View source for OpenIGTLink/Slicer 3 2

[[OpenIGTLink | &lt;&lt; OpenIGTLink]]


=Introduction=
The OpenIGTLink module is a communication interface between 3D Slicer and OpenIGTLink-compliant  devices. It enables the 3D SLicer to import various types of data such as real-time images, tracking data and other user-defined commands and data. The module supports multiple device connections. Each of connections can be configured as either server mode (the Slicer waits connections from devices) or client mode (the Slicer request connection to clients) independently. 

The module works with MRML to exchange coordinate and image data with other clinical modules e.g. NeuroNav and ProstateNav in the Slicer. The module has a dedicated graphical user interface to manage and control multiple connections.


[[Image:OpenIGTLink_Slicer_Screenshot.png]]

=Install the Software=

==From binaries==

The Open IGT Link is currently distributed as a loadable module for 3D Slicer. You need to obtain 3D Slicer and Module object.

=== 3D Slicer (Version 3.2 RC2 -- released on June 23, 2008)===
* [http://www.slicer.org/DownloadSlicer.php/Snapshots/win32/Slicer3-3.2-rc2-2008-06-23-win32.exe For Windows (32-bit)]
* [http://www.slicer.org/DownloadSlicer.php/Snapshots/linux-x86/Slicer3-3.2-rc2-2008-06-23-linux-x86.tar.gz For Linux (x86, 32-bit)]
* [http://www.slicer.org/DownloadSlicer.php/Snapshots/linux-x86_64/Slicer3-3.2-rc2-2008-06-23-linux-x86_64.tar.gz For Linux (x86, 64-bit)]
* [http://www.slicer.org/DownloadSlicer.php/Snapshots/darwin-x86/Slicer3-3.2-rc2-2008-06-23-darwin-x86.tar.gz For Mac OS X (x86)]
* [http://www.slicer.org/DownloadSlicer.php/Snapshots/darwin-ppc/Slicer3-3.2-rc2-2008-06-23-darwin-ppc.tar.gz For Mac OS X (PPC)]

=== Open IGT Link Loadable Module (for Version 3.2 RC2 -- released on June 23, 2008)===
* [[Media:OpenIGTLink_3.2rc2_Linux_x86_32.tgz| For Linux (x86, 32-bit)]].
* [[Media:OpenIGTLink_3.2rc2_Linux_x86_64.tgz| For Linux (x86, 64-bit)]].
* [[Media:OpenIGTLink_3.2rc2_Win_x86_32.zip| For Windows (32-bit)]].
* [[Media:OpenIGTLink_3.2rc2_Darwin_x86.tgz| For Mac OS X(x86)]].
* [[Media:OpenIGTLink_3.2rc2_Darwin_ppc.tgz| For Mac OS X(PPC)]].

=== Open IGT Link Loadable Module (for Version 3.2 RC1 -- outdated!)===
* [[Media:OpenIGTLink_3.2_Linux_x86_32.tgz| For Linux (x86, 32-bit)]].
* [[Media:OpenIGTLink_3.2_Linux_x86_64.tgz| For Linux (x86, 64-bit)]].
* [[Media:OpenIGTLink_3.2_Win_x86_32.zip| For Windows (32-bit)]].
* [[Media:OpenIGTLink_Darwin_3.2_x86.tgz| For Mac OS X(x86)]].
* [[Media:OpenIGTLink_Darwin_3.2_ppc.tgz| For Mac OS X(PPC)]].

=== Install ===
* Copy the binary into '''your-slicer3-build(install)-directory'''/lib/Slicer3/Modules.
* You should see '''OpenIGTLink''' in the Slicer3 module list after Slicer is started.

==Build from source==
===Build 3D Slicer===
Please refer instruction in [https://www.slicer.org/wiki/Slicer3:Build_Instructions].

===Build Open IGT Link Loadable Module===

Before build the module, please make sure that your CMake's version is higher than 2.6.
You can find it in Slicer3-lib/CMake-build directory, which was created during building 3D Slicer.

First, get the source code from the repository. For Linux and Mac:
  $ cd <working directory>
  $ svn co http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/OpenIGTLink OpenIGTLink

Create build direcotry
  $ mkdir OpenIGTLink-build
  $ cd OpenIGTLink-build

Then configure by using CMake
  $ cmake -DSlicer3_DIR=<Path to Slicer-build directory> ../OpenIGTLink
 NOTE: <Path to Slicer-build directory> should be a full-path.

If the previous command has completed without error, you can start compiling
  $ make

After the compilation, you will find libOpenIGTLink.so (Linux) libOpenIGTLink.dylib (Mac) in OpenIGTLink-build dirctory.

