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Qualisys_OpenSim

OpenSim Workflow in Qualisys Track Manager Project Automation Framework

See how it works: https://www.youtube.com/watch?v=Nz8CSuOh0xg


What does this PAF do?

  • Generate OpenSim motion files:
    • Static trial:
      • Detremine lab coordinate system based on marker data
      • Rotate marker data to be consistent with OpenSim coordinate system (XYZ)
      • Calculate hip joint center based on Harrington et al. (2007)
      • Calculate knee and ankle joint center
      • Generate TRC file
    • Gait trials:
      • Determine lab coordinate system based on GRF data (vertical, braking and propulsion peaks)
      • Rotate marker and force data to be consistent with OpenSim coordinate system (XYZ)
      • Detect which foot strikes which force plate
      • Calculate time of feet contact
      • Low-pass filter the force data
      • Generate TRC, MOT and OpenSim External Load files
  • Run OpenSim tools:
    • Scale tool:
      • Scale MaxIsometricForce based on Handsfield et al. (2014)
      • Set MaxContractionVelocity to 15 (m/s)
    • InverseKinematics tool
    • InverseDynamics tool
    • StaticOptimization tool
    • JointReaction tool

Requirements

Install miniconda/minigorge/mambaforge with the following packages:


IMPORTANT NOTES

USE IT AT YOUR OWN RISK.

If you use this PAF or any functions of the script for your project, please cite this work as:

@misc{Qualisys_OpenSim,
    title={OpenSim Workflow in Qualisys Track Manager Project Automation Framework},
    author={Rezaie, Mohammadreza},
    year={2022},
    url={https://github.com/mrrezaie/Qualisys_OpenSim}
}

The model is described by Rajagopal et al. (2016) with calibrated passive muscle force curves and improved hip abductor muscle paths: https://simtk.org/projects/fbmodpassivecal

The Workflow is inspired by Rajagopal sample simulation: https://simtk.org/projects/full_body

The PAF is inspired by Qualisys PAF example: https://github.com/qualisys/paf-opensim-example

Only Gait (Walking and Running) trials is supported.

Define subject Height and Mass accurately. They will be used in the analysis.

Personally I do not filter markers data. However, I fill the gaps and remove the spikes in QTM using 'Trajectory Editor' tool.

In QTM 'Project Options', make sure these settings are satisfied before start processing:

  • Coordinate system is set to World (Lab) in 'Force Data'
  • 3D data and Force data are checked in 'MATLAB file Export'
  • Python path is defined correctly in 'Folder Options'

Here I used MAT format instead of C3D because no C3D parser (e.g EZC3D or BTK) takes Kistler COP correction (FPCOPPOLY) prameter into account. Fortunately, QTM does it. Why don't we exclude mediums? QTM is also able to import C3D files and change force plate parameters.

The markerset:

Marker Definition Type Static Dynamic
C7 C7 spinous process Anatomical * *
T10 T10 spinous process Anatomical * *
CLAV Right sternoclavicular prominent Anatomical * *
RACR Right acromion process Anatomical * *
LACR Left acromion process Anatomical * *
RLEL Right lateral elbow (humeral lateral epicondyle) Anatomical * *
LLEL Left lateral elbow (humeral lateral epicondyle) Anatomical * *
RFAradius Right lateral wrist (radial styloid process) Anatomical * *
LFAradius Left lateral wrist (radial styloid process) Anatomical * *
RASI Right anterior superior iliac spine Anatomical * *
LASI Left anterior superior iliac spine Anatomical * *
RPSI Right posterior superior iliac spine Anatomical * *
LPSI Left posterior superior iliac spine Anatomical * *
RHJC Right hip joint center Virtual *
LHJC Left hip joint center Virtual *
RTH1-RTH4 4 clusters on right thigh Tracking *
LTH1-LTH4 4 clusters on left thigh Tracking *
RLFC Right lateral epicondyle of femur Anatomical * *
LLFC Left lateral epicondyle of femur Anatomical * *
RMFC Right medial epicondyle of femur Anatomical *
LMFC Left medial epicondyle of femur Anatomical *
RKJC Right knee joint center Virtual *
LKJC Left knee joint center Virtual *
RTB1-RTB4 4 clusters on right tibia Tracking *
LTB1-LTB4 4 clusters on left tibia Tracking *
RLMAL Right lateral malleolus Anatomical *
LLMAL Left lateral malleolus Anatomical *
RMMAL Right medial malleolus Anatomical *
LMMAL Left medial malleolus Anatomical *
RAJC Right ankle joint center Virtual *
LAJC Left ankle joint center Virtual *
RCAL Right calcaneus tuberosity Anatomical * *
LCAL Left calcaneus tuberosity Anatomical * *
RMT1 Right 1st metatarsal head Anatomical * *
LMT1 Left 1st metatarsal head Anatomical * *
RMT5 Right 5th metatarsal head Anatomical * *
LMT5 Left 5th metatarsal head Anatomical * *

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OpenSim workflow in QTM PAF

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