ERROR in Cingular Pole Projection 2 System call crashed

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

ERROR in Cingular Pole Projection 2 System call crashed

Postby francois » Wed Jun 05, 2019 1:35 pm

Hello,

We have one patient for which we get this error:

Code: Select all

Process Hip-Hop Cortical Parameterization started on 2019/06/04 15:11
progress: 0.0 / 100 ...
progress: 0.0 / 100 ...
Changing Referential...
Projection Done
Dilation Erosion Done
Topological correction...
1797 vertices have the texture value 1
Thresholding: 0
1797/57684
Computing connected component
nb cc: 1
/usr/local/brainvisa-4.6.1-beta-Mandriva2008/lib/python2.7/site-packages/scipy/sparse/sputils.py:118: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  if np.rank(M) == 0 and np.rank(N) == 0:
/usr/local/brainvisa-4.6.1-beta-Mandriva2008/lib/python2.7/site-packages/scipy/sparse/compressed.py:130: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  if np.rank(self.data) != 1 or np.rank(self.indices) != 1 or np.rank(self.indptr) != 1:
/usr/local/brainvisa-4.6.1-beta-Mandriva2008/lib/python2.7/site-packages/scipy/sparse/coo.py:195: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  if np.rank(self.data) != 1 or np.rank(self.row) != 1 or np.rank(self.col) != 1:
length of boundaries :  [178]
cleaning the longest boundary of the texture
... Done
progress: 6.25 / 100 ...
TODO project the insula spam
Projecting the insula from sulci graph
The sulci F.C.M._left does not exist at this level of translation... The sulci
F.Cal.ant.-Sc.Cal._left does not exist at this level of translation... The sulci
F.I.P._left does not exist at this level of translation... The sulci F.P.O._left
does not exist at this level of translation... The sulci F.C.M._right does not
exist at this level of translation... The sulci F.Cal.ant.-Sc.Cal._right does
not exist at this level of translation... The sulci F.I.P._right does not exist
at this level of translation... The sulci F.P.O._right does not exist at this
level of translation... The sulci S.F.inf._left does not exist at this level of
translation... The sulci S.F.inf._right does not exist at this level of
translation... The sulci S.F.inf._left does not exist at this level of
translation... The sulci S.F.sup._left does not exist at this level of
translation... The sulci S.F.inf._right does not exist at this level of
translation... The sulci S.F.sup._right does not exist at this level of
translation... The sulci F.C.M._left does not exist at this level of
translation... The sulci S.F.sup._left does not exist at this level of
translation... The sulci F.C.M._right does not exist at this level of
translation... The sulci S.F.sup._right does not exist at this level of
translation... The sulci F.Cal.ant.-Sc.Cal._left does not exist at this level of
translation... The sulci F.Coll._left does not exist at this level of
translation... The sulci F.Cal.ant.-Sc.Cal._right does not exist at this level
of translation... The sulci F.Coll._right does not exist at this level of
translation... The sulci S.F.orbitaire._left does not exist at this level of
translation... The sulci S.R.inf._left does not exist at this level of
translation... The sulci S.F.orbitaire._right does not exist at this level of
translation... The sulci S.R.inf._right does not exist at this level of
translation... The sulci S.C._left does not exist at this level of
translation... The sulci S.Po.C._left does not exist at this level of
translation... The sulci S.C._right does not exist at this level of
translation... The sulci S.Po.C._right does not exist at this level of
translation... The sulci S.C._left does not exist at this level of
translation... The sulci S.Pe.C._left does not exist at this level of
translation... The sulci S.C._right does not exist at this level of
translation... The sulci S.Pe.C._right does not exist at this level of
translation... The sulci S.O.T.lat._left does not exist at this level of
translation... The sulci S.T.i._left does not exist at this level of
translation... The sulci S.O.T.lat._right does not exist at this level of
translation... The sulci S.T.i._right does not exist at this level of
translation... The sulci S.T.i._left does not exist at this level of
translation... The sulci S.T.s._left does not exist at this level of
translation... The sulci S.T.i._right does not exist at this level of
translation... The sulci S.T.s._right does not exist at this level of
translation... The sulci S.T.s._left does not exist at this level of
translation... The sulci S.T.s._right does not exist at this level of
translation... The sulci OCCIPITAL_left does not exist at this level of
translation... The sulci S.O.T.lat._left does not exist at this level of
translation... The sulci OCCIPITAL_right does not exist at this level of
translation... The sulci S.O.T.lat._right does not exist at this level of
translation... The sulci F.Coll._left does not exist at this level of
translation... The sulci S.O.T.lat._left does not exist at this level of
translation... The sulci F.Coll._right does not exist at this level of
translation... The sulci S.O.T.lat._right does not exist at this level of
translation... The sulci F.C.M._left does not exist at this level of
translation... The sulci S.Call._left does not exist at this level of
translation... The sulci F.C.M._right does not exist at this level of
translation... The sulci S.Call._right does not exist at this level of
translation... The sulci S.Call._left does not exist at this level of
translation... The sulci ventricle_left does not exist at this level of
translation... The sulci S.Call._right does not exist at this level of
translation... The sulci ventricle_right does not exist at this level of
translation... The sulci ventricle_left does not exist at this level of
translation... The sulci ventricle_right does not exist at this level of
translation... The sulci F.Coll._left does not exist at this level of
translation... The sulci ventricle_left does not exist at this level of
translation... The sulci F.Coll._right does not exist at this level of
translation... The sulci ventricle_right does not exist at this level of
translation... The sulci ventricle_left does not exist at this level of
translation... The sulci ventricle_right does not exist at this level of
translation... The sulci F.I.P._left does not exist at this level of
translation... The sulci S.T.s._left does not exist at this level of
translation... The sulci F.I.P._right does not exist at this level of
translation... The sulci S.T.s._right does not exist at this level of
translation...
Not able to close the projected connnected component, but I continue.
Dilation Erosion Done
Topological correction...
1144 vertices have the texture value 1
Thresholding: 0
1144/57684
Computing connected component
nb cc: 2
2  connex component(s) for this value in the texture, keeping only the largest component
length of boundaries :  [116]
cleaning the longest boundary of the texture
... Done
progress: 12.5 / 100 ...
Reading textures and mesh
Cingular and Insular poles are separated by more than 4 vertices, OK
Done
progress: 18.75 / 100 ...
computing curvature texture
Done
smoothing curvature texture
Done
computing depth texture
Done
computing Graph Label
Done
Sulcal Lines extraction
Done
progress: 25.0 / 100 ...
Reading textures and mesh
Reading sulcus-label correspondences file
HIP
------------------CutMesh
labels found in the texture  [180.0, 1.0, 0.0]
------------------poles path, always from insula to cingular pole
------------------path2Boundary
reversing insula boundary
reversing cingular boundary
------------------rectConformalMapping
mapping to the rectangle   450.0  x  100.0 with fixed_boundary =  0
    Computing Laplacian
    Computing mesh weights
    -edge length threshold needed for  0  values =  0  %
    -number of Nan in weights:  0  =  0  %
    -number of Negative values in weights:  27696  =  8  %
    -nb Nan in L :  0
    -nb Inf in L :  0
/usr/local/brainvisa-4.6.1-beta-Mandriva2008/lib/python2.7/site-packages/scipy/sparse/coo.py:178: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank of a matrix see `numpy.linalg.matrix_rank`.
  if np.rank(M) != 2:
solve the linear system
(55309,)
using lgmres
67.12 seconds process time
matrix inverted
------------------number of vertices on folded triangles : 15 => 0.0135982884288
%
------------------unfolding reversed triangles
[15, 17]
[15, 17, 17]
[15, 17, 17, 17]
[15, 17, 17, 17, 17]
[15, 17, 17, 17, 17, 17]
[15, 17, 17, 17, 17, 17, 17]
[15, 17, 17, 17, 17, 17, 17, 17]
[15, 17, 17, 17, 17, 17, 17, 17, 17]
unable to solve the inverted faces
------------------evolution of the iterative unfolding : [15, 17, 17, 17, 17,
17, 17, 17, 17]
Translating the barycenter of S.C. to 0
found the following sulci in the texture :
['F.C.L.r.asc._left', 'F.C.M.ant._left', 'F.Cal.ant.-Sc.Cal._left',
'F.Coll._left', 'F.I.P.Po.C.inf._left', 'F.P.O._left', 'S.C._left',
'S.F.inf._left', 'S.F.inter._left', 'S.F.marginal._left', 'S.F.orbitaire._left',
'S.F.sup._left', 'S.O.T.lat.post._left', 'S.Olf._left', 'S.Pe.C.inf._left',
'S.Pe.C.median._left', 'S.Pe.C.sup._left', 'S.Po.C.sup._left',
'S.T.i.ant._left', 'S.T.i.post._left', 'S.T.s._left', 'S.T.s.ter.asc.ant._left',
'S.T.s.ter.asc.post._left']
associated to the following labels :
[ 7 17 23 25 27 35 43 51 57 59 63 67 81 85 99 105 107 109 115 117 121 123 125]
Writing meshes and textures
Done
progress: 31.25 / 100 ...
Reading model
read model version 3
modelVersion 3
left -242.926999774
right 207.07300168
top 100.0
bottom 0.0
insularPoleBoundaryCoord 30.0
cingularPoleBoundaryCoord 30.0
longitudeAxisID 16,40,61,281,297,339,360
longitudeAxisCoord
11.3520704418,29.9030027811,49.4981417246,-40.5930002416,-34.3914656973,-12.6077749619,3.32446671061e-17
longitudeAxisSulci
F.Cal.ant.-Sc.Cal.:(281;1.0),S.Pe.C.median.:(16;1.0),F.C.L.r.asc.:(40;1.0),S.F.orbitaire.:(61;1.0),S.Pe.C.sup.:(16;1.0),F.P.O.:(297;1.0),S.F.marginal.:(61;1.0),S.C.:(360;1.0),S.Po.C.sup.:(339;1.0),S.Pe.C.inf.:(16;1.0),F.I.P.Po.C.inf.:(339;1.0)
latitudeAxisID 1,55,56,81,92,106
latitudeAxisCoord
None,84.73323423,69.6368139884,58.9850785074,49.126326817,38.323223391
latitudeAxisSulci
S.O.T.lat.post.:(81;1.0),F.C.M.ant.:(55;1.0),S.T.s.:(106;1.0),F.Coll.:(56;1.0),S.F.sup.:(81;1.0),S.Call.:(1;1.0),S.T.i.post.:(92;1.0),S.T.s.ter.asc.ant.:(106;1.0),S.Olf.:(81;1.0),S.T.i.ant.:(92;1.0),S.T.s.ter.asc.post.:(92;1.0),S.F.inter.:(92;1.0),S.F.inf.:(106;1.0)
Reading textures and mesh
Reading sulcus-label correspondences file
found the following sulci in the texture :
['F.C.L.r.asc._left', 'F.C.M.ant._left', 'F.Cal.ant.-Sc.Cal._left',
'F.Coll._left', 'F.I.P.Po.C.inf._left', 'F.P.O._left', 'S.C._left',
'S.F.inf._left', 'S.F.inter._left', 'S.F.marginal._left', 'S.F.orbitaire._left',
'S.F.sup._left', 'S.O.T.lat.post._left', 'S.Olf._left', 'S.Pe.C.inf._left',
'S.Pe.C.median._left', 'S.Pe.C.sup._left', 'S.Po.C.sup._left',
'S.T.i.ant._left', 'S.T.i.post._left', 'S.T.s._left', 'S.T.s.ter.asc.ant._left',
'S.T.s.ter.asc.post._left']
associated to the following labels :
[ 7 17 23 25 27 35 43 51 57 59 63 67 81 85 99 105 107 109 115 117 121 123 125]
HOP
SC_label:  43
    Computing Laplacian
    Computing mesh weights
    -edge length threshold needed for  0  values =  0  %
    -number of Nan in weights:  0  =  0  %
    -number of Negative values in weights:  27696  =  8  %
    -nb Nan in L :  0
    -nb Inf in L :  0
cstr mapping in the rectangle  with cstrBalance =  200.0
F.C.L.r.asc._left weight in HOP energy : 1.0
F.Cal.ant.-Sc.Cal._left weight in HOP energy : 1.0
F.I.P.Po.C.inf._left weight in HOP energy : 1.0
F.P.O._left weight in HOP energy : 1.0
S.C._left weight in HOP energy : 1.0
S.F.marginal._left weight in HOP energy : 1.0
S.F.orbitaire._left weight in HOP energy : 1.0
S.Pe.C.inf._left weight in HOP energy : 1.0
S.Pe.C.median._left weight in HOP energy : 1.0
