External Email - Use Caution        

 
You can read from but not write to where freesurfer is installed under /usr/local/freesurfer as your normal userid.   Just change the setting of SUBJECTS_DIR to be, e.g., in your home directory or some location you can always write to as your normal userid.  It’s a good idea not to modify the distribution installed under /usr/local/freesurfer.  To change to your home directory,

… setup the freesurfer environment which by default sets SUBJECTS_DIR to be under /usr/local/freesurfer ...

$ cd $HOME

… or …

$ cd

$ mkdir subjects

$ cd subjects

… copy in you subject data …

$ export SUBJECTS_DIR=$HOME/subjects

…. then re-run your command(s) ...

- R.

On Feb 15, 2025, at 12:52, Paola Di Filippo <paola.difilippo@unifg.it> wrote:

        External Email - Use Caution        

hi everyone,

i have succesfully managed to download freesurfer with ubuntu 22 on a virtual machine. i've tried some tutorials and everything is working fine.

now i am trying to run my first recon-all, but this is the error I get:

-------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/7.4.1
FSFAST_HOME       /usr/local/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjects
MNI_DIR           /usr/local/freesurfer/7.4.1/mni
paolasofia@Freesurfer-ub22:~$ recon-all -subject angcher.02.04.91.12.09.22 -sd /usr/local/freesurfer/7.4.1/subjects  -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511174521774361.dcm -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511942168418847.dcm -i /home/paolasofia/DICOM.ANG.CHER.2.4.91/DICOM/./1.3.12.2.1107.5.2.19.146011.2022091213511945768618951.dcm -all 
mkdir: cannot create directory '/usr/local/freesurfer/7.4.1/subjects/angcher.02.04.91.12.09.22': Permission denied
fs-check-version --s angcher.02.04.91.12.09.22 --o /tmp/tmp.VZQFHn
ERROR: cannot find angcher.02.04.91.12.09.22
recon-all: version check failed
fs-check-version --s angcher.02.04.91.12.09.22 --o /tmp/tmp.VZQFHn

how could i solve this problem?

thanks in advance

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