Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Questions about BrainVisa usage and installation

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

Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby francois » Thu Oct 25, 2018 7:33 pm

Hello,

I'm having this issue when trying to run Morphologist on a FreeSurfer segmentation.
How is this possible that two files get attributed exactly the same UUID?
How can I know which is the offending file, and what can I do to get around this issue?

Thanks
Francois


Code: Select all

Process Import FreeSurfer grey/white segmentation to Morphologist started on
2018/10/25 20:00
Convert .mgz to .nii with FreeSurfer
Import data into database with brainvisa ontology
filein  : /tmp/bv_17418_9.nii
fileout : /home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/0001BAR_FreeSurfer.nii
encoding: Binary
normal  : 0
rescale : 0
format  :
type    : S16
objtype :
xdim    : 0
ydim    : 0
zdim    : 0
imin    : default
imax    : default
omin    : default
omax    : default
reading /tmp/bv_17418_9.nii as Volume / U8...
reading done
convert to Volume / S16
converting data...
convert done
writing /home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/0001BAR_FreeSurfer.nii...
done
cp /tmp/bv_17418_10.nii
/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/segmentation/voronoi_0001BAR_FreeSurfer.nii
Convert Talairach_Auto into AC-PC File
AC: [129, 129, 101] , mm: [129.38424682617188, 128.61575317382812,
101.05226135253906]
PC: [127, 154, 108] , mm: [127.1310763657093, 153.7526811361313,
107.83288529515266]
IP: [130, 174, 63] , mm: [129.52969713509083, 173.88163429498672,
63.18990504741669]
Create right/left grey white files from ribbon freesurfer data
Create brain mask file from ribbon freesurfer data
Create split brain file from ribbon freesurfer data
Launch T1BiasCorrection
ERROR Cannot insert "/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias_0001BAR_FreeSurfer.nii"
because its uuid is in conflict with the uuid of another file in the database

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riviere
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Posts: 1358
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Location: CEA NeuroSpin, Saint Aubin, France
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Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby riviere » Fri Oct 26, 2018 6:31 pm

Hi,
That's right we have been observing this for a while, and have not found the cause yet (I must admit we have not searched very thoroughly). It isn't very harmful but the database has to be updated from time to time.
I have put here a modified version of the database module which should print more info when this happens:
ftp://ftp.cea.fr/pub/dsv/anatomist/upda ... atabase.py
Maybe this will help to find out at last. It has to be placed at the same location in the brainvisa distribution (in python/brainvisa/data/).
(note: I have not tested this modification...)
Denis

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

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby francois » Tue Oct 30, 2018 8:24 am

Now I get this:

Code: Select all

Launch T1BiasCorrection
UUID conflict in database, uuid: 3f4fea27-3899-ddcc-b9ad-b9a83f3a1dbd
error: UNIQUE constraint failed: _DISKITEMS_._uuid
while inserting: /home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias_0001BAR_FreeSurfer.nii
file(s) with the same UUID:
(u'Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias_0001BAR_FreeSurfer.nii',)
UUID conflict in database, uuid: 3f4fea27-3899-ddcc-b9ad-b9a83f3a1dbd
while inserting: /home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias_0001BAR_FreeSurfer.nii
file(s) with the same UUID:
(u'Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias_0001BAR_FreeSurfer.nii',)
error: UNIQUE constraint failed: _DISKITEMS_._uuid
ERROR Cannot insert "/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias_0001BAR_FreeSurfer.nii"
because its uuid is in conflict with the uuid of another file in the database.


The problem is hence about replacing a file with itself. I thought there was no problem with re-running a process twice, that simply overwrites the existing files. Are we supposed to explicitly delete the files before re-computing them?
Or is it because the two paths are interpreted as different files because it tests the full path ('/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/...') versus the relative path ('Epilepsy/...') ?

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

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby francois » Tue Oct 30, 2018 8:41 am

In the same context, I also have this other error regularly:

Code: Select all

Launch VipGreyStatFromClassif to generate a histo analysis file
Now run the last part of the regular Morphologist pipeline.
SkipSkip  unselected unselected node: Image orientation handlingnode:
progress: Image orientation handling
 0.0 / 100 ...Skip unselected node: T1
 progress:Bias Correction 10.0 / 100 ...
SkipTraceback (most recent call last):
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/soma/qt_gui/qtThread.py", line 124, in event
 unselected node: Histogram    self.doAction()
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/soma/qt_gui/qtThread.py", line 240, in doAction
    function(*args)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processing/qt4gui/neuroProcessesGUI.py", line 1332, in setProgress
    self, value, maxval)
 analysis
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 4039, in showProgress
    Skip unselected node: Compute Brain Maskself.write('progress:', value, '/', count, '...')

  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3648, in write
    Skip unselected self._write(msg)
node:  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3674, in _write
    self._writeHTMLParser.feed(html + '<br>\n')
   File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/lib/python2.7/sgmllib.py", line 104, in feed
    self.goahead(0)
Skull-stripped  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/lib/python2.7/sgmllib.py", line 138, in goahead
     k = self.parse_starttag(i)
brain  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/lib/python2.7/sgmllib.py", line 274, in parse_starttag
 normalization    self.error('unexpected call to parse_starttag')

  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/lib/python2.7/htmllib.py", line 45, in error
    raise HTMLParseError(message)
htmllib.HTMLParseError: unexpected call to parse_starttag
Skip unselected node: Split Brain Mask

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

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby francois » Tue Oct 30, 2018 8:46 am

And a third blocking issue I get with the process Import_FROM_FreeSurfer_TO_Morpho.py.
Sometimes it works, sometimes not... what am I doing wrong?

