https://www.na-mic.org/w/api.php?action=feedcontributions&user=Vmagnotta&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-28T13:46:05ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=2011.07.18-IowaResearchScientist&diff=698932011.07.18-IowaResearchScientist2011-07-18T21:13:16Z<p>Vmagnotta: Created page with 'The Department of Psychology and Delta Center at the University of Iowa are seeking an Associate Research Scientist to coordinate the newly opened CHild Imaging Laboratory in Dev…'</p>
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<div>The Department of Psychology and Delta Center at the University of Iowa are seeking an Associate Research Scientist to coordinate the newly opened CHild Imaging Laboratory in Developmental Science ([http://www.uiowa.edu/delta-center/research/facilities.html CHILDS] ). CHILDS is equipped with a 24-channel Near-infrared Spectroscopy (fNIRS) system from TechEn, Inc., as well as multiple supportive technologies including two eye-tracking systems, stereo touch-screen display, and motion-tracking systems. The Research Scientist will also work on several projects involving simultaneous fNIRS and fMRI using the Siemens Trio 3T scanner at the [https://mri.radiology.uiowa.edu/about_facility.html Magnetic Resonance Research Facility] at the University of Iowa. The ad for this position is included below.<br />
<br />
<br />
<br />
<center><br />
'''Department of Psychology'''<br><br />
Associate Research Scientist<br><br />
(Requisition #59703)<br />
</center><br />
<br />
Associate Research Scientist wanted to perform research on typical and atypical populations to study the early development of cognitive abilities using functional neuroimaging. Work to develop new theories and methodologies to assess early cognitive function with complete responsibility for all aspects of the research project.<br />
<br />
To see a complete job description, requirements and to apply, visit the [http://jobs.uiowa.edu University of Iowa website] (Requisition #59703). The University of Iowa is an Equal Employment Opportunity / Affirmative Action employer. Women and minorities are encouraged to apply. A background check will be conducted on the final candidate for this position.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=Resources&diff=69892Resources2011-07-18T21:08:59Z<p>Vmagnotta: /* Active Job Openings */</p>
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<div>=== [[Collaborator:Resources|Resources for Collaborators]] ===<br />
<br />
[[Collaborator:Resources|This page]] contains information for investigators who would like to collaborate with NAMIC.<br />
<br />
=== Software, Data, and Tutorials ===<br />
<br />
NA-MIC Software, Data, and Tutorials are available at the following link: [[Downloads|NA-MIC Downloads]].<br />
<br />
=== Software: NA-MIC kit ===<br />
<br />
The NA-MIC Kit consists of all software that is being made available under the NA-MIC project. This software follows the NIH guidelines for open software development. In this section, we provide information about the components of the NA-MIC kit as well as supporting software tools that are being used by the software developers on the project.<br />
<br />
* [[NA-MIC-Kit|Software Resources for NA-MIC Kit]]<br />
* [[Engineering:SandBox|Development Sandbox ]]<br />
<br />
=== Acknowledgment for NA-MIC Support ===<br />
<br />
To acknowledge NA-MIC in your publications or software, please use the text provided [[Publications:NIH_Roadmap_acknowledgement|here]].<br />
<br />
=== Mailing Lists ===<br />
<br />
These are the mailing lists associated with NA-MIC. If you are a participant in the project, please make sure that you are signed up for all the mailing lists that apply to your role and interests in the projects. These lists are moderated and maintained by Kitware.<br />
<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-leadership NAMIC Leadership] (All Core and Site PIs, Administrators)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-algo-pi NAMIC Algo PIs] (Algorithms Site PIs)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-eng NAMIC-Eng] (Engineering Site PIs and members)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-dbp NAMIC-dbp] (DBPs and teams)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-service NAMIC-Service] (Service Core)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-training NAMIC Training] (Training Core)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-dissemination NAMIC-dissemination] (Dissemination Core)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-EAB NAMIC-EAB] (EAB)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-nih NAMIC-nih] (NIH programs staff)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-collaborators NAMIC-collaborators]<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-alumni NAMIC-Alumni] (Alumni)<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-info NAMIC-info]<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week NAMIC Project Week]<br />
* [http://public.kitware.com/cgi-bin/mailman/listinfo/namic-all NAMIC All]<br />
<br />
=== [[NIH-Page|NIH Page]] ===<br />
<br />
* [[NIH-Page|This page]] contains useful information provided by our NIH officers.<br />
<br />
=== [[NAMIC_Logos_Templates|NAMIC Logos and Templates]] ===<br />
<br />
* [[NAMIC_Logos_Templates|This page]] contains links to files containing the NA-MIC logo and templates.<br />
<br />
=== Active Job Openings ===<br />
* [[2010.07.25-KitwareJob | Kitware Job: Open-Source Developers for Digital Libraries, Bioinformatics, and Information Visualization]]<br />
* [[Media:Intuitive_Surgical_Senior_Research_Engineer-Software-and-UI_2010-12-1a.pdf| Intuitive Surgical Job: Senior Research Engineer - Software and UI]]<br />
*[[Media:2011_January_CONDR_Postdoc_Description.pdf|WUSTL Postdoctoral Fellow]]. Posted January 24, 2011<br />
*[[2011.02.25-YalePostdocPosition|Yale University Postdoctoral Fellow]]. Posted February 25, 2011.<br />
*[[2011.07.18-IowaResearchScientist|Iowa Associate Research Scientist - Functional Imaging]]. Posted July 18, 2011.<br />
<br />
=== Wikis ===<br />
<br />
We are often asked about mediawiki and other wikis. Here is some [[Information_on_wikis|information on wikis]].</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=2010_University.of.Iowa&diff=513842010 University.of.Iowa2010-04-12T19:41:42Z<p>Vmagnotta: /* Workshop Agenda */</p>
<hr />
<div>==Training Faculty ==<br />
* [http://www.spl.harvard.edu/~kikinis Ron Kikinis, M.D.], Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* [http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D.,] Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Kathryn Hayes, M.S.E, Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Hans Johnson, Ph.D., University of Iowa<br />
* Vince Magnotta, Ph.D., University of Iowa<br />
* Eric Axelson, University of Iowa<br />
* Joy Matsui, University of Iowa<br />
<br />
==Logistics==<br />
*Date: Friday April 9 and Saturday April 10, 2010<br />
*Location: University of Iowa, Iowa City<br />
*'''[http://www.na-mic.org/Wiki/images/0/03/NA-MIC-Flyer-Iowa-2010.pdf Workshop Flyer]'''<br />
* Slicer version: Slicer3.4 release (2009-05-21)<br />
*[https://mri.radiology.uiowa.edu// Additional information]<br />
<br />
== Workshop Agenda ==<br />
{| border="1" cellpadding="5" width="1000"<br />
|- style="background:#ebeced; color:#663300; font-size:120%" align="center" <br />
| style="width:10%" | '''Time'''<br />
| style="width:90%" colspan="2"| '''Friday, April 9, 2010'''<br />
|-<br />
| style="background:#efefef; color:#663300"| '''12:00-12:45'''<br />
| style="background:#FBF7BB; color:#522200" colspan="2"| [http://www.na-mic.org/Wiki/images/9/9c/Iowa-NA-MIC-2010-04-09.ppt NA-MIC Overview Lecture] (Vincent Magnotta) (283 EMRB - Seebohm Conference Room)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''4:00-5:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Radiation Oncology Research (Ron Kikinis) (01136 - Braley Conference Room) <br />
|-<br />
| style="background:#efefef; color:#663300"| '''5:00-6:00'''<br />
| style="background:#FBF7BB; color:#522200" colspan="2"| Neurosurgery Department Seminar: 3D Computer-Assisted Brain Mapping (Sonia Pujol) (01603 - Neurosurgery)<br />
|-<br />
| style="background:#FFFFFF; height:35px" colspan="3" | <br />
|-style="background:#ebeced; color:#663300; font-size:120%" align="center" <br />
| style="width:10%" | '''Time'''<br />
| style="width:90%" colspan="2"| '''Saturday, April 10, 2010''' <br />
|-<br />
| style="background:#efefef; color:#663300"| '''09:00-9:10'''<br />
| style="background:#FBF7BB;; color:#522200" colspan="2"| Welcome and overview of day activities (Kikinis) (2217 Seamans Center) <br />
|-<br />
| style="background:#efefef; color:#663300"| '''09:10-10:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Introduction to the NA-MIC kit for clinical research applications (Kikinis/Pujol) (2217 Seamans Center) <br />
<br />
|-<br />
| style="background:#efefef; color:#663300"| '''10:00-10:30'''<br />
| style="background:#FBF7BB; color:#522200" colspan="2"| Three ways to use the NA-MIC kit (Sonia Pujol) (2217 Seamans Center) <br />
<br />
|-<br />
| style="background:#efefef; color:#663300"| '''10:30-11:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:#663300"| '''11:00-12:30'''<br />
| style="background:#FBF7BB; width:45%; color:#522200"| 3D Visualization and Diffusion Tensor Imaging - Part 1 <br> (Sonia Pujol/Katie Hayes) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"| 3D Visualization and Programming Tutorial - Part 1 <br>(Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''12:30-1:45'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Lunch<br />
|-<br />
| style="background:#efefef; color:#663300"| '''1:45-3:00'''<br />
| style="background:#FBF7BB; color:#522200"| Diffusion Tensor Imaging - Part 2 <br>(Sonia Pujol/Katie Hayes) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"| Programming Tutorial - Part 2 <br> (Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''3:00-3:15'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:#663300"| '''3:15-4:15'''<br />
| style="background:#FBF7BB; color:#522200"|Questions from the Audience (Ron Kikinis/Sonia Pujol)<br> (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"|Programming Tutorial - Part 3 (Hans Johnson)<br> (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''4:15-5:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Concluding Remarks and Feedback<br />
|-<br />
|}<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=2010_University.of.Iowa&diff=513832010 University.of.Iowa2010-04-12T19:40:43Z<p>Vmagnotta: /* Workshop Agenda */</p>
<hr />
<div>==Training Faculty ==<br />
* [http://www.spl.harvard.edu/~kikinis Ron Kikinis, M.D.], Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* [http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D.,] Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Kathryn Hayes, M.S.E, Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Hans Johnson, Ph.D., University of Iowa<br />
* Vince Magnotta, Ph.D., University of Iowa<br />
* Eric Axelson, University of Iowa<br />
* Joy Matsui, University of Iowa<br />
<br />
==Logistics==<br />
*Date: Friday April 9 and Saturday April 10, 2010<br />
*Location: University of Iowa, Iowa City<br />
*'''[http://www.na-mic.org/Wiki/images/0/03/NA-MIC-Flyer-Iowa-2010.pdf Workshop Flyer]'''<br />
* Slicer version: Slicer3.4 release (2009-05-21)<br />
*[https://mri.radiology.uiowa.edu// Additional information]<br />
<br />
== Workshop Agenda ==<br />
{| border="1" cellpadding="5" width="1000"<br />
|- style="background:#ebeced; color:#663300; font-size:120%" align="center" <br />
| style="width:10%" | '''Time'''<br />
| style="width:90%" colspan="2"| '''Friday, April 9, 2010'''<br />
|-<br />
| style="background:#efefef; color:#663300"| '''12:00-12:45'''<br />
| style="background:#FBF7BB; color:#522200" colspan="2"| [[File:Iowa-NA-MIC-2010-04-09.ppt NA-MIC Overview Lecture]] (Vincent Magnotta) (283 EMRB - Seebohm Conference Room)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''4:00-5:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Radiation Oncology Research (Ron Kikinis) (01136 - Braley Conference Room) <br />
|-<br />
| style="background:#efefef; color:#663300"| '''5:00-6:00'''<br />
| style="background:#FBF7BB; color:#522200" colspan="2"| Neurosurgery Department Seminar: 3D Computer-Assisted Brain Mapping (Sonia Pujol) (01603 - Neurosurgery)<br />
|-<br />
| style="background:#FFFFFF; height:35px" colspan="3" | <br />
|-style="background:#ebeced; color:#663300; font-size:120%" align="center" <br />
| style="width:10%" | '''Time'''<br />
| style="width:90%" colspan="2"| '''Saturday, April 10, 2010''' <br />
|-<br />
| style="background:#efefef; color:#663300"| '''09:00-9:10'''<br />
| style="background:#FBF7BB;; color:#522200" colspan="2"| Welcome and overview of day activities (Kikinis) (2217 Seamans Center) <br />
|-<br />
| style="background:#efefef; color:#663300"| '''09:10-10:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Introduction to the NA-MIC kit for clinical research applications (Kikinis/Pujol) (2217 Seamans Center) <br />
<br />
|-<br />
| style="background:#efefef; color:#663300"| '''10:00-10:30'''<br />
| style="background:#FBF7BB; color:#522200" colspan="2"| Three ways to use the NA-MIC kit (Sonia Pujol) (2217 Seamans Center) <br />
<br />
|-<br />
| style="background:#efefef; color:#663300"| '''10:30-11:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:#663300"| '''11:00-12:30'''<br />
| style="background:#FBF7BB; width:45%; color:#522200"| 3D Visualization and Diffusion Tensor Imaging - Part 1 <br> (Sonia Pujol/Katie Hayes) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"| 3D Visualization and Programming Tutorial - Part 1 <br>(Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''12:30-1:45'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Lunch<br />
|-<br />
| style="background:#efefef; color:#663300"| '''1:45-3:00'''<br />
| style="background:#FBF7BB; color:#522200"| Diffusion Tensor Imaging - Part 2 <br>(Sonia Pujol/Katie Hayes) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"| Programming Tutorial - Part 2 <br> (Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''3:00-3:15'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:#663300"| '''3:15-4:15'''<br />
