Apply affine transformation file and deformation file estimated from high resolution images to low resolution images with the same field of view #1326

zw1989 · 2022-03-19T20:57:22Z

zw1989
Mar 19, 2022

Hi,

I try to apply the affine transformation file and the deformation field estimated from two high-resolution 3D T2-weighted images (matrix size = 256x128x16, FOV=24mmx12mmx8mm) to low-resolution functional images (matrix size = 96x48x16, FOV=24mmx12mmx8mm) by using

antsApplyTransforms -d 3 -e 3 --interpolation BSpline[5] -t run0_1Warp.nii.gz -t run0_0GenericAffine.mat -i epi.nii, -r epi.nii, -o epi_warped.nii

However, the warped epi images don't match the images that I want to register to. I thought it was the image origin mismatch causing the failure of the registration, i.e. the image origin of the fixed images used to estimate the transformation files is not the same as that for the epi images (I assume the default of origin when using "antsApplyTransforms" is the geometric center of the image). Then I tried to change --initial-fixed-transform [fixedImg, movingImg, 1] to --initial-fixed-transform [fixedImg, movingImg, 0] to use the geometric center of the images. The result is incorrect, either.

Then I tried to register one epi image to the other directly and got the run1_0GenericAffine.mat. I compared it to run0_0GenericAffine.mat. Initially, I thought the parameter AffineTransform_double_3_3 in both files should be close because the T2w images and epi images have the same FOV and image center, i.e. they are registered already except epi images bear more distortion. Surprisingly, the two _oGenericAffine.mat files are quite different, especially for the last three numbers (which according to the manual, are the translation parameters). Here are the results:

AffineTransform_double_3_3 estimated from two T2w images: [1.0309, -0.0098, -0.0038, -0.0042, 1.0523, 0.0539, 0.0032, -0.0425, 1.0423, 0.4644, 0.0467, 0.0874]
AffineTransform_double_3_3 estimated from two epi images: [0.9587, -0.0216, 0.0053, 0.0041, 0.9265, -0.0367, 0.0034, 0.0461, 1.0548, -0.4695, -0.9274, -0.1567]

I'm quite confused about the results. Could any experts explain to me why I got such results and also enlighten me how to apply transformation files estimated from high-resolution images to the corresponding low-resolution images?

Thanks

ntustison · 2022-03-19T23:05:07Z

ntustison
Mar 19, 2022
Maintainer

Can you post the original images and the commands that you used to generate the affine transform?

1 reply

zw1989 Mar 20, 2022
Author

Thanks for the quick response. Attached please find the two T2w images and the corresponding epi images. Below is the code I used to get the affine transformation file and the deformation file:

antsRegistration --dimensionality 3 --float 0 --output [run1_,run1_Warped.nii.gz,run1_inverswarped.nii.gz] --interpolation BSpline[5] --winsorize-image-intensities [0.005,0.995] --use-histogram-matching 0 --initial-fixed-transform [fixedImg,movingImg,0] --transform Rigid[0.05] --metric CC[fixedImg,movingImg,1,4,Regular,0.1] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform Affine[0.1] --metric MI[fixedImg,movingImg,1,32,Regular,0.1] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform SyN[0.1,1,0] --metric CC[fixedImg,movingImg,1,4] --convergence [100x70x50x20,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox -x [fixedImgMask, movingImgMask]

The fixedImg and movingImg are corrected_fsems_mouse_26.nii and corrected_fsems_mouse_27.nii, or epi1avg.nii and epi2avg.nii, respectively. The masks are used only for fsems images. Note corrected_fsems_mouse_26.nii and epi1avg.nii have the same FOV and slice coverage. So is the other pair.

I want to register epi2avg.nii to epi1avg.nii. My goal is to apply the transformation files estimated from fsems images to epi images.

preprocess_ANTs-test.zip

ntustison · 2022-03-21T18:54:07Z

ntustison
Mar 21, 2022
Maintainer

The epi and corrected corrected_fsems images don't reside in the same physical space (specifically, they don't share the same origin) so the affine transform derived from the "corrected_fsems" pair wouldn't apply to the epi images. Try fixing this issue and see if that corrects the problem.

1 reply

zw1989 Mar 24, 2022
Author

Thanks Nick. You are right. The fsems images has its origin shifted a few voxels which I don' know why. Then I changed the originator of both epi and fsems images to be the center of the images and it fixed the issue. In addition, I have several other questions:

In what situation do I want to use '--initial-fixed(moving)-transform [fixed, moving, 0]' in the antsRegistration function? At first, I thought this option could make the image origin at the geometric center, but it seems not.
To increase reproducibility, it is suggested to use fixed random number generator. I used the option '--random-seed 20', but I still see some variations with repeated runs. Where are those variations from?
Is there a document describing how the parameters in the AffineTransform_double_3_3 are transformed to the affine transformation matrix?

ntustison · 2022-03-24T22:11:27Z

ntustison
Mar 24, 2022
Maintainer

In what situation do I want to use '--initial-fixed(moving)-transform [fixed, moving, 0]' in the antsRegistration function? At first, I thought this option could make the image origin at the geometric center, but it seems not.

No, the origin in either image isn't changed. The calculated initial transform simply matches the fixed and moving image origins.

To increase reproducibility, it is suggested to use fixed random number generator. I used the option '--random-seed 20', but I still see some variations with repeated runs. Where are those variations from?

See further discussion here.

Is there a document describing how the parameters in the AffineTransform_double_3_3 are transformed to the affine transformation matrix?

https://itk.org/Doxygen/html/classitk_1_1AffineTransform.html

1 reply

zw1989 Mar 29, 2022
Author

Thanks Nick. Now I'm testing the registration of the T2w image to the template image. In this situation, the two sets of images are different in matrix size, resolution, and field of view. I set the originators of both images to be at the center of the 3D images, respectively. When I ran antsRegistration, I got a warning message saying no valid points were found during metric evaluation, verify that the images overlap appropriately.

Do you have an idea what causes the problem?

ntustison · 2022-03-29T23:36:39Z

ntustison
Mar 29, 2022
Maintainer

Again, you'd have to post the commands and images for us.

1 reply

zw1989 Mar 30, 2022
Author

I used the same antsRegistration command I attached previously and replaced the moving image to atlas.nii. Attached please find the images.
preprocess_ANTs-test.zip

ntustison · 2022-03-30T15:39:18Z

ntustison
Mar 30, 2022
Maintainer

Please include a script file that I can use to simply run from the command line.

1 reply

zw1989 Mar 30, 2022
Author

Here is the code I ran:
antsRegistration --dimensionality 3 --float 0 --output [run1_,run1_Warped.nii.gz,run1_inverswarped.nii.gz] --interpolation BSpline[5] --winsorize-image-intensities [0.005,0.995] --use-histogram-matching 0 --initial-fixed-transform [corrected_fsems_mouse_26_resetOrigin.nii,atlas.nii,0] --transform Rigid[0.05] --metric CC[corrected_fsems_mouse_26_resetOrigin.nii,atlas.nii,1,4,Regular,0.1] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform Affine[0.1] --metric MI[corrected_fsems_mouse_26_resetOrigin.nii,atlas.nii,1,32,Regular,0.1] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform SyN[0.1,1,0] --metric CC[corrected_fsems_mouse_26_resetOrigin.nii,atlas.nii,1,4] --convergence [100x70x50x20,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox -x mask26_resetOrigin.nii

I re-attached only the necessary data to run the code.
preprocess_ANTs-test.zip

ntustison · 2022-03-30T16:16:25Z

ntustison
Mar 30, 2022
Maintainer

I didn't have any issues running the command. Make sure your ANTs is up-to-date with the repository.

% sh command.sh
All_Command_lines_OK
Using double precision for computations.
=============================================================================
The composite transform comprises the following transforms (in order): 
  1. Image center alignment using fixed image: corrected_fsems_mouse_26_resetOrigin.nii and moving image: atlas.nii (type = Euler3DTransform)
=============================================================================
  Reading mask(s).
    Registration stage 0
      Fixed mask = mask26_resetOrigin.nii
  number of levels = 4
  number of levels = 4
  number of levels = 4
  fixed image: corrected_fsems_mouse_26_resetOrigin.nii
  moving image: atlas.nii
  fixed image: corrected_fsems_mouse_26_resetOrigin.nii
  moving image: atlas.nii
  fixed image: corrected_fsems_mouse_26_resetOrigin.nii
  moving image: atlas.nii
Dimension = 3
Number of stages = 3
Use Histogram Matching false
Winsorize image intensities true
Lower quantile = 0.005
Upper quantile = 0.995
Stage 1 State
   Image metric = CC
     Fixed image = Image (0x7fab06204a80)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 1996
  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: 1779
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 128, 16]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 128, 16]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 128, 16]
  Spacing: [0.09375, 0.09375, 0.5]
  Origin: [12, 6, -4]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.09375 0 0
0 -0.09375 0
0 0 0.5

  PointToIndexMatrix: 
-10.6667 0 0
0 -10.6667 0
0 0 2

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

  PixelContainer: 
    ImportImageContainer (0x600002a48420)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 1776
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7faad8008000
      Container manages memory: true
      Size: 524288
      Capacity: 524288

     Moving image = Image (0x7fab06204d30)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 1997
  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: 1994
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [228, 160, 264]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [228, 160, 264]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [228, 160, 264]
  Spacing: [0.05, 0.05, 0.05]
  Origin: [5.7, 6.6, -4]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.05 0 0
0 -0.05 0
0 0 0.05

