[Elastix] binary image (segmentation image) registration

litiantian litiantian2014 at 163.com
Mon Feb 9 08:31:49 CET 2015

Dear Sir/Mandam,

i came across a problem when i tried to register the binary image(segmentation result).
The registration algorithm preformed well when no mask was used. However, when i added mask on both fixed image and/or moved image the registration result became worse.

' If a mask is given, the sampler tries to find samples within the mask. ' ---> From the mannual
i thought if i added mask and kept the NumberOfSpatialSamples unchanged, the registration result should be better. Am i right??
Here is my Parameter file:

(FixedInternalImagePixelType "float")
(FixedImageDimension 3)
(MovingInternalImagePixelType "float")
(MovingImageDimension 3)

(Registration "MultiResolutionRegistration")
(FixedImagePyramid "FixedSmoothingImagePyramid")
(MovingImagePyramid "MovingSmoothingImagePyramid")
(Interpolator "BSplineInterpolator")
(Metric "AdvancedMattesMutualInformation")
(Optimizer "StandardGradientDescent")
(ResampleInterpolator "FinalBSplineInterpolator")
(Resampler "DefaultResampler")
(Transform "BSplineTransform")

// ********** Pyramid

// Total number of resolutions
(NumberOfResolutions 2)

// ********** Transform
// ********** Transform

(FinalGridSpacingInPhysicalUnits 4.0 4.0 4.0)
(GridSpacingSchedule 1.0 1.0 1.0 1.0 1.0 1.0)
(HowToCombineTransforms "Compose")

// ********** Optimizer

// Maximum number of iterations in each resolution level:
(MaximumNumberOfIterations 1000)

//SP: Param_a in each resolution level. a_k = a/(A+k+1)^alpha
(SP_a 10000.0)

//SP: Param_alpha in each resolution level. a_k = a/(A+k+1)^alpha
(SP_alpha 0.602)

//SP: Param_A in each resolution level. a_k = a/(A+k+1)^alpha
(SP_A 50.0)

// ********** Metric

//Number of grey level bins in each resolution level:
(NumberOfHistogramBins 32)
(FixedLimitRangeRatio 0.0)
(MovingLimitRangeRatio 0.0)
(FixedKernelBSplineOrder 3)
(MovingKernelBSplineOrder 3)

// ********** Several

(WriteTransformParametersEachIteration "false")
(WriteTransformParametersEachResolution "true")
(WriteResultImage "true")
(ShowExactMetricValue "false")
(ErodeFixedMask "false")
(ErodeMovingMask "false")
(UseDifferentiableOverlap "false")

// ********** ImageSampler
//Number of spatial samples used to compute the mutual information in each resolution level:
(ImageSampler "Random")
(NumberOfSpatialSamples 10000)
(NewSamplesEveryIteration "true")

// ********** Interpolator and Resampler

//Order of B-Spline interpolation used in each resolution level:
(BSplineInterpolationOrder 3)

//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)

(ResultImagePixelType "float")
(ResultImageFormat "hdr")
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