runtime error in Grey White Surface

[Hanna]

Hallo,
I'm new to BrainVisa and I would like to extract the surfaces of the cortex and head from an MRI using Morphologist 2012. I have tried with two different MRI images, but I always get the same runtime error (see below) when trying to execute the Grey White Surface step of the pipeline. I have the impression that previous steps are correctly executed. Could someone please tell me what might cause this error and how I can fix it?
I would be thankful for any help!
Hanna

This is the error message I get:

in Grey White Surface 2012 1 System command exited with non null value : 42

RuntimeError
neuroProcesses.py (2400) in _processExecution:
result = process.execution( self )
GreyWhiteSurface.py (86) in execution:
"-m", "C", "-w", "t" )
neuroProcessesGUI.py (2380) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2522) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )


in Morphologist 2012 1 System command exited with non null value : 42

RuntimeError
neuroProcesses.py (2400) in _processExecution:
result = process.execution( self )
neuroProcesses.py (1064) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1723) in run:
return self._run( context )
neuroProcesses.py (1952) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1723) in run:
return self._run( context )
neuroProcesses.py (1868) in _run:
return context.runProcess( self._process )
neuroProcesses.py (2173) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2400) in _processExecution:
result = process.execution( self )
GreyWhiteSurface.py (86) in execution:
"-m", "C", "-w", "t" )
neuroProcessesGUI.py (2380) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2522) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )

[denghien]

Hy Hanna,

Have you tried with data for demonstration (the demo_data.zip package in http://brainvisa.info/downloadpage.html#data) just to check ?

The message is too short to understand what happened. You can read more information in the "BrainVisa -> Show Log".
Could you save the log file and send me it ? (cf http://brainvisa.info/doc/axon-4.2/bv_m ... tml#N10892 )

The Morphologist pipeline is more and more robust but specific cases can have some difficulties.

Isa

[Hanna]

Hallo Isa,

I checked with the demo data for Subject 01 and I get the same error.
I attached the log file to this post.

Hanna

[riviere]

Hi Hanna,

You're right, there was a bug in the grey/white surface extraction: actually there was some debug code which had not been removed, and which wrote some intermediate images "classif_grey1" and "classif_grey2" in the current directory. Here apparently BrainVisa is running from a directory where it cannot write, and this makes the command to fail.
This bug has been fixed since the release of BrainVisa 4.2.1 and the next version will not have this problem.
For the time being, a simple solution is to run BrainVisa from within a directory where it has write permissions (/tmp for instance). It will just spuriously write a few images there.

Sorry for the inconvenience...
Denis

[Hanna]

Thank you for your response.
I checked that BrainVisa is installed in a directory where it has permission to write. This is the case. I also tried moving it to another directory where it has write permissions, but it still didn't work. Does it really try to write only in the BrainVisa directory or also somewhere else?
Maybe I should also specify that I'm running the BrainVisa release for Mac 10.5 under Mac 10.7 (using the solution described in http://brainvisa.info/forum/viewtopic.php?f=2&t=1561 to make it work). Could this be part of the problem?

Hanna

[riviere]

Hi,
It's not the directory where BV is installed which causes problem actually, but the directory where it is run from (the "current directory").
If you are using a Mac, I guess you run it by simply clicking on the Brainvisa icon. I don't really know what is the current directory of programs run from the Mac desktop. Maybe you can try opening a terminal and run it manually. You should find the terminal application on Mac somewhere in Applications / utilities.
In the terminal, type:

Code: Select all

cd /tmp
open <path_to_brainvisa>/BrainVISA.app

If it doesn't work, you can also try (in the terminal):

Code: Select all

cd /tmp
<path_to_brainvisa>/bin/brainvisa

(<path_to_brainvisa> being the root directory of BV installation, for instance /Applications/brainvisa-4.2.1)

Denis

[Hanna]

Hallo Denis,

thanks a lot, your second proposition (typing cd /tmp and <path_to_brainvisa>/bin/brainvisa in the terminal) worked!

Hanna