Theia3D itself does not output joint angles, so these must be derived from the segments. Two types of joint angles are commonly used in biomechanics:

Angles around a joint between the joint's proximal and distal segments
Progress angles – the angles between a segment and the subject's progression coordinate system

First, you define a standard joint angle:

After loading the trial, click the Variables tab and create a new Scheme (or edit an existing one).
Add a new variable.
Enter a relevant name for the variable, for example LeftKneeAngles.
For the Function, choose Angle and on the same line Euler Angle: XYZ between A and B.
For A, choose Type: Segment and Input Variable: l_thigh_4X4.
For B, choose Type: Segment and Input Variable: l_shank_4X4

The setup now looks like this:

Note that we have chosen XYZ as the Euler Angle extraction order. This is because the Theia segments are by default oriented X = mediolateral, Y = anterior-posterior, Z = proximal-distal. Thus, we extract flexion/extension first, followed by ab/adduction and finally rotation (which conforms to normal biomechanical conventions).

Also note that you have the option to negate one or more of the components if the mathematical output does not conform to convention. To do this, select the relevant combination from the Negate drop-down menu at the top right in the above image.

By repeating this procedure for other joints and their proximal/distal segments, you can define the joint angles that you want to calculate.

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