You get results in the same unit as the input image. In case of a calibrated CT, it is Hounsfield unit. In case of a non-calibrated system, it can be anything.
3 measurement points are very few. At least for initial exploration, I would add at least 5-10 points, just to have an idea about shape and amount of noise in the curve. It is highly unlikely that the calibration curve would be a line, so fitting a line to 3 points is a potential source of error.
GelDosimetry extension contains an automatic image intensity calibration and evaluation workflow that should be directly usable. @cpinter do you have any advice?
There could be many reasons, but I don’t know what that software does. Is that software open-source? Do they describe somewhere what they do?
How much is the difference? If it’s small then it may be due to forcing the calibration curve to be a line.