https://www.slicer.org/w/api.php?action=feedcontributions&feedformat=atom&user=WangkSlicer Wiki - User contributions [en]2026-04-09T08:56:27ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/MarginCalculator&diff=42929Documentation/Nightly/Extensions/MarginCalculator2015-10-09T18:13:07Z<p>Wangk: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Contributors: Kevin Wang (Princess Margaret Cancer Centre), Winnie Li (Princess Margaret Cancer Centre)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.ca</email><br><br />
Website: http://www.assembla.com/spaces/margincalculator<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|sparkit}}|SparKit<br />
|{{collaborator|logo|namic}}|NA-MIC<br />
|{{collaborator|logo|perklab}}|PerkLab<br />
|{{collaborator|logo|ocairo}}|OCAIRO<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
Multidimensional data is an extension of 3D Slicer to allow creating and visualization of higher-dimension data nodes, such as 4D volumes, models changing in time, markups changing in time, sequences of transforms, scene camera trajectory, or even sequence of sequences. Software features include:<br />
<br />
* Synthetic dose volume generation for testing.<br />
* Motion simulation for systematic and random errors.<br />
* Dose population histogram generation based on motion simulation.<br />
* A complete simulation module for margin calculation.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/DoseMorphology|Dose Morphology]]<br />
*[[Documentation/{{documentation/version}}/Modules/DosePopulationHistogram|Dose Population Histogram]]<br />
*[[Documentation/{{documentation/version}}/Modules/MarginCalculator|MarginCalculator]]<br />
*[[Documentation/{{documentation/version}}/Modules/MotionSimulator|Motion Simulator]]<br />
*[[Documentation/{{documentation/version}}/Modules/SyntheticRTDose|Synthetic RT Dose]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
<br />
* Comparison of different RT plans with specific margin using dose population histogram<br />
* Evaluation of effect of different margin in RT plan<br />
* Calculation of PTV margin<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
<br />
* TBA<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]]: SlicerRT and Margin Calculator are complementary software. Margin Calculator focuses specifically on the RT plan margin calculation, while SlicerRT aims for providing an easy-to-use interface for a wide range of stable, well-tested radiotherapy related features.<br />
* [[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<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<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<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* Source code: https://subversion.assembla.com/svn/margincalculator/trunk/MarginCalculator/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u1049984 open issues and enhancement requests]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/4.4/Extensions/MarginCalculator&diff=42928Documentation/4.4/Extensions/MarginCalculator2015-10-09T18:06:06Z<p>Wangk: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Contributors: Kevin Wang (Princess Margaret Cancer Centre), Winnie Li (Princess Margaret Cancer Centre)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.ca</email><br><br />
Website: http://www.assembla.com/spaces/margincalculator<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|sparkit}}|SparKit<br />
|{{collaborator|logo|namic}}|NA-MIC<br />
|{{collaborator|logo|perklab}}|PerkLab<br />
|{{collaborator|logo|ocairo}}|OCAIRO<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
Multidimensional data is an extension of 3D Slicer to allow creating and visualization of higher-dimension data nodes, such as 4D volumes, models changing in time, markups changing in time, sequences of transforms, scene camera trajectory, or even sequence of sequences. Software features include:<br />
<br />
* Synthetic dose volume generation for testing.<br />
* Motion simulation for systematic and random errors.<br />
* Dose population histogram generation based on motion simulation.<br />
* A complete simulation module for margin calculation.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/DoseMorphology|Dose Morphology]]<br />
*[[Documentation/{{documentation/version}}/Modules/DosePopulationHistogram|Dose Population Histogram]]<br />
*[[Documentation/{{documentation/version}}/Modules/MarginCalculator|MarginCalculator]]<br />
*[[Documentation/{{documentation/version}}/Modules/MotionSimulator|Motion Simulator]]<br />
*[[Documentation/{{documentation/version}}/Modules/SyntheticRTDose|Synthetic RT Dose]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
<br />
* Comparison of different RT plans with specific margin using dose population histogram<br />
* Evaluation of effect of different margin in RT plan<br />
* Calculation of PTV margin<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
<br />
* TBA<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]]: SlicerRT and Margin Calculator are complementary software. Margin Calculator focuses specifically on the RT plan margin calculation, while SlicerRT aims for providing an easy-to-use interface for a wide range of stable, well-tested radiotherapy related features.<br />
* [[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<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<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<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* Source code: https://subversion.assembla.com/svn/margincalculator/trunk/MarginCalculator/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u1049984 open issues and enhancement requests]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/MarginCalculator&diff=42730Documentation/Nightly/Extensions/MarginCalculator2015-09-17T14:50:27Z<p>Wangk: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Contributors: Kevin Wang (Princess Margaret Cancer Centre), Winnie Li (Princess Margaret Cancer Centre)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.ca</email><br><br />
Website: http://www.assembla.com/spaces/margincalculator<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|sparkit}}|SparKit<br />
|{{collaborator|logo|namic}}|NA-MIC<br />
|{{collaborator|logo|perklab}}|PerkLab<br />
|{{collaborator|logo|ocairo}}|OCAIRO<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
Multidimensional data is an extension of 3D Slicer to allow creating and visualization of higher-dimension data nodes, such as 4D volumes, models changing in time, markups changing in time, sequences of transforms, scene camera trajectory, or even sequence of sequences. Software features include:<br />
<br />
* Synthetic dose volume generation for testing.<br />
* Motion simulation for systematic and random errors.<br />
* Dose population histogram generation based on motion simulation.<br />
* A complete simulation module for margin calculation.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/DoseMorphology|Dose Morphology]]<br />
*[[Documentation/{{documentation/version}}/Modules/DosePopulationHistogram|Dose Population Histogram]]<br />
*[[Documentation/{{documentation/version}}/Modules/MarginCalculator|MarginCalculator]]<br />
*[[Documentation/{{documentation/version}}/Modules/MotionSimulator|Motion Simulator]]<br />
*[[Documentation/{{documentation/version}}/Modules/SyntheticRTDose|Synthetic RT Dose]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
<br />
* Sample scenes:<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneCardiacCt.mrb Cardiac CT: sequence of volumes, real-time volume rendering]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneModelDeformation.mrb Deformation of a 3D model]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneUsGuidedNeedleInsertion.mrb Ultrasound-guided needle insertion: moving tracked ultrasound image and tools, synchronized replay of image ad transforms]<br />
* Usage:<br />
** Load the downloaded .mrb scene file into Slicer<br />
** Go to the Sequence browser module to browse the data set<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
* [[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.<br />
* [[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<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<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<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* Source code: https://subversion.assembla.com/svn/margincalculator/trunk/MarginCalculator/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u1049984 open issues and enhancement requests]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=File:MarginCalculatorScreenshot1.png&diff=42712File:MarginCalculatorScreenshot1.png2015-09-15T19:38:41Z<p>Wangk: </p>
<hr />
<div></div>Wangkhttps://www.slicer.org/w/index.php?title=File:MarginCalculator_Logo2_128.png&diff=42711File:MarginCalculator Logo2 128.png2015-09-15T19:36:23Z<p>Wangk: </p>
<hr />
<div></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/4.4/Extensions/MarginCalculator&diff=42517Documentation/4.4/Extensions/MarginCalculator2015-08-21T20:12:06Z<p>Wangk: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Contributors: Kevin Wang (Princess Margaret Cancer Centre), Winnie Li (Princess Margaret Cancer Centre)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.ca</email><br><br />
Website: http://www.assembla.com/spaces/margincalculator<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|sparkit}}|SparKit<br />
|{{collaborator|logo|namic}}|NA-MIC<br />
|{{collaborator|logo|perklab}}|PerkLab<br />
|{{collaborator|logo|ocairo}}|OCAIRO<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
Multidimensional data is an extension of 3D Slicer to allow creating and visualization of higher-dimension data nodes, such as 4D volumes, models changing in time, markups changing in time, sequences of transforms, scene camera trajectory, or even sequence of sequences. Software features include:<br />
<br />
* Synthetic dose volume generation for testing.<br />
* Motion simulation for systematic and random errors.<br />
* Dose population histogram generation based on motion simulation.<br />
* A complete simulation module for margin calculation.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/DoseMorphology|Dose Morphology]]<br />
*[[Documentation/{{documentation/version}}/Modules/DosePopulationHistogram|Dose Population Histogram]]<br />
*[[Documentation/{{documentation/version}}/Modules/MarginCalculator|MarginCalculator]]<br />
*[[Documentation/{{documentation/version}}/Modules/MotionSimulator|Motion Simulator]]<br />
*[[Documentation/{{documentation/version}}/Modules/SyntheticRTDose|Synthetic RT Dose]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
<br />
* Sample scenes:<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneCardiacCt.mrb Cardiac CT: sequence of volumes, real-time volume rendering]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneModelDeformation.mrb Deformation of a 3D model]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneUsGuidedNeedleInsertion.mrb Ultrasound-guided needle insertion: moving tracked ultrasound image and tools, synchronized replay of image ad transforms]<br />
* Usage:<br />
** Load the downloaded .mrb scene file into Slicer<br />
** Go to the Sequence browser module to browse the data set<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
* [[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.<br />
* [[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<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<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<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* Source code: https://subversion.assembla.com/svn/margincalculator/trunk/MarginCalculator/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u1049984 open issues and enhancement requests]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/4.4/Extensions/MarginCalculator&diff=42516Documentation/4.4/Extensions/MarginCalculator2015-08-21T20:11:19Z<p>Wangk: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Contributors: Kevin Wang (Princess Margaret Cancer Centre), Winnie Li (Princess Margaret Cancer Centre)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.ca</email><br><br />
Website: http://www.assembla.com/spaces/margincalculator<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|sparkit}}|SparKit<br />
|{{collaborator|logo|namic}}|NA-MIC<br />
|{{collaborator|logo|perklab}}|PerkLab<br />
|{{collaborator|logo|ocairo}}|OCAIRO<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
Multidimensional data is an extension of 3D Slicer to allow creating and visualization of higher-dimension data nodes, such as 4D volumes, models changing in time, markups changing in time, sequences of transforms, scene camera trajectory, or even sequence of sequences. Software features include:<br />
<br />
* Synthetic dose volume generation for testing.<br />
* Motion simulation for systematic and random errors.<br />
* Dose population histogram generation based on motion simulation.<br />
* A complete simulation module for margin calculation.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/DoseMorphology|Dose Morphology]]<br />
*[[Documentation/{{documentation/version}}/Modules/DosePopulationHistogram|Dose Population Histogram]]<br />
*[[Documentation/{{documentation/version}}/Modules/MarginCalculator|MarginCalculator]]<br />
*[[Documentation/{{documentation/version}}/Modules/MotionSimulator|Motion Simulator]]<br />
*[[Documentation/{{documentation/version}}/Modules/SyntheticRTDose|Synthetic RT Dose]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
<br />
* Sample scenes:<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneCardiacCt.mrb Cardiac CT: sequence of volumes, real-time volume rendering]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneModelDeformation.mrb Deformation of a 3D model]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneUsGuidedNeedleInsertion.mrb Ultrasound-guided needle insertion: moving tracked ultrasound image and tools, synchronized replay of image ad transforms]<br />
