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- #---------------------------------
- # New invocation of recon-all Wed Oct 16 20:10:16 UTC 2019
- #--------------------------------------------
- #@# Tessellate rh Wed Oct 16 20:10:17 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 20:10:20 UTC 2019
- mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
- #--------------------------------------------
- #@# Inflation1 rh Wed Oct 16 20:10:24 UTC 2019
- mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
- #--------------------------------------------
- #@# QSphere rh Wed Oct 16 20:10:36 UTC 2019
- mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
- #--------------------------------------------
- #@# Fix Topology Copy rh Wed Oct 16 20:12:01 UTC 2019
- cp ../surf/rh.orig.nofix ../surf/rh.orig
- cp ../surf/rh.inflated.nofix ../surf/rh.inflated
- #@# Fix Topology rh Wed Oct 16 20:12:01 UTC 2019
- mris_fix_topology -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-07/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-07 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 20:15:35 UTC 2019
- mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-07 rh
- #--------------------------------------------
- #@# Smooth2 rh Wed Oct 16 20:18:42 UTC 2019
- mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
- #--------------------------------------------
- #@# Inflation2 rh Wed Oct 16 20:18:45 UTC 2019
- mris_inflate -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-07/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
- #--------------------------------------------
- #@# Curv .H and .K rh Wed Oct 16 20:18:57 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 20:19:41 UTC 2019
- mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-07 rh curv sulc
- #--------------------------------------------
- #@# Sphere rh Wed Oct 16 20:19:44 UTC 2019
- mris_sphere -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-07/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
- #--------------------------------------------
- #@# Surf Reg rh Wed Oct 16 20:28:36 UTC 2019
- mris_register -curv -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-07/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 20:46:50 UTC 2019
- mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
- #--------------------------------------------
- #@# AvgCurv rh Wed Oct 16 20:46:51 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 20:46:52 UTC 2019
- mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-07 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 20:47:00 UTC 2019
- mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-07 rh
- #--------------------------------------------
- #@# Surf Volume rh Wed Oct 16 20:55:51 UTC 2019
- #---------------------------------
- # New invocation of recon-all Sat Jul 25 00:15:23 PDT 2020
- #--------------------------------------------
- #@# Curv .H and .K rh Sat Jul 25 00:15:24 PDT 2020
- mris_curvature -w rh.white.preaparc
- mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated
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