External Email - Use Caution The scripts I used to manage upload, execution, and download of thousands of freesurfer runs to a cluster are available at https://github.com/mfschmidt/freesurfer-management. Seeing what I did might save you some time over scripting this from scratch. Feel free to copy/paste/take whatever you like in parts or in whole. I ran everything single-threaded since I had far more subjects than available cores. And I did not have GPU cores at my disposal. You would want to adapt the recon-all command for that, after you work out the CUDA implementation.
Mike On Fri, Dec 7, 2018 at 1:41 AM John Absher <jabs...@ghs.org> wrote: > External Email - Use Caution > > Hi, > > > > I’m planning a freesurfer analysis of a large MRI dataset, and want to use > the “380 GPU nodes” (and other cores/nodes) on the Palmetto Cluster ( > https://www.palmetto.clemson.edu/palmetto/userguide_palmetto_overview.html) > to speed up the process. Since I am not a programmer, I’m hoping someone > can give me a quick tutorial: > > > > a) Is this going to speed up recon-all and the data analysis? > > b) How much programming/expertise is required to enable freesurfer > to take advantage of a supercomputer’s resources? > > c) Has anyone done this already? > > d) The Palmetto Cluster is more or less limited to command-line. As > long as I visualize the data on another system, I assume this will not be a > problem, right? > > > > Thanks, > > > > John R. Absher, MD > > > > jabs...@ghs.org > > GHS Neuroscience Associates > > University of South Carolina School of Medicine Greenville > > 864-350-6655 (mobile) > > > _______________________________________________ > 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
