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
Thanks,
François