itk::ERROR: ImageToImageFilter Inputs do not occupy the same physical space! After two BSpline registration phases

[gdevenyi]

Followup to my comment on #74.

Built on current HEAD

The run command:

antsRegistration --dimensionality 3 --float 0 --collapse-output-transforms 1 --verbose \
--output [nifti//brain1_0.5_t1.nii.gz-brain2_0.5_t1.nii.gz,nifti//brain1_0.5_t1.nii.gz-brain2_0.5_t1.nii.gz] \
--winsorize-image-intensities [0.005,0.995] --use-histogram-matching 1 --initial-moving-transform [nifti/brain2_0.5_t1.nii.gz,nifti/brain1_0.5_t1.nii.gz,1] \
--transform Rigid[0.1] --metric Mattes[nifti/brain2_0.5_t1.nii.gz,nifti/brain1_0.5_t1.nii.gz,1,32,Regular,0.25] --convergence [2000,1e-6,10,1] --shrink-factors 16 --smoothing-sigmas 6.7945 --masks [NULL,NULL] \
--transform Similarity[0.1] --metric Mattes[nifti/brain2_0.5_t1.nii.gz,nifti/brain1_0.5_t1.nii.gz,1,32,Regular,0.25] --convergence [1000,1e-6,10,1] --shrink-factors 8 --smoothing-sigmas 3.3973 --masks [NULL,NULL] \
--transform Affine[0.1] --metric Mattes[nifti/brain2_0.5_t1.nii.gz,nifti/brain1_0.5_t1.nii.gz,1,32,Regular,0.5] --convergence [500x250,1e-6,10,1] --shrink-factors 8x8 --smoothing-sigmas 3.3973x1.6986 --masks [NULL,NULL] \
--transform Affine[0.1] --metric Mattes[nifti/brain2_0.5_t1.nii.gz,nifti/brain1_0.5_t1.nii.gz,1,32,Regular,1] --convergence [175x100x0,1e-6,10,1] --shrink-factors 8x4x1 --smoothing-sigmas 0.8493x0.4247x0 --masks [nifti/brain2_0.5_mask.nii.gz,nifti/brain1_0.5_mask.nii.gz] \
--transform BSplineSyN[0.1,26,0,3] --metric CC[nifti/brain2_0.5_t1.nii.gz,nifti/brain1_0.5_t1.nii.gz,1,4] --convergence [100x100x100x0,1e-6,10] --shrink-factors 16x8x4x2 --smoothing-sigmas 3x2x1x0 --masks [NULL,NULL] \
--transform BSplineSyN[0.1,3,0,3] --metric CC[nifti/brain2_0.5_t1.nii.gz,nifti/brain1_0.5_t1.nii.gz,1,6] --convergence [20,1e-6,10] --shrink-factors 1 --smoothing-sigmas 0 --masks [nifti/brain2_0.5_mask.nii.gz,nifti/brain1_0.5_mask.nii.gz]

Example files used:
https://www.dropbox.com/sh/5ea8lff1nb0skmr/AADughEXzPYWhQ1Q5uCw653Ga?dl=0

The log

All_Command_lines_OK
Using double precision for computations.
=============================================================================
The composite transform comprises the following transforms (in order): 
  1. Center of mass alignment using fixed image: nifti/brain2_0.5_t1.nii.gz and moving image: nifti/brain1_0.5_t1.nii.gz (type = Euler3DTransform)
=============================================================================
  Reading mask(s).
    Registration stage 0
      No fixed mask
      No moving mask
    Registration stage 1
      No fixed mask
      No moving mask
    Registration stage 2
      No fixed mask
      No moving mask
    Registration stage 3
      Fixed mask = nifti/brain2_0.5_mask.nii.gz
      Moving mask = nifti/brain1_0.5_mask.nii.gz
    Registration stage 4
      No fixed mask
      No moving mask
    Registration stage 5
      Fixed mask = nifti/brain2_0.5_mask.nii.gz
      Moving mask = nifti/brain1_0.5_mask.nii.gz
  number of levels = 1
  number of levels = 1
  number of levels = 2
  number of levels = 3
  number of levels = 4
  number of levels = 1
  fixed image: nifti/brain2_0.5_t1.nii.gz
  moving image: nifti/brain1_0.5_t1.nii.gz
  fixed image: nifti/brain2_0.5_t1.nii.gz
  moving image: nifti/brain1_0.5_t1.nii.gz
  fixed image: nifti/brain2_0.5_t1.nii.gz
  moving image: nifti/brain1_0.5_t1.nii.gz
  fixed image: nifti/brain2_0.5_t1.nii.gz
  moving image: nifti/brain1_0.5_t1.nii.gz
  fixed image: nifti/brain2_0.5_t1.nii.gz
  moving image: nifti/brain1_0.5_t1.nii.gz
  fixed image: nifti/brain2_0.5_t1.nii.gz
  moving image: nifti/brain1_0.5_t1.nii.gz
Dimension = 3
Number of stages = 6
Use Histogram Matching true
Winsorize image intensities true
Lower quantile = 0.005
Upper quantile = 0.995
Stage 1 State
   Image metric = Mattes
     Fixed image = Image (0x3f05670)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 3831
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 3652
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.0688, 87.1857, -47.7607]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f018b0)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 3649
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7f8eff493010
      Container manages memory: true
      Size: 55569260
      Capacity: 55569260

     Moving image = Image (0x3f03880)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 3832
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 3829
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.3061, 80.0497, -30.7617]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f05a70)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 3826
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7f8ee8318010
      Container manages memory: true
      Size: 48428523
      Capacity: 48428523

     Weighting = 1
     Sampling strategy = regular
     Number of bins = 32
     Radius = 4
     Sampling percentage  = 0.25
   Transform = Rigid
     Gradient step = 0.1
     Update field sigma (voxel space) = 0
     Total field sigma (voxel space) = 0
     Update field time sigma = 0
     Total field time sigma  = 0
     Number of time indices = 0
     Number of time point samples = 0
Stage 2 State
   Image metric = Mattes
     Fixed image = Image (0x3f0e860)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 4187
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 4008
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.0688, 87.1857, -47.7607]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f0eaf0)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 4005
      Debug: Off
      Object Name: 
      Observers: 
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      Pointer: 0x7f8ecdb22010
      Container manages memory: true
      Size: 55569260
      Capacity: 55569260

     Moving image = Image (0x3f0efb0)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 4188
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 4185
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.3061, 80.0497, -30.7617]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f0f240)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 4182
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7f8eb69a7010
      Container manages memory: true
      Size: 48428523
      Capacity: 48428523

     Weighting = 1
     Sampling strategy = regular
     Number of bins = 32
     Radius = 4
     Sampling percentage  = 0.25
   Transform = Similarity
     Gradient step = 0.1
     Update field sigma (voxel space) = 0
     Total field sigma (voxel space) = 0
     Update field time sigma = 0
     Total field time sigma  = 0
     Number of time indices = 0
     Number of time point samples = 0
Stage 3 State
   Image metric = Mattes
     Fixed image = Image (0x3f13d70)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 4543
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 4364
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.0688, 87.1857, -47.7607]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f14000)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 4361
      Debug: Off
      Object Name: 
      Observers: 
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      Pointer: 0x7f8e9c1b1010
      Container manages memory: true
      Size: 55569260
      Capacity: 55569260

     Moving image = Image (0x3f16770)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 4544
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 4541
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.3061, 80.0497, -30.7617]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f16a00)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 4538
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7f8e85036010
      Container manages memory: true
      Size: 48428523
      Capacity: 48428523

     Weighting = 1
     Sampling strategy = regular
     Number of bins = 32
     Radius = 4
     Sampling percentage  = 0.5
   Transform = Affine
     Gradient step = 0.1
     Update field sigma (voxel space) = 0
     Total field sigma (voxel space) = 0
     Update field time sigma = 0
     Total field time sigma  = 0
     Number of time indices = 0
     Number of time point samples = 0
Stage 4 State
   Image metric = Mattes
     Fixed image = Image (0x3f19140)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 4899
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 4720
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.0688, 87.1857, -47.7607]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f13720)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 4717
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7f8e6a840010
      Container manages memory: true
      Size: 55569260
      Capacity: 55569260

     Moving image = Image (0x3f1bd90)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 4900
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 4897
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.3061, 80.0497, -30.7617]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f1c020)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 4894
      Debug: Off
      Object Name: 
      Observers: 
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      Pointer: 0x7f8e536c5010
      Container manages memory: true
      Size: 48428523
      Capacity: 48428523

     Weighting = 1
     Sampling strategy = regular
     Number of bins = 32
     Radius = 4
     Sampling percentage  = 1
   Transform = Affine
     Gradient step = 0.1
     Update field sigma (voxel space) = 0
     Total field sigma (voxel space) = 0
     Update field time sigma = 0
     Total field time sigma  = 0
     Number of time indices = 0
     Number of time point samples = 0
Stage 5 State
   Image metric = CC
     Fixed image = Image (0x3f1e7d0)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 5255
  Debug: Off
  Object Name: 
  Observers: 
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  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 5076
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.0688, 87.1857, -47.7607]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f1ea60)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 5073
      Debug: Off
      Object Name: 
      Observers: 
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      Pointer: 0x7f8e38ecf010
      Container manages memory: true
      Size: 55569260
      Capacity: 55569260

     Moving image = Image (0x3f211b0)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 5256
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 5253
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.3061, 80.0497, -30.7617]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f1bb40)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 5250
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7f8e21d54010
      Container manages memory: true
      Size: 48428523
      Capacity: 48428523

     Weighting = 1
     Sampling strategy = none
     Number of bins = 32
     Radius = 4
     Sampling percentage  = 1
   Transform = BSplineSyN
     Gradient step = 0.1
     Update field sigma (voxel space) = 0
     Total field sigma (voxel space) = 0
     Update field time sigma = 0
     Total field time sigma  = 0
     Number of time indices = 0
     Number of time point samples = 0
Stage 6 State
   Image metric = CC
     Fixed image = Image (0x3f23bb0)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 5611
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 5432
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [340, 463, 353]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.0688, 87.1857, -47.7607]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f23e40)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 5429
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7f8e0755e010
      Container manages memory: true
      Size: 55569260
      Capacity: 55569260

     Moving image = Image (0x3f24300)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 5612
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 0
  UpdateMTime: 5609
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [333, 429, 339]
  Spacing: [0.5, 0.5, 0.5]
  Origin: [85.3061, 80.0497, -30.7617]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.5 0 0
0 -0.5 0
0 0 0.5

  PointToIndexMatrix: 
-2 0 0
0 -2 0
0 0 2

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 1

  PixelContainer: 
    ImportImageContainer (0x3f24590)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 5606
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7f8df03e3010
      Container manages memory: true
      Size: 48428523
      Capacity: 48428523

     Weighting = 1
     Sampling strategy = none
     Number of bins = 32
     Radius = 6
     Sampling percentage  = 1
   Transform = BSplineSyN
     Gradient step = 0.1
     Update field sigma (voxel space) = 0
     Total field sigma (voxel space) = 0
     Update field time sigma = 0
     Total field time sigma  = 0
     Number of time indices = 0
     Number of time point samples = 0
Registration using 6 total stages.

Stage 0
  iterations = 2000
  convergence threshold = 1e-06
  convergence window size = 10
  number of levels = 1
  using the Mattes MI metric (number of bins = 32, weight = 1)
  preprocessing:  winsorizing the image intensities
  preprocessing:  histogram matching the images
  Shrink factors (level 1 out of 1): [16, 16, 16]
  smoothing sigmas per level: [6.79449987411499]
  regular sampling (percentage = 0.25)

*** Running Euler3DTransform registration ***

DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -7.836705285958e-01, 1.797693134862e+308, 1.1463e+01, 1.1463e+01, 
 2DIAGNOSTIC,     2, -7.857861783407e-01, 1.797693134862e+308, 1.1481e+01, 1.8124e-02, 
 2DIAGNOSTIC,     3, -7.886186862220e-01, 1.797693134862e+308, 1.1498e+01, 1.7078e-02, 
 2DIAGNOSTIC,     4, -7.921870966121e-01, 1.797693134862e+308, 1.1514e+01, 1.6272e-02, 
 2DIAGNOSTIC,     5, -7.948521016086e-01, 1.797693134862e+308, 1.1531e+01, 1.6657e-02, 
 2DIAGNOSTIC,     6, -7.959243519627e-01, 1.797693134862e+308, 1.1548e+01, 1.6946e-02, 
 2DIAGNOSTIC,     7, -7.986868988893e-01, 1.797693134862e+308, 1.1567e+01, 1.9383e-02, 
 2DIAGNOSTIC,     8, -8.091715412056e-01, 1.797693134862e+308, 1.1591e+01, 2.3654e-02, 
 2DIAGNOSTIC,     9, -8.097135404881e-01, 1.797693134862e+308, 1.1609e+01, 1.7958e-02, 
 2DIAGNOSTIC,    10, -8.101094873127e-01, 2.320923246089e-03, 1.1627e+01, 1.8002e-02, 
 2DIAGNOSTIC,    11, -8.112681654886e-01, 2.064978237611e-03, 1.1647e+01, 2.0177e-02, 
 2DIAGNOSTIC,    12, -8.118117584544e-01, 1.743298498407e-03, 1.1664e+01, 1.7279e-02, 
 2DIAGNOSTIC,    13, -8.122801932526e-01, 1.398484653206e-03, 1.1686e+01, 2.1785e-02, 
 2DIAGNOSTIC,    14, -8.132035209513e-01, 1.089245848167e-03, 1.1714e+01, 2.8030e-02, 
 2DIAGNOSTIC,    15, -8.131504291719e-01, 7.878985398396e-04, 1.1742e+01, 2.8122e-02, 
 2DIAGNOSTIC,    16, -8.133907745248e-01, 4.829312657540e-04, 1.1759e+01, 1.6854e-02, 
 2DIAGNOSTIC,    17, -8.137248530061e-01, 2.283378770517e-04, 1.1778e+01, 1.9043e-02, 
 2DIAGNOSTIC,    18, -8.141602963756e-01, 1.956805775548e-04, 1.1797e+01, 1.8766e-02, 
 2DIAGNOSTIC,    19, -8.145123306381e-01, 1.649764271073e-04, 1.1818e+01, 2.0794e-02, 
 2DIAGNOSTIC,    20, -8.145665194536e-01, 1.297741174424e-04, 1.1836e+01, 1.8084e-02, 
 2DIAGNOSTIC,    21, -8.146220556173e-01, 1.065946555024e-04, 1.1857e+01, 2.1194e-02, 
 2DIAGNOSTIC,    22, -8.146611520172e-01, 8.497595296301e-05, 1.1882e+01, 2.4643e-02, 
 2DIAGNOSTIC,    23, -8.147567364748e-01, 6.558904343950e-05, 1.1906e+01, 2.4303e-02, 
 2DIAGNOSTIC,    24, -8.148615882157e-01, 5.692398530370e-05, 1.1984e+01, 7.8447e-02, 
 2DIAGNOSTIC,    25, -8.148615878681e-01, 4.300166375341e-05, 1.2005e+01, 2.0480e-02, 
 2DIAGNOSTIC,    26, -8.148615912212e-01, 2.953255417151e-05, 1.2023e+01, 1.8557e-02, 
 2DIAGNOSTIC,    27, -8.148615968893e-01, 1.867066188162e-05, 1.2045e+01, 2.1277e-02, 
 2DIAGNOSTIC,    28, -8.148616064689e-01, 1.228013310540e-05, 1.2063e+01, 1.8382e-02, 
 2DIAGNOSTIC,    29, -8.148616226528e-01, 9.523727583727e-06, 1.2084e+01, 2.0627e-02, 
 2DIAGNOSTIC,    30, -8.148616499856e-01, 6.792822686577e-06, 1.2100e+01, 1.6326e-02, 
 2DIAGNOSTIC,    31, -8.148616960940e-01, 4.347828400010e-06, 1.2117e+01, 1.7009e-02, 
 2DIAGNOSTIC,    32, -8.148617737142e-01, 2.156886716509e-06, 1.2134e+01, 1.6839e-02, 
  Elapsed time (stage 0): 1.8435e+01


Stage 1
  iterations = 1000
  convergence threshold = 1.0000e-06
  convergence window size = 10
  number of levels = 1
  using the Mattes MI metric (number of bins = 32, weight = 1.0000e+00)
  preprocessing:  winsorizing the image intensities
  preprocessing:  histogram matching the images
  Shrink factors (level 1 out of 1): [8, 8, 8]
  smoothing sigmas per level: [3.3973000049591064]
  regular sampling (percentage = 2.5000e-01)

*** Running Similarity3DTransform registration ***

DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -6.322798915387e-01, 1.797693134862e+308, 6.0301e+00, 6.0301e+00, 
 2DIAGNOSTIC,     2, -6.334991738614e-01, 1.797693134862e+308, 6.0623e+00, 3.2228e-02, 
 2DIAGNOSTIC,     3, -6.350820027709e-01, 1.797693134862e+308, 6.0915e+00, 2.9219e-02, 
 2DIAGNOSTIC,     4, -6.371873184720e-01, 1.797693134862e+308, 6.1177e+00, 2.6187e-02, 
 2DIAGNOSTIC,     5, -6.398321138393e-01, 1.797693134862e+308, 6.1448e+00, 2.7033e-02, 
 2DIAGNOSTIC,     6, -6.423239599754e-01, 1.797693134862e+308, 6.1765e+00, 3.1688e-02, 
 2DIAGNOSTIC,     7, -6.438567128911e-01, 1.797693134862e+308, 6.2082e+00, 3.1721e-02, 
 2DIAGNOSTIC,     8, -6.448282062260e-01, 1.797693134862e+308, 6.2585e+00, 5.0329e-02, 
 2DIAGNOSTIC,     9, -6.449199965507e-01, 1.797693134862e+308, 6.2851e+00, 2.6617e-02, 
 2DIAGNOSTIC,    10, -6.451310796311e-01, 1.477626732670e-03, 6.3176e+00, 3.2456e-02, 
 2DIAGNOSTIC,    11, -6.452655109343e-01, 1.155204905559e-03, 6.3516e+00, 3.3982e-02, 
 2DIAGNOSTIC,    12, -6.453556131488e-01, 8.314532501886e-04, 6.3846e+00, 3.3024e-02, 
 2DIAGNOSTIC,    13, -6.454302320510e-01, 5.392897852742e-04, 6.4168e+00, 3.2179e-02, 
 2DIAGNOSTIC,    14, -6.455806208935e-01, 3.109569947226e-04, 6.4788e+00, 6.2028e-02, 
 2DIAGNOSTIC,    15, -6.455804412239e-01, 1.618807609529e-04, 6.5116e+00, 3.2812e-02, 
 2DIAGNOSTIC,    16, -6.455972090124e-01, 8.544998699363e-05, 6.5451e+00, 3.3526e-02, 
 2DIAGNOSTIC,    17, -6.456242352265e-01, 5.036841396705e-05, 6.5794e+00, 3.4291e-02, 
 2DIAGNOSTIC,    18, -6.456529395066e-01, 3.929493816797e-05, 6.6144e+00, 3.4980e-02, 
 2DIAGNOSTIC,    19, -6.457070540167e-01, 2.917354936759e-05, 6.6468e+00, 3.2390e-02, 
 2DIAGNOSTIC,    20, -6.456727135337e-01, 2.135788389521e-05, 6.6790e+00, 3.2193e-02, 
 2DIAGNOSTIC,    21, -6.457376351590e-01, 1.669850901208e-05, 6.7270e+00, 4.8056e-02, 
 2DIAGNOSTIC,    22, -6.458178221168e-01, 1.442182752671e-05, 6.7687e+00, 4.1629e-02, 
 2DIAGNOSTIC,    23, -6.458261502744e-01, 1.259181550406e-05, 6.8080e+00, 3.9382e-02, 
 2DIAGNOSTIC,    24, -6.458291154865e-01, 1.271662077224e-05, 6.8482e+00, 4.0133e-02, 
 2DIAGNOSTIC,    25, -6.458291959475e-01, 1.179187364896e-05, 6.8920e+00, 4.3823e-02, 
 2DIAGNOSTIC,    26, -6.458294556347e-01, 1.022806376837e-05, 6.9286e+00, 3.6632e-02, 
 2DIAGNOSTIC,    27, -6.458287506456e-01, 8.325536867498e-06, 6.9700e+00, 4.1318e-02, 
 2DIAGNOSTIC,    28, -6.458281703148e-01, 6.308184263996e-06, 7.0068e+00, 3.6817e-02, 
 2DIAGNOSTIC,    29, -6.458267714068e-01, 4.790781473682e-06, 7.0446e+00, 3.7863e-02, 
 2DIAGNOSTIC,    30, -6.458253042482e-01, 2.487963804136e-06, 7.0770e+00, 3.2369e-02, 
 2DIAGNOSTIC,    31, -6.458246242560e-01, 1.083748962426e-06, 7.1123e+00, 3.5336e-02, 
  Elapsed time (stage 1): 1.3530e+01


Stage 2
  iterations = 500x250
  convergence threshold = 1.0000e-06
  convergence window size = 10
  number of levels = 2
  using the Mattes MI metric (number of bins = 32, weight = 1.0000e+00)
  preprocessing:  winsorizing the image intensities
  preprocessing:  histogram matching the images
  Shrink factors (level 1 out of 2): [8, 8, 8]
  Shrink factors (level 2 out of 2): [8, 8, 8]
  smoothing sigmas per level: [3.3973000049591064, 1.6986000537872314]
  regular sampling (percentage = 5.0000e-01)

