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recon-all.cmd

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  1. 

  2.  mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/001.mgz 
    3. 

  3. 

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

  5. #@# T2/FLAIR Input Thu Aug  8 10:54:17 CEST 2013
    6. 

  6. 

  7.  mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub002/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz 
    8. 

  8. 

  9. #--------------------------------------------
    10. 

  10. #@# MotionCor Thu Aug  8 10:54:34 CEST 2013
    11. 

  11. 

  12.  cp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz 
    13. 

  13. 

  14. 

  15.  mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz --conform --cw256 
    16. 

  16. 

  17. 

  18.  mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz 
    19. 

  19. 

  20. #--------------------------------------------
    21. 

  21. #@# Talairach Thu Aug  8 10:55:15 CEST 2013
    22. 

  22. 

  23.  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz 
    24. 

  24. 

  25. 

  26.  talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 
    27. 

  27. 

  28. 

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

  30. 

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

  32. #@# Talairach Failure Detection Thu Aug  8 10:58:20 CEST 2013
    33. 

  33. 

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

  35. 

  36. 

  37.  awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach_avi.log 
    38. 

  38. 

  39. 

  40.  tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach_avi.log 
    41. 

  41. 

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

  43. #@# Nu Intensity Correction Thu Aug  8 10:58:20 CEST 2013
    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 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/talairach.xfm nu.mgz nu.mgz 
    49. 

  49. 

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

  51. #@# Intensity Normalization Thu Aug  8 11:00:39 CEST 2013
    52. 

  52. 

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

  54. 

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

  56. #@# Skull Stripping Thu Aug  8 11:03:30 CEST 2013
    57. 

  57. 

  58.  mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta 
    59. 

  59. 

  60. 

  61.  mri_watershed -T1 -brain_atlas /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.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 Thu Aug  8 11:38:34 CEST 2013
    68. 

  68. 

  69.  mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta 
    70. 

  70. 

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

  72. #@# CA Normalize Thu Aug  8 12:03:13 CEST 2013
    73. 

  73. 

  74.  mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz 
    75. 

  75. 

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

  77. #@# CA Reg Thu Aug  8 12:05:17 CEST 2013
    78. 

  78. 

  79.  mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca transforms/talairach.m3z 
    80. 

  80. 

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

  82. #@# CA Reg Inv Thu Aug  8 16:34:50 CEST 2013
    83. 

  83. 

  84.  mri_ca_register -invert-and-save transforms/talairach.m3z 
    85. 

  85. 

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

  87. #@# Remove Neck Thu Aug  8 16:36:11 CEST 2013
    88. 

  88. 

  89.  mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca nu_noneck.mgz 
    90. 

  90. 

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

  92. #@# SkullLTA Thu Aug  8 16:37:38 CEST 2013
    93. 

  93. 

  94.  mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta 
    95. 

  95. 

  96. #--------------------------------------
    97. 

  97. #@# SubCort Seg Thu Aug  8 17:17:50 CEST 2013
    98. 

  98. 

  99.  mri_ca_label -align norm.mgz transforms/talairach.m3z /opt/freesurfer/5.3.0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz 
    100. 

  100. 

  101. 

  102.  mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/cc_up.lta sub002 
    103. 

  103. 

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

  105. #@# Merge ASeg Thu Aug  8 17:38:36 CEST 2013
    106. 

  106. 

  107.  cp aseg.auto.mgz aseg.mgz 
    108. 

  108. 

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

  110. #@# Intensity Normalization2 Thu Aug  8 17:38:36 CEST 2013
    111. 

  111. 

  112.  mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz 
    113. 

  113. 

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

  115. #@# Mask BFS Thu Aug  8 17:42:58 CEST 2013
    116. 

  116. 

  117.  mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 
    118. 

  118. 

  119. #--------------------------------------------
    120. 

  120. #@# WM Segmentation Thu Aug  8 17:43:01 CEST 2013
    121. 

  121. 

  122.  mri_segment brain.mgz wm.seg.mgz 
    123. 

