Recurring Meeting of Cleveland Clinic Core Team

Date: February 9, 2016

Time: 10:30 AM EST

Means: In person meeting


  1. Ahmet Erdemir
  2. Craig Bennetts
  3. Snehal Chokhandre
  4. Robb Colbrunn
  5. Tara Bonner
  6. Jason Halloran (Cleveland State University)
  7. Will Zaylor (Cleveland State University)


  1. Discuss immediate action items from the last meeting.
  2. Continue evaluation of drafts for 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 described tricks for overlaying multiple different MRIs in Slicer in detail in the meeting minutes, i.e. using coronal and axial ligament image sets for segmentation with the cartilage MRI as the master volume. He still needs to port these details to the image segmentation wiki.
    • Ahmet has continued segmenting the MCL. He seemed to differentiate superficial and deep layers. Yet, geometric modeling of the ligament would likely involve some art.
    • Craig worked with Diana Suciu's script to compare contact pressure metrics against those calculated by Robb. Robb exported Tekscan binary file to a csv file. For each time frame he calculated the metrics, i.e. peak pressure, contact area, etc. In following, he averaged the metrics to get a value for a static loading trial. Ahmet mentioned that Diana's code should average the contact pressure distribution through time to get a representative pressure distribution for the static loading trial. Then, the metrics are calculated. It is possible that peak pressure and contact area values calculated with these different strategies may differ. Craig noted that there is orders of magnitude differences between the metrics calculated by varying methods. This may be related to a unit mismatch. Craig and Ahmet will meet to go over the script for pressure data analysis.
    • Craig, Robb and Tara met to coordinate overlapping sections of manuscripts. They determined all cross-references, tables, and which manuscript should contain detailed information.
    • Craig discussed the geometry generation workflow he has devised. Labeled as LVTIT, he uses Slicer for Laplacian smoothing and Meshlab for VCG reconstruction, Taubin smoothing, iso-parameterization, Taubin smoothing again. This allows moving from segmented volumes to STL surfaces. Craig and Ahmet also successfully meshed the femur cartilage using tetrahedral elements in Salome. They have also discussed various node and element selection strategies for generating sets. Snehal will look into geometry generation for oks001. Ahmet will start reviewing the specifications wiki page on geometry generation.
    • Snehal provided an image of a tensile sample from cartilage. The tissue thickness appears to be variable. Getting tensile samples from the superficial zone of the cartilage is challenging due to curvature of the surface and the cutting strategy. Snehal is currently using vibratome, which can cut thicker samples. Vibratome requires one to glue the sample. Snehal avoids gluing the superficial surface. However, the curvature of the surface may result in non-uniform samples. Another alternative is to use cryostat to shave both sides of the tissue to get a uniform sample. Yet, this will require an additional freeze-thaw cycle to the specimen. It seems like the bottleneck in tissue testing is the tensile sample preparation for cartilage.
    • Snehal demonstrated the output file from the optical tissue thickness measurement system. The group discussed effective ways of using XML features, i.e. naming convention, tags, and output formatting. Snehal and Craig will go over these. They will also evaluate the reproducibility of using OTMS script.
    • Snehal implemented zero force displacement identification to the tissue testing data analysis script. Ahmet requested plotting of stress-strain curves. The script also evaluates if the actual rates match the desired rates.
    • Ahmet asked if we would be receiving new knee specimens. Snehal will check.
    • Jason has started working on the background for patellofemoral joint testing.
  2. Continue evaluation of drafts for data manuscripts.
    • All manuscripts are evolving. See discussions above on immediate action items from previous meeting.
  3. Decide immediate action items for the next meeting.
    • See Immediate Action Items above.
  4. Other.
    • Ahmet mentioned the knee segmentation and registration toolkit (KSRT). This software tool is a multi-atlas based bone and cartilage segmentation tool on knee MRIs. It may be useful for large scale segmentation problems, i.e., using data from Osteoarthritis Initiative. Ahmet also mentioned the knee segmentation challenge - SKI10. The outcome of this challenge may be beneficial to Open Knee(s).

RecurringMeetings/2016-02-09 (last edited 2016-05-04 22:09:48 by localhost)