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

[Syrine Sahmim]

Hi Ezequiel,

So happy that you are managed to solve the problem.Unfortunately, I'm just newer with ITK but if I have any thing to help every one I will do it even with the smallest knowledge that i have.
Thank you




________________________________
De : Ezequiel Geremia <t-egerem at microsoft.com>
À : Syrine Sahmim <syrine.sahmim at yahoo.fr>
Cc : "insight-users at itk.org" <insight-users at itk.org>
Envoyé le : Mercredi, 24 Juin 2009, 0h26mn 40s
Objet : RE: Re : [Insight-users] Output dicom series in new directory

 
Hi Syrine,
 
Thank you for your help
 
I managed to solve the problem by using NumericSeriesFileNames
class.
 
However some issues remain unsolved due to incompatibility between
windows and unix path separators, that forces the executable to be used in the
same file as the the header.
 
Attached the resulting code
 
Many thanks,
 
Ezequiel
 
From:Syrine Sahmim
[mailto:syrine.sahmim at yahoo.fr] 
Sent: 23 June 2009 18:55
To: Ezequiel Geremia
Cc: insight-users at itk.org
Subject: Re : [Insight-users] Output dicom series in new directory
 
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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