  123. 

  124. 

  125.  mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz 
    126. 

  126. 

  127. 

  128.  mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz 
    129. 

  129. 

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

  131. #@# Fill Thu Aug  8 17:45:39 CEST 2013
    132. 

  132. 

  133.  mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz 
    134. 

  134. 

  135. #--------------------------------------------
    136. 

  136. #@# Tessellate lh Thu Aug  8 17:46:37 CEST 2013
    137. 

  137. 

  138.  mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz 
    139. 

  139. 

  140. 

  141.  mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 
    142. 

  142. 

  143. 

  144.  rm -f ../mri/filled-pretess255.mgz 
    145. 

  145. 

  146. 

  147.  mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 
    148. 

  148. 

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

  150. #@# Smooth1 lh Thu Aug  8 17:46:46 CEST 2013
    151. 

  151. 

  152.  mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 
    153. 

  153. 

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

  155. #@# Inflation1 lh Thu Aug  8 17:46:51 CEST 2013
    156. 

  156. 

  157.  mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 
    158. 

  158. 

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

  160. #@# QSphere lh Thu Aug  8 17:47:30 CEST 2013
    161. 

  161. 

  162.  mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 
    163. 

  163. 

  164. #--------------------------------------------
    165. 

  165. #@# Fix Topology lh Thu Aug  8 17:53:01 CEST 2013
    166. 

  166. 

  167.  cp ../surf/lh.orig.nofix ../surf/lh.orig 
    168. 

  168. 

  169. 

  170.  cp ../surf/lh.inflated.nofix ../surf/lh.inflated 
    171. 

  171. 

  172. 

  173.  mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub002 lh 
    174. 

  174. 

  175. 

  176.  mris_euler_number ../surf/lh.orig 
    177. 

  177. 

  178. 

  179.  mris_remove_intersection ../surf/lh.orig ../surf/lh.orig 
    180. 

  180. 

  181. 

  182.  rm ../surf/lh.inflated 
    183. 

  183. 

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

  185. #@# Make White Surf lh Thu Aug  8 18:08:36 CEST 2013
    186. 

  186. 

  187.  mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub002 lh 
    188. 

  188. 

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

  190. #@# Smooth2 lh Thu Aug  8 18:16:43 CEST 2013
    191. 

  191. 

  192.  mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm 
    193. 

  193. 

  194. #--------------------------------------------
    195. 

  195. #@# Inflation2 lh Thu Aug  8 18:16:48 CEST 2013
    196. 

  196. 

  197.  mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated 
    198. 

  198. 

  199. 

  200.  mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated 
    201. 

  201. 

  202. 

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

  204. #@# Curvature Stats lh Thu Aug  8 18:19:36 CEST 2013
    205. 

  205. 

  206.  mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub002 lh curv sulc 
    207. 

  207. 

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

  209. #@# Sphere lh Thu Aug  8 18:19:41 CEST 2013
    210. 

  210. 

  211.  mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere 
    212. 

  212. 

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

  214. #@# Surf Reg lh Thu Aug  8 19:28:39 CEST 2013
    215. 

  215. 

  216.  mris_register -curv ../surf/lh.sphere /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg 
    217. 

  217. 

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

  219. #@# Jacobian white lh Thu Aug  8 20:02:00 CEST 2013
    220. 

  220. 

  221.  mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white 
    222. 

  222. 

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

  224. #@# AvgCurv lh Thu Aug  8 20:02:03 CEST 2013
    225. 

  225. 

  226.  mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv 
    227. 

  227. 

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

  229. #@# Cortical Parc lh Thu Aug  8 20:02:05 CEST 2013
    230. 

  230. 

  231.  mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot 
    232. 

  232. 

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

  234. #@# Make Pial Surf lh Thu Aug  8 20:03:19 CEST 2013
    235. 

  235. 

  236.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub002 lh 
    237. 

  237. 

  238. #--------------------------------------------
    239. 

  239. #@# Surf Volume lh Thu Aug  8 20:20:22 CEST 2013
    240. 

