Problem in correcting brain mask

Questions about BrainVisa usage and installation

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Nomad
Posts: 17
Joined: Tue Apr 01, 2008 3:56 am

Problem in correcting brain mask

Post by Nomad »

Hi,
Something goes wrong when i split brain mask after correcting brain mask.
The error message is :

in Vip Split Brain 5 RuntimeError: System command exited with non null value : 111

neuroProcesses.py (1641) in _processExecution:
result = process.execution( self )
VipSplitBrain.py (107) in execution:
apply( context.system, call_list+option_list )
neuroProcessesGUI.py (932) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (1721) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )





in Ana Split Brain from Brain Mask 4 RuntimeError: System command exited with non null value : 111

neuroProcesses.py (1641) in _processExecution:
result = process.execution( self )
AnaSplitBrainFromBrainMask.py (69) in execution:
Commissure_coordinates = self.Commissure_coordinates )
neuroProcesses.py (1534) in runProcess:
result = self._processExecution( _process )
neuroProcesses.py (1641) in _processExecution:
result = process.execution( self )
VipSplitBrain.py (107) in execution:
apply( context.system, call_list+option_list )
neuroProcessesGUI.py (932) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (1721) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )
User avatar
Jean-Francois Mangin
Posts: 337
Joined: Mon Mar 01, 2004 10:24 am
Location: Neurospin, CEA, France
Contact:

Re: Problem in correcting brain mask

Post by Jean-Francois Mangin »

Yes,
this topic has been answered a number of time in the forum. This procedure is not very stable...
Do a search on split.
Nomad
Posts: 17
Joined: Tue Apr 01, 2008 3:56 am

Re: Problem in correcting brain mask

Post by Nomad »

Jean-Francois Mangin wrote:Yes,
this topic has been answered a number of time in the forum. This procedure is not very stable...
Do a search on split.
The following words in your search query were ignored because they are too common words: split.
You must specify at least one word to search for. Each word must consist of at least 3 characters and must not contain more than 14 characters excluding wildcards.
User avatar
Jean-Francois Mangin
Posts: 337
Joined: Mon Mar 01, 2004 10:24 am
Location: Neurospin, CEA, France
Contact:

Re: Problem in correcting brain mask

Post by Jean-Francois Mangin »

Well I did not though you would use "split" literally...
But I agree it is not always easy to search a forum.

In fact I do not know enough about the way you use brainVISA to
give useful advise. Most of the time, the pb stem from a bad bias correction,
or from the fact that the cerebellum is missing in the brain mask.
A bad histogram analysis could be a pb too.

The right strategy for you is to use the bias correction of pipeline 05,
lock it (see validation process) and switch back to pipeline 04. There may
be some useful other things in the 2005 one, but this
would require a documentation. Anyway, I am sorry I do not find time
to converge on the various ongoing developments.

When the split brain fails, just play around with the threshold used to define white matter.
Select the "barycenter something" mode, and the ratio between grey average and white average.
After a few attempts, you should get something. If it is not perfect, click on the pen
and correct the result manually...
Last edited by Jean-Francois Mangin on Mon Sep 08, 2008 8:19 pm, edited 1 time in total.
User avatar
Jean-Francois Mangin
Posts: 337
Joined: Mon Mar 01, 2004 10:24 am
Location: Neurospin, CEA, France
Contact:

Re: Problem in correcting brain mask

Post by Jean-Francois Mangin »

In fact, I think that an even better strategy should be the use of the split brain
of the pipeline 2005 (called "4 something").
Anyway, when things are going bad, only experience can help you to play around with the parameters.
I guess it is time for us to organize a school... or to work further on the documentation...

The moral: to minimize trouble, use good quality data. I am sometime terrified by the production
of some scanners...
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