// Description: elastixpaper, euler

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

//Components
(Registration "MultiResolutionRegistration")
(FixedImagePyramid "FixedSmoothingImagePyramid")
(MovingImagePyramid "MovingSmoothingImagePyramid")
(Interpolator "BSplineInterpolator")
(Metric "AdvancedMattesMutualInformation")
(Optimizer "StandardGradientDescent")
(ResampleInterpolator "FinalBSplineInterpolator")
(Resampler "DefaultResampler")
(Transform "EulerTransform")

(ErodeMask "false")

(AutomaticScalesEstimation "true")
(AutomaticTransformInitialization "false")

(NumberOfResolutions 4)

(HowToCombineTransforms "Compose")

//Save composite ITK transform
(ITKTransformOutputFileNameExtension "h5")
(WriteITKCompositeTransform "true")

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

//Maximum number of iterations in each resolution level:
(MaximumNumberOfIterations 2000)

//Number of grey level bins in each resolution level:
(NumberOfHistogramBins 32 )
(FixedKernelBSplineOrder 3)
(MovingKernelBSplineOrder 3)
(FixedLimitRangeRatio 0.0)
(MovingLimitRangeRatio 0.0)

// sampler:
(ImageSampler "RandomCoordinate")
(FixedImageBSplineInterpolationOrder 1 )
(UseRandomSampleRegion "true")
(SampleRegionSize 50.0)
(CheckNumberOfSamples "false")
(NewSamplesEveryIteration "true" )

//Number of spatial samples used to compute the mutual information in each resolution level:
(NumberOfSpatialSamples 2000 )

//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)

//SP: Param_a in each resolution level. a_k = a/(A+k+1)^alpha
(SP_a 2000.0)

//SP: Param_A in each resolution level. a_k = a/(A+k+1)^alpha
(SP_A 200.0)

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


