Error with process Import_FROM_FreeSurfer_TO_Morpho.py

Questions about BrainVisa usage and installation

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francois
Posts: 61
Joined: Tue Jul 25, 2017 9:37 am

Error with process Import_FROM_FreeSurfer_TO_Morpho.py

Postby francois » Thu Nov 01, 2018 11:20 am

Any clue where is this error coming from?

Code: Select all

progress: 83.5714285714 / 100 ...
Building left hemisphere attributed relational sulci graph...
Traceback (most recent call last): File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/bin/real-bin/AimsFoldsGraphThickness.py",
line 84, in <module>
graph_out = fd.process() File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/soma/wip/aimsalgo/foldsgraphthickness.py",
line 173, in process self.preProcess() File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/soma/wip/aimsalgo/foldsgraphthickness.py",
line 117, in preProcess self.mid_interface_bck = f1.midInterface(self.WM_label,
self.LCR_label) Exception: unknown
ERROR in Hemisphere Sulci Thickness and Volumes 1 System command exited with non
null value : 1

--------------------------------------------------------------------------------
RuntimeError
ERROR in Hemisphere Cortical Folds Graph 3 System command exited with non null
value : 1

--------------------------------------------------------------------------------
RuntimeError
ERROR in Morphologist 2015 2 System command exited with non null value : 1

--------------------------------------------------------------------------------
RuntimeError
ERROR in Import FreeSurfer grey/white segmentation to Morphologist 4 System
command exited with non null value : 1

--------------------------------------------------------------------------------
RuntimeError
Process Import FreeSurfer grey/white segmentation to Morphologist finished on
2018/10/30 08:37 (12 minutes 19 seconds)
Traceback (most recent call last):
  File "/home/ftadel/IntrAnat/IntrAnat_ftadel/progressbar.py", line 119, in run
    self.out = self.func(self)
  File "/home/ftadel/IntrAnat/IntrAnat_ftadel/ImageImport.py", line 2478, in <lambda>
    ProgressDialog.call(lambda thr:self.runPipelineFSWorker(diOrig, diOut, thr), True, self, "Running Morphologist on FreeSurfer output...", "FreeSufer")
  File "/home/ftadel/IntrAnat/IntrAnat_ftadel/ImageImport.py", line 2493, in runPipelineFSWorker
    self.brainvisaContext.runProcess(proc)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2985, in runProcess
    six.reraise(type(e[0]), e[0], e[1])
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3261, in _processExecution
    result = process.execution(self)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/brainvisa/toolboxes/freesurfer/processes/Import/Import_FROM_FreeSurfer_TO_Morpho.py", line 360, in execution
    context.runProcess( morphologist )
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2978, in runProcess
    result = self._processExecution(_process, None)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3261, in _processExecution
    result = process.execution(self)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 1653, in execution
    return self._executionNode.run(context)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2276, in run
    return self._run(context)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2632, in _run
    result.append(node.run(context))
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2276, in run
    return self._run(context)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2705, in _run
    return super(ParallelExecutionNode, self)._run(context)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2632, in _run
    result.append(node.run(context))
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2276, in run
    return self._run(context)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2632, in _run
    result.append(node.run(context))
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2276, in run
    return self._run(context)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2513, in _run
    return context.runProcess(self._process)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2978, in runProcess
    result = self._processExecution(_process, None)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3261, in _processExecution
    result = process.execution(self)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/brainvisa/toolboxes/morphologist/processes/segmentationpipeline/components/corticalfoldsgraph.py", line 229, in execution
    sulci_voronoi=self.sulci_voronoi)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 2978, in runProcess
    result = self._processExecution(_process, None)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3261, in _processExecution
    result = process.execution(self)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/brainvisa/toolboxes/morphologist/processes/segmentationpipeline/components/CorticalFoldsGraphThickness.py", line 79, in execution
    context.pythonSystem(*cmd)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3465, in pythonSystem
    return self.system(sys.executable, exe, *args[1:], **kwargs)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3441, in system
    _t_('System command exited with non null value : %s') % str(ret))
RuntimeError: System command exited with non null value : 1
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riviere
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Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

Postby riviere » Sun Nov 04, 2018 2:30 am

Hi,
Does the input image look "nornal" ? Is it possible to send the example image to me so that I can try it ?
Denis

francois
Posts: 61
Joined: Tue Jul 25, 2017 9:37 am

Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

Postby francois » Fri Nov 09, 2018 2:19 pm

It does look normal, and it used to work on this patient, with the same FreeSurfer segmentation folder.
I sent you the FreeSurfer output by email.

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riviere
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Location: CEA NeuroSpin, Saint Aubin, France
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Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

Postby riviere » Fri Nov 09, 2018 6:31 pm

OK I have tried your image, and it seems that in the ribbon.mgz image, the values are not the ones we expect. I don't know if Freesurfer 6 has changed something here, and I don't remember if we have used this version with brainvisa. Which version are you running ?
Anyway the problem is that the grey/white values in the ribbon images used to be 2, 3, 41 and 42, and they are 10, 20, 110, 120 in your image. So all the processing was wrong.
I have put an updated process here:
ftp://ftp.cea.fr/pub/dsv/anatomist/upda ... _Morpho.py
For me it works far better :)

Denis

francois
Posts: 61
Joined: Tue Jul 25, 2017 9:37 am

Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

Postby francois » Mon Nov 12, 2018 12:46 pm

Indeed, it seems to be working a lot better.
Thanks for the quick fix!

It was generated with FreeSurfer 6 indeed. But I think we have been importing other FreeSurfer 6-processed patients previously without any problem.

francois
Posts: 61
Joined: Tue Jul 25, 2017 9:37 am

Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

Postby francois » Tue Nov 13, 2018 12:00 pm

Hi Denis,

It doesn't crash, but in fact it doesn't work very well either. After taking an abnormally long time to run, the MarsAtlas segmentation that comes out of it is totally wrong on the left hemisphere (but correct on the right). The left hemisphere also looks abnormally inflated compared to the right. See example here:
https://www.dropbox.com/s/dm0lbphw8h4va ... s.jpg?dl=0

Is there any chance this is just because you exchanged the meaning of two values when reading the ribbon.mgz?

Thanks
François

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riviere
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Re: Error with process Import_FROM_FreeSurfer_TO_Morpho.py

Postby riviere » Tue Nov 13, 2018 12:42 pm

Oh yes you're right, I have inverted the grey and white label values in the left hemisphere... Interestingly the segmentation went all right, but the left meshes were not, which caused the trouble.
I have updated the process file (same location on the ftp server)
Denis


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