Hi James,

It sounds like your target filesystem does not support symlinks? The answer to your question depends on how you are actually copying data, and you should probably contact your IT about this, but if you’re using rsync to move recons, you can supply the --copy-links flag to transform symlinks into referent file/dir.

best,

Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Park, James" <james.kunwoo.park@emory.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, October 26, 2020 at 3:03 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

        External Email - Use Caution        

Hello,

My name is James Park, and I had a question regarding some issues with Freesurfer.

We noticed that for the freesurfer recon-all output there were multiple aliases files such as surf/rh.white.K among others.

Unfortunately we have been unable to copy these types of files to secondary locations (i.e. a network server).

I have confirmed this is not an issue with the computer-network connection as I have been able to copy other alias file types to the network location.

I was wondering if there is any workaround for this issue?

This was run on a Mac with macOS Catalina Version 10.15.7 using FreeSurfer version freesurfer-darwin-macOS-7.1.1-20200811-8b40551.

Thank you for your help in advance.

Sincerely,

James Park

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