Basics of Data

Loading and 3D
Visualization in 3D
Slicer
Sonia Pujol, Ph.D.
Director of 3D Slicer Training & Education

Assistant Professor of Radiology

Brigham and Women’s Hospital
Harvard Medical School
 Overall Goal

This tutorial is an
introduction to the basics
of loading and viewing
DICOM images and 3D
models in 3D Slicer.

© Sonia Pujol, Ph.D. All Rights Reserved 2

 Learning Objectives
Following this tutorial, you will be able
• to load and visualize DICOM images in Slicer
• to perform volume rendering of CT datas
• to load and visualize 3D models reconstructed
from MRI data

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 Tutorial materials

3DVisualizationDataset.zip
3D Slicer version 4.11.0
 Tutorial dataset
• The file 3DVisualizationDataset.zip contains
two directories:
– dataset1_Thorax_Abdomen
– dataset2_Head
• Unzip the file 3DVisualizationDataset.zip on
your computer to access the datasets

© Sonia Pujol, Ph.D. All Rights Reserved 5

 • 3D Slicer is a free open source software
application distributed under a BSD style license.
Disclaimer
• The software is not FDA approved or CE-Marked,
and is for research use only.
 Tutorial Outline

Part 1: Loading and Viewing DICOM data

Part 2: Volume Rendering

Part 3: Loading and Viewing 3D models

 Part 1
DICOM Data
Loading
 Loading a DICOM volume

Drag and drop the directory dataset1_Thorax_Abdomen into Slicer

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Loading a DICOM volume

Click on OK to load
the directory in the
DICOM database

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 Loading a DICOM volume

Slicer displays the user

interface of the DICOM
module

The patient1 study contains a CT Thorax Abdomen dataset

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 Loading a DICOM volume

Select patient1 and click on Load

to load the dataset in Slicer

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 Loading a DICOM volume

Slicer displays the axial, coronal

and sagittal images of the CT
Thorax Abdomen dataset Select the CT_Thorax_Abdomen dataset

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 Loading a DICOM volume

Slicer displays the axial, coronal

and sagittal images of the CT
Thorax Abdomen dataset Select the CT_Thorax_Abdomen dataset

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Loading a DICOM volume
Left click on DICOM to display
the list of modules of Slicer

Select the module

Volumes

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Loading a DICOM volume

Click on the CT-abdomen

preset to automatically adjust
the window/level display of the
CT dataset

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Loading a DICOM volume

Position the mouse cursor

over the red banner in the
Red Viewer to display the slice
menu.

Click on the Links icon to link

the slice controls across all
Slice Viewers.

Click on the Eye icon to

display the three anatomical
slices in the 3D Viewer

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 Visualizing DICOM images
The three anatomical slices
appear in the 3D viewer.

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 Visualizing DICOM images
Click on the Slicer layout menu
icon, and select the
Conventional Widescreen layout

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 Visualizing DICOM images
Click on the Slicer layout menu
icon, and select the
Conventional Widescreen layout

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 Visualizing DICOM images
Slicer switches the layout
to Conventional
Widescreen layout

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 Visualizing DICOM images
Use the right mouse button in the
3D Viewer to zoom in and out

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 Visualizing DICOM images
Use the left mouse button in the
3D Viewer to rotate the images

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 3D Viewer Controller

Position the mouse cursor over

the pin icon in the blue banner
of the 3D viewer window to
display the 3DView controller

Click on the second icon on the

top row of the 3DView
controller to center the 3D view
on the scene

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 3D Viewer Controller

Select the Volume Rendering

module in the list of modules

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 Part 2
Volume Rendering
Volume Rendering
• Volume rendering
techniques enable 3D
visualization of 3D
datasets

• The Volume Rendering

module in Slicer enables
interactive 3D visualization
of DICOM images

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 Volume Rendering

Click on Preset in the Display tab

and select the preset CT-Cardiac3

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 Volume Rendering

Select VTK GPU Ray Casting Rendering

Click on the eye icon in the Volume tab to display
the volume rendered image in the 3D viewer

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 Volume Rendering

Use the shift slider to

change the transfer
function and display the
aorta

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 Volume Rendering

Click on Display ROI to

display a region of interest
(ROI) in the 3D viewer and
check the option Enable

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 Volume Rendering

Turn off the visibility of the

axial, sagittal and coronal
slices in the 2D viewer

Position the ROI around the

left kidney using the color
handles

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 Volume Rendering

Click on the eye icon to

display the volume rendered
image

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 Volume Rendering

Slicer displays the

volume rendered
image of the left kidney

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 Volume Rendering

Extend the ROI to generate

a volume rendered image of
the right kidney

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Volume Rendering
Click on Fileà Close Scene
in the main menu

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 Part 3
Loading and
viewing 3D models
Tutorial dataset
• The directory dataset2_Head
contains the Slicer scene called
Head_scene.mrb

• The scene contains 3D models

from the SPL brain atlas developed
by the department of Radiology at
Brigham and Women’s Hospital,
Harvard Medical School (NIH P41
RR013218, NIH R01 MH05074)

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 Slicer Scene

Slicer stores all loaded data in a repository called a

scene

Each data set, such as an image volume, surface

model, or point set, is represented as a node in a
Slicer scene.

All Slicer modules operate on the data stored in a

Slicer scene.

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Loading a Scene

Drag and drop the file

Head_Scene.mrb located in
the dataset2_Head directory
into Slicer

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 Loading a Scene

Slicer displays a 3D
surface model of the
head and 2D MRI slices

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 Viewing 3D models

Position the cursor over

the pin icon to reveal the
slice menu and click on
the eye icon to display the
axial slice in the 3D viewer

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 Viewing 3D models

Select the Models module

in the list of models

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 Viewing 3D models

Slicer displays the list of

3D models loaded in the
scene

Select the model Skin.vtk

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 Viewing 3D models

Lower the opacity of The skull bone and

the Skin model using eyeballs models appear
the visibility slider through the skin
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 Viewing 3D models

Select the skull bone

model and click on the
eye icon to turn off its The white matter and
visibility optic nerve models
appear through the skin
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Interacting with 3D models

Click on the eye icon to

display the coronal slice
in Reserved
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 Interacting with 3D models

Select the hemispheric

white matter model and
select the option Clipping © Sonia Pujol, Ph.D. All Rights Reserved 48
 Interacting with 3D models

Move the coronal slice

posteriorily to display the
optic chiasm
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 Interacting with 3D models

Slicer displays a 3D view of

the optic chiasm
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 Conclusion
• 3D Slicer provides advanced functionalities for
loading and viewing 3D medical imaging data

• The tutorial demonstrates how to use volume

rendering and 3D surface modeling for
interactive visualization of CT and MRI data

Contact: [email protected]
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 Acknowledgments

Neuroimage Analysis
Center
(NIBIB P41 EB015902)

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