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

• Tutorial slides for the Advanced Navigation Tutorial
• Atlas: download the .zip file from either the SPL-PNL Brain Atlas or the SPL Abdominal Atlas

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 2a: You have the choice of either downloading a precompiled version OR building it yourself from the source code:
  • Precompiled OpenIGTLink module (for use with Slicer 3.2): Download and unzip.
    • For Windows (32-bit).
    • For Mac OS X (x86).
    • For Linux (x86, 32-bit).
    • For Linux (x86, 64-bit).
  • Building the OpenIGTLink module from source code: Find the instructions here
• 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 3: Install IGSTK

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

• 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