Here we demonstrate how to use HAMMER registration filter in ITK for deformable registration of the two T1 MR brains. The source code can be found in source code package (/src/test/HammerRegistrationTest.cxx).

First of all, we need to initialize the HAMMER registration filter instance as follows:
typedef itk::HammerDeformableRegistrationImageFilter RegistrationFilterType;
RegistrationFilterType::Pointer hammer = RegistrationFilterType::New();

Then, the fixed and the moving images should be specified:
hammer->SetFixedImage( fImg0 );
hammer->SetMovingImage( mImg0 );

Next, we need to specify the parameters used in HAMMER:
hammer->SetIterations( iterations[0], iterations[1], iterations[2] );
hammer->SetDeformRate(0.05);
hammer->SetPointMatchingThreshold(0.8);
hammer->SetSubvolumeSimilarityThreshold(0.6);
hammer->SetSearchRadius(12);

Finally, by calling hammer->Update(), it will return a dense deformation field that points from the fixed image to the moving image. The following lines of code are used to warp the subject image with itk::WarpImageFilter:
typedef itk::WarpImageFilter  WarperType;
typedef itk::NearestNeighborInterpolateImageFunction  InterpolatorType;
WarperType::Pointer warper = WarperType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
warper->SetInput( mImg0 );
warper->SetInterpolator( interpolator );
warper->SetOutputDirection( fImg0->GetDirection() );
warper->SetOutputSpacing( fImg0->GetSpacing() );
warper->SetOutputOrigin( fImg0->GetOrigin() );
warper->SetDeformationField(hammer->GetOutput());
WriterType::Pointer writer =  WriterType::New();
writer->SetFileName( resampledFilename.c_str() );
writer->SetInput( warper->GetOutput() );
writer->Update();