The frequently asked questions about OpenSim are broken up into several categories:
A. As of version 4.0 we're only supporting 64 bit windows machines as these are the most commonly used Windows platform. If you have 32 bit windows machine you can build the API from sources or use an earlier version (e.g. OpenSim 3.3)
A. Starting with OpenSim 4.0, we provide a version of the graphical user interface compatible with Mac.
A. No. You only need Matlab to use the Matlab scripting. If you don't have Matlab, you can still use the application or GUI, the GUI or python scripting shell, and the API. Please make sure if you have Matlab that it has the same architecture (32/64 bit) as OpenSim on Windows.
A. No. You can keep old installations of OpenSim to compare your results.
A. You can access all previous releases through the OpenSim Downloads Page. Directly under the current version is the drop down menu 'List all previous releases'.
A. If you would like to run OpenSim on a Windows machine, but you don't have install privileges, you can try running OpenSim from a USB drive. This may be useful for instructors of biomechanics courses, for example, allowing students to run OpenSim on library computers. To set up the drive, insert the USB drive and install OpenSim, selecting a path the USB drive as your install directory. Note that you must do this on a Windows machine. After installing you can then run OpenSim from another Windows machine. You will likely need to update the Geometry folder under Edit -> Preferences, to the appropriate path on the new machine.
A. Open Edit/Preferences and edit the entry for "Paths: Geometry Search Path" which is a semicolon separated list of directories and add the desired path. See User Preferences for more information.
A. These are the geometry files corresponding to the bones and other objects used by your model. The "vtp" format is a format used by VTK which was used by earlier versions of OpenSim for visualization. vtp files come in two flavors (ASCII, Binary) we only support ASCII format. Both .stl, .obj are standard mesh file formats as well.
A. In version 4.0 we switched from using vtk (for parsing mesh files) to native parsers built into the SimTK libraries. Some STL, OBJ files are not handled by the SimTK parsers which try to build closed meshes from these filesfor contact purposes, for example files with multiple solids, or no solids may not be handled the same.
A. Although many models are loaded, only a single model can be marked as "Current". This is indicated in bold in the navigator.
A. Picking is restricted to "Current model" (by default non-current models are dimmed out). If you want to pick on a non-current model you'll have to make it current first.
A. Only objects that are pickable in the Visualizer window are Path Points and Markers. Moving Muscle Points are special Path Points that have Splines describing their trajectories so they can't be picked and dragged from the GUI.
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A. There are many muscle models implemented in OpenSim.
One of the most commonly used muscles is the Thelen2003Muscle, based on the model described in Thelen, 2003.
Thelen DG. Adjustment of muscle mechanics model parameters to simulate dynamic contractions in older adults. J Biomech Eng. 2003; 125(1):70-7.
We've also added some new muscle models. Watch Matt Millard's webinar to find out more.
A. Yes, the muscle models in OpenSim model the electro-mechanical delay between muscle excitation (or the electrical neural signal sent to the motor-neuron junction) and activation (i.e., the level of force production). From more details on the theory behind our muscle models, check out this great review paper by Felix Zajac: Zajac FE. Muscle and tendon: properties, models, scaling, and application to biomechanics and motor control. Crit Rev Biomed Eng. 1989, 17(4):359-411.
A. Sure! You could develop a custom controller in the OpenSim API that is based upon the stretch of muscle or tendons in the model and map that back to predicted activations.
A. Yes, we do model the orientation, or pennation angle, of muscle fibers, but no, we do not currently model slow versus fast twitch fibers. For more details on the theory behind these muscle models, check out this great review paper by Felix Zajac: Zajac FE. Muscle and tendon: properties, models, scaling, and application to biomechanics and motor control. Crit Rev Biomed Eng. 1989;17(4):359-411.
