Good afternoon, I hope this finds you well.
I am a research assistant at MGH, recently took the freesurfer course in June, trying to install it on an arm64 M3 chip Mac (OS Sequoia 15.5), 24GB RAM/memory. I followed the online installation guides and troubleshooting for V8.0.0, yet am getting stuck at the "setup and configuration" step: I successfully installed the freesurfer package file but when I enter the commands in a terminal window to "source the freesurfer environment", the terminal either says "zsh: parse error near '\n'" or it says "source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh". I copy and pasted the full terminal content below (including the error messages). I looked at older online tutorials for installation, one of them had me load a tab in freeview after installation, before sourcing the environment in a terminal. When I tried to load any volume onto freeview, the app immediately quit and generated an error report. Since the same issue happened repeatedly, I copy and pasted the full error report to a word document attached to this email.
Do you have any tips, recommendations, or ideas of what could be going wrong with my setup and configuration? Are there any videos I can consult online, or someone I could speak with to get assistance on my specific errors?
Thank you for your time! Have a good weekend. Best, Nadine
Terminal message:
Last login: Fri Jun 27 11:50:08 on ttys000 nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer/8.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh export: not valid in this context: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ % >.... Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/8.0.0 FSFAST_HOME /Applications/freesurfer/8.0.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/8.0.0/subjects MNI_DIR /Applications/freesurfer/8.0.0/mni
... install either the Matlab R2014b or R2019b runtime environment ...
$ which fs_install_mcr /Applications/freesurfer/8.0.0/bin/fs_install_mcr
$ sudo FREESURFER_HOME=$FREESURFER_HOME $FREESURFER_HOME/bin/fs_install_mcr R2019b <output deleted>
... set LD_LIBRARY_PATH to point to The Mathworks libraries ...
$ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/runtime/maci64:$FREESURFER_HOME/MCRv97/bin/maci64:$FREESURFER_HOME/MCRv97/sys/os/maci64:$FREESURFER_HOME/MCRv97/extern/bin/maci64
zsh: parse error near `\n' nadinejarrar@MGB033764 ~ % export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh source: no such file or directory: /Applications/freesurfer/SetUpFreeSurfer.sh nadinejarrar@MGB033764 ~ %