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

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[[Image:AdvancedNavigationTutorialSummary.png|300px|thumb]]
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Back to [[IGT:ToolKit|IGT:ToolKit]]
 
Back to [[IGT:ToolKit|IGT:ToolKit]]
  
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The general IGT navigation system consists of the following components:
 
The general IGT navigation system consists of the following components:
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* Slicer3 - the base platform
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* Slicer3 - the base platform plus IGT modules such as OpenIGTLink and NeuroNav
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* OpenIGTLink module - a loadable software module plugged into Slicer3
 
 
* IGSTK - an interfacing tool for common commercial tracking devices
 
* IGSTK - an interfacing tool for common commercial tracking devices
 
* A tracking device - such as the NDI Aurora magnetic tracking system
 
* A tracking device - such as the NDI Aurora magnetic tracking system
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==Tutorial Materials==
 
==Tutorial Materials==
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* Tutorial slides for the Advanced Navigation Tutorial
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* 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]
 
* 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]
  
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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.
  
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=== '''Step 2: Install the OpenIGTLink module''' ===
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=== '''Step 2: Install IGSTK Package''' ===
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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.
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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].
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* '''Step 2a:'''  You have the choice of either downloading a precompiled version '''OR''' building it yourself from the source code:
 
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** Precompiled OpenIGTLink module (for use with Slicer 3.2):  Download and unzip.
 
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*** [[Media:OpenIGTLink_3.2_Win_x86_32.zip| For Windows (32-bit)]].
 
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*** [[Media:OpenIGTLink_Darwin_3.2_x86.tgz| For Mac OS X (x86)]].
 
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*** [[Media:OpenIGTLink_3.2_Linux_x86_32.tgz| For Linux (x86, 32-bit)]].
 
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*** [[Media:OpenIGTLink_3.2_Linux_x86_64.tgz| For Linux (x86, 64-bit)]].
 
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** Building the OpenIGTLink module from source code:  [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Build-OpenIGTLink Find the instructions here]
 
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* ''' 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.
 
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=== '''Step 3: Install IGSTK''' ===
 
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IGSTK is used to acquire tracking data from the NDI Aurora tracking system.
 
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* 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''':
 
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** For Linux box (x86, 32-bit), click [[Media:IGSTKSandbox.tgz|'''here''']].
 
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** For Windows box (32-bit), click '''here'''.
 
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** For Mac box, click '''here'''.
 
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* If you'd like to build IGSTK from the source code, [[IGT:ToolKit/Build-IGSTK|find the instructions here]].
 
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=== '''Step 4: Connect NDI Aurora tracking device''' ===
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=== '''Step 3: Set up Communication between IGSTK and Slicer''' ===
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* Set up your NDI Aurora tracking device
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Here are the [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Connect-IGSTK-Slicer steps] to connect IGSTK and Slicer3.
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* Connect it to the computer where IGSTK will be run.
 
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** By default, Aurora has only serial port connection.
 
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** If your computer doesn't have a serial port, you need to have a serial-to-USB converter.
 
  
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=== '''Step 5: Perform navigation''' ===
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==People==
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* Run Slicer3
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* [http://www.spl.harvard.edu/pages/People/tokuda Junichi Tokuda]
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'''your-slicer3-build(install)-directory'''/Slicer3 (Linux/Mac) or
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* [http://www.spl.harvard.edu/pages/People/hliu Haiying Liu]
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'''your-slicer3-build(install)-directory'''/Slicer3.exe (Windows with Cygwin)
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* [http://www.spl.harvard.edu/pages/People/noby Nobuhiko Hata]
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* Configure OpenIGTLink module in Slicer3
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* [http://www.spl.harvard.edu/pages/People/dpace Danielle Pace]
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** In Slicer3, get to the interface of OpenIGTLink module
 
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** Expand '''Connector Browser'''
 
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** Press '''Add''' button to add a connector
 
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** Click '''Server''' as the connector type
 
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** Click '''Active''' for the connector
 
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Now Slicer3 is ready to receive tracking data.
 
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* Run IGSTK
 
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** Cd to IGSTKSandbox-build
 
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** Run this command
 
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./bin/igstkSandboxTests igstkAuroraTrackerToolObserverToOpenIGTLinkRelayTest localhost 18944 10000 0 1
 
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At this moment, the tracking data from NDI Aurora is being sent to Slicer3.
 
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* Load a 3D image for navigation
 
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** Download the data set from [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit]
 
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** Load the SPGR volume into Slicer3
 
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** Get to the interface of the Slicer3 data module
 
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** Inside the MRML tree, drag the SPGR volume node under the transform node
 
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* Do navigation
 
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** Move the Aurora probe
 
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** 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

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