This is probably easiest to achieve using the perl utility "pvconv". See the pvconv web page for usage. pvconv.pl will write out SPM .mat files for the images which will reorient the images to neurological orientation, and to the orientation of the subject's head within the scanner.Another way of converting the data to analyze format is ImageJ. See Emma Williams' getting WBIC scan data page for the procedure. Note that ImageJ may not get the slice thickness correctly for some standard functional protocols, and the image header files may need more tweaking before you continue.
Matthew Brett 29/01/2002