External Email - Use Caution
Hello Kirill, Is the shared folder where the “ln -s” command is running to create a soft link on a disk that is formatted to have a Windows file system, e.g., NTFS? My understanding is that Linux/Unix style soft linking via the “ln” command does not work on such a windows file system. Freesurfer scripts assume the file system supports standard Unix/Linux soft links via the ln command, e.g., where the disk partition or volume it runs on is formatted as ext3 or ext4. You can install software in Windows to *read* a linux file system. The link below talks about 2 software applications for windows - one can read linux file systems, and the other can read both linux and Mac file systems. https://www.howtogeek.com/112888/3-ways-to-access-your-linux-partitions-from... - R.
A Windows NTFS file system does not support Unix soft links
On Jan 9, 2020, at 08:58, Kirill Elin <ekirling@gmail.com> wrote: External Email - Use Caution Dear FreeSurfer Developers,I am trying to run the script and the recon-all command and gettingExited with errors output.1. FreeSurfer Version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c2. Platform, VM Ware Workstation 15, host OS: Windows 10, Guest:Ubuntu ubuntu-18.04.3-LTS, 64 Bit, 2 GB RAM3. See the log file and the screenshot.In the script I have not found any other errors so I am not even sure,what I should be looking for.If it plays a role, my MRI folder, where original T1s are as well asthe output folder are in the shared folder (shared between the hostwindows OS and the virtual machine).I would be grateful if you could help me out with this.Thank you in advance.Sincerely yours,Kirill<Finish_Errors.PNG><recon-all.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer