[Insight-users] Bspline 3D deformable registration

[Luis Ibanez]

Hi Shoosh,


You should then combine the code from the examples:


      DeformableRegistration15.cxx  (grid multi-res)

and

      MultiResImageRegistration1.cxx (image multi-res)
      MultiResImageRegistration2.cxx (image multi-res)

You will find them in the directory:


     Insight/Examples/Registration



   Regards,


       Luis


-----------------
shoosh moosh wrote:
> I need to make both multi-resolution on the images using a B-spline scaling functions for 3D deformable registration. So which code do I use, if not the demons method?
> 
> ----------------------------------------
> 
>>Date: Wed, 9 Jul 2008 17:39:13 -0400
>>From: luis.ibanez at kitware.com
>>To: babygirl_25 at hotmail.com
>>CC: insight-users at itk.org
>>Subject: Re: [Insight-users] Bspline 3D deformable registration
>>
>>Hi Shoosh,
>>
>>Do you want to make multi-resolution on the images ?
>>or do you want to make it on the BSpline grid ?
>>
>>Please let us know,
>>
>>In either case, you are starting from the wrong code.
>>The example that you posted is appropriate for
>>the Demons method but not for the BSplineDeformable
>>Transform.
>>
>>We can point you to the right framework once we know
>>if you want to do image multi-resolution or BSpline
>>multi-resolution.
>>
>>
>>
>>    Thanks
>>
>>
>>       Luis
>>
>>
>>--------------------
>>shoosh moosh wrote:
>>
>>>I'm trying to write code to register 3D images using a multiresolution first degree B-spline deformation model. I'm not sure where to include/spedify the B-spline part. The code is attached. 
>>>Thanks
>>>
>>>
>>>
>>>_________________________________________________________________
>>>Explore the seven wonders of the world
>>>http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE
>>>
>>>
>>>------------------------------------------------------------------------
>>>
>>>/*******************************************************************************
>>>Program:   Demons Registration using ITK
>>>Id:        $Id$
>>>Language:  C++
>>>*******************************************************************************/
>>>
>>>#include 
>>>using std::cerr;
>>>using std::clog;
>>>using std::endl;
>>>
>>>#include 
>>>
>>>#include "demons.h"
>>>
>>>// ITK IO includes
>>>#include "itkImage.h"
>>>#include "itkImageFileReader.h"
>>>#include "itkImageFileWriter.h"
>>>
>>>// ITK Registration includes
>>>#include "itkMultiResolutionPDEDeformableRegistration.h"
>>>#include "itkMultiResolutionImageRegistrationMethod.h"
>>>#include "itkMultiResolutionPyramidImageFilter.h"
>>>#include "itkDemonsRegistrationFilter.h" 
>>>#include "itkHistogramMatchingImageFilter.h" 
>>>#include "itkCastImageFilter.h" 
>>>#include "itkWarpImageFilter.h" 
>>>#include "itkLinearInterpolateImageFunction.h"
>>>
>>>int demons( std::vector< std::string> args )
>>>{
>>>  
>>>  // Verify the number of parameters in the command line
>>>  if( args.size() != 4 ){
>>>    clog << "usage: " << endl << args[0] << " target source deformation" << endl;
>>>    return EXIT_FAILURE;
>>>  }
>>>  
>>>  // define ITK short-hand types
>>>  const unsigned int Dimension = 3; 
>>>  typedef short PixelType;
>>>  typedef float InternalPixelType; 
>>>  typedef itk::Image< PixelType, Dimension> ImageType;
>>>  typedef itk::Image< InternalPixelType, Dimension> InternalImageType;
>>>  typedef itk::CastImageFilter< ImageType, InternalImageType> ImageCasterType;
>>>
>>>  // setup input file readers
>>>  typedef itk::ImageFileReader< ImageType>  ReaderType;
>>>  ReaderType::Pointer targetReader = ReaderType::New();
>>>  targetReader->SetFileName( args[1] );
>>>  ReaderType::Pointer sourceReader = ReaderType::New();
>>>  sourceReader->SetFileName( args[2] );
>>>
>>>  // cast target and source to float
>>>  ImageCasterType::Pointer targetImageCaster = ImageCasterType::New(); 
>>>  ImageCasterType::Pointer sourceImageCaster = ImageCasterType::New(); 
>>>  targetImageCaster->SetInput( targetReader->GetOutput() ); 
>>>  sourceImageCaster->SetInput( sourceReader->GetOutput() );
>>>  
>>>  // match the histograms between source and target
>>>  typedef itk::HistogramMatchingImageFilter< InternalImageType, InternalImageType> MatchingFilterType; 
>>>  MatchingFilterType::Pointer matcher = MatchingFilterType::New();
>>>  matcher->SetInput( sourceImageCaster->GetOutput() ); 
>>>  matcher->SetReferenceImage( targetImageCaster->GetOutput() );
>>>  matcher->SetNumberOfHistogramLevels( 1024 ); 
>>>  matcher->SetNumberOfMatchPoints( 7 );
>>>  matcher->ThresholdAtMeanIntensityOn();
>>>
>>>  // setup the deformation field and filter
>>>  typedef itk::Vector< float, Dimension> VectorPixelType; 
>>>  typedef itk::Image< VectorPixelType, Dimension> DeformationFieldType; 
>>>  typedef itk::DemonsRegistrationFilter< InternalImageType, 
>>>    InternalImageType, DeformationFieldType> RegistrationFilterType; 
>>>  RegistrationFilterType::Pointer filter = RegistrationFilterType::New();
>>>  filter->SetStandardDeviations( 1.0 );
>>>
>>>  // use multiresolution scheme
>>>  typedef itk::MultiResolutionPDEDeformableRegistration
>>>    < InternalImageType, InternalImageType, DeformationFieldType>
>>>    MultiResRegistrationFilterType;
>>>  MultiResRegistrationFilterType::Pointer 
>>>    multires = MultiResRegistrationFilterType::New();
>>>  multires->SetRegistrationFilter( filter );
>>>  multires->SetNumberOfLevels( 5 );
>>>  multires->SetFixedImage( targetImageCaster->GetOutput() );
>>>  multires->SetMovingImage( matcher->GetOutput() );
>>>  unsigned int nIterations[5] = { 25, 60, 95, 130, 165 };
>>>  multires->SetNumberOfIterations( nIterations );
>>>
>>>  // apply the registration filter
>>>  multires->Update();
>>>
>>>  // write the deformation field
>>>  typedef itk::ImageFileWriter< DeformationFieldType>  DeformationWriterType;
>>>  DeformationWriterType::Pointer defwriter = DeformationWriterType::New();
>>>  defwriter->SetFileName( args[3] );
>>>  defwriter->SetInput( multires->GetOutput() );
>>>  defwriter->Update();
>>>
>>>  return EXIT_SUCCESS;
>>>}
>>>
>>>
>>>
>>>
>>>
>>>------------------------------------------------------------------------
>>>
>>>_______________________________________________
>>>Insight-users mailing list
>>>Insight-users at itk.org
>>>http://www.itk.org/mailman/listinfo/insight-users
> 
> 
> _________________________________________________________________
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>