I am trying to clip a 6 band Micasense Altum image which is in Uint16 format, with 5 multispectral bands and a thermal band which is lower resolution. The image was aligned using the micasense alignment procedure. The image and shapefile don't have a CRS, but align perfectly in QGIS . The Clip Raster by Mask Layer tool results in the correct area being clipped, but the output is entirely black.
I have tried various compressions (LZW, JPEG, NONE) and deflation options to no avail, i.e as per the discussion here: Creating compressed GeoTIFF with QGIS Clipper tool?
My additional command line parameters include:
-to SRC_METHOD=NO_GEOTRANSFORM -crop_to_cutline
Here is a link to the dataset and below is a screenshot of the issue.