Difference between revisions of "Documentation/Nightly/Modules/PlmLANDWARP"

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This is the plastimatch landmark-based deformable image registration module.  The intended application of this method is rapid, interactive correction of registration failures with a small number of mouse clicks.  Compared to other landmark-based methods, the plastimatch registration method might offer:
 
This is the plastimatch landmark-based deformable image registration module.  The intended application of this method is rapid, interactive correction of registration failures with a small number of mouse clicks.  Compared to other landmark-based methods, the plastimatch registration method might offer:
  
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# both local and global registration
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#both local and global registration
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# regularization of the deformation field
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#regularization of the deformation field
  
 
Examples of how this module is being used:
 
Examples of how this module is being used:
  
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* Intra-subject registration for adaptive radiotherapy
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*Intra-subject registration for adaptive radiotherapy
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* Inter-subject registration for automatic segmentation
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*Inter-subject registration for automatic segmentation
  
  
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{|
 
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|[[Image:3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.png|thumb|280px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1622/3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.ppt Download tutorial]]]
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|[[Image:3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.png|thumb|280px|[https://sourceforge.net/projects/plastimatch/files/Sample%20Data/3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.ppt/download Download tutorial]]]
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|[[Image:fixed.png|thumb|230px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1619/synthetic_img.zip Download tutorial data]]]
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|[[Image:fixed.png|thumb|230px|[https://sourceforge.net/projects/plastimatch/files/Sample%20Data/landwarp-tutorial-images.zip/download Download tutorial data]]]
 
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{|
 
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* '''Input/Output panel:'''
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*'''Input/Output panel:'''
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** '''Fixed Volume:'''  Here you choose the "fixed image", which is the reference image.
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**'''Fixed Volume:'''  Here you choose the "fixed image", which is the reference image.
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** '''Moving Volume:''' Here you choose the "moving image", which will be warped to match the fixed image.
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**'''Moving Volume:''' Here you choose the "moving image", which will be warped to match the fixed image.
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** '''Output Volume:''' Here you choose where to put the warped image.  You can replace an existing image in the scene, or create a new image.
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**'''Output Volume:''' Here you choose where to put the warped image.  You can replace an existing image in the scene, or create a new image.
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** '''Basis function:''' Here you can choose either tps (thin plate splines), or gauss (Gaussian RBF), or wendland (Wendland RBF).
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**'''Basis function:''' Here you can choose either tps (thin plate splines), or gauss (Gaussian RBF), or wendland (Wendland RBF).
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** '''RBF radius:''' Here you can choose the radius of RBF.
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**'''RBF radius:''' Here you can choose the radius of RBF.
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** '''Number of clusters:''' Here you can choose the number of landmark clusters.
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**'''Number of clusters:''' Here you can choose the number of landmark clusters.
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** '''Stiffness:''' Here you can choose the regularization parameter.
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**'''Stiffness:''' Here you can choose the regularization parameter.
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** '''Default Pixel Value:''' Here you can choose the value for pixels with unknown value.
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**'''Default Pixel Value:''' Here you can choose the value for pixels with unknown value.
 
|[[Image:plastimatch_landmark_gui.png|thumb|280px|User Interface]]
 
|[[Image:plastimatch_landmark_gui.png|thumb|280px|User Interface]]
 
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{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
{{documentation/{{documentation/version}}/module-section|Similar Modules}}
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*[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
 
*[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
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*[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
 
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*[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]]
 
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*[[Documentation/{{documentation/version}}/Modules/PlmDoseComparison|Plastimatch Dose Comparison]]
 
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*[[Documentation/{{documentation/version}}/Modules/PlmDoseVolumeHistogram|Plastimatch Dose Volume Histogram]]
 
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*[[Documentation/{{documentation/version}}/Modules/PlmSyntheticImageGeneration|Plastimatch Synthetic Image Generation]]
 
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*[[Documentation/{{documentation/version}}/Modules/PlmThreshBox|Plastimatch Threshold in a box]]
 
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*[[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]]
 
  
 
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{{documentation/{{documentation/version}}/module-section|References}}
 
{{documentation/{{documentation/version}}/module-section|References}}
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* G Sharp et al. "Plastimatch - An open source software suite for radiotherapy image processing," Proceedings of the XVIth International Conference on the use of Computers in Radiotherapy, May, 2010.
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* N. Shusharina, G. Sharp "Landmark-based image registration with analytic regularization", IEEE Trans. Med. Imag., submitted, 2011.
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*G Sharp et al. "Plastimatch - An open source software suite for radiotherapy image processing," Proceedings of the XVIth International Conference on the use of Computers in Radiotherapy, May, 2010.
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*N. Shusharina, G. Sharp "Landmark-based image registration with analytic regularization", IEEE Trans. Med. Imag., submitted, 2011.
  
 
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Latest revision as of 18:58, 18 February 2022

Home < Documentation < Nightly < Modules < PlmLANDWARP


For the latest Slicer documentation, visit the read-the-docs.


Introduction and Acknowledgements

Extension: Plastimatch
Acknowledgments:

  • An Ira J Spiro translational research grant (2009)
  • NIH / NCI 6-PO1 CA 21239
  • The Federal share of program income earned by MGH on C06CA059267
  • Progetto Rocca Foundation – A collaboration between MIT and Politecnico di Milano
  • The National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant 2-U54-EB005149; information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics
  • NSF ERC Innovation Award EEC-0946463


Webpage: www.plastimatch.org
Author: Greg Sharp (Department of Radiation Oncology, Massachusetts General Hospital)
Contributor1: Julien Finet (Kitware)
Contact: Greg Sharp, <email>gcsharp@partners.org</email>

Kitware, Inc.  
National Alliance for Medical Image Computing (NA-MIC)  

Module Description

This is the plastimatch landmark-based deformable image registration module. The intended application of this method is rapid, interactive correction of registration failures with a small number of mouse clicks. Compared to other landmark-based methods, the plastimatch registration method might offer:

  1. both local and global registration
  2. regularization of the deformation field

Examples of how this module is being used:

  • Intra-subject registration for adaptive radiotherapy
  • Inter-subject registration for automatic segmentation


Use Cases

Before Registration
After Registration


Tutorials

Download tutorial
Download tutorial data


Panels and their use

  • Input/Output panel:
    • Fixed Volume: Here you choose the "fixed image", which is the reference image.
    • Moving Volume: Here you choose the "moving image", which will be warped to match the fixed image.
    • Output Volume: Here you choose where to put the warped image. You can replace an existing image in the scene, or create a new image.
    • Basis function: Here you can choose either tps (thin plate splines), or gauss (Gaussian RBF), or wendland (Wendland RBF).
    • RBF radius: Here you can choose the radius of RBF.
    • Number of clusters: Here you can choose the number of landmark clusters.
    • Stiffness: Here you can choose the regularization parameter.
    • Default Pixel Value: Here you can choose the value for pixels with unknown value.
User Interface


Similar Modules

References

  • G Sharp et al. "Plastimatch - An open source software suite for radiotherapy image processing," Proceedings of the XVIth International Conference on the use of Computers in Radiotherapy, May, 2010.
  • N. Shusharina, G. Sharp "Landmark-based image registration with analytic regularization", IEEE Trans. Med. Imag., submitted, 2011.

Information for Developers

Work in progress
 Section under construction.


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