Documentation/4.8/Extensions/SlicerRT - Revision history

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2019-11-27T02:28:51Z

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Pinter at 06:53, 27 June 2018

2018-06-27T06:53:07Z

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2017-10-18T07:04:06Z

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<noinclude>{{documentation/versioncheck}}</noinclude>

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

[[File:LogoCco.png|Cancer Care Ontario]]
[[File:Logo-SparKit.png|SparKit]]
[[File:LogoOCAIRO.jpg|OCAIRO]]


{{documentation/{{documentation/version}}/module-section|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:
* Csaba Pinter, <email>csaba.pinter@queensu.ca</email>
* Andras Lasso, <email>lasso@cs.queensu.ca</email>
* 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]]
Website: [http://slicerrt.github.io slicerrt.org] 
License: [http://www.slicer.org/pages/LicenseText Slicer license] 
'''Download/install:''' install 3D Slicer, start 3D Slicer, open the Extension Manager, install the SlicerRT extension (see more details [http://slicerrt.github.io/Download.html on the download page])



{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|
|
[[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. 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.

* Additional information for users can be found on the [[Documentation/SlicerRT/UsersGuide|User's Guide]] page 
|
|}


{{documentation/{{documentation/version}}/extension-section|Modules}}
{|
|

*[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]], [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport export]
*[[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
*[[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
*[[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
*[[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
*[[Documentation/{{documentation/version}}/Modules/SegmentComparison|Segment comparison]]
*[[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)

* Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]]
**[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]
**[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]] [[image:UnderConstruction.png|tumb|10px]]


* Former SlicerRT modules integrated to Slicer core
**[[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy]]
**[[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer]]
**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]]

| [[File:SlicerRt_Montage.jpg|512px|SlicerRT highlights]]
|}



{{documentation/{{documentation/version}}/extension-section|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


{{documentation/{{documentation/version}}/extension-section|Tutorials}}
* '''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]
** Dataset: [http://slicer.kitware.com/midas3/download/item/205391/WC2015_Gel_Slicelet_Dataset.zip download] from MIDAS
* '''Summer NA-MIC week 2013 tutorial'''
** 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
* '''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
* '''RSNA 2012 tutorial'''
** Tutorial description: [http://www.donotlink.com/bEo SlicerRT wiki: Slicer tutorials at RSNA 2012]

** Sample data: [http://slicer.kitware.com/midas3/folder/859 download] SlicerRT ART dose verification data from Midas server
* Summer NA-MIC week 2012 tutorial '''(deprecated)'''
** Tutorial presentation: [https://www.assembla.com/spaces/slicerrt/documents/aAuMq81Eqr4ztvacwqjQXA/download/aAuMq81Eqr4ztvacwqjQXA download] from the SlicerRT website



{{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}}/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


{{documentation/{{documentation/version}}/extension-section|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, [http://perk.cs.queensu.ca/sites/perk.cs.queensu.ca/files/Pinter2012_0.pdf "SlicerRT – Radiation therapy research toolkit for 3D Slicer"], Med. Phys., 39(10) pp. 6332-6338, 2012
<pre>
@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},
}
</pre>


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
* [https://www.assembla.com/spaces/slicerrt/wiki/SlicerRt_developers_page SlicerRT developers wiki page]


{{documentation/{{documentation/version}}/extension-footer}}

@@ Line 56: / Line 56: @@
 **[[Documentation/{{documentation/version}}/Modules/SegmentMorphology|Segment morphology]] (Add/remove margin, Unify, Intersect, etc.)
 * I/O
-**[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]], [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport export]
+**[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]], [[Documentation/Labs/DICOMExport|export]]
 *[https://github.com/SlicerRt/SlicerRT/tree/master/BatchProcessing Batch processing scripts] (currently only one is available for command-line conversion of RTSS to volume nodes)
@@ Line 69: / Line 69: @@
 **[[Documentation/{{documentation/version}}/Modules/Data|Subject hierarchy]]
 **[[Documentation/{{documentation/version}}/Modules/Transforms|Transform visualizer]]
-**DICOM-RT export, as [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport improved DICOM export function]
+**DICOM-RT export, as [[Documentation/Labs/DICOMExport|improved DICOM export function]]
 **[[Documentation/{{documentation/version}}/Modules/Segmentations|Segmentations]]
 **[[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]]

