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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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1QY3rGdqJouwjNSkdy2O1DaMbRHvOVLBCmyyP7lydP63wtB...
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I was able to fix the problem with this single line of command:
sudo chmod -R a+w $SUBJECTS_DIR
but thank you as always!
Il giorno sab 15 feb 2025 alle ore 23:13 fsbuild fsbuild@contbay.com ha scritto:
External Email - Use CautionYou 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=$HOME/subjects …. then re-run your command(s) ...
- R.
On Feb 15, 2025, at 12:52, Paola Di Filippo paola.difilippo@unifg.it wrote:
External Email - Use Cautionhi everyone, i have succesfully managed to download freesurfer with ubuntu 22 on a virtual machine. i've tried some tutorials and everything is working fine. now i am trying to run my first recon-all, but this is the error I get:
-------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/7.4.1 FSFAST_HOME /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/7.4.1/subjects MNI_DIR /usr/local/freesurfer/7.4.1/mni paolasofia@Freesurfer-ub22:~$ 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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Paola Di Filippo