IMALIGN is a powerful but potentially annoying tool.

Step How to Tricks with DS9Example/Filename
Select a reference image Your reference image should be the smallest of your images if they are different sizes image1.fits
Select stars in reference image Use display to display an image in DS9 (you may have to set stdimag=imt2048, then use imexamine with the a,r, or x keys to find star coordinates in pixel position Use DS9 regions to select a list of stars and use the region file starcoords.txt
Find the relative shifts between images if the shifts are greater than the bigbox parameter of imalign Use disp and imexam to find the coordinates of the same star in each image, and calculate the relative shifts between those stars. The shifts should be of the form ( refx - imagex ,refy - imagey ) Copy and paste DS9 regions between the files. It is helpful to have one ruler region included to make the measurement easier. shiftlist.txt
Make a list of input and output files Edit two files and put in the list of input/output files. Make sure your reference image is the first one. Use UNIX tricks inlist.txt, outlist.txt

imalign @inlist.txt image1.fits starcoords.txt @outlist.txt shifts=shiftlist.txt

Remember that inlist.txt, outlist.txt, and shiftlist.txt have to have the same number of items in them!
If you get segmentation violations or similar errors, make sure that the coordinates and shifts are separated by SPACES, not COMMAS.