  PointToIndexMatrix: 
-20 0 0
0 -20 0
0 0 20

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

  PixelContainer: 
    ImportImageContainer (0x600002a48a20)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 1991
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7fab10000000
      Container manages memory: true
      Size: 9630720
      Capacity: 9630720

     Weighting = 1
     Sampling strategy = regular
     Number of bins = 32
     Radius = 4
     Sampling percentage  = 0.1
   Transform = Rigid
     Gradient step = 0.05
     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 (0x7fab05704c90)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 2428
  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: 2211
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 128, 16]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 128, 16]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 128, 16]
  Spacing: [0.09375, 0.09375, 0.5]
  Origin: [12, 6, -4]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.09375 0 0
0 -0.09375 0
0 0 0.5

  PointToIndexMatrix: 
-10.6667 0 0
0 -10.6667 0
0 0 2

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

  PixelContainer: 
    ImportImageContainer (0x600002a5c2a0)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 2208
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7faae0008000
      Container manages memory: true
      Size: 524288
      Capacity: 524288

     Moving image = Image (0x7fab05704f40)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 2429
  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: 2426
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [228, 160, 264]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [228, 160, 264]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [228, 160, 264]
  Spacing: [0.05, 0.05, 0.05]
  Origin: [5.7, 6.6, -4]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.05 0 0
0 -0.05 0
0 0 0.05

  PointToIndexMatrix: 
-20 0 0
0 -20 0
0 0 20

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

  PixelContainer: 
    ImportImageContainer (0x600002a5c900)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 2423
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7faaf0000000
      Container manages memory: true
      Size: 9630720
      Capacity: 9630720

     Weighting = 1
     Sampling strategy = regular
     Number of bins = 32
     Radius = 4
     Sampling percentage  = 0.1
   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 3 State
   Image metric = CC
     Fixed image = Image (0x7fab06027970)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 2860
  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: 2643
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 128, 16]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 128, 16]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [256, 128, 16]
  Spacing: [0.09375, 0.09375, 0.5]
  Origin: [12, 6, -4]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.09375 0 0
0 -0.09375 0
0 0 0.5

  PointToIndexMatrix: 
-10.6667 0 0
0 -10.6667 0
0 0 2

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

  PixelContainer: 
    ImportImageContainer (0x600002a52700)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 2640
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7faac8008000
      Container manages memory: true
      Size: 524288
      Capacity: 524288

     Moving image = Image (0x7fab06027c20)
  RTTI typeinfo:   itk::Image<double, 3u>
  Reference Count: 2
  Modified Time: 2861
  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: 2858
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [228, 160, 264]
  BufferedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [228, 160, 264]
  RequestedRegion: 
    Dimension: 3
    Index: [0, 0, 0]
    Size: [228, 160, 264]
  Spacing: [0.05, 0.05, 0.05]
  Origin: [5.7, 6.6, -4]
  Direction: 
-1 0 0
0 -1 0
0 0 1

  IndexToPointMatrix: 
-0.05 0 0
0 -0.05 0
0 0 0.05

  PointToIndexMatrix: 
-20 0 0
0 -20 0
0 0 20

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

  PixelContainer: 
    ImportImageContainer (0x600002a52d00)
      RTTI typeinfo:   itk::ImportImageContainer<unsigned long, double>
      Reference Count: 1
      Modified Time: 2855
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0x7faad0000000
      Container manages memory: true
      Size: 9630720
      Capacity: 9630720

     Weighting = 1
     Sampling strategy = none
     Number of bins = 32
     Radius = 4
     Sampling percentage  = 1
   Transform = SyN
     Gradient step = 0.1
     Update field sigma (voxel space) = 1
     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 3 total stages.

Stage 0
  iterations = 1000x500x250x100
  convergence threshold = 1e-06
  convergence window size = 10
  number of levels = 4
  using the CC metric (radius = 4, weight = 1)
  preprocessing:  winsorizing the image intensities
  Shrink factors (level 1 out of 4): [8, 8, 1]
  Shrink factors (level 2 out of 4): [4, 4, 1]
  Shrink factors (level 3 out of 4): [2, 2, 1]
  Shrink factors (level 4 out of 4): [1, 1, 1]
  smoothing sigmas per level: [3, 2, 1, 0]
  regular sampling (percentage = 0.1)

*** Running Euler3DTransform registration ***

DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -4.725088881403e-01, 1.797693134862e+308, 4.5888e-01, 4.5888e-01, 
 2DIAGNOSTIC,     2, -4.883753973487e-01, 1.797693134862e+308, 4.9287e-01, 3.3995e-02, 
 2DIAGNOSTIC,     3, -5.148684368638e-01, 1.797693134862e+308, 5.3306e-01, 4.0185e-02, 
 2DIAGNOSTIC,     4, -5.812028555249e-01, 1.797693134862e+308, 6.9025e-01, 1.5719e-01, 
 2DIAGNOSTIC,     5, -5.812016702121e-01, 1.797693134862e+308, 7.2387e-01, 3.3620e-02, 
 2DIAGNOSTIC,     6, -5.812016971199e-01, 1.797693134862e+308, 7.5832e-01, 3.4451e-02, 
 2DIAGNOSTIC,     7, -5.812017423693e-01, 1.797693134862e+308, 7.9369e-01, 3.5369e-02, 
 2DIAGNOSTIC,     8, -5.812018181289e-01, 1.797693134862e+308, 8.2837e-01, 3.4683e-02, 
 2DIAGNOSTIC,     9, -5.812019430918e-01, 1.797693134862e+308, 8.6158e-01, 3.3211e-02, 
 2DIAGNOSTIC,    10, -5.812021470503e-01, 1.212002818048e-02, 8.9665e-01, 3.5066e-02, 
 2DIAGNOSTIC,    11, -5.812024804876e-01, 6.998551141400e-03, 9.2992e-01, 3.3274e-02, 
 2DIAGNOSTIC,    12, -5.812030928665e-01, 2.813886682514e-03, 9.6997e-01, 4.0051e-02, 
 2DIAGNOSTIC,    13, -5.812042918327e-01, 2.670950695380e-06, 1.0066e+00, 3.6604e-02, 
 2DIAGNOSTIC,    14, -5.812060413672e-01, 2.635852306920e-06, 1.0435e+00, 3.6875e-02, 
 2DIAGNOSTIC,    15, -5.812099441391e-01, 2.669887753812e-06, 1.0798e+00, 3.6391e-02, 
 2DIAGNOSTIC,    16, -5.812141607687e-01, 2.786508246228e-06, 1.1337e+00, 5.3907e-02, 
 2DIAGNOSTIC,    17, -5.812144612228e-01, 2.829565482046e-06, 1.3008e+00, 1.6708e-01, 
 2DIAGNOSTIC,    18, -5.812144612193e-01, 2.788494487205e-06, 1.4687e+00, 1.6787e-01, 
 2DIAGNOSTIC,    19, -5.812144612193e-01, 2.665780450536e-06, 1.5125e+00, 4.3764e-02, 
 2DIAGNOSTIC,    20, -5.812144612193e-01, 2.470917801797e-06, 1.5555e+00, 4.3074e-02, 
 2DIAGNOSTIC,    21, -5.812144612193e-01, 2.223072174894e-06, 1.6011e+00, 4.5556e-02, 
 2DIAGNOSTIC,    22, -5.812144612193e-01, 1.949916611253e-06, 1.6514e+00, 5.0336e-02, 
 2DIAGNOSTIC,    23, -5.812144612193e-01, 1.684193090913e-06, 1.6946e+00, 4.3212e-02, 
 2DIAGNOSTIC,    24, -5.812144612193e-01, 1.450668842273e-06, 1.7376e+00, 4.2973e-02, 
 2DIAGNOSTIC,    25, -5.812144612193e-01, 1.302295540635e-06, 1.7750e+00, 3.7412e-02, 
 2DIAGNOSTIC,    26, -5.812144612193e-01, 1.245550066233e-06, 1.8186e+00, 4.3578e-02, 
 2DIAGNOSTIC,    27, -5.812144612193e-01, 1.198617054762e-06, 1.8702e+00, 5.1548e-02, 
 2DIAGNOSTIC,    28, -5.812144612193e-01, 1.155092474621e-06, 1.9136e+00, 4.3439e-02, 
 2DIAGNOSTIC,    29, -5.812144612193e-01, 1.114618092650e-06, 1.9563e+00, 4.2709e-02, 
 2DIAGNOSTIC,    30, -5.812144612193e-01, 1.076884127205e-06, 2.0169e+00, 6.0602e-02, 
 2DIAGNOSTIC,    31, -5.812144612193e-01, 1.041621372114e-06, 2.0610e+00, 4.4058e-02, 
 2DIAGNOSTIC,    32, -5.812144612193e-01, 1.008594763915e-06, 2.1052e+00, 4.4285e-02, 
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -4.282779427748e-01, 1.797693134862e+308, 2.7288e+00, 6.2354e-01, 
 2DIAGNOSTIC,     2, -4.439504269220e-01, 1.797693134862e+308, 2.8846e+00, 1.5584e-01, 
 2DIAGNOSTIC,     3, -4.566643330046e-01, 1.797693134862e+308, 3.0720e+00, 1.8738e-01, 
 2DIAGNOSTIC,     4, -4.604286190245e-01, 1.797693134862e+308, 3.3831e+00, 3.1111e-01, 
 2DIAGNOSTIC,     5, -4.600423883438e-01, 1.797693134862e+308, 3.6621e+00, 2.7896e-01, 
 2DIAGNOSTIC,     6, -4.607588665909e-01, 1.797693134862e+308, 4.3665e+00, 7.0445e-01, 
 2DIAGNOSTIC,     7, -4.607588574881e-01, 1.797693134862e+308, 5.0523e+00, 6.8580e-01, 
 2DIAGNOSTIC,     8, -4.607588574878e-01, 1.797693134862e+308, 5.5576e+00, 5.0531e-01, 
 2DIAGNOSTIC,     9, -4.607588574878e-01, 1.797693134862e+308, 5.7983e+00, 2.4071e-01, 
 2DIAGNOSTIC,    10, -4.607588574878e-01, 3.143676998690e-03, 5.9757e+00, 1.7737e-01, 
 2DIAGNOSTIC,    11, -4.607588574878e-01, 1.190533154837e-03, 6.1547e+00, 1.7902e-01, 
 2DIAGNOSTIC,    12, -4.607588574878e-01, 2.563359563303e-04, 6.3324e+00, 1.7770e-01, 
 2DIAGNOSTIC,    13, -4.607588574878e-01, 4.824956103340e-05, 6.5738e+00, 2.4138e-01, 
 2DIAGNOSTIC,    14, -4.607588574878e-01, 3.412694167811e-05, 6.7546e+00, 1.8082e-01, 
 2DIAGNOSTIC,    15, -4.607588574878e-01, 2.137118044615e-06, 6.9326e+00, 1.7799e-01, 
 2DIAGNOSTIC,    16, -4.607588574878e-01, 2.002908197962e-06, 7.1114e+00, 1.7879e-01, 
 2DIAGNOSTIC,    17, -4.607588574878e-01, 1.884265636382e-06, 7.3186e+00, 2.0723e-01, 
 2DIAGNOSTIC,    18, -4.607588574878e-01, 1.778892658448e-06, 7.4982e+00, 1.7961e-01, 
 2DIAGNOSTIC,    19, -4.607588574878e-01, 1.684680968193e-06, 7.6803e+00, 1.8210e-01, 
 2DIAGNOSTIC,    20, -4.607588574878e-01, 1.599946424853e-06, 7.8608e+00, 1.8045e-01, 
 2DIAGNOSTIC,    21, -4.607588574878e-01, 1.523327491218e-06, 8.0412e+00, 1.8045e-01, 
 2DIAGNOSTIC,    22, -4.607588574878e-01, 1.453711518683e-06, 8.2204e+00, 1.7920e-01, 
 2DIAGNOSTIC,    23, -4.607588574878e-01, 1.390180361764e-06, 8.4582e+00, 2.3778e-01, 
 2DIAGNOSTIC,    24, -4.607588574878e-01, 1.331969656154e-06, 8.6383e+00, 1.8010e-01, 
 2DIAGNOSTIC,    25, -4.607588574878e-01, 1.278437916509e-06, 8.8179e+00, 1.7961e-01, 
 2DIAGNOSTIC,    26, -4.607588574878e-01, 1.229042797951e-06, 8.9973e+00, 1.7933e-01, 
 2DIAGNOSTIC,    27, -4.607588574878e-01, 1.183322656091e-06, 9.1792e+00, 1.8197e-01, 
 2DIAGNOSTIC,    28, -4.607588574878e-01, 1.140882075187e-06, 9.3593e+00, 1.8007e-01, 
 2DIAGNOSTIC,    29, -4.607588574878e-01, 1.101380402650e-06, 9.5396e+00, 1.8032e-01, 
 2DIAGNOSTIC,    30, -4.607588574878e-01, 1.064522585768e-06, 9.7191e+00, 1.7948e-01, 
 2DIAGNOSTIC,    31, -4.607588574878e-01, 1.030051788836e-06, 9.8972e+00, 1.7815e-01, 
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -2.362153704843e-01, 1.797693134862e+308, 1.3050e+01, 3.1530e+00, 
 2DIAGNOSTIC,     2, -2.362152466043e-01, 1.797693134862e+308, 1.5822e+01, 2.7721e+00, 
 2DIAGNOSTIC,     3, -2.362152466002e-01, 1.797693134862e+308, 1.8559e+01, 2.7370e+00, 
 2DIAGNOSTIC,     4, -2.362152466002e-01, 1.797693134862e+308, 1.9264e+01, 7.0499e-01, 
 2DIAGNOSTIC,     5, -2.362152466002e-01, 1.797693134862e+308, 1.9969e+01, 7.0449e-01, 
 2DIAGNOSTIC,     6, -2.362152466002e-01, 1.797693134862e+308, 2.0668e+01, 6.9911e-01, 
 2DIAGNOSTIC,     7, -2.362152466002e-01, 1.797693134862e+308, 2.1606e+01, 9.3847e-01, 
 2DIAGNOSTIC,     8, -2.362152466002e-01, 1.797693134862e+308, 2.2432e+01, 8.2539e-01, 
 2DIAGNOSTIC,     9, -2.362152466002e-01, 1.797693134862e+308, 2.3135e+01, 7.0293e-01, 
 2DIAGNOSTIC,    10, -2.362152466002e-01, 3.166086157594e-06, 2.3840e+01, 7.0544e-01, 
 2DIAGNOSTIC,    11, -2.362152466002e-01, 2.891810588768e-06, 2.4550e+01, 7.0967e-01, 
 2DIAGNOSTIC,    12, -2.362152466002e-01, 2.650826794195e-06, 2.5254e+01, 7.0372e-01, 
 2DIAGNOSTIC,    13, -2.362152466002e-01, 2.446917049037e-06, 2.5950e+01, 6.9661e-01, 
 2DIAGNOSTIC,    14, -2.362152466002e-01, 2.272137266390e-06, 2.6676e+01, 7.2573e-01, 
 2DIAGNOSTIC,    15, -2.362152466002e-01, 2.120661453969e-06, 2.7418e+01, 7.4241e-01, 
 2DIAGNOSTIC,    16, -2.362152466002e-01, 1.988120117452e-06, 2.8147e+01, 7.2867e-01, 
 2DIAGNOSTIC,    17, -2.362152466002e-01, 1.871171878866e-06, 2.8883e+01, 7.3646e-01, 
 2DIAGNOSTIC,    18, -2.362152466002e-01, 1.767217888624e-06, 2.9627e+01, 7.4407e-01, 
 2DIAGNOSTIC,    19, -2.362152466002e-01, 1.674206423358e-06, 3.0337e+01, 7.0967e-01, 
 2DIAGNOSTIC,    20, -2.362152466002e-01, 1.590496104396e-06, 3.1161e+01, 8.2348e-01, 
 2DIAGNOSTIC,    21, -2.362152466002e-01, 1.514758196555e-06, 3.1864e+01, 7.0311e-01, 
 2DIAGNOSTIC,    22, -2.362152466002e-01, 1.445905552885e-06, 3.2566e+01, 7.0268e-01, 
 2DIAGNOSTIC,    23, -2.362152466002e-01, 1.383040095497e-06, 3.3271e+01, 7.0506e-01, 
 2DIAGNOSTIC,    24, -2.362152466002e-01, 1.325413426109e-06, 3.3978e+01, 7.0604e-01, 
 2DIAGNOSTIC,    25, -2.362152466002e-01, 1.272396890198e-06, 3.4683e+01, 7.0553e-01, 
 2DIAGNOSTIC,    26, -2.362152466002e-01, 1.223458549235e-06, 3.5387e+01, 7.0358e-01, 
 2DIAGNOSTIC,    27, -2.362152466002e-01, 1.178145270529e-06, 3.6097e+01, 7.1083e-01, 
 2DIAGNOSTIC,    28, -2.362152466002e-01, 1.136068654491e-06, 3.6810e+01, 7.1260e-01, 
 2DIAGNOSTIC,    29, -2.362152466002e-01, 1.096893874029e-06, 3.7522e+01, 7.1157e-01, 
 2DIAGNOSTIC,    30, -2.362152466002e-01, 1.060330745525e-06, 3.8226e+01, 7.0422e-01, 
 2DIAGNOSTIC,    31, -2.362152466002e-01, 1.026126528504e-06, 3.8923e+01, 6.9735e-01, 
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -8.081948465203e-02, 1.797693134862e+308, 4.2370e+01, 3.4471e+00, 
 2DIAGNOSTIC,     2, -8.138014042182e-02, 1.797693134862e+308, 4.5127e+01, 2.7564e+00, 
 2DIAGNOSTIC,     3, -8.167378890099e-02, 1.797693134862e+308, 4.7436e+01, 2.3096e+00, 
 2DIAGNOSTIC,     4, -8.215977440063e-02, 1.797693134862e+308, 5.0192e+01, 2.7559e+00, 
 2DIAGNOSTIC,     5, -8.228736142525e-02, 1.797693134862e+308, 5.4429e+01, 4.2369e+00, 
 2DIAGNOSTIC,     6, -8.223391342265e-02, 1.797693134862e+308, 6.5045e+01, 1.0616e+01, 
 2DIAGNOSTIC,     7, -8.223391316508e-02, 1.797693134862e+308, 7.5749e+01, 1.0704e+01, 
 2DIAGNOSTIC,     8, -8.223391316507e-02, 1.797693134862e+308, 8.3276e+01, 7.5271e+00, 
 2DIAGNOSTIC,     9, -8.223391316507e-02, 1.797693134862e+308, 8.6021e+01, 2.7445e+00, 
 2DIAGNOSTIC,    10, -8.223391316507e-02, 8.977441355000e-04, 8.8878e+01, 2.8575e+00, 
 2DIAGNOSTIC,    11, -8.223391316507e-02, 4.347587424442e-04, 9.2636e+01, 3.7580e+00, 
 2DIAGNOSTIC,    12, -8.223391316507e-02, 1.723104635865e-04, 9.4932e+01, 2.2955e+00, 
 2DIAGNOSTIC,    13, -8.223391316507e-02, 9.771041001805e-06, 9.9539e+01, 4.6072e+00, 
  Elapsed time (stage 0): 1.0032e+02


