A Primer on NHP-MRI

PRIME-RE wiki for the Perplexed and Frustrated...

Initial contributions: Kep Kee Loh, Julien Sein, Ting Xu, & Rogier Mars
Further contributions: Chris Klink

This is not meant as a definitive guide. We welcome the community to keep complementing, improving, and correcting this wiki. However, we have chosen to not make the wiki completely open to the public. You can request writing access of submit an update proposal by filing an issue

Together, we can make this the information you wish you had when you started out with NHP-MRI.

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Welcome to the jungle of NHP MRI data!

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 (and all others), we try to ease you into the jungle of NHP MRI data processing.

Disclaimer. This wiki is not a text book, nor a definitive guide on how to do things. NHP MRI analysis, like all neuroimaging analysis, can be done with different methods and some are not necessarily better or worse than others. Our primary goal here is to introduce the reader to some of the possible solutions to problems they are likely to encounter sooner or later when analyzing NHP MRI data. We do not claim to be comprehensive and in fact invite our readers to contribute additional approaches that may be missing from this guide. The wiki is intended as a community-driven knowledge base, much like the PRIME-RE website itself.

Main Sections of the Guide

(Use the side-bar navigation menu to easily jump between sections)

A. Why the interest in NHP neuroimaging?
B. What makes NHP MRI challenging?
C. Typical data processing challenges and how to deal with them
D. Structural data processing steps and PRIME-RE tools
E. Functional data processing steps and PRIME-RE tools
F. Diffusion data processing steps and PRIME-RE tools
G. Cross-species comparisons and PRIME-RE tools