ITK Deformable Registration

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ITK Deformable Registration
Demons Methods
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Deformable Registration
Deformable Registration
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Deformable Transforms
Deformable Transforms
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Deformable Transformation
y
y
Transform
x
x
Fixed Image
Moving Image
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Deformable Transformation
y
y
Transform
x
x
Fixed Image
Moving Image
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Deformable Transformation
y
y
Transform
x
x
Fixed Image
Moving Image
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Image Resampling
Interpolator
FixedImage
Resample Image Filter
MovingImage
DeformedImage
Transform
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Image Resampling
Interpolator
FixedImage
Resample Image Filter
MovingImage
High Order Polynomials
Orthogonal Basis
Splines
Explicit Vector Field
DeformedImage
Transform
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Kernel Splines Transforms
Target Landmarks
Source Landmarks
Displacement Vectors
Interpolated Values
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Kernel Spline Transforms

• Thin Plates
• Thin Plates R2 log R
• Elastic Body
• Elastic Body Reciprocal
• Volume

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Kernel Spline Transforms
InsightApplications / ThinPlateSplines
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Resampling Kernel Spline Transform
include "itkImage.h" include "itkResampleImageFi
lter.h" include "itkLinearInterpolateImageFunctio
n.h" include "itkElasticBodySplineKernelTransform
.h" typedef itkImage
ImageType ImageTypeConstPointer fixedImage
GetFixedImage() ImageTypeConstPointer
movingImage GetMovingImage() typedef
itkLinearInterpolateImageFunction ImageType,
double
InterpolatorType InterpolatorTy
pePointer interpolator InterpolatorTypeNew()
typedef itkResampleImageFilter ImageType FilterType FilterTypeP
ointer resampler FilterTypeNew()
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Resampling Kernel Spline Transform

• typedef itkElasticBodySplineKernelTransform double, 2
  TransformType
• TransformTypePointer transform
  TransformTypeNew()
• resampler-SetInterpolator( interpolator )
• resampler-SetInput( movingImage )
• ImageTypeRegionType region fixedImage-GetBuff
  eredRegion()
• resampler-SetSize( region-GetSize() )
• resampler-SetOutputStartIndex(
  region-GetIndex() )
• resampler-SetOutputSpacing( fixedImage-GetSpacin
  g() )
• resampler-SetOutputOrigin( fixedImage-GetOrigin(
  ) )

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Resampling Kernel Spline Transform
resampler-SetTransform( transform ) typedef
TransformTypePointSetType
PointSetType PointSetTypePointer
sourceLandmarks PointSetTypeNew() PointSetTyp
ePointer targetLandmarks PointSetTypeNew()
transform-SetSourceLandmarks( sourceLandmarks
) transform-SetTargetLandmarks( targetLandmarks
) typedef PointSetTypePointsContainer
PointsContainer PointsContainerPointer
sources sourceLandmarks-GetPoints() PointsCont
ainerPointer targets targetLandmarks-GetPoint
s()
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Resampling Kernel Spline Transform

• sources-Reserve( numberOfLandmarks )
• targets-Reserve( numberOfLandmarks )
• typedef PointSetTypePointType PointType
• PointType source
• PointType target
• for( int i 0 i
• inputFile source
• inputFile target
• sources-InsertElement( i, source )
• targets-InsertElement( i, target )
• transform-ComputeWMatrix()
• resampler-Update() // Finally !!

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Kernel Spline Transforms
VolView ITK Plugin
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Kernel Spline Transforms
VolView ITK Plugin
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Deformable Transforms
Deformation Fields
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Deformation Vector Field
ParaView http//www.paraview.org
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Warp Image Filter
include "itkImage.h" include "itkWarpImageFilter
.h" include "itkLinearInterpolateImageFunction.h"
typedef itkImage
ImageType ImageTypeConstPointer fixedImage
GetFixedImage() ImageTypeConstPointer
movingImage GetMovingImage() typedef
itkLinearInterpolateImageFunction ImageType,
double
InterpolatorType InterpolatorTy
pePointer interpolator InterpolatorTypeNew()
typedef itkVector
VectorType typedef itkImage
VectorFieldType VectorFieldTypePointer
vectorField GetVectorField()
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Warp Image Filter

• typedef itkWarpImageFilter
• ImageType,
• VectorFieldType WarpFilterType
• WarpFilterTypePointer warpFilter
  WarpFilterTypeNew()
• warpFilter-SetInterpolator( interpolator )
• warpFilter-SetInput( movingImage )
• warpFilter-SetOutputSpacing( fixedImage-GetSpaci
  ng() )
• warpFilter-SetOutputOrigin( fixedImage-GetOrigin
  () )
• warpFilter-SetDeformationField( vectorField )
• warpFilter-Update()
• ImageTypeConstPointer deformedImage
  warpFilter-GetOutput()

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Demons Registration
Demons Registration
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Demons Registration
Demons is a Family of Algorithms
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Demons Registration
Demons Type 0
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Demons Registration Type 0
Transform
Scene
Model
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Demons Registration Type 0
Transform
Scene
Gradients
Model
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Demons Registration Type 0
Transform
Scene
Forces
Model
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Demons Registration
Demons Type 1
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Demons Registration Type 1
Transform
Scene
Model
Vector Field
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Demons Registration Type 1
Transform
Scene
Model
Vector Field
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Demons Registration Type 1
Transform
Scene
Model
Vector Field
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Demons Registration Type 1
Transform
Scene
Model
Vector Field
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Demons Registration Type 1
Gradient
Scene
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Demons Registration Type 1
Current Estimation
Intensity
Space
Gradient
Desired Displacement
Scene
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Demons Registration Type 1
Transform
Scene
Model
Vector Field
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Demons Registration Type 1
Scene
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Demons Registration Type 1
Iterations
Previous Field
Gaussian Smoothing
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Demons Registration Type 1
( s m ) . Grad(s)
V
Grad(s)2
( s m ) . Grad(s)
V
Grad(s)2 (s-m)2
K
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Image Registration Framework
FixedImage
Increment Computation
PDE Solver
MovingImage
Interpolator
DeformationField
Transform
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Demons Registration Type 1
include "itkImage.h" include "itkDemonsRegistrat
ionFilter.h" typedef itkImage
ImageType ImageTypeConstPointer fixedImage
GetFixedImage() ImageTypeConstPointer
movingImage GetMovingImage() typedef
itkVector VectorType typedef
itkImage VectorFieldType t
ypedef itkDemonsRegistrationFilter ImageType, ImageType,
VectorFieldType DemonsType DemonsType
Pointer demons DemonsTypeNew()
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Demons Registration Type 1

• demons-SetFixedImage( fixedImage )
• demons-SetMovingImage( movingImage )
• demons-SetNumberOfIterations( 200 )
• demons-SetStandardDeviations( 1.0 )
• demons-Update()
• ImageTypeConstPointer vectorField
  demons-GetOutput()

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Demons Registration Type 1
Scene
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Demons Registration Type 1
Model
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Demons Registration Type 1
After Registration
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Demons Registration Type 1
Scene
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Demons Registration Type 1
Scene
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Requirements
Fixed and Moving images should have the same
intensity distribution !
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Eventual Preprocessing
- Histogram Matching Filter- Anisotropic
Diffusion Filtering
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Image Registration Framework
FixedImage
Increment Computation
PDE Solver
MovingImage
Interpolator
DeformationField
Transform
Resampler
MovingRegistered
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Enjoy ITK !