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recon_checker.log

recon_checker.log 42 KB
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  1. -----
    2. 

  2. Running recon_checker on:
    3. 

  3. Fri Aug  9 09:39:04 CEST 2013
    4. 

  4. -----
    5. 

  5. Most recent FreeSurfer version used to process this subject:
    6. 

  6. /opt/freesurfer/5.3.0/bin/recon-all
    7. 

  7. -----
    8. 

  8. All FreeSurfer versions used to process this subject:
    9. 

  9. /opt/freesurfer/5.3.0/bin/recon-all
    10. 

  10. -----
    11. 

  11. Checking all output files exist...
    12. 

  12.      Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_output_file_checker -subjid sub002 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log -outputfileorderfile /home/fkaule/tools/QAtools_v1.1//default_FOF_FSv5.1
    13. 

  13. -----
    14. 

  14. Checking status log output...
    15. 

  15. 	Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_status_log_checker -subjid sub002 -details -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
    16. 

  16. Using status log: /home/fkaule/tools/QAtools_v1.1//default_status_log_FSv5.1.log
    17. 

  17. 

  18. ERROR: Recon-all steps missing in subject sub002 status file
    19. 

  19. 

  20.  
    21. 

  21. Expected to see the following step(s): 
    22. 

  22. #@# Surf Volume rh Fri Aug 9 00:19:17 CEST 2013 
    23. 

  23. in the recon-all-status.log file before (line # 68): 
    24. 

  24. --> Parcellation Stats lh 
    25. 

  25. --> Cortical Parc 2 lh 
    26. 

  26. --> Parcellation Stats 2 lh 
    27. 

  27. --> Tessellate rh 
    28. 

  28. --> Smooth1 rh 
    29. 

  29. --> Inflation1 rh 
    30. 

  30. --> QSphere rh 
    31. 

  31. --> Fix Topology rh 
    32. 

  32. --> Make White Surf rh 
    33. 

  33. --> Smooth2 rh 
    34. 

  34. --> Inflation2 rh 
    35. 

  35. --> Curvature Stats rh 
    36. 

  36. --> Sphere rh 
    37. 

  37. --> Surf Reg rh 
    38. 

  38. --> Jacobian white rh 
    39. 

  39. --> AvgCurv rh 
    40. 

  40. --> Cortical Parc rh 
    41. 

  41. --> Make Pial Surf rh
    42. 

  42. -----
    43. 

  43. Checking asegs for outliers...
    44. 

  44. Using asegLUT: /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt
    45. 

  45. Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_aseg_outlier_checker -subjid sub002 -LookupMeansFromFile /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
    46. 

  46. checking subcortical label: Left-Cerebral-Exterior, 0 +/- 0
    47. 

  47. checking subcortical label: Left-Cerebral-White-Matter, 0 +/- 0
    48. 

  48. checking subcortical label: Left-Cerebral-Cortex, 0 +/- 0
    49. 

  49. checking subcortical label: Left-Lateral-Ventricle, 0 +/- 0
    50. 

  50. checking subcortical label: Left-Inf-Lat-Vent, 0 +/- 0
    51. 

  51. checking subcortical label: Left-Cerebellum-Exterior, 0 +/- 0
    52. 

  52. checking subcortical label: Left-Cerebellum-White-Matter, 0 +/- 0
    53. 

  53. checking subcortical label: Left-Cerebellum-Cortex, 0 +/- 0
    54. 

  54. checking subcortical label: Left-Thalamus, 2 matches found for name Left-Thalamus... exiting ...
    55. 

  55. checking subcortical label: Left-Thalamus-Proper, 0 +/- 0
    56. 

  56. checking subcortical label: Left-Caudate, 2 matches found for name Left-Caudate... exiting ...
    57. 

  57. checking subcortical label: Left-Putamen, 0 +/- 0
    58. 

  58. checking subcortical label: Left-Pallidum, 0 +/- 0
    59. 

  59. checking subcortical label: 3rd-Ventricle, 0 +/- 0
    60. 

  60. checking subcortical label: 4th-Ventricle, 0 +/- 0
    61. 

  61. checking subcortical label: Brain-Stem, 0 +/- 0
    62. 

  62. checking subcortical label: Left-Hippocampus, 0 +/- 0
    63. 

  63. checking subcortical label: Left-Amygdala, 2 matches found for name Left-Amygdala... exiting ...
    64. 

  64. checking subcortical label: Left-Insula, 0 +/- 0
    65. 

  65. checking subcortical label: Left-Operculum, 0 +/- 0
    66. 

  66. checking subcortical label: Line-1, 0 +/- 0
    67. 

  67. checking subcortical label: Line-2, 0 +/- 0
    68. 

  68. checking subcortical label: Line-3, 0 +/- 0
    69. 

  69. checking subcortical label: CSF, 2 matches found for name CSF... exiting ...
    70. 

  70. checking subcortical label: Left-Lesion, 0 +/- 0
    71. 

  71. checking subcortical label: Left-Accumbens-area, 0 +/- 0
    72. 

  72. checking subcortical label: Left-Substancia-Nigra, 0 +/- 0
    73. 

  73. checking subcortical label: Left-VentralDC, 0 +/- 0
    74. 

  74. checking subcortical label: Left-undetermined, 0 +/- 0
    75. 

  75. checking subcortical label: Left-vessel, 0 +/- 0
    76. 

  76. checking subcortical label: Left-choroid-plexus, 0 +/- 0
    77. 

  77. checking subcortical label: Left-F3orb, 0 +/- 0
    78. 

  78. checking subcortical label: Left-lOg, 0 +/- 0
    79. 

  79. checking subcortical label: Left-aOg, 0 +/- 0
    80. 

  80. checking subcortical label: Left-mOg, 0 +/- 0
    81. 

  81. checking subcortical label: Left-pOg, 0 +/- 0
    82. 

  82. checking subcortical label: Left-Stellate, 0 +/- 0
    83. 

  83. checking subcortical label: Left-Porg, 0 +/- 0
    84. 

  84. checking subcortical label: Left-Aorg, 0 +/- 0
    85. 

  85. checking subcortical label: Right-Cerebral-Exterior, 0 +/- 0
    86. 

  86. checking subcortical label: Right-Cerebral-White-Matter, 0 +/- 0
    87. 

  87. checking subcortical label: Right-Cerebral-Cortex, 0 +/- 0
    88. 

  88. checking subcortical label: Right-Lateral-Ventricle, 0 +/- 0
    89. 

  89. checking subcortical label: Right-Inf-Lat-Vent, 0 +/- 0
    90. 

  90. checking subcortical label: Right-Cerebellum-Exterior, 0 +/- 0
    91. 

  91. checking subcortical label: Right-Cerebellum-White-Matter, 0 +/- 0
    92. 

  92. checking subcortical label: Right-Cerebellum-Cortex, 0 +/- 0
    93. 

  93. checking subcortical label: Right-Thalamus, 2 matches found for name Right-Thalamus... exiting ...
    94. 

  94. checking subcortical label: Right-Thalamus-Proper, 0 +/- 0
    95. 

  95. checking subcortical label: Right-Caudate, 2 matches found for name Right-Caudate... exiting ...
    96. 

  96. checking subcortical label: Right-Putamen, 0 +/- 0
    97. 

  97. checking subcortical label: Right-Pallidum, 0 +/- 0
    98. 

  98. checking subcortical label: Right-Hippocampus, 0 +/- 0
    99. 

  99. checking subcortical label: Right-Amygdala, 2 matches found for name Right-Amygdala... exiting ...
    100. 

  100. checking subcortical label: Right-Insula, 0 +/- 0
    101. 

  101. checking subcortical label: Right-Operculum, 0 +/- 0
    102. 

  102. checking subcortical label: Right-Lesion, 0 +/- 0
    103. 

  103. checking subcortical label: Right-Accumbens-area, 0 +/- 0
    104. 

