Documentation/4.3/Extensions/SlicerRT - Revision history

Pinter at 22:04, 23 September 2014

2014-09-23T22:04:25Z

Pinter at 21:55, 23 September 2014

2014-09-23T21:55:24Z

Pinter at 21:54, 23 September 2014

2014-09-23T21:54:30Z

Pinter: Rename from patient hierarchy to subject hierarchy

2014-02-12T17:51:29Z

Rename from patient hierarchy to subject hierarchy

Rankin: Changing reference to project name from PLUS to SlicerRt

2014-01-09T17:33:37Z

Changing reference to project name from PLUS to SlicerRt

Pinter at 17:43, 5 November 2013

2013-11-05T17:43:33Z

UpdateBot: Nightly -> 4.3

2013-09-05T03:35:32Z

Nightly -> 4.3

New page

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

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

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


{{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:
* 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)
* [https://www.assembla.com/spaces/slicerrt/wiki/How_to_report_an_error 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 [https://www.assembla.com/spaces/slicerrt/wiki/SlicerRt_users_guide in the installation section])



{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|
|
[[Image:SlicerRT_Logo_2.0_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 Ontarioand 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.
|
|}

{| class="wikitable"
|


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

*[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
*[[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
*[[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/ContourComparison|Contour comparison]]
*[[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
*[[Documentation/{{documentation/version}}/Modules/PatientHierarchy|Patient hierarchy]]
*[[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer (moved to separate extension)]]

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



{{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 image-based non-rigid patient motion compensation
* Dose accumulation with motion compensation

| [[File:SlicerRT_0.10_Montage.png|1024px|SlicerRT highlights]]
|}


{{documentation/{{documentation/version}}/extension-section|Tutorials}}
* '''Summer NA-MIC week 2013 tutorial''' (recommended)
** 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: [https://www.assembla.com/spaces/slicerrt/wiki/20121127_Slicer_tutorials_at_RSNA_2012 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
** Tutorial presentation: [https://www.assembla.com/spaces/slicerrt/documents/aAuMq81Eqr4ztvacwqjQXA/download/aAuMq81Eqr4ztvacwqjQXA download] from the SlicerRT website
** Sample data: [https://www.assembla.com/spaces/slicerrt/documents/bMuwgYTKur4yP-acwqjQWU/download/bMuwgYTKur4yP-acwqjQWU 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}}/extension-section|References}}
* [https://www.assembla.com/spaces/slicerrt/wiki/SlicerRt_users_guide SlicerRT users guide pages]


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}


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

@@ Line 70: / Line 70: @@
 * Former SlicerRT modules integrated to Slicer core
-** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy]]
+**[[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy]]
 **[[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer]]

@@ Line 105: / Line 105: @@
 {{documentation/{{documentation/version}}/extension-section|References}}
 ==How to cite==
-Please cite the following paper when referring to Plus in your publication:<br>
+Please cite the following paper when referring to SlicerRt in your publication:<br>
 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>

@@ Line 12: / Line 12: @@
 Contributors: Greg Sharp (Massachusetts General Hospital), Steve Pieper (Isomics)<br>
 Contacts:
 * 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)

@@ Line 54: / Line 54: @@
 *[[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]
 *[[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]
 * Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
@@ Line 69: / Line 67: @@
 **[[Documentation/{{documentation/version}}/Modules/PlmThreshBox|Plastimatch Threshold in a box]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]
 -->
 <!-- ---------------------------- -->
@@ Line 101: / Line 103: @@
 {{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.
 <!-- ---------------------------- -->

@@ Line 14: / Line 14: @@
 * 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)
-* [https://www.assembla.com/spaces/slicerrt/wiki/How_to_report_an_error How to report an error]
+* [[Documentation/SlicerRT/HowToReportAnError|How to report an error]]
 Website: [http://slicerrt.github.io slicerrt.org]<br>
 License: [http://www.slicer.org/pages/LicenseText Slicer license]<br>
-'''Download/install:''' install 3D Slicer, start 3D Slicer, open the Extension Manager, install the SlicerRT extension (see more details [https://www.assembla.com/spaces/slicerrt/wiki/SlicerRt_users_guide in the installation section])
+'''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])
 <!--
@@ Line 31: / Line 31: @@
 [[Image:SlicerRT_Logo_2.0_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.
+* 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.
-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.
+|
 |}
@@ Line 45: / Line 46: @@
 *[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]
 *[[Documentation/{{documentation/version}}/Modules/Contours|Contours]]
 *[[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]
@@ Line 57: / Line 59: @@
 * Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)
 **[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]] (Greg Sharp)
 **[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]] (Greg Sharp)
 **[[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] (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]]
@@ Line 73: / Line 75: @@
 * Evaluation of the effect of image-based non-rigid patient motion compensation
 * Dose accumulation with motion compensation
-| [[File:SlicerRT_0.10_Montage.png|1024px|SlicerRT highlights]]
+| [[File:SlicerRt_Montage.jpg|1024px|SlicerRT highlights]]
 |}
@@ Line 85: / Line 89: @@
 ** 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: [https://www.assembla.com/spaces/slicerrt/wiki/20121127_Slicer_tutorials_at_RSNA_2012 SlicerRT wiki: Slicer tutorials at RSNA 2012]
+** 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
-** Tutorial presentation: [https://www.assembla.com/spaces/slicerrt/documents/aAuMq81Eqr4ztvacwqjQXA/download/aAuMq81Eqr4ztvacwqjQXA download] from the SlicerRT website
+** Tutorial presentation: [http://www.donotlink.com/bEp download] from the SlicerRT website
-** Sample data: [https://www.assembla.com/spaces/slicerrt/documents/bMuwgYTKur4yP-acwqjQWU/download/bMuwgYTKur4yP-acwqjQWU download] from the SlicerRT website
+<!-- Original link: https://www.assembla.com/spaces/slicerrt/documents/aAuMq81Eqr4ztvacwqjQXA/download/aAuMq81Eqr4ztvacwqjQXA -->
 <!-- ---------------------------- -->
@@ Line 97: / Line 104: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|References}}
-* [https://www.assembla.com/spaces/slicerrt/wiki/SlicerRt_users_guide SlicerRT users guide pages]
+==How to cite==
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Information for Developers}}
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-footer}}
 <!-- ---------------------------- -->