I'm using QGIS to analyze some image of the NOLA area pre- and post-hurricanes. I'd like to calculate NDVI and a couple other indices for the images, but I want to exclude pixels with clouds in them from my final analysis. I already have an fmask band for each of the images, however I'm not sure how to incorporate that into the index calculation so that those pixels are excluded. Is this something I would need to do after calculating the indices? Ultimately I'm going to compute difference layers and use multidate classification for the change analysis.
I have access to QGIS, gdal, and otb, but not too much experience with the latter two.