• ModelDevelopment

Goals

The fundamental goal of the Model Development phase is the development of initial working knee models by each team. The term "initial working model" refers to a model that is completely defined to carry out preliminary simulations. Calibration and benchmarking of this "initial working model" are NOT anticipated at this phase.

Specific goals of the Model Development phase are

• To develop two initial knee models (inclusive of tibiofemoral and patellofemoral joints)
  • one using Open Knee(s) data
  • one using Natural Knee data
• To conduct simulations with models with a sample simulation case
• To document and disseminate virtual anatomical and mechanical representations of model components and the working models

• To document and disseminate modeling & simulation (M&S) processes, including specifications and protocol deviations

• To document and disseminate simulation results

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 MD - oks003

  • Link to package location: https://simtk.org/frs/?group_id=1061

  • File name: data-MD-oks003.zip

  • Direct link to file: https://simtk.org/frs/download_confirm.php/file/5438/data-MD-oks003.zip?group_id=1061

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
  • DU02_knee_06mm/ - CT folder (sequence of images in DICOM format)
  • DU02_fs_SAG/ - MRI folder (sequence of images in DICOM format)
• Other
  • DU02_raw_probed_points/ - Probing data
    • Points_on_Femur/ - in a local femur coordinate system
      • DU02_ACL_fem.txt
      • DU02_fem_artgeo.txt
      • DU02_fem_Bone.txt
      • DU02_fem_GSPts.txt - anatomical landmarks

      • DU02_HipBall.txt - -- aerdemir 2018-07-02 18:47:06 Added on July 2, 2018. Thanks to Will Zaylor for recognizing missing file.

      • DU02_latPFlig_fem.txt
      • DU02_LCL_fem.txt
      • DU02_MCL_fem.txt
      • DU02_PCL_fem.txt
      • DU_fem_perimeter.txt
    • Points_on_Patella/ - in a local patella coordinate system
      • DU02_latPFlig_pat.txt
      • DU02_Pat_artgeo.txt
      • DU02_Pat_GSPts.txt - anatomical landmarks
      • DU02_pat_tend_pat.txt

      • DU02_QuadTend_pat.txt

    • Points_on_Tibia/ - in a local tibia coordinate system
      • DU02_ACL_tib.txt
      • DU02_LCL_tib.txt
      • DU02_MCL_tib.txt
      • DU02_PCL_tib.txt
      • DU02_tib_artgeo.txt
      • DU02_tib_bone.txt
      • DU02_tib_GSPts.txt - anatomical landmarks
      • DU02_tib_latmeniscus_anteriorhorn.txt
      • DU02_tib_latmeniscus_posteriorhorn.txt
      • DU02_tib_lat_plateau.txt
      • DU02_tib_medmeniscus_anteriorhorn.txt
      • DU02_tib_medmeniscus_posteriorhorn.txt
      • DU02_tib_med_plateau.txt
      • DU02_tib_pattendon.txt
      • DU02_tib_plateauperimeter.txt

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

  • Package name: Data for MD - DU02

  • Link to package location: https://simtk.org/frs/?group_id=1061

  • File name: data-MD-DU02.zip

  • Direct link to file: https://simtk.org/frs/download_confirm.php/file/5437/data-MD-DU02.zip?group_id=1061

The modeling teams do not have to use all of the earmarked data. They can also utilize information in literature to define model components that may not have any associated specimen-specific data.

Simulation Case

Each team will simulate passive flexion from 0 to 90 degrees. Interpretation of the term "passive flexion", and therefore its reflection as loading and boundary conditions, will be left to individual teams. The simulations' primary aim will be the prediction of joint kinematics.

Deliverables

Modeling & Simulation Outputs

Intermediate and End-Point M&S Outputs

Two packages representing final and intermediate outcomes of Model Development phase will be the outputs of this phase. The focus is the complete curation of the results of each individual team's Model Development activities.

• Package (*.zip) collating M&S Outputs using Open Knee(s)

  • End-point M&S Outputs such as

    • Working model including simulation case in a format preferred by modeling team
    • Simulation results in a format preferred by modeling team

  • Intermediate M&S Outputs in formats preferred by modeling team

    • Model components (for included tissue structures) along M&S lifecycle

      • Representation of anatomy such as
        • 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 behavior such as
        • 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. force-displacement, stiffness
    • Models of interactions between model components such as
      • Connectivity representation, e.g. tie
      • Contact models
    • Coordinate systems
    • Loading and boundary conditions

• Package (*.zip) collating M&S Outputs using Natural Knee Data

  • Similar to package described above but utilizing Natural Knee Data

Documentation of M&S Outputs

Two document sets should provide information to help navigate the M&S output package and to describe what M&S Outputs are (not how they are obtained).

• Document (in source, e.g., *.odt, *.docx, etc., and PDF formats) describing M&S Outputs using Open Knee(s) data

  • Metadata for the document - authors, date, contact information
  • Information to navigate the package

  • Information to describe what each M&S Output is

• Document (in source, e.g., *.odt, *.docx, etc., and PDF formats) describing M&S Outputs using Natural Knee Data

  • Similar to document described above but utilizing Natural Knee Data

Modeling & Simulation Processes

An important set of deliverables are the documentation of the M&S processes, i.e. the individualized workflows to transform earmarked data to M&S outputs. The documents will include Specifications, to provide each team's initial plans for processing data to obtain M&S outputs, and Protocol Deviations, to describe modifications to Specifications during the execution of the initial plans. 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 their disseminated M&S outputs.

Specifications

Specifications documents are aimed to describe individual steps to obtain M&S outputs 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 these decisions. This document should be prepared and disseminated before M&S activities start.

• Specifications document (in source, e.g., *.odt, *.docx, etc., and PDF formats) describing M&S Processes using Open Knee(s) data

  • Metadata for the document - authors, date, contact information

  • Information to describe what each target M&S Output is

  • Information to describe how each target M&S Output will be obtained

  • Anticipated burden of the workflow

• Specifications document (in source, e.g., *.odt, *.docx, etc., and PDF formats) describing M&S Processes using Natural Knee Data

  • Similar to document described above but utilizing Natural Knee Data

Protocol Deviations

If specifications need to be updated during activities to go from earmarked data to M&S outputs, these should be documented as protocol deviations. As much insight as possible should be provided for justification of the deviation. This document should be prepared during M&S activities and disseminated along with M&S outputs.

• Protocol Deviation document (in source, e.g., *.odt, *.docx, etc., and PDF formats) describing M&S Processes using Open Knee(s) data

  • Metadata for the document - authors, date, contact information
  • Collated set of protocol deviations, each describing
    • What is the deviation in relevance to Specifications?

    • Which M&S output does the deviation impact?

    • Who implemented the modification?
    • When was the modification made?
    • What is the justification for deviation?
  • Actual burden of the workflow

• Protocol Deviation document (in source, e.g., *.odt, *.docx, etc., and PDF formats) describing M&S Processes using Natural Knee Data

  • Similar to document described above but utilizing Natural Knee Data

Package for Comparative Analysis

Two packages will be prepared to curate M&S Outputs and process documentation of each team; one starting with data from Open Knee(s), the other utilizing Natural Knee data. The M&S Output files submitted by the individual teams will be organized in these packages and provided as is with the possible exception of renaming of master package files. The documents will be provided as is. Yet, additional organization of output description and process documentation may be necessary to meet third-party requirements or recommendations (see guidance from #USFDA, #ASME, #NASA, #Erdemir2015).

• Package of M&S outputs and processes using data from Open Knee(s)

