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3DVisualizationDICOM Slicer4.8 SoniaPujol

This tutorial guides the user through loading a DICOM CT dataset into 3D Slicer and visualizing it in various ways. It shows how to import the data, adjust window/level settings, view slices in 2D and a 3D rendered view. It also demonstrates cropping the data using a region of interest to view specific anatomical structures.

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David Fernandez
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152 views26 pages

3DVisualizationDICOM Slicer4.8 SoniaPujol

This tutorial guides the user through loading a DICOM CT dataset into 3D Slicer and visualizing it in various ways. It shows how to import the data, adjust window/level settings, view slices in 2D and a 3D rendered view. It also demonstrates cropping the data using a region of interest to view specific anatomical structures.

Uploaded by

David Fernandez
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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3D Visualiza+on of DICOM Data

Sonia Pujol, Ph.D.



Assistant Professor of Radiology
Director, 3D Slicer Training & Educa+on
Brigham and Women’s Hospital
Harvard Medical School

spujol@bwh.harvard.edu



Goal of the Tutorial
The tutorial guides you
step-by-step through the
process of loading and
visualizing a DICOM CT
dataset with 3D Slicer.

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


Tutorial Materials
•  SoRware:
3D Slicer version 4.8.1

•  Dataset:
3D Visualiza+on DICOM images part 1

© Sonia Pujol, Ph.D. All Rights Reserved 3


Tutorial Dataset

Download and unzip the file


3DVisualiza+on_DICOM_images_part1.zip

© Sonia Pujol, Ph.D. All Rights Reserved 4


Loading a DICOM volume

Drag and drop the directory ‘dataset1_Thorax-Abdomen’


into Slicer

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


Loading a DICOM volume

A pop-up window appears:


Select Load directory into DICOM database and click on OK

© Sonia Pujol, Ph.D. All Rights Reserved 6


Loading a DICOM volume

The pa#ent1 DICOM dataset appears in the DICOM browser.


Select pa#ent1 and then click Load to import the data into Slicer
© Sonia Pujol, Ph.D. All Rights Reserved 7
Loading a DICOM volume
Select the Volumes
module from the
modules menu

Select the AcLve Volume


6:CT_Thorax_Abdomen

Click on the Window Level


Preset CT-abdomen to
automaLcally adjust the
window/level display of the CT
scan

© Sonia Pujol, Ph.D. All Rights Reserved 8


Loading a DICOM volume
PosiLon 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

© Sonia Pujol, Ph.D. All Rights Reserved 9


Loading a DICOM volume

The three anatomical slices


appear in the 3D viewer.
Use the right-mouse
buWon in the 3D Viewer to
zoom in and out

© Sonia Pujol, Ph.D. All Rights Reserved 10


Loading a DICOM volume

The three anatomical slices


appear in the 3D viewer.
Use the right-mouse
buWon in the 3D Viewer to
zoom in and out

© Sonia Pujol, Ph.D. All Rights Reserved 11


Loading a DICOM volume

PosiLon the mouse over the blue


banner in the 3D viewer window
to display the 3DView controller
Click on the upper leY icon to
center the 3D view on the scene

© Sonia Pujol, Ph.D. All Rights Reserved 12


Loading a DICOM volume

Click on the Slicer layout


menu icon, and select the
Conven#onal Widescreen
layout

© Sonia Pujol, Ph.D. All Rights Reserved 13


Volume Rendering

Select the module


Volume Rendering in
the modules menu

© Sonia Pujol, Ph.D. All Rights Reserved 14


Volume Rendering

Click on Preset in the Display tab


to display the list of available
presets for the transfer funcLon

Select the Preset CT-Cardiac3

© Sonia Pujol, Ph.D. All Rights Reserved 15


Volume Rendering

Click on Preset in the Display tab


to display the list of available
presets for the transfer funcLon

Select the Preset CT-Cardiac3

© Sonia Pujol, Ph.D. All Rights Reserved 16


Volume Rendering

Select the Rendering VTK


GPU Ray Cas#ng, and
click on the eye icon in
the Volume tab to
display the rendered
imaged in the 3D viewer

© Sonia Pujol, Ph.D. All Rights Reserved 17


Volume Rendering

The volume rendered


image of the thoraco-
abdominal CT scans
appears in the 3D
viewer

© Sonia Pujol, Ph.D. All Rights Reserved 18


Volume Rendering

Click on Display ROI to display


The volume rendered
a region of interest that we will
image of the aorta and rib
use for cropping the dataset
cage appears in the 3D
Check the opLon Enable
viewer

© Sonia Pujol, Ph.D. All Rights Reserved 19


Volume Rendering

Turn off the visibility of the


volume rendered image
Turn on the visibility of the
grayscale images in to the
3D Viewer
PosiLon the ROI around the
leY kidney using the ROI
controls in the 2D views and
in the 3D viewer

© Sonia Pujol, Ph.D. All Rights Reserved 20


Volume Rendering

Slicer displays the


volume rendered
image of the leY
kidney

© Sonia Pujol, Ph.D. All Rights Reserved 21


Volume Rendering

Extend the ROI to generate a volume


rendered image of the right kidney

© Sonia Pujol, Ph.D. All Rights Reserved 22


Volume Rendering

Extend the ROI to generate a volume


rendered image of the right kidney

© Sonia Pujol, Ph.D. All Rights Reserved 23


Volume Rendering

Slicer displays the


volume rendered
image of the right and
leY kidney

© Sonia Pujol, Ph.D. All Rights Reserved 24


Volume Rendering

Click on FileàClose Scene


to close the scene

© Sonia Pujol, Ph.D. All Rights Reserved 25


Acknowledgments
Na+onal Alliance for Medical Image
Compu+ng (NA-MIC)
NIH U54EB005149

Neuroimage Analysis Center (NAC)
NIH P41EB015902


© Sonia Pujol, Ph.D. All Rights Reserved 26

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