Defaced anatomical data fails BIDS validator

1

Hi,

I’m starting to use pydeface.py on my anatomical data, where in my sub-${s}/anat directory I have the files sub-${s}_T1w.nii.gz and sub-${s}_T1w_defaced.nii.gz

This leads to a bids-validation error, so I was wondering whether I need to rename the _defaced file to sub-${s}_T1w.nii.gz or is there a more appropriate method?

Thanks again

2

Renaming the defaced images to sub-${s}_T1w.nii.gz is the recommended approach.

3

Hi Chris, I’m new to this, and I was wondering if this recommendation means that you’re essentially supposed to overwrite/replace your original source file? Also I feel like defacing is a pretty typical step, and this isn’t in the BIDS spec- or if it is, could you point me to it? Thank you!

4

You can keep source images (that include facial features) in sourcedata - see https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#source-vs-raw-vs-derived-data.

5

Thank you for that! The difference between raw and source was/is a bit confusing, since we are trying to keep everything in BIDS.

6

you can leave it as sub-${s}_acq-defaced_T1w.nii.gz