Elastix 配准过程 文件

work\elastix\4.7\elastix_windows64_v4.7

中  cmd   运行  example.bat

自动生成exampleoutput路径:

TransformParameters.0.txt

TransformParameters.1.txt

Installing all components.

InstallingComponents was successful.

WARNING: The parameter "ResampleInterpolat

or", requested at entry number 0, does not exist at all.

  The default value "FinalBSplineInterpolator" is used instead.

ELASTIX version: 4.801

Command line options from ElastixBase:

-fMask    unspecified, so no fixed mask used

-mMask    unspecified, so no moving mask used

-out      output_path_not_set

-priority unspecified, so NORMAL process priority

-threads  unspecified, so all available threads are used

WARNING: The parameter "UseDirectionCosines", requested at entry number 0, does not exist at all.

  The default value "true" is used instead.

WARNING: The option "UseDirectionCosines" was not found in your parameter file.

  From elastix 4.8 it defaults to true!

This may change the behavior of your registrations considerably.

Command line options from TransformBase:

-t0       unspecified, so no initial transform used

Reading images...

Reading images took 1 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.

Transform parameters are initialized as: [0, 0, 0, 0, 0, 0]

Scales are estimated automatically.

Scales for transform parameters are: [20307.656799316406, 20467.985001752284, 21932.985396196942, 1, 1, 1]

WARNING: The parameter "FinalBSplineInterpolationOrder", requested at entry number 0, does not exist at all.

  The default value "3" is used instead.

Initialization of all components (before registration) took: 79 ms.

Preparation of the image pyramids took: 2245 ms.

Resolution: 0

ERROR: File "output_path_not_set\IterationInfo.0.R0.txt" could not be opened!

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 "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 "64" is used instead.

WARNING: The parameter "NumberOfMovingHistogramBins", requested at entry number 0, does not exist at all.

  The default value "64" 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 "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: The parameter "MaximumNumberOfSamplingAttempts", requested at entry number 0, does not exist at all.

  The default value "0" is used instead.

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 "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 "MaximumStepLength", requested at entry number 0, does not exist at all.

  The default value "0.644531" 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: 362 ms.

Initialization of AdvancedMattesMutualInformation metric took: 108 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 0.003550s

  NumberOfGradientMeasurements to estimate sigma_i: 6

  Sampling gradients ...

  Sampling the gradients took 5.129143s

Automatic parameter estimation took 5.37s

1:ItNr  2:Metric        3a:Time 3b:StepSize     4:||Gradient||  Time[ms]

0       -0.603829       0.000000        6.620830        0.035737        5801.1

1       -0.618404       0.000000        6.620830        0.017310        154.4

2       -0.601744       0.354611        6.510886        0.020102        290.4

3       -0.611541       0.000000        6.620830        0.030230        147.9

4       -0.615908       0.000000        6.620830        0.028257        140.0

5       -0.612848       0.000000        6.620830        0.018265        145.6

6       -0.603083       0.999296        6.320085        0.014969        201.2

7       -0.595240       0.299110        6.527852        0.013688        132.2

8       -0.606773       1.298886        6.235174        0.012052        109.5

9       -0.617754       2.298223        5.967727        0.043594        122.6

10      -0.589116       1.598072        6.152624        0.019090        106.6

11      -0.609391       0.897885        6.349354        0.014567        98.8

中间略过....

496     -0.684972       50.329571       1.949226        0.012318        75.5

497     -0.676327       49.630069       1.968530        0.013293        73.2

498     -0.659570       49.700812       1.966561        0.022283        75.9

499     -0.663538       50.637003       1.940861        0.011277        74.6

Time spent in resolution 0 (ITK initialization and iterating): 112.005 s.

Stopping condition: Maximum number of iterations has been reached.

Settings of AdaptiveStochasticGradientDescent in resolution 0:

( SP_a 139.037431 )

( SP_A 20.000000 )

( SP_alpha 1.000000 )

( SigmoidMax 1.000000 )

( SigmoidMin -0.700186 )

( SigmoidScale 0.000014 )

第二层配准:

Resolution: 1

ERROR: File "output_path_not_set\IterationInfo.0.R1.txt" could not be opened!

WARNING: The parameter "ShowExactMetricValue", requested at entry number 1, does not exist at all.

