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:

• Numpy, Scipy (https://anaconda.org/conda-forge/scikit-learn)
• OpenSim (https://anaconda.org/opensim_admin/opensim)

---

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	*	*