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Using Plastimatch for Landmark-Based Registration

3D Slicer Training Compendium. Using Plastimatch for Landmark-Based Registration. Tutorial Version 1.0, Jan 27, 2011. Nadya Shusharina Department of Radiation Oncology Massachusetts General Hospital. Learning Objective. This tutorial is a step-by-step guide, and includes:

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Using Plastimatch for Landmark-Based Registration

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  1. 3D Slicer Training Compendium Using Plastimatch forLandmark-Based Registration Tutorial Version 1.0, Jan 27, 2011 Nadya Shusharina Department of Radiation OncologyMassachusetts General Hospital

  2. 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

  3. 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

  4. Part 1: Downloading the Plastimatch Extension

  5. (This part of the tutorial might not workcorrectly, pending the Slicer 3.6 release)

  6. Start up 3D Slicer Choose “Extension Manager”from the “View” menu

  7. Click “Next”

  8. Find the plastimatch plugin,and click “Select” Then, click “Download and Install”

  9. The “Status” should become green Click “Next”

  10. Restart 3D Slicer

  11. Part 2: Loading the example data

  12. Start up 3D Slicer

  13. Choose “Add data” from the menu

  14. Choose “Add files” in dialog box

  15. Select (highlight) example files: fix.mha and mov.mha Then click “Open”

  16. Click “Apply”

  17. The images are now loaded

  18. Part 3: Visualizing the example data

  19. 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

  20. Choose “Red slice only”

  21. 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.

  22. Click, and select “fix” as the foreground imageand “mov” as the background.

  23. Use the “Manipulate Slice Views” slider to blend between foreground and background

  24. We can now see the alignment of the images.

  25. Part 4: Creating Fiducial Lists

  26. Choose “Fiducials” from the Modules menu

  27. Clic on Fiducial List and Create New FiducialList Rename it as “fixed” Repeat one more time to obtain “moving” list

  28. Clic on “Create-and-place” fiducials. Choose “fixed” list. Slide to the foreground image.

  29. Create fiducials by clicking on lattice corners

  30. Make “fixed” fiducials invisible. Slide to the background image.

  31. Create “moving” fiducials IN THE SAME ORDER as “fixed” fiducials. Choose “moving” list.

  32. Part 5: Running LANDWARP Landmark deformable registration

  33. Go back to the module selector. Choose “LANDWARP Landmark deformable registartion” from “Plastimatch” section

  34. Set “Fixed Volume” to “fix” Set “Moving Volume” to “mov” Set “Fixed Fiducials” to “fixed” Set “Moving Fiducials” to“moving” Set “Output Volume” to “Create New Volume” Use default RBF radius, Stiffness and Default Pixel Value Click “Apply”

  35. Check the status in the status bar The registration takes 10 to 15 seconds

  36. When the registration is complete, the warped image is automatically displayed

  37. You have to set the foreground view again to see the registration quality Your results should look like this.

  38. Part 6: Advanced Registartion Options

  39. 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.

  40. Go back to File Menu and load images square_fix.mha, square_mov_mha and fiducials square_fixed.fcsv, square_moving.fcsv

  41. Blended foreground and background images look like this To see fiducials right-click on any of them in the list You can look at them one at a time by sliding the slice view manipulator

  42. Result for LANDWARP default settings looks like this

  43. Setting “Stiffness” to 0.3 improves the result significantly

  44. NOTE THAT Increasing the “Stiffness” improves smoothness, but Declines accuracy of landmark matching

  45. Conclusion Congratulations! You have completed the tutorial. Please send corrections or suggestions to: Nadya Shusharina nshusharina@partners.org Or visit the web page at: http://plastimatch.org

  46. 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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