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recon-all-lh.cmd

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Dec 6th, 2019
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  1.  
  2.  
  3. #---------------------------------
  4. # New invocation of recon-all Fri Dec 6 03:47:54 UTC 2019
  5. #--------------------------------------------
  6. #@# Tessellate lh Fri Dec 6 03:47:54 UTC 2019
  7.  
  8. mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
  9.  
  10.  
  11. mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
  12.  
  13.  
  14. rm -f ../mri/filled-pretess255.mgz
  15.  
  16.  
  17. mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
  18.  
  19. #--------------------------------------------
  20. #@# Smooth1 lh Fri Dec 6 03:48:04 UTC 2019
  21.  
  22. mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
  23.  
  24. #--------------------------------------------
  25. #@# Inflation1 lh Fri Dec 6 03:48:12 UTC 2019
  26.  
  27. mris_inflate -no-save-sulc -n 50 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
  28.  
  29. #--------------------------------------------
  30. #@# QSphere lh Fri Dec 6 03:51:17 UTC 2019
  31.  
  32. mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
  33.  
  34. #--------------------------------------------
  35. #@# Fix Topology Copy lh Fri Dec 6 03:55:17 UTC 2019
  36.  
  37. cp ../surf/lh.orig.nofix ../surf/lh.orig
  38.  
  39.  
  40. cp ../surf/lh.inflated.nofix ../surf/lh.inflated
  41.  
  42. #@# Fix Topology lh Fri Dec 6 03:55:17 UTC 2019
  43.  
  44. mris_fix_topology -rusage /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-TOME3024 lh
  45.  
  46.  
  47. mris_euler_number ../surf/lh.orig
  48.  
  49.  
  50. mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
  51.  
  52.  
  53. rm ../surf/lh.inflated
  54.  
  55. #--------------------------------------------
  56. #@# Make White Surf lh Fri Dec 6 04:17:56 UTC 2019
  57.  
  58. mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-TOME3024 lh
  59.  
  60. #--------------------------------------------
  61. #@# Smooth2 lh Fri Dec 6 04:24:29 UTC 2019
  62.  
  63. mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
  64.  
  65. #--------------------------------------------
  66. #@# Inflation2 lh Fri Dec 6 04:24:37 UTC 2019
  67.  
  68. mris_inflate -rusage /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/touch/rusage.mris_inflate.lh.dat -n 50 ../surf/lh.smoothwm ../surf/lh.inflated
  69.  
  70. #--------------------------------------------
  71. #@# Curv .H and .K lh Fri Dec 6 04:26:10 UTC 2019
  72.  
  73. mris_curvature -w lh.white.preaparc
  74.  
  75.  
  76. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
  77.  
  78.  
  79. #-----------------------------------------
  80. #@# Curvature Stats lh Fri Dec 6 04:28:06 UTC 2019
  81.  
  82. mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-TOME3024 lh curv sulc
  83.  
  84. #--------------------------------------------
  85. #@# Sphere lh Fri Dec 6 04:28:13 UTC 2019
  86.  
  87. mris_sphere -rusage /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
  88.  
  89. #--------------------------------------------
  90. #@# Surf Reg lh Fri Dec 6 05:02:05 UTC 2019
  91.  
  92. mris_register -curv -rusage /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/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
  93.  
  94. #--------------------------------------------
  95. #@# Jacobian white lh Fri Dec 6 05:51:33 UTC 2019
  96.  
  97. mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
  98.  
  99. #--------------------------------------------
  100. #@# AvgCurv lh Fri Dec 6 05:51:36 UTC 2019
  101.  
  102. 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
  103.  
  104. #-----------------------------------------
  105. #@# Cortical Parc lh Fri Dec 6 05:51:38 UTC 2019
  106.  
  107. mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-TOME3024 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot
  108.  
  109. #--------------------------------------------
  110. #@# Make Pial Surf lh Fri Dec 6 05:52:00 UTC 2019
  111.  
  112. mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-TOME3024 lh
  113.  
  114. #--------------------------------------------
  115. #@# Refine Pial Surfs w/ T2/FLAIR Fri Dec 6 06:12:41 UTC 2019
  116.  
  117. bbregister --s sub-TOME3024 --mov /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/orig/T2raw.mgz --lta /flywheel/v0/output/5de9524af99936001ce1a19f/freesurfer/sub-TOME3024/mri/transforms/T2raw.auto.lta --init-coreg --T2
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