  The default value "false" is used instead.

WARNING: The parameter "CheckNumberOfSamples", requested at entry number 1, does not exist at all.

  The default value "true" is used instead.

WARNING: The parameter "UseMultiThreadingForMetrics", requested at entry number 1, 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 1, does not exist at all.

  The default value "64" is used instead.

WARNING: The parameter "NumberOfMovingHistogramBins", requested at entry number 1, does not exist at all.

  The default value "64" is used instead.

WARNING: The parameter "FixedLimitRangeRatio", requested at entry number 1, does not exist at all.

  The default value "0.01" is used instead.

WARNING: The parameter "MovingLimitRangeRatio", requested at entry number 1, does not exist at all.

  The default value "0.01" is used instead.

WARNING: The parameter "UseFastAndLowMemoryVersion", requested at entry number 1, does not exist at all.

  The default value "true" is used instead.

WARNING: The parameter "UseJacobianPreconditioning", requested at entry number 1, does not exist at all.

  The default value "false" is used instead.

WARNING: The parameter "FiniteDifferenceDerivative", requested at entry number 1, does not exist at all.

  The default value "false" is used instead.

WARNING: The parameter "SP_A", requested at entry number 1, does not exist at all.

  The default value "20" is used instead.

WARNING: The parameter "MaximumNumberOfSamplingAttempts", requested at entry number 1, does not exist at all.

  The default value "0" is used instead.

WARNING: The parameter "SigmoidInitialTime", requested at entry number 1, does not exist at all.

  The default value "0" is used instead.

WARNING: The parameter "MaxBandCovSize", requested at entry number 1, does not exist at all.

  The default value "192" is used instead.

WARNING: The parameter "NumberOfBandStructureSamples", requested at entry number 1, does not exist at all.

  The default value "10" is used instead.

WARNING: The parameter "AutomaticParameterEstimation", requested at entry number 1, does not exist at all.

  The default value "true" is used instead.

WARNING: The parameter "UseConstantStep", requested at entry number 1, does not exist at all.

  The default value "false" is used instead.

WARNING: The parameter "MaximumStepLength", requested at entry number 1, does not exist at all.

  The default value "0.644531" is used instead.

WARNING: The parameter "NumberOfGradientMeasurements", requested at entry number 1, does not exist at all.

  The default value "0" is used instead.

WARNING: The parameter "NumberOfJacobianMeasurements", requested at entry number 1, does not exist at all.

  The default value "1000" is used instead.

WARNING: The parameter "NumberOfSamplesForExactGradient", requested at entry number 1, does not exist at all.

  The default value "100000" is used instead.

WARNING: The parameter "SigmoidScaleFactor", requested at entry number 1, does not exist at all.

  The default value "0.1" is used instead.

Elastix initialization of all components (for this resolution) took: 367 ms.

Initialization of AdvancedMattesMutualInformation metric took: 993 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 0.008164s

  NumberOfGradientMeasurements to estimate sigma_i: 6

  Sampling gradients ...

  Sampling the gradients took 3.880090s

Automatic parameter estimation took 4.39s

1:ItNr  2:Metric        3a:Time 3b:StepSize     4:||Gradient||  Time[ms]

0       -0.503712       0.000000        5.420294        0.021302        5709.7

1       -0.519788       0.000000        5.420294        0.011595        99.3

2       -0.508978       0.203281        5.368328        0.013123        103.4

3       -0.528191       0.000000        5.420294        0.014439        103.8

4       -0.496078       0.000000        5.420294        0.015732        104.1

5       -0.506901       0.999842        5.173954        0.016209        126.1

6       -0.532203       1.998912        4.949198        0.017920        107.3

7       -0.519148       2.998897        4.742975        0.012644        107.3

8       -0.493539       3.998838        4.553259        0.018460        104.7

9       -0.510999       3.145435        4.714190        0.014446        110.2

10      -0.510662       2.292035        4.886914        0.019133        117.1

11      -0.499323       2.902048        4.762193        0.014657        110.9

12      -0.530187       3.900341        4.571270        0.005722        114.1

13      -0.529421       3.076567        4.727675        0.011831        117.8

14      -0.545803       2.419707        4.860273        0.016609        121.3

15      -0.512115       1.566584        5.044014        0.012531        122.8

16      -0.505436       2.550274        4.833327        0.015796        138.7

17      -0.520144       1.696865        5.015062        0.008069        132.4

18      -0.526575       2.680799        4.806687        0.008088        165.5

19      -0.521542       3.629595        4.621520        0.014792        122.2

496     -0.534564       18.284854       2.897457        0.015286        106.2

497     -0.535960       17.854336       2.929562        0.007900        104.7

498     -0.537392       18.336387       2.893661        0.013080        97.6

499     -0.536334       19.323855       2.822800        0.020093        103.8

Time spent in resolution 1 (ITK initialization and iterating): 364.469 s.

Stopping condition: Maximum number of iterations has been reached.

Settings of AdaptiveStochasticGradientDescent in resolution 1:

( SP_a 113.826178 )

( SP_A 20.000000 )

( SP_alpha 1.000000 )

( SigmoidMax 1.000000 )

( SigmoidMin -0.853412 )

( SigmoidScale 0.000012 )

Registration result checksum: 691526154

Final metric value  = -0.536334

Settings of AdaptiveStochasticGradientDescent for all resolutions:

( SP_a 139.037431 113.826178 )

( SP_A 20.000000 20.000000 )

( SP_alpha 1.000000 1.000000 )

( SigmoidMax 1.000000 1.000000 )

( SigmoidMin -0.700186 -0.853412 )

( SigmoidScale 0.000014 0.000012 )

Time spent on saving the results, applying the final transform etc.: 39 ms.

(Transform "EulerTransform")

(NumberOfParameters 3)

(TransformParameters -0.000178 -1.424628 -0.461868)

(InitialTransformParametersFileName "NoInitialTransform")

(HowToCombineTransforms "Compose")

// Image specific

(FixedImageDimension 2)

(MovingImageDimension 2)

(FixedInternalImagePixelType "float")

(MovingInternalImagePixelType "float")

(Size 256 256)

(Index 0 0)

(Spacing 1.0000000000 1.0000000000)

(Origin 0.0000000000 0.0000000000)

(Direction 1.0000000000 0.0000000000 0.0000000000 1.0000000000)

(UseDirectionCosines "true")

// EulerTransform specific

(CenterOfRotationPoint 127.5000000000 127.5000000000)

// ResampleInterpolator specific

(ResampleInterpolator "FinalBSplineInterpolator")

(FinalBSplineInterpolationOrder 3)

// Resampler specific

(Resampler "DefaultResampler")

(DefaultPixelValue 0.000000)

(ResultImageFormat "mhd")

(ResultImagePixelType "short")

(CompressResultImage "false")(Transform "BSplineTransform")

(NumberOfParameters 722)

