External Email - Use Caution 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 <fsbu...@contbay.com> ha scritto: > 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/1e3Y0Q-TbWFo7WRLVrFXxORH7bbufOEQGh9ubmG5k0ve9_KtWv4ybYiLU2aQCU8YWXyGabnSMdI6i2J2O3h8I6UuaNbg4T5Q0KXM6BGUNvVFOiQM6bKzY4fHNGHA3FAK-ga-ITrpuIZfGftv4sNMfHgMloZ5Qb6tY0RLJUZkufvlo5WZd2ilC7HrEcPdPRQpZ-JaIvqEW8Gb9axxAwvoksmyhAUIwaasDgkRHJJXp2u1xQvp9qojfBrAGxCJm4sOwzhG6PNRhkp3zUaTiohiOqzTy1zJS6Z1krVm9EnlreyNZJQets81Fs4ylDrERiuJxQ4n6hXwFKsEgKVma6ZYuRQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1e3Y0Q-TbWFo7WRLVrFXxORH7bbufOEQGh9ubmG5k0ve9_KtWv4ybYiLU2aQCU8YWXyGabnSMdI6i2J2O3h8I6UuaNbg4T5Q0KXM6BGUNvVFOiQM6bKzY4fHNGHA3FAK-ga-ITrpuIZfGftv4sNMfHgMloZ5Qb6tY0RLJUZkufvlo5WZd2ilC7HrEcPdPRQpZ-JaIvqEW8Gb9axxAwvoksmyhAUIwaasDgkRHJJXp2u1xQvp9qojfBrAGxCJm4sOwzhG6PNRhkp3zUaTiohiOqzTy1zJS6Z1krVm9EnlreyNZJQets81Fs4ylDrERiuJxQ4n6hXwFKsEgKVma6ZYuRQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it > is addressed. 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