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recon-all.cmd

recon-all.cmd 27 KB
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  1. 

  2.  mri_convert /data/in/sub-02/anat/sub-02_T1w.nii.gz /data/out/sub-02/mri/orig/001.mgz 
    3. 

  3. 

  4. #--------------------------------------------
    5. 

  5. #@# MotionCor Sat Jan 14 08:35:59 UTC 2017
    6. 

  6. 

  7.  cp /data/out/sub-02/mri/orig/001.mgz /data/out/sub-02/mri/rawavg.mgz 
    8. 

  8. 

  9. 

  10.  mri_convert /data/out/sub-02/mri/rawavg.mgz /data/out/sub-02/mri/orig.mgz --conform 
    11. 

  11. 

  12. 

  13.  mri_add_xform_to_header -c /data/out/sub-02/mri/transforms/talairach.xfm /data/out/sub-02/mri/orig.mgz /data/out/sub-02/mri/orig.mgz 
    14. 

  14. 

  15. #--------------------------------------------
    16. 

  16. #@# Talairach Sat Jan 14 08:36:08 UTC 2017
    17. 

  17. 

  18.  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz 
    19. 

  19. 

  20. 

  21.  talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
    22. 

  22. 

  23. 

  24.  cp transforms/talairach.auto.xfm transforms/talairach.xfm 
    25. 

  25. 

  26. #--------------------------------------------
    27. 

  27. #@# Talairach Failure Detection Sat Jan 14 08:37:15 UTC 2017
    28. 

  28. 

  29.  talairach_afd -T 0.005 -xfm transforms/talairach.xfm 
    30. 

  30. 

  31. 

  32.  awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /data/out/sub-02/mri/transforms/talairach_avi.log 
    33. 

  33. 

  34. 

  35.  tal_QC_AZS /data/out/sub-02/mri/transforms/talairach_avi.log 
    36. 

  36. 

  37. #--------------------------------------------
    38. 

  38. #@# Nu Intensity Correction Sat Jan 14 08:37:16 UTC 2017
    39. 

  39. 

  40.  mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 
    41. 

  41. 

  42. 

  43.  mri_add_xform_to_header -c /data/out/sub-02/mri/transforms/talairach.xfm nu.mgz nu.mgz 
    44. 

  44. 

  45. #--------------------------------------------
    46. 

  46. #@# Intensity Normalization Sat Jan 14 08:38:18 UTC 2017
    47. 

  47. 

  48.  mri_normalize -g 1 nu.mgz T1.mgz 
    49. 

  49. 

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

  51. #@# Skull Stripping Sat Jan 14 08:39:56 UTC 2017
    52. 

  52. 

  53.  mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta 
    54. 

  54. 

  55. 

  56.  mri_watershed -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 
    57. 

  57. 

  58. 

  59.  cp brainmask.auto.mgz brainmask.mgz 
    60. 

  60. 

  61. #-------------------------------------
    62. 

  62. #@# EM Registration Sat Jan 14 09:04:38 UTC 2017
    63. 

  63. 

  64.  mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta 
    65. 

  65. 

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

  67. #@# CA Normalize Sat Jan 14 09:23:36 UTC 2017
    68. 

  68. 

  69.  mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz 
    70. 

  70. 

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

  72. #@# CA Reg Sat Jan 14 09:24:59 UTC 2017
    73. 

  73. 

  74.  mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z 
    75. 

  75. 

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

  77. #@# CA Reg Inv Sat Jan 14 11:57:34 UTC 2017
    78. 

  78. 

  79.  mri_ca_register -invert-and-save transforms/talairach.m3z 
    80. 

  80. 

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

  82. #@# Remove Neck Sat Jan 14 11:58:33 UTC 2017
    83. 

  83. 

  84.  mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz 
    85. 

  85. 

  86. #--------------------------------------
    87. 

  87. #@# SkullLTA Sat Jan 14 11:59:36 UTC 2017
    88. 

  88. 

  89.  mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta 
    90. 

  90. 

  91. #--------------------------------------
    92. 

  92. #@# SubCort Seg Sat Jan 14 12:20:20 UTC 2017
    93. 

  93. 

  94.  mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz 
    95. 

  95. 

  96. 

  97.  mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /data/out/sub-02/mri/transforms/cc_up.lta sub-02 
    98. 

  98. 

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

  100. #@# Merge ASeg Sat Jan 14 12:37:57 UTC 2017
    101. 

  101. 

  102.  cp aseg.auto.mgz aseg.mgz 
    103. 

  103. 

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

  105. #@# Intensity Normalization2 Sat Jan 14 12:37:57 UTC 2017
    106. 

  106. 

  107.  mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz 
    108. 

  108. 

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

  110. #@# Mask BFS Sat Jan 14 12:40:46 UTC 2017
    111. 

  111. 

  112.  mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 
    113. 

  113. 

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

  115. #@# WM Segmentation Sat Jan 14 12:40:48 UTC 2017
    116. 

  116. 

  117.  mri_segment brain.mgz wm.seg.mgz 
    118. 

  118. 

  119. 

  120.  mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz 
    121. 

  121. 

  122. 

  123.  mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz 
    124. 

  124. 

  125. #--------------------------------------------
    126. 

  126. #@# Fill Sat Jan 14 12:42:25 UTC 2017
    127. 

  127. 

  128.  mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz 
    129. 

  129. 

  130. #--------------------------------------------
    131. 

  131. #@# Tessellate lh Sat Jan 14 12:43:03 UTC 2017
    132. 

  132. 

  133.  mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz 
    134. 

  134. 

  135. 

  136.  mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 
    137. 

  137. 

  138. 

  139.  rm -f ../mri/filled-pretess255.mgz 
    140. 

  140. 

  141. 

  142.  mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 
    143. 

  143. 

  144. #--------------------------------------------
    145. 

  145. #@# Smooth1 lh Sat Jan 14 12:43:08 UTC 2017
    146. 

  146. 

  147.  mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 
    148. 

  148. 

  149. #--------------------------------------------
    150. 

  150. #@# Inflation1 lh Sat Jan 14 12:43:10 UTC 2017
    151. 

  151. 

  152.  mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 
    153. 

  153. 

  154. #--------------------------------------------
    155. 

  155. #@# QSphere lh Sat Jan 14 12:43:30 UTC 2017
    156. 

  156. 

  157.  mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 
    158. 

  158. 

  159. #--------------------------------------------
    160. 

  160. #@# Fix Topology lh Sat Jan 14 12:46:21 UTC 2017
    161. 

  161. 

  162.  cp ../surf/lh.orig.nofix ../surf/lh.orig 
    163. 

  163. 

  164. 

  165.  cp ../surf/lh.inflated.nofix ../surf/lh.inflated 
    166. 

  166. 

  167. 

  168.  mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub-02 lh 
    169. 

  169. 

  170. 

  171.  mris_euler_number ../surf/lh.orig 
    172. 

  172. 

  173. 

  174.  mris_remove_intersection ../surf/lh.orig ../surf/lh.orig 
    175. 

  175. 

  176. 

  177.  rm ../surf/lh.inflated 
    178. 

  178. 

  179. #--------------------------------------------
    180. 

  180. #@# Make White Surf lh Sat Jan 14 12:59:01 UTC 2017
    181. 

  181. 

  182.  mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-02 lh 
    183. 

  183. 

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

  185. #@# Smooth2 lh Sat Jan 14 13:02:29 UTC 2017
    186. 

  186. 

  187.  mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm 
    188. 

  188. 

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

  190. #@# Inflation2 lh Sat Jan 14 13:02:32 UTC 2017
    191. 

  191. 

  192.  mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated 
    193. 

  193. 

  194. 

  195.  mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated 
    196. 

  196. 

  197. 

  198. #-----------------------------------------
    199. 

  199. #@# Curvature Stats lh Sat Jan 14 13:03:48 UTC 2017
    200. 

  200. 

  201.  mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-02 lh curv sulc 
    202. 

  202. 

  203. #--------------------------------------------
    204. 

  204. #@# Sphere lh Sat Jan 14 13:03:51 UTC 2017
    205. 

  205. 

  206.  mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 
    207. 

  207. 

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

  209. #@# Surf Reg lh Sat Jan 14 13:30:11 UTC 2017
    210. 

  210. 

  211.  mris_register -curv ../surf/lh.sphere /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg 
    212. 

  212. 

  213. #--------------------------------------------
    214. 

  214. #@# Jacobian white lh Sat Jan 14 13:44:00 UTC 2017
    215. 

  215. 

  216.  mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white 
    217. 