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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Posts: 1358
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Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby riviere » Wed Oct 31, 2018 7:08 pm

Hi,
(it would probably better to use several topics for several problems, here the answers will not be clear).
For now I only answer to the 1st problem.
The problem occurs when re-inserting or updating a file in the database when it has already been inserted. Normally the system should check and update whenever it occurs, so there's probably a bug somewhere here. But there was also a bug in my debug prints, so could you please try again after updating the sqlFSODatabase.py file (same location of the ftp server) ?
As I understand I think the file UUID was already in the database, the filename was also in the database, but was registered under a different UUID so there is an inconsistency. The debug info was printing the files associated with the "other" UUID so didn't bring the info I was expecting. I hope I have fixed that.
Denis

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

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby francois » Thu Nov 01, 2018 1:10 pm

Here is the complete sequence of error messages I get with the first execution of the FreeSurfer=>Morphologist process.
It starts with a warning saying that the UUID of the nobias volume had to be changed (while this file didn't exist previously in the DB):

Code: Select all

Launch T1BiasCorrection
Warning: changed uuid of "u'/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias_0001BAR_FreeSurfer.nii'" because another file has the same uuid: ce5f96fe-c8c7-9f51-d529-3bd55aedc301
Launch VipGreyStatFromClassif to generate a histo analysis file
Now run the last part of the regular Morphologist pipeline.
models: 6
SPAM models are present.
Skip unselected node: Image orientation handlingSkip
 unselected node: Image orientation handlingprogress: 0.0 / 100
 progress: ...
Skip unselected0.0 / 100  node: ...
SkipT1 unselected node: T1  Bias Correction
Bias Correctionprogress:
 10.0 / 100 ...
Skipprogress: 10.0 / 100 ...
unselectedSkip node: Histogram analysis
 unselected node: HistogramSkip  analysisunselected node: Compute Brain Mask
>progress:> 20.0 / 100 ... Skip unselected progress:node: Skull-stripped
brain normalization 40.0 / 100 ...
Skip unselected
 Skipnode:  unselected Splitnode: Brain Mask
 Split Brain MaskSkip 50.0 / 100 ... unselected node: Talairach transformation from manual
progress: 60.0 AC/PC / 100
Skip... Traceback (most recent call last):
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/soma/qt_gui/qtThread.py", line 124, in event
unselected     self.doAction()
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/soma/qt_gui/qtThread.py", line 240, in doAction
    function(*args)
node:  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processing/qt4gui/neuroProcessesGUI.py", line 1332, in setProgress
    self, value, maxval)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 4039, in showProgress
     self.write('progress:', value, '/', count, '...')
Head   File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3648, in write
    self._write(msg)
Mesh  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3674, in _write

    self._writeHTMLParser.feed(html + '<br>\n')
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/lib/python2.7/sgmllib.py", line 104, in feed
    self.goahead(0)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/lib/python2.7/sgmllib.py", line 138, in goahead
    k = self.parse_starttag(i)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/lib/python2.7/sgmllib.py", line 274, in parse_starttag
    self.error('unexpected call to parse_starttag')
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/lib/python2.7/htmllib.py", line 45, in error
    raise HTMLParseError(message)
htmllib.HTMLParseError: unexpected call to parse_starttag
Skip unselected Skipnode: Grey unselected node: Grey White Classification White Classification

progress: 70.0 / 100 ...
progress: 80.0 / 100 ...
progress: 80.0 / 100 ...
progress: 80.0 / 100 ...
progress: 80.7142857143 / 100 ...
Detecting left hemisphere spherical inner cortical interface...
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex
------------------------------ ------------------------------ ! VIP Warning:
Empty bucket list in VipGetNthBiggest3DBucket_S16BIT
------------------------------ ------------------------------ ! VIP Warning:
Nothing is left in VipConnexVolumeFilter ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex
------------------------------ ------------------------------ ! VIP Warning:
Empty bucket list in VipGetNthBiggest3DBucket_S16BIT
------------------------------ ------------------------------ ! VIP Warning:
Nothing is left in VipConnexVolumeFilter ------------------------------
progress: 81.4285714286 / 100 ...
Reconstructing left hemisphere white mesh...
progress: 82.1428571429 / 100 ...
Computing left sulci skeleton and buried gyrus watershed...
progress: 82.8571428571 / 100 ...
Detecting left hemisphere spherical outer cortical surface...
Reconstructing left hemisphere pial mesh...
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 1 System command exited with non null
value : 1

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

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

--------------------------------------------------------------------------------
RuntimeError
Process Import FreeSurfer grey/white segmentation to Morphologist finished on
2018/11/01 11:42 (29 minutes 53 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


I start the same process again, I get this:

Code: Select all

Process Import FreeSurfer grey/white segmentation to Morphologist started on
2018/11/01 12:14
ERROR in Import FreeSurfer grey/white segmentation to Morphologist 2 The file:
/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/0001BAR_FreeSurfer.nii
is locked. It cannot be opened for writing. You can unlock it if necessary using
the contextual menu of the parameter T1_output