S.Pe.C.sup._left weight in HOP energy : 1.0
S.Po.C.sup._left weight in HOP energy : 1.0
F.C.M.ant._left weight in HOP energy : 1.0
F.Coll._left weight in HOP energy : 1.0
S.F.inf._left weight in HOP energy : 1.0
S.F.inter._left weight in HOP energy : 1.0
S.F.sup._left weight in HOP energy : 1.0
S.O.T.lat.post._left weight in HOP energy : 1.0
S.Olf._left weight in HOP energy : 1.0
S.T.i.ant._left weight in HOP energy : 1.0
S.T.i.post._left weight in HOP energy : 1.0
S.T.s._left weight in HOP energy : 1.0
S.T.s.ter.asc.ant._left weight in HOP energy : 1.0
S.T.s.ter.asc.post._left weight in HOP energy : 1.0
solve the linear system
15.69 seconds process time for x
10.65 seconds process time for y
matrix inverted
------------------number of vertices on folded triangles : 1518 => 1.37614678899
%
------------------unfolding reversed triangles
[1518, 405]
[1518, 405, 168]
[1518, 405, 168, 77]
[1518, 405, 168, 77, 34]
[1518, 405, 168, 77, 34, 21]
[1518, 405, 168, 77, 34, 21, 18]
[1518, 405, 168, 77, 34, 21, 18, 17]
[1518, 405, 168, 77, 34, 21, 18, 17, 17]
[1518, 405, 168, 77, 34, 21, 18, 17, 17, 17]
[1518, 405, 168, 77, 34, 21, 18, 17, 17, 17, 17]
[1518, 405, 168, 77, 34, 21, 18, 17, 17, 17, 17, 17]
[1518, 405, 168, 77, 34, 21, 18, 17, 17, 17, 17, 17, 17]
[1518, 405, 168, 77, 34, 21, 18, 17, 17, 17, 17, 17, 17, 17]
unable to solve the inverted faces
------------------number of vertices on folded triangles : [1518, 405, 168, 77,
34, 21, 18, 17, 17, 17, 17, 17, 17, 17]
Writing meshes and textures
Done
progress: 37.5 / 100 ...
Reading textures, meshes and model
read model version 3
modelVersion 3
left -242.926999774
right 207.07300168
top 100.0
bottom 0.0
insularPoleBoundaryCoord 30.0
cingularPoleBoundaryCoord 30.0
longitudeAxisID 16,40,61,281,297,339,360
longitudeAxisCoord
11.3520704418,29.9030027811,49.4981417246,-40.5930002416,-34.3914656973,-12.6077749619,3.32446671061e-17
longitudeAxisSulci
F.Cal.ant.-Sc.Cal.:(281;1.0),S.Pe.C.median.:(16;1.0),F.C.L.r.asc.:(40;1.0),S.F.orbitaire.:(61;1.0),S.Pe.C.sup.:(16;1.0),F.P.O.:(297;1.0),S.F.marginal.:(61;1.0),S.C.:(360;1.0),S.Po.C.sup.:(339;1.0),S.Pe.C.inf.:(16;1.0),F.I.P.Po.C.inf.:(339;1.0)
latitudeAxisID 1,55,56,81,92,106
latitudeAxisCoord
None,84.73323423,69.6368139884,58.9850785074,49.126326817,38.323223391
latitudeAxisSulci
S.O.T.lat.post.:(81;1.0),F.C.M.ant.:(55;1.0),S.T.s.:(106;1.0),F.Coll.:(56;1.0),S.F.sup.:(81;1.0),S.Call.:(1;1.0),S.T.i.post.:(92;1.0),S.T.s.ter.asc.ant.:(106;1.0),S.Olf.:(81;1.0),S.T.i.ant.:(92;1.0),S.T.s.ter.asc.post.:(92;1.0),S.F.inter.:(92;1.0),S.F.inf.:(106;1.0)
mapping the insula to a disk
    Computing Laplacian
    Computing mesh weights
    -edge length threshold needed for  0  values =  0  %
    -number of Nan in weights:  0  =  0  %
    -number of Negative values in weights:  376  =  7  %
    -nb Nan in L :  0
    -nb Inf in L :  0
Boundary Size: (116,)
Laplacian Size: (886, 886)
mapping the cingular pole to a disk
    Computing Laplacian
    Computing mesh weights
    -edge length threshold needed for  0  values =  0  %
    -number of Nan in weights:  0  =  0  %
    -number of Negative values in weights:  736  =  7  %
    -nb Nan in L :  0
    -nb Inf in L :  0
Boundary Size: (178,)
Laplacian Size: (1797, 1797)
Writing textures
progress: 43.75 / 100 ...
read model version 3
WARNING: NOTE: in every parcellation textures, CINGULAR POLE = 0 and PATH
BETWEEN POLES = 255
number of parcels created for the model-based parcellation (including the
cingular pole) :
63
Writing texture
number of parcels created for the marsAtlas parcellation (including the cingular
pole) :
43
Writing texture
number of parcels created for the lobes parcellation (including the cingular
pole) :
8
Writing texture
number of parcels created for the gyri parcellation (including the cingular
pole) :
27
Writing texture
Done
progress: 50.0 / 100 ...
progress: 50.0 / 100 ...
progress: 50.0 / 100 ...
Changing Referential...
ERROR in Cingular Pole Projection 2 System call crashed

