• ModelDevelopment

Goals

• To develop and disseminate two initial working models (one from Open Knee(s) including intermediate virtual representations of tissue structures; one from Natural Knee Data) along with the documentation of modeling outputs, simulation outcomes, and modeling & simulation processes.

Tentative Timeline

Earmarked Data

oks003 from Open Knee(s):

• Demographics
  • Left knee
  • Age: 25 years
  • Gender: Female
  • Height: 1.73 m
  • Weight: 68 kg
  • BMI: 22.8
• Specimen-specific medical imaging data sets
  • 1.3.12.2.1107.5.2.19.45406.2014120210113013368841431.0.0.0.nii - General purpose imaging (MRI in NIfTI format)
  • 1.3.12.2.1107.5.2.19.45406.2014120210325342222042395.0.0.0.nii - Cartilage imaging (MRI in NIfTI format)
  • 1.3.12.2.1107.5.2.19.45406.2014120211145041394943484.0.0.0.nii - Soft tissue imaging - axial plane (MRI in NIfTI format)
  • 1.3.12.2.1107.5.2.19.45406.2014120211045428131243076.0.0.0.nii - Soft tissue imaging - sagittal plane (MRI in NIfTI format)
  • 1.3.12.2.1107.5.2.19.45406.2014120211095362283243280.0.0.0.nii - Soft tissue imaging - coronal plane (MRI in NIfTI format)
• Other

  • Imaging data sets also contain registration markers that were probed for joint testing (probing data, including anatomical and registration markers, are not provided as part of Model Development and will be provided in upcoming M&S phases)

• Download data in the downloads section of project site, https://simtk.org/projects/kneehub

  • Package name: Data for Model Development - oks003
  • Link to package location:
  • File name: data-MD-oks003.zip
  • Direct link to file:

DU02 from Natural Knee Data:

• Demographics
  • Right knee
  • Age: 44 years
  • Gender: Male
  • Height: 1.83 m
  • Weight: 70.31 kg
  • BMI: 21.02
• Specimen-specific medical imaging data sets
• Other

• Download data in the downloads section of project site, https://simtk.org/projects/kneehub

  • Package name: Data for Model Development - DU02
  • Link to package location:
  • File name: data-MD-DU02.zip
  • Direct link to file:

Start with

• Specimen-specific medial imaging datasets (MRIs, CTs)
• Other specimen-specific anatomical information (digitization)
• Literature
• Earmarked data (provided in the downloads section of project site)
  • Specimen? - Open Knee(s) - MRI (general purpose, cartilage, three orthogonal connective tissue) in NIfTI format
  • Specimen? - DU - CT, MRI in DICOM format, anatomical landmarks + ligament insertion origin sites in text format

Simulation Case

Passive flexion

Deliverables

Modeling & Simulation Process Outputs

• Modeling and simulation outputs
  • Initial working models simulating passive flexion in native simulation software formats
  • Representation of anatomy for each included tissue component, e.g.,
    • Segmentation
    • Geometry
    • Mesh
  • Representation of material/structural behavior for each included tissue component, e.g.,
    • Constitutive models
    • Tissue stress-strain response
    • Tissue bulk response
  • Coordinate systems
  • Representation of loading and boundary conditions

Intermediate and Final M&S Outputs

• Outcomes (to be uploaded to the downloads section of project site)
  • Model 1 from Specimen? - Open Knee(s)
    • Working capacity, i.e., simulating passive flexion OR other type of activity?
    • Representation of anatomy (in formats preferred by modeling team)
      • Segmentations of modeled tissues, e.g., binary image label
      • Geometry of modeled tissues, e.g., triangulated surface representation
      • Mesh, e.g. tetrahedral/hexahedral volume mesh
    • Representation of tissue behaviour
      • Constitutive models, e.g. coefficients and equation of strain energy potential
      • Tissue stress-strain response, e.g. raw data or calculated from constitutive model
      • Tissue bulk response?, e.g. total ligament force under simplified loading
  • Model 2 from Specimen? - DU
    • Same as above.