--------------------------------------------------------------------------------
IOError
Process Import FreeSurfer grey/white segmentation to Morphologist finished on
2018/11/01 12:14 (0 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 3205, in _processExecution
    HTMLMessage(_t_('<b>The file: <em>%s</em> is locked</b>. It cannot be opened for writing. You can unlock it if necessary using  the contextual menu of the parameter %s') % (str(v), n)))
IOError: <b>The file: <em>/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/0001BAR_FreeSurfer.nii</em> is locked</b>. It cannot be opened for writing. You can unlock it if necessary using  the contextual menu of the parameter T1_output


I delete all the .lock files, start again, and then I get the error I first mentioned:

Code: Select all

Launch T1BiasCorrection
UUID conflict in database, uuid: 6f90f9d9-e5dc-2d69-6288-9be5f847a9e9
while inserting: Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias_0001BAR_FreeSurfer.nii
file(s) with the same UUID:
UUID conflict in database, uuid: 6f90f9d9-e5dc-2d69-6288-9be5f847a9e9
while inserting: Epilepsy/0001BAR_FreeSurfer/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias_0001BAR_FreeSurfer.nii
file(s) with the same UUID:
ERROR Error binding parameter 0 - probably unsupported type.

--------------------------------------------------------------------------------
InterfaceError
processes.py (3303) in _processExecution:

item, update=True)

sqlFSODatabase.py (296) in insertDiskItem:

self.insertDiskItems((item, ), **kwargs)

sqlFSODatabase.py (2288) in insertDiskItems:

insertParentDirs=insertParentDirs)

sqlFSODatabase.py (1335) in insertDiskItems:

'WHERE _uuid=?', (diskItem._uuid, ))

Launch VipGreyStatFromClassif to generate a histo analysis file
Now run the last part of the regular Morphologist pipeline.
progress:progress:  0.0 0.0 / 100 ...
/Skip 100 ...
unselected node: Image orientation handlingprogress:
 progress: 10.0 10.0/ 100 ...
 / 100 ...Skip
 unselected node: T1 Bias Correctionprogress: 20.0 /
 progress: 100 20.0 / 100 ...
Skip...
 unselected node: Histogram analysisprogress: 30.0
 progress:/  30.0 / 100 ...100
 Skip unselected...
node: Compute Brain Maskprogress:
 progress: 40.040.0 / 100 ... /
Skip  unselected node: Skull-stripped brain normalization100
 ...progress:
 progress:50.0 50.0 / 100 ...
Skip unselected/
100 ...
node: Split Brain Maskprogress: progress: 60.0 / 100 ... 60.0 / 100 ...

Skip Skip unselected node: Talairachunselected  transformation from node: manual AC/PC
Skip unselected node: Talairach transformation from manualHead  AC/PCMesh

Skip unselected progress:node: 70.0 / 100  Head Mesh
...progress: 80.0 / 100 ...
Skip unselected node: GreySkip White  Classification
unselected node: Grey White Classificationprogress: 80.0 / 100 ...
progress: 80.0 / 100 ...
progress: 80.7142857143 / 100 ...
Detecting left hemisphere spherical inner cortical interface...
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex
------------------------------ ------------------------------ ! VIP Warning:
Empty bucket list in VipGetNthBiggest3DBucket_S16BIT
------------------------------ ------------------------------ ! VIP Warning:
Nothing is left in VipConnexVolumeFilter ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex
------------------------------ ------------------------------ ! VIP Warning:
Empty bucket list in VipGetNthBiggest3DBucket_S16BIT
------------------------------ ------------------------------ ! VIP Warning:
Nothing is left in VipConnexVolumeFilter ------------------------------
progress: 81.4285714286 / 100 ...
Reconstructing left hemisphere white mesh...
progress: 82.1428571429 / 100 ...
Computing left sulci skeleton and buried gyrus watershed...
progress: 82.8571428571 / 100 ...
Detecting left hemisphere spherical outer cortical surface...
Reconstructing left hemisphere pial mesh...
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 2 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 3 System
command exited with non null value : 1

--------------------------------------------------------------------------------
RuntimeError
Process Import FreeSurfer grey/white segmentation to Morphologist finished on
2018/11/01 12:46 (29 minutes 16 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


I posted the other messages as separate topics:
viewtopic.php?f=2&t=1868
viewtopic.php?f=2&t=1869

User avatar
riviere
Site Admin
Posts: 1358
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
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Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby riviere » Sun Nov 04, 2018 2:24 am

Oh I'm sorry I left again a bug in the debug info prints. Could you please replace again the file sqlFSODatabase.py and try again ?
Denis

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

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby francois » Fri Nov 09, 2018 2:58 pm

It looks like I am getting this error with most of the subjects now... this is totally blocking us for adding new patients to our SEEG database...
This was working before. I'm not sure if it changed after a change I made, or after I upgraded to the last compiled version you sent me.

Here is another patient, with your updated debugging info.
First execution => Warning, then crashes:

Code: Select all

Process Import FreeSurfer grey/white segmentation to Morphologist started on
2018/11/09 14:44
Convert .mgz to .nii with FreeSurfer
Import data into database with brainvisa ontology
filein  : /tmp/bv_3923_15.nii
fileout : /home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/0010GRE_20092010.nii
encoding: Binary
normal  : 0
rescale : 0
format  :
type    : S16
objtype :
xdim    : 0
ydim    : 0
zdim    : 0
imin    : default
imax    : default
omin    : default
omax    : default
reading /tmp/bv_3923_15.nii as Volume / U8...
reading done
convert to Volume / S16
converting data...
convert done
writing /home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/0010GRE_20092010.nii...
done
cp /tmp/bv_3923_16.nii
/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/default_analysis/segmentation/voronoi_0010GRE_20092010.nii
Convert Talairach_Auto into AC-PC File
AC: [129, 119, 153] , mm: [128.9222869873047, 119.40118408203125,
153.4657440185547]
PC: [129, 148, 149] , mm: [128.99389399122447, 148.36766636371613,
148.55385622382164]
IP: [129, 151, 99] , mm: [128.65103408135474, 150.55316454172134,
99.38857114315033]
Create right/left grey white files from ribbon freesurfer data
Create brain mask file from ribbon freesurfer data
Create split brain file from ribbon freesurfer data
Launch T1BiasCorrection
Warning: changed uuid of "u'/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/default_analysis/nobias_0010GRE_20092010.nii'" because another file has the same uuid: ef015eb9-2428-e50a-e6a5-6c6514e15f4f
Launch VipGreyStatFromClassif to generate a histo analysis file
Now run the last part of the regular Morphologist pipeline.
models: 6
SPAM models are present.
progress: 0.0 / 100 ...
Skip unselected node: Image orientation handling
progress: 10.0 / 100 ...
Skip unselected node: T1 Bias Correction
progress: 20.0 / 100 ...
Skip unselected node: Histogram analysis
progress: 30.0 / 100 ...
Skip unselected node: Compute Brain Mask
progress: 40.0 / 100 ...
Skip unselected node: Skull-stripped brain normalization
progress: 50.0 / 100 ...
Skip unselected node: Split Brain Mask
progress: 60.0 / 100 ...
Skip unselected node: Talairach transformation from manual AC/PC
progress: 70.0 / 100 ...
Skip unselected node: Head Mesh
progress: 80.0 / 100 ...
progress: 80.0 / 100 ...
progress: 80.0 / 100 ...
Skip unselected node: Grey White Classification
progress: 80.7142857143 / 100 ...
Detecting left hemisphere spherical inner cortical interface...
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex
------------------------------ ------------------------------ ! VIP Warning:
Empty bucket list in VipGetNthBiggest3DBucket_S16BIT
------------------------------ ------------------------------ ! VIP Warning:
Nothing is left in VipConnexVolumeFilter ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex
------------------------------ ------------------------------ ! VIP Warning:
Empty bucket list in VipGetNthBiggest3DBucket_S16BIT
------------------------------ ------------------------------ ! VIP Warning:
Nothing is left in VipConnexVolumeFilter ------------------------------
progress: 81.4285714286 / 100 ...
Reconstructing left hemisphere white mesh...
progress: 82.1428571429 / 100 ...
Computing left sulci skeleton and buried gyrus watershed...
progress: 82.8571428571 / 100 ...
Detecting left hemisphere spherical outer cortical surface...
Reconstructing left hemisphere pial mesh...
progress: 83.5714285714 / 100 ...
Building left hemisphere attributed relational sulci graph...
label: 404 ------------------------------ !! VIP Error: Strange label
------------------------------ ------------------------------ !! VIP Error:
Execution aborted in function 'FillSurfaceSimpleEdges'.
------------------------------
ERROR in Hemisphere Cortical Folds Graph 1 System command exited with non null
value : 111

--------------------------------------------------------------------------------
RuntimeError
ERROR in Morphologist 2015 1 System command exited with non null value : 111

--------------------------------------------------------------------------------
RuntimeError
ERROR in Import FreeSurfer grey/white segmentation to Morphologist 1 System
command exited with non null value : 111

--------------------------------------------------------------------------------
RuntimeError
Process Import FreeSurfer grey/white segmentation to Morphologist finished on
2018/11/09 14:46 (2 minutes 25 seconds)
Traceback (most recent call last):
  File "/home/ftadel/IntrAnat/IntrAnat_ftadel/ImageImport.py", line 2481, in runPipelineFS
    self.runPipelineFSWorker(diOrig, diOut)
  File "/home/ftadel/IntrAnat/IntrAnat_ftadel/ImageImport.py", line 2495, 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 173, in execution
    context.system(*command)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3455, in system
    _t_('System command exited with non null value : %s') % str(ret))
RuntimeError: System command exited with non null value : 111


Second execution (after deleting all the .lock files) => error, then crashes:

