I am using the nightly build of Freesurfer 6.0 (Dec 18, 2015) on Ubuntu 14.04 with a high resolution image (0.5mm isotropic).  I set OMP_NUM_THREADS=16 and then passed the -openmp 16 and -itkthreads 16 flags in my autorecon 2 line command.  Autorecon1 and the beginning parts of Autorecon2 ran in a reasonable amount of time. 

Currently the program is running the mri_segment -keep -mprage brain.mgz wm.seg.mgz line command however it has been at this step for approximately 5 days!  I used top line command to verify that the program is still running and it seems to be still running.  I wasn't sure if this time for this step is typical for a high-res image (as this is my first time processing data higher than 1mm iso), or if there is a potential bug.

I ran this same subject on another computer using the same version of Freesurfer and Ubuntu (8 core machine) and mri_segment (~ step 15) has been running for over a day so far.  Any feedback would be appreciated as to if this amount of processing time is typical for this type of resolution, or if it could be a potential bug and that I should wait for a new beta release?

Thanks,

Ajay