elastixParams_affine.txt

(FixedImageDimension 3)
(MovingImageDimension 3)

(Registration "MultiMetricMultiResolutionRegistration")

(FixedImagePyramid "FixedRecursiveImagePyramid")
(MovingImagePyramid "MovingRecursiveImagePyramid")

(Optimizer "AdaptiveStochasticGradientDescent")
(ASGDParameterEstimationMethod "DisplacementDistribution")
(NumberOfSpatialSamples 2000)
(CheckNumberOfSamples "true")
(RequiredRatioOfValidSamples 0.05)
(MaximumNumberOfSamplingAttempts 3)
(NewSamplesEveryIteration "true")
(ImageSampler "RandomCoordinate")


(Transform "AffineTransform")
(AutomaticTransformInitialization "true")
(AutomaticTransformInitializationMethod "CenterOfGravity")
(AutomaticScalesEstimation "true")
(HowToCombineTransforms "Compose")

(Interpolator "LinearInterpolator")
//(Interpolator "BSplineInterpolator")
//(BSplineInterpolationOrder 1)


(Metric "AdvancedNormalizedCorrelation") //This line can be modified by run_elastix. Do not change
//(Metric1Use "true" "true" "true" "true") //This line can be modified by run_elastix. Do not change, except as instructed below
  //If your corresponding points are placed accurately, using them for the whole
  //alignment is a good idea, so have all "true"s in the line above. However,
  //accurately placing correspondence points in 3D stacks is hard, so if you
  //want your points to guide the alignment into roughly the right spot but then
  //let the image correlations drive the final alignment, the line above should
  //start with one or two "true"s but then end with a few "false"s.


(NumberOfResolutions 4)

(MaximumNumberOfIterations 3000)


//Output
(Resampler "DefaultResampler")
(ResampleInterpolator "FinalBSplineInterpolator")
(FinalBSplineInterpolationOrder 3)
(DefaultPixelValue 0)
(ResultImagePixelType "float")
(ResultImageFormat "nrrd")
(CompressResultImage "true")
//(WriteResultImageAfterEachResolution "true" "false" "false" "false" "false" "false" "false" "false" "false")
(WriteResultImage "true") //This is the default, but this line can be changed by run_elastix's -p option, so don't remove this line