Difference between revisions of "Modules:NeuroNav-Documentation-3.6"

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[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
 
[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
  
−
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]
+
[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]
  
 
__NOTOC__
 
__NOTOC__
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* Haiying Liu, BWH
 
* Haiying Liu, BWH
 
* Nobuhiko Hata, BWH
 
* Nobuhiko Hata, BWH
 +
* Ron Kikinis, BWH
 
* Contact: Haiying Liu, hliu@bwh.harvard.edu
 
* Contact: Haiying Liu, hliu@bwh.harvard.edu
  
 
===Module Description===
 
===Module Description===
−
NeuroNav module is developed to guide neurosurgeons by images to perform surgical procedures in OR. The workflow is composed of the following steps:
+
NeuroNav module is developed to guide neurosurgeons by images to perform surgical procedures in OR.
−
#Connect to a tracking source, a tracking simulator or real tracking device.
 
−
#Perform patient to image registration.
 
−
#Execute surgical navigation.
 
  
 
== Usage ==
 
== Usage ==
 +
===Regular Neurosurgical Navigation===
 +
Follow the following steps to make the module work properly:
 +
#Connect to a tracking source, which could be a tracking simulator or real tracking device such as NDI Aurora. The tracking source sends tracking data, i.e. the orientation and tip location of the probe, to Slicer at a defined rate.
 +
#Perform patient to image registration. Load preoperative image(s) or scene into Slicer. Choose 4-6 landmarks on the patient head and then find those points on the loaded image to perform the patient to image registration.
 +
#Execute surgical navigation. Navigation is driven by the tracking probe. As long as the probe tip moves within the tracking scope of the device, Slicer will update the image display to give a visual feedback to the neurorsurgeon. The image update will offer useful real-time guidance during the surgical procedure.
  
−
===Use Cases, Examples===
+
===Integration with BioImage Suite and BrainLab===
 +
Integration of Slicer with BioImage Suite and BrainLab has been a recent successful example of collaboration between academia and industry.
 +
BioImage Suite is an integrated image analysis software suite developed at Yale University. BrainLab is an FDA approved neurosurgical navigation system. This integration will interface Slicer to the BrainLab system and allow neurosurgeons to use Slicer to perform some research in DTI visualization in OR while using BrainLab as the navigation system. Please check sections below for details.
  
−
This module is especially appropriate for these use cases:
+
===Examples, Use Cases & Tutorials===
−
 
+
[[Slicer3:BrainLab_Integration|Tutorial for the integration of Slicer with BioImage Suite and BrainLab system.]]
−
* Use Case 1:
 
−
* Use Case 2:
 
−
 
 
−
Examples of the module in use:
 
−
 
 
−
* Example 1
 
−
* Example 2
 
−
 
 
−
===Tutorials===
 
−
 
 
−
Links to tutorials explaining how to use this module:
 
−
 
 
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* Tutorial 1
 
−
** Data Set 1
 
  
 
===Quick Tour of Features and Use===
 
===Quick Tour of Features and Use===
  
−
A list panels in the interface, their features, what they mean, and how to use them. For instance:
+
* '''Connection:''' Connect to a tracking source through OpenIGTLink. This step is not visible on NeuroNav module interface.
−
 
+
* '''Registration:''' Perform patient to image registration.
−
{|
+
* '''Navigation:''' Execute surgical navigation.
−
|
 
−
* '''Input panel:'''
 
−
** '''First input'''
 
−
** '''Second input'''
 
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* '''Parameters panel:'''
 
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** '''First parameter'''
 
−
** '''Second parameter'''
 
−
* '''Output panel:'''
 
−
** '''First output'''
 
−
** '''Second output'''
 
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* '''Viewing panel:'''
 
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|[[Image:screenshotBlankNotOptional.png|thumb|280px|User Interface]]
 
−
|}
 
  
 
== Development ==
 
== Development ==
  
 
===Notes from the Developer(s)===
 
===Notes from the Developer(s)===
−
 
−
Algorithms used, library classes depended upon, use cases, etc.
 
  
 
===Dependencies===
 
===Dependencies===
−
 
+
Fiducial<br>
−
Other modules or packages that are required for this module's use.
+
OpenIGTLink<br>
 +
DTMRI<br>
 +
FiducialSeeding<br>
  
 
===Tests===
 
===Tests===
  
−
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:
+
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms.
−
 
 
−
* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
 
−
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]
 
  
 
===Known bugs===
 
===Known bugs===
−
 
+
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.
−
Links to known bugs in the Slicer3 bug tracker
 
−
 
 
−
* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]  
 
−
 
 
  
 
===Usability issues===
 
===Usability issues===
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===Source code & documentation===
 
===Source code & documentation===
 +
Follow this [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Volumes/ link] to the Volumes source code in ViewVC.
  