  217. 

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

  219. #@# AvgCurv lh Sat Jan 14 13:44:02 UTC 2017
    220. 

  220. 

  221.  mrisp_paint -a 5 /opt/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv 
    222. 

  222. 

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

  224. #@# Cortical Parc lh Sat Jan 14 13:44:03 UTC 2017
    225. 

  225. 

  226.  mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot 
    227. 

  227. 

  228. #--------------------------------------------
    229. 

  229. #@# Make Pial Surf lh Sat Jan 14 13:44:33 UTC 2017
    230. 

  230. 

  231.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub-02 lh 
    232. 

  232. 

  233. #--------------------------------------------
    234. 

  234. #@# Surf Volume lh Sat Jan 14 13:51:02 UTC 2017
    235. 

  235. 

  236.  mris_calc -o lh.area.mid lh.area add lh.area.pial 
    237. 

  237. 

  238. 

  239.  mris_calc -o lh.area.mid lh.area.mid div 2 
    240. 

  240. 

  241. 

  242.  mris_calc -o lh.volume lh.area.mid mul lh.thickness 
    243. 

  243. 

  244. #-----------------------------------------
    245. 

  245. #@# WM/GM Contrast lh Sat Jan 14 13:51:03 UTC 2017
    246. 

  246. 

  247.  pctsurfcon --s sub-02 --lh-only 
    248. 

  248. 

  249. #-----------------------------------------
    250. 

  250. #@# Parcellation Stats lh Sat Jan 14 13:51:07 UTC 2017
    251. 

  251. 

  252.  mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-02 lh white 
    253. 

  253. 

  254. #-----------------------------------------
    255. 

  255. #@# Cortical Parc 2 lh Sat Jan 14 13:51:15 UTC 2017
    256. 

  256. 

  257.  mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot 
    258. 

  258. 

  259. #-----------------------------------------
    260. 

  260. #@# Parcellation Stats 2 lh Sat Jan 14 13:51:53 UTC 2017
    261. 

  261. 

  262.  mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-02 lh white 
    263. 

  263. 

  264. #-----------------------------------------
    265. 

  265. #@# Cortical Parc 3 lh Sat Jan 14 13:52:01 UTC 2017
    266. 

  266. 

  267.  mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot 
    268. 

  268. 

  269. #-----------------------------------------
    270. 

  270. #@# Parcellation Stats 3 lh Sat Jan 14 13:52:30 UTC 2017
    271. 

  271. 

  272.  mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab sub-02 lh white 
    273. 

  273. 

  274. #--------------------------------------------
    275. 

  275. #@# Tessellate rh Sat Jan 14 13:52:38 UTC 2017
    276. 

  276. 

  277.  mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz 
    278. 

  278. 

  279. 

  280.  mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 
    281. 

  281. 

  282. 

  283.  rm -f ../mri/filled-pretess127.mgz 
    284. 

  284. 

  285. 

  286.  mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 
    287. 

  287. 

  288. #--------------------------------------------
    289. 

  289. #@# Smooth1 rh Sat Jan 14 13:52:42 UTC 2017
    290. 

  290. 

  291.  mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 
    292. 

  292. 

  293. #--------------------------------------------
    294. 

  294. #@# Inflation1 rh Sat Jan 14 13:52:45 UTC 2017
    295. 

  295. 

  296.  mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 
    297. 

  297. 

  298. #--------------------------------------------
    299. 

  299. #@# QSphere rh Sat Jan 14 13:53:04 UTC 2017
    300. 

  300. 

  301.  mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 
    302. 

  302. 

  303. #--------------------------------------------
    304. 

  304. #@# Fix Topology rh Sat Jan 14 13:55:27 UTC 2017
    305. 

  305. 

  306.  cp ../surf/rh.orig.nofix ../surf/rh.orig 
    307. 

  307. 

  308. 

  309.  cp ../surf/rh.inflated.nofix ../surf/rh.inflated 
    310. 

  310. 

  311. 

  312.  mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub-02 rh 
    313. 

  313. 

  314. 

  315.  mris_euler_number ../surf/rh.orig 
    316. 

  316. 

  317. 

  318.  mris_remove_intersection ../surf/rh.orig ../surf/rh.orig 
    319. 

  319. 

  320. 

  321.  rm ../surf/rh.inflated 
    322. 

  322. 

  323. #--------------------------------------------
    324. 

  324. #@# Make White Surf rh Sat Jan 14 14:09:18 UTC 2017
    325. 

  325. 

  326.  mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-02 rh 
    327. 

  327. 

  328. #--------------------------------------------
    329. 

  329. #@# Smooth2 rh Sat Jan 14 14:12:18 UTC 2017
    330. 

  330. 

  331.  mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm 
    332. 

  332. 

  333. #--------------------------------------------
    334. 

  334. #@# Inflation2 rh Sat Jan 14 14:12:20 UTC 2017
    335. 

  335. 

  336.  mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated 
    337. 

  337. 

  338. 

  339.  mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated 
    340. 

  340. 

  341. 

  342. #-----------------------------------------
    343. 

  343. #@# Curvature Stats rh Sat Jan 14 14:13:26 UTC 2017
    344. 

  344. 

  345.  mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-02 rh curv sulc 
    346. 

  346. 

  347. #--------------------------------------------
    348. 

  348. #@# Sphere rh Sat Jan 14 14:13:29 UTC 2017
    349. 

  349. 

  350.  mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 
    351. 

  351. 

  352. #--------------------------------------------
    353. 

  353. #@# Surf Reg rh Sat Jan 14 14:28:17 UTC 2017
    354. 

  354. 

  355.  mris_register -curv ../surf/rh.sphere /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg 
    356. 

  356. 

  357. #--------------------------------------------
    358. 

  358. #@# Jacobian white rh Sat Jan 14 14:41:19 UTC 2017
    359. 

  359. 

  360.  mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white 
    361. 

  361. 

  362. #--------------------------------------------
    363. 

  363. #@# AvgCurv rh Sat Jan 14 14:41:21 UTC 2017
    364. 

  364. 

  365.  mrisp_paint -a 5 /opt/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv 
    366. 

  366. 

  367. #-----------------------------------------
    368. 

  368. #@# Cortical Parc rh Sat Jan 14 14:41:22 UTC 2017
    369. 

  369. 

  370.  mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot 
    371. 

  371. 

  372. #--------------------------------------------
    373. 

  373. #@# Make Pial Surf rh Sat Jan 14 14:41:51 UTC 2017
    374. 

  374. 

  375.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub-02 rh 
    376. 

  376. 

  377. #--------------------------------------------
    378. 

  378. #@# Surf Volume rh Sat Jan 14 14:47:58 UTC 2017
    379. 

  379. 

  380.  mris_calc -o rh.area.mid rh.area add rh.area.pial 
    381. 

  381. 

  382. 

  383.  mris_calc -o rh.area.mid rh.area.mid div 2 
    384. 

  384. 

  385. 

  386.  mris_calc -o rh.volume rh.area.mid mul rh.thickness 
    387. 

  387. 

  388. #-----------------------------------------
    389. 

  389. #@# WM/GM Contrast rh Sat Jan 14 14:47:59 UTC 2017
    390. 

  390. 

  391.  pctsurfcon --s sub-02 --rh-only 
    392. 

  392. 

  393. #-----------------------------------------
    394. 

  394. #@# Parcellation Stats rh Sat Jan 14 14:48:03 UTC 2017
    395. 

  395. 

  396.  mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-02 rh white 
    397. 

  397. 

  398. #-----------------------------------------
    399. 

  399. #@# Cortical Parc 2 rh Sat Jan 14 14:48:10 UTC 2017
    400. 

  400. 

  401.  mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot 
    402. 

  402. 

  403. #-----------------------------------------
    404. 

  404. #@# Parcellation Stats 2 rh Sat Jan 14 14:48:47 UTC 2017
    405. 

  405. 

  406.  mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-02 rh white 
    407. 

  407. 

  408. #-----------------------------------------
    409. 

  409. #@# Cortical Parc 3 rh Sat Jan 14 14:48:55 UTC 2017
    410. 

  410. 

  411.  mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub-02 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot 
    412. 

  412. 

  413. #-----------------------------------------
    414. 

  414. #@# Parcellation Stats 3 rh Sat Jan 14 14:49:24 UTC 2017
    415. 

  415. 

  416.  mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab sub-02 rh white 
    417. 

  417. 

  418. #--------------------------------------------
    419. 

  419. #@# Cortical ribbon mask Sat Jan 14 14:49:31 UTC 2017
    420. 

