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Slicer User Training 101 IGT Edition Haiying Liu Nobuhiko Hata.

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Presentation on theme: "Slicer User Training 101 IGT Edition Haiying Liu Nobuhiko Hata."— Presentation transcript:

1 Slicer User Training 101 IGT Edition Haiying Liu Nobuhiko Hata

2 © NIH National Center for Image-Guided Therapy, October 2006 Slide 2 Acknowledgements National Center for Image- Guided Therapy NIH U41RR019703 National Alliance for Medical Image Computing NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218

3 © NIH National Center for Image-Guided Therapy, October 2006 Slide 3 Disclaimer It is the responsibility of the user of Slicer IGT to comply with both the terms of the license and with the applicable laws, regulations and rules.

4 © NIH National Center for Image-Guided Therapy, October 2006 Slide 4 Goal of this tutorial Simulate the brain surgical navigation using a plastic skull, a tracking sensor and Slicer IGT

5 © NIH National Center for Image-Guided Therapy, October 2006 Slide 5 Outline of this tutorial 1)Introduction to 3D Slicer 2)Required materials 3)System set-up 4)Patient to image registration 5)Navigation

6 © NIH National Center for Image-Guided Therapy, October 2006 Slide 6 Welcome to 3D Slicer IGT

7 © NIH National Center for Image-Guided Therapy, October 2006 Slide 7 What is 3D Slicer? 3D Slicer is… – An end-user application for 3D medical image computing research and Image Guided Therapy – A platform for research where new techniques can be plugged into a useful framework – A freely-downloadable program with source and binaries for Windows, Linux, Solaris and (increasingly) Mac OSX – NOT an FDA approved medical device and CANNOT be used clinically without proper research controls (IRB etc.) – NOT finished – some parts will work better than others and it is constantly evolving

8 © NIH National Center for Image-Guided Therapy, October 2006 Slide 8 Slicer background SPL Image Guided Surgery and Visualization (Kikinis, Westin, Hata, Halle, others) Slicer Application Pulled Together by Dave Gering 1997-1999 with VTK and Tcl Further Development and Architecture by Lauren O’Donnell 1999-2001 Ongoing Development of Slicer’s Base Primarily by Steve Pieper and Nicole Aucoin Many Modules and Contributions by Various Authors – BWH, MIT, MGH, Georgia Tech, UCSD, JHU... Now being used as a reference application platform for NA- MIC and NCIGT

9 © NIH National Center for Image-Guided Therapy, October 2006 Slide 9 Features Load Medical Image Data: MR, CT in DICOM, GE, Analyze… XML-based File Format: MRML (Medical Reality Markup Language) Interactive Editor: Draw, Threshold, Math Morphology… Automated Segmenters: EM Segmentation, Fast Marching, Level Sets… Visualization: Model Building, Stereo Rendering, Animation… Registration: Manual, ITK… Measurement: Fiducial-Based, Volumetric, Polyhedral Intersection, Vessel Cross-Section, Osteotomy Planning IGT: Tracked Probes, Real-Time Images, Robot Control Additional Application-Specific Features in Modules…

10 © NIH National Center for Image-Guided Therapy, October 2006 Slide 10 Materials for this tutorial A plastic skull A tracking device Slicer IGT SPLOT server CT scan of the plastic skull

11 © NIH National Center for Image-Guided Therapy, October 2006 Slide 11 Buy a plastic skull A life-size plastic skull can be bought at any of the following companies: Anatomical Chart Company, Skokie, IL. www.anatomical.cm. $29.95 (as of Nov. 2006)www.anatomical.cm Lippincott Williams & Wilkins (lww.com) Amazon.com Other international Amazon sites

12 © NIH National Center for Image-Guided Therapy, October 2006 Slide 12 Obtain a tracking system –Our preferred tracking systems are Aurora, Polaris, and Polaris Vicra from Northern Digital, Inc. (Ontario, Canada) –Aurora with a 6 DOF sensor is selected and tested for this tutorial. Users may choose other tracking sensors. (http://www.ndigital.com/aurora.php)

13 © NIH National Center for Image-Guided Therapy, October 2006 Slide 13 One download Slicer-IGT may be downloaded here: http://www.na-mic.org/Wiki/index.php/IGT-Tutorials The current package is for Windows XP. Slicer- IGT for Linux will be available soon. Unzip Slicer-IGT.zip by WinZip and you will have:  skull_CT: the 3D CT image of the plastic skull  SPLOT_server: SPLOT server, dtd and configuration files  slicer2.6-opt-win32-x86-2006-11-15.zip: Slicer2.6 for IGT

14 © NIH National Center for Image-Guided Therapy, October 2006 Slide 14 Install Slicer IGT 1) Unzip file slicer2.6-opt-win32-x86-2006-11- 15.zip to any location on your computer and a directory named slicer2.6-opt-win32-x86-2006- 11-15 will be created. This is the top directory of the Slicer IGT 2) Change to that directory using Windows Explorer 3) Create a shortcut for slicer2-win32-x86.exe 4) Double click the shortcut to start the Slicer IGT

15 © NIH National Center for Image-Guided Therapy, October 2006 Slide 15 Learn the basics of Slicer Those who have not used Slicer are strongly encouraged to learn the basics of Slicer before trying Slicer-IGT Basic tutorial for Slicer is available at http://www.na- mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 Users are expected to know the following (non-IGT) functions of the Slicer: – Load volumes – Import a scene – Segment – Make models

16 © NIH National Center for Image-Guided Therapy, October 2006 Slide 16 Set up Aurora tracking device (1) 1)Follow the manufacturer's user manual to set up the Aurora tracking system. Connect the device by a serial port to the computer where the Slicer IGT has been installed. 2)Install the NDI ToolViewer on your computer from the CD, which came with the product. ToolViewer can be used to test the system setup and more importantly to find the tool ID for the 6 DOF sensor to be used for tracking. 3)Replace the toolID field of this file splotConfig.xml (in the SPLOT_server directory) by the value obtained above.