  104. checking subcortical label: Right-Substancia-Nigra, 0 +/- 0
    105. 

  105. checking subcortical label: Right-VentralDC, 0 +/- 0
    106. 

  106. checking subcortical label: Right-undetermined, 0 +/- 0
    107. 

  107. checking subcortical label: Right-vessel, 0 +/- 0
    108. 

  108. checking subcortical label: Right-choroid-plexus, 0 +/- 0
    109. 

  109. checking subcortical label: Right-F3orb, 0 +/- 0
    110. 

  110. checking subcortical label: Right-lOg, 0 +/- 0
    111. 

  111. checking subcortical label: Right-aOg, 0 +/- 0
    112. 

  112. checking subcortical label: Right-mOg, 0 +/- 0
    113. 

  113. checking subcortical label: Right-pOg, 0 +/- 0
    114. 

  114. checking subcortical label: Right-Stellate, 0 +/- 0
    115. 

  115. checking subcortical label: Right-Porg, 0 +/- 0
    116. 

  116. checking subcortical label: Right-Aorg, 0 +/- 0
    117. 

  117. checking subcortical label: 5th-Ventricle, 0 +/- 0
    118. 

  118. checking subcortical label: Left-Interior, 0 +/- 0
    119. 

  119. checking subcortical label: Right-Interior, 0 +/- 0
    120. 

  120. checking subcortical label: Left-Lateral-Ventricles, 0 +/- 0
    121. 

  121. checking subcortical label: Right-Lateral-Ventricles, 0 +/- 0
    122. 

  122. checking subcortical label: WM-hypointensities, 6 matches found for name WM-hypointensities... exiting ...
    123. 

  123. checking subcortical label: Left-WM-hypointensities, 0 +/- 0
    124. 

  124. checking subcortical label: Right-WM-hypointensities, 0 +/- 0
    125. 

  125. checking subcortical label: non-WM-hypointensities, 3 matches found for name non-WM-hypointensities... exiting ...
    126. 

  126. checking subcortical label: Left-non-WM-hypointensities, 0 +/- 0
    127. 

  127. checking subcortical label: Right-non-WM-hypointensities, 0 +/- 0
    128. 

  128. checking subcortical label: Left-F1, 0 +/- 0
    129. 

  129. checking subcortical label: Right-F1, 0 +/- 0
    130. 

  130. checking subcortical label: Optic-Chiasm, 0 +/- 0
    131. 

  131. checking subcortical label: Corpus_Callosum, 0 +/- 0
    132. 

  132. checking subcortical label: Left-Amygdala-Anterior, 0 +/- 0
    133. 

  133. checking subcortical label: Right-Amygdala-Anterior, 0 +/- 0
    134. 

  134. checking subcortical label: Dura, 0 +/- 0
    135. 

  135. checking subcortical label: Left-wm-intensity-abnormality, 0 +/- 0
    136. 

  136. checking subcortical label: Left-caudate-intensity-abnormality, 0 +/- 0
    137. 

  137. checking subcortical label: Left-putamen-intensity-abnormality, 0 +/- 0
    138. 

  138. checking subcortical label: Left-accumbens-intensity-abnormality, 0 +/- 0
    139. 

  139. checking subcortical label: Left-pallidum-intensity-abnormality, 0 +/- 0
    140. 

  140. checking subcortical label: Left-amygdala-intensity-abnormality, 0 +/- 0
    141. 

  141. checking subcortical label: Left-hippocampus-intensity-abnormality, 0 +/- 0
    142. 

  142. checking subcortical label: Left-thalamus-intensity-abnormality, 0 +/- 0
    143. 

  143. checking subcortical label: Left-VDC-intensity-abnormality, 0 +/- 0
    144. 

  144. checking subcortical label: Right-wm-intensity-abnormality, 0 +/- 0
    145. 

  145. checking subcortical label: Right-caudate-intensity-abnormality, 0 +/- 0
    146. 

  146. checking subcortical label: Right-putamen-intensity-abnormality, 0 +/- 0
    147. 

  147. checking subcortical label: Right-accumbens-intensity-abnormality, 0 +/- 0
    148. 

  148. checking subcortical label: Right-pallidum-intensity-abnormality, 0 +/- 0
    149. 

  149. checking subcortical label: Right-amygdala-intensity-abnormality, 0 +/- 0
    150. 

  150. checking subcortical label: Right-hippocampus-intensity-abnormality, 0 +/- 0
    151. 

  151. checking subcortical label: Right-thalamus-intensity-abnormality, 0 +/- 0
    152. 

  152. checking subcortical label: Right-VDC-intensity-abnormality, 0 +/- 0
    153. 

  153. checking subcortical label: Epidermis, 0 +/- 0
    154. 

  154. checking subcortical label: Conn-Tissue, 0 +/- 0
    155. 

  155. checking subcortical label: SC-Fat/Muscle, 0 +/- 0
    156. 

  156. checking subcortical label: CSF-SA, 0 +/- 0
    157. 

  157. checking subcortical label: Muscle, 2 matches found for name Muscle... exiting ...
    158. 

  158. checking subcortical label: Ear, 0 +/- 0
    159. 

  159. checking subcortical label: Adipose, 0 +/- 0
    160. 

  160. checking subcortical label: Spinal-Cord, 0 +/- 0
    161. 

  161. checking subcortical label: Soft-Tissue, 0 +/- 0
    162. 

  162. checking subcortical label: Nerve, 0 +/- 0
    163. 

  163. checking subcortical label: Bone, 0 +/- 0
    164. 

  164. checking subcortical label: Air, 0 +/- 0
    165. 

  165. checking subcortical label: Orbital-Fat, 0 +/- 0
    166. 

  166. checking subcortical label: Tongue, 0 +/- 0
    167. 

  167. checking subcortical label: Nasal-Structures, 0 +/- 0
    168. 

  168. checking subcortical label: Globe, 0 +/- 0
    169. 

  169. checking subcortical label: Teeth, 0 +/- 0
    170. 

  170. checking subcortical label: Left-Caudate/Putamen, 0 +/- 0
    171. 

  171. checking subcortical label: Right-Caudate/Putamen, 0 +/- 0
    172. 

  172. checking subcortical label: Left-Claustrum, 0 +/- 0
    173. 

  173. checking subcortical label: Right-Claustrum, 0 +/- 0
    174. 

  174. checking subcortical label: Cornea, 0 +/- 0
    175. 

  175. checking subcortical label: Diploe, 0 +/- 0
    176. 

  176. checking subcortical label: Vitreous-Humor, 0 +/- 0
    177. 

  177. checking subcortical label: Lens, 0 +/- 0
    178. 

  178. checking subcortical label: Aqueous-Humor, 0 +/- 0
    179. 

  179. checking subcortical label: Outer-Table, 0 +/- 0
    180. 

  180. checking subcortical label: Inner-Table, 0 +/- 0
    181. 

  181. checking subcortical label: Periosteum, 0 +/- 0
    182. 

  182. checking subcortical label: Endosteum, 0 +/- 0
    183. 

  183. sub002 has 0 outliers ...
    184. 

  184. -----
    185. 

  185. Checking white matter SNR measurements...
    186. 

  186. 

  187. SNR: Anatomical signal-to-noise ratio in white matter
    188. 

  188. mWM: Mean white matter intensity value
    189. 

  189. stdWM: Standard deviation of white matter intensity value
    190. 

  190. voxWM: Total number of white matter voxels in eroded mask
    191. 

  191. Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_wm-anat-snr_checker -subjid sub002 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
    192. 

  192. wm-anat-snr results (sub002):
    193. 

  193. SNR	meanWM	stdWM	voxWM	
    194. 

  194. 17.84	106.04	5.94	55548
    195. 

  195. -----
    196. 

  196. -----
    197. 

