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=$HOME/subjects…. then re-run your command(s) ... - R. On Feb 15, 2025, at 12:52, Paola Di Filippo <paola.difili...@unifg.it> wrote: External Email - Use Caution hi everyone,i have succesfully managed to download freesurfer with ubuntu 22 on a virtual machine. i've tried some tutorials and everything is working fine.now i am trying to run my first recon-all, but this is the error I get: -------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni paolasofia@Freesurfer-ub22:~$ 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1QY3rGdqJouwjNSkdy2O1DaMbRHvOVLBCmyyP7lydP63wtBNZVDFiezDaZSBtd9_TzsnAqKjhTvwk7kKrEc2vJ8YexUDjFd8JDQtsMXU8uexJtzymBwbhzHsAxRdjZ-wvdmByWYiDZY5jIXKEIcK7MeZMVV5oe0EFiOrqW7UIyOT9DlaRPQhdDON84XbAlBejLPxdz6QTBhHBS1DuisMcMeGRP9x37fnOuOe48NopnMvArX681L19zYhnSxNKuhmaH2DMTdpajsT1xc0YTJ2fSvXCAiMpYr5Xb6BKRfIRsGyfg2zOp7BwoNG2-fvQeXReITIArmAxB9F8HkgW6KS8JA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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