*** Running AffineTransform registration ***

DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -6.412757654181e-01, 1.797693134862e+308, 6.2212e+00, 6.2212e+00, 
 2DIAGNOSTIC,     2, -6.441293999004e-01, 1.797693134862e+308, 6.2810e+00, 5.9745e-02, 
 2DIAGNOSTIC,     3, -6.488158458183e-01, 1.797693134862e+308, 6.3409e+00, 5.9907e-02, 
 2DIAGNOSTIC,     4, -6.562740323322e-01, 1.797693134862e+308, 6.4003e+00, 5.9442e-02, 
 2DIAGNOSTIC,     5, -6.680782723484e-01, 1.797693134862e+308, 6.4581e+00, 5.7767e-02, 
 2DIAGNOSTIC,     6, -7.027618919844e-01, 1.797693134862e+308, 6.5387e+00, 8.0624e-02, 
 2DIAGNOSTIC,     7, -7.261136788946e-01, 1.797693134862e+308, 6.5985e+00, 5.9771e-02, 
 2DIAGNOSTIC,     8, -7.369930888939e-01, 1.797693134862e+308, 6.6560e+00, 5.7549e-02, 
 2DIAGNOSTIC,     9, -7.456882694082e-01, 1.797693134862e+308, 6.7156e+00, 5.9530e-02, 
 2DIAGNOSTIC,    10, -7.541103071695e-01, 1.239087030017e-02, 6.7878e+00, 7.2191e-02, 
 2DIAGNOSTIC,    11, -7.612519883361e-01, 1.138974166674e-02, 6.8592e+00, 7.1486e-02, 
 2DIAGNOSTIC,    12, -7.637271126187e-01, 9.719376880808e-03, 6.9285e+00, 6.9284e-02, 
 2DIAGNOSTIC,    13, -7.655654695290e-01, 7.664633675960e-03, 7.0062e+00, 7.7661e-02, 
 2DIAGNOSTIC,    14, -7.659534153908e-01, 5.465905371706e-03, 7.0696e+00, 6.3381e-02, 
 2DIAGNOSTIC,    15, -7.662131668027e-01, 3.385102554553e-03, 7.1389e+00, 6.9317e-02, 
 2DIAGNOSTIC,    16, -7.665601734758e-01, 2.123971351614e-03, 7.2076e+00, 6.8664e-02, 
 2DIAGNOSTIC,    17, -7.668398177386e-01, 1.369214698168e-03, 7.2711e+00, 6.3596e-02, 
 2DIAGNOSTIC,    18, -7.670315328471e-01, 8.168726572661e-04, 7.3548e+00, 8.3630e-02, 
 2DIAGNOSTIC,    19, -7.673072994864e-01, 4.325370869060e-04, 7.4264e+00, 7.1575e-02, 
 2DIAGNOSTIC,    20, -7.676100826540e-01, 2.157916033092e-04, 7.4883e+00, 6.1973e-02, 
 2DIAGNOSTIC,    21, -7.677170476148e-01, 1.340645260880e-04, 7.5590e+00, 7.0705e-02, 
 2DIAGNOSTIC,    22, -7.677692537754e-01, 9.154559320981e-05, 7.6212e+00, 6.2133e-02, 
 2DIAGNOSTIC,    23, -7.678631929617e-01, 7.696111391375e-05, 7.6993e+00, 7.8176e-02, 
 2DIAGNOSTIC,    24, -7.679460273889e-01, 6.407003530655e-05, 7.7690e+00, 6.9616e-02, 
 2DIAGNOSTIC,    25, -7.680494374493e-01, 5.181999021255e-05, 7.8313e+00, 6.2328e-02, 
 2DIAGNOSTIC,    26, -7.682408925022e-01, 4.371274829055e-05, 7.9011e+00, 6.9856e-02, 
 2DIAGNOSTIC,    27, -7.682812549818e-01, 3.677017889164e-05, 7.9728e+00, 7.1632e-02, 
 2DIAGNOSTIC,    28, -7.682906530306e-01, 2.972773540170e-05, 8.0349e+00, 6.2102e-02, 
 2DIAGNOSTIC,    29, -7.683075588464e-01, 2.429515968858e-05, 8.1048e+00, 6.9975e-02, 
 2DIAGNOSTIC,    30, -7.683149307384e-01, 2.096658060534e-05, 8.2079e+00, 1.0303e-01, 
 2DIAGNOSTIC,    31, -7.683159140291e-01, 1.728099345995e-05, 8.2792e+00, 7.1317e-02, 
 2DIAGNOSTIC,    32, -7.683149762576e-01, 1.289703512621e-05, 8.3424e+00, 6.3230e-02, 
 2DIAGNOSTIC,    33, -7.683144522182e-01, 8.763740164647e-06, 8.4126e+00, 7.0211e-02, 
 2DIAGNOSTIC,    34, -7.683135999602e-01, 5.060212364384e-06, 8.4768e+00, 6.4185e-02, 
 2DIAGNOSTIC,    35, -7.683115998544e-01, 2.235085244873e-06, 8.5396e+00, 6.2808e-02, 
 2DIAGNOSTIC,    36, -7.683133985477e-01, 1.483798612176e-06, 8.6151e+00, 7.5502e-02, 
 2DIAGNOSTIC,    37, -7.683141322562e-01, 1.142001566357e-06, 8.6769e+00, 6.1736e-02, 
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -6.874362331971e-01, 1.797693134862e+308, 1.2841e+01, 4.1643e+00, 
 2DIAGNOSTIC,     2, -6.879166701681e-01, 1.797693134862e+308, 1.2903e+01, 6.1760e-02, 
 2DIAGNOSTIC,     3, -6.886567428966e-01, 1.797693134862e+308, 1.2977e+01, 7.4499e-02, 
 2DIAGNOSTIC,     4, -6.887429114593e-01, 1.797693134862e+308, 1.3034e+01, 5.6451e-02, 
 2DIAGNOSTIC,     5, -6.890651156581e-01, 1.797693134862e+308, 1.3091e+01, 5.7252e-02, 
 2DIAGNOSTIC,     6, -6.892058433994e-01, 1.797693134862e+308, 1.3179e+01, 8.7418e-02, 
 2DIAGNOSTIC,     7, -6.892096592536e-01, 1.797693134862e+308, 1.3235e+01, 5.6647e-02, 
 2DIAGNOSTIC,     8, -6.892273563762e-01, 1.797693134862e+308, 1.3292e+01, 5.6477e-02, 
 2DIAGNOSTIC,     9, -6.892424329904e-01, 1.797693134862e+308, 1.3350e+01, 5.7999e-02, 
 2DIAGNOSTIC,    10, -6.892483242958e-01, 1.522200460206e-04, 1.3421e+01, 7.1646e-02, 
 2DIAGNOSTIC,    11, -6.892493153111e-01, 8.828388043823e-05, 1.3483e+01, 6.2025e-02, 
 2DIAGNOSTIC,    12, -6.892597794385e-01, 4.370510240435e-05, 1.3547e+01, 6.3222e-02, 
 2DIAGNOSTIC,    13, -6.892840494286e-01, 2.663791510933e-05, 1.3628e+01, 8.1480e-02, 
 2DIAGNOSTIC,    14, -6.892868375111e-01, 1.218756811093e-05, 1.3756e+01, 1.2770e-01, 
 2DIAGNOSTIC,    15, -6.892869757618e-01, 7.529062791056e-06, 1.3821e+01, 6.5309e-02, 
 2DIAGNOSTIC,    16, -6.892894850350e-01, 6.668177047572e-06, 1.3890e+01, 6.8862e-02, 
 2DIAGNOSTIC,    17, -6.892907799951e-01, 5.589105181530e-06, 1.3955e+01, 6.4700e-02, 
 2DIAGNOSTIC,    18, -6.892917136236e-01, 4.695001666152e-06, 1.4018e+01, 6.3028e-02, 
 2DIAGNOSTIC,    19, -6.892948001084e-01, 4.016053182600e-06, 1.4082e+01, 6.3848e-02, 
 2DIAGNOSTIC,    20, -6.892963270092e-01, 3.349031327239e-06, 1.4144e+01, 6.2318e-02, 
 2DIAGNOSTIC,    21, -6.893008460802e-01, 2.689996398915e-06, 1.4208e+01, 6.3877e-02, 
 2DIAGNOSTIC,    22, -6.893049741520e-01, 2.240623889108e-06, 1.4270e+01, 6.2735e-02, 
 2DIAGNOSTIC,    23, -6.893131110816e-01, 2.335226908873e-06, 1.4334e+01, 6.3050e-02, 
 2DIAGNOSTIC,    24, -6.893378717781e-01, 2.804024794280e-06, 1.4396e+01, 6.2158e-02, 
 2DIAGNOSTIC,    25, -6.894114361291e-01, 4.301820314814e-06, 1.4460e+01, 6.4747e-02, 
 2DIAGNOSTIC,    26, -6.895346538745e-01, 7.366019612293e-06, 1.4561e+01, 1.0062e-01, 
 2DIAGNOSTIC,    27, -6.895504792030e-01, 9.850705830566e-06, 1.4625e+01, 6.3948e-02, 
 2DIAGNOSTIC,    28, -6.895775087757e-01, 1.178098911098e-05, 1.4688e+01, 6.2953e-02, 
 2DIAGNOSTIC,    29, -6.896250664452e-01, 1.330402743854e-05, 1.4774e+01, 8.5851e-02, 
 2DIAGNOSTIC,    30, -6.896308591536e-01, 1.363725797651e-05, 1.4838e+01, 6.4366e-02, 
 2DIAGNOSTIC,    31, -6.896540598029e-01, 1.311151414730e-05, 1.4903e+01, 6.5107e-02, 
 2DIAGNOSTIC,    32, -6.896836596714e-01, 1.191606768447e-05, 1.4968e+01, 6.4684e-02, 
 2DIAGNOSTIC,    33, -6.897247969077e-01, 1.038566048969e-05, 1.5047e+01, 7.9329e-02, 
 2DIAGNOSTIC,    34, -6.897593791152e-01, 8.749600995128e-06, 1.5165e+01, 1.1803e-01, 
 2DIAGNOSTIC,    35, -6.897626704580e-01, 7.331528997109e-06, 1.5244e+01, 7.9111e-02, 
 2DIAGNOSTIC,    36, -6.897627993348e-01, 6.807150566210e-06, 1.5319e+01, 7.4229e-02, 
 2DIAGNOSTIC,    37, -6.897622505927e-01, 5.914920382481e-06, 1.5390e+01, 7.1596e-02, 
 2DIAGNOSTIC,    38, -6.897624965353e-01, 4.864922369809e-06, 1.5462e+01, 7.1788e-02, 
 2DIAGNOSTIC,    39, -6.897632507164e-01, 3.993996464557e-06, 1.5533e+01, 7.0768e-02, 
 2DIAGNOSTIC,    40, -6.897630838594e-01, 2.923106100262e-06, 1.5606e+01, 7.3606e-02, 
 2DIAGNOSTIC,    41, -6.897619082426e-01, 1.925142679521e-06, 1.5677e+01, 7.0521e-02, 
 2DIAGNOSTIC,    42, -6.897616489903e-01, 1.146606169438e-06, 1.5749e+01, 7.2008e-02, 
  Elapsed time (stage 2): 2.2510e+01


Stage 3
  iterations = 175x100x0
  convergence threshold = 1.0000e-06
  convergence window size = 10
  number of levels = 3
  using the Mattes MI metric (number of bins = 32, weight = 1.0000e+00)
  preprocessing:  winsorizing the image intensities
  preprocessing:  histogram matching the images
  Shrink factors (level 1 out of 3): [8, 8, 8]
  Shrink factors (level 2 out of 3): [4, 4, 4]
  Shrink factors (level 3 out of 3): [1, 1, 1]
  smoothing sigmas per level: [0.8493000268936157, 0.424699991941452, 0]
  regular sampling (percentage = 1.0000e+00)

