3D Slicer Plastimatch Registration Tutorial by yTQ20o

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									                                 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



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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) 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

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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/85/1004/rider-lung-images.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 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) both example files:
                                         fix.nrrd and mov.nrrd




                                                       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 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 image.
                                       Repeat for all three views.

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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. To see it better, we
                                 need to increase the viewport size.

                                 Click on the layout chooser button




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                 Choose “Red slice only”




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




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




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                                 Set it to “Warm Tint 1”




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          Part 4: Running Plastimatch




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                                 Go back to the module selector




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                                 Choose “B-spline deformable
                                 registration” from the
                                 “Plastimatch” section




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                                 Set “Fixed Volume” to “fix”
                                 Set “Moving Volume” to “mov”


                                 Set “Output Volume” to
                                 “Create New Volume”




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                                 Click “Apply”


                                 (You might need to scroll down)


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                                 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


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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




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                                                          Your results
                                                          should look
                                                          like this.




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          Part 5: Optimizing Your Registration




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




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                                 Click on “Enable Stage 2”
                                 Then click “Apply”

                                 This takes 12 seconds on
                                 the Tesla C1060. Might be
                                 3-4 minutes on a laptop.
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                                                 Like before, the
                                                 output is automatically
                                                 loaded.




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                                                    Your results should
                                                    look like this.

                                                    Note improvement
                                                    in the alignment of
                                                    the mediastinum




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          Part 6: Advanced Plastimatch Options




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                                 By default, plastimatch optimizes
                                 Mean-squared error (MSE).

                                 But you can choose Mutual
                                 Information (MI) instead




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                                 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.

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                                 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.




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                                 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




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                                 Decreasing max iterations
                                 improves registration speed

                                 Increasing max iterations
                                 improves registration accuracy




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                                 Decreasing the grid spacing
                                 improves accuracy

                                 Increasing the grid spacing
                                 improves reliability




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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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