Hi Ursula,

I was just reminded that we purposely don’t include MCR in the container due to redistribution-restrictions by the MCR license. So, it’s up to the user to install or provide the MCR library if needed.

best

Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew <AHOOPES@mgh.harvard.edu>
Date: Friday, March 19, 2021 at 1:06 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer 6.0.0 Container & MCR

Hi Ursula,

Thanks for pointing this out. I think it’s just the case that MCR wasn’t installed in that container. I’m surprised this hasn’t been brought up before. We’ll update the container with it.

best

Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ursula Tooley <utooley@gmail.com>
Date: Friday, March 19, 2021 at 12:23 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer 6.0.0 Container & MCR

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Hi Freesurfer experts,

I’m trying to use the official FS 6.0.0 container from Dockerhub on a new HPC (for consistency with previous pipelines), and got the error below about not finding the Matlab Compiler Runtime in the container. I have worked around it by explicitly binding the mcr on the HPC to the container with “-B /cbica/software/external/matlab/mcr/v711/:/opt/freesurfer/MCRv80”, but is this the expected behavior? Or is there some issue? My understanding was that one of the advantages of mcr was that you could include it in containers and distribute compiled code, so was surprised to find this come up.

Thanks in advance,

Ursula

---

Ursula Tooley

Ph.D. Candidate

Neuroscience Graduate Group

University of Pennsylvania

she/her/hers

utooley@gmail.com

202.413.5627