*** Running AffineTransform registration ***

DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -1.358874621575e-01, 1.797693134862e+308, 6.1831e+00, 6.1831e+00, 
 2DIAGNOSTIC,     2, -1.370737055522e-01, 1.797693134862e+308, 6.2226e+00, 3.9533e-02, 
 2DIAGNOSTIC,     3, -1.384631291551e-01, 1.797693134862e+308, 6.2603e+00, 3.7735e-02, 
 2DIAGNOSTIC,     4, -1.402845493714e-01, 1.797693134862e+308, 6.2940e+00, 3.3703e-02, 
 2DIAGNOSTIC,     5, -1.427556151029e-01, 1.797693134862e+308, 6.3283e+00, 3.4304e-02, 
 2DIAGNOSTIC,     6, -1.551851169171e-01, 1.797693134862e+308, 6.3699e+00, 4.1551e-02, 
 2DIAGNOSTIC,     7, -1.647938902862e-01, 1.797693134862e+308, 6.4145e+00, 4.4591e-02, 
 2DIAGNOSTIC,     8, -1.689614713120e-01, 1.797693134862e+308, 6.4546e+00, 4.0107e-02, 
 2DIAGNOSTIC,     9, -1.747808553726e-01, 1.797693134862e+308, 6.4999e+00, 4.5328e-02, 
 2DIAGNOSTIC,    10, -1.781676550498e-01, 2.037616069982e-02, 6.5463e+00, 4.6354e-02, 
 2DIAGNOSTIC,    11, -1.802011867674e-01, 1.918515467243e-02, 6.5856e+00, 3.9295e-02, 
 2DIAGNOSTIC,    12, -1.823818899693e-01, 1.698871845379e-02, 6.6244e+00, 3.8872e-02, 
 2DIAGNOSTIC,    13, -1.861875332992e-01, 1.435394535282e-02, 6.6637e+00, 3.9247e-02, 
 2DIAGNOSTIC,    14, -1.913771833699e-01, 1.172041273874e-02, 6.7188e+00, 5.5114e-02, 
 2DIAGNOSTIC,    15, -1.921994436149e-01, 8.776791917842e-03, 6.7685e+00, 4.9655e-02, 
 2DIAGNOSTIC,    16, -1.922850883098e-01, 6.789622553749e-03, 6.8128e+00, 4.4343e-02, 
 2DIAGNOSTIC,    17, -1.937265200862e-01, 5.552910049409e-03, 6.8601e+00, 4.7317e-02, 
 2DIAGNOSTIC,    18, -1.941959638071e-01, 4.376848597307e-03, 6.9259e+00, 6.5772e-02, 
 2DIAGNOSTIC,    19, -1.942141050190e-01, 3.438909977649e-03, 6.9642e+00, 3.8285e-02, 
 2DIAGNOSTIC,    20, -1.945223681859e-01, 2.597115102515e-03, 7.0121e+00, 4.7916e-02, 
 2DIAGNOSTIC,    21, -1.947454879205e-01, 1.786154527664e-03, 7.0525e+00, 4.0441e-02, 
 2DIAGNOSTIC,    22, -1.949189012423e-01, 1.062235084206e-03, 7.0981e+00, 4.5550e-02, 
 2DIAGNOSTIC,    23, -1.950073832470e-01, 5.744367991151e-04, 7.1459e+00, 4.7832e-02, 
 2DIAGNOSTIC,    24, -1.951772889499e-01, 4.395338412726e-04, 7.1926e+00, 4.6675e-02, 
 2DIAGNOSTIC,    25, -1.953127032326e-01, 3.382805305764e-04, 7.2343e+00, 4.1696e-02, 
 2DIAGNOSTIC,    26, -1.954077776869e-01, 2.226468696348e-04, 7.2804e+00, 4.6158e-02, 
 2DIAGNOSTIC,    27, -1.956795967380e-01, 1.963802461201e-04, 7.3264e+00, 4.5975e-02, 
 2DIAGNOSTIC,    28, -1.957101269447e-01, 1.822340387771e-04, 7.3723e+00, 4.5844e-02, 
 2DIAGNOSTIC,    29, -1.956826469883e-01, 1.514384607860e-04, 7.4204e+00, 4.8116e-02, 
 2DIAGNOSTIC,    30, -1.961133561635e-01, 1.476321851648e-04, 7.4670e+00, 4.6645e-02, 
 2DIAGNOSTIC,    31, -1.962733335849e-01, 1.489147463669e-04, 7.5159e+00, 4.8831e-02, 
 2DIAGNOSTIC,    32, -1.964978053080e-01, 1.555327049233e-04, 7.5662e+00, 5.0312e-02, 
 2DIAGNOSTIC,    33, -1.971221694373e-01, 1.809313520063e-04, 7.6125e+00, 4.6306e-02, 
 2DIAGNOSTIC,    34, -1.975890801686e-01, 2.163941685902e-04, 7.6531e+00, 4.0619e-02, 
 2DIAGNOSTIC,    35, -1.989085411736e-01, 2.936315163281e-04, 7.6935e+00, 4.0401e-02, 
 2DIAGNOSTIC,    36, -1.995389619464e-01, 3.682418621114e-04, 7.7423e+00, 4.8757e-02, 
 2DIAGNOSTIC,    37, -1.999740162044e-01, 4.333980097633e-04, 7.7836e+00, 4.1341e-02, 
 2DIAGNOSTIC,    38, -2.002148927923e-01, 4.652627087761e-04, 7.8313e+00, 4.7701e-02, 
 2DIAGNOSTIC,    39, -2.003276792844e-01, 4.540386754290e-04, 7.8721e+00, 4.0765e-02, 
 2DIAGNOSTIC,    40, -2.011733341962e-01, 4.489799085439e-04, 7.9422e+00, 7.0170e-02, 
 2DIAGNOSTIC,    41, -2.012143247191e-01, 4.080249809395e-04, 7.9940e+00, 5.1736e-02, 
 2DIAGNOSTIC,    42, -2.012260111047e-01, 3.393605888068e-04, 8.0476e+00, 5.3634e-02, 
 2DIAGNOSTIC,    43, -2.012233429489e-01, 2.647472120574e-04, 8.0955e+00, 4.7883e-02, 
 2DIAGNOSTIC,    44, -2.012028315817e-01, 1.831417022213e-04, 8.1348e+00, 3.9271e-02, 
 2DIAGNOSTIC,    45, -2.012060131264e-01, 1.320939537144e-04, 8.1813e+00, 4.6580e-02, 
 2DIAGNOSTIC,    46, -2.011960640702e-01, 9.103335111872e-05, 8.2240e+00, 4.2712e-02, 
 2DIAGNOSTIC,    47, -2.011902432830e-01, 5.736149541273e-05, 8.2641e+00, 4.0064e-02, 
 2DIAGNOSTIC,    48, -2.011430423155e-01, 2.615222975102e-05, 8.3095e+00, 4.5395e-02, 
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -1.775418219168e-01, 1.797693134862e+308, 1.5020e+01, 6.7110e+00, 
 2DIAGNOSTIC,     2, -1.781271566262e-01, 1.797693134862e+308, 1.5253e+01, 2.3291e-01, 
 2DIAGNOSTIC,     3, -1.785057650730e-01, 1.797693134862e+308, 1.5475e+01, 2.2129e-01, 
 2DIAGNOSTIC,     4, -1.788323594755e-01, 1.797693134862e+308, 1.5734e+01, 2.5944e-01, 
 2DIAGNOSTIC,     5, -1.790408095000e-01, 1.797693134862e+308, 1.5981e+01, 2.4710e-01, 
 2DIAGNOSTIC,     6, -1.797260526538e-01, 1.797693134862e+308, 1.6289e+01, 3.0804e-01, 
 2DIAGNOSTIC,     7, -1.797750323505e-01, 1.797693134862e+308, 1.6547e+01, 2.5760e-01, 
 2DIAGNOSTIC,     8, -1.797815389174e-01, 1.797693134862e+308, 1.6817e+01, 2.6980e-01, 
 2DIAGNOSTIC,     9, -1.797906814263e-01, 1.797693134862e+308, 1.7076e+01, 2.5915e-01, 
 2DIAGNOSTIC,    10, -1.797852580812e-01, 8.197969489895e-04, 1.7403e+01, 3.2747e-01, 
 2DIAGNOSTIC,    11, -1.797838649590e-01, 5.510995280979e-04, 1.7653e+01, 2.4943e-01, 
 2DIAGNOSTIC,    12, -1.797807446996e-01, 3.542353077899e-04, 1.7914e+01, 2.6103e-01, 
 2DIAGNOSTIC,    13, -1.797814035169e-01, 2.027540644678e-04, 1.8226e+01, 3.1245e-01, 
 2DIAGNOSTIC,    14, -1.797809764829e-01, 9.203757942292e-05, 1.8484e+01, 2.5805e-01, 
 2DIAGNOSTIC,    15, -1.797833375652e-01, 8.203193666290e-06, 1.8708e+01, 2.2426e-01, 
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -1.672836261518e-01, 1.797693134862e+308, 6.2267e+01, 4.3559e+01, 
  Elapsed time (stage 3): 6.8850e+01


Stage 4
  iterations = 100x100x100x0
  convergence threshold = 1.0000e-06
  convergence window size = 10
  number of levels = 4
  using the CC metric (radius = 4, weight = 1.0000e+00)
  preprocessing:  winsorizing the image intensities
  preprocessing:  histogram matching the images
  Shrink factors (level 1 out of 4): [16, 16, 16]
  Shrink factors (level 2 out of 4): [8, 8, 8]
  Shrink factors (level 3 out of 4): [4, 4, 4]
  Shrink factors (level 4 out of 4): [2, 2, 2]
  smoothing sigmas per level: [3, 2, 1, 0]
  Using default NONE metricSamplingStrategy 

