csci 6971: image registration lecture 10: registration components february 13, 2004 prof. chuck...

CSci 6971: Image Registration Lecture 10: Registration Components

February 13, 2004

CSci 6971: Image Registration Lecture 10: Registration Components

February 13, 2004

Prof. Chuck Stewart, RPIDr. Luis Ibanez, KitwareProf. Chuck Stewart, RPIDr. Luis Ibanez, Kitware

Image Registration Lecture 10 2

Registration ComponentsRegistration Components

Basic Registration Framework


Image Registration FrameworkImage Registration Framework

FixedImage

MovingImage

Metric

Transform

Interpolator Optimizer

Parameters


Image RegistrationImage Registration

#include ”itkImageRegistrationMethod.h”#include ”itkTranslationTransform.h”#include ”itkMeanSquaresImageToImageMetric.h”#include ”itkLinearInterpolateImageFunction.h”#include ”itkRegularStepGradientDescentOptimizer.h”#include ”itkImage.h”#include ”itkImageFileReader.h”#include ”itkImageFileWriter.h”#include ”itkResampleImageFilter.h”



const unsigned int Dimension = 2;

typedef unsigned char PixelType;

typedef itk::Image< PixelType , Dimension > FixedImageType;

typedef itk::Image< PixelType , Dimension > MovingImageType;

typedef itk::TranslationTransform< double, Dimension > TransformType;

typedef itk::RegularStepGradientDescentOptimizer OptimizerType;

typedef itk::LinearInterpolateImageFunction< MovingImageType , double > InterpolatorType;

typedef itk::MeanSquaresImageToImageMetric< FixedImageType , MovingImageType > MetricType;

typedef itk::ImageRegistrationMethod< FixedImageType , MovingImageType > RegistrationType;



TransformType::Pointer transform = TransformType::New();

OptimizerType::Pointer optimizer = OptimizerType::New();

InterpolatorType::Pointer interpolator = InterpolatorType::New();

MetricType::Pointer metric = MetricType::New();

RegistrationType::Pointer registrator = RegistrationType::New();

registrator->SetTransform( transform );

registrator->SetOptimizer( optimizer );

registrator->SetInterpolator( interpolator );

registrator->SetMetric( metric );

registrator->SetFixedImage( fixedImageReader->GetOutput() );

registrator->SetMovingImage( movingImageReader->GetOutput() );



registrator->SetFixedImageRegion( fixedImageReader->GetOutput()->GetBufferedRegion() );

typedef RegistrationType::ParametersType ParametersType;

transform->SetIdentity();

registrator->SetInitialTransformParameters( transform->GetParameters() );

optimizer->SetMaximumStepLength( 4.00 );

optimizer->SetMinimumStepLength( 0.01 );

optimizer->SetNumberOfIterations( 100 );

optimizer->MaximizeOff();



try { registrator->StartRegistration (); }catch( itk::ExceptionObject & excp ) { std::cerr << “Error in registration” << std::endl; std::cerr << excp << std::endl; }

transform->SetParameters( registrator->GetLastTransformParameters() );



FixedImage

MovingImage

Metric

Transform

Interpolator

Optimizer

Parameters

Resampler

MovingRegistered



typedef itk::ResampleImageFilter< FixedImageType , MovingImageType > ResamplerType;

ResamplerType ::Pointer resampler = ResamplerType::New();

resampler->SetTransform ( transform );

resampler->SetInput( movingImageReader->GetOutput() );

FixedImageType ::Pointer fixedImage = fixedImageReader->GetOutput();

resampler->SetOrigin( fixedImage->GetOrigin() );

resampler->SetSpacing( fixedImage->GetSpacing() );

resampler->SetSize( fixedImage->GetLargestPossibleRegion()->GetSize() );

resampler->Update();



Tracking the

Registration Process


Observing RegistrationObserving Registration

#include ”itkCommand.h”

class CommandIteration : public itk::Command {

public: typedef CommandIteration Self;

typedef itk::Command SuperClass;

typedef itk::SmartPointer< Self > Pointer;

itkNewMacro( Self );

protected:

