Using fMRIPrep on the SCC

fMRIPrep is a preprocessing pipeline for task-based and resting-state functional MRI. It takes a BIDS dataset and applies a standard, well-validated sequence of steps — skull stripping, susceptibility distortion correction, head-motion correction, coregistration, normalization to a standard space, and confound estimation — while writing a detailed visual report for every subject it touches.

This guide covers running fMRIPrep on Boston University's Shared Computing Cluster (SCC). It documents fMRIPrep 25.2.5.

Before You Start

fMRIPrep requires a BIDS-valid dataset as input. We recommend running MRIQC first, so that you screen out unusable scans before committing the compute time fMRIPrep needs.

Contents

• Getting Started — loading the fMRIPrep module on the SCC.
• Running fMRIPrep — what the command-line options do.
• Running fMRIPrep on the SCC — the participant-level batch job.
• Checking Your Output — reading the HTML reports and the derivatives.
• Appendix — resource recommendations and version support.

Additional Resources

• fMRIPrep documentation
• RCS fMRIPrep software page
• RCS modules page

Questions? Contact us at help@scc.bu.edu.