A. Under Y-Quantity, select "Load file..." and then you can read data files in the storage or motion format.
A. Under the "curves list", right click on the top level node and select "Export Data...". OpenSim will prompt you for a file name to save the data into. This file can be later re-imported into OpenSim or used by other applications.
A. OpenSim does not use a database for scaling. The model is scaled based on measurements of experimental markers. See How Scaling Works for more information.
A. Scaling in OpenSim scales each body segment independently based on measurements of markers placed on that segment. See the section on Scaling for more details.
A. Yes, the optimal force or max strength of the muscles in the model used in many studies are based on Delp, 1990 (see reference below), which determined muscle parameters from cadavers. While the strength of the model was not increased to study running (Hamner et al., 2010), other researchers have noticed that the "strength" (i.e., optimal force) of the muscles has to be increased for movements with higher forces and accelerations, like running and cutting, or for pathological gaits, such as crouch gait. Delp SL et al., An interactive graphics-based model of the lower extremity to study orthopedic surgical procedures. IEEE Trans Biomed Eng. 1990; 37(8):757-67.
A. No, the scale tool in OpenSim does not automatically scale muscle forces based on the geometric based scaling (i.e., scaling based on distance measurements between markers) or the mass scaling. However, you can scale muscle forces in the model based manually if you have a criterion for doing this. See the Scripting chapter for info about how to do this with a script.
A. BIODEX data can be used to determine the strength, or torque generating capacity of your subject. Researchers have used this information to modify the optimal muscle forces used in their model. For an example, check out the paper by Anderson & Pandy from 2001. They explain, "Values of peak isometric muscle force and tendon slack length were adjusted so that the maximum isometric torque angle curves for each joint in the model matched average torque-angle curves measured for the five subjects." Anderson FC, Pandy MG. Dynamic optimization of human walking. J Biomech Eng. 2001;123(5):381-90.
A. RRA is an optimization algorithm whose goal is to minimize the non-physical “residual” forces acting on a dynamic simulation. The settings modified for RRA are the inputs to the optimization algorithm, which include the excitation limits (i.e., min/max controls) for the residual actuators along with the tracking weights for each of the coordinates (i.e., joint angles). See Getting Started with RRA for more information.
A. Yes, OpenSim has another tool called Static Optimization, which has been used by numerous researchers to estimate muscle forces. Check out this paper describing static optimization: Anderson FC, Pandy MG. Static and dynamic optimization solutions for gait are practically equivalent. J Biomech. 2001,34 (2):153-61.
A. No, we do not explicitly model synergistic muscle groups. Computed muscle control treats each muscle as an independently controlled actuator. However, our results show that muscles are still activated in the observed synergistic groups.
See our Musculoskeletal Models page for a list of OpenSim models that we've developed at Stanford, as well as a link to the library of models from our team and other researchers on Simtk.org. Please also see our page on Evaluating a Musculoskeletal Model. It has a list of questions to review when deciding what model to use in your research.
A. Yes, students and researchers in the Neuromuscular Biomechanics Lab at Stanford have created muscle-actuated simulations of individuals with cerebral palsy with a crouch gait. Check out a recent study led by Kat Steele. Steele, K.M., Seth, A., Hicks, J.L., Schwartz, M.S., Delp, S.L. Muscle contributions to support and progression during single-limb stance in crouch gait. Journal of Biomechanics, vol 43, pp 2099-2105 and other papers on the Neuromuscular Biomechanics Lab Page. See the OpenSim Website for more research applications.
A. For dynamic simulations of rigid body systems, like a double pendulum, check out Simbody(TM), which is the rigid-body dynamics engine used by OpenSim. It is open-source and freely available with a well-tested and stable API. The project page is https://simtk.org/home/simbody.
A. Importing data can sometimes be time consuming and require troubleshooting. The most difficult part is setting up a custom workflow that fits our lab and needs. See Preparing Your Data for more information about this process. We've added Scripting to make it easier to customize your workflows. Other users have also contributed their tools in the OpenSim Utilities library. We also plan to continue to improve our usability going forward, as one of our top priorities.
