1. -1- Massachusetts General Hospital National Alliance for Medical Image Computing Using Plastimatch for DICOM / DICOM-RT Import Gregory C. Sharp Department of Radiation Oncology Massachusetts General Hospital 3D Slicer Training Compendium Tutorial Version 1.0, Jun 8, 2010

2. -2- Massachusetts General Hospital National Alliance for Medical Image Computing Learning Objective This tutorial is a step-by-step guide, and includes: 1) Downloading the Plastimatch extension to 3D Slicer 2) Loading the DICOM and DICOM-RT data 3) Inspecting the results The plastimatch web site is: http://plastimatch.org

3. -3- Massachusetts General Hospital National Alliance for Medical Image Computing 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/85/934/chest-phantom-dicomrt-xio-4.33.02.tar.gz

4. -4- Massachusetts General Hospital National Alliance for Medical Image Computing Part 1: Downloading the Plastimatch Extension

5. -5- Massachusetts General Hospital National Alliance for Medical Image Computing (This part of the tutorial might not work correctly, pending the Slicer 3.6 release)

6. -6- Massachusetts General Hospital National Alliance for Medical Image Computing Start up 3D Slicer Choose “Extension Manager” from the “View” menu

7. -7- Massachusetts General Hospital National Alliance for Medical Image Computing Click “Next”

8. -8- Massachusetts General Hospital National Alliance for Medical Image Computing Find the plastimatch plugin, and click “Select” Then, click “Download and Install”

9. -9- Massachusetts General Hospital National Alliance for Medical Image Computing The “Status” should become green Click “Next”

10. -10- Massachusetts General Hospital National Alliance for Medical Image Computing Restart 3D Slicer

11. -11- Massachusetts General Hospital National Alliance for Medical Image Computing Part 2: Loading the DICOM and DICOM-RT data

12. -12- Massachusetts General Hospital National Alliance for Medical Image Computing Start up 3D Slicer

13. -13- Massachusetts General Hospital National Alliance for Medical Image Computing In the Plastimatch menu, choose DICOM / DICOM-RT Import

14. -14- Massachusetts General Hospital National Alliance for Medical Image Computing First we need to choose the input directory

15. -15- Massachusetts General Hospital National Alliance for Medical Image Computing Click on any file in the directory

16. -16- Massachusetts General Hospital National Alliance for Medical Image Computing Next, we need to specify three outputs: image, labelmap, and dose

17. -17- Massachusetts General Hospital National Alliance for Medical Image Computing For each of these three output items, choose: “Create New Volume”

18. -18- Massachusetts General Hospital National Alliance for Medical Image Computing The tutorial data contains a CT. So you don't need to specify a reference image. A reference image is needed when your input data does not contain a CT image.

19. -19- Massachusetts General Hospital National Alliance for Medical Image Computing Click “Apply” Importing the data will take about 20 seconds.

20. -20- Massachusetts General Hospital National Alliance for Medical Image Computing You should see something like this. The structures in the DICOM-RT structure set will be imported as a labelmap.

21. -21- Massachusetts General Hospital National Alliance for Medical Image Computing Part 3: Inspecting the results

22. -22- Massachusetts General Hospital National Alliance for Medical Image Computing To see the CT image and dose, click on the “label opacity” button (the little green button)

23. -23- Massachusetts General Hospital National Alliance for Medical Image Computing Move the slider back and forth, and choose a good level where you can see both the structures and the dose.

24. -24- Massachusetts General Hospital National Alliance for Medical Image Computing By default, the dose is loaded as the background image. You can choose the foreground and background images by choosing the menus to the right of the “F” and “B”.

25. -25- Massachusetts General Hospital National Alliance for Medical Image Computing Here, I set the background to be the CT, and the foreground to be the dose

26. -26- Massachusetts General Hospital National Alliance for Medical Image Computing To make the dose look better, we need to change the colormap. Choose “Volumes” in the module menu.

27. -27- Massachusetts General Hospital National Alliance for Medical Image Computing Set “Import Volume2” to be the active volume.

28. -28- Massachusetts General Hospital National Alliance for Medical Image Computing Modify the alpha blending value until you see both the dose and anatomy at the same time

29. -29- Massachusetts General Hospital National Alliance for Medical Image Computing Change the dose “lookup table” to Discrete / FullRainbow

30. -30- Massachusetts General Hospital National Alliance for Medical Image Computing Next, change the threshold from Off to Manual.

31. -31- Massachusetts General Hospital National Alliance for Medical Image Computing Use the slider bars to change the lower threshold to about 10. These thresholds are in units of Gy, just like the DICOM-RT dose.

32. -32- Massachusetts General Hospital National Alliance for Medical Image Computing Conclusion Congratulations! You have completed the tutorial. Please send corrections or suggestions to: Greg Sharp gcsharp@partners.org gcsharp@partners.org Or visit the web page at: http://plastimatch.org

33. -33- Massachusetts General Hospital National Alliance for Medical Image Computing National Alliance for Medical Image Computing NIH U54EB005149 Acknowledgements 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