AFNI GUI crashes on Sierra 10.12.2

AFNI Message Board
1

Hi,

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/com.apple.launchd.A13EsOlrk4/org.macosforge.xquartz:0”

Any suggestions on how to fix this?
Thanks!
Galit

2

Hi Galit,

What is the system check output?

afni_system_check.py -check_all

  • rick
3

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
4

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!
Galit

5

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.

6

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!

7

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,

Galit