[Insight-users] Surface extraction seg. fault at meshSource->Update()

[Luis Ibanez]

Hi Catherine,


BTW, If your final goal is to actually extract surfaces
out of a *Series* of DICOM files, then what you may consider
to do first is to use the

                   SeriesImageReader

To load all the DICOM slices into a single 3D Volume.
You will find instructions on how to do this in the
ITK Software Guide:

     http://www.itk.org/ItkSoftwareGuide.pdf

in the Chapter "Reading and Writing Images".



Once you have a 3D volume into an itk::Image, you will be
able to use the mesh3D extraction filter,

            or as a second option

You could also convert the 3D volume to a vtkImageData and
then use the vtkContour filter.


Please let us know what your final goal actually is.


    Thanks


       Luis



------------------------
Catherine Peloquin wrote:
> My image only contains one slice. It has 512 rows and 512 columns.
>  
> Catherine
> 
>  
> On 4/30/07, *Luis Ibanez* <luis.ibanez at kitware.com 
> <mailto:luis.ibanez at kitware.com>> wrote:
> 
> 
>     Hi Catherine,
> 
>     Does your image CT0001.dcm contain multiple slices ?
> 
> 
>     Otherwise it is going to be considered as a 1 slice
>     3D image, and it is reasonable that it will fail to
>     produce a 3D surface when passed as input to the
>     BinaryMask3DMeshSource.
> 
> 
>     Please let us know how many pixels along each one
>     of the three dimensions does CT0001.dcm has.
> 
> 
> 
>        Regards,
> 
> 
>           Luis
> 
> 
> 
>     --------------------------
>     Catherine Peloquin wrote:
>      > I am trying to get a version of the example surface extraction code
>      > running.  I had problems with the CMakeLists.txt file, but that
>     has been
>      > resolved.  My problem now is that I am getting a segmentation
>     fault at
>      > the line "meshSource->Update()".  I tried using .ima files, and .dcm
>      > files located in the same directory as my .cxx and CMakeLists
>     files.  I
>      > added a try/catch block around this line as Luis suggested and
>     re-built
>      > the example, but the program still faults out at that location.  I am
>      > running the executable with the command "SurfaceExtraction CT0001.dcm
>      > 400".
>      >
>      > The relevant .cxx file code is as follows:
>      >
>      > //Surface Extraction code modified from ITK Surface Extraction
>     Example
>      > included in ITK build
>      > #if defined(_MSC_VER)
>      > #pragma warning ( disable : 4786 )
>      > #endif
>      >
>      > #ifdef __BORLANDC__
>      > #define ITK_LEAN_AND_MEAN
>      > #endif
>      >
>      > #include "itkImageFileReader.h"
>      > #include " itkBinaryMask3DMeshSource.h"
>      > #include " itkImage.h"
>      > #include "itkMesh.h"
>      > #include <iostream>
>      > using namespace std;
>      >
>      > int main(int argc, char * argv[] )
>      > {
>      >
>      >   if( argc < 3 )
>      >     {
>      >     std::cerr << "Usage: IsoSurfaceExtraction  inputImageFile
>      > objectValue " << std::endl;
>      >     return EXIT_FAILURE;
>      >     }
>      >
>      >   const unsigned int Dimension = 3;
>      >   typedef unsigned char  PixelType;
>      >
>      >   typedef itk::Image< PixelType, Dimension >   ImageType;
>      >   typedef itk::ImageFileReader< ImageType >    ReaderType;
>      >   ReaderType::Pointer reader = ReaderType::New();
>      >   reader->SetFileName( argv[1] );
>      >
>      >   try
>      >     {
>      >     reader->Update();
>      >     }
>      >   catch( itk::ExceptionObject & exp )
>      >     {
>      >     std::cerr << "Exception thrown while reading the input file " <<
>      > std::endl;
>      >     std::cerr << exp << std::endl;
>      >     return EXIT_FAILURE;
>      >     }
>      >
>      >   typedef itk::Mesh<double>                         MeshType;
>      >   typedef itk::BinaryMask3DMeshSource< ImageType, MeshType >
>      > MeshSourceType;
>      >   MeshSourceType::Pointer meshSource = MeshSourceType::New();
>      >
>      >   const PixelType objectValue = static_cast<PixelType>( atof(
>     argv[2] ) );
>      >
>      >   meshSource->SetObjectValue( objectValue );
>      >
>      >     cout << "Before meshSource input set." << endl;
>      >     try
>      >       {
>      >           meshSource->SetInput( reader->GetOutput() );
>      >         }
>      >       catch( itk::ExceptionObject & exp )
>      >       {
>      >         std::cerr << "Exception thrown during setting mesh
>     input() " <<
>      > std::endl;
>      >         std::cerr << exp << std::endl;
>      >         return EXIT_FAILURE;
>      >         }
>      >
>      >     cout << "Before meshSource update" << endl;
>      >   try
>      >     {
>      >     meshSource->Update();  //--------------------------SEGMENTATION
>      > FAULT HERE--------------------------------------------
>      >     }
>      >   catch( itk::ExceptionObject & exp )
>      >     {
>      >     cerr << "Exception thrown during Update() " << std::endl;
>      >     cerr << exp << std::endl;
>      >     return EXIT_FAILURE;
>      >     }
>      >
>      >   cout << "Nodes = " << meshSource->GetNumberOfNodes() << std::endl;
>      >   cout << "Cells = " << meshSource->GetNumberOfCells() << std::endl;
>      >
>      >   return EXIT_SUCCESS;
>      > }
>      >
>      > Does anyone have any suggestions?
>      >
>      > Thanks,
>      > Catherine
>      >
>      >
>      >
>     ------------------------------------------------------------------------
>      >
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