[vtkusers] DICOM images flipped ITK-VTK

[Darshan Pai]

When I used VTKDICOMReader directly on a axial slice data I get the right
answer in radiological convention. But using the same data in ITK gives me
an orientation mismatch error . But anyway you can just use vtkImageFlip or
just multiple the necessary rotation matrix to the direction cosines.

Regards
Darshan

On Sun, Feb 27, 2011 at 12:59 PM, Alexander Taghva <alextaghva at gmail.com>wrote:

> Hello,
> I am relatively new to ITK and VTK.  I am trying to read a DICOM series
> into ITK and display it with a simple viewer using VTK and KWWidgets.  When
> I load the series in ITK, the axial images are upside-down and the sagittal
> images are flipped left-right.    If I try doing it all in VTK
> (vtkDicomImageReader), the sagittal and coronal images are upside-down.  I
> have seen this issue touched on before, but I couldn't find a good solution.
> Key parts of my code are below.  I am using ITK 3.20 and VTK 5.6.1 on Ubuntu
> Linux 10.10.
>
> ******************************
>
> **********************************************************************************************************************
>
>     // initialize ITK DICOM reader
>     typedef unsigned short PixelType;
>     const unsigned int Dimension = 3;
>
>     typedef itk::Image<PixelType, Dimension> ImageType;
>     typedef itk::ImageSeriesReader< ImageType > ReaderType;
>     ReaderType::Pointer reader = ReaderType::New();
>
>
>
>     typedef itk::GDCMImageIO ImageIOType;
>     ImageIOType::Pointer dicomIO = ImageIOType::New();
>     reader->SetImageIO( dicomIO );
>
>     typedef itk::GDCMSeriesFileNames NamesGeneratorType;
>     NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
>     nameGenerator->SetUseSeriesDetails( true );
>     nameGenerator->SetInputDirectory( "DICOM" );
>     const ReaderType::FileNamesContainer & filenames =
> nameGenerator->GetInputFileNames();
>
>     reader->SetFileNames( filenames );
>
>     try
>     {
>     reader->Update();
>     }
>     catch (itk::ExceptionObject &ex)
>     {
>     std::cout << ex << std::endl;
>     return EXIT_FAILURE;
>     }
>
>    // now connect to VTK
>     typedef itk::ImageToVTKImageFilter< ImageType> ConnectorType;
>     ConnectorType::Pointer connector = ConnectorType::New();
>     connector->SetInput( reader->GetOutput() );
>
>      vtkImageViewer2     *viewer = vtkImageViewer2::New();
>
>     //Create a VTK image viewer, set it up so that it uses our render
> widget, set its input to the output of the reader, reset the camera to
> center the whole slice
>     viewer->SetRenderWindow(rw->GetRenderWindow());
>     viewer->SetRenderer(rw->GetRenderer());
>     viewer->SetInput(connector->GetOutput());
>     viewer->SetupInteractor(rw->GetRenderWindow()->GetInteractor());
>     rw->ResetCamera();
>
>     //Retrieve the corner annotation object from the render widget, point
> it to the viewer actor and window/level filter, and let it display both
> slice and window/level in different corners using tags
>     vtkCornerAnnotation *ca = rw->GetCornerAnnotation();
>     ca->SetImageActor(viewer->GetImageActor());
>     ca->SetWindowLevel(viewer->GetWindowLevel());
>     ca->SetText(2,"<slice>");
>     ca->SetText(3,"<window>\n<level>");
>
>     //Create a scale object in our window, set its range to match the
> number of slices, set its callback to use its value to set the slice in the
> viewer, pack the scale in our window below the render widget
>     vtkKWScale *slice_scale = vtkKWScale::New();
>     slice_scale->SetParent(win->GetViewFrame());
>     slice_scale->Create();
>     slice_scale->SetRange(viewer->GetSliceMin(),viewer->GetSliceMax());
>     slice_scale->SetCommand(viewer, "SetSlice");
>     app->Script("pack %s -side top -expand n -fill x",
> slice_scale->GetWidgetName());
>
>
>
> ******************************************************************************************************************************************************
>
> Alex
>
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