The bones are shoulders, back, hips, head, lthigh, lknee, lankle, lfoot, rthigh, rknee, rankle, rfoot, lshoulder, lelbow, lhand, rshoulder, relbow and rhand, respectively



Structure:



For some reason, the character stays too big and intersects with itself using the most obvious choices.

Can you provide us the character file itself so we can test it?

Yes.

How do I assign the bones of the model I uploaded in iPi Mocap Studio?

Please reply as I made the effort of preparing and uploading the file.

I have checked the file. The best result I could get is attached (retargeting profile for Mocap Studio).
It seems that this rig is not adequate for retargeting in Mocap Studio. The joint structure differs significantly from the model used by Mocap Studio. If you author this character, consider making another rig, with root at hips and connections between joints similar to model in Mocap Studio.
PS. The "l" and "r" prefixes for joint names are confusing, because they reference the opposite side of the character - joints of the right side have prefix "l", and vice versa.

Thank you.

Your keks.fbx character has a very unusual structure with root bone at shoulders. It is impossible to retarget from iPi skeleton. (Default iPi skeleton root bone is hips).

Please read http://www.mit.edu/~ibaran/autorig/pinocchio.html for more information.

Given my skeleton, which approach do you suggest to get the best template for ipi desktop?