| style="background:#FBF7BB; color:#522200"|Questions from the Audience (Ron Kikinis/Sonia Pujol)<br> (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"|Programming Tutorial - Part 3 (Hans Johnson)<br> (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''4:15-5:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Concluding Remarks and Feedback<br />
|-<br />
|}<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=2010_University.of.Iowa&diff=513822010 University.of.Iowa2010-04-12T19:39:48Z<p>Vmagnotta: /* Workshop Agenda */</p>
<hr />
<div>==Training Faculty ==<br />
* [http://www.spl.harvard.edu/~kikinis Ron Kikinis, M.D.], Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* [http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D.,] Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Kathryn Hayes, M.S.E, Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Hans Johnson, Ph.D., University of Iowa<br />
* Vince Magnotta, Ph.D., University of Iowa<br />
* Eric Axelson, University of Iowa<br />
* Joy Matsui, University of Iowa<br />
<br />
==Logistics==<br />
*Date: Friday April 9 and Saturday April 10, 2010<br />
*Location: University of Iowa, Iowa City<br />
*'''[http://www.na-mic.org/Wiki/images/0/03/NA-MIC-Flyer-Iowa-2010.pdf Workshop Flyer]'''<br />
* Slicer version: Slicer3.4 release (2009-05-21)<br />
*[https://mri.radiology.uiowa.edu// Additional information]<br />
<br />
== Workshop Agenda ==<br />
{| border="1" cellpadding="5" width="1000"<br />
|- style="background:#ebeced; color:#663300; font-size:120%" align="center" <br />
| style="width:10%" | '''Time'''<br />
| style="width:90%" colspan="2"| '''Friday, April 9, 2010'''<br />
|-<br />
| style="background:#efefef; color:#663300"| '''12:00-12:45'''<br />
| style="background:#FBF7BB; color:#522200" colspan="2"| [File:Iowa-NA-MIC-2010-04-09.ppt NA-MIC Overview Lecture] (Vincent Magnotta) (283 EMRB - Seebohm Conference Room)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''4:00-5:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Radiation Oncology Research (Ron Kikinis) (01136 - Braley Conference Room) <br />
|-<br />
| style="background:#efefef; color:#663300"| '''5:00-6:00'''<br />
| style="background:#FBF7BB; color:#522200" colspan="2"| Neurosurgery Department Seminar: 3D Computer-Assisted Brain Mapping (Sonia Pujol) (01603 - Neurosurgery)<br />
|-<br />
| style="background:#FFFFFF; height:35px" colspan="3" | <br />
|-style="background:#ebeced; color:#663300; font-size:120%" align="center" <br />
| style="width:10%" | '''Time'''<br />
| style="width:90%" colspan="2"| '''Saturday, April 10, 2010''' <br />
|-<br />
| style="background:#efefef; color:#663300"| '''09:00-9:10'''<br />
| style="background:#FBF7BB;; color:#522200" colspan="2"| Welcome and overview of day activities (Kikinis) (2217 Seamans Center) <br />
|-<br />
| style="background:#efefef; color:#663300"| '''09:10-10:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Introduction to the NA-MIC kit for clinical research applications (Kikinis/Pujol) (2217 Seamans Center) <br />
<br />
|-<br />
| style="background:#efefef; color:#663300"| '''10:00-10:30'''<br />
| style="background:#FBF7BB; color:#522200" colspan="2"| Three ways to use the NA-MIC kit (Sonia Pujol) (2217 Seamans Center) <br />
<br />
|-<br />
| style="background:#efefef; color:#663300"| '''10:30-11:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:#663300"| '''11:00-12:30'''<br />
| style="background:#FBF7BB; width:45%; color:#522200"| 3D Visualization and Diffusion Tensor Imaging - Part 1 <br> (Sonia Pujol/Katie Hayes) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"| 3D Visualization and Programming Tutorial - Part 1 <br>(Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''12:30-1:45'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Lunch<br />
|-<br />
| style="background:#efefef; color:#663300"| '''1:45-3:00'''<br />
| style="background:#FBF7BB; color:#522200"| Diffusion Tensor Imaging - Part 2 <br>(Sonia Pujol/Katie Hayes) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"| Programming Tutorial - Part 2 <br> (Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''3:00-3:15'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:#663300"| '''3:15-4:15'''<br />
| style="background:#FBF7BB; color:#522200"|Questions from the Audience (Ron Kikinis/Sonia Pujol)<br> (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"|Programming Tutorial - Part 3 (Hans Johnson)<br> (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:#663300"| '''4:15-5:00'''<br />
| style="background:#F5EBD6; color:#522200" colspan="2"| Concluding Remarks and Feedback<br />
|-<br />
|}<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=File:Iowa-NA-MIC-2010-04-09.ppt&diff=51381File:Iowa-NA-MIC-2010-04-09.ppt2010-04-12T19:38:39Z<p>Vmagnotta: </p>
<hr />
<div></div>Vmagnottahttps://www.na-mic.org/w/index.php?title=2010_University.of.Iowa&diff=504012010 University.of.Iowa2010-03-15T20:55:17Z<p>Vmagnotta: /* Tentative Agenda */</p>
<hr />
<div>(under construction)<br />
<br />
<br />
==Training Faculty ==<br />
<br />
* Ron Kikinis, M.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Sonia Pujol, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Kathryn Hayes, M.S.E, Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Stuart Wallace, M.Sc., Athinoula Martinos Center, Harvard Medical School, Boston, MA<br />
* Hans Johnson, Ph.D., University of Iowa<br />
* Technical Support (TBN),University of Iowa <br />
<br />
== Tentative Agenda ==<br />
<br />
'''[http://www.na-mic.org/Wiki/images/0/03/NA-MIC-Flyer-Iowa-2010.pdf Workshop Flyer]'''<br />
<br />
'''Friday April 9'''<br />
*12pm - NA-MIC Overview Lecture (Ron Kikinis) (283 - Seebohm Conference Room)<br />
*4-5pm – Radiation Oncology Research (Ron Kikinis) (01600 PFP W- Radiation Oncology Conference Room)<br />
*5-6pm – Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC toolkit (Sonia Pujol) (1603 JCP)<br />
<br />
'''Saturday April 10'''<br />
*9:00 am - 9:10 am Welcome and overview of day activities (Ron Kikinis)<br />
*9:10 am - 10:00 am Introduction to the NA-MIC kit for clinical research applications (Ron Kikinis/Sonia Pujol)<br />
*10:00 am - 10:45 am Loading and Viewing Data (Sonia Pujol)<br />
*10:45 am - 11:00 am Coffee break<br />
<br />
Parallel sessions ( Room 2217 & 2229 Seamans Center)<br />
*11: 00 am - 12:30 pm: Diffusion Tensor Imaging - Part 1 (Sonia Pujol) ( Room 2217)<br />
*11:00 am - 12:30 pm Programming Tutorial (Hans Johnson) ( Room 2229)<br />
*12:30 pm - 1:45 pm Lunch<br />
<br />
*1:45 pm - 3:00 pm DTI: Diffusion Tensor Imaging - Part 2 (Sonia Pujol) ( Room 2217 )<br />
*1:45 pm - 3:00 pm Programming Tutorial - Part 2 (Hans Johnson) ( Room 2229)<br />
<br />
*3:00 pm - 3:15 pm: Coffee Break<br />
*3:15 pm - 4:15 pm: Free Surfer Tutorial (Hans Johnson) ( Room 2229)<br />
*3:15 pm - 4:15 pm: Questions from audience (Ron Kikinis/Sonia Pujol) ( Room 2217)<br />
*4:15 pm - 4:30 pm: Concluding remarks and feedback<br />
<br />
==Logistics==<br />
<br />
*Date: Friday April 9 and Saturday April 10, 2010<br />
*Location: University of Iowa, Iowa City<br />
<br />
==Preparation for the workshop==<br />
TBA<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#ebeced; color:maroon" align="left" <br />
| style="width:6%" | '''Time'''<br />
| style="width:30%" | '''Friday, April 9, 2010'''<br />
| style="width:64%" colspan="2"| '''Saturday, April 10, 2010''' <br />
|-<br />
| style="background:#efefef; color:maroon"| 09.00-9:10<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB;; color:#522200" colspan="2"| Welcome and overview of day activities (Kikinis)<br />
|-<br />
| style="background:#efefef; color:maroon"| 09.10-10:00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Introduction to the NA-MIC kit for clinical research applications (Kikinis/Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10:00-10:45<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200" colspan="2"|Loading and Viewing Data (Sonia Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10.45-11:00<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 11.00-12.30<br />
| style="background:#FBF7BB; color:#522200"| 12:00 NA-MIC Overview Lecture (Ron Kikinis) (283 EMRB - Seebohm Conference Room)<br />
| style="background:#FBF7BB; color:#522200"| Diffusion Tensor Imaging - Part 1 (Sonia Pujol) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"| Programming Tutorial - Part 1 (Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:maroon"| 12.30-1.45<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Lunch<br />
|-<br />
| style="background:#efefef; color:maroon"| 1.45-3.00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"|Diffusion Tensor Imaging - Part 2 (Sonia Pujol) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"|Programming Tutorial - Part 2 (Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.00-3.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.15-4.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#FBF7BB; color:#522200"|Questions from the Audience (Ron Kikinis/Sonia Pujol) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"|Free Surfer Tutorial (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:maroon"| 4:00-5:00<br />
| style="background:#EEDDBB; color:#522200"| Radiation Oncology Research (Ron Kikinis)<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
|-<br />
| style="background:#efefef; color:maroon"| 5:00-6:00<br />
| style="background:#FBF7BB; color:#522200"| Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC kit (Sonia Pujol)<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"| <br />
|}<br />
<br />
<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=2010_University.of.Iowa&diff=504002010 University.of.Iowa2010-03-15T20:54:08Z<p>Vmagnotta: /* Tentative Agenda */</p>
<hr />
<div>(under construction)<br />
<br />
<br />
==Training Faculty ==<br />
<br />
* Ron Kikinis, M.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Sonia Pujol, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Kathryn Hayes, M.S.E, Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Stuart Wallace, M.Sc., Athinoula Martinos Center, Harvard Medical School, Boston, MA<br />
* Hans Johnson, Ph.D., University of Iowa<br />
* Technical Support (TBN),University of Iowa <br />
<br />
== Tentative Agenda ==<br />
<br />
'''[[File:NA-MIC-Flyer-Iowa-2010.pdf| Flyer]]'''<br />
<br />
'''Friday April 9'''<br />
*12pm - NA-MIC Overview Lecture (Ron Kikinis) (283 - Seebohm Conference Room)<br />
*4-5pm – Radiation Oncology Research (Ron Kikinis) (01600 PFP W- Radiation Oncology Conference Room)<br />
*5-6pm – Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC toolkit (Sonia Pujol) (1603 JCP)<br />
<br />
'''Saturday April 10'''<br />
*9:00 am - 9:10 am Welcome and overview of day activities (Ron Kikinis)<br />
*9:10 am - 10:00 am Introduction to the NA-MIC kit for clinical research applications (Ron Kikinis/Sonia Pujol)<br />
*10:00 am - 10:45 am Loading and Viewing Data (Sonia Pujol)<br />
*10:45 am - 11:00 am Coffee break<br />
<br />
Parallel sessions ( Room 2217 & 2229 Seamans Center)<br />
*11: 00 am - 12:30 pm: Diffusion Tensor Imaging - Part 1 (Sonia Pujol) ( Room 2217)<br />
*11:00 am - 12:30 pm Programming Tutorial (Hans Johnson) ( Room 2229)<br />
*12:30 pm - 1:45 pm Lunch<br />
<br />
*1:45 pm - 3:00 pm DTI: Diffusion Tensor Imaging - Part 2 (Sonia Pujol) ( Room 2217 )<br />
*1:45 pm - 3:00 pm Programming Tutorial - Part 2 (Hans Johnson) ( Room 2229)<br />
<br />
*3:00 pm - 3:15 pm: Coffee Break<br />
*3:15 pm - 4:15 pm: Free Surfer Tutorial (Hans Johnson) ( Room 2229)<br />
*3:15 pm - 4:15 pm: Questions from audience (Ron Kikinis/Sonia Pujol) ( Room 2217)<br />
*4:15 pm - 4:30 pm: Concluding remarks and feedback<br />
<br />
==Logistics==<br />
<br />
*Date: Friday April 9 and Saturday April 10, 2010<br />
*Location: University of Iowa, Iowa City<br />
<br />
==Preparation for the workshop==<br />
TBA<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#ebeced; color:maroon" align="left" <br />
| style="width:6%" | '''Time'''<br />
| style="width:30%" | '''Friday, April 9, 2010'''<br />
| style="width:64%" colspan="2"| '''Saturday, April 10, 2010''' <br />
|-<br />
| style="background:#efefef; color:maroon"| 09.00-9:10<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB;; color:#522200" colspan="2"| Welcome and overview of day activities (Kikinis)<br />
|-<br />
| style="background:#efefef; color:maroon"| 09.10-10:00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Introduction to the NA-MIC kit for clinical research applications (Kikinis/Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10:00-10:45<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200" colspan="2"|Loading and Viewing Data (Sonia Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10.45-11:00<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 11.00-12.30<br />
| style="background:#FBF7BB; color:#522200"| 12:00 NA-MIC Overview Lecture (Ron Kikinis) (283 EMRB - Seebohm Conference Room)<br />
| style="background:#FBF7BB; color:#522200"| Diffusion Tensor Imaging - Part 1 (Sonia Pujol) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"| Programming Tutorial - Part 1 (Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:maroon"| 12.30-1.45<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Lunch<br />
|-<br />
| style="background:#efefef; color:maroon"| 1.45-3.00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"|Diffusion Tensor Imaging - Part 2 (Sonia Pujol) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"|Programming Tutorial - Part 2 (Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.00-3.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.15-4.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#FBF7BB; color:#522200"|Questions from the Audience (Ron Kikinis/Sonia Pujol) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"|Free Surfer Tutorial (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:maroon"| 4:00-5:00<br />
| style="background:#EEDDBB; color:#522200"| Radiation Oncology Research (Ron Kikinis)<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
|-<br />
| style="background:#efefef; color:maroon"| 5:00-6:00<br />
| style="background:#FBF7BB; color:#522200"| Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC kit (Sonia Pujol)<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"| <br />
|}<br />
<br />
<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=File:NA-MIC-Flyer-Iowa-2010.pdf&diff=50399File:NA-MIC-Flyer-Iowa-2010.pdf2010-03-15T20:53:11Z<p>Vmagnotta: </p>
