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

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


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

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


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

// Total number of resolutions
(NumberOfResolutions 5)
(ImagePyramidSchedule 16 16 16 8 8 8 4 4 4 2 2 2 1 1 1)
//16mm 8mm 4mm 2mm 1mm

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

(FinalGridSpacingInPhysicalUnits 10.0 10.0 10.0)
(GridSpacingSchedule 16.0 8.0 4.0 2.0 1.0)
//160mm every 10 voxel, 80mm, every 10 voxel, 40mm, every 10 voxel, 20mm, every 10 voxel, 10mm, every 10 voxel
(HowToCombineTransforms "Compose")


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

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

//SP: Param_a in each resolution level. a_k = a/(A+k+1)^alpha
(SP_a 10000.0 10000.0 5000.0 1000.0 1000.0)
//(SP_a 8000.0 2000.0 2000.0 2000.0 2000.0)

//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 32 32 32 32 32)
(UseFastAndLowMemoryVersion "true")


// ********** 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 2000)
(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)