Macapype: An open multi-software framework for non-human primate anatomical MRI processing

Non-human primates (NHP) are increasingly used for cross-species neuroimaging studies, either for anatomical or functional comparison with human. Anatomical MR images are typically segmented in order to define regions of interest for fMRI and diffusion MRI analyses, work on surface reconstruction or localize implanted electrodes for electrophysiology. Although MRI processing is largely standardized in humans, it is still a challenge to define robust processing pipelines for segmentation of NHP anatomical images. Because acquisition parameters and experimental settings are much more variable in NHP than in human studies (size of animals, resolution, field of view, signal-to-noise ratio, availability of T2w images, etc.), there are multiple ways to perform each processing step (see for example Balbastre et al., 2017; Tasserie et al, 2019).
To unify processing of NHP anatomical MRI, we propose Macapype (https://github.com/Macatools/macapype), an open-source framework to create custom pipelines based on Nipype (Gorgolewski et al., 2011).