IGT:ToolKit/Navigation-with-Aurora

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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

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

  • You have the choice of either downloading a precompiled version (binary)


  • 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:
    • For Linux box (x86, 32-bit), click here.
    • For Windows box (32-bit), click here.
    • For Mac box, click here.
  • If you'd like to build IGSTK from the source code, find the instructions here.



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