Page Comparison

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• Prepare the model by adding additional markers. When previously scaling the model using OpenSim, additional markers, specific to the laboratory marker setup, were added from another file. Since AddBiomechanics does not currently support this feature, follow the steps below to add these markers to a new, modified model file.
• Copy the original model file (Rajagopal2015.osim) to a new file (e.g., Rajagopal2015_CustomerMarkerSetCustomMarkerSet.osim) before making any changes.
• The model file is an XML file. Open both the new model file and the additional marker set file (Scale/markerset_walk_preScale.xml) in a text editor. More info about the model format and suggestions for text editors can be found in the OpenSim Models File Format documentation.
• Add the additional markers to the new model file. For both files, all of the Markers can be found under the section <MarkerSet>, under a subsection called <objects>. Copy all of the Markers from the additional marker set file to the new model file (appending them to the list of markers, not replacing them), and save the new model file.
• Open the new model in OpenSim and check if additional markers have been added to the model. If the model does not load, check if the new model file has the required XML opening and closing tag (e.g., <Marker> and a corresponding </Marker>).
• Prepare the marker and ground reaction force data files.
• Copy the original marker (ExpData/motion_capture_walk.trc) and ground reaction force (grf_walk.mot) data files to new files (e.g., motion_capture_walk_trimmed.trc and grf_walk_trimmed.mot) before making any changes.
• In the new files, trim the beginning and end of the trial so that the time range remaining only contains times that are valid for use with Inverse Dynamics (as you did previously for RRA). It could be helpful to use an advanced text editor (e.g., Notepad++), Excel, or MATLAB to perform this step.

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• Set the <fixed> tag to true for Markers that could be causing issues in the generic model with added markers (e.g., Rajagopal2015_CustomerMakerSetCustomMakerSet.osim). There are two ways to do this:
  • Load the model in the GUI and navigate to the Markers to be updated.
    • Click on an individual marker, then in the Properties pane (bottom left), check the box next to “fixed”.
    • Repeat this for all Markers that need to be updated.
    • Save the model.
  • Load the model file in a text editor.
    • Navigate to a Marker to be updated and change the XML tag <fixed> to be true.
    • Repeat this for all Markers that need to be updated.
    • Save the model file.
• Update the AddBiomechanics setup page and re-run the tool.
  • Navigate back to the original Subject page that you set up before.
  • Update the model by clicking on the box on the right hand side of the OpenSim Model and Markerset and choosing your updated generic model file.
  • Click Reprocess.
• Download the results.

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1. Assess the quality of the Inverse Dynamics results. In the ID results folder, open the file ending in “summary.txt”.
   1. What are the average residual force and torque?
   2. How do these values compare to the residuals after RRA?
   3. Look at all 6 residual values over the trial by opening the file ending in “id.pdf” provided in the ID results folder. How do these values compare with the residuals after RRA?
2. Investigate some of the changes that were made by the tool to reduce residuals. Similar to RRA, the inertial parameters of bodies and kinematics can be changed to reduce residuals.
   1. In the top folder of the downloaded results, open README.txt. How does the total mass of the model compare to the mass of the subject that was used as an input to the tool?
   2. Which bodies had some of the largest changes, both as percentage changes and absolute changes. Are these changes changes reasonable? Why or why not?
3. Assess the quality of your ID results .by comparing your ID results from those obtained in the original paper (Rajagopal et al., 2016). Plot your results for the three sagittal plane coordinates (hip_flexion, knee_angle, and ankle_angle) through either: 1) plotting in the GUI, or 2) opening the file ending in “id.pdf” provided in the ID results folder.
    
   1. How well do your results match with the original work? Some aspects to consider include the timing of peaks, the relative magnitude of the different joint moments, and the absolute magnitude of the different joint moments.
   2. Compare your ID results from those obtained in the original paper (Rajagopal et al., 2016). Are these results differences surprising given that the processing steps were performed differently?
   3. Plot your results for the three sagittal plane coordinates (hip_flexion, knee_angle, and ankle_angle) through either: 1) plotting in the GUI, or 2) opening the file ending in “id.pdf” provided in the ID results folder.