Hi all,
I have encountered some strange behavior with mri_deface.
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
<https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface>
1: When I ran that, many of the files defaced correctly, but a sizable number
had only the inside of the face removed (eg. nasal cavity, inside of mouth,
etc), 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? As it is,
they are still very much identifiable.
2: Thinking I may have an outdated version of mri_deface, I tried downloading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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