Manual-Correction

If you want to re-run the pipeline with manually corrected FreeSurfer output, please make a copy of the original data and then replace the FreeSurfer directory in the bids/derivatives folder of your project.

You can then re-run a portion of the pipeline with the relevant arguments supplying your manually corrected FreeSurfer reconstructions:

QSIPrep : –freesurfer-input /path/to/bids/derivatives/freesurfer fMRIPrep : –fs-subjects-dir /path/to/bids/derivatives/freesurfer