Recurring Meeting of the Advisory Board
Date(s): November 19, 2015
Due to scheduling conflicts, the group meeting with the Advisory Board members were scheduled on an individual basis with each member. Please refer to Meeting Minutes for more details.
Contents
Progress Report
Project Specific Aims
- To provide an open, freely available, and collaborative development, testing, simulation and dissemination platform for in silico exploration of the biomechanics of healthy and diseased knees.
- To develop in silico biomechanical models of healthy and diseased knee joints of different genders and ages, supported by specimen-specific joint and tissue level experimental mechanics.
Project Infrastructure
https://simtk.org/home/openknee (project website)
http://wiki.simtk.org/openknee (project wiki)
Project Contact
Ahmet Erdemir, PhD, erdemira@ccf.org, https://simtk.org/users/aerdemir
Advisory Board
Clinical. Jack Andrish, MD; Carl Winalski, MD; Morgan Jones, MD, MPH; Paul Saluan, MD (Cleveland Clinic)
Engineering. Yasin Dhaher, PhD (Northwestern University); Trent Guess, PhD (University of Missouri), Rami Korhonen, PhD (University of Eastern Finland)
Progress Period
- May 9, 2015 - November 19, 2015
Development Team during Progress Period
Cleveland Clinic Core Team. Craig Bennetts, Tara Bonner, Snehal Chokhandre, Robb Colbrunn, Ahmet Erdemir
Stanford University. Scott Delp, Joy Ku, Henry Kwong
University of Utah. Ben Ellis, Jeff Weiss, Steve Maas
Community. Shannon Donnola, Chris Flask, Omar Gad, Raghav Malik, Diana Suciu, Connor Lough
See https://simtk.org/project/xml/team.xml?group_id=485 for full details on the project team.
Goals of Progress Period
- Launch and test usability of web based computation infrastructure (Stanford University)
- Publish in situ strain feature and implement additional features in simulation software (University of Utah)
- Disseminate joint mechanics data for oks001, oks002, oks003, oks004, oks006, oks007 (Cleveland Clinic)
- Complete joint imaging and joint mechanics experimentation on oks008, oks009, oks010, oks011 (Cleveland Clinic)
- Start tissue mechanics testing of all specimens (Cleveland Clinic)
Continue development and review of modeling & simulation specifications (Cleveland Clinic & Community)
- Start developing models for all specimens (Cleveland Clinic)
- Follow up publication of previous work on Open Knee - Generation 1 (Cleveland Clinic)
Please also refer to previous meeting minutes of the Advisory Board at RecurringMeetings/2015-05-08. It should be noted that the timeline of activities has deviated from the original proposal, i.e., see the Roadmap and the proposed timeline of the proposal in GrantInformation/proposal.pdf.
Activities of Progress Period
- Cloud computing prototype
The team at the Stanford University mainly focused on the upgrade of the SimTk.org infrastructure. Internal testing of the updated site has been taking longer than expected. As a result, the launch of the updated site has been delayed. With the upgrade of !Simtk.org, a beta release of the cloud computing infrastructure will be launched for usability testing. Cleveland Clinic team has Open Knee(s) - Generation 1 model ready with pre- and post-processing scripts for the beta release. The usability testing will facilitate the development of a model administration interface and the implementation of quota management features.
Cleveland Clinic and Stanford University teams cancelled majority of the conference calls, awaiting upgrade of SimTk.org and launch of Open Knee(s) cloud computing beta release. For those which were held, please refer to meeting minutes in Cleveland Clinic - Stanford University section of RecurringMeetings.
Detailed specifications on a prototype for web-based computing infrastructure can be found at the wiki page Revision as of November 17, 2015 or current version.
- Simulation software features
Cleveland Clinic and University of Utah teams continued to have monthly conference calls to discuss enhancements in FEBio, the simulation software used in Open Knee(s). Please refer to meeting minutes in Cleveland Clinic - University of Utah section of RecurringMeetings.
Detailed specifications for desired features can be found at the wiki page Revision as of November 17, 2015 or current version.
- Studies for implementing and testing in situ ligament strain feature has completed. A manuscript was submitted to the Journal of the Mechanical Behaviour of Biomedical Materials for publication.
- Rigid body movement related features, e.g. definition of cylindrical joints to represent anatomical joint coordinate systems and movement conventions, were implemented and ready for continued testing.
- Future efforts will likely build upon the implemented set definitions feature to allow definition of parts/components for assembly of models.
- Overall, FEBio team has implemented many critical features for modeling and simulation of musculoskeletal joints. Additional work will likely focus on testing and evaluation of these features and implementation of convenience features to facilitate modeling workflow.
