Weekly Update in lieu of Recurring Meeting of Cleveland Clinic Core Team
Date: May 09, 2017
Provided by: Snehal Chokhandre
Ongoing Action Items:
- Review drafts of data manuscripts for submission.
- Complete studies for tissue testing reproducibility.
- Continue tissue testing of Open Knee(s) specimens.
- Continue segmentation of Open Knee(s) specimens.
- Tissue testing.
- No tissue testing was done last week as Snehal was waiting for supplies.
- Snehal is currently conducting unconfined compression tests on a cartilage sample from the 78 yr old specimen. The tests will be conducted all week (5 tests). This set is the second set in the testing plan for cartilage (Use of PBS, longer times between tests and starting preconditioning and stress relaxation with a 300 micron buffer from the 10g 'find contact' position). Next test sets will be for confined compression and tension for cartilage samples from the 48 yr old and 78 yr old specimens.
- Snehal has conducted two tests for this week's set so far and the results are updated on the Specifications/ExperimentationTissueMechanics wiki page.
- The two tests appear repeatable (1.5% error). The sample experienced load earlier in the second test.
- Data manuscripts.
- No progress.
- No progress.
- Snehal has been working on the simulation test case to assess effects of variations in patella cartilage surface topology due to manual segmentation attempts by multiple users on the finite element model predictions.
- To gain understanding of the manual process of meshing and model development using Salome and FEBio, Snehal worked on a patellofemoral cartilage compression model; see Cases/ImageSegmentationVariability.
- Geometries generated by Craig were used for this trial. Both cartilage geometries were reoriented in Blender to overlap each other and for easier application of boundary conditions. Femur cartilage was also truncated in the region not overlapped by the patella cartilage.
- Snehal used the following meshing and FEA procedures:
- Imported geometries in Salome (stl files created from Slicer 3D, smoothed surfaces).
- Created tetrahedral meshes and node sets in Salome. Exported as .unv files.
- Converted .unv to .inp files using unv2abaqus.py.
- Removed surface elements from the .inp file using text editor before importing in FEBio Preview.
- Imported .inp files in FEBio Preview, applied boundary conditions, defined materials (Mooney-Rivlin), defined contact, exported as .feb.
Ran simulation using FEBio and visualized results PostView.
- As a follow up, Snehal will use the pipeline created by Ben to automatically mesh and assemble the model using the same example.
- To progress towards the goal of the use case, Snehal will take unsmoothed surfaces created by Craig and Connor for oks001 patella and femur cartilage and apply exactly the same smoothing, meshing etc parameters to both sets and run compression simulations.
- To further expand the models to be able to incorporate loading scenarios from patellofemoral joint testing, models including patella, femur, quadriceps tendon and patellar ligament will be built next from oks001 geometries created by Craig and Connor.
- Snehal will update all the relevant information including example files, Python scripts etc. on the use case wiki page and repository.