(WriteResultImage "false")
(AutomaticTransformInitialization "true")
(HowToCombineTransforms "Compose")

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

(ErodeMask "false")

(ImageSampler "RandomSparseMask")

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

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

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

//Order of B-Spline interpolation used for applying the final deformation:
(FinalBSplineInterpolationOrder 0)

(AutomaticScalesEstimation "true")

(NumberOfResolutions 4)

//Maximum number of iterations in each resolution level:
(MaximumNumberOfIterations 256)

//Number of grey level bins in each resolution level:
(NumberOfHistogramBins 32)

(NewSamplesEveryIteration "true")
(UseAllPixels "false")
(WriteTransformParametersEachResolution "false")
(WriteTransformParametersEachIteration "false")

//Number of spatial samples used to compute the mutual information in each resolution level:
(NumberOfSpatialSamples 5000)

(MaximumNumberOfSamplingAttempts 10)

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

(ImagePyramidSchedule 8 4 4 2 1)

//SP: Param_a in each resolution level. a_k = a/(A+k+1)^alpha
(SP_a 500.0)

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

//SP: Param_alpha in each resolution level. a_k = a/(A+k+1)^alpha
(SP_alpha 0.602) 





