Andries, I am not aware of usage of Freesurfer in a (Sun) Grid Engine environment (such as that used by the Cohen group at UCLA).
However, here at the MGH/MIT/HMS Martinos Center we use a cluster of some 100+ nodes configured with Linux Centos 4, and governed by PBS (Portable Batch System). Researchers here often conduct studies with dozens to hundreds of brains, and for each subject, an instance of Freesurfer's 'recon-all -s <subject> -all' script is submitted to the batch system, which, under the hood, gets submitted to one computing node. Thus, several dozen brains can be processed in a day (and a half). Freesurfer does not currently support fine-grain parallelism. Some coarse-grain parallelism, whereby each brain hemisphere is processed independently (benefiting multiprocessor nodes) is possible, but not currently implemented in our 'recon-all' script, as the error handling and logging for doing so is somewhat tricky (and so this feature is in- the-works-but-not-anytime-soon). In short, if you plan on using Freesurfer in studies with large numbers of subjects, I would recommend some kind of computing cluster, and some fairly simple batch software (like PBS) should be sufficient. For instance, I know of one group that has successfully run Freesurfer on their Altix Itanium Linux cluster. Groetjes, Nick On Wed, 2006-12-06 at 18:44 +0100, Andries van der Leij wrote: > > > > > > ______________________________________________________________________ > > From: Andries van der Leij > Sent: Wednesday, December 06, 2006 5:59 PM > To: 'freesurfer@nmr.mgh.harvard.edu' > Subject: Freesurfer and Grid computing > > > > > Dear Freesurfer community, > > > > I’m a PHD student at the university of Amsterdam and I’m currently > investigating the possibilities to streamline our MRI data processing > stream. Next summer we’ll obtain a research-only scanner. I’m trying > to push the group to also invest in computing power and am currently > investigating the applications that researchers will most probably > use. > > > > I came across a project of the group of Cohen at UCLA. They have > configured a Apple (unix) grid and have proposed a more or less > standard setup specially designed for MRI analyses: > > > > http://airto.bmap.ucla.edu/mt- > static/NICluster/archives/2005/06/welcome.html > > > > It is my understanding that one of the members has rewritten the FSL > code which allow distributed parallel processing in a Grid. See the > benchmarks here: > > > > http://airto.bmap.ucla.edu/bmcweb/bmc_bios/MarkCohen/Apple/Benchmarks.htm > > > > My question is fairly simple: Are similar steps taken in the > Freesurfer community? I have no experience with this app myself, but > it is my understanding that Freesurfer consumes a lot of resources. > > > > Thank you very much in advance, > > > > Andries van der Leij > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
