[Insight-users] The behavior of itk::OrientImageFilter

[kurt Zhao]

Hi guys,

I am confused by the behavior of itk::OrientImageFilter.

If I re-orient an image from RPI to LPI, the output image is visualized  as
same as the input file using Slicer3 as the visualization tool.

As I look closer, it appears to me that the filter do the thing below if the
input and output both are meta format:

1. change the orientation of the data stored ( however the
AnatomicalOrientation remains unchanged, is it a bug?).
2. change the TransformMatrix.

To change the orientation of image, a filter may have to do either 1 or 2,
preferably 1, because it means Anatomical Orientation. However, since the
filter does both 1 and 2, so the visualization seems unchanged.

Does somebody know if it is a bug or implemented in purpose?

The data can be downloaded at
http://www.duke.edu/~kurtzhao/RPI_original.zipand the code is
enclosed.

Any input is highly appreciated.

-Kurt

#include <metaCommand.h>
#include <itkImageFileWriter.h>
#include <itkImageFileReader.h>
#include <itkAnalyzeImageIO.h>
#include <itkNiftiImageIO.h>
#include <itkOrientImageFilter.h>
#include <itkSpatialOrientation.h>



int main(int argc, char **argv)
  {

  const unsigned int    Dimension  =  3;
  typedef short PixelType;

  typedef itk::Image< PixelType, Dimension >      ImageType;
  typedef itk::ImageFileReader< ImageType >       ReaderType;
  typedef itk::ImageIOBase                        ImageIOBaseType;

  ReaderType::Pointer reader = ReaderType::New();

  itk::AnalyzeImageIO::Pointer io = itk::AnalyzeImageIO::New();

  std::string inputFileName;
  inputFileName = "C:/data/formatConversion/RPI_original.mha";

  reader->SetFileName( inputFileName.c_str() );


  try
    {
    reader -> Update ( ) ;
    }
  catch( itk::ExceptionObject  &  err  )
    {
    std::cerr  << "ExceptionObject caught !"  << std::endl;
    std::cerr  << err <<  std::endl;
    return EXIT_FAILURE;
    }

  typedef itk::OrientImageFilter<ImageType,ImageType> OrienterType;
  OrienterType::Pointer orienter =  OrienterType::New();
  orienter->UseImageDirectionOn();

orienter->SetDesiredCoordinateOrientation(itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_LPI);

  orienter->SetInput( reader -> GetOutput ( ) );
  try
    {
    orienter->Update();
    }
  catch( itk::ExceptionObject  &  err  )
    {
    std::cerr  << "ExceptionObject caught !"  << std::endl;
    std::cerr  << err <<  std::endl;
    return EXIT_FAILURE;
    }

  typedef itk::ImageFileWriter < ImageType >      WriterType;

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

  itk::NiftiImageIO::Pointer niftIio = itk::NiftiImageIO::New();


  std::string outputFileName;

  outputFileName = "C:/data/formatConversion/LPI.mha";

  writer ->SetFileName( outputFileName.c_str() );

  writer -> SetInput ( orienter -> GetOutput ( ) ) ;

  writer -> UseCompressionOn ( ) ;

  try
    {
    writer -> Update ( ) ;
    }
  catch( itk::ExceptionObject  &  err  )
    {
    std::cerr  << "ExceptionObject caught !"  << std::endl;
    std::cerr  << err <<  std::endl;
    return EXIT_FAILURE;
    }

  return EXIT_SUCCESS;
  }
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