Hi all, I am working on defacing around 70 scans, and was using the mri_deface program to do so. To start off with, I ran them using the version of mri_deface from version 5.3, along with the .gca files included here: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface
When I ran that, many of the files defaced correctly, but a sizable number had only the inside of the face removed, maintaining the outward facial structure. Is there a way to adjust the thresholding/settings, such that we can prevent this from happening, and thereby reduce the need to do hand-editing? On a second note, thinking I may have an outdated version of mri_deface, I tried downloading and running both 32-bit and 64-bit versions from that site (v1.22), and when I ran them, I obtained different results from the 5.3 version. The results from v1.22 (both versions) actually took out large sections of brain/skull from the right side of the head, instead of the face. We are running on 64-bit linux. Any idea what may be causing this? All the gca files were downloaded directly from the site. Let me know if any more information would be helpful! Thanks! Andrew Schoen Center for Investigating Healthy Minds Waisman Center University of Wisconsin - Madison
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