Difference between revisions of "Documentation/Nightly/Extensions/SlicerRT"

From Slicer Wiki
Jump to: navigation, search
(Updated module list and use case list)
(11 intermediate revisions by 3 users not shown)
Line 5: Line 5:
 
[[File:LogoCco.png|Cancer Care Ontario]]
 
[[File:LogoCco.png|Cancer Care Ontario]]
 
[[File:Logo-SparKit.png|SparKit]]
 
[[File:Logo-SparKit.png|SparKit]]
[[File:LogoOCAIRO.jpg|SparKit]]
+
[[File:LogoOCAIRO.jpg|OCAIRO]]
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
  
Line 14: Line 14:
 
* Csaba Pinter, <email>csaba.pinter@queensu.ca</email>
 
* Csaba Pinter, <email>csaba.pinter@queensu.ca</email>
 
* Andras Lasso, <email>lasso@cs.queensu.ca</email>
 
* Andras Lasso, <email>lasso@cs.queensu.ca</email>
* Mailing list, <email>slicerrt@alerts.assembla.com</email> (need to register to [http://www.assembla.com Assembla] using the email address from which the email is sent)
+
* SlicerRT@Assembla messages, register to [http://www.assembla.com Assembla], create new thread in [https://app.assembla.com/spaces/slicerrt/messages SlicerRT messages]
 +
* [https://discourse.slicer.org Slicer Forum]
 
* [[Documentation/SlicerRT/HowToReportAnError|How to report an error]]
 
* [[Documentation/SlicerRT/HowToReportAnError|How to report an error]]
 
Website: [http://slicerrt.github.io slicerrt.org]<br>
 
Website: [http://slicerrt.github.io slicerrt.org]<br>
Line 32: Line 33:
 
[[Image:SlicerRT_Logo_3.0_128x128.png]]
 
[[Image:SlicerRT_Logo_3.0_128x128.png]]
 
|
 
|
* SlicerRT is one of the themes of the SparKit (Software Platform and Adaptive Radiotherapy Kit) project with the goal of making 3D Slicer a powerful radiotherapy research platform.<br>SparKit is a project funded by Cancer Care Ontarioand the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.
+
* SlicerRT is one of the themes of the SparKit (Software Platform and Adaptive Radiotherapy Kit) project with the goal of making 3D Slicer a powerful radiotherapy research platform.<br>SparKit is a project funded by Cancer Care Ontario and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.
  
 
* The SlicerRT extension incorporates [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] modules and algorithms.
 
* The SlicerRT extension incorporates [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] modules and algorithms.
  
* Additional information for users can be found on the [[Documentation/SlicerRT/UsersGuide|User's guide]] page <br>
+
* Additional information for users can be found on the [[Documentation/SlicerRT/UsersGuide|User's Guide]] page <br>
 
|
 
|
 
|}
 
|}
 
{| class="wikitable"
 
|
 
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/extension-section|Modules}}
 
{{documentation/{{documentation/version}}/extension-section|Modules}}
 +
{|
 +
|
  
*[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
+
*[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]], [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport export]
*[[Documentation/{{documentation/version}}/Modules/Segmentations|Segmentations]]
 
 
*[[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
 
*[[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
 
*[[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
 
*[[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
 
*[[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
 
*[[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
 
*[[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
 
*[[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
*[[Documentation/{{documentation/version}}/Modules/ContourComparison|Segment comparison]]
+
*[[Documentation/{{documentation/version}}/Modules/SegmentComparison|Segment comparison]]
*[[Documentation/{{documentation/version}}/Modules/ContourMorphology|Segment morphology]]
+
*[[Documentation/{{documentation/version}}/Modules/SegmentMorphology|Segment morphology]]
 
*[https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/BatchProcessing/ Batch processing scripts] (currently only one is available for command-line conversion of RTSS to volume nodes)
 
*[https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/BatchProcessing/ Batch processing scripts] (currently only one is available for command-line conversion of RTSS to volume nodes)
  
* Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
+
* Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]]
**[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]] (Greg Sharp)
+
**[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
**[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]] (Greg Sharp)
+
**[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]] [[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
 
 
<!--
 
<!--
**[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]] (Greg Sharp)
 
**[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
 
**[[Documentation/{{documentation/version}}/Modules/PlmDoseComparison|Plastimatch Dose Comparison]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
 
**[[Documentation/{{documentation/version}}/Modules/PlmDoseVolumeHistogram|Plastimatch Dose Volume Histogram]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
 
 
**[[Documentation/{{documentation/version}}/Modules/PlmSyntheticImageGeneration|Plastimatch Synthetic Image Generation]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
 
**[[Documentation/{{documentation/version}}/Modules/PlmSyntheticImageGeneration|Plastimatch Synthetic Image Generation]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
**[[Documentation/{{documentation/version}}/Modules/PlmThreshBox|Plastimatch Threshold in a box]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
 
 
-->
 
-->
  
Line 72: Line 65:
 
**[[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy]]
 
**[[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy]]
 
**[[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer]]
 
**[[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer]]
**[[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]], as [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport improved DICOM export function]
+
**DICOM-RT export, as [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport improved DICOM export function]
 +
**[[Documentation/{{documentation/version}}/Modules/Segmentations|Segmentations]]
 +
**[[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]]
 +
<!--
 +
* Experimental modules
 +
**[[Documentation/{{documentation/version}}/Modules/ExternalBeamPlanning|External beam planning]] [[image:UnderConstruction.png|tumb|10px]]
 +
-->
 +
| [[File:SlicerRt_Montage.jpg|512px|SlicerRT highlights]]
 +
|}
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 +
 +
 
{{documentation/{{documentation/version}}/extension-section|Use Cases}}
 
{{documentation/{{documentation/version}}/extension-section|Use Cases}}
 
* Comparison of dose maps and dose volume histograms from various treatment planning systems
 
* Comparison of dose maps and dose volume histograms from various treatment planning systems
Line 87: Line 90:
 
* Batch structure set conversion
 
* Batch structure set conversion
  
| [[File:SlicerRt_Montage.jpg|1024px|SlicerRT highlights]]
 
|}
 
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/extension-section|Tutorials}}
 
{{documentation/{{documentation/version}}/extension-section|Tutorials}}
* '''World Congress 2015 tutorial''' (recommended)
+
* '''World Congress 2015 tutorial''' ''(recommended)''
 
** Tutorial presentation: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/doc/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pptx pptx] [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/doc/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pdf pdf]
 
** Tutorial presentation: [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/doc/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pptx pptx] [https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/doc/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pdf pdf]
 
** Dataset: [http://slicer.kitware.com/midas3/download/item/205391/WC2015_Gel_Slicelet_Dataset.zip download] from MIDAS
 
** Dataset: [http://slicer.kitware.com/midas3/download/item/205391/WC2015_Gel_Slicelet_Dataset.zip download] from MIDAS
* Summer NA-MIC week 2013 tutorial
+
* '''Summer NA-MIC week 2013 tutorial'''
 
** Tutorial presentation: [http://wiki.na-mic.org/Wiki/images/b/b0/SlicerRT_TutorialContestSummer2013.pdf download] from Slicer wiki
 
** Tutorial presentation: [http://wiki.na-mic.org/Wiki/images/b/b0/SlicerRT_TutorialContestSummer2013.pdf download] from Slicer wiki
 
** Sample data: [http://slicer.kitware.com/midas3/download/folder/1345/SlicerRtTutorial_Namic2013June.zip download] from MIDAS
 
** Sample data: [http://slicer.kitware.com/midas3/download/folder/1345/SlicerRtTutorial_Namic2013June.zip download] from MIDAS
* ECR 2013 - Medical University Vienna workshop
+
* '''ECR 2013 - Medical University Vienna workshop'''
 