Code: Select all

Process Import FreeSurfer grey/white segmentation to Morphologist started on
2018/11/09 14:48
Convert .mgz to .nii with FreeSurfer
Import data into database with brainvisa ontology
filein  : /tmp/bv_3923_75.nii
fileout : /home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/0010GRE_20092010.nii
encoding: Binary
normal  : 0
rescale : 0
format  :
type    : S16
objtype :
xdim    : 0
ydim    : 0
zdim    : 0
imin    : default
imax    : default
omin    : default
omax    : default
reading /tmp/bv_3923_75.nii as Volume / U8...
reading done
convert to Volume / S16
converting data...
convert done
writing /home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/0010GRE_20092010.nii...
done
cp /tmp/bv_3923_76.nii
/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/default_analysis/segmentation/voronoi_0010GRE_20092010.nii
Convert Talairach_Auto into AC-PC File
AC: [129, 119, 153] , mm: [128.9222869873047, 119.40118408203125,
153.4657440185547]
PC: [129, 148, 149] , mm: [128.99389399122447, 148.36766636371613,
148.55385622382164]
IP: [129, 151, 99] , mm: [128.65103408135474, 150.55316454172134,
99.38857114315033]
Create right/left grey white files from ribbon freesurfer data
Create brain mask file from ribbon freesurfer data
Create split brain file from ribbon freesurfer data
Launch T1BiasCorrection
UUID conflict in database, uuid: 7d5d72d2-ae3e-cf38-ec05-bca484797355
error: UNIQUE constraint failed: _DISKITEMS_._uuid
while inserting: Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/default_analysis/nobias_0010GRE_20092010.nii
file(s) with the same UUID:
(u'Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/0010GRE_20092010.nii',)
Launch VipGreyStatFromClassif to generate a histo analysis file
Now run the last part of the regular Morphologist pipeline.
progress: 41.7857142857 / 100 ...
Skip unselected node: Image orientation handling
progress: 46.7857142857 / 100 ...
Skip unselected node: T1 Bias Correction
progress: 51.7857142857 / 100 ...
Skip unselected node: Histogram analysis
progress: 56.7857142857 / 100 ...
Skip unselected node: Compute Brain Mask
progress: 61.7857142857 / 100 ...
Skip unselected node: Skull-stripped brain normalization
progress: 66.7857142857 / 100 ...
Skip unselected node: Split Brain Mask
progress: 71.7857142857 / 100 ...
Skip unselected node: Talairach transformation from manual AC/PC
progress: 76.7857142857 / 100 ...
Skip unselected node: Head Mesh
progress: 81.7857142857 / 100 ...
progress: 81.7857142857 / 100 ...
progress: 81.7857142857 / 100 ...
Skip unselected node: Grey White Classification
progress: 82.1428571429 / 100 ...
Detecting left hemisphere spherical inner cortical interface...
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex
------------------------------ ------------------------------ ! VIP Warning:
Empty bucket list in VipGetNthBiggest3DBucket_S16BIT
------------------------------ ------------------------------ ! VIP Warning:
Nothing is left in VipConnexVolumeFilter ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex
------------------------------ ------------------------------ ! VIP Warning:
Empty bucket list in VipGetNthBiggest3DBucket_S16BIT
------------------------------ ------------------------------ ! VIP Warning:
Nothing is left in VipConnexVolumeFilter ------------------------------
progress: 82.5 / 100 ...
Reconstructing left hemisphere white mesh...
progress: 82.8571428571 / 100 ...
Computing left sulci skeleton and buried gyrus watershed...
progress: 83.2142857143 / 100 ...
Detecting left hemisphere spherical outer cortical surface...
Reconstructing left hemisphere pial mesh...
progress: 83.5714285714 / 100 ...
Building left hemisphere attributed relational sulci graph...
label: 534 ------------------------------ !! VIP Error: Strange label
------------------------------ ------------------------------ !! VIP Error:
Execution aborted in function 'FillSurfaceSimpleEdges'.
------------------------------
ERROR in Hemisphere Cortical Folds Graph 3 System command exited with non null
value : 111

--------------------------------------------------------------------------------
RuntimeError
ERROR in Morphologist 2015 2 System command exited with non null value : 111

--------------------------------------------------------------------------------
RuntimeError
UUID conflict in database, uuid: 7d5d72d2-ae3e-cf38-ec05-bca484797355
error: UNIQUE constraint failed: _DISKITEMS_._uuid
while inserting: Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/default_analysis/nobias_0010GRE_20092010.nii
file(s) with the same UUID:
(u'Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/0010GRE_20092010.nii',)
ERROR Cannot insert "/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/default_analysis/nobias_0010GRE_20092010.nii"
because its uuid is in conflict with the uuid of another file in the database.

--------------------------------------------------------------------------------
DatabaseError
processes.py (3320) in _processExecution:

item, update=True)

sqlFSODatabase.py (296) in insertDiskItem:

self.insertDiskItems((item, ), **kwargs)

sqlFSODatabase.py (2288) in insertDiskItems:

insertParentDirs=insertParentDirs)

sqlFSODatabase.py (1343) in insertDiskItems:

% diskItem.fullPath())

ERROR in Import FreeSurfer grey/white segmentation to Morphologist 3 System
command exited with non null value : 111

--------------------------------------------------------------------------------
RuntimeError
Process Import FreeSurfer grey/white segmentation to Morphologist finished on
2018/11/09 14:50 (2 minutes 20 seconds)
Traceback (most recent call last):
  File "/home/ftadel/IntrAnat/IntrAnat_ftadel/ImageImport.py", line 2481, in runPipelineFS
    self.runPipelineFSWorker(diOrig, diOut)
  File "/home/ftadel/IntrAnat/IntrAnat_ftadel/ImageImport.py", line 2495, 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 173, in execution
    context.system(*command)
  File "/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/brainvisa/processes.py", line 3455, in system
    _t_('System command exited with non null value : %s') % str(ret))
RuntimeError: System command exited with non null value : 111

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

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby francois » Fri Nov 09, 2018 3:01 pm