===!! Note: Building on Mac OS X 10.5 (Leopard) !!===
If you are working in the Mac OS X 10.5 (Leopard) environment, you may get a linker error: 

  ld: cycle in dylib re-exports with /usr/X11R6/lib/libGL.dylib

This is caused by a known bug of the Open GL library in Mac OS X 10.5 (see [http://wiki.finkproject.org/index.php/Fink:Packaging:Preparing_for_10.5#OpenGL_Bug] for detail).
To avoid this error, specify following option when you run cmake.

 $ cmake -DSlicer3_DIR=<Path to Slicer-build directory> -DCMAKE_SHARED_LINKER_FLAGS=-Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib ../OpenIGTLink

<BR>

=Tracker Simulator for Testing Open IGT Link=

To test the Open IGT Link module (or other Open-IGT-Link-complaint devices and software), tracking simulator software is provided. This software simply sends dummy coordinate data to the server with specified frame rate.
You can either obtain the software as a binary code or build from source.

==From binaries==
Obtain a binary file for your environment. 
* [[Media:TrackerSimulator_Linux_x86_32.tgz|For Linux (x86, 32-bit)]].
* [[Media:TrackerSimulator_Linux_x86_64.tgz|For Linux (x86, 64-bit)]].
* [[Media:TrackerSimulator_Win_x86_32.zip|For Windows (32-bit)]].
* [[Media:TrackerSimulator_Darwin_x86.tgz |For Mac OS X (x86)]].
* [[Media:TrackerSimulator_Darwin_ppc.tgz |For Mac OS X (PPC)]].

==From Source==

To get the source code, run following commands:
 $ mkdir <working directory>
 $ svn co http://svn.na-mic.org/NAMICSandBox/trunk/BRPTools/ScannerIO ScannerIO

Then configure the source code
 $ cd ScannerIO
 $ ccmake .

Usually, you don't need to change any setting. Just press 'c' key by 'g' key to generate Makefiles. Press 'q' to quit the ccmake interface. Now you are ready to build the program.
 $ make

The executable file '''TrackerSim''' can be found in '''ScannerIO/bin''' directory.

<br>

=Testing Open IGT Link Module -- Show Tracking Device in the 3D Space=

==Set up Open IGT Link Module==

# Select "OpenIGTLink" from "Modules:" menu
# Open "Connector Browser" frame, and press "Add" button below the "Connectors" list to add a new connector
# Configure and start the connector. Choose "Server" check box in the "Type" option, then clinck "Active" check box. Now the Slicer is ready to accept connections through Open IGT Link.

==Run Tracker Simulator==
To send dummy coordinate data to the Slicer running on localhost with frame rate of 10 fps, run:
 $ ./TrackerSim  10  c  localhost 18944

==Visualize Tracker Position==
To see the coordinate from the Tracker Simulator,
# Open "Visualization / Slice Control" frame in the OpenIGTLink module interface.
# Click the "Show Locator" check button. A locator model shows up on the 3D viewer.
# Open "Data" module. Choose "Data" from "Modules:" menu.
# Edit MRML tree. Put "IGTLocator" under the "Tracker" by dragging "IGTLocator" node.
# You should see the locator model moves in the 3D viewer.

<br>

=Testing Open IGT Link Module -- Reslice 3D image=
We can reslice 3D image according to the locator position with following steps:
# Load 3D volume from the "Volumes" module.
# Start Tracking as we did in the previous section.
# In the "Visualization / Slice Control" frame in the OpenIGTLink module interface, click Red menu and choose "Locator".
# The image in the left 2D slice viewer (Red) should start to move. You can change the orientation by changing slice orientation menu in the 2D slice viewer.
# If you click the "Oblique" check button in the "Visualization / Slicer Control" frame, the slice orientation is set according to the locator orientation.
# You can use other 2D viewers (Yellow and Green) by choosing "Locator" from the Yellow and Green menu in the "Visualization / Slice Control" frame.

<br>


=Loadmap=
The current version of the Open IGT Link module supports only incoming data. In future, the module will also support outgoing data, which is useful for
*exporting registration result to other software
*exporting result images of registration / segmentation
*sending control commands to devices and imagers
*synchronizing multiple navigation software

The idea of outgoing data support is that the Open IGT Link module detects MRML update events (linear transforms and images) and put the new data into Open IGT Link data stream. This mechanism allows other Slicer3 modules to communicate with other OpenIGTLink-compatible software or devices through MRML.

In the next version, the Open IGT Link module handles MRML events to detect updates in MRML nodes (linear transforms and images)

Currently, the new version of Open IGT Link module is being developed. The code is available from SVN repository at:
 http://svn.na-mi.org/NAMICSandBox/trunk/IGTLodableModules/OpenIGTLinkPrototype
Please make sure not to load the current version of OpenIGTLink module and OpenIGTLinkPrototype module at the same time.

<BR>

=Other Resources=
*[[OpenIGTLink/Simulators]]

=People=
*[http://www.spl.harvard.edu/pages/People/tokuda  Junichi Tokuda]
*[http://www.spl.harvard.edu/pages/People/hliu Haiying Liu]