Difference between revisions of "Slicer3:BrainLab Integration"
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= Introduction = | = Introduction = | ||
| − | This | + | BrainLab has recently introduced VV Link, an open API (but not free) to communicate with the IGT environment. This API allows to receive tracker information from the BrainLab system. This tutorial describes in detail how to interface 3D Slicer to the BrainLab system and to use it for research. Specifically, we describe 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 still | + | *The BrainLab system will still run as usual; we won't install any software and hardware on the computer running the BrainLab system and will not affect the FDA status of the BrainLab system. In our current scenario we are using the BioImage Suite from Yale as a "bridge". Slicer3 and BioImage Suite run on a different computer than the BrainLab system. These two computers need to be connected to each other using a network or router 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 in compliance with applicable laws, rules, and regulations. | + | *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 and Linux. If you are using a Mac, please share your experience with us. | ||
<br> | <br> | ||
| − | + | = '''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. For Windows users, the computer should have Windows XP Pro installed. For Linux users, Ubuntu 8.04 is used as the testbed. We have used NVIDIA graphics cards with good success. | |
| − | |||
| − | |||
* Install BioImage Suite | * 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 | + | ** 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 | * Install Slicer3 | ||
** Slicer3 binary download site: http://www.slicer.org/DownloadSlicer.php/Nightly | ** Slicer3 binary download site: http://www.slicer.org/DownloadSlicer.php/Nightly | ||
| − | ** Choose one | + | ** Choose one of the available (and dated) versions for your system and download it |
| − | ** | + | ** For Windows users, run the installer to install Slicer3 on your Windows XP computer. For Linux users, unzip the binary to your preferred location |
| + | <br> | ||
| + | |||
| + | = '''STEP 2:''' Set up the System = | ||
| + | * The computers running the BrainLab system and the one running Slicer3 should be connected through a Ethernet network or a router. We have been testing the system in OR with a wired router (e.g. Netgear or Linsys). | ||
| + | * Steps to set up the system can be found in [[media:system_setup_brainlab_bioimage_slicer3.ppt|this file]] | ||
| + | <br> | ||
| − | + | = '''STEP 3:''' Test 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. |
| − | + | * Steps to test the system connectivity can be found in [[media:system_test_brainlab_bioimage_slicer3.ppt|this file]] | |
| − | * | + | <br> |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | = '''STEP 4:''' Visualize DTI in Slicer3 = | |
| − | *The tutorial | + | *The tutorial, '''Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3''', 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 No. 1.4) |
| − | *The procedure to visualize DTI tractography: | + | *The procedure to visualize DTI tractography while tracking by BrainLab is described in [[media:dti_vis_brainlab_bioimage_slicer3.ppt|this file]] |
| + | <br> | ||
= Terminology = | = Terminology = | ||
| − | *'''Slicer3''' | + | *'''Slicer3''' [http://www.slicer.org/] 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.<br> |
| − | *'''BrainLab''' | + | *'''BrainLab''' [http://www.brainlab.com/scripts/website_english.asp] 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.<br> |
| − | *'''BioImage Suite''' | + | *'''BioImage Suite''' [http://www.bioimagesuite.org/] 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.<br> | *'''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.<br> | ||
| − | *'''OpenIGTLink''' is a simple network protocol intended for trackers, robots and other devices to send data to the main application.<br> | + | *'''OpenIGTLink''' is a simple network protocol intended for trackers, robots and other devices to send data to the main application. |
| + | <br> | ||
| − | = Contact | + | = Contact us = |
If you have any comments or requests, please contact Dr. Nobuhiko Hata (hata at bwh.harvard.edu). | If you have any comments or requests, please contact Dr. Nobuhiko Hata (hata at bwh.harvard.edu). | ||
Latest revision as of 21:56, 15 February 2009
Home < Slicer3:BrainLab Integration
Contents
Introduction
BrainLab has recently introduced VV Link, an open API (but not free) to communicate with the IGT environment. This API allows to receive tracker information from the BrainLab system. This tutorial describes in detail how to interface 3D Slicer to the BrainLab system and to use it for research. Specifically, we describe 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 and will not affect the FDA status of the BrainLab system. In our current scenario we are using the BioImage Suite from Yale as a "bridge". Slicer3 and BioImage Suite run on a different computer than the BrainLab system. These two computers need to be connected to each other using a network or router 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 and Linux. If you are using a Mac, please share your experience with us.
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. For Windows users, the computer should have Windows XP Pro installed. For Linux users, Ubuntu 8.04 is used as the testbed. 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 of the available (and dated) versions for your system and download it
- For Windows users, run the installer to install Slicer3 on your Windows XP computer. For Linux users, unzip the binary to your preferred location
STEP 2: Set up the System
- The computers running the BrainLab system and the one running Slicer3 should be connected through a Ethernet network or a router. We have been testing the system in OR with a wired router (e.g. Netgear or Linsys).
- Steps to set up the system can be found in this file
STEP 3: Test 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.
- Steps to test the system connectivity can be found in this file
STEP 4: Visualize DTI in Slicer3
- The tutorial, Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3, 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 No. 1.4)
- The procedure to visualize DTI tractography while tracking by BrainLab is described in this file
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).
