Using Plastimatch for DICOM / DICOM-RT Import

3D Slicer Training Compendium
Using Plastimatch for
DICOM / DICOM-RT Import
Tutorial Version 1.1, Dec 28, 2010
Gregory C. Sharp
Department of Radiation Oncology
Massachusetts General Hospital
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Learning Objective
This tutorial is a step-by-step guide, and includes:
1) Downloading the Plastimatch extension to 3D Slicer
2) Loading the DICOM and DICOM-RT data
3) Inspecting the results
The plastimatch web site is: http://plastimatch.org
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Prerequisites
This tutorial assumes that you have already downloaded the
sample data. You can get the data from here:
http://forge.abcd.harvard.edu/gf/download/frsrelease/85/934/chest-phantom-dicomrt-xio-4.33.02.tar.gz
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Part 1: Downloading the Plastimatch Extension
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(This part of the tutorial might not work
correctly, pending the Slicer 3.6 release)
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Start up 3D Slicer
Choose “Extension Manager”
from the “View” menu
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Click “Next”
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Find the plastimatch plugin,
and click “Select”
Then, click “Download and Install”
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The “Status” should become green
Click “Next”
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Restart 3D Slicer
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Part 2: Loading the DICOM and DICOM-RT data
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Start up 3D Slicer
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In the Plastimatch menu,
choose DICOM / DICOM-RT Import
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First we need to choose
the input directory
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Click on any
file in the directory
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Next, we need to
specify three outputs:
image, labelmap, and dose
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Depending on your
plugin version, you
might have a choice
for “Output SS Image”.
You can ignore that.
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For each output item,
choose: “Create New Volume”
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A reference image is needed
when your input data does
not contain a CT image.
The tutorial data contains a CT.
So you don't need to specify
a reference image.
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Click “Apply”
Importing the data will
take about 20 seconds.
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You should see something
like this. The structures in
the DICOM-RT structure set
will be imported as a labelmap.
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Part 3: Inspecting the results
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To see the CT image and
dose, click on the
“label opacity” button
(the little green button)
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Move the slider back and
forth, and choose a good
level where you can see
both the structures and the dose.
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By default, the dose is loaded as the background
image. You can choose the foreground and
background images by choosing the menus
to the right of the “F” and “B”.
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Here, I set the background
to be the CT, and the foreground
to be the dose
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To make the dose look better,
we need to change the colormap.
Choose “Volumes” in the module
menu.
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Set “Import Volume2” to be the
active volume.
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Modify the alpha blending value
until you see both the dose
and anatomy at the same time
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Change the dose “lookup table”
to Discrete / FullRainbow
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Next, change the threshold
from Off to Manual.
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Use the slider bars to change
the lower threshold to about 10.
These thresholds are in units of
Gy, just like the DICOM-RT dose.
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Conclusion
Congratulations! You have completed the tutorial.
Please send corrections or suggestions to:
Greg Sharp
gcsharp@partners.org
Or visit the web page at:
http://plastimatch.org
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Acknowledgements
National Alliance for Medical Image Computing
NIH U54EB005149
National Institutes of Health
NIH / NCI 6-PO1 CA 21239
Federal share of program income earned by MGH on C06CA059267
Progetto Rocca Foundation
A collaboration between MIT and Politecnico di Milano
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