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Please try the following, … open a new terminal and run the bash shell … I am cd’d to /tmp though it should not matter ... $ cd /tmp$ bash The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For more details, please visit https://secure-web.cisco.com/1G4FPb9n4t6EAd65_hmtnkfEITITNTkf9OQlUdDQs6VJF-T...
… check the version of Quartz by starting an xterm. When the xterm window opens check the version from the upper left hand corner XQuartz application pull down menu and check what “About X11” reports. In the example below, Quartz 2.8.5 is running on a late 2019 Intel MacBook Pro with MacOS 12.6.7 (Monterey) installed … Mac:/tmp> which xterm /opt/X11/bin/xtermMac:/tmp> xterm &
… check you have Quartz 2.8.2 or later and then quit the xterm window … … copy your license.txt file into your home directory. For example if you downloaded your license attached to the email notification into your Downloads folder, then copy it from there into $HOME … Mac:/tmp> cd $HOME Mac:~> cp -p -f Downloads/license.txt . … set the environment variable FS_LICENSE to point to the license file … later you can put this in your shell init file to be the default when you launch a new terminal window with your default shell … Mac:~> export FS_LICENSE=$HOME/license.txt Mac:~> head -1 $FS_LICENSEyou@somedomain.com <— email you used to register for the license … setup the freesurfer environment … Mac:~> export FREESURFER_HOME=/Applications/freesurfer/7.4.1 Mac:~> source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.4.1 FSFAST_HOME /Applications/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects MNI_DIR /Applications/freesurfer/7.4.1/mni … first check freeview with no arguments opens an empty window … Mac:~> which freeview/Applications/freesurfer/7.4.1/bin/freeviewMac:~> freeview … close the window and try to open a volume or surface ...
… check the volume file exists … Mac:~> ls -l $SUBJECTS_DIR/bert/mri/T1.mgz -rwxr-xr-x 1 root wheel 4502402 Jul 13 2021 /Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz* … try opening the volume file …Mac:~> freeview $SUBJECTS_DIR/bert/mri/T1.mgz The above works on the Mac configuration listed above. - R. On Aug 11, 2023, at 18:59, Irakli Kaloiani <ikalo@stanford.edu> wrote: External Email - Use Caution Dear Freesurfer team,Several members of our lab tried setting up Freesurfer (V.7.4.1) and about 5-6 people have encountered the same problem (all of the on macOS) of freeview crashing when we are trying to load the T1 from the folder bert>mri>T1. We already have license file placed in an appropriate folder.Additionally, there’s an issue with XQuartz (V.2.8.5) when I am trying to run xclock in terminal – “Error: Can't open display:”Do you know what could be an issue? Google and stackoverflow wasn’t useful.Your advice would be greatly appreciated,Thankfully,Irakli Irakli Kaloiani, M.D.TMS LeadBrain Stimulation Lab, Stanford UniversityDepartment of Psychiatry and Behavioral SciencesMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1ZkGWHgZJw-3zmLYe8yrmEG28cyI9K8rL_avCqmNmtLv0Pzo... 446 - 1596 _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer