Difference between revisions of "2010 Summer Project Week Shape Analysis UNC"

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Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
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Image:surgworkflow.png|SPHARM-PDM shape Analysis workflow to detect stability after Orthognatic Surgery.
 
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==Motivations: Clinical Applications in Orthodontics==
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We are aiming to develop methods to compute Shape Correspondence and Shape Analysis to the Orthodontic Clinical field. The main challenge in this approach is the complexity of the surfaces processed, i.e. Cranio-Maxillo-Facial anatomy. Until now, Shape Correspondence was applied almost entirely to brain morphometry studies. SPHARM-PDM Toolbox has been used until now for different Ortho applications ([1-5] see figure 1), however the performance of this methodological framework does not work satisfactorily for Full Mandibles. Our main interest focuses right now in Entropy-Based Particle Systems [6], that does not rely in parametric fields or spherical topology for establishing correspondence in a Surface Ensemble. Since it is relevant to expand our research topics, we are interested in linear distance map visualization in Slicer3, as well as how to best use transformation nodes provided by Slicer3 for Surgical planning.
  
 
==Key Investigators==
 
==Key Investigators==
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* MIT: Tammy Riklin Raviv
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* UNC SPHARM: Beatriz Paniagua, Martin Styner, Corentin Hamel
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* BWH: Sylvain Bouix
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* UNC Particle System: Beatriz Paniagua, Ipek Oguz, Clement Vachet
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* UNC Shape Analysis, Application and Visualization: Beatriz Paniagua, Martin Styner, Lucia Cevidanes
 
   
 
   
 
==Project==
 
==Project==
 
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<div style="width: 30%; float: left; padding-right: 2%;">
 
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<h3>Objective</h3>
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<h3>Objectives</h3>
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Group-wise statistical analysis of brain structures is significant for clinical and neuroanatomy studies. Nevertheless, due to the inherent difficulty to properly represent the morphology of the structures of interest, the statistics is usually limited to volume and surface area measurements. Ideally, we would require an injective shape representation that is invariant rigid or even affine transformations and form a vector space. In the absence of shape representation that meets all of these requirements, it is difficult to define fundamental concepts such as the median or average shape.
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'''1.''' Integrate tools developed to be used with ShapeWorks particle-optimization shape correspondence program, developed by Utah U.
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'''2.''' Slicer3 color map visualization
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'''3.''' UNC SPHARM-PDM shape analysis module integration in Slicer3.
 +
 
 +
'''4.''' Application of Slicer3 for Cranio maxillo facial surgical planning, discussions about how Slicer3 clips, rotates, mirrors, etc.
  
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We defined a novel measure for shape dissimilarity that is based on shape boundaries. This measure allows us to construct the 'median' of shapes of the same class that provides reacher morphological characteristics of the ensemble. Our goal in this project is to apply the proposed method to a population study of brain structures and test its discriminative power.
 
 
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</div>
  
 
<div style="width: 30%; float: left; padding-right: 2%;">
 
<div style="width: 30%; float: left; padding-right: 2%;">
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<h3>Approach, Plan</h3>
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<h3>Approach Plan</h3>
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We use a variational framework based on level-sets to deform a representative (canonical) shape such that the sum of its distances from each of the shapes in the group is minimized.
+
'''1.''' Entropy-Based Particle Systems: Meet with Manasi Datar and Josh Cates (Utah U.) to discuss integration of our auxiliary post and pre processing tools.
−
We will first test the approach on a set of synthetic shapes where the resulting median shape can be validated. The outcomes of this preliminary stage are expected to guide us in planning more advanced experiments.
+
 
 +
'''2.''' Slicer3 color map visualization: Talk with Nicole Augier about how to use Color module in Slicer3. Some tools were coded to adapt Slicer3 to our needs, but they are not optimal and it would be desirable to integrate this in Slicer3.
 +
 
 +
'''3.''' UNC SPHARM-PDM shape analysis module integration in Slicer3: Corentin Hamel is the main person in charge for that, but I will be happy to help if needed.
 +
 
 +
'''4.''' Application of Slicer3 for Cranio maxillo facial surgical planning, discussions about how Slicer3 clips, rotates, mirrors, etc: Talk with Steve Piper (?) about Transformation Nodes usage.
 +
 
 
</div>
 
</div>
  
 
<div style="width: 35%; float: left;">
 
<div style="width: 35%; float: left;">
 
<h3>Progress</h3>
 
<h3>Progress</h3>
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 +
'''*''' Worked with Manasi Datar in the integration of particle consistency code.
 +
 +
'''*''' Slicer3 color map visualization: Demian and Nicole are working in future upgrades of the color module that most likely will cover our needs with regards to color visualization in Slicer3. In the meantime a stand-alone tool is up and running for mapping colors that might be displayed in Slicer3.
 +
 +
'''*''' Possibilities and scope of Cranio maxillo facial surgical planning module were discussed with Steve. In the meantime while that evolves, further idea on clipping, rotation functionality in Slicer3 will allow to go further in our surgery simulation studies.
  
