External Email - Use Caution
Dear FreeSurfer supporter,
We are working on a PTSD project and we used FreeSurfer to obtain the subcortical and cortical volumes for our MRI images in our patients. We ran our images through the recon-all pipeline. We then extracted the volumes from the lh/rh.aparc.stats files. We plotted the volume data for all the subjects for all the structures using SPSS to compare the volumes between the right and left hemispheres to identify outliers. After further inspection of our plots for the cingulate
structure, we believe the volumes are not accurate. The cingulate is very important in the pathogenesis of PTSD and we want to make sure the volumes we are getting are correct. We loaded the data into Freeview to check the gray and white matter segmentations and it appears that the white matter segmentation is including gray matter. We used the following command to edit the wm.mgz:
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 editing/cleaning we saved the new wm.mgz image and ran the following command:
recon-all -autorecon2-wm -autorecon3 -subjid#
Following completion we checked the new lh/rh.aparc.stats files? and the total white matter volume is increasing in some patients and decreasing in others while the gray matter is increasing in some of the subjects (which is what we expect). Do you have any suggestions for why the WM volumes would be increasing if we are removing what we think is not WM? Are we running the correct commands to edit the WM segmentation?
Any suggestions or help would greatly appreciated.
Thanks,
Leen F. Abazid Ph.D. Student Neuroscience Imaging at the Research Imaging Institute UT Health Science Center at San Antonio (210) 823-3532