  197. Running recon_checker on:
    198. 

  198. Fri Aug  9 10:02:31 CEST 2013
    199. 

  199. -----
    200. 

  200. Most recent FreeSurfer version used to process this subject:
    201. 

  201. /opt/freesurfer/5.3.0/bin/recon-all
    202. 

  202. -----
    203. 

  203. All FreeSurfer versions used to process this subject:
    204. 

  204. /opt/freesurfer/5.3.0/bin/recon-all
    205. 

  205. -----
    206. 

  206. Checking all output files exist...
    207. 

  207.      Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_output_file_checker -subjid sub002 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log -outputfileorderfile /home/fkaule/tools/QAtools_v1.1//default_FOF_FSv5.1
    208. 

  208. -----
    209. 

  209. Checking status log output...
    210. 

  210. 	Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_status_log_checker -subjid sub002 -details -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
    211. 

  211. Using status log: /home/fkaule/tools/QAtools_v1.1//default_status_log_FSv5.1.log
    212. 

  212. 

  213. ERROR: Recon-all steps missing in subject sub002 status file
    214. 

  214. 

  215.  
    216. 

  216. Expected to see the following step(s): 
    217. 

  217. #@# Surf Volume rh Fri Aug 9 00:19:17 CEST 2013 
    218. 

  218. in the recon-all-status.log file before (line # 68): 
    219. 

  219. --> Parcellation Stats lh 
    220. 

  220. --> Cortical Parc 2 lh 
    221. 

  221. --> Parcellation Stats 2 lh 
    222. 

  222. --> Tessellate rh 
    223. 

  223. --> Smooth1 rh 
    224. 

  224. --> Inflation1 rh 
    225. 

  225. --> QSphere rh 
    226. 

  226. --> Fix Topology rh 
    227. 

  227. --> Make White Surf rh 
    228. 

  228. --> Smooth2 rh 
    229. 

  229. --> Inflation2 rh 
    230. 

  230. --> Curvature Stats rh 
    231. 

  231. --> Sphere rh 
    232. 

  232. --> Surf Reg rh 
    233. 

  233. --> Jacobian white rh 
    234. 

  234. --> AvgCurv rh 
    235. 

  235. --> Cortical Parc rh 
    236. 

  236. --> Make Pial Surf rh
    237. 

  237. -----
    238. 

  238. Checking asegs for outliers...
    239. 

  239. Using asegLUT: /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt
    240. 

  240. Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_aseg_outlier_checker -subjid sub002 -LookupMeansFromFile /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
    241. 

  241. checking subcortical label: Left-Cerebral-Exterior, 0 +/- 0
    242. 

  242. checking subcortical label: Left-Cerebral-White-Matter, 0 +/- 0
    243. 

  243. checking subcortical label: Left-Cerebral-Cortex, 0 +/- 0
    244. 

  244. checking subcortical label: Left-Lateral-Ventricle, 0 +/- 0
    245. 

  245. checking subcortical label: Left-Inf-Lat-Vent, 0 +/- 0
    246. 

  246. checking subcortical label: Left-Cerebellum-Exterior, 0 +/- 0
    247. 

  247. checking subcortical label: Left-Cerebellum-White-Matter, 0 +/- 0
    248. 

  248. checking subcortical label: Left-Cerebellum-Cortex, 0 +/- 0
    249. 

  249. checking subcortical label: Left-Thalamus, 2 matches found for name Left-Thalamus... exiting ...
    250. 

  250. checking subcortical label: Left-Thalamus-Proper, 0 +/- 0
    251. 

  251. checking subcortical label: Left-Caudate, 2 matches found for name Left-Caudate... exiting ...
    252. 

  252. checking subcortical label: Left-Putamen, 0 +/- 0
    253. 

  253. checking subcortical label: Left-Pallidum, 0 +/- 0
    254. 

  254. checking subcortical label: 3rd-Ventricle, 0 +/- 0
    255. 

  255. checking subcortical label: 4th-Ventricle, 0 +/- 0
    256. 

  256. checking subcortical label: Brain-Stem, 0 +/- 0
    257. 

  257. checking subcortical label: Left-Hippocampus, 0 +/- 0
    258. 

  258. checking subcortical label: Left-Amygdala, 2 matches found for name Left-Amygdala... exiting ...
    259. 

  259. checking subcortical label: Left-Insula, 0 +/- 0
    260. 

  260. checking subcortical label: Left-Operculum, 0 +/- 0
    261. 

  261. checking subcortical label: Line-1, 0 +/- 0
    262. 

  262. checking subcortical label: Line-2, 0 +/- 0
    263. 

  263. checking subcortical label: Line-3, 0 +/- 0
    264. 

  264. checking subcortical label: CSF, 2 matches found for name CSF... exiting ...
    265. 

  265. checking subcortical label: Left-Lesion, 0 +/- 0
    266. 

  266. checking subcortical label: Left-Accumbens-area, 0 +/- 0
    267. 

  267. checking subcortical label: Left-Substancia-Nigra, 0 +/- 0
    268. 

  268. checking subcortical label: Left-VentralDC, 0 +/- 0
    269. 

  269. checking subcortical label: Left-undetermined, 0 +/- 0
    270. 

  270. checking subcortical label: Left-vessel, 0 +/- 0
    271. 

  271. checking subcortical label: Left-choroid-plexus, 0 +/- 0
    272. 

  272. checking subcortical label: Left-F3orb, 0 +/- 0
    273. 

  273. checking subcortical label: Left-lOg, 0 +/- 0
    274. 

  274. checking subcortical label: Left-aOg, 0 +/- 0
    275. 

  275. checking subcortical label: Left-mOg, 0 +/- 0
    276. 

  276. checking subcortical label: Left-pOg, 0 +/- 0
    277. 

  277. checking subcortical label: Left-Stellate, 0 +/- 0
    278. 

  278. checking subcortical label: Left-Porg, 0 +/- 0
    279. 

  279. checking subcortical label: Left-Aorg, 0 +/- 0
    280. 

  280. checking subcortical label: Right-Cerebral-Exterior, 0 +/- 0
    281. 

  281. checking subcortical label: Right-Cerebral-White-Matter, 0 +/- 0
    282. 

  282. checking subcortical label: Right-Cerebral-Cortex, 0 +/- 0
    283. 

  283. checking subcortical label: Right-Lateral-Ventricle, 0 +/- 0
    284. 

  284. checking subcortical label: Right-Inf-Lat-Vent, 0 +/- 0
    285. 

  285. checking subcortical label: Right-Cerebellum-Exterior, 0 +/- 0
    286. 

  286. checking subcortical label: Right-Cerebellum-White-Matter, 0 +/- 0
    287. 

  287. checking subcortical label: Right-Cerebellum-Cortex, 0 +/- 0
    288. 

  288. checking subcortical label: Right-Thalamus, 2 matches found for name Right-Thalamus... exiting ...
    289. 

  289. checking subcortical label: Right-Thalamus-Proper, 0 +/- 0
    290. 

  290. checking subcortical label: Right-Caudate, 2 matches found for name Right-Caudate... exiting ...
    291. 

  291. checking subcortical label: Right-Putamen, 0 +/- 0
    292. 

  292. checking subcortical label: Right-Pallidum, 0 +/- 0
    293. 

  293. checking subcortical label: Right-Hippocampus, 0 +/- 0
    294. 

  294. checking subcortical label: Right-Amygdala, 2 matches found for name Right-Amygdala... exiting ...
    295. 

  295. checking subcortical label: Right-Insula, 0 +/- 0
    296. 

  296. checking subcortical label: Right-Operculum, 0 +/- 0
    297. 

  297. checking subcortical label: Right-Lesion, 0 +/- 0
    298. 

  298. checking subcortical label: Right-Accumbens-area, 0 +/- 0
    299. 

  299. checking subcortical label: Right-Substancia-Nigra, 0 +/- 0
    300. 

