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??Hello,
I am a PhD student at the University of Texas in San Antonio. I am working on the PTSD project and we used the FreeSurfer to clean the MRI images of the patients. After we were done cleaning, the statistics analysis of the cingulate structure in the brain was not accurate, this part of the brain is one of the most important structure in the pathogenesis of PTSD. We believe that the FreeSurfer is messing the white matter with the gray matter and interpret what is supposed to be a gray matter as a white matter. So the values are not accurate which is affecting our results. We tried to use the command to edit the white matter but we are not sure if we are doing the correct thing. After the edit and re-running the FreeSurfer again on the white matter, the gray matter values are slightly increasing but the white matter values are increasing and decreasing, so we are not sure what the FreeSurfer is doing exactly and if our edit is correct.
This is the command we are using to edit the white matter:
freeview -v mri/brainmask.mgz \
mri/wm.mgz:colormap=heat:opacity=0.4 \
-f surf/lh.white:edgecolor=blue \
surf/lh.pial:edgecolor=red \
surf/rh.white:edgecolor=blue \
surf/rh.pial:edgecolor=red \
surf/rh.inflated:visible=0 \
surf/lh.inflated:visible=0
After done cleaning the white matter
recon-all -autorecon2-wm -autorecon3 -subjid#
Leen F. Abazid Ph.D. Student Neuroscience Imaging at the Research Imaging Institute UT Health Science Center at San Antonio (210) 823-3532