Slicer3:BrainLab Integration

Introduction

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

• The BrainLab system will still run as usual; we won't install any software and hardware on the computer running the brainlab system. Slicer3 and BioImage Suite run on a separate machine. These two computers need to be connected to each other using a network connection. During surgical procedures, the BrainLab sends real-time data from its tracking system and/or images to Slicer3 through BioImage Suite. The information from the Brainlab tracker can be used to manipulate 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 is 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 decent computer with a minimum of 2GB of RAM and a Graphics Card with at least 256MB of dedicated graphics memory. The computer should have Windows XP Pro installed. We have used NVIDIA graphics cards with good success.
• 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 computers running the BrainLab system and the one running Slicer3 should be connected through a Ethernet network. We are using ... for this purpose.
• Steps to set up the system can be found in this file

STEP 3: Testing the System

• Testing the individual components and the interoperation of the components should be done during setup to ensure proper operation of the research part of the setup. In order to test the clinical part of the brain lab system, please follow the vendor guidelines.
• To test Slicer....
• To test BioImage Suite ...
• To test the connection between Slicer and the brainlab system ....

STEP 4: Visualize DTI in Slicer3

• The tutorial (called ...) and sample data sets for processing DTI images in Slicer3 can be found at http://www.na-mic.org/Wiki/index.php/Slicer3.2:Training (see module number ...)
• The procedure to visualize DTI tractography: In progress

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).