Using Plastimatch for DICOM / DICOM-RT Import
Transcription
Using Plastimatch for DICOM / DICOM-RT Import
3D Slicer Training Compendium Using Plastimatch for DICOM / DICOM-RT Import Tutorial Version 1.1, Dec 28, 2010 Gregory C. Sharp Department of Radiation Oncology Massachusetts General Hospital Massachusetts General Hospital National Alliance for Medical Image Computing -1- 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 Massachusetts General Hospital National Alliance for Medical Image Computing -2- 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 Massachusetts General Hospital National Alliance for Medical Image Computing -3- Part 1: Downloading the Plastimatch Extension Massachusetts General Hospital National Alliance for Medical Image Computing -4- (This part of the tutorial might not work correctly, pending the Slicer 3.6 release) Massachusetts General Hospital National Alliance for Medical Image Computing -5- Start up 3D Slicer Choose “Extension Manager” from the “View” menu Massachusetts General Hospital National Alliance for Medical Image Computing -6- Click “Next” Massachusetts General Hospital National Alliance for Medical Image Computing -7- Find the plastimatch plugin, and click “Select” Then, click “Download and Install” Massachusetts General Hospital National Alliance for Medical Image Computing -8- The “Status” should become green Click “Next” Massachusetts General Hospital National Alliance for Medical Image Computing -9- Restart 3D Slicer Massachusetts General Hospital National Alliance for Medical Image Computing -10- Part 2: Loading the DICOM and DICOM-RT data Massachusetts General Hospital National Alliance for Medical Image Computing -11- Start up 3D Slicer Massachusetts General Hospital National Alliance for Medical Image Computing -12- In the Plastimatch menu, choose DICOM / DICOM-RT Import Massachusetts General Hospital National Alliance for Medical Image Computing -13- First we need to choose the input directory Massachusetts General Hospital National Alliance for Medical Image Computing -14- Click on any file in the directory Massachusetts General Hospital National Alliance for Medical Image Computing -15- Next, we need to specify three outputs: image, labelmap, and dose Massachusetts General Hospital National Alliance for Medical Image Computing -16- Depending on your plugin version, you might have a choice for “Output SS Image”. You can ignore that. Massachusetts General Hospital National Alliance for Medical Image Computing -17- For each output item, choose: “Create New Volume” Massachusetts General Hospital National Alliance for Medical Image Computing -18- A reference image is needed when your input data does not contain a CT image. The tutorial data contains a CT. So you don't need to specify a reference image. Massachusetts General Hospital National Alliance for Medical Image Computing -19- Click “Apply” Importing the data will take about 20 seconds. Massachusetts General Hospital National Alliance for Medical Image Computing -20- You should see something like this. The structures in the DICOM-RT structure set will be imported as a labelmap. Massachusetts General Hospital National Alliance for Medical Image Computing -21- Part 3: Inspecting the results Massachusetts General Hospital National Alliance for Medical Image Computing -22- To see the CT image and dose, click on the “label opacity” button (the little green button) Massachusetts General Hospital National Alliance for Medical Image Computing -23- Move the slider back and forth, and choose a good level where you can see both the structures and the dose. Massachusetts General Hospital National Alliance for Medical Image Computing -24- 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”. Massachusetts General Hospital National Alliance for Medical Image Computing -25- Here, I set the background to be the CT, and the foreground to be the dose Massachusetts General Hospital National Alliance for Medical Image Computing -26- To make the dose look better, we need to change the colormap. Choose “Volumes” in the module menu. Massachusetts General Hospital National Alliance for Medical Image Computing -27- Set “Import Volume2” to be the active volume. Massachusetts General Hospital National Alliance for Medical Image Computing -28- Modify the alpha blending value until you see both the dose and anatomy at the same time Massachusetts General Hospital National Alliance for Medical Image Computing -29- Change the dose “lookup table” to Discrete / FullRainbow Massachusetts General Hospital National Alliance for Medical Image Computing -30- Next, change the threshold from Off to Manual. Massachusetts General Hospital National Alliance for Medical Image Computing -31- 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. Massachusetts General Hospital National Alliance for Medical Image Computing -32- Conclusion Congratulations! You have completed the tutorial. Please send corrections or suggestions to: Greg Sharp [email protected] Or visit the web page at: http://plastimatch.org Massachusetts General Hospital National Alliance for Medical Image Computing -33- 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 Massachusetts General Hospital National Alliance for Medical Image Computing -34-
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