We tried make an orthomosaic from multispectral tiffs (70m above ground, forest trees), but Pix4Dmatic makes error at orthomosaic (ORTHO-5 error). It shows green twitch only at half of the pictures.
You may want to try out PIX4Dfields that can create orthomosaics from multispectral imagery. Have you given it a try? It’s usually more thought for “flat” areas like fields, but it may work in your case too. It’s worth a try.
What information are you looking at when mapping the forest?
The last trying with Pix4DFields became successful. We are trying to find an algorithm to accurately delineate tree crowns from othomosaic.