// Parameter file to register Parelsnoer T1 to MNI space

(UseDirectionCosines "true")

//ImageTypes
(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 "EulerTransform")

(ErodeMask "false" )

(NumberOfResolutions 5)

(HowToCombineTransforms "Compose")
(AutomaticTransformInitialization "true")
(AutomaticScalesEstimation "true")
(AutomaticTransformInitializationMethod "GeometricalCenter")

(WriteTransformParametersEachIteration "false")
(WriteResultImage "true")
(CompressResultImage "false")
(WriteResultImageAfterEachResolution "false") 
(ShowExactMetricValue "false")
(ResultImageFormat "nii") 
(ResultImagePixelType "unsigned short") 

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

//Number of grey level bins in each resolution level:
(NumberOfHistogramBins 64 )
(FixedLimitRangeRatio 0.0)
(MovingLimitRangeRatio 0.0)
(FixedKernelBSplineOrder 3)
(MovingKernelBSplineOrder 3)

//Number of spatial samples used to compute the mutual information in each resolution level:
(ImageSampler "RandomCoordinate")
(FixedImageBSplineInterpolationOrder 1 )
(UseRandomSampleRegion "false")
(NumberOfSpatialSamples 4000 )
(NewSamplesEveryIteration "true")
(CheckNumberOfSamples "true")
(MaximumNumberOfSamplingAttempts 10)

//Order of B-Spline interpolation used in each resolution level:
(BSplineInterpolationOrder 1)

//Order of B-Spline interpolation used for applying the final deformation:
(FinalBSplineInterpolationOrder 1)

//Default pixel value for pixels that come from outside the picture:
(DefaultPixelValue 0)

//SP: Param_A in each resolution level. a_k = a/(A+k+1)^alpha
(SP_A 20.0 )