[Insight-users] DICOM and Nrrd registration

[Guilhem Chéron]

Hi,I'm trying to register one set of DICOM and one Nrrd file.I’ve used the exemple : ImageRegistration8, which use “mha” files.I just want to replace the two mha files by my DICOM serie and my nrrd file.So I replace this part of code :typedef itk::ImageFileReader< FixedImageType  > FixedImageReaderType;
typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
FixedImageReaderType::Pointer  fixedImageReader  = FixedImageReaderType::New();
MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();
fixedImageReader->SetFileName(  argv[1] );
movingImageReader->SetFileName( argv[2] );
registration->SetFixedImage(    fixedImageReader->GetOutput()    );
registration->SetMovingImage(   movingImageReader->GetOutput()   );
fixedImageReader->Update();
registration->SetFixedImageRegion(
   fixedImageReader->GetOutput()->GetBufferedRegion() );
  By this (loading) part :     typedef itk::ImageSeriesReader< FixedImageType > FixedImageReaderType;
    typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
    FixedImageReaderType::Pointer  fixedImageReader  = FixedImageReaderType::New();
    MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();
    
/*    fixedImageReader->SetFileName(  argv[1] );
    movingImageReader->SetFileName( argv[2] );*/


    registration->SetFixedImage(    fixedImageReader->GetOutput()    );
    registration->SetMovingImage(   movingImageReader->GetOutput()   );

    // lecture première image (DICOM)
    std::cout << "Le fichier " << argv[1] << " est une serie de DICOM " << std::endl;

    typedef itk::GDCMImageIO ImageIOType; // une image DICOM
    typedef itk::GDCMSeriesFileNames InputNamesGeneratorType;

    // DICOM LOADING
    ImageIOType::Pointer gdcmIO = ImageIOType::New();

    // on crée le générateur de noms de fichier
    InputNamesGeneratorType::Pointer namesGenerator = InputNamesGeneratorType::New();
    // on indique au générateur de nom le dossier d'entrée
    namesGenerator->SetInputDirectory( argv[1] );
    // on récupère à présent la liste des fichiers à lire
    const FixedImageReaderType::FileNamesContainer & filenames =
        namesGenerator->GetInputFileNames();

    // on lui indique que ce sont des DICOM
    fixedImageReader->SetImageIO( gdcmIO );
    // on lui fournit la liste des fichiers à charger
    fixedImageReader->SetFileNames( filenames );
    try
    {// on lance le processus de lecture
        fixedImageReader->Update();
    }
    catch (itk::ExceptionObject &excp)
    {
        std::cerr << "Exception thrown while reading the series" << std::endl;
        std::cerr << excp << std::endl;
    }
        std::cout << "The input series in directory " << argv[1]
    << " has " << fixedImageReader->GetFileNames().size() << " files "
        << " of size " << fixedImageReader->GetOutput()->GetBufferedRegion().GetSize()
        << std::endl;



    // lecture deuxieme image (nrrd)
    typedef itk::NrrdImageIO nrrdType; // une image nrrd

    std::cout << "Le fichier  " <<  argv[2]  << " est un nrrd" << std::endl;

    //  nrrd LOADING
    nrrdType::Pointer nrrdIO = nrrdType::New();
    // on lui indique que ce sont des nrrd
    movingImageReader->SetImageIO( nrrdIO );
    // on lui fournit la liste des fichiers à charger
    movingImageReader->SetFileName(  argv[2]  );
    try
    {// on lance le processus de lecture
        movingImageReader->Update();
    }
    catch (itk::ExceptionObject &excp)
    {
        std::cerr << "Exception thrown while reading the series" << std::endl;
        std::cerr << excp << std::endl;
    }


    fixedImageReader->Update();
    registration->SetFixedImageRegion(
        fixedImageReader->GetOutput()->GetBufferedRegion() );


//////////////////////////// end of loading


when I use these loading I had a bad alloc error at calling “update()” methode of the registration...
when I try to register the nrrd on the other same nrrd, I’ve no problem : the soft do one iteration and stop with error = 0.

So the problem seem to come from the DICOM...


I join you my code,

Regards,

Guilhem



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