Wrong “Spacing” and “Origin” of a DICOM series in ITK

Question

When I read a dicom series with a series reader in itk,

I always find the origin=[0 0 0] and spacing=[1 1 1], the same for all different datasets.

* main function:-

    void main()
    {
        reader = READ_DCM(Input_DCM_Paths[0]);
        cout<<" Reading Done!!"<<endl;
        cout<< " Origin: " <<reader->GetOutput()->GetOrigin()<< endl;
        cout<< " Spacing: " <<reader->GetOutput()->GetSpacing()<< endl;
    }

* reader function:-

    SeriesReaderType::Pointer READ_DCM (std::string InputFolder)
    {
      SeriesReaderType::Pointer seriesReader = SeriesReaderType::New();
      seriesReader->SetImageIO(itk::GDCMImageIO::New());
      itk::GDCMSeriesFileNames::Pointer nameGenerator = itk::GDCMSeriesFileNames::New();
      nameGenerator->SetUseSeriesDetails(true);
      nameGenerator->SetDirectory(InputFolder);
      std::string seriesID = nameGenerator->GetSeriesUIDs().begin()->c_str();
      seriesReader->SetFileNames(nameGenerator->GetFileNames(seriesID));
      seriesReader->Update();
      return seriesReader;
    }

* 1st series output in itk:-

enter image description here

* 1st series output in matlab:-

enter image description here

What's worng with my 'series reader' code ?? I followed the "reading part" in this example.

you forgot to specify which DICOM Instance you are reading. The attribute Pixel Spacing may belong to an extended SOP Class UID. — malat
sorry, I don't know about that? is it the dicom tag (0008,0016) = << SOP Class UID = '1.2.840.10008.5.1.4.1.1.7' >> ? or << (0008,0016) = SOP Instance UID = '1.2.276.0.28.3.2418833.1095761920.42.5040.2012041216272628700 ' >> ? — Sonnenschein
Just use gdcminfo next time. You are dealing with a Secondary Capture Image Storage instance. This instance does not define Pixel Spacing attribute therefore it is correct to assume (1,1) for pixel spacing (same goes for IPP). — malat

kshahim kshahim · Accepted Answer · 2015-04-16T09:22:28

I have the same problem, i use following similar codes to read dicom series, but the output of spacing between slices is sometimes correct BUT not always:

// 1) Read the input series

typedef itk::GDCMImageIO ImageIOType;
typedef itk::GDCMSeriesFileNames InputNamesGeneratorType;

ImageIOType::Pointer gdcmIO = ImageIOType::New();
InputNamesGeneratorType::Pointer inputNames=InputNamesGeneratorType::New();
inputNames->SetInputDirectory( dirPath );
inputNames->AddSeriesRestriction("0020|0013");

// then i select a serie identifier and pass it to the reader

typedef itk::ImageSeriesReader< CTImageType > ReaderType;
ReaderType::Pointer reader = ReaderType::New(); ;
reader->SetImageIO( gdcmIO );
reader->SetFileNames(  inputNames->GetFileNames(  seriesIdentifier.c_str() ));
reader->UpdateOutputInformation();

--->>> reader->GetOutput()->GetSpacing()[2] is not correct always!!!