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| + | {{documentation/banner |
| − | {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}} | + | | text = [https://slicer.readthedocs.io/en/latest/user_guide/modules/volumerendering.html This page has been moved to read-the-docs.] |
| − | {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}} }}
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| − | {{documentation/{{documentation/version}}/module-introduction-row}}
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| − | {{documentation/{{documentation/version}}/module-acknowledgements}}<br>
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| − | Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br>
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| − | Author: Julien Finet, Kitware Inc.<br>
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| − | Contributor1: Alex Yarmarkovich, Isomics, Inc.<br>
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| − | Contributor2: Yanling Liu, NCI-Frederick/SAIC-Frederick<br>
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| − | Contributor3: Andreas Freudling, Intern at SPL, University of Heidelberg (Germany)<br>
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| − | Contact: Julien Finet, <email>julien.finet@kitware.com</email><br>
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| − | {{documentation/{{documentation/version}}/module-introduction-row}}
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| − | {{documentation/{{documentation/version}}/module-introduction-logo-gallery
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| − | |{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}
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| − | |{{collaborator|logo|isomics}}|{{collaborator|longname|isomics}}
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| − | |{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
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| − | |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
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| − | }}
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| − | {{documentation/{{documentation/version}}/module-introduction-end}}
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| − | <!-- ---------------------------- -->
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| − | {{documentation/{{documentation/version}}/module-section|Module Description}}
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| − | {{documentation/{{documentation/version}}/module-description}}
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| − | Only UNSIGNED CHAR images are supported for now. You can convert your images into UCHAR by using the [[Documentation/{{documentation/version}}/Modules/CastScalarVolume|Cast Scalar Volume]] module.
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| − | <!-- ---------------------------- -->
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| − | {{documentation/{{documentation/version}}/module-section|Use Cases}}
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| − | <gallery widths="200px" perrow="4">
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| − | Image:Tumor-Volume-Rendering-PostGad-2011.png|Tumor post pad <br><small>(preset: MR-Default)</small>
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| − | Image:Modules-VolumeRendering-LabelMap.png|Segmented (labelmap) knee<br><small>(interpolation: nearest neighbor, shading: off)</small>
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| − | Image:QSlicerVolumeRendering-default.png|Default view of the module.<br><small>Inputs and Advanced... are hidden by default</small>
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| − | Image:VolumeRenderingSettings.png|Volume Rendering settings<br><small>''Edit -> Application Settings -> Volume Rendering settings''</small>
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| − | </gallery>
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| − | <!-- ---------------------------- -->
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| − | {{documentation/{{documentation/version}}/module-section|Tutorials}}
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| − | Tutorial about [http://www.slicer.org/slicerWiki/index.php/Slicer3:Volume_Rendering_Tutorials using the volume rendering module].
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| − | | |
| − | ===Labelmap rendering===
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| − | [[File:Modules-VolumeRendering-LabelMap.png|right|500px]]
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| − | A labelmap is a volume, and as such it can be visualized using the Volume Rendering method. It can be an alternative from [[Documentation/{{documentation/version}}/Modules/ModelMaker|creating surface models]] from labelmap.
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| − | # First you need to load your labelmap.
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| − | ## Make sure you check the "Labelmap" check box at load time.
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| − | ## Make sure the labelmap is a Unsigned Char image, not Unsigned/Signed Short, Int or Long. If needed, you can [[Documentation/{{documentation/version}}/Modules/CastScalarVolume| cast]] the labelmap to UCHAR.
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| − | # Open the Volume Rendering module
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| − | ## As usual, click on the eye to start the Volume Rendering.
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| − | # To turn off shading:
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| − | ## go to Advanced../Volume Properties/Advanced group box and uncheck the "Shade" checkbox
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| − | # To turn on/off a specific label:
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| − | ## Go to the Advanced.../Volume Properties/Scalar Opacity Mapping group box
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| − | ## Toggle down the '>>' button to show the Opacity controls.