<hr />
<div></div>Vmagnottahttps://www.na-mic.org/w/index.php?title=File:NA-MIC_Flyer-Iowa-2010.pdf&diff=50398File:NA-MIC Flyer-Iowa-2010.pdf2010-03-15T20:50:51Z<p>Vmagnotta: </p>
<hr />
<div></div>Vmagnottahttps://www.na-mic.org/w/index.php?title=2010_University.of.Iowa&diff=503972010 University.of.Iowa2010-03-15T20:49:41Z<p>Vmagnotta: /* Preparation for the workshop */</p>
<hr />
<div>(under construction)<br />
<br />
<br />
==Training Faculty ==<br />
<br />
* Ron Kikinis, M.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Sonia Pujol, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Kathryn Hayes, M.S.E, Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Stuart Wallace, M.Sc., Athinoula Martinos Center, Harvard Medical School, Boston, MA<br />
* Hans Johnson, Ph.D., University of Iowa<br />
* Technical Support (TBN),University of Iowa <br />
<br />
== Tentative Agenda ==<br />
<br />
'''Friday April 9'''<br />
*12pm - NA-MIC Overview Lecture (Ron Kikinis) (283 - Seebohm Conference Room)<br />
*4-5pm – Radiation Oncology Research (Ron Kikinis) (01600 PFP W- Radiation Oncology Conference Room)<br />
*5-6pm – Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC toolkit (Sonia Pujol) (1603 JCP)<br />
<br />
'''Saturday April 10'''<br />
*9:00 am - 9:10 am Welcome and overview of day activities (Ron Kikinis)<br />
*9:10 am - 10:00 am Introduction to the NA-MIC kit for clinical research applications (Ron Kikinis/Sonia Pujol)<br />
*10:00 am - 10:45 am Loading and Viewing Data (Sonia Pujol)<br />
*10:45 am - 11:00 am Coffee break<br />
<br />
Parallel sessions ( Room 2217 & 2229 Seamans Center)<br />
*11: 00 am - 12:30 pm: Diffusion Tensor Imaging - Part 1 (Sonia Pujol) ( Room 2217)<br />
*11:00 am - 12:30 pm Programming Tutorial (Hans Johnson) ( Room 2229)<br />
*12:30 pm - 1:45 pm Lunch<br />
<br />
*1:45 pm - 3:00 pm DTI: Diffusion Tensor Imaging - Part 2 (Sonia Pujol) ( Room 2217 )<br />
*1:45 pm - 3:00 pm Programming Tutorial - Part 2 (Hans Johnson) ( Room 2229)<br />
<br />
*3:00 pm - 3:15 pm: Coffee Break<br />
*3:15 pm - 4:15 pm: Free Surfer Tutorial (Hans Johnson) ( Room 2229)<br />
*3:15 pm - 4:15 pm: Questions from audience (Ron Kikinis/Sonia Pujol) ( Room 2217)<br />
*4:15 pm - 4:30 pm: Concluding remarks and feedback<br />
<br />
==Logistics==<br />
<br />
*Date: Friday April 9 and Saturday April 10, 2010<br />
*Location: University of Iowa, Iowa City<br />
<br />
==Preparation for the workshop==<br />
TBA<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#ebeced; color:maroon" align="left" <br />
| style="width:6%" | '''Time'''<br />
| style="width:30%" | '''Friday, April 9, 2010'''<br />
| style="width:64%" colspan="2"| '''Saturday, April 10, 2010''' <br />
|-<br />
| style="background:#efefef; color:maroon"| 09.00-9:10<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB;; color:#522200" colspan="2"| Welcome and overview of day activities (Kikinis)<br />
|-<br />
| style="background:#efefef; color:maroon"| 09.10-10:00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Introduction to the NA-MIC kit for clinical research applications (Kikinis/Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10:00-10:45<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200" colspan="2"|Loading and Viewing Data (Sonia Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10.45-11:00<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 11.00-12.30<br />
| style="background:#FBF7BB; color:#522200"| 12:00 NA-MIC Overview Lecture (Ron Kikinis) (283 EMRB - Seebohm Conference Room)<br />
| style="background:#FBF7BB; color:#522200"| Diffusion Tensor Imaging - Part 1 (Sonia Pujol) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"| Programming Tutorial - Part 1 (Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:maroon"| 12.30-1.45<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Lunch<br />
|-<br />
| style="background:#efefef; color:maroon"| 1.45-3.00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"|Diffusion Tensor Imaging - Part 2 (Sonia Pujol) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"|Programming Tutorial - Part 2 (Hans Johnson) (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.00-3.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.15-4.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#FBF7BB; color:#522200"|Questions from the Audience (Ron Kikinis/Sonia Pujol) (2217 Seamans Center)<br />
| style="background:#FBF7BB; color:#522200"|Free Surfer Tutorial (2229 Seamans Center)<br />
|-<br />
| style="background:#efefef; color:maroon"| 4:00-5:00<br />
| style="background:#EEDDBB; color:#522200"| Radiation Oncology Research (Ron Kikinis)<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
|-<br />
| style="background:#efefef; color:maroon"| 5:00-6:00<br />
| style="background:#FBF7BB; color:#522200"| Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC kit (Sonia Pujol)<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"| <br />
|}<br />
<br />
<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=2010_University.of.Iowa&diff=503962010 University.of.Iowa2010-03-15T20:48:38Z<p>Vmagnotta: /* Preparation for the workshop */</p>
<hr />
<div>(under construction)<br />
<br />
<br />
==Training Faculty ==<br />
<br />
* Ron Kikinis, M.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Sonia Pujol, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Kathryn Hayes, M.S.E, Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Stuart Wallace, M.Sc., Athinoula Martinos Center, Harvard Medical School, Boston, MA<br />
* Hans Johnson, Ph.D., University of Iowa<br />
* Technical Support (TBN),University of Iowa <br />
<br />
== Tentative Agenda ==<br />
<br />
'''Friday April 9'''<br />
*12pm - NA-MIC Overview Lecture (Ron Kikinis) (283 - Seebohm Conference Room)<br />
*4-5pm – Radiation Oncology Research (Ron Kikinis) (01600 PFP W- Radiation Oncology Conference Room)<br />
*5-6pm – Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC toolkit (Sonia Pujol) (1603 JCP)<br />
<br />
'''Saturday April 10'''<br />
*9:00 am - 9:10 am Welcome and overview of day activities (Ron Kikinis)<br />
*9:10 am - 10:00 am Introduction to the NA-MIC kit for clinical research applications (Ron Kikinis/Sonia Pujol)<br />
*10:00 am - 10:45 am Loading and Viewing Data (Sonia Pujol)<br />
*10:45 am - 11:00 am Coffee break<br />
<br />
Parallel sessions ( Room 2217 & 2229 Seamans Center)<br />
*11: 00 am - 12:30 pm: Diffusion Tensor Imaging - Part 1 (Sonia Pujol) ( Room 2217)<br />
*11:00 am - 12:30 pm Programming Tutorial (Hans Johnson) ( Room 2229)<br />
*12:30 pm - 1:45 pm Lunch<br />
<br />
*1:45 pm - 3:00 pm DTI: Diffusion Tensor Imaging - Part 2 (Sonia Pujol) ( Room 2217 )<br />
*1:45 pm - 3:00 pm Programming Tutorial - Part 2 (Hans Johnson) ( Room 2229)<br />
<br />
*3:00 pm - 3:15 pm: Coffee Break<br />
*3:15 pm - 4:15 pm: Free Surfer Tutorial (Hans Johnson) ( Room 2229)<br />
*3:15 pm - 4:15 pm: Questions from audience (Ron Kikinis/Sonia Pujol) ( Room 2217)<br />
*4:15 pm - 4:30 pm: Concluding remarks and feedback<br />
<br />
==Logistics==<br />
<br />
*Date: Friday April 9 and Saturday April 10, 2010<br />
*Location: University of Iowa, Iowa City<br />
<br />
==Preparation for the workshop==<br />
TBA<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#ebeced; color:maroon" align="left" <br />
| style="width:6%" | '''Time'''<br />
| style="width:30%" | '''Friday, April 9, 2010'''<br />
| style="width:64%" colspan="2"| '''Saturday, April 10, 2010''' <br />
|-<br />
| style="background:#efefef; color:maroon"| 09.00-9:10<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB;; color:#522200" colspan="2"| Welcome and overview of day activities (Kikinis)<br />
|-<br />
| style="background:#efefef; color:maroon"| 09.10-10:00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Introduction to the NA-MIC kit for clinical research applications (Kikinis/Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10:00-10:45<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200" colspan="2"|Loading and Viewing Data (Sonia Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10.45-11:00<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 11.00-12.30<br />
| style="background:#FBF7BB; color:#522200"| 12:00 NA-MIC Overview Lecture (Ron Kikinis) (283 EMRB - Seebohm Conference Room)<br />
| style="background:#FBF7BB; color:#522200"| Diffusion Tensor Imaging - Part 1 (Sonia Pujol) (Please add room number)<br />
| style="background:#FBF7BB; color:#522200"| Programming Tutorial - Part 1 (Hans Johnson) (Please add room number)<br />
|-<br />
| style="background:#efefef; color:maroon"| 12.30-1.45<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Lunch<br />
|-<br />
| style="background:#efefef; color:maroon"| 1.45-3.00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"|Diffusion Tensor Imaging - Part 2 (Sonia Pujol) (Please add room number)<br />
| style="background:#FBF7BB; color:#522200"|Programming Tutorial - Part 2 (Hans Johnson) (Please add room number)<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.00-3.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.15-4.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#FBF7BB; color:#522200"|Questions from the Audience (Ron Kikinis/Sonia Pujol)<br />
| style="background:#FBF7BB; color:#522200"|Free Surfer Tutorial (Hans Johnson)<br />
|-<br />
| style="background:#efefef; color:maroon"| 4:00-5:00<br />
| style="background:#EEDDBB; color:#522200"| Radiation Oncology Research (Ron Kikinis)<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
|-<br />
| style="background:#efefef; color:maroon"| 5:00-6:00<br />
| style="background:#FBF7BB; color:#522200"| Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC kit (Sonia Pujol)<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"| <br />
|}<br />
<br />
<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=2010_University.of.Iowa&diff=503952010 University.of.Iowa2010-03-15T20:47:08Z<p>Vmagnotta: /* Tentative Agenda */</p>
<hr />
<div>(under construction)<br />
<br />
<br />
==Training Faculty ==<br />
<br />
* Ron Kikinis, M.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Sonia Pujol, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Kathryn Hayes, M.S.E, Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Stuart Wallace, M.Sc., Athinoula Martinos Center, Harvard Medical School, Boston, MA<br />
* Hans Johnson, Ph.D., University of Iowa<br />
* Technical Support (TBN),University of Iowa <br />
<br />
== Tentative Agenda ==<br />
<br />
'''Friday April 9'''<br />
*12pm - NA-MIC Overview Lecture (Ron Kikinis) (283 - Seebohm Conference Room)<br />
*4-5pm – Radiation Oncology Research (Ron Kikinis) (01600 PFP W- Radiation Oncology Conference Room)<br />
*5-6pm – Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC toolkit (Sonia Pujol) (1603 JCP)<br />
<br />
'''Saturday April 10'''<br />
*9:00 am - 9:10 am Welcome and overview of day activities (Ron Kikinis)<br />
*9:10 am - 10:00 am Introduction to the NA-MIC kit for clinical research applications (Ron Kikinis/Sonia Pujol)<br />
*10:00 am - 10:45 am Loading and Viewing Data (Sonia Pujol)<br />
*10:45 am - 11:00 am Coffee break<br />
<br />
Parallel sessions ( Room 2217 & 2229 Seamans Center)<br />
*11: 00 am - 12:30 pm: Diffusion Tensor Imaging - Part 1 (Sonia Pujol) ( Room 2217)<br />
*11:00 am - 12:30 pm Programming Tutorial (Hans Johnson) ( Room 2229)<br />
*12:30 pm - 1:45 pm Lunch<br />
<br />
*1:45 pm - 3:00 pm DTI: Diffusion Tensor Imaging - Part 2 (Sonia Pujol) ( Room 2217 )<br />
*1:45 pm - 3:00 pm Programming Tutorial - Part 2 (Hans Johnson) ( Room 2229)<br />
<br />
*3:00 pm - 3:15 pm: Coffee Break<br />
*3:15 pm - 4:15 pm: Free Surfer Tutorial (Hans Johnson) ( Room 2229)<br />
*3:15 pm - 4:15 pm: Questions from audience (Ron Kikinis/Sonia Pujol) ( Room 2217)<br />
*4:15 pm - 4:30 pm: Concluding remarks and feedback<br />
<br />
==Logistics==<br />
<br />
*Date: Friday April 9 and Saturday April 10, 2010<br />
*Location: University of Iowa, Iowa City<br />
<br />
==Preparation for the workshop==<br />
TBA<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#ebeced; color:maroon" align="left" <br />
| style="width:6%" | '''Time'''<br />
| style="width:30%" | '''Friday, April 9, 2010'''<br />
| style="width:64%" colspan="2"| '''Saturday, April 10, 2010''' <br />
|-<br />
| style="background:#efefef; color:maroon"| 09.00-9:10<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB;; color:#522200" colspan="2"| Welcome and overview of day activities (Kikinis)<br />
|-<br />
| style="background:#efefef; color:maroon"| 09.10-10:00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Introduction to the NA-MIC kit for clinical research applications (Kikinis/Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10:00-10:45<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200" colspan="2"|Loading and Viewing Data (Sonia Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10.45-11:00<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 11.00-12.30<br />
| style="background:#FBF7BB; color:#522200"| 12:00 NA-MIC Overview Lecture (Ron Kikinis) (Please add room number)<br />
| style="background:#FBF7BB; color:#522200"| Diffusion Tensor Imaging - Part 1 (Sonia Pujol) (Please add room number)<br />
| style="background:#FBF7BB; color:#522200"| Programming Tutorial - Part 1 (Hans Johnson) (Please add room number)<br />
|-<br />
| style="background:#efefef; color:maroon"| 12.30-1.45<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Lunch<br />
|-<br />
| style="background:#efefef; color:maroon"| 1.45-3.00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"|Diffusion Tensor Imaging - Part 2 (Sonia Pujol) (Please add room number)<br />
| style="background:#FBF7BB; color:#522200"|Programming Tutorial - Part 2 (Hans Johnson) (Please add room number)<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.00-3.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.15-4.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#FBF7BB; color:#522200"|Questions from the Audience (Ron Kikinis/Sonia Pujol)<br />
| style="background:#FBF7BB; color:#522200"|Free Surfer Tutorial (Hans Johnson)<br />
|-<br />
| style="background:#efefef; color:maroon"| 4:00-5:00<br />
| style="background:#EEDDBB; color:#522200"| Radiation Oncology Research (Ron Kikinis)<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
|-<br />
| style="background:#efefef; color:maroon"| 5:00-6:00<br />
