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

From NAMIC Wiki
Jump to: navigation, search
Line 1: Line 1:
 
Back to [[IGT:ToolKit|IGT:ToolKit]]
 
Back to [[IGT:ToolKit|IGT:ToolKit]]
  
The general navigation system consists of the following components:<br>
+
=Advanced Slicer3 Navigation Tutorial=
* Slicer3: the base platform for navigation
+
 
* IGT loadable modules: Software modules, pluginned into Slicer3, for supporting IGT specific functionality
+
==Overview:==
* IGSTK: An interfacing tool for common commercial tracking devices
+
 
* Tracking device: e.g. NDI Aurora tracking system
+
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.
This tutorial explains how to set up these components to build and use a general purpose navigation system.
+
 
<br><br>
+
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 [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial Basic Navigation Tutorial].
 +
 
 +
==Tutorial Materials==
 +
* Tutorial slides for the Advanced Navigation Tutorial
 +
* Atlas: download the .zip file from either the [http://www.na-mic.org/pages/Special:PubDB_View?dspaceid=1265 SPL-PNL Brain Atlas] or the [http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1266 SPL Abdominal Atlas]
 +
 
 +
==Required Hardware==
 +
* [http://www.ndigital.com 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''' ===
 
=== '''Step 1: Install Slicer3''' ===
 
Go to the [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Install-Slicer3 Slicer3 Install] site.
 
Go to the [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Install-Slicer3 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.
 +
*** [[Media:OpenIGTLink_3.2_Win_x86_32.zip| For Windows (32-bit)]].
 +
*** [[Media:OpenIGTLink_Darwin_3.2_x86.tgz| For Mac OS X (x86)]].
 +
*** [[Media:OpenIGTLink_3.2_Linux_x86_32.tgz| For Linux (x86, 32-bit)]].
 +
*** [[Media:OpenIGTLink_3.2_Linux_x86_64.tgz| For Linux (x86, 64-bit)]].
 +
** Building the OpenIGTLink module from source code:  [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Build-OpenIGTLink 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 2: Install OpenIGTLink module''' ===
 
OpenIGTLink protocol handles data communication between Slicer3 and tracking device ([http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink Click here for details]). As a loadable module in Slicer3, OpenIGTLink will receive tracking data from the NDI Aurora system.
 
* If you can find a proper binary here for your computer, download it and unzip the file:
 
** For Linux box (x86, 32-bit), click [[Media:OpenIGTLink.tgz|'''here''']].
 
** For Linux box (x86, 64-bit), click [[Media:OpenIGTLink_Linux_x86_64.tgz|'''here''']].
 
** For Windows box (32-bit), click '''here'''.
 
** For Mac OS X(Leopard x86), click [[Media:OpenIGTLink_MacOSX10.5_Intel.tgz|'''here''']].
 
* If you'd like to build OpenIGTLink module from the source code, [[IGT:ToolKit/Build-OpenIGTLink|find the instructions here]].
 
* Copy the binary into '''your-slicer3-build(install)-directory'''/lib/Slicer3/Modules.
 
* You should see '''OpenIGTLink''' in the Slicer3 module list after Slicer is started.
 
  
 
=== '''Step 3: Install IGSTK''' ===
 
=== '''Step 3: Install IGSTK''' ===
IGSTK is used to acquire tracking data from NDI Aurora tracking system.
+
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''':
 
* 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 [[Media:IGSTKSandbox.tgz|'''here''']].
 
** For Linux box (x86, 32-bit), click [[Media:IGSTKSandbox.tgz|'''here''']].
Line 30: Line 51:
 
** For Mac box, click '''here'''.
 
** For Mac box, click '''here'''.
 
* If you'd like to build IGSTK from the source code, [[IGT:ToolKit/Build-IGSTK|find the instructions here]].
 
* If you'd like to build IGSTK from the source code, [[IGT:ToolKit/Build-IGSTK|find the instructions here]].
 +
 +
 +
  
 
=== '''Step 4: Connect NDI Aurora tracking device''' ===
 
=== '''Step 4: Connect NDI Aurora tracking device''' ===

Revision as of 04:28, 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

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