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Hello Freesurfer experts,
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
------------ Keith G. Jones, Ph.D. Postdoctoral Researcher Laboratory of Dr. Robert C. Welsh Department of Psychiatry and Biobehavioral Sciences University of California, Los Angeles