An automated approach to analyze motion capture trials in OpenSim

A repository containing an OpenSim template pipeline structure for performing common analyses (extraction from c3d, scaling, inverse kinematics, inverse dynamics, residual reduction analysis, static optimization, computed muscle controls, muscle analysis, joint reaction analysis, etc.). The user can include his c3d files, and with minimum changes to the scripts, one can perform different analyses through OpenSim.

Each folder has a specific structure and name convention that should be preserved so that the different setup files (.xml) can locate the files needed for the analyses. The user should navigate into the script folder located in each sub-folder. Scripts for converting c3d files and performing standard analyses in OpenSim are provided. A caution note here is that the user should manually inspect the results between individual steps (e.g., scaling). Sometimes a mismatch in the marker placement can cause problems, especially when we work with new data sets. We provide the marker placement in these examples, but the user should define this carefully for a different setting.

The examples are organized as follows:

• tutorial: a very simple example that demonstrates how to extract marker positions, EMG, and ground reaction forces from c3d files, perform scaling, inverse kinematics, inverse dynamics, and static optimization using OpenSim.
• simple: does the same thing as the tutorial but goes one step further and performs additional analysis such as joint reaction calculations.
• complex: does the same as simple, but the residual reduction algorithm is involved in the pipeline. Sometimes, users prefer not to use this algorithm, so we provide simple and complex variants. In the complex example, we also perform computed muscle controls in OpenSim.
• opensim_example: application of the analysis on the OpenSim gait examples. In these examples, no c3d files are provided, and we work directly with the .trc and .mot files. This is used as a test between the GUI and the scripts.

If you are experiencing issues with visualizing the models, please include the Geometry folder in OPENSIM_HOME.

Acknowledge

If you find this useful you can acknowledge it as follows:

@misc{opensim-automated-pipeline,
  author = {Stanev, Dimitar},
  title = {An automated approach to analyze motion capture trials in OpenSim},
  year = {2021},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/mitkof6/opensim_automated_pipeline}
}

No worries, I do not mind not being acknowledged. Most of the things presented here are based on things available on SimTK and the user-guide. I hope I will have more time to improve and provide additional scripts for performing useful manipulations on the data in the future.