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Add pydeface to Prep subworkflow #29

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adam2392 opened this issue Jul 2, 2020 · 0 comments
Open

Add pydeface to Prep subworkflow #29

adam2392 opened this issue Jul 2, 2020 · 0 comments
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enhancement New feature or request good first issue Good for newcomers

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@adam2392
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adam2392 commented Jul 2, 2020

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.

@adam2392 adam2392 added enhancement New feature or request good first issue Good for newcomers labels Jul 2, 2020
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