−
Links to the module's source code:
+
[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html Documentation] generated by doxygen.
−
 
 
−
Source code:
 
−
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
 
−
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]
 
−
 
−
Doxygen documentation:
 
−
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]
 
  
 
== More Information ==  
 
== More Information ==  
  
 
===Acknowledgment===
 
===Acknowledgment===
−
Include funding and other support here.
+
This work is part of the National Center for Image Guided Therapy (NCIGT), funded by the National Institutes of Health, Grant 5U41RR019703. This study is also in part supported by Intelligent Surgical Instruments Project of METI (Japan).
  
 
===References===
 
===References===
−
Publications related to this module go here. Links to pdfs would be useful.
+
H Elhawary, Haiying Liu, Pratik Patel, Isaiah Norton, Laura Rigolo, Xenophon Papademetris, Nobuhiko Hata, Alexandra J. Golby, Intra-operative Real-time Querying of White Mater Tracts during Frameless Stereotactic Neuronavigation, in press, Neurosurgery, 2010

Latest revision as of 13:55, 29 April 2010

Home < Modules:NeuroNav-Documentation-3.6

Return to Slicer 3.6 Documentation

Gallery of New Features


Module Name

NeuroNav

Patient to image registration
Surgical navigation
NeuroNav used in OR
NeuroNav with DTI tractography

General Information

Module Type & Category

Type: Interactive

Category: IGT

Authors, Collaborators & Contact

  • Haiying Liu, BWH
  • Nobuhiko Hata, BWH
  • Ron Kikinis, BWH
  • Contact: Haiying Liu, hliu@bwh.harvard.edu

Module Description

NeuroNav module is developed to guide neurosurgeons by images to perform surgical procedures in OR.

Usage

Regular Neurosurgical Navigation

Follow the following steps to make the module work properly:

  1. Connect to a tracking source, which could be a tracking simulator or real tracking device such as NDI Aurora. The tracking source sends tracking data, i.e. the orientation and tip location of the probe, to Slicer at a defined rate.
  2. Perform patient to image registration. Load preoperative image(s) or scene into Slicer. Choose 4-6 landmarks on the patient head and then find those points on the loaded image to perform the patient to image registration.
  3. Execute surgical navigation. Navigation is driven by the tracking probe. As long as the probe tip moves within the tracking scope of the device, Slicer will update the image display to give a visual feedback to the neurorsurgeon. The image update will offer useful real-time guidance during the surgical procedure.

Integration with BioImage Suite and BrainLab

Integration of Slicer with BioImage Suite and BrainLab has been a recent successful example of collaboration between academia and industry. BioImage Suite is an integrated image analysis software suite developed at Yale University. BrainLab is an FDA approved neurosurgical navigation system. This integration will interface Slicer to the BrainLab system and allow neurosurgeons to use Slicer to perform some research in DTI visualization in OR while using BrainLab as the navigation system. Please check sections below for details.

Examples, Use Cases & Tutorials

Tutorial for the integration of Slicer with BioImage Suite and BrainLab system.

Quick Tour of Features and Use

  • Connection: Connect to a tracking source through OpenIGTLink. This step is not visible on NeuroNav module interface.
  • Registration: Perform patient to image registration.
  • Navigation: Execute surgical navigation.

Development

Notes from the Developer(s)

Dependencies

Fiducial
OpenIGTLink
DTMRI
FiducialSeeding

Tests

On the Dashboard, these tests verify that the module is working on various platforms.

Known bugs

Follow this link to the Slicer3 bug tracker.

Usability issues

Follow this link to the Slicer3 bug tracker. Please select the usability issue category when browsing or contributing.

Source code & documentation

Follow this link to the Volumes source code in ViewVC.

Documentation generated by doxygen.

More Information

Acknowledgment

This work is part of the National Center for Image Guided Therapy (NCIGT), funded by the National Institutes of Health, Grant 5U41RR019703. This study is also in part supported by Intelligent Surgical Instruments Project of METI (Japan).

References

H Elhawary, Haiying Liu, Pratik Patel, Isaiah Norton, Laura Rigolo, Xenophon Papademetris, Nobuhiko Hata, Alexandra J. Golby, Intra-operative Real-time Querying of White Mater Tracts during Frameless Stereotactic Neuronavigation, in press, Neurosurgery, 2010

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