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reference-preprocessing
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ABIDE_fs-6.0.0
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ABIDE_fs-6.0.0
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0050309
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scripts
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recon-all.cmd

recon-all.cmd 9.4 KB
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  1. 

  2. 

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

  4. # New invocation of recon-all Sun Oct 22 20:25:40 CEST 2017 
    5. 

  5. 

  6.  mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050309/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/orig/001.mgz 
    7. 

  7. 

  8. #--------------------------------------------
    9. 

  9. #@# MotionCor Sun Oct 22 20:25:45 CEST 2017
    10. 

  10. 

  11.  cp /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/rawavg.mgz 
    12. 

  12. 

  13. 

  14.  mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/orig.mgz --conform 
    15. 

  15. 

  16. 

  17.  mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/orig.mgz 
    18. 

  18. 

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

  20. #@# Talairach Sun Oct 22 20:25:55 CEST 2017
    21. 

  21. 

  22.  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 
    23. 

  23. 

  24. 

  25.  talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
    26. 

  26. 

  27. talairach_avi log file is transforms/talairach_avi.log...
    28. 

  28. 

  29.  cp transforms/talairach.auto.xfm transforms/talairach.xfm 
    30. 

  30. 

  31. #--------------------------------------------
    32. 

  32. #@# Talairach Failure Detection Sun Oct 22 20:27:59 CEST 2017
    33. 

  33. 

  34.  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
    35. 

  35. 

  36. 

  37.  awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/transforms/talairach_avi.log 
    38. 

  38. 

  39. 

  40.  tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/transforms/talairach_avi.log 
    41. 

  41. 

  42. #--------------------------------------------
    43. 

  43. #@# Nu Intensity Correction Sun Oct 22 20:27:59 CEST 2017
    44. 

  44. 

  45.  mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 
    46. 

  46. 

  47. 

  48.  mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/transforms/talairach.xfm nu.mgz nu.mgz 
    49. 

  49. 

  50. #--------------------------------------------
    51. 

  51. #@# Intensity Normalization Sun Oct 22 20:30:15 CEST 2017
    52. 

  52. 

  53.  mri_normalize -g 1 -mprage nu.mgz T1.mgz 
    54. 

  54. 

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

  56. #@# Skull Stripping Sun Oct 22 20:32:40 CEST 2017
    57. 

  57. 

  58.  mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 
    59. 

  59. 

  60. 

  61.  mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 
    62. 

  62. 

  63. 

  64.  cp brainmask.auto.mgz brainmask.mgz 
    65. 

  65. 

  66. #-------------------------------------
    67. 

  67. #@# EM Registration Sun Oct 22 20:55:56 CEST 2017
    68. 

  68. 

  69.  mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta 
    70. 

  70. 

  71. #--------------------------------------
    72. 

  72. #@# CA Normalize Sun Oct 22 21:14:11 CEST 2017
    73. 

  73. 

  74.  mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz 
    75. 

  75. 

  76. #--------------------------------------
    77. 

  77. #@# CA Reg Sun Oct 22 21:16:00 CEST 2017
    78. 

  78. 

  79.  mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z 
    80. 

  80. 

  81. #--------------------------------------
    82. 

  82. #@# SubCort Seg Mon Oct 23 00:50:41 CEST 2017
    83. 

  83. 

  84.  mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 
    85. 

  85. 

  86. 

  87.  mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/transforms/cc_up.lta 0050309 
    88. 

  88. 

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

  90. #@# Merge ASeg Mon Oct 23 01:57:23 CEST 2017
    91. 

  91. 

  92.  cp aseg.auto.mgz aseg.presurf.mgz 
    93. 

  93. 

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

  95. #@# Intensity Normalization2 Mon Oct 23 01:57:24 CEST 2017
    96. 

  96. 

  97.  mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz 
    98. 

  98. 

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

  100. #@# Mask BFS Mon Oct 23 02:01:19 CEST 2017
    101. 

  101. 

  102.  mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 
    103. 

  103. 

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

  105. #@# WM Segmentation Mon Oct 23 02:01:21 CEST 2017
    106. 

  106. 

  107.  mri_segment -mprage brain.mgz wm.seg.mgz 
    108. 

  108. 

  109. 

  110.  mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz 
    111. 

  111. 

  112. 

  113.  mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz 
    114. 

  114. 

  115. #--------------------------------------------
    116. 

  116. #@# Fill Mon Oct 23 02:05:49 CEST 2017
    117. 

  117. 

  118.  mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz 
    119. 

  119. 

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

  121. #@# Tessellate lh Mon Oct 23 02:06:38 CEST 2017
    122. 

  122. 

  123.  mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz 
    124. 

  124. 

  125. 

  126.  mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 
    127. 

  127. 

  128. 

  129.  rm -f ../mri/filled-pretess255.mgz 
    130. 

  130. 

  131. 

  132.  mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 
    133. 

  133. 

  134. #--------------------------------------------
    135. 

  135. #@# Tessellate rh Mon Oct 23 02:06:43 CEST 2017
    136. 

  136. 

  137.  mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz 
    138. 

  138. 

  139. 

  140.  mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 
    141. 

  141. 

  142. 

  143.  rm -f ../mri/filled-pretess127.mgz 
    144. 

  144. 

  145. 

  146.  mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 
    147. 

  147. 

  148. #--------------------------------------------
    149. 

  149. #@# Smooth1 lh Mon Oct 23 02:06:49 CEST 2017
    150. 

  150. 

  151.  mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 
    152. 

  152. 

  153. #--------------------------------------------
    154. 

  154. #@# Smooth1 rh Mon Oct 23 02:06:49 CEST 2017
    155. 

  155. 

  156.  mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 
    157. 

  157. 

  158. #--------------------------------------------
    159. 

  159. #@# Inflation1 lh Mon Oct 23 02:07:00 CEST 2017
    160. 

  160. 

  161.  mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 
    162. 

  162. 

  163. #--------------------------------------------
    164. 

  164. #@# Inflation1 rh Mon Oct 23 02:07:00 CEST 2017
    165. 

  165. 

  166.  mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 
    167. 

  167. 

  168. #--------------------------------------------
    169. 

  169. #@# QSphere lh Mon Oct 23 02:08:33 CEST 2017
    170. 

  170. 

  171.  mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 
    172. 

  172. 

  173. #--------------------------------------------
    174. 

  174. #@# QSphere rh Mon Oct 23 02:08:33 CEST 2017
    175. 

  175. 

  176.  mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 
    177. 

  177. 

  178. #--------------------------------------------
    179. 

  179. #@# Fix Topology Copy lh Mon Oct 23 02:18:13 CEST 2017
    180. 

  180. 

  181.  cp ../surf/lh.orig.nofix ../surf/lh.orig 
    182. 

  182. 

  183. 

  184.  cp ../surf/lh.inflated.nofix ../surf/lh.inflated 
    185. 

  185. 

  186. #--------------------------------------------
    187. 

  187. #@# Fix Topology Copy rh Mon Oct 23 02:18:13 CEST 2017
    188. 

  188. 

  189.  cp ../surf/rh.orig.nofix ../surf/rh.orig 
    190. 

  190. 

  191. 

  192.  cp ../surf/rh.inflated.nofix ../surf/rh.inflated 
    193. 

  193. 

  194. #@# Fix Topology lh Mon Oct 23 02:18:13 CEST 2017
    195. 

  195. 

  196.  mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050309 lh 
    197. 

  197. 

  198. #@# Fix Topology rh Mon Oct 23 02:18:13 CEST 2017
    199. 

  199. 

  200.  mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050309 rh 
    201. 

  201. 

  202. 

  203. 

  204. #---------------------------------
    205. 

  205. # New invocation of recon-all Tue May 29 16:19:41 CEST 2018 
    206. 

  206. 

  207. 

  208. #---------------------------------
    209. 

  209. # New invocation of recon-all Tue May 29 16:25:19 CEST 2018 
    210. 

  210. 

  211. 

  212. #---------------------------------
    213. 

  213. # New invocation of recon-all Tue May 29 16:56:44 CEST 2018 
    214. 

  214. #--------------------------------------------
    215. 

  215. #@# Qdec Cache preproc lh w-g.pct.00.mgh fsaverage Tue May 29 16:56:46 CEST 2018
    216. 

  216. 

  217.  mris_preproc --s 0050309 --hemi lh --meas w-g.pct.00.mgh --target fsaverage --out lh.w-g.pct.00.mgh.fsaverage.mgh 
    218. 

  218. 

  219. 

  220. 

  221. #---------------------------------
    222. 

  222. # New invocation of recon-all Wed May 30 14:45:30 CEST 2018 
    223. 

  223. #--------------------------------------------
    224. 

  224. #@# Qdec Cache preproc lh w-g.pct.mgh fsaverage Wed May 30 14:45:36 CEST 2018
    225. 

  225. 

  226.  mris_preproc --s 0050309 --hemi lh --meas w-g.pct.mgh --target fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh 
    227. 

  227. 

  228. 

  229. 

  230. #---------------------------------
    231. 

  231. # New invocation of recon-all Thu Jul 12 13:52:33 CEST 2018 
    232. 

  232. #--------------------------------------------
    233. 

  233. #@# Qdec Cache preproc lh thickness fsaverage Thu Jul 12 13:52:37 CEST 2018
    234. 

  234. 

  235.  mris_preproc --s 0050309 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh 
    236. 

  236. 

  237. 

  238. 

  239. #---------------------------------
    240. 

  240. # New invocation of recon-all Thu Oct 17 17:47:29 CEST 2019 
    241. 

  241. #--------------------------------------------
    242. 

  242. #@# Qdec Cache preproc lh thickness fsaverage4 Thu Oct 17 17:47:41 CEST 2019
    243. 

  243. 

  244.  mris_preproc --s 0050309 --hemi lh --meas thickness --target fsaverage4 --out lh.thickness.fsaverage4.mgh 
    245. 

  245.