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Hi everyone,
I am running Freesurfer on some multi-echo MPRAGE data in order to extract
cortical thickness. I would like to use the multi-echo data to improve the
surfaces, and I found example code to do that on a previous post. However,
it's not clear to me if there are any steps after this. Do I need to rerun
any part of recon-all in order to use these newly created surfaces for
cortical parcellation and thickness extraction? My exact code is below:
Step 1: Run recon-all
recon-all -subject ${SUBJECT} -i {T1RMS} -sd ${OUTPUT} -mprage -3T -T2
${T2} -T2pial -hires -threads 16 -all
Step 2: Adjusting dura
mris_make_surfaces -dura memprage_echo%d.mgz 4 -sdir ${OUTPUT} ${SUBJECT}
${HEMI}
Step 3: Rerun part of recon-all to use the new surfaces?
Step 4: Extract data with aparcstats2table
Thanks for the help!
Sincerely,
Keith Jones
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