External Email - Use Caution
It would help to know what OS you are running on. Some users have experienced issues with running the default shell, now zsh, on the Silicon Macs with M1 … M4 processors. If you are on a silicon mac, then I would try running bash shell, e.g., see below for setting up the freesurfer environment on MacOS after running the freesurfer 8.0.0 .pkg installer. You could also change your default shell to bash. No matter what OS you are running on, don’t forget to change SUBJECTS_DIR to a directory you can write to before processing your own subject data. You don’t have write permission to modify where freesurfer is installed and where SUBJECTS_DIR points to by default. - R.
% 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/1NDBetOHTkHPkMteD2_GKgTsbI3gNgJ8PTsSsy9e3qS8Zhd... export FREESURFER_HOME=/Applications/freesurfer/8..0.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME /Applications/freesurfer/8.0.0FSFAST_HOME /Applications/freesurfer/8.0.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR /Applications/freesurfer/8.0.0/subjectsMNI_DIR /Applications/freesurfer/8.0.0/mni $ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects <--- copy in your subject data to here
On Mar 5, 2025, at 11:11, Sebastian Adolfo Rios Quintanilla <sebas.riosq99@gmail.com> wrote: External Email - Use Caution Hello FreeSurfer Developers, I try using SAMSEG for my subjects' data. I acquired 3 subjects in 3 different months and everytime I wanted to use samseg for brain segmentation I encountered "zsh: command not found" and found myself in the need to re-do all the installation steps. At first, after going from subject 1 to subject 2 I thought It was a mistake I may have made in the installation. But now after around a month, trying to work on subject 3 I get the same error. I reach out to the dev team because I plan to scan more subjects in the coming months and having to reinstall everytime is not efficient and time consuming. Thank you very much for your time, help and support. -Sebastian RiosMSc. student at Polytechnique Montreal, MTL, CA_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh..harvard.edu https://secure-web.cisco.com/1NyLa77_UEWtBNlbB1RgpkAgEBy-TX0mp6BnMjWNcHDqNmF...