Slicer3:Registration

Slicer 3 includes linear and nonlinear registration tools built as command line modules. On this page we are working to collect a variety of example data sets which test the boundary cases in order to optimize the registration performance and accuracy.

See also additional use cases collected for nonlinear registration optimization.

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T2 to FA Affine Registration

Results using slicer2

Results using slicer3 as of 2008-04-07

• Input Volumes
  • media:T2 Aligned.nrrd (Sagittal)
  • media:FA-slicer3-2008-04-08.nrrd (Rotated Axial)

• Reference 'Gold Standard'
  • Slicer2 calculation using Mattes MI Affine (also uses ITK implementation)
  • Result transform:

   0.998582 0.0548244 0.00874164 1.86596 
   -0.051956 0.957673 0.0339914 -12.8223 
   -0.00506141 -0.00847398 0.994165 16.2862 
   0 0 0 1 

• Software
  • Slicer3 svn trunk 2008-04-07

• Parameters
  • Defaults

• Method
  • Use T2 as fixed, FA as moving
  • Create new output transform and output volume (no input transform)
  • In data module drag FA volume under the newly calculated transform
  • In Transform Module select the output transform and click Invert

• Results 2008-04-07
  • Output volume appears to be all 0
  • Output transform looks correct, see image to the right.

0.924175 0.0524361 0.0617505 -0.457981 
0.0453017 0.99089 0.0283234 -8.79902 
-0.0525653 -0.0657896 1.11031 18.5389 
-0 0 -0 1

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T1 to Average Gradient Affine Registration

Results using slicer2

Results using slicer3 as of 2008-04-10

• Input Volumes
  • [1]
  • [2]

• Reference 'Gold Standard'
  • Slicer2 calculation using Mattes MI Affine (also uses ITK implementation)
  • Result transform:

   0.950655 0.024335 0.0259082 0.857786 
   0.0086567 0.8889 -0.379321 -6.77365 
   -0.0395529 0.39257 0.835359 14.664 
   0 0 0 1 

• Software
  • Slicer3 svn trunk 2008-04-10

• Parameters
  • Defaults

• Method
  • Use T1 as fixed, Gradient as moving

• Results 2008-04-10
  • Cannot run due to sampling issue

itk::ExceptionObject (0x1990140)
Location: "void itk::MattesMutualInformationImageToImageMetric<TFixedImage, TMovingImage>::GetValueAndDerivative(const typename itk::ImageToImageMetric<TFixedImage, TMovingImage>::ParametersType&, typename itk::ImageToImageMetric<TFixedImage, TMovingImage>::MeasureType&, typename itk::ImageToImageMetric<TFixedImage, TMovingImage>::DerivativeType&) const [with TFixedImage = itk::OrientedImage<short int, 3u>, TMovingImage = itk::OrientedImage<short int, 3u>]" 
File: /Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/Algorithms/itkMattesMutualInformationImageToImageMetric.txx
Line: 1036
Description: itk::ERROR: MattesMutualInformationImageToImageMetric(0x198d470): Too many samples map outside moving image buffer: 2481 / 10000





ERROR: In /Users/pieper/slicer3/latest/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1326
vtkCommandLineModuleLogic (0x1d265ac0): Affine registration completed with errors