Difference between revisions of "Projects:ShapeCorrespondence UNCOrthoApp"

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(Created page with '__NOTOC__ <gallery> Image:PW2009-v3.png|Project Week Main Page Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus ...')
 
 
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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:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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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).
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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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|'''(3)''' Shape Analysis is applied to find correspondent models between two different screenings on the same subject (red, postsurgery, white presurgery).
 
</gallery>
 
</gallery>
  
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==Instructions for Use of this Template==
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==Motivations: Clinical Applications in Orthodontics==
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# EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED EDITED
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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.
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#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
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#Copy the entire text of this page into the page created above
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Three projects are currently in progress:
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#Link the created page into the list of projects for the project event
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#Delete this section from the created page
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<div style="margin: 20px;">
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#Send an email to tkapur at bwh.harvard.edu if you are stuck
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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.
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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. Shape analysis can give useful stability information.
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</div>
  
 
==Key Investigators==
 
==Key Investigators==
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
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* UNC: Beatriz Paniagua
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* Utah: Tom Fletcher, Ross Whitaker
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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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We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
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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).  
  
 
</div>
 
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.
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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
  
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Our plan for the project week is to first try out <bar>,...
 
 
</div>
 
</div>
  
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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.
 +
 
 +
''' ... 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 ([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...
  
 
</div>
 
</div>
 
</div>
 
</div>
  
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=References=
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==References==
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* '''"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.
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*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
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* '''"Parameter space warping: shape-based correspondence between morphologically different objects"''' Meier, D. Fisher, E. IEEE Transactions on Medical Imaging, 2002
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* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
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* '''"Craniofacial Surgery"''' Seth Thaller, Joe I. Garri, James P. Bradley, Henry K. (INT) Kawamoto Contributor Henry K. (INT) Kawamoto. CRC Press, 2007
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* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
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* '''"Principles of Surgery"''' I. Schwartz., Single Volume. McGraw-Hill Professional, 7 edition, 1998.
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* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .
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* '''"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

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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