I think the problem is that the file system does not support preserving permissions with cp -p. I've never seen this before. I'm guessing it is your file system that is configured in this way, but it is possible that it is the container. Can you try to execute the cp command outside of the container? If that fails, you might ask your sys admins to change the way the file system is configured. You can also try editing recon-all at that line to use
cp --preserve=timestamps  instead of cp -p

On 4/1/2026 1:35 PM, fsbuild wrote:

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You could make sure every directory is writeable under subjects, e.g.,
$ find /subjects -type d -exec chmod u+w {} +   

If /subjects is located outside of the container, then this might help,
https://stackoverflow..com/questions/45236106/why-does-docker-cp-of-directory-hierarchy-out-of-container-fail-with-permission

- R.

On Apr 1, 2026, at 16:04, Camacho, Paul <pcamach2@illinois.edu> wrote:

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cp -p /subjects/sub-SAY118/mri/filled.mgz /subjects/sub-SAY118_ses-B.long.sub-SAY118/mri/filled.mgz
cp: preserving permissions for '/subjects/sub-SAY118_ses-B.long.sub-SAY118/mri/filled.mgz': Invalid argument
Linux ccc0425.campuscluster.illinois.edu 5.14.0-570.76.1.el9_6.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Dec 17 04:36:29 EST 2025 x86_64 x86_64 x86_64 GNU/Linux



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