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| − | ## Browse each label with the "Point:" spinbox. When the spinbox shows the current label value,
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| − | ## Set the Opacity spinbox value to 0.0/1.0 to hide/show the label.
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| − | | |
| − | ===Render 2 volumes in 2 views===
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| − | [[File:DualVR.png|right|500px]]
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| − | # [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Change layout]] into "Dual 3D"
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| − | # [[Documentation/{{documentation/version}}/SlicerApplication/LoadingData|Load]] your 2 volumes
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| − | # [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Module_Selection_.26_Navigation|Open]] Volume Rendering module
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| − | # For the first volume:
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| − | ## Open the "Inputs" section
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| − | ## Uncheck "View2" -> only "View1" is checked
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| − | ## Don't click the "eye" icon yet.
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| − | # Select the 2nd volume
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| − | ## Check "View2"
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| − | ## Uncheck "View1" -> only "View2" is checked
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| − | ## Click the eye icon for the VR to show up in View2
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| − | # Select the 1st volume
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| − | ## Click the eye icon for the VR to show up in View1
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| − | <!-- ---------------------------- -->
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| − | {{documentation/{{documentation/version}}/module-section|Panels and their use}}
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| − | [[File:VolumeRenderingPanel.png|right|]]
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| − | {{documentation/{{documentation/version}}/module-parametersdescription}}
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| − | <!-- ---------------------------- -->
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| − | {{documentation/{{documentation/version}}/module-section|Similar Modules}}
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| − | [[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]]
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| − | <!-- ---------------------------- -->
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| − | {{documentation/{{documentation/version}}/module-section|References}}
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| − | Publications related to this module go here. Links to pdfs would be useful.
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| − | For extensions: link to the source code repository and additional documentation
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| − | <!-- ---------------------------- -->
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| − | {{documentation/{{documentation/version}}/module-section|Information for Developers}}
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| − | ===Limitations===
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| − | *To date, only 1 volume can be visible at a time. This happens because the current volume rendering displayable node is hidden when changing to a different volume node.
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| − | *Only UNSIGNED CHAR images are supported for now. You can convert your images into UCHAR by using the [[Documentation/{{documentation/version}}/Modules/CastScalarVolume|Cast Scalar Volume]] module.
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| − | | |
| − | ===Key [[Documentation/{{documentation/version}}/Developers/MRML|nodes]] and classes===
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| − | * [http://slicer.org/doc/html/classvtkMRMLVolumeRenderingDisplayNode.html vtkMRMLVolumeRenderingDisplayNode] controls the volume rendering properties. Each volume rendering technique has its own subclass.
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| − | * [http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html vtkSlicerVolumeRenderingLogic] contains utility functions
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| − | * [http://slicer.org/doc/html/classvtkMRMLScalarVolumeNode.html vtkMRMLScalarVolumeNode] contains the volume itself
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| − | * [http://slicer.org/doc/html/classvtkMRMLVolumePropertyNode.html vtkMRMLVolumePropertyNode] points to the transfer functions
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| − | * [http://slicer.org/doc/html/classvtkMRMLAnnotationROINode.html vtkMRMLAnnotationROINode] controls the clipping planes
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| − | * [http://slicer.org/doc/html/classvtkMRMLVolumeRenderingDisplayableManager.html vtkMRMLVolumeRenderingDisplayableManager] adds the volume renderings into the views
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| − | | |
| − | ===How Tos===
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| − | *How to programmatically volume render your volume node?
