Hello,
I would like to use the data that is included when downloading the program (MOtoNMS) for the following procedure.
I'd like to take the .trc and mot. files from the GU subject (one of the subjects that is among the examples in MOtoNMS download) and use them in OpenSim to execute Computed Muscle Control. But I am not sure this is possible, so please, find below my doubts.
(1) I had thought of the possibility of scaling and then applying Inverse Kinematics, RRA and finally CMC.
(2) In case (1) is possible, I first need to scale a model. For this purpose, the static .trc marker file is also provided in MOtoNMS download, for the GU subject. Assuming I already have a musculoskeletal model, however, I would need to provide the Scale Tool with the marker virtual set .xml file, which I don't know how to define, since the location of markers is unknown. So I have the experimental markers (static .trc file elaborated by MOtoNMS) but not the virtual ones.
I'd like to thank in advance any kind of help or comment about this problem I'm posing, which may be wrongly posed.
Thank you for your attention,
Ana
Using MOtoNMS example files for CMC in OpenSim
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Ana Algora
- Posts: 6
- Joined: Wed Jun 22, 2016 2:42 am
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Alice Mantoan
- Posts: 29
- Joined: Fri Feb 24, 2012 11:51 am
Re: Using MOtoNMS example files for CMC in OpenSim
Dear Ana,
your idea is certainly good, and also possible. Said that, your doubts are rightful.
In the MOtoNMS Test Data package, we intentionally do not provide the OpenSim models, since our focus is in the processing of input experimental data, not the following workflow with the OpenSim Tools that MOtoNMS aims to facilitate.
However, we have been developing another tool, called BOPS, that aims to represent an aid in performing batch processing of the most common OpenSim Tools (e.g. Inverse Kinematics, Inverse Dynamics, Muscle Analysis and Static Optimization). You can find the project here:
https://simtk.org/projects/bops
Test Data from this project exploits most of the input data used to test MOtoNMS (i.e. UMGsubject, UNIPDsubject and UWAsubject, while unfortunately we could not include the GUsubject). In this package, OpenSim scaled models are already included, as they are required for the subsequent steps implemented in BOPS.
From the scaled models, you can export an .xml file describing the position of the virtual makers (see at the end of this page: http://simtk-confluence.stanford.edu:80 ... ker+Editor).
Therefore, I would suggest you to integrate MOtoNMS Test Data with the scaled models you can find in the BOPS Test Data package.
If you are interested also in using BOPS source code, I would suggest you to download the latest version from our Github repository (https://github.com/RehabEngGroup/BOPS/tree/develop), until we will release BOPS 1.0 in the SimTK project page.
I'm glad to help if you have any other doubts. Please, just remember that if you are using our data for your research, we kindly ask you to cite the following paper:
Mantoan et al. Source Code for Biology and Medicine (2015) 10:12
DOI 10.1186/s13029-015-0044-4
http://www.scfbm.org/content/10/1/12
Kind regards,
Alice
your idea is certainly good, and also possible. Said that, your doubts are rightful.
In the MOtoNMS Test Data package, we intentionally do not provide the OpenSim models, since our focus is in the processing of input experimental data, not the following workflow with the OpenSim Tools that MOtoNMS aims to facilitate.
However, we have been developing another tool, called BOPS, that aims to represent an aid in performing batch processing of the most common OpenSim Tools (e.g. Inverse Kinematics, Inverse Dynamics, Muscle Analysis and Static Optimization). You can find the project here:
https://simtk.org/projects/bops
Test Data from this project exploits most of the input data used to test MOtoNMS (i.e. UMGsubject, UNIPDsubject and UWAsubject, while unfortunately we could not include the GUsubject). In this package, OpenSim scaled models are already included, as they are required for the subsequent steps implemented in BOPS.
From the scaled models, you can export an .xml file describing the position of the virtual makers (see at the end of this page: http://simtk-confluence.stanford.edu:80 ... ker+Editor).
Therefore, I would suggest you to integrate MOtoNMS Test Data with the scaled models you can find in the BOPS Test Data package.
If you are interested also in using BOPS source code, I would suggest you to download the latest version from our Github repository (https://github.com/RehabEngGroup/BOPS/tree/develop), until we will release BOPS 1.0 in the SimTK project page.
I'm glad to help if you have any other doubts. Please, just remember that if you are using our data for your research, we kindly ask you to cite the following paper:
Mantoan et al. Source Code for Biology and Medicine (2015) 10:12
DOI 10.1186/s13029-015-0044-4
http://www.scfbm.org/content/10/1/12
Kind regards,
Alice
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Ana Algora
- Posts: 6
- Joined: Wed Jun 22, 2016 2:42 am
Re: Using MOtoNMS example files for CMC in OpenSim
Thank you very much; it seems to be just what I need to continue working.
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Ana Algora
- Posts: 6
- Joined: Wed Jun 22, 2016 2:42 am
Re: Using MOtoNMS example files for CMC in OpenSim
Dear Alice,
I have another problem that prevents me from continuing my work. I finally used the UNIPD subject and used the desired kinematics file that is provided by BOPS. Before computing CMC, I want to compute RRA algorithm, but I am lacking two important files. The ground reaction forces file .xml I think is written adequately. However, for RRA, I also need two other files: tracking tasks (.xml) and reserve actuators (.xml). I copied them from another model, just to run RRA. Even though it runs, of course, RRA doesn't finish and is computed wrongly. I think I should modify the code inside those files. For example, variables 'point' and 'direction' in the reserve actuators file or variables 'kp', 'kv' and 'gain' in the tracking tasks file.
Otherwise, what could I do? And I have to indeed modify those pieces of code, which criteria should I follow? I tried reading the user guide, but I could not get any clear idea.
I have another problem that prevents me from continuing my work. I finally used the UNIPD subject and used the desired kinematics file that is provided by BOPS. Before computing CMC, I want to compute RRA algorithm, but I am lacking two important files. The ground reaction forces file .xml I think is written adequately. However, for RRA, I also need two other files: tracking tasks (.xml) and reserve actuators (.xml). I copied them from another model, just to run RRA. Even though it runs, of course, RRA doesn't finish and is computed wrongly. I think I should modify the code inside those files. For example, variables 'point' and 'direction' in the reserve actuators file or variables 'kp', 'kv' and 'gain' in the tracking tasks file.
Otherwise, what could I do? And I have to indeed modify those pieces of code, which criteria should I follow? I tried reading the user guide, but I could not get any clear idea.
-
Alice Mantoan
- Posts: 29
- Joined: Fri Feb 24, 2012 11:51 am
Re: Using MOtoNMS example files for CMC in OpenSim
Dear Ana,
I'm sorry but this forum is about doubts and problems related to the use of MOtoNMS software.
RRA is an OpenSim tool, and thus I suggest you to post your last question in the OpenSim forum.
Best Regards,
Alice
I'm sorry but this forum is about doubts and problems related to the use of MOtoNMS software.
RRA is an OpenSim tool, and thus I suggest you to post your last question in the OpenSim forum.
Best Regards,
Alice