* Usage:<br />
** Load the downloaded .mrb scene file into Slicer<br />
** Go to the Sequence browser module to browse the data set<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
* [[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.<br />
* [[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<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* Source code: https://subversion.assembla.com/svn/margincalculator/trunk/MarginCalculator/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u1049984 open issues and enhancement requests]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/4.4/Extensions/MarginCalculator&diff=42515Documentation/4.4/Extensions/MarginCalculator2015-08-21T20:09:30Z<p>Wangk: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Contributors: Kevin Wang (Princess Margaret Cancer Centre), Winnie Li (Princess Margaret Cancer Centre)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.ca</email><br><br />
Website: http://www.assembla.com/spaces/margincalculator<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|sparkit}}|SparKit<br />
|{{collaborator|logo|namic}}|NA-MIC<br />
|{{collaborator|logo|perklab}}|PerkLab<br />
|{{collaborator|logo|ocairo}}|OCAIRO<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
Multidimensional data is an extension of 3D Slicer to allow creating and visualization of higher-dimension data nodes, such as 4D volumes, models changing in time, markups changing in time, sequences of transforms, scene camera trajectory, or even sequence of sequences. Software features include:<br />
<br />
* Synthetic dose volume generation for testing.<br />
* Motion simulation for systematic and random errors.<br />
* Dose population histogram generation based on motion simulation.<br />
* A complete simulation module for margin calculation.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/DoseMorphology|Dose Morphology]]<br />
*[[Documentation/{{documentation/version}}/Modules/DosePopulationHistogram|Dose Population Histogram]]<br />
*[[Documentation/{{documentation/version}}/Modules/MarginCalculator|MarginCalculator]]<br />
*[[Documentation/{{documentation/version}}/Modules/MotionSimulator|Motion Simulator]]<br />
*[[Documentation/{{documentation/version}}/Modules/SyntheticRTDose|Synthetic RT Dose]]<br />
<br />
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{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
<br />
* Sample scenes:<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneCardiacCt.mrb Cardiac CT: sequence of volumes, real-time volume rendering]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneModelDeformation.mrb Deformation of a 3D model]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneUsGuidedNeedleInsertion.mrb Ultrasound-guided needle insertion: moving tracked ultrasound image and tools, synchronized replay of image ad transforms]<br />
* Usage:<br />
** Load the downloaded .mrb scene file into Slicer<br />
** Go to the Sequence browser module to browse the data set<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* Source code: https://subversion.assembla.com/svn/margincalculator/trunk/MarginCalculator/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u1049984 open issues and enhancement requests]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/4.4/Extensions/MarginCalculator&diff=42514Documentation/4.4/Extensions/MarginCalculator2015-08-21T20:09:11Z<p>Wangk: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Contributors: Kevin Wang (Princess Margaret Cancer Centre), Winnie Li (Princess Margaret Cancer Centre)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.ca</email><br><br />
Website: http://www.assembla.com/spaces/margincalculator<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|sparkit}}|SparKit<br />
|{{collaborator|logo|namic}}|NA-MIC<br />
|{{collaborator|logo|perklab}}|PerkLab<br />
|{{collaborator|logo|ocairo}}|OCAIRO<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
Multidimensional data is an extension of 3D Slicer to allow creating and visualization of higher-dimension data nodes, such as 4D volumes, models changing in time, markups changing in time, sequences of transforms, scene camera trajectory, or even sequence of sequences. Software features include:<br />
<br />
* Synthetic dose volume generation for testing.<br />
* Motion simulation for systematic and random errors.<br />
* Dose population histogram generation based on motion simulation.<br />
* A complete simulation module for margin calculation.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/DoseMorphology|Dose Morphology]]<br />
*[[Documentation/{{documentation/version}}/Modules/DosePopulationHistogram|Dose Population Histogram]]<br />
*[[Documentation/{{documentation/version}}/Modules/MarginCalculator|MarginCalculator]]<br />
*[[Documentation/{{documentation/version}}/Modules/MotionSimulator|Motion Simulator]]<br />
*[[Documentation/{{documentation/version}}/Modules/SyntheticRTDose|Synthetic RT Dose]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://plastimatch.org/data_sources.html Sample data] to use with modules.<br />
<gallery widths="200px" perrow="4"><br />
Image:plastimatch_dicomrt_ss.png|DICOM-RT Structure Set<br />
Image:plastimatch_dicomrt_dose.png|DICOM-RT Dose<br />
Image:plastimatch_image_1.png|Before Registration<br />
Image:plastimatch_image_2.png|After Registration<br />
Image:before_reg.png|Before Registration<br />
Image:after_reg.png|After Registration<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
<br />
* Sample scenes:<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneCardiacCt.mrb Cardiac CT: sequence of volumes, real-time volume rendering]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneModelDeformation.mrb Deformation of a 3D model]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneUsGuidedNeedleInsertion.mrb Ultrasound-guided needle insertion: moving tracked ultrasound image and tools, synchronized replay of image ad transforms]<br />
* Usage:<br />
** Load the downloaded .mrb scene file into Slicer<br />
** Go to the Sequence browser module to browse the data set<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* Source code: https://subversion.assembla.com/svn/margincalculator/trunk/MarginCalculator/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u1049984 open issues and enhancement requests]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/4.4/Extensions/MarginCalculator&diff=42513Documentation/4.4/Extensions/MarginCalculator2015-08-21T20:08:08Z<p>Wangk: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Contributors: Kevin Wang (Princess Margaret Cancer Centre), Winnie Li (Princess Margaret Cancer Centre)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.ca</email><br><br />
Website: http://www.assembla.com/spaces/margincalculator<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|sparkit}}|SparKit<br />
|{{collaborator|logo|namic}}|NA-MIC<br />
|{{collaborator|logo|perklab}}|PerkLab<br />
|{{collaborator|logo|ocairo}}|OCAIRO<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
Multidimensional data is an extension of 3D Slicer to allow creating and visualization of higher-dimension data nodes, such as 4D volumes, models changing in time, markups changing in time, sequences of transforms, scene camera trajectory, or even sequence of sequences. Software features include:<br />
<br />
* Synthetic dose volume generation for testing.<br />
* Motion simulation for systematic and random errors.<br />
* Dose population histogram generation based on motion simulation.<br />
* A complete simulation module for margin calculation.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/DoseMorphology|Dose Morphology]]<br />
*[[Documentation/{{documentation/version}}/Modules/DosePopulationHistogram|Dose Population Histogram]]<br />
*[[Documentation/{{documentation/version}}/Modules/MarginCalculator|MarginCalculator]]<br />
*[[Documentation/{{documentation/version}}/Modules/MotionSimulator|Motion Simulator]]<br />
*[[Documentation/{{documentation/version}}/Modules/SyntheticRTDose|Synthetic RT Dose]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://plastimatch.org/data_sources.html Sample data] to use with modules.<br />
<gallery widths="200px" perrow="4"><br />
Image:plastimatch_dicomrt_ss.png|DICOM-RT Structure Set<br />
Image:plastimatch_dicomrt_dose.png|DICOM-RT Dose<br />
Image:plastimatch_image_1.png|Before Registration<br />
Image:plastimatch_image_2.png|After Registration<br />
Image:before_reg.png|Before Registration<br />
Image:after_reg.png|After Registration<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:plastimatch_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1023/3D_Slicer_Plastimatch_Registration_Tutorial.ppt Download tutorial]<br />
Image:plastimatch_tutorial_data.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1004/rider-lung-images.tar.gz Download tutorial data]<br />
Image:plastimatch_dicomrt_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1568/3D_Slicer_Plastimatch_DICOM_RT_Tutorial_2010_12_28.pdf Download tutorial (PDF)]<br />
Image:plastimatch_dicomrt_ss.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/934/chest-phantom-dicomrt-xio-4.33.02.tar.gz (Download tutorial data)]<br />
Image:3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1622/3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.ppt Download tutorial]<br />
Image:fixed.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1619/synthetic_img.zip Download tutorial data]<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* Source code: https://subversion.assembla.com/svn/margincalculator/trunk/MarginCalculator/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u1049984 open issues and enhancement requests]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/4.4/Extensions/MarginCalculator&diff=42512Documentation/4.4/Extensions/MarginCalculator2015-08-21T20:03:54Z<p>Wangk: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Contributors: Kevin Wang (Princess Margaret Cancer Centre), Winnie Li (Princess Margaret Cancer Centre)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.ca</email><br><br />
Website: http://www.assembla.com/spaces/margincalculator<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|sparkit}}|SparKit<br />
|{{collaborator|logo|namic}}|NA-MIC<br />
|{{collaborator|logo|perklab}}|PerkLab<br />
|{{collaborator|logo|ocairo}}|OCAIRO<br />
}}<br />
<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
Multidimensional data is an extension of 3D Slicer to allow creating and visualization of higher-dimension data nodes, such as 4D volumes, models changing in time, markups changing in time, sequences of transforms, scene camera trajectory, or even sequence of sequences. Software features include:<br />
<br />
* Synthetic dose volume generation for testing.<br />
* Motion simulation for systematic and random errors.<br />
* Dose population histogram generation based on motion simulation.<br />
* A complete simulation module for margin calculation.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/Sequences|Sequences]]<br />
*[[Documentation/{{documentation/version}}/Modules/SequenceBrowser|Sequence browser]]<br />
*[[Documentation/{{documentation/version}}/Modules/MetafileImporter|Tracked ultrasound sequence importer]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://plastimatch.org/data_sources.html Sample data] to use with modules.<br />
<gallery widths="200px" perrow="4"><br />
Image:plastimatch_dicomrt_ss.png|DICOM-RT Structure Set<br />
Image:plastimatch_dicomrt_dose.png|DICOM-RT Dose<br />
Image:plastimatch_image_1.png|Before Registration<br />
Image:plastimatch_image_2.png|After Registration<br />
Image:before_reg.png|Before Registration<br />
Image:after_reg.png|After Registration<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:plastimatch_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1023/3D_Slicer_Plastimatch_Registration_Tutorial.ppt Download tutorial]<br />
Image:plastimatch_tutorial_data.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1004/rider-lung-images.tar.gz Download tutorial data]<br />
Image:plastimatch_dicomrt_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1568/3D_Slicer_Plastimatch_DICOM_RT_Tutorial_2010_12_28.pdf Download tutorial (PDF)]<br />
Image:plastimatch_dicomrt_ss.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/934/chest-phantom-dicomrt-xio-4.33.02.tar.gz (Download tutorial data)]<br />
Image:3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1622/3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.ppt Download tutorial]<br />
Image:fixed.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1619/synthetic_img.zip Download tutorial data]<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* Source code: https://subversion.assembla.com/svn/margincalculator/trunk/MarginCalculator/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u1049984 open issues and enhancement requests]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/4.4/Extensions/MarginCalculator&diff=42511Documentation/4.4/Extensions/MarginCalculator2015-08-21T19:51:43Z<p>Wangk: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
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<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
Acknowledgments:<br />
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by ... <br><br />
Author:Greg Sharp<br><br />
Contributors: Jean-Christophe Fillion-Robin ({{collaborator|name|kitware}})<br><br />
Contact: Greg Sharp, <email>gcsharp@partners.org</email><br><br />
Website: http://plastimatch.org/<br><br />
License: [http://forge.abcd.harvard.edu/gf/project/plastimatch/scmsvn/?action=browse&path=%2F*checkout*%2Fplastimatch%2Ftrunk%2Fsrc%2Fplastimatch%2FLICENSE.TXT&revision=2388 BSD]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
Plastimatch is an open source software for image computation. Our main focus is high-performance volumetric registration of medical images, such as X-ray computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). Software features include:<br />
<br />
*B-spline method for deformable image registration (GPU and multicore accelerated)<br />
*Demons method for deformable image registration (GPU accelerated)<br />
*ITK-based algorithms for translation, rigid, affine, demons, and B-spline registration<br />
*Pipelined, multi-stage registration framework with seamless conversion between most algorithms and transform types<br />
*Landmark-based deformable registration using thin-plate splines for global registration<br />
*Landmark-based deformable registration using radial basis functions for local corrections<br />
*Broad support for 3D image file formats (using ITK), including DICOM, Nifti, NRRD, MetaImage, and Analyze<br />
*DICOM and DICOM-RT import and export<br />
*XiO import and export<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
*[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]<br />
*[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]]<br />
*[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://plastimatch.org/data_sources.html Sample data] to use with modules.<br />
<gallery widths="200px" perrow="4"><br />
Image:plastimatch_dicomrt_ss.png|DICOM-RT Structure Set<br />
Image:plastimatch_dicomrt_dose.png|DICOM-RT Dose<br />
Image:plastimatch_image_1.png|Before Registration<br />
Image:plastimatch_image_2.png|After Registration<br />
Image:before_reg.png|Before Registration<br />
Image:after_reg.png|After Registration<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:plastimatch_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1023/3D_Slicer_Plastimatch_Registration_Tutorial.ppt Download tutorial]<br />
Image:plastimatch_tutorial_data.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1004/rider-lung-images.tar.gz Download tutorial data]<br />
Image:plastimatch_dicomrt_tutorial_ppt.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1568/3D_Slicer_Plastimatch_DICOM_RT_Tutorial_2010_12_28.pdf Download tutorial (PDF)]<br />
Image:plastimatch_dicomrt_ss.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/934/chest-phantom-dicomrt-xio-4.33.02.tar.gz (Download tutorial data)]<br />
Image:3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/110/1622/3D_Slicer_Plastimatch_Landmark_Registration_Tutorial.ppt Download tutorial]<br />
Image:fixed.png|[http://forge.abcd.harvard.edu/gf/download/frsrelease/85/1619/synthetic_img.zip Download tutorial data]<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* G Sharp, N Kandasamy, H Singh, M Folkert, "GPU-based streaming architectures for fast cone-beam CT image reconstruction and demons deformable registration," Physics in Medicine and Biology, 52(19), pp 5771-83, 2007. <br />
* V Boldea, G Sharp, SB Jiang, D Sarrut, "4D-CT lung motion estimation with deformable registration: Quantification of motion nonlinearity and hysteresis," Medical Physics, 33(3), pp 1008-18, 2008.<br />
* Z Wu, E Rietzel, V Boldea, D Sarrut, G Sharp, "Evaluation of deformable registration of patient lung 4DCT with sub-anatomical region segmentations," Medical Physics, 35(2), pp 775-81, 2008. <br />
* 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.<br />
* N. Shusharina, G. Sharp "Landmark-based image registration with analytic regularization", IEEE Trans. Med. Imag., submitted, 2011.<br />
<br />
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{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/extension-developerinfo}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/4.4/Extensions&diff=42510Documentation/4.4/Extensions2015-08-21T19:51:04Z<p>Wangk: /* Cat 2 */</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<noinclude><br />
__TOC__<br />
</noinclude>= Extensions by Category =<br />
<br />
==Cat 1==<br />
<br />
==Cat 2==<br />
*[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<br />
* [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )<br />
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)<br />
* [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)<br />
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)<br />
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)<br />
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)<br />
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)<br />
* [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Kevin Wang, Adam Rankin, Greg Sharp, Andras Lasso, Steve Pieper)<br />
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br />
** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br />
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br />
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br />
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br />
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br />
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br />
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br />
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br />
<!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]] --><br />
<!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]] --><br />
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br />
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]<br />
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]<br />
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)<br />
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)<br />
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)<br />
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)<br />
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)<br />
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)<br />
** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)<br />
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)<br />
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)<br />
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/MeshToLabelMap|MeshToLabelMap]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)<br />
* [[Documentation/{{documentation/version}}/Extensions/IntensitySegmenter|IntensitySegmenter]] (Francois Budin, Pengdong Xiao, Beatriz Paniagua)<br />
* [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)<br />
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)<br />
* [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)<br />
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)<br />
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)<br />
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)<br />
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br />
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)<br />
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)<br />
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]<br />
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]<br />
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)<br />
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)<br />
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)<br />
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)<br />
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)<br />
* [[Documentation/{{documentation/version}}/Extensions/VolumeClip|VolumeClip]] (Andras Lasso, Matt Lougheed)<br />
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)<br />
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)<br />
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)<br />
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)<br />
* [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)<br />
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)<br />
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)<br />
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)<br />
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)<br />
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]<br />
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]<br />
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]<br />
* [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)<br />
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)<br />
* [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)<br />
* [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)<br />
* [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)<br />
* [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)<br />
* [[Documentation/{{documentation/version}}/Extensions/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Atsushi Yamada, Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)<br />
* [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)<br />
** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]<br />
** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]<br />
* [[Documentation/{{documentation/version}}/Extensions/CurveMaker|CurveMaker]] (Junichi Tokuda)<br />
* [[Documentation/{{documentation/version}}/Extensions/CBC_3D_I2MConversion | CBC 3D I2MConversion]] (Fotis Drakopoulos, Yixun Liu, Andrey Fedorov and Nikos Chrisochoides)<br />
** [[Documentation/{{documentation/version}}/Modules/BodyCentricCubicMesh|Body Centric Cubic Mesh]]<br />
** [[Documentation/{{documentation/version}}/Modules/MeshCompression|Mesh Compression]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PBNRR|Physics-Based Non-Rigid Registration (PBNRR)]] (Fotis Drakopoulos, Yixun Liu, Andriy Kot, Andrey Fedorov, Olivier Clatz and Nikos Chrisochoides)<br />
* [[Documentation/{{documentation/version}}/Extensions/ResectionPlanner|ResectionVolume]] (Matt Lougheed)<br />
* [[Documentation/{{documentation/version}}/Extensions/PETDICOM|PET DICOM]] (Andrey Fedorov, Ethan Ulrich)<br />
* [[Documentation/{{documentation/version}}/Extensions/PETTumorSegmentation|PET Tumor Segmentation]] (Christian Bauer, Markus van Tol)<br />
* [[Documentation/{{documentation/version}}/Extensions/CornerAnnotation|CornerAnnotation]] (Atsushi Yamada)<br />
* [[Documentation/{{documentation/version}}/Extensions/Wasp|Watershed Annotation and Segmentation Plugin.]] (Thomas Lawson)<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerPetSpectAnalysis|SlicerPetSpectAnalysis]] (Martín Bertran,Natalia Martínez, Guillermo Carbajal, Álvaro Gómez)<br />
** [[Documentation/{{documentation/version}}/Modules/dPetBrainQuantification|dPetBrainQuantification]]<br />
* [[Documentation/{{documentation/version}}/Extensions/IGTWizard|IGTWizard]] (Junichi Tokuda and Atsushi Yamada)<br />
* [[Documentation/{{documentation/version}}/Extensions/MarginCalculator|MarginCalculator]] (Kevin Wang and Winnie Li)<br />
<br />
==Cat 3==<br />
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)<br />
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)<br />
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)<br />
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)<br />
* [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)<br />
<noinclude><br />
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}<br />
</noinclude></div>Wangkhttps://www.slicer.org/w/index.php?title=Developer_Meetings/20150113&diff=40660Developer Meetings/201501132015-01-13T20:15:44Z<p>Wangk: </p>
<hr />
<div>== To discuss ==<br />
<br />
The following topics are the continuation of discussion from 20141230 meeting.<br />
* DICOM export improvements<br />
** possible improvements to deal with all types of objects versus just one and ignoring the rest, as well as having to pass information between plugins<br />
* possibility to add multidimen data to slicer superbuild and ask people to migrate their modules to use it in stead of the multivolume module.<br />
* a new PET SUV module and how best to display results (data probe mouse over showing calculation at each voxel vs returning a new volume with the calculation as the image data)<br />
<br />
== Conclusion ==<br />
<br />
* Discussed Dicom export - Kevin will talk to Csaba to continue the work.<br />
* Discussed integrating multidimen data into slicer superbuild and agreed it is a natural step to do. Kevin to discuss with Andras to get final approval and then will start the integration.<br />
* Discussed PET SUV calculation work in Slicer community. <br />
** http://www.slicer.org/slicerWiki/index.php/Documentation/4.4/Extensions/LongitudinalPETCT<br />
** http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/dPetBrainQuantification<br />
* Discussed how to work around for extensions that are only built and tested on certain platform (such as windows). <br />
** Developers should keep in mind to make their code cross-platform but can state that they can only support in certain platform.<br />
** in extension CMakeLists.txt, check build platform and disable building for other unsupported platforms.</div>Wangkhttps://www.slicer.org/w/index.php?title=Developer_Meetings/20150113&diff=40587Developer Meetings/201501132014-12-30T21:00:22Z<p>Wangk: /* To discuss */</p>
<hr />
<div>== To discuss ==<br />
<br />
The following topics are the continuation of discussion from 20141230 meeting.<br />
* DICOM export improvements<br />
** possible improvements to deal with all types of objects versus just one and ignoring the rest, as well as having to pass information between plugins<br />
* possibility to add multidimen data to slicer superbuild and ask people to migrate their modules to use it in stead of the multivolume module.<br />
* a new PET SUV module and how best to display results (data probe mouse over showing calculation at each voxel vs returning a new volume with the calculation as the image data)</div>Wangkhttps://www.slicer.org/w/index.php?title=Developer_Meetings/20150113&diff=40586Developer Meetings/201501132014-12-30T20:59:13Z<p>Wangk: </p>
<hr />
<div>== To discuss ==<br />
<br />
* DICOM export improvements<br />
