Image Registration

[jeng87]

Hello, I am rookie to image field. I am trying to preform atlas registration in a Fiji Plugin, but it seems doesn't work out, I am wondering if I installed elastix correctly? Thank you.

And I had errors in log like this:

Running elastix with parameter file 0: "C:/Users/jg4493/Downloads/BrainJ Atlases/ABA_CCF_25_2017//Registration_Parameters/MB49_Param_Affine.txt".

Current time: Thu Mar 17 12:03:44 2022. Reading the elastix parameters from file ...

Installing all components. InstallingComponents was successful.

ELASTIX version: 5.000 Command line options from ElastixBase: -f C:/Users/jg4493/Downloads/50/3_Registered_Sections/DAPI_25.tif -m C:/Users/jg4493/Downloads/BrainJ Atlases/ABA_CCF_25_2017/Template.tif -fMask unspecified, so no fixed mask used -mMask unspecified, so no moving mask used -out C:\Users\jg4493\Downloads\50\5_Analysis_Output\Temp\Template_aligned
-p C:/Users/jg4493/Downloads/BrainJ Atlases/ABA_CCF_25_2017//Registration_Parameters/MB49_Param_Affine.txt -p C:/Users/jg4493/Downloads/BrainJ Atlases/ABA_CCF_25_2017//Registration_Parameters/MB49_Param_BSpline.txt -priority unspecified, so NORMAL process priority -threads unspecified, so all available threads are used Command line options from TransformBase: -t0 unspecified, so no initial transform used

Reading images... Reading images took 556 ms.

WARNING: the fixed pyramid schedule is not fully specified! A default pyramid schedule is used. WARNING: the moving pyramid schedule is not fully specified! A default pyramid schedule is used. WARNING: The parameter "AutomaticTransformInitializationMethod", requested at entry number 0, does not exist at all. The default value "GeometricalCenter" is used instead. Transform parameters are initialized as: [1, 0, 0, 0, 1, 0, 0, 0, 1, 112, 65.5, 251] InitializeTransform took 0.00s Scales are estimated automatically. Scales for transform parameters are: [4600.25, 3006.5, 72.91666666666667, 4600.25, 3006.5, 72.91666666666667, 4600.25, 3006.5, 72.91666666666667, 1, 1, 1] Initialization of all components (before registration) took: 5 ms. Preparation of the image pyramids took: 3277 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 "UseMultiThreadingForMetrics", 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 "NumberOfFixedHistogramBins", requested at entry number 0, does not exist at all. The default value "32" is used instead. WARNING: The parameter "NumberOfMovingHistogramBins", requested at entry number 0, does not exist at all. The default value "32" is used instead. WARNING: The parameter "FixedLimitRangeRatio", requested at entry number 0, does not exist at all. The default value "0.01" is used instead. WARNING: The parameter "MovingLimitRangeRatio", requested at entry number 0, does not exist at all. The default value "0.01" is used instead. WARNING: The parameter "FixedKernelBSplineOrder", requested at entry number 0, does not exist at all. The default value "0" is used instead. WARNING: The parameter "MovingKernelBSplineOrder", requested at entry number 0, does not exist at all. The default value "3" is used instead. WARNING: The parameter "UseFastAndLowMemoryVersion", requested at entry number 0, does not exist at all. The default value "true" is used instead. WARNING: The parameter "UseJacobianPreconditioning", requested at entry number 0, does not exist at all. The default value "false" is used instead. WARNING: The parameter "FiniteDifferenceDerivative", requested at entry number 0, does not exist at all. The default value "false" is used instead. WARNING: The parameter "SP_A", requested at entry number 0, does not exist at all. The default value "20" is used instead.

WARNING: You have set MaximumNumberOfSamplingAttempts to 10. This functionality is known to cause problems (stack overflow) for large values. If elastix stops or segfaults for no obvious reason, reduce this value. You may select the RandomSparseMask image sampler to fix mask-related problems.

WARNING: The parameter "SigmoidInitialTime", requested at entry number 0, does not exist at all. The default value "0" is used instead. WARNING: The parameter "MaxBandCovSize", requested at entry number 0, does not exist at all. The default value "192" is used instead. WARNING: The parameter "NumberOfBandStructureSamples", requested at entry number 0, does not exist at all. The default value "10" is used instead. WARNING: The parameter "UseAdaptiveStepSizes", requested at entry number 0, does not exist at all. The default value "true" is used instead. WARNING: The parameter "AutomaticParameterEstimation", requested at entry number 0, does not exist at all. The default value "true" is used instead. WARNING: The parameter "UseConstantStep", requested at entry number 0, does not exist at all. The default value "false" is used instead. WARNING: The parameter "MaximumStepLengthRatio", requested at entry number 0, does not exist at all. The default value "1" is used instead. WARNING: The parameter "MaximumStepLength", requested at entry number 0, does not exist at all. The default value "1" is used instead. WARNING: The parameter "NumberOfGradientMeasurements", requested at entry number 0, does not exist at all. The default value "0" is used instead. WARNING: The parameter "NumberOfJacobianMeasurements", requested at entry number 0, does not exist at all. The default value "1000" is used instead. WARNING: The parameter "NumberOfSamplesForExactGradient", requested at entry number 0, does not exist at all. The default value "100000" is used instead. WARNING: The parameter "SigmoidScaleFactor", requested at entry number 0, does not exist at all. The default value "0.1" is used instead. Elastix initialization of all components (for this resolution) took: 1 ms. Computing the fixed image extrema took 1 ms. Computing the moving image extrema took 63 ms. Initialization of AdvancedMattesMutualInformation metric took: 3252 ms. Starting automatic parameter estimation for AdaptiveStochasticGradientDescent ... WARNING: The parameter "ASGDParameterEstimationMethod", requested at entry number 0, does not exist at all. The default value "Original" is used instead. Computing JacobianTerms ... Computing the Jacobian terms took 0.001499s NumberOfGradientMeasurements to estimate sigma_i: 3 Sampling gradients ... Sampling the gradients took 0.297805s Automatic parameter estimation took 0.30s