  300. checking subcortical label: Right-VentralDC, 0 +/- 0
    301. 

  301. checking subcortical label: Right-undetermined, 0 +/- 0
    302. 

  302. checking subcortical label: Right-vessel, 0 +/- 0
    303. 

  303. checking subcortical label: Right-choroid-plexus, 0 +/- 0
    304. 

  304. checking subcortical label: Right-F3orb, 0 +/- 0
    305. 

  305. checking subcortical label: Right-lOg, 0 +/- 0
    306. 

  306. checking subcortical label: Right-aOg, 0 +/- 0
    307. 

  307. checking subcortical label: Right-mOg, 0 +/- 0
    308. 

  308. checking subcortical label: Right-pOg, 0 +/- 0
    309. 

  309. checking subcortical label: Right-Stellate, 0 +/- 0
    310. 

  310. checking subcortical label: Right-Porg, 0 +/- 0
    311. 

  311. checking subcortical label: Right-Aorg, 0 +/- 0
    312. 

  312. checking subcortical label: 5th-Ventricle, 0 +/- 0
    313. 

  313. checking subcortical label: Left-Interior, 0 +/- 0
    314. 

  314. checking subcortical label: Right-Interior, 0 +/- 0
    315. 

  315. checking subcortical label: Left-Lateral-Ventricles, 0 +/- 0
    316. 

  316. checking subcortical label: Right-Lateral-Ventricles, 0 +/- 0
    317. 

  317. checking subcortical label: WM-hypointensities, 6 matches found for name WM-hypointensities... exiting ...
    318. 

  318. checking subcortical label: Left-WM-hypointensities, 0 +/- 0
    319. 

  319. checking subcortical label: Right-WM-hypointensities, 0 +/- 0
    320. 

  320. checking subcortical label: non-WM-hypointensities, 3 matches found for name non-WM-hypointensities... exiting ...
    321. 

  321. checking subcortical label: Left-non-WM-hypointensities, 0 +/- 0
    322. 

  322. checking subcortical label: Right-non-WM-hypointensities, 0 +/- 0
    323. 

  323. checking subcortical label: Left-F1, 0 +/- 0
    324. 

  324. checking subcortical label: Right-F1, 0 +/- 0
    325. 

  325. checking subcortical label: Optic-Chiasm, 0 +/- 0
    326. 

  326. checking subcortical label: Corpus_Callosum, 0 +/- 0
    327. 

  327. checking subcortical label: Left-Amygdala-Anterior, 0 +/- 0
    328. 

  328. checking subcortical label: Right-Amygdala-Anterior, 0 +/- 0
    329. 

  329. checking subcortical label: Dura, 0 +/- 0
    330. 

  330. checking subcortical label: Left-wm-intensity-abnormality, 0 +/- 0
    331. 

  331. checking subcortical label: Left-caudate-intensity-abnormality, 0 +/- 0
    332. 

  332. checking subcortical label: Left-putamen-intensity-abnormality, 0 +/- 0
    333. 

  333. checking subcortical label: Left-accumbens-intensity-abnormality, 0 +/- 0
    334. 

  334. checking subcortical label: Left-pallidum-intensity-abnormality, 0 +/- 0
    335. 

  335. checking subcortical label: Left-amygdala-intensity-abnormality, 0 +/- 0
    336. 

  336. checking subcortical label: Left-hippocampus-intensity-abnormality, 0 +/- 0
    337. 

  337. checking subcortical label: Left-thalamus-intensity-abnormality, 0 +/- 0
    338. 

  338. checking subcortical label: Left-VDC-intensity-abnormality, 0 +/- 0
    339. 

  339. checking subcortical label: Right-wm-intensity-abnormality, 0 +/- 0
    340. 

  340. checking subcortical label: Right-caudate-intensity-abnormality, 0 +/- 0
    341. 

  341. checking subcortical label: Right-putamen-intensity-abnormality, 0 +/- 0
    342. 

  342. checking subcortical label: Right-accumbens-intensity-abnormality, 0 +/- 0
    343. 

  343. checking subcortical label: Right-pallidum-intensity-abnormality, 0 +/- 0
    344. 

  344. checking subcortical label: Right-amygdala-intensity-abnormality, 0 +/- 0
    345. 

  345. checking subcortical label: Right-hippocampus-intensity-abnormality, 0 +/- 0
    346. 

  346. checking subcortical label: Right-thalamus-intensity-abnormality, 0 +/- 0
    347. 

  347. checking subcortical label: Right-VDC-intensity-abnormality, 0 +/- 0
    348. 

  348. checking subcortical label: Epidermis, 0 +/- 0
    349. 

  349. checking subcortical label: Conn-Tissue, 0 +/- 0
    350. 

  350. checking subcortical label: SC-Fat/Muscle, 0 +/- 0
    351. 

  351. checking subcortical label: CSF-SA, 0 +/- 0
    352. 

  352. checking subcortical label: Muscle, 2 matches found for name Muscle... exiting ...
    353. 

  353. checking subcortical label: Ear, 0 +/- 0
    354. 

  354. checking subcortical label: Adipose, 0 +/- 0
    355. 

  355. checking subcortical label: Spinal-Cord, 0 +/- 0
    356. 

  356. checking subcortical label: Soft-Tissue, 0 +/- 0
    357. 

  357. checking subcortical label: Nerve, 0 +/- 0
    358. 

  358. checking subcortical label: Bone, 0 +/- 0
    359. 

  359. checking subcortical label: Air, 0 +/- 0
    360. 

  360. checking subcortical label: Orbital-Fat, 0 +/- 0
    361. 

  361. checking subcortical label: Tongue, 0 +/- 0
    362. 

  362. checking subcortical label: Nasal-Structures, 0 +/- 0
    363. 

  363. checking subcortical label: Globe, 0 +/- 0
    364. 

  364. checking subcortical label: Teeth, 0 +/- 0
    365. 

  365. checking subcortical label: Left-Caudate/Putamen, 0 +/- 0
    366. 

  366. checking subcortical label: Right-Caudate/Putamen, 0 +/- 0
    367. 

  367. checking subcortical label: Left-Claustrum, 0 +/- 0
    368. 

  368. checking subcortical label: Right-Claustrum, 0 +/- 0
    369. 

  369. checking subcortical label: Cornea, 0 +/- 0
    370. 

  370. checking subcortical label: Diploe, 0 +/- 0
    371. 

  371. checking subcortical label: Vitreous-Humor, 0 +/- 0
    372. 

  372. checking subcortical label: Lens, 0 +/- 0
    373. 

  373. checking subcortical label: Aqueous-Humor, 0 +/- 0
    374. 

  374. checking subcortical label: Outer-Table, 0 +/- 0
    375. 

  375. checking subcortical label: Inner-Table, 0 +/- 0
    376. 

  376. checking subcortical label: Periosteum, 0 +/- 0
    377. 

  377. checking subcortical label: Endosteum, 0 +/- 0
    378. 

  378. sub002 has 0 outliers ...
    379. 

  379. -----
    380. 

  380. Checking white matter SNR measurements...
    381. 

  381. 

  382. SNR: Anatomical signal-to-noise ratio in white matter
    383. 

  383. mWM: Mean white matter intensity value
    384. 

  384. stdWM: Standard deviation of white matter intensity value
    385. 

  385. voxWM: Total number of white matter voxels in eroded mask
    386. 

  386. Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_wm-anat-snr_checker -subjid sub002 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/QA/recon_checker.ALL.summary.log
    387. 

  387. wm-anat-snr results (sub002):
    388. 

  388. SNR	meanWM	stdWM	voxWM	
    389. 

  389. 17.84	106.04	5.94	55548
    390. 

  390. -----
    391. 

  391. -----
    392. 

  392. Running recon_checker on:
    393. 

  393. Mon Aug 12 12:55:18 CEST 2013
    394. 

  394. -----
    395. 

