pujol s, gollub r -1- national alliance for medical image computing data loading and visualization...
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Pujol S, Gollub R
-1-National Alliance for Medical Image Computing
Data Loading and Visualization
Sonia Pujol, Ph.D.
Surgical Planning LaboratoryHarvard Medical School
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Slicer3
• An end-user application for image analysis
• An open-source environment for software development
• A software platform that is both easy to use for clinical researchers and easy to extend for programmers
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Material
This course requires the installation of the Slicer3 softwareand training dataset accessible at the following locations:
• Slicer 3 Softwarehttp://www.na-mic.org/Wiki/index.php/Slicer:Slicer3
• Training Dataset 1http://www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
DisclaimerIt is the responsibility of the user of 3DSlicer tocomply with both the terms of the license and withthe applicable laws, regulations and rules.
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Data
This course is built upon three datasets of a single
healthy subject brain:
MR DICOM GRASS
MR Nrrd SPGR
Pre-computed Label Map
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Learning objective
Following this tutorial, you’ll be able to load and visualize volumes within Slicer3, and to interact in 3D with structural images and models.
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Overview• Loading and visualizing multiple volumes
simultaneously
• Loading and visualizing segmented structures overlaid on grayscale images
• Loading and visualizing 3D models
• Loading and saving a scene
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Launch Slicer3
Slicer3
Slicer3-build
Slicer3-lib
• Launch Slicer3 from the directory Slicer3-build
Mac/LinuxRun ‘./Slicer3’ in Slicer3-build/
WindowsRun ‘./Slicer3.exe’ in Slicer3-build/
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Slicer3 GUI
The Graphical User Interface (GUI) of Slicer3 integrates five components:
•the Menu Toolbar
•the Module GUI Panel
•the 3D Viewer
•the Slice Viewer
•the Slice and 3D View Controller
Slice Viewer
3DViewerModule GUI Panel
Slice and 3D View
Controller
Menu Toolbar
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Part 1: Loading and visualizing
multiple volumes simultaneously
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Loading Volumes
The Data module is the module displayed by default in the GUI.
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Loading VolumesLeft-click on the module selection menu to load the module Volumes
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Loading Volumes
The panel of the module Volumes appears in the interface.
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Loading Volumes
Click on Select Volume File
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Loading Volumes
Browse to find the first image 001.dcm of the dataset located in the directory
SlicerSampleVisualization/dicom
and click on Open
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Loading Volumes
Select Image Origin: Centered
Click on Apply to load the DICOM dataset
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Loading Volumes
The DICOM images appear in the Background display of the 2DViewer.
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Loading Volumes
Click on the tab Info to display the characteristics of the DICOM volume
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Viewing Volume Information
The information contained in the DICOM header appears in the interface:
•Volume dimensions: 256 x 256 x 124
•Volume Spacing: 0.9375x0.9375x1.3 mm
•Scan Order: LR
•Scalar Type: Short
•Image Origin: (-79.95, 119.53,119.53)
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Click on the choose view icon
Exploring the data
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Select the red slice only layout
from the menu
Exploring the data
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Exploring the data
The axial slices of the dicom volume appear in the 3D viewer.
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Exploring the data
Click on the slices fit to window icon
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Exploring the data
Slicer automatically adjusts the dimensions of the image to the size of the window.
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Exploring the dataBrowse the images using the slider to display the ventricles (~slice 38)
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Exploring the data
Click on the conventional layout icon to come back to the standard view
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Loading Volumes
Click on the ‘adjust slices fit to window’ icon
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Loading Volumes
Click on Select Volume File
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Loading Volumes
Browse to find the header file of the spgr volume spgr.nhdr located in the directory SlicerSampleVisualization/nrrd and click on Open.
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Loading Volumes
Select Image Origin: Centered
and Click on Apply
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Loading Volumes
The spgr images appear in the Background display of the 2DViewer.
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Visualizing multiple volumes
To simultaneously view the dicom and the nrrd volumes, left click on the drop-down menu to the right of the Foreground icon and select the image 001.dcm
Click on the links icon.
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Visualizing multiple volumes
Use the slider from the Slice View controller to fade between Background and Foreground views.
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Visualizing multiple volumes
Click on either
the Background icon
or the Foreground icon
to display the Nrrd or
the DICOM volumes in
the Slice Viewer
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Overview• Loading and visualizing multiple volumes
simultaneously
• Loading and visualizing segmented structures overlaid on grayscale images
• Loading and visualizing 3D models
• Loading and saving a scene
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Part 2: Loading and visualizing segmented structures overlaid on
grayscale images
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Loading a label mapClick on Select Volume File
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Loading a label map
Browse to find the header file all.nhdr of the label map dataset located in the directory
SlicerSampleVisualization/nrrd
and click on Open
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Visualizing a label map
Set Image Origin to Centered, Check the Label Map box and click on Apply
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Visualizing a label map
Slicer displays the label map all in the Label layer
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Visualizing Multiple Volumes
Background Viewer
Left click the drop-down menu to the right of the B icon and select the labelmap all
Label Viewer
Left click the drop-down menu to the right of the L icon and select None
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Visualizing Multiple Volumes
Foreground Viewer
Left click on the drop-down menu to the right of the F icon and select the volume spgr
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Visualizing Multiple Volumes
Select Manipulate Slice Views
Use the slider to fade between the labelmap all (Background) and the spgr volume (Foreground).