  • Cleveland Clinic team

    • M&S outputs package file

    • M&S outputs documentation files

    • M&S processes specifications documents

    • M&S processes protocol deviation documents

  • University of Denver team

    • M&S outputs package file

    • M&S outputs documentation files

    • M&S processes specifications documents

    • M&S processes protocol deviation documents

  • Cleveland State University team

    • M&S outputs package file

    • M&S outputs documentation files

    • M&S processes specifications documents

    • M&S processes protocol deviation documents

  • Auckland Bioengineering Institute team

    • M&S outputs package file

    • M&S outputs documentation files

    • M&S processes specifications documents

    • M&S processes protocol deviation documents

  • Hospital for Special Surgery team

    • M&S outputs package file

    • M&S outputs documentation files

    • M&S processes specifications documents

    • M&S processes protocol deviation documents

• Package of M&S outputs and processes using Natural Knee data

  • Cleveland Clinic team

    • M&S outputs package file

    • M&S outputs documentation files

    • M&S processes specifications documents

    • M&S processes protocol deviation documents

  • University of Denver team

    • M&S outputs package file

    • M&S outputs documentation files

    • M&S processes specifications documents

    • M&S processes protocol deviation documents

  • Cleveland State University team

    • M&S outputs package file

    • M&S outputs documentation files

    • M&S processes specifications documents

    • M&S processes protocol deviation documents

  • Auckland Bioengineering Institute team

    • M&S outputs package file

    • M&S outputs documentation files

    • M&S processes specifications documents

    • M&S processes protocol deviation documents

  • Hospital for Special Surgery team

    • M&S outputs package file

    • M&S outputs documentation files

    • M&S processes specifications documents

    • M&S processes protocol deviation documents

Guidance

Where to get the Earmarked Data?

The teams can download data in the downloads section of project site, https://simtk.org/projects/kneehub, check packages

• Data for Model Development - oks003, from Open Knee(s)
• Data for Model Development - DU02, from Natural Knee Data

How to prepare and submit Specifications?

Specifications are concerned about documentation of the 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. Specifications 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.

Recommended content for Specifications includes:

• Metadata for the document - contributors, contact information for corresponding author, date of document.

• Summary of data utilized with the M&S processes.

• Overview of target M&S outputs and M&S processes - similar to summarizing it in a scholarly publication.

• Detailed descriptions of target M&S outputs (consult Erdemir et al. (2012), for completeness)

  • Complete model
    • Anatomy
    • Mechanical properties
    • Coordinate systems
    • Loading and boundary conditions (for the simulation case)
    • Interactions between model components (contacts, ties)
  • Intermediate and final virtual representations of individual model components
    • anatomy (mesh, segmentation, geometry)
    • mechanics (stress-strain data, constitutive models, constitutive coefficients/material properties, structural properties, etc.)
  • Simulation case
    • Loading and boundary conditions
    • Target metrics for predictions
    • Numerical analysis settings
    • Anticipated results

• Detailed descriptions of M&S processes to get the target M&S outputs

  • Steps to generate intermediate and final anatomical representation(s)
  • Steps to generate intermediate and final mechanical representation(s)
  • Steps to implement full model - assembly, interactions, coordinate systems, loading and boundary conditions
  • Steps to perform simulations
  • Burden
    • Software requirements
    • Hardware requirements
    • Anticipated man hours and expertise level
    • Computational cost
• References

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. The documents should be submitted by any convenient means - e-mail, file sharing, upload to project site, etc. Ahmet Erdemir, erdemira@ccf.org, will push the submitted documents to the project site in the Documents section with labeling indicative of modeling phase, development teams, and data source.

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 it along with specifications to reproduce M&S outputs. This document should also include the actual burden of M&S activities including changes in software and hardware requirements, and deviations from anticipated labor effort and computational cost. Protocol Deviations should 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 after execution of Model Development activities in source form, i.e., in preferred format that it is written, and as a PDF copy. The documents should be submitted by any convenient means - e-mail, file sharing, upload to project site, etc. Ahmet Erdemir, erdemira@ccf.org, will push the submitted documents to the project site in the Documents section with labeling indicative of modeling phase, development teams, and data source.

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' workflows. 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). For each package, an accompanying document should describe M&S outputs - in source form, i.e., in preferred format that it is written, and as a PDF copy. 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. The packages should be submitted by any convenient means - e-mail, file sharing, upload to project site, etc. Ahmet Erdemir, erdemira@ccf.org, will push the submitted packages to the project site in the Downloads section with labeling indicative of modeling phase, development teams, and data source.

Preparing a package for Comparative Analysis

All material will likely need to be reorganized and converted to respond to third-party requirements for comparative analysis (see guidance from #USFDA, #ASME, #NASA, #Erdemir2015). Nonetheless, this should not prevent individual M&S teams to personalize their workflows and documentation style. Preparation of a package for comparative analysis will collate M&S outputs and documents submitted by the individual teams. M&S outputs will be provided in formats as delivered by the teams. Documentation may need to be reorganized using source copies of documentation from individual teams. Ahmet Erdemir, erdemira@ccf.org, will submit the prepared package to the third-party by any convenient means - e-mail, file sharing, upload to project site, etc.

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.