AFNI GUI crashes on Sierra 10.12.2


I have updated my Mac’s OS, and ever since AFNI doesn’t work properly. Every time I open the GUI and want to add an overlay, for instance, the window from which to choose a file looks very small such that I can’t read the list from it but I must enlarge it. When I choose a file there is no “Apply” button etc. When I close the window the whole program shuts down.
Any other window that I open (clusterize, underlay, …) has the same program - it looks compressed, and closing it would close the whole program.
This is the error that I get:
XIO: fatal IO error 35 (Resource temporarily unavailable) on X server “/private/tmp/”

Any suggestions on how to fix this?

Hi Galit,

What is the system check output? -check_all

  • rick

Check which version of XQuartz you are running (from the “About XQuartz” menu item on the Mac menu bar item for “XQuartz”). Here’s a message from AFNI that might be relevant (or might not be):

++ If you are using XQuartz 2.7.10 (or later), and
 + AFNI crashes when opening windows, you might need
 + to set an environment variable to solve this problem:
 +   setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace

Thank you Rick and Bob!
the version was XQuartz 2.7.11, and copy-pasting the command that Bob mentioned solved the problem!
So many thanks. Happy 2017!

Just one minor thing - the ‘set p-value’ by right-clicking on the slider does not open any chooser window anymore where I could type the p-value. I suppose the OS update somehow deleted this feature - what’s the way to get it back?
Many thanks again.

The absence of the “Set p-value” popup is secular. I am also using XQuartz 2.7.11 on my Mac laptop and I get that popup. Do other popups go missing as well (like the Underlay chooser, or the “Set q-value” chooser)?

Try minimizing the AFNI controller window (to the Dock), then bring it back. Does that help? I’m really just guessing here, since your problem doesn’t happen to me!

Hi Bob,

Thanks for the advice. Unfortunately it didn’t work… All the other popout windows work just fine (clustering, overlay), but they require a regular left click with the mouse, not a right click. I wanted to say that right-clicks don’t work on my AFNI but they actually do - right clicking on a brain image does open a navigation window like it used to be. Right clicking on the slider does nothing (neither setting p-value nor setting q-value).

UPDATE: I moved to work on a different user on the Mac and setting the p-value works fine on that other user now. Perhaps there was some discrepancy between the two AFNI versions (although I did update AFNI on both users). I don’t know, at least it works! :slight_smile:

Thank you so much for the help,