3D Data Loading and

Visualization


Sonia Pujol, Ph.D.

Surgical Planning Laboratory
Harvard University
3DSlicer
Slicer is a freely available open-source
pla@orm for segmentaBon, registraBon
and 3D visualizaBon of medical imaging
data.

3DSlicer is a mulB-insBtuBonal effort
supported by the NaBonal InsBtute of
Health.
 Translational research

An open-source environment An end-user application

for software developers for clinical investigators
and scientists

3D Slicer: an open-source platform for

translating innovative algorithms into
clinical research applications
 3DSlicer History
•  1997: Slicer started as a
research project between the
Surgical Planning Lab (Harvard)
and the CSAIL (MIT)

Image Courtesy of the CSAIL, MIT

3DSlicer History
•  1997: Slicer started as a
research project between the
Surgical Planning Lab (Harvard)
and the CSAIL (MIT)

•  2016: Multi-institution effort to

share the latest advances in
image analysis with clinicians
and scientists
 A MulB-insBtuBon Effort

-  Infrastructure grants fund the pla@orm

-  CollaboraBve projects (e.g. Canada, Japan, Australia, Italy) fund
the applicaBon packages
 Slicer Is Open Madrid 2012

•  Open Science
= Iowa City, USA 2012

Open Source
+
Open Data
+
Open Community

Courtesy R. Kikinis
Slicer Open Community
•  80 authorized developers
contributing to the source
code of Slicer

•  Over 700 subscribers on

Slicer user and Slicer
developer mailing list
3D Slicer in practice


•  Slicer is open-source

•  Slicer works on Windows, Linux,

and Mac

•  Slicer is distributed under a

BSD-style license agreement
with no restriction on use
Slicer: Behind the scenes
Slicer is built every night
on Windows, Mac and
Linux platforms
Slicer Training
•  Hands-on training
workshops at national
and international
venues

•  >2,300 clinicians,
clinical researchers
and scientists trained
since 2005
 3D VisualizaBon of the Anatomy
Following this tutorial,
you will be able to load
and visualize volumes
within Slicer4, and to
interact in 3D with
structural images and
models of the anatomy.
 3DSlicer Version4

The Welcome module

is the default start-up
module

SlicerWelcome Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015

 3DSlicer Version4
Each module of Slicer includes a series
of tabs, which gives access to different
functionalities

Click on the arrow symbol to display

the content of each tab

SlicerWelcome Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015

 3DSlicer Version4

The Main Window tab contains

information on the basic organization of
Slicer’s user interface

Scroll down to see all the contents

SlicerWelcome Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015

 Slicer User Interface

User Interface (UI) panel of Toolbar

the Slicer Welcome Module

3D Viewer

2D anatomical viewers

Data Probe
SlicerWelcome Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Slicer4
Browse to the locaBon of the
MR dataset MR-head.nrrd
on your disk.

Drag and drop it into Slicer

Slicer automatically opens

the ‘Add data into the Click on OK to load the
scene’ window. dataset into Slicer

 Loading a volume

The axial, sagittal and coronal views appear

in the 2D viewers

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

Click on the Slicer layout

icon

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

Click on the Red slice only

option

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

Position your mouse over the

pin icon to display the slice
viewer toolbar

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

Once the slice viewer toolbar

is displayed, click on the “>>“

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

This menu will appear once

the “>>“ button is pressed

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

Click on the Lightbox menu

and chose the option “6x6
view”

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

Slicer displays 36
consecutive images of the
dicom volume. Use the red
slice slider to browse through
the data

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

Click on the Slicer layout

icon and select
Conventional

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

Position your arrow again on

the pin icon of the red
viewer, select the Lightbox
menu and change it back to
“1x1 view”

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

Position your arrow again on

the pin icon of the red viewer
and click on the links icon to
link all three viewers

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

Once the icons are linked,

click on the eye icon to
display all 3 anatomical slices
in the 3D viewer

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume
c

All three anatomical slices

are shown in the 3D viewer

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a volume

Use the left mouse button to

rotate the camera and the
right mouse button to zoom in
and out

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Close the scene
To close the scene, click on
File and select Close Scene

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Exit Slicer

To exit Slicer, click on Slicer

and select Exit

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a Scene

Drag and drop the file

‘3DHeadScene.mrml’ into Slicer

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading a Scene

Slicer automatically
opens the ‘Add data
into the scene’
window.

Click on OK to load
the scene file.

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading the Slicer Scene

A 3D surface model of the head, and

2D anatomical slices appear in the
Slicer Viewer

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Loading the Slicer Scene

Select the Modules menu and select

Models

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Models Module

The list of 3D scenes appear in the

Models panel

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Position the cursor over the pin icon

to reveal the slice menu and click on
the eye icon to reveal the axial slice

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Notice the axial slice through the 3D

model of the head

Once the axial slice is displayed in the

3D viewer, click on Skin in the list of
3D scenes

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Scroll down the Models tabs and

locate the “Color” tab. Lower the
Opacity to a transparent level,
around .30

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Notice the skin has become almost

fully transparent

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Scroll back up to the 3D scenes

menu and select skull_bone

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Turn off its visibility by unchecking

the Visibility option and notice the
bone disappearing from the 3D
view of the head

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Position your mouse over the pin

icon in the coronal slice view and
select the eye icon to reveal the
coronal slice in the 3D view

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

The coronal slice is shown in the

3D viewer.

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon
Scroll up and select the 3D scene
hemispheric_white_matter, then
check off the option for Clip under
the Visibility tab

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Scroll down and find the tab

Clipping, and check off the options
for Green Slice Clipping and
Negative Space

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

The optic chiasm appears in the

3D viewer

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Scroll up and uncheck the option

for Clip and lower the Opacity of
hemispheric_white_matter

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

The intersection of the white matter

surface with the 2D anatomical
slices are shown in the 2D viewers

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Position your cursor over the pin

icon in the corona slice view and
unselect the eye icon

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Click on the Slicer Layout icon

and select Conventional

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 3D VisualizaBon

Position your cursor over the pin

icon in the 3D viewer to display the
3D control windows. Select the A
(Anterior) view of the 3D models
3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Part 3:

Saving a scene

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Saving a Scene

Click on File and select Save

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Saving a Scene
The Save Scene and Unsaved Data
window lists all the elements of the
slicer scene.

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Saving a Scene

Check off the box next to the scene

named 3DHeadScene.mrml and
double click on it.
Rename it myNewScene.mrml
and select Save
3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Saving a Scene

Click on File and select Quit to

close myNewScene.mrml and exit
Slicer

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Scene Restore

Restart Slicer and click on Load

Data

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Scene Restore
Click Choose File(s) to Add and
Browse your folders to find the file
myNewScene.mrml in the
3DHeadData folder

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Scene Restore

Click OK

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Slicer4

The 3D scene myNewScene.mrml

appears in the viewer

3D Data Loading and VisualizaBon Sonia Pujol, Ph.D. NA-MIC ARR 2012-2015
 Acknowledgments
•  NaBonal Alliance for Medical Image CompuBng
(NA-MIC)
NIH U54EB005149

•  Neuroimage Analysis Center (NAC)
NIH P41RR013218

•  Fan Zhang, The University of Sydney

Sonia Pujol, Ph.D. NaBonal Alliance for

3D Data Loading and Visualization
Medical Image CompuBng
ARR 2012-2015