ncsl / seek

(Stereotatic ElectroEncephalography Kit) Run reconstruction, co-registration, electrode localization and surface/atlas rendering for iEEG, T1 MRI and CT data.

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Add pydeface to Prep subworkflow

adam2392 opened this issue · comments

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.