Thank you!

This has been super helpful.

Sincerely,

James Park

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
Date: Tuesday, October 27, 2020 at 2:21 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

Hi James,

Rsync is a very common unix command for syncing/copying across filesystems. There’s plenty of information about it online, and you can access the help text through `man rysnc`. This might be useful https://www.tecmint.com/rsync-local-remote-file-synchronization-commands/

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: Tuesday, October 27, 2020 at 12:12 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

External Email - Use Caution

Hi Andrew,

Thank you so much for your prompt response.

Our IT department was unfortunately a bit unfamiliar with these types of files.

We were not using rsync to move our files but instead just copying the files over through a file explorer.

Could you please point me in the right direction as to where I could access more information on rsync or moving data to a different location?

That would be super helpful!

Thank you again for your help.

Sincerely,

James Park

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew <AHOOPES@mgh.harvard.edu>
Sent: Monday, October 26, 2020 7:16 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] Troubleshooting: Question Regarding Copying Freesurfer Output to Secondary Location

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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