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With contributions by: Kep Kee Loh, Julien Sein, Ting Xu, Rogier Mars
Setting out on processing your first NHP data set can be a daunting affair, even for those who might already have considerable prior experience with human MRI data processing. Stable processing pipelines from well-known neuroimaging packages that worked perfectly across all your human subjects just keep failing/crashing or giving weirdly shaped blobs for your NHP images at the various pre-processing steps, e.g. skull-stripping, segmentation or even simply trying to register your subject image to a template. In this guide for the perplexed (and frustrated), we try to ease you into the jungle of NHP MRI data processing.
A. Why the interest in NHP neuroimaging?
B. Why is NHP neuroimaging research/data so perplexing and challenging?
C. What are the typical challenges encountered during NHP MR processing and how to deal with them?
D. Main steps in NHP structural data processing and available PRIME-RE tools
E. Main steps in NHP functional data processing and available PRIME-RE tools
F. Main steps in NHP diffusion data processing and available PRIME-RE tools
G. Cross-species comparisons and available PRIME-RE tools