[Insight-users] MRIBiasCorrector program
Jisung Kim
bahrahm at yahoo . com
Tue, 30 Jul 2002 06:37:17 -0700 (PDT)
Hello.
Yesterday, I finally fixed the problem and I also made
some modifications that removes depreceated feature
warnings. I will check in the modified code right now.
MRIBiasCorrection example is more than a year old and
there has been lots of changes in ITK. I tried to
"mordernize" my example and filter codes.
The "max-iteration" command line option is replaced
with two separate options, "volume-max-iteration" and
"inter-slice-max-iteration". The former is the maximal
number of iterations for 3D bias correction and the
latter for 2D zero degree inter slice bias correction
that is a preprocess of 3D bias correction.
I tested the example against Brainweb dataset. It
seems works fine.
If you have more problems, please let me know.
Thank you,
Jisung.
--- "Hans J. Johnson" <hjohnson@engineering.uiowa.edu>
wrote:
> Jisung,
>
> Any luck so far? I will have some time at the end
> of this week to look
> at this program again, and I was just wondering if
> you were able to get
> it to work.
>
> I realize that you probably have many other things
> to do, so if I can be
> of any assistance, please let me know.
>
> Thanks,
> Hans
>
> Jisung Kim wrote:
>
> >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
> >>
>
>=============================================================================
> >
> >>
> >>
> >>
>
=== message truncated ===
=====
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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