Checking Your Output

fMRIPrep writes one self-contained HTML report per subject into your output directory. Open them in a browser on the SCC:

[scc4]$ module load firefox
[scc4]$ firefox --new-window /projectnb/your_project/bids/derivatives/fmriprep/sub-01.html &

Read every report. fMRIPrep is designed to run unattended, but it will happily produce a complete, confident-looking report for a subject whose registration failed. The reports are the only place that failure is visible.

Reading the Report

Anatomical Processing

Susceptibility Distortion Correction

BOLD to Anatomical Registration

The Carpet Plot and Confounds

The Derivatives

File	What it is	When you need it

Confounds

Confound	What it measures	Notes

The Boilerplate

fMRIPrep writes a methods paragraph describing exactly what it did to your data, with citations, into the output directory.