[Insight-users] MRIBiasCorrector program

[Hans J. Johnson]

Hello,

I trying to use the MRIBiasCorrector program, and I am getting a 
segmentation fault.

I am using the most generic command line, with a floating point input 
image with Meta data header:
==============
NDims = 3
DimSize = 256 256 124
ElementType = MET_FLOAT
ElementSpacing = 0.703125 0.703125 1.500000
ElementByteOrderMSB = False
ElementDataFile = /home/hjohnson/T1_float.img
===============

COMMANDLINE:
/usr/robin/people/hjohnson/src/buildhome/athlon/DEBUG/bin/BiasCorrector 
--input /home/hjohnson/T1_float.mhd --output xxx.img --class-mean 1500 
570  --class-sigma 100 70 --use-log yes --degree 3 --growth 1.05 
--shrink 0.9


********The following warnings are produced within a few seconds of startup

Loading images...
WARNING: In 
/IPLlinux/robin_home/hjohnson/src/buildhome/athlon/DEBUG/include/Insight/Code/Common/itkImageSource.txx, 
line 94
ReadMetaImage (0x8134528): SetOutput(): This method is slated to be 
removed from ITK.  Please use GraftOutput() in possible combination with 
DisconnectPipeline() instead.

Input image loaded.
Images loaded.
WARNING: In 
/IPLlinux/robin_home/hjohnson/src/buildhome/athlon/DEBUG/include/Insight/Code/Common/itkImageSource.txx, 
line 94
MRIBiasFieldCorrectionFilter (0x81320f0): SetOutput(): This method is 
slated to be removed from ITK.  Please use GraftOutput() in possible 
combination with DisconnectPipeline() instead.

*******After about 2 minutes the program seg faults
*******
====================Stack Trace =================
chunk_free,              FP=bfffd558
__cfree,                 FP=bfffd578
__builtin_delete,        FP=bfffd598
__builtin_vec_delete,    FP=bfffd5b8
vnl_c_vector_dealloc,    FP=bfffd5d8
                     [282]-->  delete [] static_cast<char*>(v);
vnl_c_vector<double>::deallocate, FP=bfffd5f8
                     [309]-->  vnl_c_vector_dealloc(v, n, sizeof (T));
vnl_vector<double>::destroy, FP=bfffd618
                     [252]-->   vnl_vector_free_blah;
vnl_vector<double>::~vnl_vector, FP=bfffd638
                     [107]-->   ~vnl_vector() { if (data) destroy(); }
itk::Array<double>::~Array, FP=bfffd658
                     [71]-->   ~Array() {};
...gned int)3> >::EstimateBiasField, FP=bfffd6e8
                    
[277]-->bias->SetCoefficients(m_Optimizer->GetCurrentPosition());
...(unsigned int)3> >::GenerateData, FP=bfffe328
                     [447]-->this->EstimateBiasField(bias, *iter) ;
...:ProcessObject::UpdateOutputData, FP=bfffe488
                     [814]-->this->GenerateData();                     
itk::DataObject::UpdateOutputData, FP=bfffe4a8
                     [403]-->m_Source->UpdateOutputData(this);         
        itk::DataObject::Update, FP=bfffe4c8
                     [328]-->this->UpdateOutputData();  
itk::ProcessObject::Update, FP=bfffe4e8
                     [482]  void
                     [483]  ProcessObject
                     [484]  ::Update()
                     [485]  {
                     [486]     if (this->GetOutput(0))
                     [487]       {
                     [488]-->       this->GetOutput(0)->Update();
                     [489]       }
                     [490]   }
main,                    FP=bfffe818
                     [212]   filter->SetBiasFieldDegree(degree) ;
                     [213]   
filter->SetUsingSlabIdentification(usingSlabIdentification) ;
                     [214]   filter->SetSlicingDirection(sliceDirection) ;
                     [215]-->filter->Update() ;
    __libc_start_main,       FP=bfffe858
==============================================

Any suggestions or help would be greatly appreciated.

-- 
Regards,
Hans

============================================================================= 

Hans J. Johnson                                                          
   305 MEB
hans-johnson@uiowa.edu                                             Dept. 
of Psychiatry
http://moniz.psychiatry.uiowa.edu/~hjohnson             The University 
of Iowa
(319) 353-5593                                                          
   Iowa City, IA 52242
=============================================================================