How can I fit shapes to my sensor data (e.g. CT scan mesh)?

[adamkewley]

AK: this question was ported from an email. The content was edited/redacted to make it suitable for a public discussions thread.

As you know the process of building subject specific OpenSim model, it is necessary to have joint centers. For example, when you have a mesh file of femur which is segmented from medical images, the center of a sphere fitted to the femoral head would be hip joint center. Similarly, the axis of a cylinder fitted to femoral condyles would be knee flexion/extension axis. So, is there any way to:

1. Select a specific area (point clouds) of a mesh. e.g selecting the femoral head (point clouds) of the entire femur
2. Fit analytic geometry to the selection, e.g. a sphere, a cylinder, etc.. It would be useful to fit a sphere to the selected point clouds from the above feature.
3. Report required parameters of the fitted geometries from the above feature for building OpenSim model. e.g center, radius, axis and etc.

These features would ease the process of building OpenSim models from bone geometries created via medical images segmentation software.

Please find the following projects that do similar things via MATLAB:

https://simtk.org/projects/subj-spec-model/
https://simtk.org/projects/auto-sk-models/

[adamkewley]

OpenSim Creator has basic facilities for fitting analytic geometry to meshes in an OpenSim model. The way that's done is:

• Right-click a mesh in the model
• Go to the Fit Analytic Geometry to This menu
• Click on a desired geometry (e.g. Sphere)

At time of writing (v0.5.12), this is limited to fitting the entire mesh, not a manually-selected subset (as requested). The fitting algorithms are were ported to C++ from the MATLAB code that's in the supplementary information of this paper:

• Bishop PJ, Cuff AR, Hutchinson JR. How to build a dinosaur: Musculoskeletal modeling and simulation of locomotor biomechanics in extinct animals. Paleobiology. 2021;47(1):1-38. doi:10.1017/pab.2020.46

Practically speaking, if you want a "hacky" way to fit only part of a mesh, then you could:

• Select points you care about in VFX software like Blender, invert the selection, delete all other points
• Re-export this butchered mesh to the same location as the original one
• Re-load your model in OpenSim Creator (there's a button in the toolbar, or do it manually)
• Fit the geometry as-described above
• Un-butcher the mesh in your VFX software and re-export it
• Reload your model in OpenSim Creator
• You'll then have the fit you want, but with the original (un-butchered) mesh.