https://www.na-mic.org/w/api.php?action=feedcontributions&feedformat=atom&user=AndreasNAMIC Wiki - User contributions [en]2026-05-20T06:24:47ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering_Tutorials&diff=23531Slicer3:Volume Rendering Tutorials2008-04-02T09:53:00Z<p>Andreas: /* Tutorials */</p>
<hr />
<div>==Known limitations for the module==<br />
<br />
==Preparation for the tutorials==<br />
* Download an [http://wiki.na-mic.org/Wiki/images/f/f8/Tutorial-with-dicom.zip example dataset] of the head.<br />
* Download the [http://www.slicer.org/pages/Special:Slicer_Downloads/Snapshots latest slicer snapshot] and install it.<br />
* Start Slicer and load the example set<br />
** Click on File->"Load Scene"<br />
** Select the following file "Tutorial-with-dicom"/tutorial/tutorial.xml of the tutorial dataset that you just downloaded<br />
<br />
===Load and save parametersets===<br />
<flash>file=VR_Load_Basics.swf|width=1000|height=800|quality=best</flash><br />
<br />
===Tresholding===<br />
<flash>file=VR_Threshold.swf|width=1000|height=800|quality=best</flash><br />
===Performance===<br />
<flash>file=VR_Performance.swf|width=1000|height=800|quality=best</flash><br />
===Cropping===<br />
===Advanced===<br />
===Other features===</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering_Tutorials&diff=23530Slicer3:Volume Rendering Tutorials2008-04-02T09:51:06Z<p>Andreas: </p>
<hr />
<div>==Known limitations for the module==<br />
<br />
==Preparation for the tutorials==<br />
* Download an [http://wiki.na-mic.org/Wiki/images/f/f8/Tutorial-with-dicom.zip example dataset] of the head.<br />
* Download the [http://www.slicer.org/pages/Special:Slicer_Downloads/Snapshots latest slicer snapshot] and install it.<br />
* Start Slicer and load the example set<br />
** Click on File->"Load Scene"<br />
** Select the following file "Tutorial-with-dicom"/tutorial/tutorial.xml of the tutorial dataset that you just downloaded<br />
<br />
==Tutorials==<br />
At the moment the tutorials can be downloaded from [[Image:VolumeRenderingTutorials.zip| here]]. You will need a [http://www.eolsoft.com/download/ SWF Player] to view it until now, but this functionality will be included into the wiki soon<br />
===Load and save parametersets===<br />
<flash>file=VR_Load_Basics.swf|width=1000|height=800|quality=best</flash><br />
<br />
===Tresholding===<br />
<flash>file=VR_Threshold.swf|width=1000|height=800|quality=best</flash><br />
===Performance===<br />
<flash>file=VR_Performance.swf|width=1000|height=800|quality=best</flash><br />
===Cropping===<br />
===Advanced===<br />
===Other features===</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering_Tutorials&diff=23529Slicer3:Volume Rendering Tutorials2008-04-02T09:50:33Z<p>Andreas: </p>
<hr />
<div>==Known limitations for the module==<br />
<br />
==Preparation for the tutorials==<br />
* Download an [http://wiki.na-mic.org/Wiki/images/f/f8/Tutorial-with-dicom.zip example dataset] of the head.<br />
* Download the [http://www.slicer.org/pages/Special:Slicer_Downloads/Snapshots latest slicer snapshot] and install it.<br />
* Start Slicer and load the example set<br />
** Click on File->"Load Scene"<br />
** Select the following file "Tutorial-with-dicom"/tutorial/tutorial.xml of the tutorial dataset that you just downloaded<br />
<br />
==Tutorials==<br />
At the moment the tutorials can be downloaded from [[Image:VolumeRenderingTutorials.zip| here]]. You will need a [http://www.eolsoft.com/download/ SWF Player] to view it until now, but this functionality will be included into the wiki soon<br />
===Load and save parametersets===<br />
<flash>file=VR_Load_Basics.swf|width=1000|height=800|quality=best</flash><br />
<br />
===Tresholding===<br />
<flash>file=VR_Treshold.swf|width=1000|height=800|quality=best</flash><br />
===Performance===<br />
<flash>file=VR_Performance.swf|width=1000|height=800|quality=best</flash><br />
===Cropping===<br />
===Advanced===<br />
===Other features===</div>Andreashttps://www.na-mic.org/w/index.php?title=File:VR_Threshold.swf&diff=23528File:VR Threshold.swf2008-04-02T09:47:53Z<p>Andreas: </p>
<hr />
<div></div>Andreashttps://www.na-mic.org/w/index.php?title=File:VR_Performance.swf&diff=23527File:VR Performance.swf2008-04-02T09:39:43Z<p>Andreas: </p>
<hr />
<div></div>Andreashttps://www.na-mic.org/w/index.php?title=File:VR_Load_Basics.swf&diff=23526File:VR Load Basics.swf2008-04-02T09:34:24Z<p>Andreas: </p>
<hr />
<div></div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering_Tutorials&diff=23444Slicer3:Volume Rendering Tutorials2008-03-31T16:28:18Z<p>Andreas: /* Load and save parametersets */</p>
<hr />
<div>==Known limitations for the module==<br />
<br />
==Preparation for the tutorials==<br />
* Download an [http://wiki.na-mic.org/Wiki/images/f/f8/Tutorial-with-dicom.zip example dataset] of the head.<br />
* Download the [http://www.slicer.org/pages/Special:Slicer_Downloads/Snapshots latest slicer snapshot] and install it.<br />
* Start Slicer and load the example set<br />
** Click on File->"Load Scene"<br />
** Select the following file "Tutorial-with-dicom"/tutorial/tutorial.xml of the tutorial dataset that you just downloaded<br />
<br />
==Tutorials==<br />
At the moment the tutorials can be downloaded from [[Image:VolumeRenderingTutorials.zip| here]]. You will need a [http://www.eolsoft.com/download/ SWF Player] to view it until now, but this functionality will be included into the wiki soon<br />
===Load and save parametersets===<br />
<flash>file=Load_Basics.swf|width=1000|height=800|quality=best</flash><br />
<br />
===Tresholding===<br />
===Performance===<br />
===Cropping===<br />
===Advanced===<br />
===Other features===</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering_Tutorials&diff=21994Slicer3:Volume Rendering Tutorials2008-02-07T18:32:09Z<p>Andreas: </p>
<hr />
<div>==Known limitations for the module==<br />
<br />
==Preparation for the tutorials==<br />
* Download an [http://wiki.na-mic.org/Wiki/images/f/f8/Tutorial-with-dicom.zip example dataset] of the head.<br />
* Download the [http://www.slicer.org/pages/Special:Slicer_Downloads/Snapshots latest slicer snapshot] and install it.<br />
* Start Slicer and load the example set<br />
** Click on File->"Load Scene"<br />
** Select the following file "Tutorial-with-dicom"/tutorial/tutorial.xml of the tutorial dataset that you just downloaded<br />
<br />
==Tutorials==<br />
At the moment the tutorials can be downloaded from [[Image:VolumeRenderingTutorials.zip| here]]. You will need a [http://www.eolsoft.com/download/ SWF Player] to view it until now, but this functionality will be included into the wiki soon<br />
===Load and save parametersets===<br />
===Tresholding===<br />
===Performance===<br />
===Cropping===<br />
===Advanced===<br />
===Other features===</div>Andreashttps://www.na-mic.org/w/index.php?title=File:VolumeRenderingTutorials.zip&diff=21993File:VolumeRenderingTutorials.zip2008-02-07T18:28:40Z<p>Andreas: </p>
<hr />
<div></div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering_Tutorials&diff=21992Slicer3:Volume Rendering Tutorials2008-02-07T18:28:13Z<p>Andreas: /* Tutorials */</p>
<hr />
<div>==Known limitations for the module==<br />
<br />
==Preparation for the tutorials==<br />
* Download an [http://wiki.na-mic.org/Wiki/images/f/f8/Tutorial-with-dicom.zip example dataset] of the head.<br />
* Download the [http://www.slicer.org/pages/Special:Slicer_Downloads/Snapshots latest slicer snapshot] and install it.<br />
* Start Slicer and load the example set<br />
** Click on File->"Load Scene"<br />
** Select the following file "Tutorial-with-dicom"/tutorial/tutorial.xml of the tutorial dataset that you just downloaded<br />
<br />
==Tutorials==<br />
At the moment the tutorials can be downloaded from here. You will need a [http://www.eolsoft.com/download/ SWF Player] to view it until now, but this functionality will be included into the wiki soon<br />
===Load and save parametersets===<br />
===Tresholding===<br />
===Performance===<br />
===Cropping===<br />
===Advanced===<br />
===Other features===</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:DocumentationWink&diff=21976Slicer3:DocumentationWink2008-02-07T14:24:08Z<p>Andreas: /* What are the best settings if using Wink with Slicer */</p>
<hr />
<div>This page describes how to get wink and what the best settings are in combination with Slicer3. Please feel free to add settings, tips and tricks etc.<br />
==What is Wink?==<br />
"Wink is a Tutorial and Presentation creation software, primarily aimed at creating tutorials on how to use software (like a tutor for MS-Word/Excel etc). Using Wink you can capture screenshots, add explanations boxes, buttons, titles etc and generate a highly effective tutorial for your users." See more details here [http://www.debugmode.com/wink/ here].<br />
==How do I get Wink?==<br />
Wink can be downloaded [http://www.debugmode.com/wink/download.php here]<br />
==What are the best settings if using Wink with Slicer==<br />
* Record Slicer at a window size of about 1400x1050.<br />
* Set Slicer's font size to largest.<br />
* Choose a "Time Captured Rate" of 4 frames per second.<br />
* Write down the steps that you want to do in your tutorial before recording it.<br />
* Record your tutorial.<br />
* Go to "Resize All Frames" (Projects menu), select Resize "Only frame" and "Resize to percent" this what that you reach a resolution of about 800x600.<br />
* Add annotations and text boxes to your animation.<br />
* If you add an annotation set "Stay in this frame for" to 5 seconds.<br />
* When creating your project choose 10 frames per second.</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:DocumentationWink&diff=21975Slicer3:DocumentationWink2008-02-07T14:22:40Z<p>Andreas: /* What are the best settings if using Wink with Slicer */</p>
<hr />
<div>This page describes how to get wink and what the best settings are in combination with Slicer3. Please feel free to add settings, tips and tricks etc.<br />
==What is Wink?==<br />
"Wink is a Tutorial and Presentation creation software, primarily aimed at creating tutorials on how to use software (like a tutor for MS-Word/Excel etc). Using Wink you can capture screenshots, add explanations boxes, buttons, titles etc and generate a highly effective tutorial for your users." See more details here [http://www.debugmode.com/wink/ here].<br />
==How do I get Wink?==<br />
Wink can be downloaded [http://www.debugmode.com/wink/download.php here]<br />
==What are the best settings if using Wink with Slicer==<br />
* Record Slicer at a window size of about 1400x1050.<br />
* Set Slicer's font size to largest.<br />
* Choose a "Time Captured Rate" of 4 frames per second.<br />
* Write down about the steps that you want to do in your tutorial before recording it.<br />
* Record your tutorial.<br />
* Go to "Resize All Frames" (Projects menu), select Resize "Only frame" and "Resize to percent" this what that you reach a resolution of about 800x600.<br />
* Add annotations and text boxes to your animation.<br />
* If you add an annotation set "Stay in this frame for" to 5 seconds.<br />
* When creating your project choose 10 frames per second.</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:DocumentationWink&diff=21974Slicer3:DocumentationWink2008-02-07T14:22:11Z<p>Andreas: /* What are the best settings if using Wink with Slicer */</p>
<hr />
<div>This page describes how to get wink and what the best settings are in combination with Slicer3. Please feel free to add settings, tips and tricks etc.<br />
==What is Wink?==<br />
"Wink is a Tutorial and Presentation creation software, primarily aimed at creating tutorials on how to use software (like a tutor for MS-Word/Excel etc). Using Wink you can capture screenshots, add explanations boxes, buttons, titles etc and generate a highly effective tutorial for your users." See more details here [http://www.debugmode.com/wink/ here].<br />
==How do I get Wink?==<br />
Wink can be downloaded [http://www.debugmode.com/wink/download.php here]<br />
==What are the best settings if using Wink with Slicer==<br />
* Record Slicer at a window size of about 1400x1050<br />
* Set Slicer's font size to largest<br />
* Choose a "Time Captured Rate" of 4 frames per second<br />
* Write down about the steps that you want to do in your tutorial before recording it<br />
* Record your tutorial<br />
* Go to "Resize All Frames" (Projects menu), select Resize "Only frame" and "Resize to percent" this what that you reach a resolution of about 800x600<br />
* Add annotations and text boxes to your animation<br />
* If you add an annotation set "Stay in this frame for" to 5 seconds<br />
* When creating your project choose 10 frames per second</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:DocumentationWink&diff=21973Slicer3:DocumentationWink2008-02-07T14:19:15Z<p>Andreas: New page: This page describes how to get wink and what the best settings are in combination with Slicer3. Please feel free to add settings, tips and tricks etc. ==What is Wink?== "Wink is a Tutorial...</p>
<hr />
<div>This page describes how to get wink and what the best settings are in combination with Slicer3. Please feel free to add settings, tips and tricks etc.<br />
==What is Wink?==<br />
"Wink is a Tutorial and Presentation creation software, primarily aimed at creating tutorials on how to use software (like a tutor for MS-Word/Excel etc). Using Wink you can capture screenshots, add explanations boxes, buttons, titles etc and generate a highly effective tutorial for your users." See more details here [http://www.debugmode.com/wink/ here].<br />
==How do I get Wink?==<br />
Wink can be downloaded [http://www.debugmode.com/wink/download.php here]<br />
==What are the best settings if using Wink with Slicer==<br />
* Record Slicer at a window size of about 1400x1050<br />
* Set Slicer's font size to largest<br />
* Choose a "Time Captured Rate" of 4 frames per second<br />
* Record your tutorial<br />
* Go to "Resize All Frames" (Projects menu), select Resize "Only frame" and "Resize to percent" this what that you reach a resolution of about 800x600<br />
* Add annotations and text boxes to your animation<br />
* If you add an annotation set "Stay in this frame for" to 5 seconds<br />
* When creating your project choose 10 frames per second</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Developers&diff=21972Slicer3:Developers2008-02-07T14:05:13Z<p>Andreas: /* Documenting your module */</p>
<hr />
<div>{| class="toccolours" style="margin-right: 25px" align="right"<br />
! bgcolor="#ccccff" align="center" | Slicer3<br />
|-<br />
|<br />
[[Slicer3|Home]]<br />
|-<br />
|<br />
[[Slicer3:About|About]]<br />
|-<br />
|<br />
[[Slicer3:FAQ|FAQ]]<br />
|-<br />
|<br />
[[Slicer3:Status|Status]]<br />
|-<br />
|<br />
[[Slicer3:Downloads|Downloads]]<br />
|-<br />
|<br />
[[Slicer3:Documentation|Documentation]]<br />
|-<br />
|<br />
[[Slicer3:Community_Support|Community Support]]<br />
|-<br />
| '''Developers'''<br />
|-<br />
|<br />
[[Slicer3:Acknowledgements|Acknowledgements]]<br />
|-<br />
|<br />
[[Slicer3:Links|Links]]<br />
|}<br />
<br />
== Slicer 3 Overview ==<br />
[[Image:Slicer3LogoHorizontalBeta.png]]<br />
<br />
* For more details on the slicer architecture see: [[media:Slicer 3-beta-2007-04-16.ppt | Architecture Slides]] (updated April, 2007).<br />
* Highlights of the new architecture<br />
<br />
{|<br />
|[[Image:Slicer3-Architecture.jpg|thumb|200px]]<br />
|[[Image:Slicer3-Architecture-MRML.jpg|thumb|200px]]<br />
|[[Image:Slicer3-Architecture-Layers.jpg|200px|thumb]]<br />
|[[Image:ExecutionModelPlugins.png|200px|thumb]]<br />
|}<br />
<br />
== Information for Developers ==<br />
This section centrally locates many existing (and developing) wiki pages useful to Slicer3 developers. The content developed for the January 2007 AHM.<br />
<br />
=== Introduction to Slicer3 ===<br />
* [[Media:SlicerHistoricalTimeline.ppt | Slicer3 Historical Timeline]]<br />
* [[Slicer3:Status_Summary | Status overview]] and [http://slicerl.bwh.harvard.edu/tmp/slicer3-PreAHMBeta%20Demo/slicer3-PreAHMBeta.htm Demo]<br />
* Schematic of application interface & functionality: [[Media:GUIMap.png]]<br />
* Schematic of slice GUI: [[Media:SliceGUI.png ]]<br />
* [[Slicer3:Build_Instructions | Getting the software and troubleshooting]]<br />
* [[media:Slicer 3-beta-2007-01-10.ppt | Overall Architecture]] and [[Slicer3:Style|Slicer 3 Coding Style]]<br />
* [[Slicer3:Contributing_codes_to_Slicer3| Contributing codes to Slicer3]]<br />
<br />
=== Two module types (Command line and Interactive) ===<br />
* [[Slicer3:Execution_Model_Documentation | Command line modules and how to implement one]] (Jim and Bill) [[media:Slicer3-ExecutionModelJune2006.ppt| Intro]]<br />
*[[Slicer3:How_to_implement_an_Interactive_Module_GUI | How to implement an interactive module]] (wjp)<br />
<br />
=== MRML [http://www.na-mic.org/Wiki/images/e/e3/Slicer3_MRML.ppt MRML Slides](Alex) ===<br />
Medical Reality Modeling Language (MRML) is a language implemented as a type of XML document, with new tags defined to handle medical image data types such as volumes, models or coordinate transforms.<br />
<br />
* [[Slicer3:Data_Model#Creating_Custom_MRML_Node_Classes | Creating and using new MRML node types]] (Alex)<br />
* [[Slicer3:Data_Model#References_to_MRML_Nodes | Keeping references to MRML nodes ]] (Alex)<br />
* [[Slicer3:Data_Model#Undo/Redo_Mechanism | How undo/redo works, and how to enable it in your code]] (Alex)<br />
<br />
=== GUI ===<br />
* [[Slicer3:StatelessGUI | Keeping the GUI stateless]] (wjp)<br />
* [[Slicer3:EventBindings | Adding keyboard shortcuts]] (wjp)<br />
* [[Slicer3:Human_Interface_and_Style_Guide_for_Developers | GUI style guidelines]] (wjp)<br />
* [[Slicer3:Usability#User-centered_design_practice_for_3DSlicer | User-centered design practice]] (wjp)<br />
* [[Slicer3:Slicer3Brand | 3DSlicer's logo and visual communication guidelines]] (wjp)<br />
* [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3 | Incorporating your group's logo and attributions]] (Jim)<br />
* [[Slicer3:GUI_Experiments | Some experiments/advanced techniques for developing slicer3 interfaces]] (Steve)<br />
<br />
=== Engineering ===<br />
* Tips for avoiding memory leaks<br />
** Current Practice (Steve)<br />
** [[Slicer3:Memory Management | Suggested change to SmartPointers]] (Jim)<br />
* Generating tests (Bill)<br />
* [[Slicer3:Testing | Setting up Testing]]<br />
* [[Slicer3:Launcher| The Launcher]]<br />
<br />
=== Documenting your module ===<br />
* As soon as the wiki page template is finalized, and the infrastructure is added to link to this wiki page from the "Help & Acknowledgment" panel in your module's GUI, we will ask developers to fill out a brief document describing your module and its use. Stay tuned for developments...<br />
* [[Slicer3:DocumentationWink|Documenting a module with wink]]<br />
<br />
=== Integrate Slicer3 into a development environment ===<br />
* [[Slicer3::Eclipse | Eclipse]] (keilhack)<br />
* [[Slicer3::MSVS200X | Microsoft Visual Studio 200x]]<br />
<br />
== Slicer 3 Projects ==<br />
<br />
Projects should correspond to the outstanding issues listed on the '''[[Slicer3:Status_Summary|Status Summary]]'''. Please refer to the '''[[Slicer3:FeatureRequests|Feature Requests]]''' from users when planning your implementations.<br />
<br />
''If your name is in bold, you are responsible for that aspect of the project''<br />
<br />
* '''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)<br />
* '''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)<br />
* '''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)<br />
* '''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan)<br />
* '''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)<br />
** [[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>'''Alex''' with help from Diffusion Images: '''Raul''', Tractography: '''Lauren''' [http://lmi.bwh.harvard.edu LMI]<br />
** [[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''<br />
** [[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''<br />
** [[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''<br />
** [[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''<br />
** [[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''<br />
* '''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)<br />
* '''[[Slicer3:Pipeline_Integration|Loni Pipeline Integration]]''' ('''Jags''')<br />
* '''[[Slicer3:Batchmake_Integration|Batchmake/GRID Integration]]''' ('''Julien Jomier''')<br />
* '''[http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization Improvements to the registration framework]''' ('''Stephen Aylward''')<br />
* '''[[Slicer3:Python|Python Integration]]''' ('''Dan Blezek''')<br />
* '''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)<br />
* '''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')<br />
* '''[[Slicer3:ThreadingToolKit|Threading ToolKit]]''' ('''Dan Blezek, James Miller, Stephen Aylward''')<br />
* '''[[Slicer3:Volume Rendering |Volume Rendering]]''' ('''Andy''')<br />
* '''[[Slicer3:Volume Rendering With Cuda|Volume Rendering With CUDA]]''' ('''Ben''')<br />
* '''[[Slicer3:XNAT |XNAT Interface]]''' ('''Steve''', Wendy, Dan Marcus, Tim Olsen)<br />
* '''[[Slicer3:LDDMM |LDDMM Interface]]''' ('''Steve''', Anthony Kolasny)<br />
* '''[[Slicer3:Web Presence |Web Presence]]''' ('''Nicole Aucoin'''), Zack Galbreath<br />
* '''[[Slicer3:Loadable Modules |Loadable Modules]]''' ('''Alex Yarmarkovich'''), Steve Pieper<br />
* '''[[Slicer3:DWI Gradient Editor |DWI Gradient Editor]]''' ('''Kerstin''')<br />
* '''[[Slicer3:TimeSeries and Multi-Volume Data | TimeSeries and Multi-Volume Data]]''' (Steve Pieper, Daniel Blezek, Dominik Meier, Wendy Plesniak)<br />
* '''[[Slicer3:Remote Data Handling | Remote Data Handling]]''' (Steve Pieper, Nicole Aucoin, Wendy Plesniak)<br />
* '''[[Slicer3:Module:QueryAtlas |Query Atlas]]''' ('''Wendy Plesniak''')<br />
<br />
== Slicer 3 Quick links to the Source code ==<br />
<br />
The Slicer3 svn repository:<br />
<br />
svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
<br />
Use [http://www.na-mic.org/ViewVC/index.cgi/ ViewVC to browse the repository]<br />
<br />
[[Engineering:SandBox|Instructions for NA-MIC svn]]<br />
<br />
[[Slicer3:Build_Instructions|Slicer3 build instructions]]<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Doxygen documentation for Slicer3].<br />
<br />
The [[Slicer3:VisualBlog|Slicer3 VisualBlog]] shows screenshots of slicer developments.<br />
<br />
Developers should follow the [[Slicer3:Style|Slicer 3 Coding Style]].<br />
<br />
[http://www.na-mic.org/Slicer3/Dashboard Slicer3 Dashboard]<br />
<br />
[http://na-mic.org/Mantis/main_page.php Slicer Bug Tracker]<br />
<br />
Discussion of slicer3 takes place on the slicer-devel@massmail.spl.harvard.edu list. To join developer's mailing list, send a request to: [mailto:slicer-devel-request@massmail.spl.harvard.edu slicer-devel-request@massmail.spl.harvard.edu] with the keyword ''subscribe'' as the subject. Or access the [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel slicer-devel archives and web administration interface].<br />
<br />
== Design Information ==<br />
<br />
May 23, 2006: [[Algorithms:Core1Visit_May06|Algorithm Core workshop.]]<br />
<br />
<br /> April 3, 2006: [[Media:Slicer_3-alpha-2006-04-03.ppt| Slicer 3 alpha]] technical powerpoint presentation.<br />
<br />
<br /><br />
<br />
= Events =<br />
<br />
== Upcoming ==<br />
<br />
=== Slicer3.0 ===<br />
<br />
* the first product release of Slicer3 is scheduled for the AHM in January of 2008<br />
* there will be a code freeze on Nov. 15 2007<br />
** if you want your module to be part of Slicer3.0 submit it by then<br />
** After that date, we will only accept bug fixes. It means that there will be no features added after the freeze in the main trunk.<br />
<br />
** Any people working on new features can do so in their own branch and they will be responsible for merging these back into the trunk after the freeze is lifted (at which point the release will be in a maintenance branch). <br />
<br />
<br />
== Retrospective ==<br />
<br />
=== Slicer 3 Snapshot Builds ===<br />
<br />
* Initial releases began end of March 2007<br />
** Base code functional and usable<br />
** Several usable modules include (auto segmentaiton, editor, registration...)<br />
** Image Guided Therapy example modules<br />
* Updated versions summer 2007<br />
** With DTI and other application modules<br />
** Bug fixes and performance enhancements<br />
<br />
=== Migration Tutorials (from Slicer 2.x to 3.0) ===<br />
<br />
The first set of user tutorials will be released in Fall 2007. <br />
Slicer3 programming courses will be released in January 2008.<br />
<br />
== Past ==<br />
<br />
=== Slicer3.0 Beta ===<br />
<br />
* Official release at [[AHM_2007 | AHM January 2007]]<br />
<br />
=== April 3, 2006 ===<br />
<br />
There was a [[Slicer3:_Alpha1_Meeting|Slicer3 Alpha1 Design Review]] meeting.<br />
<br />
'''[[Slicer3:Alpha|Definition of Alpha Milestone]]'''<br />
<br />
=== Slicer3 Alpha2/Beta1 by End of July 2006 ===<br />
<br />
* Initial Testing with Core 3 participation<br />
* Base functionality in place, but still subject to API changes and other improvements.<br />
* Packaged versions not yet available, but testers are able to easily build their own versions.<br />
<br />
=== Implementation of Slicer3 Alpha1 by end of March 2006 ===</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering_Tutorials&diff=21934Slicer3:Volume Rendering Tutorials2008-02-06T17:42:33Z<p>Andreas: /* Preparation for the tutorials */</p>
<hr />
<div>==Known limitations for the module==<br />
<br />
==Preparation for the tutorials==<br />
* Download an [http://wiki.na-mic.org/Wiki/images/f/f8/Tutorial-with-dicom.zip example dataset] of the head.<br />
* Download the [http://www.slicer.org/pages/Special:Slicer_Downloads/Snapshots latest slicer snapshot] and install it.<br />
* Start Slicer and load the example set<br />
** Click on File->"Load Scene"<br />
** Select the following file "Tutorial-with-dicom"/tutorial/tutorial.xml of the tutorial dataset that you just downloaded<br />
<br />
==Tutorials==<br />
===Load and save parametersets===<br />
===Tresholding===<br />
===Performance===<br />
===Cropping===<br />
===Advanced===<br />
===Other features===</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering_Tutorials&diff=21742Slicer3:Volume Rendering Tutorials2008-02-01T18:36:30Z<p>Andreas: New page: ==Known limitations for the module== ==Preparation for the tutorials== ==Tutorials== ===Load and save parametersets=== ===Tresholding=== ===Performance=== ===Cropping=== ===Advanced=== ...</p>
<hr />
<div>==Known limitations for the module==<br />
<br />
==Preparation for the tutorials==<br />
<br />
==Tutorials==<br />
===Load and save parametersets===<br />
===Tresholding===<br />
===Performance===<br />
===Cropping===<br />
===Advanced===<br />
===Other features===</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21741Slicer3:Volume Rendering2008-02-01T18:33:14Z<p>Andreas: /* Tutorials */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
==Tutorials==<br />
[[Slicer3:Volume_Rendering_Tutorials|Tutorials]] for volume rendering will soon be available.<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector<br />
<br />
===Details GUI is recreated everytime a new volume is selected===<br />
* Create GUI on startup of slicer<br />
* Split existing class in several new classes and completely integrate every widget into the MRML architecture<br />
<br />
===vtkSlicerVRGrayscaleHelper is not maintainable===<br />
* Split it into several different widget classes and into one class that holds all rendering logic<br />
* Completely implement MRML pattern<br />
* Details see class diagramm below<br />
<br />
===GUI offers too much configuring options at the same time===<br />
* Make own page for tresholding<br />
* Make tresholding page the default page<br />
<br />
===It is not possible to use parameters from existing MRML-Volume rendering nodes===<br />
* Add a transfer configuration from node NodeSelector to Details frame<br />
<br />
===Questions for Steve===<br />
* Which coordinate system for clipping sliders<br />
* Can I use vtkVolumeProperty in the MRML-Node<br />
* Discuss new class architecture <br />
* Restructuring achievable in the small time frame?<br />
* if labelmaps or tresholding is enabled, disable the other ones (labelmaps, treshold or VolumePropertyWidget)<br />
* where should all the important logic go one class?<br />
* what about the integration of snapshot functionality<br />
<br />
===Notes for new class diagramm===<br />
* SetVolumeRenderingNode(NULL) in all classes disables the widget and sets values back to start configuration.<br />
* SetVolumeRenderingNode(aMRMLNode) populates the widgets with values from node, (initial calculations are done, the internally update is called)<br />
* ForceInvokeModifiedEvent is used for changes to vtkVolumeProperty (doesn' trigger events on its own)<br />
* clipping planes are part of mapper => cannot be saved in vtkVolumeProperty<br />
<br />
* Should threshold settings go into MRML<br />
* Include vtkMRMLVolumeRendering into Undo/Redo Stack at the following situations<br />
** Transfer parametersets<br />
** Enable labelmaps<br />
** Enable threshold<br />
** When selecting preset<br />
** etc.<br />
<br />
===New Architecture===<br />
[[Image:NewArchitecture.jpg]]</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21740Slicer3:Volume Rendering2008-02-01T18:33:00Z<p>Andreas: /* Tutorials */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
