scaling failed

[Isotta Rigoni]

Good morning,
I am a new user of OpenSim, so my question might sound banal to most of you. I am trying to import my own static trial (.trc file) to scale the gait2392 model. Because I used the PIG marker set, I modified marker names and positions in the Scale_MarkerSet.xml file directly with Notepad++ . Of course I modified them also in the Setup_Scale.xml file (see attachment). Even though the markers are perfectly shown on the model, the scaling features are not working: no scale factors are calculated (apart from the manual scaling) and the markers are "NOT FOUND!" (see pictures). I don't know what I am missing: are there any other files used during the scaling process, where the markers at defined (and therefore I need to redefine them)? Is it a problem if the Vicon segment names are different from those used by OpenSim? If some markers in the .trc file are not modelled in MarkerSet.xml, can this be a problem? Do I need to delete them before importing the .trc file or the software does know how to ignore them? I hope some of you will find the time to answer me, in the meantime, if you could indicate a webpage where the content of the .xml files is described, that would be appreciated.
Thank you very much in advance,
Best,
Isotta

[Thomas Uchida]

indicate a webpage where the content of the .xml files is described

The Scale Tool is described in the "Scaling" section of the Confluence documentation (https://simtk-confluence.stanford.edu/d ... im/Scaling); there are a couple pages in that section that describe the format of the associated XML files. There are also a few scaling-related videos that might be helpful:
- Two at the bottom of this page: https://simtk-confluence.stanford.edu/d ... Scale+Tool
- "OpenSim Webinar: Tips and Tricks for Data Collection, Scaling and Inverse Kinematics in OpenSim": https://youtu.be/ZG7wzvQC6eU
Also see Tutorial 3: https://simtk-confluence.stanford.edu/d ... e+Dynamics.

[Isotta Rigoni]

Thanks for the tips. Anyway, I have another question regarding the marker tracking phase. I am following all the steps described in the "scaling" video tutorial: I created my own marker set (with 27 markers) and my own Scale_Setup.xml file, where I define the static trial with the experimental marker. When I load the last one, the model has only the virtual markers (pink) and no blue markers, but still it looks like the model has been scaled (the segment masses are different from those of the original model). How is this possible? And how do I perform marker tracking before running InverseDynamics? I don't know what I am doing differently from the tutorial...
Thank you in advance,
Best,
Isotta

[Cai Birch]

Hi Isotta, I had a similar issue with the scaling tool saying 'from file --- NOT FOUND' when I exported trc files directly from Vicon Nexus. I found that these errors were occuring because Vicon Nexus was including the subjects name and marker name. For example instead of just the marker name "RAcromion" in the trc file; it would instead give me "Subjectname: RAcromion" instead. I'm not sure how to fix this in Vicon, so I just open up the trc file in excel and remove the subjects name using the 'find & select' function.

It sounds from your last message that you've resolved that issue yourself though!

In order to view your blue experimental markers and the pink model/virtual markers, right click on your output e.g. static pose/cutting motion/etc under the 'Motions' tab in the Navigator window and select 'Associate motion data'. This will allow you to select the respective trc file that you used and load the blue markers to see how closely your scaled model markers match the experimental data.

[jimmy d]

Isotta

When I load the last one, the model has only the virtual markers (pink) and no blue markers, but still it looks like the model has been scaled (the segment masses are different from those of the original model). How is this possible?

I assume you mean the last model? Sounds like you saved over the model at some stage. Start with the generic version of gait2392 (unscaled) and repeat the scaling step with your experimental markers.

And how do I perform marker tracking before running InverseDynamics?

Please go through Tutorial 3 and pay close attention to the tools that you use. In the tutorial, you scale a model, perform inverse kinematics, and inverse dynamics. If your analysis is similar, then make a copy of all the files from the tutorial and edit them for your particular model, markerset, file system, and experimental data