Download - Data Loading and Visualization
![Page 1: Data Loading and Visualization](https://reader036.vdocuments.us/reader036/viewer/2022062407/56812cf9550346895d91c639/html5/thumbnails/1.jpg)
Pujol S, Gollub R
-1-National Alliance for Medical Image Computing
Data Loading and Visualization
Sonia Pujol, PhDRandy Gollub, MD, PhD
Slicer3 Training Compendium
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Pujol S, Gollub R
-2-National Alliance for Medical Image Computing
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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Pujol S, Gollub R
-3-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
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Pujol S, Gollub R
-4-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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Pujol S, Gollub R
-5-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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Pujol S, Gollub R
-6-National Alliance for Medical Image Computing
Part 1: Loading and visualizing
multiple volumes simultaneously
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Pujol S, Gollub R
-7-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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-8-National Alliance for Medical Image Computing
Loading Volumes
The Data module is the module displayed by default in the GUI.
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-9-National Alliance for Medical Image Computing
Loading VolumesLeft-click on the module selection menu to load the module Volumes
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-10-National Alliance for Medical Image Computing
Loading Volumes
The panel of the module Volumes appears in the interface.
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Pujol S, Gollub R
-11-National Alliance for Medical Image Computing
Loading Volumes
Click on Select Volume File
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Pujol S, Gollub R
-12-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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-13-National Alliance for Medical Image Computing
Loading Volumes
Select Image Origin: Centered
Click on Apply to load the DICOM dataset
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-14-National Alliance for Medical Image Computing
Loading Volumes
The DICOM images appear in the Background display of the 2DViewer.
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Pujol S, Gollub R
-15-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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-16-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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-17-National Alliance for Medical Image Computing
Click on the choose view icon
Exploring the data
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-18-National Alliance for Medical Image Computing
Select the red slice only layout
from the menu
Exploring the data
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-19-National Alliance for Medical Image Computing
Exploring the data
The axial slices of the dicom volume appear in the 3D viewer.
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-20-National Alliance for Medical Image Computing
Exploring the data
Click on the slices fit to window icon
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-21-National Alliance for Medical Image Computing
Exploring the data
Slicer automatically adjusts the dimensions of the image to the size of the window.
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Pujol S, Gollub R
-22-National Alliance for Medical Image Computing
Exploring the dataBrowse the images using the slider to display the ventricles (~slice 38)
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-23-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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-24-National Alliance for Medical Image Computing
Loading Volumes
Click on the ‘adjust slices fit to window’ icon
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Pujol S, Gollub R
-25-National Alliance for Medical Image Computing
Loading Volumes
Click on Select Volume File
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Pujol S, Gollub R
-26-National Alliance for Medical Image Computing
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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Pujol S, Gollub R
-27-National Alliance for Medical Image Computing
Loading Volumes
Select Image Origin: Centered
and Click on Apply
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Pujol S, Gollub R
-28-National Alliance for Medical Image Computing
Loading Volumes
The spgr images appear in the Background display of the 2DViewer.
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Pujol S, Gollub R
-29-National Alliance for Medical Image Computing
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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-30-National Alliance for Medical Image Computing
Visualizing multiple volumes
Use the slider from the Slice View controller to fade between Background and Foreground views.
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Pujol S, Gollub R
-31-National Alliance for Medical Image Computing
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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Pujol S, Gollub R
-32-National Alliance for Medical Image Computing
Part 2: Loading and visualizing segmented structures overlaid on
grayscale images
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-33-National Alliance for Medical Image Computing
Loading a label mapClick on Select Volume File
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Pujol S, Gollub R
-34-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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-35-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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-36-National Alliance for Medical Image Computing
Visualizing a label map
Slicer displays the label map all in the Label layer
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-37-National Alliance for Medical Image Computing
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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Pujol S, Gollub R
-38-National Alliance for Medical Image Computing
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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-39-National Alliance for Medical Image Computing
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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-40-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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-41-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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-42-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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-43-National Alliance for Medical Image Computing
Part 3: Loading and visualizing 3D models
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-44-National Alliance for Medical Image Computing
Loading a 3D model
Select the module Models from the main menu
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-45-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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-46-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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-47-National Alliance for Medical Image Computing
Loading a 3D model
Click on the panel Display to access the module’s display components
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-48-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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-49-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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-50-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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-51-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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-52-National Alliance for Medical Image Computing
Manipulating a 3D model
Click on the R letter (Right) in the control window
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-53-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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-54-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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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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-56-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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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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-60-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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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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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
Click on the letter S to display a Superior view of the dataset, and click on Create Scene Snapshot
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Pujol S, Gollub R
-76-National Alliance for Medical Image Computing
Creating Scene Snapshots
Enter the name MySceneSnapshot2 and click on OK
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Pujol S, Gollub R
-77-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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Pujol S, Gollub R
-78-National Alliance for Medical Image Computing
Saving Data
Select FileClose Scene in the main menu and click on OK
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Pujol S, Gollub R
-79-National Alliance for Medical Image Computing
Saving Data
The elements of the previous scene disappear from the Viewer.
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Pujol S, Gollub R
-80-National Alliance for Medical Image Computing
Saving Data
Select FileLoad Scene from the main menu
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Pujol S, Gollub R
-81-National Alliance for Medical Image Computing
Saving Data
Select the file myScene.mrml and click on Open
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Pujol S, Gollub R
-82-National Alliance for Medical Image Computing
Loading a Scene
Slicer loads the elements from the scene myScene.mrml
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Pujol S, Gollub R
-83-National Alliance for Medical Image Computing
Loading a Scene
Browse to select MySceneSnapshot2, and click on Restore
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Pujol S, Gollub R
-84-National Alliance for Medical Image Computing
Loading a Scene
Slicer restores scene snapshot MySceneSnapshot2
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Pujol S, Gollub R
-85-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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Pujol S, Gollub R
-86-National Alliance for Medical Image Computing
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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Pujol S, Gollub R
-87-National Alliance for Medical Image Computing
Acknowledgments
National Alliance for Medical Image ComputingNIH U54EB005149
Neuroimage Analysis Center NIH P41RR013218