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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