General
- fmriprep Resource Allocation Page
- fmriprep Confound documentation
- TemplateFlow
- fMRIprep slides (PDF of google slides used for this lesson and the previous one)
FreeSurfer
Readings
- Esteban O, Ciric R, Finc K, Blair R, Markiewicz CJ, Moodie CA et al. (2020) Analysis of task-based functional MRI data preprocessed with fMRIPrep. Nature Protocols 1-17.
- Power JD, Barnes KA, Snyder AZ, Schlaggar BL, Petersen SE (2012) Spurious but systematic correlations in functional connectivity MRI networks arise from subject motion. NeuroImage 59: 2142-2154.
- Provins C, Markiewicz C, Ciric R, Goncalves M, Caballera-Gaudes C, Poldrak R et al. (2021) Quality control and nuisance regression of fMRI, looking out where signal should not be found. Neuroimage Preprint: 2142-2154.
Troubleshooting
- Github Issues Page
- Intend4 tool
- NeuroStars
Versions
fmriprep post tools
- As of November 2024, BIDS apps are being developed to process the outputs of fMRIprep:
  - BIDSMReye provides software-based eye-tracking on fmri data.
  - fmripost-aroma runs AROMA ICA on fMRIprep derivatives.
  - fmripost-rapidtide removes time varying, physiological blood signals from fMRI.
  - XCP-D does data cleaning (e.g. confound removal), surface parcellation, and statistics for participant-level resting state scans.

fMRIPrep 3 (10 pts): Output