Does bold_confounds_wf rely on freesurfer outputs?

See post indexed_gzip.indexed_gzip.ZranError: zran_read returned error: ZRAN_READ_FAIL for details of this issue.

I am running into the error described in the above post where every time I rerun fmriprep, it requires me to rerun freesurfer otherwise it errors out midway through autorecon1 even though freesurfer is complete. Currently I believe fMRIprep is just hitting memory or hard drive related errors in bold_confounds_wf with dvars, compcor, acompcor, crowncompcor.

Do any of these modules depend on freesurfer outputs? If not, then I will just rerun fMRIprep with the “no freesurfer” flag to complete confound generation. I am able to successfully generate registered processed bold images but it just randomly errors out on some of the confounds.

Slightly. Anatomical masks are transformed into BOLD space in order to perform compcor and extract white matter and CSF signals. The transform depends on FreeSurfer in order to do bbregister.