Documentation of M&S Outputs

Process Documentation

• Workflow documentation (to be uploaded to the documents section of project site)
  • Specifications. A document describing individual steps to obtain outcomes from earmarked data. The detail should be provided in a manner that other teams can reproduce the decision making process of the modeler. Any subjective and arbitrary decisions should be noted and as much insight as possible should be provided for justification and reproduction this decision.
  • Protocol deviations. If specifications need to be updated during activities to go from earmarked data to outcomes, these should be documented as protocol deviations. As much insight as possible should be provided for justification of deviation.
  • Ideally, when a third-party modeler has the earmarked data, specifications, and protocol deviations, they can follow the steps of the modeling team to reproduce the outcomes.
  • The documentation should list all the resources used and note estimated and actual effort level of personnel (and the expertise level of personnel) to estimate cost burden.

Specifications

Protocol Deviations

Package for Comparative Analysis

Guidance

Where to get the Earmarked Data?

How to prepare and submit Specifications?

Specifications are concerned about documentation of processes to transform earmarked data to M&S outputs. This information is intended to be provided separately for processing of both data sets to capture nuances in response to variable data content and quality. This documentation will be provided before execution of Model Development activities to demonstrate the path each modeling team has chosen. It should be in a detail such that other modeling teams can follow the steps to reproduce M&S outputs. When possible, justifications to support modeling & simulation decisions should be provided.

Content

• Document metadata; contributors to document, corresponding contact, date document finalized.
• Summary of data used including citations
• Overview of model components

• Description of target intermediate and final M&S products (consult Erdemir et al. (2012), for completeness)

• For each tissue structure
  • Anatomy
  • Material/structural properties
• Loading and boundary conditions
• Interactions between tissue structures
• Software requirements
• Hardware requirements
• Anticipated man hours and expertise level

Each team will submit two sets of documents, one for Model Development using Open Knee(s) data and another for Model Development using Natural Knee data. Each set will include the source document, i.e., in preferred format that it is written, and as a PDF copy.

How to prepare and submit Protocol Deviations?

It is likely that initial specifications may need to be modified to accomplish Model Development activities. These modifications, i.e. Protocol Deviations, should be documented during Model Development activities. Each protocol deviation should include information to understand who did, what and when, and why. The documentation should be in a detail such that other modeling teams can utilize along with specifications to reproduce M&S outputs. Protocol Deviations will be collated in two sets of documents (one for using Open Knee(s) data and another for Natural Knee data). The documents will be provided before execution of Model Development activities in source form, i.e., in preferred format that it is written, and as a PDF copy.

How to curate, document and submit Modeling and Simulation Outputs?

All M&S outputs (intermediate and final) should be provided in their preferred format, i.e., accommodating individual teams workflow. Each team should provide two packages (one for Open Knee(s) data and another for Natural Knee data) as a compressed archive (e.g. zip). An accompanying document should describe M&S outputs. This information should focus on i) file descriptors and formats, and folder organization to help navigate the provided content and ii) what actually each M&S output is (NOT how they are obtained). The latter should be reflective of the description of target intermediate and final M&S products of Specifications. It should also be indicative of necessary information for other modeling teams to judge the nature and extent of the provided content.

Preparing a package for Comparative Analysis

All material may need to be reorganized and converted to response to third-party requirements for comparative analysis. Nonetheless, this should not prevent individual M&S teams to personalize their workflows and documentation style.

References

Erdemir, A., Mulugeta, L. and Lytton, W. W. Ten “not so” simple rules for credible practice of modeling and simulation in healthcare: a multidisciplinary committee perspective, 2015 Biomedical Engineering Society / Food and Drug Administration Frontiers in Medical Devices Conference: Innovations in Modeling and Simulation, May 18-20, 2015, Washington, DC. Available at: https://simtk.org/svn/cpms/doc/posters/fmd_2015.pdf.

Erdemir, A., Guess, T. M., Halloran, J. P., Tadepalli, S. C. and Morrison, T. M. (2012) Considerations for reporting finite element analysis studies in biomechanics, Journal of Biomechanics, 45, 625-633. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278509/.

U.S. Food and Drug Administration. Reporting of Computational Modeling Studies in Medical Device Submissions. Available at: https://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/GuidanceDocuments/UCM381813.

NASA-STD-7009: Standard for Models and Simulations. Available at: https://standards.nasa.gov/standard/nasa/nasa-std-7009.

ASME V&V American Society of Mechanical Engineers - Committee Pages - V&V 40 Verification and Validation in Computational Modeling of Medical Devices. Available at: https://cstools.asme.org/csconnect/CommitteePages.cfm?Committee=100108782.