issue when using morphologist 2012 cortical fold graph

[Sarrazin]

Dear experts,

I'm trying to process a database of t1 images using the morphologist 2012 pipeline (BV 4.3.0) in ubuntu 14.04.

With some but not all subjects, the pipeline ends with an error during the step cortical fold graph (3.1). I have checked the outputs from all the previous steps and all seem to be correct.
I have also tried to process these images with BV 4.4.0 to see if that could fix the problem but the problem remains the same, during the same step.
The problems seems to come from AimsSulciVoronoi.py
This is the first time that I'm facing such an issue, and I did not find any post related to this problem.

I don't think that it is related to this problem, but I faced a problem with libpng12.so after installing brainvisa. I had to remove some files (libpng12.so & libpng12.so.0 & libpng12.so.0.1.2.8 ) from the /lib repertory to fix the problem and to be able to lauch brainvisa (cf error log at the end of the post)

Here is the log from morphologist 2012 (4.3.0) :

Skip unselected node: AC/PC Or Normalization
Skip unselected node: 1 - T1 Bias Correction
Skip unselected node: 2 - Histogram analysis
Skip unselected node: 3 - Compute Brain Mask
Skip unselected node: 4 - Split Brain Mask
Skip unselected node: Talairach Transformation
Skip unselected node: Grey White Classification 2012
Skip unselected node: Grey White Surface 2012
Skip unselected node: Get Spherical Hemi Surface
Skip unselected node: Head Mesh
Masking Bias corrected image with hemisphere masks...
Computing skeleton and buried gyrus watershed...
Building Attributed Relational Graph...
Traceback (most recent call last): File "/home/prudentia-ubuntu/brainvisa-4.3.0/bin/real-bin/AimsSulciVoronoi.py", line 78, in <module> f1.doit( voronoi_vol, [-100], seed_label_list ) Exception: unknown



in Sulci Voronoi 1 System command exited with non null value : 1


RuntimeError
processes.py (2150) in _processExecution:
?
sulcivoronoi.py (71) in execution:
?
neuroProcessesGUI.py (2504) in system:
?
processes.py (2274) in system:
?

in Cortical Fold Graph (3.1+) 1 System command exited with non null value : 1

RuntimeError
processes.py (2150) in _processExecution:
?
processes.py (1083) in execution:
?
processes.py (1473) in run:
?
processes.py (1702) in _run:
?
processes.py (1473) in run:
?
processes.py (1618) in _run:
?
processes.py (1922) in runProcess:
?
processes.py (2150) in _processExecution:
?
sulcivoronoi.py (71) in execution:
?
neuroProcessesGUI.py (2504) in system:
?
processes.py (2274) in system:
?

in Cortical Fold Graph (general) 1 System command exited with non null value : 1

RuntimeError
processes.py (2150) in _processExecution:
?
processes.py (1083) in execution:
?
processes.py (1473) in run:
?
processes.py (1752) in _run:
?
processes.py (1473) in run:
?
processes.py (1731) in _run:
?
processes.py (1702) in _run:
?
processes.py (1473) in run:
?
processes.py (1618) in _run:
?
processes.py (1922) in runProcess:
?
processes.py (2150) in _processExecution:
?
processes.py (1083) in execution:
?
processes.py (1473) in run:
?
processes.py (1702) in _run:
?
processes.py (1473) in run:
?
processes.py (1618) in _run:
?
processes.py (1922) in runProcess:
?
processes.py (2150) in _processExecution:
?
sulcivoronoi.py (71) in execution:
?
neuroProcessesGUI.py (2504) in system:
?
processes.py (2274) in system:
?

in Morphologist 2012 1 System command exited with non null value : 1


RuntimeError
processes.py (2150) in _processExecution:
?
processes.py (1083) in execution:
?
processes.py (1473) in run:
?
processes.py (1702) in _run:
?
processes.py (1473) in run:
?
processes.py (1618) in _run:
?
processes.py (1922) in runProcess:
?
processes.py (2150) in _processExecution:
?
processes.py (1083) in execution:
?
processes.py (1473) in run:
?
processes.py (1752) in _run:
?
processes.py (1473) in run:
?
processes.py (1731) in _run:
?
processes.py (1702) in _run:
?
processes.py (1473) in run:
?
processes.py (1618) in _run:
?
processes.py (1922) in runProcess:
?
processes.py (2150) in _processExecution:
?
processes.py (1083) in execution:
?
processes.py (1473) in run:
?
processes.py (1702) in _run:
?
processes.py (1473) in run:
?
processes.py (1618) in _run:
?
processes.py (1922) in runProcess:
?
processes.py (2150) in _processExecution:
?
sulcivoronoi.py (71) in execution:
?
neuroProcessesGUI.py (2504) in system:
?
processes.py (2274) in system:
?

