[Elastix] Running multi-metric registration

Jihun Kim jihun at umich.edu
Thu Apr 4 21:34:37 CEST 2013


Sorry that I did not attach this file.

Regards,
Jihun
--
*Jihun Kim*
Ph. D. candidate
Mechanical Engineering
University of Michigan, Ann Arbor
734-276-7167


On Thu, Apr 4, 2013 at 3:27 PM, Jihun Kim <jihun at umich.edu> wrote:

> Dear Elastix-subscribers,
>
> I am trying to run multi-metric registration with AdvancedMeanSquares and
> TransformRigidityPenalty. I attached a parameter file to run a
> registration. I have got the following a command window message:
>
> =====Message
> Begins======================================================================================
> elastix is started at Thu Apr 04 15:20:05 2013.
>
> elastix runs at: Jihun-PC
>   Windows 7, Service Pack 1 (Build 7601)
>   with 3956 MB memory, and 4 cores @ 2393 MHz.
> -------------------------------------------------------------------------
>
> Running elastix with parameter file 0:
> "D:\elastix\hncbm8\ct7\staring-ms\Parameters.txt".
>
> Current time: Thu Apr 04 15:20:05 2013.
> Reading the elastix parameters from file ...
>
> Installing all components.
> InstallingComponents was successful.
>
> ELASTIX version: 4.600
> Command line options from ElastixBase:
> -f        D:\hncbm8\fect1-7.mhd
> -m        D:\hncbm8\ct7.mhd
> -fMask    unspecified, so no fixed mask used
> -mMask    unspecified, so no moving mask used
> -out      D:\elastix\hncbm8\ct7\staring-ms/
> -p        D:\elastix\hncbm8\ct7\staring-ms\Parameters.txt
> -priority unspecified, so NORMAL process priority
> -threads  unspecified, so all available threads are used
> Command line options from TransformBase:
> -t0       D:\hncbm8\ct7toct1.txt
> WARNING: The parameter "BSplineTransformSplineOrder", requested at entry
> number 0, does not exist at all.
>   The default value "3" is used instead.
> WARNING: The parameter "UseCyclicTransform", requested at entry number 0,
> does not exist at all.
>   The default value "false" is used instead.
>
> Reading images...
> Reading images took 489 ms.
>
> Reading the elastix parameters from file ...
>
> Initialization of all components (before registration) took: 43 ms.
> Preparation of the image pyramids took: 2882 ms.
>
> Resolution: 0
> WARNING: The parameter "ShowExactMetricValue", requested at entry number
> 0, does not exist at all.
>   The default value "false" is used instead.
> WARNING: The parameter "CheckNumberOfSamples", requested at entry number
> 0, does not exist at all.
>   The default value "true" is used instead.
> WARNING: The parameter "ShowExactMetricValue", requested at entry number
> 0, does not exist at all.
>   The default value "false" is used instead.
> WARNING: The parameter "CheckNumberOfSamples", requested at entry number
> 0, does not exist at all.
>   The default value "true" is used instead.
> Setting the fixed masks took: 0 ms.
> Setting the moving masks took: 0 ms.
> WARNING: The parameter "UseRelativeWeights", requested at entry number 0,
> does not exist at all.
>   The default value "false" is used instead.
> WARNING: The parameter "NumberOfSamplesForSelfHessian", requested at entry
> number 0, does not exist at all.
>   The default value "100000" is used instead.
> WARNING: The parameter "SelfHessianSmoothingSigma", requested at entry
> number 0, does not exist at all.
>   The default value "1" is used instead.
> WARNING: The parameter "SelfHessianNoiseRange", requested at entry number
> 0, does not exist at all.
>   The default value "1" is used instead.
> WARNING: The parameter "MaximumNumberOfSamplingAttempts", requested at
> entry number 0, does not exist at all.
>   The default value "0" is used instead.
> Elastix initialization of all components (for this resolution) took: 2 ms.
> Initialization of AdvancedMeanSquares metric took: 0 ms.
> Initialization of TransformRigidityPenalty term took: 0 ms.
> 1:ItNr 2:Metric 2:Metric0 2:Metric1 3:StepSize 4:||Gradient0||
> 4:||Gradient1|| 4:||Gradient|| Metric-LC Metric-OC Metric-PC Time0[ms]
> Time1[ms] Time[ms] ||Gradient-LC|| ||Gradient-OC|| ||Gradient-PC||
> SGD
> elxTemplate
> 0 13224.394736 13224.394736 0.000000 7457.268480 593.852296 0.000000
> 593.852296 0.0000000000 0.0000000000 0.0000000000 103 115 295 0.0000000000
> 0.0000000000 0.0000000000
> Time spent in resolution 0 (ITK initialisation and iterating): 0.333 s.
> Stopping condition: Error in metric.
>
> itk::ExceptionObject (0178FA88)
> Location: "ElastixTemplate - Run()"
> File:
> d:\src4\elastix_sources_v4.6\src\common\costfunctions\itkAdvancedImageToImageMetric.hxx
> Line: 628
> Description: itk::ERROR: AdvancedMeanSquaresMetric(03ABCAB0): Too many
> samples map outside moving image buffer: 0 / 5000
>
> Error occurred during actual registration.
>
> Errors occurred!
> =====Message
> Ends======================================================================================
>
> Following the instruction given in FAQ, I applied an initial transform but
> I don't know what to try further. I am wondering if you could give me some
> suggestions.
> Thanks very much.
>
> Regards,
> Jihun
> --
> *Jihun Kim*
> Ph. D. candidate
> Mechanical Engineering
> University of Michigan, Ann Arbor
> 734-276-7167
>
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// **************** Image Types ******************************

