AFNI dialogue boxes on Mac OS

AFNI Message Board
1

Hi-

I have encountered a problem where I cannot type into an AFNI dialogue box, since the latest update (on Mac OS Sierra).

So, if I want to enter a p threshold in to a dialogue box, I cannot. If I want to clusterize, I cannot enter a minimum cluster size.

Have you seen this before, and what can I do about it?

Thanks,

Jim Waltz

2

Yeah, that is an Xquartz-related bundle of joy.

You need to set an environment variable called DYLD_LIBRARY_PATH to have the value /opt/X11/lib/flat_namespace.

To do that in either tcsh or bash, see Step 1b here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_mac.html

(you can see which shell you are using by typing “echo $0” into the terminal.)

–pt

3

→ and note that, for the change to take effect once you have set the variable, you can either open a new terminal or source the ~/.*rc file that you edited with either:


source ~/.bashrc

or


source ~/.cshrc

depending on your shell.

–pt

4

Ok. That helps me a lot. Thank you very much.

A few more, related questions.

  1. Why does it always say, when I enter “afni &”, “AFNI is detached from terminal”?
  2. Why do dialogue boxes always start out teeny-tiny, until I stretch them?
  3. Do I have to type “source ~/.bashrc” every time I open a terminal window?

Thanks,

Jim Waltz

5

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?

–pt