[Insight-users] Conversion from DICOM to NIFTI

[Daniele Domenichelli]

Hello,

I'm trying to convert dicom images into nifti images, but i found some
strange behaviors

1) Nifti header is too big: it should be 348 bytes, but it is 352
bytes instead. This is the same for ".hdr" and for ".nii" files.
This does not happen if I use AnalyzeImageIO instead of NiftiImageIO
2) Orientation of the output nifti file is wrong. In the header For
example I have a coronal acquisition and converting it in nifti in the
header is saved as "LPS" but image is written as "LIP".

This is the code I'm using.

Am I doing something wrong?

I'm using the last ITK version...

Thanks,
Daniele Domenichelli


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#include <itkDICOMImageIO2Factory.h>
#include <itkDICOMImageIO2.h>
#include <itkImageSeriesReader.h>
#include <itkDICOMSeriesFileNames.h>

#include <itkImageFileWriter.h>
#include <itkImageFileReader.h>
#include <itkImageIOFactory.h>
#include <itkNiftiImageIOFactory.h>
#include <itkNiftiImageIO.h>

#include <string>


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

    if (argc!=4)
    {
        std::cout << "Usage: " << argv[0] << " <dicom_dir>
<output_filename> <reverse_order>" << std::endl;
        return EXIT_FAILURE;
    }


    std::string m_DirectoryName = argv[1];
    std::string m_OutputFileName = argv[2];
    unsigned char m_ReverseOrder = atoi(argv[2]);

    typedef itk::Image<unsigned short,3> DICOMImageType;
    typedef itk::ImageSeriesReader<DICOMImageType> ReaderType;

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

    // Get the DICOM filenames from the directory
    itk::DICOMSeriesFileNames::Pointer names = itk::DICOMSeriesFileNames::New();
    names->SetDirectory(m_DirectoryName.c_str());

    ReaderType::Pointer reader = ReaderType::New();
    reader->SetFileNames(names->GetFileNames());
    reader->SetImageIO(io);

    if (m_ReverseOrder)
    {
        reader->ReverseOrderOn();
    }


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

    typedef itk::NiftiImageIO OutImageIO;
    OutImageIO::Pointer outImageIO = OutImageIO::New();
    writer->SetImageIO(outImageIO);

    writer->SetFileName(m_OutputFileName.c_str());
    writer->SetInput( reader->GetOutput() );


    try
    {
        reader->Update();
        writer->Update();
        writer->Write();
    }
    catch ( itk::ExceptionObject & ex )
    {
        std::string message;
        message = ex.GetLocation();
        message += "\n";
        message += ex.GetDescription();
        std::cerr << message << std::endl;
        return EXIT_FAILURE;
    }
    return EXIT_SUCCESS;
}


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