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Hello,
I am using FreeSurfer version v7.1.1. For few subjects who have already been through the complete recon-all pipeline, I would like to re-run the recon steps downstream of “-fill”. I am using the following commands to do so. Can an expert check and let me know if this encompasses all the downstream steps accurately for v7.1.1?
### Recon commands begin ###
recon-all -s [subjid] -tessellate -smooth1 -inflate1 -qsphere -fix
cd [subdir]/mri
#-------------------------------------------- #@# AutoDetGWStats lh mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh #-------------------------------------------- #@# AutoDetGWStats rh mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh #-------------------------------------------- #@# WhitePreAparc lh mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 #-------------------------------------------- #@# WhitePreAparc rh mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 #-------------------------------------------- #@# CortexLabel lh mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label #-------------------------------------------- #@# CortexLabel+HipAmyg lh mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label #-------------------------------------------- #@# CortexLabel rh mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label #-------------------------------------------- #@# CortexLabel+HipAmyg rh mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label
recon-all -s [subjid] -smooth2 -inflate2 -curvHK -autorecon3
### Recon commands end ###
Additional question – Is there an individual flag that replaces the hardcoded commands above for AutoDetGWStats, CortexLabel, WhitePreAparc and CortexLabel+HipAmyg? According to the [subjid]/scripts/recon-all.cmd file, I see that these additional commands are added to v7.1.1 but are not present in the recon steps listed here for stable 7.1.1 release https://secure-web.cisco.com/1mh5NrCnQZwjol6BqUWZ3zVU1wUDX0ceM5QaWcfAsgmEUHY....
Thank you in advance for your response.
Sincerely, Jaiashre.