Yes. You can model Hunt Crossley Contact Forces and add contact geometry. See the OpenSim Doxygen for more information. Check out the XML Browser in the GUI (under Help) to find the xml tags to add the force to your model.
A. Yes, OpenSim version 3.2 and later supports scripting in Python, Jython (an implementation of Python in Java), and MATLAB. In the OpenSim application, the scripting shell is a Jython shell. All scripting capabilities use a technique (called wrapping) to invoke the OpenSim C++ API from Python, Java, or MATLAB.
A. You should be able to leverage the extensive Doxygen documentation of the OpenSim API to use it in Scripts. You'll also find the examples included with the distribution as well as the help page on Scripting (Common Scripting Commands) helpful.
A. Starting with OpenSim 4.0, we only provide 64-bit versions of the software. You can use OpenSim with 64-bit Matlab by downloading and installing the 64-bit version of the OpenSim GUI. This assumes you are using Windows. Read more in Scripting with Matlab.
A. No, the OpenSim application and the scripting interface both utilize the same libraries, but are unrelated otherwise. While scripting in the GUI, you have access to all the API and some GUI functionality (e.g. control of view, plotter, loading models, motions, etc.). While in MATLAB you have access to the API and you can use the MATLAB tools for plotting and the API Visualizer. You can also use the scripting interface from a standalone Python or Jython shell but you have access to neither the GUI functionality nor MATLAB's. See Common Scripting Commands for more information.
A. You can invoke almost any menu command and many other functions (e.g. Plotting) from the GUI scripting layer, but not all dialogs/tools/options are exposed. Please consult the page Common Scripting Commands#GUIScriptingShell for specific examples.
A. You can turn on more verbose messages so you get more feedback while running scripts by calling modeling.setDebugLevel(3), but for syntax errors you usually get the error message displayed in the scripting shell directly.
In general, we strongly discourage doing raw parsing of XML files in a Matlab script. This approach is not robust and does not take advantage of the OpenSim API in Matlab. Instead you should instantiate tools/objects from setup files and let the code do the parsing internally. The XML format changes with different versions of the software and the version number of the documents written by newer versions of the software may even be different from the one you read due to backward compatibility built into the code and assumptions about default values, etc. You'll keep changing your code endlessly rather than rely on a robust API that makes calls to set/get values (rather than parse XML files). In essence the assumptions about the contents of the XML files and the XML file header are all built into the code that is exercised by the API but ignored by any XML parsing code. Violating these assumptions will break the functionality downstream.
An example using parsing (not recommended for OpenSim 3.0):
% get initial and inal time from first and last entry in time column
initial_time = trcData(1,1);
final_time=trcData(end,1);
xmlDoc.getElementsByTagName('IKTool').item(0).getAttributes.item(0).setValue(name);
xmlDoc.getElementsByTagName('marker_file').item(0).getFirstChild.setNodeValue([trialsForIKPath markerFile{1}]);
xmlDoc.getElementsByTagName('output_motion_file').item(0).getFirstChild.setNodeValue([results_folder '\' name '_ik.mot']);
xmlDoc.getElementsByTagName('time_range').item(0).getFirstChild.setNodeValue([num2str(initial_time) ' ' num2str(final_time)]); |
An example of calling the API (recommended):
% Get trc data to determine time range
markerData = MarkerData(markerDateFileName);
% Get initial and intial time
initial_time = markerData.getStartFrameTime();
final_time = markerData.getLastFrameTime();
% Setup the ikTool for this trial
ikTool.setName(name);
ikTool.setMarkerDataFileName(fullpath);
ikTool.setStartTime(initial_time);
ikTool.setEndTime(final_time); |
The code snippet above is take from the example "setupAndRunIKBatchExample.m".
Q. What is the relationship between SIMM and OpenSim
A. Please review this PDF (updated March 2010)