Troubleshooting various qdec, tkmedit, tksurfer,tkregister error messages.

If you get any of the following error messages please try the recommended solution.

Error message: 

dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib
  Referenced from: /Applications/freesurfer/bin/qdec.bin
  Reason: image not found
Trace/BPT trap

or 

Couldn't create output file .xdebug_tkmeditGLUT: Fatal Error in tkmedit.bin: could not open display

Solution: You need to install XQuartz. Pre-Yosemite versions of OS X require XQuartz 2.7.5, Yosemite requires XQuartz 2.7.6 or higher.

Error message: 

Bus error

Solution: You are encountering an oft encountered problem when installing XQuartz on top of the existing X11. To solve this you will have to completely remove XQuartz and reinstall. This is done as follows: 

sudo rm -rf /System/Library/Launch*/org.x.*
sudo rm -rf /Applications/Utilities/XQuartz.app
sudo rm -rf /opt/X11
sudo mv /usr/X11 /usr/X11.orig
sudo rm /usr/X11R6

Then reinstall XQuartz and reboot the system. Pre-Yosemite versions of OS X require XQuartz 2.7.5, Yosemite requires XQuartz 2.7.6 or higher.

At this point, if you try to open qdec (or another Freesurfer GUI) and the terminal just hangs, you will need to goto Applications->Utilities and open XQuartz. If opening any of the GUIs still doesnt work, then you might have to logout then login again. XQuartz can be a finicky install, requiring one or more reboot and logout/logins, but once the GUI opens, it should no longer be a problem.

Error message: 

Opening window subj
Window type not found
register: tkoinitwindow(name) failed.

Solution: You have a compatibility issue between Exceed OpenGL and Mesa GLX. It turns out if your system's libGL.so library is provided by Mesa 7.1 or later, OpenGL applications may not run remotely. Setting the following environment variable should solve the problem: 

export LIBGL_ALWAYS_INDIRECT=y

Error message: 

X Error of failed request:  GLXBadContext
  Major opcode of failed request:  0 ()
  Serial number of failed request:  1171
  Current serial number in output stream:  1171

Solution: You have a system with graphics card that is incompatible with qdec. You will have to use another system or get a more powerful graphics card in order to run qdec.

Error message: 

Segfault
Setting global interpreter
xDebug stack (length: 2)
   01: main()
   01: Setting global interpreter
 00:
 00:

or 

Segfault
Initializing glut
xDebug stack (length: 1)
  00:
  00: Initializing glut

Solution: The XQuartz upgrade from v2.7.5 to v2.7.6 broke some of the FreeSurfer GUIs. Please reinstall XQuartz v2.7.5. It can be downloaded from this page (http://xquartz.macosforge.org/trac/wiki/Releases).

Contact zkaufman@nmr.mgh.harvard.edu if you have additional questions.