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 JAbsher@ghs.org wrote:
External Email - Use CautionHi,
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
jabsher@ghs.org
GHS Neuroscience Associates
University of South Carolina School of Medicine Greenville
864-350-6655 (mobile)
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