Difference between revisions of "IGT:ToolKit"

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The wiki pages here present the tool kit we are using or developing at Brigham and Women's Hospital for the purpose of image guided therapy (IGT). The IGT kit is a set of open source software tools with supported hardware devices. We encourage you download and use the free tools if you find them useful to you and welcome any comments or feedback from your experience
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__NOTOC__
  
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The '''Image Guided Therapy Toolkit''' is a toolkit being developed at the Brigham and Women's Hospital.  The IGT toolkit is a set of open source software tools integrated with supported hardware devices: [http://www.slicer.org www.slicer.org 3D Slicer] is our main platform for software development and dissemination, and
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[http://www.na-mic.org/Wiki/index.php/OpenIGTLink OpenIGTLink] is a communication protocol that allows Slicer3 to communicate with imaging devices, trackers and medical robots. We encourage you to download and use the free tools and welcome any comments or feedback.
  
  
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==='''Slicer 3 for IGT'''===
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='''Tutorials'''=
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;[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Install-Slicer3 Install Slicer3]
 
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;[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Datasets IGT example data]
 
  
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==='''Tutorials'''===
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See the [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training Slicer3 Training page] for additional tutorials on Slicer3 capabilities.
  
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;[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Training Slicer3 Training]
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{| border="1" cellpadding="5"
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;[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-with-Aurora Navigation Tutorial]
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|- style="background:#BBE9E2; color:black" align="left"
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;[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial Navigation Tutorial]
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| style="width:5%" | '''Level'''
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;[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Volume-Rendering Volume rendering with Real-time Imaging]
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| style="width:45%" | '''Tutorial'''
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| style="width:20%" | '''Hardware Requirements'''
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| style="width:10%" | '''Tutorial'''
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|-
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| style="background:#9BF2C5; color:black" align="Center"| '''1'''
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| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-tutorial Basic Navigation Tutorial]
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Illustrates Slicer3's tracking capabilities using a tracking simulator in place of an actual tracking device
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| style="background:#D1FFF9; color:black"| None
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| style="background:#C3D1C3; color:black" align="Center"|
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[[Image:IGTBasicNavigationSummary.png|200px|Basic Navigation]]  
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|-
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| style="background:#9BF2C5; color:black" align="Center"| '''1'''
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| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning in Slicer3]
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Demonstrate's Slicer3's IGT capabilities by using image registration, model making and DTI to create a preoperative plan for neurosurgery
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| style="background:#D1FFF9; color:black"| None
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| style="background:#C3D1C3; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|200px|Neurosurgical Planning Overview]]
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|-
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| style="background:#9BF2C5; color:black" align="Center"| '''1'''
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| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Prostate-Planning Prostate Therapy Planning in Slicer3]
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Demonstrates Slicer3's IGT capabilities by using deformable registration and model making to create a preoperative plan for prostate therapy
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| style="background:#D1FFF9; color:black"| None
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| style="background:#C3D1C3; color:black" align="Center"|
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[[Image:ProstatePlanningOverview.jpg|200px|Prostate Planning Overview]]
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|-
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| style="background:#9BF2C5; color:black" align="Center"| '''1'''
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| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/LEGO_IGT_and_Medical_Robotics_Tutorial Lego IGT and Medical Robotics Tutorial]
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Provides an overview of all of the main components of IGT and medical robotics, including imaging, pre-operative planning, targetting by tracking, navigation and registration
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| style="background:#D1FFF9; color:black"| Lego Mindstorms NXT robot
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Lego Deluxe Brick Box
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| style="background:#C3D1C3; color:black" align="Center"| [[Image:Slicer3-IGT-LEGOTutorial-biopsy.jpg|200px|Lego Tutorial]]
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|-
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| style="background:#8EDEB5; color:black" align="Center"| '''2'''
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| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Navigation-with-Aurora Advanced Navigation Tutorial with a tracking device]
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Illustrates Slicer3's tracking capabilities using a tracking device, and provides a more advanced overview of the OpenIGTLink protocol
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| style="background:#D1FFF9; color:black"| Tracking device e.g. NDI Aurora
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| style="background:#C3D1C3; color:black" align="Center"| [[Image:AdvancedNavigationTutorialSummary.png|200px|Advanced Navigation Tutorial]]
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|}
  
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==='''Advanced Tutorial'''===
 
  
  
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=== '''Step 3: Install IGSTK''' ===
 
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IGSTK is used to acquire tracking data from 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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* Set up your NDI Aurora tracking device
 
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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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='''Contact Information'''=
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* Run Slicer3
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If you have any comments or requests, please contact Dr. Nobuhiko Hata (''hata at bwh.harvard.edu'').
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'''your-slicer3-build(install)-directory'''/Slicer3 (Linux/Mac) or
 
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  '''your-slicer3-build(install)-directory'''/Slicer3.exe (Windows with Cygwin)
 
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* Configure OpenIGTLink module in Slicer3
 
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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
 
  
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==='''Anatomy of IGT Tool Kit'''===
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Dr. Hata leads the development of '''Slicer IGT''' at the [http://www.ncigt.org/ National Center for Image Guided Therapy].  See the website of his [http://snr.spl.harvard.edu/ Surgical Navigation and Robotics Laboratory].
  
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==Core Open Source Software and Protocol==
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=Sponsors=
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;[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit/Slicer-IGT Slicer IGT]
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<gallery perrow="4" widths="150px">
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;[http://www.na-mic.org/Wiki/index.php/OpenIGTLink Open IGT Link]
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Image:NCIGTlogo.gif|[http://www.ncigt.org National Center for Image Guided therapy]
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Image:Logo_CIMIT.png|[http://www.cimit.org CIMIT]
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==Optional Open Source Tool Kit==
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Image:NAMIC 380x463.jpg|[http://www.na-mic.org National Alliance for Medical Image Computing]
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;[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/IGSTK IGSTK, an interface to commercial IGT tracking device]
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Image:Isip.jpg|[http://www.intelli-si.org/index_e.html Intelligent Surgical Instrument Project, Japan]
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;[http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Robot Robot Control Toolkit, an interface to surgical robots]
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</gallery>
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==='''Contact Info'''===
 
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If you have any comments or requests, please contact Dr. Nobuhiko Hata at: ''hata {at-mark} bwh.harvard.edu''. Dr. Hata leads the development of '''Slicer IGT''' at National Center for Image Guided Therapy.
 

Latest revision as of 17:02, 11 April 2023

Home < IGT:ToolKit


The Image Guided Therapy Toolkit is a toolkit being developed at the Brigham and Women's Hospital. The IGT toolkit is a set of open source software tools integrated with supported hardware devices: www.slicer.org 3D Slicer is our main platform for software development and dissemination, and OpenIGTLink is a communication protocol that allows Slicer3 to communicate with imaging devices, trackers and medical robots. We encourage you to download and use the free tools and welcome any comments or feedback.


Tutorials

See the Slicer3 Training page for additional tutorials on Slicer3 capabilities.

Level Tutorial Hardware Requirements Tutorial
1 Basic Navigation Tutorial

Illustrates Slicer3's tracking capabilities using a tracking simulator in place of an actual tracking device

None

Basic Navigation

1 Neurosurgical Planning in Slicer3

Demonstrate's Slicer3's IGT capabilities by using image registration, model making and DTI to create a preoperative plan for neurosurgery

None Neurosurgical Planning Overview
1 Prostate Therapy Planning in Slicer3

Demonstrates Slicer3's IGT capabilities by using deformable registration and model making to create a preoperative plan for prostate therapy

None

Prostate Planning Overview

1 Lego IGT and Medical Robotics Tutorial

Provides an overview of all of the main components of IGT and medical robotics, including imaging, pre-operative planning, targetting by tracking, navigation and registration

Lego Mindstorms NXT robot

Lego Deluxe Brick Box

Lego Tutorial
2 Advanced Navigation Tutorial with a tracking device

Illustrates Slicer3's tracking capabilities using a tracking device, and provides a more advanced overview of the OpenIGTLink protocol

Tracking device e.g. NDI Aurora Advanced Navigation Tutorial



Contact Information

If you have any comments or requests, please contact Dr. Nobuhiko Hata (hata at bwh.harvard.edu).

Dr. Hata leads the development of Slicer IGT at the National Center for Image Guided Therapy. See the website of his Surgical Navigation and Robotics Laboratory.

Sponsors

Retrieved from "https://www.na-mic.org/w/index.php?title=IGT:ToolKit&oldid=98875"