species studies. The modifications needed to adapt CIVET from the macaque to the chimpanzee brain are detailed and cortical thickness maps obtained for the NCBR subjects are compared to other published maps. The open usage of CIVET-Macaque and CIVET-Chimp is expected to promote collaborative efforts in data collection and processing, automated analyses, and data sharing, thereby contributing to advances in the field of non-human primate brain imaging.