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.
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
pydefacepydeface to the installation python dependencies and also the Docker recipe.Implement
rule deface_scans:inprep.smkfile.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.