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I'm trying to fine tune my scaling of a generic model to fit a subjects static mocap data. Experimental and virtual markers will not match perfectly despite my best (but novice) efforts and I'm wondering what is being scaled exactly. I've computed measurement based scale factors for all segments but I'd like to know if the model is scaling only the bone geometry e.g. femoral condyle to femoral head; or from joint center to joint center? I've read the 'How Scaling Works' documentation but I'd like to be certain of what it means..Thank you!

Scaling only adjusts the bony geometries along their primary axes (X,Y,Z). The long axis of the femur passes from the mid-condyle point to the center of the femoral head. Assigning the appropriate scaling factors is very challenging and can be a bit easier if you go through a functional joint center definition for the hips and knees to find their true axes in order for scaling. The ankle joint is pretty easy to identify by palpating the malleoli.