[ITK-users] Symmetric Demons registration
Matt McCormick
matt.mccormick at kitware.com
Sun Sep 27 19:16:19 EDT 2015
During the pipeline updates, these may be reset. But, the Size's have
to be the same, too.
One of the images may have to be resampled with the ResampleImageFilter.
HTH,
Matt
On Sun, Sep 27, 2015 at 6:56 PM, stefano serviddio
<s.serviddio at gmail.com> wrote:
> Hi Matt,
> I have added this code:
> "
> Image2->SetOrigin(Image1->GetOrigin());
> Image2->SetSpacing(Image1->GetSpacing());
> Image2->SetDirection(Image1->GetDirection());"
> but the problem remain the same.
>
> 2015-09-28 0:10 GMT+02:00 Matt McCormick <matt.mccormick at kitware.com>:
>>
>> Hi Stefano,
>>
>> The means that the images must occupy the same spatial domain. The
>> domain is determined by the Origin, Spacing, Direction, and
>> ImageRegion Size of the Image's. This is explained more in the ITK
>> Software Guide:
>>
>>
>> http://itk.org/ITKSoftwareGuide/html/Book1/ITKSoftwareGuide-Book1ch4.html#x40-430004
>>
>> HTH,
>> Matt
>>
>> On Sun, Sep 27, 2015 at 5:56 PM, stefano serviddio
>> <s.serviddio at gmail.com> wrote:
>> > HI,
>> > I have always the same issue with my demons registration code, "Inputs
>> > do
>> > not occupy the same physical space".
>> > the fixed image is a Ct 512x512 dicom and the second one is a Pet
>> > 256x256
>> > dicom.
>> > May you help me to find out what is the problem?
>> > Thank you very much.
>> >
>> >
>> >
>> > #include "itkImageFileReader.h"
>> > #include "itkImageFileWriter.h"
>> > #include <time.h>
>> > #include <fstream>
>> > #include "itkSymmetricForcesDemonsRegistrationFilter.h"
>> > #include "itkHistogramMatchingImageFilter.h"
>> > #include "itkCastImageFilter.h"
>> > #include "itkWarpImageFilter.h"
>> >
>> > #include "itkGDCMImageIO.h"
>> > #include "itkShrinkImageFilter.h"
>> >
>> >
>> >
>> > class CommandIterationUpdate : public itk::Command
>> > {
>> > public:
>> > typedef CommandIterationUpdate Self;
>> > typedef itk::Command Superclass;
>> > typedef itk::SmartPointer<CommandIterationUpdate> Pointer;
>> > itkNewMacro( CommandIterationUpdate );
>> > protected:
>> > CommandIterationUpdate() {};
>> >
>> > typedef itk::Image< double, 2 > InternalImageType;
>> > typedef itk::Vector< double, 2 > VectorPixelType;
>> > typedef itk::Image< VectorPixelType, 2 > DisplacementFieldType;
>> >
>> > typedef itk::SymmetricForcesDemonsRegistrationFilter<
>> > InternalImageType,
>> > InternalImageType,
>> > DisplacementFieldType>
>> > RegistrationFilterType;
>> >
>> > public:
>> >
>> > void Execute(itk::Object *caller, const itk::EventObject & event)
>> > ITK_OVERRIDE
>> > {
>> > Execute( (const itk::Object *)caller, event);
>> > }
>> >
>> > void Execute(const itk::Object * object, const itk::EventObject &
>> > event)
>> > ITK_OVERRIDE
>> > {
>> > const RegistrationFilterType * filter = static_cast< const
>> > RegistrationFilterType * >( object );
>> > if( !(itk::IterationEvent().CheckEvent( &event )) )
>> > {
>> > return;
>> > }
>> > std::cout << filter->GetMetric() << std::endl;
>> > }
>> > };
>> >
>> >
>> > int main( int argc, char *argv[] )
>> > {
>> > /*if( argc < 4 )
>> > {
>> > std::cerr << "Missing Parameters " << std::endl;
>> > std::cerr << "Usage: " << argv[0];
>> > std::cerr << " fixedImageFile movingImageFile ";
>> > std::cerr << " outputImageFile " << std::endl;
>> > std::cerr << " [outputDisplacementFieldFile] " << std::endl;
>> > return EXIT_FAILURE;
>> > }*/
>> >
>> >
>> > time_t now = time(0);
>> > struct tm tstruct;
>> > char buf[80];
>> > tstruct = *localtime(&now);
>> > strftime(buf, sizeof(buf), "%Y-%m-%d %X", &tstruct);
>> >
>> > std::ofstream resultfile;
>> > char Risultati[] = "D:/Images/MetricResultDeformaion.txt";
>> >
>> > resultfile.open(Risultati, std::ios::app);
>> > if (resultfile.is_open())
>> > {
>> > std::cout << "File Open exists\n";
>> >
>> > }
>> >
>> > resultfile<<"Data :"<<buf<<std::endl;
>> >
>> >
>> >
>> >
>> > const unsigned int Dimension = 2;
>> > typedef unsigned int PixelType;
>> >
>> > typedef itk::Image< PixelType, Dimension > FixedImageType;
>> > typedef itk::Image< PixelType, Dimension > MovingImageType;
>> >
>> >
>> >
>> >
>> > typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
>> > typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
>> > typedef itk::GDCMImageIO GDCMType;
>> > GDCMType::Pointer gdcm=GDCMType::New();
>> > FixedImageReaderType::Pointer fixedImageReader =
>> > FixedImageReaderType::New();
>> > MovingImageReaderType::Pointer movingImageReader =
>> > MovingImageReaderType::New();
>> >
>> > char* filename1="D:/Images/def00001.dcm";
