// Description
// Stage: non-rigid
//
// Author:      Roy van Pelt
// Affiliation: Eindhoven University of Technology
// Year:        2013

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

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


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

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


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

// Total number of resolutions
(NumberOfResolutions 3)
(ImagePyramidSchedule 4 4 4 2 2 2 1 1 1)


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

(GridSpacingSchedule 8 8 8 4 4 4 2 2 2)
(HowToCombineTransforms "Compose")


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

// Maximum number of iterations in each resolution level:
(MaximumNumberOfIterations 300 200 100)

(AutomaticParameterEstimation "true")
(UseAdaptiveStepSizes "true")
(NumberOfHistogramBins 32 32)
(NumberOfFixedHistogramBins 32 32)
(NumberOfMovingHistogramBins 32 32)

(NumberOfGradientMeasurements 0)
(NumberOfJacobianMeasurements 4056)
(NumberOfBandStructureSamples 10)
(MaximumStepLength 2.29829)
(MaxBandCovSize 192)
(SigmoidInitialTime 0 0 0)
(SigmoidScaleFactor 0.1)


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

(WriteTransformParametersEachIteration "false")
(WriteTransformParametersEachResolution "false")
(WriteResultImageAfterEachResolution "false")
(WritePyramidImagesAfterEachResolution "false")
(ShowExactMetricValue "false")
(ErodeFixedMask "false" "false")
(ErodeMovingMask "false" "false")
(UseDirectionCosines "true")
(FixedLimitRangeRatio 0.01 0.01)
(MovingLimitRangeRatio 0.01 0.01)
(UseFastAndLowMemoryVersion "true")
(SP_A 20.0 )


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

//Number of spatial samples used to compute the mutual information in each resolution level:
(ImageSampler "RandomCoordinate")
(CheckNumberOfSamples "false" "false" "false")
(NumberOfSpatialSamples 2048 4096 4096)
(NumberOfSamplesForSelfHessian 10000)
(NumberOfSamplesForExactGradient 10000)
(NewSamplesEveryIteration "true")
(UseRandomSampleRegion "false")
(MaximumNumberOfSamplingAttempts 0 0 0)


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

//Order of B-Spline interpolation used in each resolution level:
(BSplineInterpolationOrder 1 1 1)
(FixedImageBSplineInterpolationOrder 1 1 1)
(MovingImageBSplineInterpolationOrder 1 1 1)
(FixedKernelBSplineOrder 3 3 3) // 0 for binary
(MovingKernelBSplineOrder 3 3 3)

//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)

(WriteResultImage "true")
(CompressResultImage "false")

// The pixel type and format of the resulting deformed moving image
(ResultImagePixelType "float")
(ResultImageFormat "mhd")