*** Running B-spline SyN registration (updateMeshSizeAtBaseLevel = [7, 9, 7], totalMeshSizeAtBaseLevel = [0, 0, 0]) ***

XDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
WDIAGNOSTIC,     1, -6.813203278684e-01, 1.797693134862e+308, 5.0787e+00, 5.0787e+00, 
WDIAGNOSTIC,     2, -6.869521433785e-01, 1.797693134862e+308, 5.2447e+00, 1.6596e-01, 
WDIAGNOSTIC,     3, -6.909457963749e-01, 1.797693134862e+308, 5.4070e+00, 1.6227e-01, 
WDIAGNOSTIC,     4, -6.937703794525e-01, 1.797693134862e+308, 5.5733e+00, 1.6637e-01, 
WDIAGNOSTIC,     5, -6.962419247136e-01, 1.797693134862e+308, 5.7422e+00, 1.6888e-01, 
WDIAGNOSTIC,     6, -6.982821721804e-01, 1.797693134862e+308, 5.8931e+00, 1.5088e-01, 
WDIAGNOSTIC,     7, -6.996576062238e-01, 1.797693134862e+308, 6.0505e+00, 1.5740e-01, 
WDIAGNOSTIC,     8, -7.006983068655e-01, 1.797693134862e+308, 6.2099e+00, 1.5938e-01, 
WDIAGNOSTIC,     9, -7.013911252527e-01, 1.797693134862e+308, 6.3687e+00, 1.5882e-01, 
WDIAGNOSTIC,    10, -7.016943937963e-01, 1.758131662497e-03, 6.5435e+00, 1.7485e-01, 
WDIAGNOSTIC,    11, -7.018177976706e-01, 1.188130600224e-03, 6.7009e+00, 1.5738e-01, 
WDIAGNOSTIC,    12, -7.014041160358e-01, 7.830916458327e-04, 6.8900e+00, 1.8906e-01, 
WDIAGNOSTIC,    13, -7.018919388648e-01, 5.102121332192e-04, 7.0493e+00, 1.5927e-01, 
WDIAGNOSTIC,    14, -7.012828701867e-01, 2.933693534637e-04, 7.2064e+00, 1.5714e-01, 
WDIAGNOSTIC,    15, -7.019326102715e-01, 1.634016959343e-04, 7.3696e+00, 1.6318e-01, 
WDIAGNOSTIC,    16, -7.012343242585e-01, 6.827899406450e-05, 7.5493e+00, 1.7972e-01, 
WDIAGNOSTIC,    17, -7.019232503411e-01, 2.790704227862e-05, 7.7103e+00, 1.6104e-01, 
WDIAGNOSTIC,    18, -7.014137074800e-01, 8.414691616832e-07, 7.8761e+00, 1.6580e-01, 
XDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
WDIAGNOSTIC,     1, -6.326028474288e-01, 1.797693134862e+308, 1.2196e+01, 4.3199e+00, 
WDIAGNOSTIC,     2, -6.444565228150e-01, 1.797693134862e+308, 1.3126e+01, 9.2994e-01, 
WDIAGNOSTIC,     3, -6.579332600073e-01, 1.797693134862e+308, 1.4013e+01, 8.8747e-01, 
WDIAGNOSTIC,     4, -6.692999071275e-01, 1.797693134862e+308, 1.4935e+01, 9.2128e-01, 
WDIAGNOSTIC,     5, -6.797860781687e-01, 1.797693134862e+308, 1.5862e+01, 9.2735e-01, 
WDIAGNOSTIC,     6, -6.886267128505e-01, 1.797693134862e+308, 1.6754e+01, 8.9158e-01, 
WDIAGNOSTIC,     7, -6.960064197347e-01, 1.797693134862e+308, 1.7749e+01, 9.9577e-01, 
WDIAGNOSTIC,     8, -7.018551885445e-01, 1.797693134862e+308, 1.8650e+01, 9.0050e-01, 
WDIAGNOSTIC,     9, -7.069231326298e-01, 1.797693134862e+308, 1.9634e+01, 9.8405e-01, 
WDIAGNOSTIC,    10, -7.112836539879e-01, 7.455882112055e-03, 2.0509e+01, 8.7492e-01, 
WDIAGNOSTIC,    11, -7.147975434062e-01, 5.869488066626e-03, 2.1422e+01, 9.1355e-01, 
WDIAGNOSTIC,    12, -7.180826440143e-01, 4.549108898347e-03, 2.2322e+01, 8.9940e-01, 
WDIAGNOSTIC,    13, -7.211842881603e-01, 3.551920481890e-03, 2.3223e+01, 9.0074e-01, 
WDIAGNOSTIC,    14, -7.240001616767e-01, 2.792994668370e-03, 2.4169e+01, 9.4601e-01, 
WDIAGNOSTIC,    15, -7.266022370023e-01, 2.238805205855e-03, 2.5068e+01, 8.9906e-01, 
WDIAGNOSTIC,    16, -7.288885058985e-01, 1.833080594278e-03, 2.5954e+01, 8.8664e-01, 
WDIAGNOSTIC,    17, -7.310898901358e-01, 1.536166609536e-03, 2.6885e+01, 9.3078e-01, 
WDIAGNOSTIC,    18, -7.331155025117e-01, 1.307680738795e-03, 2.7821e+01, 9.3632e-01, 
WDIAGNOSTIC,    19, -7.349828071021e-01, 1.129501009864e-03, 2.8759e+01, 9.3741e-01, 
WDIAGNOSTIC,    20, -7.365632090864e-01, 9.840692754058e-04, 2.9693e+01, 9.3456e-01, 
WDIAGNOSTIC,    21, -7.380510513019e-01, 8.567067780783e-04, 3.0585e+01, 8.9204e-01, 
WDIAGNOSTIC,    22, -7.395006173617e-01, 7.472509260557e-04, 3.1494e+01, 9.0842e-01, 
WDIAGNOSTIC,    23, -7.407859141902e-01, 6.536312428645e-04, 3.2408e+01, 9.1436e-01, 
WDIAGNOSTIC,    24, -7.420582742002e-01, 5.745246940459e-04, 3.3319e+01, 9.1097e-01, 
WDIAGNOSTIC,    25, -7.431526613839e-01, 5.067482810431e-04, 3.4237e+01, 9.1800e-01, 
WDIAGNOSTIC,    26, -7.441892671313e-01, 4.473619720087e-04, 3.5213e+01, 9.7626e-01, 
WDIAGNOSTIC,    27, -7.451548607677e-01, 3.967609541146e-04, 3.6148e+01, 9.3464e-01, 
WDIAGNOSTIC,    28, -7.461423912485e-01, 3.549318626852e-04, 3.7092e+01, 9.4381e-01, 
WDIAGNOSTIC,    29, -7.469465150553e-01, 3.188800462122e-04, 3.8009e+01, 9.1710e-01, 
WDIAGNOSTIC,    30, -7.476996341930e-01, 2.858309340455e-04, 3.8946e+01, 9.3701e-01, 
WDIAGNOSTIC,    31, -7.484573249586e-01, 2.564413998931e-04, 3.9910e+01, 9.6359e-01, 
WDIAGNOSTIC,    32, -7.492115253660e-01, 2.317022715172e-04, 4.0827e+01, 9.1752e-01, 
WDIAGNOSTIC,    33, -7.499374668358e-01, 2.103891906903e-04, 4.1739e+01, 9.1166e-01, 
WDIAGNOSTIC,    34, -7.506295939564e-01, 1.930585906562e-04, 4.2666e+01, 9.2746e-01, 
WDIAGNOSTIC,    35, -7.513022026695e-01, 1.782026087042e-04, 4.3612e+01, 9.4551e-01, 
WDIAGNOSTIC,    36, -7.519014595979e-01, 1.650303408585e-04, 4.4537e+01, 9.2560e-01, 
WDIAGNOSTIC,    37, -7.525777835658e-01, 1.542032529473e-04, 4.5476e+01, 9.3830e-01, 
WDIAGNOSTIC,    38, -7.532206859470e-01, 1.460193967090e-04, 4.6388e+01, 9.1275e-01, 
WDIAGNOSTIC,    39, -7.537689091949e-01, 1.378772767677e-04, 4.7344e+01, 9.5596e-01, 
WDIAGNOSTIC,    40, -7.543255440717e-01, 1.297972181607e-04, 4.8301e+01, 9.5707e-01, 
WDIAGNOSTIC,    41, -7.548585734567e-01, 1.220056345735e-04, 4.9239e+01, 9.3732e-01, 
WDIAGNOSTIC,    42, -7.553232082723e-01, 1.142269070857e-04, 5.0203e+01, 9.6471e-01, 
WDIAGNOSTIC,    43, -7.557887960053e-01, 1.066845628688e-04, 5.1130e+01, 9.2682e-01, 
WDIAGNOSTIC,    44, -7.561813084330e-01, 9.888301522030e-05, 5.2137e+01, 1.0072e+00, 
WDIAGNOSTIC,    45, -7.565623392706e-01, 9.110939030617e-05, 5.3079e+01, 9.4140e-01, 
WDIAGNOSTIC,    46, -7.569127726509e-01, 8.297199581742e-05, 5.3991e+01, 9.1212e-01, 
WDIAGNOSTIC,    47, -7.572604230854e-01, 7.569856862603e-05, 5.4888e+01, 8.9756e-01, 
WDIAGNOSTIC,    48, -7.575935486392e-01, 6.938551718784e-05, 5.5820e+01, 9.3186e-01, 
WDIAGNOSTIC,    49, -7.580028880688e-01, 6.426937332584e-05, 5.6756e+01, 9.3575e-01, 
WDIAGNOSTIC,    50, -7.583165630743e-01, 5.993234337540e-05, 5.7687e+01, 9.3096e-01, 
WDIAGNOSTIC,    51, -7.586339037823e-01, 5.649948854653e-05, 5.8601e+01, 9.1387e-01, 
WDIAGNOSTIC,    52, -7.588403958709e-01, 5.278538011518e-05, 5.9496e+01, 8.9557e-01, 
WDIAGNOSTIC,    53, -7.590518341289e-01, 4.912052153545e-05, 6.0476e+01, 9.7941e-01, 
WDIAGNOSTIC,    54, -7.592815335412e-01, 4.534447062784e-05, 6.1413e+01, 9.3695e-01, 
WDIAGNOSTIC,    55, -7.594105451346e-01, 4.094358925146e-05, 6.2325e+01, 9.1169e-01, 
WDIAGNOSTIC,    56, -7.596034390805e-01, 3.655795425375e-05, 6.3436e+01, 1.1117e+00, 
WDIAGNOSTIC,    57, -7.597803413041e-01, 3.240035403010e-05, 6.4376e+01, 9.4019e-01, 
WDIAGNOSTIC,    58, -7.599688345902e-01, 2.875197551407e-05, 6.5313e+01, 9.3647e-01, 
WDIAGNOSTIC,    59, -7.602052190177e-01, 2.670392752504e-05, 6.6229e+01, 9.1637e-01, 
WDIAGNOSTIC,    60, -7.603893385970e-01, 2.536086754406e-05, 6.7145e+01, 9.1556e-01, 
WDIAGNOSTIC,    61, -7.605722367619e-01, 2.482006818773e-05, 6.8087e+01, 9.4263e-01, 
WDIAGNOSTIC,    62, -7.607592849110e-01, 2.437984219140e-05, 6.9039e+01, 9.5139e-01, 
WDIAGNOSTIC,    63, -7.609477464985e-01, 2.406455235246e-05, 7.0007e+01, 9.6860e-01, 
WDIAGNOSTIC,    64, -7.611667067039e-01, 2.417003258243e-05, 7.0980e+01, 9.7226e-01, 
WDIAGNOSTIC,    65, -7.613581165049e-01, 2.385770718025e-05, 7.1905e+01, 9.2486e-01, 
WDIAGNOSTIC,    66, -7.615327112708e-01, 2.343089856989e-05, 7.2864e+01, 9.5946e-01, 
WDIAGNOSTIC,    67, -7.617043187707e-01, 2.279095066127e-05, 7.3847e+01, 9.8343e-01, 
WDIAGNOSTIC,    68, -7.618924903777e-01, 2.211817043019e-05, 7.4846e+01, 9.9865e-01, 
WDIAGNOSTIC,    69, -7.620449265314e-01, 2.151528208323e-05, 7.5777e+01, 9.3117e-01, 
WDIAGNOSTIC,    70, -7.622112326554e-01, 2.080404123019e-05, 7.6782e+01, 1.0047e+00, 
WDIAGNOSTIC,    71, -7.623799340170e-01, 2.003484172739e-05, 7.7715e+01, 9.3255e-01, 
WDIAGNOSTIC,    72, -7.625527056227e-01, 1.929611312280e-05, 7.8684e+01, 9.6915e-01, 
WDIAGNOSTIC,    73, -7.626962543212e-01, 1.847626927213e-05, 7.9594e+01, 9.0997e-01, 
WDIAGNOSTIC,    74, -7.628649083035e-01, 1.792983310120e-05, 8.0522e+01, 9.2798e-01, 
WDIAGNOSTIC,    75, -7.630293622735e-01, 1.750915392032e-05, 8.1455e+01, 9.3319e-01, 
WDIAGNOSTIC,    76, -7.631844944091e-01, 1.709187129247e-05, 8.2379e+01, 9.2392e-01, 
WDIAGNOSTIC,    77, -7.633530315333e-01, 1.674696611005e-05, 8.3324e+01, 9.4550e-01, 
WDIAGNOSTIC,    78, -7.635012491123e-01, 1.646955959126e-05, 8.4255e+01, 9.3028e-01, 
WDIAGNOSTIC,    79, -7.636661553886e-01, 1.617013076279e-05, 8.5200e+01, 9.4546e-01, 
WDIAGNOSTIC,    80, -7.638327708415e-01, 1.592754114253e-05, 8.6135e+01, 9.3546e-01, 
WDIAGNOSTIC,    81, -7.639964847334e-01, 1.574004969314e-05, 8.7050e+01, 9.1485e-01, 
WDIAGNOSTIC,    82, -7.641531379566e-01, 1.559644848025e-05, 8.7961e+01, 9.1107e-01, 
WDIAGNOSTIC,    83, -7.643076300879e-01, 1.534307810210e-05, 8.8943e+01, 9.8181e-01, 
WDIAGNOSTIC,    84, -7.644623624452e-01, 1.510484963362e-05, 8.9924e+01, 9.8078e-01, 
WDIAGNOSTIC,    85, -7.645787611564e-01, 1.469436263648e-05, 9.0902e+01, 9.7813e-01, 
WDIAGNOSTIC,    86, -7.647258904486e-01, 1.423832419528e-05, 9.1839e+01, 9.3644e-01, 
WDIAGNOSTIC,    87, -7.648741460073e-01, 1.382753798156e-05, 9.2837e+01, 9.9836e-01, 
WDIAGNOSTIC,    88, -7.650261751919e-01, 1.340895596468e-05, 9.3787e+01, 9.5058e-01, 
WDIAGNOSTIC,    89, -7.651514690929e-01, 1.296618700671e-05, 9.4726e+01, 9.3839e-01, 
WDIAGNOSTIC,    90, -7.653059479559e-01, 1.266443779148e-05, 9.5636e+01, 9.1062e-01, 