PS: if I update the database, I get messages like this:

Code: Select all

/home/ftadel/IntrAnat/brainvisa-4.6.1-beta-Ubuntu-16.04_x86_64/python/soma/html.py:104: UnicodeWarning: Unicode equal comparison failed to convert both arguments to Unicode - interpreting them as being unequal
  u'ô', u'î', u'û', u'ù', u'ö', )])
WARNING: internal error: an sqlite connection on u'/home/ftadel/IntrAnat/freesurfer/subjects/database-2.3.sqlite' is opened for thread Dummy-1 but the corresponding ThreadSafeSQLiteConnection instance (number 1) is being deleted in thread Thread-2. Method currentThreadCleanup() should have been called from Dummy-1 to supress this warning.
WARNING: internal error: an sqlite connection on u'/home/ftadel/IntrAnat/brainvisa_db/database-2.3.sqlite' is opened for thread Dummy-1 but the corresponding ThreadSafeSQLiteConnection instance (number 2) is being deleted in thread Thread-2. Method currentThreadCleanup() should have been called from Dummy-1 to supress this warning.
Warning: changed uuid of "u'/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0010GRE_20092010/t1mri/FreesurferAtlaspre_2010-9-20/default_analysis/nobias_0010GRE_20092010.nii'" because another file has the same uuid: ef015eb9-2428-e50a-e6a5-6c6514e15f4f
Warning: changed uuid of "u'/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0011GRE_19112013/t1mri/FreesurferAtlaspre_2013-11-19/default_analysis/nobias_0011GRE_19112013.nii'" because another file has the same uuid: 531f53f0-edc0-5c6f-ea5c-cbadd1290093

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

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby francois » Fri Nov 09, 2018 4:30 pm

It seems to work if I run it from BrainVISA, with the process FreeSurfer > Import > Import FreeSurfer grey/white segmentation to Morphologist. I select two entries only:
- T1_orig: /home/ftadel/IntrAnat/freesurfer/subjects/0001BAR_27112016/mri/orig.mgz
- T1_output: /home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_27112016/t1mri/FreesurferAtlaspre_2016-11-27/0001BAR_27112016.nii

The code I use to try and reproduce the same prcedure:

Code: Select all

        proc = getProcessInstance('Import_FROM_FreeSurfer_TO_Morpho')
        proc.T1_orig = str(diOrig.fullPath())
        proc.T1_output = str(diOut.fullPath())
        self.brainvisaContext.runProcess(proc)
       
        # diOrig.fullPath() => u'/home/ftadel/IntrAnat/freesurfer/subjects/0001BAR_27112016/mri/orig.mgz'
        # diOut.fullPath() => u'/home/ftadel/IntrAnat/brainvisa_db/Epilepsy/0001BAR_27112016/t1mri/FreesurferAtlaspre_2016-11-27/0001BAR_27112016.nii'


The execution log from BrainVISA is different. There is no warning in this case.
Why is that? Aren't two executions supposed to be equivalent (from the BrainVISA interface or from my python functions)?

Code: Select all

Process Import FreeSurfer grey/white segmentation to Morphologist started on 2018/11/09 16:23
Convert .mgz to .nii with FreeSurfer
Import data into database with brainvisa ontology

cp /tmp/bv_142_101.nii /home/ftadel/IntrAnat/brainvisa_db/subjects/0001BAR_27112016/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/segmentation/voronoi_0001BAR_27112016.nii
Convert Talairach_Auto into AC-PC File
AC: [129, 129, 101] , mm: [129.38424682617188, 128.61575317382812, 101.05226135253906]
PC: [127, 154, 108] , mm: [127.1310763657093, 153.7526811361313, 107.83288529515266]
IP: [130, 174, 63] , mm: [129.52969713509083, 173.88163429498672, 63.18990504741669]
Create right/left grey white files from ribbon freesurfer data
Create brain mask file from ribbon freesurfer data
Create split brain file from ribbon freesurfer data
Launch T1BiasCorrection
Launch VipGreyStatFromClassif to generate a histo analysis file
Now run the last part of the regular Morphologist pipeline.
Skip unselected node: Image orientation handling
Skip unselected node: T1 Bias Correction
Skip unselected node: Histogram analysis
Skip unselected node: Compute Brain Mask
Skip unselected node: Skull-stripped brain normalization
Skip unselected node: Split Brain Mask
Skip unselected node: Talairach transformation from manual AC/PC
Skip unselected node: Head Mesh
Skip unselected node: Grey White Classification
Detecting left hemisphere spherical inner cortical interface...
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------ ------------------------------ ! VIP Warning: Empty bucket list in VipGetNthBiggest3DBucket_S16BIT ------------------------------ ------------------------------ ! VIP Warning: Nothing is left in VipConnexVolumeFilter ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------ ------------------------------ ! VIP Warning: Empty bucket list in VipGetNthBiggest3DBucket_S16BIT ------------------------------ ------------------------------ ! VIP Warning: Nothing is left in VipConnexVolumeFilter ------------------------------
Reconstructing left hemisphere white mesh...
Computing left sulci skeleton and buried gyrus watershed...
Detecting left hemisphere spherical outer cortical surface...
Reconstructing left hemisphere pial mesh...
...

