API tools faq
paste
Advertisement
Guest User

recon-all-lh.cmd

a guest
Dec 6th, 2019
172
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 4.59 KB | None | 0 0
raw download clone embed print report
  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
Advertisement
Add Comment
Please, Sign In to add comment
Advertisement
Public Pastes
Advertisement
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy.  OK, I Understand
Not a member of Pastebin yet?
Sign Up, it unlocks many cool features!