** possible improvements to deal with all types of objects versus just one and ignoring the rest, as well as having to pass information between plugins<br />
* possibility to add multidimen data to slicer superbuild and ask people to migrate their modules to use it in stead of the multivolume module.<br />
* a new PET SUV module and how best to display results (data probe mouse over showing calculation at each voxel vs returning a new volume with the calculation as the image data)</div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerRT&diff=38063Documentation/Nightly/Extensions/SlicerRT2014-05-29T18:34:46Z<p>Wangk: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
[[File:LogoCco.png|Cancer Care Ontario]]<br />
[[File:Logo-SparKit.png|SparKit]]<br />
[[File:LogoOCAIRO.jpg|SparKit]]<br />
<!-- ---------------------------- --><br />
<br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: <b>Csaba Pinter</b> (PerkLab, Queen's University), <b>Andras Lasso</b> (PerkLab, Queen's University), <b>Kevin Wang</b> (Princess Margaret Cancer Centre)<br><br />
Contributors: Greg Sharp (Massachusetts General Hospital), Steve Pieper (Isomics)<br><br />
Contacts:<br />
* Andras Lasso, <email>lasso@cs.queensu.ca</email><br />
* 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)<br />
* [[Documentation/SlicerRT/HowToReportAnError|How to report an error]]<br />
Website: [http://slicerrt.github.io slicerrt.org]<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
'''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])<br />
<br />
<!--<br />
<div style="float:right; margin-left:12px;"><br />
importScript('http://www.ohloh.net/p/641228/widgets/project_basic_stats.js');<br />
<wiki:gadget url="http://www.ohloh.net/p/641228/widgets/project_search_code.xml" height="195" border="1"/><br />
</div><br />
--><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
|<br />
[[Image:SlicerRT_Logo_2.0_128x128.png]]<br />
|<br />
* 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.<br />
<br />
* The SlicerRT extension incorporates [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] modules and algorithms.<br />
<br />
* Additional information for users can be found on the [[Documentation/SlicerRT/UsersGuide|User's guide]] page <br><br />
|<br />
|}<br />
<br />
{| class="wikitable"<br />
|<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br />
*[[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br />
*[[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br />
*[[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br />
*[[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br />
*[[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br />
*[[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br />
*[[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br />
*[[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br />
<!-- *[[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]] --><br />
<!-- *[[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]] --><br />
*[[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]<br />
*[[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer (moved to separate extension)]]<br />
<br />
* Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
<!--<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDoseComparison|Plastimatch Dose Comparison]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDoseVolumeHistogram|Plastimatch Dose Volume Histogram]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmSyntheticImageGeneration|Plastimatch Synthetic Image Generation]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmThreshBox|Plastimatch Threshold in a box]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
* Comparison of dose maps and dose volume histograms from various treatment planning systems<br />
* Evaluation of the effect of image-based non-rigid patient motion compensation<br />
* Dose accumulation with motion compensation<br />
* Evaluation of gel dosimetry<br />
* Testing of treatment planning algorithms<br />
<br />
| [[File:SlicerRt_Montage.jpg|1024px|SlicerRT highlights]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
* '''Summer NA-MIC week 2013 tutorial''' (recommended)<br />
** Tutorial presentation: [http://wiki.na-mic.org/Wiki/images/b/b0/SlicerRT_TutorialContestSummer2013.pdf download] from Slicer wiki<br />
** Sample data: [http://slicer.kitware.com/midas3/download/folder/1345/SlicerRtTutorial_Namic2013June.zip download] from MIDAS<br />
* ECR 2013 - Medical University Vienna workshop<br />
** Workshop material: [http://www.na-mic.org/Wiki/index.php/File:Pinter_MedUni2013_Workshop.pdf download] from NA-MIC.org<br />
* RSNA 2012 tutorial<br />
** Tutorial description: [http://www.donotlink.com/bEo SlicerRT wiki: Slicer tutorials at RSNA 2012]<br />
<!-- Original link: https://www.assembla.com/spaces/slicerrt/wiki/20121127_Slicer_tutorials_at_RSNA_2012 --><br />
** Sample data: [http://slicer.kitware.com/midas3/folder/859 download] SlicerRT ART dose verification data from Midas server<br />
* Summer NA-MIC week 2012 tutorial<br />
** Tutorial presentation: [http://www.donotlink.com/bEp download] from the SlicerRT website<br />
<!-- Original link: https://www.assembla.com/spaces/slicerrt/documents/aAuMq81Eqr4ztvacwqjQXA/download/aAuMq81Eqr4ztvacwqjQXA --><br />
** Sample data: [http://www.donotlink.com/bEq download] from the SlicerRT website<br />
<!-- Original link: https://www.assembla.com/spaces/slicerrt/documents/bMuwgYTKur4yP-acwqjQWU/download/bMuwgYTKur4yP-acwqjQWU --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
* [[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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
==How to cite==<br />
Please cite the following paper when referring to SlicerRt in your publication:<br><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<br />
<pre><br />
@ARTICLE{Pinter2012,<br />
author = {Pinter, C. and Lasso, A. and Wang, A. and Jaffray, D. and Fichtinger, G.},<br />
title = {SlicerRT – Radiation therapy research toolkit for 3D Slicer},<br />
journal = {Med. Phys.},<br />
year = {2012},<br />
volume = {39},<br />
number = {10},<br />
pages = {6332-6338},<br />
}<br />
</pre><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* [http://www.donotlink.com/bEr SlicerRT developers wiki page]<br />
<!-- Original link: https://www.assembla.com/spaces/slicerrt/wiki/SlicerRt_developers_page --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions&diff=38062Documentation/Nightly/Extensions2014-05-29T18:34:03Z<p>Wangk: /* Cat 2 */</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<noinclude><br />
__TOC__<br />
</noinclude>= Extensions by Category =<br />
<br />
==Cat 1==<br />
<br />
==Cat 2==<br />
*[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<br />
* [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )<br />
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)<br />
* [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)<br />
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)<br />
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)<br />
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)<br />
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)<br />
* [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)<br />
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br />
** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br />
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br />
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br />
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br />
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br />
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br />
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br />
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br />
<!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]] --><br />
<!-- ** [[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]] --><br />
** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]<br />
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br />
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]<br />
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]<br />
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)<br />
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)<br />
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)<br />
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)<br />
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)<br />
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)<br />
** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)<br />
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)<br />
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)<br />
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)<br />
* [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)<br />
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)<br />
* [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)<br />
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)<br />
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)<br />
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)<br />
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br />
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)<br />
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)<br />
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]<br />
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]<br />
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)<br />
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)<br />
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)<br />
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)<br />
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)<br />
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)<br />
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)<br />
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)<br />
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)<br />
* [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)<br />
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)<br />
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)<br />
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)<br />
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)<br />
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]<br />
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]<br />
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]<br />
* [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)<br />
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)<br />
* [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)<br />
* [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)<br />
* [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)<br />
* [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)<br />
* [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)<br />
* [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)<br />
** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]<br />
** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]<br />
<br />
==Cat 3==<br />
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)<br />
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)<br />
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)<br />
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)<br />
* [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)<br />
<noinclude><br />
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}<br />
</noinclude></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DicomSroImport&diff=38061Documentation/Nightly/Modules/DicomSroImport2014-05-29T16:35:48Z<p>Wangk: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the SparKit project, funded by An Applied Cancer Research Unit of Cancer Care Ontario with funds provided by the Ministry of Health and Long-Term Care and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.<br><br />
Authors: Kevin Wang (Princess Margaret Cancer Centre), Greg Sharp (MGH)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.ca</email><br><br />
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT Back to SlicerRT home]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|cco}}|{{collaborator|longname|cco}}<br />
|{{collaborator|logo|sparkit}}|{{collaborator|longname|sparkit}}<br />
|{{collaborator|logo|ocairo}}|{{collaborator|longname|ocairo}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{| class="wikitable"<br />
|<br />
<br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
The {{documentation/modulename}} module enables importing and loading DICOM SRO files into the Slicer DICOM database and the Slicer scene.<br />
<br />
{{documentation/modulename}} does not have a separate module GUI. Instead, it is a DICOM import plugin that extends the DICOM module.<br />
<br />
When the user selects a patient in the DICOM management module interface, the import mechanism allows each DICOM import module to interpret the data. The DICOM import modules parse the data and return a list of items that they can read from the selected DICOM objects. This module will return with the RT objects. The DICOM module displays the consolidated list of all loadable objects to the user, and loads the items that are selected by the user.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Import and load DICOM SRO data<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
See [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT#Tutorials SlicerRT main page]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
See module description<br />
<!--<br />
{{documentation/{{documentation/version}}/module-parametersdescription}}<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Reporting Reporting extension]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
N/A<br />
<br />
| [[File:SlicerRT_0.14_DicomSROPlugin.png|thumb|720px| DICOM browser with SlicerRT]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions&diff=38060Documentation/Nightly/Extensions2014-05-29T16:32:38Z<p>Wangk: /* Cat 2 */</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<noinclude><br />
