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I am attempting to use the scale tool for the model I am using. I have made sure the markers on the model that are in the xml match the markers that are found in the trc file. What I have done was followed along with the webinar for tips and tricks on scaling, then put in the pairs for the pelvis and the right femur. For some reason it will not produce a scale factor. Not sure what I am doing wrong, does anyone know other things I could try to get the scale tool to work?

Not sure, but those boxes can be highlighted red when those measurements don't have any pairs of markers assigned to them (in the Edit Measurement Set). You could check out some of the files provided OpenSim files for Gait2392 (see your Documents/OpenSim/4.1/Models/Gait2392_Simbody) for an example. Load in the model and then open the Scale tool and load the setup file, and then check out how the "Edit Measurement Set" is filled out.