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
Solution:
You need to install XQuartz. OSX versions 10.6 - 10.9 require XQuartz 2.7.5. OSX versions 10.10 and higher require XQuartz 2.7.6.
Error message:
GLUT: Fatal Error in tkmedit.bin: could not open display:
Solution:
You need to install XQuartz. OSX versions 10.6 - 10.9 require XQuartz 2.7.5. OSX versions 10.10 and higher require XQuartz 2.7.6.
If you've already installed XQuartz then you probably need to log out and log back in.
Error message:
ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu
Solution:
If you are getting this error on Mac OSX systems, it is most likely because you are running a version of XQuartz that is incompatible with your version of OSX. OSX versions 10.6 - 10.9 require XQuartz 2.7.5. OSX versions 10.10 and higher require XQuartz 2.7.6.
To see your version of XQuartz double click the XQuartz icon located in Applications -> Utlities -> XQuartz, then in the upper left hand corner of your screen click X11 -> About X11.
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. OSX versions 10.6 - 10.9 require XQuartz 2.7.5. OSX versions 10.10 and higher require XQuartz 2.7.6.
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 (https://www.xquartz.org/releases/).
Contact zkaufman@nmr.mgh.harvard.edu if you have additional questions.