External Email - Use Caution
Hello FreeSurfer developers,
I am in the process of learning how to use FreeSurfer and attempting to run the recon-all on FreeSurfer 7.4.1 on a 2019 MacBook Pro (Sonoma 14.5).
The response is attached as a pdf, but I have also copied and pasted the environment and commands below.
Last login: Thu Jun 6 14:07:57 on ttys000 jack@Jack-MacBook-Pro ~ % export FREESURFER_HOME=/Applications/freesurfer/7.4.1 jack@Jack-MacBook-Pro ~ % export SUBJECTS_DIR=$FREESURFER_HOME/subjects jack@Jack-MacBook-Pro ~ % echo $FREESURFER_HOME /Applications/freesurfer/7.4.1 jack@Jack-MacBook-Pro ~ % echo $SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects jack@Jack-MacBook-Pro ~ % 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 jack@Jack-MacBook-Pro ~ % which freeview /Applications/freesurfer/7.4.1/bin/freeview jack@Jack-MacBook-Pro ~ % which recon-all /Applications/freesurfer/7.4.1/bin/recon-all jack@Jack-MacBook-Pro ~ % cd SUBJECTS_DIR cd: no such file or directory: SUBJECTS_DIR jack@Jack-MacBook-Pro ~ % cd $SUBJECTS_DIR jack@Jack-MacBook-Pro subjects % ls HYPE_shared cvs_avg35_inMNI152 fsaverage_sym README fsaverage lh.EC_average Test.nii fsaverage3 rh.EC_average V1_average fsaverage4 sample-001.mgz bert fsaverage5 sample-002.mgz cvs_avg35 fsaverage6 tutorial_data_20190918_1558 jack@Jack-MacBook-Pro subjects % recon-all -all -i sample-001.mgz -s SAMPLE001J6 fs_temp_file: Command not found. fs-check-version --s SAMPLE001J6 --o ERROR: flag --o requires one argument
I see that there is not an EXIT as is typical with FreeSurfer hard failures... Do you have any advice on where I might have gone wrong? I could not find any information posted/previous issues with this command online.
I appreciate any help you can provide.
Jack