Dear Doug, We are trying to compute partial volume correction in DWI images, using your PEtsurf approach, to correct CSF contamination. Afterwards, we will compute whatever DTI metric from the corrected data and project it to surface.
As you suggested in your previous post (https://www.mail-archive.com/ freesurfer@nmr.mgh.harvard.edu/msg52436.html), we used the psf=0, so the algorithm will just perform TFE. However, we have some concerns. When we perform this correction in symptomatic subjects (e.g AD patients), we have seen that in certain regions (mainly non atrophied areas), the PVC effect is overestimated. If I am not wrong, the WM coefficient obtained from the SGTM takes into account ALL the superficial WM, and thus, will take intro account both atrophied and non atrophied regions. This is important because, unlike PET, the superficial WM diffusion, resembles the GM diffusion and it would be interesting to treat them as one compartment. Therefore, my question is if there is any option in mri_gtmpvc to use a 3-compartiment model (WM+GM, CSF, SKULL) instead of the default 4-compartment. Once we have the PVC volume, we project our DTI metric to surface using mri_vol2surf with proj-fract 0.5. However, since we used a GM thr of 30% (as in your NI paper), there are several regions with no signal (i.e 0 in the native surface). How do you solve this issue? Smooth of the data? Exclude those vertices from further analysis? Thank you in advance for your help!! Regards, Victor M
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
