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Slicer4Minute Tutorial Sonia Pujol, Ph.D. Surgical Planning Laboratory Harvard University

Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

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Page 1: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D.

Surgical Planning Laboratory

Harvard University

Page 2: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

First, click on Load Data

Page 3: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

The “Add data into the

scene” table appears.

Click Choose Directory

to Add

Page 4: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Locate and select the

file Slicer4minute and

click Choose

Page 5: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Check off ONLY the box

with the Description

“MRML Scene” and

click OK

Page 6: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Slicer displays the elements

of the slicer4minute scene,

which contains the MR

volume of the brain and a

series of 3D surface models

Page 7: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Next, click the viewing

mode menu and select

the Conventional

Widescreen option

Page 8: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Select the Models

module

Page 9: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

The Models module

GUI displays the list of

models loaded in the

slicer4minute scene,

their color, and the

value of their opacity

(between 0.0 an 1.0)

Page 10: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Click on the pin icon in

the top left corner of the

Red axial slice to

display the slice viewer

menu, then click on the

eye icon to display the

axial slice in the 3D

Viewer

Page 11: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Slicer simultaneously

displays the slices in the

3D viewer. Use the

slider of the red viewer

to browse through the

axial MR slices.

Page 12: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Under the Scene tab,

select the scene

Skin.vtk, then click on

the Display tab

Page 13: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Under the Display tab,

locate the option

Opacity and lower the

opacity of Skin.vtk

Page 14: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Click on the pin icons

of the axial and coronal

slices and select both

eye icons to display

both the axial and

coronal slices in the 3D

viewer

Page 15: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Select the scene

skull_bone.vtk and click on

the Display tab

Page 16: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Under the Display tab,

uncheck the option for

Visible. The white

matter surface, as well

as the left and right

optic nerves, appear in

the 3D viewer

Page 17: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Select the scene

hemispheric_white_matter.vtk,

and under the Display tab check

the option Clip

Page 18: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Scroll down the Models

module and select the

tab Clipping, and check

off the options for

Green Slice Clipping in

the Negative space

Page 19: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Use the slider of the

axial and coronal slices

to expose the optic

chiasm

Page 20: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Select the scene

Skin.vtk again, and

under the Display tab

slightly increase the

opacity

Page 21: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

Click on the viewing

mode menu and select

the 3D only view

Page 22: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

The slice viewers

disappear. Click on the

pin icon of the 3D

viewer and select the

option Spin the 3D view

Page 23: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

The 3D model starts to

spin. Click the same

option to stop the model

from spinning

Page 24: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Slicer4Minute Tutorial

Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014

Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Hospital, Boston, MA..

Slicer4Minute Tutorial

This tutorial was a short introduction to the 3D visualization capabilities

of Slicer. Visit the Slicer4 training compendium for more information on

the software

http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Training

Page 25: Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol, Ph.D. NA-MIC ARR 2012-2014 Image Courtesy of Dr. Alexandra Golby, Brigham and Women’s

Acknowledgments

Sonia Pujol, Ph.D. National Alliance for Medical Image Computing

ARR 2012-2014

Slicer4Minute Tutorial

• National Alliance for Medical Image Computing (NA-MIC)

NIH U54EB005149

• Neuroimage Analysis Center (NAC)

NIH P41RR013218

• Parth Amin, WIT ’16

• Matthew Flynn, WIT ‘16