Part I: Computing Joint Moments with OpenSim

1. Scaling a model

1. By looking at the mass of the subject and generic model, as well as the scale factors, is the subject generally larger or smaller than the generic model? Support your answer by providing the mass and a few scale factors.
2. What is the time range of data that was used to adjust the model’s markers? Compared to a typical movement to capture, such as one full stride of walking, is this range short or long? Why might the time range be short or long for a static trial?

2. Visualizing input motion data

1. Over what time range is marker data provided?
2. Over what time range is GRF data provided (i.e., what is the earliest time and latest time that contain non-zero forces)?
3. This walking trial was collected overground (i.e., not on a treadmill) with force plates located in the middle of the motion laboratory. 
1. How many foot strikes have GRF data?
2. Over what time range do you have complete GRF data (i.e., all external loads are accounted for)?

3. Inverse Kinematics

1. List a few markers with higher weights. Why do these markers have higher weights when studying a motion like walking and for a model like this one? It may be helpful to refer to the IK documentation, and specifically How Inverse Kinematics Works.
2. List a few markers with lower weights. Why do these markers have lower weights when studying a motion like walking and for a model like this one?
3. At what times is the overall error, as measured by RMSE, highest? What are some possible reasons why this could happen?
4. Which marker(s) have particularly high errors? Why might these marker(s) be prone to higher errors?

4. Inverse Dynamics

1. Plot the applied forces (i.e., pelvis_tx_force, pelvis_ty_force, and pelvis_tz_force) and torques (i.e., pelvis_tilt_moment, pelvis_list_moment, pelvis_rotation_moment) that act on the pelvis as functions of time. The data are in the ID/inverse_dynamics.sto file. These applied forces and torques are the residuals. 
1. To better understand on which degrees of freedom and along which directions each of these forces and torques act, use the coordinate sliders to investigate how each pelvis degree of freedom (pelvis_tx, pelvis_ty, pelvis_tz, pelvit_tilt, pelvis_list, and pelvis_moment) moves the model. It may be helpful to reset the pose by clicking Poses -> Default when investigating each degree of freedom. In particular, note the following:
1. For each translational degree of freedom, which direction does the model move (e.g., forward/back, up/down, left/right). These directions indicate the coordinate frame of the pelvis (e.g., pelvis_tx motion will indicate the x-axis direction of the pelvis coordinate frame).
2. For each rotational degree of freedom, about which axis of the pelvis frame does that degree of freedom move the model?
2. When are these residuals the highest?
3. Of the three forces, which residual force is the highest? Why might this be? 
2. Plot the experimentally measured vertical ground reaction forces (ground_force_r_vy [right leg] and ground_force_l_vy [left leg]) from the grf_walk.mot file and the pelvis_ty_force from the ID results as functions of time. 
1. How do the vertical ground reaction forces compare to the pelvis_ty_force residual?
2. Looking at this plot, why are residuals highest at the times specified by question 1a?
3. During what times is it valid to analyze the inverse dynamics data? How do these times compare to those from the questions in the section “Visualizing input motion data”?

5. Residual Reduction Algorithm

1. Open the Messages pane and locate the recommended overall mass adjustment from the last run of RRA (e.g., "pelvis: orig mass = xxxxx, new mass = yyyyy"). Note that the units are in kilograms (kg). What is the recommended mass adjustment?
2. Investigate how the kinematics were adjusted by RRA. The positional errors between the RRA adjusted kinematics and the input IK kinematics can be found in your RRA results folder in the file ending in “pErr.sto”. Plot all of the errors for all coordinates (note: a quick way to do this is to use the plotter and choose “select all shown” and then deselect “time”). 
1. What are the two coordinates with the largest maximum changes? 
2. What is the maximum value for each of these coordinates? Rotational coordinates have units of radians, and translational coordinates have units of meters. 
3. Why or why not are the magnitude of these changes reasonable?
3. Compare the residuals from the ID results with those from the RRA results. The RRA results can be found in your RRA results folder in the file ending in “Actuation_force.sto” under the quantities for FX, FY, FZ, MX, MY, MZ. For each of the 6 residual measures, quantify how well RRA reduced residuals.

Part II: Computing Joint Moments with AddBiomechanics

4. Upload data and run the AddBiomechanics tool

1. Assess the IK results by looking at the marker errors.
1. In the IK folder, open the file that ends in “summary.txt”. What was the average marker RMSE and the average marker max error?
2. Open the file containing the marker errors between the IK solution and the experimental data (in the IK folder, find the file that ends in “marker_errors.pdf”). Markers that are on both limbs are plotted together. For both legs, which Marker has the highest RMSE?
2. Look at the Marker with the highest error by visualizing the results in the OpenSim GUI. Load the model (final.osim) and the IK results (in the IK folder, find the .mot file). Find the Marker of interest on the model. How did the tool move the Marker?
3. Overlay the experimental data with the IK solution. To do this, under the model, expand the “Motions” section, right-click “Coordinates” and click Associate Motion Data…. Go to the MarkerData subfolder and choose the .trc file. Does the Marker with the highest error track closely to the experimental data (blue marker)?

5. Adjusting settings for marker tracking

1. Assess the new IK results. Were results improved by the change by “fixing” the Marker? Support your answer with quantitative data from any plots and other output, and with visualizing the model and results.
2. Plot the coordinates that are located closest to the updated Marker for both the results in the previous section and this section. How did the IK results change for this coordinate? Coordinates can be plotted in a couple ways: 1) in the GUI, or 2) in the file ending in “ik.pdf” provided in the IK results folder.
3. Overlay the experimental data on the new IK motion as done in the previous section.
1. Does the Marker with the highest error track closely to the experimental data (blue marker)?
2. Recall that the Scale and IK steps were completed at the same time when using AddBiomechanics. 
1. How can this explain any issues with the placement of this Marker? 
2. What is a downside to performing these steps at the same time?
4. Why might it have been necessary to set this Marker as “fixed” for AddBiomechanics when it was not “fixed” when using the OpenSim Scale Tool (i.e., scaling a model during a static trial)?
5. Looking at all of the marker errors, suggest other Markers that you may consider “fixing” in future iterations.

6. Assessing Inverse Dynamics Results

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. Are these differences surprising given that the processing steps were performed differently?