Recurring Meeting of the Advisory Board
Date(s): October 28 - November 1, 2013
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.
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.
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)
- September 16, 2013 - October 28, 2013
Development Team during Progress Period
Cleveland Clinic Core Team. Craig Bennetts, Tara Bonner, Snehal Chokhandre, Robb Colbrunn, Ahmet Erdemir, Jason Halloran
Stanford University. Scott Delp, Joy Ku, Henry Kwong
University of Utah. Ben Ellis, Jeff Weiss, Steve Maas
Community. Scott Sibole
See https://simtk.org/project/xml/team.xml?group_id=485 for full details on the project team.
Goals of Progress Period
- Organize workload of Cleveland Clinic, Stanford University, and University of Utah teams
- Start recurring meetings with team members
- Establish web based collaboration infrastructure
- Start development of web based computation infrastructure
- Start development of simulation software improvements
- Start development and review of experimentation specifications
For more details, see the proposed timeline of the proposal in GrantInformation/proposal.pdf.
Activities of Progress Period
As part of a specifications task entitled Roadmap, a wiki page was created; see Revision as of October 27, 2013 or current version. The document provides centralized access to descriptions of infrastructure, specifications, and development milestones for Open Knee(s) utilities and models.
First set of meetings with Cleveland Clinic Core Team, between Cleveland Clinic & Stanford University, and between Cleveland Clinic & University of Utah were conducted to distribute project workload, clarify expectations, and pinpoint deliverables.
- Recurring meetings
- Web based collaboration infrastructure
The project site at https://simtk.org/home/openknee provides the web based collaboration infrastructure for development and dissemination. Please refer to InstructionsForProjectSite to learn specific components of the web site.
The wiki at http://wiki.simtk.org/openknee provides the capacity for collaborative development of scientific content, e.g. specifications. Please refer to InstructionsForWiki to get accustomed to using the wiki.
The source code repository located at https://simtk.org/svn/openknee provides a version control system and the means for collaborative development of software, data analysis code, and models. Please refer to InstructionsForSourceCodeRepository to learn using this system.
Public has read access to all components of the web based collaboration infrastructure. The activity is an open development activity, also see Licensing.
The project site, wiki, and source code repository was updated to move the previous Open Knee work as Open Knee - Generation 1.
- Web based computation infrastructure
Cleveland Clinic and Stanford University had a conference call to discuss web based computation infrastructure. Please refer to meeting minutes.
A specifications task entitled Test workflow for cloud computing prototype was created to provide a simple test problem on the wiki, in order to support development of a cloud computing prototype.
- Simulation software improvements
As part of specifications task entitled Febio feature requests, Cleveland Clinic team provided prioritization of desired FEBio features and a test problem in the wiki; see Revision as of October 27, 2013 or current version.
Details of FEBio, simulation software for finite element analysis, can be found in Infrastructure/SimulationSoftware.
- Experimentation specifications
Various specifications tasks were started and corresponding wiki pages have been created to document operation procedures to conduct experimentation on specimens. These pages are aimed to guide anyone to follow up the steps to reach the targeted outcome of a given experimentation procedure, in a nutshell to collect specimen-specific anatomical and mechanical data. The specifications wiki page lists all these along with an illustration of the overall experimentation workflow, see Revision as of October 27, 2013 or current version.
A high priority specification is related to specimens in order to start acquisition of knee samples. A related wiki page is complete; see Revision as of October 27, 2013 or current version. An anticipated difficulty in this procedure is the potentially limited access to osteoarthritic knee specimens.
Before conducting anatomical imaging and mechanical testing, specimens need to be prepared appropriately. Relevant information has been accumulated in wiki pages related to preparation (Revision as of October 27, 2013 or current version) and registration (Revision as of October 27, 2013 or current version). Anticipated difficulties in these procedures are i) potential redesign of brass components to minimize imaging artifacts, ii) development of new holding fixtures to transport specimens, and iii) redesign of registration markers for femur and tibia.
Anatomical imaging, e.g. MRI, will lead into geometric representation of the knee joint. The Cleveland Clinic team has established collaborations with imaging facilities at the University Hospitals. A wiki page is in progress to identify a suitable imaging protocol based on our previous experiences, see Revision as of October 27, 2013 or current version. The Cleveland Clinic team and the imaging facility will explore different protocols to facilitate segmentation of tissues within the knee.
Primary and secondary mechanical testing conditions to characterize tibiofemoral and patellofemoral joint responses were decided upon. The Cleveland Clinic team, supported by the BioRobotics Core previously devised approaches for such testing. Detailed specifications are under development in a wiki page, see Revision as of October 27, 2013 or current version.
Tissue testing will provide constitutive relationships for ligaments, tendons, meniscus, and cartilage for development of computational models. The Cleveland Clinic team, supported by the BioRobotics Core previously devised approaches for such testing. Detailed specifications on the extent of tissue samples and testing protocols are under development in a wiki page, see Revision as of October 27, 2013 or current version. Tissue testing can be costly due to large number of samples and long testing durations for appropriate characterization. Alternative strategies, such as acquisition of testing equipment dedicated to the project, are under consideration.
Open Knee was presented at the ASME/FDA 2013 1st Annual Frontiers in Medical Devices: Applications of Computer Modeling and Simulation, September 11-13, 2013, Washington, DC, see abstract. An abridged version of this abstract was submitted to Journal of Medical Devices as one page article for publication.
For publication of previous work on Open Knee, various publication tasks were created. An outline and a draft of Open Knee - Generation 1 manuscript can be found in source code repository.
For a complete list of various tasks (finished or in progress), please refer to https://simtk.org/pm/?group_id=485.
Plans for Next Progress Period (October 29, 2013 - May 2014)
- Complete a prototype of web based computation infrastructure (Stanford University)
- Complete implementation of high priority features in simulation software (University of Utah)
- Complete experimentation (specifications and data collection) for Specimen 001 (Cleveland Clinic)
- Disseminate data from Specimen 001 (Cleveland Clinic)
Start development and review of modeling specifications (Cleveland Clinic & Community)
Start development and review of simulation specifications (Cleveland Clinic & Community)
Launch community projects program (reviews, internships, and collaborations) (Cleveland Clinic & Community)
- Publish previous work on Open Knee - Generation 1 (Cleveland Clinic)
For more details, see the proposed timeline of the proposal in GrantInformation/proposal.pdf.
Date, Time, Means:
- October 28, 2013, 7:00 AM EST, in person meeting (AE,PS)
- October 29, 2013, 8:00 AM EST, in person meeting (AE,JH,CW)
- Ocbober 30, 2013, 2:00 PM EST, conference call (AE,JH, YD,TG,RK)
- November 1, 2013, 9:00 AM EST, in person meeting (AE,JA,MJ)
- Ahmet Erdemir (Cleveland Clinic)
- Jason Halloran (Cleveland Clinic)
- Jack Andrish (Cleveland Clinic)
- Morgan Jones (Cleveland Clinic)
- Paul Saluan (Cleveland Clinic)
- Carl Winalski (Cleveland Clinic)
- Yasin Dhaher (Northwestern University)
- Trent Guess (University of Missouri)
- Rami Korhonen (University of Eastern Finland)
- Project description
- Expectations from Advisory Board
- Progress update
- Scheduling of biannual meetings
- Action items for following meeting
Immediate Action Items:
See notes for details.
All Advisory Board Members
Get an account at https://simtk.org for Ahmet Erdemir to add them as team members with write access to project site.
- Get accustomed to the project site.
- Comment on current progress and planned activities in case some issues were overlooked during the meeting.
- Spread the word about Open Knee(s).
- Update specifications on specimens to acquire knees with moderate (not severe) osteoarthritis and to ask for x-rays under axial loading for osteoarthritis grading.
- Arrange meeting with Chris Flask of University Hospitals and Carl Winalski to explore imaging modalities.
- Arrange meeting with Jack Andrish, Jason Halloran, and Paul Saluan to discuss MPFL work.
- Explore the possibility of a community project on MRI segmentation reproducibility.
- Identify investigators of knee experimentation and reach out.
- Reach out Qmetrics to explore synergistic work on segmentation.
- Due to scheduling conflicts, a series of meetings were conducted to inform the Advisory Board about Open Knee(s) activities and get feedback.
- Project description.
- Ahmet iterated the specific aims of the project. He summarized the organization between (and roles of) Cleveland Clinic, Stanford University, and University of Utah teams and the Advisory Board and the community. Public nature of the project and the open development approach were emphasized. Budget cuts in the project and shortened first year were noted.
- The project's minimum requirements (primary conditions for exprimentation and modeling and simulation) are proposed in the grant application. There may be possibilities to explore secondary conditions if timing and resources allow. There are also project branching possibilities based on ideas emerging from Open Knee(s), synergistic yet with different focus. The latter can be accomplished through spinning off separate projects and seeking for additional funding.
