[Insight-users] Re : Output dicom series in new directory

[Syrine Sahmim]

this is my code and you must verify your cmake file
#include "itkImageSeriesReader.h"
#include "itkDICOMImageIO2.h"
#include "itkDICOMSeriesFileNames.h"
#include "itkImageFileWriter.h"

int main( int argc, char* argv[] )
{
/*
  if( argc < 3 )
    {
    std::cerr << "Usage: " << argv[0] << " DicomDirectory  outputFileName  [seriesName]" << std::endl;
    return EXIT_FAILURE;
    }
*/

    argc = 2;
    argv[1] = "dicom";
    argv[2] = "dicomMRA.hdr";
    
  typedef itk::Image<short,3>            ImageType;
  typedef itk::ImageSeriesReader< ImageType >     ReaderType;

  itk::DICOMImageIO2::Pointer dicomIO = itk::DICOMImageIO2::New();

  // Get the DICOM filenames from the directory
  itk::DICOMSeriesFileNames::Pointer nameGenerator = itk::DICOMSeriesFileNames::New();
  nameGenerator->SetDirectory( argv[1] );
  

  try
    {
    typedef std::vector<std::string> seriesIdContainer;
    const seriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();

    seriesIdContainer::const_iterator seriesItr = seriesUID.begin();
    seriesIdContainer::const_iterator seriesEnd = seriesUID.end();
  
    std::cout << std::endl << "The directory: " << std::endl;
    std::cout << std::endl << argv[1] << std::endl << std::endl;
    std::cout << "Contains the following DICOM Series: ";
    std::cout << std::endl << std::endl;

    while( seriesItr != seriesEnd )
      {
      std::cout << seriesItr->c_str() << std::endl;
      seriesItr++;
      }
  
    std::cout << std::endl << std::endl;
    std::cout << "Now reading series: " << std::endl << std::endl;

    typedef std::vector<std::string> fileNamesContainer;
    fileNamesContainer fileNames;

    if( argc < 4 ) // If no optional third argument
      {
      std::cout << seriesUID.begin()->c_str() << std::endl;
      fileNames = nameGenerator->GetFileNames();
      }
    else
      {
      std::cout << argv[3] << std::endl;
      fileNames = nameGenerator->GetFileNames( argv[3] );
      }
    std::cout << std::endl << std::endl;

    ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileNames( fileNames );
    reader->SetImageIO( dicomIO );

    try
      {
      reader->Update();
      }
    catch (itk::ExceptionObject &ex)
      {
      std::cout << ex << std::endl;
      return EXIT_FAILURE;
      }

    typedef itk::ImageFileWriter< ImageType > WriterType;
    WriterType::Pointer writer = WriterType::New();

    std::cout  << "Writing the image as " << std::endl << std::endl;
    std::cout  << argv[2] << std::endl << std::endl;

    writer->SetFileName( argv[2] );
    
    writer->SetInput( reader->GetOutput() );

    try
      {
      writer->Update();
      }
    catch (itk::ExceptionObject &ex)
      {
      std::cout << ex;
      return EXIT_FAILURE;
      }
    }
  catch (itk::ExceptionObject &ex)
    {
    std::cout << ex;
    return EXIT_FAILURE;
    }

  return EXIT_SUCCESS;

}

i hope that will help you. tell wether your program goes on or not








________________________________
De : Ezequiel Geremia <t-egerem at microsoft.com>
À : Mathieu Malaterre <mathieu.malaterre at gmail.com>
Cc : "insight-users at itk.org" <insight-users at itk.org>
Envoyé le : Mardi, 23 Juin 2009, 16h18mn 52s
Objet : Re: [Insight-users] Output dicom series in new directory

No exception is thrown. The output dicom series are not created in the requested Directory.

Moreover Syrine, there is not a matter of reading nrrd format, it is just a matter of outputting generated files in the right directory.

If already have had that problem and resolve it you can send me the file so that I can compare it with mine. It will help me solving that issue.

Thanks,

Ezequiel

-----Original Message-----
From: Mathieu Malaterre [mailto:mathieu.malaterre at gmail.com] 
Sent: 23 June 2009 16:11
To: Ezequiel Geremia
Cc: insight-users at itk.org
Subject: Re: [Insight-users] Output dicom series in new directory

On Tue, Jun 23, 2009 at 4:45 PM, Ezequiel Geremia<t-egerem at microsoft.com> wrote:
> Hi insight-users,
>
> I wrote a code inspired from itkSoftwraeGuide to convert nrrd files into dicom series.
>
> When running the executable on windows vista, the latter does not output the dicom slices in the directory specified through
>
> typedef itk::GDCMSeriesFileNames NamesGeneratorType;
> NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
>
> namesGenerator->SetOutputDirectory( outputDirectory );
>
> Do you have an idea on how to resolve that issue ?

I have absolutely no idea. But if you send the output of the
executable, I might help. just print the exception that's thrown
during the call to Update() (or Write()) and send it to the list.

2cts

-- 
Mathieu

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