2009 Winter Project Week ShapePipeline - Revision history

Datar: /* Key Investigators */

2009-01-09T15:25:43Z

Key Investigators

Tkapur at 02:29, 1 January 2009

2009-01-01T02:29:59Z

Tkapur at 20:32, 31 December 2008

2008-12-31T20:32:33Z

Cates at 03:40, 27 December 2008

2008-12-27T03:40:27Z

Cates: New page: {| |Project Week Main Page ]] |[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium using MR...

2008-12-27T03:39:49Z

New page: {| |thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page ]] |[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium using MR...

New page

{|
|[[Image:NAMIC-SLC.jpg|thumb|320px|Return to [[2009_Winter_Project_Week|Project Week Main Page]] ]]
|[[Image:scarmri_namic.jpg|thumb|320px|Image showing scar in the left atrium using MRI]]
|[[Image:scar_carto_namic.jpg|thumb|320px|Image of scar by MRI registered to MR Angiogram, and to the EP RF ablation site data.]]
|}

__NOTOC__

===Key Investigators===
* Univ Utah, SCI Institute: Manasi Datar, Josh Cates, Ross Whitaker

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<h1>Objective</h1>
We will investigate the use of BatchMake for automating and packaging
our particle-based shape analysis pipeline. Major tasks include learning
to use BatchMake, and designing compatible command-line interfaces for our
existing software.

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<h1>Approach, Plan</h1>
Our goal during project week is to spec out a design and API for a shape analysis
pipeline that strings together a number of our existing software tools. If time
allows, we will also construct a prototype system. Existing code that we hope to
convert for use by BatchMake includes preprocessing routines, correspondence optimization
routines, and visualization tools.

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<h1>Progress</h1>

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===References===
* J Cates, P T Fletcher, M Styner, H Hazlett, R Whitaker. Particle-Based Shape Analysis of Multi-Object Complexes. Proceedings of the 11th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI '08), to appear.

* J Cates, P T Fletcher, Z Warnock, R Whitaker. A Shape Analysis Framework for Small Animal Phenotyping with Application to Mice with a Targeted Disruption of Hoxd11. Proceedings of the 5th IEEE International Symposium on Biomedical Imaging (ISBI '08), pp. 512-516, 2008.

* I Oguz, J Cates, P T Fletcher, R Whitaker, D Cool, S Aylward, M Styner. Entropy-Based Particle Systems and Local Features for Cortical Correspondence Optimization Proceedings of the 5th IEEE International Symposium on Biomedical Imaging (ISBI '08), pp. 1637-1641, 2008.

* J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker. Shape Modeling and Analysis with Entropy-Based Particle Systems. Information Processing in Medical Imaging IPMI 2007, LNCS 4584, pp. 333-345, 2007.

* J Cates, P T Fletcher, R Whitaker. Entropy-Based Particle Systems for Shape Correspondence. Mathematical Foundations of Computational Anatomy Workshop, MICCAI 2006. pp. 90-99 Oct 2006. pdf

← Older revision		Revision as of 15:25, 9 January 2009
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	<h1>Progress</h1>		<h1>Progress</h1>
		+	Strategy:<br>
		+	Create individual Batchmake scripts for the various components identified during discussions with the UNC group <br>
		+	String these (as required) into a master Batchmake script to run a customized pipeline <br>
		+	As a separate step, integrate these into Slicer3 as command line modules <br>
		+
		+	Action: <br>
		+	Created a prototype Batchmake script which: <br>
		+	requires the user to set the data directory <br>
		+	dynamically creates the parameter file required for one of the pre-processing operations <br>
		+	runs the pre-processing operation on all images present in the data directory <br>
		+
		+	Problems: <br>
		+	1. The command appendFile(...) is used to create the parameter file dynamically - unable to print '(' and ')' to the file - e.g. appendFile('<path>/xyz.params','(inputs\n') does not work <br>
		+	2. What are the components that need to be bundled with this script when distributing it ? <br>

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 ===Key Investigators===
 * Univ Utah, SCI Institute: Manasi Datar, Josh Cates, Ross Whitaker
-* Kitware: Stephen Aylward?
+* Kitware: Stephen Aylward
-* UNC: Martin Styner?
+* UNC: Martin Styner
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