Is it possible to get mri_reface to save the masks it applied to the input image? This would make it easier in QC to identify cases where alignment failed and brain voxels were included.

Hi Paul,
We have plans to add a more full featured QC interface in a future release. The program is not really "mask"-based because there's some "as-needed" logic applied in the regions, but what we recommend is simply displaying abs(original.nii-deFaced.nii)>0 overlaid on the original in your favorite nii viewer (fsleyes for us), for inspection of "were brain voxels modified". You can use fslmaths or similar for that operation quite easily. This should always be in addition to also viewing the produced .png files for the "was the whole face replaced" question. 

Best regards,
Chris Schwarz

Originally posted by Christopher Schwarz:

Hi Paul,
We have plans to add a more full featured QC interface in a future release. The program is not really "mask"-based because there's some "as-needed" logic applied in the regions, but what we recommend is simply displaying abs(original.nii-deFaced.nii)>0 overlaid on the original in your favorite nii viewer (fsleyes for us), for inspection of "were brain voxels modified". You can use fslmaths or similar for that operation quite easily. This should always be in addition to also viewing the produced .png files for the "was the whole face replaced" question. 

Best regards,
Chris Schwarz

Thank you Chris. I had already done pretty much that for my test run, so glad we're thinking the same. I'll let you know what we learn testing mri_reface at scale and developing our QC approach.