==Tutorials==<br />
[[Slicer3:Volume_Rendering_Tutorials|Tutorials]]for volume rendering will soon be available.<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector<br />
<br />
===Details GUI is recreated everytime a new volume is selected===<br />
* Create GUI on startup of slicer<br />
* Split existing class in several new classes and completely integrate every widget into the MRML architecture<br />
<br />
===vtkSlicerVRGrayscaleHelper is not maintainable===<br />
* Split it into several different widget classes and into one class that holds all rendering logic<br />
* Completely implement MRML pattern<br />
* Details see class diagramm below<br />
<br />
===GUI offers too much configuring options at the same time===<br />
* Make own page for tresholding<br />
* Make tresholding page the default page<br />
<br />
===It is not possible to use parameters from existing MRML-Volume rendering nodes===<br />
* Add a transfer configuration from node NodeSelector to Details frame<br />
<br />
===Questions for Steve===<br />
* Which coordinate system for clipping sliders<br />
* Can I use vtkVolumeProperty in the MRML-Node<br />
* Discuss new class architecture <br />
* Restructuring achievable in the small time frame?<br />
* if labelmaps or tresholding is enabled, disable the other ones (labelmaps, treshold or VolumePropertyWidget)<br />
* where should all the important logic go one class?<br />
* what about the integration of snapshot functionality<br />
<br />
===Notes for new class diagramm===<br />
* SetVolumeRenderingNode(NULL) in all classes disables the widget and sets values back to start configuration.<br />
* SetVolumeRenderingNode(aMRMLNode) populates the widgets with values from node, (initial calculations are done, the internally update is called)<br />
* ForceInvokeModifiedEvent is used for changes to vtkVolumeProperty (doesn' trigger events on its own)<br />
* clipping planes are part of mapper => cannot be saved in vtkVolumeProperty<br />
<br />
* Should threshold settings go into MRML<br />
* Include vtkMRMLVolumeRendering into Undo/Redo Stack at the following situations<br />
** Transfer parametersets<br />
** Enable labelmaps<br />
** Enable threshold<br />
** When selecting preset<br />
** etc.<br />
<br />
===New Architecture===<br />
[[Image:NewArchitecture.jpg]]</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21739Slicer3:Volume Rendering2008-02-01T18:32:46Z<p>Andreas: /* Tutorials */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
==Tutorials==<br />
[[Slicer3:Volume_Rendering_Tutorials]|Tutorials]for volume rendering will soon be available.<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector<br />
<br />
===Details GUI is recreated everytime a new volume is selected===<br />
* Create GUI on startup of slicer<br />
* Split existing class in several new classes and completely integrate every widget into the MRML architecture<br />
<br />
===vtkSlicerVRGrayscaleHelper is not maintainable===<br />
* Split it into several different widget classes and into one class that holds all rendering logic<br />
* Completely implement MRML pattern<br />
* Details see class diagramm below<br />
<br />
===GUI offers too much configuring options at the same time===<br />
* Make own page for tresholding<br />
* Make tresholding page the default page<br />
<br />
===It is not possible to use parameters from existing MRML-Volume rendering nodes===<br />
* Add a transfer configuration from node NodeSelector to Details frame<br />
<br />
===Questions for Steve===<br />
* Which coordinate system for clipping sliders<br />
* Can I use vtkVolumeProperty in the MRML-Node<br />
* Discuss new class architecture <br />
* Restructuring achievable in the small time frame?<br />
* if labelmaps or tresholding is enabled, disable the other ones (labelmaps, treshold or VolumePropertyWidget)<br />
* where should all the important logic go one class?<br />
* what about the integration of snapshot functionality<br />
<br />
===Notes for new class diagramm===<br />
* SetVolumeRenderingNode(NULL) in all classes disables the widget and sets values back to start configuration.<br />
* SetVolumeRenderingNode(aMRMLNode) populates the widgets with values from node, (initial calculations are done, the internally update is called)<br />
* ForceInvokeModifiedEvent is used for changes to vtkVolumeProperty (doesn' trigger events on its own)<br />
* clipping planes are part of mapper => cannot be saved in vtkVolumeProperty<br />
<br />
* Should threshold settings go into MRML<br />
* Include vtkMRMLVolumeRendering into Undo/Redo Stack at the following situations<br />
** Transfer parametersets<br />
** Enable labelmaps<br />
** Enable threshold<br />
** When selecting preset<br />
** etc.<br />
<br />
===New Architecture===<br />
[[Image:NewArchitecture.jpg]]</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21738Slicer3:Volume Rendering2008-02-01T18:31:07Z<p>Andreas: </p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
==Tutorials==<br />
[[Link title]|Tutorials]for volume rendering will soon be available.<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector<br />
<br />
===Details GUI is recreated everytime a new volume is selected===<br />
* Create GUI on startup of slicer<br />
* Split existing class in several new classes and completely integrate every widget into the MRML architecture<br />
<br />
===vtkSlicerVRGrayscaleHelper is not maintainable===<br />
* Split it into several different widget classes and into one class that holds all rendering logic<br />
* Completely implement MRML pattern<br />
* Details see class diagramm below<br />
<br />
===GUI offers too much configuring options at the same time===<br />
* Make own page for tresholding<br />
* Make tresholding page the default page<br />
<br />
===It is not possible to use parameters from existing MRML-Volume rendering nodes===<br />
* Add a transfer configuration from node NodeSelector to Details frame<br />
<br />
===Questions for Steve===<br />
* Which coordinate system for clipping sliders<br />
* Can I use vtkVolumeProperty in the MRML-Node<br />
* Discuss new class architecture <br />
* Restructuring achievable in the small time frame?<br />
* if labelmaps or tresholding is enabled, disable the other ones (labelmaps, treshold or VolumePropertyWidget)<br />
* where should all the important logic go one class?<br />
* what about the integration of snapshot functionality<br />
<br />
===Notes for new class diagramm===<br />
* SetVolumeRenderingNode(NULL) in all classes disables the widget and sets values back to start configuration.<br />
* SetVolumeRenderingNode(aMRMLNode) populates the widgets with values from node, (initial calculations are done, the internally update is called)<br />
* ForceInvokeModifiedEvent is used for changes to vtkVolumeProperty (doesn' trigger events on its own)<br />
* clipping planes are part of mapper => cannot be saved in vtkVolumeProperty<br />
<br />
* Should threshold settings go into MRML<br />
* Include vtkMRMLVolumeRendering into Undo/Redo Stack at the following situations<br />
** Transfer parametersets<br />
** Enable labelmaps<br />
** Enable threshold<br />
** When selecting preset<br />
** etc.<br />
<br />
===New Architecture===<br />
[[Image:NewArchitecture.jpg]]</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21681Slicer3:Volume Rendering2008-01-31T17:20:43Z<p>Andreas: /* Problems, issues with current implementation */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector<br />
<br />
===Details GUI is recreated everytime a new volume is selected===<br />
* Create GUI on startup of slicer<br />
* Split existing class in several new classes and completely integrate every widget into the MRML architecture<br />
<br />
===vtkSlicerVRGrayscaleHelper is not maintainable===<br />
* Split it into several different widget classes and into one class that holds all rendering logic<br />
* Completely implement MRML pattern<br />
* Details see class diagramm below<br />
<br />
===GUI offers too much configuring options at the same time===<br />
* Make own page for tresholding<br />
* Make tresholding page the default page<br />
<br />
===It is not possible to use parameters from existing MRML-Volume rendering nodes===<br />
* Add a transfer configuration from node NodeSelector to Details frame<br />
<br />
===Questions for Steve===<br />
* Which coordinate system for clipping sliders<br />
* Can I use vtkVolumeProperty in the MRML-Node<br />
* Discuss new class architecture <br />
* Restructuring achievable in the small time frame?<br />
* if labelmaps or tresholding is enabled, disable the other ones (labelmaps, treshold or VolumePropertyWidget)<br />
* where should all the important logic go one class?<br />
* what about the integration of snapshot functionality<br />
<br />
===Notes for new class diagramm===<br />
* SetVolumeRenderingNode(NULL) in all classes disables the widget and sets values back to start configuration.<br />
* SetVolumeRenderingNode(aMRMLNode) populates the widgets with values from node, (initial calculations are done, the internally update is called)<br />
* ForceInvokeModifiedEvent is used for changes to vtkVolumeProperty (doesn' trigger events on its own)<br />
* clipping planes are part of mapper => cannot be saved in vtkVolumeProperty<br />
<br />
* Should threshold settings go into MRML<br />
* Include vtkMRMLVolumeRendering into Undo/Redo Stack at the following situations<br />
** Transfer parametersets<br />
** Enable labelmaps<br />
** Enable threshold<br />
** When selecting preset<br />
** etc.<br />
<br />
===New Architecture===<br />
[[Image:NewArchitecture.jpg]]</div>Andreashttps://www.na-mic.org/w/index.php?title=File:NewArchitecture.jpg&diff=21680File:NewArchitecture.jpg2008-01-31T17:19:44Z<p>Andreas: Volume Rendering and MRML, architecture suggestion</p>
<hr />
<div>Volume Rendering and MRML, architecture suggestion</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21679Slicer3:Volume Rendering2008-01-31T17:07:29Z<p>Andreas: /* Problems, issues with current implementation */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector<br />
<br />
===Details GUI is recreated everytime a new volume is selected===<br />
* Create GUI on startup of slicer<br />
* Split existing class in several new classes and completely integrate every widget into the MRML architecture<br />
<br />
===vtkSlicerVRGrayscaleHelper is not maintainable===<br />
* Split it into several different widget classes and into one class that holds all rendering logic<br />
* Completely implement MRML pattern<br />
* Details see class diagramm below<br />
<br />
===GUI offers too much configuring options at the same time===<br />
* Make own page for tresholding<br />
* Make tresholding page the default page<br />
<br />
===It is not possible to use parameters from existing MRML-Volume rendering nodes===<br />
* Add a transfer configuration from node NodeSelector to Details frame<br />
<br />
===Questions for Steve===<br />
* Which coordinate system for clipping sliders<br />
* Can I use vtkVolumeProperty in the MRML-Node<br />
* Discuss new class architecture <br />
* Restructuring achievable in the small time frame?<br />
* if labelmaps or tresholding is enabled, disable the other ones (labelmaps, treshold or VolumePropertyWidget)<br />
* where should all the important logic go one class?<br />
* what about the integration of snapshot functionality<br />
<br />
===Notes for new class diagramm===<br />
* SetVolumeRenderingNode(NULL) in all classes disables the widget and sets values back to start configuration.<br />
* SetVolumeRenderingNode(aMRMLNode) populates the widgets with values from node, (initial calculations are done, the internally update is called)<br />
* ForceInvokeModifiedEvent is used for changes to vtkVolumeProperty (doesn' trigger events on its own)<br />
* clipping planes are part of mapper => cannot be saved in vtkVolumeProperty<br />
<br />
* Should threshold settings go into MRML<br />
* Include vtkMRMLVolumeRendering into Undo/Redo Stack at the following situations<br />
** Transfer parametersets<br />
** Enable labelmaps<br />
** Enable threshold<br />
** When selecting preset<br />
** etc.</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21668Slicer3:Volume Rendering2008-01-31T15:53:31Z<p>Andreas: /* Notes for new class diagramm */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector<br />
<br />
===Details GUI is recreated everytime a new volume is selected===<br />
* Create GUI on startup of slicer<br />
* Split existing class in several new classes and completely integrate every widget into the MRML architecture<br />
<br />
===vtkSlicerVRGrayscaleHelper is not maintainable===<br />
* Split it into several different widget classes and into one class that holds all rendering logic<br />
* Completely implement MRML pattern<br />
* Details see class diagramm below<br />
<br />
===GUI offers too much configuring options at the same time===<br />
* Make own page for tresholding<br />
* Make tresholding page the default page<br />
<br />
===It is not possible to use parameters from existing MRML-Volume rendering nodes===<br />
* Add a transfer configuration from node NodeSelector to Details frame<br />
<br />
===Questions for Steve===<br />
* Which coordinate system for clipping sliders<br />
* Can I use vtkVolumeProperty in the MRML-Node<br />
* Discuss new class architecture <br />
* Restructuring achievable in the small time frame?<br />
* if labelmaps or tresholding is enabled, disable the other ones (labelmaps, treshold or VolumePropertyWidget)<br />
* where should all the important logic go one class?<br />
<br />
===Notes for new class diagramm===<br />
* SetVolumeRenderingNode(NULL) in all classes disables the widget and sets values back to start configuration.<br />
* SetVolumeRenderingNode(aMRMLNode) populates the widgets with values from node, (initial calculations are done, the internally update is called)<br />
* ForceInvokeModifiedEvent is used for changes to vtkVolumeProperty (doesn' trigger events on its own)<br />
* clipping planes are part of mapper => cannot be saved in vtkVolumeProperty<br />
<br />
* Should threshold settings go into MRML<br />
* Include vtkMRMLVolumeRendering into Undo/Redo Stack at the following situations<br />
** Transfer parametersets<br />
** Enable labelmaps<br />
** Enable threshold<br />
** When selecting preset<br />
** etc.</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21666Slicer3:Volume Rendering2008-01-31T15:47:14Z<p>Andreas: /* Questions for Steve */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector<br />
<br />
===Details GUI is recreated everytime a new volume is selected===<br />
* Create GUI on startup of slicer<br />
* Split existing class in several new classes and completely integrate every widget into the MRML architecture<br />
<br />
===vtkSlicerVRGrayscaleHelper is not maintainable===<br />
* Split it into several different widget classes and into one class that holds all rendering logic<br />
* Completely implement MRML pattern<br />
* Details see class diagramm below<br />
<br />
===GUI offers too much configuring options at the same time===<br />
* Make own page for tresholding<br />
* Make tresholding page the default page<br />
<br />
===It is not possible to use parameters from existing MRML-Volume rendering nodes===<br />
* Add a transfer configuration from node NodeSelector to Details frame<br />
<br />
===Questions for Steve===<br />
* Which coordinate system for clipping sliders<br />
* Can I use vtkVolumeProperty in the MRML-Node<br />
* Discuss new class architecture <br />
* Restructuring achievable in the small time frame?<br />
* if labelmaps or tresholding is enabled, disable the other ones (labelmaps, treshold or VolumePropertyWidget)<br />
* where should all the important logic go one class?<br />
<br />
===Notes for new class diagramm===<br />
* SetVolumeRenderingNode(NULL) in all classes disables the widget and sets values back to start configuration.<br />
* SetVolumeRenderingNode(aMRMLNode) populates the widgets with values from node, (initial calculations are done, the internally update is called)<br />
* ForceInvokeModifiedEvent is used for changes to vtkVolumeProperty (doesn' trigger events on its own)<br />
* clipping planes are part of mapper => cannot be saved in vtkVolumeProperty<br />
<br />
* Should threshold settings go into MRML<br />
*</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21663Slicer3:Volume Rendering2008-01-31T15:14:41Z<p>Andreas: /* Details GUI is recreated everytime a new volume is selected */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector<br />
<br />
===Details GUI is recreated everytime a new volume is selected===<br />
* Create GUI on startup of slicer<br />
* Split existing class in several new classes and completely integrate every widget into the MRML architecture<br />
<br />
===vtkSlicerVRGrayscaleHelper is not maintainable===<br />
* Split it into several different widget classes and into one class that holds all rendering logic<br />
* Completely implement MRML pattern<br />
* Details see class diagramm below<br />
<br />
===GUI offers too much configuring options at the same time===<br />
* Make own page for tresholding<br />
* Make tresholding page the default page<br />
<br />
===It is not possible to use parameters from existing MRML-Volume rendering nodes===<br />
* Add a transfer configuration from node NodeSelector to Details frame<br />
<br />
===Questions for Steve===<br />
* Which coordinate system for clipping sliders<br />
* Can I use vtkVolumeProperty in the MRML-Node<br />
* Discuss new class architecture <br />
* Restructuring achievable in the small time frame?<br />
* if labelmaps or tresholding is enabled, disable the other ones (labelmaps, treshold or VolumePropertyWidget)<br />
<br />
===Notes for new class diagramm===<br />
* SetVolumeRenderingNode(NULL) in all classes disables the widget and sets values back to start configuration.<br />
* SetVolumeRenderingNode(aMRMLNode) populates the widgets with values from node, (initial calculations are done, the internally update is called)<br />
* ForceInvokeModifiedEvent is used for changes to vtkVolumeProperty (doesn' trigger events on its own)<br />
* clipping planes are part of mapper => cannot be saved in vtkVolumeProperty<br />
<br />
* Should threshold settings go into MRML<br />
*</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21662Slicer3:Volume Rendering2008-01-31T15:14:26Z<p>Andreas: /* Problems, issues with current implementation */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector<br />
<br />
===Details GUI is recreated everytime a new volume is selected===<br />
* Create GUI on startup of slicer<br />
* Split existing class in several new classes and completely integrate every widget into the MRML architecture<br />
<br />
<br />
===vtkSlicerVRGrayscaleHelper is not maintainable===<br />
* Split it into several different widget classes and into one class that holds all rendering logic<br />
* Completely implement MRML pattern<br />
* Details see class diagramm below<br />
<br />
===GUI offers too much configuring options at the same time===<br />
* Make own page for tresholding<br />
* Make tresholding page the default page<br />
<br />
===It is not possible to use parameters from existing MRML-Volume rendering nodes===<br />
* Add a transfer configuration from node NodeSelector to Details frame<br />
<br />
===Questions for Steve===<br />
* Which coordinate system for clipping sliders<br />
* Can I use vtkVolumeProperty in the MRML-Node<br />
* Discuss new class architecture <br />
* Restructuring achievable in the small time frame?<br />
* if labelmaps or tresholding is enabled, disable the other ones (labelmaps, treshold or VolumePropertyWidget)<br />
<br />
===Notes for new class diagramm===<br />
* SetVolumeRenderingNode(NULL) in all classes disables the widget and sets values back to start configuration.<br />
* SetVolumeRenderingNode(aMRMLNode) populates the widgets with values from node, (initial calculations are done, the internally update is called)<br />
* ForceInvokeModifiedEvent is used for changes to vtkVolumeProperty (doesn' trigger events on its own)<br />
* clipping planes are part of mapper => cannot be saved in vtkVolumeProperty<br />
<br />
* Should threshold settings go into MRML<br />
*</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21654Slicer3:Volume Rendering2008-01-31T14:34:39Z<p>Andreas: /* Problems, issues with current implementation */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector<br />
<br />
===Details GUI is recreated everytime a new volume is selected===<br />
* Create GUI on startup of slicer<br />
* Split existing class in several new classes and completely integrate every widget into the MRML architecture<br />
<br />
<br />
===vtkSlicerVRGrayscaleHelper is not maintainable===<br />
* Split it into several different widget classes and into one class that holds all rendering logic<br />
* Completely implement MRML pattern<br />
* Details see class diagramm below</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=21652Slicer3:Volume Rendering2008-01-31T14:29:16Z<p>Andreas: </p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps<br />
<br />
==Problems, issues with current implementation==<br />
===Load and Save Frame is much too complicated===<br />
* Include "Name new Parameterset:" and "Create Visualization Parameterset" into one Parameterset "Node Selector"<br />
* Don't allow n:m relationships between volumes and vtkMRMLVolumeRenderingNodes but only 1:1 relationships<br />
* Select parameterset before selecting volume<br />
* Rename "Current Parametersets" to "Presets" and put only real presets in the corresponding node selector</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week_VolumeRendering&diff=212152008 Winter Project Week VolumeRendering2008-01-11T15:55:52Z<p>Andreas: </p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]<br />
|valign="top"|[[Image:AbdomenLung.jpg |thumb|320px|Volume Rendering, mapping functions optimized for lung]]<br />
|valign="top"|[[Image:VolumeRenderingBoxWidget.jpg |thumb|320px|Edit clipping planes using vtkBoxWidget]]<br />
|}<br />
<br />
__NOTOC__<br />
===Key Investigators===<br />
* Isomics: Steve Pieper<br />
* SPL/IGT: Benjamin Grauer, Andreas Freudling<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
Integration of interactive volume rendering into Slicer 3 using hardware and software based rendering techniques.<br />
<br />
Improve the existing framework using new algorithms / frameworks like [http://en.wikipedia.org/wiki/CUDA| CUDA] or other rendering algorithms.<br />
<br />
Use volume rendering for 4D IGT.<br />
<br />
See [[Slicer3:Volume_Rendering| integration of volume rendering in Slicer 3]] and [http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques| new volume rendering techniques] for details.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan </h1><br />
Discuss which further efforts have to be taken to get a better usability of volume rendering (How can mapping functions be edited more intuitive, what are good presets etc.)<br />
<br />
What are essential features for volume rendering in Slicer.<br />
<br />
What are difficulties, issues when using volume rendering in connection with other modules.<br />
<br />
How should a different rendering, GUI for DTI, label maps and gray scale volumes look like.<br />
<br />
Figure out how difficult it is to integrate CUDA or other rendering algorithms into VTK and Slicer.<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
====June 2007 Project Week====<br />
The work on this project started in August 2007.<br />
====Jan 2007 Project Half Week====<br />
We added additional usability features, including a vtkBoxWidget and a GUI for volume rendering of labelmaps. We could also improve performance issues and are working on adding scene snapshot functionality.<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
===References===</div>Andreashttps://www.na-mic.org/w/index.php?title=File:VolumeRenderingBoxWidget.jpg&diff=21209File:VolumeRenderingBoxWidget.jpg2008-01-11T15:49:42Z<p>Andreas: Edit clipping planes by using the vtkBoxWidget</p>
<hr />
<div>Edit clipping planes by using the vtkBoxWidget</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week_VolumeRendering&diff=211982008 Winter Project Week VolumeRendering2008-01-11T15:23:58Z<p>Andreas: /* Jan 2007 Project Half Week */</p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]<br />
|valign="top"|[[Image:AbdomenLung.jpg |thumb|320px|Volume Rendering, mapping functions optimized for lung]]<br />
|}<br />
<br />
__NOTOC__<br />
===Key Investigators===<br />
* Isomics: Steve Pieper<br />
* SPL/IGT: Benjamin Grauer, Andreas Freudling<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
Integration of interactive volume rendering into Slicer 3 using hardware and software based rendering techniques.<br />
<br />
Improve the existing framework using new algorithms / frameworks like [http://en.wikipedia.org/wiki/CUDA| CUDA] or other rendering algorithms.<br />
<br />
Use volume rendering for 4D IGT.<br />
<br />
See [[Slicer3:Volume_Rendering| integration of volume rendering in Slicer 3]] and [http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques| new volume rendering techniques] for details.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan </h1><br />
Discuss which further efforts have to be taken to get a better usability of volume rendering (How can mapping functions be edited more intuitive, what are good presets etc.)<br />
<br />
What are essential features for volume rendering in Slicer.<br />
<br />
What are difficulties, issues when using volume rendering in connection with other modules.<br />
<br />
How should a different rendering, GUI for DTI, label maps and gray scale volumes look like.<br />
<br />
Figure out how difficult it is to integrate CUDA or other rendering algorithms into VTK and Slicer.<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
====June 2007 Project Week====<br />
The work on this project started in August 2007.<br />
====Jan 2007 Project Half Week====<br />
We added additional usability features, including a vtkBoxWidget and a GUI for volume rendering of labelmaps. We could also improve performance issues and are working on adding scene snapshot functionality.<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
===References===</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=20837Slicer3:Volume Rendering2008-01-07T21:40:05Z<p>Andreas: </p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
*[http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques Cuda Support for 4D imaging]<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
* Use Cuda for 3D projection algorithm<br />
<br />
* Integrate [http://www.na-mic.org/Wiki/images/f/ff/Volumerenderer.h.txt code from MIST projects] into Slicer for higher software rendering performance<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.<br />
<br />
==Feature Requests==<br />
* Show cropping boundaries in slice view<br />
* Save cropping boundaries<br />
* Extend GUI for easier usability<br />
* Include scene snapshot functionality<br />
* Enhance functionality differentiation for DTI and label maps</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week_VolumeRendering&diff=207902008 Winter Project Week VolumeRendering2008-01-07T02:14:44Z<p>Andreas: </p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]<br />
|valign="top"|[[Image:AbdomenLung.jpg |thumb|320px|Volume Rendering, mapping functions optimized for lung]]<br />
|}<br />
<br />
__NOTOC__<br />
===Key Investigators===<br />
* Isomics: Steve Pieper<br />
* SPL/IGT: Benjamin Grauer, Andreas Freudling<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
Integration of interactive volume rendering into Slicer 3 using hardware and software based rendering techniques.<br />
<br />
Improve the existing framework using new algorithms / frameworks like [http://en.wikipedia.org/wiki/CUDA| CUDA] or other rendering algorithms.<br />
<br />
Use volume rendering for 4D IGT.<br />
<br />
See [[Slicer3:Volume_Rendering| integration of volume rendering in Slicer 3]] and [http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques| new volume rendering techniques] for details.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan </h1><br />
Discuss which further efforts have to be taken to get a better usability of volume rendering (How can mapping functions be edited more intuitive, what are good presets etc.)<br />
<br />
What are essential features for volume rendering in Slicer.<br />
<br />
What are difficulties, issues when using volume rendering in connection with other modules.<br />
<br />
How should a different rendering, GUI for DTI, label maps and gray scale volumes look like.<br />
<br />
Figure out how difficult it is to integrate CUDA or other rendering algorithms into VTK and Slicer.<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
====June 2007 Project Week====<br />
The work on this project started in August 2007.<br />
====Jan 2007 Project Half Week====<br />
<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
<br />
===References===</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week_VolumeRendering&diff=207842008 Winter Project Week VolumeRendering2008-01-07T02:09:38Z<p>Andreas: </p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]<br />
|valign="top"|[[Image:AbdomenLung.jpg |thumb|320px|Volume Rendering, mapping functions optimized for lung]]<br />
|}<br />
<br />
__NOTOC__<br />
===Key Investigators===<br />
* Isomics: Steve Pieper<br />
