[Insight-users] Visualizing a 2D deformation field - the answer

[Boettcher, Dr. Peter]

Thank you Karthikö. This is what I found out ...

 

Here are the answers I was looking for when I tried to visualize the deformation fields produced by the 2D deformable image registration examples

 

First one has to change the 2D-vector declaration to a 3D-vector declaration. 

 

const     unsigned int   Dimension = 2;

  typedef   float          VectorComponentType;

  typedef   itk::Vector< VectorComponentType, 3 >    VectorType;

  typedef   itk::Image< VectorType,  Dimension >   DeformationFieldType;

 

 

Then we have to fill the third component of the vector with zero (after computation of the deformation field).

 

try

    {

    deformer->UpdateLargestPossibleRegion();

    }

  catch( itk::ExceptionObject & excp )

    {

    std::cerr << "Exception thrown " << std::endl;

    std::cerr << excp << std::endl;

    return EXIT_FAILURE;

    }

 

  DeformationFieldType::Pointer deformationField = deformer->GetOutput();

 

Now we have to loop over all vectors within the deformation field and set the 3rd component to the desired value:

 

DeformationFieldType::PixelType VectorValue;

  DeformationFieldType::SizeType size = deformationField->GetLargestPossibleRegion().GetSize();

 

 

  DeformationFieldType::IndexType vectorIndex;

                

  for(int y = 0; y < size[1]; y++)

  for(int x = 0; x < size[0]; x++)

  {

                  vectorIndex[0] = x; // x position

                vectorIndex[1] = y; // y position

                

 

                  VectorValue = deformationField->GetPixel( vectorIndex);

                  VectorValue[2] = 0.0; // z component

                  deformationField->SetPixel(vectorIndex, VectorValue);

  }

 

Finally we save the deformation field using the meta-image file format (*.mdh). This file can be loaded with Paraview. 

 

typedef itk::ImageFileWriter<  DeformationFieldType  > FieldWriterType;

 

  FieldWriterType::Pointer Fieldwriter = FieldWriterType::New();

 

  Fieldwriter->SetInput (  deformationField );

 

  Fieldwriter->SetFileName( argv[5] );

 

  deformer->Print( std::cout );

 

  try

    {

    Fieldwriter->Update();

    }

  catch( itk::ExceptionObject & excp )

    {

    std::cerr << "Exception thrown by writer" << std::endl;

    std::cerr << excp << std::endl;

    return EXIT_FAILURE;

    }

  

Putting some glyphs onto the image makes the deformation visible.

 

Regards, Peter.

 
------------------------------------
Peter Böttcher, Dr med vet, DipECVS
European Veterinary Specialist in Surgery
Fachtierarzt für Kleintierchirurgie
Klinik für Kleintiere 
Universität Leipzig 
An den Tierkliniken 23 
D-04103 Leipzig (Germany)
Tel: +49-341-9738700 
Fax: +49-341-9738799
email: boettcher at kleintierklinik.uni-leipzig.de

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