Tips and Tricks


Tips and Tricks

When you upload your data to AddBiomechanics, several preprocessing steps are performed in order to produce the best possible results from the automated optimization pipeline. AddBiomechanics will try to correct any data quality issues (e.g., occluded marker(s) in a frame), but we cannot make guarantees that all issues will be addressed. Therefore, it is recommended to perform the following data checks before uploading your files to AddBiomechanics.

  1. Anatomical versus tracking markers. Anatomical markers (i.e., markers on bony landmarks) will be moved much less than tracking markers (i.e., markers on soft tissue) during optimization. AddBiomechanics relies on <fixed>true</fixed> and <fixed>false</fixed> annotations in your *.osim model file to tell the difference between anatomical and tracking markers. If you do not provide these annotations, the AddBiomechanics will try to guess, but may not be successful. For best performance,

  2. Compare model markers to experimental markers. Make sure that the markers in your generic model match the markers in your experimental marker (TRC) files. If your *.osim file doesn't contain the markers that are used in your marker files, AddBiomechanics will not produce any results.

  3. Prioritize data with diverse joint motions. AddBiomechanics relies on movement to optimize the scaling of the model. Upload trials with plenty of joint movement for optimal results.

  4. Check for consistent marker trajectories. AddBiomechanics will try to correct common human error in marker trajectory data (like having a pair of markers trade labels partway through a trial) but for best results try to keep your input data as clean as possible.

  5. Check the quality of the ground reaction forces. If performing inverse dynamics, check that your ground reaction force data is free of artifacts (e.g., due to filtering) and contains accurate center of pressure information. Make sure that the column labels follow a naming convention supported by OpenSim (e.g., ground_force_r_v#, ground_force_r_p#, ground_torque_r_#). Finally, providing force plate geometry (e.g., via C3D files), can improve automatic registration of the contact forces to the model.

  6. Check for consistency between ground reactions and markers. Check that your ground reaction force data and marker data have matching time columns. If the data were recorded at different sampling rates, AddBiomechanics will resample the data to create a matching time grid. If the time columns differ, AddBiomechanics will automatically detect a common time range that is the intersection of both time ranges.

  7. Review trial warnings to correct data issues. AddBiomechanics will generate warning messages (yellow text box) if it detects something in your uploaded data that will likely lead to a problem.

  8. Error messaging. If the automated processing fails, AddBiomechanics will generate an error message (red text box) including the reason for the failure and the processing step at which it occurred. You can use this information to update your data files and/or processing settings to address the issue.

  9. Post issues to the user forum. If you are unable to resolve issues yourself, please create a post on the AddBiomechanics forum. Be sure to include the error message in your post to help us resolve your issue.

Sample data

Want to try out AddBiomechanics but don't have any data to upload? Download the sample data below from the supplementary material distributed with the OpenSim model publication by Rajagopal et al. (2016).

How to use Custom Markersets

Using custom marker sets with AddBiomechanics is easy:

  1. Start by downloading the OpenSim GUI
  2. You'll also want to download a skeleton model to base yours off of: Rajagopal 2015 and Lai Arnold 2017 are popular options.
  3. Then you can use the Marker Editor in OpenSim to add your marker set to your skeleton. Export a *.osim file when you're done.
  4. Now you can use your new *.osim file as your Custom OpenSim Skeleton and Markerset in AddBiomechanics!