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Visualizing Multiple Volumes
Select the Red Slice View mode
Select the red slice only layout
from the menu
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Visualizing Multiple Volumes
Browse to display the segmented ventricles overlaid on the spgr images (slice 41)
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Visualizing Multiple Volumes
Browse to display the segmented ventricles overlaid on the spgr images (~slice 41)
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Overview• Loading and visualizing multiple volumes
simultaneously
• Loading and visualizing segmented structures overlaid on grayscale images
• Loading and visualizing 3D models
• Loading and saving a scene
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Part 3: Loading and visualizing 3D models
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Loading a 3D model
Select the module Models from the main menu
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Loading a 3D model
Click on Load Model Directory
and select the directory models:
SlicerSampleVisualization/models/
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Loading a 3D model
Slicer loads the 3D models of the skin, the ventricles and the vessels.
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Loading a 3D model
Click on the panel Hierachy and Display to access the module’s display components
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Visualizing a 3D model
Select the model Skin.vtk
Click on the icon Set Color and choose a new color for the 3D model of the head.
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Visualizing a 3D model
Use the slider to lower the opacity of the 3D model.
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Visualizing a 3D model
The 3D models of the vessels and the ventricles appear through the skin.
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Visualizing a 3D model
Select the model Vessels.vtk and change the color of the vasculature
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Manipulating a 3D model
Click on the R letter (Right) in the control window
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Manipulating a 3D model
The 3D Viewer shows the model from the right side of the patient
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Manipulating a 3D model
Position the mouse in the 3D Viewer, hold down the left mouse button and drag to rotate the model.
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Manipulating a 3D model
Hold down the right mouse button, and move the mouse up and down to zoom out and in.
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Manipulating a 3D model
Click on the A letter to display the standard Anterior View.
Click on the Spin icon
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Manipulating a 3D model
The model starts spinning inside the Viewer Panel.
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Manipulating a 3D model
Click on the icon Rock
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Manipulating a 3D model
The model starts rocking inside the Viewer Panel.
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Manipulating a 3D model
Click on the Slice Visibility icon to display the slices in the 3D Viewer
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Manipulating the images
The anatomical slices appear in the 3D Viewer.
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Manipulating the images
Use the sliders to slice through the volume in the anterior-posterior direction.
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Manipulating the images
Set the opacity of the Skin model to 1.0, and select the option clipping
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Manipulating the images
Scroll down and expand the component Clipping.
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Manipulating the images
Set the Red Slice Clipping, Yellow Slice Clipping and Green Slice Clipping to Negative Space
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Manipulating the images
Slicer displays the result of the clipping.
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Overview• Loading and visualizing multiple volumes
simultaneously
• Loading and visualizing segmented structures overlaid on grayscale images
• Loading and visualizing 3D models
• Loading and saving a scene
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Part 4: Loading and saving a Scene
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Saving Data
Click on File and Select Save
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Saving DataThe list of elements currently loaded into Slicer3 appears.
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Saving Data
Click on Scene File to browse to the location where the scene will be saved
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Saving Data
Enter the name MyScene.mrml, and click on Save
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Saving Data
Check the box Save Scene
and click on Save
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Creating Scene Snapshots
Select the module Data, and click on Create Scene Snapshot
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Creating Scene Snapshots
Enter the Snapshot Name MySceneSnapshot1 and click on OK
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Creating Scene Snapshots
Select a Superior view of the dataset, and click on Create Scene Snapshot
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Creating Scene Snapshots
Enter the name MySceneSnapshot2 and click on OK
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Creating Scene Snapshots
Select File Save and click on Save to include the two scene snapshots in the saved scene
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Saving Data
Select FileClose Scene in the main menu and click on OK
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Saving Data
The elements of the previous scene disappear from the Viewer.
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Saving Data
Select FileLoad Scene from the main menu
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Saving Data
Select the file myScene.mrml and click on Open
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Loading a Scene
Slicer loads the elements from the scene myScene.mrml
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Loading a Scene
Browse to select MySceneSnapshot2, and click on Restore
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Loading a Scene
Slicer restores scene snapshot MySceneSnapshot2
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Overview• Loading and visualizing multiple volumes
simultaneously
• Loading and visualizing segmented structures overlaid on grayscale images
• Loading and visualizing 3D models
• Loading and saving a scene
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Conclusion
• Interactive interface to load and manipulate grayscale volumes and labelmaps
• 3D interaction with anatomical views
• Open-source platforms for Linux, Mac and Windows
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Acknowledgments
National Alliance for Medical Image ComputingNIH U54EB005149
Neuroimage Analysis Center NIH P41RR013218