Post on 31-Dec-2015
description
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
3D Visualization
Sonia Pujol, Ph.D.
Surgical Planning Laboratory
Harvard Medical School
Leonardo da Vinci (1452-1519), Virgin and Child Alte Pinakothek, München
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Material
This course requires the installation of the Slicer3 softwareand training dataset
• Slicer 3 Software: www.slicer.org/pages/Downloads
• Training Dataset: SlicerSampleVisualization.tar.gz
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Data
This course is built upon three datasets of a single
healthy subject brain:
MR DICOM GRASS
MR Nrrd SPGR
Pre-computed Label Map
tar –zxvf SlicerSampleVisualization.tar.gz
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
• If you have downloaded a pre-compiled version of the software, launch Slicer3 from the directory Slicer3 3.2.2008-08-08/:
Mac/LinuxRun ‘./Slicer3’ in Slicer3-3.2.2008-08-08/
WindowsRun ‘./Slicer3’ in Program Files/Slicer3 3.2.2008-08-08/
or launch Start All Programs Slicer3 3.2.2008-08-08/Slicer
Launch Slicer3
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
• If you have built a version of Slicer3 on your machine, launch Slicer3 from the directory Slicer3-build:
Mac/Linux/WindowsRun ‘./Slicer3’ in Slicer3-build/
Launch Slicer3
Slicer3
Slicer3-build
Slicer3-lib
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Part 1: Loading and visualizing
multiple volumes simultaneously
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
The Data module is the module displayed by default in the GUI.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading VolumesLeft-click on the module selection menu to load the module Volumes
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
The panel of the module Volumes appears in the interface.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
Click on Select Volume File
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
Select Image Origin: Centered
Click on Apply to load the DICOM dataset
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
The DICOM images appear in the Background display of the 2DViewer.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
Click on the tab Info to display the characteristics of the DICOM volume
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Click on the choose view icon
Exploring the data
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Select the red slice only layout
from the menu
Exploring the data
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Exploring the data
The axial slices of the dicom volume appear in the 3D viewer. Slicer automatically adjusts the dimensions of the image to the size of the window.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Exploring the dataBrowse the images using the slider to display the ventricles (~slice 38)
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Exploring the data
Click on the conventional layout icon to come back to the standard view
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
Click on the ‘adjust slices fit to window’ icon
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
Click on Select Volume File
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
Browse to find the header file of the volume spgr.nhdr located in the directory SlicerSampleVisualization/nrrd and click on Open.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
Select Image Origin: Centered
and Click on Apply
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
The spgr images appear in the Background display of the 2DViewer.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
Select the module Data from the Modules Menu.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading Volumes
The two datasets 001.dcm ad spgr.nhdr are loaded in Slicer.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Part 2: Loading and visualizing segmented structures overlaid on
grayscale images
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading a label mapCome back to the module Volumes and click on Select Volume File
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Visualizing a label map
Set Image Origin to Centered,
Check the Label Map box and click on Apply
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Visualizing a label map
Slicer displays the label map all in the Label layer
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Visualizing Multiple Volumes
Foreground Viewer
Left click the drop-down menu to the right of the F 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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Visualizing Multiple Volumes
Background Viewer
Left click on the drop-down menu to the right of the B icon and select the volume spgr
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Visualizing Multiple Volumes
Select Manipulate Slice Views
Use the slider to fade between the labelmap all (Foreground) and the spgr volume (Background).
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Visualizing Multiple Volumes
Select the Red Slice View mode
Select the red slice only layout
from the menu
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Visualizing Multiple Volumes
Browse to display the segmented ventricles overlaid on the spgr images (~slice 41)
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Part 3: Loading and visualizing 3D models
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading a 3D model
Select the module Models from the main menu
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading a 3D model
Click on Load Model Directory
and select the directory models:
SlicerSampleVisualization/models/
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading a 3D model
Slicer loads the 3D models of the skin, the ventricles and the vessels.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading a 3D model
Click on the Display panel to access the module’s display components
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading a 3D model
Select the model Skin.vtk and scroll down in the Display window to display the icon Set Color.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Visualizing a 3D model
Click on the icon Set Color and choose a new color for the 3D model of the head.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Visualizing a 3D model
Use the slider to lower the opacity of the 3D model.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Visualizing a 3D model
The 3D models of the vessels and the ventricles appear through the skin.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Visualizing a 3D model
Select the model Vessels.vtk and change the color of the vasculature
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating a 3D model
Click on the R letter (Right) in the control window
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating a 3D model
The 3D Viewer shows the model from the right side of the patient
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating a 3D model
Click on the A letter to display the standard Anterior View.
Click on the Spin icon
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating a 3D model
The model starts spinning inside the Viewer Panel.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating a 3D model
Click on the icon Rock
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating a 3D model
The model starts rocking inside the Viewer Panel.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating a 3D model
Click on the Slice Visibility icon to display the slices in the 3D Viewer
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating the images
The anatomical slices appear in the 3D Viewer.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating the images
Use the sliders to slice through the volume in the anterior-posterior direction.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating the images
Select the model Skin and set the opacity to 1.0
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating the images
Select the option Clipping
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating the images
Scroll down and expand the component Clipping.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating the images
Set the Red Slice Clipping, Yellow Slice Clipping and Green Slice Clipping to Negative Space
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Manipulating the images
Slicer displays the result of the clipping.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Part 4: Loading and saving a Scene
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Saving Data
Click on File and Select Save
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Saving DataThe list of elements currently loaded into Slicer3 appears.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Saving Data
Click on Scene File to browse to the location where the scene will be saved
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Saving Data
Enter the name MyScene.mrml, and click on Save
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Saving Data
Check the box Save Scene
and click on Save
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Creating Scene Snapshots
Choose a 3D view of the scene and select the module Data.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Creating Scene Snapshots
Click on the capture snapshot icon
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Creating Scene Snapshots
Enter the Snapshot Name MySceneSnapshot1 and click on OK
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Creating Scene Snapshots
Select a Superior view of the dataset, and click on the capture snapshot icon
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Creating Scene Snapshots
Enter the name MySceneSnapshot2 and click on OK
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Creating Scene Snapshots
Select File Save and click on Save to include the two scene snapshots in the saved scene
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Saving Data
Select FileClose Scene in the main menu and click on OK
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Saving Data
The elements of the previous scene disappear from the Viewer.
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Saving Data
Select FileLoad Scene from the main menu
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Saving Data
Select the file myScene.mrml and click on Open
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading a Scene
Slicer loads the elements from the scene myScene.mrml
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading a Scene
Left-click on the restore snapshot icon.
Select MySceneSnapshot2 and click on restore
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Loading a Scene
Slicer restores the scene snapshot MySceneSnapshot2
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
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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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Conclusion
• Interactive interface to load and manipulate greyscale volumes, labelmaps and 3D models.
• 3D interaction with anatomical views
• Open-source platforms for Linux, Mac and Windows
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3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image Computing
Acknowledgments
National Alliance for Medical Image ComputingNIH U54EB005149
Neuroimage Analysis Center NIH P41RR013218