- Expectations from Advisory Board.
- The expected role of Advisory Board members were summarized.
- Biannual review of progress report.
- Biannual meeting with Ahmet Erdemir to evaluate progress and provide input for upcoming activities.
- Intermittent, possibly individual, interactions with team members to consult on relevant specific activities to accomplish components of Open Knee(s).
- Paul Saluan noted that additional individual meetings (maybe quarterly) with Advisory Board members may be useful.
- The expected role of Advisory Board members were summarized.
- Progress update.
- The progress report was summarized and relevant individual items were discussed in detail. No issues were raised in terms of the level of current and planned activities.
- Target specimen population and specimen acquisition was a major topic of discussions.
- Many Advisory Board members raised the suitability of an Open Knee(s) specimen to represent the target population. Ahmet Erdemir emphasized that logistically this is not possible to warrant before testing. Specimen acquisition can ensure age, gender, and osteoarthritis level requirements. As the experimentation goes on, one can utilize imaging and mechanical testing data to see how a given specimen fits to a certain population.
- Paul Saluan runs the surgical skills laboratory at the Cleveland Clinic. Specimens may be acquired through that channel. If necessary, one-to-one specimen exchange may be possible to allow Open Knee(s) team access to specimens with desired specifications. Specimens in Paul Saluan's other scientific studies may also be used for Open Knee(s).
- Morgan Jones and Jack Andrish noted that severe osteoarthritis may not be something that Open Knee(s) would like to aim for. Such knees will likely go through total knee replacement anyway. Knees with moderate osteoarthritis, as indicated by x-ray, will be adequate. Specimen providers should be asked to acquire x-rays with the specimens loaded axially.
- Carl Winalski was concerned about knee storage. The knees (and tissues) may need to go through multiple cycles of freeze and thaw. Ahmet described that this is necessary due to logistics of experimentation at many levels but it will be kept to a minimum.
- Some Advisory Board members noted additional tissues of interest, which may need to be included in experimentation and modeling.
- Per Paul Saluan, the illiotibial tract (IT band) may need to be explored. The IT band has importance for knee stabilization. It may be possible to include secondary testing conditions to joint and tissue experimentation to quantify mechanics of the IT band.
- Advisory Board members provided feedback on experimentation on joint mechanics, particularly the use of robotics for testing.
- Jack Andrish asked for clarification of the capabilities of robotics testing. Ahmet Erdemir responded that the robot can be used in an adaptive fashion, i.e., joint movements can be measured as a function of joint loading before and after a change in knee condition. The robot allows at desired degrees of freedom by ensuring zero loads (forces or moments) at that direction.
- Morgan Jones advised to conduct experiments for physiological loading of daily activities and for testing pathological conditions, e.g. ligament release, meniscal interventions, etc. Knowledge of joint mechanics under such conditions may strengthen validity of prospective models, particularly from a clinical perspective. For example, it can shown that the simulations predict both the healthy and pathological state. Such testing scenarios may be added as secondary conditions, or possibly as a branching project.
- Imaging of cadaver specimens was discussed with Advisory Board members.
- Carl Winalski has concerns about dissection of specimens before imaging. The air surrounding the tissue (instead of a full tissue envelope) may deter image quality.
- CT was proposed by Carl Winalski as an additional imaging modality, particularly to acquire information about bone. CT arthrogram may allow imaging of tissues, e.g. cartilage as well. However, injection of a contrast agent may inflate the capsule and deform the tissues.
- Carl Winalski has been working with the imaging facility at the University Hospitals, and with Chris Flask who is directing this facility. The Cleveland Clinic team will be meeting Chris Flask about imaging and they will inform Carl about the outcome. Carl also has connections with researchers in University of Eastern Finland and with investigators in Brigham and Women's Hospital (developers of Slicer). He may also have access to MR images of knees in case the project needs.
- Carl Winalski noted that some companies may be interested in contributing, particularly for (semi-)automated image segmentation. Such arrangements may be beneficial to both parties; Open Knee(s) having a solution for segmentation and companies having access to MR images of knees and visibility through their work with Open Knee(s). He specifically mentioned Saraa Totterman from Qmetrics.
- Yasin Dhaher emphasized the need for powerful (semi-)automated methods for segmentation. Supported by appropriate imaging modalities, Open Knee(s) team may invest in the development of reliable segmentation processes during the modeling phase.