>> > char* filename2="D:/Images/def100001.dcm";
>> > fixedImageReader->SetFileName( filename1 );
>> > movingImageReader->SetFileName( filename2 );
>> > fixedImageReader->SetImageIO(gdcm);
>> > movingImageReader->SetImageIO(gdcm);
>> >
>> > resultfile<<filename1<<std::endl;
>> > resultfile<<filename2<<std::endl;
>> >
>> > fixedImageReader->Update();
>> > movingImageReader->Update();
>> >
>> > typedef itk::ShrinkImageFilter<MovingImageType,MovingImageType>
>> > ShrinkFilterType;
>> > ShrinkFilterType::Pointer shrinkFilter = ShrinkFilterType::New();
>> > shrinkFilter->SetShrinkFactors( 2 );
>> > shrinkFilter->SetInput( fixedImageReader->GetOutput() );
>> > shrinkFilter->Update();
>> >
>> > typedef double InternalPixelType;
>> > typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
>> > typedef itk::CastImageFilter< FixedImageType, InternalImageType >
>> > FixedImageCasterType;
>> > typedef itk::CastImageFilter< MovingImageType, InternalImageType >
>> > MovingImageCasterType;
>> >
>> > FixedImageCasterType::Pointer fixedImageCaster =
>> > FixedImageCasterType::New();
>> > MovingImageCasterType::Pointer movingImageCaster=
>> > MovingImageCasterType::New();
>> >
>> > fixedImageCaster->SetInput( shrinkFilter->GetOutput() );
>> > movingImageCaster->SetInput( fixedImageReader->GetOutput() );
>> >
>> > fixedImageCaster->Update();
>> > movingImageCaster->Update();
>> >
>> > typedef itk::HistogramMatchingImageFilter<
>> > InternalImageType,InternalImageType > MatchingFilterType;
>> > MatchingFilterType::Pointer matcher = MatchingFilterType::New();
>> >
>> > matcher->SetInput( movingImageCaster->GetOutput() );
>> >
>> > matcher->SetReferenceImage( fixedImageCaster->GetOutput() );
>> >
>> >
>> > matcher->SetNumberOfHistogramLevels(1024);
>> > matcher->SetNumberOfMatchPoints(7 );
>> >
>> >
>> > matcher->ThresholdAtMeanIntensityOn();
>> >
>> > typedef itk::Vector< double, Dimension > VectorPixelType;
>> > typedef itk::Image< VectorPixelType, Dimension >
>> > DisplacementFieldType;
>> >
>> >
>> >
>> > typedef
>> >
>> > itk::SymmetricForcesDemonsRegistrationFilter<InternalImageType,InternalImageType,
>> > DisplacementFieldType> RegistrationFilterType;
>> > RegistrationFilterType::Pointer filter =
>> > RegistrationFilterType::New();
>> >
>> >
>> >
>> > CommandIterationUpdate::Pointer observer =
>> > CommandIterationUpdate::New();
>> > filter->AddObserver( itk::IterationEvent(), observer );
>> >
>> >
>> >
>> > filter->SetFixedImage( fixedImageCaster->GetOutput() );
>> > filter->SetMovingImage( matcher->GetOutput());
>> > filter->SetNumberOfIterations( 256 );
>> > filter->SetStandardDeviations( 4.0 );
>> >
>> >
>> >
>> > try
>> > {
>> > filter->Update();
>> > }
>> > catch( itk::ExceptionObject & err )
>> > {
>> > std::cerr << "ExceptionObject caught !" << std::endl;
>> > std::cerr << err << std::endl;
>> > return EXIT_FAILURE;
>> > }
>> >
>> >
>> > typedef itk::WarpImageFilter< MovingImageType, MovingImageType,
>> > DisplacementFieldType > WarperType;
>> > typedef itk::LinearInterpolateImageFunction< MovingImageType, double
>> > >
>> > InterpolatorType;
>> > WarperType::Pointer warper = WarperType::New();
>> > InterpolatorType::Pointer interpolator = InterpolatorType::New();
>> > FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
>> >
>> > warper->SetInput( movingImageReader->GetOutput() );
>> > warper->SetInterpolator( interpolator );
>> > warper->SetOutputSpacing( fixedImage->GetSpacing() );
>> > warper->SetOutputOrigin( fixedImage->GetOrigin() );
>> > warper->SetOutputDirection( fixedImage->GetDirection() );
>> >
>> > warper->SetDisplacementField( filter->GetOutput() );
>> >
>> > warper->Update();
>> >
>> >
>> >
>> > typedef unsigned char OutputPixelType;
>> > typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
>> > typedef itk::CastImageFilter<
>> > MovingImageType,
>> > OutputImageType > CastFilterType;
>> > typedef itk::ImageFileWriter< OutputImageType > WriterType;
>> >
>> > WriterType::Pointer writer = WriterType::New();
>> > CastFilterType::Pointer caster = CastFilterType::New();
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > std::cout<<"last metric value "<<filter->GetMetric()<<std::endl;
>> > resultfile<<"last metric value "<<filter->GetMetric()<<std::endl;
>> > writer->SetFileName( "D:/Images/new.dcm" );
>> >
>> > caster->SetInput( warper->GetOutput() );
>> > caster->Update();
>> > writer->SetInput( caster->GetOutput() );
>> > writer->SetImageIO(gdcm);
>> > writer->Update();
>> >
>> >
>> > return EXIT_SUCCESS;
>> > }
>> >
>> >
>> >
>> >
>> >
>> >
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