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Using Plastimatch for Deformable Registration

3D Slicer Training Compendium. Using Plastimatch for Deformable Registration. Tutorial Version 1.0, Apr 26, 2010. Gregory C. Sharp 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 Deformable Registration

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  1. 3D Slicer Training Compendium Using Plastimatch forDeformable Registration Tutorial Version 1.0, Apr 26, 2010 Gregory C. Sharp 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) Running deformable registration on the CPU 4) Running deformable registration on the GPU 5) Inspecting registration quality in 3D Slicer 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/85/1004/rider-lung-images.tar.gz

  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) both example files: fix.nrrd and mov.nrrd Then click “Open”

  16. Click “Apply”

  17. The images are now loaded

  18. Part 3: Visualizing the example data

  19. 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.

  20. Click, and select “fix” as the foreground image.Repeat for all three views.

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

  22. We can now see the alignment of the images. To see it better, we need to increase the viewport size. Click on the layout chooser button

  23. Choose “Red slice only”

  24. Much better! Next we're going to try color blending. Choose the “Volumes module.

  25. We're going to modify the color of the moving volume. Choose “mov”as the active volume.

  26. Set it to “Warm Tint 1”

  27. Part 4: Running Plastimatch

  28. Go back to the module selector

  29. Choose “B-spline deformableregistration” from the “Plastimatch” section

  30. Set “Fixed Volume” to “fix” Set “Moving Volume” to “mov” Set “Output Volume” to “Create New Volume”

  31. Click “Apply” (You might need to scroll down)

  32. Check the status in the status bar With a Tesla C1060 GPU, the registration takes 6 seconds A laptop might take 1 or 2 minutes

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

  34. You have to set the foreground view again to see the registration quality

  35. Your results should look like this.

  36. Part 5: Optimizing Your Registration

  37. We're going to try to improve the registration result.

  38. Click on “Enable Stage 2” Then click “Apply” This takes 12 seconds on the Tesla C1060. Might be 3-4 minutes on a laptop.

  39. Like before, the output is automatically loaded.

  40. Your results should look like this. Note improvement in the alignment of the mediastinum

  41. Part 6: Advanced Plastimatch Options

  42. By default, plastimatch optimizes Mean-squared error (MSE). But you can choose Mutual Information (MI) instead

  43. By default, plastimatch uses the GPU. But you can choose to use the CPU instead. Plastimatch CPU uses OpenMP to take advantage of modern multi-core systems However, in Plastimatch 1.4, mutual information does not take advantage of the GPU, nor is it multi-threaded.

  44. In our tutorial, the images were sufficiently well aligned that we could use B-spline registration. But if they are not well aligned, you can do a “rough alignment” using translation, rigid, or affine registration. Click “Enable Stage 0” to enable the rough alignment.

  45. For each stage, you can modify the subsampling rate, grid size, and maximum iterations Decreasing the subsampling rate improves accuracy Increasing the subsampling rate improves reliability

  46. Decreasing max iterations improves registration speed Increasing max iterations improves registration accuracy

  47. Decreasing the grid spacing improves accuracy Increasing the grid spacing improves reliability

  48. Conclusion Congratulations! You have completed the tutorial. Please send corrections or suggestions to: Greg Sharpgcsharp@partners.org Or visit the web page at: http://plastimatch.org

  49. 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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