WDIAGNOSTIC,    91, -7.654585570999e-01, 1.248840527736e-05, 9.6580e+01, 9.4370e-01, 
WDIAGNOSTIC,    92, -7.656084170352e-01, 1.239337852862e-05, 9.7529e+01, 9.4880e-01, 
WDIAGNOSTIC,    93, -7.657555128394e-01, 1.235465458670e-05, 9.8447e+01, 9.1846e-01, 
WDIAGNOSTIC,    94, -7.659011183329e-01, 1.236325719014e-05, 9.9382e+01, 9.3452e-01, 
WDIAGNOSTIC,    95, -7.660426301947e-01, 1.222875563168e-05, 1.0032e+02, 9.3311e-01, 
WDIAGNOSTIC,    96, -7.661797000570e-01, 1.205837255357e-05, 1.0126e+02, 9.4925e-01, 
WDIAGNOSTIC,    97, -7.663134527568e-01, 1.184913053271e-05, 1.0220e+02, 9.3949e-01, 
WDIAGNOSTIC,    98, -7.664411521525e-01, 1.160567981960e-05, 1.0315e+02, 9.4303e-01, 
WDIAGNOSTIC,    99, -7.665614593880e-01, 1.120644928688e-05, 1.0411e+02, 9.6099e-01, 
WDIAGNOSTIC,   100, -7.666822729015e-01, 1.079675260734e-05, 1.0504e+02, 9.3253e-01, 
XDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
WDIAGNOSTIC,     1, -6.994412673803e-01, 1.797693134862e+308, 1.1382e+02, 8.7835e+00, 
WDIAGNOSTIC,     2, -7.061146360336e-01, 1.797693134862e+308, 1.2016e+02, 6.3407e+00, 
WDIAGNOSTIC,     3, -7.120266550070e-01, 1.797693134862e+308, 1.2647e+02, 6.3078e+00, 
WDIAGNOSTIC,     4, -7.176192507011e-01, 1.797693134862e+308, 1.3280e+02, 6.3311e+00, 
WDIAGNOSTIC,     5, -7.230355579993e-01, 1.797693134862e+308, 1.3908e+02, 6.2717e+00, 
WDIAGNOSTIC,     6, -7.277239403158e-01, 1.797693134862e+308, 1.4549e+02, 6.4134e+00, 
WDIAGNOSTIC,     7, -7.316817720051e-01, 1.797693134862e+308, 1.5178e+02, 6.2926e+00, 
WDIAGNOSTIC,     8, -7.351022163382e-01, 1.797693134862e+308, 1.5822e+02, 6.4375e+00, 
WDIAGNOSTIC,     9, -7.383794663566e-01, 1.797693134862e+308, 1.6458e+02, 6.3603e+00, 
WDIAGNOSTIC,    10, -7.406930963068e-01, 3.657286623301e-03, 1.7092e+02, 6.3430e+00, 
WDIAGNOSTIC,    11, -7.427274390533e-01, 2.943862896100e-03, 1.7735e+02, 6.4306e+00, 
WDIAGNOSTIC,    12, -7.445471890289e-01, 2.362392594799e-03, 1.8377e+02, 6.4200e+00, 
WDIAGNOSTIC,    13, -7.463710872200e-01, 1.888915788699e-03, 1.9009e+02, 6.3193e+00, 
WDIAGNOSTIC,    14, -7.480594895307e-01, 1.512994872568e-03, 1.9647e+02, 6.3732e+00, 
WDIAGNOSTIC,    15, -7.497796953793e-01, 1.233293403823e-03, 2.0281e+02, 6.3464e+00, 
WDIAGNOSTIC,    16, -7.513226673932e-01, 1.026104174071e-03, 2.0919e+02, 6.3737e+00, 
WDIAGNOSTIC,    17, -7.527503920628e-01, 8.710288391217e-04, 2.1547e+02, 6.2876e+00, 
WDIAGNOSTIC,    18, -7.539872707376e-01, 7.519664797780e-04, 2.2183e+02, 6.3587e+00, 
WDIAGNOSTIC,    19, -7.551634949260e-01, 6.658890729649e-04, 2.2810e+02, 6.2645e+00, 
WDIAGNOSTIC,    20, -7.560864122742e-01, 5.885685187483e-04, 2.3456e+02, 6.4601e+00, 
WDIAGNOSTIC,    21, -7.570456218942e-01, 5.184871989549e-04, 2.4093e+02, 6.3783e+00, 
WDIAGNOSTIC,    22, -7.579829680160e-01, 4.543108298883e-04, 2.4728e+02, 6.3493e+00, 
WDIAGNOSTIC,    23, -7.588345628510e-01, 3.976725120002e-04, 2.5354e+02, 6.2553e+00, 
WDIAGNOSTIC,    24, -7.597209576251e-01, 3.494169375035e-04, 2.5990e+02, 6.3567e+00, 
WDIAGNOSTIC,    25, -7.606738069173e-01, 3.129966201973e-04, 2.6624e+02, 6.3415e+00, 
WDIAGNOSTIC,    26, -7.617622533829e-01, 2.884392053122e-04, 2.7264e+02, 6.4055e+00, 
WDIAGNOSTIC,    27, -7.629726608235e-01, 2.756187718091e-04, 2.7907e+02, 6.4324e+00, 
WDIAGNOSTIC,    28, -7.641654568639e-01, 2.705736919385e-04, 2.8541e+02, 6.3392e+00, 
WDIAGNOSTIC,    29, -7.653785514477e-01, 2.716136978026e-04, 2.9176e+02, 6.3433e+00, 
WDIAGNOSTIC,    30, -7.663094514643e-01, 2.702605590992e-04, 2.9819e+02, 6.4351e+00, 
WDIAGNOSTIC,    31, -7.671938875018e-01, 2.659390983758e-04, 3.0452e+02, 6.3288e+00, 
WDIAGNOSTIC,    32, -7.680059698838e-01, 2.573722130508e-04, 3.1091e+02, 6.3904e+00, 
WDIAGNOSTIC,    33, -7.688057913766e-01, 2.438140656364e-04, 3.1723e+02, 6.3143e+00, 
WDIAGNOSTIC,    34, -7.695612925294e-01, 2.261512738237e-04, 3.2353e+02, 6.3021e+00, 
WDIAGNOSTIC,    35, -7.700749935163e-01, 2.038453888449e-04, 3.2979e+02, 6.2596e+00, 
WDIAGNOSTIC,    36, -7.707204286018e-01, 1.816522077403e-04, 3.3617e+02, 6.3776e+00, 
WDIAGNOSTIC,    37, -7.711940308550e-01, 1.605097015347e-04, 3.4253e+02, 6.3657e+00, 
WDIAGNOSTIC,    38, -7.717876431462e-01, 1.428700563455e-04, 3.4888e+02, 6.3497e+00, 
WDIAGNOSTIC,    39, -7.720947498229e-01, 1.271862084706e-04, 3.5524e+02, 6.3551e+00, 
WDIAGNOSTIC,    40, -7.725690398061e-01, 1.134576274875e-04, 3.6160e+02, 6.3653e+00, 
WDIAGNOSTIC,    41, -7.730837829771e-01, 1.024268603353e-04, 3.6801e+02, 6.4071e+00, 
WDIAGNOSTIC,    42, -7.735989745362e-01, 9.397681065634e-05, 3.7447e+02, 6.4639e+00, 
WDIAGNOSTIC,    43, -7.741203496138e-01, 8.846676604836e-05, 3.8082e+02, 6.3453e+00, 
WDIAGNOSTIC,    44, -7.746644990799e-01, 8.590328872322e-05, 3.8725e+02, 6.4346e+00, 
WDIAGNOSTIC,    45, -7.751971366689e-01, 8.395637996727e-05, 3.9362e+02, 6.3632e+00, 
WDIAGNOSTIC,    46, -7.756352905238e-01, 8.289764700276e-05, 3.9990e+02, 6.2829e+00, 
WDIAGNOSTIC,    47, -7.761471389150e-01, 8.179276172630e-05, 4.0637e+02, 6.4687e+00, 
WDIAGNOSTIC,    48, -7.767891621711e-01, 8.259516254011e-05, 4.1269e+02, 6.3234e+00, 
WDIAGNOSTIC,    49, -7.772363561782e-01, 8.117653758934e-05, 4.1915e+02, 6.4589e+00, 
WDIAGNOSTIC,    50, -7.778352416987e-01, 8.009900169435e-05, 4.2545e+02, 6.2967e+00, 
WDIAGNOSTIC,    51, -7.783865082471e-01, 7.921213168311e-05, 4.3187e+02, 6.4256e+00, 
WDIAGNOSTIC,    52, -7.789137760431e-01, 7.825428958606e-05, 4.3833e+02, 6.4633e+00, 
WDIAGNOSTIC,    53, -7.792469963607e-01, 7.583096181958e-05, 4.4468e+02, 6.3490e+00, 
WDIAGNOSTIC,    54, -7.795237509198e-01, 7.192815451074e-05, 4.5101e+02, 6.3242e+00, 
WDIAGNOSTIC,    55, -7.798338841946e-01, 6.703406414306e-05, 4.5737e+02, 6.3621e+00, 
WDIAGNOSTIC,    56, -7.801786955645e-01, 6.108915759129e-05, 4.6371e+02, 6.3447e+00, 
WDIAGNOSTIC,    57, -7.804970439661e-01, 5.488856602987e-05, 4.7005e+02, 6.3310e+00, 
WDIAGNOSTIC,    58, -7.808165310668e-01, 4.986031984080e-05, 4.7637e+02, 6.3285e+00, 
WDIAGNOSTIC,    59, -7.811234971139e-01, 4.499577866680e-05, 4.8270e+02, 6.3281e+00, 
WDIAGNOSTIC,    60, -7.814065594947e-01, 4.145082295050e-05, 4.8907e+02, 6.3630e+00, 
WDIAGNOSTIC,    61, -7.816564644531e-01, 3.891459340673e-05, 4.9546e+02, 6.3902e+00, 
WDIAGNOSTIC,    62, -7.819722698824e-01, 3.780352813490e-05, 5.0180e+02, 6.3422e+00, 
WDIAGNOSTIC,    63, -7.819869604364e-01, 3.515835399509e-05, 5.0811e+02, 6.3161e+00, 
WDIAGNOSTIC,    64, -7.821638251870e-01, 3.191231816217e-05, 5.1455e+02, 6.4341e+00, 
WDIAGNOSTIC,    65, -7.823257342546e-01, 2.841246820687e-05, 5.2087e+02, 6.3228e+00, 
WDIAGNOSTIC,    66, -7.824787207233e-01, 2.509589236444e-05, 5.2716e+02, 6.2916e+00, 
WDIAGNOSTIC,    67, -7.827779282249e-01, 2.291008192431e-05, 5.3353e+02, 6.3677e+00, 
WDIAGNOSTIC,    68, -7.829257442100e-01, 2.114981296863e-05, 5.3991e+02, 6.3792e+00, 
WDIAGNOSTIC,    69, -7.830870019834e-01, 1.996847422059e-05, 5.4624e+02, 6.3294e+00, 
WDIAGNOSTIC,    70, -7.832806139787e-01, 1.945147120921e-05, 5.5259e+02, 6.3496e+00, 
WDIAGNOSTIC,    71, -7.836741805637e-01, 2.043215247071e-05, 5.5891e+02, 6.3227e+00, 
WDIAGNOSTIC,    72, -7.837850415744e-01, 2.162203046914e-05, 5.6525e+02, 6.3441e+00, 
WDIAGNOSTIC,    73, -7.841935383425e-01, 2.289227835037e-05, 5.7154e+02, 6.2877e+00, 
WDIAGNOSTIC,    74, -7.846041364454e-01, 2.488431041005e-05, 5.7790e+02, 6.3612e+00, 
WDIAGNOSTIC,    75, -7.852356636826e-01, 2.835196801837e-05, 5.8426e+02, 6.3535e+00, 
WDIAGNOSTIC,    76, -7.859695441521e-01, 3.327729401757e-05, 5.9068e+02, 6.4193e+00, 
WDIAGNOSTIC,    77, -7.868101955205e-01, 4.034678397334e-05, 5.9700e+02, 6.3217e+00, 
WDIAGNOSTIC,    78, -7.878327359062e-01, 4.890026927660e-05, 6.0343e+02, 6.4311e+00, 
WDIAGNOSTIC,    79, -7.886431176183e-01, 5.703437526665e-05, 6.0973e+02, 6.3012e+00, 
WDIAGNOSTIC,    80, -7.894818844298e-01, 6.420707137026e-05, 6.1613e+02, 6.3972e+00, 
WDIAGNOSTIC,    81, -7.904277198149e-01, 7.113496767881e-05, 6.2255e+02, 6.4208e+00, 
WDIAGNOSTIC,    82, -7.911316860707e-01, 7.464480857359e-05, 6.2891e+02, 6.3649e+00, 
WDIAGNOSTIC,    83, -7.917774051345e-01, 7.555309190815e-05, 6.3529e+02, 6.3717e+00, 
WDIAGNOSTIC,    84, -7.925659073146e-01, 7.441659530890e-05, 6.4174e+02, 6.4570e+00, 
WDIAGNOSTIC,    85, -7.930735647509e-01, 7.103669456253e-05, 6.4816e+02, 6.4225e+00, 
WDIAGNOSTIC,    86, -7.936635498559e-01, 6.654316034249e-05, 6.5460e+02, 6.4349e+00, 
WDIAGNOSTIC,    87, -7.940630738513e-01, 6.094291298571e-05, 6.6096e+02, 6.3571e+00, 
WDIAGNOSTIC,    88, -7.946583014405e-01, 5.637446122347e-05, 6.6741e+02, 6.4584e+00, 
WDIAGNOSTIC,    89, -7.950191933349e-01, 5.127380217099e-05, 6.7379e+02, 6.3797e+00, 
WDIAGNOSTIC,    90, -7.955527154757e-01, 4.692635617769e-05, 6.8021e+02, 6.4120e+00, 
WDIAGNOSTIC,    91, -7.959533908456e-01, 4.358324135121e-05, 6.8654e+02, 6.3340e+00, 
WDIAGNOSTIC,    92, -7.963262774799e-01, 4.041232038487e-05, 6.9291e+02, 6.3681e+00, 
WDIAGNOSTIC,    93, -7.966935698579e-01, 3.739070247371e-05, 6.9924e+02, 6.3320e+00, 
WDIAGNOSTIC,    94, -7.970152907273e-01, 3.516814328605e-05, 7.0559e+02, 6.3506e+00, 
WDIAGNOSTIC,    95, -7.973271608941e-01, 3.275660594346e-05, 7.1188e+02, 6.2878e+00, 
WDIAGNOSTIC,    96, -7.976297461861e-01, 3.065955560032e-05, 7.1827e+02, 6.3894e+00, 
WDIAGNOSTIC,    97, -7.979218689486e-01, 2.825243748391e-05, 7.2466e+02, 6.3913e+00, 
WDIAGNOSTIC,    98, -7.981685722891e-01, 2.633788327008e-05, 7.3102e+02, 6.3643e+00, 
WDIAGNOSTIC,    99, -7.984279870806e-01, 2.421323842050e-05, 7.3734e+02, 6.3163e+00, 
WDIAGNOSTIC,   100, -7.986429969443e-01, 2.254604186358e-05, 7.4378e+02, 6.4393e+00, 
  Elapsed time (stage 4): 7.5322e+02