Process Morphologist 2012 finished on 2015/03/04 00:20 (12 minutes 2 seconds)





and from morphologist 2013 (bv 4.4.0) :

System command exited with non null value : 1

RuntimeError
processes.py (2554) in _processExecution:
result = process.execution( self )
corticalfoldsgraph.py (216) in execution:
sulci_voronoi = self.sulci_voronoi)
processes.py (2314) in runProcess:
result = self._processExecution( _process, None )
processes.py (2554) in _processExecution:
result = process.execution( self )
sulcivoronoi.py (71) in execution:
'-f', self.graph, '-g', self.hemi_cortex, '-o', self.sulci_voronoi )
neuroProcessesGUI.py (2741) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
processes.py (2678) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )


Here is the terminal log concerning the problem with libpng12.so

prudentia-ubuntu@ordi-prudentia:~$ brainvisa
Traceback (most recent call last):
File "<string>", line 27, in <module>
File "/home/prudentia-ubuntu/brainvisa-4.3.0/brainvisa/neuro.py", line 71, in <module>
from brainvisa.toolboxes import readToolboxes, allToolboxes
File "/neurospin/brainvisa/build/Fedora-4-i686/bug_fix/python/brainvisa/toolboxes.py", line 33, in <module>
File "/neurospin/brainvisa/build/Fedora-4-i686/bug_fix/python/brainvisa/processes.py", line 187, in <module>
File "/home/prudentia-ubuntu/brainvisa-4.3.0/brainvisa/neuroData.py", line 75, in <module>

File "/neurospin/brainvisa/build/Fedora-4-i686/bug_fix/python/brainvisa/processing/neuroException.py", line 50, in <module>
File "/neurospin/brainvisa/build/Fedora-4-i686/bug_fix/python/brainvisa/processing/qtgui/neuroExceptionGUI.py", line 33, in <module>
File "/neurospin/brainvisa/build/Fedora-4-i686/bug_fix/python/brainvisa/processing/qt4gui/neuroExceptionGUI.py", line 33, in <module>
File "/home/prudentia-ubuntu/brainvisa-4.3.0/brainvisa/backwardCompatibleQt.py", line 37, in <module>
#print 'called from:'
ImportError: /usr/lib/i386-linux-gnu/libfreetype.so.6: symbol png_set_expand_gray_1_2_4_to_8, version PNG12_0 not defined in file libpng12.so.0 with link time reference


Many thanks in advance for your help,
Samuel

[riviere]

Hi Samuel,

I don't think I have ever run into this specific problem. As the only message here is that the SulciVornoi command failed (and probably crashed), we may need to have a look at your data to try and understand.

The libpng problem has been seen, it is due to BV embedded libs and systems libs incompatibilities: the brainvisa distribution is built on a very old system (especially the 32 bits version) because these binaries are able to run on a wider range of systems, but we get into problems with recent ones. Maybe we will switch to a "not so old" system for newer releases. More precisely, freetype (on the system) needs functions that are not present in the libpng provided with BV, but if we do not ship libpng, some other system may miss it, or have an incompatible one... On the other hand I think I remember at one time we shipped a freetype lib, and it causes other problems on even other systems...

Denis

[Sarrazin]

Thank you Denis, I'm going to check the images again. Do you have any idea on what could specifically interfere with the process at that particular step ?
Thanks,
samuel

[riviere]

Hi,
I don't exactly know without seing the data... Maybe look at the sulci skeleton if it looks good. Sometimes when the segmentation goes bad, the skeleton gets completely crappy with thousands of little branches. I don't know if it could be the cause of your problem.
Denis