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Dear Freesurfer experts,
I’m trying to do a group comparison of cortical mean diffusivity. The study subjects form 2 groups (demented vs. non-demented). I’ve run recon-all and dt_recon on all of my study subjects. My goal is to create a surface, that has the mean diffusivity values sampled from the midpoint of the cortical thickness (50% the distance between WM and pia). I’m puzzled about three things;
1) Can I use the adc.nii created by dt_recon to represent the mean diffusivity or should I use something else?
2) Can I obtain the MD values from the midpoint of cortical thickness using mri_vol2surf command, using the optional ”–projfrac 0.5” flag? i.e. mri_vol2surf –src adc.nii.gz --out adc-to-midthick.mgz --hemi lh --projfrac 0.5 --srcreg register.dat
3) I want to smooth the the data with FWHM 15mm. Should I apply the smoothing in the mri_vol2surf (as registering the adc.nii to cortical ribbon) or in the mri_surf2surf phase (as registering the adc-to-midthick.mgz to fsaverage)?
Thank you already in advance!
Best, Antti Cajanus