• RecurringMeetings
• 2018-09-11

Recurring Meeting of Cleveland Clinic Core Team

Date: September 11, 2018

Time: 2:00 PM EST

Means: In person meeting

Attendees:

1. Ahmet Erdemir
2. Tammy Owings
3. Tyler Schimmoeller
4. Sean Doherty
5. Rici Neumann
6. Ben Landis (skype)

Agenda:

1. Manuscripts update.
2. Data dissemination update.
3. In vitro testing status.

4. Modeling & simulation status.

5. Review of action items from past meeting.

   • https://simtk.org/plugins/moinmoin/multis/RecurringMeetings/2018-08-28

6. Decide action items for next meeting.
7. Other.

Ongoing Action Items:

• Rici
  • Meet with Ahmet weekly to discuss progress on indentation paper.
  • Assist Tyler with surgical tools testing.
• Tyler
  • Continue development of manuscript on tissue thickness measurement comparisons.
  • Revisit repeatability testing for tissue characterization.
  • Perform surgical tools testing.
• Ben
  • Work to get SOFA working in Windows (with customized scripts).
  • Finalize strategy for meshing with Gmsh.
  • Meet with Ahmet on a weekly basis regarding the model assembly paper.
• Sean
  • Pick out a model to stress FEBio to be used as part of a test suite.
  • Continue mesh convergence.
  • Begin working to develop layered models for the male and female subject.
• Ariel
  • Assist Tyler with surgical tools testing as needed.
  • Assist Sean in the model building process as needed.
• Ahmet
  • Meet with Rici on a weekly basis regarding the indentation paper.
  • Meet with Ben on a weekly basis regarding the model assembly paper.
  • Compile haptics libraries and SofaHAPI.
  • Write annual report (due at the end of September).

Notes:

1. Manuscripts update.
   • We recieved the proofs for the in vivo data paper, which were reviewed and sent back to Scientific Data for publication within the next 2-3 weeks.
   • Rici, Tyler, and Ahmet had a meeting with Jim Bena from Quantitaive Health Sciences to discuss statistics for the indentation paper as well as the image modality paper. Rici has developed an R script to perform the mixed effect model analysis for the indentation paper. She is still working to finalize the power analysis. For analyses related to image modality comparison, Jim also suggested defining an acceptable range for the differences between image modalities and present that data as a percentage that fall within the range. He asked if using the intraperson variation would be an acceptable range. Rici replied for clarification prior to moving forward with analysis.
   • Tyler is waiting on data DOIs from SimTK for the instrumented ultrasound paper prior to submission to Journal of Biomechanics.
   • Ben and Ahmet met last week about the model assembly paper. He asked about the recent change with meshing and if that should be changed for the paper as well. Ahmet is not worried about changing the paper because it is not the focus for the paper.
   • Ben is working on re-running the test problems for the model assembly paper on Windows.
2. Data dissemination update.
   • Rici and Ahmet met with Stanford University team today to discuss progress. There are still bugs in the system that Tod is working on. The SimTK integrated system will be ready for initial testing by the end of the week.
3. In vitro testing status.
   • Rici provided a spreadsheet for Tyler that includes the rates and maximum strain for in vitro tests. Ahmet suggested setting the target compression to about 30% of sample thickness and at a rate of 20%/second based on the average peak compression and rates from the in vitro ultrasound indentation tests for initial testing.
   • For surgical tool testing, Ahmet asked Tyler to update the protocol in regard to when taring of instrumented tools occurs.
   • Tyler will adjust the cadaver request age to be under 45 years now (instead of 30). We plan to get 3 additional specimen sets (arm and leg) so that we have a group of 10 donors for in vitro testing. Target donor characteristics are a male in 50s and a male and female under 45.
   • Ahmet would like videos and images throughout the surgical tool experiments.

4. Modeling & simulation status.

   • Sean got the high performance computing account and ran a test model with large compression. However, the output was too large to visualize on his computer. He ran it on 1 node using single processor and it took about 4 hours. Ahmet suggested using multiple cores to see if there is improvement in computation time. The computing platform has FEBio version 2.5 and 2.8.
   • Ben has a Python script to strip out some time points of the output. He will try to find it so Sean can read his results on his local computer.
   • Salome's mesh density adjustment is not working as expected, so Sean has switched to using Gmsh for developing meshes for mesh convergence.
   • Sean remeshed some of the old models and they all run with 5 mm of deformation.
   • Ahmet suggested working on layered models in parallel with the mesh density work. Sean will begin making the explicitly defined layered models. The surfaces will share nodes at tissue interfaces.
   • Ben has been working on how to script the work in Gmsh. He is able to script it from the command line. Ahmet would like them to come up with a strategy for meshing in Gmsh and then the team can review and determine if modifications need to be made for this pipeline.
   • Ben has tried some test problems in Sofa, however tie conditions are not allowing it to run. Ahmet suggested putting the model in a forum after reproducing the problem on a Mac or Linux.
5. Review of action items from past meeting.
   • All action items were related to the agenda items; refer to discussions above.
6. Decide action items for next meeting.
   • See Ongoing Action Items above.
7. Other.
   • Ahmet will be working on the annual report. He will use a picture of all eight models, as well as surface strain measurments for each surgical tool. The surgical tools summary data in the femur coordinate system will also be included.