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 <pwigh...@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-Jmdbyp1mCHd4Pn6kIwrd4hImk8VOXD8pdbEW12POtXk5HPyMvNnQxSAoP5vx9XaJJmSGC9aX3PkSnL40nNY6DHaHkV9mwZgGoEQeNgIaY_oLpMUJL-kX2Rfwf-lGB4zy2vZ-4pbGm_iCQJ68z95XYjV4xpE90dWdskTq6DWHlyzYs3OTBCSFchJhhALovTp_pCK_4rUeRBXfW72RlVMmWLYZNTEhe2HR6wocWgbTHxXgxtGjTSbru09mFYDCsS1pDz3ocpcwwerw0HqTF8_RtQEwy735EIa2dDums3F4LFVHw/https%3A%2F%2Fgithub.com%2FReproNim%2Fneurodocker). > > This template should give you a good idea of the pre-reqs for a FreeSurfer > container. > https://secure-web.cisco.com/1ry5yeGZuLl-9xVuUZw7MASqFRoQ5jitZcduS8Q_TyX8PfdWT4QeXCp90PheZCw0eHYZHapPSe_CA5qKafW6ctRNwlcolk55oq2bXWukiaJQRwIyaat8DOGhqFbtDRLCaRACsaq85D-kUvUr5ukxxHGnoZSvGIddCiv9eyoAzJ56G6AQ1x1SGNWmApKIeMLuj1CiUfuVamJLhJkU7nfWH3Rrt2D3qoatOksOoHMUJL0LaDv8TPX7nU2M1pPIA5YuwAswVsyinG6vtuVKXh6s40MFwuuN09Dzk6LEztzHRK1YwRU2cEKhYiW1WGHBfvdX-s2vyD-H2V_fbHIV-8p_hNQ/https%3A%2F%2Fgithub.com%2FReproNim%2Fneurodocker%2Fblob%2Fmaster%2Fneurodocker%2Ftemplates%2Ffreesurfer.yaml > > 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_0o4QP4rhXdQnBCVMfybvU5stQ7ju7c04JmdpM9riBZ-pxwyrDxZGslwKD5a_N2mN0M_s6vp_XtpTigTFFRQ5TmF7RR-JomSTIpfoobfyfkEyK67EdRXwUfyWw9dTwIVII8sBE8R2Y8ZKm25c03ORibIGH5pmAHKa2E1wx4G9CGy81mHKc6sA9yvtpYqW7vMPNYTLmDi09uRFc5-ABGFNYTQmZR9HlBtm4b9S-s0IKpxvKFb4Hc50i2KKRzWAMTRreXR11MY-qzRi83OMRlmDGl7heK30GC9y2UVNXsw/https%3A%2F%2Fgithub.com%2FReproNim%2Fneurodocker%2Fpull%2F445 > > Hope this helps, > > -Paul > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bennet Fauber > <ben...@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://secure-web.cisco.com/1cJ5_CrhkobOUfRAJt2CnlYoi-khH-m87gazPwr-uKJ6aTNXP3ymPJHJobIQyRkU0wPl_XcGgXPeoBbvEiu1v_SZDMqyj20JPVJ1fk8OVfDjLh_0D6hdkvMjOJ53jyYe0tfHtkq2e55qX2bFNwIpaOVm2Ol8y1ZnumxDWgGosurAa5Ko3AsuJcyRiEsE0H-n66Ws0TCwGdh3SJqN2fDWwXv_DuGSuqn4PNXPmuvO2_luiv9CE8i1HxQlwKffOsGDGGWrzAjl2KHjkdl47DAq_FwR2HBpnOwIXL1C6SYrsBw0IPZjjGPA_Vh2CrRdJSO3I0aavew30ZPR6pt2W5tHDqw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1cJ5_CrhkobOUfRAJt2CnlYoi-khH-m87gazPwr-uKJ6aTNXP3ymPJHJobIQyRkU0wPl_XcGgXPeoBbvEiu1v_SZDMqyj20JPVJ1fk8OVfDjLh_0D6hdkvMjOJ53jyYe0tfHtkq2e55qX2bFNwIpaOVm2Ol8y1ZnumxDWgGosurAa5Ko3AsuJcyRiEsE0H-n66Ws0TCwGdh3SJqN2fDWwXv_DuGSuqn4PNXPmuvO2_luiv9CE8i1HxQlwKffOsGDGGWrzAjl2KHjkdl47DAq_FwR2HBpnOwIXL1C6SYrsBw0IPZjjGPA_Vh2CrRdJSO3I0aavew30ZPR6pt2W5tHDqw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > The information in this e-mail is intended only for the person to whom it is > addressed. 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