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

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