‘fs_temp_file’ should be in the same directory as recon-all.  Can you check if it exists -  ‘ls -l $FREESURFER_HOME/bin/fs_temp_file’?

Also,  ‘/Applications/freesurfer/7.4.1/subjects’ is part of Freesurfer distribution. You should change SUBJECTS_DIR to point to some other directory you have write permission.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Cameron, Jack
Sent: Thursday, June 6, 2024 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] fs_temp_file: Command not found

        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