[ITK Community] OrientImageFilter ASL >> RAI wrong output?

[Matt McCormick]

Hi Pascal,

Welcome to the list and good first post!

The OrientImageFilter class is deprecated and not supported.

For more information, see [1] [2]

Thanks,
Matt

[1] http://www.slicer.org/slicerWiki/index.php/Slicer:VTK_ITK_Coordinates
[2] http://www.slicer.org/slicerWiki/index.php/Coordinate_systems


On Thu, Nov 28, 2013 at 10:32 AM, <p.wettmann at hispeed.ch> wrote:

> hi,
>
> I intend to read an arbitrary MRI file (e.g. RAI, ASL, ...) and convert it
> to RAI for further use. If i enter RAI, use orientImageFilter, output is
> correct RAI. However, if i enter ASL, output is not RAI. L/R axis is
> inverse. If I use LAI or a axis flip afterwards, the image seems to be
> correct, despite the fact that it is shifted.
>
> Here a code snipets:
>
>          typedef short PixelType;
>          const unsigned int VolumeDimension = 3;
>          typedef itk::Image< PixelType, VolumeDimension > ImageType;
>          typedef itk::ImageSeriesReader< ImageType >    ReaderType;
>
>          [...]
>
>          ReaderType::Pointer reader = ReaderType::New();
>
>          itk::OrientImageFilter<ImageType,ImageType>::Pointer orienter =
>          itk::OrientImageFilter<ImageType,ImageType>::New();
>
>          FlipImageFilterType::Pointer flipFilter
>             = FlipImageFilterType::New ();
>
>          [...]
>
>          reader->SetFileNames(fileNamesNew);
>          reader->Update();
>
>          rval = reader->GetOutput();
>
>          orienter->UseImageDirectionOn();
>
>  orienter->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAI);
>          //orienter->SetDesiredCoordinateOrientationToAxial();
>          orienter->SetInput(rval);
>          orienter->Update();
>
>          rval = orienter->GetOutput();
>
> //         itk::FixedArray<bool, 3> flipAxes;
> //         flipAxes[0] = true;
> //         flipAxes[1] = false;
> //         flipAxes[2] = false;
>
> //         flipFilter->SetInput(rval);
> //         flipFilter->SetFlipAxes(flipAxes);
>
>
> Am I missing something? This is my first e-mail to a mailing list, so
> please let me know any improvements of posting or style. :)
>
> Thanks for any help!
>
> Pascal
>
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