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Dec 4th, 2018
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  1. darasan@imecas10:/data/Team_Caspers/Arasan$ bash 2import_update_morphologist.sh -s /data/Team_Caspers/Arasan/brainvisa_test/test_subjects_list.txt -d /data/Team_Caspers/Arasan/brainvisa_test/sbr95
  2. MAKING DATABASE FOLDER /data/Team_Caspers/Arasan/brainvisa_test/sbr95 AS IT DOES NOT EXIST
  3. SINGULARITY IMAGE TO BE USED: /data/Team_Caspers/lmod/installed/brainvisa_extra/brainvisa_4_6_0_xenial_with_updatedb_createdb_added-2018-12-03-86a7458d4613.simg
  4. SPECIFIED DATABASE PATH: /data/Team_Caspers/Arasan/brainvisa_test/sbr95
  5. CREATING DATABASE: /data/Team_Caspers/Arasan/brainvisa_test/sbr95
  6. ############################################################## CREATING /mnt2
  7. Loading toolbox cortical_surface
  8. Loading toolbox data management
  9. Loading toolbox datamind
  10. Loading toolbox freesurfer
  11. Loading toolbox morphologist
  12. Loading toolbox spm
  13. Loading toolbox structural_analysis
  14. Loading toolbox tools
  15. Loading toolbox viewers
  16. Loading toolbox My processes
  17. The log file for this session is
  18. '/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
  19. Headless Anatomist running in normal (non-headless) mode
  20. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  21.  
  22. Process Create database started on 2018/12/04 16:15
  23. /mnt2: parse directories and insert items
  24. /mnt2: 2 files are stored as 2 DiskItems in 0 seconds
  25. Generating database tables for /mnt2
  26. /mnt2: parse directories and insert items
  27. /mnt2: 2 files are stored as 2 DiskItems in 0 seconds
  28. Process Create database finished on 2018/12/04 16:15 (8 seconds)
  29. IMPORTING SUBJECT: /data/Team_Caspers/Arasan/brainvisa_test/sbr51/100408_1-T1w_acpc_dc_restore_1mm.nii.gz
  30. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ IMPORTING 100408_1-T1w_acpc_dc_restore_1mm
  31. DATABASE MOUNTED /mnt2
  32. SUBJECT NIFTI DIR MOUNTED /mnt1
  33. SUBJECT NIFTI FILE NAME 100408_1-T1w_acpc_dc_restore_1mm.nii.gz
  34. SUBJECT NIFTI PREFIX 100408_1-T1w_acpc_dc_restore_1mm
  35. Loading toolbox cortical_surface
  36. Loading toolbox data management
  37. Loading toolbox datamind
  38. Loading toolbox freesurfer
  39. Loading toolbox morphologist
  40. Loading toolbox spm
  41. Loading toolbox structural_analysis
  42. Loading toolbox tools
  43. Loading toolbox viewers
  44. Loading toolbox My processes
  45. The log file for this session is
  46. '/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
  47. Database /mnt2 must be updated because there is no database file.
  48. Headless Anatomist running in normal (non-headless) mode
  49. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  50. WARNING: Cannot question database /mnt2. You should update this database.
  51. WARNING: Cannot question database /mnt2. You should update this database.
  52. WARNING: Cannot question database /mnt2 : no such table: Bvsession . You should
  53. update this database.
  54. WARNING: Cannot question database /mnt2 : no such table: Bvsession . You should
  55. update this database.
  56.  
  57. Process Import T1 MRI started on 2018/12/04 16:15
  58. filein : /tmp/tmpy6JRMm.nii.gz
  59. fileout : /mnt2/subjects/100408_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100408_1-T1w_acpc_dc_restore_1mm.nii.gz
  60. encoding: Binary
  61. normal : 0
  62. rescale : 1
  63. format :
  64. type : S16
  65. objtype :
  66. xdim : 0
  67. ydim : 0
  68. zdim : 0
  69. imin : default
  70. imax : default
  71. omin : 0
  72. omax : 4095
  73. reading /tmp/tmpy6JRMm.nii.gz as Volume / FLOAT...
  74. reading done
  75. convert to Volume / S16
  76. converting data...
  77. convert done
  78. writing /mnt2/subjects/100408_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100408_1-T1w_acpc_dc_restore_1mm.nii.gz...