- Scheduling of biannual meetings.
- The Advisory Board agreed on the scheduling of biannual meetings to evaluate progress; in late October - early November, and in late April - early May.
- As indicated by the clinicians of the Advisory Board, advanced notice may be necessary to schedule group meetings, e.g., two months before the meeting.
- Paul Saluan can also meet quarterly, for example by arranging early morning meetings at Yours Truly.
- Action items for following meeting.
- Each Advisory Board member were asked to get an account in simtk.org. Ahmet will add them as team members to give them write access to the project site.
- The Advisory Board members will familiarize themselves with the project site. They will provide feedback on the ease navigation of the site.
- The Advisory Board members were also encouraged to comment on current progress and planned activities in case they did not raise such issues during these meetings.
- Ahmet informed the members from the Cleveland Clinic that a desk space was made available in the Biomechanics Laboratory of the Department of Biomedical Engineering.
- Open Knee(s) may be useful to branch into experimentation, and modeling and simulation studies for individual clinical and research directions of the Advisory Board members.
- Paul Saluan has interests in growth plate, MPFL, ACL reconstructions.
- Jack Andrish is interested in patellofemoral joint problems.
- Morgan Jones is interested in models to explore progress of pathological conditions. He is wondering about the possibility to develop a database of models from publicly available MRI, e.g. Osteoarthritis Initiative, to explore mechanics of the knee as disease progress. This may be framed in a simplified manner focusing on a target region of the knee.
- Carl Winalski has interests in quantitative imaging of active and passive components of the knee, e.g. imaging of muscles.
- Yasin Dhaher has interests in rehabilitation interventions following neurological and musculoskeletal disabilities.
- Trent Guess works in physical therapy and orthopaedics with knee joint work bridging body level mechanics with joint and tissue mechanics.
- Rami Korhonen works in multiscale mechanics of cartilage and has interests in imaging modalities to characterize microstructure of cartilage, e.g. T2 mapping for collagen orientation.
- Imaging interests of Carl Winalski, Chris Flask of the imaging facility at the University Hospitals, and Rami Korhonen may result in branching projects for development and evaluation of tissue imaging modalities. If clinical imaging, e.g. using 3T machines, can achieve high resolution, with the possibility of acquiring fiber level information and extracting mechanical properties, in vivo applicability for patient-specific analysis may be possible.
- As brought up by Yasin Dhaher and supported by Trent Guess and Rami Korhonen, a reproducibility analysis to quantify uncertainty in segmentation of MR images may be branched from Open Knee(s). Yasin has MRI and segmentation from 6 female and ~6-7 male knees and has already conducted preliminary work in this area. Trent has already disseminated MRI and geometry data for 3 knees. Combined with MRI of Open Knee(s), a community driven project can be devised. This will be a good contribution to literature and will fit in community outreach of Open Knee(s).
- Jack Andrish wondered whether open nature of the project will affect scholarly publications, i.e. will the journals consider the work as previously published? Ahmet described that the public information at the project site is still not peer reviewed in the traditional sense and therefore may not necessarily be considered as a previous scholarly publication. He also noted that many scientific journals allow investigators to provide pre-print versions of their work. Nonetheless, management of copyright may be necessary to accommodate the use of information for scholarly publishing.
- As the project is truly open, numerous possibilities to get feedback from the community exist: wiki, e-mails, forums. Jack Andrish raised concerns about potential Brownian movement and wondered how requests should be kept seriously. Ahmet responded that this will likely be something for the Advisory Board to manage and prioritize.
Carl Winalski mentioned various pathways for community reach out; a video channel, e.g. through YouTube, raising additional funds through mechanisms like Kickstarter, and scientific exhibits, posters, papers in AAOS, ORS, PNAS, etc.
- Yasin Dhaher emphasized the importance of disseminating the lessons learned throughout the project, e.g. for segmentation, meshing, etc., to provide the know-how to the next generation of researchers. Open Knee(s) already does this by public development and display of specifications essentially serve for this purpose.
- Yasin Dhaher also asked about engagement with the Interagency Modeling and Analysis Group (IMAG) and Multiscale Modeling (MSM) Consortium. Ahmet has been active in these communities and made Open Knee(s) visible within that group.
- Jason Halloran asked to add a knee experimentation expert to the Advisory Board.
- All members of the Advisory Board were encouraged to spread the word about Open Knee(s); to pass the project site information to others that may have an interest.