- Experimentation
- Joint level testing continued during the progress period:
Joint imaging and joint mechanics testing were completed on oks008, see Revision as of November 17, 2015.
A new specimen was acquired - oks009, see Revision as of November 17, 2015.
- Additional specimens were ordered to increase the diversity of Open Knee(s) (by adding specimens from mid-age donors) and augment data from young knees (by additional specimens).
- Tissue testing has not started as the team decided to confirm and expand upon tissue testing capabilities:
- New load transducers with higher resolutions were purchased to increase accuracy of force measurements for soft specimens, e.g. meniscus under compression.
An optical tissue thickness measurement system was developed; see the wiki page, Revision as of November 17, 2015 or current version. The system is currently evaluated.
A detailed protocol evaluation plan was developed; see the wiki page, Revision as of November 17, 2015 or current version.
- Testing of tissue for Open Knee(s) - Generation 2 specimens will commence after in-depth evaluation of protocols.
- Joint level testing continued during the progress period:
Modeling & simulation
- Open Knee(s) - Generation 1 development continued.
- Pre- and post-processing scripts have been developed to change loading conditions of the Open Knee(s) - Generation 1 model and to analyze results to describe joint kinematics and to quantify convergence characteristics. These scripts, written in Python, can be found in the source code repository.
Open Knee(s) - Generation 1 model modifications mostly focused on improvement of meniscal constraints. During the summer internship program (see Community projects below), students implemented springs to represent the transverse ligament between menisci, the attachment of medial collateral ligament to medial meniscus, and the circumference of the menisci to tibia imitating capsular restraints. These modifications are available in the source code repository currently tested to evaluate their influence on convergence and on predicted joint kinematics/kinetics, see relevant wiki page Revision as of November 17, 2015 or current version.
- A case study on the mechanics of transverse ligament, in particular its influence on tibiofemoral joint mechanics and cartilage loading, has been started. Omar Gad is leading the study (see Community projects below).
- Open Knee(s) - Generation 2 development has started.
- Pre-processing scripts for the analysis of joint mechanics data were developed in Python (see Community projects below).
- Segmentation attempts were made by the students during the summer internship program (see Community projects below). These activities allowed evaluation of specifications for geometry generation and documented in relevant wiki pages.
- Detailed segmentation of oks001 has started. Ongoing work will be documented in the wiki and recorder in the source code repository.
- Open Knee(s) - Generation 1 development continued.
- Dissemination
As of November 17, 2015, Open Knee(s) provided 8 packages (1,834 total downloads, 950 unique downloads), see Open Knee(s) download page:
- oks001 version g2-s1-v0.2.0.20150825 (72 unique users as of November 17, 2015)
- oks002 version g2-s2-v0.2.0.20150916 (14 unique users as of November 17, 2015)
- oks003 version g2-s3-v0.2.0.20151013 (8 unique users as of November 17, 2015)
- oks004 version g2-s4-v0.2.0.20151029 (8 unique users as of November 17, 2015)
- oks006 version g2-s6-v0.2.0.20150915 (6 unique users as of November 17, 2015)
- oks007 version g2-s7-v0.2.0.20151021 (9 unique users as of November 17, 2015)
- oks008 version g2-s8-v0.2.0.20151021 (11 unique users as of November 17, 2015)
Open Knee - Generation 1 versions g1-s1-v1.1.0.391 & g1-s1-v1.0.1.202 (617 unique users as of November 17, 2015):
As of November 17, 2015, Open Knee(s) provided 5 developer, 3 user documentation in release form, see Open Knee(s) documents page.
- With a few exceptions (as requested by a collaborating team), all of the project website; wiki site, e.g. specifications, meeting minutes; and source code repository are publicly accessible.
As of November 17, 2015, Open Knee(s) website received 111,769 page hits in the past 180 days with 19,572 unique visitors, see Open Knee(s) project activity.
As of November 17, 2015, Open Knee(s) enabled 17 studies by external research teams, see Open Knee(s) publications page.
At this moment joint imaging and mechanical testing data are disseminated for seven knees: oks001, oks002, oks003, oks004, oks006, oks007 & oks008 (see Open Knee(s) download page).
- Community projects
There were no feedback from the community on specifications disseminated through documents for developers in Open Knee(s) documents page. These specifications are still open for feedback through Open Knee(s) public forums and public write discussion pages at the wiki.
- 2015 summer internship program was completed with participation by four students.
