[Insight-users] converting mhd/raw data to dicom problem

[Moti Freiman]

Hi,
I'm trying to convert a mhd/raw CT volume to dicom, to import it to a
Phillips workstation.
The conversion succeed, and when I'm reading the dicom series using
itk-snap, everything is fine.
However, when I'm trying to import it to the Phillips workstation, the
order of the slices becomes wrong, and slices appear
not in the anatomical order.
Any Idea?
The conversion code  is basically the ITK example and attached below:
Thanks,
Moti


/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: ImageReadDicomSeriesWrite.cxx,v $
  Language:  C++
  Date:      $Date: 2006-03-21 01:00:08 $
  Version:   $Revision: 1.1 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/
#if defined(_MSC_VER)
#pragma warning ( disable : 4786 )
#endif

#ifdef __BORLANDC__
#define ITK_LEAN_AND_MEAN
#endif

#include "itkGDCMImageIO.h"
#include "itkNumericSeriesFileNames.h"
#include "itkImageFileReader.h"
#include "itkImageSeriesWriter.h"
#include "itkMetaDataObject.h"

#include <vector>
#include <itksys/SystemTools.hxx>

//  Software Guide : BeginLatex
//
//  This example illustrates how to read a 3D image from a non DICOM
file and write it as a series of DICOM slices.
//  with some changed header information. Header
//
//  Please note that modifying the content of a DICOM header is a very risky
//  operation. The Header contains fundamental information about the patient
//  and therefore its consistency must be protected from any data corruption.
//  Before attempting to modify the DICOM headers of your files, you must make
//  sure that you have a very good reason for doing so, and that you can ensure
//  that this information change will not result in a lower quality of health
//  care to be delivered to the patient.
//
//  \index{DICOM!Writing Series}
//
//  Software Guide : EndLatex


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

  if( argc < 3 )
    {
    std::cerr << "Usage: " << argv[0];
    std::cerr << "InputImage  OutputDicomDirectory" << std::endl;
    return EXIT_FAILURE;
    }


  typedef signed short    PixelType;
  const unsigned int      Dimension = 3;

  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 &excp)
    {
    std::cerr << "Exception thrown while writing the image" << std::endl;
    std::cerr << excp << std::endl;
    return EXIT_FAILURE;
    }




  typedef itk::GDCMImageIO                        ImageIOType;
  typedef itk::NumericSeriesFileNames             NamesGeneratorType;

  ImageIOType::Pointer gdcmIO = ImageIOType::New();

  const char * outputDirectory = argv[2];

  itksys::SystemTools::MakeDirectory( outputDirectory );


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

  typedef itk::Image< OutputPixelType, OutputDimension >    Image2DType;

  typedef itk::ImageSeriesWriter<
                         ImageType, Image2DType >  SeriesWriterType;

  NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();

  itk::MetaDataDictionary & dict = gdcmIO->GetMetaDataDictionary();
  std::string tagkey, value;
  tagkey = "0008|0060"; // Modality
  value = "MR";
  itk::EncapsulateMetaData<std::string>(dict, tagkey, value );
  tagkey = "0008|0008"; // Image Type
  value = "DERIVED\\SECONDARY";
  itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
  tagkey = "0008|0064"; // Conversion Type
  value = "DV";
  itk::EncapsulateMetaData<std::string>(dict, tagkey, value);


  SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();

  seriesWriter->SetInput( reader->GetOutput() );
  seriesWriter->SetImageIO( gdcmIO );


  ImageType::RegionType region =
     reader->GetOutput()->GetLargestPossibleRegion();

  ImageType::IndexType start = region.GetIndex();
  ImageType::SizeType  size  = region.GetSize();


  std::string format = outputDirectory;

  format += "/image%03d.dcm";

  namesGenerator->SetSeriesFormat( format.c_str() );

  namesGenerator->SetStartIndex( start[2] );
  namesGenerator->SetEndIndex( start[2] + size[2] - 1 );
  namesGenerator->SetIncrementIndex( 1 );


  seriesWriter->SetFileNames( namesGenerator->GetFileNames() );


  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 EXIT_SUCCESS;
}




-- 
__
Moti Freiman, Ph.D Student.
Medical Image Processing and Computer-Assisted Surgery Laboratory.
School of Computer Science and Engineering.
The Hebrew University of Jerusalem Givat Ram, Jerusalem 91904, Israel
Phone: +(972)-2-658-5371 (laboratory)
WWW site: http://www.cs.huji.ac.il/~freiman