Slicer 101 IGT Edition

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Acknowledgements
National Center for Image-Guided Therapy NIH
U41RR019703 National Alliance for Medical Image
Computing NIH U54EB005149 Neuroimage Analysis
Center NIH P41RR013218
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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.

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Goal of this tutorial

• Simulate the brain surgical navigation using a
  plastic skull, a tracking sensor and Slicer IGT

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Outline of this tutorial

1. Introduction to 3D Slicer
2. Required materials
3. System set-up
4. Patient to image registration
5. Navigation

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Welcome to 3D Slicer IGT
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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

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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
  ODonnell 1999-2001
• Ongoing Development of Slicers 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

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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

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Materials for this tutorial

• A plastic skull
• A tracking device
• Slicer IGT
• SPLOT server
• CT scan of the plastic skull

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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)
• Lippincott Williams Wilkins (lww.com)
• Amazon.com
• Other international Amazon sites

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Obtain a tracking system
(http//www.ndigital.com/aurora.php)

• 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.

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One download

• Slicer-IGT may be downloaded here
• http//www.na-mic.org/Wiki/index.php/IGT-Tutor
  ials
• 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

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Install Slicer IGT

• 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

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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/SlicerWo
  rkshopsUser_Training_101
• Users are expected to know the following
  (non-IGT) functions of the Slicer
• Load volumes
• Import a scene
• Segment
• Make models

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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.

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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!
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Connect Slicer IGT to Aurora (1)
1) Click Locator button
2) Click Server tab
3) Choose Opentracker as the Active Server
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Connect Slicer IGT to Aurora (2)

1. Click Locator button

2) Click Tracking tab
3) Click Connect button
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Load the CT scan of the skull

• 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-gtImport Scene-gtskull.xml
• Display the image as the Background (Bg) volume
• Adjust window and level to its best view

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Make a model for the skull (1)

• In Slicer IGT, make a model for the skull from
  its CT scan by using Threshold method

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Make a model for the skull (2)

• 1) Set Or to Axial

2) Set Or to Sagittal
3) Set Or to Coronal
4) Set all 3 Fg's to None
5) Set all 3 Lb's to None
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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

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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-gtServer-gt
  OpenTracker-gtRegistration tab). Then perform
  registration. See next 4 slides for details.
• The fiducial points on the skull model helps a
  lot to match points.

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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
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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.

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Get coordinates in Slicer IGT (2)
2) The point coordinates (RAS) are saved here in
the entry of Slicer space
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Perform the registration

• Click OK to add one pair of points

All added point pairs are displayed in this list
Load point pairs from a file
Save all point pairs to a file
Delete a point pair from the list
Remove current registration
Get at least 4 point pairs and then click
Register to perform registration
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Navigation (1)
1) Click Locator button
2) Click Tracking tab
4) Click Handle button
3) Click Show Locator button
5) Click Driver button to change the driver from
User to Locator
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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

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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.

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Navigation (4)
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Slicer resources

• www.slicer.org
• www.na-mic.org/Wiki
• www.na-mic.org/Bug
• www.na-mic.org/Testing
• slicer-devel_at_bwh.harvard.edu
• slicer-users_at_bwh.harvard.edu