Running Atropos for 3-dimensional images.

Progress: 
  Iteration 0 (of 5): posterior probability = 0 (annealing temperature = 1)
  Iteration 1 (of 5): posterior probability = 0.596973 (annealing temperature = 1)

Writing output:
  Writing posterior image (class 1)
  Writing posterior image (class 2)
  Writing posterior image (class 3)
  Writing posterior image (class 4)
  Writing posterior image (class 5)
  Writing posterior image (class 6)

  AtroposSegmentationImageFilter (0x14edbc0)
    RTTI typeinfo:   itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >
    Reference Count: 1
    Modified Time: 4933
    Debug: Off
    Object Name: 
    Observers: 
      IterationEvent(Command)
    Inputs: 
      Primary: (0x14fb330) *
      _1: (0x14f5620)
    Indexed Inputs: 
      0: Primary (0x14fb330)
      1: _1 (0x14f5620)
    Required Input Names: Primary
    NumberOfRequiredInputs: 1
    Outputs: 
      Primary: (0xa996bf00)
    Indexed Outputs: 
      0: Primary (0xa996bf00)
    NumberOfRequiredOutputs: 1
    Number Of Work Units: 80
    ReleaseDataFlag: Off
    ReleaseDataBeforeUpdateFlag: Off
    AbortGenerateData: Off
    Progress: 0
    Multithreader: 
      RTTI typeinfo:   itk::PoolMultiThreader
      Reference Count: 1
      Modified Time: 203
      Debug: Off
      Object Name: 
      Observers: 
        none
      Number of Work Units: 80
      Number of Threads: 20
      Global Maximum Number Of Threads: 128
      Global Default Number Of Threads: 20
      Global Default Threader Type: itk::MultiThreaderBaseEnums::Threader::Pool
      SingleMethod: 0
      SingleData: 0
    DynamicMultiThreading: On
    CoordinateTolerance: 1e-06
    DirectionTolerance: 1e-06
    Maximum number of iterations: 5
    Convergence threshold: 0.0001
    Number of tissue classes: 6
    Number of partial volume classes: 0
    Minimize memory usage: false
    Initialization strategy: Random
    Posterior probability formulation: Socrates
      initial annealing temperature = 1
      annealing rate = 1
      minimum annealing temperature = 0.1
    MRF parameters
      MRF smoothing factor = 1
      MRF radius = [1, 1, 1]
    Use asynchronous updating of the labels.
      ICM parameters
        maximum ICM code = 14
        maximum number of ICM iterations = 1
    No outlier handling.
    Tissue class 1: proportion = 0.166628
      HistogramParzenWindowsListSampleFunction (0x1500000)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 2: proportion = 0.166864
      HistogramParzenWindowsListSampleFunction (0x14fe490)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 3: proportion = 0.167286
      HistogramParzenWindowsListSampleFunction (0x14fe550)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 4: proportion = 0.166422
      HistogramParzenWindowsListSampleFunction (0x14fe610)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 5: proportion = 0.166279
      HistogramParzenWindowsListSampleFunction (0x14fe6d0)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 6: proportion = 0.166034
      HistogramParzenWindowsListSampleFunction (0x14fe790)
        Sigma: 1
        Number of histogram bins: 32
Elapsed time: 287.229

Running Atropos for 3-dimensional images.

Progress: 
  Iteration 0 (of 5): posterior probability = 0 (annealing temperature = 1)
  Iteration 1 (of 5): posterior probability = 0.596973 (annealing temperature = 1)

Writing output:
  Writing posterior image (class 1)
  Writing posterior image (class 2)
  Writing posterior image (class 3)

