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You can import .c3d file in blender like this:

https://stackoverflow.com/questions/20499320/how-to-import-c3d-files-into-blender

The problem is it won't be an armature, but animated locations of points:

Some points will be dead in the center (marked).

1. Adjust the frame range to fit the mocap data

2. Delete the dead markers

3. Re-build the armature - add armature to scene

   • looks like we have markers from both sides for each leg - that means the bones will be somewhere in between markers

   • Building the armature:

     • select a marker (or two if I want position in between) and align 3D cursor with 'Shift-S > Cursor to Selected'
     • then enter edit-mode of armature and select a joint and 'Shift-S > Selection to Cursor'
     • this way I can place all the bones (joints) precisely

     

     • also recalculate the Roll of the bones with 'Ctrl+N > Cursor' with 3D cursor on some reference marker

   • Name the bones properly

   • Constraining location of root bones:

     • use copy_location constraint
     • or two of them with second on 50% influence to get in-between position of two markers
     • similar for center of 3 markers, you get the idea

   • Constraining bones direction

     • use damped_track constraint
     • also multiple of them with adjusted influence for center of group of markers

     

4. Bake the animation to Action with Pose > Animation

   Bake Action: visual_keying_ON, clear_constraints_ON

5. Export armature as .bvh from the blender main menu (you might need to enable BVH addon).

These steps will result in having a .c3d file converted to a .bvh file. A sample .blend file with rigged markers here: