I am interested in using Freesurfer 7.3.2 to extract cortical thickness values from multi-echo MPRAGE data. I ran recon-all using the T1 RMS and T2 images, and then I ran dura correction using the four T1 echo images to create updated pial surfaces (examples of code below).
Next, can I simply run -parcstats to extract the relevant stats from the newly created surfaces, or are there additional processing steps that are necessary? Thank you for the help!
Example steps:
Step 1: Run recon-all
recon-all -subject ${SUBJECT} -i {$T1RMS} -sd ${OUTPUT} -mprage -3T -T2 ${T2} -T2pial -hires -threads 16 -all
Step 2: Dura correction
mris_make_surfaces -dura memprage_echo%d.mgz 4 -sdir ${OUTPUT} ${SUBJECT} ${HEMI}
Step 3: Extract values from new surfaces??
recon-all -subject ${SUBJECT} -parcstats
Sincerely,
Keith Jones