  AtroposSegmentationImageFilter (0x2988bc0)
    RTTI typeinfo:   itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >
    Reference Count: 1
    Modified Time: 2952
    Debug: Off
    Object Name: 
    Observers: 
      IterationEvent(Command)
    Inputs: 
      Primary: (0x2996330) *
      _1: (0x2990620)
    Indexed Inputs: 
      0: Primary (0x2996330)
      1: _1 (0x2990620)
    Required Input Names: Primary
    NumberOfRequiredInputs: 1
    Outputs: 
      Primary: (0x15f9a4e60)
    Indexed Outputs: 
      0: Primary (0x15f9a4e60)
    NumberOfRequiredOutputs: 1
    Number Of Work Units: 80
    ReleaseDataFlag: Off
    ReleaseDataBeforeUpdateFlag: Off
    AbortGenerateData: Off
    Progress: 0
    Multithreader: 
      RTTI typeinfo:   itk::PoolMultiThreader
      Reference Count: 1
      Modified Time: 203
      Debug: Off
      Object Name: 
      Observers: 
        none
      Number of Work Units: 80
      Number of Threads: 20
      Global Maximum Number Of Threads: 128
      Global Default Number Of Threads: 20
      Global Default Threader Type: itk::MultiThreaderBaseEnums::Threader::Pool
      SingleMethod: 0
      SingleData: 0
    DynamicMultiThreading: On
    CoordinateTolerance: 1e-06
    DirectionTolerance: 1e-06
    Maximum number of iterations: 5
    Convergence threshold: 0.0001
    Number of tissue classes: 3
    Number of partial volume classes: 0
    Minimize memory usage: false
    Initialization strategy: Random
    Posterior probability formulation: Socrates
      initial annealing temperature = 1
      annealing rate = 1
      minimum annealing temperature = 0.1
    MRF parameters
      MRF smoothing factor = 1
      MRF radius = [1, 1, 1]
    Use asynchronous updating of the labels.
      ICM parameters
        maximum ICM code = 14
        maximum number of ICM iterations = 1
    No outlier handling.
    Tissue class 1: proportion = 0.332749
      HistogramParzenWindowsListSampleFunction (0x299b000)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 2: proportion = 0.331848
      HistogramParzenWindowsListSampleFunction (0x2999490)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 3: proportion = 0.335199
      HistogramParzenWindowsListSampleFunction (0x2999550)
        Sigma: 1
        Number of histogram bins: 32
Elapsed time: 190.734

Running Atropos for 3-dimensional images.

Progress: 
  Iteration 0 (of 5): posterior probability = 0 (annealing temperature = 1)
  Iteration 1 (of 5): posterior probability = 0.596973 (annealing temperature = 1)

Writing output:
  Writing posterior image (class 1)
  Writing posterior image (class 2)
  Writing posterior image (class 3)

  AtroposSegmentationImageFilter (0x13d8bc0)
    RTTI typeinfo:   itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >
    Reference Count: 1
    Modified Time: 407268300
    Debug: Off
    Object Name: 
    Observers: 
      IterationEvent(Command)
    Inputs: 
      Primary: (0x13e6330) *
      _1: (0x13e0620)
    Indexed Inputs: 
      0: Primary (0x13e6330)
      1: _1 (0x13e0620)
    Required Input Names: Primary
    NumberOfRequiredInputs: 1
    Outputs: 
      Primary: (0x66f2c9b0)
    Indexed Outputs: 
      0: Primary (0x66f2c9b0)
    NumberOfRequiredOutputs: 1
    Number Of Work Units: 80
    ReleaseDataFlag: Off
    ReleaseDataBeforeUpdateFlag: Off
    AbortGenerateData: Off
    Progress: 0
    Multithreader: 
      RTTI typeinfo:   itk::PoolMultiThreader
      Reference Count: 1
      Modified Time: 203
      Debug: Off
      Object Name: 
      Observers: 
        none
      Number of Work Units: 80
      Number of Threads: 20
      Global Maximum Number Of Threads: 128
      Global Default Number Of Threads: 20
      Global Default Threader Type: itk::MultiThreaderBaseEnums::Threader::Pool
      SingleMethod: 0
      SingleData: 0
    DynamicMultiThreading: On
    CoordinateTolerance: 1e-06
    DirectionTolerance: 1e-06
    Maximum number of iterations: 5
    Convergence threshold: 0.0001
    Number of tissue classes: 3
    Number of partial volume classes: 0
    Minimize memory usage: false
    Initialization strategy: K means clustering
    Posterior probability formulation: Socrates
      initial annealing temperature = 1
      annealing rate = 1
      minimum annealing temperature = 0.1
    MRF parameters
      MRF smoothing factor = 1
      MRF radius = [1, 1, 1]
    Use asynchronous updating of the labels.
      ICM parameters
        maximum ICM code = 14
        maximum number of ICM iterations = 1
    No outlier handling.
    Tissue class 1: proportion = 0.596973
      HistogramParzenWindowsListSampleFunction (0x13eb080)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 2: proportion = 0.0364827
      HistogramParzenWindowsListSampleFunction (0x13e9490)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 3: proportion = 0.0153199
      HistogramParzenWindowsListSampleFunction (0x13e9550)
        Sigma: 1
        Number of histogram bins: 32
Elapsed time: 176.519

