2011 Winter Project Week:SPECTRE Integration

2010-12-15T15:30:15Z

Mchen55: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Nicole Aucoin
* JHU: Min Chen

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<h3>Objective</h3>

To advance the integration of the Java based SPECTRE algorithm into Slicer3 (and Slicer4), to find validation data sets.

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<h3>Approach, Plan</h3>

Our approach is to fine tune the integration for Slicer3, write a python wrapping script for Slicer4, fine tune the ACPC algorithm. The main challenge to this approach is coordinate system transforms.

Our plan for the project week is:
<ul>
<li>Add a memory argument to the SPECTRE xml and use it to set Java heap sizes
<li>Fine tune the Java handling in Slicer3 to fail gracefully if Java is not available on a build machine
<li>Debug the ACPC algorithm in SPECTRE
<ul>
<li>Add a transform output to SPECTRE
</ul>
<li>Debug y flip on reading in output images into Slicer
<li>
<li>Find collaborators with segemented data sets for the validation portion of our project. Ron has suggested talking with:
<ul>
<li>Sylvain Bioux
<li>Hans Johnson
</ul>
<li>Write a python wrapper so we can integrate SPECTRE into Slicer4
<li>Work on documentation so that the manual steps are as clear as possible
<li>Remove the requirement to have to run MIPAV before running the SPECTRE extension in Slicer.
<li>Set volume types in SPECTRE outputs
</ul>

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<h3>Progress</h3>

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==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a
#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable

==References==

*[[2010_Summer_Project_Week_SPECTRE | 2010 Summer Project Week]]
*[[2010_Winter_Project_Week_SPECTRE_3DSlicer_Integration | 2010 Winter Project Week]] (has manual steps for integration)

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2010 Summer Project Week SPECTRE

2010-06-15T15:15:37Z

Mchen55: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]

</gallery>

==Key Investigators==
* BWH: Nicole Aucoin
* JHU: Min Chen

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

<h3>Objective</h3>

Futher integration of the Java SPECTRE skull tripping module into Slicer3.

</div>

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

<h3>Approach, Plan</h3>

Our approach is to integrate SPECTRE as an extension.
The main challenge to this approach is setting up a web site with a stable jar file and tcl wrapper.

Our plan for the project week is to first try out a temporary location for the jar file and tcl wrapper and then come up with a plan for updates.

SPECTRE outputs will be modified to be compatible with Slicer image types(i.e. intensity, mask, etc.)

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<h3>Progress</h3>

Tcl wrapped Java jar files have been integrated into Slicer3 already, so hopefully no major infrastructur changes will be required.

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</div>

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

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline YES
##Extension -- loadable
#Other (Please specify)

==References==

</div>

NAMIC Wiki - User contributions [en]

2011 Winter Project Week:SPECTRE Integration

2010 Summer Project Week SPECTRE