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=profil...
Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Linden Parkes [linden.parkes@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