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
MailScanner
has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0.
Thank
you in advance for your response.
Sincerely,
Jaiashre.