| style="background:#FBF7BB; color:#522200"| Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC kit (Sonia Pujol)<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"| <br />
|}<br />
<br />
<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=2010_University.of.Iowa&diff=503942010 University.of.Iowa2010-03-15T20:45:45Z<p>Vmagnotta: /* Tentative Agenda */</p>
<hr />
<div>(under construction)<br />
<br />
<br />
==Training Faculty ==<br />
<br />
* Ron Kikinis, M.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Sonia Pujol, Ph.D., Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Kathryn Hayes, M.S.E, Surgical Planning Laboratory, Harvard Medical School, Boston, MA<br />
* Stuart Wallace, M.Sc., Athinoula Martinos Center, Harvard Medical School, Boston, MA<br />
* Hans Johnson, Ph.D., University of Iowa<br />
* Technical Support (TBN),University of Iowa <br />
<br />
== Tentative Agenda ==<br />
<br />
'''Friday April 9'''<br />
*12pm - NA-MIC Overview Lecture (Ron Kikinis) (283 - Seebohm Conference Room)<br />
*4-5pm – Radiation Oncology Research (Ron Kikinis) (01600 PFP W- Radiation Oncology Conference Room)<br />
*5-6pm – Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC toolkit (Sonia Pujol) (1603 JCP)<br />
<br />
'''Saturday April 10'''<br />
*9:00 am - 9:10 am Welcome and overview of day activities (Ron Kikinis)<br />
*9:10 am - 10:00 am Introduction to the NA-MIC kit for clinical research applications (Ron Kikinis/Sonia Pujol)<br />
*10:00 am - 10:45 am Loading and Viewing Data (Sonia Pujol)<br />
*10:45 am - 11:00 am Coffee break<br />
<br />
Parallel sessions ( Room 2217 & 2229 Seamans Center)<br />
*11: 00 am - 12:30 pm: Diffusion Tensor Imaging - Part 1 (Sonia Pujol) ( Room xxx)<br />
*11:00 am - 12:30 pm Programming Tutorial (Hans Johnson) ( Room yyy)<br />
*12:30 pm - 1:45 pm Lunch<br />
<br />
*1:45 pm - 3:00 pm DTI: Diffusion Tensor Imaging - Part 2 (Sonia Pujol) ( Room xxx )<br />
*1:45 pm - 3:00 pm Programming Tutorial - Part 2 (Hans Johnson) ( Room yyy)<br />
<br />
*3:00 pm - 3:15 pm: Coffee Break<br />
*3:15 pm - 4:15 pm: Free Surfer Tutorial (Hans Johnson) ( Room yyy)<br />
*3:15 pm - 4:15 pm: Questions from audience (Ron Kikinis/Sonia Pujol) ( Room xxx)<br />
*4:15 pm - 4:30 pm: Concluding remarks and feedback<br />
<br />
==Logistics==<br />
<br />
*Date: Friday April 9 and Saturday April 10, 2010<br />
*Location: University of Iowa, Iowa City<br />
<br />
==Preparation for the workshop==<br />
TBA<br />
<br />
{| border="1" cellpadding="5"<br />
|- style="background:#ebeced; color:maroon" align="left" <br />
| style="width:6%" | '''Time'''<br />
| style="width:30%" | '''Friday, April 9, 2010'''<br />
| style="width:64%" colspan="2"| '''Saturday, April 10, 2010''' <br />
|-<br />
| style="background:#efefef; color:maroon"| 09.00-9:10<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB;; color:#522200" colspan="2"| Welcome and overview of day activities (Kikinis)<br />
|-<br />
| style="background:#efefef; color:maroon"| 09.10-10:00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Introduction to the NA-MIC kit for clinical research applications (Kikinis/Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10:00-10:45<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200" colspan="2"|Loading and Viewing Data (Sonia Pujol)<br />
|-<br />
| style="background:#efefef; color:maroon"| 10.45-11:00<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 11.00-12.30<br />
| style="background:#FBF7BB; color:#522200"| 12:00 NA-MIC Overview Lecture (Ron Kikinis) (Please add room number)<br />
| style="background:#FBF7BB; color:#522200"| Diffusion Tensor Imaging - Part 1 (Sonia Pujol) (Please add room number)<br />
| style="background:#FBF7BB; color:#522200"| Programming Tutorial - Part 1 (Hans Johnson) (Please add room number)<br />
|-<br />
| style="background:#efefef; color:maroon"| 12.30-1.45<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Lunch<br />
|-<br />
| style="background:#efefef; color:maroon"| 1.45-3.00<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"|Diffusion Tensor Imaging - Part 2 (Sonia Pujol) (Please add room number)<br />
| style="background:#FBF7BB; color:#522200"|Programming Tutorial - Part 2 (Hans Johnson) (Please add room number)<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.00-3.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#EEDDBB; color:#522200" colspan="2"| Coffee Break<br />
|-<br />
| style="background:#efefef; color:maroon"| 3.15-4.15<br />
| style="background:#FBF7BB; color:#522200"|<br />
| style="background:#FBF7BB; color:#522200"|Questions from the Audience (Ron Kikinis/Sonia Pujol)<br />
| style="background:#FBF7BB; color:#522200"|Free Surfer Tutorial (Hans Johnson)<br />
|-<br />
| style="background:#efefef; color:maroon"| 4:00-5:00<br />
| style="background:#EEDDBB; color:#522200"| Radiation Oncology Research (Ron Kikinis)<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
| style="background:#EEDDBB; color:#522200"| 4:15-4:30 Concluding Remarks and Feedback<br />
|-<br />
| style="background:#efefef; color:maroon"| 5:00-6:00<br />
| style="background:#FBF7BB; color:#522200"| Neurosurgery Department Seminar: Image-guided neurosurgery research using the NA-MIC kit (Sonia Pujol)<br />
| style="background:#FBF7BB; color:#522200"| <br />
| style="background:#FBF7BB; color:#522200"| <br />
|}<br />
<br />
<br />
<br />
Back to [http://www.na-mic.org/Wiki/index.php/Events NA-MIC Events]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49630NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-03-01T20:31:31Z<p>Vmagnotta: /* Publications */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
#Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
#Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
#Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
#Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
#Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
#Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
#DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
#Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
#Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
#Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
#Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
#Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
#Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
***[[2007 Project Half Week]]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]]<br />
***[[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]]<br />
*'''2008'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
***[[2008 Winter Project Week:Finite Element Meshing into NA-MIC]]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]]<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[MeshingSummer2009]]<br />
** [[Meshing Tcon September 26]]<br />
<br />
*'''2010'''<br />
**[http://www.na-mic.org/Wiki/images/4/44/NA-MIC-Mesh-Collaboration-2010.ppt NA-MIC Update 2010]<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49579NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T18:01:37Z<p>Vmagnotta: /* Image Registration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
#Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
#Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
#Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
#Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
#Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
#Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
#DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
#Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
#Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
#Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
#Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
#Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
#Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
***[[2007 Project Half Week]]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]]<br />
***[[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]]<br />
*'''2008'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
***[[2008 Winter Project Week:Finite Element Meshing into NA-MIC]]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]]<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[MeshingSummer2009]]<br />
** [[Meshing Tcon September 26]]<br />
<br />
*'''2010'''<br />
**[http://www.na-mic.org/Wiki/images/4/44/NA-MIC-Mesh-Collaboration-2010.ppt NA-MIC Update 2010]<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=Mapped_Hexahedral_Meshing&diff=49578Mapped Hexahedral Meshing2010-02-28T17:59:08Z<p>Vmagnotta: </p>
<hr />
<div>'''Objective:'''<br />
<br />
* Develop a tool for mapped meshing that will warp a template mesh onto a surface for a new subject<br />
* Determine the limits that the warping algorithm will succeed and fail<br />
* Apply these techniques to a sample of data to determine the reliability of the algorithm with respect to mesh quality<br />
<br />
'''Progress:'''<br />
* Previous work on this project was performed at the 2007 AHM - [http://www.na-mic.org/Wiki/images/3/34/2007_AHM_Programming_Half_Week_MappedMesh.ppt Mapped Mesh 4 Block]<br />
* Warped meshing framework has been developed using VTK and ITK using a finite element approach<br />
**VTK<br />
***Support the reading and writing of meshes (vtkUnstructuredGrid) and surfaces (vtkPolyData)<br />
***Distance measures between the deforming mesh and the subject surface<br />
***Initial registration - [http://www.vtk.org/doc/nightly/html/classvtkIterativeClosestPointTransform.html Iterative Closest Point] or [http://www.vtk.org/doc/nightly/html/classvtkProcrustesAlignmentFilter.html Procrustes] <br />
**ITK<br />
***Finite element framework used to warped the template mesh onto the subject surface<br />
*Registration made hierarchical to speed up the registration process<br />
**Requires multiple template meshes to exist<br />
**This is readily supported using the interactive meshing tools by changing the average edge length <br />
**Subsequent meshes are initialized using a thin plate splines<br />
*Parameters allowed to vary at each level of the registration<br />
**Iterations<br />
**Young's Modulus<br />
*Convergence based on distance between the warped template and the subject surface<br />
**User specified convergence threshold in mm<br />
**Convergence can be based on average or maximum distance<br />
*Boundary conditions can be applied<br />
**Center of the mesh - Holds the eight nodes closest to the center of the mesh fixed <br />
**External - Applies boundary conditions to the mesh as they fall within a user specified tolerance of the subject surface<br />
* Initial testing done by warping a cube mesh onto a sphere<br />
**Evaluation:<br />
***Distance between warped mesh and subject surface<br />
***Mesh quality<br />
<br />
'''Publications:'''<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
<br />
'''Key Investigators:'''<br />
<br />
* Iowa: Nicole Grosland, Vincent Magnotta, Ritesh Bafna<br />
<br />
'''Links:'''<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)]<br />
<br />
<br />
'''Figures:'''<br />
<br />
[[Image:MappedHexMeshSquareSphereInit.jpg|left|thumb|300px|Initial position of the cube template mesh and the sphere surface prior to registration using the itk::FEM mapped meshing algorithm]]<br />
<br />
[[Image:MappedMeshCubeSphereQuality.jpg|left|thumb|325px|Mesh quality evaluation of the warped cube]]<br />
<br />
[[Image:MappedMeshSquareSphere.jpg|left|thumb|300px|a)Position of the template cube mesh and surface after ICP registration. b) Resulting warped cube after itk::FEM mapped meshing. c) Distance map between the warped cube and the sphere surface]]<br />
<br />
[[Image:MappedMeshProximalPhalanxTrial.jpg|left|thumb|300px|Initial attempt to apply mapped meshing algorithm to the proximal phalanx]]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49577NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:57:25Z<p>Vmagnotta: /* Publications */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
#Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
#Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
#Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
#Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
#Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
#Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
#DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
#Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
#Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
#Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
#Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
#Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
#Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
***[[2007 Project Half Week]]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]]<br />
***[[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]]<br />
*'''2008'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
***[[2008 Winter Project Week:Finite Element Meshing into NA-MIC]]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]]<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[MeshingSummer2009]]<br />
** [[Meshing Tcon September 26]]<br />
<br />
*'''2010'''<br />
**[http://www.na-mic.org/Wiki/images/4/44/NA-MIC-Mesh-Collaboration-2010.ppt NA-MIC Update 2010]<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49576NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:56:48Z<p>Vmagnotta: /* Publications */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
#Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
#Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
#Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
#Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
#Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
#Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
#DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
#Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
#Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
#Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
#Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
#Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
#Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
***[[2007 Project Half Week]]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]]<br />
***[[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]]<br />
*'''2008'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
