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- arasan@arasan-VirtualBox:~/brainvisa_test/sbr42$ bash 3without_bvproc.sh
- 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
- Loading toolbox cortical_surface
- Loading toolbox data management
- Loading toolbox datamind
- Loading toolbox freesurfer
- Loading toolbox morphologist
- Loading toolbox spm
- Loading toolbox structural_analysis
- Loading toolbox tools
- Loading toolbox viewers
- Loading toolbox My processes
- The log file for this session is '/home/arasan/.brainvisa/brainvisa4.log'
- Headless Anatomist running in normal (non-headless) mode
- exec: /home/arasan/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
- /home/arasan/brainvisa_test/fsl/data: parse directories and insert items
- /home/arasan/brainvisa_test/fsl/data: 1 files are stored as 1 DiskItems in 0
- seconds
- /home/arasan/brainvisa_test/spm8: parse directories and insert items
- /home/arasan/brainvisa_test/spm8: 1 files are stored as 1 DiskItems in 0 seconds
- Process Check SPAM models installation started on 2018/10/18 17:24
- models: 6
- SPAM models are present.
- Process Check SPAM models installation finished on 2018/10/18 17:24 (0 seconds)
- Process Morphologist 2015 started on 2018/10/18 17:24
- progress: 0.0 % ...
- progress: 0.0 % ...
- progress: 0.0 % ...
- progress: 0.0 % ...
- smoothing anatomy_data...
- Registering to the template...
- WARNING: Test image is a floating point data Volume ==> Conversion to int16
- Managing transformations chain...
- done.
- progress: 5.0 % ...
- progress: 5.0 % ...
- ERROR in AC/PC Or Normalization 1 Mandatory argument source_referential has no
- value
- --------------------------------------------------------------------------------
- Exception
- ERROR in Morphologist 2015 1 Mandatory argument source_referential has no value
- --------------------------------------------------------------------------------
- Exception
- Process Morphologist 2015 finished on 2018/10/18 17:26 (1 minutes 43 seconds)
- Traceback (most recent call last):
- File "/home/arasan/brainvisa-4.6.0/lib/python2.7/runpy.py", line 174, in _run_module_as_main
- "__main__", fname, loader, pkg_name)
- File "/home/arasan/brainvisa-4.6.0/lib/python2.7/runpy.py", line 72, in _run_code
- exec code in run_globals
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/axon/runprocess.py", line 448, in <module>
- keep_failed_workflow=options.keep_failed_workflow)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/axon/runprocess.py", line 242, in run_process_with_distribution
- brainvisa.processes.defaultContext().runProcess(process)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2901, in runProcess
- six.reraise(e[0], None, e[1])
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 3174, in _processExecution
- result = process.execution(self)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 1583, in execution
- return self._executionNode.run(context)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
- return self._run(context)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2554, in _run
- result.append(node.run(context))
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
- return self._run(context)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2435, in _run
- return context.runProcess(self._process)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2894, in runProcess
- result = self._processExecution(_process, None)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 3174, in _processExecution
- result = process.execution(self)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 1583, in execution
- return self._executionNode.run(context)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
- return self._run(context)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2660, in _run
- res = node.run(context)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
- return self._run(context)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2554, in _run
- result.append(node.run(context))
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
- return self._run(context)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2435, in _run
- return context.runProcess(self._process)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2893, in runProcess
- self._setArguments(_process, *args, **kwargs)
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 2854, in _setArguments
- _process.checkArguments()
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/processes.py", line 878, in checkArguments
- o.checkValue(p, getattr(self, p, None))
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/data/readdiskitem.py", line 188, in checkValue
- Parameter.checkValue( self, name, value )
- File "/home/arasan/brainvisa-4.6.0/python/brainvisa/data/neuroData.py", line 209, in checkValue
- raise Exception( HTMLMessage(_t_('Mandatory argument <em>%s</em> has no value') % name) )
- Exception: Mandatory argument <em>source_referential</em> has no value
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