External Email - Use Caution
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://support.apple.com/kb/HT208050.
… 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. Check you have Quartz 2.8.2 or later and then quit the xterm window.
Mac:/tmp> which xterm
/opt/X11/bin/xterm
Mac:/tmp> xterm &
… copy your license.txt file into your home directory. For example if you downloaded the license by default 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_LICENSE
you@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/freeview
Mac:~> freeview
… close the freeview window and try to open a knoen to be good volume file ...
… 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
If the above works try opening one of your own volume or surface files.
BTW - you should update MacOS on your machine from 12.6.7 to 12.7 as there are important security fixes in 12.7.
- R.
On Oct 4, 2023, at 00:53, Clara Massaneda Tuneu <c.massaneda_tuneu@blackdog.org.au> wrote:
External Email - Use Caution
Hi,
I'm attempting to install and run FreeSurfer, but every time I try to load data, the program unexpectedly quits. I downloaded the license from the email sent by FreeSurfer and followed the instructions of the video tutorial.
I've also downloaded and installed the latest version of XQuartz before installing and executing FreeSurfer.. When I tried to open FreeView in my terminal and load the image, there was no message in my terminal explaining why the program crashes.
The version of FreeSurfer that I'm using is freesurfer-macOS-darwin_x86_64-7.4.1. My device is a MacBook Pro (2016) running version 12.6.7, with a 2 GHz Dual-Core Intel Core i5 processor and 8GB of memory.
I've searched the list, and no similar errors have been reported. Does anyone have any thoughts on how to troubleshoot this issue?
Thanks for your help.