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reference-preprocessing
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ABIDE_fs-6.0.0
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شاخه: master
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ABIDE_fs-6.0.0
/
0050276
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scripts
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recon-all.cmd

recon-all.cmd 9.4 KB
لینک دائمی تاريخچه Download

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  1. 

  2. 

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

  4. # New invocation of recon-all Sat Oct  7 23:29:49 CEST 2017 
    5. 

  5. 

  6.  mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050276/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig/001.mgz 
    7. 

  7. 

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

  9. #@# MotionCor Sat Oct  7 23:29:51 CEST 2017
    10. 

  10. 

  11.  cp /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/rawavg.mgz 
    12. 

  12. 

  13. 

  14.  mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig.mgz --conform 
    15. 

  15. 

  16. 

  17.  mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig.mgz 
    18. 

  18. 

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

  20. #@# Talairach Sat Oct  7 23:30:00 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 Sat Oct  7 23:31:58 CEST 2017
    33. 

  33. 

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

  35. 

  36. #--------------------------------------------
    37. 

  37. #@# Talairach Sat Oct  7 23:31:59 CEST 2017
    38. 

  38. 

  39.  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 
    40. 

  40. 

  41. 

  42.  talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig 
    43. 

  43. 

  44. talairach_avi log file is transforms/talairach_avi.log...
    45. 

  45. 

  46.  cp transforms/talairach.auto.xfm transforms/talairach.xfm 
    47. 

  47. 

  48. #--------------------------------------------
    49. 

  49. #@# Talairach Failure Detection Sat Oct  7 23:33:55 CEST 2017
    50. 

  50. 

  51.  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
    52. 

  52. 

  53. #--------------------------------------------
    54. 

  54. #@# Talairach Sat Oct  7 23:33:55 CEST 2017
    55. 

  55. 

  56.  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 
    57. 

  57. 

  58. 

  59.  talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
    60. 

  60. 

  61. 

  62.  cp transforms/talairach.auto.xfm transforms/talairach.xfm 
    63. 

  63. 

  64. #--------------------------------------------
    65. 

  65. #@# Talairach Failure Detection Sat Oct  7 23:35:11 CEST 2017
    66. 

  66. 

  67.  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
    68. 

  68. 

  69. 

  70. 

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

  72. # New invocation of recon-all Tue Oct 10 18:42:45 CEST 2017 
    73. 

  73. #--------------------------------------------
    74. 

  74. #@# MotionCor Tue Oct 10 18:42:46 CEST 2017
    75. 

  75. 

  76.  cp /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/rawavg.mgz 
    77. 

  77. 

  78. 

  79.  mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig.mgz --conform 
    80. 

  80. 

  81. 

  82.  mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig.mgz 
    83. 

  83. 

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

  85. #@# Talairach Tue Oct 10 18:42:54 CEST 2017
    86. 

  86. 

  87.  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 
    88. 

  88. 

  89. 

  90.  talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
    91. 

  91. 

  92. talairach_avi log file is transforms/talairach_avi.log...
    93. 

  93. 

  94. INFO: transforms/talairach.xfm already exists!
    95. 

  95. The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm
    96. 

  96. This is done to retain any edits made to transforms/talairach.xfm
    97. 

  97. Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm
    98. 

  98. 

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

  100. #@# Talairach Failure Detection Tue Oct 10 18:44:29 CEST 2017
    101. 

  101. 

  102.  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
    103. 

  103. 

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

  105. #@# Talairach Tue Oct 10 18:44:29 CEST 2017
    106. 

  106. 

  107.  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 
    108. 

  108. 

  109. 

  110.  talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig 
    111. 

  111. 

  112. talairach_avi log file is transforms/talairach_avi.log...
    113. 

  113. 

  114.  cp transforms/talairach.auto.xfm transforms/talairach.xfm 
    115. 

  115. 

  116. #--------------------------------------------
    117. 

  117. #@# Talairach Failure Detection Tue Oct 10 18:46:03 CEST 2017
    118. 

  118. 

  119.  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
    120. 

  120. 

  121. #--------------------------------------------
    122. 

  122. #@# Talairach Tue Oct 10 18:46:03 CEST 2017
    123. 

  123. 

  124.  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 
    125. 

  125. 

  126. 

  127.  talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
    128. 

  128. 

  129. 

  130.  cp transforms/talairach.auto.xfm transforms/talairach.xfm 
    131. 

  131. 

  132. #--------------------------------------------
    133. 

  133. #@# Talairach Failure Detection Tue Oct 10 18:47:12 CEST 2017
    134. 

  134. 

  135.  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
    136. 

  136. 

  137. 

  138. 

  139. #---------------------------------
    140. 

  140. # New invocation of recon-all Fri Oct 20 11:09:32 CEST 2017 
    141. 

  141. #--------------------------------------------
    142. 

  142. #@# MotionCor Fri Oct 20 11:09:34 CEST 2017
    143. 