***[[2008 Winter Project Week:Finite Element Meshing into NA-MIC]]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]]<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[MeshingSummer2009]]<br />
** [[Meshing Tcon September 26]]<br />
<br />
*'''2010'''<br />
**[http://www.na-mic.org/Wiki/images/4/44/NA-MIC-Mesh-Collaboration-2010.ppt NA-MIC Update 2010]<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49575NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:56:19Z<p>Vmagnotta: /* Publications */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
#Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
***[[2007 Project Half Week]]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]]<br />
***[[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]]<br />
*'''2008'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
***[[2008 Winter Project Week:Finite Element Meshing into NA-MIC]]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]]<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[MeshingSummer2009]]<br />
** [[Meshing Tcon September 26]]<br />
<br />
*'''2010'''<br />
**[http://www.na-mic.org/Wiki/images/4/44/NA-MIC-Mesh-Collaboration-2010.ppt NA-MIC Update 2010]<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49574NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:55:56Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
***[[2007 Project Half Week]]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]]<br />
***[[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]]<br />
*'''2008'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
***[[2008 Winter Project Week:Finite Element Meshing into NA-MIC]]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]]<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[MeshingSummer2009]]<br />
** [[Meshing Tcon September 26]]<br />
<br />
*'''2010'''<br />
**[http://www.na-mic.org/Wiki/images/4/44/NA-MIC-Mesh-Collaboration-2010.ppt NA-MIC Update 2010]<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49573NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:54:14Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
***[[2007 Project Half Week]]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]]<br />
***[[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]]<br />
*'''2008'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
***[[2008 Winter Project Week:Finite Element Meshing into NA-MIC]]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[NA-MIC/Projects/External Collaboration/Mesh Generation Summer 2008]]<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
** [[Meshing Tcon September 26]]<br />
*'''2010'''<br />
**[http://www.na-mic.org/Wiki/images/4/44/NA-MIC-Mesh-Collaboration-2010.ppt NA-MIC Update 2010]<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49572NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:52:18Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
***[[2007 Project Half Week]]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
**'''NA-MIC Summer Project Week'''<br />
***[[Collaboration/Iowa/Meshing/Adding VTK Interactive WWidgets to Slicer3]]<br />
***[[Collaboration/Iowa/Meshing/Migrate Iowa Neural Net code to pure ITK]]<br />
*'''2008'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
***[[2008 Winter Project Week:Finite Element Meshing into NA-MIC]]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
** [[Meshing Tcon September 26]]<br />
*'''2010'''<br />
**[http://www.na-mic.org/Wiki/images/4/44/NA-MIC-Mesh-Collaboration-2010.ppt NA-MIC Update 2010]<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49571NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:49:43Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
***[[2007 Project Half Week]]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
*'''2008'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
***[[2008 Winter Project Week:Finite Element Meshing into NA-MIC]]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
** [[Meshing Tcon September 26]]<br />
*'''2010'''<br />
**[http://www.na-mic.org/Wiki/images/4/44/NA-MIC-Mesh-Collaboration-2010.ppt NA-MIC Update 2010]<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49570NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:46:57Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
*'''2008'''<br />
**'''NA-MIC AHM'''<br />
***[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
***[[2008 Winter Project Week:Finite Element Meshing into NA-MIC]]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
** [[Meshing Tcon September 26]]<br />
*'''2010'''<br />
**[http://www.na-mic.org/Wiki/images/4/44/NA-MIC-Mesh-Collaboration-2010.ppt NA-MIC Update 2010]<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49569NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:44:19Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
*'''2008'''<br />
**[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
** [[Meshing Tcon September 26]]<br />
*'''2010'''<br />
**[http://www.na-mic.org/Wiki/images/4/44/NA-MIC-Mesh-Collaboration-2010.ppt NA-MIC Update 2010]<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49568NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:43:02Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
*'''2008'''<br />
**[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''NA-MIC All Hands Meeting'''<br />
***[http://www.na-mic.org/Wiki/images/d/d7/NA-MIC_Mesh_Collaboration_2009.ppt AHM Update]<br />
***[[Iowa Meshing Tutorial]]<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
** [[Meshing Tcon September 26]]<br />
*'''2010'''<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49567NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:41:23Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
*'''2008'''<br />
**[http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update]<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
** [[Meshing Tcon September 26]]<br />
*'''2010'''<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49566NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:39:31Z<p>Vmagnotta: /* Publications */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, Patient, Toward the development of virtual surgical tools to aid orthopaedic FE analyses, EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
*'''2008'''<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
** [[Meshing Tcon September 26]]<br />
*'''2010'''<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49565NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:38:14Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
*'''2008'''<br />
**'''Annual BMES Meeting'''<br />
***Gandhi, A.A., D. Fredericks, N.M. Grosland, and J. Smucker. Assessment of Bioplex interbody device in a sheep lumbar fusion model. in Annual BMES Meeting. 2008. St. Louis, MO.<br />
**'''Pre ORS'''<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient -Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning. in 16th Annual pre-ors meeting. 2008. San Francisco, CA.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme, A.J., N.A. DeVries, N.A. Kallemeyn, V.A. Magnotta, and N.M. Grosland. [http://www.ors.org/web/Transactions/54/1563.PDF Comparison of the EM algorithm and an artifical neural network for automated bone segmentation.] in 54th Annual Meeting of the Orthopaedic Research Society. 2008. San Francisco, CA.<br />
**'''ASME Summer Bioengineering Conference'''<br />
***Shivanna, K.H., N.A. Kallemeyn, S.C. Tadepalli, N.A. DeVries, V.A. Magnotta, and N.M. Grosland. [http://www.x-cd.com/sbc08/index.html IA-FEMesh: An Interactive all hexahedral mesh generator for discrete anatomic closed surfaces.] in ASME Summer Bioengineering Conference. 2008. Marco Island, FL.<br />
**'''MICCAI'''<br />
***Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*'''2009'''<br />
**'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing [Poster]. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
***Ramme, A.J., V.A. Magnotta, and N.M. Grosland. Automated building block assignments for finite element mesh development of patient-specific orthopaedic models. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Shivanna, K.H., S.C. Tadepalli, V.A. Magnotta, and N.M. Grosland. A framework for finite element mesh quality improvement and visualization in orthopaedic biomechanics. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Semi-Automated Patient Specific Hexahedral Mesh Generation of Articular Cartilage. in ASME Summer Bioengineering Conference. 2009. Lake Tahoe, CA.<br />
**'''American Society of Biomechanics Annual Meeting'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. A Combinatorial Approach to Automated Patient-Specific Finite Element Meshing. American Society of Biomechanics Annual Meeting, State College, PA, August 26-29, 2009.<br />
** [[Meshing Tcon September 26]]<br />
*'''2010'''<br />
**'''Pre ORS'''<br />
***Ramme AJ, Shivanna KH, Magnotta VA, Grosland NM. Semi-Automated Block Definitions in Multi-Block Finite Element Meshing. 18th Annual Symposium on Computational Methods in Orthopaedic Biomechanics. Tulane University; New Orleans, LA, March 5, 2010.<br />
**'''Orthopaedic Research Society'''<br />
***Ramme AJ, Magnotta VA, Grosland NM. Automating Hexahedral Finite Element Meshing of Bony Structures. Orthopaedic Research Society Annual Meeting, New Orleans, LA, March 6-9, 2010.<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49564NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:29:08Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
*'''2006'''<br />
**Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
**'''Orthopaedic Research Society - 2006'''<br />
***Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
**'''MICCAI - 2006'''<br />
***Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
**[[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
*'''2007'''<br />
**[http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
**'''American Society of Biomechanics 2007'''<br />
***Grosland, N.M., C. Lisle, K.H. Shivanna, S. Pieper, and V.A. Magnotta. [http://www.asbweb.org/conferences/2007/40.pdf A check of mesh quality.] in American Society of Biomechanics. 2007. Palo Alto, CA. Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
***Tadepalli, S.C., K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Patient-specific orthopaedic surgical planning: Image data sets to FE models. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***DeVries, N.A., E.E. Gassman, N.A. Kallemeyn, K.H. Shivanna, V.A. Magnotta, and N.M. Grosland. Validation of orthopaedic related image segmentation techniques. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
***Bafna, R., V.A. Magnotta, and N.M. Grosland. Automated hexahedral meshing of anatomical structures using deformable registration. in American Society of Biomechanics. 2007. Palo Alto, CA.<br />
<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
<br />
*'''Orthopaedic Research Society - 2008'''<br />
**Ramme A, Magnotta V, Grosland NM. Comparison of the Expectation Maximization Algorithm and an Artificial Neural Network for Automated Bone Segmentation.<br />
*'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
**Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. IA-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces.<br />
**Tadepalli SC, Kallemeyn NA, Shivanna KH, Smucker J, Fredericks DC, Grosland NM. Cervical Laminoplasty Construct Stability: A Finite Element Study.<br />
**Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. Toward Patient-Specific Cervical Spine Functional Spinal Unit FE Modeling and Validation.<br />
<br />
<br />
* [[Meshing Tcon September 26]]<br />
*'''Pre-ORS meeting - 2009'''<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM. Patient –Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning.<br />
*'''Orthopaedic Research Society - 2009'''<br />
*'''ASME Summer Bioengineering Conference - 2009 - Lake Tahoe, CA'''<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM. A Semi-Automated Hexahedral Mesh Generation of the Articular Cartilage.<br />
**Kiran H Shivanna, Srinivas C Tadepalli, Vincent A Magnotta, Nicole M Grosland, A Framework for Finite Element Mesh Quality Improvement and Visualization in Orthopaedic Biomechanics.<br />
*'''American Society of Biomechanics - 2009 - State College PA'''<br />
**Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. Feature based all hexahedral mesh generation in orthopaedic applications<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=49563NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-02-28T17:25:22Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
<br />
* Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
*'''Orthopaedic Research Society - 2006'''<br />
**Gassman, E.E., S.M. Powell, V.A. Magnotta, and N.M. Grosland. Automating the identification of bony structures using artificial neural networks. in 52nd Annual Meeting of the Orthopaedic Research Society. 2006. Chicago, IL.<br />
*'''MICCAI - 2006'''<br />
**Shivanna, K.H., B.D. Adams, V.A. Magnotta, and N.M. Grosland. Automating patient-specific finite element model development. in 9th MICCAI Conference. 2006. Copenhagen.<br />
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
* [http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
* Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
* [http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update 2008]<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
<br />
*'''Orthopaedic Research Society - 2008'''<br />
**Ramme A, Magnotta V, Grosland NM. Comparison of the Expectation Maximization Algorithm and an Artificial Neural Network for Automated Bone Segmentation.<br />
*'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
**Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. IA-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces.<br />
**Tadepalli SC, Kallemeyn NA, Shivanna KH, Smucker J, Fredericks DC, Grosland NM. Cervical Laminoplasty Construct Stability: A Finite Element Study.<br />
**Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. Toward Patient-Specific Cervical Spine Functional Spinal Unit FE Modeling and Validation.<br />
<br />
<br />
* [[Meshing Tcon September 26]]<br />
*'''Pre-ORS meeting - 2009'''<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM. Patient –Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning.<br />
*'''Orthopaedic Research Society - 2009'''<br />
*'''ASME Summer Bioengineering Conference - 2009 - Lake Tahoe, CA'''<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM. A Semi-Automated Hexahedral Mesh Generation of the Articular Cartilage.<br />
