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Field regularisation low contrast

https://brainvisa.info/forum/viewtopic.php?f=2&t=1537

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Field regularisation low contrast

Posted: Mon Jan 31, 2011 10:24 pm
by guisepps
I am coming across the following problem when usinf 2007 pipeline with a T1 MRI : VIP Warning: Impossible to distinguish gray and white matter: insufficient grey white contrast, you have to increase field regularization in VipBiasCorrection) ------------------------------



in 4 - Split Brain Mask 1 System command exited with non null value : 111


RuntimeError
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
SplitBrain.py (112) in execution:
apply( context.system, call_list+option_list )
neuroProcessesGUI.py (1495) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2133) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )




in Split Brain Mask 1 System command exited with non null value : 111


RuntimeError
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1694) in _run:
res = node.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
SplitBrain.py (112) in execution:
apply( context.system, call_list+option_list )
neuroProcessesGUI.py (1495) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2133) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )




in T1 Pipeline 2007 1 System command exited with non null value : 111


RuntimeError
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1694) in _run:
res = node.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
SplitBrain.py (112) in execution:
apply( context.system, call_list+option_list )
neuroProcessesGUI.py (1495) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2133) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) ).

I saw some information for the same kind of error in a previous topic but the link providing some explanation is down.
What is field regularisation ? Field rigidity , what are the good default values to enter

Many thanks

Guisepps

Re: Field regularisation low contrast

Posted: Tue Feb 01, 2011 8:54 am
by Dominique Geffroy
Hello,

First, you can try the alternative method for bias correction step : unroll the bias correction step in the pipeline and change the selected method. The parameters are not the same and in some cases, one works better than the other.

Dominique

Re: Field regularisation low contrast

Posted: Tue Feb 01, 2011 2:11 pm
by guisepps
I had tried with slection of Vip Bias instead of the defalult one but there is still the same problem .
Thanks for your help.

Guisepps

Re: Field regularisation low contrast

Posted: Sun Feb 06, 2011 9:18 pm
by Jean-Francois Mangin
If your data have a good contrast, it could be related to
a failure of histogram Analysis. Switch from auto to a couple
of other fixel values for the sampling.

Re: Field regularisation low contrast

Posted: Wed Feb 16, 2011 10:21 pm
by guisepps
Thanks for your answer ,I tried to change the value in histogram analysis (2 instead of auto) and 32 (instead of auto)
and this is what I get :
OK, the image seems to be in the correct orientation.
------------------------------ ! VIP Warning: Impossible to distinguish gray and white matter: insufficient grey white contrast, you have to increase field regularization in VipBiasCorrection) ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------



in Vip Split Brain 1 System command exited with non null value : 111


RuntimeError
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
VipSplitBrain.py (110) in execution:
apply( context.system, call_list+option_list )
neuroProcessesGUI.py (1495) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2133) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )




in Ana Split Brain from Brain Mask 1 System command exited with non null value : 111


RuntimeError
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
AnaSplitBrainFromBrainMask.py (73) in execution:
Commissure_coordinates = self.Commissure_coordinates )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
VipSplitBrain.py (110) in execution:
apply( context.system, call_list+option_list )
neuroProcessesGUI.py (1495) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2133) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )




in Split Brain Mask 1 System command exited with non null value : 111


RuntimeError
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1694) in _run:
res = node.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
AnaSplitBrainFromBrainMask.py (73) in execution:
Commissure_coordinates = self.Commissure_coordinates )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
VipSplitBrain.py (110) in execution:
apply( context.system, call_list+option_list )
neuroProcessesGUI.py (1495) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2133) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )




in T1 Pipeline 2007 1 System command exited with non null value : 111


RuntimeError
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1541) in _run:
result.append( node.run( context ) )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
neuroProcesses.py (749) in execution:
return self._executionNode.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1694) in _run:
res = node.run( context )
neuroProcesses.py (1347) in run:
return self._run( context )
neuroProcesses.py (1464) in _run:
return context.runProcess( self._process )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
AnaSplitBrainFromBrainMask.py (73) in execution:
Commissure_coordinates = self.Commissure_coordinates )
neuroProcesses.py (1829) in runProcess:
result = self._processExecution( _process, None )
neuroProcesses.py (2028) in _processExecution:
result = process.execution( self )
VipSplitBrain.py (110) in execution:
apply( context.system, call_list+option_list )
neuroProcessesGUI.py (1495) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (2133) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )


Process T1 Pipeline 2007 1 finished on 2011/02/16 22:15 (4 minutes 4 seconds)


Thanks for your help.

Guisepps

Re: Field regularisation low contrast

Posted: Fri Feb 18, 2011 9:48 am
by Jean-Francois Mangin
Is the brain mask OK?
IS the histogram analysis OK (I mean you can check easily the mean value for grey and white matter,
to see if they fit the nobias image (use the profile window in Anatomist)
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