runtime error in T1 Bias correction

Questions about BrainVisa usage and installation

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tizianod
Posts: 21
Joined: Fri Apr 06, 2012 9:52 am

runtime error in T1 Bias correction

Postby tizianod » Wed May 30, 2012 12:32 pm

The Morpohologist 2012 pipeline stops in the estimation of the bias:

Code: Select all

Process Morphologist 2012 started on 2012/05/30 13:25
Skip unselected node: Check SPAM models installation
OK, the image seems to be in the correct orientation.
------------------------------ ! VIP Warning: empty volume in VipComputeRobustStatInMaskVolume ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------ ------------------------------ ! VIP Warning: Empty bucket list in VipGetNthBiggest3DBucket_S16BIT ------------------------------ ------------------------------ ! VIP Warning: Nothing is left in VipConnexVolumeFilter ------------------------------
------------------------------ ! VIP Warning: empty volume in VipComputeRobustStatInMaskVolume ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------ ------------------------------ ! VIP Warning: Empty bucket list in VipGetNthBiggest3DBucket_S16BIT ------------------------------ ------------------------------ ! VIP Warning: Nothing is left in VipConnexVolumeFilter ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------ ------------------------------ ! VIP Warning: Empty bucket list in VipGetNthBiggest3DBucket_S16BIT ------------------------------ ------------------------------ ! VIP Warning: Nothing is left in VipConnexVolumeFilter ------------------------------
------------------------------ ! VIP Warning: Empty volume in VipGet3DConnex ------------------------------ ------------------------------ ! VIP Warning: Empty bucket list in VipGetNthBiggest3DBucket_S16BIT ------------------------------
------------------------------ ! VIP Warning: Empty histogram! ------------------------------ ------------------------------ !! VIP Error: Execution aborted in function 'VipGetHistoEntropy'. ------------------------------
------------------------------ !! VIP Error: Empty image ------------------------------ ------------------------------ !! VIP Error: Execution aborted in function 'VipComputeBiasFieldMultiGrid'. ------------------------------



in 1 - T1 Bias Correction 7 System command exited with non null value : 111


RuntimeError
neuroProcesses.py (2400) in _processExecution:
result = process.execution( self )
T1BiasCorrection.py (127) in execution:
?
neuroProcessesGUI.py (2380) in system:
?
neuroProcesses.py (2522) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )




in Morphologist 2012 6 System command exited with non null value : 111


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 )
T1BiasCorrection.py (127) in execution:
?
neuroProcessesGUI.py (2380) in system:
?
neuroProcesses.py (2522) in system:
raise RuntimeError( _t_( 'System command exited with non null value : %s' ) % str( ret ) )
-


The image looks fine, not particularly noisy and it's well oriented. Here is the GIS header:

Code: Select all

256 256 124 1
-type S16
-dx 0.9375 -dy 0.9375 -dz 1.3 -dt 1
-bo DCBA
-om binar


May the error have something to do with the fact that on the Z-direction the sampling is 1.3mm ?

Thanks a lot
Tiziano

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