#---------------------------------
# New invocation of recon-all Wed Oct 16 20:18:38 UTC 2019 
#--------------------------------------------
#@# Tessellate rh Wed Oct 16 20:18:39 UTC 2019

 mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz 


 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 


 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 

#--------------------------------------------
#@# Smooth1 rh Wed Oct 16 20:18:42 UTC 2019

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

#--------------------------------------------
#@# Inflation1 rh Wed Oct 16 20:18:46 UTC 2019

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

#--------------------------------------------
#@# QSphere rh Wed Oct 16 20:19:00 UTC 2019

 mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 

#--------------------------------------------
#@# Fix Topology Copy rh Wed Oct 16 20:20:43 UTC 2019

 cp ../surf/rh.orig.nofix ../surf/rh.orig 


 cp ../surf/rh.inflated.nofix ../surf/rh.inflated 

#@# Fix Topology rh Wed Oct 16 20:20:44 UTC 2019

 mris_fix_topology -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-09/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-09 rh 


 mris_euler_number ../surf/rh.orig 


 mris_remove_intersection ../surf/rh.orig ../surf/rh.orig 


 rm ../surf/rh.inflated 

#--------------------------------------------
#@# Make White Surf rh Wed Oct 16 20:23:01 UTC 2019

 mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-09 rh 

#--------------------------------------------
#@# Smooth2 rh Wed Oct 16 20:26:58 UTC 2019

 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm 

#--------------------------------------------
#@# Inflation2 rh Wed Oct 16 20:27:02 UTC 2019

 mris_inflate -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-09/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 

#--------------------------------------------
#@# Curv .H and .K rh Wed Oct 16 20:27:16 UTC 2019

 mris_curvature -w rh.white.preaparc 


 mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated 


#-----------------------------------------
#@# Curvature Stats rh Wed Oct 16 20:28:07 UTC 2019

 mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-09 rh curv sulc 

#--------------------------------------------
#@# Sphere rh Wed Oct 16 20:28:10 UTC 2019

 mris_sphere -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-09/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 

#--------------------------------------------
#@# Surf Reg rh Wed Oct 16 20:35:41 UTC 2019

 mris_register -curv -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-09/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 

#--------------------------------------------
#@# Jacobian white rh Wed Oct 16 20:55:40 UTC 2019

 mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white 

#--------------------------------------------
#@# AvgCurv rh Wed Oct 16 20:55:41 UTC 2019

 mrisp_paint -a 5 /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv 

#-----------------------------------------
#@# Cortical Parc rh Wed Oct 16 20:55:43 UTC 2019

 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-09 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot 

#--------------------------------------------
#@# Make Pial Surf rh Wed Oct 16 20:55:52 UTC 2019

 mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-09 rh 

#--------------------------------------------
#@# Surf Volume rh Wed Oct 16 21:06:18 UTC 2019


#---------------------------------
# New invocation of recon-all Sat Jul 25 00:16:00 PDT 2020 
#--------------------------------------------
#@# Curv .H and .K rh Sat Jul 25 00:16:01 PDT 2020

 mris_curvature -w rh.white.preaparc 


 mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated