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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-windows/

- 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:

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Dear FreeSurfer Developers,
I am trying to run the script and the recon-all command and getting
Exited with errors output.
1. FreeSurfer Version freesurfer-Linux-centos6_x86_64-stable-pub-v6..0.0-2beb96c
2. Platform, VM Ware Workstation 15, host OS: Windows 10, Guest:
Ubuntu ubuntu-18.04.3-LTS, 64 Bit, 2 GB RAM
3. 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 as
the output folder are in the shared folder (shared between the host
windows 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>_______________________________________________
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