--------------------------------------------------------------------------------
SignalException
ERROR in Hip-Hop Hemispheric Parameterization 2 System call crashed

--------------------------------------------------------------------------------
SignalException
ERROR in Hip-Hop Cortical Parameterization 1 System call crashed

--------------------------------------------------------------------------------
SignalException
Process Hip-Hop Cortical Parameterization finished on 2019/06/04 15:30 (19
minutes 10 seconds)
Traceback (most recent call last):
  File "/usr/local/IntrAnat/progressbar.py", line 119, in run
    self.out = self.func(self)
  File "ImageImport.py", line 2506, in <lambda>
    ProgressDialog.call(lambda thr:self.runPipelineFSWorker(diOrig, diOut, thr), True, self, "Running Morphologist on FreeSurfer output...", "FreeSufer")
  File "ImageImport.py", line 2532, in runPipelineFSWorker
    self.hiphopStart(diOut.attributes()['center'], diOut.attributes()['subject'], diOut.attributes()['acquisition'])
  File "ImageImport.py", line 2861, in hiphopStart
    self.brainvisaContext.runProcess('Hip-Hop Cortical Parameterization', Lgraph = Lrdi[0], Rgraph = Rrdi[0], sulcus_identification ='label')
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2985, in runProcess
    six.reraise(type(e[0]), e[0], e[1])
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 3261, in _processExecution
    result = process.execution(self)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 1653, in execution
    return self._executionNode.run(context)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2276, in run
    return self._run(context)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2705, in _run
    return super(ParallelExecutionNode, self)._run(context)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2632, in _run
    result.append(node.run(context))
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2276, in run
    return self._run(context)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2513, in _run
    return context.runProcess(self._process)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2978, in runProcess
    result = self._processExecution(_process, None)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 3261, in _processExecution
    result = process.execution(self)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 1653, in execution
    return self._executionNode.run(context)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2276, in run
    return self._run(context)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2632, in _run
    result.append(node.run(context))
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2276, in run
    return self._run(context)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2513, in _run
    return context.runProcess(self._process)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 2978, in runProcess
    result = self._processExecution(_process, None)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 3261, in _processExecution
    result = process.execution(self)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/brainvisa/toolboxes/cortical_surface/processes/anatomy/tools/CingularPoleProjection.py", line 86, in execution
    context.system(*command)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 3449, in system
    nativeEnv=nativeEnv, cwd=cwd, env=env)
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processes.py", line 3607, in _system
    result = c.wait()
  File "/usr/local/brainvisa-4.6.1-beta-Mandriva2008/python/brainvisa/processing/qt4gui/command.py", line 161, in wait
    raise self.SignalException(_t_('System call crashed'))
brainvisa.processing.qt4gui.command.SignalException: System call crashed
./t1mri/FreesurferAtlaspre_2018-2-5/registration/RawT1-Gre_2019_AUBa_FreesurferAtlaspre_2018-2-5_TO_Talairach-ACPC.trm.lock


Do you know where this is coming from?

Thanks,
François

User avatar
riviere
Site Admin
Posts: 1352
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
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Re: ERROR in Cingular Pole Projection 2 System call crashed

Postby riviere » Thu Jun 06, 2019 1:11 am

Hi François,
A program run by the process has crashed, the log should provide more details (the exact command which was run with its parameters).

The cingular pole extraction seems to cause problems on this specific patient. Do the segmentation and meshes look OK ?
Denis


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