1. Why does it always say, when I enter “afni &”, “AFNI is detached from terminal”?
Default behavior is to detach AFNI, so you shouldn’t even need the “&”. If you run “afni -no_detach”, then it won’t detach from the terminal, but you also won’t be able to keep typing commands in the terminal (until you, for example, interrupt it and put it in the background).
2. Why do dialogue boxes always start out teeny-tiny, until I stretch them?
Hmm, doesn’t the flatnamespace change from earlier in the thread fix that?
3. Do I have to type “source ~/.bashrc” every time I open a terminal window?
You shouldn’t. Perhaps you have a ~/.bash_profile file, and so instead of sourcing ~/.bashrc when you open a new terminal, ~/.bash_profile is getting preferential treatment-- so, if you do have ~/.bash_profile existing, then you should put a line inside that to source your ~/.bashrc. For example, you could open the file with an editor of your choice and add “source $HOME/.bashrc” to it, or run the following from the command line:
echo 'source $HOME/.bashrc' >> ~/.bash_profile
—> again, open a new terminal or “source ~/.bash_profile” for the change to take effect.
Also, is your default shell bash? Hopefully you have set your computer up that way, if you want to be using bash as your shell. You can set that in your Mac’s preferences → user profile.
(I edited this to have “$HOME” instead of “~” in the ~/. files, because I think that might be more known.)
In addition, does the output from running “afni_system_check.py -check_all” in a terminal have suggestions for your setup?