17 © NIH National Center for Image-Guided Therapy, October 2006 Slide 17 Set Aurora tracking device (2) 4) Create a command prompt and change directory to SPLOT_server 5) Power off and then on the tracking device. In directory SPLOT_server within the command prompt, run this command: opentracker_spl.exe splotConfig.xml 6) Now, move the 6 DOF sensor within the tracking scope (500 x 500 x 500 mm) and then you should see the position and orientation values change in the prompt. The tracking device is working!

18 © NIH National Center for Image-Guided Therapy, October 2006 Connect Slicer IGT to Aurora (1) 1) Click Locator button 3) Choose Opentracker as the Active Server 2) Click Server tab

19 © NIH National Center for Image-Guided Therapy, October 2006 Connect Slicer IGT to Aurora (2) 1)Click Locator button 2) Click Tracking tab 3) Click Connect button

20 © NIH National Center for Image-Guided Therapy, October 2006 Slide 20 Load the CT scan of the skull 1)In the directory skull_CT, the CT scan of the plastic skull is saved as a Slicer scene. Load the 3D CT image into Slicer IGT by importing the scene: File->Import Scene->skull.xml 2)Display the image as the Background (Bg) volume 3)Adjust window and level to its best view

21 © NIH National Center for Image-Guided Therapy, October 2006 Slide 21 Make a model for the skull (1) In Slicer IGT, make a model for the skull from its CT scan by using Threshold method

22 © NIH National Center for Image-Guided Therapy, October 2006 Slide 22 Make a model for the skull (2) 1) Set Or to Axial 5) Set all 3 Lb's to None 4) Set all 3 Fg's to None 2) Set Or to Sagittal 3) Set Or to Coronal

23 © NIH National Center for Image-Guided Therapy, October 2006 Slide 23 Why do we need registration? Slicer IGT uses RAS coordinate system Aurora tracking device has a different coordinate system (XYZ) We need to match points between the two systems

24 © NIH National Center for Image-Guided Therapy, October 2006 Slide 24 Patient to image registration Put the plastic skull inside the tracking scope of the device (500 x 500 x 500 mm) On the plastic skull, find at least 4 unique points. Record their coordinates in both patient (device) and image (Slicer IGT) spaces. Input these values into Slicer IGT (Locator->Server-> OpenTracker- >Registration tab). Then perform registration. See next 4 slides for details. The fiducial points on the skull model helps a lot to match points.

25 © NIH National Center for Image-Guided Therapy, October 2006 Slide 25 Get coordinates in patient space 1) Touch a desired point on the skull with the sensor 2) Click Get button to save the point coordinates in the entry of Patient space

26 © NIH National Center for Image-Guided Therapy, October 2006 Slide 26 Get coordinates in Slicer IGT (1) 1) For the same point on the skull, find its corresponding point in the CT image by looking into the 3 slice windows, with the help of the skull model in the 3D view. Then click it.

27 © NIH National Center for Image-Guided Therapy, October 2006 Slide 27 Get coordinates in Slicer IGT (2) 2) The point coordinates (RAS) are saved here in the entry of Slicer space

28 © NIH National Center for Image-Guided Therapy, October 2006 Slide 28 Perform the registration Click OK to add one pair of points All added point pairs are displayed in this list Get at least 4 point pairs and then click Register to perform registration Remove current registration Delete a point pair from the list Save all point pairs to a file Load point pairs from a file

29 © NIH National Center for Image-Guided Therapy, October 2006 Navigation (1) 1) Click Locator button 5) Click Driver button to change the driver from User to Locator 4) Click Handle button 3) Click Show Locator button 2) Click Tracking tab

30 © NIH National Center for Image-Guided Therapy, October 2006 Navigation (2) Now, the system is ready for navigation. Move the sensor around the skull and you should see the following happen:  The 6 DOF tracking sensor is represented by a green needle and displayed in the 3D view window of the Slicer IGT  The position and orientation of the green needle update as the sensor moves

31 © NIH National Center for Image-Guided Therapy, October 2006 Navigation (3)  The blue images displayed in the 3 slice windows of Slicer IGT are the 2D views (Axial, Sagittal and Coronal) of the plastic skull. These images update accordingly as the sensor moves.  One or more of the 2D images may also be displayed in the 3D view of the Slicer IGT. In next slide, the Coronal image is selected as the example.

32 © NIH National Center for Image-Guided Therapy, October 2006 Navigation (4)

33 © NIH National Center for Image-Guided Therapy, October 2006 Slide 33 Slicer resources www.slicer.org www.na-mic.org/Wiki www.na-mic.org/Bug www.na-mic.org/Testing slicer-devel@bwh.harvard.edu slicer-users@bwh.harvard.edu

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