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

[Luis Ibanez]

Hi Matthias,

The ITK pipeline does not propagate the MetaDataDictionaries.
The reason is that we cannot guarantee that the values in
the dictionaries are still valid after passing one image through
a filter. [e.g. a regions of interest filter should edit also
the meta data dictionary in order to reflect the new number of
pixels in the image].

As a result, it is upto you to pass the MetaDataDictionaries to
the ImageIO class used for writing.

You may want to look at the example:


      Insight/Examples/IO/
          ImageReadDicomSeriesWrite.cxx



Regards,



     Luis


------------------------
Matthias Schabel wrote:
> 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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