Stage 1
  iterations = 1000x500x250x100
  convergence threshold = 1.0000e-06
  convergence window size = 10
  number of levels = 4
  using the Mattes MI metric (number of bins = 32, weight = 1.0000e+00)
  preprocessing:  winsorizing the image intensities
  Shrink factors (level 1 out of 4): [8, 8, 1]
  Shrink factors (level 2 out of 4): [4, 4, 1]
  Shrink factors (level 3 out of 4): [2, 2, 1]
  Shrink factors (level 4 out of 4): [1, 1, 1]
  smoothing sigmas per level: [3, 2, 1, 0]
  regular sampling (percentage = 1.0000e-01)

*** Running AffineTransform registration ***

DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -1.427588186732e+00, 1.797693134862e+308, 4.3999e-01, 4.3999e-01, 
 2DIAGNOSTIC,     2, -1.529167617246e+00, 1.797693134862e+308, 4.4014e-01, 1.5783e-04, 
 2DIAGNOSTIC,     3, -1.541650576627e+00, 1.797693134862e+308, 4.4027e-01, 1.2994e-04, 
 2DIAGNOSTIC,     4, -1.546287380104e+00, 1.797693134862e+308, 4.4040e-01, 1.2994e-04, 
 2DIAGNOSTIC,     5, -1.556608815224e+00, 1.797693134862e+308, 4.4059e-01, 1.8406e-04, 
 2DIAGNOSTIC,     6, -1.562389341595e+00, 1.797693134862e+308, 4.4070e-01, 1.1206e-04, 
 2DIAGNOSTIC,     7, -1.577299256548e+00, 1.797693134862e+308, 4.4081e-01, 1.1206e-04, 
 2DIAGNOSTIC,     8, -1.582261942635e+00, 1.797693134862e+308, 4.4092e-01, 1.1110e-04, 
 2DIAGNOSTIC,     9, -1.585598069619e+00, 1.797693134862e+308, 4.4103e-01, 1.1086e-04, 
 2DIAGNOSTIC,    10, -1.587955422661e+00, 4.654400860161e-03, 4.4141e-01, 3.7217e-04, 
 2DIAGNOSTIC,    11, -1.592367619868e+00, 2.425943292876e-03, 4.4178e-01, 3.7003e-04, 
 2DIAGNOSTIC,    12, -1.596531848209e+00, 1.961727860166e-03, 4.4213e-01, 3.5095e-04, 
 2DIAGNOSTIC,    13, -1.597548058570e+00, 1.581818949798e-03, 4.4248e-01, 3.5620e-04, 
 2DIAGNOSTIC,    14, -1.600869893905e+00, 1.217709944347e-03, 4.4289e-01, 4.0793e-04, 
 2DIAGNOSTIC,    15, -1.604135868854e+00, 9.568927715861e-04, 4.4323e-01, 3.3784e-04, 
 2DIAGNOSTIC,    16, -1.604807726718e+00, 7.099833226175e-04, 4.4362e-01, 3.8695e-04, 
 2DIAGNOSTIC,    17, -1.605311066886e+00, 5.908887963838e-04, 4.4397e-01, 3.4904e-04, 
 2DIAGNOSTIC,    18, -1.606756771563e+00, 4.953475166677e-04, 4.4430e-01, 3.3021e-04, 
 2DIAGNOSTIC,    19, -1.612090853470e+00, 4.462784562793e-04, 4.4466e-01, 3.6693e-04, 
 2DIAGNOSTIC,    20, -1.590248460796e+00, 1.831443957673e-04, 4.4501e-01, 3.5000e-04, 
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -9.500049983743e-01, 1.797693134862e+308, 8.9579e-01, 4.5078e-01, 
 2DIAGNOSTIC,     2, -1.003632589124e+00, 1.797693134862e+308, 8.9642e-01, 6.2513e-04, 
 2DIAGNOSTIC,     3, -1.013554451274e+00, 1.797693134862e+308, 8.9702e-01, 6.0296e-04, 
 2DIAGNOSTIC,     4, -1.008811993927e+00, 1.797693134862e+308, 8.9754e-01, 5.2118e-04, 
 2DIAGNOSTIC,     5, -1.013778561706e+00, 1.797693134862e+308, 8.9789e-01, 3.4404e-04, 
 2DIAGNOSTIC,     6, -1.021101673234e+00, 1.797693134862e+308, 8.9823e-01, 3.4189e-04, 
 2DIAGNOSTIC,     7, -1.021700575458e+00, 1.797693134862e+308, 8.9867e-01, 4.4680e-04, 
 2DIAGNOSTIC,     8, -1.021879652967e+00, 1.797693134862e+308, 8.9902e-01, 3.4094e-04, 
 2DIAGNOSTIC,     9, -1.022049438333e+00, 1.797693134862e+308, 8.9936e-01, 3.3998e-04, 
 2DIAGNOSTIC,    10, -1.022457691665e+00, 2.862831633199e-03, 8.9995e-01, 5.9104e-04, 
 2DIAGNOSTIC,    11, -1.023655998580e+00, 1.049975169396e-03, 9.0054e-01, 5.9795e-04, 
 2DIAGNOSTIC,    12, -1.026999159314e+00, 7.741188850591e-04, 9.0124e-01, 6.9118e-04, 
 2DIAGNOSTIC,    13, -1.029411350056e+00, 7.426524376146e-04, 9.0187e-01, 6.3705e-04, 
 2DIAGNOSTIC,    14, -1.024992528135e+00, 4.643136879780e-04, 9.0251e-01, 6.4015e-04, 
 2DIAGNOSTIC,    15, -1.032179573171e+00, 4.078716072028e-04, 9.0307e-01, 5.5408e-04, 
 2DIAGNOSTIC,    16, -1.033144083674e+00, 4.615339538665e-04, 9.0377e-01, 7.0691e-04, 
 2DIAGNOSTIC,    17, -1.033662192067e+00, 4.835519345748e-04, 9.0435e-01, 5.7697e-04, 
 2DIAGNOSTIC,    18, -1.034021318318e+00, 4.684652699182e-04, 9.0498e-01, 6.3205e-04, 
 2DIAGNOSTIC,    19, -1.034366416332e+00, 4.208994450923e-04, 9.0564e-01, 6.5923e-04, 
 2DIAGNOSTIC,    20, -1.034497076846e+00, 3.458976715860e-04, 9.0637e-01, 7.3004e-04, 
 2DIAGNOSTIC,    21, -1.035048729273e+00, 2.669145838816e-04, 9.0706e-01, 6.9094e-04, 
 2DIAGNOSTIC,    22, -1.036611653649e+00, 2.321159012312e-04, 9.0764e-01, 5.8103e-04, 
 2DIAGNOSTIC,    23, -1.036885571459e+00, 2.135054217831e-04, 9.0826e-01, 6.1202e-04, 
 2DIAGNOSTIC,    24, -1.037398563332e+00, 1.293674980327e-04, 9.0888e-01, 6.2299e-04, 
 2DIAGNOSTIC,    25, -1.037817331159e+00, 1.244311609084e-04, 9.0958e-01, 6.9785e-04, 
 2DIAGNOSTIC,    26, -1.037927602546e+00, 1.195412387587e-04, 9.1027e-01, 6.9690e-04, 
 2DIAGNOSTIC,    27, -1.038126427294e+00, 1.110063578683e-04, 9.1100e-01, 7.2289e-04, 
 2DIAGNOSTIC,    28, -1.038623340650e+00, 1.011180799019e-04, 9.1177e-01, 7.6795e-04, 
 2DIAGNOSTIC,    29, -1.038867165520e+00, 8.817821086238e-05, 9.1254e-01, 7.7295e-04, 
 2DIAGNOSTIC,    30, -1.038961552771e+00, 6.996338931993e-05, 9.1315e-01, 6.0701e-04, 
 2DIAGNOSTIC,    31, -1.039039170817e+00, 5.178066121876e-05, 9.1374e-01, 5.9700e-04, 
 2DIAGNOSTIC,    32, -1.039164307055e+00, 4.456218549296e-05, 9.1433e-01, 5.8794e-04, 
 2DIAGNOSTIC,    33, -1.039431830510e+00, 3.803595498963e-05, 9.1492e-01, 5.8889e-04, 
 2DIAGNOSTIC,    34, -1.039836337832e+00, 3.569181378744e-05, 9.1582e-01, 9.0599e-04, 
 2DIAGNOSTIC,    35, -1.039895916597e+00, 3.394729721162e-05, 9.1659e-01, 7.6890e-04, 
 2DIAGNOSTIC,    36, -1.039938614347e+00, 3.040939277416e-05, 9.1733e-01, 7.3910e-04, 
 2DIAGNOSTIC,    37, -1.040039288629e+00, 2.644006627442e-05, 9.1802e-01, 6.8378e-04, 
 2DIAGNOSTIC,    38, -1.040289414214e+00, 2.558634055146e-05, 9.1861e-01, 5.9199e-04, 
 2DIAGNOSTIC,    39, -1.040572041147e+00, 2.605463917628e-05, 9.1959e-01, 9.8491e-04, 
 2DIAGNOSTIC,    40, -1.040583029504e+00, 2.480392869569e-05, 9.2016e-01, 5.6791e-04, 
 2DIAGNOSTIC,    41, -1.040602988127e+00, 2.206324828094e-05, 9.2073e-01, 5.6720e-04, 
 2DIAGNOSTIC,    42, -1.040670597638e+00, 1.868623647476e-05, 9.2136e-01, 6.3396e-04, 
 2DIAGNOSTIC,    43, -1.040785291635e+00, 1.609663044917e-05, 9.2196e-01, 5.9390e-04, 
 2DIAGNOSTIC,    44, -1.040976803258e+00, 1.584799526102e-05, 9.2255e-01, 5.8889e-04, 
 2DIAGNOSTIC,    45, -1.052199335736e+00, 8.326820216795e-05, 9.2320e-01, 6.5207e-04, 
 2DIAGNOSTIC,    46, -1.055199714684e+00, 1.561468677785e-04, 9.2405e-01, 8.4805e-04, 
 2DIAGNOSTIC,    47, -1.057719369690e+00, 2.265983090767e-04, 9.2463e-01, 5.8913e-04, 
 2DIAGNOSTIC,    48, -1.058178390403e+00, 2.772631423614e-04, 9.2530e-01, 6.6209e-04, 
 2DIAGNOSTIC,    49, -1.058582550950e+00, 3.032933099247e-04, 9.2595e-01, 6.5088e-04, 
 2DIAGNOSTIC,    50, -1.058864900339e+00, 2.999706006355e-04, 9.2660e-01, 6.4802e-04, 
 2DIAGNOSTIC,    51, -1.060219711676e+00, 2.749773499433e-04, 9.2720e-01, 6.0606e-04, 
 2DIAGNOSTIC,    52, -1.061786517031e+00, 2.338061780717e-04, 9.2784e-01, 6.3491e-04, 
 2DIAGNOSTIC,    53, -1.063415461699e+00, 1.815925746551e-04, 9.2857e-01, 7.3719e-04, 
 2DIAGNOSTIC,    54, -1.064286087701e+00, 1.180732805613e-04, 9.2917e-01, 5.9509e-04, 
 2DIAGNOSTIC,    55, -1.064535907650e+00, 1.026579939761e-04, 9.2975e-01, 5.7983e-04, 
 2DIAGNOSTIC,    56, -1.064914311868e+00, 9.425140957154e-05, 9.3037e-01, 6.2490e-04, 
