Most AFNI programs save a copy of their command lines into a file named .afni.log in your home directory. This is done to make it easy for you to find out how you ran some program a while ago. A recent example from my own .afni.log file:
[Sat Apr 4 12:26:59 2009] 3dmaskSVD -mask 'Ethresh+orig<999..32222>' -vnorm -input 'epi_vr+orig[1..$]'
showing that I ran the new 3dmaskSVD program today at 12:26.
If you are using some program many many times in a loop, you might get a gigantic .afni.log file. To prevent this, you can turn off logging by setting the environment variable AFNI_DONT_LOGFILE to YES.
If your .afni.log file goes over about 10 Mbytes in size, the interactive afni program will print out a warning message when it starts. This message is in honor of Kevin Murphy, the only person I ever knew who filled up his hard disk with his .afni.log file. Raise a pint of Guinness to Kevin!