* SPL/IGT: Benjamin Grauer, Andreas Freudling<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
Integration of interactive volume rendering into Slicer 3 using hardware and software based rendering techniques.<br />
<br />
Improve the existing framework using new algorithms / frameworks like [http://en.wikipedia.org/wiki/CUDA| CUDA] or other rendering algorithms.<br />
<br />
Use volume rendering for 4D IGT.<br />
<br />
See [[Slicer3:Volume_Rendering| integration of volume rendering in Slicer 3]] and [http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques| new volume rendering techniques] for details.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan </h1><br />
Discuss which further efforts have to be taken to get a better usability of volume rendering (How can mapping functions be edited more intuitive, what are good presets etc.)<br />
<br />
What are essential features for volume rendering in Slicer.<br />
<br />
What are difficulties, issues when using volume rendering in connection with other modules.<br />
<br />
Figure out how difficult it is to integrate CUDA or other rendering algorithms into VTK and Slicer.<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
====June 2007 Project Week====<br />
The work on this project started in August 2007.<br />
====Jan 2007 Project Half Week====<br />
<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
<br />
===References===</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week_VolumeRendering&diff=207822008 Winter Project Week VolumeRendering2008-01-07T02:07:17Z<p>Andreas: </p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]<br />
|valign="top"|[[Image:AbdomenLung.jpg |thumb|320px|Volume Rendering, mapping functions optimized for lung]]<br />
|}<br />
<br />
__NOTOC__<br />
===Key Investigators===<br />
* Isomics: Steve Pieper<br />
* SPL/IGT: Benjamin Grauer, Andreas Freudling<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
Integration of interactive volume rendering into Slicer 3 using hardware and software based rendering techniques.<br />
<br />
Improve the existing framework using new algorithms / frameworks like [http://en.wikipedia.org/wiki/CUDA| CUDA] or other rendering algorithms.<br />
<br />
Use volume rendering for 4D IGT.<br />
<br />
See [[Slicer3:Volume_Rendering| integration of volume rendering in Slicer 3]] and [http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques| new volume rendering techniques] for details.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan </h1><br />
Discuss which further efforts have to be taken to get a better usability of volume rendering (How can mapping functions be edited more intuitive etc.)<br />
<br />
What are essential features for volume rendering in Slicer.<br />
<br />
What are difficulties, issues when using volume rendering in connection with other modules.<br />
<br />
(Figure out how difficult it is to integrate CUDA or other rendering algorithms into VTK and Slicer.)<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
====June 2007 Project Week====<br />
The work on this project started in August 2007.<br />
====Jan 2007 Project Half Week====<br />
<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
<br />
===References===</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week&diff=190942008 Winter Project Week2007-12-12T02:40:09Z<p>Andreas: /* NA-MIC Kit - Slicer 3 */</p>
<hr />
<div>Back to [[Project Events]], [[AHM_2008]], [[Events]]<br />
<br />
== Projects ==<br />
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]<br />
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]<br />
<br />
Please note that we would like to have four clinical application focused parallel tracks at the meeting, each corresponding to a DBP problem. <br />
<br />
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br />
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br />
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br />
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br />
<br />
<br />
<br />
===Structural Analysis===<br />
#DBP Analysis of Brain Lesions in Lupus: [[2008_Winter_Project_Week:Lesions|Lesions]], Towards an end to end lesion analysis feature in Slicer3 (Mark Scully, Jeremy, Brad, Marcel Prastawa, others)<br />
#Groupwise Registration and Atlas Building (Brad, Serdar?, Casey) [[2008_Winter_Project_Week_GroupwiseReg|'''Template''']]<br />
# Cortical thickness analysis of pediatric brains (Clement Vachet, Martin Styner), [[DBP2:UNC:Cortical_Thickness_Roadmap | Roadmap]]<br />
# [[2008_Winter_Project_Week:Prostate_Segmentation|Prostate Segmentation]], (Yi Gao, Ponnappan Arumuganainar, John Melonakos, Allen Tannenbaum, Gabor Fichtinger)<br />
# Dorsolateral Prefrontal Cortex [[DBP2:Harvard:Brain_Segmentation_Roadmap|Segmentation]] (Marek, Sylvain, John, Brad, Polina)<br />
<br />
===Diffusion Image Analysis===<br />
#Incorporating DTI data into entropy-based particle system for cortical correspondence (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)<br />
#[[2008_Winter_Project_Week:Population_DTI|Integrating population based DTI tools into NAMIC Kit]] (Casey Goodlett)<br />
#[[2008_Winter_Project_Week:Population_DTI_Application|Application of population based DTI tools to Schizophrenia]] (Casey Goodlett, Marek Kubicki)<br />
#Stochastic tractography of the arcuate fasciculus in schizophrenia (Marek Kubicki, Tri Ngo, Doug Markant)<br />
# [[2008_Winter_Project_Week:Geodesic_Tractography_Segmentation|Geodesic Tractography Segmentation]], (John Melonakos, Allen Tannenbaum, Core2 Slicer3ist, Marek Kubicki)<br />
#Fluid Mechanics Based DTI Tractography (Nathan Hageman)<br />
<br />
===Image Guided Therapy===<br />
#IGSTK-Slicer (Liu, w. Georgetown team, Hata, Tokuda) '''NA-MIC supplement''' [[NA-MIC_NCBC_Collaboration:An_Integrated_System_for_Image-Guided_Radiofrequency_Ablation_of_Liver_Tumors || Description]]<br />
#Japanese Intelligent Surgical Instrument Project (Hata, Chinzei, Hong)<br />
#Robotic Prostate Interventions (Fichtinger, Gobbi, Csoma) [[NA-MIC_NCBC_Collaboration:Robotic_Prostate_Interventions || Description]]<br />
<br />
===NA-MIC Kit - Slicer 3===<br />
<br />
#MRML Scenes for the Execution Model including Transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)<br />
#Unstructured Grids and Mesh Support(Curt, Nicole, Alex, Steve, Will, Vince, Bob O'Bara)<br />
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith)<br />
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca, Steve)<br />
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)<br />
#Drafting Human Interface and Slicer Style Guidelines (Wendy,Sebastien)<br />
#Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith, Padma, Martin Styner)<br />
#Revisit - ROIs in Slicer3 (Wendy, Jim, Nicole, Steve, Ron)<br />
#[[2008_Winter_Project_Week_VolumeRendering|Volume rendering]] (Andy Freudling, Steve Pieper, Grauer) <br />
#Stereo Displays (Katharina, Curt)<br />
#3D W Widgets and Picking (Will, Nicole, Curt, Kiran, Nicole)<br />
#MRML support for out of core processing with fMRI and DTI as use cases (Steve, Jim, Wendy, Alex, Will)<br />
#[http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake] Integration (Dan Marcus, Steve, Stephen, Jeff, Julien)<br />
#KWWidgets Roadmap (Sebastien, Wendy, Katie)<br />
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)<br />
<br />
===External Collaborations===<br />
#Finite Element Meshing into NA-MIC [Univ. of Iowa] (Nicole, Vince, Kiran, Steve, Brad, Curt)<br />
#Evaluating NA-MIC Tools for Small Animal Imaging Workflows [NCI] (Curt, Jack Collins, Killian)<br />
#[[2008_Winter_Project_Week:GoFigure |'''GoFigure''']] High-Level Microscopy Image analysis Application and Algorithms [CalTech-Harvard Medical School] (Alex. G, Sean Megason, Arnaud Gelas?)<br />
#microSlicer3:Doing microscopy image analysis with Slicer3[Ohio State U](Kishore M., Raghu M.), NAMIC(Brad D.,Stephen A., Steve P.)<br />
#fmri image analysis with Slicer 3[Ohio State U](Firdaus J.,Raghu M.), NAMIC [Luis I.,Steve P., Wendy P.]<br />
<br />
===Non-Medical Collaborations===<br />
<br />
== Dates.Venue.Registration ==<br />
<br />
'''Dates:''' <br />
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''. <br />
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.<br />
<br />
'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.<br />
<br />
<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big><br />
<br />
<br />
Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]<br />
<br />
([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br />
<br />
===Introduction to NA-MIC Project Week===<br />
<br />
Please read the introduction to these events [[Project_Events#Introduction|here]].<br />
<br />
=== Agenda===<br />
<br />
[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]<br />
<br />
=== Preparation ===<br />
<br />
# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]<br />
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]<br />
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]<br />
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]<br />
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]<br />
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)<br />
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# By 3pm ET on Jan 3, 2008: [[2008_Winter_Project_Week_Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
<br />
== Previous Project Events ==<br />
<br />
A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week_VolumeRendering&diff=189922008 Winter Project Week VolumeRendering2007-12-10T15:20:49Z<p>Andreas: </p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]<br />
|valign="top"|[[Image:AbdomenLung.jpg |thumb|320px|Volume Rendering, mapping functions optimized for lung]]<br />
|}<br />
<br />
__NOTOC__<br />
===Key Investigators===<br />
* Isomics: Steve Pieper<br />
* SPL/IGT: Benjamin Grauer, Andreas Freudling<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
Integration of interactive volume rendering into Slicer 3 using hardware and software based rendering techniques.<br />
<br />
Improve the existing framework using new algorithms / frameworks like [http://en.wikipedia.org/wiki/CUDA| CUDA] or other rendering algorithms.<br />
<br />
Use volume rendering for 4D IGT.<br />
<br />
See [[Slicer3:Volume_Rendering| integration of volume rendering in Slicer 3]] and [http://www.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT#Volume_Rendering_Techniques| new volume rendering techniques] for details.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan </h1><br />
Figure out how difficult it is to integrate CUDA or other rendering algorithms into VTK and Slicer.<br />
<br />
Discuss which further efforts have to be taken to get a better usability of volume rendering (How can mapping functions be edited more intuitive etc.)<br />
<br />
What are essential features for volume rendering in Slicer.<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
====June 2007 Project Week====<br />
The work on this project started in August 2007.<br />
====Jan 2007 Project Half Week====<br />
<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
<br />
===References===</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week_VolumeRendering&diff=189902008 Winter Project Week VolumeRendering2007-12-10T15:13:49Z<p>Andreas: /* Key Investigators */</p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]<br />
|valign="top"|[[Image:AbdomenLung.jpg |thumb|320px|Volume Rendering, mapping functions optimized for lung]]<br />
|}<br />
<br />
__NOTOC__<br />
===Key Investigators===<br />
* Isomics: Steve Pieper<br />
* SPL/IGT: Benjamin Grauer, Andreas Freudling<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
Integration of interactive volume rendering into Slicer 3 using hardware and software based rendering techniques.<br />
<br />
Improve the existing framework using new algorithms / frameworks like [http://en.wikipedia.org/wiki/CUDA| CUDA] or <br />
<br />
Use volume rendering for 4D IGT.<br />
<br />
See [[Slicer3:Volume_Rendering| Project Page]] for more details.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan </h1><br />
Figure out how difficult it is to integrate CUDA or ... into VTK and Slicer.<br />
<br />
Discuss which further efforts have to be taken to get a better usability of volume rendering (How can mapping functions be edited more intuitive etc.)<br />
<br />
What are essential features for volume rendering in Slicer.<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
====June 2007 Project Week====<br />
The work on this project started in August 2007.<br />
====Jan 2007 Project Half Week====<br />
<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
<br />
===References===</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week_VolumeRendering&diff=189872008 Winter Project Week VolumeRendering2007-12-10T15:09:31Z<p>Andreas: </p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]<br />
|valign="top"|[[Image:AbdomenLung.jpg |thumb|320px|Volume Rendering, mapping functions optimized for lung]]<br />
|}<br />
<br />
__NOTOC__<br />
===Key Investigators===<br />
* Insomics: Steve Pieper<br />
* SPL/IGT: Benjamin Grauer, Andreas Freudling<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
Integration of interactive volume rendering into Slicer 3 using hardware and software based rendering techniques.<br />
<br />
Improve the existing framework using new algorithms / frameworks like [http://en.wikipedia.org/wiki/CUDA| CUDA] or <br />
<br />
Use volume rendering for 4D IGT.<br />
<br />
See [[Slicer3:Volume_Rendering| Project Page]] for more details.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan </h1><br />
Figure out how difficult it is to integrate CUDA or ... into VTK and Slicer.<br />
<br />
Discuss which further efforts have to be taken to get a better usability of volume rendering (How can mapping functions be edited more intuitive etc.)<br />
<br />
What are essential features for volume rendering in Slicer.<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
====June 2007 Project Week====<br />
The work on this project started in August 2007.<br />
====Jan 2007 Project Half Week====<br />
<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
<br />
===References===</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week_VolumeRendering&diff=189862008 Winter Project Week VolumeRendering2007-12-10T13:45:01Z<p>Andreas: </p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]<br />
|valign="top"|[[Image:AbdomenLung.jpg |thumb|320px|Volume Rendering, mapping functions optimized for lung]]<br />
|}<br />
<br />
__NOTOC__<br />
===Key Investigators===<br />
* Insomics: Steve Pieper<br />
* SPL/IGT: Benjamin Grauer, Andreas Freudling<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
Integration of interactive volume rendering into Slicer 3 using hardware and software based rendering techniques.<br />
<br />