**Kiran H Shivanna, Srinivas C Tadepalli, Vincent A Magnotta, Nicole M Grosland, A Framework for Finite Element Mesh Quality Improvement and Visualization in Orthopaedic Biomechanics.<br />
*'''American Society of Biomechanics - 2009 - State College PA'''<br />
**Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. Feature based all hexahedral mesh generation in orthopaedic applications<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=Engineering:TCON_2010&diff=48147Engineering:TCON 20102010-01-28T20:15:37Z<p>Vmagnotta: /* 2010-01-28 */</p>
<hr />
<div>Back to [[TCON:Main|TCON:Main]], [[Events]]<br />
<br />
==2010-01-28==<br />
Attendees: Xiaodong, Tina, John M, Katie, Nicole, Dominik, Vince, Casey<br />
<br />
Agenda<br />
* data update (john m)<br />
**example downloadable resources page: http://www.ncigt.org/pages/Downloads<br />
<br />
*Iowa Data<br />
**Visible Human Datasets https://mri.radiology.uiowa.edu//visible_human_datasets.html<br />
<br />
==2010-01-21==<br />
Attendees: Jim, Katie, Nicole, Wendy, Curt, Ron, Dominic, Steve, Dan<br />
<br />
* Update wiki pages in preparation for the review of the NA-MIC renewal<br />
<br />
==2010-01-14==<br />
<br />
Attendees: Katie Ben Casey Yin Tina Vince Jim Satra Nicole Lauren Hiro Fernando Chris Brian Dominik Ron<br />
<br />
* Discussion of [http://ipython.scipy.org/doc/rel-0.10/html/parallel/index.html parallel processing using ipython] for use with [[NA-MIC_NCBC_Collaboration:NA-MIC_virtual_colonoscopy|NA-MIC CT Colonography collaboration project]]. (confirmed).<br />
** As a follow up people may be interested in the [http://www.enthought.com/training/webinars.php Enthought webinar on this topic 3pm eastern on Jan 22, 2010].<br />
** Need real time processing speed. 10 fps for volume rendering. 5 minutes of image processing (down from 30 minutes)<br />
** 512x512x1000 voxels<br />
** GPU solutions or ipython solutions<br />
** Python package for accessing to Slicer internals in a headless mode, i.e. run Slicer internals from Python instead of running Python from within Slicer<br />
** iPython distinct from MPI (meet different needs)<br />
** Microsoft interest in iPython<br />
* Jim fell on the sword to take minutes<br />
* Follow up information from Fernando about the new version of ipython in development:<br />
** the docs for the in-testing ipython are at: http://ipython.scipy.org/doc/bzr.r1321/<br />
** and downloads in various formats are at: http://ipython.scipy.org/dist/testing/<br />
** ''Note:'' the files with .bzr.r1321 in the names are the relevant ones for today's call, NOT the 'nightly' ones.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=47980NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-01-21T22:52:18Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
<br />
* Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
* [http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
* Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
* [http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update 2008]<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
<br />
*'''Orthopaedic Research Society - 2008'''<br />
**Ramme A, Magnotta V, Grosland NM. Comparison of the Expectation Maximization Algorithm and an Artificial Neural Network for Automated Bone Segmentation.<br />
*'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
**Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. IA-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces.<br />
**Tadepalli SC, Kallemeyn NA, Shivanna KH, Smucker J, Fredericks DC, Grosland NM. Cervical Laminoplasty Construct Stability: A Finite Element Study.<br />
**Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. Toward Patient-Specific Cervical Spine Functional Spinal Unit FE Modeling and Validation.<br />
<br />
<br />
* [[Meshing Tcon September 26]]<br />
*'''Pre-ORS meeting - 2009'''<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM. Patient –Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning.<br />
*'''Orthopaedic Research Society - 2009'''<br />
*'''ASME Summer Bioengineering Conference - 2009 - Lake Tahoe, CA'''<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM. A Semi-Automated Hexahedral Mesh Generation of the Articular Cartilage.<br />
**Kiran H Shivanna, Srinivas C Tadepalli, Vincent A Magnotta, Nicole M Grosland, A Framework for Finite Element Mesh Quality Improvement and Visualization in Orthopaedic Biomechanics.<br />
*'''American Society of Biomechanics - 2009 - State College PA'''<br />
**Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. Feature based all hexahedral mesh generation in orthopaedic applications<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=47979NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-01-21T22:46:56Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
<br />
* Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
* [http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
* Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
* [http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update 2008]<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
<br />
*'''Orthopaedic Research Society - 2008'''<br />
**Ramme A, Magnotta V, Grosland NM. Comparison of the Expectation Maximization Algorithm and an Artificial Neural Network for Automated Bone Segmentation.<br />
*'''ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.'''<br />
**Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. IA-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces.<br />
**Srinivas C Tadepalli., Nicole A Kallemeyn., Kiran H Shivanna., Joseph Smucker., Douglas C Fredericks., Nicole M Grosland., Cervical Laminoplasty Construct Stability: A Finite Element Study.<br />
**Nicole A Kallemeyn., Srinivas C Tadepalli., Kiran H Shivanna., Nicole M Grosland., Toward Patient-Specific Cervical Spine Functional Spinal Unit FE Modeling and Validation.<br />
<br />
<br />
* [[Meshing Tcon September 26]]<br />
*'''Pre-ORS meeting - 2009'''<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM. Patient –Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning.<br />
*'''Orthopaedic Research Society - 2009'''<br />
*'''ASME Summer Bioengineering Conference - 2009 - Lake Tahoe, CA'''<br />
**Srinivas C Tadepalli, Kiran H Shivanna, Vincent A Magnotta, Nicole M Grosland, A Semi-Automated Hexahedral Mesh Generation of the Articular Cartilage.<br />
**Kiran H Shivanna, Srinivas C Tadepalli, Vincent A Magnotta, Nicole M Grosland, A Framework for Finite Element Mesh Quality Improvement and Visualization in Orthopaedic Biomechanics.<br />
*'''American Society of Biomechanics - 2009 - State College PA'''<br />
**Kiran H Shivanna, Srinivas C Tadepalli , Vincent A Magnotta, Nicole M Grosland, Feature based all hexahedral mesh generation in orthopaedic applications<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=47978NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-01-21T22:46:10Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
<br />
* Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
* [http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
* Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
* [http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update 2008]<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
<br />
*Orthopaedic Research Society - 2008<br />
**Ramme A, Magnotta V, Grosland NM. Comparison of the Expectation Maximization Algorithm and an Artificial Neural Network for Automated Bone Segmentation.<br />
*ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.<br />
**Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. IA-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces.<br />
**Srinivas C Tadepalli., Nicole A Kallemeyn., Kiran H Shivanna., Joseph Smucker., Douglas C Fredericks., Nicole M Grosland., Cervical Laminoplasty Construct Stability: A Finite Element Study.<br />
**Nicole A Kallemeyn., Srinivas C Tadepalli., Kiran H Shivanna., Nicole M Grosland., Toward Patient-Specific Cervical Spine Functional Spinal Unit FE Modeling and Validation.<br />
<br />
<br />
* [[Meshing Tcon September 26]]<br />
*'''Pre-ORS meeting - 2009'''<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM. Patient –Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning.<br />
*'''Orthopaedic Research Society - 2009'''<br />
*ASME Summer Bioengineering Conference - 2009 - Lake Tahoe, CA<br />
**Srinivas C Tadepalli, Kiran H Shivanna, Vincent A Magnotta, Nicole M Grosland, A Semi-Automated Hexahedral Mesh Generation of the Articular Cartilage.<br />
**Kiran H Shivanna, Srinivas C Tadepalli, Vincent A Magnotta, Nicole M Grosland, A Framework for Finite Element Mesh Quality Improvement and Visualization in Orthopaedic Biomechanics.<br />
*American Society of Biomechanics - 2009 - State College PA<br />
**Kiran H Shivanna, Srinivas C Tadepalli , Vincent A Magnotta, Nicole M Grosland, Feature based all hexahedral mesh generation in orthopaedic applications<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=47977NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-01-21T22:41:21Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
<br />
* Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
* [http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
* Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
* [http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update 2008]<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*Pre-ORS meeting - 2009<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM. Patient –Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning.<br />
*Orthopaedic Research Society - 2008<br />
**Ramme A, Magnotta V, Grosland NM. Comparison of the Expectation Maximization Algorithm and an Artificial Neural Network for Automated Bone Segmentation.<br />
*ASME Summer Bioengineering Conference - 2008 - Marco Island, FL.<br />
**Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. IA-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces.<br />
**Srinivas C Tadepalli., Nicole A Kallemeyn., Kiran H Shivanna., Joseph Smucker., Douglas C Fredericks., Nicole M Grosland., Cervical Laminoplasty Construct Stability: A Finite Element Study.<br />
**Nicole A Kallemeyn., Srinivas C Tadepalli., Kiran H Shivanna., Nicole M Grosland., Toward Patient-Specific Cervical Spine Functional Spinal Unit FE Modeling and Validation.<br />
<br />
<br />
* [[Meshing Tcon September 26]]<br />
*Orthopaedic Research Society - 2009<br />
*ASME Summer Bioengineering Conference - 2009 - Lake Tahoe, CA<br />
**Srinivas C Tadepalli, Kiran H Shivanna, Vincent A Magnotta, Nicole M Grosland, A Semi-Automated Hexahedral Mesh Generation of the Articular Cartilage.<br />
**Kiran H Shivanna, Srinivas C Tadepalli, Vincent A Magnotta, Nicole M Grosland, A Framework for Finite Element Mesh Quality Improvement and Visualization in Orthopaedic Biomechanics.<br />
*American Society of Biomechanics - 2009 - State College PA<br />
**Kiran H Shivanna, Srinivas C Tadepalli , Vincent A Magnotta, Nicole M Grosland, Feature based all hexahedral mesh generation in orthopaedic applications<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=47924NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-01-20T18:34:23Z<p>Vmagnotta: /* Mesh Improvement */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Mesh Quality Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
<br />
* Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
* [http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
* Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
* [http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update 2008]<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*Pre-ORS meeting - 2009<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM. Patient –Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning.<br />
*Orthopaedic Research Society - 2008<br />
**Ramme A, Magnotta V, Grosland NM. Comparison of the Expectation Maximization Algorithm and an Artificial Neural Network for Automated Bone Segmentation.<br />
*ASME Summer Bioengineering Conference - 2008<br />
**Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. IA-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces.<br />
* [[Meshing Tcon September 26]]<br />
*Orthopaedic Research Society - 2009<br />
*ASME Summer Bioengineering Conference - 2009<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning&diff=47923Validation of Defined Regions of Interest Using Surface Scanning2010-01-20T18:32:42Z<p>Vmagnotta: </p>
<hr />
<div>'''Objective:'''<br />
<br />
* To evaluate manual and automated segmentation routines using surface scans of disected bones from cadaveric specimens<br />
<br />
'''Progress:'''<br />
<br />
* CT images of the hand and wrist have been obtained<br />
* Four hands have been disected and bones extracted<br />
* Surface scanning for these disected bones is completed using a Roland LPX-250 Laser Scanner<br />
* Manual tracing of the CT images is completed<br />
* Evaluate reliability of the manual tracers is complete using relative overlap<br />
* Tools have been developed to reorient surface axes and to register the manually defined model and the surface resulting from laser scanning<br />
* Distance maps for the manual segmentation have been generated.<br />
* The effect of various post processing routines have been studied relative to changes in the surface geometry relative to the laser scan.<br />
<br />
<br />
'''Publications:'''<br />
* DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008. <br />
<br />
<br />
'''Key Investigators:'''<br />
<br />
* Iowa: Nicole Grosland, Vincent Magnotta, Nicole DeVries<br />
<br />
'''Links:'''<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modelling and Experimentation (MIMX)]<br />
<br />
'''References:'''<br />
* [http://www.springerlink.com/content/u36v5957k17536wt/ Devries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. Validation of Phalanx Bone 3D Surface Segmentation from CT Images Using Laser Scanning, Skeletal Radiology, 2007] <br />
<br />
'''Figures:'''<br />
<br />
[[Image:DistanceMapTool.jpg|left|thumb|300px|Surface distance mapping tool developed in FLTK]]<br />
<br />
[[Image:DistanceMap.png|left|thumb|300px|Surface Distance Map for a phalanx bone between a surface manually defined via CT and a physical surface laser scan.]]<br />
<br />