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

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby francois » Fri Nov 09, 2018 5:33 pm

Erratum: It does NOT work from Brainvisa, I get the same error message: Cannot insert "/home/ftadel/IntrAnat/brainvisa_db/subjects/0001BAR_27112016/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/nobias_0001BAR_27112016.nii" because its uuid is in conflict with the uuid of another file in the database.

Therefore you should be able to reproduce it on your end, right?

The full log (for the patient I sent you by email):

Code: Select all

Process Import FreeSurfer grey/white segmentation to Morphologist started on 2018/11/09 16:38
Convert .mgz to .nii with FreeSurfer
Import data into database with brainvisa ontology

cp /tmp/bv_961_20.nii /home/ftadel/IntrAnat/brainvisa_db/subjects/0001BAR_27112016/t1mri/FreesurferAtlaspre_2016-11-27/default_analysis/segmentation/voronoi_0001BAR_27112016.nii
Convert Talairach_Auto into AC-PC File
AC: [129, 129, 101] , mm: [129.38424682617188, 128.61575317382812, 101.05226135253906]
PC: [127, 154, 108] , mm: [127.1310763657093, 153.7526811361313, 107.83288529515266]
IP: [130, 174, 63] , mm: [129.52969713509083, 173.88163429498672, 63.18990504741669]
Create right/left grey white files from ribbon freesurfer data
Create brain mask file from ribbon freesurfer data
Create split brain file from ribbon freesurfer data
Launch T1BiasCorrection
Launch VipGreyStatFromClassif to generate a histo analysis file
Now run the last part of the regular Morphologist pipeline.
Skip unselected node: Image orientation handling
Skip unselected node: T1 Bias Correction
Skip unselected node: Histogram analysis
Skip unselected node: Compute Brain Mask
Skip unselected node: Skull-stripped brain normalization
Skip unselected node: Split Brain Mask
Skip unselected node: Talairach transformation from manual AC/PC
Skip unselected node: Head Mesh
Skip unselected node: Grey White Classification
Detecting left hemisphere spherical inner cortical interface...
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------ ------------------------------ ! VIP Warning: Empty bucket list in VipGetNthBiggest3DBucket_S16BIT ------------------------------ ------------------------------ ! VIP Warning: Nothing is left in VipConnexVolumeFilter ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------ ------------------------------ ! VIP Warning: Empty bucket list in VipGetNthBiggest3DBucket_S16BIT ------------------------------ ------------------------------ ! VIP Warning: Nothing is left in VipConnexVolumeFilter ------------------------------
Reconstructing left hemisphere white mesh...
Computing left sulci skeleton and buried gyrus watershed...
Detecting left hemisphere spherical outer cortical surface...
Reconstructing left hemisphere pial mesh...
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



in Hemisphere Sulci Thickness and Volumes 1 System command exited with non null value : 1


RuntimeError





in Hemisphere Cortical Folds Graph 1 System command exited with non null value : 1


RuntimeError





in Morphologist 2015 1 System command exited with non null value : 1


RuntimeError





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


RuntimeError


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

Re: Error message: Cannot insert ... because its uuid is in conflict with the uuid of another file in the database

Postby francois » Wed Jun 05, 2019 1:32 pm

Hello,

We're still getting the same error message with some patients:

Code: Select all

Process Import FreeSurfer grey/white segmentation to Morphologist started on
2019/06/04 14:49
Convert .mgz to .nii with FreeSurfer
Import data into database with brainvisa ontology
filein  : /tmp/bv_17664_8.nii
fileout : /mnt/epilepsie/brainvisa_db/Epilepsy/Gre_2019_AUBa/t1mri/FreesurferAtlaspre_2018-2-5/Gre_2019_AUBa.nii
encoding: Binary
normal  : 0
rescale : 0
format  :
type    : S16
objtype :
xdim    : 0
ydim    : 0
zdim    : 0
imin    : default
imax    : default
omin    : default
omax    : default
reading /tmp/bv_17664_8.nii as Volume / U8...
reading done
convert to Volume / S16
converting data...
convert done
writing /mnt/epilepsie/brainvisa_db/Epilepsy/Gre_2019_AUBa/t1mri/FreesurferAtlaspre_2018-2-5/Gre_2019_AUBa.nii...
done
cp /tmp/bv_17664_9.nii
/mnt/epilepsie/brainvisa_db/Epilepsy/Gre_2019_AUBa/t1mri/FreesurferAtlaspre_2018-2-5/default_analysis/segmentation/voronoi_Gre_2019_AUBa.nii
Convert Talairach_Auto into AC-PC File
AC: [130, 118, 113] , mm: [130.04425048828125, 118.35255432128906,
113.19630432128906]
PC: [130, 146, 118] , mm: [129.82522860635072, 145.80412137508392,
118.01352444291115]
IP: [132, 161, 77] , mm: [131.9522107206285, 160.7505724132061,
77.04973566532135]
Create right/left grey white files from ribbon freesurfer data
Create brain mask file from ribbon freesurfer data
Create split brain file from ribbon freesurfer data
Launch T1BiasCorrection
UUID conflict in database, uuid: 36da6c27-dfc8-652a-d30b-115644c2616a
while inserting: Epilepsy/Gre_2019_AUBa/t1mri/FreesurferAtlaspre_2018-2-5/default_analysis/nobias_Gre_2019_AUBa.nii
file(s) with the same UUID:
(u'Epilepsy/Gre_2019_AUBa/t1mri/FreesurferAtlaspre_2018-2-5/Gre_2019_AUBa.nii',)
error: column _uuid is not unique
Launch VipGreyStatFromClassif to generate a histo analysis file
Now run the last part of the regular Morphologist pipeline.
models: 6
SPAM models are present.
Skip unselected Skip node: Image orientation handling
unselected node: Image orientation handlingprogress: 0.0 / 100 ...

