recon-all.cmd 33 KB

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  1. mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/highres001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/001.mgz
  2. #--------------------------------------------
  3. #@# T2/FLAIR Input Thu Aug 8 10:54:34 CEST 2013
  4. mri_convert /home/data/exppsy/forrest_gump/openfmri.org/sub010/anatomy/other/t2w001.nii.gz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz
  5. #--------------------------------------------
  6. #@# MotionCor Thu Aug 8 10:54:48 CEST 2013
  7. cp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/001.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz
  8. mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/rawavg.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz --conform --cw256
  9. mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/talairach.xfm /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz
  10. #--------------------------------------------
  11. #@# Talairach Thu Aug 8 10:55:26 CEST 2013
  12. mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
  13. talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm
  14. cp transforms/talairach.auto.xfm transforms/talairach.xfm
  15. #--------------------------------------------
  16. #@# Talairach Failure Detection Thu Aug 8 10:57:50 CEST 2013
  17. talairach_afd -T 0.005 -xfm transforms/talairach.xfm
  18. awk -f /opt/freesurfer/5.3.0/bin/extract_talairach_avi_QA.awk /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/talairach_avi.log
  19. tal_QC_AZS /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/talairach_avi.log
  20. #--------------------------------------------
  21. #@# Nu Intensity Correction Thu Aug 8 10:57:50 CEST 2013
  22. mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
  23. mri_add_xform_to_header -c /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/talairach.xfm nu.mgz nu.mgz
  24. #--------------------------------------------
  25. #@# Intensity Normalization Thu Aug 8 10:59:47 CEST 2013
  26. mri_normalize -g 1 nu.mgz T1.mgz
  27. #--------------------------------------------
  28. #@# Skull Stripping Thu Aug 8 11:02:38 CEST 2013
  29. mri_em_register -skull nu.mgz /opt/freesurfer/5.3.0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta
  30. 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
  31. cp brainmask.auto.mgz brainmask.mgz
  32. #-------------------------------------
  33. #@# EM Registration Thu Aug 8 11:37:48 CEST 2013
  34. 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
  35. #--------------------------------------
  36. #@# CA Normalize Thu Aug 8 12:04:43 CEST 2013
  37. 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
  38. #--------------------------------------
  39. #@# CA Reg Thu Aug 8 12:06:45 CEST 2013
  40. 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
  41. #--------------------------------------
  42. #@# CA Reg Inv Thu Aug 8 15:51:55 CEST 2013
  43. mri_ca_register -invert-and-save transforms/talairach.m3z
  44. #--------------------------------------
  45. #@# Remove Neck Thu Aug 8 15:53:50 CEST 2013
  46. 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
  47. #--------------------------------------
  48. #@# SkullLTA Thu Aug 8 15:55:38 CEST 2013
  49. 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
  50. #--------------------------------------
  51. #@# SubCort Seg Thu Aug 8 16:36:09 CEST 2013
  52. 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
  53. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/cc_up.lta sub010
  54. #--------------------------------------
  55. #@# Merge ASeg Thu Aug 8 16:55:43 CEST 2013
  56. cp aseg.auto.mgz aseg.mgz
  57. #--------------------------------------------
  58. #@# Intensity Normalization2 Thu Aug 8 16:55:43 CEST 2013
  59. mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
  60. #--------------------------------------------
  61. #@# Mask BFS Thu Aug 8 17:00:10 CEST 2013
  62. mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
  63. #--------------------------------------------
  64. #@# WM Segmentation Thu Aug 8 17:00:12 CEST 2013
  65. mri_segment brain.mgz wm.seg.mgz
  66. mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz
  67. mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
  68. #--------------------------------------------
  69. #@# Fill Thu Aug 8 17:02:36 CEST 2013
  70. mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
  71. #--------------------------------------------
  72. #@# Tessellate lh Thu Aug 8 17:03:30 CEST 2013
  73. mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
  74. mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
  75. rm -f ../mri/filled-pretess255.mgz
  76. mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
  77. #--------------------------------------------
  78. #@# Smooth1 lh Thu Aug 8 17:03:38 CEST 2013
  79. mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
  80. #--------------------------------------------
  81. #@# Inflation1 lh Thu Aug 8 17:03:42 CEST 2013
  82. mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
  83. #--------------------------------------------
  84. #@# QSphere lh Thu Aug 8 17:04:09 CEST 2013
  85. mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
  86. #--------------------------------------------
  87. #@# Fix Topology lh Thu Aug 8 17:08:04 CEST 2013
  88. cp ../surf/lh.orig.nofix ../surf/lh.orig
  89. cp ../surf/lh.inflated.nofix ../surf/lh.inflated
  90. mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub010 lh
  91. mris_euler_number ../surf/lh.orig
  92. mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
  93. rm ../surf/lh.inflated
  94. #--------------------------------------------
  95. #@# Make White Surf lh Thu Aug 8 17:31:24 CEST 2013
  96. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub010 lh
  97. #--------------------------------------------
  98. #@# Smooth2 lh Thu Aug 8 17:37:09 CEST 2013
  99. mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm
  100. #--------------------------------------------
  101. #@# Inflation2 lh Thu Aug 8 17:37:12 CEST 2013
  102. mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated
  103. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated
  104. #-----------------------------------------
  105. #@# Curvature Stats lh Thu Aug 8 17:39:11 CEST 2013
  106. mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub010 lh curv sulc
  107. #--------------------------------------------
  108. #@# Sphere lh Thu Aug 8 17:39:15 CEST 2013
  109. mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
  110. #--------------------------------------------
  111. #@# Surf Reg lh Thu Aug 8 18:29:35 CEST 2013
  112. mris_register -curv ../surf/lh.sphere /opt/freesurfer/5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg
  113. #--------------------------------------------
  114. #@# Jacobian white lh Thu Aug 8 18:52:14 CEST 2013
  115. mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white
  116. #--------------------------------------------
  117. #@# AvgCurv lh Thu Aug 8 18:52:16 CEST 2013
  118. 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
  119. #-----------------------------------------
  120. #@# Cortical Parc lh Thu Aug 8 18:52:18 CEST 2013
  121. mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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
  122. #--------------------------------------------
  123. #@# Make Pial Surf lh Thu Aug 8 18:53:08 CEST 2013
  124. mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub010 lh
  125. #--------------------------------------------
  126. #@# Surf Volume lh Thu Aug 8 19:04:31 CEST 2013
  127. mris_calc -o lh.area.mid lh.area add lh.area.pial
  128. mris_calc -o lh.area.mid lh.area.mid div 2
  129. mris_calc -o lh.volume lh.area.mid mul lh.thickness
  130. #-----------------------------------------
  131. #@# WM/GM Contrast lh Thu Aug 8 19:04:31 CEST 2013
  132. pctsurfcon --s sub010 --lh-only
  133. #-----------------------------------------
  134. #@# Parcellation Stats lh Thu Aug 8 19:04:42 CEST 2013
  135. 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 sub010 lh white
  136. #-----------------------------------------
  137. #@# Cortical Parc 2 lh Thu Aug 8 19:04:55 CEST 2013
  138. mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot
  139. #-----------------------------------------
  140. #@# Parcellation Stats 2 lh Thu Aug 8 19:05:53 CEST 2013
  141. 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 sub010 lh white
  142. #-----------------------------------------
  143. #@# Cortical Parc 3 lh Thu Aug 8 19:06:06 CEST 2013
  144. mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 lh ../surf/lh.sphere.reg /opt/freesurfer/5.3.0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot
  145. #-----------------------------------------
  146. #@# Parcellation Stats 3 lh Thu Aug 8 19:06:56 CEST 2013
  147. 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 sub010 lh white
  148. #--------------------------------------------
  149. #@# Tessellate rh Thu Aug 8 19:07:09 CEST 2013
  150. mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
  151. mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
  152. rm -f ../mri/filled-pretess127.mgz
  153. mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix
  154. #--------------------------------------------
  155. #@# Smooth1 rh Thu Aug 8 19:07:16 CEST 2013
  156. mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
  157. #--------------------------------------------
  158. #@# Inflation1 rh Thu Aug 8 19:07:20 CEST 2013
  159. mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
  160. #--------------------------------------------
  161. #@# QSphere rh Thu Aug 8 19:07:48 CEST 2013
  162. mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
  163. #--------------------------------------------
  164. #@# Fix Topology rh Thu Aug 8 19:11:42 CEST 2013
  165. cp ../surf/rh.orig.nofix ../surf/rh.orig
  166. cp ../surf/rh.inflated.nofix ../surf/rh.inflated
  167. mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 sub010 rh
  168. mris_euler_number ../surf/rh.orig
  169. mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
  170. rm ../surf/rh.inflated
  171. #--------------------------------------------
  172. #@# Make White Surf rh Thu Aug 8 19:26:28 CEST 2013
