Difference between revisions of "Slicer3:Registration"

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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.
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<big>'''Note:''' We are migrating this content to the slicer.org domain - <font color="orange">The newer page is [https://www.slicer.org/wiki/Slicer3:Registration  here]</font></big>
 
 
 
 
See also [[ITK_Registration_Optimization#Algorithmic_Requirements_and_Use_Cases | additional use cases collected for nonlinear registration optimization]].
 
 
 
__TOC__
 
 
 
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= T2 to FA Affine Registration =
 
 
 
 
 
[[Image:T2-FA-registration-slicer2-2008-04-08.png|thumb|right|250px|Results using slicer2]]
 
 
 
[[Image:T2-fa-registration-2008-04-08.png|thumb|right|250px|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 =
 
 
 
 
 
[[Image:Debrecen-slicer2-affine.png|thumb|right|250px|Results using slicer2]]
 
 
 
[[Image:Derecen-slicer3-affine.png|thumb|right|250px|Results using slicer3 as of 2008-04-10]]
 
 
 
 
 
* Input Volumes
 
** Provided by András Jakab, University of Debrecen Medical School and Health Science Center
 
** [http://cooler.underground.hu/docs/imaging/send/extract_brain_3dt1_manual_volume.nrrd]
 
** [http://cooler.underground.hu/docs/imaging/send/AVGgradient.nrrd]
 
 
 
* 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
 
 
 
<pre>
 
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
 
</pre>
 

Latest revision as of 18:07, 10 July 2017

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Note: We are migrating this content to the slicer.org domain - The newer page is here