  420. 

  421.  mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub-02 
    422. 

  422. 

  423. #--------------------------------------------
    424. 

  424. #@# ASeg Stats Sat Jan 14 14:54:33 UTC 2017
    425. 

  425. 

  426.  mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-02 
    427. 

  427. 

  428. #-----------------------------------------
    429. 

  429. #@# AParc-to-ASeg Sat Jan 14 14:56:30 UTC 2017
    430. 

  430. 

  431.  mri_aparc2aseg --s sub-02 --volmask 
    432. 

  432. 

  433. 

  434.  mri_aparc2aseg --s sub-02 --volmask --a2009s 
    435. 

  435. 

  436. #-----------------------------------------
    437. 

  437. #@# WMParc Sat Jan 14 14:57:52 UTC 2017
    438. 

  438. 

  439.  mri_aparc2aseg --s sub-02 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz 
    440. 

  440. 

  441. 

  442.  mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-02 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv 
    443. 

  443. 

  444. #--------------------------------------------
    445. 

  445. #@# BA Labels lh Sat Jan 14 15:04:52 UTC 2017
    446. 

  446. 

  447.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA1.label --trgsubject sub-02 --trglabel ./lh.BA1.label --hemi lh --regmethod surface 
    448. 

  448. 

  449. 

  450.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA2.label --trgsubject sub-02 --trglabel ./lh.BA2.label --hemi lh --regmethod surface 
    451. 

  451. 

  452. 

  453.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3a.label --trgsubject sub-02 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface 
    454. 

  454. 

  455. 

  456.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3b.label --trgsubject sub-02 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface 
    457. 

  457. 

  458. 

  459.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4a.label --trgsubject sub-02 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface 
    460. 

  460. 

  461. 

  462.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4p.label --trgsubject sub-02 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface 
    463. 

  463. 

  464. 

  465.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA6.label --trgsubject sub-02 --trglabel ./lh.BA6.label --hemi lh --regmethod surface 
    466. 

  466. 

  467. 

  468.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA44.label --trgsubject sub-02 --trglabel ./lh.BA44.label --hemi lh --regmethod surface 
    469. 

  469. 

  470. 

  471.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA45.label --trgsubject sub-02 --trglabel ./lh.BA45.label --hemi lh --regmethod surface 
    472. 

  472. 

  473. 

  474.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V1.label --trgsubject sub-02 --trglabel ./lh.V1.label --hemi lh --regmethod surface 
    475. 

  475. 

  476. 

  477.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V2.label --trgsubject sub-02 --trglabel ./lh.V2.label --hemi lh --regmethod surface 
    478. 

  478. 

  479. 

  480.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.MT.label --trgsubject sub-02 --trglabel ./lh.MT.label --hemi lh --regmethod surface 
    481. 

  481. 

  482. 

  483.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.perirhinal.label --trgsubject sub-02 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface 
    484. 

  484. 

  485. 

  486.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA1.thresh.label --trgsubject sub-02 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface 
    487. 

  487. 

  488. 

  489.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA2.thresh.label --trgsubject sub-02 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface 
    490. 

  490. 

  491. 

  492.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub-02 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface 
    493. 

  493. 

  494. 

  495.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub-02 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface 
    496. 

  496. 

  497. 

  498.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub-02 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface 
    499. 

  499. 

  500. 

  501.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub-02 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface 
    502. 

  502. 

  503. 

  504.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA6.thresh.label --trgsubject sub-02 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface 
    505. 

  505. 

  506. 

  507.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA44.thresh.label --trgsubject sub-02 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface 
    508. 

  508. 

  509. 

  510.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.BA45.thresh.label --trgsubject sub-02 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface 
    511. 

  511. 

  512. 

  513.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V1.thresh.label --trgsubject sub-02 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface 
    514. 

  514. 

  515. 

  516.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.V2.thresh.label --trgsubject sub-02 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface 
    517. 

  517. 

  518. 

  519.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/lh.MT.thresh.label --trgsubject sub-02 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface 
    520. 

  520. 

  521. 

  522.  mris_label2annot --s sub-02 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose 
    523. 

  523. 

  524. 

  525.  mris_label2annot --s sub-02 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose 
    526. 

  526. 

  527. 

  528.  mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub-02 lh white 
    529. 

  529. 

  530. 

