2011 Winter Project Week:ParticleShapeAnalysis - Revision history

Bpaniagua: /* Project */

2011-01-12T20:18:19Z

Project

Bpaniagua at 20:16, 12 January 2011

2011-01-12T20:16:22Z

Bpaniagua at 17:13, 2 December 2010

2010-12-02T17:13:53Z

Bpaniagua at 16:32, 2 December 2010

2010-12-02T16:32:28Z

Bpaniagua at 16:31, 2 December 2010

2010-12-02T16:31:40Z

Bpaniagua at 16:28, 2 December 2010

2010-12-02T16:28:47Z

Bpaniagua at 16:10, 2 December 2010

2010-12-02T16:10:09Z

Bpaniagua at 16:07, 2 December 2010

2010-12-02T16:07:42Z

Bpaniagua at 16:06, 2 December 2010

2010-12-02T16:06:58Z

Bpaniagua: Created page with 'NOTOC Image:PW-MIT2010.png|Projects List Image:surgworkflow.png|SPHARM-PDM shape Analysis workflow to detect stability after O…'

2010-12-02T16:06:01Z

Created page with '__NOTOC__ <gallery> Image:PW-MIT2010.png|Projects List Image:surgworkflow.png|SPHARM-PDM shape Analysis workflow to detect stability after O…'

New page

__NOTOC__
<gallery>
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
Image:surgworkflow.png|SPHARM-PDM shape Analysis workflow to detect stability after Orthognatic Surgery.
</gallery>

==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==
<div style="margin: 10px;">
<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Objectives</h3>

'''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.

</div>

<div style="width: 30%; float: left; padding-right: 2%;">
<h3>Approach Plan</h3>
'''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.

</div>

<div style="width: 35%; float: left;">
<h3>Progress</h3>

'''*''' 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>

==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.

@@ Line 43: / Line 43: @@
 '''*''' On Tuesday 11th, we had a breakout meeting in which the next steps for the particle system development were decided:
 - Manasi has to commit her work on geodesics distances and normal penalties.
-- The whole Shape Works has to migrate from GForge (CVS) to NITRC (svn) - Clement will work with Josh
+'''-''' Manasi has to commit her work on geodesics distances and normal penalties.
 - Beatriz and Lucile will work into implementing a quality control module for Slicer3 in which the results of the correspondence obtained can be evaluated.
 '''*''' Applying satisfactorily the recent upgrades (geodesics and normal penalty) to mandibular data (Jaws)

@@ Line 42: / Line 42: @@
 <h3>Progress</h3>
-'''*'''
+'''*''' On Tuesday 11th, we had a breakout meeting in which the next steps for the particle system development were decided:
-'''*'''
+'''*''' Applying satisfactorily the recent upgrades (geodesics and normal penalty) to mandibular data (Jaws)
 '''*'''

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
-Image:ReconstructionProblems.png|Particle Correspondence has problems with regard to representing thin areas correctly, and thus with reconstructing them
+Image:ReconstructionProblems.png|Fig1. Particle Correspondence has problems with regard to representing thin areas correctly, and thus with reconstructing them
-Image:NormalFeatures.png|First attempts into incorporating normal directions into Particle Correspondence
+Image:NormalFeatures.png|Fig2. First attempts into incorporating normal directions into Particle Correspondence
 </gallery>
 ==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,  correspondence was obtained almost entirely for 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.
+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,  correspondence was obtained almost entirely for brain morphometry studies. SPHARM-PDM Toolbox has been used until now for different Ortho applications ([1-5] ), 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.
-PROBLEMS WHY NORMALS ARE NEEDED
+Particle systems performance in mandibles is not very good with the curent implementation. Correspondence in thin areas is ill-defined, and that causes a number of reconstruction problems (see figure 1). We think that acknowledging for particles normal directions in this application is necessary. For this we did several attempts to incorporate normal directions into particles, without interfering with the optimization process (see figure 2). Still those seem not to be enough and we have implemented some code to incorporate normal directions into the optimization.
 ==Key Investigators==
@@ Line 22: / Line 21: @@
 <h3>Objectives</h3>
-'''1.''' Integrate tools developed to be used with ShapeWorks particle-optimization shape correspondence program, developed by Utah U.
+'''1.''' Integrate normal directions optimization  code in ShapeWorks particle-optimization shape correspondence program, developed by Utah U., altogether with the code that acknowledges for geodesic distances from Manasi Datar and Ross Whitacker.
-'''2.''' Slicer3 color map visualization
+'''2.''' Meet with Joshua Cates to resolve coding questions regarding to the current implementation of ShapeWorks
-'''3.''' UNC SPHARM-PDM shape analysis module integration in Slicer3.
+'''3.''' Particle Correspondence in Slicer3: yes or no discussions
 </div>
@@ Line 34: / Line 31: @@
 <div style="width: 30%; float: left; padding-right: 2%;">
 <h3>Approach Plan</h3>
-'''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.
+'''1.''' Entropy-Based Particle Systems: Meet with Manasi Datar (Utah U.) to discuss integration of our code
-'''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.
+'''2.''' Meet with Josh Cates in a Q&A session to figure out specific details
-'''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.
+'''3.''' Attend discussions between Ross Whitacker and Steve Piper (?)
 </div>
@@ Line 47: / Line 42: @@
 <h3>Progress</h3>
-'''*''' 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>

@@ Line 7: / Line 7: @@
 ==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,  t 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.
+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,  correspondence was obtained almost entirely for 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.
 PROBLEMS WHY NORMALS ARE NEEDED

@@ Line 6: / Line 6: @@
 ==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.
+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,  t 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.
 ==Key Investigators==
-* UNC SPHARM: Beatriz Paniagua, Martin Styner, Corentin Hamel
+* UNC SPHARM: Beatriz Paniagua, Martin Styner, Corentin Hamel, Lucile Bompard
-* UNC Particle System: Beatriz Paniagua, Ipek Oguz, Clement Vachet
+* UNC Particle System: Manasi Datar, Ross Witacker, Martin Styner, Beatriz Paniagua, Ipek Oguz, Clement Vachet
 * UNC Shape Analysis, Application and Visualization: Beatriz Paniagua, Martin Styner, Lucia Cevidanes

@@ Line 1: / Line 1: @@
 __NOTOC__
 <gallery>
-Image:PW-SLC2011.png|[[AHM_2011#Projects|Projects List]]
+Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
 Image:surgworkflow.png|SPHARM-PDM shape Analysis workflow to detect stability after Orthognatic Surgery.
 </gallery>