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poldracklab / pydeface

defacing utility for MRI images
MIT License
110 stars 42 forks source link

[feature request] provide dicom directory as input #37

Open greydongilmore opened 3 years ago

greydongilmore commented 3 years ago

There are some great workflows to convert a directory of dicoms into a BIDS compliant format. However, the source dicoms remain identifiable which limits the ability to share source data. At our institute, we have encountered some instances where the source dicoms were requested in-place of the nifti files.

Would it be possible to add functionality for pydeface to accept a directory of dicoms and return defaced dicoms (assuming conversion to nifti and back)?

poldrack commented 3 years ago

we would be open to a contribution to add that feature, but I'm not sure anyone on our team right now has the time to add it.

On Tue, Oct 27, 2020 at 11:28 AM Greydon Gilmore notifications@github.com wrote:

There are some great workflows to convert a directory of dicoms into a BIDS compliant format. However, the source dicoms remain identifiable which limits the ability to share source data. At our institute, we have encountered some instances where the source dicoms were requested in-place of the nifti files.

Would it be possible to add functionality for pydeface to accept a directory of dicoms and return defaced dicoms (assuming conversion to nifti and back)?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/poldracklab/pydeface/issues/37, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGUVEHXLLJ64G654AVBNULSM4GNFANCNFSM4TBHAS5Q .

-- Russell A. Poldrack Albert Ray Lang Professor of Psychology Director, DSI Center for Open and Reproducible Science Building 420 Stanford University Stanford, CA 94305

poldrack@stanford.edu http://www.poldracklab.org/

greydongilmore commented 3 years ago

can certainly do that. The approach I would take would be convert input dicoms to nifti with dcm2niix, run pydeface, convert back to dicom using Nifti2Dicom. Would this be suitable?

poldrack commented 3 years ago

sounds reasonable to me...

On Tue, Oct 27, 2020 at 2:58 PM Greydon Gilmore notifications@github.com wrote:

can certainly do that. The approach I would take would be convert input dicoms to nifti with dcm2niix, run pydeface, convert back to dicom using Nifti2Dicom. Would this be suitable?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/poldracklab/pydeface/issues/37#issuecomment-717564419, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGUVEFOHUKIWPQHN235QODSM467PANCNFSM4TBHAS5Q .

-- Russell A. Poldrack Albert Ray Lang Professor of Psychology Director, DSI Center for Open and Reproducible Science Building 420 Stanford University Stanford, CA 94305

poldrack@stanford.edu http://www.poldracklab.org/

effigies commented 11 months ago

IMO, time would be better spent making sure pydeface integrates nicely with a third-party tool that wraps a DICOM-NIfTI-DICOM round trip.

@greydongilmore Did you ever work on this?