External Email - Use Caution
In reply to mail from Mitchell Horn, Douglas Greve replied
The math libraries changed between 7 and 8, nothing we can do about it. When I have to run things on a centos8 machine, I generally run in a centos7 singularity container (which we might be able to make available, without support:)
Would it be possible to get just the Singularity definition file for the CentOS 7 Singularity image that you use posted to the FS wiki?
We're happy to do the building, but having a file that lists the needed prerequisites that need to be installed via yum prior to installing FreeSurfer would be very helpful. It would also help to see how you handle the needed FSL components, and I think at least some portion of ANTs is needed for TRACULA, so even just which binaries are needed would be a help, too..
Thanks for considering this request, which I hope is not as burdensome as providing the fully built container.
Hi Bennet,
I've been doing my best to support building FreeSurfer containers via neurodocker (https://github.com/ReproNim/neurodocker).
This template should give you a good idea of the pre-reqs for a FreeSurfer container. https://github.com/ReproNim/neurodocker/blob/master/neurodocker/templates/fr...
And you can also use neurodocker to install other required components like FSL, niftyreg, ants, etc.
I also have a PR in the works to support compiling FreeSurfer from source, but it's a mess right now and I haven't had time to clean it up. https://github.com/ReproNim/neurodocker/pull/445
Hope this helps,
-Paul ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bennet Fauber bennet@umich.edu Sent: Thursday, April 6, 2023 7:34 AM To: Freesurfer support list Subject: [Freesurfer] FreeSurfer container recipe?
External Email - Use Caution
In reply to mail from Mitchell Horn, Douglas Greve replied
The math libraries changed between 7 and 8, nothing we can do about it. When I have to run things on a centos8 machine, I generally run in a centos7 singularity container (which we might be able to make available, without support:)
Would it be possible to get just the Singularity definition file for the CentOS 7 Singularity image that you use posted to the FS wiki?
We're happy to do the building, but having a file that lists the needed prerequisites that need to be installed via yum prior to installing FreeSurfer would be very helpful. It would also help to see how you handle the needed FSL components, and I think at least some portion of ANTs is needed for TRACULA, so even just which binaries are needed would be a help, too..
Thanks for considering this request, which I hope is not as burdensome as providing the fully built container.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Paul,
That's super helpful and very much appreciated. The template source is definitely helpful!
On Thu, Apr 6, 2023 at 11:57 AM Wighton, Paul PWIGHTON@mgh.harvard.edu wrote:
Hi Bennet,
I've been doing my best to support building FreeSurfer containers via neurodocker (https://secure-web.cisco.com/1HCtlZ_46Lc5mEomj3KvdN9SeqbUDClJAUn0DaP42-Jmdby...).
This template should give you a good idea of the pre-reqs for a FreeSurfer container. https://secure-web.cisco.com/1ry5yeGZuLl-9xVuUZw7MASqFRoQ5jitZcduS8Q_TyX8Pfd...
And you can also use neurodocker to install other required components like FSL, niftyreg, ants, etc.
I also have a PR in the works to support compiling FreeSurfer from source, but it's a mess right now and I haven't had time to clean it up. https://secure-web.cisco.com/1s1naXRXHnGUHtOyYiH6kV1qayJ70T7_mmoJdCqzj-28f-h...
Hope this helps,
-Paul ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bennet Fauber bennet@umich.edu Sent: Thursday, April 6, 2023 7:34 AM To: Freesurfer support list Subject: [Freesurfer] FreeSurfer container recipe?
External Email - Use CautionIn reply to mail from Mitchell Horn, Douglas Greve replied
The math libraries changed between 7 and 8, nothing we can do about it. When I have to run things on a centos8 machine, I generally run in a centos7 singularity container (which we might be able to make available, without support:)
Would it be possible to get just the Singularity definition file for the CentOS 7 Singularity image that you use posted to the FS wiki?
We're happy to do the building, but having a file that lists the needed prerequisites that need to be installed via yum prior to installing FreeSurfer would be very helpful. It would also help to see how you handle the needed FSL components, and I think at least some portion of ANTs is needed for TRACULA, so even just which binaries are needed would be a help, too..
Thanks for considering this request, which I hope is not as burdensome as providing the fully built container.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1cJ5_CrhkobOUfRAJt2CnlYoi-khH-m87gazPwr-uKJ6aTN...
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freesurfer@nmr.mgh.harvard.edu
-
Bennet Fauber -
Wighton, Paul