[Insight-users] modifying and writing dicom for 3D mri data set

[Matthias Schabel]

I am trying to output post-processed data that preserves most of the  
DICOM metadata from the input DICOM files, but with a few fields  
modified. Unfortunately, while the data itself is output and appears  
correct, I can't seem to get ITK to include anything but what I guess  
is the default GDCM DICOM stuff. A snippet of the code that I'm using  
(InputType is Image<float,3>, OutputType is Image<short,3>) is below.  
The dumpITKMetadata function just prints all the tag/value pairs to  
std::cout - in this case, the first call includes altered/added  
fields, so my changes are propagating correctly into the gdcmImageIO  
variable, but don't seem to make it the rest of the way through the  
pipeline. Any suggestions on what I may be doing wrong?

Regards,

Matthias



     // set up ITK DICOM image series writer
     typedef itk::ImageFileWriter<OutputType>	WriterType;

     WriterType::Pointer		writer = WriterType::New();

     static const std::string    output_name = "/Users/ 
matthiasschabel/Temporary/Ktrans.dcm";

     typedef itk::GDCMImageIO    ImageIOType;

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

     metadata_type&   dict = gdcmImageIO->GetMetaDataDictionary();

     copyITKMetadata(metadata(0),dict);

     // DICOM dictionary values
     static const std::string	modalityTag             = "0008|0060",
                                 seriesDescriptionTag    = "0008|103e",
                                 seriesNumberTag         = "0020|0011",
                                 windowCenterTag         = "0028|1050",
                                 windowWidthTag          = "0028|1051",
                                 rescaleInterceptTag     = "0028|1052",
                                 rescaleSlopeTag         = "0028|1053";

     itk::EncapsulateMetaData<std::string>(dict,modalityTag,"MR");
     itk::EncapsulateMetaData<std::string> 
(dict,seriesDescriptionTag,"Ktrans");
     itk::EncapsulateMetaData<std::string> 
(dict,windowCenterTag,"500.0");
     itk::EncapsulateMetaData<std::string> 
(dict,windowWidthTag,"1000.0");
     itk::EncapsulateMetaData<std::string> 
(dict,rescaleInterceptTag,"0.0");
     itk::EncapsulateMetaData<std::string> 
(dict,rescaleSlopeTag,"1000.0");

     dumpITKMetadata(dict,std::cout);
     dumpITKMetadata(metadata(0),std::cout);

     writer->SetInput(rescaler->GetOutput());
     writer->SetFileName(output_name.c_str());
     writer->SetImageIO(gdcmImageIO);

     try
     {
         writer->Update();
     }
     catch (itk::ExceptionObject& e)
     {
         std::cerr << "exception in file reader " << std::endl;
         std::cerr << e << std::endl;

         throw;
     }
}



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