  79. done
  80. Process Import T1 MRI finished on 2018/12/04 16:15 (5 seconds)
  81. ERROR no such table: _FILENAMES_
  82.  
  83. --------------------------------------------------------------------------------
  84. OperationalError
  85. processes.py (3216) in _processExecution:
  86.  
  87. item, update=True)
  88.  
  89. sqlFSODatabase.py (278) in insertDiskItem:
  90.  
  91. self.insertDiskItems( ( item, ), **kwargs )
  92.  
  93. sqlFSODatabase.py (2020) in insertDiskItems:
  94.  
  95. insertParentDirs=insertParentDirs )
  96.  
  97. sqlFSODatabase.py (1127) in insertDiskItems:
  98.  
  99. diSet = self._diskItemsWithParents( diskItems )
  100.  
  101. sqlFSODatabase.py (1115) in _diskItemsWithParents:
  102.  
  103. ( reldirname, ) ).fetchone()
  104.  
  105. ERROR no such table: _FILENAMES_
  106.  
  107. --------------------------------------------------------------------------------
  108. OperationalError
  109. processes.py (3216) in _processExecution:
  110.  
  111. item, update=True)
  112.  
  113. sqlFSODatabase.py (278) in insertDiskItem:
  114.  
  115. self.insertDiskItems( ( item, ), **kwargs )
  116.  
  117. sqlFSODatabase.py (2020) in insertDiskItems:
  118.  
  119. insertParentDirs=insertParentDirs )
  120.  
  121. sqlFSODatabase.py (1127) in insertDiskItems:
  122.  
  123. diSet = self._diskItemsWithParents( diskItems )
  124.  
  125. sqlFSODatabase.py (1115) in _diskItemsWithParents:
  126.  
  127. ( reldirname, ) ).fetchone()
  128.  
  129. IMPORTING SUBJECT: /data/Team_Caspers/Arasan/brainvisa_test/sbr51/100610_1-T1w_acpc_dc_restore_1mm.nii.gz
  130. @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ IMPORTING 100610_1-T1w_acpc_dc_restore_1mm
  131. DATABASE MOUNTED /mnt2
  132. SUBJECT NIFTI DIR MOUNTED /mnt1
  133. SUBJECT NIFTI FILE NAME 100610_1-T1w_acpc_dc_restore_1mm.nii.gz
  134. SUBJECT NIFTI PREFIX 100610_1-T1w_acpc_dc_restore_1mm
  135. Loading toolbox cortical_surface
  136. Loading toolbox data management
  137. Loading toolbox datamind
  138. Loading toolbox freesurfer
  139. Loading toolbox morphologist
  140. Loading toolbox spm
  141. Loading toolbox structural_analysis
  142. Loading toolbox tools
  143. Loading toolbox viewers
  144. Loading toolbox My processes
  145. The log file for this session is
  146. '/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
  147. Database /mnt2 must be updated because there is no database file.
  148. Headless Anatomist running in normal (non-headless) mode
  149. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  150. WARNING: Cannot question database /mnt2. You should update this database.
  151. WARNING: Cannot question database /mnt2. You should update this database.
  152. WARNING: Cannot question database /mnt2 : no such table: Bvsession . You should
  153. update this database.
  154. WARNING: Cannot question database /mnt2 : no such table: Bvsession . You should
  155. update this database.
  156.  
  157. Process Import T1 MRI started on 2018/12/04 16:15
  158. filein : /tmp/tmpsE_qpS.nii.gz
  159. fileout : /mnt2/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100610_1-T1w_acpc_dc_restore_1mm.nii.gz
  160. encoding: Binary
  161. normal : 0
  162. rescale : 1
  163. format :
  164. type : S16
  165. objtype :
  166. xdim : 0
  167. ydim : 0
  168. zdim : 0
  169. imin : default
  170. imax : default
  171. omin : 0
  172. omax : 4095
  173. reading /tmp/tmpsE_qpS.nii.gz as Volume / FLOAT...
  174. reading done
  175. convert to Volume / S16
  176. converting data...
  177. convert done
  178. writing /mnt2/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100610_1-T1w_acpc_dc_restore_1mm.nii.gz...
  179. done
  180. Process Import T1 MRI finished on 2018/12/04 16:15 (4 seconds)
  181. ERROR no such table: _FILENAMES_
  182.  