  173. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub010 rh
  174. #--------------------------------------------
  175. #@# Smooth2 rh Thu Aug 8 19:32:21 CEST 2013
  176. mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm
  177. #--------------------------------------------
  178. #@# Inflation2 rh Thu Aug 8 19:32:25 CEST 2013
  179. mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated
  180. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated
  181. #-----------------------------------------
  182. #@# Curvature Stats rh Thu Aug 8 19:34:14 CEST 2013
  183. mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub010 rh curv sulc
  184. #--------------------------------------------
  185. #@# Sphere rh Thu Aug 8 19:34:18 CEST 2013
  186. mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
  187. #--------------------------------------------
  188. #@# Surf Reg rh Thu Aug 8 20:18:43 CEST 2013
  189. mris_register -curv ../surf/rh.sphere /opt/freesurfer/5.3.0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg
  190. #--------------------------------------------
  191. #@# Jacobian white rh Thu Aug 8 20:44:27 CEST 2013
  192. mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white
  193. #--------------------------------------------
  194. #@# AvgCurv rh Thu Aug 8 20:44:29 CEST 2013
  195. 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
  196. #-----------------------------------------
  197. #@# Cortical Parc rh Thu Aug 8 20:44:30 CEST 2013
  198. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 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
  199. #--------------------------------------------
  200. #@# Make Pial Surf rh Thu Aug 8 20:45:21 CEST 2013
  201. mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs sub010 rh
  202. #--------------------------------------------
  203. #@# Surf Volume rh Thu Aug 8 20:56:57 CEST 2013
  204. mris_calc -o rh.area.mid rh.area add rh.area.pial
  205. mris_calc -o rh.area.mid rh.area.mid div 2
  206. mris_calc -o rh.volume rh.area.mid mul rh.thickness
  207. #-----------------------------------------
  208. #@# WM/GM Contrast rh Thu Aug 8 20:56:57 CEST 2013
  209. pctsurfcon --s sub010 --rh-only
  210. #-----------------------------------------
  211. #@# Parcellation Stats rh Thu Aug 8 20:57:09 CEST 2013
  212. 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 sub010 rh white
  213. #-----------------------------------------
  214. #@# Cortical Parc 2 rh Thu Aug 8 20:57:21 CEST 2013
  215. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot
  216. #-----------------------------------------
  217. #@# Parcellation Stats 2 rh Thu Aug 8 20:58:19 CEST 2013
  218. 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 sub010 rh white
  219. #-----------------------------------------
  220. #@# Cortical Parc 3 rh Thu Aug 8 20:58:32 CEST 2013
  221. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 sub010 rh ../surf/rh.sphere.reg /opt/freesurfer/5.3.0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot
  222. #-----------------------------------------
  223. #@# Parcellation Stats 3 rh Thu Aug 8 20:59:23 CEST 2013
  224. 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 sub010 rh white
  225. #--------------------------------------------
  226. #@# Refine Pial Surfs w/ T2/FLAIR Thu Aug 8 20:59:35 CEST 2013
  227. bbregister --s sub010 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta --init-fsl --T2
  228. mri_convert -at /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/transforms/T2raw.lta -rl /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/T2.mgz
  229. mri_normalize -aseg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/aseg.mgz -sigma 4 -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.white identity.nofile -surface /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.white identity.nofile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/T2.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/mri/T2.mgz
  230. cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/lh.woT2.pial
  231. mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub010 lh
  232. cp -v /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.pial /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub010/surf/rh.woT2.pial
  233. mris_make_surfaces -orig_white white -orig_pial woT2.pial -white NOWRITE -mgz -T1 brain.finalsurfs -T2 ../mri/T2 sub010 rh
  234. #--------------------------------------------
  235. #@# Surf Volume lh Thu Aug 8 21:42:01 CEST 2013
  236. mris_calc -o lh.area.mid lh.area add lh.area.pial
  237. mris_calc -o lh.area.mid lh.area.mid div 2
  238. mris_calc -o lh.volume lh.area.mid mul lh.thickness
  239. #--------------------------------------------
  240. #@# Surf Volume rh Thu Aug 8 21:42:01 CEST 2013
  241. mris_calc -o rh.area.mid rh.area add rh.area.pial
  242. mris_calc -o rh.area.mid rh.area.mid div 2
  243. mris_calc -o rh.volume rh.area.mid mul rh.thickness
  244. #--------------------------------------------
  245. #@# Cortical ribbon mask Thu Aug 8 21:42:01 CEST 2013
  246. mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub010
  247. #--------------------------------------------
  248. #@# ASeg Stats Thu Aug 8 21:55:18 CEST 2013
  249. 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 sub010
  250. #-----------------------------------------
  251. #@# AParc-to-ASeg Thu Aug 8 21:58:44 CEST 2013
  252. mri_aparc2aseg --s sub010 --volmask
  253. mri_aparc2aseg --s sub010 --volmask --a2009s
  254. #-----------------------------------------
  255. #@# WMParc Thu Aug 8 22:02:45 CEST 2013
  256. mri_aparc2aseg --s sub010 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz
  257. 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 sub010 --surf-wm-vol --ctab /opt/freesurfer/5.3.0/WMParcStatsLUT.txt --etiv
  258. #--------------------------------------------
  259. #@# BA Labels lh Thu Aug 8 22:12:37 CEST 2013
  260. INFO: fsaverage subject does not exist in SUBJECTS_DIR
  261. INFO: Creating symlink to fsaverage subject...
  262. cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer; ln -s /opt/freesurfer/5.3.0/subjects/fsaverage; cd -
  263. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.label --trgsubject sub010 --trglabel ./lh.BA1.label --hemi lh --regmethod surface
  264. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.label --trgsubject sub010 --trglabel ./lh.BA2.label --hemi lh --regmethod surface
  265. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.label --trgsubject sub010 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface
  266. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.label --trgsubject sub010 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface
  267. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.label --trgsubject sub010 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface
  268. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.label --trgsubject sub010 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface
  269. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.label --trgsubject sub010 --trglabel ./lh.BA6.label --hemi lh --regmethod surface
  270. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.label --trgsubject sub010 --trglabel ./lh.BA44.label --hemi lh --regmethod surface
  271. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.label --trgsubject sub010 --trglabel ./lh.BA45.label --hemi lh --regmethod surface
  272. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.label --trgsubject sub010 --trglabel ./lh.V1.label --hemi lh --regmethod surface
  273. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.label --trgsubject sub010 --trglabel ./lh.V2.label --hemi lh --regmethod surface
  274. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.label --trgsubject sub010 --trglabel ./lh.MT.label --hemi lh --regmethod surface
  275. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.perirhinal.label --trgsubject sub010 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface
  276. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject sub010 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface
  277. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA2.thresh.label --trgsubject sub010 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface
  278. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3a.thresh.label --trgsubject sub010 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface
  279. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA3b.thresh.label --trgsubject sub010 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface
  280. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4a.thresh.label --trgsubject sub010 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface
  281. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA4p.thresh.label --trgsubject sub010 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface
  282. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA6.thresh.label --trgsubject sub010 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface
  283. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA44.thresh.label --trgsubject sub010 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface
  284. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.BA45.thresh.label --trgsubject sub010 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface
  285. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V1.thresh.label --trgsubject sub010 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface
  286. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.V2.thresh.label --trgsubject sub010 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface
  287. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/lh.MT.thresh.label --trgsubject sub010 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface
  288. mris_label2annot --s sub010 --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
  289. mris_label2annot --s sub010 --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
  290. mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab sub010 lh white
  291. mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab sub010 lh white
  292. #--------------------------------------------
  293. #@# BA Labels rh Thu Aug 8 22:16:23 CEST 2013
  294. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.label --trgsubject sub010 --trglabel ./rh.BA1.label --hemi rh --regmethod surface
  295. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.label --trgsubject sub010 --trglabel ./rh.BA2.label --hemi rh --regmethod surface
  296. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.label --trgsubject sub010 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface
  297. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.label --trgsubject sub010 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface
  298. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.label --trgsubject sub010 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface
  299. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.label --trgsubject sub010 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface
  300. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.label --trgsubject sub010 --trglabel ./rh.BA6.label --hemi rh --regmethod surface
  301. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.label --trgsubject sub010 --trglabel ./rh.BA44.label --hemi rh --regmethod surface
  302. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.label --trgsubject sub010 --trglabel ./rh.BA45.label --hemi rh --regmethod surface
  303. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.label --trgsubject sub010 --trglabel ./rh.V1.label --hemi rh --regmethod surface
  304. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.label --trgsubject sub010 --trglabel ./rh.V2.label --hemi rh --regmethod surface
  305. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.label --trgsubject sub010 --trglabel ./rh.MT.label --hemi rh --regmethod surface
  306. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.perirhinal.label --trgsubject sub010 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface
  307. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA1.thresh.label --trgsubject sub010 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface
  308. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA2.thresh.label --trgsubject sub010 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface
  309. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3a.thresh.label --trgsubject sub010 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface
  310. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA3b.thresh.label --trgsubject sub010 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface
  311. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4a.thresh.label --trgsubject sub010 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface
  312. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA4p.thresh.label --trgsubject sub010 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface
  313. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA6.thresh.label --trgsubject sub010 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface
  314. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA44.thresh.label --trgsubject sub010 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface
  315. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.BA45.thresh.label --trgsubject sub010 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface
  316. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V1.thresh.label --trgsubject sub010 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface
  317. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.V2.thresh.label --trgsubject sub010 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface
  318. mri_label2label --srcsubject fsaverage --srclabel /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/fsaverage/label/rh.MT.thresh.label --trgsubject sub010 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface
  319. mris_label2annot --s sub010 --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
  320. mris_label2annot --s sub010 --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
  321. mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab sub010 rh white
  322. mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab sub010 rh white
  323. #--------------------------------------------
  324. #@# Ex-vivo Entorhinal Cortex Label lh Thu Aug 8 22:20:09 CEST 2013
  325. INFO: lh.EC_average subject does not exist in SUBJECTS_DIR
  326. INFO: Creating symlink to lh.EC_average subject...
  327. cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer; ln -s /opt/freesurfer/5.3.0/subjects/lh.EC_average; cd -
  328. mris_spherical_average -erode 1 -orig white -t 0.4 -o sub010 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
  329. mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label sub010 lh white
  330. #--------------------------------------------
  331. #@# Ex-vivo Entorhinal Cortex Label rh Thu Aug 8 22:20:22 CEST 2013
  332. INFO: rh.EC_average subject does not exist in SUBJECTS_DIR
  333. INFO: Creating symlink to rh.EC_average subject...
  334. cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer; ln -s /opt/freesurfer/5.3.0/subjects/rh.EC_average; cd -
  335. mris_spherical_average -erode 1 -orig white -t 0.4 -o sub010 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
  336. mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label sub010 rh white