Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol,...
Transcript of Slicer4Minute Tutorial - Harvard University · 2017. 1. 6. · Slicer4Minute Tutorial Sonia Pujol,...
Slicer4Minute Tutorial
Sonia Pujol, Ph.D.
Surgical Planning Laboratory
Harvard University
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
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
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
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
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
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
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
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)
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
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.
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
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
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
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
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
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
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
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
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
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
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
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
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
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