Hi Experts!
I am a newbie to the motion capture and kinematic analysis. We are planning to use an optitrack MOCAP system to examine gait parameters during some walking experiment. we dont have any force plates or EMG sensors and have only passive marker data to use.
So far I am trying to use opensim to scale a body model and do inverse kinematics. I extract movement traces from optitrack in .c3d format and convert them to .trc using MOKKA(I understand I could also export .trc files as well).
Now I am trying to use opensim scaling tool to scale a body model to match my subjects anatomy. I was wondering if anyone might have had done this before and could help me along the way?
Do I need to rename the markers? it seems like optitrack markers name do not match opensim markers (if I want to scale to gait2354)? is there any way I can do it automatically? any software available?
Thanks,
optitrack system
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Kaitlin Lostroscio
- Posts: 4
- Joined: Wed Jan 25, 2017 2:59 pm
Re: optitrack system
I am working on this as well.
- Marker names need only match (so you could either change the marker names in the OpenSim model or open the .c3d/ .trc in a text editor or Excel and change the names there)
- You can create & move markers in your OpenSim model as well
- Since your mocap won't have joint center markers, it may be worth while to create "Virtual Markers" to help with scaling. (And for scaling, uncheck any markers that don't exist in both the OpenSim model and the experimental marker set)
Hope this helps, and best of luck!
PS: if you are having trouble with the .trc export from OptiTrack, it may be fixed in the Motive update to be released in the next couple months
- Marker names need only match (so you could either change the marker names in the OpenSim model or open the .c3d/ .trc in a text editor or Excel and change the names there)
- You can create & move markers in your OpenSim model as well
- Since your mocap won't have joint center markers, it may be worth while to create "Virtual Markers" to help with scaling. (And for scaling, uncheck any markers that don't exist in both the OpenSim model and the experimental marker set)
Hope this helps, and best of luck!
PS: if you are having trouble with the .trc export from OptiTrack, it may be fixed in the Motive update to be released in the next couple months
Re: optitrack system
You can change the name of the markers in OpenSim GUI. Each markers name, body it is fixed to, and location in the local frame, can all be edited in the GUI.
You could also do it in Matlab, but since you should only have to customize your markerset once (you use the same markerset on every subject and trial), then it is quicker to do it in the GUI.
If you are new to scaling, I will refer you to the OpenSim scaling documentation. There is also a recently done webinar on scaling that it now on youtube
You could also do it in Matlab, but since you should only have to customize your markerset once (you use the same markerset on every subject and trial), then it is quicker to do it in the GUI.
If you are new to scaling, I will refer you to the OpenSim scaling documentation. There is also a recently done webinar on scaling that it now on youtube
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mahsa Malekmohammadi
- Posts: 2
- Joined: Wed Mar 15, 2017 9:29 am
Re: optitrack system
Thanks for your comments! I really appreciate the insight.
I tried creating my own markerset in optitrack to match the GAIT2354 model in opensim but realized that while doing the experiment the optitrack motiv software doesnt track/interpolate my marker locations automatically so there are episodes of time when I dont have any data for some of the markers
Now in the optitrack system I see they introduce the rizouli's markerset and visual 3d to process the gait and they dont really allow for adding a custom markerset thay I can repeatedly use on my subjects
this makes me feel trapped somewhat that I have to purchase their suggested software (Visual 3D) to be able to analyze gait data
Do you happen to have any experience defining the gait2354 model in any of your expeiemtns with optitrack?
Thanks,
I tried creating my own markerset in optitrack to match the GAIT2354 model in opensim but realized that while doing the experiment the optitrack motiv software doesnt track/interpolate my marker locations automatically so there are episodes of time when I dont have any data for some of the markers
Now in the optitrack system I see they introduce the rizouli's markerset and visual 3d to process the gait and they dont really allow for adding a custom markerset thay I can repeatedly use on my subjects
this makes me feel trapped somewhat that I have to purchase their suggested software (Visual 3D) to be able to analyze gait data
Do you happen to have any experience defining the gait2354 model in any of your expeiemtns with optitrack?
Thanks,
-
Kaitlin Lostroscio
- Posts: 4
- Joined: Wed Jan 25, 2017 2:59 pm
Re: optitrack system
While I believe you are correct that OptiTrack does not currently support complete custom markersets for models (for creating custom skeletons), and so reconstruction & auto-label is not available, you can still use manual labeling methods and the editing tools in Motive to fill the gaps. (Although more tedious, you can get the job done with it)
Data Editing: http://wiki.optitrack.com/index.php?title=Data_Editing
Manual Labeling: http://wiki.optitrack.com/index.php?title=Labeling
Edit Tools: http://wiki.optitrack.com/index.php?tit ... Tools_Pane
Assets: http://wiki.optitrack.com/index.php?title=Assets (could use the markerset creation feature to help group while manually labeling)
You could further explore the OptiTrack documentation and forum for your data editing questions:
OptiTrack forum: https://forums.naturalpoint.com/viewforum.php?f=78
One hurdle on the OpenSim side is getting data in the proper format (if you are unable to export a .trc properly in your version of Motive). If your .c3d exports correctly, you can look to these tools to aid in converting - Tools for Preparing Motion Data: http://simtk-confluence.stanford.edu:80 ... otion+Data
Data Editing: http://wiki.optitrack.com/index.php?title=Data_Editing
Manual Labeling: http://wiki.optitrack.com/index.php?title=Labeling
Edit Tools: http://wiki.optitrack.com/index.php?tit ... Tools_Pane
Assets: http://wiki.optitrack.com/index.php?title=Assets (could use the markerset creation feature to help group while manually labeling)
You could further explore the OptiTrack documentation and forum for your data editing questions:
OptiTrack forum: https://forums.naturalpoint.com/viewforum.php?f=78
One hurdle on the OpenSim side is getting data in the proper format (if you are unable to export a .trc properly in your version of Motive). If your .c3d exports correctly, you can look to these tools to aid in converting - Tools for Preparing Motion Data: http://simtk-confluence.stanford.edu:80 ... otion+Data