Questions regarding OpenSim Scaling. Markers

[Ayman Habib]

Hello,

Currently, the Physical Activity Lab at Colorado State University is
attempting to make a msculoskeletal model utilizing OpenSims simulation
software. We recently collected kinematic data using a motion capturing
system and I am trying to create a scaled model and motion file (.MOT) using
this information. We are new at this and need some guidance on the
following topics:

1. When scaling a current model (one that I've downloaded as an example),
where can I find the origin of that model in order to convert the lab
coordinates to the model coordinates?
2. Am I corrent when assuming that the location of each marker that I
specify in the MarkerSet.xml file needs to be scaled to the COM of its
respective segment?
3. Some models use "bodies" as bones and not actual segments (ie, instead of
using the foot as a "body", it will use the talus or calcaneous). How
should I scale the coordinates of different markers to these bones? Or
should I use a different segment?
4. Do you have any advice on what markers are crucial in obtaining
simulation of a walking lower extreminty? For instance, what markers on the
torso would you recommend? We currently have markers on the right and left
ASIS, T1, T10, and sternum. Would you recommend using all of these in our
model?

Any input you could provide would be greatly appreciated and I will post a
summary of responses once I have everything figured out.

Robby Ketchell
Robby.Ketchell@gmail.com
Colorado State University
Department of Health and Exercise Science
Fort Collins, CO

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[Ayman Habib]

Hi Robby,

Some quick answers to your message (reposted from Biomech-L)
1. The model origin is the same as the origin of the "ground" segment which you can visualize by adding a new "Marker" at the point 0,0,0 of the ground body.
2. Throughout OpenSim, locations are specified relative to the geometric "origin" of a segment and not its "COM" (which was a convention used by SD/Fast).
3. The bones are used exclusively for visualization. You should always refer to "segments" and not "bones". Segments could have multiple or no geometry files/bones.

Hope this helps,
-Ayman

[Travis Peterson]

Ayman,

I have both .jnt and .msl files for a SIMM model. The .jnt file gives sections for SEGMENTS and for JOINTS. You said previously that coordinates are in relation to the ground origin. I want to change positions of certain segments only in the "y" direction, essentially just lowering the height of the segments. Exactly which data do I need to change to make this happen?

Thank you,
Travis

[J.J. Mordang]

Hi,


I've a question about point 2. Is there an easy way to modify the geometric origin of the segments? Like editing the .osim file or do you have to edit the .vtp files?

Cheers,

Jan-Jurre

[Anne Schmitz]

Hello,

In response to segment origins. I too am working with a coordinate system different than the one used in OpenSim. I am using local frames from Sheehan's dynamic MRI papers on bone tracking. The only way I found to do this was to modify the .vtp file.

Anne

[Ayman Habib]

J.J,

I'm not sure why you want to change the geometric origin. You can change location and location_in_parent (of the Joint) if all you need is to change where the geometry is displayed relative to the joint.

Keep in mind that the center-of-mass is specified relative to the geometric origin.

Hope this helps,
-Ayman

[J.J. Mordang]

Hi Ayman,

Thank you very much for your reply.
The problem is that the model is correct visual wise. But when I change the location in parent to the coordinates the segment should be the visual segment is shifted because, I think, the segment is virtually bigger than you can see and that's why the center of geometric origin lies outside the segment. The problem is that I don't know how to make the segment smaller (e.g. the actual dimensions of the visual segment), or change the geometric origin.

I hope this is a bit more clear.

Jan-Jurre

[Moon Ki Jung]

Hi Jan-Jurre,

I saw this discussion by chance. And I understood that your problem is related to the scaling problem of geometry files of segments. If I misunderstood your problem, I’d like to say sorry.

There is an open-source geometry modification software that you can use. Its name is MeshLab.
http://meshlab.sourceforge.net/

I think this software is very good to use. It supports various file formats like STL and OBJ.

If you want to scale the bone geometry files of OpenSim human models, you’d better to change their formats as OBJ. The vtp(VTK format) file format can’t be imported in MeshLab.

In MeshLab software, go to the ‘Filters->Normals, Curvatures and Orientation->Transform: Scale’ menu. Then you can resize your geometry files.

If you want to change your vtp files to OBJ files, please give me a private message.

Best regards,
Moonki

[J.J. Mordang]

Hi Moonki,


Thanks for your reply.
I don't think I've to scale the geometry files because I edited the .vtp files of OpenSim and I think they are already scaled. My problem is that in my OpenSim model the model looks all right. But the geometric origins of each segment are not in the right place. For instance the big toe (a seperate segment) has it's geometric origin somewhere in the lateral forefoot (another segment). When I want to place this big toe in the right coordinates of the parent (here the midfoot, a third segment), OpenSim uses the geometric origin causing the toe to shift away from the whole foot. And I think this can be solved by changing the geometric origin of the segment but I don't know how to achieve that.


Kind regards,

Jan-Jurre

[Moon Ki Jung]

Hi,

In MeshLab, there is the menu 'Transform: Move, Translate, Center'. Then you can get new geometry files that is transformed.

Best regards,
Moonki