The Princeton Handbook for Reproducible Neuroimaging


Welcome to the Princeton Handbook for Reproducible Neuroimaging! The handbook is currently under active development—expect substantial changes in the near future. The goal of this handbook is to provide a reference for best practices in reproducible fMRI research. There’s no single “right” answer for many questions in fMRI, but here we try to provide helpful references and recommendations. Many elements of the handbook are specific to the Princeton Neuroscience Institute computing infrastructure, but the principles are widely applicable. This document will be updated over time as best practices evolve. We hope that this handbook will be useful as you embark on your own journey doing fMRI experiments!

Please contact us if you have any questions, feedback, or suggestions!

Brand new to neuroimaging?

Familiarize yourself with important background reading material here. If you’re unsure about any terms, check out the glossary.

Using BIDS

After running your first subject, go from raw DICOMs to preprocessed niftis. Make sure everything works before running more subjects!

Managing your preprocessed data