External Email - Use Caution
The install location of freesurfer under /usr/local is on purpose read only (like the location of most Linux package installs) so you should not be trying to process and write subject data there. We provide example subjects under /usr/local/freesurfer/7.4.0/subjects for read only purposes. Neither can you set SUBJECTS_DIR or write files in the process of running recon-all to your mounted or shared C drive. This is because the the Windows file system does not support creating soft links. So please try the following. In your Ubuntu linux terminal window, go to your HOME directory and create a subjects directory there, i.e., you can always read/write to your HOME directory. Then copy in your subject data to be processed there via recon-all and set SUBJECTS_DIR appropriately or pass the path on the recon-all command line. … in WSL linux terminal window …$ cd $HOME$ mkdir subjects$ cd subjects$ pwd/home/naily/subjects$ export SUBJECTS_DIR=/home/naily/subjects… copy in your data to process for recon-all to live under SUBJECTS_DIR … It also looks like your license file is not being found. You can set the environment variable FS_LICENSE to point to that so it will be found and read, $ export FS_LICENSE=/home/naiy/license.txt$ head -1 $FS_LICENSEyou@somewhere.com <---- email address you used to register … then try running some Freesurfer commands again … - R. On Nov 17, 2023, at 17:49, Nai, Ying Hwey <naiy@wustl..edu> wrote:<FSissues.txt>