Improve the existing framework using new algorithms / frameworks like [http://en.wikipedia.org/wiki/CUDA| CUDA] or <br />
<br />
Use volume rendering for 4D IGT.<br />
<br />
See [[Slicer3:Volume_Rendering| Project Page]] for more details.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan </h1><br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
====June 2007 Project Week====<br />
The work on this project started in August 2007.<br />
====Jan 2007 Project Half Week====<br />
<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
<br />
===References===</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week_VolumeRendering&diff=189852008 Winter Project Week VolumeRendering2007-12-10T13:29:10Z<p>Andreas: </p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]<br />
|valign="top"|[[Image:AbdomenLung.jpg |thumb|320px|Volume Rendering, mapping functions optimized for lung]]<br />
|}<br />
<br />
__NOTOC__<br />
===Key Investigators===<br />
* Insomics: Steve Pieper<br />
* SPL/IGT: Benjamin Grauer, Andreas Freudling<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
<br />
See [[Slicer3:Volume_Rendering| Project Page]] for more details.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan </h1><br />
<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
====June 2007 Project Week====<br />
The work on this project started in August 2007.<br />
====Jan 2007 Project Half Week====<br />
<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
<br />
===References===</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week_VolumeRendering&diff=189842008 Winter Project Week VolumeRendering2007-12-10T13:17:16Z<p>Andreas: New page: {| |Return to [[2008_Winter_Project_Week ]] |valign="top"|The Cingulum Bundle Anchor Tract |} __...</p>
<hr />
<div>{|<br />
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2008_Winter_Project_Week]] ]]<br />
|valign="top"|[[Image:Case24-coronal-tensors-edit.png |thumb|320px|The Cingulum Bundle Anchor Tract]]<br />
|}<br />
<br />
__NOTOC__<br />
===Key Investigators===<br />
* Insomics: Steve Pieper<br />
* SPL/IGT: Benjamin Grauer, Andreas Freudling<br />
<br />
<div style="margin: 20px;"><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Objective</h1><br />
We have developed techniques for finding the optimal geodesic path (or anchor tract) between two regions of interest in DWMRI data.<br />
<br />
The objectives of this project are to port the Fast Sweeping and optimal geodesic path tractography code to ITK as well as the code to provide for volumetric segmentation of DW-MRI data.<br />
<br />
See our [[Algorithm:GATech:Finsler_Active_Contour_DWI| Project Page]] for more details.<br />
<br />
</div><br />
<br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<br />
<h1>Approach, Plan </h1><br />
Our approach is described by the references below. Our challenge is to build the ITK infrastructure (such as new ITK iterators) to support this algorithm. Our main purpose at the Project Week is to collaborate on new algorithms and clinical data to provide the best solutions for our DBP partners.<br />
</div><br />
<br />
<div style="width: 40%; float: left;"><br />
<br />
<h1>Progress</h1><br />
<br />
====June 2007 Project Week====<br />
The work on this project started in August 2007.<br />
====Jan 2007 Project Half Week====<br />
<br />
<br />
</div><br />
<br />
<br style="clear: both;" /><br />
<br />
</div><br />
<br />
<br />
===References===</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week&diff=189052008 Winter Project Week2007-12-07T19:21:08Z<p>Andreas: /* NA-MIC Kit - Slicer 3 */</p>
<hr />
<div>Back to [[Project Events]], [[AHM_2008]], [[Events]]<br />
<br />
== Projects ==<br />
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]<br />
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]<br />
<br />
Please note that we would like to have four clinical application focused parallel tracks at the meeting, each corresponding to a DBP problem. <br />
<br />
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br />
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br />
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br />
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br />
<br />
<br />
<br />
===Structural Analysis===<br />
#DBP Analysis of Brain Lesions in Lupus: [[2008_Winter_Project_Week:Lesions|Lesions]], Towards an end to end lesion analysis feature in Slicer3 (Mark Scully, Jeremy, Brad, Marcel Prastawa, others)<br />
#Groupwise Registration and Atlas Building (Brad, Serdar?, Casey) [[2008_Winter_Project_Week_GroupwiseReg|'''Template''']]<br />
# Cortical thickness analysis of pediatric brains (Clement Vachet, Martin Styner), [[DBP2:UNC:Cortical_Thickness_Roadmap | Roadmap]]<br />
<br />
===Diffusion Image Analysis===<br />
#Incorporating DTI data into entropy-based particle system for cortical correspondence (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)<br />
#Integrating population based DTI tools into NAMIC Kit (Casey Goodlett) [[2008_Winter_Project_Week:Population_DTI|'''Template''']]<br />
#Application of population based DTI tools to Schizophrenia (Casey Goodlett, Marek Kubicki)<br />
#Stochastic tractography of the arcuate fasciculus in schizophrenia (Marek Kubicki, Tri Ngo, Doug Markant)<br />
<br />
===Image Guided Therapy===<br />
#IGSTK-Slicer (Liu, w. Georgetown team, Hata, Tokuda) '''NA-MIC supplement''' [[NA-MIC_NCBC_Collaboration:An_Integrated_System_for_Image-Guided_Radiofrequency_Ablation_of_Liver_Tumors || Description]]<br />
#Japanese Intelligent Surgical Instrument Project (Hata, Chinzei, Hong)<br />
#Robotic Prostate Interventions (Fichtinger, Gobbi, Csoma) [[NA-MIC_NCBC_Collaboration:Robotic_Prostate_Interventions || Description]]<br />
<br />
===NA-MIC Kit - Slicer 3===<br />
<br />
#MRML Scenes for the Execution Model including Transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)<br />
#Unstructured Grids and Mesh Support(Curt, Nicole, Alex, Steve, Will, Vince, Bob O'Bara)<br />
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith)<br />
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca, Steve)<br />
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)<br />
#Drafting Human Interface and Slicer Style Guidelines (Wendy,Sebastien)<br />
#Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith, Padma, Martin Styner)<br />
#Revisit - ROIs in Slicer3 (Wendy, Jim, Nicole, Steve, Ron)<br />
#[[2008_Winter_Project_Week_VolumeRendering|'''Volume rendering ''']] (Andy Freudling, Steve Pieper, Grauer) <br />
#Stereo Displays (Katharina, Curt)<br />
#3D W Widgets and Picking (Will, Nicole, Curt, Kiran, Nicole)<br />
#MRML support for out of core processing with fMRI and DTI as use cases (Steve, Jim, Wendy, Alex, Will)<br />
#[http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake] Integration (Dan Marcus, Steve, Stephen, Jeff, Julien)<br />
#KWWidgets Roadmap (Sebastien, Wendy, Katie)<br />
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)<br />
<br />
===External Collaborations===<br />
#Finite Element Meshing into NA-MIC [Univ. of Iowa] (Nicole, Vince, Kiran, Steve, Brad, Curt)<br />
#Evaluating NA-MIC Tools for Small Animal Imaging Workflows [NCI] (Curt, Jack Collins, Killian)<br />
# [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:3D+t_Cells_Lineage:GoFigure GoFigure] High-Level Microscopy Image analysis Application and Algorithms [CalTech-Harvard Medical School] (Alex. G, Sean Megason, Arnaud Gelas?)<br />
#microSlicer3:Doing microscopy image analysis with Slicer3[Ohio State U](Kishore M., Raghu M.), NAMIC(Brad D.,Stephen A., Steve P.)<br />
#fmri image analysis with Slicer 3[Ohio State U](Firdaus J.,Raghu M.), NAMIC [Luis I.,Steve P., Wendy P.]<br />
<br />
===Non-Medical Collaborations===<br />
<br />
== Dates.Venue.Registration ==<br />
<br />
'''Dates:''' <br />
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''. <br />
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.<br />
<br />
'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.<br />
<br />
<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big><br />
<br />
<br />
Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]<br />
<br />
([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br />
<br />
===Introduction to NA-MIC Project Week===<br />
<br />
Please read the introduction to these events [[Project_Events#Introduction|here]].<br />
<br />
=== Agenda===<br />
<br />
[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]<br />
<br />
=== Preparation ===<br />
<br />
# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]<br />
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]<br />
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]<br />
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]<br />
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]<br />
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)<br />
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# By 3pm ET on Jan 3, 2008: [[2008_Winter_Project_Week_Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
<br />
== Previous Project Events ==<br />
<br />
A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].</div>Andreashttps://www.na-mic.org/w/index.php?title=2008_Winter_Project_Week&diff=189042008 Winter Project Week2007-12-07T19:20:05Z<p>Andreas: /* NA-MIC Kit - Slicer 3 */</p>
<hr />
<div>Back to [[Project Events]], [[AHM_2008]], [[Events]]<br />
<br />
== Projects ==<br />
*2008 Project Week [[2008_Winter_Project_Week_Template|'''Template''']]<br />
*[[2007_Programming/Project_Week_MIT#Projects|Last Year's Projects as a reference]]<br />
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]<br />
<br />
Please note that we would like to have four clinical application focused parallel tracks at the meeting, each corresponding to a DBP problem. <br />
<br />
#[[DBP2:Harvard|Velocardio Facial Syndrome (VCFS) as a Genetic Model for Schizophrenia]] (Harvard: Marek Kubicki, PI)<br />
#[[DBP2:UNC|Longitudinal MRI Study of Early Brain Development in Autism]] (UNC: Heather Hazlett, Joseph Piven, PI)<br />
#[[DBP2:MIND|Analysis of Brain Lesions in Lupus]] (MIND/UNM: Jeremy Bockholt, Charles Gasparovic PI)<br />
#[[DBP2:JHU|Segmentation and Registration Tools for Robotic Prostate Intervention]] (Queens/JHU: Gabor Fichtinger, PI)<br />
<br />
<br />
<br />
===Structural Analysis===<br />
#DBP Analysis of Brain Lesions in Lupus: [[2008_Winter_Project_Week:Lesions|Lesions]], Towards an end to end lesion analysis feature in Slicer3 (Mark Scully, Jeremy, Brad, Marcel Prastawa, others)<br />
#Groupwise Registration and Atlas Building (Brad, Serdar?, Casey) [[2008_Winter_Project_Week_GroupwiseReg|'''Template''']]<br />
# Cortical thickness analysis of pediatric brains (Clement Vachet, Martin Styner), [[DBP2:UNC:Cortical_Thickness_Roadmap | Roadmap]]<br />
<br />
===Diffusion Image Analysis===<br />
#Incorporating DTI data into entropy-based particle system for cortical correspondence (Ipek Oguz, Josh Cates, Tom Fletcher, Martin Styner)<br />
#Integrating population based DTI tools into NAMIC Kit (Casey Goodlett) [[2008_Winter_Project_Week:Population_DTI|'''Template''']]<br />
#Application of population based DTI tools to Schizophrenia (Casey Goodlett, Marek Kubicki)<br />
#Stochastic tractography of the arcuate fasciculus in schizophrenia (Marek Kubicki, Tri Ngo, Doug Markant)<br />
<br />
===Image Guided Therapy===<br />
#IGSTK-Slicer (Liu, w. Georgetown team, Hata, Tokuda) '''NA-MIC supplement''' [[NA-MIC_NCBC_Collaboration:An_Integrated_System_for_Image-Guided_Radiofrequency_Ablation_of_Liver_Tumors || Description]]<br />
#Japanese Intelligent Surgical Instrument Project (Hata, Chinzei, Hong)<br />
#Robotic Prostate Interventions (Fichtinger, Gobbi, Csoma) [[NA-MIC_NCBC_Collaboration:Robotic_Prostate_Interventions || Description]]<br />
<br />
===NA-MIC Kit - Slicer 3===<br />
<br />
#MRML Scenes for the Execution Model including Transforms (Jim Miller, Brad Davis, Nicole Aucoin, Alex Yarmarkovich, Steve Pieper)<br />
#Unstructured Grids and Mesh Support(Curt, Nicole, Alex, Steve, Will, Vince, Bob O'Bara)<br />
#[[2008_Winter_Project_Week:PythonSupport |Python Support in Slicer 3]] (Luca, Bryan Smith)<br />
#[[2008_Winter_Project_Week:MRMLTransformHardening |Transform hardening in MRML]] (Luca, Steve)<br />
#[[2008_Winter_Project_Week:CPack |CPack]], CTest, CMake infrastructure Improvements(Katie, Steve, Bill Hoffman, Sebastien)<br />
#Drafting Human Interface and Slicer Style Guidelines (Wendy,Sebastien)<br />
#Shape Descriptor Functions for Dendritic Spine Morphometrics (Bryan Smith, Padma, Martin Styner)<br />
#Revisit - ROIs in Slicer3 (Wendy, Jim, Nicole, Steve, Ron)<br />
#Volume rendering (Andy Freudling, Steve Pieper, Grauer) [[2008_Winter_Project_Week_VolumeRendering|'''Template''']]<br />
#Stereo Displays (Katharina, Curt)<br />
#3D W Widgets and Picking (Will, Nicole, Curt, Kiran, Nicole)<br />
#MRML support for out of core processing with fMRI and DTI as use cases (Steve, Jim, Wendy, Alex, Will)<br />
#[http://www.xnat.org XNAT], [http://www.slicer.org Slicer], [http://www.Xcede.org XCEDE], [http://www.batchmake.org Batchmake] Integration (Dan Marcus, Steve, Stephen, Jeff, Julien)<br />
#KWWidgets Roadmap (Sebastien, Wendy, Katie)<br />
#Circuit Annotation Capability (for example drawing arrows above regions that are connected functionally, structurally, etc), (Mark Scully, others)<br />
<br />
===External Collaborations===<br />
#Finite Element Meshing into NA-MIC [Univ. of Iowa] (Nicole, Vince, Kiran, Steve, Brad, Curt)<br />
#Evaluating NA-MIC Tools for Small Animal Imaging Workflows [NCI] (Curt, Jack Collins, Killian)<br />
# [http://www.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:3D+t_Cells_Lineage:GoFigure GoFigure] High-Level Microscopy Image analysis Application and Algorithms [CalTech-Harvard Medical School] (Alex. G, Sean Megason, Arnaud Gelas?)<br />
#microSlicer3:Doing microscopy image analysis with Slicer3[Ohio State U](Kishore M., Raghu M.), NAMIC(Brad D.,Stephen A., Steve P.)<br />
#fmri image analysis with Slicer 3[Ohio State U](Firdaus J.,Raghu M.), NAMIC [Luis I.,Steve P., Wendy P.]<br />
<br />
===Non-Medical Collaborations===<br />
<br />
== Dates.Venue.Registration ==<br />
<br />
'''Dates:''' <br />
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 10th'''. <br />
* Project Activities will be held rest of the week between '''Monday, January 7th and Friday, January 11th'''.<br />
<br />
'''Venue:''' The venue for the meeting is [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ Marriot City Center, Salt Lake City, Utah] Mariott City Center, Salt Lake City, Utah. [http://marriott.com/property/meetingsandevents/floorplans/slccc (Floorplan)]. To reserve rooms at the meeting rate of $129/night, please call the hotel at 1-801-961-8700 or 1-866-961-8700 (toll free) and mention that you are attending the NAMIC meeting. Please note that we do need attendees to use this hotel in order to not incur additional charges for the use of conference rooms.<br />
