Landmarks on generic bones (problem in aligning a CT bone on the generic bone)

[Seyyed Hamed Hosseini Nasab]

Hello everybody,

I want to develop a subject specific musculoskeletal model of a TKA subject based on lowerlimb2010 model. I have coordinates of some bony landmarks on femur (femural head center, medial epicondyle and lateral epicondyle) and some others on the tibia (medial and lateral malleolies) in the CT coordinate system. In addition I have 3D pose of implant components in the CT coordinate system. The problem is that, I don't know the 3D pose of the generic bones in the model. What I know is that, in stand pose, the origin of hip, knee and ankle frames are aligned. This only determines the bone pose in sagital plane. Therefore one of the following options may help me to align the bone geometry obtained from CT to that of opensim:
1- Orientation of the line connecting medial and lateral epicondyles in the femural frame of the generic model
2- Orientation of the line connecting medial and lateral malleolies in the tibial frame of the generic model
or
3- STL files of the generic bones
If you have any information that can help me in this matter, I will appreciate it.

With kind regards,
Hamed

[John O Connor]

Hi Seyyed,

All the geometries in OpenSim models are available in the directory specified under the "bodies>femur_r>display geometry" tree in the GUI. These can be in many formats such as .vtp but you can convert them to .stl file using (http://www.kitware.com/opensource/paraview.html). You can then use some registration method to align your CT scanned femur to the model. Note also that there is often a scale mismatch between opensim and CT femurs as Opensim geometry tends to be in metres, you may have to scale the resulting geometry to millimetres.

Best of luck
John