Sulcus Parametrization 2015 , bvproc

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f4bry
Posts: 29
Joined: Wed Mar 25, 2009 1:46 pm

Sulcus Parametrization 2015 , bvproc

Post by f4bry »

Hi,
I am trying to run the 'Sulcus Parametrization 2015' function using BrainVISA 4.5 (OS X 10.11.4) from the command line.
I saved a .bvproc process from the GUI and then I run it like:

Code: Select all

/Applications/brainvisa-4.5/bin/brainvisa -r file.bvproc
but I got the following error messages:

Code: Select all

Loading toolbox .DS_Store
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Loading toolbox My processes

Process Sulcus Parameterization 2015 started on 2016/08/09 18:06
Extracting sulcus and buckets from graph
ERROR in Sulcus Parameterization 2015 1 Could not get process "'Create Sulcus
Label Volume'": invalid identifier or process file: IOError(2, 'No such file or
directory')

--------------------------------------------------------------------------------
KeyError
processes.py (2725) in _processExecution:

result = process.execution( self )

ParameterizeSulcus2015.py (374) in execution:

node_edge_types='All' )

processes.py (2480) in runProcess:

_process = getProcessInstance( _process )

processes.py (3902) in getProcessInstance:

+ '": invalid identifier or process file: ' + repr(e))

Process Sulcus Parameterization 2015 finished on 2016/08/09 18:06 (1 seconds)
ERROR Could not get process "'Create Sulcus Label Volume'": invalid identifier
or process file: IOError(2, 'No such file or directory')

--------------------------------------------------------------------------------
KeyError
processes.py (167) in initializeProcesses:

exec f in localsStartup, localsStartup

<string> (1) in <module>:

?

processes.py (2725) in _processExecution:

result = process.execution( self )

ParameterizeSulcus2015.py (374) in execution:

node_edge_types='All' )

processes.py (2480) in runProcess:

_process = getProcessInstance( _process )

processes.py (3902) in getProcessInstance:

+ '": invalid identifier or process file: ' + repr(e))

ERROR temporary file /Applications/brainvisa/temp_bv/bv_2892_0.ima not deleted
'NoneType' object has no attribute 'removePath'

--------------------------------------------------------------------------------
AttributeError
neuroDiskItems.py (2314) in __del__:

temporary.manager.removePath( f )

Exception SystemExit: 1 in <bound method TemporaryDiskItem.__del__ of u'/Applications/brainvisa/temp_bv/bv_2892_0.ima'> ignored
ERROR temporary file /Applications/brainvisa/temp_bv/bv_2892_1.ima not deleted
'NoneType' object has no attribute 'removePath'

--------------------------------------------------------------------------------
AttributeError
neuroDiskItems.py (2314) in __del__:

temporary.manager.removePath( f )

Exception SystemExit: 1 in <bound method TemporaryDiskItem.__del__ of u'/Applications/brainvisa/temp_bv/bv_2892_1.ima'> ignored
ERROR temporary file /Applications/brainvisa/temp_bv/bv_2892_2.ima not deleted
'NoneType' object has no attribute 'removePath'

--------------------------------------------------------------------------------
AttributeError
neuroDiskItems.py (2314) in __del__:

temporary.manager.removePath( f )

Exception SystemExit: 1 in <bound method TemporaryDiskItem.__del__ of u'/Applications/brainvisa/temp_bv/bv_2892_2.ima'> ignored
ERROR temporary file /Applications/brainvisa/temp_bv/bv_2892_3.ima not deleted
'NoneType' object has no attribute 'removePath'

--------------------------------------------------------------------------------
AttributeError
neuroDiskItems.py (2314) in __del__:

temporary.manager.removePath( f )

Exception SystemExit: 1 in <bound method TemporaryDiskItem.__del__ of u'/Applications/brainvisa/temp_bv/bv_2892_3.ima'> ignored
ERROR temporary file /Applications/brainvisa/temp_bv/bv_2892_4.ima not deleted
'NoneType' object has no attribute 'removePath'

--------------------------------------------------------------------------------
AttributeError
neuroDiskItems.py (2314) in __del__:

temporary.manager.removePath( f )

Exception SystemExit: 1 in <bound method TemporaryDiskItem.__del__ of u'/Applications/brainvisa/temp_bv/bv_2892_4.ima'> ignored
ERROR temporary file /Applications/brainvisa/temp_bv/bv_2892_5.ima not deleted
'NoneType' object has no attribute 'removePath'

--------------------------------------------------------------------------------
AttributeError
neuroDiskItems.py (2314) in __del__:

temporary.manager.removePath( f )

Exception SystemExit: 1 in <bound method TemporaryDiskItem.__del__ of u'/Applications/brainvisa/temp_bv/bv_2892_5.ima'> ignored
ERROR temporary file /Applications/brainvisa/temp_bv/bv_2892_6.mesh not deleted
'NoneType' object has no attribute 'removePath'

--------------------------------------------------------------------------------
AttributeError
neuroDiskItems.py (2314) in __del__:

temporary.manager.removePath( f )

Exception SystemExit: 1 in <bound method TemporaryDiskItem.__del__ of u'/Applications/brainvisa/temp_bv/bv_2892_6.mesh'> ignored
ERROR temporary file /Applications/brainvisa/temp_bv/bv_2892_7.mesh not deleted
'NoneType' object has no attribute 'removePath'

--------------------------------------------------------------------------------
AttributeError
neuroDiskItems.py (2314) in __del__:

temporary.manager.removePath( f )

Exception SystemExit: 1 in <bound method TemporaryDiskItem.__del__ of u'/Applications/brainvisa/temp_bv/bv_2892_7.mesh'> ignored
ERROR temporary file /Applications/brainvisa/temp_bv/bv_2892_8.tex not deleted
'NoneType' object has no attribute 'removePath'

--------------------------------------------------------------------------------
AttributeError
neuroDiskItems.py (2314) in __del__:

temporary.manager.removePath( f )

Exception SystemExit: 1 in <bound method TemporaryDiskItem.__del__ of u'/Applications/brainvisa/temp_bv/bv_2892_8.tex'> ignored
ERROR temporary file /Applications/brainvisa/temp_bv/bv_2892_9.tex not deleted
'NoneType' object has no attribute 'removePath'

--------------------------------------------------------------------------------
AttributeError
neuroDiskItems.py (2314) in __del__:

temporary.manager.removePath( f )

Exception SystemExit: 1 in <bound method TemporaryDiskItem.__del__ of u'/Applications/brainvisa/temp_bv/bv_2892_9.tex'> ignored
If I open the .bvproc file with the GUI it runs well.
Do you know why I can not run it from the command line?

Thank you!
Fab
User avatar
riviere
Site Admin
Posts: 1361
Joined: Tue Jan 06, 2004 12:21 pm
Location: CEA NeuroSpin, Saint Aubin, France
Contact:

Re: Sulcus Parametrization 2015 , bvproc

Post by riviere »

Hi,
Sorry for the delay, I was on vacation...
The "brainvisa -r" commandline does not perform the complete initialization of brainvisa, but a "fast" version instead. In this mode some internal variables are not initialized, and here the list of processes indexed by name is missing (only the index by identifier is present).
It would have worked if the process ParameterizeSulcus2015 had used the process identifier "sulcuslabelvolume" instead of its name "Create Sulcus Label Volume" in runProcess(...) calls.
It is possible to run brainvisa as commandline with full features (enabling databases etc), using the newer "axon-runprocess" commandline, which is a commandline-only version of brainvisa with mode options than the older "brainvisa" command:

Code: Select all

axon-runprocess --enabledb file.bvproc
Denis
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