External Email - Use Caution
Something is probably not right trying to launch the window since it works to run the binary and produce the help output.
You can check the following command produces no output,
$ otool -L /Applications/freesurfer/7.1.1/Freeview.app/Contents/MacOS/freeview | grep not
If Xquartz is installed, then you should be able to run the following and see a clock,
$ /opt/X11/bin/xclock
If the above work, then reproduce the segfault and the system should display a window with the crash report. You should be able to select all the crash report text and paste it into an email to send along.
- R.
Sahil Bajaj (sahil.brain@gmail.com) July 16, 2021 at 20:35 Yes, actually I have the environment already set up, please see below: When I open the terminal I get:
Last login: Fri Jul 16 16:46:38 on ttys000-------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /Applications/freesurfer/7.1.1FSFAST_HOME /Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Applications/freesurfer/7.1.1/subjectsMNI_DIR /Applications/freesurfer/7.1.1/mniFSL_DIR /usr/local/fsl 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/1TfCfDsXw-5fFic1YizTPgQdjE3Hh6816iInHxunF-GQ7d6.... When I type freeview, I get:
BT136080:~ bajsah$ freeview /Applications/freesurfer/7.1.1/bin/freeview: line 2: 8086 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" When I type which freeview and --help, I get:
BT136080:~ bajsah$ which freeview
/Applications/freesurfer/7.1.1/bin/freeview BT136080:~ bajsah$ freeview --helpUsage: freeview [OPTION <ARGUMENT:SUB-OPTION>]...
Volume and surface viewer and editor for freesurfer.-v, --volume <FILE>....
Load one or multiple volume files. Available sub-options are: ....... Screenshot for the above stuff is attached below:
fsbuild (fsbuild@contbay.com) July 16, 2021 at 19:49 External Email - Use Caution Just wondering if you already tried using bash to setup the environment. - R.
%] bashbash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1bash-3..2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /Applications/freesurfer/7.1.1FSFAST_HOME /Applications/freesurfer/7.1.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Applications/freesurfer/7.1.1/subjects bash-3.2$ which freeview/Applications/freesurfer/7.1.1/bin/freeviewbash-3.2$ freeview --help. . . output deleted . . .. . . if that succeeds then see if freeview will open an empty window . . .bash-3.2$ freeview
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