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
Code: Select all
Loading toolbox .DS_Store
Loading toolbox brainrat
Loading toolbox connectomist
Loading toolbox cortical_surface
Loading toolbox data management
Loading toolbox datamind
Loading toolbox freesurfer
Loading toolbox morphologist
Loading toolbox structural_analysis
Loading toolbox tools
Loading toolbox viewers
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
Do you know why I can not run it from the command line?
Thank you!
Fab