Omar Gad, from University of Toledo, worked on i) pre-processing of tibiofemoral joint kinematics and kinetics data, ii) implementation of transverse ligament representation in Open Knee(s) - Generation 1 model, and iii) exploration of image segmentation approaches. Omar was supported by NSF Research Experience for Undergraduates program at the Department of Biomedical Engineering, Cleveland Clinic. He presented his work in the Department of Biomedical Engineering and at the 2015 Research Experiences for Undergraduates Symposium in Arlington, VA. For the latter, Omar was also nominated to present his work in Posters on the Hill. He will continue modeling & simulation with the Open Knee(s) - Generation 1 model to explore the role of transverse ligament on joint and cartilage mechanics.
- Connor Lough, from Saint Louis University, worked on i) pre-processing of registration data to align coordinate systems of joint mechanical testing and imaging, ii) representation of capsular restraints of meniscus as springs in Open Knee(s) - Generation 1 model, and exploration of image segmentation approaches.
- Diana Suciu, from Case Western Reserve University, worked on i) pre-processing and analysis of patellofemoral joint contact pressure data, ii) representation of medial collateral ligament and medial meniscus attachment as springs in Open Knee(s) - Generation 1 model, and exploration of image segmentation approaches.
- Raghav Malik, from Mentor High School, worked on software development for automated measurement of tissue thickness using a camera-based system.
- All the contributions by summer students are available in the wiki and source code repository.
- Leonardo Ruggiero informed Ahmet that his post-doctoral fellowship application was not funded. Leonard had expressed interest in contributing to the development of next generation knee models as part of his post-doctoral fellowship application.
- Petri Tanska, from Rami Korhonen's laboratory at the University of Eastern Finland, applied for travel funds to visit Erdemir laboratory. His application was funded; he will most likely be visiting Cleveland Clinic during summer 2016.
- Publications
- A manuscript with University of Utah team was submitted to the Journal of the Mechanical Behaviour of Biomedical Materials on the implementation of in situ strain feature in FEBio.
- Multiple manuscripts are being prepared to document anatomical imaging and joint mechanics testing of the Open Knee(s) - Generation 2 specimens.
- Open Knee(s) team published articles in peer-reviewer journals:
- Erdemir, A. (in press) Open Knee: open source modeling and simulation in knee biomechanics, Journal of Knee Surgery.
- Open Knee(s) team presented work in various national and international conferences:
- Gad, O. M., Bennetts, C. J., Chokhandre, S. and Erdemir, A. Open Knee(s): the role of the transverse ligament in cartilage and menisci mechanics predicted by finite element analysis of the knee, Research Experiences for Undergraduates Symposium, October 25-26, 2015, Arlington, VA.
- Colbrunn, R. W., Bonner, T. F., Chokhandre, S. K., Bennetts, C. J., Halloran, J. and Erdemir, A. Open Knee(s): comprehensive patellofemoral joint testing for specimen-specific next generation knee models, 39th Annual Meeting of the American Society of Biomechanics, August 5-8, 2015, Columbus, OH.
- Bennetts, C., Chokhandre, S., Donnola, S., Flask, C., Bonner, T., Colbrunn, R. and Erdemir, A. Open Knee(s): magnetic resonance imaging for specimen-specific next generation knee models, Summer Biomechanics, Bioengineering, and Biotransport Conference, June 17-20, 2015, Snowbird, UT.
- Bonner, T. F., Colbrunn, R. W., Chokhandre, S., Bennetts, C. and Erdemir, A. Open Knee(s): comprehensive tibiofemoral joint testing for specimen-specific next generation knee models, Summer Biomechanics, Bioengineering, and Biotransport Conference, June 17-20, 2015, Snowbird, UT.
- Maas, S., Erdemir, A., Halloran, J. P. and Weiss, J. A. Computational framework for application of residual stress when the stress-free configuration is unknown , Summer Biomechanics, Bioengineering, and Biotransport Conference, June 17-20, 2015, Snowbird, UT.
- Erdemir A., Bennetts, C., Bonner, T., Chokhandre, S. and Colbrunn, R. Open Knee(s): founding data for next generation knee models, 2015 Biomedical Engineering Society / Food and Drug Administration Frontiers in Medical Devices Conference: Innovations in Modeling and Simulation, May 18-20, 2015, Washington, DC.
- Other
- Open Knee(s) has been promoted at Cleveland Clinic's philanthropy site for support:
- Ahmet promoted dissemination of joint mechanics data sets for Open Knee(s) - Generation 2 in Biomch-L forums:
Joint mechanics data for Open Knee(s) - Generation 2 specimens
- Ahmet presented Open Knee(s) project to collaborators:
- Erdemir, A., Open Knee(s): founding data for next generation knee models, Cleveland Clinic Orthopaedic Research Center Basic Science Day, June 5, 2015, Lerner Research Institute, Cleveland Clinic, Cleveland, OH.
