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

[Karthik Krishnan]

Bryn,

Just committed a fix in CVS. Let me know if it works ok.

Thanks
regards
Karthik

Gordon Kindlmann wrote:

> 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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>
>
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