Tim,

So to be sure, are you planning to run everything as 'root'? If so, you
should either change your root shell to /bin/tcsh, or you should fix the
path in your root's .bashrc or .profile.

Note that the '.' directory is generally not in the path, for security reasons.
So if you want to 'cd' to the afni directory and run afni, you need to type
./afni instead of just afni. Or you could run the command directly from
the installation directory, as in '/usr/local/afni/afni'.

In any case, if you are going to stay as root or not, you probably just
need to get your shell and path set correctly.

Which shell do you plan to use?

- rick