[[Image:SurfaceOverlay.png|left|thumb|200px|Overlay of the physical surface (White) and CT based surface (Purple)]]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning&diff=47922Validation of Defined Regions of Interest Using Surface Scanning2010-01-20T18:32:00Z<p>Vmagnotta: </p>
<hr />
<div>'''Objective:'''<br />
<br />
* To evaluate manual and automated segmentation routines using surface scans of disected bones from cadaveric specimens<br />
<br />
'''Progress:'''<br />
<br />
* CT images of the hand and wrist have been obtained<br />
* Four hands have been disected and bones extracted<br />
* Surface scanning for these disected bones is completed using a Roland LPX-250 Laser Scanner<br />
* Manual tracing of the CT images is completed<br />
* Evaluate reliability of the manual tracers is complete using relative overlap<br />
* Tools have been developed to reorient surface axes and to register the manually defined model and the surface resulting from laser scanning<br />
* Distance maps for the manual segmentation have been generated.<br />
* The effect of various post processing routines have been studied relative to changes in the surface geometry relative to the laser scan.<br />
<br />
<br />
'''Publications:'''<br />
* DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning. Skeletal Radiol. 37(1):35-42, 2008. <br />
<br />
<br />
'''Key Investigators:'''<br />
<br />
* Iowa: Nicole Grosland, Vincent Magnotta, Nicole DeVries<br />
<br />
'''Links:'''<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modelling and Experimentation (MIMX)]<br />
<br />
'''References:'''<br />
* [http://www.springerlink.com/content/u36v5957k17536wt/ Devries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. Validation of Phalanx Bone 3D Surface Segmentation from CT Images Using Laser Scanning, Skeletal Radiology, 2007] <br />
<br />
'''Figures:'''<br />
<br />
[[Image:DistanceMapTool.jpg|left|thumb|300px|Surface distance mapping tool developed in FLTK]]<br />
<br />
[[Image:DistanceMap.png|left|thumb|300px|Surface Distance Map for a phalanx bone between a surface manually defined via CT and a physical surface laser scan.]]<br />
<br />
[[Image:SurfaceOverlay.png|left|thumb|200px|Overlay of the physical surface (White) and CT based surface (Purple)]]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=EM_Segmentation_For_Orthopaedic_Applications&diff=47921EM Segmentation For Orthopaedic Applications2010-01-20T18:30:51Z<p>Vmagnotta: </p>
<hr />
<div>'''Objective:'''<br />
<br />
* To utilize the Slicer3 Expectation Maximization Algorithm for segmentation of the phalanx bones of the hand.<br />
<br />
'''Progress:'''<br />
<br />
* We have utilized the Slicer2.7 EM Segmentation Module for segmentation of the phalanx bones<br />
*# Registration was performed outside of Slicer using ITK registration algorithms that are available in the IaFeMesh software. This includes Thin plate spline, B-Spline and rigid registration algorithms.<br />
*# Probability map information was created from a single subject used as the atlas image and filtered using a Gaussian filter.<br />
* Initial evaluation has been performed <br />
**Reliability assessed on fourteen specimens that also had the index finger segmented, and two specimens that had the index, middle, ring and little fingers manually segmented<br />
**Validation assessed using the laser scanning of the index finger (proximal, middle, and distal) phalanx bones in five specimens<br />
* Work is underway to develop a Slicer2.7 tutorial for this segmentation ([[Image:Draft_EM_Segment_Tutorial_9_12.pdf|Draft Copy]])<br />
<br />
'''Results:'''<br />
<br />
{| class="wikitable" border="1" cellpadding="2"<br />
|+Relative Overlap with Manual Rater<br />
|-<br />
! Finger !! Phalanx Segment !! Average Relative Overlap<br />
|-<br />
! Index (14 subjects)<br />
| Proximal || 0.87<br />
|-<br />
!<br />
| Medial || 0.80<br />
|-<br />
!<br />
| Distal || 0.70<br />
|-<br />
! Middle (2 subjects)<br />
| Proximal || 0.79<br />
|-<br />
!<br />
| Medial || 0.77<br />
|-<br />
!<br />
| Distal || 0.71<br />
|-<br />
! Ring (2 subjects)<br />
| Proximal || 0.76<br />
|-<br />
!<br />
| Medial || 0.82<br />
|-<br />
!<br />
| Distal || 0.80<br />
|-<br />
! Pinky (2 subjects)<br />
| Proximal || 0.70<br />
|-<br />
!<br />
| Medial || 0.73<br />
|-<br />
!<br />
| Distal || 0.72<br />
|}<br />
<br />
* Example of Validation Results is shown below in the figures<br />
<br />
<br />
<br />
<br />
<br />
'''To Do:'''<br />
*Update the the tutorial to support the Slicer3 Workflow<br />
**Tutorial will be developed by Austin Ramme - In progress<br />
*Slicer3 Segmentation applied to the femur<br />
**Using BRAINSFit for mapping of probability information to the subject images<br />
<br />
'''Manuscript:'''<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
<br />
<br />
'''Key Investigators:'''<br />
<br />
* Iowa: Austin Ramme, Nicole Grosland, and Vincent Magnotta<br />
<br />
'''Links:'''<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)]<br />
<br />
<br />
'''Figures:'''<br />
<br />
[[Image:EM-Segment-Phalanx.png|left|thumb|300px|Surface models from EM Segmentation generated via Slicer3]]<br />
<br />
[[Image:EM-Segment-Proximal.png|left|thumb|450px|Results of the EM Segmentation for the Proximal Pahalanx]]<br />
<br />
[[Image:EMSegment-Phalanx-DistanceMap.jpg|left|thumb|300px|Validation of EM Segmentation for the phalanx bones of the hand. Distance of automated segmentation versus physical laser surface scanning]]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=Novel_Hexahedral_Meshing_Algorithms&diff=47920Novel Hexahedral Meshing Algorithms2010-01-20T18:27:01Z<p>Vmagnotta: </p>
<hr />
<div>'''Objective:'''<br />
<br />
* Develop and integrate novel hexahedral meshing algorithms into the NA-MIC kit<br />
<br />
'''Progress:'''<br />
<br />
* Base projection algorithms have been developed and will be integrated into the toolkit. The algorithms have been implemented in KWWidgets in IaFeMesh to simplify integration into Slicer3.<br />
* The base code and algorithms have been brought into Slicer3 for integration within the GUI and MRML. Curt Lisle has been working on a this integration.<br />
*# The sort term goal is to get a single editable bounding box working within Slicer3 for the next release.<br />
*# Projection based morphing and mesh interpolation will be required.<br />
*# Include export to Abaqus format<br />
<br />
* Develop mapped meshing techniques that include an FE based solution using ITK that registers a template mesh with a subject specific surface. <br />
* Building of meshing code has now been turned on by default for the latest Slicer3 release.<br />
** Fully support all bounding box editing options<br />
**# Vertex manipulation<br />
**# Add<br />
**# Delete<br />
**# Split<br />
**# Merge<br />
**# Extrude<br />
**# Face manipulation<br />
**Allow the user to undo and redo operations - This should be supported by the inherent logic in the MRML scene description.<br />
** Extract mesh material properties from the images<br />
** Export to Abaqus format<br />
<br />
'''To Do:'''<br />
*Develop testing modules using the GUI framework being developed by Kitware.<br />
*Refine integration with Slicer. This is mainly related to the handling of data objects between Slicer3 and the meshing module interface.<br />
<br />
'''Publications:'''<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
<br />
'''Key Investigators:'''<br />
<br />
* Iowa: Nicole Grosland, Vincent Magnotta, Kiran Shivanna, Curt Lisle, and Steve Pieper<br />
<br />
'''Links:'''<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)]<br />
<br />
<br />
[[Image:MeshBoundingBox.png|left|thumb|300px|Basic Bounding Box Widget Integrated into Slicer3. Editing of bounding box vertices is not yet working]]<br />
<br />
[[Image:Slicer3MeshExample1.png|left|thumb|400px|Bounding Box Mesh Workflow shown in Slicer3 ]]<br />
<br />
<br />
[[Image:MeshDisplayProperties.png|left|thumb|300px|Mesh Display Properties]]<br />
[[Image:MeshDisplayElementSet.png|left|thumb|300px|Display of only element sets of interest]]<br />
[[Image:Femesh-in-trunk-120808.png|left|thumb|300px|Full Meshing Module Integration with Slicer3]]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=Mapped_Hexahedral_Meshing&diff=47919Mapped Hexahedral Meshing2010-01-20T18:24:58Z<p>Vmagnotta: </p>
<hr />
<div>'''Objective:'''<br />
<br />
* Develop a tool for mapped meshing that will warp a template mesh onto a surface for a new subject<br />
* Determine the limits that the warping algorithm will succeed and fail<br />
* Apply these techniques to a sample of data to determine the reliability of the algorithm with respect to mesh quality<br />
<br />
'''Progress:'''<br />
* Previous work on this project was performed at the 2007 AHM - [http://www.na-mic.org/Wiki/images/3/34/2007_AHM_Programming_Half_Week_MappedMesh.ppt Mapped Mesh 4 Block]<br />
* Warped meshing framework has been developed using VTK and ITK using a finite element approach<br />
**VTK<br />
***Support the reading and writing of meshes (vtkUnstructuredGrid) and surfaces (vtkPolyData)<br />
***Distance measures between the deforming mesh and the subject surface<br />
***Initial registration - [http://www.vtk.org/doc/nightly/html/classvtkIterativeClosestPointTransform.html Iterative Closest Point] or [http://www.vtk.org/doc/nightly/html/classvtkProcrustesAlignmentFilter.html Procrustes] <br />
**ITK<br />
***Finite element framework used to warped the template mesh onto the subject surface<br />
*Registration made hierarchical to speed up the registration process<br />
**Requires multiple template meshes to exist<br />
**This is readily supported using the interactive meshing tools by changing the average edge length <br />
**Subsequent meshes are initialized using a thin plate splines<br />
*Parameters allowed to vary at each level of the registration<br />
**Iterations<br />
**Young's Modulus<br />
*Convergence based on distance between the warped template and the subject surface<br />
**User specified convergence threshold in mm<br />
**Convergence can be based on average or maximum distance<br />
*Boundary conditions can be applied<br />
**Center of the mesh - Holds the eight nodes closest to the center of the mesh fixed <br />
**External - Applies boundary conditions to the mesh as they fall within a user specified tolerance of the subject surface<br />
* Initial testing done by warping a cube mesh onto a sphere<br />
**Evaluation:<br />
***Distance between warped mesh and subject surface<br />
***Mesh quality<br />
<br />
'''Publications:'''<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
<br />
'''Key Investigators:'''<br />
<br />
* Iowa: Nicole Grosland, Vincent Magnotta, Ritesh Bafna<br />
<br />
'''Links:'''<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)]<br />
<br />
'''Execution Model Program Description:'''<br />
* To be filled in once developed<br />
<br />
This tool was developed as part of an NIH NA-MIC Collaboration Grant EB005973.<br />
<br />
'''Program Usage:'''<br />
* To be filled in once developed<br />
<br />
'''Figures:'''<br />
<br />
[[Image:MappedHexMeshSquareSphereInit.jpg|left|thumb|300px|Initial position of the cube template mesh and the sphere surface prior to registration using the itk::FEM mapped meshing algorithm]]<br />
<br />
[[Image:MappedMeshCubeSphereQuality.jpg|left|thumb|325px|Mesh quality evaluation of the warped cube]]<br />
<br />
[[Image:MappedMeshSquareSphere.jpg|left|thumb|300px|a)Position of the template cube mesh and surface after ICP registration. b) Resulting warped cube after itk::FEM mapped meshing. c) Distance map between the warped cube and the sphere surface]]<br />
<br />
[[Image:MappedMeshProximalPhalanxTrial.jpg|left|thumb|300px|Initial attempt to apply mapped meshing algorithm to the proximal phalanx]]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=Hex_vs_Tet_Mesh_Comparisons&diff=47918Hex vs Tet Mesh Comparisons2010-01-20T18:23:31Z<p>Vmagnotta: </p>
<hr />
<div>'''Objective:'''<br />
<br />
* Comparison of Hexahedral versus Tetrahedral meshing algorithms Orthopaedic applications<br />
<br />
'''Progress:'''<br />
<br />
* Currently evaluating open source tetrahedral meshing algorithms<br />
**VTK<br />
***Slivers exist in resulting mesh<br />
**[http://www.hpfem.jku.at/netgen/ Netgen]<br />
***LGPL license<br />
***Issues have been found regarding invalid memory references<br />
***Does not always converge to a solution<br />
***Difficult to specify desired mesh density<br />
**[http://tetgen.berlios.de/ Tetgen]<br />
***Non commercial license. Commercial license can be purchased<br />
***Has been used for medical applications including heart, vertebral body, and head meshes <br />
<br />
* Performed an initial comparison of hexahedral versus tetrahedral algorithms<br />
**Study included comparison of hexahedral and tetrahedral meshing tools<br />
**Evaluated the results based the following criteria<br />
***Time to generate the mesh<br />
***mesh quality<br />
***Results of a static load analysis versus the number of elements<br />
'''Pulbication:'''<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009<br />
<br />
'''Key Investigators:'''<br />
<br />
* Iowa: Nicole DeVries, Nicole Grosland, Vincent Magnotta<br />
<br />
'''Links:'''<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)]<br />
<br />
<br />
'''Images:'''<br />
[[Image:FEmesh_comparisons.JPG|left|thumb|600px|The von Mises stress distribution for the various meshing techniques: IA-FEMesh (a) hexahedral mesh, (b) NETGEN tetrahedral mesh, and PATRAN (c) hexahedral mesh, (d) tetrahedral mesh with average element length of 1mm, and (e) tetrahedral mesh with average element length of 2mm.]]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=Mapped_Hexahedral_Meshing&diff=47917Mapped Hexahedral Meshing2010-01-20T18:22:10Z<p>Vmagnotta: </p>
<hr />
<div>'''Objective:'''<br />
<br />
* Develop a tool for mapped meshing that will warp a template mesh onto a surface for a new subject<br />
* Determine the limits that the warping algorithm will succeed and fail<br />
* Apply these techniques to a sample of data to determine the reliability of the algorithm with respect to mesh quality<br />
<br />
'''Progress:'''<br />
* Previous work on this project was performed at the 2007 AHM - [http://www.na-mic.org/Wiki/images/3/34/2007_AHM_Programming_Half_Week_MappedMesh.ppt Mapped Mesh 4 Block]<br />
