Recurring Meeting of Cleveland Clinic Core Team

Date: February 2, 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. Will Zaylor (Cleveland State University)


  1. Discuss immediate action items from the last meeting.
  2. Continue evaluation of drafts for data manuscripts.
  3. Discuss tissue mechanical testing protocol evaluation.
  4. Decide immediate action items for the next meeting.
  5. Other.

Immediate Action Items:

Ongoing Action Items:



  1. Discuss immediate action items from the last meeting.
    • Ahmet has been working on the segmentation of oks001 MCL. He was able to identify sueprficial and deep layers of the MCL and noted that generation of the geometry requires some art. He committed a rough segmentation in the repository.
    • Ahmet also learned a few tricks in Slicer that can facilitate segmentation.
      • Different MRIs can be displayed in different windows, e.g. those that are ligament specific and cartilage specific. When linked, Slicer uses interpolation for coupled viewing of the image sets that are already spatially aligned. This feature may be useful to generate images of zoomed-in regions to see how a given tissue type looks like in different imaging sequences. This feature also helps segmentation, i.e. one can use one image set as the master volume but segment in the other allowing high resolution segmentation volume from images with lower resolution.
      • Ahmet provided some tips using manual segmentation tools. The pencil works to draw straight lines, e.g. by simply clicking. The eraser changes the behaviour of the tool, e.g. brush or pencil, to erase rather than draw.
      • Ahmet will document the tips for the use of Slicer in image segmentation specifications.
    • Craig updated manual segmentation on wiki. He clarified Slicer STL output to emphasize no smoothing and no decimation. He is documenting smoothing and decimation in Slicer in the specifications page for geometry generation. He has been exploring geometry generation workflow using oks001 segmentations.
    • Snehal showed the script for interactive optical thickness measurement system (OTMS). She discussed the workflow including trade-offs to different approaches. The group provided recommendations for the GUI to facilitate interactive point-pair picking. The output file format was discussed and Ahmet recommended to use XML. She will continue working on the script to finalize it for use. Other features can be added on an ongoing basis.
    • Snehal has not worked on tissue testing analysis script. She had a question about the motivation to find zero displacement. Ahmet noted that this essentially gets rid of slack length and allows appropriate calculation of average modulus.
    • Jason did not attend the meeting. He has not provided the background on patellofemoral joint testing manuscript.
  2. Continue evaluation of drafts for data manuscripts.
    • Craig started modifying the anatomical imaging manuscript. He added a table for 'Data Records'. The group also discussed file naming in the Downloads section of Open Knee(s) project site.
    • Robb, Tara and Craig scheduled a meeting to go over overlapping parts of the manuscripts. Robb and Craig coordinated analysis of pressure sensor data to use Diana Suicu's script.
    • Tara will look at patellofemoral joint testing when the first draft is done.
    • Tara has been working on the technical validation section of tibiofemoral joint testing manuscript:
      • She used a LabView function for sphere fit to output centers and radii of registration markers. All radius values were about 10 mm as expected. She used the centers of the registration markers to calculate distances in between. This information can be used to compare similar calculations done using anatomical imaging data. For each bone, it is anticipated that these distances, as measured in the tibiofemoral joint testing and as extracted from MRI, would be similar.

      • Tara provided a table indicating maximum RMS error in loads during laxity testing of each knee, at each flexion angle and testing condition. oks004 and oks007 have higher errors than others. Ahmet emphasized that to be able to call a trial as "laxity test", off-axis loads should be close to zero. In that sense, for off-axis loading. the absolute RMS error will ideally be zero. For the dominant axis, a relative RMS error can be reported, normalized by the maximum load applied. Tara, Ahmet and Will will meet to go over Python scripts for laxity analysis from SimVitro tdms files, which may help streamline these analysis.

  3. Discuss tissue mechanical testing protocol evaluation.
    • See relevant discussion in the agenda item above on previous meeting's immediate action items.
  4. Decide immediate action items for the next meeting.
    • See Immediate Action Items above.
  5. Other.
    • None noted.

RecurringMeetings/2016-02-02 (last edited 2016-05-04 22:09:50 by localhost)