  183. --------------------------------------------------------------------------------
  184. OperationalError
  185. processes.py (3216) in _processExecution:
  186.  
  187. item, update=True)
  188.  
  189. sqlFSODatabase.py (278) in insertDiskItem:
  190.  
  191. self.insertDiskItems( ( item, ), **kwargs )
  192.  
  193. sqlFSODatabase.py (2020) in insertDiskItems:
  194.  
  195. insertParentDirs=insertParentDirs )
  196.  
  197. sqlFSODatabase.py (1127) in insertDiskItems:
  198.  
  199. diSet = self._diskItemsWithParents( diskItems )
  200.  
  201. sqlFSODatabase.py (1115) in _diskItemsWithParents:
  202.  
  203. ( reldirname, ) ).fetchone()
  204.  
  205. ERROR no such table: _FILENAMES_
  206.  
  207. --------------------------------------------------------------------------------
  208. OperationalError
  209. processes.py (3216) in _processExecution:
  210.  
  211. item, update=True)
  212.  
  213. sqlFSODatabase.py (278) in insertDiskItem:
  214.  
  215. self.insertDiskItems( ( item, ), **kwargs )
  216.  
  217. sqlFSODatabase.py (2020) in insertDiskItems:
  218.  
  219. insertParentDirs=insertParentDirs )
  220.  
  221. sqlFSODatabase.py (1127) in insertDiskItems:
  222.  
  223. diSet = self._diskItemsWithParents( diskItems )
  224.  
  225. sqlFSODatabase.py (1115) in _diskItemsWithParents:
  226.  
  227. ( reldirname, ) ).fetchone()
  228.  
  229. UPDATING DATABSE 2: /data/Team_Caspers/Arasan/brainvisa_test/sbr95
  230. ############################################################## UPDATING /mnt2
  231. Loading toolbox cortical_surface
  232. Loading toolbox data management
  233. Loading toolbox datamind
  234. Loading toolbox freesurfer
  235. Loading toolbox morphologist
  236. Loading toolbox spm
  237. Loading toolbox structural_analysis
  238. Loading toolbox tools
  239. Loading toolbox viewers
  240. Loading toolbox My processes
  241. The log file for this session is
  242. '/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
  243. Database /mnt2 must be updated because there is no database file.
  244. Headless Anatomist running in normal (non-headless) mode
  245. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  246. WARNING: Cannot question database /mnt2. You should update this database.
  247.  
  248. Process Update databases started on 2018/12/04 16:15
  249. Generating database tables for /mnt2
  250. Clear database: /mnt2
  251. Update database: /mnt2
  252. /mnt2: parse directories and insert items
  253. /mnt2: 12 files are stored as 12 DiskItems in 0 seconds
  254. Process Update databases finished on 2018/12/04 16:15 (3 seconds)
  255. MORPHOLOGIST SUBJECT: /data/Team_Caspers/Arasan/brainvisa_test/sbr51/100408_1-T1w_acpc_dc_restore_1mm.nii.gz
  256. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MORPHOLOGIST 100408_1-T1w_acpc_dc_restore_1mm
  257. DATABASE MOUNTED /mnt2
  258. SUBJECT NIFTI PREFIX 100408_1-T1w_acpc_dc_restore_1mm
  259. Loading toolbox cortical_surface
  260. Loading toolbox data management
  261. Loading toolbox datamind
  262. Loading toolbox freesurfer
  263. Loading toolbox morphologist
  264. Loading toolbox spm
  265. Loading toolbox structural_analysis
  266. Loading toolbox tools
  267. Loading toolbox viewers
  268. Loading toolbox My processes
  269. The log file for this session is
  270. '/home/homeGlobal/darasan/.brainvisa/brainvisa3.log'
  271. Headless Anatomist running in normal (non-headless) mode
  272. exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  273.  
  274. Process Check SPAM models installation started on 2018/12/04 16:16
  275. models: 6
  276. SPAM models are present.
  277. Process Check SPAM models installation finished on 2018/12/04 16:16 (0 seconds)
  278.  
  279. Process Morphologist 2015 started on 2018/12/04 16:16
  280. progress: 0.0 % ...
  281. progress: 0.0 % ...
  282. progress: 0.0 % ...
  283. progress: 0.0 % ...
  284. smoothing anatomy_data...
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