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

// **************** Main Components **************************

(Registration "MultiMetricMultiResolutionRegistration")
(Interpolator "BSplineInterpolator")
(ResampleInterpolator "FinalBSplineInterpolator")
(Resampler "DefaultResampler")
(FixedImagePyramid "FixedRecursiveImagePyramid")
(MovingImagePyramid "MovingRecursiveImagePyramid")
(Optimizer "StandardGradientDescent")
(Transform "BSplineTransform")
(Metric "AdvancedMeanSquares" "TransformRigidityPenalty")

// ***************** Transformation **************************

(FinalGridSpacingInVoxels 8.0 8.0 1.0)
(UpsampleGridOption "true")
(AutomaticTransformInitialization "false")
(HowToCombineTransforms "Compose")
// ******************** Multiresolution **********************

(NumberOfResolutions 3)
(ImagePyramidSchedule 4 4 1  2 2 1  1 1 1 )

// ******************* Sampling ****************************

(ImageSampler "Random")
(NewSamplesEveryIteration "true" "true" "true")
(NumberOfSpatialSamples 5000 5000 5000)
(ErodeMask "false")

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

(MaximumNumberOfIterations 300 300 1200)
(SP_a 3200.0 3200.0 3200.0)
(SP_alpha 0.602 0.602 0.602)
(SP_A 100.0 100.0 100.0)

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

(UseNormalization "false")

// MMIWRR specific
(Metric0Weight 1.0)
(Metric1Weight 0.0 1000.0 1000.0)
(LinearityConditionWeight 100.0)
(OrthonormalityConditionWeight 1.0)
(PropernessConditionWeight 2.0)
(UseLinearityCondition "true")
(UseOrthonormalityCondition "true")
(UsePropernessCondition "true")
(CalculateLinearityCondition "true")
(CalculateOrthonormalityCondition "true")
(CalculatePropernessCondition "true")
(DilateRigidityImages "false" "false" "false")
(DilationRadiusMultiplier 2.0)
(UseFixedRigidityImage "true")
(FixedRigidityImageName D:\hncbm8\segbinary.mhd)
(UseMovingRigidityImage "false")
// ************* Interpolation and Resampling ****************

(BSplineInterpolationOrder 1)
(FinalBSplineInterpolationOrder 3)
(DefaultPixelValue -1000)
(WriteResultImage "true")
(ResultImagePixelType "short")
(ResultImageFormat "mhd")


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