Improper defacing before reorient

[pstetz]

Hello,

For some subjects we have, parts of the brain are cut off instead of the face (see below images). However, pydeface seems to work when the image is reoriented first

You should be able to reproduce this issue by doing

curl https://patrickstetz.com/pydeface/in.nii.gz --output in.nii.gz
singularity run --cleanenv -B ./:/tmp/0 docker://poldracklab/pydeface pydeface ./in.nii.gz

Input Image

After defacing

Defacing after reorienting first

Would be happy to help by submitting a PR for this!!

Best,
Patrick

[pstetz]

Looks like this is already reported in #9

[ofgulban]

@pstetz , thanks for opening this issue 👍 . You are welcome to submit a pull request.

[effigies]

#9 covers this. PRs still welcome.