 2DIAGNOSTIC,    57, -1.065370499483e+00, 9.128538668027e-05, 9.3099e-01, 6.1989e-04, 
 2DIAGNOSTIC,    58, -1.067214176673e+00, 9.044925292651e-05, 9.3212e-01, 1.1261e-03, 
 2DIAGNOSTIC,    59, -1.067988019073e+00, 8.633225471285e-05, 9.3279e-01, 6.7186e-04, 
 2DIAGNOSTIC,    60, -1.068127787987e+00, 7.605788279017e-05, 9.3364e-01, 8.5306e-04, 
 2DIAGNOSTIC,    61, -1.068560776413e+00, 6.694986461040e-05, 9.3425e-01, 6.0892e-04, 
 2DIAGNOSTIC,    62, -1.069249536709e+00, 6.149377860760e-05, 9.3491e-01, 6.5517e-04, 
 2DIAGNOSTIC,    63, -1.071794920032e+00, 6.817198419335e-05, 9.3575e-01, 8.3804e-04, 
 2DIAGNOSTIC,    64, -1.062017418674e+00, 2.981712279914e-05, 9.3632e-01, 5.7101e-04, 
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -5.069982497818e-01, 1.797693134862e+308, 1.3834e+00, 4.4712e-01, 
 2DIAGNOSTIC,     2, -5.082978061688e-01, 1.797693134862e+308, 1.3847e+00, 1.2760e-03, 
 2DIAGNOSTIC,     3, -5.086612098097e-01, 1.797693134862e+308, 1.3859e+00, 1.2021e-03, 
 2DIAGNOSTIC,     4, -5.107542285941e-01, 1.797693134862e+308, 1.3871e+00, 1.1952e-03, 
 2DIAGNOSTIC,     5, -5.186564166232e-01, 1.797693134862e+308, 1.3886e+00, 1.4679e-03, 
 2DIAGNOSTIC,     6, -5.264952296004e-01, 1.797693134862e+308, 1.3901e+00, 1.4729e-03, 
 2DIAGNOSTIC,     7, -5.284897327435e-01, 1.797693134862e+308, 1.3919e+00, 1.8010e-03, 
 2DIAGNOSTIC,     8, -5.291985704367e-01, 1.797693134862e+308, 1.3933e+00, 1.4038e-03, 
 2DIAGNOSTIC,     9, -5.267753216886e-01, 1.797693134862e+308, 1.3944e+00, 1.1580e-03, 
 2DIAGNOSTIC,    10, -5.394342885267e-01, 3.966817171126e-03, 1.3961e+00, 1.7350e-03, 
 2DIAGNOSTIC,    11, -5.421701565108e-01, 3.824118986898e-03, 1.3982e+00, 2.0602e-03, 
 2DIAGNOSTIC,    12, -5.427734144096e-01, 3.455250983304e-03, 1.3996e+00, 1.4389e-03, 
 2DIAGNOSTIC,    13, -5.435321217261e-01, 2.896073787957e-03, 1.4011e+00, 1.4951e-03, 
 2DIAGNOSTIC,    14, -5.445777130615e-01, 2.274708301490e-03, 1.4026e+00, 1.4479e-03, 
 2DIAGNOSTIC,    15, -5.461080346790e-01, 1.854970520583e-03, 1.4050e+00, 2.4431e-03, 
 2DIAGNOSTIC,    16, -5.466341174110e-01, 1.593624050750e-03, 1.4067e+00, 1.6830e-03, 
 2DIAGNOSTIC,    17, -5.467641335714e-01, 1.289532197072e-03, 1.4087e+00, 1.9741e-03, 
 2DIAGNOSTIC,    18, -5.468507339441e-01, 9.332805868989e-04, 1.4106e+00, 1.8609e-03, 
 2DIAGNOSTIC,    19, -5.467219561801e-01, 4.481241596975e-04, 1.4121e+00, 1.5941e-03, 
 2DIAGNOSTIC,    20, -5.468671067671e-01, 3.105709059151e-04, 1.4136e+00, 1.4141e-03, 
 2DIAGNOSTIC,    21, -5.471106589105e-01, 2.330114377265e-04, 1.4150e+00, 1.4892e-03, 
 2DIAGNOSTIC,    22, -5.476012050344e-01, 1.676320320692e-04, 1.4167e+00, 1.6282e-03, 
 2DIAGNOSTIC,    23, -5.495094319156e-01, 1.538447323583e-04, 1.4188e+00, 2.0890e-03, 
 2DIAGNOSTIC,    24, -5.513316993523e-01, 1.886203481210e-04, 1.4211e+00, 2.2881e-03, 
 2DIAGNOSTIC,    25, -5.521387070089e-01, 2.517504801457e-04, 1.4225e+00, 1.4920e-03, 
 2DIAGNOSTIC,    26, -5.544817355929e-01, 3.451043263646e-04, 1.4243e+00, 1.7729e-03, 
 2DIAGNOSTIC,    27, -5.552305058519e-01, 4.152700083781e-04, 1.4263e+00, 2.0301e-03, 
 2DIAGNOSTIC,    28, -5.556318176599e-01, 4.502290219782e-04, 1.4278e+00, 1.4889e-03, 
 2DIAGNOSTIC,    29, -5.562787865324e-01, 4.497735857513e-04, 1.4292e+00, 1.3750e-03, 
 2DIAGNOSTIC,    30, -5.568660521984e-01, 4.198093614781e-04, 1.4306e+00, 1.3881e-03, 
 2DIAGNOSTIC,    31, -5.576999218878e-01, 3.703622992705e-04, 1.4320e+00, 1.3721e-03, 
 2DIAGNOSTIC,    32, -5.596614902957e-01, 3.285927581242e-04, 1.4341e+00, 2.1620e-03, 
 2DIAGNOSTIC,    33, -5.604650023339e-01, 3.007021369893e-04, 1.4355e+00, 1.4071e-03, 
 2DIAGNOSTIC,    34, -5.609558459886e-01, 2.820257079314e-04, 1.4370e+00, 1.4451e-03, 
 2DIAGNOSTIC,    35, -5.615789541440e-01, 2.585853595319e-04, 1.4385e+00, 1.5130e-03, 
 2DIAGNOSTIC,    36, -5.637902163612e-01, 2.777923096730e-04, 1.4404e+00, 1.8840e-03, 
 2DIAGNOSTIC,    37, -5.667497609728e-01, 3.208101635799e-04, 1.4420e+00, 1.6220e-03, 
 2DIAGNOSTIC,    38, -5.673795894078e-01, 3.442536001742e-04, 1.4436e+00, 1.5612e-03, 
 2DIAGNOSTIC,    39, -5.681076235271e-01, 3.530051504299e-04, 1.4459e+00, 2.3160e-03, 
 2DIAGNOSTIC,    40, -5.682580293353e-01, 3.377124859184e-04, 1.4473e+00, 1.3969e-03, 
 2DIAGNOSTIC,    41, -5.691187566796e-01, 3.116350456127e-04, 1.4488e+00, 1.4760e-03, 
 2DIAGNOSTIC,    42, -5.704215788377e-01, 2.966269837192e-04, 1.4504e+00, 1.6100e-03, 
 2DIAGNOSTIC,    43, -5.707417782307e-01, 2.674465812894e-04, 1.4520e+00, 1.6019e-03, 
 2DIAGNOSTIC,    44, -5.719816851715e-01, 2.353164254517e-04, 1.4535e+00, 1.4899e-03, 
 2DIAGNOSTIC,    45, -5.742631383348e-01, 2.152839305348e-04, 1.4556e+00, 2.1100e-03, 
 2DIAGNOSTIC,    46, -5.747071429311e-01, 2.040706929023e-04, 1.4573e+00, 1.7090e-03, 
 2DIAGNOSTIC,    47, -5.748782171381e-01, 2.083816029246e-04, 1.4587e+00, 1.4582e-03, 
 2DIAGNOSTIC,    48, -5.754647214139e-01, 2.059136953642e-04, 1.4601e+00, 1.3769e-03, 
 2DIAGNOSTIC,    49, -5.780597177872e-01, 2.187810048151e-04, 1.4620e+00, 1.9069e-03, 
 2DIAGNOSTIC,    50, -5.803926606988e-01, 2.346505109039e-04, 1.4636e+00, 1.5950e-03, 
 2DIAGNOSTIC,    51, -5.810048344804e-01, 2.417573900547e-04, 1.4654e+00, 1.7791e-03, 
 2DIAGNOSTIC,    52, -5.820266001024e-01, 2.493469990568e-04, 1.4668e+00, 1.3902e-03, 
 2DIAGNOSTIC,    53, -5.822538222295e-01, 2.380509181119e-04, 1.4682e+00, 1.3771e-03, 
 2DIAGNOSTIC,    54, -5.822854701906e-01, 2.156011150786e-04, 1.4696e+00, 1.4021e-03, 
 2DIAGNOSTIC,    55, -5.823381867276e-01, 1.948389477993e-04, 1.4710e+00, 1.4710e-03, 
 2DIAGNOSTIC,    56, -5.825414525427e-01, 1.623574829631e-04, 1.4737e+00, 2.6360e-03, 
 2DIAGNOSTIC,    57, -5.825726388861e-01, 1.176050302660e-04, 1.4785e+00, 4.8029e-03, 
 2DIAGNOSTIC,    58, -5.825726388584e-01, 6.803839118666e-05, 1.4836e+00, 5.1129e-03, 
 2DIAGNOSTIC,    59, -5.825726388584e-01, 3.588473116046e-05, 1.4857e+00, 2.1360e-03, 
 2DIAGNOSTIC,    60, -5.825726388584e-01, 2.129846535261e-05, 1.4876e+00, 1.8330e-03, 
 2DIAGNOSTIC,    61, -5.825726388584e-01, 1.009191252239e-05, 1.4895e+00, 1.9269e-03, 
 2DIAGNOSTIC,    62, -5.825726388584e-01, 6.697495752394e-06, 1.4911e+00, 1.5831e-03, 
 2DIAGNOSTIC,    63, -5.825726388584e-01, 4.685075491444e-06, 1.4928e+00, 1.7169e-03, 
 2DIAGNOSTIC,    64, -5.825726388584e-01, 2.601678782434e-06, 1.4943e+00, 1.5011e-03, 
DIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 2DIAGNOSTIC,     1, -2.983909686382e-01, 1.797693134862e+308, 1.5312e+00, 3.6961e-02, 
 2DIAGNOSTIC,     2, -3.158997308531e-01, 1.797693134862e+308, 1.5383e+00, 7.0522e-03, 
 2DIAGNOSTIC,     3, -3.178681539010e-01, 1.797693134862e+308, 1.5438e+00, 5.4712e-03, 
 2DIAGNOSTIC,     4, -2.762891381785e-01, 1.797693134862e+308, 1.5504e+00, 6.6519e-03, 
 2DIAGNOSTIC,     5, -2.697864242387e-01, 1.797693134862e+308, 1.5557e+00, 5.2800e-03, 
 2DIAGNOSTIC,     6, -2.721016567136e-01, 1.797693134862e+308, 1.5613e+00, 5.6190e-03, 
 2DIAGNOSTIC,     7, -2.723266799128e-01, 1.797693134862e+308, 1.5658e+00, 4.4761e-03, 
 2DIAGNOSTIC,     8, -2.740358676860e-01, 1.797693134862e+308, 1.5741e+00, 8.3401e-03, 
 2DIAGNOSTIC,     9, -2.744586215916e-01, 1.797693134862e+308, 1.5791e+00, 4.9629e-03, 
  Elapsed time (stage 1): 1.8589e+00


