-1- Massachusetts General Hospital National Alliance for Medical Image Computing Using Plastimatch for Landmark-Based Registration Nadya Shusharina Department

-1-Massachusetts General Hospital National Alliance for Medical Image Computing

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


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


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


Part 1: Downloading the Plastimatch Extension


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


Start up 3D Slicer

Choose “Extension Manager”from the “View” menu


Click “Next”


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


The “Status” should become green

Click “Next”


Restart 3D Slicer


Part 2: Loading the example data


Start up 3D Slicer


Choose “Add data” from the menu


Choose “Add files” in dialog box


Select (highlight) example files:fix.mha and mov.mha

Then click “Open”


Click “Apply”


The images are now loaded


Part 3: Visualizing the example data


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


Choose “Red slice only”


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.


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


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


We can now see the alignment

of the images.


Part 4: Creating Fiducial Lists


Choose “Fiducials” from the Modules menu


Clic on Fiducial List and Create New FiducialList

Rename it as “fixed”

Repeat one more time to obtain “moving” list


Choose “fixed” list.

Slide to the foreground image.

Clic on “Create-and-place” fiducials.


Create fiducials by clicking on lattice corners


Slide to the background image.

Make “fixed” fiducials invisible.


Choose “moving” list.

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


Part 5: Running LANDWARP Landmark deformable registration


Go back to the module selector.

Choose “LANDWARP Landmark deformable registartion” from “Plastimatch” section


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”


Check the status in the status bar

The registration takes 10 to 15 seconds


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


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

Your results should look like this.


Part 6: Advanced Registartion Options


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.


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


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


Result for LANDWARP default settings looks like this


Setting “Stiffness” to 0.3 improves the result significantly


Increasing the “Stiffness” improves smoothness,

but

Declines accuracy of landmark matching

NOTE THAT


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


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

Documents

-1- Massachusetts General Hospital National Alliance for Medical Image Computing Using Plastimatch for Landmark-Based Registration Nadya Shusharina Department