[Insight-users] Default orientation of an Analyze image

[Luis Ibanez]

Hi Wenjia,

Yes,
you will be able to make your programs assume an
identity transform by default if you do:


   - Use itk::Image, and not itk::OrientedImage, and
   - Set ITK_IMAGE_BEHAVES_AS_ORIENTED_IMAGE = OFF


Note that this is just to recover the previous behavior of your
code, however, it will be very dangerous to use this configuration
for any clinical application in which you need to produce reliable
locations associated with the image data.


E.g. Don't do this if you are working in surgery planning or
       surgery guidance.


    Regards,


          Luis


---------------------------------------------------------------------------
On Sun, Aug 16, 2009 at 8:45 AM, wenjia <wenjia at robots.ox.ac.uk> wrote:

> Hi Luis,
>
> I have not noticed the orientation problem before and written a lot of
> programs assuming the default direction to be identity. These programs work
> fine in ITK 3.8. However, after upgrading to ITK 3.14, a lot of programs
> function abnormally because itkImageBase starts using orientation
> information in conversion between index and physical point and the Analyze
> image has a non-identity direction.
>
> Is it possible to disable the default orientation of AnalyzeImageIO by
> setting ITK_USE_ORIENTED_IMAGE_DIRECTION=OFF when installing ITK 3.14?
>
> Many thanks,
> Wenjia
>
> On 15 Aug 22:13, Luis Ibanez wrote:
> >
> > Hi Wenjia,
> >
> >
> > Yes,
> > this is the default orientation for Analyze images.
> >
> >
> >    Regards
> >
> >
> >        Luis
> >
> >
> > ---------------------------
> > On Sat, Aug 15, 2009 at 10:15 AM, wenjia <wenjia at robots.ox.ac.uk> wrote:
> >
> >     Dear all,
> >
> >     I have just found that when ITK reads an Analyze image with unknown
> >     orientation, it does not set the default image direction to identity.
> >     Instead, it sets the direction to
> >
> >      [1 0 0
> >      0 0 -1
> >      0 1 0].
> >
> >     I am wondering why it uses this direction as default. Is this
> direction
> >     defined in any Analyze format standard? Is it possible to change the
> >     default to an identity matrix since it is easy to cope with?
> >
> >     I have put a test Analyze file on the website:
> http://www.robots.ox.ac.uk/
> >     ~wenjia/data/
> >
> >     In addition, my ITK version is 3.14. I am using the following code
> for
> >     reading the direction,
> >
> >     #include "itkImage.h"
> >     #include "itkImageFileReader.h"
> >
> >     int main(int argc, char *argv[])
> >     {
> >      // Check the number of input arguments
> >      if(argc < 2){
> >        std::cout << "Read an image and show its direction" << std::endl;
> >        std::cout << "Usage: " << argv[0] << " image" << std::endl;
> >        return -1;
> >      }
> >
> >      const char *filename = argv[1];
> >
> >      // Read the image
> >      const unsigned int Dimension = 3;
> >      typedef double InternalPixelType;
> >      typedef itk::Image<InternalPixelType, Dimension> ImageType;
> >      typedef itk::ImageFileReader<ImageType> ImageReaderType;
> >
> >      ImageReaderType::Pointer reader = ImageReaderType::New();
> >      reader->SetFileName(filename);
> >      reader->Update();
> >      ImageType::Pointer image = reader->GetOutput();
> >
> >      // Show the direction
> >      std::cout << "The image direction is:" << std::endl;
> >      std::cout << image->GetDirection() << std::endl;
> >
> >      return 0;
> >     }
> >
> >
> >     Many thanks,
> >     Wenjia
> >     --
> >     Wenjia Bai
> >     D.Phil Student
> >     Wolfson Medical Vision Laboratory
> >     Department of Engineering
> >     University of Oxford
> >     _____________________________________
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