Stage 5
  iterations = 20
  convergence threshold = 1.0000e-06
  convergence window size = 10
  number of levels = 1
  using the CC metric (radius = 6, weight = 1.0000e+00)
  preprocessing:  winsorizing the image intensities
  preprocessing:  histogram matching the images
  Shrink factors (level 1 out of 1): [1, 1, 1]
  smoothing sigmas per level: [0]
  Using default NONE metricSamplingStrategy 

*** Running B-spline SyN registration (updateMeshSizeAtBaseLevel = [57, 77, 59], totalMeshSizeAtBaseLevel = [0, 0, 0]) ***

XDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
WDIAGNOSTIC,     1, -3.201500593608e-01, 1.797693134862e+308, 3.6407e+02, 3.6407e+02, 
WDIAGNOSTIC,     2, -3.220976440412e-01, 1.797693134862e+308, 7.2665e+02, 3.6258e+02, 
WDIAGNOSTIC,     3, -3.241317250008e-01, 1.797693134862e+308, 1.0985e+03, 3.7189e+02, 
WDIAGNOSTIC,     4, -3.262190673352e-01, 1.797693134862e+308, 1.4689e+03, 3.7033e+02, 
WDIAGNOSTIC,     5, -3.283410212855e-01, 1.797693134862e+308, 1.8290e+03, 3.6016e+02, 
WDIAGNOSTIC,     6, -3.305217165298e-01, 1.797693134862e+308, 2.1911e+03, 3.6204e+02, 
WDIAGNOSTIC,     7, -3.327696684938e-01, 1.797693134862e+308, 2.5567e+03, 3.6565e+02, 
WDIAGNOSTIC,     8, -3.350973554878e-01, 1.797693134862e+308, 2.9225e+03, 3.6581e+02, 
WDIAGNOSTIC,     9, -3.374806633589e-01, 1.797693134862e+308, 3.2938e+03, 3.7127e+02, 
WDIAGNOSTIC,    10, -3.398449156693e-01, 3.818132618973e-03, 3.6612e+03, 3.6739e+02, 
WDIAGNOSTIC,    11, -3.422264944764e-01, 3.540091928278e-03, 4.0239e+03, 3.6275e+02, 
WDIAGNOSTIC,    12, -3.445921605645e-01, 3.295696171427e-03, 4.3895e+03, 3.6556e+02, 
WDIAGNOSTIC,    13, -3.468562865783e-01, 3.070730887458e-03, 4.7578e+03, 3.6827e+02, 
WDIAGNOSTIC,    14, -3.490177761408e-01, 2.854896087782e-03, 5.1269e+03, 3.6913e+02, 
WDIAGNOSTIC,    15, -3.510926396677e-01, 2.642585702892e-03, 5.4943e+03, 3.6743e+02, 
WDIAGNOSTIC,    16, -3.531326554243e-01, 2.435794023526e-03, 5.8596e+03, 3.6528e+02, 
WDIAGNOSTIC,    17, -3.551733040088e-01, 2.240003994128e-03, 6.2268e+03, 3.6716e+02, 
WDIAGNOSTIC,    18, -3.572137020906e-01, 2.061285913830e-03, 6.5989e+03, 3.7217e+02, 
WDIAGNOSTIC,    19, -3.592718332921e-01, 1.904689037664e-03, 6.9603e+03, 3.6140e+02, 
WDIAGNOSTIC,    20, -3.613619705308e-01, 1.771232660940e-03, 7.3256e+03, 3.6524e+02, 
  Elapsed time (stage 5): 7.3347e+03


