I am sorry that I did not provide enough information. I suspect that I do not understand enough to even ask the correct questions to get the information needed, but I am trying.
I do not know specifically what format the .img files are in. I know that it is not ANALYZE.
We created header files in SPM99, by giving values for Image Dimension - pixels in x, y, z; Voxel Dimension - mm in x, y, z; Scalefactor; Data Type; Offset into file - bytes; Origin (x, y, z of voxel). I have tried using AFNI with the header files created (opening AFNI in the directory containing the .hdr and .img files), but it says it cannot read the first file and presumably all the following files. I tried opening the files in emacs and matlab so I could tell you what was in them, but they produced gibberish. I have a copy of the matlab script that creates the .img files, at another location, would there be information there that would help? These files are for the functional runs only.
I looked at the information on to3d and near as I can figure I should be able to use the information that I have to create a header which could be read. But I have no idea how one might go about creating such a header.
The anatomical files we get are also in a merged_ file, which is different from that expected by AFNI, I think.
I am changing from SPM, because I want to work with someone who has created programs to align the scans across subjects based preferentially on the position of the hippocampus. These programs were created and run in his lab alongside/within AFNI. Faced with the choice of trying to integrate them into SPM or learn AFNI, I chose the later. I have had some concerns/problems with SPM, which added to the decision. Unfortunately, I am/will be the only person at this University actively using AFNI so it is up to me to figure out how to get it to work.

Thanks for any help you can give.