Running Atropos for 3-dimensional images.

Progress: 
  Iteration 0 (of 5): posterior probability = 0 (annealing temperature = 1)
  Iteration 1 (of 5): posterior probability = 0.999974 (annealing temperature = 1)

Writing output:
  Writing posterior image (class 1)
  Writing posterior image (class 2)
  Writing posterior image (class 3)

  AtroposSegmentationImageFilter (0x15baac0)
    RTTI typeinfo:   itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >
    Reference Count: 1
    Modified Time: 49900104
    Debug: Off
    Object Name: 
    Observers: 
      IterationEvent(Command)
    Inputs: 
      Primary: (0x15c8310) *
      _1: (0x15c2530)
    Indexed Inputs: 
      0: Primary (0x15c8310)
      1: _1 (0x15c2530)
    Required Input Names: Primary
    NumberOfRequiredInputs: 1
    Outputs: 
      Primary: (0xef8bcb0)
    Indexed Outputs: 
      0: Primary (0xef8bcb0)
    NumberOfRequiredOutputs: 1
    Number Of Work Units: 80
    ReleaseDataFlag: Off
    ReleaseDataBeforeUpdateFlag: Off
    AbortGenerateData: Off
    Progress: 0
    Multithreader: 
      RTTI typeinfo:   itk::PoolMultiThreader
      Reference Count: 1
      Modified Time: 203
      Debug: Off
      Object Name: 
      Observers: 
        none
      Number of Work Units: 80
      Number of Threads: 20
      Global Maximum Number Of Threads: 128
      Global Default Number Of Threads: 20
      Global Default Threader Type: itk::MultiThreaderBaseEnums::Threader::Pool
      SingleMethod: 0
      SingleData: 0
    DynamicMultiThreading: On
    CoordinateTolerance: 1e-06
    DirectionTolerance: 1e-06
    Maximum number of iterations: 5
    Convergence threshold: 0.0001
    Number of tissue classes: 3
    Number of partial volume classes: 0
    Minimize memory usage: false
    Initialization strategy: K means clustering
    Posterior probability formulation: Socrates
      initial annealing temperature = 1
      annealing rate = 1
      minimum annealing temperature = 0.1
    MRF parameters
      MRF smoothing factor = 1
      MRF radius = [1, 1, 1]
    Use asynchronous updating of the labels.
      ICM parameters
        maximum ICM code = 14
        maximum number of ICM iterations = 1
    No outlier handling.
    Tissue class 1: proportion = 0.00121519
      HistogramParzenWindowsListSampleFunction (0x15ccf10)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 2: proportion = 0.998583
      HistogramParzenWindowsListSampleFunction (0x15cb400)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 3: proportion = 0.000202552
      HistogramParzenWindowsListSampleFunction (0x15cb4c0)
        Sigma: 1
        Number of histogram bins: 32
Elapsed time: 20.4935

Running Atropos for 3-dimensional images.