 
</div>
 
</div>
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==References==
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'''[1]''' LHS Cevidanes, B Paniagua, L De Paula, M Styner: Shape Analysis of Stability following Skeletal Class III Surgery. IADR Barcelona, July 14-17, 2010.
 +
 +
'''[2]''' B Paniagua, LHS Cevidanes, H Zhu, M Styner: Surgical Outc ome Quantification using SPHARM-PDM Toolbox. IADR Barcelona, July 14-17, 2010.
 +
 +
'''[3]''' D Walker, LHS Cevidanes, B Paniagua, H Zhu, M Styner, PF Lim: Validation of Shape Correspondence for Quantification of Condylar Resorption. J Dent Res. 2010 ;89 (Spec Iss A):1200.
 +
 +
'''[4]''' LHS Cevidanes, A Alhadidi, B Paniagua, M Styner, WR Proffit, J Ludlow, A Mol, E Russouw: 3D quantification of mandibular asymmetry. Submitted to Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology & Endodontics April 2010.
 +
 +
'''[5]''' LHS Cevidanes, AK Hajati, B Paniagua, PF Lim, DG Walker, G Palconet, AG Nackley, JB Ludlow, MA Styner, H Zhu, C Phillips. Quantification of Condylar Resorption in TMJ Osteoarthritis. Oral Surg Oral Med Oral Pathol Oral Radiol Endod Oral Surg. Epub April 08 2010.
 +
 +
'''[6]''' 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.

Latest revision as of 13:58, 25 June 2010

Home < 2010 Summer Project Week Shape Analysis UNC

  • SPHARM-PDM shape Analysis workflow to detect stability after Orthognatic Surgery.

Motivations: Clinical Applications in Orthodontics

We are aiming to develop methods to compute Shape Correspondence and Shape Analysis to the Orthodontic Clinical field. The main challenge in this approach is the complexity of the surfaces processed, i.e. Cranio-Maxillo-Facial anatomy. Until now, Shape Correspondence was applied almost entirely to brain morphometry studies. SPHARM-PDM Toolbox has been used until now for different Ortho applications ([1-5] see figure 1), however the performance of this methodological framework does not work satisfactorily for Full Mandibles. Our main interest focuses right now in Entropy-Based Particle Systems [6], that does not rely in parametric fields or spherical topology for establishing correspondence in a Surface Ensemble. Since it is relevant to expand our research topics, we are interested in linear distance map visualization in Slicer3, as well as how to best use transformation nodes provided by Slicer3 for Surgical planning.

Key Investigators

  • UNC SPHARM: Beatriz Paniagua, Martin Styner, Corentin Hamel
  • UNC Particle System: Beatriz Paniagua, Ipek Oguz, Clement Vachet
  • UNC Shape Analysis, Application and Visualization: Beatriz Paniagua, Martin Styner, Lucia Cevidanes

Project

Objectives

1. Integrate tools developed to be used with ShapeWorks particle-optimization shape correspondence program, developed by Utah U.

2. Slicer3 color map visualization

3. UNC SPHARM-PDM shape analysis module integration in Slicer3.

4. Application of Slicer3 for Cranio maxillo facial surgical planning, discussions about how Slicer3 clips, rotates, mirrors, etc.

Approach Plan

1. Entropy-Based Particle Systems: Meet with Manasi Datar and Josh Cates (Utah U.) to discuss integration of our auxiliary post and pre processing tools.

2. Slicer3 color map visualization: Talk with Nicole Augier about how to use Color module in Slicer3. Some tools were coded to adapt Slicer3 to our needs, but they are not optimal and it would be desirable to integrate this in Slicer3.

3. UNC SPHARM-PDM shape analysis module integration in Slicer3: Corentin Hamel is the main person in charge for that, but I will be happy to help if needed.

4. Application of Slicer3 for Cranio maxillo facial surgical planning, discussions about how Slicer3 clips, rotates, mirrors, etc: Talk with Steve Piper (?) about Transformation Nodes usage.

Progress

* Worked with Manasi Datar in the integration of particle consistency code.

* Slicer3 color map visualization: Demian and Nicole are working in future upgrades of the color module that most likely will cover our needs with regards to color visualization in Slicer3. In the meantime a stand-alone tool is up and running for mapping colors that might be displayed in Slicer3.

* Possibilities and scope of Cranio maxillo facial surgical planning module were discussed with Steve. In the meantime while that evolves, further idea on clipping, rotation functionality in Slicer3 will allow to go further in our surgery simulation studies.

References

[1] LHS Cevidanes, B Paniagua, L De Paula, M Styner: Shape Analysis of Stability following Skeletal Class III Surgery. IADR Barcelona, July 14-17, 2010.

[2] B Paniagua, LHS Cevidanes, H Zhu, M Styner: Surgical Outc ome Quantification using SPHARM-PDM Toolbox. IADR Barcelona, July 14-17, 2010.

[3] D Walker, LHS Cevidanes, B Paniagua, H Zhu, M Styner, PF Lim: Validation of Shape Correspondence for Quantification of Condylar Resorption. J Dent Res. 2010 ;89 (Spec Iss A):1200.

[4] LHS Cevidanes, A Alhadidi, B Paniagua, M Styner, WR Proffit, J Ludlow, A Mol, E Russouw: 3D quantification of mandibular asymmetry. Submitted to Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology & Endodontics April 2010.

[5] LHS Cevidanes, AK Hajati, B Paniagua, PF Lim, DG Walker, G Palconet, AG Nackley, JB Ludlow, MA Styner, H Zhu, C Phillips. Quantification of Condylar Resorption in TMJ Osteoarthritis. Oral Surg Oral Med Oral Pathol Oral Radiol Endod Oral Surg. Epub April 08 2010.

[6] 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.

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