[Insight-users] vtk to dicom converstion

[Ming Chao]

Hi Mathieu,

Thanks for your reply. I could read in a 3D vtk file and write out a series
of 2D dicome files with taking the headers from a series of original 2D
dicom files. So what I did is the following test. Originally I had a series
of 2D dicom files, then I used volview and paraview to form a 3D vtk file. I
fed this 3D vtk as the image body data and the header is taken from the
original 2D dicom files. I have two questions about this procedure. 1) is
this procedure correct? 2) I checked the output 2D dicom files by forming a
3D image using volview but found that AP position was reversed. Don't know
why. Hope somebody can have an idea. I attach my code in the following.
Thanks,
Ming




// ----------------------------------------------------------------------
//
// a program used to convert 3D vtk file to a series of 2D dicom files
//
//

#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkImageSeriesWriter.h"
#include "itkImageSeriesReader.h"

#include <list>
#include <fstream>

int main( int argc, char* argv[] ) {

 // Verify the number of parameters in the command line
 if( argc < 4 ) {
  std::cerr << "Usage: " << std::endl;
  std::cerr << argv[0] << " vtkImage InputDicomImage ";
  std::cerr << " OutputImage \n";
  return EXIT_FAILURE;
    }

 typedef signed short InputPixelType;
 //typedef float InputPixelType;
 const unsigned int   InputDimension = 3;

 typedef itk::Image< InputPixelType, InputDimension > ImageType;

 typedef itk::ImageSeriesReader< ImageType >     ReaderType;

 typedef itk::ImageFileReader< ImageType > ReaderType2;
 ReaderType2::Pointer reader2 = ReaderType2::New();
 reader2->SetFileName( argv[1] );


 typedef itk::GDCMImageIO           ImageIOType;
 ImageIOType::Pointer gdcmIO = ImageIOType::New();

 typedef itk::GDCMSeriesFileNames                NamesGeneratorType;
 NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();


 namesGenerator->SetInputDirectory( argv[2] );
 const ReaderType::FileNamesContainer & filenames =
                            namesGenerator->GetInputFileNames();

 unsigned int numberOfFilenames =  filenames.size();
 std::cout << numberOfFilenames << std::endl;
 for(unsigned int fni = 0; fni<numberOfFilenames; fni++)
    {
     std::cout << "filename # " << fni << " = ";
     std::cout << filenames[fni] << std::endl;
    }

 ReaderType::Pointer reader = ReaderType::New();
 reader->SetImageIO( gdcmIO );
 reader->SetFileNames( filenames );

 try {
  reader->Update();
    }
 catch (itk::ExceptionObject & e) {
  std::cerr << "exception in file reader " << std::endl;
  std::cerr << e << std::endl;
  return EXIT_FAILURE;
 }

 const char * outputDirectory = argv[3];
 itksys::SystemTools::MakeDirectory( outputDirectory );

 typedef signed short    OutputPixelType;
 //typedef float    OutputPixelType;
 const unsigned int      OutputDimension = 2;

 typedef itk::Image< OutputPixelType, OutputDimension >    Image2DType;
 typedef itk::ImageSeriesWriter< ImageType, Image2DType >  SeriesWriterType;

 SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
 seriesWriter->SetInput( reader2->GetOutput() );
 seriesWriter->SetImageIO( gdcmIO );

 namesGenerator->SetOutputDirectory( outputDirectory );
 seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames() );

 seriesWriter->SetMetaDataDictionaryArray(
        reader->GetMetaDataDictionaryArray() );


 try {
  seriesWriter->Update();
    }
 catch( itk::ExceptionObject & excp ) {
  std::cerr << "Exception thrown while writing the series " << std::endl;
  std::cerr << excp << std::endl;
  return EXIT_FAILURE;
    }


 return 0;


}



On 6/6/06, Mathieu Malaterre <mathieu.malaterre at kitware.com> wrote:
>
> Ming Chao wrote:
> > Hi,
> >
> > Does anybody know whether a 3D vtk file can be converted into a series
> > of 2D dicom images in ITK? Thanks.


Yes and no :)
> Yes, you can read a 3D vtk image file, and yes you can write an
> itk::Image into a series of DICOM files.
>
> No, because by default GDCM is writing Secondary Image Capture which
> does not have the Patient Module and therefore cannot be reconstructed
> as a volume (no Image Position/Orientation (Patient)) if you use any
> serious DICOM reader.
> So you'll need an additional step in defining what is your DICOM Object
> (MR, CT, RT...)
>
> 2 cents
> Mathieu
>
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