[Elastix] problem with non-rigid

Floris Berendsen floris at isi.uu.nl
Tue Feb 24 14:26:05 CET 2015


Hi Esmeralda,

The black hole could be caused by the finite domain of the moving image.
You can see if this is the case by setting the DefaultPixelValue to a
specific value, e.g. 10. Any pixel with this value showing up in the result
image is likely to be from outside the original moving domain and cannot be
considered part of the object nor the background, but must be considered
'undefined'.

Best,
Floris

On Tue, Feb 24, 2015 at 12:57 PM, Esmeralda Ruiz Pujadas <
esmeralda.ruizpujadas at gmail.com> wrote:

> Dear all,
>
> I am writing because I got some artifacts in non-rigid registration
> and I am wondering if someone had the same problem. I attach
> the image the moving obtect is applying a non-rigid registration
> using the script below, it is simply a non registration having
> certain limits in their bending as i do not want to lose the details.
> But as a results the first 3 frames I get that the biggest object
> is cropped and only the border is presenved when the other moving image
> is very similar to this one, so i do not understand this result.
>
> Thank you so much
> Sincerely
> Esmeralda
>
>
>
> // ********** Image Types
>
> (FixedInternalImagePixelType "float")
> (FixedImageDimension 3)
> (MovingInternalImagePixelType "float")
> (MovingImageDimension 3)
> (UseDirectionCosines "true")
> (Direction 1 0 0 0 1 0 0 0 1)
> (ComputeZYX "false")
>
> // ********** Components
>
> (Registration "MultiMetricMultiResolutionRegistration")
> (FixedImagePyramid "FixedSmoothingImagePyramid")
> (MovingImagePyramid "MovingSmoothingImagePyramid")
> (Transform "BSplineTransform")
> (Metric "AdvancedMattesMutualInformation" "TransformBendingEnergyPenalty")
> (Optimizer "AdaptiveStochasticGradientDescent")
> (Interpolator "BSplineInterpolator")
> (ResampleInterpolator "FinalBSplineInterpolator")
> (Resampler "DefaultResampler")
>
> // ********** Pyramid Scheme
>
> //Identical scheme for fixed and moving image:
> (NumberOfResolutions 2)
> (ImagePyramidSchedule 1 1 1 0 0 0)
>
> // ********** Transform
>
> (BSplineTransformSplineOrder 3) //Default: 3
> //Can also be specified with a parameter for each dimension
> (FinalGridSpacingInVoxels 2.0)
> (GridSpacingSchedule 8.0 4.0)
> (HowToCombineTransforms "Compose")
>
> // ********** Metric
>
> //Can also be specified with a parameter for each resolution
> (SubtractMean "true") //Default: true
> (Metric0Weight 0.6)
> (Metric1Weight 0.4)
>
> // ********** Optimizer
>
> //Can also be specified with a parameter for each resolution
> (MaximumNumberOfIterations 250)
> (AutomaticParameterEstimation "true")
> (UseAdaptiveStepSizes "true")
>
> (NumberOfJacobianMeasurements 65536)
> (NumberOfSamplesForExactGradient 32768)
>
> // ********** Masks
>
> (ErodeMask "false")
>
> // ********** ImageSampler
>
> (ImageSampler "RandomCoordinate")
> (NewSamplesEveryIteration "true")
> (NumberOfSpatialSamples 32768)
>
> (UseRandomSampleRegion "false")
>
> // ********** Interpolator and Resampler
>
> //B-Spline interp order used in each resolution:
> //Can also be specified with a parameter for each resolution:
> (BSplineInterpolationOrder 2)
>
> //B-Spline interp order used for applying the final deformation:
> (FinalBSplineInterpolationOrder 0)
>
> //Default pixel value for pixels outside the picture:
> (DefaultPixelValue 0)
>
> // ********** Several/MISC
>
> (WriteTransformParametersEachIteration "false")
> (WriteTransformParametersEachResolution "false")
> (WriteResultImageAfterEachResolution "false")
> (WriteResultImage "true")
> (CompressResultImage "false")
> (ResultImageFormat "nii")
> (ShowExactMetricValue "false")
>
>
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