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

From NAMIC Wiki
Jump to: navigation, search
 
(17 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 +
[[Image:AdvancedNavigationTutorialSummary.png|300px|thumb]]
 +
 
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 plus IGT modules such as OpenIGTLink and NeuroNav
 +
* 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: [[Media:IGTAdvancedNavigation.pdf|pdf (recommended)]] or [[Media:IGTAdvancedNavigation.ppt|ppt]]
 +
* 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 IGSTK Package''' ===
 +
IGSTK package is used to acquire tracking data from the NDI Aurora tracking system. To build it from the source code, [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Build-IGSTK find the instructions here].
  
−
=== '''Step 2: Install OpenIGTLink module''' ===
+
=== '''Step 3: Set up Communication between IGSTK and Slicer''' ===
−
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.
+
Here are the [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Connect-IGSTK-Slicer steps] to connect IGSTK and Slicer3.
−
* 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''' ===
 
−
IGSTK is used to acquire tracking data from 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 [[Media:IGSTKSandbox.tgz|'''here''']].
 
−
** For Windows box (32-bit), 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]].
 
−
 
 
−
=== '''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''' ===
+
==People==
−
* Run Slicer3
+
* [http://www.spl.harvard.edu/pages/People/tokuda Junichi Tokuda]
−
'''your-slicer3-build(install)-directory'''/Slicer3 (Linux/Mac) or
+
* [http://www.spl.harvard.edu/pages/People/hliu Haiying Liu]
−
'''your-slicer3-build(install)-directory'''/Slicer3.exe (Windows with Cygwin)
+
* [http://www.spl.harvard.edu/pages/People/noby Nobuhiko Hata]
−
* Configure OpenIGTLink module in Slicer3
+
* [http://www.spl.harvard.edu/pages/People/dpace Danielle Pace]
−
** 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 [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit]
 
−
** 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
 

Latest revision as of 18:08, 25 May 2009

Home < IGT:ToolKit < Navigation-with-Aurora
AdvancedNavigationTutorialSummary.png

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 plus IGT modules such as OpenIGTLink and NeuroNav
  • 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 IGSTK Package

IGSTK package is used to acquire tracking data from the NDI Aurora tracking system. To build it from the source code, find the instructions here.

Step 3: Set up Communication between IGSTK and Slicer

Here are the steps to connect IGSTK and Slicer3.

People

Retrieved from "https://www.na-mic.org/w/index.php?title=IGT:ToolKit/Navigation-with-Aurora&oldid=37728"