In your case, you cannot apply the alignment procedure based on homography. Why not? Because it is not suitable in this use case. It was designed to level flat surfaces. Faces (3D objects) with markers in different places and depths obviously do not have a flat surface.
Instead, you can:
- try to match markers between images, then interpolate the offset field of the other pixels. Classic ways to do this would include least squares interpolation or RBF 's;
- "Face Processing" (, AAM) .