pass refine_pial args for autorecon resume

bids-apps / freesurfer

BIDS app wrapping recon-all from FreeSurfer

Apache License 2.0

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Open bpinsard opened 11 months ago

bpinsard commented 11 months ago

T2/FLAIR can be input on resumed recon-all, so we want that option. Usecase:

run autorecon1: this without passing T2/FLAIR (otherwise autorecon1 crashes trying to load surfaces not yet produced)
fix horrible fs brainmask (eg. using AntsBrainExtraction/sMRIPrep)
run autorecon2/3 while inputting T2/FLAIR.

Another usecase:

bpinsard commented 3 months ago

getting back to this, if anyone has time to review. @Remi-Gau I don't know how the CI is setup, it skips non-authorized steps but returns as failed.