  531.  mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub-02 lh white 
    532. 

  532. 

  533. #--------------------------------------------
    534. 

  534. #@# BA Labels rh Sat Jan 14 15:07:16 UTC 2017
    535. 

  535. 

  536.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA1.label --trgsubject sub-02 --trglabel ./rh.BA1.label --hemi rh --regmethod surface 
    537. 

  537. 

  538. 

  539.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA2.label --trgsubject sub-02 --trglabel ./rh.BA2.label --hemi rh --regmethod surface 
    540. 

  540. 

  541. 

  542.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3a.label --trgsubject sub-02 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface 
    543. 

  543. 

  544. 

  545.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3b.label --trgsubject sub-02 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface 
    546. 

  546. 

  547. 

  548.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4a.label --trgsubject sub-02 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface 
    549. 

  549. 

  550. 

  551.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4p.label --trgsubject sub-02 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface 
    552. 

  552. 

  553. 

  554.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA6.label --trgsubject sub-02 --trglabel ./rh.BA6.label --hemi rh --regmethod surface 
    555. 

  555. 

  556. 

  557.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA44.label --trgsubject sub-02 --trglabel ./rh.BA44.label --hemi rh --regmethod surface 
    558. 

  558. 

  559. 

  560.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA45.label --trgsubject sub-02 --trglabel ./rh.BA45.label --hemi rh --regmethod surface 
    561. 

  561. 

  562. 

  563.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V1.label --trgsubject sub-02 --trglabel ./rh.V1.label --hemi rh --regmethod surface 
    564. 

  564. 

  565. 

  566.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V2.label --trgsubject sub-02 --trglabel ./rh.V2.label --hemi rh --regmethod surface 
    567. 

  567. 

  568. 

  569.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.MT.label --trgsubject sub-02 --trglabel ./rh.MT.label --hemi rh --regmethod surface 
    570. 

  570. 

  571. 

  572.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.perirhinal.label --trgsubject sub-02 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface 
    573. 

  573. 

  574. 

  575.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA1.thresh.label --trgsubject sub-02 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface 
    576. 

  576. 

  577. 

  578.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA2.thresh.label --trgsubject sub-02 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface 
    579. 

  579. 

  580. 

  581.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub-02 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface 
    582. 

  582. 

  583. 

  584.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub-02 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface 
    585. 

  585. 

  586. 

  587.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub-02 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface 
    588. 

  588. 

  589. 

  590.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub-02 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface 
    591. 

  591. 

  592. 

  593.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA6.thresh.label --trgsubject sub-02 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface 
    594. 

  594. 

  595. 

  596.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA44.thresh.label --trgsubject sub-02 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface 
    597. 

  597. 

  598. 

  599.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.BA45.thresh.label --trgsubject sub-02 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface 
    600. 

  600. 

  601. 

  602.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V1.thresh.label --trgsubject sub-02 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface 
    603. 

  603. 

  604. 

  605.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.V2.thresh.label --trgsubject sub-02 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface 
    606. 

  606. 

  607. 

  608.  mri_label2label --srcsubject fsaverage --srclabel /data/out/fsaverage/label/rh.MT.thresh.label --trgsubject sub-02 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface 
    609. 

  609. 

  610. 

  611.  mris_label2annot --s sub-02 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose 
    612. 

  612. 

  613. 

  614.  mris_label2annot --s sub-02 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose 
    615. 

  615. 

  616. 

  617.  mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub-02 rh white 
    618. 

  618. 

  619. 

  620.  mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub-02 rh white 
    621. 

  621. 

  622. #--------------------------------------------
    623. 

  623. #@# Ex-vivo Entorhinal Cortex Label lh Sat Jan 14 15:09:37 UTC 2017
    624. 

  624. 

  625.  mris_spherical_average -erode 1 -orig white -t 0.4 -o sub-02 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 
    626. 

  626. 

  627. 

  628.  mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub-02 lh white 
    629. 

  629. 

  630. #--------------------------------------------
    631. 

  631. #@# Ex-vivo Entorhinal Cortex Label rh Sat Jan 14 15:09:47 UTC 2017
    632. 

  632. 

  633.  mris_spherical_average -erode 1 -orig white -t 0.4 -o sub-02 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label 
    634. 

  634. 

  635. 

  636.  mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub-02 rh white 
    637. 

  637.