Stage 2
  iterations = 100x70x50x20
  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
  Shrink factors (level 1 out of 4): [8, 8, 1]
  Shrink factors (level 2 out of 4): [4, 4, 1]
  Shrink factors (level 3 out of 4): [2, 2, 1]
  Shrink factors (level 4 out of 4): [1, 1, 1]
  smoothing sigmas per level: [3, 2, 1, 0]
  Using default NONE metricSamplingStrategy 

*** Running SyN registration (varianceForUpdateField = 1.0000e+00, varianceForTotalField = 0.0000e+00) ***

XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 1DIAGNOSTIC,     1, -4.262779020134e-01, 1.797693134862e+308, 5.6628e-01, 5.6628e-01, 
 1DIAGNOSTIC,     2, -4.336168577477e-01, 1.797693134862e+308, 6.9755e-01, 1.3127e-01, 
 1DIAGNOSTIC,     3, -4.399917903590e-01, 1.797693134862e+308, 8.2518e-01, 1.2763e-01, 
 1DIAGNOSTIC,     4, -4.466908071998e-01, 1.797693134862e+308, 9.5392e-01, 1.2874e-01, 
 1DIAGNOSTIC,     5, -4.520989170543e-01, 1.797693134862e+308, 1.0825e+00, 1.2853e-01, 
 1DIAGNOSTIC,     6, -4.571134831598e-01, 1.797693134862e+308, 1.2108e+00, 1.2832e-01, 
 1DIAGNOSTIC,     7, -4.623665082782e-01, 1.797693134862e+308, 1.3397e+00, 1.2896e-01, 
 1DIAGNOSTIC,     8, -4.667969036092e-01, 1.797693134862e+308, 1.4673e+00, 1.2757e-01, 
 1DIAGNOSTIC,     9, -4.688156234649e-01, 1.797693134862e+308, 1.5962e+00, 1.2890e-01, 
 1DIAGNOSTIC,    10, -4.717987264373e-01, 6.486619635898e-03, 1.7248e+00, 1.2859e-01, 
 1DIAGNOSTIC,    11, -4.744940282591e-01, 5.228186870555e-03, 1.8544e+00, 1.2964e-01, 
 1DIAGNOSTIC,    12, -4.767627216278e-01, 4.210530861256e-03, 1.9848e+00, 1.3039e-01, 
 1DIAGNOSTIC,    13, -4.787129615047e-01, 3.367301402600e-03, 2.1159e+00, 1.3106e-01, 
 1DIAGNOSTIC,    14, -4.745806647060e-01, 2.457422284866e-03, 2.2430e+00, 1.2716e-01, 
 1DIAGNOSTIC,    15, -4.758215511148e-01, 1.726569668639e-03, 2.3727e+00, 1.2965e-01, 
 1DIAGNOSTIC,    16, -4.733475315217e-01, 1.023256064853e-03, 2.5016e+00, 1.2890e-01, 
 1DIAGNOSTIC,    17, -4.732799792784e-01, 4.952354474092e-04, 2.6297e+00, 1.2815e-01, 
 1DIAGNOSTIC,    18, -4.732307624253e-01, 1.308999330395e-04, 2.7526e+00, 1.2287e-01, 
 1DIAGNOSTIC,    19, -4.731316441937e-01, -1.441307577252e-04, 2.8750e+00, 1.2238e-01, 
XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 1DIAGNOSTIC,     1, -5.589833668050e-01, 1.797693134862e+308, 3.7662e+00, 8.9121e-01, 
 1DIAGNOSTIC,     2, -5.598000748348e-01, 1.797693134862e+308, 4.2452e+00, 4.7898e-01, 
 1DIAGNOSTIC,     3, -5.603877376878e-01, 1.797693134862e+308, 4.7237e+00, 4.7857e-01, 
 1DIAGNOSTIC,     4, -5.614530732582e-01, 1.797693134862e+308, 5.2068e+00, 4.8308e-01, 
 1DIAGNOSTIC,     5, -5.623444095265e-01, 1.797693134862e+308, 5.6855e+00, 4.7865e-01, 
 1DIAGNOSTIC,     6, -5.642167219613e-01, 1.797693134862e+308, 6.1658e+00, 4.8028e-01, 
 1DIAGNOSTIC,     7, -5.658593545415e-01, 1.797693134862e+308, 6.6424e+00, 4.7664e-01, 
 1DIAGNOSTIC,     8, -5.667808987910e-01, 1.797693134862e+308, 7.1206e+00, 4.7824e-01, 
 1DIAGNOSTIC,     9, -5.668307110511e-01, 1.797693134862e+308, 7.6079e+00, 4.8722e-01, 
 1DIAGNOSTIC,    10, -5.683073008952e-01, 1.128990639126e-03, 8.0913e+00, 4.8345e-01, 
 1DIAGNOSTIC,    11, -5.690987376251e-01, 1.026081302404e-03, 8.5733e+00, 4.8201e-01, 
 1DIAGNOSTIC,    12, -5.693574982006e-01, 8.925554280905e-04, 9.0549e+00, 4.8160e-01, 
 1DIAGNOSTIC,    13, -5.698011513454e-01, 7.398962173719e-04, 9.5359e+00, 4.8094e-01, 
 1DIAGNOSTIC,    14, -5.699570471954e-01, 5.867555889853e-04, 1.0008e+01, 4.7230e-01, 
 1DIAGNOSTIC,    15, -5.701843533568e-01, 4.369289921536e-04, 1.0483e+01, 4.7519e-01, 
 1DIAGNOSTIC,    16, -5.706288056789e-01, 3.371879764096e-04, 1.0980e+01, 4.9653e-01, 
 1DIAGNOSTIC,    17, -5.710510826910e-01, 2.788575834831e-04, 1.1472e+01, 4.9217e-01, 
 1DIAGNOSTIC,    18, -5.711772772203e-01, 2.311685595894e-04, 1.1978e+01, 5.0624e-01, 
 1DIAGNOSTIC,    19, -5.714621061316e-01, 1.754593727248e-04, 1.2477e+01, 4.9834e-01, 
 1DIAGNOSTIC,    20, -5.717224371057e-01, 1.523001560502e-04, 1.2984e+01, 5.0728e-01, 
 1DIAGNOSTIC,    21, -5.718683601480e-01, 1.394229788793e-04, 1.3480e+01, 4.9622e-01, 
 1DIAGNOSTIC,    22, -5.719990419610e-01, 1.234289965907e-04, 1.3977e+01, 4.9647e-01, 
 1DIAGNOSTIC,    23, -5.718163670193e-01, 1.031767614799e-04, 1.4474e+01, 4.9743e-01, 
 1DIAGNOSTIC,    24, -5.717080270951e-01, 7.625885834269e-05, 1.4975e+01, 5.0057e-01, 
 1DIAGNOSTIC,    25, -5.720025214942e-01, 5.474676524340e-05, 1.5471e+01, 4.9638e-01, 
 1DIAGNOSTIC,    26, -5.724133072662e-01, 4.589344891671e-05, 1.5975e+01, 5.0364e-01, 
 1DIAGNOSTIC,    27, -5.728011982134e-01, 4.835274102939e-05, 1.6471e+01, 4.9606e-01, 
 1DIAGNOSTIC,    28, -5.725490728705e-01, 4.392195437946e-05, 1.6965e+01, 4.9398e-01, 
 1DIAGNOSTIC,    29, -5.726471294659e-01, 4.264179701721e-05, 1.7445e+01, 4.8035e-01, 
 1DIAGNOSTIC,    30, -5.728922177006e-01, 4.575243280903e-05, 1.7921e+01, 4.7633e-01, 
 1DIAGNOSTIC,    31, -5.729434897886e-01, 4.717241477376e-05, 1.8405e+01, 4.8334e-01, 
 1DIAGNOSTIC,    32, -5.727678319863e-01, 4.350354914329e-05, 1.8880e+01, 4.7548e-01, 
 1DIAGNOSTIC,    33, -5.730522367057e-01, 3.795122394075e-05, 1.9360e+01, 4.7945e-01, 
 1DIAGNOSTIC,    34, -5.735213812437e-01, 3.439423427050e-05, 1.9839e+01, 4.7960e-01, 
 1DIAGNOSTIC,    35, -5.736311863017e-01, 3.321961417058e-05, 2.0320e+01, 4.8035e-01, 
 1DIAGNOSTIC,    36, -5.734005458373e-01, 3.144636501363e-05, 2.0806e+01, 4.8680e-01, 
 1DIAGNOSTIC,    37, -5.736946718186e-01, 3.645904633216e-05, 2.1284e+01, 4.7804e-01, 
 1DIAGNOSTIC,    38, -5.737126660461e-01, 3.455494424263e-05, 2.1765e+01, 4.8058e-01, 
 1DIAGNOSTIC,    39, -5.731529505377e-01, 2.338519938971e-05, 2.2247e+01, 4.8179e-01, 
 1DIAGNOSTIC,    40, -5.730098623455e-01, 1.213828307776e-05, 2.2728e+01, 4.8169e-01, 
 1DIAGNOSTIC,    41, -5.731975756750e-01, 3.463784625880e-06, 2.3200e+01, 4.7122e-01, 
 1DIAGNOSTIC,    42, -5.731139795855e-01, -8.379446753387e-06, 2.3681e+01, 4.8144e-01, 
XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 1DIAGNOSTIC,     1, -5.732798830973e-01, 1.797693134862e+308, 2.6147e+01, 2.4658e+00, 
 1DIAGNOSTIC,     2, -5.734906941535e-01, 1.797693134862e+308, 2.8234e+01, 2.0868e+00, 
 1DIAGNOSTIC,     3, -5.739524851086e-01, 1.797693134862e+308, 3.0340e+01, 2.1060e+00, 
 1DIAGNOSTIC,     4, -5.751237452628e-01, 1.797693134862e+308, 3.2392e+01, 2.0526e+00, 
 1DIAGNOSTIC,     5, -5.754528538596e-01, 1.797693134862e+308, 3.4358e+01, 1.9657e+00, 
 1DIAGNOSTIC,     6, -5.762688478244e-01, 1.797693134862e+308, 3.6299e+01, 1.9406e+00, 
 1DIAGNOSTIC,     7, -5.765596883516e-01, 1.797693134862e+308, 3.8249e+01, 1.9504e+00, 
 1DIAGNOSTIC,     8, -5.765679753238e-01, 1.797693134862e+308, 4.0323e+01, 2.0742e+00, 
 1DIAGNOSTIC,     9, -5.769631990519e-01, 1.797693134862e+308, 4.2409e+01, 2.0855e+00, 
 1DIAGNOSTIC,    10, -5.772157614301e-01, 4.778346552279e-04, 4.4495e+01, 2.0860e+00, 
 1DIAGNOSTIC,    11, -5.772527833258e-01, 3.831937642417e-04, 4.6462e+01, 1.9670e+00, 
 1DIAGNOSTIC,    12, -5.773009874014e-01, 2.812023714858e-04, 4.8418e+01, 1.9565e+00, 
 1DIAGNOSTIC,    13, -5.777314239357e-01, 2.030515134219e-04, 5.0396e+01, 1.9783e+00, 
 1DIAGNOSTIC,    14, -5.778816663572e-01, 1.639682346337e-04, 5.2412e+01, 2.0160e+00, 
 1DIAGNOSTIC,    15, -5.779284935686e-01, 1.269261112837e-04, 5.4383e+01, 1.9704e+00, 
 1DIAGNOSTIC,    16, -5.779352139213e-01, 1.085643463247e-04, 5.6473e+01, 2.0903e+00, 
 1DIAGNOSTIC,    17, -5.783326734073e-01, 1.027762067488e-04, 5.8536e+01, 2.0625e+00, 
 1DIAGNOSTIC,    18, -5.783915479416e-01, 8.943455672853e-05, 6.0600e+01, 2.0644e+00, 
 1DIAGNOSTIC,    19, -5.781745698614e-01, 7.382025374307e-05, 6.2594e+01, 1.9942e+00, 
 1DIAGNOSTIC,    20, -5.785049896821e-01, 6.788878212099e-05, 6.4551e+01, 1.9568e+00, 
 1DIAGNOSTIC,    21, -5.783617847507e-01, 5.370279168511e-05, 6.6629e+01, 2.0780e+00, 
 1DIAGNOSTIC,    22, -5.783184835086e-01, 3.577518477243e-05, 6.8670e+01, 2.0414e+00, 
 1DIAGNOSTIC,    23, -5.784247078999e-01, 2.768457047574e-05, 7.0702e+01, 2.0314e+00, 
 1DIAGNOSTIC,    24, -5.788132112176e-01, 2.889211041313e-05, 7.2656e+01, 1.9545e+00, 
 1DIAGNOSTIC,    25, -5.788014351796e-01, 2.792427717449e-05, 7.4622e+01, 1.9659e+00, 
 1DIAGNOSTIC,    26, -5.786120767291e-01, 2.094987672102e-05, 7.6539e+01, 1.9164e+00, 
 1DIAGNOSTIC,    27, -5.786723653021e-01, 2.123086713986e-05, 7.8577e+01, 2.0388e+00, 
 1DIAGNOSTIC,    28, -5.788335408934e-01, 2.348004320690e-05, 8.0583e+01, 2.0060e+00, 
 1DIAGNOSTIC,    29, -5.791995271385e-01, 2.555494254803e-05, 8.2606e+01, 2.0223e+00, 
 1DIAGNOSTIC,    30, -5.791819856969e-01, 3.026721765888e-05, 8.4593e+01, 1.9872e+00, 
 1DIAGNOSTIC,    31, -5.789495372501e-01, 2.625475236292e-05, 8.6603e+01, 2.0104e+00, 
 1DIAGNOSTIC,    32, -5.790874917802e-01, 2.175797951947e-05, 8.8653e+01, 2.0500e+00, 
 1DIAGNOSTIC,    33, -5.790654784347e-01, 1.643757896991e-05, 9.0700e+01, 2.0464e+00, 
 1DIAGNOSTIC,    34, -5.790768049631e-01, 1.561612573848e-05, 9.2690e+01, 1.9899e+00, 
 1DIAGNOSTIC,    35, -5.788785958205e-01, 1.063931137429e-05, 9.4680e+01, 1.9901e+00, 
 1DIAGNOSTIC,    36, -5.792360168425e-01, 7.517361252408e-06, 9.6663e+01, 1.9833e+00, 
 1DIAGNOSTIC,    37, -5.789148755960e-01, 2.753367007759e-07, 9.8687e+01, 2.0242e+00, 
XXDIAGNOSTIC,Iteration,metricValue,convergenceValue,ITERATION_TIME_INDEX,SINCE_LAST
 1DIAGNOSTIC,     1, -5.843794639696e-01, 1.797693134862e+308, 1.0665e+02, 7.9676e+00, 
 1DIAGNOSTIC,     2, -5.843812106469e-01, 1.797693134862e+308, 1.1470e+02, 8.0473e+00, 
 1DIAGNOSTIC,     3, -5.843273112237e-01, 1.797693134862e+308, 1.2261e+02, 7.9063e+00, 
 1DIAGNOSTIC,     4, -5.842752635729e-01, 1.797693134862e+308, 1.3052e+02, 7.9113e+00, 
 1DIAGNOSTIC,     5, -5.842166297219e-01, 1.797693134862e+308, 1.3958e+02, 9.0644e+00, 
 1DIAGNOSTIC,     6, -5.842179912999e-01, 1.797693134862e+308, 1.4792e+02, 8.3391e+00, 
 1DIAGNOSTIC,     7, -5.842877784927e-01, 1.797693134862e+308, 1.5664e+02, 8.7185e+00, 
 1DIAGNOSTIC,     8, -5.842276378280e-01, 1.797693134862e+308, 1.6479e+02, 8.1477e+00, 
 1DIAGNOSTIC,     9, -5.842013820104e-01, 1.797693134862e+308, 1.7291e+02, 8.1192e+00, 
 1DIAGNOSTIC,    10, -5.841612809161e-01, -1.818346030111e-05, 1.8074e+02, 7.8282e+00, 
  Elapsed time (stage 2): 181.1


