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constructed_import_db_FAILED

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Oct 19th, 2018
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  1. arasan@arasan-VirtualBox:~/brainvisa_test/sbr42$ bash 3without_bvproc.sh
  2. python -m brainvisa.axon.runprocess --enabledb morphologist t1mri=/home/arasan/brainvisa_test/sbr42/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/100610_1-T1w_acpc_dc_restore_1mm.nii.gz perform_normalization=1 anterior_commissure=none posterior_commissure=none interhemispheric_point=none left_hemisphere_point=none t1mri_nobias=/home/arasan/brainvisa_test/sbr42/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/default_analysis/nobias_100610_1-T1w_acpc_dc_restore_1mm.nii.gz histo_analysis=/home/arasan/brainvisa_test/sbr42/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/default_analysis/nobias_100610_1-T1w_acpc_dc_restore_1mm.han split_brain=/home/arasan/brainvisa_test/sbr42/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/default_analysis/segmentation/voronoi_100610_1-T1w_acpc_dc_restore_1mm.nii.gz left_graph=/home/arasan/brainvisa_test/sbr42/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/default_analysis/folds/3.1/L100610_1-T1w_acpc_dc_restore_1mm.arg right_graph=/home/arasan/brainvisa_test/sbr42/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/default_analysis/folds/3.1/R100610_1-T1w_acpc_dc_restore_1mm.arg perform_sulci_recognition=1 left_labelled_graph=/home/arasan/brainvisa_test/sbr42/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/default_analysis/folds/3.1/default_session_auto/L100610_1-T1w_acpc_dc_restore_1mm_default_session_auto.arg right_labelled_graph=/home/arasan/brainvisa_test/sbr42/subjects/100610_1-T1w_acpc_dc_restore_1mm/t1mri/default_acquisition/default_analysis/folds/3.1/default_session_auto/R100610_1-T1w_acpc_dc_restore_1mm_default_session_auto.arg
  3. Loading toolbox cortical_surface
  4. Loading toolbox data management
  5. Loading toolbox datamind
  6. Loading toolbox freesurfer
  7. Loading toolbox morphologist
  8. Loading toolbox spm
  9. Loading toolbox structural_analysis
  10. Loading toolbox tools
  11. Loading toolbox viewers
  12. Loading toolbox My processes
  13. The log file for this session is '/home/arasan/.brainvisa/brainvisa4.log'
  14. Headless Anatomist running in normal (non-headless) mode
  15. exec: /home/arasan/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
  16. /home/arasan/brainvisa_test/fsl/data: parse directories and insert items
  17. /home/arasan/brainvisa_test/fsl/data: 1 files are stored as 1 DiskItems in 0
  18. seconds
  19. /home/arasan/brainvisa_test/spm8: parse directories and insert items
  20. /home/arasan/brainvisa_test/spm8: 1 files are stored as 1 DiskItems in 0 seconds
  21.  
  22. Process Check SPAM models installation started on 2018/10/18 17:24
  23. models: 6
  24. SPAM models are present.
  25. Process Check SPAM models installation finished on 2018/10/18 17:24 (0 seconds)
  26.  
  27. Process Morphologist 2015 started on 2018/10/18 17:24
  28. progress: 0.0 % ...
  29. progress: 0.0 % ...
  30. progress: 0.0 % ...
  31. progress: 0.0 % ...
  32. smoothing anatomy_data...
  33. Registering to the template...
  34. WARNING: Test image is a floating point data Volume ==> Conversion to int16
  35. Managing transformations chain...
  36. done.
  37. progress: 5.0 % ...
  38. progress: 5.0 % ...
  39. ERROR in AC/PC Or Normalization 1 Mandatory argument source_referential has no
  40. value
  41.  
  42. --------------------------------------------------------------------------------
  43. Exception
  44. ERROR in Morphologist 2015 1 Mandatory argument source_referential has no value
  45.  
  46. --------------------------------------------------------------------------------
  47. Exception
  48. Process Morphologist 2015 finished on 2018/10/18 17:26 (1 minutes 43 seconds)
  49. Traceback (most recent call last):
  50. File "/home/arasan/brainvisa-4.6.0/lib/python2.7/runpy.py", line 174, in _run_module_as_main
  51. "__main__", fname, loader, pkg_name)
  52. File "/home/arasan/brainvisa-4.6.0/lib/python2.7/runpy.py", line 72, in _run_code
  53. exec code in run_globals
  54. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/axon/runprocess.py", line 448, in <module>
  55. keep_failed_workflow=options.keep_failed_workflow)
  56. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/axon/runprocess.py", line 242, in run_process_with_distribution
  57. brainvisa.processes.defaultContext().runProcess(process)
  58. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2901, in runProcess
  59. six.reraise(e[0], None, e[1])
  60. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 3174, in _processExecution
  61. result = process.execution(self)
  62. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 1583, in execution
  63. return self._executionNode.run(context)
  64. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
  65. return self._run(context)
  66. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2554, in _run
  67. result.append(node.run(context))
  68. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
  69. return self._run(context)
  70. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2435, in _run
  71. return context.runProcess(self._process)
  72. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2894, in runProcess
  73. result = self._processExecution(_process, None)
  74. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 3174, in _processExecution
  75. result = process.execution(self)
  76. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 1583, in execution
  77. return self._executionNode.run(context)
  78. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
  79. return self._run(context)
  80. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2660, in _run
  81. res = node.run(context)
  82. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
  83. return self._run(context)
  84. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2554, in _run
  85. result.append(node.run(context))
  86. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
  87. return self._run(context)
  88. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2435, in _run
  89. return context.runProcess(self._process)
  90. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2893, in runProcess
  91. self._setArguments(_process, *args, **kwargs)
  92. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2854, in _setArguments
  93. _process.checkArguments()
  94. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 878, in checkArguments
  95. o.checkValue(p, getattr(self, p, None))
  96. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/data/readdiskitem.py", line 188, in checkValue
  97. Parameter.checkValue( self, name, value )
  98. File "/home/arasan/brainvisa-4.6.0/python/brainvisa/data/neuroData.py", line 209, in checkValue
  99. raise Exception( HTMLMessage(_t_('Mandatory argument <em>%s</em> has no value') % name) )
  100. Exception: Mandatory argument <em>source_referential</em> has no value
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