  143. 

  144.  cp /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/rawavg.mgz 
    145. 

  145. 

  146. 

  147.  mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig.mgz --conform 
    148. 

  148. 

  149. 

  150.  mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050276/mri/orig.mgz 
    151. 

  151. 

  152. #--------------------------------------------
    153. 

  153. #@# Talairach Fri Oct 20 11:09:42 CEST 2017
    154. 

  154. 

  155.  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 
    156. 

  156. 

  157. 

  158.  talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
    159. 

  159. 

  160. talairach_avi log file is transforms/talairach_avi.log...
    161. 

  161. 

  162. INFO: transforms/talairach.xfm already exists!
    163. 

  163. The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm
    164. 

  164. This is done to retain any edits made to transforms/talairach.xfm
    165. 

  165. Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm
    166. 

  166. 

  167. #--------------------------------------------
    168. 

  168. #@# Talairach Failure Detection Fri Oct 20 11:11:19 CEST 2017
    169. 

  169. 

  170.  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
    171. 

  171. 

  172. #--------------------------------------------
    173. 

  173. #@# Talairach Fri Oct 20 11:11:19 CEST 2017
    174. 

  174. 

  175.  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 
    176. 

  176. 

  177. 

  178.  talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig 
    179. 

  179. 

  180. talairach_avi log file is transforms/talairach_avi.log...
    181. 

  181. 

  182.  cp transforms/talairach.auto.xfm transforms/talairach.xfm 
    183. 

  183. 

  184. #--------------------------------------------
    185. 

  185. #@# Talairach Failure Detection Fri Oct 20 11:12:54 CEST 2017
    186. 

  186. 

  187.  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
    188. 

  188. 

  189. #--------------------------------------------
    190. 

  190. #@# Talairach Fri Oct 20 11:12:54 CEST 2017
    191. 

  191. 

  192.  mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 
    193. 

  193. 

  194. 

  195.  talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
    196. 

  196. 

  197. 

  198.  cp transforms/talairach.auto.xfm transforms/talairach.xfm 
    199. 

  199. 

  200. #--------------------------------------------
    201. 

  201. #@# Talairach Failure Detection Fri Oct 20 11:14:02 CEST 2017
    202. 

  202. 

  203.  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
    204. 

  204. 

  205. 

  206. 

  207. #---------------------------------
    208. 

  208. # New invocation of recon-all Tue May 29 16:19:39 CEST 2018 
    209. 

  209. #--------------------------------------------
    210. 

  210. #@# Qdec Cache preproc lh w-g.pct..00.mgh fsaverage Tue May 29 16:19:40 CEST 2018
    211. 

  211. 

  212.  mris_preproc --s 0050276 --hemi lh --meas w-g.pct..00.mgh --target fsaverage --out lh.w-g.pct..00.mgh.fsaverage.mgh 
    213. 

  213. 

  214. 

  215. 

  216. #---------------------------------
    217. 

  217. # New invocation of recon-all Tue May 29 16:25:19 CEST 2018 
    218. 

  218. #--------------------------------------------
    219. 

  219. #@# Qdec Cache preproc lh w-g.pct.00.mgh fsaverage Tue May 29 16:25:25 CEST 2018
    220. 

  220. 

  221.  mris_preproc --s 0050276 --hemi lh --meas w-g.pct.00.mgh --target fsaverage --out lh.w-g.pct.00.mgh.fsaverage.mgh 
    222. 

  222. 

  223. 

  224. 

  225. #---------------------------------
    226. 

  226. # New invocation of recon-all Wed May 30 14:45:30 CEST 2018 
    227. 

  227. #--------------------------------------------
    228. 

  228. #@# Qdec Cache preproc lh w-g.pct.mgh fsaverage Wed May 30 14:45:36 CEST 2018
    229. 

  229. 

  230.  mris_preproc --s 0050276 --hemi lh --meas w-g.pct.mgh --target fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh 
    231. 

  231. 

  232. 

  233. 

  234. #---------------------------------
    235. 

  235. # New invocation of recon-all Thu Jul 12 13:52:32 CEST 2018 
    236. 

  236. #--------------------------------------------
    237. 

  237. #@# Qdec Cache preproc lh thickness fsaverage Thu Jul 12 13:52:39 CEST 2018
    238. 

  238. 

  239.  mris_preproc --s 0050276 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh 
    240. 

  240. 

  241. 

  242. 

  243. #---------------------------------
    244. 

  244. # New invocation of recon-all Thu Oct 17 17:47:27 CEST 2019 
    245. 

  245. #--------------------------------------------
    246. 

  246. #@# Qdec Cache preproc lh thickness fsaverage4 Thu Oct 17 17:47:33 CEST 2019
    247. 

  247. 

  248.  mris_preproc --s 0050276 --hemi lh --meas thickness --target fsaverage4 --out lh.thickness.fsaverage4.mgh 
    249. 

  249.