bvproc : parameter is not readable or does not exist ERROR

Questions about BrainVisa usage and installation

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durai2323
Posts: 8
Joined: Thu Sep 13, 2018 8:53 am
Location: Forschungszentrum Jülich, Jülich, Germany

bvproc : parameter is not readable or does not exist ERROR

Postby durai2323 » Mon Oct 01, 2018 9:55 am

Hello forum members,

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


and I get the following error. It says a parameter is not readable or not found ( the normalization_transformation parameter) -

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


I have attached the bvproc that was used as well. Unfortunately the forum does not allow me to upload bvprocs with the extension bvproc. So I changed the bvproc's extension to txt. So the file is called Morphologist_220071_1.txt.

Please let me know if the issue makes sense to you.

Thanks,
Durai

durai2323
Posts: 8
Joined: Thu Sep 13, 2018 8:53 am
Location: Forschungszentrum Jülich, Jülich, Germany

Re: bvproc : parameter is not readable or does not exist ERROR

Postby durai2323 » Mon Oct 01, 2018 9:57 am

OK I could not attach the file, there is a "could not upload error". I am working on it..

Durai

User avatar
riviere
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Posts: 1358
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
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Re: bvproc : parameter is not readable or does not exist ERROR

Postby riviere » Sat Oct 06, 2018 4:09 pm

Hi,
There was probably a problem of access right on the attachments directory on our server. I have changed it, I hope it works better but I haven't tested it.
What kind of normalization have you configured in brainvisa (SPM, FSL...), and which one is selected in your pipeline ? Depending on it the behavior should be different so I need to know that before investigating further.
Denis


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