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1.291089 1.333829 1.345783 1.029643 -4.708690 -5.263420 -5.086854 -4.394870 -2.816933 -0.899484 5.202614 -3.853728 -1.220574 2.582464 0.795553 -0.557611 1.758487 -0.485983 -0.001410 0.134053 0.463320 0.595024 0.531243 -5.267274 -6.135555 -6.252397 -5.832511 -4.084302 -4.392882 -2.024639 3.415236 -1.544800 -6.215153 -3.974017 5.604398 2.595218 -1.892481 -1.674439 -1.355740 -0.541678 -0.230458 -0.081087 -5.711824 -6.849014 -7.222577 -7.027357 -5.568541 -3.938147 -0.752778 1.801734 2.467183 -3.059552 4.542775 5.726862 -0.374466 1.081628 -1.819459 -2.147349 -1.628751 -1.171631 -0.793522 -5.933695 -6.831075 -6.900533 -6.481111 -4.526897 -3.449279 5.281076 5.185606 4.250948 5.524911 5.068123 -4.045985 -5.866662 3.230596 -0.725740 -2.188439 -2.126530 -1.946802 -1.597121 -6.013334 -6.423493 -5.974788 -5.013222 -2.974729 -1.968814 3.998068 3.335815 -1.746072 3.747601 2.945503 -0.844208 -1.120942 4.474537 1.566895 -1.424251 -2.600493 -2.759183 -2.428849 -6.021470 -5.918313 -4.811735 -3.125926 0.179862 1.797125 0.342625 2.587259 -2.317095 -7.146149 -3.550504 1.955419 5.287158 5.138320 1.731050 -1.232811 -2.958357 -3.346213 -3.205660 -6.001221 -5.461036 -3.903368 -1.751396 0.140209 -1.407179 -1.172123 0.649200 0.372325 -0.776596 -0.758333 2.849968 2.372647 3.906849 1.342965 -1.451494 -3.109012 -3.961976 -3.923376 -6.010028 -5.379156 -3.743329 -1.969246 -0.659274 2.340074 0.501070 0.162096 6.911466 5.097637 0.951101 3.190237 -2.676680 2.550547 1.420396 -1.874968 -3.426793 -4.391471 -4.467526 -5.996250 -5.486799 -4.061536 -1.812295 1.501051 5.139122 1.110487 2.662996 5.492555 -1.871861 -1.646265 4.787595 -0.126221 2.270284 1.540431 -0.557465 -3.839430 -4.897717 -4.914927 -5.938408 -5.683421 -4.589747 -2.356865 1.483426 1.405792 7.804199 5.867406 0.227499 -2.200556 -0.893996 1.850690 -5.708892 -1.142669 -1.760569 -1.642082 -4.415886 -5.373641 -5.232821 -5.793653 -5.837515 -4.989927 -3.553700 -1.147263 0.479214 0.797113 3.782897 3.957811 1.857528 -2.852519 -0.467367 1.549899 3.303914 -0.293413 -3.395393 -4.791059 -5.525470 -5.388663 -5.457763 -5.651818 -5.030289 -3.779626 -1.216955 2.796333 0.412170 1.977772 4.343635 1.665250 -2.949788 -1.723266 -2.038868 1.410657 -1.227989 -3.588951 -4.800098 -5.537406 -5.391021 -5.042687 -5.418429 -4.894212 -3.738298 -1.910949 0.530025 0.403036 2.485423 -4.108577 6.431977 3.574931 0.357706 -4.191449 -7.127765 -4.720383 -4.381197 -4.920362 -5.465416 -5.275857 -4.551994 -5.094303 -4.665762 -3.821774 -2.569077 -1.551708 -2.740241 -2.007746 -2.710926 2.014191 2.443109 0.649396 -2.579619 -5.545824 -5.299243 -4.900675 -5.092487 -5.312958 -5.027621 -4.076468 -4.645640 -4.392586 -3.884793 -3.149200 -2.787350 -3.647165 -4.281798 -2.989016 -1.307309 -0.715204 -1.328664 -3.256158 -4.915648 -5.134740 -4.863261 -4.988565 -5.134724 -4.733023 -2.763624 -3.251033 -3.207432 -3.067273 -2.861244 -2.799529 -3.059140 -3.271614 -3.013550 -2.538976 -2.084266 -1.980492 -2.556963 -3.226087 -3.499139 -3.617384 -3.805748 -3.928953 -3.574482)

(InitialTransformParametersFileName "exampleoutput\TransformParameters.0.txt")

(HowToCombineTransforms "Compose")

// Image specific

(FixedImageDimension 2)

(MovingImageDimension 2)

(FixedInternalImagePixelType "float")

(MovingInternalImagePixelType "float")

(Size 256 256)

(Index 0 0)

(Spacing 1.0000000000 1.0000000000)

(Origin 0.0000000000 0.0000000000)

(Direction 1.0000000000 0.0000000000 0.0000000000 1.0000000000)

(UseDirectionCosines "true")

// BSplineTransform specific

(GridSize 19 19)

(GridIndex 0 0)

(GridSpacing 16.0028513433 16.0028513433)

(GridOrigin -17.9502905293 -16.9875303662)

(GridDirection 1.0000000000 0.0000000000 0.0000000000 1.0000000000)

(BSplineTransformSplineOrder 3)

(UseCyclicTransform "false")

// ResampleInterpolator specific

(ResampleInterpolator "FinalBSplineInterpolator")

(FinalBSplineInterpolationOrder 3)

// Resampler specific

(Resampler "DefaultResampler")

(DefaultPixelValue 0.000000)

(ResultImageFormat "mhd")

(ResultImagePixelType "short")

(CompressResultImage "false")

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