Add pydeface to Prep subworkflow
adam2392 opened this issue · comments
Adam Li commented
Describe the problem
Defacing a MRI and CT scan should ideally be automatic and part of the workflow to enable sharing of the results of the data trivially via OpenNeuro.
Describe your solution
Add pydeface
pydeface to the installation python dependencies and also the Docker recipe.
Implement rule deface_scans:
in prep.smk
file.
Describe possible alternatives
Defacing can always occur via fiducials and mne_bids.write_anat
, but pydeface seems like a way simpler solution.
Additional context
Thanks Greydon Gilmore for bringing it up.