It's been a while since I've done some thermal ortho's, but we used to take .tiff images, and put a raster transformation on it with the raster calculator.
So the single input band (B1) is transformed in the raster calculator with "B1*0.04-273" as a base, then we would take measurements from flir tools and adjust the offset accordingly.
As I said, it's been a while since I've done this, but hopefully this gets you a little further.