yes, the 20-24 hour numbers are several years old at this point, and we
have made some improvements to speed so 6 hours is not unheard of. That
said, definitely visually inspect the results! I'll leave the
hyperthreading question for Zeke or Nick
cheers
Bruce
On Tue, 17 Jun 2014, Peter
Goodin wrote:
When in doubt, check the tissue and surface segmentations
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview)
but ultimately celebrations seem to be in order...
__________________________
Peter Goodin, BSc (Hons), Ph.D Candidate.
Brain and Psychological Sciences Research Centre (BPsych)
Swinburne University,
Hawthorn, Vic, 3122
http://www.swinburne.edu.au/swinburneresearchers/index.php?fuseaction=profi
le&pid=4149
Monash Alfred Psychiatry Research Centre (MAPrc)
Level 4, 607 St Kilda Road,
Melbourne 3004
____________________________________________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Linden Parkes
[linden.par...@monash.edu]
Sent: Tuesday, 17 June 2014 8:50 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Version 5.3 recon-all run time
Hi FSers,
I have an Ubuntu machine (14.04 LTS) with a quad-core i7 4770k/32gb RAM and
recon-all is taking me approximately 6 hours per subject without using
openmp (haven't tried this yet). According to the terminal, it finishes
without errors.
I've read (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FsQuizAnswers)
and heard that recon-all should take 20-24 hours per participant to
complete. So, should I be celebrating my 6 hour run time or should I be very
suspicious of it?
Also, how does freesurfer go with hyper threaded CPUs? (as is the case with
the 4770k; 4 cores, 8 threads). I've read that you should restrict parallel
processing to one subject per core. Can I take advantage of the hyper
threading and run 8 subjects simultaneously or should I be more conservative
and only run 4?
Cheers,
Linden
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