** Workshop material: [http://www.na-mic.org/Wiki/index.php/File:Pinter_MedUni2013_Workshop.pdf download] from NA-MIC.org
 
** Workshop material: [http://www.na-mic.org/Wiki/index.php/File:Pinter_MedUni2013_Workshop.pdf download] from NA-MIC.org
* RSNA 2012 tutorial
+
* '''RSNA 2012 tutorial'''
 
** Tutorial description: [http://www.donotlink.com/bEo SlicerRT wiki: Slicer tutorials at RSNA 2012]
 
** Tutorial description: [http://www.donotlink.com/bEo SlicerRT wiki: Slicer tutorials at RSNA 2012]
 
<!-- Original link: https://www.assembla.com/spaces/slicerrt/wiki/20121127_Slicer_tutorials_at_RSNA_2012 -->
 
<!-- Original link: https://www.assembla.com/spaces/slicerrt/wiki/20121127_Slicer_tutorials_at_RSNA_2012 -->
 
** Sample data: [http://slicer.kitware.com/midas3/folder/859 download] SlicerRT ART dose verification data from Midas server
 
** Sample data: [http://slicer.kitware.com/midas3/folder/859 download] SlicerRT ART dose verification data from Midas server
* Summer NA-MIC week 2012 tutorial
+
* Summer NA-MIC week 2012 tutorial '''(deprecated)'''
** Tutorial presentation: [http://www.donotlink.com/bEp download] from the SlicerRT website
+
** Tutorial presentation: [https://www.assembla.com/spaces/slicerrt/documents/aAuMq81Eqr4ztvacwqjQXA/download/aAuMq81Eqr4ztvacwqjQXA download] from the SlicerRT website
<!-- Original link: https://www.assembla.com/spaces/slicerrt/documents/aAuMq81Eqr4ztvacwqjQXA/download/aAuMq81Eqr4ztvacwqjQXA -->
 
** Sample data: [http://www.donotlink.com/bEq download] from the SlicerRT website
 
 
<!-- Original link: https://www.assembla.com/spaces/slicerrt/documents/bMuwgYTKur4yP-acwqjQWU/download/bMuwgYTKur4yP-acwqjQWU -->
 
<!-- Original link: https://www.assembla.com/spaces/slicerrt/documents/bMuwgYTKur4yP-acwqjQWU/download/bMuwgYTKur4yP-acwqjQWU -->
  
Line 113: Line 112:
 
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
 
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
 
* [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]]: SlicerRT and Plastimatch are complementary software libraries. Plastimatch focuses on delivering new computational methods radiotherapy, while SlicerRT aims for providing an easy-to-use interface for a wide range of stable, well-tested radiotherapy related features. SlicerRT uses Plastimatch internally for certain operations.
 
* [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]]: SlicerRT and Plastimatch are complementary software libraries. Plastimatch focuses on delivering new computational methods radiotherapy, while SlicerRT aims for providing an easy-to-use interface for a wide range of stable, well-tested radiotherapy related features. SlicerRT uses Plastimatch internally for certain operations.
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|Gel Dosimetry]]: Slicelet facilitating a streamlined workflow to perform gel dosimetry analysis for commissioning linacs and evaluating new dose calculation procedures
+
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|Gel Dosimetry]]: Slicelet facilitating a streamlined workflow to perform true 3D gel dosimetry analysis for commissioning linacs and evaluating new dose calculation procedures
 +
* [[Documentation/{{documentation/version}}/Modules/FilmDosimetry|Film Dosimetry]]: Slicelet supporting workflow to perform 2D film dosimetry analysis for commissioning new radiation techniques and to validate the accuracy of radiation treatment by enabling visual comparison of the planned dose to the delivered dose
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
Line 134: Line 134:
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
 
