I am trying to run the morphologist pipeline using a bvproc form the command line using the following command -
Code: Select all
python -m brainvisa.axon.runprocess --enabledb /mnt3/bvprocs_for_singularity_c4/Morphologist_220071_1.bvproc
Code: Select all
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/homeGlobal/darasan/.brainvisa/brainvisa2.log'
Headless Anatomist running in normal (non-headless) mode
exec: /home/brainvisauser/brainvisa-4.6.0/brainvisa/toolboxes/morphologist/startup.py
Process Check SPAM models installation started on 2018/10/01 08:37
models: 0
WARNING: SPAM models have not be installed yet.
Process Check SPAM models installation finished on 2018/10/01 08:37 (0 seconds)
Process Morphologist 2015 started on 2018/10/01 08:37
progress: 0.0 % ...
progress: 0.0 % ...
progress: 0.0 % ...
progress: 0.0 % ...
progress: 5.0 % ...
ERROR in AC/PC Or Normalization 1 the parameter normalization_transformation is
not readable or does not exist :
/mnt2/1000BRAINS_with_bvproc_test_c4/subjects/220071_1-t1/t1mri/default_acquisition/registration/RawT1-220071_1-t1_default_acquisition_TO_Talairach-MNI.trm
--------------------------------------------------------------------------------
RuntimeError
ERROR in Morphologist 2015 1 the parameter normalization_transformation is not
readable or does not exist :
/mnt2/1000BRAINS_with_bvproc_test_c4/subjects/220071_1-t1/t1mri/default_acquisition/registration/RawT1-220071_1-t1_default_acquisition_TO_Talairach-MNI.trm
--------------------------------------------------------------------------------
RuntimeError
Process Morphologist 2015 finished on 2018/10/01 08:37 (0 seconds)
Traceback (most recent call last):
File "/home/brainvisauser/brainvisa-4.6.0/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"__main__", fname, loader, pkg_name)
File "/home/brainvisauser/brainvisa-4.6.0/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/axon/runprocess.py", line 448, in <module>
keep_failed_workflow=options.keep_failed_workflow)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/axon/runprocess.py", line 242, in run_process_with_distribution
brainvisa.processes.defaultContext().runProcess(process)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2901, in runProcess
six.reraise(e[0], None, e[1])
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 3174, in _processExecution
result = process.execution(self)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 1583, in execution
return self._executionNode.run(context)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
return self._run(context)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2554, in _run
result.append(node.run(context))
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
return self._run(context)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2435, in _run
return context.runProcess(self._process)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2894, in runProcess
result = self._processExecution(_process, None)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 3174, in _processExecution
result = process.execution(self)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 1583, in execution
return self._executionNode.run(context)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
return self._run(context)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2660, in _run
res = node.run(context)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
return self._run(context)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2554, in _run
result.append(node.run(context))
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2199, in run
return self._run(context)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2435, in _run
return context.runProcess(self._process)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2893, in runProcess
self._setArguments(_process, *args, **kwargs)
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 2854, in _setArguments
_process.checkArguments()
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/processes.py", line 878, in checkArguments
o.checkValue(p, getattr(self, p, None))
File "/home/brainvisauser/brainvisa-4.6.0/python/brainvisa/data/readdiskitem.py", line 191, in checkValue
raise RuntimeError( HTMLMessage(_t_( 'the parameter <em>%s</em> is not readable or does not exist : %s' ) % (unicode(name), unicode(value))) )
RuntimeError: the parameter <em>normalization_transformation</em> is not readable or does not exist : /mnt2/1000BRAINS_with_bvproc_test_c4/subjects/220071_1-t1/t1mri/default_acquisition/registration/RawT1-220071_1-t1_default_acquisition_TO_Talairach-MNI.trm
Please let me know if the issue makes sense to you.
Thanks,
Durai