CommandIteration() {};

public:

typedef itk::RegularStepGradientDescentOptimizer OptimizerType;

typedef const OptimizerType * OptimizerPointer;



void Execute( itk::Object * caller, const itk::EventObject & event ) { this-> Execute( (const itk::Object *) caller, event ); }

void Execute( const itk::Object * caller, const itk::EventObject & event ) { OptimizerPointer optimizer = dynamic_cast< OptimizerPointer >( caller );

if( typeid( event ) == typeid( itk::IterationEvent ) ) { std::cout << optimizer->GetCurrentIteration() << “ : “; std::cout << optimizer->GetValue() << “ : “; std::cout << optimizer->GetCurrentPosition() << std::endl; } }



CommandIteration::Pointer observer = CommandIteration::New();

optimizer->AddObserver( itk::IterationEvent(), observer )



Registration dirty little secretsRegistration dirty little secrets

Rotation – Translation

Parameter Scaling


Registration dirty little secretsRegistration dirty little secrets

Fixed Image Moving Image Registered Moving Image


Gradient Descent OptimizerGradient Descent Optimizer

f( x , y )

S = L ∙ G( x , y )f( x , y )

∆

G( x , y ) =



f( x , y )

S = L ∙ G( x , y )f( x , y )

∆

G( x , y ) =



f( x , y )

S = L ∙ G( x , y )f( x , y )

∆

G( x , y ) =

How about a factor 1:100 ?


Radians & MillimetersRadians & Millimeters

0.0 rad x

y

1.57 rad

180 mm


Radians & MillimetersRadians & Millimeters

0.0 rad x

y

1.57 rad

180 mm

1.57 rad

180 mm

1:100


Other TransformsOther Transforms

Centered Rigid 2D


Rotation around the Center Rotation around the Center

y

Fixed

Transform

10o

x

y

Moving

x


Centered Rigid 2D TransformCentered Rigid 2D Transform

#include ”itkImageRegistrationMethod.h”#include ”itkCenteredRigid2DTransform.h”#include ”itkMeanSquaresImageToImageMetric.h”#include ”itkLinearInterpolateImageFunction.h”#include ”itkRegularStepGradientDescentOptimizer.h”#include ”itkCenteredTransformInitializer.h”#include ”itkImage.h”#include ”itkImageFileReader.h”#include ”itkImageFileWriter.h”#include ”itkResampleImageFilter.h”



const unsigned int Dimension = 2;typedef unsigned char PixelType;

typedef itk::Image< PixelType , Dimension > FixedImageType;typedef itk::Image< PixelType , Dimension > MovingImageType;

typedef itk::CenteredRigid2DTransform< double > TransformType;

typedef itk:: CenteredTransformInitializer< TransformType , FixedImageType , MovingImageType > InitializerType;




InitializerType::Pointer initializer = InitializerType::New();












Centered Transform InitializerCentered Transform Initializer

y

Fixed Image

Transform

x

y

Moving Image

x

Geometry On



y

Fixed Image

Transform

x

y

Moving Image

x

Moments On

Xm = Sum( x ∙ I ) / Sum( I )Ym = Sum( y ∙ I ) / Sum( I )




initializer->SetTransform ( transform );

initializer->SetFixedImage( fixedImageReader->GetOutput() );

initializer->SetMovingImage( movingImageReader->GetOutput() );

initializer->MomentsOn();

initializer->InitializeTransform();




y

x

Array of

Parameters

P[ 0 ]

P[ 1 ]

P[ 2 ]

P[ 3 ]

P[ 4 ]

Angle

Center X

Center Y

Trans X

Trans Y



typedef OptimizerType::ScaleType OptimizerScalesType;

OptimizerScalesType optimizerScales( optimizer->SetMaximumStepLength() );

const double translationScale = 1.0 / 1000.0 ;

optimizerScales[ 0 ] = 1.0;

optimizerScales[ 1 ] = translationScale;




optimizer->SetScales( optimizerScales );



