[Insight-users] MRIBiasCorrector program

[Jisung Kim]

Hello.

I am the developer of the program. I just ran it and
had same seg fault error. The example is kind of old
and there wasn't any change since I implemented and
tested it on Windows and Linux. 

At this moment, I don't know what caused it. I will 
fix it and let you know. By the way, could you send an
email with information about your system such as types
and versions of OS and compiler?

Thank you for pointing it out,

Jisung.

--- "Hans J. Johnson" <hans-johnson@uiowa.edu> wrote:
> 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
>
=============================================================================
> 
> 
> 
> 
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> Insight-users@public.kitware.com
>
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=====
Jisung Kim
bahrahm@yahoo.com
106 Mason Farm Rd.
129 Radiology Research Lab., CB# 7515
Univ. of North Carolina at Chapel Hill
Chapel Hill, NC 27599-7515

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