Do you have a ~/.bash_profile as well as ~/.profile? If so bash will preferentially read the former and ignore the latter. This could be the source of your problem. Have you tried opening ~/.profile in an text editor to ensure that the lines to add afni to the path are actually in ~/.profile?
Also I notice that you commands above refer to .profile. Were you in ~/ when you executed these commands? If not the .profile you created will not be in ~/ and hence bash will not be able to find it.
.profile must be in ~/ for bash to find it.
Edited 1 time(s). Last edit at 06/25/2013 03:16PM by Colm Connolly.