-1- 3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image...

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

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

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.

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

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.

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

• 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

• 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

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

Part 1: Loading and visualizing

multiple volumes simultaneously

Loading Volumes

The Data module is the module displayed by default in the GUI.

Loading VolumesLeft-click on the module selection menu to load the module Volumes

Loading Volumes

The panel of the module Volumes appears in the interface.

Loading Volumes

Click on Select Volume File

Loading Volumes

Browse to find the first image 001.dcm of the dataset located in the directory

SlicerSampleVisualization/dicom

and click on Open

Loading Volumes

Select Image Origin: Centered

Click on Apply to load the DICOM dataset

Loading Volumes

The DICOM images appear in the Background display of the 2DViewer.

Loading Volumes

Click on the tab Info to display the characteristics of the DICOM volume

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)

Click on the choose view icon

Exploring the data

Select the red slice only layout

from the menu

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.

Exploring the dataBrowse the images using the slider to display the ventricles (~slice 38)

Exploring the data

Click on the conventional layout icon to come back to the standard view

Loading Volumes

Click on the ‘adjust slices fit to window’ icon

Loading Volumes

Click on Select Volume File

Loading Volumes

Browse to find the header file of the volume spgr.nhdr located in the directory SlicerSampleVisualization/nrrd and click on Open.

Loading Volumes

Select Image Origin: Centered

and Click on Apply

Loading Volumes

The spgr images appear in the Background display of the 2DViewer.

Loading Volumes

Select the module Data from the Modules Menu.

Loading Volumes

The two datasets 001.dcm ad spgr.nhdr are loaded in Slicer.

simultaneously

Part 2: Loading and visualizing segmented structures overlaid on

grayscale images

Loading a label mapCome back to the module Volumes and click on Select Volume File

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

Visualizing a label map

Set Image Origin to Centered,

Check the Label Map box and click on Apply

Visualizing a label map

Slicer displays the label map all in the Label layer

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

Background Viewer

Left click on the drop-down menu to the right of the B icon and select the volume spgr

Select Manipulate Slice Views

Use the slider to fade between the labelmap all (Foreground) and the spgr volume (Background).

Select the Red Slice View mode

Select the red slice only layout

from the menu

Browse to display the segmented ventricles overlaid on the spgr images (~slice 41)

simultaneously

Part 3: Loading and visualizing 3D models

Loading a 3D model

Select the module Models from the main menu

Loading a 3D model

Click on Load Model Directory

and select the directory models:

SlicerSampleVisualization/models/

Loading a 3D model

Slicer loads the 3D models of the skin, the ventricles and the vessels.

Loading a 3D model

Click on the Display panel to access the module’s display components

Loading a 3D model

Select the model Skin.vtk and scroll down in the Display window to display the icon Set Color.

Visualizing a 3D model

Click on the icon Set Color and choose a new color for the 3D model of the head.

Use the slider to lower the opacity of the 3D model.

The 3D models of the vessels and the ventricles appear through the skin.

Select the model Vessels.vtk and change the color of the vasculature

Manipulating a 3D model

Click on the R letter (Right) in the control window

The 3D Viewer shows the model from the right side of the patient

Position the mouse in the 3D Viewer, hold down the left mouse button and drag to rotate the model.

Hold down the right mouse button, and move the mouse up and down to zoom out and in.

Click on the A letter to display the standard Anterior View.

Click on the Spin icon

The model starts spinning inside the Viewer Panel.

Click on the icon Rock

The model starts rocking inside the Viewer Panel.

Click on the Slice Visibility icon to display the slices in the 3D Viewer

Manipulating the images

The anatomical slices appear in the 3D Viewer.

Use the sliders to slice through the volume in the anterior-posterior direction.

Select the model Skin and set the opacity to 1.0

Select the option Clipping

Scroll down and expand the component Clipping.

Set the Red Slice Clipping, Yellow Slice Clipping and Green Slice Clipping to Negative Space

Slicer displays the result of the clipping.

simultaneously

Part 4: Loading and saving a Scene

Saving Data

Click on File and Select Save

Saving DataThe list of elements currently loaded into Slicer3 appears.

Saving Data

Click on Scene File to browse to the location where the scene will be saved

Saving Data

Enter the name MyScene.mrml, and click on Save

Saving Data

Check the box Save Scene

and click on Save

Creating Scene Snapshots

Choose a 3D view of the scene and select the module Data.

Click on the capture snapshot icon

Enter the Snapshot Name MySceneSnapshot1 and click on OK

Select a Superior view of the dataset, and click on the capture snapshot icon

Enter the name MySceneSnapshot2 and click on OK

Select File Save and click on Save to include the two scene snapshots in the saved scene

Saving Data

Select FileClose Scene in the main menu and click on OK

Saving Data

The elements of the previous scene disappear from the Viewer.

Saving Data

Select FileLoad Scene from the main menu

Saving Data

Select the file myScene.mrml and click on Open

Loading a Scene

Slicer loads the elements from the scene myScene.mrml

Loading a Scene

Left-click on the restore snapshot icon.

Select MySceneSnapshot2 and click on restore

Loading a Scene

Slicer restores the scene snapshot MySceneSnapshot2

simultaneously

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

Acknowledgments

National Alliance for Medical Image ComputingNIH U54EB005149

Neuroimage Analysis Center NIH P41RR013218

-1- 3D Visualization. Sonia Pujol, Ph.D., Harvard Medical School National Alliance for Medical Image...

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