Thanks Alexey.
Following Appendix A and the workflow suggest by a previous user I:
1. Generate the mask for one single picture using the SELECTION TOOLS
2. TOOLS > EXPORT > EXPORT MASKS. Save as a single channel mask image.
3. TOOLS > IMPORT > IMPORT MASK and select OK.
I do not see a cropped image, I assume that the algorithm just uses it to compute an average value over this area and then uses the value for the reflectance calibration, correct? So no cropped image is physically stored anywhere.