// **************** ImageTypes **************************
(FixedInternalImagePixelType "float")
(FixedImageDimension 2)
(MovingImagePixelType  "float")
(MovingImageDimension 2)
(UseDirectionCosines "true")

// **************** Main Components **************************
(Registration "MultiResolutionRegistration")
//(Metric "AdvancedMeanSquares")
(Metric "AdvancedMattesMutualInformation")
//(ImageSampler "Random") 
(ImageSampler "RandomCoordinate")
(Interpolator "BSplineInterpolator")
(ResampleInterpolator "FinalBSplineInterpolator")
(Resampler "DefaultResampler")
(Transform "AffineTransform")
//(Transform "SimilarityTransform")
(Optimizer "AdaptiveStochasticGradientDescent")
(FixedImagePyramid "FixedSmoothingImagePyramid")  
(MovingImagePyramid "MovingSmoothingImagePyramid")


// ***************** Transformation **************************
( AutomaticScalesEstimation "true" ) 
(AutomaticTransformInitialization "true") 
(HowToCombineTransforms "Compose")

// ******************* Optimization **************************
(MaximumNumberOfIterations 1000)
(AutomaticParameterEstimation "true")
//(MaximumStepLength 1.0)


// ******************** Multiresolution **********************
(NumberOfResolutions 4)


// ************************ Metric **************************
//(UseComplement "false")
//(ForeGroundvalue 255)
(NumberOfHistogramBins 32)
(ShowExactMetricValue "true")



// ************************ Image Sampler *******************
(NumberOfSpatialSamples 8000)
(NewSamplesEveryIteration "true")

// ************* Interpolation and Resampling ****************
(BSplineInterpolationOrder 1)
(FinalBSplineInterpolationOrder 3)
(DefaultPixelValue 0)

(WriteResultImage "true")

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