error early in anatomic pipeline

[amit]

All,

I am trying to take an SPGR T1 anatomic and create a 3-D surface mesh for rendering group activation on. It gets through the VIPbiascorrection then crashes on the histogram step with the following error. I am running BrainVisa on Mac OSX and have used the standard settings on "Ana do a lot of things from T1 MRI" (though changing some of the settings seems to make no difference). Does anybody have any ideas why this is and how I can fix it?

thanks,
Amit

Process Ana Do A Lot of Things from T1 MRI 1 startedVipBiasCorrection
VipHistoAnalysis



in Ana Do A Lot of Things from T1 MRI 1 RuntimeError: System call interrupted with signal SIGSEGV

neuroProcesses.py (1003) in _processExecution:
result = process.execution( self )
AnaDoAll.py (126) in execution:
lesion_mask=self.lesion_mask)
neuroProcesses.py (813) in runProcess:
result = self._processExecution( _process )
neuroProcesses.py (1003) in _processExecution:
result = process.execution( self )
AnaT1toBrainMask.py (71) in execution:
context.runProcess('Vip Histogram analysis', self.mri_corrected, self.histo_analysis,0)
neuroProcesses.py (813) in runProcess:
result = self._processExecution( _process )
neuroProcesses.py (1003) in _processExecution:
result = process.execution( self )
VipHistoAnalysis.py (60) in execution:
context.system( 'VipHistoAnalysis', '-i', self.mri_corrected.fullName(), '-o',self.histo_analysis.fullName(), '-S', 'y', '-m', 'a')
neuroProcessesGUI.py (626) in system:
ret = apply( ExecutionContextGUI.system, (self,) + args, kwargs )
neuroProcesses.py (1072) in system:
ret = self._system( command, self._systemStdout, self._systemStderr )
neuroProcesses.py (1131) in _system:
result = c.wait()
neuroProcesses.py (548) in wait:
raise RuntimeError( _t_( 'System call interrupted with signal <em>%s</em>') % signalName( sig ) )


Process Ana Do A Lot of Things from T1 MRI 1 finished

[Jean-Francois Mangin]

Well,
I have no guess for the moment. A few questions:

did you manage to process some other datasets? (for instance the example
in the distribution)
did you spatially normalize your data before importation?
are you sure your normalized data is not in a floating point format (I am
not sure our importation process deals correctly with such data).

Jeff

[riviere]

Normally the importation process should take care of converting data to short int data format. Doesn't it work ?
Denis