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I need to register some cardiac MR data (10 grayscale 2D images with 256x96 pixels), and I am trying to avoid having to select a reference image by using a groupwise registration method. The current problem I am facing is that the data, although well registered is significantly distorted.
Any suggestions on what parameters I should tweak first to minimise non-rigid distortions when using groupwise registration?
I am a bit lost with all the recipes and parameters, and everything feels like a dark art at the moment. I don't seem to be able to use the metric "TransformBendingEnergyPenalty" when doing groupwise registration.
I cannot show an example as this is clinical data, but I can list my current recipe:
(AutomaticParameterEstimation"true")
(CheckNumberOfSamples"true")
(DefaultPixelValue0)
(FinalBSplineInterpolationOrder3)
(FinalGridSpacingInVoxels16)
(FixedImagePyramid"FixedSmoothingImagePyramid")
(GridSpacingSchedule2.8032211.9881001.4100001.000000)
(ImageSampler"RandomCoordinate")
(Interpolator"ReducedDimensionBSplineInterpolator")
(MaximumNumberOfIterations256)
(MaximumNumberOfSamplingAttempts8)
(MovingImagePyramid"MovingSmoothingImagePyramid")
(NewSamplesEveryIteration"true")
(NumberOfResolutions4)
(NumberOfSamplesForExactGradient4096)
(NumberOfSpatialSamples2048)
(Optimizer"AdaptiveStochasticGradientDescent")
(Registration"MultiResolutionRegistration")
(ResampleInterpolator"FinalReducedDimensionBSplineInterpolator")
(Resampler"DefaultResampler")
(ResultImageFormat"nii")
(Transform"BSplineStackTransform")
(WriteIterationInfo"false")
(WriteResultImage"true")
//Choose one of the following groupwise metrics://(Metric "PCAMetric2")//(Metric "PCAMetric")//(Metric "LinearGroupwiseMI")//(Metric "SumOfPairwiseCorrelationCoefficientsMetric")
(Metric"VarianceOverLastDimensionMetric")
////Specific for the LinearGroupwiseMI metric//(TemplateImage "ArithmeticAverage" "ArithmeticAverage")//(Combination "Sum" "Sum")//(UseFastAndLowMemoryVersion "true")//(NumberOfFixedHistogramBins 32)//(NumberOfMovingHistogramBins 32)////Specific for the PCAMetric//(NumEigenValues 7)
Many thanks.
The text was updated successfully, but these errors were encountered:
Hello @Pedro-Filipe, did you find an answer to this ? I'm facing a similar problem: I would like to do group wise registration of a 4DCT (10 breathing phases of shape 128,128,128).
Hi,
I need to register some cardiac MR data (10 grayscale 2D images with 256x96 pixels), and I am trying to avoid having to select a reference image by using a groupwise registration method. The current problem I am facing is that the data, although well registered is significantly distorted.
Any suggestions on what parameters I should tweak first to minimise non-rigid distortions when using groupwise registration?
I am a bit lost with all the recipes and parameters, and everything feels like a dark art at the moment. I don't seem to be able to use the metric
"TransformBendingEnergyPenalty"
when doing groupwise registration.I cannot show an example as this is clinical data, but I can list my current recipe:
Many thanks.
The text was updated successfully, but these errors were encountered: