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Using Plastimatch forLandmark-Based Registration
Nadya Shusharina
Department of Radiation Oncology
Massachusetts General Hospital
3D Slicer Training Compendium
Tutorial Version 1.0, Jan 27, 2011
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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 sample images
3) Visualizing the example data
4) Creating fiducial lists
5) Running LANDWARP Landmark deformable registration
6) Advanced Registartion Options
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/85/1596/synthetic_img.zip
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Part 1: Downloading the Plastimatch Extension
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(This part of the tutorial might not workcorrectly, 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 example data
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Start up 3D Slicer
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Choose “Add data” from the menu
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Choose “Add files” in dialog box
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Select (highlight) example files:fix.mha and mov.mha
Then click “Open”
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Click “Apply”
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The images are now loaded
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Part 3: Visualizing the example data
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We can now see the alignment of the images. To see it better, we need to increase the viewpoint size.
Click on the layout chooser button
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Choose “Red slice only”
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Much better! We want to look at how well the images are aligned before we start
3D Slicer can view a “foreground” (F) and “background” (B) image at the same time. After loading, (F) is set to “None” in all views.
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Click, and select “fix” as the foreground imageand “mov” as the background.
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Use the “Manipulate Slice Views” slider to blend between foreground and background
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We can now see the alignment
of the images.
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Part 4: Creating Fiducial Lists
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Choose “Fiducials” from the Modules menu
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Clic on Fiducial List and Create New FiducialList
Rename it as “fixed”
Repeat one more time to obtain “moving” list
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Choose “fixed” list.
Slide to the foreground image.
Clic on “Create-and-place” fiducials.
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Create fiducials by clicking on lattice corners
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Slide to the background image.
Make “fixed” fiducials invisible.
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Choose “moving” list.
Create “moving” fiducials IN THE SAME ORDER as“fixed” fiducials.
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Part 5: Running LANDWARP Landmark deformable registration
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Go back to the module selector.
Choose “LANDWARP Landmark deformable registartion” from “Plastimatch” section
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Set “Fixed Volume” to “fix”Set “Moving Volume” to “mov”
Set “Output Volume” to “Create New Volume”
Set “Fixed Fiducials” to “fixed”Set “Moving Fiducials” to“moving”
Use default RBF radius, Stiffness and Default Pixel ValueClick “Apply”
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Check the status in the status bar
The registration takes 10 to 15 seconds
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When the registration is complete, the warped image is automatically displayed
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You have to set the foreground view again to see the registration quality
Your results should look like this.
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Part 6: Advanced Registartion Options
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By default, registration does not include regularization of the vector field, i.e. “Stiffness” is set to “0”
But for some images regularization is a need.
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Go back to File Menu and load images square_fix.mha, square_mov_mha and fiducials square_fixed.fcsv, square_moving.fcsv
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Blended foreground and background images look like this
You can look at them one at a time by sliding the slice view manipulator
To see fiducials right-click on any of them in the list
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Result for LANDWARP default settings looks like this
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Setting “Stiffness” to 0.3 improves the result significantly
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Increasing the “Stiffness” improves smoothness,
but
Declines accuracy of landmark matching
NOTE THAT
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Conclusion
Congratulations! You have completed the tutorial.
Please send corrections or suggestions to:
Nadya Shusharina
[email protected]
Or visit the web page at:
http://plastimatch.org
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National Alliance for Medical Image ComputingNIH U54EB005149
Acknowledgements
National Institutes of HealthNIH / NCI 6-PO1 CA 21239Federal share of program income earned by MGH on C06CA059267
Progetto Rocca FoundationA collaboration between MIT and Politecnico di Milano