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oesteban
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ds000114
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ds000114
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freesurfer-6.0.1
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sub-10
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scripts
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recon-all-rh.cmd

recon-all-rh.cmd 4.6 KB
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  1. 

  2. 

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

  4. # New invocation of recon-all Wed Oct 16 19:48:33 UTC 2019 
    5. 

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

  6. #@# Tessellate rh Wed Oct 16 19:48:34 UTC 2019
    7. 

  7. 

  8.  mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz 
    9. 

  9. 

  10. 

  11.  mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 
    12. 

  12. 

  13. 

  14.  rm -f ../mri/filled-pretess127.mgz 
    15. 

  15. 

  16. 

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

  18. 

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

  20. #@# Smooth1 rh Wed Oct 16 19:48:37 UTC 2019
    21. 

  21. 

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

  23. 

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

  25. #@# Inflation1 rh Wed Oct 16 19:48:40 UTC 2019
    26. 

  26. 

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

  28. 

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

  30. #@# QSphere rh Wed Oct 16 19:48:51 UTC 2019
    31. 

  31. 

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

  33. 

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

  35. #@# Fix Topology Copy rh Wed Oct 16 19:50:01 UTC 2019
    36. 

  36. 

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

  38. 

  39. 

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

  41. 

  42. #@# Fix Topology rh Wed Oct 16 19:50:01 UTC 2019
    43. 

  43. 

  44.  mris_fix_topology -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-10/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-10 rh 
    45. 

  45. 

  46. 

  47.  mris_euler_number ../surf/rh.orig 
    48. 

  48. 

  49. 

  50.  mris_remove_intersection ../surf/rh.orig ../surf/rh.orig 
    51. 

  51. 

  52. 

  53.  rm ../surf/rh.inflated 
    54. 

  54. 

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

  56. #@# Make White Surf rh Wed Oct 16 19:54:12 UTC 2019
    57. 

  57. 

  58.  mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-10 rh 
    59. 

  59. 

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

  61. #@# Smooth2 rh Wed Oct 16 19:57:00 UTC 2019
    62. 

  62. 

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

  64. 

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

  66. #@# Inflation2 rh Wed Oct 16 19:57:03 UTC 2019
    67. 

  67. 

  68.  mris_inflate -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-10/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated 
    69. 

  69. 

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

  71. #@# Curv .H and .K rh Wed Oct 16 19:57:14 UTC 2019
    72. 

  72. 

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

  74. 

  75. 

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

  77. 

  78. 

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

  80. #@# Curvature Stats rh Wed Oct 16 19:57:53 UTC 2019
    81. 

  81. 

  82.  mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-10 rh curv sulc 
    83. 

  83. 

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

  85. #@# Sphere rh Wed Oct 16 19:57:56 UTC 2019
    86. 

  86. 

  87.  mris_sphere -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-10/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 
    88. 

  88. 

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

  90. #@# Surf Reg rh Wed Oct 16 20:02:18 UTC 2019
    91. 

  91. 

  92.  mris_register -curv -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-10/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 
    93. 

  93. 

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

  95. #@# Jacobian white rh Wed Oct 16 20:17:44 UTC 2019
    96. 

  96. 

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

  98. 

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

  100. #@# AvgCurv rh Wed Oct 16 20:17:45 UTC 2019
    101. 

  101. 

  102.  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 
    103. 

  103. 

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

  105. #@# Cortical Parc rh Wed Oct 16 20:17:46 UTC 2019
    106. 

  106. 

  107.  mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-10 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot 
    108. 

  108. 

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

  110. #@# Make Pial Surf rh Wed Oct 16 20:17:54 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-10 rh 
    113. 

  113. 

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

  115. #@# Surf Volume rh Wed Oct 16 20:25:43 UTC 2019
    116. 

  116. 

  117. 

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

  119. # New invocation of recon-all Sat Jul 25 00:15:20 PDT 2020 
    120. 

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

  121. #@# Curv .H and .K rh Sat Jul 25 00:15:21 PDT 2020
    122. 

  122. 

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

  124. 

  125. 

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

  127.