Hi-

For converting img/hdr files to NIFTI, you can use 3dcopy, for example:

3dcopy FILE_IN.hdr FILE_OUT.nii

In terms of setting up a pipeline for RS-FMRI, using Rick's tool afni_proc.py is probably the best way to go. There is an interactive GUI for setting up the command the first time, as well as a number of complete examples in the help file for that function; for RS-FMRI, examples #9-11 are the most modern, I believe:

afni_proc.py -hview

or

afni_proc.py -help

I think it might be fair to say that Daniel is the inhuman expert here... I mean, expert on non-human data analyses. As proof, see:
[afni.nimh.nih.gov]
Perhaps as you develop your pipeline he might be able to weigh in more about rat-specific options/settings that would be useful.

For group analysis, there are tools like 3dttest++, 3dANOVA, 3dMVM, 3dLME, etc. depending on your data and questions of interest. Gang has put several examples of various cases in each of those.

So, those would be the initial places to look, I think, and any questions can be asked here, of course. There might be additionally useful documents/scripts in the AFNI Bootcamp demo, which can be gotten most easily through Step #2 here:
[afni.nimh.nih.gov]

--pt