// ********** 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")