Erdemir, A., Open Knee(s): open source modeling & simulation for in silico knee biomechanics, October 2, 2015, Department of Applied Physics, University of Eastern Finland, Kuopio, Finland.
Ahmet, along with Jason Halloran (Cleveland State University) had a conference call with Kevin Shelburne and Peter Laz (University of Denver), Carl Imhauser (Hospital for Special Surgery), and Thor Besier (Auckland Bioengineering Institute) to identify paths for synergy in modeling & simulation of the knee joint. The group will continue discussions on an ongoing basis.
Details of activities can be found in past meeting minutes of various teams at RecurringMeetings.
Plans for Next Progress Period (November 20, 2015 - May 2016)
- Launch and test usability of web based computation infrastructure (Stanford University)
- Explore the possibility to implement additional convenience related features in simulation software (University of Utah)
- Complete joint imaging and joint mechanics experimentation on oks009, oks010, oks011 (Cleveland Clinic)
- Start tissue mechanics testing of all specimens (Cleveland Clinic)
Continue development and review of modeling & simulation specifications (Cleveland Clinic & Community)
- Continue developing models for all specimens (Cleveland Clinic)
Plan 2016 summer internship program as part of community projects (Cleveland Clinic & Community)
Follow up with case studies on modeling & simulation (Cleveland Clinic & Community)
- Follow up publications for Open Knee(s) - Generation 2 data sets (Cleveland Clinic)
It should be noted that the timeline of activities has deviated from the original proposal, i.e., see the Roadmap and the proposed timeline of the proposal in GrantInformation/proposal.pdf.
Meeting Minutes
Date, Time, Means:
- November 19, 2015, 9:00 AM EST, conference call (AE,PS,CW,RK)
- November 19, 2015, 2:00 PM EST, conference call (AE,JA,MJ,TG)
Attendees:
- Ahmet Erdemir (Cleveland Clinic)
- Jack Andrish (Cleveland Clinic)
- Morgan Jones (Cleveland Clinic)
- Paul Saluan (Cleveland Clinic)
- Carl Winalski (Cleveland Clinic)
- Trent Guess (University of Missouri)
- Rami Korhonen (University of Eastern Finland)
Agenda:
- Progress update, see progress report at:
- Recap of previous meeting minutes, see meeting minutes at:
- Action items for following meeting.
- Other.
Immediate Action Items:
See notes for details.
All Advisory Board Members
- Start thinking potential projects for Open Knee(s) related grant applications.
Ahmet Erdemir
- Provide Carl Winalski copies of Open Knee(s) specimens' MRIs.
- Send Jack Andrish a copy of the Open Knee(s) - Generation 1 article.
- Share with Rami Korhonen ideas for Summer 2016 projects.
Carl Winalski
- Send Ahmet Erdemir literature on MRI scoring of knees.
Notes:
- Due to scheduling conflicts, a series of meetings were conducted to inform the Advisory Board about Open Knee(s) activities and get feedback.
- Progress update.
- Ahmet provided a summary of progress emphasizing the dissemination, summer internship program, and upcoming activities. An update on experimentation and modeling work was provided along with the progress of collaborators at the University of Utah and Stanford University. Published, submitted, and planned manuscripts were discussed. Discussions included many other topics, which were summarized in here.
- Two sets of conference calls were arranged. First one included Rami Korhonen, Carl Winalski, and Paul Saluan:
- Carl and Rami had a chance to meet and introduce themselves to each other. They have common connections through the Oulu research group.
- Carl identified an MRI scoring strategy, referred as MOKS. This scoring will help evaluate and report health status of Open Knee(s) specimens particularly from the perspective of osteoarthritis and it will be part of a data publication. Carl will send a relevant manuscript on MOKS to Ahmet. Carl also mentioned other scoring techniques that may be used. He will check with his colleagues for selection of the scoring method. He mentioned that given the number of knee specimens (7 to 12), it may be possible to utilize multiple methods and report. The team needs to provide Carl, the MRIs of Open Knee(s) specimens. Carl can download these from a website or the team can give him a copy in an external harddrive. Carl mentioned that he can upload these images to a research PACS system where they can be accessed easily within the Cleveland Clinic by radiologists.