<br />
<big> '''Registration:''' We are charging a registration fee to all participants. The fee covers the costs of the facilities and food provided. In order to keep the fee low, we need to get a sufficient number of hotel nights by our participants. See above for more on this. Please click [http://www.sci.utah.edu/namic2008/registration.html '''here'''] for online registration. This registration must be completed by Friday, December 14, 2007. </big><br />
<br />
<br />
Please note that this information can also be found [[AHM_2008#Dates.Venue.Registration|here.]]<br />
<br />
([[Project Week Logistics Checklist|This is a checklist for the onsite planning items]])<br />
<br />
===Introduction to NA-MIC Project Week===<br />
<br />
Please read the introduction to these events [[Project_Events#Introduction|here]].<br />
<br />
=== Agenda===<br />
<br />
[[AHM_2008#Agenda|Agenda for AHM 2008 and Project Week]]<br />
<br />
=== Preparation ===<br />
<br />
# Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]<br />
# [[Engineering:TCON_2007#2007-11-29|November 29, 2007: Kickoff TCON#1 (w/ NA-MIC Engeering Core only) to discuss Projects and Assign/Verify Teams]]<br />
# [[Engineering:TCON_2007#2007-12-06|December 6, 2007: TCON#2 with all participants to Assign/Verify Teams]]<br />
# [[Engineering:TCON_2007#2007-12-13|December 13, 2007: TCON#3 with Breakout Session owners to review agendas]]<br />
# [[Engineering:TCON_2007#2007-12-13|December 20, 2007: TCON#4 to discuss outstanding projects and teams]]<br />
# [[Engineering:TCON_2007#2008-01-03|January 3, 2008: TCON#5 to discuss outstanding projects and teams]]<br />
# December 20, 2007: Create a Wiki page per project (the participants must do this, hopefully jointly)<br />
# January 3, 2008: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)<br />
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]<br />
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)<br />
## Gather test images in any of the Data sharing resources we have (e.g. the BIRN). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)<br />
## Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)<br />
# By 3pm ET on Jan 3, 2008: [[2008_Winter_Project_Week_Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.<br />
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...<br />
<br />
== Previous Project Events ==<br />
<br />
A history of all the programming/project events in NA-MIC is available by following [[Project Events|this link]].</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:VisualBlog&diff=18485Slicer3:VisualBlog2007-12-02T22:40:48Z<p>Andreas: </p>
<hr />
<div>__NOTOC__<br />
<br />
<gallery caption="2007" widths="200px" perrow="4"><br />
Image:Arcuatetractvolume2.png|'''Image from Tri Ngo and Steve Pieper, November 2007'''<br>Display of Stochastic Tractography results using volume rendering inside Slicer3. See [[Algorithm:MIT:DTI_StochasticTractography|'''here''']] for more information.<br />
Image:VolumeRenderingBoneDetection.png|'''Image from Andy Freudling on October 2007'''<br>First results of volume rendering inside Slicer3. See [[Slicer3:Volume_Rendering|'''here''']] for more information.<br />
Image:sirp1.png|'''Image from wjp on Wednesday, October 24, 2007'''<br>QueryAtlas visualizing combined morphology and functional analyses generated by running FreeSurfer and a FIPS pipeline on a BIRN phaseII SIRP dataset. Interactive annotations (on mouse-over) are being translated thru Slicer's controlled vocabulary.<br />
Image:SlicerReformat.png|'''Image from Jim on Saturday, September 15, 2007'''<br>Slice viewers can be used to specify oblique reformats using the 'Reformat' orientation (instead of axial, coronal, sagittal) and CTRL-Right-Button-Move<br>(subject to change).<br />
Image:Livers.png|'''Image from Dirk, Matthew, Jim, and Steve on Monday, August 13, 2007'''<br>A new label map smoothing tool has been added to help with our [[NA-MIC_Collaborations#Children.27s_Pediatric_Cardiology_Collaboration_with_SCI.2FSPL.2FNortheastern | collaboration with Children's Hospital Boston, SCI at University of Utah and Northeastern University]]. The unfiltered labelmap is shown in blue, and the filtered results are shown in peach.<br />
Image:Editbox.png|'''Image from Steve and Wendy on Monday, August 6, 2007'''<br>New Editor functionality, with EditBox which is invoked using the F1 key (will soon be moved to the space bar).<br />
Image:EMSegment31Structures.png|'''Image from Brad and Kilian on Wednesday, June, 21, 2007'''<br>Example of [[Projects/Structural/2007_Project_Week_EMSegmentation_Validation | EMSegmenter in Slicer3]]<br />
Image:ConnectivityMap.png|'''Image from pieper on Friday, June, 9, 2007'''<br>Slicer3 Module for [[Algorithm:MIT:DTI_StochasticTractography | Stochastic Tractography]] from MIT (Ngo, Golland) and BWH (Westin, Kubicki).<br />
Image:kwmeshvisu-slicer-logo.png|'''Image from ipek on Wednesday, June, 6, 2007'''<br>UNC Logo in Slicer3 for KWMeshVisu (Ipek Oguz, Martin Styner).<br />
Image:CineDisplayDesigns.png|'''Image from wjp on Wednesday, May, 30, 2007'''<br>Design mockups for Slicer3's Cine Display interface (William Leue, Wendy Plesniak).<br />
Image:Atlas-2007-05-16.png|'''Image from pieper on Tuesday, May, 30, 2007'''<br>The SPL-PNL brain atlas loaded in Slicer3. Demonstrates model hierarchy and clipping.<br />
Image:EMSegmentation_Results_Screenshot.png|'''Image from davisb on Monday, April, 27, 2007'''<br>EMSegment screenshot---segmentation results and work-flow GUI<br />
Image:Mimx.png|'''Image from magnotta on Monday, April, 16, 2007'''<br>Mimx Logo in Slicer3 for VoxelMeshingModule<br />
Image:PythonMenu.png |'''Image from blezek on Tuesday, April, 10, 2007 at 8:00AM'''<br>Python incorporated into [[Slicer3:Python | Slicer]]. [[Slicer3:VisualBlog_Extension#Image from blezek on Tuesday, April, 10, 2007 at 8:00AM | More ...]]<br />
Image:ZoomWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM'''<br>New GUI elements: Shows a magnified view in the GUI panel of an area around the mouse in any Slice Window.<br />
Image:NavigationWindow.png|'''Image from wjp on Thursday, March 22, 2007 at 10:00AM'''<br>New GUI elements: Shows birds-eye-view of the scene relative to the outline of the 3D Viewer's window in the 'Manipulate 3D View' GUI panel.<br />
Image:Slicer3FirstTractography.png|'''Image from pieper on Tuesday, January 16, 2007 at 7:58PM'''<br>From Lauren, shows fiber tracts loaded from a file and with display properties controlled by the GUI.<br />
</gallery><br />
<gallery caption="2006" widths="200px" perrow="4"><br />
Image:S3GUI-12-29-06.png|'''Image from wjp on Friday, December 29, 2006 at 3:23PM'''<br>Module choose and navigation functionality integrated into the application toolbar to create more space for module GUIs on the side panel. Slice Controller widgets also updated to have more functionality available, a button to link and unlink their control, and an improved visual design.<br />
Image:S3GUIWithLogo.png|'''Image from wjp on Monday, November 28, 2006 at 6:40M'''<br>New 3D Slicer logo integrated with slicer GUI.<br />
Image:QueryAtlas-fBIRN-Slicer3-2006-10-23.png|'''Image from pieper on Thursday, October 26, 2006 at 1:54M'''<br>FreeSurfer structural data (cortical and subcortical segmentation) with fBIRN functional overlay, shown as part of Slicer3-based BIRN Query Atlas project.<br />
Image:Clipping.png|'''Image from pieper on Thursday, October 05, 2006 at 1:08PM'''<br>Clipping with the slice plane is now supported, along with thresholded image display.<br />
Image:FreeSurfer-Curvature-2006-09-08.png|'''Image from naucoin on Friday, September 08, 2006 at 12:14pm'''<br>The FreeSurfer colour lookup table has been added to the Slicer3 FreeSurfer Library. A curvature overlay file was loaded and displayed on bert/surf/lh.pial as loaded in via the Models module.<br />
Image:FreeSurfer-Annotation-2006-09-08-B.png|'''Image from naucoin on Friday, September 08, 2006 at 11:24am'''<br>The FreeSurfer scalar reader has been integrated as a Slicer 3 Library, and surfaces can be read via the Models module. Shot shows standard bert/surf/lh.pial plus a test script to load the annotation labels file.<br />
Image:Editor-module-prototype.png|'''Image from pieper on Tuesday, August 08, 2006 at 4:26PM'''<br>A number of things have come together to allow the new prototype editor module. [[Slicer3:VisualBlog_Extension#Image from pieper on Tuesday, August 08, 2006 at 4:26PM | More ...]]<br />
Image:Oblique-slice-test.png|'''Image from pieper on Friday, July 28, 2006 at 9:04AM'''<br>Test of making a non-orthogonal slice plane. This was created by manually setting the SliceToRAS matrix in the vtkMRMLSliceNode. GUI is not yet hooked up for oblique slices.<br />
Image:Single-pixel.png|'''Image from pieper on Thursday, July 27, 2006 at 5:21PM'''<br>Shows that a single pixel voxel in black is exactly bounded by a unit cube in RAS space. Also the blinking eye buttons for slice visiblility are hooked up and there is now a red-yellow-green color coding for the slice windows (carried over from slicer2).<br />
Image:Textured-slice-planes.png|'''Image from pieper on Thursday, July 13, 2006 at 4:49PM'''<br>Test of interactive slice textured plane control. Not yet eneabled through GUI, but driven by a [http://www.na-mic.org:8000/websvn/filedetails.php?repname=Slicer3&amp;path=%2Ftrunk%2FBase%2FGUI%2FTesting%2FTestSliceModels.tcl&amp;rev=0&amp;sc=1 test script] that you can source into the console. [[Slicer3:VisualBlog_Extension#Image from pieper on Thursday, July 13, 2006 at 4:49PM | More ...]]<br />
Image:Slicer3-lung.png|'''Image from pieper on Tuesday, July 11, 2006 at 3:39PM'''<br>Example model read from vtk file and loaded in slicer3<br />
Image:Logo-widget.png|'''Image from pieper on Monday, July 03, 2006 at 3:35PM'''<br>Test of the new logo widget for adding module-specific watermark logos directly in the 3d view. Uses a vtkLogoWidget from VTK cvs head. Kitware is working on cmake support to notify developers when a VTK cvs update is needed. Once that is done, the logo code will be added to slicer3 svn.<br />
Image:Slicer3-pan-zoom-anno-2006-06-26.png|'''Image from pieper on Monday, June 26, 2006 at 10:38AM'''<br>New annotations and key bindings. Middle mouse to pan, right mouse to zoom.<br />
Image:Slicer3_command-line-median-filter-2006-06-21.png|'''Image by pieper on Wednesday, June 21, 2006 at 1:01PM'''<br>results of the command line median filter module<br />
Image:SlicerScreenShot7.png|'''Image by millerjv on Tuesday, June 20, 2006 at 4:37PM'''<br>{First command line module to export data, execute, and import data back into Slicer}<br />
Image:SlicerScreenShot5.png|'''Image by millerjv on Friday, June 16, 2006 at 11:15AM'''<br>{Command line module with an enumerated parameter as a radio button}<br />
Image:Slicer3ApplicationSettings.png|'''Image by millerjv on Wednesday, June 14, 2006 at 10:20AM'''<br>{Slicer applications settings panel showing the module search path}<br />
Image:SlicerScreenShot2.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:23PM'''<br>Another command line module example from Jim<br />
Image:SlicerScreenShot1.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:20PM'''<br>Example from Jim Miller showing the automatic GUI generation from XML collected from execution module commands<br />
Image:Slicer-sample-2006-06-13.png|'''Image from pieper on Tuesday, June 13, 2006 at 8:18PM'''<br>Example screen shot showing that there is a basic interface in place.<br />
</gallery><br />
<br><br />
<br />
<br />
== About the VisualBlog ==<br />
<br />
The VisualBlog is meant to be an easy place to upload screenshot so that both developers and outside observes can track the progress of the project.<br />
<br />
Many thanks to developers and users for contributing their images here.</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Developers&diff=18406Slicer3:Developers2007-11-29T19:51:55Z<p>Andreas: /* Slicer 3 Projects */</p>
<hr />
<div>{| class="toccolours" style="margin-right: 25px" align="right"<br />
! bgcolor="#ccccff" align="center" | Slicer3<br />
|-<br />
|<br />
[[Slicer3|Home]]<br />
|-<br />
|<br />
[[Slicer3:About|About]]<br />
|-<br />
|<br />
[[Slicer3:FAQ|FAQ]]<br />
|-<br />
|<br />
[[Slicer3:Status|Status]]<br />
|-<br />
|<br />
[[Slicer3:Downloads|Downloads]]<br />
|-<br />
|<br />
[[Slicer3:Documentation|Documentation]]<br />
|-<br />
|<br />
[[Slicer3:Community_Support|Community Support]]<br />
|-<br />
| '''Developers'''<br />
|-<br />
|<br />
[[Slicer3:Acknowledgements|Acknowledgements]]<br />
|-<br />
|<br />
[[Slicer3:Links|Links]]<br />
|}<br />
<br />
== Slicer 3 Overview ==<br />
[[Image:Slicer3LogoHorizontalBeta.png]]<br />
<br />
* For more details on the slicer architecture see: [[media:Slicer 3-beta-2007-04-16.ppt | Architecture Slides]] (updated April, 2007).<br />
* Highlights of the new architecture<br />
<br />
{|<br />
|[[Image:Slicer3-Architecture.jpg|thumb|200px]]<br />
|[[Image:Slicer3-Architecture-MRML.jpg|thumb|200px]]<br />
|[[Image:Slicer3-Architecture-Layers.jpg|200px|thumb]]<br />
|[[Image:ExecutionModelPlugins.png|200px|thumb]]<br />
|}<br />
<br />
== Information for Developers ==<br />
This section centrally locates many existing (and developing) wiki pages useful to Slicer3 developers. The content developed for the January 2007 AHM.<br />
<br />
=== Introduction to Slicer3 ===<br />
* [[Media:SlicerHistoricalTimeline.ppt | Slicer3 Historical Timeline]]<br />
* [[Slicer3:Status_Summary | Status overview]] and [http://slicerl.bwh.harvard.edu/tmp/slicer3-PreAHMBeta%20Demo/slicer3-PreAHMBeta.htm Demo]<br />
* Schematic of application interface & functionality: [[Media:GUIMap.png]]<br />
* Schematic of slice GUI: [[Media:SliceGUI.png ]]<br />
* [[Slicer3:Build_Instructions | Getting the software and troubleshooting]]<br />
* [[media:Slicer 3-beta-2007-01-10.ppt | Overall Architecture]] and [[Slicer3:Style|Slicer 3 Coding Style]]<br />
* [[Slicer3:Contributing_codes_to_Slicer3| Contributing codes to Slicer3]]<br />
<br />
=== Two module types (Command line and Interactive) ===<br />
* [[Slicer3:Execution_Model_Documentation | Command line modules and how to implement one]] (Jim and Bill) [[media:Slicer3-ExecutionModelJune2006.ppt| Intro]]<br />
*[[Slicer3:How_to_implement_an_Interactive_Module_GUI | How to implement an interactive module]] (wjp)<br />
<br />
=== MRML [http://www.na-mic.org/Wiki/images/e/e3/Slicer3_MRML.ppt MRML Slides](Alex) ===<br />
Medical Reality Modeling Language (MRML) is a language implemented as a type of XML document, with new tags defined to handle medical image data types such as volumes, models or coordinate transforms.<br />
<br />
* [[Slicer3:Data_Model#Creating_Custom_MRML_Node_Classes | Creating and using new MRML node types]] (Alex)<br />
