------ IMPORTANT message regarding afni_proc.py ------ You may not be aware of the afni_proc.py super-script. It can carry out almost all single-subject analysis task in AFNI, with one command line. It creates a script of all the AFNI commands needed to carry out the analysis, and then runs that script. We STRONGLY RECOMMEND that you start using afni_proc.py to manage your single subject analyses. Making this switch will have several benefits: - If you need help, we'll have a common starting point. If you instead are using a custom script, helping you figure out what happened when the results are confusing will be much much harder. - We have seen several groups using somewhat peculiar and 'rococo' scripts to analyze their data -- often scripts that have been handed down from people no longer in the lab, and no one present really understands what is being done, or why. This situation is not good for anyone. - afni_proc.py is continually being improved (by the estimable and invaluable Rick Reynolds), and if it can't do what you need now, it probably will soon -- especially if you ask (nicely). - The script that afni_proc.py writes is itself quite clearly formatted and commented, and afni_proc.py is well documented, including examples of how to do various 'standard' analyses: http://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html In short, unless you are doing something unusual AND you understand in depth what your script is doing, you should be using afni_proc.py. It will soon become your best friend.