- Ahmet, Rami, and Carl discussed the segmentation process. The group agreed that a fully automated segmentation, particularly for cartilage, is not necessarily possible. A reasonable path appears to be a semi-automatic system where manual corrections are done in a facilitated manner, e.g. through interactive tools. This is essentially the anticipated strategy by the Open Knee(s) team. Currently, Craig Bennetts, Open Knee(s) engineer, utilizes grow cut for automation of a gross initial segmentation followed by slice by slice manual corrections to delineate the tissue boundary appropriately. The process takes about half a day for a tissue segment. Rami's group has similar experience. Carl also mentioned a commonly used strategy to quantify variability of segmentation process when there is a lack of gold standard, i.e., multiple people segmenting and each segmentation compared to average.
- Ahmet mentioned Carl and Rami that about 15 research groups used Open Knee(s) or its data for modeling and simulation. He mentioned that it may be interesting to compile the results from these studies to see if they are similar.
- Rami and Ahmet talked about his student's (Petri Tanska) visit to Cleveland Clinic next summer. Petri will be a post-doc at that moment. Ideally, he will work on a project relevant to Rami's currently funded research activity, which is also synergistic with Ahmet's multiscale cartilage mechanics work. Nonetheless, Petri may be able to do some work relevant to Open Knee(s). Ahmet will send some ideas to Rami and in return, Rami will think about combining these to Petri's project.
- Ahmet and Rami also talked about experimentation and modeling and simulation of muscle's influence on knee mechanics.
- The second conference call included Jack Andrish, Morgan Jones, and Trent Guess:
- Ahmet noted that Open Knee(s) - Generation 1 model was published in a special issue of the Journal of Knee Surgery. The special issue was organized by Trent Guess. Per Ahmet's request, Trent described the special issue to Morgan and Jack. The issue brought together experimentation and modeling studies from prominent knee researchers. In general, the journal commonly focuses on publication of surgical techniques for management of knee problems and the audience is predominantly clinicians. Jack asked for the article information to be able to access it. Ahmet will e-mail him the article information.
Ahmet mentioned future plans for Open Knee(s) in relation to submissions grants for renewal, e.g. continued development of Open Knee(s) and other synergistic projects that utilize Open Knee(s) for scientific research and clinical translation. Ahmet asked Morgan and Jack how Open Knee(s) can be integrated to orthopaedic residents training or research, acknowledging that a lot needs to be done first to streamline the modeling & simulation workflow. Morgan mentioned that understanding how interventions work for different pathologies and for different knees is a key aspect. Jack emphasized that similar concerns had been raised in early modeling studies focusing on clinical translation. In this regard computational modeling may provide the capacity to understand robustness of the operation, i.e. to see if it will have very different results or not. Ahmet noted that one possibility is to change an existing model to simulation different patient populations. The other possibility is to build a set of specimen-specific models including both anatomical and mechanical properties from the same specimen. Open Knee(s) fit in the latter category and may serve as a virtual patient population
Morgan mentioned motivation for prospective modeling & simulation study, which may help understand appropriateness of X-ray imaging strategies to assess joint space. These studies may help increase the accuracy of diagnosis and prognosis of osteoarthritis and anterior cruciate ligament deficiency from X-ray imaging. Role of weight bearing and joint positioning may be explored systematically with the models.
- Jack wondered how long it would take to validate the models such that clinicians can utilize them. Ahmet first talked about a stringent validation scheme based on specimen-specific models being able to predict specimen-specific response. This is possible with Open Knee(s) data, which provides comprehensive information including specimen-specific anatomical and tissue properties, and specimen-specific joint response. Nonetheless, he noted that this will likely require multiple modifications in the models to iteratively improve their capacity to represent measured response. He also noted that clinical translation may not necessarily require this stringent validation process as long as the model indicates the correct path for decision making. This was confirmed by Jack.
- Trent emphasized the lack of data on properties of tissues that stabilize the menisci. Ahmet reminded him that the group dissects as much tissue as possible for prospective quantification of specimen-specific properties. He also noted the limited number of studies which actually collected mechanics data for characterization of tissue, e.g. anterior cruciate ligament.
- Ahmet described his plans to both groups on publishing anatomical imaging and joint mechanics data by submitting manuscripts to Scientific Data, a journal specifically designed for publishing data collection strategies and to disseminate data. In response to Rami, Ahmet clarified the difference between Scientific Data and Scientific Reports, which are both journals of Nature Publishing Group. He also described the concept of data journals to Morgan Jones and others in the latter conference call. It may be possible to include the physicians in these publications, particularly to provide a clinical perspective for potential use of disseminated data.
- Recap of previous meeting minutes.
- The discussions mainly focused on progress (see item above).
- Action items for following meeting.
- See Immediate Action Items above.
- Other.
- Refer to notes above for the agenda item on progress update.