'fs_temp_file' should be in the same directory as recon-all. Can you check if
it exists - 'ls -l $FREESURFER_HOME/bin/fs_temp_file'?
Also, '/Applications/freesurfer/7.4.1/subjects' is part of Freesurfer
distribution. You should change SUBJECTS_DIR to point to some other directory
you have write permission.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Cameron, Jack
Sent: Thursday, June 6, 2024 9:36 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] fs_temp_file: Command not found
External Email - Use Caution
Hello FreeSurfer developers,
I am in the process of learning how to use FreeSurfer and attempting to run the
recon-all on FreeSurfer 7.4.1 on a 2019 MacBook Pro (Sonoma 14.5).
The response is attached as a pdf, but I have also copied and pasted the
environment and commands below.
Last login: Thu Jun 6 14:07:57 on ttys000
jack@Jack-MacBook-Pro ~ % export FREESURFER_HOME=/Applications/freesurfer/7.4.1
jack@Jack-MacBook-Pro ~ % export SUBJECTS_DIR=$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
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