Perform cloud mask over ROI only

It would be very useful to be able to run the CHRIS cloud mask screening only on pre-selected portions of an image (ROI). For example, I have images in which clouds are distributed only in the upper part of the image, and in which equally bright non-cloudy surfaces (urban) are present in the lower portion of the image but also labelled as clouds by the clustering algorithm. If we could determine ROI beforehand and run the cloud screening only for these ROIs, that would be marvellous!