Difference between revisions of "Projects:ShapeCorrespondence UNCOrthoApp"

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Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
 
Image:PW2009-v3.png|[[2009_Summer_Project_Week|Project Week Main Page]]
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Image:TMJOAWorkflow.png|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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Image:TMJOAWorkflow.png|'''(1)''' Shape Analysis workflow to detect morphological differences in the progression of the Temporomandibular Joint Disease (TMJ OA).
 
Image:Asymmetry.png| '''(2)''' Showing a rotation of a surface mirror (left) and an anterior occlusal cant view (right) to detect asymmetries in 3D.
 
Image:Asymmetry.png| '''(2)''' Showing a rotation of a surface mirror (left) and an anterior occlusal cant view (right) to detect asymmetries in 3D.
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Image:OrthoSurgery.png|EDITED Trying to add more images into the current layout.
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Image:OrthoSurgery.png|'''(3)''' Shape Analysis is applied to find correspondent models between two different screenings on the same subject (red, postsurgery, white presurgery).
 
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==This template page is under construction, read under your risk and responsibility :P==
 
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==Instructions for Use of this Template==
 
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# EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED
 
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#'''Link the created page into the list of projects for the project event''' TO DO!!
 
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#Send an email to tkapur at bwh.harvard.edu if you are stuck PROBABLY TO DO!
 
  
 
==Motivations: Clinical Applications in Orthodontics==
 
==Motivations: Clinical Applications in Orthodontics==
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<div style="margin: 20px;">
 
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* '''Temporomandibular Joint (TMJ) Osteoarthritis (OA).''' Shape analysis used to localize and quantify the condylar morphological differences in the progression of the Temporomandibular Joint Osteoarthritic disease. The information obtained can be used in the clinical field to better elucidate the nature of the disease and therefore aim for a better treatment planning.
 
* '''Temporomandibular Joint (TMJ) Osteoarthritis (OA).''' Shape analysis used to localize and quantify the condylar morphological differences in the progression of the Temporomandibular Joint Osteoarthritic disease. The information obtained can be used in the clinical field to better elucidate the nature of the disease and therefore aim for a better treatment planning.
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* '''Asymmetry.''' 3D cephalometries, measuring the distances between the structure and its mirror is an approach to localize asymmetry and to quantify the left and right differences in the anatomy of interest.  This information can be used in corrective surgery planning.  
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* '''Asymmetry.''' Shape analysis is used to measure distances between an anatomical structure and its mirror is an approach to localize asymmetry and to quantify the left and right differences in the anatomy of interest (3D cephalometries).  This information can be used in corrective surgery planning.  
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* '''Skeletodental deformities corrective surgery.''' Test the changes in hard-tissue after corrective surgery for skeletal dento-facial deformities.  
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* '''Skeletodental deformities corrective surgery.''' Test the changes in hard-tissue after corrective surgery for skeletal dento-facial deformities. Shape analysis can give useful stability information.
 
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==Key Investigators==
 
==Key Investigators==
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* UNC: Beatriz Paniagua, Martin Styner, Lucia Cevidanes
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* UNC: Beatriz Paniagua  
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* Supervision (UNC): Martin Styner
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* Clinical supervision (UNC): Lucia Cevidanes
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* Methodology and Programming Aid (UNC): Clement Vachet, Marc Niethammer, Ipek Oguz
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* Beta-testing and collaborations: Joost Jansen (Spain), Mark Walterfang (Australia)
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* Finite Element Meshing in Slicer: Curtis Lisle (KnowledgeVis/Isomics)
  
 
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<h3>Objective</h3>
 
<h3>Objective</h3>
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Trying to merge our tools into the Slicer3 program, providing to the clinical people a friendly framework to get the measurements that are currently obtained by people with technical background. Apart from that, there are many other possibilities, but one focus for these Project Week could be the incorporation of XNAT in Slicer3 for defining groups and patient variables in our sample groups.  
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Trying to merge our tools into the Slicer3 program, providing to the clinical people a friendly framework to get the measurements that are currently obtained by people with technical background. This passes for integrating our Shape Correspondence tools and Statistical Analysis tools into Slicer3. Therefore one focus for these Project Week could be the incorporation of XNAT in Slicer3 for defining groups and patient variables in our sample groups (Batchmake).  
  
