Hi-
I think we'll need some more specifics to know what might be happening. What system are you on (linux, mac, windows-linux)?
What does this mean: "whenever I put any directory change in"? Can you please copy+paste an example of:
+ a command you are using,
+ the output given
+ and the directory run from (output of typing "pwd" in a terminal)
What is the output of "afni_system_check.py -check_all"?
--pt