View source for 2011 Summer Project Week normal consistency particles

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Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:ReconstructionProblems.png|Fig1. Particle Correspondence has problems with regard to representing thin areas correctly, and thus with reconstructing them
Image:NormalFeatures.png|Fig2. First attempts into incorporating normal directions into Particle Correspondence
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==Key Investigators==
* University of North Carolina at Chapel Hill: Beatriz Paniagua, Sungkyu Jung, Martin Styner, Steve Pizer
* University of Utah: Josh Cates, Manasi Datar, Ross Whitacker


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<h3>Objective</h3>

A well established method for performing statistics on an ensemble of shapes is to compare corresponding landmarks placed automatically on the individual shapes. Particle ensemble-systems, designed initially by Cates et all [1], has sometimes problems to correctly represent medical or biological shapes that have sharp features and regions of high curvature. Normal directions should be consistent in each individual particle during the optimization, that should try to minimize normal entropy. The problem of computing entropy in normals is that they are not in Euclidean space so a dimensionality reduction method is needed. Jung et al [2] created a dimension reduction and data visualization for highdimensional data method that can be applied to entropy computing in normals.

Our objective is incorporate a new entropy term into [1] based in [2] that accounts for normal consistency during landmark positioning.  


ALSO, talk with Steve and Ron about discontinued projects in CMF applications [3]

Iowa Data (Huntington's disease DBP), with Clement Vachet.

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<h3>Approach, Plan</h3>

# Coding-debugging in collaboration with Josh Cates and Manasi Datar.
# Revise the engineering details of the code with Josh Cates.
# (hopefully) Test the code to asses the validity of the method. 


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<h3>Progress</h3>

* Particle systems: 
#Josh, Manasi, Clement and I had engineering meeting to decide how the code is going to be branched and to talk abt the last additions to the method.
#Started to work with Manasi in testing the new core architecture in mandible studies.
#Debugging with Josh and Lucile.
#Coding PNS, still not finished (but close!). Started to incorporate it into the particle system core.
#Follow-up paper
* CMF
#Follow-up in the CMF applications (Osteo-plan) with Laurent Chauvin.
#Help from Sonia Pujol to distribute the materials of our CMF workshops in the dentistry community within Slicer wiki.
#Ron Kikinis suggested how to use Fiducials and Measurement tapes to perform cephalometries.
* IOWA Data, coordinated efforts to start shape correspondence projects with HD data.
*Slicer translation: Gracias to Demian W. and Antonio V.!
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==References==

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1. Shape Modeling and Analysis with Entropy-Based Particle Systems. Joshua Cates1, P. Thomas Fletcher1, Martin Styner2, Martha Shenton3, and Ross Whitaker1

2. Analysis of Principal Nested Spheres, SUNGKYU JUNG, IAN L. DRYDEN AND J. S. MARRON. Submitted to Biometrika 2010.

3. Development of a three-dimensional treatment planning system based on computed tomographic data. M. J. Troulis, P. Everett, E. B. Seldin, R. Kikinis, L. B. Kaban: Development of a three-dimensional treatment planning system based on computed tomographic data. Int. J. Oral Maxillofac. Surg. 2002

==Delivery Mechanism==

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This work will be delivered to the NAMIC Kit as a 

#NITRIC distribution
#Slicer Module
##Built-in: 
##Extension -- commandline:  
##Extension -- loadable: