Recurring Meeting of Cleveland Clinic Core Team

Date: February 2, 2016

Time: 10:30 AM EST

Means: In person meeting

Attendees:

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

Agenda:

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:

• Ahmet
  • Work on segmentation of MCL of oks001.
  • Document manual segmentation and image overlaying tricks to facilitate workflow.
• Craig
  • Continue working on recommendations discussed in the meeting for the imaging manuscript.
  • Explore and document geometry generation workflow.
• Snehal
  • Update tissue testing analysis script to identify zero force displacement (next two weeks).
  • Expand tissue testing evaluation documentation to provide quantitative information for conclusions.
  • Continue working on tissue testing evaluation for sample thickness measurements.
• Jason
  • Provide the background for the patellofemoral joint testing manuscript.
• Robb
  • Complete the first draft of the patellofemoral joint testing manuscript.
  • Work with Craig to get patellofemoral joint contact pressures analyzed.
• Tara
  • Continue working on tables for the tibiofemoral joint testing manuscript.

• Robb, Tara, & Craig

  • Meet to work on overlapping content of data manuscripts.

• Tara, Ahmet, & Will

  • Meet to go over student Python scripts for analysis of SimVitro TDMS and state configuration files.

• Will
  • Put tdmsParser in Open Knee(s) source code repository.

Ongoing Action Items:

DEADLINE FOR SECOND DRAFT DATA PAPERS IS APRIL 1, 2016

• Ahmet
  • Prepare flowcharts to describe data flow for pre-processing of joint kinematics/kinetics data.
• Craig
  • Anatomical imaging manuscript.
  • Large-scale analysis of simulation parameters for convergence.
• Snehal
  • Add citations and summaries to tissue data papers to the wiki for potential use to model tissue properties.
  • Pivot shift manuscript.

  • Cruciate ligament modeling & simulation.

• Robb
  • Patellofemoral joint experimentation manuscript.
• Tara
  • Tibiofemoral joint experimentation manuscript.

Notes:

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 showed 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.
   • TBD
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.