Plastimatch Dose Warping - National Alliance for Medical Image

3D Slicer Training Compendium
Plastimatch Dose Warping
Tutorial Version 1.0, May 19, 2011
Nadya Shusharina, Gregory C. Sharp
Department of Radiation Oncology
Massachusetts General Hospital
Massachusetts General Hospital
National Alliance for Medical Image Computing
-1-
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) Running deformable registration
4) Running dose warping
5) Exporting DICOM-RT data
The plastimatch web site is: http://plastimatch.org
Massachusetts General Hospital
National Alliance for Medical Image Computing
-2-
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/85/1828/popi-plan.tar.gz
Massachusetts General Hospital
National Alliance for Medical Image Computing
-3-
Part 1: Downloading the Plastimatch Extension
Massachusetts General Hospital
National Alliance for Medical Image Computing
-4-
(This part of the tutorial might not work
correctly, pending the Slicer 3.6 release)
Massachusetts General Hospital
National Alliance for Medical Image Computing
-5-
Start up 3D Slicer
Choose “Extension Manager”
from the “View” menu
Massachusetts General Hospital
National Alliance for Medical Image Computing
-6-
Click “Next”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-7-
Find the plastimatch plugin,
and click “Select”
Then, click “Download and Install”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-8-
The “Status” should become green
Click “Next”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-9-
Restart 3D Slicer
Massachusetts General Hospital
National Alliance for Medical Image Computing
-10-
Part 2: Loading the DICOM and DICOM-RT data
Massachusetts General Hospital
National Alliance for Medical Image Computing
-11-
Start up 3D Slicer
Massachusetts General Hospital
National Alliance for Medical Image Computing
-12-
In the “Plastimatch” menu,
choose “DICOM/DICOM-RT Import”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-13-
Choose “t00” as “Input DICOM directory”
by clicking on any file in it
Massachusetts General Hospital
National Alliance for Medical Image Computing
-14-
Specify the “Output Image” by
choosing “Create New Volume”
and Renaming it as “t00”
Then click “Open”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-15-
Click “Apply”
Importing the data takes
about 12 seconds on
Intel Xeon 2GHz CPU
Massachusetts General Hospital
National Alliance for Medical Image Computing
-16-
You should see something like this.
To adjust the views click on “Fit to window”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-17-
Specify the second “Input DICOM directory”
by clicking on any file in “t50” directory
Massachusetts General Hospital
National Alliance for Medical Image Computing
-18-
Specify three outputs: Image,
Labelmap and Dose Image
Choose “Create New Volume” and
Rename as “t50”, “t50-lm”, and “t50-d”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-19-
After you click “Apply”
importing the data takes
about 18 seconds on
Intel Xeon 2GHz CPU
The structures in the DICOM-RT
structure set will be imported as a labelmap
Massachusetts General Hospital
National Alliance for Medical Image Computing
-20-
Part 3: Running Deformable Registration
Massachusetts General Hospital
National Alliance for Medical Image Computing
-21-
Choose “t00” as a foreground
and “t50” as a background
image in all panels and select
“None” in labelmap window
Use the “Manipulate Slice Views”
slider to blend between foreground
and background
Massachusetts General Hospital
National Alliance for Medical Image Computing
-22-
First, the images
have to be aligned
in PA direction
Click on the transform chooser button
Choose “Create New Linear Transform”
in Transform Node and type -84.4 in
PA Translation selector, then
press Enter
Massachusetts General Hospital
National Alliance for Medical Image Computing
-23-
Click on the scene chooser button
Drug “t50” into Linear Transform sub-tree
and click on “Harden Transforms”
Repeat with “t50-lm” and “t50-d”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-24-
Go back to “Plastimatch” module and
choose “B-spline deformable registration”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-25-
Set “Fixed Volume” to “t00”
We'reSet
going
to modify
the color
of
“Moving
Volume”
to “t50”
the moving volume. Choose “mov”
Set
“Output
Volume” to
as the
active
volume.
“Create New Volume”
Set “Output B-spline transform” to
“Create New BSpline Transform”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-26-
In “Stage 1 Options” set
“Grid Size (mm)” to 80 and
click “Apply”
Registration takes about 90 seconds
on Intel Xeon 2GHz CPU
Massachusetts General Hospital
National Alliance for Medical Image Computing
-27-
When the registration is complete, the
warped image is automatically displayed
You can check on the registration
quality by manipulating the slice view
between foreground and background
Massachusetts General Hospital
National Alliance for Medical Image Computing
-28-
There is now B-spline deformable
registration Transform in the MRML Tree
Massachusetts General Hospital
National Alliance for Medical Image Computing
-29-
Part 4: Running Structures and Dose Warping
Massachusetts General Hospital
National Alliance for Medical Image Computing
-30-
Go back to “Plastimatch” module and choose
“XFORMWARP Warping with transform”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-31-
To warp the structures set
“Input Volume” to “t50-lm”
Set “Input transform (MRML)” to
“B-spline deformable registration
transform”
In “Output Volume” choose “Create
New Volume” and Rename as “t00-lm”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-32-
After you click “Apply” warping
takes about 3.5 minutes on
Intel Xeon 2GHz CPU
The structures will be displayed
automatically as a volume
Massachusetts General Hospital
National Alliance for Medical Image Computing
-33-
To warp the dose
set “Input Volume” to “t50-d”
In “Output Volume” choose “Create
New Volume” and Rename as “t00-d”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-34-
After you click “Apply” warping
takes about 7 seconds on
Intel Xeon 2GHz CPU
The dose will be displayed
automatically as a volume
Massachusetts General Hospital
National Alliance for Medical Image Computing
-35-
Part 5: Exporting DICOM-RT Data
Massachusetts General Hospital
National Alliance for Medical Image Computing
-36-
Go back to “Plastimatch” module and
choose “DICOM/DICOM-RT Export”
Massachusetts General Hospital
National Alliance for Medical Image Computing
-37-
Set “Output directory” to “t00”
Set “Dose Volume” to “t00-d”
Click “Apply”
Exporting the data is instant
on Intel Xeon 2GHz CPU
Massachusetts General Hospital
National Alliance for Medical Image Computing
-38-
Conclusion
Congratulations! You have completed the tutorial.
Please send corrections or suggestions to:
Greg Sharp
[email protected]
Or visit the web page at:
http://plastimatch.org
Massachusetts General Hospital
National Alliance for Medical Image Computing
-39-
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
Massachusetts General Hospital
National Alliance for Medical Image Computing
-40-