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pass refine_pial args for autorecon resume #81

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bpinsard wants to merge 1 commit into bids-apps:master from courtois-neuromod:fix/pial_refine_resume

bpinsard commented Oct 5, 2023

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:

run all recon-all with T1 only
rerun autorecon3 adding the T2/FLAIR pial refining.


          pass refine_pial args for resume

d11d2f4

Author

bpinsard commented May 21, 2024

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.

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