Recurring Meeting of Cleveland Clinic Core Team

Date: January 19, 2016

Time: 10:30 AM EST

Means: In person meeting


  1. Ahmet Erdemir
  2. Craig Bennetts
  3. Robb Colbrunn
  4. Tara Bonner


  1. Discuss immediate action items from the last meeting.
  2. Discuss first drafts of data manuscripts.
  3. Decide immediate action items for the next meeting.
  4. Other.

Immediate Action Items:

Ongoing Action Items:



  1. Discuss immediate action items from the last meeting.
    • Ahmet worked with Slicer to familiarize loading image sets and segmentations and to start segmenting the medial collateral ligament (MCL). Based on his experience, he recommended Craig to briefly summarize tools available for manual segmentation in the specifications page. In addition, he mentioned surface (STL) output options that need to be documented in the specifications. Ahmet also showed some FreeCAD features that may be useful to work with STL surfaces, e.g. manual trimming of triangular surface meshes, sketching on planes that are arbitrarily oriented, etc.
    • Craig added documentation for registration marker segmentation. He still needs to evaluate registration marker segmentations done by summer students. Craig and Ahmet previously discussed approaches for segmentation and modeling workflows and how best to use available resources and time. Ahmet noted that a team member (or a group) will likely focus on getting the whole modeling workflow completed on one knee, while the other members can focus on the analysis of other knees based on matured specifications, e.g. segmentation.
    • Snehal was out of town for most of the week. The group will catch up with her in the following week.
    • Jason has not provided background for patellofemoral joint testing manuscript. The group will follow up with him next week.
    • Robb did some work on the patellofemoral joint manuscript and he is part way through reviewing the manuscript on imaging.
    • Tara needs to look at the patellofemoral joint testing manuscript to help Robb. She is planning to add some RMS error calculations to the tibiofemoral joint testing manuscript. She will work with Snehal to find literature on tibiofemoral joint laxity data to incorporate into the manuscript.
  2. Discuss first drafts of data manuscripts.
    • Ahmet took a look at the imaging manuscript. He also reviewed the format and content description of Scientific Data articles. In following he came up with recommendations to fill-in different sections of the manuscript:
      • The Data Records section should include a table listing all specimens with the relevant files for each specimen. This fits into data citation request of the journal. Ahmet also mentioned that we may need to create a package that represents the data in a fixed, e.g. static, form as submitted to the journal. This package can be uploaded to Dryad, where it can get a DOI and can be referred in the journal as the data at the time of submission. He also noted that the data can be simultaneously provided in This serves as a mirror site but also allows expansion of data with additional specimens or with derivative data obtained after data analysis.

      • It is likely that grading of the knees for osteoarthritis will be part of the Methods section. The Technical Validation section can include a clinician, e.g. Carl Winalski, verifying the MRI. This section may also include experiments and analysis to support technical quality of data. It may be useful to consult Chris Flask to ask about MRI calibration and its documentation in relation to the manuscript. We can also compare different MRIs for visual delineation of the boundaries of the same tissue, i.e. by zooming in to the region of interest.
      • The Usage Notes section can summarize the segmentation work done on oks001, referring to the software used and to the relevant specifications at the wiki site.
    • Ahmet also provided other comments to improve the manuscript
      • The abstract should include the number of specimens, different types of MRI designed for segmentation and modeling. He emphasized that per journal's guidelines this section should not include any new scientific findings.
      • For the background, the journal recommends a figure about the workflow to obtain the data. Craig will think about it.
      • In the methods section, different types of spherical registration markers need to be described along with the identification of specimens that use these.
      • Ahmet reminded the group that all MRI data sets are in same coordinate system. This has important implications for the modeling workflow and need to be emphasized in the manuscript, e.g. segmentation from one MRI data set overlaid on another.
      • Sphere fits to registration markers may validate dimensions obtained from images against their design dimensions. Distances between registration markers placed on the same bone can also be used to evaluate rigidity of the assembly at the MRI and during joint testing.
    • Craig will follow up with the recommendations listed above.
  3. Decide immediate action items for the next meeting.
    • See Immediate Action Items above.
  4. Other.
    • Ahmet noted that our activities are at an inflection point in between experimentation and modeling. He mentioned that the Open Knee(s) funding will end by the end of May 2017. He discussed with the group potential proposals he will be submitting. Ideally, a renewal application need to be submitted by June 2016, i.e. if funded, this will ensure continuity. Yet, he suspects that he will submit a renewal application on February 2017. He will likely be submitting a proposal for structured and elaborate evaluation of Open Knee(s) models. Ahmet and Jason are also interacting with other knee researchers to submit a proposal for the explorations of data exchange and model reproducibility. He also mentioned knee data provided by other researchers including those data sets pros an cons when compared to Open Knee(s).

RecurringMeetings/2016-01-19 (last edited 2016-05-04 22:09:50 by localhost)