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- #---------------------------------
- # New invocation of recon-all Wed Oct 16 19:25:28 UTC 2019
- #--------------------------------------------
- #@# Tessellate lh Wed Oct 16 19:25:29 UTC 2019
- mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
- mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
- rm -f ../mri/filled-pretess255.mgz
- mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
- #--------------------------------------------
- #@# Smooth1 lh Wed Oct 16 19:25:32 UTC 2019
- mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
- #--------------------------------------------
- #@# Inflation1 lh Wed Oct 16 19:25:36 UTC 2019
- mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
- #--------------------------------------------
- #@# QSphere lh Wed Oct 16 19:25:50 UTC 2019
- mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
- #--------------------------------------------
- #@# Fix Topology Copy lh Wed Oct 16 19:27:26 UTC 2019
- cp ../surf/lh.orig.nofix ../surf/lh.orig
- cp ../surf/lh.inflated.nofix ../surf/lh.inflated
- #@# Fix Topology lh Wed Oct 16 19:27:26 UTC 2019
- mris_fix_topology -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-06 lh
- mris_euler_number ../surf/lh.orig
- mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
- rm ../surf/lh.inflated
- #--------------------------------------------
- #@# Make White Surf lh Wed Oct 16 19:38:00 UTC 2019
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-06 lh
- #--------------------------------------------
- #@# Smooth2 lh Wed Oct 16 19:41:45 UTC 2019
- mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
- #--------------------------------------------
- #@# Inflation2 lh Wed Oct 16 19:41:49 UTC 2019
- mris_inflate -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
- #--------------------------------------------
- #@# Curv .H and .K lh Wed Oct 16 19:42:02 UTC 2019
- mris_curvature -w lh.white.preaparc
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
- #-----------------------------------------
- #@# Curvature Stats lh Wed Oct 16 19:42:53 UTC 2019
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-06 lh curv sulc
- #--------------------------------------------
- #@# Sphere lh Wed Oct 16 19:42:56 UTC 2019
- mris_sphere -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
- #--------------------------------------------
- #@# Surf Reg lh Wed Oct 16 19:53:59 UTC 2019
- mris_register -curv -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg
- #--------------------------------------------
- #@# Jacobian white lh Wed Oct 16 20:13:56 UTC 2019
- mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv lh Wed Oct 16 20:13:57 UTC 2019
- mrisp_paint -a 5 /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
- #-----------------------------------------
- #@# Cortical Parc lh Wed Oct 16 20:13:58 UTC 2019
- mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-06 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot
- #--------------------------------------------
- #@# Make Pial Surf lh Wed Oct 16 20:14:08 UTC 2019
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-06 lh
- #--------------------------------------------
- #@# Surf Volume lh Wed Oct 16 20:24:09 UTC 2019
- #---------------------------------
- # New invocation of recon-all Sat Jul 25 00:14:37 PDT 2020
- #--------------------------------------------
- #@# Curv .H and .K lh Sat Jul 25 00:14:42 PDT 2020
- mris_curvature -w lh.white.preaparc
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
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