MarkerSet

[John Chow]

I have gait data (in .trc files) collected using a MAC system with Helen-Hayes marker set. My question is whether the current version of OpenSim allows me to run my data. The tutorials give a very nice overview of the software and its capabilities. The Workflow section describe different files involved. But it is not clear to me whether the MarkerSet.xml can be modified to suit different marker sets.

[Daniel Leib]

Hi John,

It can be edited, but I believe they're still in the process of putting together the documentation on how the expected location of the markers is defined. I found it easier in the short term to put together a marker set (I'm using a Vicon system) that matches the one used in the demos. You don't have to use all of them - individual markers can be disabled as you perform the simulation. As a for instance, I don't use the medial markers of the knee, ankle, or foot for dynamic trials as they tend to be unreliable in what I'm collecting. The dialogue box will simply say "NOT FOUND IN FILE" and you can uncheck the marker before you hit run.

You can edit the *_marker_set.xml either by using the built-in edit function (Edit tab on top -> file -> file of interest) or by using a standalone XML editor. If you Google "open xml editor" several will pop up, I prefer a standalone since it looks more like a standard textual programming environment.

Have a good one,

Dan

[Ayman Habib]

Hi Daniel,

Do you mind sharing the file you created? Other users may find it useful.

Thanks,
-Ayman

[Daniel Leib]

Sure, I'd love to. I don't see a way to attach the file to this post, so I'll send it your way in an email. The attachment should be named SIMM.mkr.

-Dan

[Daniel Leib]

*edit - realized that might be confusing with SIMM being a different system, renamed to OpenSim.mkr

-Dan

[Chen-Hua Yeow]

Hi Dan,
I'm using the Vicon system too but I'm still figuring out how to make OpenSim accept PIG marker set. Does the markers in PIG and OpenSim overlap exactly? Do you observe any significant difference in the joint angles calculated by Vicon and by OpenSim. I'm interested to know how you approached this problem using your personal marker set (based on OpenSim) for Vicon. Would you mind sharing your mkr file at raydenyeow@yahoo.com.sg? Thanks a lot!

Yeow

[Daniel Leib]

Hi Yeow,

The marker sets don't quite overlap exactly, but that's not a huge problem as the "expected location" of the markers is moved to match where the markers are actually appearing in your data file. There are a couple differences that make a significant impact, though, so I went ahead and put together an XML marker set file for PiG and a scaling file for it. I've sent it to Dr. Habib to be distributed, but we're not sure that it's ready for mass use yet so I'm still doing some testing with it to make sure. If you'd like the files (SIMM.mkr, the PiG marker set XML, and the scaling file), feel free to send me an email at daniel.leib@gmail.com and I'll send them your way to try out.

So far the kinematics look pretty similar for normal gait and for cycling, with the exception of non-sagittal angles for the knee and ankle as those aspects of the joints are tightly constrained in the model file I've been using.

-Dan

[Ayman Habib]

I went ahead and uploaded the files provided by Daniel to the opensim-utils project. They should be accessible at the URL below so that other users can try them out.

https://simtk.org/websvn/wsvn/opensim-u ... _MarkerSet_

Please be aware that since these are not part of the OpenSim release, no support or guarantees are made about them from the OpenSim team.

Thanks Daniel.

[Daniel Leib]

Cool, thanks for uploading them! If anyone has any questions or finds a bug, feel free to send them my way or to the forum and I'll see what I can do.

Just a quick note for anyone who uses the PiG files - you can autoscale the model you're using using marker data, but the feet always come out a little bit small due to the difference between using a toe tip marker and the PiG toe marker. Manually scale the foot a little larger than the autoscale does it and you should be good to go.

Have a good one,

-Dan

[John Chow]

Hi Dan:

I collected a trial using the markersets in subject01_static.trc and subject01_walk1.trc. I went thru the 2nd tutorial and played around with the Scale Model and Inverse Kinematics in OpenSim but haven't had much luck in creating the motion (.mot) file I expected. Any suggestions will be much appreciated.

John