Difference between revisions of "IGT:ToolKit/Navigation-tutorial"

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[[Image:IGTBasicNavigationSummary.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 navigation system consists of the following components:<br>
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=Basic Slicer3 Navigation Tutorial=
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* Slicer3: the base platform for navigation
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* IGT loadable modules: Software modules, pluginned into Slicer3, for supporting IGT specific functionality
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==Overview:==
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* IGSTK: An interfacing tool for common commercial tracking devices
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* Tracking device: e.g. NDI Aurora tracking system
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This tutorial uses a tracking simulator to explain how navigation works in Slicer3.
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<br>
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This tutorial explains how to set up a general navigation system with a tracking simulator.
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A general IGT navigation system consists of the following components:
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<br><br>
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* Slicer3 - the base platform
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=== '''Step 1: Install Slicer3''' ===
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* IGSTK - an interfacing tool for common commercial tracking devices
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* Download one of the Slicer3 binaries (version 3.2 release)
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* A tracking device - such as the NDI Aurora magnetic tracking system
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** [http://www.slicer.org/DownloadSlicer.php/Nightly/Slicer3-3.2.2008-06-02-win32.exe For Windows (32-bit)]
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** [http://www.slicer.org/DownloadSlicer.php/Nightly/Slicer3-3.2.2008-06-02-linux-x86.tar.gz For Linux (x86, 32-bit)]
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The tracking simulator simulates the tracking device and the IGSTK interfacing software.
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** [http://www.slicer.org/DownloadSlicer.php/Nightly/Slicer3-3.2.2008-06-02-linux-x86_64.tar.gz For Linux (x86, 64-bit)]
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** [http://www.slicer.org/DownloadSlicer.php/Nightly/Slicer3-3.2.2008-06-02-darwin-x86.tar.gz For Mac OS X (x86)]
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Those wishing to connect a real tracking system to Slicer3 should see the [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-with-Aurora Advanced Navigation Tutorial].
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** [http://www.slicer.org/DownloadSlicer.php/Nightly/Slicer3-3.2.2008-06-02-darwin-ppc.tar.gz For Mac OS X (PPC)]
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* Unzip or install the Slicer3 on your computer
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==Tutorial Materials==
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* [[Media:IGTBasicNavigation.pdf|Tutorial slides]] for the Basic Navigation Tutorial
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* 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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* [[Media:Tool.vtk|Tool model]] (right-click to download)
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** If Windows saves the file as Tool.htm intstead of Tool.vtk: Select Start->Run, type "cmd", type "cd <directory where Tool.htm is>", type "move Tool.htm Tool.vtk"
  
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=== '''Step 2: Install OpenIGTLink module''' ===
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==Software Installation Instructions==
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* Download one of the following binaires of OpenIGTLink module. These binaries have been tested working in Slicer3.2.
 
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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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** [[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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* Unzip the binary and copy all files into '''your-slicer3-build(install)-directory'''/lib/Slicer3/Modules.
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=== '''Step 1: Install Slicer3''' ===
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* You should see '''OpenIGTLink''' in the Slicer3 module list after Slicer is started.
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* Go to the [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Install-Slicer3 Slicer3 Install] site.
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* Download a Slicer binary for your platform.
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* Install Slicer.
  
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==='''Step 3: Install tracker simulator'''===
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==='''Step 2: Install the tracker simulator'''===
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* This tracker simulator will generate and send fake tracking data to Slicer3. Download one of the following binaries:
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The tracking simulator will be used to generate and send fake tracking data to Slicer3.
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** For Linux (x86, 32-bit), click [[Media:TrackerSimulator_Linux_x86_32.tgz|'''here''']].
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* You have the choice of either downloading a precompiled version (binary) '''OR''' building it yourself from the source code:
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** For Linux (x86, 64-bit), click [[Media:TrackerSimulator_Linux_x86_64.tgz|'''here''']].
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** Precompiled tracking simulator:  Download and unzip.
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** For Windows (32-bit), click [[Media:TrackerSimulator_Win_x86_32.zip|'''here''']].
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*** [[Media:TrackerClient_Win_x86_32.zip|For Windows (32-bit)]].
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** For Mac OS X (x86), click [[Media:TrackerSimulator_Darwin_x86.tgz |'''here''']].
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*** [[Media:TrackerSimulator_Darwin_x86.tgz |For Mac OS X(x86)]].
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* Unzip the binary to some place on your computer.
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*** [[Media:TrackerClient_Linux_x86_32.tgz|For Linux (x86, 32-bit)]].
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*** [[Media:TrackerClient_Linux_x86_64.tgz|For Linux (x86, 64-bit)]].
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** Building the tracker simulator from source code:  [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Build-Tracker-Simulator Find the instructions here]
  
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==='''Step 4: Perform navigation'''===
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==People==
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* Run Slicer3. In the top directory of your Slicer3 installation, run this command to start up Slicer3:
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* [http://www.spl.harvard.edu/pages/People/tokuda Junichi Tokuda]
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./Slicer3
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* [http://www.spl.harvard.edu/pages/People/hliu Haiying Liu]
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* Set up OpenIGTLink module
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* [http://www.spl.harvard.edu/pages/People/noby Nobuhiko Hata]
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** Choose OpenIGTLink from Slicer Module list:[[Image:Slicer3_Select_OpenIGTLinkModule.png]]
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* [http://www.spl.harvard.edu/pages/People/dpace Danielle Pace]
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** Set up OpenIGTLink module to receive tracking data: [[Image:Slicer3_Enable_OpenIGT_Server.png]]
 
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* Run tracker simulator to send tracking data to Slicer3:
 
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cd to the install directory of TrackerSimulator
 
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./TrackerSim  10  c  local 18944
 

Latest revision as of 16:06, 10 April 2009

Home < IGT:ToolKit < Navigation-tutorial
IGTBasicNavigationSummary.png

Back to IGT:ToolKit

Basic Slicer3 Navigation Tutorial

Overview:

This tutorial uses a tracking simulator to explain how navigation works in Slicer3.

A general IGT navigation system consists of the following components:

  • Slicer3 - the base platform
  • IGSTK - an interfacing tool for common commercial tracking devices
  • A tracking device - such as the NDI Aurora magnetic tracking system

The tracking simulator simulates the tracking device and the IGSTK interfacing software.

Those wishing to connect a real tracking system to Slicer3 should see the Advanced Navigation Tutorial.

Tutorial Materials

  • Tutorial slides for the Basic Navigation Tutorial
  • Atlas: download the .zip file from either the SPL-PNL Brain Atlas or the SPL Abdominal Atlas
  • Tool model (right-click to download)
    • If Windows saves the file as Tool.htm intstead of Tool.vtk: Select Start->Run, type "cmd", type "cd <directory where Tool.htm is>", type "move Tool.htm Tool.vtk"

Software Installation Instructions

Step 1: Install Slicer3

  • Go to the Slicer3 Install site.
  • Download a Slicer binary for your platform.
  • Install Slicer.

Step 2: Install the tracker simulator

The tracking simulator will be used to generate and send fake tracking data to Slicer3.

People

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