Documentation/Nightly/Modules/PlmLANDWARP - Revision history

Gregsharp: Fix tutorial links, remove obsolete links.

2022-02-18T18:58:24Z

Fix tutorial links, remove obsolete links.

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

2013-06-14T07:58:42Z

Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

JChris.FillionR: 4.1 -> Nightly

2012-08-22T17:03:53Z

4.1 -> Nightly

New page

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
Extension: [[Documentation/{{documentation/version}}/Extensions/Plastimatch|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: [http://www.plastimatch.org www.plastimatch.org] 
Author: Greg Sharp (Department of Radiation Oncology, Massachusetts General Hospital) 
Contributor1: Julien Finet ({{collaborator|name|kitware}}) 
Contact: Greg Sharp, <email>gcsharp@partners.org</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}

{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|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:

# both local and global registration
# 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


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:before_reg.png|thumb|280px|Before Registration]]
|[[Image:after_reg.png|thumb|280px|After Registration]]
|}


{{documentation/{{documentation/version}}/module-section|Tutorials}}

{|
|[[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]]]
|[[Image:fixed.png|thumb|230px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1619/synthetic_img.zip Download tutorial data]]]
|}


{{documentation/{{documentation/version}}/module-section|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.
|[[Image:plastimatch_landmark_gui.png|thumb|280px|User Interface]]
|}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
*[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
*[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]
*[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]]
*[[Documentation/{{documentation/version}}/Modules/PlmDoseComparison|Plastimatch Dose Comparison]]
*[[Documentation/{{documentation/version}}/Modules/PlmDoseVolumeHistogram|Plastimatch Dose Volume Histogram]]
*[[Documentation/{{documentation/version}}/Modules/PlmSyntheticImageGeneration|Plastimatch Synthetic Image Generation]]
*[[Documentation/{{documentation/version}}/Modules/PlmThreshBox|Plastimatch Threshold in a box]]
*[[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]]


{{documentation/{{documentation/version}}/module-section|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.


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}


{{documentation/{{documentation/version}}/module-footer}}

@@ Line 1: / Line 1: @@
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+<noinclude>{{documentation/versioncheck}}
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 {{documentation/{{documentation/version}}/module-header}}
@@ Line 34: / Line 35: @@
 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:
-# both local and global registration
+#both local and global registration
-# regularization of the deformation field
+#regularization of the deformation field
 Examples of how this module is being used:
-* Intra-subject registration for adaptive radiotherapy
+*Intra-subject registration for adaptive radiotherapy
-* Inter-subject registration for automatic segmentation
+*Inter-subject registration for automatic segmentation
@@ Line 55: / Line 56: @@
 {|
-|[[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]]]
+|[[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]]]
-|[[Image:fixed.png|thumb|230px|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1619/synthetic_img.zip Download tutorial data]]]
+|[[Image:fixed.png|thumb|230px|[https://sourceforge.net/projects/plastimatch/files/Sample%20Data/landwarp-tutorial-images.zip/download Download tutorial data]]]
 |}
@@ Line 64: / Line 65: @@
 {|
+|
-* '''Input/Output panel:'''
+*'''Input/Output panel:'''
-** '''Fixed Volume:'''  Here you choose the "fixed image", which is the reference image.
+**'''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.
+**'''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.
+**'''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).
+**'''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.
+**'''RBF radius:''' Here you can choose the radius of RBF.
-** '''Number of clusters:''' Here you can choose the number of landmark clusters.
+**'''Number of clusters:''' Here you can choose the number of landmark clusters.
-** '''Stiffness:''' Here you can choose the regularization parameter.
+**'''Stiffness:''' Here you can choose the regularization parameter.
-** '''Default Pixel Value:''' Here you can choose the value for pixels with unknown value.
+**'''Default Pixel Value:''' Here you can choose the value for pixels with unknown value.
 |[[Image:plastimatch_landmark_gui.png|thumb|280px|User Interface]]
 |}
@@ Line 79: / Line 80: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Similar Modules}}
 *[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|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.
+*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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