* Warped meshing framework has been developed using VTK and ITK using a finite element approach<br />
**VTK<br />
***Support the reading and writing of meshes (vtkUnstructuredGrid) and surfaces (vtkPolyData)<br />
***Distance measures between the deforming mesh and the subject surface<br />
***Initial registration - [http://www.vtk.org/doc/nightly/html/classvtkIterativeClosestPointTransform.html Iterative Closest Point] or [http://www.vtk.org/doc/nightly/html/classvtkProcrustesAlignmentFilter.html Procrustes] <br />
**ITK<br />
***Finite element framework used to warped the template mesh onto the subject surface<br />
*Registration made hierarchical to speed up the registration process<br />
**Requires multiple template meshes to exist<br />
**This is readily supported using the interactive meshing tools by changing the average edge length <br />
**Subsequent meshes are initialized using a thin plate splines<br />
*Parameters allowed to vary at each level of the registration<br />
**Iterations<br />
**Young's Modulus<br />
*Convergence based on distance between the warped template and the subject surface<br />
**User specified convergence threshold in mm<br />
**Convergence can be based on average or maximum distance<br />
*Boundary conditions can be applied<br />
**Center of the mesh - Holds the eight nodes closest to the center of the mesh fixed <br />
**External - Applies boundary conditions to the mesh as they fall within a user specified tolerance of the subject surface<br />
* Initial testing done by warping a cube mesh onto a sphere<br />
**Evaluation:<br />
***Distance between warped mesh and subject surface<br />
***Mesh quality<br />
<br />
<br />
'''Key Investigators:'''<br />
<br />
* Iowa: Nicole Grosland, Vincent Magnotta, Ritesh Bafna<br />
<br />
'''Links:'''<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)]<br />
<br />
'''Execution Model Program Description:'''<br />
* To be filled in once developed<br />
<br />
This tool was developed as part of an NIH NA-MIC Collaboration Grant EB005973.<br />
<br />
'''Program Usage:'''<br />
* To be filled in once developed<br />
<br />
'''Figures:'''<br />
<br />
[[Image:MappedHexMeshSquareSphereInit.jpg|left|thumb|300px|Initial position of the cube template mesh and the sphere surface prior to registration using the itk::FEM mapped meshing algorithm]]<br />
<br />
[[Image:MappedMeshCubeSphereQuality.jpg|left|thumb|325px|Mesh quality evaluation of the warped cube]]<br />
<br />
[[Image:MappedMeshSquareSphere.jpg|left|thumb|300px|a)Position of the template cube mesh and surface after ICP registration. b) Resulting warped cube after itk::FEM mapped meshing. c) Distance map between the warped cube and the sphere surface]]<br />
<br />
[[Image:MappedMeshProximalPhalanxTrial.jpg|left|thumb|300px|Initial attempt to apply mapped meshing algorithm to the proximal phalanx]]</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=47916NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-01-20T18:19:32Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Utilization of Mesquite for Mesh Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
<br />
* Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
* [http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
* Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
* [http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update 2008]<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*Pre-ORS meeting - 2009<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM. Patient –Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning.<br />
*Orthopaedic Research Society - 2008<br />
**Ramme A, Magnotta V, Grosland NM. Comparison of the Expectation Maximization Algorithm and an Artificial Neural Network for Automated Bone Segmentation.<br />
*ASME Summer Bioengineering Conference - 2008<br />
**Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. IA-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces.<br />
* [[Meshing Tcon September 26]]<br />
*Orthopaedic Research Society - 2009<br />
*ASME Summer Bioengineering Conference - 2009<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=47915NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-01-20T18:18:11Z<p>Vmagnotta: /* Meetings and Events Specific to this Collaboration */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Utilization of Mesquite for Mesh Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
<br />
* Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
* [http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
* Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
* [http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update 2008]<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
*Pre-ORS meeting - 2009<br />
**Tadepalli SC, Shivanna KH, Magnotta VA, Grosland NM, Patient –Specific Hexahedral Mesh Generation for Orthopaedic Surgical Planning.<br />
*Orthopaedic Research Society - 2008<br />
**Ramme A, Magnotta V, Grosland NM. Comparison of the Expectation Maximization Algorithm and an Artificial Neural Network for Automated Bone Segmentation.<br />
*ASME Summer Bioengineering Conference<br />
**Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. IA-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces<br />
* [[Meshing Tcon September 26]]<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=47914NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-01-20T18:03:36Z<p>Vmagnotta: /* Publications */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Utilization of Mesquite for Mesh Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
<br />
* Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
* [http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
* Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
* [http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update 2008]<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
* [[Meshing Tcon September 26]]<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=47913NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-01-20T18:02:54Z<p>Vmagnotta: /* Publications */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Utilization of Mesquite for Mesh Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/1926/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
<br />
* Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
* [http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
* Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
* [http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update 2008]<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
* [[Meshing Tcon September 26]]<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnottahttps://www.na-mic.org/w/index.php?title=NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development&diff=47912NA-MIC NCBC Collaboration:Automated FE Mesh Development2010-01-20T18:01:05Z<p>Vmagnotta: /* Publications */</p>
<hr />
<div>Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]]<br />
<br />
[[Image:Cli-mesh-quality-small-062607.png|thumb|right|300px|Visualization of mesh quality]]<br />
==Abstract==<br />
Musculoskeletal finite element (FE) analysis is an invaluable tool in orthopedic-related research. While it has provided significant biomechanical insight, the demands associated with modeling the geometrically complex structures of the human body often limit its utility. The often-prohibitive amount of model development time is further compounded by the time required to process medical image datasets to identify the distinct anatomical structures of interest. Yet this process is a necessary preprocessing step for model development. As a result, most of the analyses reported in the literature refer to 'average' bone geometry. The broad objective of our research plan is to integrate and expand methods to automate the development of specimen- / patient-specific finite element (FE) models into the NA-MIC toolkit. In pursuit of this objective we propose to merge unique technologies to automate image dataset segmentation; material property extraction and assignment; and direct FE model development (automated meshing). While direct physical scans of the bones of interest will be used to validate the automated image segmentation routines, experimental cadaveric contact stress measurements will provide a standard against which to validate the FE contact formulations. Furthermore, the FE models generated by our software package will be compared to models of the same bone(s) created via a commercial pre-processing package. While the bones/joints of the upper extremity represent the primary structures of interest proposed in this application, the tools will be applicable to many orthopedic applications. In addition to expanding the NA-MIC toolkit beyond the brain, the proposed project will expand the image segmentation routines and finite element meshing routines currently available. This proposal will ultimately yield specimen-specific FE models of the various joints of the upper extremity. Such models will position us to provide information about the load transfer, characteristics of the normal joints and in the future to demonstrate, for example, the effects of ligamentous instabilities, posttraumatic misalignments, fractures, and various surgical procedures.<br />
<br />
==Grant#==<br />
R01EB005973 <br />
<br />
==Key Personnel==<br />
*[http://www.ccad.uiowa.edu/mimx Musculoskeletal Imaging, Modeling and Experimentation (MIMX)] at the University of Iowa: Nicole Grosland, PI, Vincent Magnotta, Tech Lead, Kiran Shivanna, Austin Ramme, Amla Natarajan <br />
*NA-MIC: Steve Pieper ([http://www.isomics.com/ Isomics]), Curt Lisle ([http://knowledgevis.com/Kvis/Welcome.html KnowledgeVis])<br />
<br />
==Funding Duration==<br />
09/20/2006-06/30/2010<br />
==Projects==<br />
An initial version of the meshing tool was recently released as a standalone application called [http://www.ccad.uiowa.edu/mimx/IA-FEMesh/ IA-FEMesh]. This application is built completely on NA-MIC tools including ITK, VTK, and KWWidgets.<br />
<br />
<br />
Active projects in this collaboration are: <br />
<br />
=== Meshing Algorithms ===<br />
<br />
# [[Voxel_Meshing_Module| Voxel Meshing Module]] (Iowa)<br />
# [[Novel_Hexahedral_Meshing_Algorithms|Novel Hexahedral Meshing Algorithms]] (Iowa)<br />
# [[Mapped Hexahedral Meshing|Mapped Hexahedral Meshing]] (Iowa)<br />
# [[Hex_vs_Tet_Mesh_Comparisons|Hex vs Tet Mesh Comparisons]] (Iowa/Isomics/BWH)<br />
<br />
=== Automated Segmentation ===<br />
<br />
# [[EM_Segmentation_For_Orthopaedic_Applications|EM Segmentation For Orthopaedic Applications]] (Iowa)<br />
# [[Integration_of_Neural_Network_Algorithms|Integration of Neural Network Algorithms]] (Iowa)<br />
<br />
=== Image Registration ===<br />
<br />
# [[Evaluation_of_Inter-Modality_Registration|Evaluation of Inter-Modality Registration]] (Iowa/Isomics)<br />
<br />
=== Validation ===<br />
<br />
# [[Validation_of_Defined_Regions_of_Interest_Using_Surface_Scanning| Validation of Defined Regions of Interest Using Surface Scanning]] (Iowa)<br />
# [[FE_Mesh_Validation|FE Mesh Validation]] (Iowa)<br />
<br />
=== Mesh Quality Visualization ===<br />
# [[FE Mesh Quality Visualization]] (Iowa/Isomics)<br />
# [[Standalone FE Mesh Quality Viewer]]<br />
# [[Mesh Quality Command Line Module]]<br />
<br />
=== Mesh Improvement ===<br />
# [[Utilization of Mesquite for Mesh Improvement]]<br />
<br />
=== Slicer3 Integration ===<br />
# [http://www.slicer.org/slicerWiki/index.php/Slicer_Interactive_Module Slicer Interactive Module]<br />
# [[Mesh KWWidgets Interface]]<br />
# [[Slicer3 Mesh Meeting October 2008]]<br />
<br />
=== Slicer3 Meshing Tutorial ===<br />
#[[Iowa Meshing Tutorial]] - Tutorial showing how to mesh the proximal phalanx bone with an example dataset<br />
<br />
==Publications==<br />
*Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.<br />
*Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.<br />
*Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.<br />
*Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.<br />
*Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.<br />
*DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.<br />
*Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.<br />
*Magnotta V, Li W, Grosland N. [http://hdl.handle.net/1926/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/1926/1490 , 2008.<br />
*Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.<br />
*Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.<br />
*Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.<br />
*Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine], 2006.<br />
<br />
==Meetings and Events Specific to this Collaboration==<br />
<br />
* Vincent Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).<br />
* [[2006_November_Meshing_Project_Visit|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]<br />
* [http://www.na-mic.org/Wiki/images/4/40/NA-MIC_Mesh_Collaboration.ppt NA-MIC All Hands Meeting Update 2007]<br />
* Nicole Grosland presents at the [http://www.asbweb.org/conferences/2007/40.pdf American Society of Biomechanics 2007, Palo Alto, CA]<br />
* [http://www.na-mic.org/Wiki/images/2/23/NA-MIC_Mesh_Collaboration_-_2008.ppt NA-MIC All Hands Meeting Update 2008]<br />
* Kiran Shivanna presents at the [http://www.x-cd.com/sbc08/index.html ASME 2008 Summer Bioengineering Conference], Marriott Resort, Marco Island, Florida, June 25 - 29, 2008.<br />
* Austin Ramme presents at [http://www.ors.org/web/Transactions/54/1563.PDF Orthopaedic Research Society (ORS)], San Francisco, CA 2008.<br />
* Vincent Magnotta presents at the [http://hdl.handle.net/1926/1490 MICCAI Workshop - Computational Biomechanics for Medicine], New York, NY 2008.<br />
* [[Meshing Tcon September 26]]<br />
<br />
==Resource Links==<br />
<br />
* [http://www.hpfem.jku.at/netgen/ netget]<br />
* [http://tetgen.berlios.de/ tetgen]<br />
* [http://libmesh.sourceforge.net/ libmesh]<br />
* [http://www.cs.sandia.gov/optimization/knupp/Mesquite.html Mesquite]<br />
* [http://www-unix.mcs.anl.gov/~freitag/Opt-MS/software.html Opt-ms]<br />
<br />
<br />
* Mesh warping project at the SPL - Steve Haker:<br />
** Haker S, Warfield S, Tempany C. [http://www.na-mic.org/Special:PubDB_View?dspaceid=633 Landmark-Guided Surface Matching and Volumetric Warping for Improved Prostate Biopsy Targeting and Guidance.] Proceedings of the 7th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2004, LNCS 3217, pp. 267-275, 2004.</div>Vmagnotta