FixedImage

MovingImage

Metric

Transform

Interpolator

Optimizer

Parameters

Resampler

MovingRegistered


Other TransformsOther Transforms

Affine 2D


Affine TransformsAffine Transforms

M11 M12 T1

M21 M22 T2


Affine TransformsAffine Transforms

Qx M11 M12 Px T1

Qy M21 M22 Py T2

= ∙ +


Affine Transform – ShearingAffine Transform – Shearing

Qx 1 a Px T1

Qy 0 1 Py T2

= ∙ +


Shearing ComponentShearing Component

y

x

a

1

(x,y)

( x + ay , y )



y’

x

y

x’


Affine Transform – ShearingAffine Transform – Shearing

Qx 1 0 Px T1

Qy b 1 Py T2

= ∙ +



y

x

b

1(x,y)

( x , y + bx )



y

x

y’

x’


Coefficients - Orders of MagnitudeCoefficients - Orders of Magnitude

Qx 1.0 0.1 Px 100

Qy 0.1 1.0 Py 100

= ∙ +


Affine Transform – RotationAffine Transform – Rotation

Qx cosθ -sinθ Px T1

Qy sinθ cosθ Py T2

= ∙ +


Affine Transform – ScalingAffine Transform – Scaling

Qx Sx 0 Px T1

Qy 0 Sy Py T2

= ∙ +


Affine Transform - ParameterizationAffine Transform - Parameterization

M11 M12 T1

M21 M22 T2

[ P0 P1 P2 P3 P4 P5 ]


Parameter ScalingParameter Scaling

M11 M12 T1

M21 M22 T2

[ P0 P1 P2 P3 P4 P5 ]

range [ 1.0 0.1 0.1 1.0 100 100 ]

scale [ 1.0 10 10 1.0 0.01 0.01 ]


Centered Affine TransformCentered Affine Transform

#include ”itkImageRegistrationMethod.h”#include ”itkCenteredAffineTransform.h”#include ”itkMeanSquaresImageToImageMetric.h”#include ”itkLinearInterpolateImageFunction.h”#include ”itkRegularStepGradientDescentOptimizer.h”#include ”itkCenteredTransformInitializer.h”#include ”itkImage.h”#include ”itkImageFileReader.h”#include ”itkImageFileWriter.h”#include ”itkResampleImageFilter.h”



const unsigned int Dimension = 2;typedef unsigned char PixelType;

typedef itk::Image< PixelType , Dimension > FixedImageType;typedef itk::Image< PixelType , Dimension > MovingImageType;

typedef itk::CenteredAffineTransform< double > TransformType;

typedef itk:: CenteredTransformInitializer< TransformType , FixedImageType , MovingImageType > InitializerType;




InitializerType::Pointer initializer = InitializerType::New();













y

Fixed Image

Transform

x

y

Moving Image

x

Geometry On



y

Fixed Image

Transform

x

y

Moving Image

x

Moments On

Xm = Sum( x ∙ I ) / Sum( I )Ym = Sum( y ∙ I ) / Sum( I )




initializer->SetTransform ( transform );

initializer->SetFixedImage( fixedImageReader->GetOutput() );

initializer->SetMovingImage( movingImageReader->GetOutput() );

initializer->MomentsOn();

initializer->InitializeTransform();



Affine Transform - ParameterizationAffine Transform - Parameterization

M11 M12 T1

M21 M22 T2

P[0] P[1] P[2] P[3] P[4] P[5]



typedef OptimizerType::ScaleType OptimizerScalesType;

OptimizerScalesType optimizerScales( optimizer->GetNumberOfParameters() );







optimizer->SetScales( optimizerScales );



FixedImage

MovingImage

Metric

Transform

Interpolator

Optimizer

Parameters

Resampler

MovingRegistered


Final ResamplingFinal Resampling











EndEnd

Enjoy ITK !

csci 6971: image registration lecture 10: registration components february 13, 2004 prof. chuck...

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