  240. 

  241.  mris_calc -o lh.area.mid lh.area add lh.area.pial 
    242. 

  242. 

  243. 

  244.  mris_calc -o lh.area.mid lh.area.mid div 2 
    245. 

  245. 

  246. 

  247.  mris_calc -o lh.volume lh.area.mid mul lh.thickness 
    248. 

  248. 

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

  250. #@# WM/GM Contrast lh Thu Aug  8 20:20:22 CEST 2013
    251. 

  251. 

  252.  pctsurfcon --s sub002 --lh-only 
    253. 

  253. 

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

  255. #@# Parcellation Stats lh Thu Aug  8 20:20:37 CEST 2013
    256. 

  256. 

  257.  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 sub002 lh white 
    258. 

  258. 

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

  260. #@# Cortical Parc 2 lh Thu Aug  8 20:21:03 CEST 2013
    261. 

  261. 

  262.  mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot 
    263. 

  263. 

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

  265. #@# Parcellation Stats 2 lh Thu Aug  8 20:22:26 CEST 2013
    266. 

  266. 

  267.  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 sub002 lh white 
    268. 

  268. 

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

  270. #@# Cortical Parc 3 lh Thu Aug  8 20:22:56 CEST 2013
    271. 

  271. 

  272.  mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot 
    273. 

  273. 

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

  275. #@# Parcellation Stats 3 lh Thu Aug  8 20:24:13 CEST 2013
    276. 

  276. 

  277.  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 sub002 lh white 
    278. 

  278. 

  279. #--------------------------------------------
    280. 

  280. #@# Tessellate rh Thu Aug  8 20:24:49 CEST 2013
    281. 

  281. 

  282.  mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz 
    283. 

  283. 

  284. 

  285.  mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 
    286. 

  286. 

  287. 

  288.  rm -f ../mri/filled-pretess127.mgz 
    289. 

  289. 

  290. 

  291.  mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 
    292. 

  292. 

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

  294. #@# Smooth1 rh Thu Aug  8 20:24:59 CEST 2013
    295. 

  295. 

  296.  mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 
    297. 

  297. 

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

  299. #@# Inflation1 rh Thu Aug  8 20:25:04 CEST 2013
    300. 

  300. 

  301.  mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 
    302. 

  302. 

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

  304. #@# QSphere rh Thu Aug  8 20:25:50 CEST 2013
    305. 

  305. 

  306.  mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 
    307. 

  307. 

  308. #--------------------------------------------
    309. 

  309. #@# Fix Topology rh Thu Aug  8 20:33:25 CEST 2013
    310. 

  310. 

  311.  cp ../surf/rh.orig.nofix ../surf/rh.orig 
    312. 

  312. 

  313. 

  314.  cp ../surf/rh.inflated.nofix ../surf/rh.inflated 
    315. 

  315. 

  316. 

  317.  mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub002 rh 
    318. 

  318. 

  319. 

  320.  mris_euler_number ../surf/rh.orig 
    321. 

  321. 

  322. 

  323.  mris_remove_intersection ../surf/rh.orig ../surf/rh.orig 
    324. 

  324. 

  325. 

  326.  rm ../surf/rh.inflated 
    327. 

  327. 

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

  329. #@# Make White Surf rh Thu Aug  8 20:53:51 CEST 2013
    330. 

  330. 

  331.  mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub002 rh 
    332. 

  332. 

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

  334. #@# Smooth2 rh Thu Aug  8 21:02:09 CEST 2013
    335. 

  335. 

  336.  mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm 
    337. 

  337. 

  338. #--------------------------------------------
    339. 

  339. #@# Inflation2 rh Thu Aug  8 21:02:15 CEST 2013
    340. 

  340. 

  341.  mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated 
    342. 

  342. 

  343. 

  344.  mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated 
    345. 

  345. 

  346. 

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

  348. #@# Curvature Stats rh Thu Aug  8 21:05:03 CEST 2013
    349. 

  349. 

  350.  mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub002 rh curv sulc 
    351. 