  395. Most recent FreeSurfer version used to process this subject:
    396. 

  396. /opt/freesurfer/5.3.0/bin/recon-all
    397. 

  397. -----
    398. 

  398. All FreeSurfer versions used to process this subject:
    399. 

  399. /opt/freesurfer/5.3.0/bin/recon-all
    400. 

  400. -----
    401. 

  401. Checking all output files exist...
    402. 

  402.      Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_output_file_checker -subjid sub002 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log -outputfileorderfile /home/fkaule/tools/QAtools_v1.1//default_FOF_FSv5.1
    403. 

  403. -----
    404. 

  404. Checking status log output...
    405. 

  405. 	Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_status_log_checker -subjid sub002 -details -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log
    406. 

  406. Using status log: /home/fkaule/tools/QAtools_v1.1//default_status_log_FSv5.1.log
    407. 

  407. 

  408. ERROR: Recon-all steps missing in subject sub002 status file
    409. 

  409. 

  410.  
    411. 

  411. Expected to see the following step(s): 
    412. 

  412. #@# Surf Volume rh Fri Aug 9 00:19:17 CEST 2013 
    413. 

  413. in the recon-all-status.log file before (line # 68): 
    414. 

  414. --> Parcellation Stats lh 
    415. 

  415. --> Cortical Parc 2 lh 
    416. 

  416. --> Parcellation Stats 2 lh 
    417. 

  417. --> Tessellate rh 
    418. 

  418. --> Smooth1 rh 
    419. 

  419. --> Inflation1 rh 
    420. 

  420. --> QSphere rh 
    421. 

  421. --> Fix Topology rh 
    422. 

  422. --> Make White Surf rh 
    423. 

  423. --> Smooth2 rh 
    424. 

  424. --> Inflation2 rh 
    425. 

  425. --> Curvature Stats rh 
    426. 

  426. --> Sphere rh 
    427. 

  427. --> Surf Reg rh 
    428. 

  428. --> Jacobian white rh 
    429. 

  429. --> AvgCurv rh 
    430. 

  430. --> Cortical Parc rh 
    431. 

  431. --> Make Pial Surf rh
    432. 

  432. -----
    433. 

  433. Checking asegs for outliers...
    434. 

  434. Using asegLUT: /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt
    435. 

  435. Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_aseg_outlier_checker -subjid sub002 -LookupMeansFromFile /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log
    436. 

  436. checking subcortical label: Left-Cerebral-Exterior, 0 +/- 0
    437. 

  437. checking subcortical label: Left-Cerebral-White-Matter, 0 +/- 0
    438. 

  438. checking subcortical label: Left-Cerebral-Cortex, 0 +/- 0
    439. 

  439. checking subcortical label: Left-Lateral-Ventricle, 0 +/- 0
    440. 

  440. checking subcortical label: Left-Inf-Lat-Vent, 0 +/- 0
    441. 

  441. checking subcortical label: Left-Cerebellum-Exterior, 0 +/- 0
    442. 

  442. checking subcortical label: Left-Cerebellum-White-Matter, 0 +/- 0
    443. 

  443. checking subcortical label: Left-Cerebellum-Cortex, 0 +/- 0
    444. 

  444. checking subcortical label: Left-Thalamus, 2 matches found for name Left-Thalamus... exiting ...
    445. 

  445. checking subcortical label: Left-Thalamus-Proper, 0 +/- 0
    446. 

  446. checking subcortical label: Left-Caudate, 2 matches found for name Left-Caudate... exiting ...
    447. 

  447. checking subcortical label: Left-Putamen, 0 +/- 0
    448. 

  448. checking subcortical label: Left-Pallidum, 0 +/- 0
    449. 

  449. checking subcortical label: 3rd-Ventricle, 0 +/- 0
    450. 

  450. checking subcortical label: 4th-Ventricle, 0 +/- 0
    451. 

  451. checking subcortical label: Brain-Stem, 0 +/- 0
    452. 

  452. checking subcortical label: Left-Hippocampus, 0 +/- 0
    453. 

  453. checking subcortical label: Left-Amygdala, 2 matches found for name Left-Amygdala... exiting ...
    454. 

  454. checking subcortical label: Left-Insula, 0 +/- 0
    455. 

  455. checking subcortical label: Left-Operculum, 0 +/- 0
    456. 

  456. checking subcortical label: Line-1, 0 +/- 0
    457. 

  457. checking subcortical label: Line-2, 0 +/- 0
    458. 

  458. checking subcortical label: Line-3, 0 +/- 0
    459. 

  459. checking subcortical label: CSF, 2 matches found for name CSF... exiting ...
    460. 

  460. checking subcortical label: Left-Lesion, 0 +/- 0
    461. 

  461. checking subcortical label: Left-Accumbens-area, 0 +/- 0
    462. 

  462. checking subcortical label: Left-Substancia-Nigra, 0 +/- 0
    463. 

  463. checking subcortical label: Left-VentralDC, 0 +/- 0
    464. 

  464. checking subcortical label: Left-undetermined, 0 +/- 0
    465. 

  465. checking subcortical label: Left-vessel, 0 +/- 0
    466. 

  466. checking subcortical label: Left-choroid-plexus, 0 +/- 0
    467. 

  467. checking subcortical label: Left-F3orb, 0 +/- 0
    468. 

  468. checking subcortical label: Left-lOg, 0 +/- 0
    469. 

  469. checking subcortical label: Left-aOg, 0 +/- 0
    470. 

  470. checking subcortical label: Left-mOg, 0 +/- 0
    471. 

  471. checking subcortical label: Left-pOg, 0 +/- 0
    472. 

  472. checking subcortical label: Left-Stellate, 0 +/- 0
    473. 

  473. checking subcortical label: Left-Porg, 0 +/- 0
    474. 

  474. checking subcortical label: Left-Aorg, 0 +/- 0
    475. 

  475. checking subcortical label: Right-Cerebral-Exterior, 0 +/- 0
    476. 

  476. checking subcortical label: Right-Cerebral-White-Matter, 0 +/- 0
    477. 

  477. checking subcortical label: Right-Cerebral-Cortex, 0 +/- 0
    478. 

  478. checking subcortical label: Right-Lateral-Ventricle, 0 +/- 0
    479. 

  479. checking subcortical label: Right-Inf-Lat-Vent, 0 +/- 0
    480. 

  480. checking subcortical label: Right-Cerebellum-Exterior, 0 +/- 0
    481. 

  481. checking subcortical label: Right-Cerebellum-White-Matter, 0 +/- 0
    482. 

  482. checking subcortical label: Right-Cerebellum-Cortex, 0 +/- 0
    483. 

  483. checking subcortical label: Right-Thalamus, 2 matches found for name Right-Thalamus... exiting ...
    484. 

  484. checking subcortical label: Right-Thalamus-Proper, 0 +/- 0
    485. 

  485. checking subcortical label: Right-Caudate, 2 matches found for name Right-Caudate... exiting ...
    486. 

  486. checking subcortical label: Right-Putamen, 0 +/- 0
    487. 

  487. checking subcortical label: Right-Pallidum, 0 +/- 0
    488. 

  488. checking subcortical label: Right-Hippocampus, 0 +/- 0
    489. 

  489. checking subcortical label: Right-Amygdala, 2 matches found for name Right-Amygdala... exiting ...
    490. 

  490. checking subcortical label: Right-Insula, 0 +/- 0
    491. 

  491. checking subcortical label: Right-Operculum, 0 +/- 0
    492. 

  492. checking subcortical label: Right-Lesion, 0 +/- 0
    493. 

  493. checking subcortical label: Right-Accumbens-area, 0 +/- 0
    494. 

  494. checking subcortical label: Right-Substancia-Nigra, 0 +/- 0
    495. 

  495. checking subcortical label: Right-VentralDC, 0 +/- 0
    496. 

  496. checking subcortical label: Right-undetermined, 0 +/- 0
    497. 

  497. checking subcortical label: Right-vessel, 0 +/- 0
    498. 

  498. checking subcortical label: Right-choroid-plexus, 0 +/- 0
    499. 

  499. checking subcortical label: Right-F3orb, 0 +/- 0
    500. 

  500. checking subcortical label: Right-lOg, 0 +/- 0
    501. 

  501. checking subcortical label: Right-aOg, 0 +/- 0
    502. 

  502. checking subcortical label: Right-mOg, 0 +/- 0
    503. 

  503. checking subcortical label: Right-pOg, 0 +/- 0
    504. 

  504. checking subcortical label: Right-Stellate, 0 +/- 0
    505. 

  505. checking subcortical label: Right-Porg, 0 +/- 0
    506. 

  506. checking subcortical label: Right-Aorg, 0 +/- 0
    507. 

  507. checking subcortical label: 5th-Ventricle, 0 +/- 0
    508. 

  508. checking subcortical label: Left-Interior, 0 +/- 0
    509. 

  509. checking subcortical label: Right-Interior, 0 +/- 0
    510. 

  510. checking subcortical label: Left-Lateral-Ventricles, 0 +/- 0
    511. 

  511. checking subcortical label: Right-Lateral-Ventricles, 0 +/- 0
    512. 

  512. checking subcortical label: WM-hypointensities, 6 matches found for name WM-hypointensities... exiting ...
    513. 

  513. checking subcortical label: Left-WM-hypointensities, 0 +/- 0
    514. 

  514. checking subcortical label: Right-WM-hypointensities, 0 +/- 0
    515. 

  515. checking subcortical label: non-WM-hypointensities, 3 matches found for name non-WM-hypointensities... exiting ...
    516. 

  516. checking subcortical label: Left-non-WM-hypointensities, 0 +/- 0
    517. 

  517. checking subcortical label: Right-non-WM-hypointensities, 0 +/- 0
    518. 

  518. checking subcortical label: Left-F1, 0 +/- 0
    519. 

  519. checking subcortical label: Right-F1, 0 +/- 0
    520. 

  520. checking subcortical label: Optic-Chiasm, 0 +/- 0
    521. 

  521. checking subcortical label: Corpus_Callosum, 0 +/- 0
    522. 

  522. checking subcortical label: Left-Amygdala-Anterior, 0 +/- 0
    523. 

  523. checking subcortical label: Right-Amygdala-Anterior, 0 +/- 0
    524. 

  524. checking subcortical label: Dura, 0 +/- 0
    525. 

  525. checking subcortical label: Left-wm-intensity-abnormality, 0 +/- 0
    526. 

  526. checking subcortical label: Left-caudate-intensity-abnormality, 0 +/- 0
    527. 

  527. checking subcortical label: Left-putamen-intensity-abnormality, 0 +/- 0
    528. 

  528. checking subcortical label: Left-accumbens-intensity-abnormality, 0 +/- 0
    529. 

  529. checking subcortical label: Left-pallidum-intensity-abnormality, 0 +/- 0
    530. 

  530. checking subcortical label: Left-amygdala-intensity-abnormality, 0 +/- 0
    531. 

  531. checking subcortical label: Left-hippocampus-intensity-abnormality, 0 +/- 0
    532. 

  532. checking subcortical label: Left-thalamus-intensity-abnormality, 0 +/- 0
    533. 

  533. checking subcortical label: Left-VDC-intensity-abnormality, 0 +/- 0
    534. 

  534. checking subcortical label: Right-wm-intensity-abnormality, 0 +/- 0
    535. 

  535. checking subcortical label: Right-caudate-intensity-abnormality, 0 +/- 0
    536. 

  536. checking subcortical label: Right-putamen-intensity-abnormality, 0 +/- 0
    537. 

  537. checking subcortical label: Right-accumbens-intensity-abnormality, 0 +/- 0
    538. 

  538. checking subcortical label: Right-pallidum-intensity-abnormality, 0 +/- 0
    539. 

  539. checking subcortical label: Right-amygdala-intensity-abnormality, 0 +/- 0
    540. 

  540. checking subcortical label: Right-hippocampus-intensity-abnormality, 0 +/- 0
    541. 

  541. checking subcortical label: Right-thalamus-intensity-abnormality, 0 +/- 0
    542. 

  542. checking subcortical label: Right-VDC-intensity-abnormality, 0 +/- 0
    543. 

  543. checking subcortical label: Epidermis, 0 +/- 0
    544. 

  544. checking subcortical label: Conn-Tissue, 0 +/- 0
    545. 

  545. checking subcortical label: SC-Fat/Muscle, 0 +/- 0
    546. 

  546. checking subcortical label: CSF-SA, 0 +/- 0
    547. 

  547. checking subcortical label: Muscle, 2 matches found for name Muscle... exiting ...
    548. 

  548. checking subcortical label: Ear, 0 +/- 0
    549. 

  549. checking subcortical label: Adipose, 0 +/- 0
    550. 

  550. checking subcortical label: Spinal-Cord, 0 +/- 0
    551. 

  551. checking subcortical label: Soft-Tissue, 0 +/- 0
    552. 

  552. checking subcortical label: Nerve, 0 +/- 0
    553. 

  553. checking subcortical label: Bone, 0 +/- 0
    554. 

  554. checking subcortical label: Air, 0 +/- 0
    555. 

  555. checking subcortical label: Orbital-Fat, 0 +/- 0
    556. 

  556. checking subcortical label: Tongue, 0 +/- 0
    557. 

  557. checking subcortical label: Nasal-Structures, 0 +/- 0
    558. 

  558. checking subcortical label: Globe, 0 +/- 0
    559. 

  559. checking subcortical label: Teeth, 0 +/- 0
    560. 

  560. checking subcortical label: Left-Caudate/Putamen, 0 +/- 0
    561. 

  561. checking subcortical label: Right-Caudate/Putamen, 0 +/- 0
    562. 

  562. checking subcortical label: Left-Claustrum, 0 +/- 0
    563. 

  563. checking subcortical label: Right-Claustrum, 0 +/- 0
    564. 

  564. checking subcortical label: Cornea, 0 +/- 0
    565. 

  565. checking subcortical label: Diploe, 0 +/- 0
    566. 

  566. checking subcortical label: Vitreous-Humor, 0 +/- 0
    567. 

  567. checking subcortical label: Lens, 0 +/- 0
    568. 

  568. checking subcortical label: Aqueous-Humor, 0 +/- 0
    569. 

  569. checking subcortical label: Outer-Table, 0 +/- 0
    570. 

  570. checking subcortical label: Inner-Table, 0 +/- 0
    571. 

  571. checking subcortical label: Periosteum, 0 +/- 0
    572. 

  572. checking subcortical label: Endosteum, 0 +/- 0
    573. 

  573. sub002 has 0 outliers ...
    574. 

  574. -----
    575. 

  575. Checking white matter SNR measurements...
    576. 

  576. 

  577. SNR: Anatomical signal-to-noise ratio in white matter
    578. 

  578. mWM: Mean white matter intensity value
    579. 

  579. stdWM: Standard deviation of white matter intensity value
    580. 

  580. voxWM: Total number of white matter voxels in eroded mask
    581. 

  581. Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_wm-anat-snr_checker -subjid sub002 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log
    582. 

  582. wm-anat-snr results (sub002):
    583. 

  583. SNR	meanWM	stdWM	voxWM	
    584. 

  584. 17.84	106.04	5.94	55548
    585. 

  585. -----
    586. 

  586. -----
    587. 

  587. Running recon_checker on:
    588. 

  588. Mon Aug 12 12:59:49 CEST 2013
    589. 

  589. -----
    590. 