Total elapsed time: 8.2113e+03
Exception Object caught: 

itk::ExceptionObject (0x3f28920)
Location: "unknown" 
File: /opt/quarantine/ANTs/git/src/build/ITKv4-install/include/ITK-4.11/itkImageToImageFilter.hxx
Line: 250
Description: itk::ERROR: ImageToImageFilter(0x3f162a0): Inputs do not occupy the same physical space! 
InputImage Origin: [8.4818802e+01, 8.6685699e+01, -4.7260700e+01], InputImage_1 Origin: [8.5068802e+01, 8.7185699e+01, -4.7760700e+01]
    Tolerance: 1.0000000e-06
InputImage Spacing: [1.0000000e+00, 1.0000000e+00, 1.0000000e+00], InputImage_1 Spacing: [5.0000000e-01, 5.0000000e-01, 5.0000000e-01]
    Tolerance: 1.0000000e-06

[ntustison]

The shrink factors specified in the second to last stage are your problem:

--transform BSplineSyN[0.1,26,0,3] --metric CC[nifti/brain2_0.5_t1.nii.gz,nifti/brain1_0.5_t1.nii.gz,1,4] --convergence [100x100x100x0,1e-6,10] --shrink-factors 16x8x4x2 --smoothing-sigmas 3x2x1x0 --masks [NULL,NULL] \
--transform BSplineSyN[0.1,3,0,3] --metric CC[nifti/brain2_0.5_t1.nii.gz,nifti/brain1_0.5_t1.nii.gz,1,6] --convergence [20,1e-6,10] --shrink-factors 1 --smoothing-sigmas 0 --masks [nifti/brain2_0.5_mask.nii.gz,nifti/brain1_0.5_mask.nii.gz]

The last level of that stage will have a shrink factor of 2. The program doesn't automatically upsample the resulting displacement field so when it tries to combine the two displacement fields of different resolutions, it throws that error. You should do this:

--transform BSplineSyN[0.1,26,0,3] --metric CC[nifti/brain2_0.5_t1.nii.gz,nifti/brain1_0.5_t1.nii.gz,1,4] --convergence [100x100x100x0x0,1e-6,10] --shrink-factors 16x8x4x2x1 --smoothing-sigmas 3x2x1x0x0 --masks [NULL,NULL] \
--transform BSplineSyN[0.1,3,0,3] --metric CC[nifti/brain2_0.5_t1.nii.gz,nifti/brain1_0.5_t1.nii.gz,1,6] --convergence [20,1e-6,10] --shrink-factors 1 --smoothing-sigmas 0 --masks [nifti/brain2_0.5_mask.nii.gz,nifti/brain1_0.5_mask.nii.gz]

[gdevenyi]

Cheers! That's a crazy corner case!

[ntustison]

Yeah, it's not one which anybody else has pointed out before. I've thought about doing something (a warning, perhaps) but I'm reluctant to make an assumption of intended usage on the part of the user. But given how often it comes up, it's not a priority to deal with at the moment.

[lazypoet]

SimpleITK on python gives a similar bug. I'm using the MICCAI BRATS database. Here's my code:

def N43D(fl):

    im = SimpleITK.ReadImage(fl)

    msk = SimpleITK.BinaryThreshold(im, 0, 0)

    msk = SimpleITK.BinaryNot(msk)

    msk = SimpleITK.Cast(msk, SimpleITK.sitkUInt8)

    im = SimpleITK.Cast(im, SimpleITK.sitkFloat32)

    im_n4 = SimpleITK.N4BiasFieldCorrection(im, msk)

    SimpleITK.WriteImage(im_n4, os.path.splitext(fl)[0]+'_n4.mha', useCompression=True)

Also, I'm using multiple cores for a list of files:
dview.map_sync(N43D, fl)

The program runs fine for about 40 files. Then I get this error on all my engines:

[0:apply]: 
RuntimeErrorTraceback (most recent call last)<string> in <module>()
<ipython-input-56-03a02a993653> in N43D(fl)
c:\users\shreyas_v\anaconda2\lib\site-packages\SimpleITK\SimpleITK.pyc in N4BiasFieldCorrection(*args, **kwargs)
  43368 
  43369     """
> 43370     return _SimpleITK.N4BiasFieldCorrection(*args, **kwargs)
  43371 class NaryAddImageFilter(ImageFilter_3):
  43372     """
RuntimeError: Exception thrown in SimpleITK N4BiasFieldCorrection: c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageToImageFilter.hxx:248:
itk::ERROR: SubtractImageFilter(00000000065D8220): Inputs do not occupy the same physical space! 
InputImage Origin: [0.0000000e+000, -2.3900000e+002, 0.0000000e+000], InputImage_1 Origin: [-5.9750000e+001, -5.9750000e+001, -3.8500000e+001]
	Tolerance: 1.0000000e-006
InputImage Spacing: [1.0000000e+000, 1.0000000e+000, 1.0000000e+000], InputImage_1 Spacing: [5.9750000e+001, 5.9750000e+001, 3.8500000e+001]
	Tolerance: 1.0000000e-006

[ntustison]

This looks like an N4 issue as opposed to a registration issue although the same exception is being thrown in the parent itkImageToImageFilter class. Can you reproduce this using the latest N4BiasFieldCorrection from the ANTs repo?

[lazypoet]

I'm sorry, I'm using Windows server 2012 standard edition. I don't know how to use ANTs on it.

[ntustison]

Okay, there's a couple other things you can do:

1. Contact the people who created SimpleITK and ask them about this issue.
2. You can try temporarily changing the header of the input image to have an origin of 0x0x0 and an identity direction matrix during processing and then changing it back after processing. Sometimes that helps.

[lazypoet]

Actually, I did contact them but have yet to find a solution.
If you look at my code, the mask was created using the image itself, so there's no way that the headers would change. Still I'll check it.

[ntustison]

If you look at my code, the mask was created using the image itself, so there's no way that the headers would change. Still I'll check it.

You're not understanding what I'm saying. I'm suggesting that you change the orientation/position of the input image prior to processing. Also, see here.

[lazypoet]

Yes I did change the origin to 0x0x0 still: [0:apply]: RuntimeErrorTraceback (most recent call last)<string> in <module>()<ipython-input-14-c593781f045f> in N43D(fl)c:\users\shreyas_v\anaconda2\lib\site-packages\SimpleITK\SimpleITK.pyc in N4BiasFieldCorrection(*args, **kwargs) 43368 43369 """> 43370 return _SimpleITK.N4BiasFieldCorrection(*args, **kwargs) 43371 class NaryAddImageFilter(ImageFilter_3): 43372 """RuntimeError: Exception thrown in SimpleITK N4BiasFieldCorrection: c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageToImageFilter.hxx:248: itk::ERROR: SubtractImageFilter(00000000065B3F10): Inputs do not occupy the same physical space! InputImage Origin: [0.0000000e+000, 0.0000000e+000, 0.0000000e+000], InputImage_1 Origin: [-5.9750000e+001, -5.9750000e+001, -3.8500000e+001] Tolerance: 1.0000000e-006 InputImage Spacing: [1.0000000e+000, 1.0000000e+000, 1.0000000e+000], InputImage_1 Spacing: [5.9750000e+001, 5.9750000e+001, 3.8500000e+001] Tolerance: 1.0000000e-006 [1:apply]: RuntimeErrorTraceback (most recent call last)<string> in <module>()<ipython-input-14-c593781f045f> in N43D(fl)c:\users\shreyas_v\anaconda2\lib\site-packages\SimpleITK\SimpleITK.pyc in N4BiasFieldCorrection(*args, **kwargs) 43368 43369 """> 43370 return _SimpleITK.N4BiasFieldCorrection(*args, **kwargs) 43371 class NaryAddImageFilter(ImageFilter_3): 43372 """RuntimeError: Exception thrown in SimpleITK N4BiasFieldCorrection: c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageToImageFilter.hxx:248: itk::ERROR: SubtractImageFilter(0000000006554440): Inputs do not occupy the same physical space! InputImage Origin: [0.0000000e+000, 0.0000000e+000, 0.0000000e+000], InputImage_1 Origin: [-1.1950000e+002, -1.1950000e+002, -7.7000000e+001] Tolerance: 1.0000000e-006 InputImage Spacing: [1.0000000e+000, 1.0000000e+000, 1.0000000e+000], InputImage_1 Spacing: [1.1950000e+002, 1.1950000e+002, 7.7000000e+001] Tolerance: 1.0000000e-006 [2:apply]: RuntimeErrorTraceback (most recent call last)<string> in <module>()<ipython-input-14-c593781f045f> in N43D(fl)c:\users\shreyas_v\anaconda2\lib\site-packages\SimpleITK\SimpleITK.pyc in N4BiasFieldCorrection(*args, **kwargs) 43368 43369 """> 43370 return _SimpleITK.N4BiasFieldCorrection(*args, **kwargs) 43371 class NaryAddImageFilter(ImageFilter_3): 43372 """RuntimeError: Exception thrown in SimpleITK N4BiasFieldCorrection: c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageToImageFilter.hxx:248: itk::ERROR: SubtractImageFilter(000000000661C230): Inputs do not occupy the same physical space! InputImage Origin: [0.0000000e+000, 0.0000000e+000, 0.0000000e+000], InputImage_1 Origin: [-1.1950000e+002, -1.1950000e+002, -7.7000000e+001] Tolerance: 1.0000000e-006 InputImage Spacing: [1.0000000e+000, 1.0000000e+000, 1.0000000e+000], InputImage_1 Spacing: [1.1950000e+002, 1.1950000e+002, 7.7000000e+001] Tolerance: 1.0000000e-006 [3:apply]: RuntimeErrorTraceback (most recent call last)<string> in <module>()<ipython-input-14-c593781f045f> in N43D(fl)c:\users\shreyas_v\anaconda2\lib\site-packages\SimpleITK\SimpleITK.pyc in N4BiasFieldCorrection(*args, **kwargs) 43368 43369 """> 43370 return _SimpleITK.N4BiasFieldCorrection(*args, **kwargs) 43371 class NaryAddImageFilter(ImageFilter_3): 43372 """RuntimeError: Exception thrown in SimpleITK N4BiasFieldCorrection: c:\d\vs9-pkg\simpleitk-build\itk\modules\core\common\include\itkImageToImageFilter.hxx:248: itk::ERROR: SubtractImageFilter(00000000065905C0): Inputs do not occupy the same physical space! InputImage Origin: [0.0000000e+000, 0.0000000e+000, 0.0000000e+000], InputImage_1 Origin: [-2.3900000e+002, -2.3900000e+002, -1.5400000e+002] Tolerance: 1.0000000e-006 InputImage Spacing: [1.0000000e+000, 1.0000000e+000, 1.0000000e+000], InputImage_1 Spacing: [2.3900000e+002, 2.3900000e+002, 1.5400000e+002] Tolerance: 1.0000000e-006 ... 20 more exceptions ...

…

On Wed, Jan 25, 2017 at 8:39 PM, Nick Tustison ***@***.***> wrote: If you look at my code, the mask was created using the image itself, so there's no way that the headers would change. Still I'll check it. You're not understanding what I'm saying. I'm suggesting that you change the orientation/position of the input image prior to processing. Also, see here <#396>. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#375 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ATN71nGibWeSfb77y7Y14Pl319S4X4r-ks5rV2WzgaJpZM4Kiv3Y> .

[ntustison]

That's unfortunate but not that surprising. It looks like you need to log an issue with the SimpleITK people.