Hello Freesurfer experts,
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
Hi Ajay
it's kind of dicey to use an arbitrary nightly build as we have no idea what was in that that might have been fixed the next day. I would wait for a beta, or at the very least try a new version as I don't think our current version exhibits the behavior you are experiencing.
cheers Bruce On Tue, 29 Dec 2015, Ajay Kurani wrote:
Hello Freesurfer experts,
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
freesurfer@nmr.mgh.harvard.edu