[Elastix] problem with non-rigid

Esmeralda Ruiz Pujadas esmeralda.ruizpujadas at gmail.com
Tue Feb 24 12:57:08 CET 2015


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")
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.bigr.nl/pipermail/elastix/attachments/20150224/c766f89d/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: doubt.jpg
Type: image/jpeg
Size: 34583 bytes
Desc: not available
URL: <http://lists.bigr.nl/pipermail/elastix/attachments/20150224/c766f89d/attachment-0001.jpg>


More information about the Elastix mailing list