__TOC__<br />
</noinclude>= Extensions by Category =<br />
<br />
==Cat 1==<br />
<br />
==Cat 2==<br />
*[[Documentation/{{documentation/version}}/Extensions/CarreraSliceInteractiveSegmenter|CarreraSlice Interactive Segmenter]] (Ivan Kolesov, LiangJia Zhu, Yi Gao, Peter Karasev, Patricio Vela, Allen Tannenbaum, Karl Fritscher, Steve Pieper )<br />
* [[Documentation/{{documentation/version}}/Extensions/SurfaceReconstruction|SurfaceReconstruction]] (Chenxi-Zhang David-Doria Arnaud-Gelas Michael-Kazhdan Matthew-Bolitho Hugues-Hoppe Jean-Christophe Fillion-Robin )<br />
* [[Documentation/{{documentation/version}}/Extensions/SkullStripper|SkullStripper]] (Xiaodong Tao)<br />
* [[Documentation/{{documentation/version}}/Extensions/MABMIS|MABMIS]] (Xiaofeng Liu)<br />
* [[Documentation/{{documentation/version}}/Extensions/SwissSkullStripper|SwissSkullStripper]] (Bill Lorensen)<br />
* [[Documentation/{{documentation/version}}/Extensions/CARMA|Cardiac MRI Toolkit]] (Alan Morris, Salma Bengali)[[image:UnderConstruction.png|tumb|10px]]<br />
* [[Documentation/{{documentation/version}}/Extensions/PkModeling|PkModeling]] (Emma Zhu, Jim Miller)<br />
* [[Documentation/{{documentation/version}}/Extensions/FacetedVisualizer|FacetedVisualizer]] (Harini Veeraraghavan, Jim Miller)<br />
* [[Documentation/{{documentation/version}}/Extensions/Reporting|Reporting]] (Andrey Fedorov, Nicole Aucoin, Steve Pieper) (work in progress)<br />
* [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIA Browser]] (Alireza Mehrtash, Andrey Fedorov) (work in progress)<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT]] (Csaba Pinter, Andras Lasso, Kevin Wang, Greg Sharp, Steve Pieper)<br />
** [[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br />
** [[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br />
** [[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br />
** [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br />
** [[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br />
** [[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br />
** [[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br />
** [[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br />
** [[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br />
** [[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]]<br />
** [[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]]<br />
** [[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]<br />
** Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br />
*** [[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]]<br />
*** [[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]]<br />
*** [[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] [[image:UnderConstruction.png|tumb|10px]]<br />
* [[Documentation/{{documentation/version}}/Extensions/SlicerIGT|SlicerIGT]] (Tamas Ungi, Adam Rankin, Andras Lasso, Junichi Tokuda, Laurent Chauvin)<br />
** [[Documentation/{{documentation/version}}/Modules/CollectFiducials|CollectFiducials]] (Tamas Ungi)<br />
** [[Documentation/{{documentation/version}}/Modules/CreateModels|CreateModels]] (Tamas Ungi, Matthew Holden)<br />
** [[Documentation/{{documentation/version}}/Modules/OpenIGTLinkRemote|OpenIGTLinkRemote]] (Tamas Ungi, Andras Lasso)<br />
** [[Documentation/{{documentation/version}}/Modules/UltrasoundSnapshots|UltrasoundSnapshots]] (Tamas Ungi, Franklin King)<br />
** [[Documentation/{{documentation/version}}/Extensions/VolumeResliceDriver|VolumeResliceDriver]] (Junichi Tokuda, Tamas Ungi, Laurent Chauvin)<br />
** [[Documentation/{{documentation/version}}/Extensions/PathExplorer|PathExplorer]] (Laurent Chauvin, Junichi Tokuda)<br />
* [[Documentation/{{documentation/version}}/Extensions/MatlabBridge|Matlab Bridge]] (Andras Lasso, Jean-Christophe Fillion-Robin, Kevin Wang)<br />
* [[Documentation/{{documentation/version}}/Extensions/iGyne|iGyne]] (Xiaojun Chen and iGyne Team)<br />
* [[Documentation/{{documentation/version}}/Extensions/LongitudinalPETCT|LongitudinalPETCT]] (Paul Mercea, Andrey Fedorov)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIProcess|DTIProcess]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasFiberAnalyzer|DTIAtlasFiberAnalyzer]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/FiberViewerLight|FiberViewerLight]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIPrep|DTIPrep]] (Francois Budin)<br />
* [[Documentation/{{documentation/version}}/Extensions/DTIAtlasBuilder|DTIAtlasBuilder]] (Adrien Kaiser)<br />
* [[Documentation/{{documentation/version}}/Extensions/ShapePopulationViewer|ShapePopulationViewer]] (Alexis Girault)<br />
* [[Documentation/{{documentation/version}}/Extensions/ModelToModelDistance|ModelToModelDistance]] (Francois Budin, Juliette Pera, Beatriz Paniagua)<br />
* [[Documentation/{{documentation/version}}/Extensions/SpharmPdm|SPHARM-PDM]] (Beatriz Paniagua, Francois Budin, Martin Styner)<br />
* [[Documentation/{{documentation/version}}/Extensions/TubeTK|TubeTK]] (Stephen Aylward, Jean-Christophe Fillion-Robin, Christopher Mullins, Michael Jeulin-L, Matthew McCormick)<br />
* [[Documentation/{{documentation/version}}/Extensions/UKFTractography|UKFTractography]] (Ryan Eckbo, Yogesh Rathi)<br />
* [[Documentation/{{documentation/version}}/Extensions/TrackerStabilizer|TrackerStabilizer]] (Laurent Chauvin, Jayender Jagadeesan)<br />
* [[Documentation/{{documentation/version}}/Extensions/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br />
* [[Documentation/{{documentation/version}}/Extensions/SobolevSegmenter|SobolevSegmenter]] (Arie Nakhmani)<br />
* [[Documentation/{{documentation/version}}/Extensions/QuickTools|QuickTools]] (Julien Finet)<br />
** [[Documentation/{{documentation/version}}/Modules/ImageMaker|Image Maker]]<br />
* [[Documentation/{{documentation/version}}/Extensions/XNATSlicer|XNATSlicer]]<br />
* [[Documentation/{{documentation/version}}/Extensions/ErodeDilateLabel|ErodeDilateLabel]] (Junichi)<br />
* [[Documentation/{{documentation/version}}/Extensions/ThingiverseBrowser|ThingiverseBrowser]] (Nigel Goh)<br />
* [[Documentation/{{documentation/version}}/Extensions/VirtualFractureReconstruction|Virtual Fracture Reconstruction]] (Karl Fritscher, Peter Karasev)<br />
* [[Documentation/{{documentation/version}}/Extensions/AirwaySegmentation|AirwaySegmentation]] (Pietro Nardelli)<br />
* [[Documentation/{{documentation/version}}/Extensions/ModelClip|ModelClip]] (Jun Lin, Xiaojun Chen)<br />
* [[Documentation/{{documentation/version}}/Extensions/SurfaceMirror|SurfaceMirror]] (Jiaxi Luo, Ruqing Ye, Xiaojun Chen)<br />
* [[Documentation/{{documentation/version}}/Extensions/Scoliosis|Scoliosis]] (Franklin King, Tamas Ungi)<br />
**[[Documentation/{{documentation/version}}/Modules/SpinalCurvatureMeasurement|Spinal Curvature Measurement]] (Franklin King, Tamas Ungi)<br />
* [[Documentation/{{documentation/version}}/Extensions/PortPlacement|Port Placement]] (Luis G. Torres and Andinet Enquobahrie)<br />
* [[Documentation/{{documentation/version}}/Extensions/AutoPortPlacement|Auto Port Placement]] (Luis G. Torres, Andinet Enquobahrie)<br />
* [[Documentation/{{documentation/version}}/Extensions/PlusRemote|Plus Remote]] (Franklin King, Tamas Ungi)<br />
* [[Documentation/{{documentation/version}}/Extensions/TransformVisualizer|Transform Visualizer]] (Franklin King, Andras Lasso, Csaba Pinter)<br />
* [[Documentation/{{documentation/version}}/Extensions/WindowLevelEffect|WindowLevelEffect]] (Andrey Fedorov, Steve Pieper)<br />
* [[Documentation/{{documentation/version}}/Extensions/PerkTutor|PerkTutor]] (Tamas Ungi, Matthew Holden)<br />
** [[Documentation/{{documentation/version}}/Modules/PerkEvaluator|PerkEvaluator]]<br />
** [[Documentation/{{documentation/version}}/Modules/TransformRecorder|TransformRecorder]]<br />
** [[Documentation/{{documentation/version}}/Modules/WorkflowSegmentation|WorkflowSegmentation]]<br />
* [[Documentation/{{documentation/version}}/Modules/SlicerToKiwiExporter|SlicerToKiwiExporter]] (Jean-Christophe Fillion-Robin)<br />
* [[Documentation/{{documentation/version}}/Modules/GelDosimetry|GelDosimetry]] (Csaba Pinter)<br />
* [[Documentation/{{documentation/version}}/Extensions/MultidimData|Multidimensional data]] (Andras Lasso, Matthew Holden, Kevin Wang)<br />
* [[Documentation/{{documentation/version}}/Extensions/GyroGuide|GyroGuide]] (Ruifeng Chen,Luping Fang, Qing Pan, Xiaolei Chen, Jiashu Zhang)<br />
* [[Documentation/{{documentation/version}}/Modules/MRI SNR Measurement|MRI SNR Measurement]] (Babak Matinfar)<br />
* [[Documentation/{{documentation/version}}/Extensions/OpenCAD|OpenCAD]] (Vivek Narayan, Jayender Jagadeesan)<br />
* [[Documentation/{{documentation/version}}/PercutaneousApproachAnalysis|Percutaneous Approach Analysis]] (Koichiro Murakami, Laurent Chauvin, Junichi Tokuda)<br />
* [[Documentation/{{documentation/version}}/Extensions/FinslerTractography|Finsler Tractography]] (Antonio Tristan Vega, Demian Wassermann and Carl-Fredrik Westin)<br />
** [[Documentation/{{documentation/version}}/Modules/FinslerTractography|Finsler Tractography]]<br />
** [[Documentation/{{documentation/version}}/Modules/FinslerBacktracing|Finsler Backtracing]]<br />
<br />
==Cat 3==<br />
* [[Documentation/{{documentation/version}}/Extensions/LesionSegmentation|LesionSegmentation]] (Mark Scully)<br />
**[[Documentation/{{documentation/version}}/Modules/TrainModel|LesionSegmentation->TrainModel]] (Mark Scully)<br />
**[[Documentation/{{documentation/version}}/Modules/PredictLesions|LesionSegmentation->PredictLesions]] (Mark Scully)<br />
* [[Documentation/{{documentation/version}}/Extensions/IASEM|IASEM]] (Bradley Lowekamp)<br />
* [[Documentation/{{documentation/version}}/Extensions/PyDevRemoteDebug|Python debugger]] (Andras Lasso)<br />
<noinclude><br />
{{:Documentation/{{documentation/version}}/FAQ/Extensions|Extensions}}<br />
</noinclude></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DicomSroExport&diff=38059Documentation/Nightly/Modules/DicomSroExport2014-05-29T16:29:52Z<p>Wangk: Created page with '<noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- -----------------------…'</p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the SparKit project, funded by An Applied Cancer Research Unit of Cancer Care Ontario with funds provided by the Ministry of Health and Long-Term Care and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.<br><br />
Authors: Greg Sharp (MGH), Kevin Wang (Princess Margaret Cancer Centre)<br><br />
Contact: Greg Sharp, <email>GCSHARP@PARTNERS.ORG</email><br><br />
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT Back to SlicerRT home]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|cco}}|{{collaborator|longname|cco}}<br />
|{{collaborator|logo|sparkit}}|{{collaborator|longname|sparkit}}<br />
|{{collaborator|logo|ocairo}}|{{collaborator|longname|ocairo}}<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{| class="wikitable"<br />
|<br />
<br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
The {{documentation/modulename}} module enables exporting DICOM SRO to local storage. The module has a basic UI that allows selecting a fixed image (source in Dicom term), a moving image (registered in Dicom term) and a transform node.<br><br />
Transform node object can be created in the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/Transforms Transform] module or Brainsfit and Plastimatch registration modules. See that page for further instructions.<br><br><br />
The module is under development. More advanced export features can be expected in the future.<br />
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{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Export DICOM SRO data to local storage<br />
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{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
See [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT#Tutorials SlicerRT main page]<br />
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
See module description<br />
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N/A<br />
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| [[File:SlicerRT_0.14_DicomSroExportModuleUi.png|thumb|720px| DICOM Export module UI]]<br />
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N/A<br />
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<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=File:SlicerRT_0.14_DicomSroExportModuleUi.png&diff=38058File:SlicerRT 0.14 DicomSroExportModuleUi.png2014-05-29T16:25:17Z<p>Wangk: </p>
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<div></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerRT&diff=38057Documentation/Nightly/Extensions/SlicerRT2014-05-29T16:13:23Z<p>Wangk: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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[[File:LogoCco.png|Cancer Care Ontario]]<br />
[[File:Logo-SparKit.png|SparKit]]<br />
[[File:LogoOCAIRO.jpg|SparKit]]<br />
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<br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: <b>Csaba Pinter</b> (PerkLab, Queen's University), <b>Andras Lasso</b> (PerkLab, Queen's University), <b>Kevin Wang</b> (Princess Margaret Cancer Centre)<br><br />
Contributors: Greg Sharp (Massachusetts General Hospital), Steve Pieper (Isomics)<br><br />
Contacts:<br />
* Andras Lasso, <email>lasso@cs.queensu.ca</email><br />
* 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)<br />
* [[Documentation/SlicerRT/HowToReportAnError|How to report an error]]<br />
Website: [http://slicerrt.github.io slicerrt.org]<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
'''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])<br />
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
|<br />
[[Image:SlicerRT_Logo_2.0_128x128.png]]<br />
|<br />
* 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.<br />
<br />
* The SlicerRT extension incorporates [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] modules and algorithms.<br />
<br />
* Additional information for users can be found on the [[Documentation/SlicerRT/UsersGuide|User's guide]] page <br><br />
|<br />
|}<br />
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{| class="wikitable"<br />
|<br />
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{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
*[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br />
*[[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br />
*[[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br />
*[[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br />
*[[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br />
*[[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br />
*[[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br />
*[[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br />
*[[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br />
*[[Documentation/{{documentation/version}}/Modules/DicomSroImport|DICOM-SRO import]]<br />
*[[Documentation/{{documentation/version}}/Modules/DicomSroExport|DICOM-SRO export]]<br />
*[[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy (integrated into Slicer trunk)]]<br />
*[[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer (moved to separate extension)]]<br />
<br />
* Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
<!--<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDoseComparison|Plastimatch Dose Comparison]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDoseVolumeHistogram|Plastimatch Dose Volume Histogram]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmSyntheticImageGeneration|Plastimatch Synthetic Image Generation]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmThreshBox|Plastimatch Threshold in a box]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
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{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
* Comparison of dose maps and dose volume histograms from various treatment planning systems<br />
* Evaluation of the effect of image-based non-rigid patient motion compensation<br />
* Dose accumulation with motion compensation<br />
* Evaluation of gel dosimetry<br />
* Testing of treatment planning algorithms<br />
<br />
| [[File:SlicerRt_Montage.jpg|1024px|SlicerRT highlights]]<br />
|}<br />
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{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
* '''Summer NA-MIC week 2013 tutorial''' (recommended)<br />
** Tutorial presentation: [http://wiki.na-mic.org/Wiki/images/b/b0/SlicerRT_TutorialContestSummer2013.pdf download] from Slicer wiki<br />
** Sample data: [http://slicer.kitware.com/midas3/download/folder/1345/SlicerRtTutorial_Namic2013June.zip download] from MIDAS<br />
* ECR 2013 - Medical University Vienna workshop<br />
** Workshop material: [http://www.na-mic.org/Wiki/index.php/File:Pinter_MedUni2013_Workshop.pdf download] from NA-MIC.org<br />
* RSNA 2012 tutorial<br />
** Tutorial description: [http://www.donotlink.com/bEo SlicerRT wiki: Slicer tutorials at RSNA 2012]<br />
<!-- Original link: https://www.assembla.com/spaces/slicerrt/wiki/20121127_Slicer_tutorials_at_RSNA_2012 --><br />
** Sample data: [http://slicer.kitware.com/midas3/folder/859 download] SlicerRT ART dose verification data from Midas server<br />
* Summer NA-MIC week 2012 tutorial<br />
** Tutorial presentation: [http://www.donotlink.com/bEp download] from the SlicerRT website<br />
<!-- Original link: https://www.assembla.com/spaces/slicerrt/documents/aAuMq81Eqr4ztvacwqjQXA/download/aAuMq81Eqr4ztvacwqjQXA --><br />
** Sample data: [http://www.donotlink.com/bEq download] from the SlicerRT website<br />
<!-- Original link: https://www.assembla.com/spaces/slicerrt/documents/bMuwgYTKur4yP-acwqjQWU/download/bMuwgYTKur4yP-acwqjQWU --><br />
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{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
* [[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.<br />
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{{documentation/{{documentation/version}}/extension-section|References}}<br />
==How to cite==<br />
Please cite the following paper when referring to SlicerRt in your publication:<br><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<br />
<pre><br />
@ARTICLE{Pinter2012,<br />
author = {Pinter, C. and Lasso, A. and Wang, A. and Jaffray, D. and Fichtinger, G.},<br />
title = {SlicerRT – Radiation therapy research toolkit for 3D Slicer},<br />
journal = {Med. Phys.},<br />
year = {2012},<br />
volume = {39},<br />
number = {10},<br />
pages = {6332-6338},<br />
}<br />
</pre><br />
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{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* [http://www.donotlink.com/bEr SlicerRT developers wiki page]<br />
<!-- Original link: https://www.assembla.com/spaces/slicerrt/wiki/SlicerRt_developers_page --><br />
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{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/Sequences&diff=37354Documentation/Nightly/Extensions/Sequences2014-02-20T17:35:13Z<p>Wangk: </p>
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Author: Andras Lasso (PerkLab, Queen's University), Matthew Holden (PerkLab, Queen's University), Kevin Wang (Princess Margaret Cancer Centre), Gabor Fichtinger (PerkLab, Queen's University)<br><br />
Contact: Andras Lasso, <email>lasso@cs.queensu.ca</email><br><br />
Project website: http://www.slicerrt.org<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|sparkit}}|SparKit<br />
|{{collaborator|logo|namic}}|NA-MIC<br />
|{{collaborator|logo|perklab}}|PerkLab<br />
|{{collaborator|logo|ocairo}}|OCAIRO<br />
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
[[Image:MultidimDataLogo.png|left]]<br />
|<br />
Multidimensional data is an extension of 3D Slicer to allow creating and visualization of higher-dimension data nodes, such as 4D volumes, models changing in time, markups changing in time, sequences of transforms, scene camera trajectory, or even sequence of sequences.<br />
<br />
Highlights:<br />
* Sequences can be created from any MRML nodes<br />
* Multiple sequences can be replayed sycnhronized, in real-time, visualizing the contents in 2D and 3D<br />
|<br />
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{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
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*[[Documentation/{{documentation/version}}/Modules/Sequences|Sequences]]<br />
*[[Documentation/{{documentation/version}}/Modules/SequenceBrowser|Sequence browser]]<br />
*[[Documentation/{{documentation/version}}/Modules/MetafileImporter|Tracked ultrasound sequence importer]]<br />
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{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
<br />
<gallery widths="200px" perrow="3"><br />
Image:CardiacCtReplay.gif|4D Cardiac CT ([https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneCardiacCt.mrb download scene])<br />
Image:UltrasoundToolGuidance3dOnly.gif|Tracked ultrasound with tool tracking ([https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneUsGuidedNeedleInsertion.mrb download scene])<br />
Image:ShapeModelSequenceBrowsing3dOnly.gif|Model deformation ([https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneModelDeformation.mrb download scene])<br />
Image:SequenceEditor.png|Sequences module for creating and editing sequences<br />
Image:SequenceBrowser.png|Sequence browser module for browsing and replaying sequences<br />
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* Sample scenes:<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneCardiacCt.mrb Cardiac CT: sequence of volumes, real-time volume rendering]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneModelDeformation.mrb Deformation of a 3D model]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneUsGuidedNeedleInsertion.mrb Ultrasound-guided needle insertion: moving tracked ultrasound image and tools, synchronized replay of image ad transforms]<br />
* Usage:<br />
** Load the downloaded .mrb scene file into Slicer<br />
** Go to the Sequence browser module to browse the data set<br />
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* Sequence: Contains an ordered array of data nodes, each data node is tagged with an index value.<br />
* Data node: A regular MRML node, one item in the sequence. Data nodes are stored privately inside the sequence, therefore not visible in the main scene (where the sequence node is in). Singleton nodes are not allowed to be stored as data nodes. Sequence nodes can be data nodes, therefore sequence of sequence nodes can be used to represent higher-dimensional data sets.<br />
* Sequence index: The index describes the dimension of the data node sequence. The index name (such as "time"), unit (such as "s"), and type (such as "numeric" or "text") is the same for the whole sequence. The index value is specified for each data node. The index type information is used for sorting (numerical or string sorting) and matching of the index values (in case of a numerical index we can find the closest data node even if there is no perfectly matching index value).<br />
* Sequence browsing: A sequence node only contains the data nodes, but does not store any node relationships, such as parent transform, display properties, etc. These relationships can be only defined for the virtual output nodes that are generated by the Sequence browser module. Several browser nodes can be created to visualize data from the same sequence, which allows visualization, comparison of multiple different time points from the same sequence.<br />
* Virtual output node: The sequence browser node creates a copy of the selected privately stored data node in the main scene. This copy is the virtual output node.<br />
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{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
* Source code: https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u1049984 open issues and enhancement requests]<br />
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<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/MatlabBridge&diff=37353Documentation/Nightly/Extensions/MatlabBridge2014-02-20T17:32:22Z<p>Wangk: </p>
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Author: Andras Lasso (PerkLab, Queen's University), Jean-Christophe Fillion-Robin (Kitware), Kevin Wang (Princess Margaret Cancer Centre), Gabor Fichtinger (PerkLab, Queen's University)<br><br />
Contact: Andras Lasso, <email>lasso@cs.queensu.ca</email><br><br />
Project website: http://www.slicerrt.org<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|sparkit}}|SparKit<br />
|{{collaborator|logo|namic}}|NA-MIC<br />
|{{collaborator|logo|perklab}}|PerkLab<br />
|{{collaborator|logo|ocairo}}|OCAIRO<br />
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
[[Image:MatlabBridgeLogo.png|left]]<br />
|<br />
MatlabBridge is an extension of 3D Slicer to allow running Matlab functions directly in 3D Slicer.<br />
<br />
Highlights:<br />
* The extension allows running of Matlab functions directly from 3D Slicer: it takes the input from the data loaded into Slicer and visualizes the results in Slicer right after the execution is completed<br />
* If you change any input on the GUI (and the “AutoRun” option is enabled) the bridge automatically re-runs the Matlab script with the updated parameters and shows the new results<br />
* If you change your Matlab function then you can re-run the function and see the updated results with a single click<br />
* The graphical user interface is generated automatically from a standard command-line interface definition XML file (no GUI programming needed)<br />
* You can get started quickly by generating a skeleton Matlab function and interface definition XML file using the Matlab Module Generator module<br />
* No building of 3D Slicer or MEX files, etc. are needed – the only requirements are to download and install 3D Slicer with the MatlabBridge extension and have Matlab on your computer<br />
The Matlab module behaves exactly as any other command-line-interface module, the Matlab engine is started automatically in the background (and it is kept running in the background so that you don’t have to wait for Matlab startup each time you run your function)<br />
<br />
Demo videos:<br />
* [http://screencast.com/t/TgAVE6Wa8mf Creating and using a Matlab module]<br />
* [http://screencast.com/t/LcdrCx9l0 Editing and debugging a Matlab module]<br />
<br />
Tutorial: [[Media:MatlabBridgeTutorial.pdf|How to create, run, customize Matlab modules]]<br />
<br />
|<br />
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*[[Documentation/{{documentation/version}}/Modules/MatlabModuleGenerator|Matlab Module Generator]] (in the module list: Developer Tools / Matlab)<br />
*[[Documentation/{{documentation/version}}/Modules/MatlabCommander|Matlab Commander]] (in the module list: Developer Tools / Matlab)<br />
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<br />
<gallery widths="200px" perrow="4"><br />
Image:MatlabBridgeScreenshot1.png|Example Matlab module user interface in Slicer<br />
Image:MatlabBridgeScreenshot2.png|Matlab Bridge modules appear under the Developer Tools / Matlab category<br />
Image:MatlabBridgeScreenshot3.png|A skeleton Matlab script can be created and installed using the Matlab module generator.<br />
Image:MatlabBridgeScreenshot4.png|The Matlab Commander allows running any commands from the user interface or from another Slicer module.<br />
</gallery><br />
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{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
*'''[[Media:MatlabBridgeTutorial.pdf|Comprehensive MatlabBridge tutorial: how to create, run, customize Matlab modules]]'''<br />
*[https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/src/Examples/ A few example modules]<br />
* Demo video: [http://screencast.com/t/TgAVE6Wa8mf Creating and using a Matlab module]<br />
* Demo video: [http://screencast.com/t/LcdrCx9l0 Editing and debugging a Matlab module]<br />
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* Source code: https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u783013 open issues and enhancement requests]<br />
* Design overview: [https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/doc/MatlabBridgeDesign.pptx].<br />
* Running Matlab modules without accessing a Matlab license: You can run your Matlab modules on a computer that does not have Matlab license by using the Matlab Compiler.<br />
** On the development computer (with Matlab and Matlab Compiler license) create an executable (let's call it MyModuleCollection.exe) with the Matlab Compiler:<br />
*** include all the MatlabBridge CommandServer functions (https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/src/MatlabCommander/commandserver/) as Shared Resources<br />
*** include your custom .m files (including the .m file that the slicer module generator creates) as Shared Resources<br />
*** choose cli_commandserver.m as "Main File"<br />
** Installation on the target computer:<br />
*** Copy the MyModuleCollection.exe to the target computer (it can be anywhere, but make sure it's not in a directory that is listed in Slicer additional module paths)<br />
*** Set the location of your Matlab module proxy (.bat file or shell script) and CLI descriptor (.xml) files as additional module paths in Slicer<br />
** Running on the target computer:<br />
*** Start MyModuleCollection.exe (anytime ''before'' you start Slicer)<br />
*** Start Slicer<br />
* Tested with Matlab R2009b, R2012a, and R2013a on Windows7.<br />
<br />
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{{documentation/{{documentation/version}}/extension-section|Troubleshooting}}<br />
* Problem: When I try to run my Matlab module, the Matlab process does not start (Matlab window does not appear on the taskbar)<br />
** Solution [on Windows Vista/7/8]: Please go to the Matlab module generator module and in the “Matlab executable” editbox set the path to your “.../bin/matlab.exe” (not to "activate_matlab.exe" or other exe files in the Matlab program directory or any file in the bin/win64 directory).<br />
** Solution [on Mac OS X]: Please go to the Matlab module generator module and in the “Matlab executable” editbox set the path to your “/Applications/MATLAB.app/bin/matlab” (instead of MATLAB.app you may have MATLAB_<Release>.app, where <Release> is the MATLAB Release's version, i.e., R2009a, R2012b, etc.).<br />
* Problem: When I try to run my Matlab module, the Matlab process starts (Matlab window appears on the taskbar and it displays the message "Starting OpenIGTLink command server at port 4100 Waiting for client connections..."), but the Matlab module execution fails (in the Slicer error log the "igtl::ClientSocket (...): Failed to connect to server 127.0.0.1:4100" message is displayed)<br />
** Solution [on Windows Vista/7/8]: Firewall settings prevent Matlab-Slicer communication. Please add a firewall exception by the following steps:<br />
**# Start ''cmd.exe'' as administrator (open the Windows Start menu, type "cmd", hit Ctrl + Shift + Enter)<br />
**# Click ''Yes'', if a dialog box appears asking "''Do you want to allow the following program to make changes to this computer?''"<br />
**# Enter the following command: ''netsh firewall add portopening tcp 4100 MatlabBridge''<br />
** Solution [on Mac OS X]: Firewall settings prevent Matlab-Slicer communication. Please disable firewal or add a firewall exception.<br />
* Problem: module execution is not completed<br />
** Solution: make sure you've selected .../MATLAB/.../bin/matlab.exe as Matlab executable (and not .../MATLAB/.../bin/win64/MATLAB.exe)<br />
<!-- ---------------------------- --><br />
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{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/Isodose&diff=37352Documentation/Nightly/Modules/Isodose2014-02-20T17:29:54Z<p>Wangk: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the SparKit project, funded by An Applied Cancer Research Unit of Cancer Care Ontario with funds provided by the Ministry of Health and Long-Term Care and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.<br><br />
Author: Kevin Wang (Princess Margaret Cancer Centre)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.on.ca</email><br><br />
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT Back to SlicerRT home]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
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}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
The {{documentation/modulename}} module creates isosurfaces from an input dose volume and a series of defined isodose levels. The output is a series of surface models grouped under a hierarchy node parent that can be visualized either in the 3D viewer or overlaid on image slices.<br />
<br />
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{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Generate isodose lines and surfaces for a dose distribution<br />
<br />
{|align="center"<br />
|[[File:SlicerRT_IsodoseModuleUi.png|thumb|407px|Isodose module UI]]<br />
|[[File:SlicerRT0.6_Isodose.png|thumb|720px|Isodose views]]<br />
|}<br />
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{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
See [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT#Tutorials SlicerRT main page]<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
* Input<br />
** Dose volume<br />
** Number of Iso levels<br />
** Iso levels table: color, label and opacity can be set to the isodose surfaces individually<br />
** Apply: Create isodose surfaces<br />
* Display options<br />
** Show isodose lines: Show/hide isodose lines in 2D slice viewers<br />
** Show isodose surfaces: Show/hide isodose surfaces in the 3D view<br />
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<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DicomRtExport&diff=37351Documentation/Nightly/Modules/DicomRtExport2014-02-20T17:28:26Z<p>Wangk: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the SparKit project, funded by An Applied Cancer Research Unit of Cancer Care Ontario with funds provided by the Ministry of Health and Long-Term Care and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.<br><br />
Authors: Andras Lasso (PerkLab, Queen's University), Steve Pieper (Isomics), Kevin Wang (Princess Margaret Cancer Centre), Csaba Pinter (PerkLab, Queen's University)<br><br />
Contact: Andras Lasso, <email>lasso@cs.queensu.ca</email><br><br />
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT Back to SlicerRT home]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|cco}}|{{collaborator|longname|cco}}<br />
|{{collaborator|logo|sparkit}}|{{collaborator|longname|sparkit}}<br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
The {{documentation/modulename}} module enables exporting basic DICOM RT studies to local storage. The module has a basic UI that allows selecting an anatomical image, a dose volume and a structure set.<br><br />
Structure set object can be created in the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/PatientHierarchy Patient Hierarchy] module. See that page for further instructions.<br><br><br />
The module is under development. More advanced export features can be expected in the future.<br />
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{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Export DICOM RT data to local storage<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
See [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT#Tutorials SlicerRT main page]<br />
<br />
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
See module description<br />
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| [[File:SlicerRT 0.12 DicomRtExportModuleUi.png|thumb|720px| DICOM Export module UI]]<br />
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<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DicomRtImport&diff=37350Documentation/Nightly/Modules/DicomRtImport2014-02-20T17:26:53Z<p>Wangk: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the SparKit project, funded by An Applied Cancer Research Unit of Cancer Care Ontario with funds provided by the Ministry of Health and Long-Term Care and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.<br><br />
Authors: Andras Lasso (PerkLab, Queen's University), Steve Pieper (Isomics), Kevin Wang (Princess Margaret Cancer Centre), Csaba Pinter (PerkLab, Queen's University)<br><br />
Contact: Andras Lasso, <email>lasso@cs.queensu.ca</email><br><br />
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT Back to SlicerRT home]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|cco}}|{{collaborator|longname|cco}}<br />
|{{collaborator|logo|sparkit}}|{{collaborator|longname|sparkit}}<br />
|{{collaborator|logo|ocairo}}|{{collaborator|longname|ocairo}}<br />
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{| class="wikitable"<br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
The {{documentation/modulename}} module enables importing and loading DICOM RT files into the Slicer DICOM database and the Slicer scene.<br />
<br />
{{documentation/modulename}} does not have a separate module GUI. Instead, it is a DICOM import plugin that extends the DICOM module.<br />
<br />
When the user selects a patient in the DICOM management module interface, the import mechanism allows each DICOM import module to interpret the data. The DICOM import modules parse the data and return a list of items that they can read from the selected DICOM objects. This module will return with the RT objects. The DICOM module displays the consolidated list of all loadable objects to the user, and loads the items that are selected by the user.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Import and load DICOM RT data<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
See [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT#Tutorials SlicerRT main page]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
See module description<br />
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[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/Reporting Reporting extension]<br />
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{{documentation/{{documentation/version}}/module-section|References}}<br />
N/A<br />
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| [[File:SlicerRT0.3 Screenshot DicomBrowser.png|thumb|720px| DICOM browser with SlicerRT]]<br />
|}<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
Custom attributes:<br />
* DicomRtImport.DoseVolume: identifier attribute that is set to each imported dose volume. Facilitates easier distinction between dose and non-dose volumes (without tampering in the Patient Hierarchy tree, see below)<br />
* DicomRtImport.DoseUnitName: set in the study of each imported dose volume, the value of this attribute is read from the Dose Units (3004,0002) attribute of the RTDOSE DICOM volume<br />
* DicomRtImport.DoseUnitValue: set in the study of each imported dose volume, the value of this attribute is read from the Dose Grid Scaling (3004,000E) attribute of the RTDOSE DICOM volume. This value defines a scaling factor to convert the integer voxel values of the dose volume in the DICOM file to real dose values. This conversion is performed during DICOM importing, but this value is stored to let other modules know what was the original scaling factor (e.g., see how it is used in the documentation of the [[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose Volume Histogram]] module)<br />
* DicomRtImport.ContourHierarchy: identifier attribute for structure sets (contour hierarchy vtkMRMLDisplayableHierarchyNode nodes)<br />
* DicomRtImport.RtImage: identifier attribute for RT images<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer}}<br />
<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Modules/DoseAccumulation&diff=37349Documentation/Nightly/Modules/DoseAccumulation2014-02-20T17:24:39Z<p>Wangk: </p>
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{{documentation/{{documentation/version}}/module-header}}<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the SparKit project, funded by An Applied Cancer Research Unit of Cancer Care Ontario with funds provided by the Ministry of Health and Long-Term Care and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.<br><br />
Author: Kevin Wang (Princess Margaret Cancer Centre)<br><br />
Contact: Kevin Wang, <email>kevin.wang@rmp.uhn.on.ca</email><br><br />
[http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/SlicerRT Back to SlicerRT home]<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|{{collaborator|logo|cco}}|{{collaborator|longname|cco}}<br />
|{{collaborator|logo|sparkit}}|{{collaborator|longname|sparkit}}<br />
|{{collaborator|logo|ocairo}}|{{collaborator|longname|ocairo}}<br />
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{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
The {{documentation/modulename}} module computes accumulated dose for multiple input dose volumes as a weighted sum of the dose values. The weight of each input volume is specified in the module’s user interface. The dose volumes have to be spatially aligned prior the dose accumulation to obtain a meaningful summation. This can be achieved by utilizing image registration algorithms already available in the 3D Slicer core. First, the alignment transformation is computed by registering the anatomical volumes and then the same transformation is applied to the corresponding dose volumes.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Evaluate total delivered dose for multiple treatment fractions.<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