 
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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We would like to provide a homogeneous framework for our clinical research needs. Integration of our tools and functionalities to existing programs (Slicer3?)
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We would like to provide a homogeneous framework for our clinical research needs. Explore the possibilities to  
  
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# Integration of the UNC statistical core  
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'''1. ''' Integration of the UNC statistical core (XNAT?)
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# Integration of the UNC pre-processing steps
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# Incorporation of XNAT functionalities
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'''2. ''' Integration of the UNC shape correspondence (XNAT?)
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'''3. ''' Ortho-Application wise... trouble-solving, meet mesh-people, ITK VTK programming etc etc
  
 
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<div style="width: 40%; float: left;">
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<div style="width: 40%; float: left;">  
  
 
<h3>Progress</h3>
 
<h3>Progress</h3>
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Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
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The application of Shape Analysis to Orthodontic applications is quite recent. The group already counts with preliminary results, but more technical development regarding to the usability of these results is needed.
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''' ... after few days... '''
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''' 1.'''  and ''' 2.'''  have been studied and discussed and we should be ready to go soon. Thanks to Wendy Plesniak, Dan Marcus, Tim Olsen and the rest of the XNAT crew for an interesting breakout session!
 +
 
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''' 3.'''  In touch with new tools ([http://www.paraview.org/ Sebastian B., Luis I.], [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ Curtis L.]), new functionalities such as Python ([http://ipython.scipy.org/moin/ Demian W.]), more knowledge on ITK and VTK after a VERY interesting ITK breakout session (Luis I.) and debugging sessions (Arnaud G. [http://www.vtk.org/doc/release/5.0/html/a01886.html 1] and [http://www.itk.org/Doxygen314/html/classitk_1_1QuadEdgeMesh.html 2])
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''' Moreover ''' new books and papers to read, new code to develop, new paths...
  
 
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=References=
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==References==
 
 
* '''"Shape Modeling and Analysis with Entropy-Based Particle Systems"''' J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker. IPMI 2007, LNCS 4584, pp. 333-345, 2007.
 
* '''"Shape Modeling and Analysis with Entropy-Based Particle Systems"''' J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker. IPMI 2007, LNCS 4584, pp. 333-345, 2007.
 
* '''"Parameter space warping: shape-based correspondence between morphologically different objects"''' Meier, D.  Fisher, E.  IEEE Transactions on Medical Imaging, 2002  
 
* '''"Parameter space warping: shape-based correspondence between morphologically different objects"''' Meier, D.  Fisher, E.  IEEE Transactions on Medical Imaging, 2002  

Latest revision as of 14:40, 26 June 2009

Home < Projects:ShapeCorrespondence UNCOrthoApp

  • (1) Shape Analysis workflow to detect morphological differences in the progression of the Temporomandibular Joint Disease (TMJ OA).

  • (2) Showing a rotation of a surface mirror (left) and an anterior occlusal cant view (right) to detect asymmetries in 3D.

  • (3) Shape Analysis is applied to find correspondent models between two different screenings on the same subject (red, postsurgery, white presurgery).

Motivations: Clinical Applications in Orthodontics

We are aiming to develop methods to apply Shape Correspondence and Shape Analysis to the Orthodontic Clinical field. The main challenge this approach is the big amount of pre-processing required to adapt the current methods to the new data (until now, Shape Correspondence was applied almost entirely to brain morphometry studies). Different NAMIC Tools are used for this purpose, and also some tools have been already developed. Many others are under current development, but some desirable thing would be to merge all the tools in the same framework, in order our work can be useful in other applications.

