Slicer3:BrainLab Integration

Introduction

This turorial describes detailed steps for neurosurgeons to use Slicer3 to perform some research in DTI visualization in OR while using BrainLab as navigation system.

• The BrainLab system still runs as usual; we won't install any software and hardware on the machine. Slicer3 and related software run on a separate computer. These two computers connect each other on networking. During procedures, the BrainLab sends realtime tracking data and/or images to Slicer3. The update of tracking data triggers dynamic DTI visualization in Slicer3.

• Slicer3 is not an FDA approved product and we make no claims on specific capabilities. It is the surgeon's responsibility to ensure that Slicer3 will perform whatever tasks s/he is trying to do and to ensure that s/he in compliance with applicable laws, rules, and regulations.

• This tutorial is being developed and tested on Windows XP. If you are using a different OS (e.g. Linux, or Mac), please let us know.

STEP 1: Download and Install Software Packages

Slicer3 connects with BrainLab navigation system through BioImage Suite, which is an integrated image analysis software suite developed at Yale University. Thus, we will install both BioImage Suite and Slicer3 on a designated machine.

• Get a descent computer with Windows XP installed
• Install BioImage Suite
  • The latest binary of BioImage Suite (2.6 Release Candidate 1) can be installed from here: http://research.yale.edu/bioimagesuite/forum/index.php?topic=257.msg
• Install Slicer3
  • Slicer3 binary download site: http://www.slicer.org/DownloadSlicer.php/Nightly
  • Choose one Win32 installer and download it
  • Run the installer to install Slicer3 on your Windows XP computer

STEP 2: Set up the System

• The BrainLab and Slicer3 communicate on networking. In OR, plugin both computers into two ethernet jackets using cables.
• On the BrainLab computer, turn ON VVLink. This requires a license. If you don't have one, contact BrainLab to get one (purchase or loan)
• Configure BioImage Suite
  • Preferences -> Advances/Miscelleneous -> VectorVisionLink: Enabled & OpenIGTLink: Enabled -> Save -> Restart BioImage Suite
• Configure Slicer3
  • Modules -> OpenIGTLink -> configure Slicer3 as a data receiver (Server)
• Connect BioImage Suite with BrainLab
  • Neurosurgery -> VVLink/OpenIGTLink Bridge
  • Features -> VVLink Tool -> Add Server -> (input hostname and password from BrainLab) -> Save Setup -> Connect
• Connect BioImage Suite with Slicer3:
  • VVLink Tool -> IGTL Bridge -> (input OpenIGTL Server and OpenIGTL Port) -> Connect

STEP 3: Visualize DTI in Slicer3

• The tutorial ans sample data sets for processing DTI images in Slicer3 can be found at http://www.na-mic.org/Wiki/index.php/Slicer3.2:Training
• The procedure to visualize DTI tractography:

Terminology

• Slicer3 [1] is cross-platform end user application for analyzing and visualizing medical images. It contails collection of Open Source libraries for developing and deploying new image computing technologies.
  
• BrainLab [2] currently offers a set of integrated OR solutions, for instance neurosurgery, orthopedic, and RT/Oncology. The BrainLab component we're working with is VectorVision Cranial Navigation System.
  
• BioImage Suite [3] is an integrated image analysis software suite developed at Yale University.
• VectorVision Link (VVLink) is a custom designed client/server tool which extends functionality from the Visualization Toolkit. VV Link enables bi-directional data transfer such as image data sets, visualizations and tool positions in real time.
  
• OpenIGTLink is a simple network protocol intended for trackers, robots and other devices to send data to the main application.

Contact US

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