Skip unselected node: T1 Bias Correction
progress: 0.0 / 100 ...

SkipSkip unselected node: T1 unselected node: Bias T1 Bias Correction
 progress: 10.0 /Correction
 progress: 10.0100  / ...
100 Skip unselected...
 Skip unselected node: node: Histogram Histogram analysis
analysis
progress: 20.0 / 100 ...
Skip unselected node:
Compute Skip unselected Brain Mask
node: Compute Brain Maskprogress: 30.0 / 100 ...

progress: 30.0Skip unselected node: Skull-stripped brain normalization
 / 100 ...Skip unselected node: Skull-stripped brain normalization

progress: 40.0 /Skip unselected node: 100 ... Skull-stripped brain normalization
progress:
40.0Skip unselected / node: Split 100 ...
BrainSkip unselected node:  Mask
Split Brain Maskprogress: 50.0 / 100 ...

progress: Skip unselected50.0 / 100 ...
 node: Talairach transformationSkip unselected node: from manual AC/PC Talairach transformation from
manual AC/PCprogress: 60.0 /

100 ...progress:
Skip unselected node:  60.0 / 100 ...
HeadSkip  Mesh
Skip unselected node: Grey White Classification
unselected node: Head Meshprogress: 70.0 / 100 ...
progress: 80.0 / 100 ...
progress: 80.0 / 100 ...
progress: 80.0 / 100 ...
progress: 80.7142857143 / 100 ...
Detecting left hemisphere spherical inner cortical interface...
progress: 81.4285714286 / 100 ...
Reconstructing left hemisphere white mesh...
progress: 82.1428571429 / 100 ...
Computing left sulci skeleton and buried gyrus watershed...
progress: 82.8571428571 / 100 ...
Detecting left hemisphere spherical outer cortical surface...
Reconstructing left hemisphere pial mesh...
progress: 83.5714285714 / 100 ...
Building left hemisphere attributed relational sulci graph...
progress: 84.2857142857 / 100 ...
progress: 84.2857142857 / 100 ...
progress: 84.2857142857 / 100 ...
progress: 84.6428571429 / 100 ...
progress: 84.6428571429 / 100 ...
progress: 85.0 / 100 ...
progress: 85.0 / 100 ...
progress: 85.0 / 100 ...
progress:progress: 85.0 / 85.0 /  100 ...100 ...

progress: 85.0 / 100 ...progress: 85.0 / 100 ...
progress: 85.7142857143 / 100 ...
Detecting right hemisphere spherical inner cortical interface...
progress: 86.4285714286 / 100 ...
Reconstructing right hemisphere white mesh...
progress: 87.1428571429 / 100 ...
Computing right sulci skeleton and buried gyrus watershed...
progress: 87.8571428571 / 100 ...
Detecting right hemisphere spherical outer cortical surface...
Reconstructing right hemisphere pial mesh...
progress: 88.5714285714 / 100 ...
Building right hemisphere attributed relational sulci graph...
progress: 89.2857142857 / 100 ...
progress: 89.2857142857 / 100 ...
progress: 89.2857142857 / 100 ...
progress: 89.6428571429 / 100 ...
progress: 89.6428571429 / 100 ...
progress: 90.0 / 100 ...
progress: 90.0 / 100 ...
progress: 90.0 / 100 ...
progress: 90.0 / 100 ...
progress: 90.0 / 100 ...
progress: 90.0 / 100 ...
Reading FGraph version 3.1
Reading FGraph version 3.1
progress: 100.0 / 100 ...
UUID conflict in database, uuid: 36da6c27-dfc8-652a-d30b-115644c2616a
while inserting: Epilepsy/Gre_2019_AUBa/t1mri/FreesurferAtlaspre_2018-2-5/default_analysis/nobias_Gre_2019_AUBa.nii
file(s) with the same UUID:
(u'Epilepsy/Gre_2019_AUBa/t1mri/FreesurferAtlaspre_2018-2-5/Gre_2019_AUBa.nii',)
error: column _uuid is not unique
ERROR Cannot insert "/mnt/epilepsie/brainvisa_db/Epilepsy/Gre_2019_AUBa/t1mri/FreesurferAtlaspre_2018-2-5/default_analysis/nobias_Gre_2019_AUBa.nii"
because its uuid is in conflict with the uuid of another file in the database.

--------------------------------------------------------------------------------
DatabaseError
processes.py (3320) in _processExecution:

item, update=True)

sqlFSODatabase.py (296) in insertDiskItem:

self.insertDiskItems((item, ), **kwargs)

sqlFSODatabase.py (2288) in insertDiskItems:

insertParentDirs=insertParentDirs)

sqlFSODatabase.py (1343) in insertDiskItems:

% diskItem.fullPath())

OK
Process Import FreeSurfer grey/white segmentation to Morphologist finished on
2019/06/04 15:11 (22 minutes 15 seconds)


Any suggestion on how we could get around this error?

Thanks,
François


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