View source for 2010 Winter Project Week SPECTRE 3DSlicer Integration

__NOTOC__
<gallery>
Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
<! --Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.-- >
</gallery>

==Key Investigators==
* BWH: Nicole Aucoin
* JHU: Aaron Carass, Min Chen
* GE: Jim Miller

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>

Integration of SPECTRE Skull Stripping software into the NAMIC Toolkit via the Slicer3 CLI framework. 








</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach: integration of software which will segment and provide coordinate reference frames for the Cerebrum (akin to the Talairach space), the Cerebellum (see reference below for K. Rehm), and for the Brainstem. 

This will be achieved through integration of the Java Imaging Software Toolkit (JIST) into the Slicer3 framework and then testing and evaluation of JIST components for completing the necessary components to provide this system. 

The main challenge is supporting Java command line executables in 3D Slicer.

Our plan is first to facilitate Java command line module discovery and execution, by adding support for the --xml argument to SPECTRE, and adding support for tcl wrapping scripts in 3DSlicer.
Then integrate SPECTRE into the NAMIC toolkit by crafing a CMakeLists.txt file to allow it to be built easily.
Create a NITRC project and a 3D Slicer extension that can be either downloaded or built on any platform.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>

A proof of concept sample Java HelloWorld application has been added to 3D Slicer.

Changes to the Command Line Module logic and Module Factory were made to support launching the tcl script with tclsh, for cross platform compatibility.

Changes made to the Java classes to support the --xml argument, Slicer recognises SPECTRE as a command line module.

Working on reading in the output images from SPECTRE back into Slicer.


</div>
</div>

==Presentations==
[[Media:2010-NA-MIC-Prince.ppt|Powerpoint]] presentation given by Jerry L. Prince on the status of the integration of SPECTRE as a module within Slicer, given at the 2010 Winter AHM in Utah.


<div style="width: 97%; float: left;">

==References==
*K. Rehm's 2000 HBM abstract, 'Use of Cerebellar Landmarks To Define a Coordinate System and an Isolation Strategy'
</div>