  351. 

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

  353. #@# Sphere rh Thu Aug  8 21:05:09 CEST 2013
    354. 

  354. 

  355.  mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere 
    356. 

  356. 

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

  358. #@# Surf Reg rh Thu Aug  8 22:21:45 CEST 2013
    359. 

  359. 

  360.  mris_register -curv ../surf/rh.sphere /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg 
    361. 

  361. 

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

  363. #@# Jacobian white rh Thu Aug  8 22:58:34 CEST 2013
    364. 

  364. 

  365.  mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white 
    366. 

  366. 

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

  368. #@# AvgCurv rh Thu Aug  8 22:58:37 CEST 2013
    369. 

  369. 

  370.  mrisp_paint -a 5 /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv 
    371. 

  371. 

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

  373. #@# Cortical Parc rh Thu Aug  8 22:58:41 CEST 2013
    374. 

  374. 

  375.  mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot 
    376. 

  376. 

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

  378. #@# Make Pial Surf rh Thu Aug  8 23:00:14 CEST 2013
    379. 

  379. 

  380.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub002 rh 
    381. 

  381. 

  382. #--------------------------------------------
    383. 

  383. #@# Surf Volume rh Thu Aug  8 23:16:44 CEST 2013
    384. 

  384. 

  385.  mris_calc -o rh.area.mid rh.area add rh.area.pial 
    386. 

  386. 

  387. 

  388.  mris_calc -o rh.area.mid rh.area.mid div 2 
    389. 

  389. 

  390. 

  391.  mris_calc -o rh.volume rh.area.mid mul rh.thickness 
    392. 

  392. 

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

  394. #@# WM/GM Contrast rh Thu Aug  8 23:16:45 CEST 2013
    395. 

  395. 

  396.  pctsurfcon --s sub002 --rh-only 
    397. 

  397. 

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

  399. #@# Parcellation Stats rh Thu Aug  8 23:17:00 CEST 2013
    400. 

  400. 

  401.  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 sub002 rh white 
    402. 

  402. 

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

  404. #@# Cortical Parc 2 rh Thu Aug  8 23:17:33 CEST 2013
    405. 

  405. 

  406.  mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot 
    407. 

  407. 

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

  409. #@# Parcellation Stats 2 rh Thu Aug  8 23:18:57 CEST 2013
    410. 

  410. 

  411.  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 sub002 rh white 
    412. 

  412. 

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

  414. #@# Cortical Parc 3 rh Thu Aug  8 23:19:22 CEST 2013
    415. 

  415. 

  416.  mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub002 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot 
    417. 

  417. 

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

  419. #@# Parcellation Stats 3 rh Thu Aug  8 23:20:34 CEST 2013
    420. 

  420. 

  421.  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 sub002 rh white 
    422. 

  422. 

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

  424. #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug  8 23:21:01 CEST 2013
    425. 

  425. 

  426.  bbregister --s sub002 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta --init-fsl --T2 
    427. 

  427. 

  428. 

  429.  mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/T2.mgz 
    430. 

  430. 

  431. 

  432.  mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/mri/T2.mgz 
    433. 

  433. 

  434. 

  435.  cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/lh.woT2.pial 
    436. 

  436. 

  437. 

  438.  mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub002 lh 
    439. 

  439. 

  440. 

  441.  cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/surf/rh.woT2.pial 
    442. 

  442. 

  443. 

  444.  mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub002 rh 
    445. 

  445. 

  446. #--------------------------------------------
    447. 

  447. #@# Surf Volume lh Fri Aug  9 00:19:15 CEST 2013
    448. 

  448. 

  449.  mris_calc -o lh.area.mid lh.area add lh.area.pial 
    450. 

  450. 

  451. 

  452.  mris_calc -o lh.area.mid lh.area.mid div 2 
    453. 

  453. 

  454. 

  455.  mris_calc -o lh.volume lh.area.mid mul lh.thickness 
    456. 

  456. 

  457. #--------------------------------------------
    458. 

