Difference between revisions of "IGT:ToolKit/Navigation-with-Aurora"

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* ''' Step 2b:''' Copy the binary into '''your-slicer3-build(install)-directory'''/lib/Slicer3/Modules.  You should see the OpenIGTLink module in the Slicer3 module list once Slicer3 is started.
 
* ''' Step 2b:''' Copy the binary into '''your-slicer3-build(install)-directory'''/lib/Slicer3/Modules.  You should see the OpenIGTLink module in the Slicer3 module list once Slicer3 is started.
  
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=== '''Step 3: Install IGSTK''' ===
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=== '''Step 3: Install IGSTK and IGSTKSandbox''' ===
 
IGSTK is used to acquire tracking data from the NDI Aurora tracking system.
 
IGSTK is used to acquire tracking data from the NDI Aurora tracking system.
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* You have the choice of either downloading a precompiled version (binary)
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* You have the choice of either downloading a precompiled version (binary) '''OR''' building it yourself from the source code:
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** Precompiled IGSTK:  Download and unzip - you should find the directory '''IGSTKSandbox-build'''
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*** '''For Windows (32-bit).'''
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*** '''For Mac OS X (x86).'''
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*** [[Media:IGSTKSandbox.tgz| For Linux (x86, 32-bit)]].
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*** '''For Linux (x86, 64-bit).'''
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** Building IGSTK and IGSTKSandbox from source code: [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Build-IGSTK Find the instructions here]
  
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==People==
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* [http://www.spl.harvard.edu/pages/People/tokuda Junichi Tokuda]
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* [http://www.spl.harvard.edu/pages/People/hliu Haiying Liu]
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* [http://www.spl.harvard.edu/pages/People/noby Nobuhiko Hata]
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* [http://www.spl.harvard.edu/pages/People/dpace Danielle Pace]
  
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* If you can find a proper binary here for your computer, download the file and unzip it to igt-tutorial. You should find directory '''IGSTKSandbox-build''':
 
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** For Linux box (x86, 32-bit), click [[Media:IGSTKSandbox.tgz|'''here''']].
 
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** For Windows box (32-bit), click '''here'''.
 
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** For Mac box, click '''here'''.
 
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* If you'd like to build IGSTK from the source code, [[IGT:ToolKit/Build-IGSTK|find the instructions here]].
 
  
  
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-------Danielle should delete all of this once she makes the ppt----------
  
  

Revision as of 04:38, 5 June 2008

Home < IGT:ToolKit < Navigation-with-Aurora

Back to IGT:ToolKit

Advanced Slicer3 Navigation Tutorial

Overview:

This tutorial uses an NDI Aurora tracking system to explain how navigation works in Slicer3. It also contains a more advanced description of the OpenIGTLink protocol.

The general IGT navigation system consists of the following components:

  • Slicer3 - the base platform
  • OpenIGTLink module - a loadable software module plugged into Slicer3
  • IGSTK - an interfacing tool for common commercial tracking devices
  • A tracking device - such as the NDI Aurora magnetic tracking system

Before you start the advanced tutorial, you should go through the Basic Navigation Tutorial.

Tutorial Materials

Required Hardware

  • NDI Aurora tracking device with tracked tool
  • If your computer does not have a serial port, you will need a Serial-to-USB converter

Software Installation Instructions

Step 1: Install Slicer3

Go to the Slicer3 Install site.

Step 2: Install the OpenIGTLink module

OpenIGTLink is a communication protocol used to interface Slicer3 with external devices, such as trackers, imaging devices and robots. OpenIGTLink is currently distributed as a loadable module for Slicer3.

Step 3: Install IGSTK and IGSTKSandbox

IGSTK is used to acquire tracking data from the NDI Aurora tracking system.

  • You have the choice of either downloading a precompiled version (binary) OR building it yourself from the source code:
    • Precompiled IGSTK: Download and unzip - you should find the directory IGSTKSandbox-build
    • Building IGSTK and IGSTKSandbox from source code: Find the instructions here

People


Danielle should delete all of this once she makes the ppt----------


Step 4: Connect NDI Aurora tracking device

  • Set up your NDI Aurora tracking device
  • Connect it to the computer where IGSTK will be run.
    • By default, Aurora has only serial port connection.
    • If your computer doesn't have a serial port, you need to have a serial-to-USB converter.

Step 5: Perform navigation

  • Run Slicer3
your-slicer3-build(install)-directory/Slicer3 (Linux/Mac) or
your-slicer3-build(install)-directory/Slicer3.exe (Windows with Cygwin)
  • Configure OpenIGTLink module in Slicer3
    • In Slicer3, get to the interface of OpenIGTLink module
    • Expand Connector Browser
    • Press Add button to add a connector
    • Click Server as the connector type
    • Click Active for the connector

Now Slicer3 is ready to receive tracking data.

  • Run IGSTK
    • Cd to IGSTKSandbox-build
    • Run this command
./bin/igstkSandboxTests igstkAuroraTrackerToolObserverToOpenIGTLinkRelayTest localhost 18944 10000 0 1

At this moment, the tracking data from NDI Aurora is being sent to Slicer3.

  • Load a 3D image for navigation
    • Download the data set from [1]
    • Load the SPGR volume into Slicer3
    • Get to the interface of the Slicer3 data module
    • Inside the MRML tree, drag the SPGR volume node under the transform node
  • Do navigation
    • Move the Aurora probe
    • You should see the updated view of the SPGR image following the movement of probe
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