  590. Most recent FreeSurfer version used to process this subject:
    591. 

  591. /opt/freesurfer/5.3.0/bin/recon-all
    592. 

  592. -----
    593. 

  593. All FreeSurfer versions used to process this subject:
    594. 

  594. /opt/freesurfer/5.3.0/bin/recon-all
    595. 

  595. -----
    596. 

  596. Checking all output files exist...
    597. 

  597.      Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_output_file_checker -subjid sub002 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log -outputfileorderfile /home/fkaule/tools/QAtools_v1.1//default_FOF_FSv5.1
    598. 

  598. -----
    599. 

  599. Checking status log output...
    600. 

  600. 	Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_status_log_checker -subjid sub002 -details -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log
    601. 

  601. Using status log: /home/fkaule/tools/QAtools_v1.1//default_status_log_FSv5.1.log
    602. 

  602. 

  603. ERROR: Recon-all steps missing in subject sub002 status file
    604. 

  604. 

  605.  
    606. 

  606. Expected to see the following step(s): 
    607. 

  607. #@# Surf Volume rh Fri Aug 9 00:19:17 CEST 2013 
    608. 

  608. in the recon-all-status.log file before (line # 68): 
    609. 

  609. --> Parcellation Stats lh 
    610. 

  610. --> Cortical Parc 2 lh 
    611. 

  611. --> Parcellation Stats 2 lh 
    612. 

  612. --> Tessellate rh 
    613. 

  613. --> Smooth1 rh 
    614. 

  614. --> Inflation1 rh 
    615. 

  615. --> QSphere rh 
    616. 

  616. --> Fix Topology rh 
    617. 

  617. --> Make White Surf rh 
    618. 

  618. --> Smooth2 rh 
    619. 

  619. --> Inflation2 rh 
    620. 

  620. --> Curvature Stats rh 
    621. 

  621. --> Sphere rh 
    622. 

  622. --> Surf Reg rh 
    623. 

  623. --> Jacobian white rh 
    624. 

  624. --> AvgCurv rh 
    625. 

  625. --> Cortical Parc rh 
    626. 

  626. --> Make Pial Surf rh
    627. 

  627. -----
    628. 

  628. Checking asegs for outliers...
    629. 

  629. Using asegLUT: /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt
    630. 

  630. Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_aseg_outlier_checker -subjid sub002 -LookupMeansFromFile /home/fkaule/tools/QAtools_v1.1//DefaultAsegMeans.txt -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log
    631. 

  631. checking subcortical label: Left-Cerebral-Exterior, 0 +/- 0
    632. 

  632. checking subcortical label: Left-Cerebral-White-Matter, 0 +/- 0
    633. 

  633. checking subcortical label: Left-Cerebral-Cortex, 0 +/- 0
    634. 

  634. checking subcortical label: Left-Lateral-Ventricle, 0 +/- 0
    635. 

  635. checking subcortical label: Left-Inf-Lat-Vent, 0 +/- 0
    636. 

  636. checking subcortical label: Left-Cerebellum-Exterior, 0 +/- 0
    637. 

  637. checking subcortical label: Left-Cerebellum-White-Matter, 0 +/- 0
    638. 

  638. checking subcortical label: Left-Cerebellum-Cortex, 0 +/- 0
    639. 

  639. checking subcortical label: Left-Thalamus, 2 matches found for name Left-Thalamus... exiting ...
    640. 

  640. checking subcortical label: Left-Thalamus-Proper, 0 +/- 0
    641. 

  641. checking subcortical label: Left-Caudate, 2 matches found for name Left-Caudate... exiting ...
    642. 

  642. checking subcortical label: Left-Putamen, 0 +/- 0
    643. 

  643. checking subcortical label: Left-Pallidum, 0 +/- 0
    644. 

  644. checking subcortical label: 3rd-Ventricle, 0 +/- 0
    645. 

  645. checking subcortical label: 4th-Ventricle, 0 +/- 0
    646. 

  646. checking subcortical label: Brain-Stem, 0 +/- 0
    647. 

  647. checking subcortical label: Left-Hippocampus, 0 +/- 0
    648. 

  648. checking subcortical label: Left-Amygdala, 2 matches found for name Left-Amygdala... exiting ...
    649. 

  649. checking subcortical label: Left-Insula, 0 +/- 0
    650. 

  650. checking subcortical label: Left-Operculum, 0 +/- 0
    651. 

  651. checking subcortical label: Line-1, 0 +/- 0
    652. 

  652. checking subcortical label: Line-2, 0 +/- 0
    653. 

  653. checking subcortical label: Line-3, 0 +/- 0
    654. 

  654. checking subcortical label: CSF, 2 matches found for name CSF... exiting ...
    655. 

  655. checking subcortical label: Left-Lesion, 0 +/- 0
    656. 

  656. checking subcortical label: Left-Accumbens-area, 0 +/- 0
    657. 

  657. checking subcortical label: Left-Substancia-Nigra, 0 +/- 0
    658. 

  658. checking subcortical label: Left-VentralDC, 0 +/- 0
    659. 

  659. checking subcortical label: Left-undetermined, 0 +/- 0
    660. 

  660. checking subcortical label: Left-vessel, 0 +/- 0
    661. 

  661. checking subcortical label: Left-choroid-plexus, 0 +/- 0
    662. 

  662. checking subcortical label: Left-F3orb, 0 +/- 0
    663. 

  663. checking subcortical label: Left-lOg, 0 +/- 0
    664. 

  664. checking subcortical label: Left-aOg, 0 +/- 0
    665. 

  665. checking subcortical label: Left-mOg, 0 +/- 0
    666. 

  666. checking subcortical label: Left-pOg, 0 +/- 0
    667. 

  667. checking subcortical label: Left-Stellate, 0 +/- 0
    668. 

  668. checking subcortical label: Left-Porg, 0 +/- 0
    669. 

  669. checking subcortical label: Left-Aorg, 0 +/- 0
    670. 

  670. checking subcortical label: Right-Cerebral-Exterior, 0 +/- 0
    671. 

  671. checking subcortical label: Right-Cerebral-White-Matter, 0 +/- 0
    672. 

  672. checking subcortical label: Right-Cerebral-Cortex, 0 +/- 0
    673. 

  673. checking subcortical label: Right-Lateral-Ventricle, 0 +/- 0
    674. 

  674. checking subcortical label: Right-Inf-Lat-Vent, 0 +/- 0
    675. 

  675. checking subcortical label: Right-Cerebellum-Exterior, 0 +/- 0
    676. 

  676. checking subcortical label: Right-Cerebellum-White-Matter, 0 +/- 0
    677. 

  677. checking subcortical label: Right-Cerebellum-Cortex, 0 +/- 0
    678. 

  678. checking subcortical label: Right-Thalamus, 2 matches found for name Right-Thalamus... exiting ...
    679. 

  679. checking subcortical label: Right-Thalamus-Proper, 0 +/- 0
    680. 

  680. checking subcortical label: Right-Caudate, 2 matches found for name Right-Caudate... exiting ...
    681. 

  681. checking subcortical label: Right-Putamen, 0 +/- 0
    682. 

  682. checking subcortical label: Right-Pallidum, 0 +/- 0
    683. 

  683. checking subcortical label: Right-Hippocampus, 0 +/- 0
    684. 

  684. checking subcortical label: Right-Amygdala, 2 matches found for name Right-Amygdala... exiting ...
    685. 

  685. checking subcortical label: Right-Insula, 0 +/- 0
    686. 

  686. checking subcortical label: Right-Operculum, 0 +/- 0
    687. 

  687. checking subcortical label: Right-Lesion, 0 +/- 0
    688. 

  688. checking subcortical label: Right-Accumbens-area, 0 +/- 0
    689. 

  689. checking subcortical label: Right-Substancia-Nigra, 0 +/- 0
    690. 

  690. checking subcortical label: Right-VentralDC, 0 +/- 0
    691. 

