Thanks for the reply Torsten, that was extremely useful.  My images are always roughly in the same orientation (+- 10 degrees) so I just proceeded with the warping without paying much attention to the warning message.  After running the reformatx command I am now getting a totally black image, which I guess may be because I have not chosen the correct parameters when warping.  I will fiddle a bit more with this and post again if I continue to have problems.
Best,
Ruben