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| − | {|width = "100%"
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| − | ! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
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| − | ! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
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| − | |-
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| − | | valign="top" |
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| − | qSlicerAbstractCoreModule* volumeRenderingModule =
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| − | qSlicerCoreApplication::application()->moduleManager()->module("VolumeRendering");
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| − | vtkSlicerVolumesLogic* volumeRenderingLogic =
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| − | volumeRenderingModule ? vtkSlicerVolumesLogic::SafeDownCast(volumesModule->logic()) : 0;
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| − | vtkMRMLVolumeNode* volumeNode = mrmlScene->GetNodeByID('vtkMRMLScalarVolumeNode1');
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| − | if (volumeRenderingLogic)
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| − | {
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| − | vtkMRMLVolumeRenderingDisplayNode* displayNode =
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| − | volumeRenderingLogic->CreateVolumeRenderingDisplayNode();
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| − | mrmlScene->AddNode(displayNode);
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| − | displayNode->Delete();
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| − | volumeRenderingLogic->UpdateDisplayNodeFromVolumeNode(displayNode, volumeNode);
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| − | volumeNode->AddAndObserveDisplayNodeID(displayNode->GetID());
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| − | }
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| − | See [[Documentation/{{documentation/version}}/Developers/Tutorials/CreateLoadableModule#Dependency_between_modules|here]] for more about volume dependency.
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| − | | valign="top" |
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| − | >>> logic = slicer.modules.volumerendering.logic()
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| − | >>> volumeNode = slicer.mrmlScene.GetNodeByID('vtkMRMLScalarVolumeNode1')
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| − | >>> displayNode = logic.CreateVolumeRenderingDisplayNode()
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| − | >>> slicer.mrmlScene.AddNode(displayNode)
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| − | >>> displayNode.UnRegister(logic)
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| − | >>> logic.UpdateDisplayNodeFromVolumeNode(displayNode, volumeNode)
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| − | >>> volumeNode.AddAndObserveDisplayNodeID(displayNode.GetID())
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| − | |}
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| − | | |
| − | *How to programmatically apply a custom color/opacity transfer function?
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| − | {|width = "100%"
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| − | ! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
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| − | ! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
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| − | |-
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| − | | valign="top" |
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| − | vtkColorTransferFunction* colors = ...
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| − | vtkPiecewiseFunction* opacities = ...
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| − | vtkMRMLVolumeRenderingDisplayNode* displayNode = ...
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| − | vtkMRMLVolumePropertyNode* propertyNode = displayNode->GetVolumePropertyNode();
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| − | propertyNode->SetColor(colorTransferFunction);
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| − | propertyNode->SetScalarOpacity(opacities);
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| − | // optionally set the gradients opacities with SetGradientOpacity
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| − | The logic has utility functions to help you create those transfer functions:
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| − | volumeRenderingLogic->[http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#ab8dbda38ad81b39b445b01e1bf8c7a86 SetWindowLevelToVolumeProp](...)
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| − | volumeRenderingLogic->[http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#a1dcbe614493f3cbb9aa50c68a64764ca SetThresholdToVolumeProp](...)
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| − | volumeRenderingLogic->[http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#a359314889c2b386fd4c3ffe5414522da SetLabelMapToVolumeProp](...)
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| − | | valign="top" |
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| − | >>> propertyNode = displayNode.GetVolumePropertyNode()
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| − | >>> ...
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| − | |}
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| − | | |
| − | *How to programmatically limit volume rendering to a subset of the volume?
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| − | {|width = "100%"
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| − | ! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
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| − | ! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
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| − | |-
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| − | | valign="top" |
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| − | [http://slicer.org/doc/html/classvtkMRMLAnnotationROINode.html vtkMRMLAnnotationROINode]* roiNode =...
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| − | vtkMRMLVolumeRenderingDisplayNode* displayNode = ...
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| − | displayNode->SetAndObserveROINodeID(roiNode->GetID());
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| − | displayNode->SetCroppingEnabled(1);
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| − | | valign="top" |
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| − | >>> displayNode.SetAndObserveROINodeID(roiNode.GetID())
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| − | >>> displayNode.CroppingEnabled = 1
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| − | |}
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| − | | |
| − | <!-- ---------------------------- -->
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| − | {{documentation/{{documentation/version}}/module-footer}}
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| − | <!-- ---------------------------- -->
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