[Insight-users] ImageWriter does not write Orientation (Direction Cosines)

[Gordon Kindlmann]

hello,

One possible option, if you are using the latest CVS version of ITK, is 
to save the image in NRRD format (filename ends with ".nhdr" for 
separate header and data, or ".nrrd" for one file).  This saves the 
direction cosines (after scaling by the spacings) in the "space 
directions:" field of the NRRD header.  Right now this only handles 
scalar datasets; non-scalar datasets should be handled soon.

Gordon

On Jul 14, 2005, at 3:29 PM, Bryn Lloyd wrote:

> Hi Bill, anybody!
>
> I am working with images that have a variable orientation relative to
> another image. Which is why I decided to use the itkOrientedImage 
> class.
> My problem is when I try to write the image. Somehow the orientation is
> lost. I try to save the image using the meta-header format (.mhd).
>
> Is this a bug or am I doing something wrong?
>
> Thanks!
>
> Bryn
>
>
> --------------
>
> the header looks like this
>
> ObjectType = Image
> NDims = 3
> BinaryData = True
> BinaryDataByteOrderMSB = False
> TransformMatrix = 1 0 0 0 1 0 0 0 1
> Offset = 0 0 0
> CenterOfRotation = 0 0 0
> AnatomicalOrientation = RSP
> ElementSpacing = 0.859375 0.859375 5
> DimSize = 256 256 1
> ElementType = MET_DOUBLE
> ElementDataFile = I020.raw
>
>
> I would assume the TransformMatrix should contain the direction 
> cosines!?
>
> ------------------
>
>   const unsigned int Dimension = 3;
>   typedef   double  PixelType;
>
>   typedef itk::OrientedImage< PixelType,   Dimension >        
> ImageType;
>
>   typedef itk::ImageFileReader< ImageType >      ReaderType;
>   typedef itk::ImageFileWriter< ImageType >      WriterType;
>
>   ReaderType::Pointer reader = ReaderType::New();
>    reader->SetFileName( filenameGE5 );
>    reader->Update();
>
>  ImageType::Pointer image = reader->GetOutput();
>   this->ReadHeader( filenameGE5 );
>
>
> /* set direction cosines */
>
>  typedef itk::Matrix<double,3,3>  DirectionType;
>   DirectionType direction;
>   direction.Fill(0.0);
>   direction[0][0] = 1.0;   // 1 0 0
>   direction[1][2] = 1.0;   // 0 0 1
>   direction[2][1] = 1.0;   // 0 1 0
>
>
>   std::cout << "New Direction Cosines " << std::endl << direction <<
> std::endl;
>
>   image->SetDirection(direction);
>   std::cout << "Image Direction Cosines " << std::endl <<
> image->GetDirection() << std::endl;
>
>
>  WriterType::Pointer writer = WriterType::New();
>   writer->SetInput( image );
>   writer->SetFileName( filenameOut );
>   writer->Update();
>
>
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