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3D_Slicer_Plastimatch_Landmark_Registration_Tutorial

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					                                 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



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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 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) 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
     Massachusetts in all views.
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                                 Click, and select “fix”
                                 as the foreground image
                                 and “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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                                     Clic on “Create-and-place” fiducials.



                 Choose “fixed” list.




Slide to the foreground image.




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                    Create fiducials by clicking on lattice corners




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                              Make “fixed” fiducials invisible.




Slide to the background image.




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


         Choose “moving” list.




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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 “Fixed Fiducials” to “fixed”
                                     Set “Moving Fiducials” to“moving”

                                     Set “Output Volume” to
                                     “Create New Volume”

                                     Use default RBF radius, Stiffness
Click “Apply”                        and Default Pixel Value




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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
 To see fiducials                     images look like this
 right-click on any
 of them in the list




You can look at
them one at a time
by sliding the slice
view manipulator




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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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     NOTE THAT

Increasing the “Stiffness”
improves smoothness,

       but

Declines accuracy of
landmark matching




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                                                      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



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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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