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
External Email - Use Caution 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.commailto:utooley@gmail.com 202.413.5627