IGT:ToolKit/Navigation-with-Aurora
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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 (binary) OR building it yourself from the source code:
- Precompiled OpenIGTLink module (for use with Slicer 3.2): Download and unzip.
- 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.
- 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.
- 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