@@ Line 3: / Line 3: @@
 {{documentation/{{documentation/version}}/module-header}}
 <!-- ---------------------------- -->
-[[File:LogoCco.png|Cancer Care Ontario]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+[[{{collaborator|logo|cco}}]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-[[File:Logo-SparKit.png|SparKit]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+[[{{collaborator|logo|canarie}}]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-[[File:LogoOCAIRO.jpg|OCAIRO]]
+[[{{collaborator|logo|ocairo}}]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 <!-- ---------------------------- -->
@@ Line 14: / Line 15: @@
 * Csaba Pinter, <email>csaba.pinter@queensu.ca</email>
 * Andras Lasso, <email>lasso@cs.queensu.ca</email>
 * [https://discourse.slicer.org Slicer Forum]
 * [[Documentation/SlicerRT/HowToReportAnError|How to report an error]]
@@ Line 57: / Line 57: @@
 * I/O
 **[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]], [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport export]
-*[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://github.com/SlicerRt/SlicerRT/tree/master/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]]
@@ Line 99: / Line 99: @@
 {{documentation/{{documentation/version}}/extension-section|Tutorials}}
 * '''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://www.dropbox.com/s/b7qx3n10s52o5f8/SlicerRT_WorldCongress_TutorialIGRT.pptx?dl=0 pptx] [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pdf pdf]
 ** Dataset: [http://slicer.kitware.com/midas3/download/item/205391/WC2015_Gel_Slicelet_Dataset.zip download] from MIDAS
 * '''Summer NA-MIC week 2013 tutorial'''

@@ Line 3: / Line 3: @@
 {{documentation/{{documentation/version}}/module-header}}
 <!-- ---------------------------- -->
-[[File:LogoCco.png|Cancer Care Ontario]]
+[[File:LogoCco.png|Cancer Care Ontario]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-[[File:Logo-SparKit.png|SparKit]]
+[[File:Logo-SparKit.png|SparKit]]&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 [[File:LogoOCAIRO.jpg|OCAIRO]]
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
-Authors: <b>Csaba Pinter</b> (PerkLab, Queen's University), <b>Andras Lasso</b> (PerkLab, Queen's University), <b>Kevin Wang</b> (Radiation Medicine Program, Princess Margaret Hospital, University Health Network Toronto)<br>
+Authors: <b>Csaba Pinter</b> (PerkLab, Queen's University), <b>Andras Lasso</b> (PerkLab, Queen's University)<br>
-Contributors: Greg Sharp (Massachusetts General Hospital), Steve Pieper (Isomics)<br>
+Contributors: Greg Sharp (Massachusetts General Hospital), <b>Kevin Wang</b> (Princess Margaret Hospital, UHN Toronto), Steve Pieper (Isomics)<br>
 Contacts:
 * Csaba Pinter, <email>csaba.pinter@queensu.ca</email>
@@ Line 46: / Line 46: @@
+|
-*[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]], [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport export]
+*[[Documentation/{{documentation/version}}/Modules/ExternalBeamPlanning|External Beam Planning]] (Treatment planning)
-*[[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
+* Dose analysis
-*[[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
+**[[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
-*[[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]
+**[[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]
-*[[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
+**[[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]] (Gamma dose similarity index)
-*[[Documentation/{{documentation/version}}/Modules/SegmentComparison|Segment comparison]]
+**[[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]
-*[[Documentation/{{documentation/version}}/Modules/SegmentMorphology|Segment morphology]]
+* Contour analysis
 *[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)
@@ Line 63: / Line 67: @@
 * Former SlicerRT modules integrated to Slicer core
-**[[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy]]
+**[[Documentation/{{documentation/version}}/Modules/Data|Subject hierarchy]]
-**[[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer]]
+**[[Documentation/{{documentation/version}}/Modules/Transforms|Transform visualizer]]
 **DICOM-RT export, as [http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DICOMExport improved DICOM export function]
 **[[Documentation/{{documentation/version}}/Modules/Segmentations|Segmentations]]
@@ Line 87: / Line 91: @@
 * Proton dose calculation
 * Gel dosimetry analysis
 * Treatment plan similarity measurement in the cloud
 * Batch structure set conversion