Hi Emad, If there is something like that I would be quite interested in a way to do so as well as I'm working on a scalable Freesurfer cloud setup, but all I know so far is, that you can parallelize parts of the freesurfer pipeline to two parallel tasks. I think it's autorecon2, probably even autorecon3 which has an optional parameter for the hemisphere to use, and if you call it without it calculates them in a row, first the left hemisphere and then the right (or vice versa). If you instead call it twice in separate processes once with left and once with right hemisphere, you parallelize this step accordingly.
If there's anything more I have no idea - but I would be interested in it as well (provided that it's not on the cost of numerical stability or something like that)
regards Peter
Am 07.11.2013 21:42, schrieb Emad Ahmadi:
Hello,
I'm using FreeSurfer on a 6-core Mac Pro machine. It takes quite a bit for commands like recon-all to complete, while I've noticed that my CPU and memory resources are mostly idle.
I just wanted to know if there's anyway to define multiple cores for FreeSurfer (something like matlabpool in matlab parallel computing toolbox).
Thank you, Emad
Emad Ahmadi, MD
Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School
25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad@nmr.mgh.harvard.edu
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