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If you use a shared drive that is formatted in a way that is not compatible with the linux (ext3, ext4) file system, e.g., a shared windows drive, then running the linux software is not expected to work.  A Windows file system does not support soft links, permissions etc. which means recon-all will fail when it tries to use soft links to point to files.  So SUBJECTS_DIR has to point to a directory you can write to (on a linux file system).   Similarly, the linux packaging tools (apt, dpkg, yum, rpm) expect to install Freesurfer on to a linux file system in order to set permissions, etc.

- R.

On Apr 23, 2024, at 11:50, Gregory Book <gregory.a.book@gmail.com> wrote:

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I did not see that message, which is why I posted again. Sorry about that!
I will try using the package installer. We're using the .tar.gz method because it is located on a shared drive, but maybe we'll just need to install it locally if that works.

On Tue, Apr 23, 2024 at 11:23 AM fsbuild <fsbuild@contbay.com> wrote:
 
Did you try the instructions  you were sent yesterday to run the actual installer and not use the tar file (which is not an installer) ?

- R.

I would try downloading and running the actual package installer, 


on to the target system..  Then change directories to where you downloaded the package and try,

$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb

I cannot guarantee the installer will work as the Debian linux packaging tools may find requirements in the Ubuntu package they cannot resolve/satisfy on your Debian system.  We don’t test on debian linux.  But the installer should notify you if it fails and why that is.



On 4/23/24 09:21, Gregory Book (gregory.a.book@gmail.com) wrote:

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I recently installed freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 22 .tar.gz). When running recon-all, I get the following error:

-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required file not found

Paths are all set, and all scripts and executables have execute permissions.
What might be happening?

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