  691. checking subcortical label: Right-undetermined, 0 +/- 0
    692. 

  692. checking subcortical label: Right-vessel, 0 +/- 0
    693. 

  693. checking subcortical label: Right-choroid-plexus, 0 +/- 0
    694. 

  694. checking subcortical label: Right-F3orb, 0 +/- 0
    695. 

  695. checking subcortical label: Right-lOg, 0 +/- 0
    696. 

  696. checking subcortical label: Right-aOg, 0 +/- 0
    697. 

  697. checking subcortical label: Right-mOg, 0 +/- 0
    698. 

  698. checking subcortical label: Right-pOg, 0 +/- 0
    699. 

  699. checking subcortical label: Right-Stellate, 0 +/- 0
    700. 

  700. checking subcortical label: Right-Porg, 0 +/- 0
    701. 

  701. checking subcortical label: Right-Aorg, 0 +/- 0
    702. 

  702. checking subcortical label: 5th-Ventricle, 0 +/- 0
    703. 

  703. checking subcortical label: Left-Interior, 0 +/- 0
    704. 

  704. checking subcortical label: Right-Interior, 0 +/- 0
    705. 

  705. checking subcortical label: Left-Lateral-Ventricles, 0 +/- 0
    706. 

  706. checking subcortical label: Right-Lateral-Ventricles, 0 +/- 0
    707. 

  707. checking subcortical label: WM-hypointensities, 6 matches found for name WM-hypointensities... exiting ...
    708. 

  708. checking subcortical label: Left-WM-hypointensities, 0 +/- 0
    709. 

  709. checking subcortical label: Right-WM-hypointensities, 0 +/- 0
    710. 

  710. checking subcortical label: non-WM-hypointensities, 3 matches found for name non-WM-hypointensities... exiting ...
    711. 

  711. checking subcortical label: Left-non-WM-hypointensities, 0 +/- 0
    712. 

  712. checking subcortical label: Right-non-WM-hypointensities, 0 +/- 0
    713. 

  713. checking subcortical label: Left-F1, 0 +/- 0
    714. 

  714. checking subcortical label: Right-F1, 0 +/- 0
    715. 

  715. checking subcortical label: Optic-Chiasm, 0 +/- 0
    716. 

  716. checking subcortical label: Corpus_Callosum, 0 +/- 0
    717. 

  717. checking subcortical label: Left-Amygdala-Anterior, 0 +/- 0
    718. 

  718. checking subcortical label: Right-Amygdala-Anterior, 0 +/- 0
    719. 

  719. checking subcortical label: Dura, 0 +/- 0
    720. 

  720. checking subcortical label: Left-wm-intensity-abnormality, 0 +/- 0
    721. 

  721. checking subcortical label: Left-caudate-intensity-abnormality, 0 +/- 0
    722. 

  722. checking subcortical label: Left-putamen-intensity-abnormality, 0 +/- 0
    723. 

  723. checking subcortical label: Left-accumbens-intensity-abnormality, 0 +/- 0
    724. 

  724. checking subcortical label: Left-pallidum-intensity-abnormality, 0 +/- 0
    725. 

  725. checking subcortical label: Left-amygdala-intensity-abnormality, 0 +/- 0
    726. 

  726. checking subcortical label: Left-hippocampus-intensity-abnormality, 0 +/- 0
    727. 

  727. checking subcortical label: Left-thalamus-intensity-abnormality, 0 +/- 0
    728. 

  728. checking subcortical label: Left-VDC-intensity-abnormality, 0 +/- 0
    729. 

  729. checking subcortical label: Right-wm-intensity-abnormality, 0 +/- 0
    730. 

  730. checking subcortical label: Right-caudate-intensity-abnormality, 0 +/- 0
    731. 

  731. checking subcortical label: Right-putamen-intensity-abnormality, 0 +/- 0
    732. 

  732. checking subcortical label: Right-accumbens-intensity-abnormality, 0 +/- 0
    733. 

  733. checking subcortical label: Right-pallidum-intensity-abnormality, 0 +/- 0
    734. 

  734. checking subcortical label: Right-amygdala-intensity-abnormality, 0 +/- 0
    735. 

  735. checking subcortical label: Right-hippocampus-intensity-abnormality, 0 +/- 0
    736. 

  736. checking subcortical label: Right-thalamus-intensity-abnormality, 0 +/- 0
    737. 

  737. checking subcortical label: Right-VDC-intensity-abnormality, 0 +/- 0
    738. 

  738. checking subcortical label: Epidermis, 0 +/- 0
    739. 

  739. checking subcortical label: Conn-Tissue, 0 +/- 0
    740. 

  740. checking subcortical label: SC-Fat/Muscle, 0 +/- 0
    741. 

  741. checking subcortical label: CSF-SA, 0 +/- 0
    742. 

  742. checking subcortical label: Muscle, 2 matches found for name Muscle... exiting ...
    743. 

  743. checking subcortical label: Ear, 0 +/- 0
    744. 

  744. checking subcortical label: Adipose, 0 +/- 0
    745. 

  745. checking subcortical label: Spinal-Cord, 0 +/- 0
    746. 

  746. checking subcortical label: Soft-Tissue, 0 +/- 0
    747. 

  747. checking subcortical label: Nerve, 0 +/- 0
    748. 

  748. checking subcortical label: Bone, 0 +/- 0
    749. 

  749. checking subcortical label: Air, 0 +/- 0
    750. 

  750. checking subcortical label: Orbital-Fat, 0 +/- 0
    751. 

  751. checking subcortical label: Tongue, 0 +/- 0
    752. 

  752. checking subcortical label: Nasal-Structures, 0 +/- 0
    753. 

  753. checking subcortical label: Globe, 0 +/- 0
    754. 

  754. checking subcortical label: Teeth, 0 +/- 0
    755. 

  755. checking subcortical label: Left-Caudate/Putamen, 0 +/- 0
    756. 

  756. checking subcortical label: Right-Caudate/Putamen, 0 +/- 0
    757. 

  757. checking subcortical label: Left-Claustrum, 0 +/- 0
    758. 

  758. checking subcortical label: Right-Claustrum, 0 +/- 0
    759. 

  759. checking subcortical label: Cornea, 0 +/- 0
    760. 

  760. checking subcortical label: Diploe, 0 +/- 0
    761. 

  761. checking subcortical label: Vitreous-Humor, 0 +/- 0
    762. 

  762. checking subcortical label: Lens, 0 +/- 0
    763. 

  763. checking subcortical label: Aqueous-Humor, 0 +/- 0
    764. 

  764. checking subcortical label: Outer-Table, 0 +/- 0
    765. 

  765. checking subcortical label: Inner-Table, 0 +/- 0
    766. 

  766. checking subcortical label: Periosteum, 0 +/- 0
    767. 

  767. checking subcortical label: Endosteum, 0 +/- 0
    768. 

  768. sub002 has 0 outliers ...
    769. 

  769. -----
    770. 

  770. Checking white matter SNR measurements...
    771. 

  771. 

  772. SNR: Anatomical signal-to-noise ratio in white matter
    773. 

  773. mWM: Mean white matter intensity value
    774. 

  774. stdWM: Standard deviation of white matter intensity value
    775. 

  775. voxWM: Total number of white matter voxels in eroded mask
    776. 

  776. Running command: /home/fkaule/tools/QAtools_v1.1//recon_all_wm-anat-snr_checker -subjid sub002 -slog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//sub002/scripts/recon_checker.log -sumlog /home/data/exppsy/forrest_gump/openfmri.org/freesurfer//QA/recon_checker.ALL.summary.log
    777. 

  777. wm-anat-snr results (sub002):
    778. 

  778. SNR	meanWM	stdWM	voxWM	
    779. 

  779. 17.84	106.04	5.94	55548
    780. 

  780. -----
    781.