[Elastix] problem with non-rigid

Esmeralda Ruiz Pujadas esmeralda.ruizpujadas at gmail.com
Tue Feb 24 14:34:21 CET 2015


Dear Floris,

Thank you so much for your answer, so I suppose that it is located points
away from the moving
domain so it is a way to say undefined. But I wonder why it does this, is
there any way
to solve this problem?.

Thanks again !!
Sicnerely
Esmeralda

On Tue, Feb 24, 2015 at 2:26 PM, Floris Berendsen <floris at isi.uu.nl> wrote:

> 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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>>
>>
>
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