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
* [http://www.donotlink.com/bEr SlicerRT developers wiki page]
+
* [https://www.assembla.com/spaces/slicerrt/wiki/SlicerRt_developers_page SlicerRT developers wiki page]
<!-- Original link: https://www.assembla.com/spaces/slicerrt/wiki/SlicerRt_developers_page -->
 
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/extension-footer}}
 
{{documentation/{{documentation/version}}/extension-footer}}
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->

Revision as of 17:51, 16 June 2017

Home < Documentation < Nightly < Extensions < SlicerRT


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


Cancer Care Ontario SparKit OCAIRO

Introduction and Acknowledgements

Authors: Csaba Pinter (PerkLab, Queen's University), Andras Lasso (PerkLab, Queen's University), Kevin Wang (Radiation Medicine Program, Princess Margaret Hospital, University Health Network Toronto)
Contributors: Greg Sharp (Massachusetts General Hospital), Steve Pieper (Isomics)
Contacts:

Website: slicerrt.org
License: Slicer license
Download/install: install 3D Slicer, start 3D Slicer, open the Extension Manager, install the SlicerRT extension (see more details on the download page)

Extension Description

SlicerRT Logo 3.0 128x128.png

  • SlicerRT is one of the themes of the SparKit (Software Platform and Adaptive Radiotherapy Kit) project with the goal of making 3D Slicer a powerful radiotherapy research platform.
    SparKit is a project funded by Cancer Care Ontario and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.
  • The SlicerRT extension incorporates Plastimatch modules and algorithms.
  • Additional information for users can be found on the User's Guide page

Modules

SlicerRT highlights


Use Cases

  • Comparison of dose maps and dose volume histograms from various treatment planning systems
  • Evaluation of the effect of different adaptive techniques (IGRT, image-based non-rigid patient motion compensation, etc.)
    • Calculate couch shift parameters for patient setup correction in IGRT
  • Dose accumulation with motion compensation
  • Testing of treatment planning algorithms
  • Calculation of PTV margin
  • Proton dose calculation
  • Gel dosimetry analysis
  • Treatment plan similarity measurement in the cloud
  • Batch structure set conversion


Tutorials

  • World Congress 2015 tutorial (recommended)
  • Summer NA-MIC week 2013 tutorial
    • Tutorial presentation: download from Slicer wiki
    • Sample data: download from MIDAS
  • ECR 2013 - Medical University Vienna workshop
    • Workshop material: download from NA-MIC.org
  • RSNA 2012 tutorial
  • Summer NA-MIC week 2012 tutorial (deprecated)
    • Tutorial presentation: download from the SlicerRT website

Similar Extensions

  • Plastimatch: SlicerRT and Plastimatch are complementary software libraries. Plastimatch focuses on delivering new computational methods radiotherapy, while SlicerRT aims for providing an easy-to-use interface for a wide range of stable, well-tested radiotherapy related features. SlicerRT uses Plastimatch internally for certain operations.
  • Gel Dosimetry: Slicelet facilitating a streamlined workflow to perform true 3D gel dosimetry analysis for commissioning linacs and evaluating new dose calculation procedures
  • Film Dosimetry: Slicelet supporting workflow to perform 2D film dosimetry analysis for commissioning new radiation techniques and to validate the accuracy of radiation treatment by enabling visual comparison of the planned dose to the delivered dose

References

How to cite

Please cite the following paper when referring to SlicerRt in your publication:
C. Pinter, A. Lasso, A. Wang, D. Jaffray and G. Fichtinger, "SlicerRT – Radiation therapy research toolkit for 3D Slicer", Med. Phys., 39(10) pp. 6332-6338, 2012

@ARTICLE{Pinter2012,
  author = {Pinter, C. and Lasso, A. and Wang, A. and Jaffray, D. and Fichtinger, G.},
  title = {SlicerRT – Radiation therapy research toolkit for 3D Slicer},
  journal = {Med. Phys.},
  year = {2012},
  volume = {39},
  number = {10},
  pages = {6332-6338},
}

Information for Developers