  458. #@# Surf Volume rh Fri Aug  9 00:19:17 CEST 2013
    459. 

  459. 

  460.  mris_calc -o rh.area.mid rh.area add rh.area.pial 
    461. 

  461. 

  462. 

  463.  mris_calc -o rh.area.mid rh.area.mid div 2 
    464. 

  464. 

  465. 

  466.  mris_calc -o rh.volume rh.area.mid mul rh.thickness 
    467. 

  467. 

  468. #--------------------------------------------
    469. 

  469. #@# Cortical ribbon mask Fri Aug  9 00:19:18 CEST 2013
    470. 

  470. 

  471.  mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub002 
    472. 

  472. 

  473. #--------------------------------------------
    474. 

  474. #@# ASeg Stats Fri Aug  9 00:44:43 CEST 2013
    475. 

  475. 

  476.  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/5.3.0/ASegStatsLUT.txt --subject sub002 
    477. 

  477. 

  478. #-----------------------------------------
    479. 

  479. #@# AParc-to-ASeg Fri Aug  9 00:47:43 CEST 2013
    480. 

  480. 

  481.  mri_aparc2aseg --s sub002 --volmask 
    482. 

  482. 

  483. 

  484.  mri_aparc2aseg --s sub002 --volmask --a2009s 
    485. 

  485. 

  486. #-----------------------------------------
    487. 

  487. #@# WMParc Fri Aug  9 00:53:00 CEST 2013
    488. 

  488. 

  489.  mri_aparc2aseg --s sub002 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz 
    490. 

  490. 

  491. 

  492.  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 sub002 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv 
    493. 

  493. 

  494. #--------------------------------------------
    495. 

  495. #@# BA Labels lh Fri Aug  9 01:05:30 CEST 2013
    496. 

  496. 

  497.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub002 --trglabel ./lh.BA1.label --hemi lh --regmethod surface 
    498. 

  498. 

  499. 

  500.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub002 --trglabel ./lh.BA2.label --hemi lh --regmethod surface 
    501. 

  501. 

  502. 

  503.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub002 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface 
    504. 

  504. 

  505. 

  506.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub002 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface 
    507. 

  507. 

  508. 

  509.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub002 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface 
    510. 

  510. 

  511. 

  512.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub002 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface 
    513. 

  513. 

  514. 

  515.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub002 --trglabel ./lh.BA6.label --hemi lh --regmethod surface 
    516. 

  516. 

  517. 

  518.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub002 --trglabel ./lh.BA44.label --hemi lh --regmethod surface 
    519. 

  519. 

  520. 

  521.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub002 --trglabel ./lh.BA45.label --hemi lh --regmethod surface 
    522. 

  522. 

  523. 

  524.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub002 --trglabel ./lh.V1.label --hemi lh --regmethod surface 
    525. 

  525. 

  526. 

  527.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub002 --trglabel ./lh.V2.label --hemi lh --regmethod surface 
    528. 

  528. 

  529. 

  530.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub002 --trglabel ./lh.MT.label --hemi lh --regmethod surface 
    531. 

  531. 

  532. 

  533.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub002 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface 
    534. 

  534. 

  535. 

  536.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub002 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface 
    537. 

  537. 

  538. 

  539.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub002 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface 
    540. 

  540. 

  541. 

  542.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub002 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface 
    543. 

  543. 

  544. 

  545.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub002 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface 
    546. 

  546. 

  547. 

  548.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub002 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface 
    549. 

  549. 

  550. 

  551.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub002 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface 
    552. 

  552. 

  553. 

  554.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub002 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface 
    555. 

  555. 

  556. 

  557.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub002 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface 
    558. 

  558. 

  559. 

  560.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub002 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface 
    561. 

  561. 

  562. 

  563.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub002 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface 
    564. 

  564. 

  565. 

  566.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub002 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface 
    567. 

  567. 

  568. 

  569.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub002 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface 
    570. 

  570. 

  571. 

  572.  mris_label2annot --s sub002 --hemi lh --ctab /opt/freesurfer/5.3.0/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 
    573. 

  573. 

  574. 

  575.  mris_label2annot --s sub002 --hemi lh --ctab /opt/freesurfer/5.3.0/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 
    576. 

  576. 

  577. 

  578.  mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub002 lh white 
    579. 

  579. 

  580. 

  581.  mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub002 lh white 
    582. 

  582. 

  583. #--------------------------------------------
    584. 

  584. #@# BA Labels rh Fri Aug  9 01:10:42 CEST 2013
    585. 

  585. 

  586.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub002 --trglabel ./rh.BA1.label --hemi rh --regmethod surface 
    587. 

  587. 

  588. 

  589.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub002 --trglabel ./rh.BA2.label --hemi rh --regmethod surface 
    590. 

  590. 

  591. 

  592.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub002 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface 
    593. 

  593. 

  594. 

  595.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub002 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface 
    596. 

  596. 

  597. 

  598.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub002 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface 
    599. 

  599. 

  600. 

  601.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub002 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface 
    602. 

  602. 

  603. 

  604.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub002 --trglabel ./rh.BA6.label --hemi rh --regmethod surface 
    605. 

  605. 

  606. 

  607.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub002 --trglabel ./rh.BA44.label --hemi rh --regmethod surface 
    608. 

  608. 

  609. 

  610.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub002 --trglabel ./rh.BA45.label --hemi rh --regmethod surface 
    611. 

  611. 

  612. 

  613.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub002 --trglabel ./rh.V1.label --hemi rh --regmethod surface 
    614. 

  614. 

  615. 

  616.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub002 --trglabel ./rh.V2.label --hemi rh --regmethod surface 
    617. 

  617. 

  618. 

  619.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub002 --trglabel ./rh.MT.label --hemi rh --regmethod surface 
    620. 

  620. 

  621. 

  622.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub002 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface 
    623. 

  623. 

  624. 

  625.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub002 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface 
    626. 

  626. 

  627. 

  628.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub002 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface 
    629. 

  629. 

  630. 

  631.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub002 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface 
    632. 

  632. 

  633. 

  634.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub002 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface 
    635. 

  635. 

  636. 

  637.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub002 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface 
    638. 

  638. 

  639. 

  640.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub002 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface 
    641. 

  641. 

  642. 

  643.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub002 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface 
    644. 

  644. 

  645. 

  646.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub002 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface 
    647. 

  647. 

  648. 

  649.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub002 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface 
    650. 

  650. 

  651. 

  652.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub002 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface 
    653. 

  653. 

  654. 

  655.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub002 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface 
    656. 

  656. 

  657. 

  658.  mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub002 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface 
    659. 

  659. 

  660. 

  661.  mris_label2annot --s sub002 --hemi rh --ctab /opt/freesurfer/5.3.0/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 
    662. 

  662. 

  663. 

  664.  mris_label2annot --s sub002 --hemi rh --ctab /opt/freesurfer/5.3.0/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 
    665. 

  665. 

  666. 

  667.  mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub002 rh white 
    668. 

  668. 

  669. 

  670.  mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub002 rh white 
    671. 

  671. 

  672. #--------------------------------------------
    673. 

  673. #@# Ex-vivo Entorhinal Cortex Label lh Fri Aug  9 01:15:48 CEST 2013
    674. 

  674. 

  675.  mris_spherical_average -erode 1 -orig white -t 0.4 -o sub002 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label 
    676. 

  676. 

  677. 

  678.  mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub002 lh white 
    679. 

  679. 

  680. #--------------------------------------------
    681. 

  681. #@# Ex-vivo Entorhinal Cortex Label rh Fri Aug  9 01:16:04 CEST 2013
    682. 

  682. 

  683.  mris_spherical_average -erode 1 -orig white -t 0.4 -o sub002 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label 
    684. 

  684. 

  685. 

  686.  mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub002 rh white 
    687. 

  687.