Three projects are currently in progress:

  • Temporomandibular Joint (TMJ) Osteoarthritis (OA). Shape analysis used to localize and quantify the condylar morphological differences in the progression of the Temporomandibular Joint Osteoarthritic disease. The information obtained can be used in the clinical field to better elucidate the nature of the disease and therefore aim for a better treatment planning.
  • Asymmetry. Shape analysis is used to measure distances between an anatomical structure and its mirror is an approach to localize asymmetry and to quantify the left and right differences in the anatomy of interest (3D cephalometries). This information can be used in corrective surgery planning.
  • Skeletodental deformities corrective surgery. Test the changes in hard-tissue after corrective surgery for skeletal dento-facial deformities. Shape analysis can give useful stability information.

Key Investigators

  • UNC: Beatriz Paniagua
  • Supervision (UNC): Martin Styner
  • Clinical supervision (UNC): Lucia Cevidanes
  • Methodology and Programming Aid (UNC): Clement Vachet, Marc Niethammer, Ipek Oguz
  • Beta-testing and collaborations: Joost Jansen (Spain), Mark Walterfang (Australia)
  • Finite Element Meshing in Slicer: Curtis Lisle (KnowledgeVis/Isomics)

Objective

Trying to merge our tools into the Slicer3 program, providing to the clinical people a friendly framework to get the measurements that are currently obtained by people with technical background. This passes for integrating our Shape Correspondence tools and Statistical Analysis tools into Slicer3. Therefore one focus for these Project Week could be the incorporation of XNAT in Slicer3 for defining groups and patient variables in our sample groups (Batchmake).

Approach, Plan

We would like to provide a homogeneous framework for our clinical research needs. Explore the possibilities to

1. Integration of the UNC statistical core (XNAT?)

2. Integration of the UNC shape correspondence (XNAT?)

3. Ortho-Application wise... trouble-solving, meet mesh-people, ITK VTK programming etc etc

Progress

The application of Shape Analysis to Orthodontic applications is quite recent. The group already counts with preliminary results, but more technical development regarding to the usability of these results is needed.

... after few days...

1. and 2. have been studied and discussed and we should be ready to go soon. Thanks to Wendy Plesniak, Dan Marcus, Tim Olsen and the rest of the XNAT crew for an interesting breakout session!

3. In touch with new tools (Sebastian B., Luis I., Curtis L.), new functionalities such as Python (Demian W.), more knowledge on ITK and VTK after a VERY interesting ITK breakout session (Luis I.) and debugging sessions (Arnaud G. 1 and 2)

Moreover new books and papers to read, new code to develop, new paths...

References

  • "Shape Modeling and Analysis with Entropy-Based Particle Systems" J Cates, P T Fletcher, M Styner, M Shenton, R Whitaker. IPMI 2007, LNCS 4584, pp. 333-345, 2007.
  • "Parameter space warping: shape-based correspondence between morphologically different objects" Meier, D. Fisher, E. IEEE Transactions on Medical Imaging, 2002
  • "Craniofacial Surgery" Seth Thaller, Joe I. Garri, James P. Bradley, Henry K. (INT) Kawamoto Contributor Henry K. (INT) Kawamoto. CRC Press, 2007
  • "Principles of Surgery" I. Schwartz., Single Volume. McGraw-Hill Professional, 7 edition, 1998.
  • "Condylar Resorption in Subjects with TMJ Osteoarthritis" Lucia H.S. Cevidanes, Anna-Kari Hajati, Beatriz Paniagua, David G. Walker, Martin Styner, Pei Feng Lim. Submitted to the Journal of Dental Research, 2009
  • "Closed and Open Source Neuroimage Analysis Tools and Libraries at UNC" Styner, Jomier, Gerig, ISBI 2006
  • "Open Source Statistical Surface Shape Analysis Package" Niethammer, Styner, Paniagua, Pantazis, Macenko, in preparation for InsightJournal
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