// ********** Image Types

(FixedInternalImagePixelType "float")
(FixedImageDimension 3)
(MovingInternalImagePixelType "float")
(MovingImageDimension 3)


// ********** Components

(Registration "MultiResolutionRegistration")
(FixedImagePyramid "FixedRecursiveImagePyramid")
(MovingImagePyramid "MovingRecursiveImagePyramid")
(Interpolator "BSplineInterpolator")
//(Metric "AdvancedMattesMutualInformation")
(Metric "MattesMutualInformationWithRigidityPenalty")
(Optimizer "StandardGradientDescent")
(ResampleInterpolator "FinalBSplineInterpolator")
(Resampler "DefaultResampler")
(Transform "BSplineTransform")


// ********** Pyramid

// Total number of resolutions
// (NumberOfResolutions 2)
// (ImagePyramidSchedule 4 4 4 1 1 1)
(NumberOfResolutions 6)
(ImagePyramidSchedule 16 16 16 8 8 8 4 4 4 2 2 2 1 1 1 1 1 1)

// ********** Transform

// (FinalGridSpacingInPhysicalUnits 8.0 8.0 8.0)
// (GridSpacingSchedule 16.0 8.0 4.0 2.0 1.0)
(FinalGridSpacingInPhysicalUnits 4.0 4.0 4.0)
(GridSpacingSchedule 32.0 16.0 8.0 4.0 2.0 1.0)
(HowToCombineTransforms "Compose")


// ********** Optimizer

// Maximum number of iterations in each resolution level:
(MaximumNumberOfIterations 500 500 500 500 20 20)

//SP: Param_a in each resolution level. a_k = a/(A+k+1)^alpha
//good(SP_a 50000.0 30000.0 10000.0 10000.0 5000.0)
//from paper
(SP_a 50000.0 10000.0 2000.0 500.0 100.0 100.0)

//SP: Param_alpha in each resolution level. a_k = a/(A+k+1)^alpha
(SP_alpha 0.6)

//SP: Param_A in each resolution level. a_k = a/(A+k+1)^alpha
(SP_A 50.0)


// ********** Metric

(NumberOfHistogramBins 16 32 32 32 32 32)
(UseFastAndLowMemoryVersion "true")
//RigidPenaly
//RigidityPenaltyWeight: A parameter to weigh the rigidity penalty term against the mutual information metric. 
(RigidityPenaltyWeight 4.0) 

//LinearityConditionWeight: A parameter to weigh the linearity condition term of the rigidity term. 
(LinearityConditionWeight 100.0)
//OrthonormalityConditionWeight: A parameter to weigh the orthonormality condition term of the rigidity term.
(OrthonormalityConditionWeight 1.0) 
//PropernessConditionWeight: A parameter to weigh the properness condition term of the rigidity term.
(PropernessConditionWeight 2.0) 
//UseFixedRigidityImage: flag to specify the use of the fixed rigidity image when calculating the rigidity coefficient image.
(UseFixedRigidityImage "true") 
//FixedRigidityImageName: the name of a coefficient image to specify the rigidity index of voxels in the fixed image.
(FixedRigidityImageName "/max/home00/kding/lungmech/2009_04_20_4DCTPulmonaryFunction/CASE8/resample/BeforeRT_Static-tumorphantom.nii.gz") 
//UseMovingRigidityImage: flag to specify the use of the moving rigidity image when calculating the rigidity coefficient image.
(UseMovingRigidityImage "false")
//DilateRigidityImages: flag to specify the dilation of the rigidity coefficient images. With this the region of rigidity can be extended to force rigidity of the inner region.
(DilateRigidityImages "false")


// ********** Several

(WriteTransformParametersEachIteration "false")
(WriteTransformParametersEachResolution "true")
(WriteResultImageAfterEachResolution "false")
(WriteResultImage "true")
(ShowExactMetricValue "false")
(ErodeMask "false")


// ********** ImageSampler

//Number of spatial samples used to compute the mutual information in each resolution level:
(ImageSampler "RandomCoordinate")
(NumberOfSpatialSamples 5000)
(NewSamplesEveryIteration "true")
//(UseRandomSampleRegion "true")
//(SampleRegionSize 50.0 50.0 50.0)
//(MaximumNumberOfSamplingAttempts 50)


// ********** Interpolator and Resampler

//Order of B-Spline interpolation used in each resolution level:
(BSplineInterpolationOrder 1)

//Order of B-Spline interpolation used for applying the final deformation:
(FinalBSplineInterpolationOrder 3)

//Default pixel value for pixels that come from outside the picture:
(DefaultPixelValue 0)