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poldracklab / pydeface

defacing utility for MRI images
MIT License
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pydeface usage #57

Closed ironb25 closed 7 months ago

ironb25 commented 7 months ago

Hello,

I wanted to get thoughts on if it matters to use pydeface either before preprocessing of MRI or after preprocessing of MRI? Preprocessing steps include registration, bias correction and skull stripping.

Thanks, Rohan

ofgulban commented 7 months ago

Hi @ironb25 ,

Thanks for your question. Skull stripping means that everything other than the brain is removed from the image (face included). Therefore, defacing afterwards does not make sense. If you are planning to share the skull stripped version of your data, you can skip defacing. If you decide to share the "unpreprocessed" version of your data, then you should probably have defacing. All these assume that you have the face included in your MRI coverage to begin with, which is not always the case for e.g. very high resolution datasets with partial brain coverage.

Hope this helps, Faruk

ironb25 commented 7 months ago

Yes, thats very helpful. Thank you for quick help.