External Email - Use Caution
If you setup the Freesurfer environment ... here using bash and not zsh ...
hostname ~ 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.
$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1
$ 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
... and point FS_LICENSE to your license.txt file, e.g., in your $HOME directory ....
$ cd
$ pwd
/Users/myuserid
$ ls license.txt
license.txt
$ export FS_LICENSE=license.txt
$ head -1 license.txt
you@somewhere.com <---- email you used to register
... then try running from the command line ...
$ freeview $SUBJECTS_DIR/bert/mri/T1.mgz
Please keep in mind you will need to change SUBJECTS_DIR to some other path, e.g., $HOME/subjects
$ mkdir -p $HOME/subjects
$ export SUBJECTS_DIR=$HOME/subjects
... and put files there if you want to write /modify subject files and data since /Applications/freesurfer/7.4.1/subjects is read only by default (not intended to be used to write data).
- R.
On Apr 15, 2024, at 21:55, Angenelle Rosal <angenelle.rosal@mail.utoronto.ca> wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I am currently using FreeSurfer 7.4.1 and I am attempting to upload the T1 image from subject “bert” using the terminal (I am using MacOS Ventura 13.5), as described in the demo video. However, freeview keeps quitting unexpectedly showing “2406 Segmentation fault: 11 $FREESURFER_HOME/Freeview..app/Contents/MAC0S/freeview “$@” when I type in “freeview/Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz”.
When I manually open Freeview without the terminal and load such image using the “Load Volume” tab, it works fine. I’ve searched the archives list and it might be due to the location of my license. However, I believe my license is located in the correct file, as it is located in my Freesurfer file (/Applications/freesurfer/license.txt). And so, any advice to also solve this problem would be greatly appreciated!
Thanks