Progress: 
  Iteration 0 (of 5): posterior probability = 0 (annealing temperature = 1)
  Iteration 1 (of 5): posterior probability = 0.910161 (annealing temperature = 1)
  Iteration 2 (of 5): posterior probability = 0.965199 (annealing temperature = 1)
  Iteration 3 (of 5): posterior probability = 0.971929 (annealing temperature = 1)
  Iteration 4 (of 5): posterior probability = 0.975874 (annealing temperature = 1)

Writing output:
  Writing posterior image (class 1)
  Writing posterior image (class 2)
  Writing posterior image (class 3)

  AtroposSegmentationImageFilter (0x27e2ac0)
    RTTI typeinfo:   itk::ants::AtroposSegmentationImageFilter<itk::Image<float, 3u>, itk::Image<unsigned int, 3u>, itk::Image<unsigned int, 3u> >
    Reference Count: 1
    Modified Time: 5219
    Debug: Off
    Object Name: 
    Observers: 
      IterationEvent(Command)
    Inputs: 
      Primary: (0x27f0310) *
      _1: (0x27ea530)
    Indexed Inputs: 
      0: Primary (0x27f0310)
      1: _1 (0x27ea530)
    Required Input Names: Primary
    NumberOfRequiredInputs: 1
    Outputs: 
      Primary: (0x11d53fe0)
    Indexed Outputs: 
      0: Primary (0x11d53fe0)
    NumberOfRequiredOutputs: 1
    Number Of Work Units: 80
    ReleaseDataFlag: Off
    ReleaseDataBeforeUpdateFlag: Off
    AbortGenerateData: Off
    Progress: 0
    Multithreader: 
      RTTI typeinfo:   itk::PoolMultiThreader
      Reference Count: 1
      Modified Time: 203
      Debug: Off
      Object Name: 
      Observers: 
        none
      Number of Work Units: 80
      Number of Threads: 20
      Global Maximum Number Of Threads: 128
      Global Default Number Of Threads: 20
      Global Default Threader Type: itk::MultiThreaderBaseEnums::Threader::Pool
      SingleMethod: 0
      SingleData: 0
    DynamicMultiThreading: On
    CoordinateTolerance: 1e-06
    DirectionTolerance: 1e-06
    Maximum number of iterations: 5
    Convergence threshold: 0.0001
    Number of tissue classes: 3
    Number of partial volume classes: 0
    Minimize memory usage: false
    Initialization strategy: Random
    Posterior probability formulation: Socrates
      initial annealing temperature = 1
      annealing rate = 1
      minimum annealing temperature = 0.1
    MRF parameters
      MRF smoothing factor = 1
      MRF radius = [1, 1, 1]
    Use asynchronous updating of the labels.
      ICM parameters
        maximum ICM code = 14
        maximum number of ICM iterations = 1
    No outlier handling.
    Tissue class 1: proportion = 0.290977
      HistogramParzenWindowsListSampleFunction (0x27f4f10)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 2: proportion = 0.358764
      HistogramParzenWindowsListSampleFunction (0x27f3400)
        Sigma: 1
        Number of histogram bins: 32
    Tissue class 3: proportion = 0.350217
      HistogramParzenWindowsListSampleFunction (0x27f34c0)
        Sigma: 1
        Number of histogram bins: 32
Elapsed time: 40.8808
mean maximum posterior for 6 classes at out-random-6class with mask redacted-brainmask-map.nii.gz = 0.9782532804268764
raw mean maximum posterior (disregarding mask) = 0.15025240482942107

mean maximum posterior for 3 classes at out-random-3class with mask redacted-brainmask-map.nii.gz = 0.9855073267560869
raw mean maximum posterior (disregarding mask) = 0.15136657222095007

mean maximum posterior for 3 classes at out-kmeans-3class with mask redacted-brainmask-map.nii.gz = 0.9995354349536029
raw mean maximum posterior (disregarding mask) = 0.15352118497212258

mean maximum posterior for 3 classes at out-nobug-kmeans-3class with mask brainmask.nii.gz = 0.9999531303537921
raw mean maximum posterior (disregarding mask) = 0.1554687011973653

mean maximum posterior for 3 classes at out-nobug-random-3class with mask brainmask.nii.gz = 0.9785478443309583
raw mean maximum posterior (disregarding mask) = 0.15214069319807974