Is your feature request related to a problem? Please describe.
My lab is currently running recon-all outside of [fs]mriprep, editing the brain mask, then running the rest of the steps outside [fs]mriprep and using the --fs-no-resume flag when running fmriprep, since the autoresume workflow seems to wipe brain mask edits.
Describe the solution you'd like
It would be nice to be able to run [fs]mriprep with a flag --fs-from-mask-edits (or something similar) that starts the recon-all pipeline assuming that brain mask edits have been done, instead of needing to run the rest of the pipeline outside of [fs]mriprep then using --fs-no-resume.
Describe alternatives you've considered
See above
Additional context
No additional context
Is your feature request related to a problem? Please describe.
My lab is currently running
recon-alloutside of [fs]mriprep, editing the brain mask, then running the rest of the steps outside [fs]mriprep and using the--fs-no-resumeflag when running fmriprep, since the autoresume workflow seems to wipe brain mask edits.Describe the solution you'd like
It would be nice to be able to run [fs]mriprep with a flag
--fs-from-mask-edits(or something similar) that starts therecon-allpipeline assuming that brain mask edits have been done, instead of needing to run the rest of the pipeline outside of [fs]mriprep then using--fs-no-resume.Describe alternatives you've considered
See above
Additional context
No additional context