See [[Documentation/{{documentation/version}}/Extensions/SlicerRT|SlicerRT extension page]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
* Input<br />
** Reference dose volume: The output dose volume will have the same size, spacing, position, and orientation as the reference dose volume and will have the same dose unit. Voxel values of the reference dose volume do not influence the output.<br />
** Show dose volumes only: If checked, only the volumes that have been created by a SlicerRT module (such as DicomRtImport or DoseAccumulation) are displayed<br />
** Dose volume table<br />
*** The checked dose volumes are accumulated<br />
*** Weight can be assigned to the dose distributions for the accumulation<br />
* Output<br />
** Accumulated dose volume: The output volume<br />
** Apply: Compute accumulated dose and save it in the output volume<br />
<!--<br />
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| [[File:SlicerRT_DoseAccumulationModuleUi.png|thumb|445px|Dose accumulation module UI]]<br />
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
Custom attributes:<br />
* DicomRtImport.DoseVolume: identifier attribute that is set to each imported dose volume. Facilitates easier distinction between dose and non-dose volumes (without tampering in the Patient Hierarchy tree, see below)<br />
* DicomRtImport.DoseUnitName: set in the study of each imported dose volume, the value of this attribute is read from the Dose Units (3004,0002) attribute of the RTDOSE DICOM volume<br />
* DicomRtImport.DoseUnitValue: set in the study of each imported dose volume, the value of this attribute is read from the Dose Grid Scaling (3004,000E) attribute of the RTDOSE DICOM volume. This value defines a scaling factor to convert the integer voxel values of the dose volume in the DICOM file to real dose values. This conversion is performed during DICOM importing, but this value is stored to let other modules know what was the original scaling factor<br />
<br />
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<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/SlicerRT&diff=37348Documentation/Nightly/Extensions/SlicerRT2014-02-20T17:22:47Z<p>Wangk: </p>
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[[File:LogoCco.png|Cancer Care Ontario]]<br />
[[File:Logo-SparKit.png|SparKit]]<br />
[[File:LogoOCAIRO.jpg|SparKit]]<br />
<!-- ---------------------------- --><br />
<br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: <b>Csaba Pinter</b> (PerkLab, Queen's University), <b>Andras Lasso</b> (PerkLab, Queen's University), <b>Kevin Wang</b> (Princess Margaret Cancer Centre)<br><br />
Contributors: Greg Sharp (Massachusetts General Hospital), Steve Pieper (Isomics)<br><br />
Contacts:<br />
* Andras Lasso, <email>lasso@cs.queensu.ca</email><br />
* 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)<br />
* [[Documentation/SlicerRT/HowToReportAnError|How to report an error]]<br />
Website: [http://slicerrt.github.io slicerrt.org]<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
'''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])<br />
<br />
<!--<br />
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importScript('http://www.ohloh.net/p/641228/widgets/project_basic_stats.js');<br />
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
{|<br />
|<br />
[[Image:SlicerRT_Logo_2.0_128x128.png]]<br />
|<br />
* 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.<br />
<br />
* The SlicerRT extension incorporates [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] modules and algorithms.<br />
<br />
* Additional information for users can be found on the [[Documentation/SlicerRT/UsersGuide|User's guide]] page <br><br />
|<br />
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{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
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*[[Documentation/{{documentation/version}}/Modules/DicomRtImport|DICOM-RT import]]<br />
*[[Documentation/{{documentation/version}}/Modules/DicomRtExport|DICOM-RT export]]<br />
*[[Documentation/{{documentation/version}}/Modules/Contours|Contours]]<br />
*[[Documentation/{{documentation/version}}/Modules/DoseVolumeHistogram|Dose volume histogram]]<br />
*[[Documentation/{{documentation/version}}/Modules/DoseAccumulation|Dose accumulation]]<br />
*[[Documentation/{{documentation/version}}/Modules/DoseComparison|Dose comparison]]<br />
*[[Documentation/{{documentation/version}}/Modules/Isodose|Isodose line and surface display]]<br />
*[[Documentation/{{documentation/version}}/Modules/ContourComparison|Contour comparison]]<br />
*[[Documentation/{{documentation/version}}/Modules/ContourMorphology|Contour morphology]]<br />
*[[Documentation/{{documentation/version}}/Modules/SubjectHierarchy|Subject hierarchy]]<br />
*[[Documentation/{{documentation/version}}/Modules/DeformationFieldVisualizer|Transform visualizer (moved to separate extension)]]<br />
<br />
* Modules from [[Documentation/{{documentation/version}}/Extensions/Plastimatch|Plastimatch]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmBSplineDeformableRegistration|Plastimatch Automatic deformable image registration]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmLANDWARP|Plastimatch LANDWARP Landmark]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmXFORMWARP|Plastimatch XFORMWARP]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
<!--<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTImport|Plastimatch DICOM-RT import]] (Greg Sharp)<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDICOMRTExport|Plastimatch DICOM-RT export]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDoseComparison|Plastimatch Dose Comparison]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmDoseVolumeHistogram|Plastimatch Dose Volume Histogram]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmSyntheticImageGeneration|Plastimatch Synthetic Image Generation]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/{{documentation/version}}/Modules/PlmThreshBox|Plastimatch Threshold in a box]] (Greg Sharp)[[image:UnderConstruction.png|tumb|10px]]<br />
--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
* Comparison of dose maps and dose volume histograms from various treatment planning systems<br />
* Evaluation of the effect of image-based non-rigid patient motion compensation<br />
* Dose accumulation with motion compensation<br />
* Evaluation of gel dosimetry<br />
* Testing of treatment planning algorithms<br />
<br />
| [[File:SlicerRt_Montage.jpg|1024px|SlicerRT highlights]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
* '''Summer NA-MIC week 2013 tutorial''' (recommended)<br />
** Tutorial presentation: [http://wiki.na-mic.org/Wiki/images/b/b0/SlicerRT_TutorialContestSummer2013.pdf download] from Slicer wiki<br />
** Sample data: [http://slicer.kitware.com/midas3/download/folder/1345/SlicerRtTutorial_Namic2013June.zip download] from MIDAS<br />
* ECR 2013 - Medical University Vienna workshop<br />
** Workshop material: [http://www.na-mic.org/Wiki/index.php/File:Pinter_MedUni2013_Workshop.pdf download] from NA-MIC.org<br />
* RSNA 2012 tutorial<br />
** Tutorial description: [http://www.donotlink.com/bEo SlicerRT wiki: Slicer tutorials at RSNA 2012]<br />
<!-- Original link: https://www.assembla.com/spaces/slicerrt/wiki/20121127_Slicer_tutorials_at_RSNA_2012 --><br />
** Sample data: [http://slicer.kitware.com/midas3/folder/859 download] SlicerRT ART dose verification data from Midas server<br />
* Summer NA-MIC week 2012 tutorial<br />
** Tutorial presentation: [http://www.donotlink.com/bEp download] from the SlicerRT website<br />
<!-- Original link: https://www.assembla.com/spaces/slicerrt/documents/aAuMq81Eqr4ztvacwqjQXA/download/aAuMq81Eqr4ztvacwqjQXA --><br />
** Sample data: [http://www.donotlink.com/bEq download] from the SlicerRT website<br />
<!-- Original link: https://www.assembla.com/spaces/slicerrt/documents/bMuwgYTKur4yP-acwqjQWU/download/bMuwgYTKur4yP-acwqjQWU --><br />
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* [[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.<br />
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==How to cite==<br />
Please cite the following paper when referring to SlicerRt in your publication:<br><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<br />
<pre><br />
@ARTICLE{Pinter2012,<br />
author = {Pinter, C. and Lasso, A. and Wang, A. and Jaffray, D. and Fichtinger, G.},<br />
title = {SlicerRT – Radiation therapy research toolkit for 3D Slicer},<br />
journal = {Med. Phys.},<br />
year = {2012},<br />
volume = {39},<br />
number = {10},<br />
pages = {6332-6338},<br />
}<br />
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* [http://www.donotlink.com/bEr SlicerRT developers wiki page]<br />
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<!-- ---------------------------- --></div>Wangkhttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/Sequences&diff=37347Documentation/Nightly/Extensions/Sequences2014-02-20T17:21:41Z<p>Wangk: </p>
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Author: Andras Lasso (PerkLab, Queen's University), Matthew Holden (PerkLab, Queen's University), Kevin Wang (Princess Margaret Cancer Centre), Gabor Fichtinger (PerkLab, Queen's University)<br><br />
Contact: Andras Lasso, <email>lasso@cs.queensu.ca</email><br><br />
Project website: http://www.slicerrt.org<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
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{|<br />
[[Image:MultidimDataLogo.png|left]]<br />
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Multidimensional data is an extension of 3D Slicer to allow creating and visualization of higher-dimension data nodes, such as 4D volumes, models changing in time, markups changing in time, sequences of transforms, scene camera trajectory, or even sequence of sequences.<br />
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Highlights:<br />
* Sequences can be created from any MRML nodes<br />
* Multiple sequences can be replayed sycnhronized, in real-time, visualizing the contents in 2D and 3D<br />
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*[[Documentation/{{documentation/version}}/Modules/Sequences|Sequences]]<br />
*[[Documentation/{{documentation/version}}/Modules/SequenceBrowser|Sequence browser]]<br />
*[[Documentation/{{documentation/version}}/Modules/MetafileImporter|Tracked ultrasound sequence importer]]<br />
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<gallery widths="200px" perrow="3"><br />
Image:CardiacCtReplay.gif|4D Cardiac CT ([https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneCardiacCt.mrb download scene])<br />
Image:UltrasoundToolGuidance3dOnly.gif|Tracked ultrasound with tool tracking ([https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneUsGuidedNeedleInsertion.mrb download scene])<br />
Image:ShapeModelSequenceBrowsing3dOnly.gif|Model deformation ([https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneModelDeformation.mrb download scene])<br />
Image:SequenceEditor.png|Sequences module for creating and editing sequences<br />
Image:SequenceBrowser.png|Sequence browser module for browsing and replaying sequences<br />
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* Sample scenes:<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneCardiacCt.mrb Cardiac CT: sequence of volumes, real-time volume rendering]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneModelDeformation.mrb Deformation of a 3D model]<br />
** [https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/data/SampleSceneUsGuidedNeedleInsertion.mrb Ultrasound-guided needle insertion: moving tracked ultrasound image and tools, synchronized replay of image ad transforms]<br />
* Usage:<br />
** Load the downloaded .mrb scene file into Slicer<br />
** Go to the Sequence browser module to browse the data set<br />
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* Sequence: Contains an ordered array of data nodes, each data node is tagged with an index value.<br />
* Data node: A regular MRML node, one item in the sequence. Data nodes are stored privately inside the sequence, therefore not visible in the main scene (where the sequence node is in). Singleton nodes are not allowed to be stored as data nodes. Sequence nodes can be data nodes, therefore sequence of sequence nodes can be used to represent higher-dimensional data sets.<br />
* Sequence index: The index describes the dimension of the data node sequence. The index name (such as "time"), unit (such as "s"), and type (such as "numeric" or "text") is the same for the whole sequence. The index value is specified for each data node. The index type information is used for sorting (numerical or string sorting) and matching of the index values (in case of a numerical index we can find the closest data node even if there is no perfectly matching index value).<br />
* Sequence browsing: A sequence node only contains the data nodes, but does not store any node relationships, such as parent transform, display properties, etc. These relationships can be only defined for the virtual output nodes that are generated by the Sequence browser module. Several browser nodes can be created to visualize data from the same sequence, which allows visualization, comparison of multiple different time points from the same sequence.<br />
* Virtual output node: The sequence browser node creates a copy of the selected privately stored data node in the main scene. This copy is the virtual output node.<br />
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* Source code: https://subversion.assembla.com/svn/slicerrt/trunk/MultidimData/<br />
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u1049984 open issues and enhancement requests]<br />
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