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ds000114
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freesurfer-6.0.1
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sub-09
/
scripts
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recon-all-lh.cmd

recon-all-lh.cmd 4.6 KB
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  1. 

  2. 

  3. #---------------------------------
    4. 

  4. # New invocation of recon-all Wed Oct 16 19:29:07 UTC 2019 
    5. 

  5. #--------------------------------------------
    6. 

  6. #@# Tessellate lh Wed Oct 16 19:29:08 UTC 2019
    7. 

  7. 

  8.  mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz 
    9. 

  9. 

  10. 

  11.  mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 
    12. 

  12. 

  13. 

  14.  rm -f ../mri/filled-pretess255.mgz 
    15. 

  15. 

  16. 

  17.  mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 
    18. 

  18. 

  19. #--------------------------------------------
    20. 

  20. #@# Smooth1 lh Wed Oct 16 19:29:12 UTC 2019
    21. 

  21. 

  22.  mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 
    23. 

  23. 

  24. #--------------------------------------------
    25. 

  25. #@# Inflation1 lh Wed Oct 16 19:29:16 UTC 2019
    26. 

  26. 

  27.  mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 
    28. 

  28. 

  29. #--------------------------------------------
    30. 

  30. #@# QSphere lh Wed Oct 16 19:29:29 UTC 2019
    31. 

  31. 

  32.  mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 
    33. 

  33. 

  34. #--------------------------------------------
    35. 

  35. #@# Fix Topology Copy lh Wed Oct 16 19:30:59 UTC 2019
    36. 

  36. 

  37.  cp ../surf/lh.orig.nofix ../surf/lh.orig 
    38. 

  38. 

  39. 

  40.  cp ../surf/lh.inflated.nofix ../surf/lh.inflated 
    41. 

  41. 

  42. #@# Fix Topology lh Wed Oct 16 19:30:59 UTC 2019
    43. 

  43. 

  44.  mris_fix_topology -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-09/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-09 lh 
    45. 

  45. 

  46. 

  47.  mris_euler_number ../surf/lh.orig 
    48. 

  48. 

  49. 

  50.  mris_remove_intersection ../surf/lh.orig ../surf/lh.orig 
    51. 

  51. 

  52. 

  53.  rm ../surf/lh.inflated 
    54. 

  54. 

  55. #--------------------------------------------
    56. 

  56. #@# Make White Surf lh Wed Oct 16 19:36:07 UTC 2019
    57. 

  57. 

  58.  mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-09 lh 
    59. 

  59. 

  60. #--------------------------------------------
    61. 

  61. #@# Smooth2 lh Wed Oct 16 19:40:11 UTC 2019
    62. 

  62. 

  63.  mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm 
    64. 

  64. 

  65. #--------------------------------------------
    66. 

  66. #@# Inflation2 lh Wed Oct 16 19:40:15 UTC 2019
    67. 

  67. 

  68.  mris_inflate -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-09/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated 
    69. 

  69. 

  70. #--------------------------------------------
    71. 

  71. #@# Curv .H and .K lh Wed Oct 16 19:40:29 UTC 2019
    72. 

  72. 

  73.  mris_curvature -w lh.white.preaparc 
    74. 

  74. 

  75. 

  76.  mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated 
    77. 

  77. 

  78. 

  79. #-----------------------------------------
    80. 

  80. #@# Curvature Stats lh Wed Oct 16 19:41:21 UTC 2019
    81. 

  81. 

  82.  mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-09 lh curv sulc 
    83. 

  83. 

  84. #--------------------------------------------
    85. 

  85. #@# Sphere lh Wed Oct 16 19:41:24 UTC 2019
    86. 

  86. 

  87.  mris_sphere -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-09/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 
    88. 

  88. 

  89. #--------------------------------------------
    90. 

  90. #@# Surf Reg lh Wed Oct 16 19:48:36 UTC 2019
    91. 

  91. 

  92.  mris_register -curv -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-09/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. 

  93. 

  94. #--------------------------------------------
    95. 

  95. #@# Jacobian white lh Wed Oct 16 20:08:21 UTC 2019
    96. 

  96. 

  97.  mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white 
    98. 

  98. 

  99. #--------------------------------------------
    100. 

  100. #@# AvgCurv lh Wed Oct 16 20:08:23 UTC 2019
    101. 

  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. 

  103. 

  104. #-----------------------------------------
    105. 

  105. #@# Cortical Parc lh Wed Oct 16 20:08:24 UTC 2019
    106. 

  106. 

  107.  mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-09 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot 
    108. 

  108. 

  109. #--------------------------------------------
    110. 

  110. #@# Make Pial Surf lh Wed Oct 16 20:08:34 UTC 2019
    111. 

  111. 

  112.  mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-09 lh 
    113. 

  113. 

  114. #--------------------------------------------
    115. 

  115. #@# Surf Volume lh Wed Oct 16 20:18:34 UTC 2019
    116. 

  116. 

  117. 

  118. #---------------------------------
    119. 

  119. # New invocation of recon-all Sat Jul 25 00:14:54 PDT 2020 
    120. 

  120. #--------------------------------------------
    121. 

  121. #@# Curv .H and .K lh Sat Jul 25 00:14:59 PDT 2020
    122. 

  122. 

  123.  mris_curvature -w lh.white.preaparc 
    124. 

  124. 

  125. 

  126.  mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated 
    127. 

  127.