Total elapsed time: 283.3
%

1 reply

zw1989 Mar 30, 2022
Author

Yes. I logged on another server and ran again and it works. However, the result is off from what I expected. Have you checked yours?

Here is an image slice that supposed to show the similar structure but actually it is not.

ntustison · 2022-03-30T17:40:31Z

ntustison
Mar 30, 2022
Maintainer

For this specific imaging pair, you will probably need to have both brains extracted.

10 replies

ntustison Mar 30, 2022
Maintainer

antsRegistration masking (-x) limits the region for similarity metric calculation. This is different from mask * image where the entire image is still considered in the similarity metric calculation which is particularly useful around the masked boundaries for driving registration.

Ok. That's a fundamental problem, but is there anything that I can do to improve the results?

One possibility is using landmarks. Otherwise, for an automated process, the best you can probably hope for is a rigid alignment.

zw1989 Mar 31, 2022
Author

Hi Nick,

I have another test where I cut several slices from the template image to roughly fit the brain area covered by the T2w image. I also extracted the brain from both images. Then I ran the same ansRegistration code attached above without -x and '--initial-fixed-transform' options. The results are much better. For your convenience, here I attached the code again:

'antsRegistration --dimensionality 3 --float 0 --interpolation Linear --use-histogram-matching 0 --winsorize-image-intensities [0.005,0.995] --random-seed 25 --transform Rigid[0.05] --metric CC[ corrected_fsems_mouse_26_resetOrigin.nii , atlas.nii , 1, 4, Regular, 0.1 ] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform Affine[0.1] --metric MI[ corrected_fsems_mouse_26_resetOrigin.nii , atlas.nii , 1, 32, Regular, 0.1 ] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform SyN[0.1,1,0] --metric CC[ corrected_fsems_mouse_26_resetOrigin.nii , atlas.nii , 1, 4 ] --convergence [100x70x50x20,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --output [ atlas_,atlas_warped.nii.gz,atlas_inverswarped.nii.gz] '

I'm pretty satisfied with the results. However, I also find some other issues:

When I use mask option -x, the results are very off. I'm not sure whether it is a bug or not.
When I use option --initial-fixed-transform, the results are off, too.

Below is the test data and the test results. test1.png is the good result and test2.png shows the failure due to the use of mask and initial transform option, respectively.
testData.zip

ntustison Mar 31, 2022
Maintainer

Great. Glad you got it to work.

When I use mask option -x, the results are very off. I'm not sure whether it is a bug or not.

Given the vetting of ANTs by multiple users over several years, the chances that it is a bug is pretty small relative to alternative explanations. I'm guessing that your assumptions about masking and how they relate to setting up the registration problem are the issue. As I mentioned above, the mask dictates the ROI for similarity metric calculation. Many users assume that the optimal mask is one which strictly encompasses the ROI. However, this is oftentimes incorrect because the boundary edges often form strong features for driving the registration which aren't included in this naive masking scenario.

When I use option --initial-fixed-transform, the results are off, too.

You shouldn't need to use that option. Use --initial-moving-transform.

zw1989 Mar 31, 2022
Author

Thanks for the further explanation. If the boundary of the image subject (here is the brain) provides strong features, can the mask option be used to get improved results if the mask includes some area outside of the brain? In this case, the brain boundary information should be kept. Is my understanding correct?

When should I use --initial-fixed-transform? My understanding is that --initial-fixed-transform and --initial-moving-transform are equivalent. The difference is just apply the initial translation vector to which image.

zw1989 Apr 7, 2022
Author

Any responses to my previous questions? Thanks.

ntustison · 2022-04-07T20:38:33Z

ntustison
Apr 7, 2022
Maintainer

Thanks for the further explanation. If the boundary of the image subject (here is the brain) provides strong features, can the mask option be used to get improved results if the mask includes some area outside of the brain? In this case, the brain boundary information should be kept. Is my understanding correct?

yes.

When should I use --initial-fixed-transform?

You shouldn't. It's not a usable feature at this point in time.

9 replies

zw1989 Apr 8, 2022
Author

Attached please find the test data.
testdata.zip

Here is the code to run it:
antsRegistration --dimensionality 3 --float 0 --output [run1_,run1_Warped.nii.gz,run1_inverswarped.nii.gz] --interpolation BSpline[5] --winsorize-image-intensities [0.005,0.995] --use-histogram-matching 0 --transform Rigid[0.05] --metric CC[corrected_fsems_mouse_26_resetOrigin.nii,atlas.nii,1,4,Regular,0.1] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform Affine[0.1] --metric MI[corrected_fsems_mouse_26_resetOrigin.nii,atlas.nii,1,32,Regular,0.1] --convergence [1000x500x250x100,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox --transform SyN[0.1,1,0] --metric CC[corrected_fsems_mouse_26_resetOrigin.nii,atlas.nii,1,4] --convergence [100x70x50x20,1e-6,10] --shrink-factors 8x4x2x1 --smoothing-sigmas 3x2x1x0vox -x mask26_resetOriginDiluted.nii

You can run the above command with and without the -x option to compare the results.

ntustison Apr 8, 2022
Maintainer

The set of parameters you chose are overkill (i.e., you're running longer than is needed). You can probably get away with antsRegistrationSyNQuick.sh -d 3 -m atlas.nii -f corrected_fsems_mouse_26_resetOrigin.nii -o run . However, with respect to your call, you missed the crucial parameter -r to do the initial alignment. You asked about the fixed option above which is not usable but the moving option is usable and very much necessary to get a good alignment for most cases.

antsRegistration --dimensionality 3 --verbose 1 --float 0 \
--output [run1_,run1_Warped.nii.gz,run1_inverswarped.nii.gz] \
--interpolation BSpline[5] \
-r [corrected_fsems_mouse_26_resetOrigin.nii,atlas.nii,1] \
--winsorize-image-intensities [0.005,0.995] \
--use-histogram-matching 0 \
--transform Rigid[0.05] \
  --metric CC[corrected_fsems_mouse_26_resetOrigin.nii,atlas.nii,1,4,Regular,0.1] \
  --convergence [1000x500x250x100,1e-6,10] \
  --shrink-factors 8x4x2x1 \
  --smoothing-sigmas 3x2x1x0vox \
--transform Affine[0.1] \
  --metric MI[corrected_fsems_mouse_26_resetOrigin.nii,atlas.nii,1,32,Regular,0.1] \
  --convergence [1000x500x250x100,1e-6,10] \
  --shrink-factors 8x4x2x1 \
  --smoothing-sigmas 3x2x1x0vox \
--transform SyN[0.1,1,0] \
  --metric CC[corrected_fsems_mouse_26_resetOrigin.nii,atlas.nii,1,4] \
  --convergence [100x70x50x20,1e-6,10] \
  --shrink-factors 8x4x2x1 \
  --smoothing-sigmas 3x2x1x0vox 
# -x mask26_resetOriginDiluted.nii

zw1989 Apr 8, 2022
Author

The initial moving alignment option is crucial to have a good starting point. Does it use the mask to calculate if -x option is provided?

In addition, you said the parameters I chose are overkill. I compare the default parameters in antsRegsitrationSyNQuick.sh with mine. There are several differences:

The gradient step for the rigid transformation is 1 in the file and I used 0.05, which can take a bit longer time
The metric used in rigid transformation evaluation is MI in the file and I used CC.
The updateFieldVarianceInVoxelSpace option in the SyN transform is 3 and I used 1 to make the update field less smoother
The radius in CC in SyN transform is 2 in the file and I used 4, which can be more robust.

Which one do you think is an overkill?

ntustison Apr 8, 2022
Maintainer

The initial moving alignment option is crucial to have a good starting point. Does it use the mask to calculate if -x option is provided?

No.

Which one do you think is an overkill?

Basically, iterations at higher resolution are time consuming and MI is typically faster than CC. If you want a more detailed answer, you're going to need to do your own exploration.

zw1989 Apr 8, 2022
Author

Got it. Thanks.

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