* [[Slicer3:Data_Model#References_to_MRML_Nodes | Keeping references to MRML nodes ]] (Alex)<br />
* [[Slicer3:Data_Model#Undo/Redo_Mechanism | How undo/redo works, and how to enable it in your code]] (Alex)<br />
<br />
=== GUI ===<br />
* [[Slicer3:StatelessGUI | Keeping the GUI stateless]] (wjp)<br />
* [[Slicer3:EventBindings | Adding keyboard shortcuts]] (wjp)<br />
* [[Slicer3:Human_Interface_and_Style_Guide_for_Developers | GUI style guidelines]] (wjp)<br />
* [[Slicer3:Usability#User-centered_design_practice_for_3DSlicer | User-centered design practice]] (wjp)<br />
* [[Slicer3:Slicer3Brand | 3DSlicer's logo and visual communication guidelines]] (wjp)<br />
* [[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3 | Incorporating your group's logo and attributions]] (Jim)<br />
* [[Slicer3:GUI_Experiments | Some experiments/advanced techniques for developing slicer3 interfaces]] (Steve)<br />
<br />
=== Engineering ===<br />
* Tips for avoiding memory leaks<br />
** Current Practice (Steve)<br />
** [[Slicer3:Memory Management | Suggested change to SmartPointers]] (Jim)<br />
* Generating tests (Bill)<br />
* [[Slicer3:Testing | Setting up Testing]]<br />
* [[Slicer3:Launcher| The Launcher]]<br />
<br />
=== Documenting your module ===<br />
* As soon as the wiki page template is finalized, and the infrastructure is added to link to this wiki page from the "Help & Acknowledgment" panel in your module's GUI, we will ask developers to fill out a brief document describing your module and its use. Stay tuned for developments...<br />
<br />
=== Integrate Slicer3 into a development environment ===<br />
* [[Slicer3::Eclipse | Eclipse]] (keilhack)<br />
* [[Slicer3::MSVS200X | Microsoft Visual Studio 200x]]<br />
<br />
== Slicer 3 Projects ==<br />
<br />
Projects should correspond to the outstanding issues listed on the '''[[Slicer3:Status_Summary|Status Summary]]'''. Please refer to the '''[[Slicer3:FeatureRequests|Feature Requests]]''' from users when planning your implementations.<br />
<br />
''If your name is in bold, you are responsible for that aspect of the project''<br />
<br />
* '''[[Slicer3:Architecture/Features|Architecture/Features]]''' ('''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata)<br />
* '''[[Slicer3:Data_Model|Data Model / libMRML]]''' ('''Alex''', Steve)<br />
* '''[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]''' ('''Jim Miller''', Bill Lorensen)<br />
* '''[[Slicer3:Interface_Design|Interface Design and Usability ]]''' ('''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan)<br />
* '''[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]''' ('''Nicole''', Katie, Wendy, Mathieu)<br />
** [[Slicer3:DTMRI|DTMRI]]<nowiki>: </nowiki>Diffusion Images: '''Raul''', Tractography: '''Lauren''' [http://lmi.bwh.harvard.edu LMI]<br />
** [[Slicer3:Editor|Editor]]<nowiki>: </nowiki>'''Steve'''<br />
** [[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]<nowiki>: </nowiki>'''Nicole'''<br />
** [[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]<nowiki>: </nowiki>'''Haiying'''<br />
** [[Slicer3:EM|EMSegment Interface]]<nowiki>: </nowiki>'''Brad Davis'''<br />
** [[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]<nowiki>: </nowiki>'''Steve Pieper'''<br />
* '''[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]''' ('''Andy''', Katie)<br />
* '''[[Slicer3:Pipeline_Integration|Loni Pipeline Integration]]''' ('''Jags''')<br />
* '''[[Slicer3:Batchmake_Integration|Batchmake/GRID Integration]]''' ('''Stephen Aylward''')<br />
* '''[http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization Improvements to the registration framework]''' ('''Stephen Aylward''')<br />
* '''[[Slicer3:Python|Python Integration]]''' ('''Dan Blezek''')<br />
* '''[[Slicer3:Grid_Interface|Grid Integration]]''' ('''Jeff Grethe''', Neil)<br />
* '''[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]''' ('''Katie''')<br />
* '''[[Slicer3:ThreadingToolKit|Threading ToolKit]]''' ('''Dan Blezek, James Miller, Stephen Aylward''')<br />
* '''[[Slicer3:Volume Rendering |Volume Rendering]]''' ('''Andy''')<br />
* '''[[Slicer3:XNAT |XNAT Interface]]''' ('''Steve''', Wendy, Dan Marcus, Tim Olsen)<br />
* '''[[Slicer3:LDDMM |LDDMM Interface]]''' ('''Steve''', Anthony Kolasny)<br />
* '''[[Slicer3:Web Presence |Web Presence]]''' ('''Nicole Aucoin'''), Zack Galbreath<br />
* '''[[Slicer3:Loadable Modules |Loadable Modules]]''' ('''Alex Yarmarkovich'''), Steve Pieper<br />
* '''[[Slicer3:Gradient Editor |Gradient Editor]]''' ('''Kerstin''')<br />
<br />
== Slicer 3 Quick links to the Source code ==<br />
<br />
The Slicer3 svn repository:<br />
<br />
svn co http://www.na-mic.org/svn/Slicer3/trunk Slicer3<br />
<br />
Use [http://www.na-mic.org/ViewVC/index.cgi/ ViewVC to browse the repository]<br />
<br />
[[Engineering:SandBox|Instructions for NA-MIC svn]]<br />
<br />
[[Slicer3:Build_Instructions|Slicer3 build instructions]]<br />
<br />
[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Doxygen documentation for Slicer3].<br />
<br />
The [[Slicer3:VisualBlog|Slicer3 VisualBlog]] shows screenshots of slicer developments.<br />
<br />
Developers should follow the [[Slicer3:Style|Slicer 3 Coding Style]].<br />
<br />
[http://www.na-mic.org/Slicer3/Dashboard Slicer3 Dashboard]<br />
<br />
[http://na-mic.org/Mantis/main_page.php Slicer Bug Tracker]<br />
<br />
Discussion of slicer3 takes place on the slicer-devel@massmail.spl.harvard.edu list. To join developer's mailing list, send a request to: [mailto:slicer-devel-request@massmail.spl.harvard.edu slicer-devel-request@massmail.spl.harvard.edu] with the keyword ''subscribe'' as the subject. Or access the [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel slicer-devel archives and web administration interface].<br />
<br />
== Design Information ==<br />
<br />
May 23, 2006: [[Algorithms:Core1Visit_May06|Algorithm Core workshop.]]<br />
<br />
<br /> April 3, 2006: [[Media:Slicer_3-alpha-2006-04-03.ppt| Slicer 3 alpha]] technical powerpoint presentation.<br />
<br />
<br /><br />
<br />
= Events =<br />
<br />
== Upcoming ==<br />
<br />
=== Slicer3.0 ===<br />
<br />
* the first product release of Slicer3 is scheduled for the AHM in January of 2008<br />
* there will be a code freeze on Nov. 15 2007<br />
** if you want your module to be part of Slicer3.0 submit it by then<br />
** After that date, we will only accept bug fixes. It means that there will be no features added after the freeze in the main trunk.<br />
<br />
** Any people working on new features can do so in their own branch and they will be responsible for merging these back into the trunk after the freeze is lifted (at which point the release will be in a maintenance branch). <br />
<br />
<br />
== Retrospective ==<br />
<br />
=== Slicer 3 Snapshot Builds ===<br />
<br />
* Initial releases began end of March 2007<br />
** Base code functional and usable<br />
** Several usable modules include (auto segmentaiton, editor, registration...)<br />
** Image Guided Therapy example modules<br />
* Updated versions summer 2007<br />
** With DTI and other application modules<br />
** Bug fixes and performance enhancements<br />
<br />
=== Migration Tutorials (from Slicer 2.x to 3.0) ===<br />
<br />
The first set of user tutorials will be released in Fall 2007. <br />
Slicer3 programming courses will be released in January 2008.<br />
<br />
== Past ==<br />
<br />
=== Slicer3.0 Beta ===<br />
<br />
* Official release at [[AHM_2007 | AHM January 2007]]<br />
<br />
=== April 3, 2006 ===<br />
<br />
There was a [[Slicer3:_Alpha1_Meeting|Slicer3 Alpha1 Design Review]] meeting.<br />
<br />
'''[[Slicer3:Alpha|Definition of Alpha Milestone]]'''<br />
<br />
=== Slicer3 Alpha2/Beta1 by End of July 2006 ===<br />
<br />
* Initial Testing with Core 3 participation<br />
* Base functionality in place, but still subject to API changes and other improvements.<br />
* Packaged versions not yet available, but testers are able to easily build their own versions.<br />
<br />
=== Implementation of Slicer3 Alpha1 by end of March 2006 ===</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=17267Slicer3:Volume Rendering2007-11-05T14:06:53Z<p>Andreas: /* Screenshots */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
<br />
==Screen shots==<br />
*The following screen shots are all captured on the same abdominal data set. Only the visualization parameter sets are different. <br />
<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.</div>Andreashttps://www.na-mic.org/w/index.php?title=Slicer3:Volume_Rendering&diff=17266Slicer3:Volume Rendering2007-11-05T14:05:02Z<p>Andreas: /* Screenshots */</p>
<hr />
<div>== Overview ==<br />
The topic of the new Volume Rendering Module is the integration of hardware accelerated volume rendering into the Slicer 3 environment. There is a special focus of achieving interactive update rates, easy user interaction (e.g. by offering several presets) and the use of label maps. Goals also include incremental updates (if module is used with Editor module), saving and loading of the configuration etc.<br />
<br />
<br />
==Screenshots==<br />
{|<br />
|[[Image:AbdomenBones.jpg|thumb|300px]]<br />
|[[Image:AbdomenLung.jpg|thumb|300px]]<br />
|[[Image:AbdomenSoftTisssue.jpg|300px|thumb]]<br />
|}<br />
<br />
==How to compile the module==<br />
*Switch the compile option "VolumeRenderingModule" on (in cmake)<br />
*Make sure that you recompile "Slicer3.cxx"<br />
*Compile<br />
<br/><br />
*Note: if you also want to us the latest labelmap support add the following steps before compiling<br />
**Switch the compile option "VR_Labelmaps" on (in cmake)<br />
**Make sure that you recompile "vtkSlicerVolumeRenderingModuleGui.cxx"<br />
<br />
==Current Features==<br />
*Visualize grayscale volumes<br />
*Create Visualization Parameter sets, load and save them<br />
*Use preset Visualization Parameter sets and link already created Parameter sets with current Volume<br />
*Edit parameters like shading; color , opacity and gradient transfer functions<br />
*Interactive render rates, achieved through 3 step rendering<br />
*Select different qualities of rendering and performance levels of rendering<br />
*Receive exact progress about rendering<br />
<br />
==Future Features==<br />
*Render labelmaps properly<br />
<br />
==How to use the module==<br />
===First steps===<br />
*Step 1: Load a MRML Scene or add a volume to a new Scene (see other module descriptions for better instructions)<br />
<br />
*Step2: A standard Visualization Parameter Set will be generated automatically and your volume will show up in the render window.<br />
<br />
*Step3: Adjust the parameter set:<br />
**To change interpolation use the interpolation drop down menu.<br />
**To enable shading click on the material button.<br />
**To change the transfer functions just click into the particular histogram to add a point, drag a point outside the editor to delete it or click on the point to change its color, position etc.<br />
**If you choose "Interactive Apply" all changes in the transfer functions will be processed immediately otherwise just interact with the volume to use the new parameters <br />
<br />
===Quality/Performance===<br />
Volume rendering in Slicer 3 uses a 3 step rendering technology. To achieve interactive render rates the quality of the volume will drop down every time you interact with the volume or change parameter sets. If you don't interact with it the quality increases. You can see the progress of the rendering in the right bottom corner. If you have a high end computer and you want to get rid off the low quality rendering try to change the Performance /Quality drop down menu. Using middle quality, the lowest resolution will be skipped. Using highest quality only the highest resolution will be used.<br />
<br />
===Work with Visualization Parameter Sets===<br />
Visualization Parameter Sets are used to save your configuration. If you save your MRML Scene all Visualization Parameter Sets will be saved so that next time you load the Scene every configuration will be available again.<br />
*If you want to create a new Parameter Set just type a name into the text field and click on "Create Visualization Parameter Set". A new default Parameter Set will be created. Now you can edit all your parameters like described in first steps.<br />
* To switch between Parameter Sets use the drop down menu "Current Visualization Parameter Set".<br />
* If you already created a Parameter Set while editing another volume in the same Scene just select it in the drop down menu "Use Existing Visualization Parameter Sets" (below the separator). Aft that this Parameter Set will also be linked to the current volume. (CAUTION: Any changes to this Parameter will effect the Parameters in both volumes (as it is still the same Parameter Set)).<br />
* If you are looking for some default Parameter Sets look into the "Use existing Visualization Parameter Set" drop down. All Parameter Sets shown above the separator are default Parameter Sets. If you choose one of them, your current Parameter Set will be filled with the values from the default Parameter Set.<br />
<br />
<br />
== Goals ==<br />
<br />
Volume rendering presets :<br />
* MIP (Maximum Intensity Projection) <br />
**[http://en.wikipedia.org/wiki/Maximum_intensity_projection Wikipedia]<br />
**[http://www.vtk.org/doc/release/5.0/html/a01399.html vtkFixedPointVolumeRayCastMapper Class Reference]<br />
* CT Bone and vessel <br />
**Use Hounsfield units<br />
***Bone +400->+1000<br />
***Soft tissue +40->+80<br />
***Water 0<br />
***Fat -60->-100<br />
***Lung -400->-600<br />
***Air -1000<br />
**Problem with Vessels: Different contrast mediums?!<br />
* T1 MR Air/skin interface<br />
* Label map per-label object rendering<br />
<br />
Slicer3 module interface:<br />
* Select from loaded volumes<br />
* Specify preset transfer functions or use KWWidgets tools<br />
<br />
Slicer3 internals:<br />
* Correct coordinates including transforms<br />
* Level of detail rendering<br />
* Proper integration with surface rendering<br />
<br />
Different Volume Rendering Algorithms<br />
*RayCast<br />
*2D Texture Mapping<br />
*3D Texture Mapping<br />
*...<br />
<br />
== Wish List ==<br />
<br />
<br />
* 2D Transfer functions - may require specialized opengl code integrated with VTK. Talk with Gordon about latest work from Utah.<br />
<br />
* use glTexSubImage3D so that incremental changes to the volume can be quickly reflected<br />
<br />
* use distance maps (inlcude several components) in rendering<br />
<br />
==Glossar==<br />
*Visualization Parameter Set: A Visualization Parameter is the combination of different mapping options. This includes color, opacity, gradient transfer functions as well as the type of interpolation (nearest neighbor or linear) and shading.</div>Andreas