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elastixParams_Bspline.txt
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elastixParams_Bspline.txt
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(FixedImageDimension 3)
(MovingImageDimension 3)
(Registration "MultiMetricMultiResolutionRegistration")
(FixedImagePyramid "FixedRecursiveImagePyramid")
(MovingImagePyramid "MovingRecursiveImagePyramid")
(ErodeMask "false")
(Optimizer "AdaptiveStochasticGradientDescent")
(ASGDParameterEstimationMethod "DisplacementDistribution")
(NumberOfSpatialSamples 16000)
(CheckNumberOfSamples "false") //This check is useful for making sure the alignment doesn't diverge catastrophically. After checking that the affine alignment went well, catastrophic divergence is rare, so can skip this check
(MaximumNumberOfSamplingAttempts 3)
(NewSamplesEveryIteration "true")
(ImageSampler "RandomCoordinate")
(Transform "RecursiveBSplineTransform")
(FinalGridSpacingInPhysicalUnits _GRIDSPACING_) //This line can be modified by run_elastix. Do not change
(GridSpacingSchedule 8 4 2 1 1)
(HowToCombineTransforms "Compose")
(Interpolator "LinearInterpolator")
(Metric "AdvancedNormalizedCorrelation" "TransformBendingEnergyPenalty") //This line can be modified by run_elastix. Do not change
(Metric0Weight 1)
(Metric1Weight _METRIC1WEIGHT_) //This line can be modified by run_elastix. Do not change
//(Metric2Weight 0.01) //This line can be modified by run_elastix. Do not change
//(Metric2Use "true" "true" "true" "true" "true") //This line can be modified by run_elastix. Do not change, except:
//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, turn the final "true"
//to "false" in the Metric2Use line above. Or turn Metric2Weight down to 0.0001
//(ShowExactMetricValue "true")
//(ExactMetricEveryXIterations 25 25 25 100 100 100 100)
//(ExactMetricSampleGridSpacing 1 1 1 2 2 2 4 4 4 8 8 8 8 8 8 8 8 8 8 8 8)
(NumberOfResolutions 5)
(ImagePyramidSchedule 8 8 8 4 4 4 2 2 2 1 1 1 1 1 1)
(MaximumNumberOfIterations 500 1000 2000 4000 6000)
//Output
(Resampler "DefaultResampler")
//(Resampler "OpenCLResampler")
//(OpenCLResamplerUseOpenCL "true")
(ResampleInterpolator "FinalBSplineInterpolator")
(FinalBSplineInterpolationOrder 3)
(DefaultPixelValue 0)
(ResultImagePixelType "float")
(ResultImageFormat "nrrd")
(CompressResultImage "true")
//(WriteResultImageAfterEachResolution "false" "false" "false" "true" "false") //No need to specify in this line that the final image needs writing, since WriteResultsImage takes care of that
(WriteResultImage "true") //This line can be modified by run_elastix. Do not change