Slicer 101 IGT Edition

1
Slicer 101IGT Edition

• Haiying Liu, M.S.
• Nobuhiko Hata, Ph.D.

2
Acknowledgements
National Center for Image-Guided Therapy NIH
1U41RR019703 National Alliance for Medical Image
Computing NIH U54EB005149
3
Outline of tutorial

• Download and install Slicer-IGT
• Learn Slicer basics
• Obtain a plastic skull
• Obtain a tracking device and setup the system
• Connect Slicer to the tracking device
• Register the tracking space to Slicer space
• Perform navigation

4
Disclaimer

• It is the responsibility of the user of 3DSlicer
• to comply with both the terms of the license
• and with the applicable laws, regulations
• and rules.

5
Welcome to 3D Slicer IGT
6
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

7
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 NCITG

8
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

9
Goal of tutorial

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

10
Download and install Slicer-IGT

• Slicer-IGT may be downloaded here
• http//www.na-mic.org/Wiki/index.php/IGT-Tutor
  ials
• Install the Slicer as follows
• 1) The binary is for Windows XP. Be sure you have
  WinZip installed on your computer
• 2) Unzip the binary to any directory on your
  computer. A directory named
• slicer2.6-opt-win32-x86-2006-11-15 will be
  created. This is the top directory of the Slicer
• 3) Change to that directory using Windows
  Explorer
• 4) Create a shortcut for slicer2-win32-x86.exe

11
Learn the basics of Slicer

• Slicer-IGT may be run by double-clicking its
  shortcut on the desktop of your computer
• Sample data and tutorials of how to use 3D Slicer
  can be found at http//wiki.na-mic.org/Wiki/index
  .php/SlicerWorkshopsUser_Training_101Slicer_Tra
  ining. Make sure you are confident to do the
  following
• Load volumes
• Segment
• Make models

12
Buy a plastic skull

• Budget Life-size Skull (29.95), Anatomical Chart
  Company (anatomical.com)
• Also available at
• Lippincott Williams Wilkins (lww.com)
• Amazon.com and other international Amazon sites

13
Obtain a tracking system from NDI
(The left picture is a copy from NDI website
http//www.ndigital.com/aurora.php)

• Choose one of these tracking systems Aurora,
  Polaris, or Polaris Vicra. Aurora is used to
  create this tutorial material.
• Make sure you have a 6 DOF tracking sensor

14
Set up the NDI tracking system (1)
The following steps are valid for Aurora tracking
system 1) Set the tracking system up following
the documentation coming with the device and
connect it by a serial port to the computer where
the Slicer is running 2) Download IGT server and
data form http//www.na-mic.org/Wiki/index.php/IG
T-Tutorials. Unzip the file and you'll find two
directories server and skull_CT. Save skull_CT
for later use. 3) Create a command prompt and
change directory to server
15
Set up the NDI tracking system (2)
4) Install NDI ToolViewer on your computer from
the CD. Power on the tracking device and run NDI
ToolViewer. Find the tool ID for the 6 DOF
tracking sensor. Put the value into this file
splotConfig.xml (the toolID field) in the
server directory. 5) Power off and on the
tracking system. Then in the command prompt in
the server directory, run this command
opentracker_spl.exe splotConfig.xml Now,
move your tracking sensor and you should see the
position and orientation values change in the
prompt. The server is running!
16
Connect Slicer to tracking device (1)

• Click Locator button
• Click Server tab
• Choose Opentracker as the Active Server

17
Connect to tracking device (2)

• Click Locator button
• Click Tracking tab
• Click Connect button

18
Space registration (1)
19
Space registration (2)

• Load the CT scan of plastic skull into Slicer
  (File-gtImport Scene-gtskull.xml)
• Adjust window and level to its best view
• Create a 3D model for the skull out of its CT
  volume. You can see 14 fiducial points on the
  surface
• Put the plastic skull inside the tracking scope
  of the device (500 x 500 x 500 mm)
• On the plastic skull, find 4 unique points.
  Record their coordinates in both device and
  Slicer spaces. Add them into Locator-gtServer-gtOpen
  Tracker-gtRegistration tab. The skull model helps
  a lot to match points.

20
Space registration (3)

• For Pat (device) space, touch the point with the
  sensor and then hit button Get to save values in
  Slicer
• For Slicer space, click the point in any 2D
  window and the coordinates will be automatically
  saved in the entry field
• Click OK to add one pair of points. Repeat it to
  add 4 pairs. Then click Register to perform
  registration
• Other useful buttons Save to write all values
  into a file. Load to load values from a file.
  Delete to remove one point pair at a time. Reset
  to ignore the current registration.

21
Navigation (1)

• Click Locator button
• Click Server tab
• Click Tracking tab
• Click Show Locator button
• Click Handle button
• Change the Driver from User to Locator

22
Navigation (2)

• Now, move the tracking sensor around the skull
  surface and you are navigating the brain in
  Slicer
• The position and orientation of the sensor (the
  needle) are displayed in the 3D view. The
  display updates as you move the needle.
• The CT images of the plastic skull in 3D
  dimensioins also update accordingly

23
Navigation (3)
24
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