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

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


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

(Registration "MultiResolutionRegistration")
(FixedImagePyramid "FixedSmoothingImagePyramid")
(MovingImagePyramid "MovingSmoothingImagePyramid")
(Interpolator "BSplineInterpolator")
(Metric "AdvancedMattesMutualInformation")
(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

(FinalGridSpacingInPhysicalUnits 10.0 10.0 10.0)
(GridSpacingSchedule 4.0 2.0 1.0)
(HowToCombineTransforms "Compose")


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

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

(AutomaticParameterEstimation "true")
(UseAdaptiveStepSizes "true")
(GradientEstimationMethod 3)


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

(NumberOfHistogramBins 32)
(FixedLimitRangeRatio 0.0)
(MovingLimitRangeRatio 0.0)
(FixedKernelBSplineOrder 1)
(MovingKernelBSplineOrder 3)
(UseFastAndLowMemoryVersion "true")


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

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


// ********** 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)

//the format of resulting deformed moving image
//(ResultImageFormat "mha")

(ResultImageFormat "nii")
(ResultImagePixelType "float")
(ResultImageName "result_image")