fyi, attached is the grep "time:: " output from a recent run (which took
27.5 hours). this should at least spare you from having to run
recon-all -time yourself. it was run on a 2GHz amd opteron.
n.
On Thu, 2010-07-29 at 11:38 -0400, Nick Schmansky wrote:
> no, but if you add the flag -time to recon-all, you will get lines
> like this in the recon-all.log:
>
> time:: 0:11.49 cmd:: mris_anatomical_stats
>
> where you can grep on 'time::' to get command run times, although you'd
> have to add together some commands to get times for a stage.
>
> note: runtimes can vary quite a bit, some subjects take a lot longer to
> correct than others, and the newer intel nehalem architecture runs in
> less than half the time as the older amd opteron and p4s.
>
> n
>
> On Wed, 2010-07-28 at 17:19 -0400, Chris Watson wrote:
> > Hello,
> > Do you guys have a script that parses recon-all.log and spits out the
> > processing time for each step? Something that would be similar to this
> > in recon-all --help:
> > -motioncor< 5 min
> > -nuintensitycor 3 min
> > -talairach 4 min
> > -normalization 3 min
> > -skullstrip 1 min
> > -gcareg 8 min
> > -canorm 1 min
> > -careg 10 hours
> >
> > and so on.
> >
> > Thanks,
> > Chris
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
time:: 0:05.93 cmd:: mri_convert
time:: 0:05.93 cmd:: mri_convert
time:: 0:10.52 cmd:: mri_convert
time:: 0:03.88 cmd:: mri_add_xform_to_header
time:: 2:41.60 cmd:: mri_nu_correct.mni
time:: 1:26.74 cmd:: talairach_avi
time:: 0:00.28 cmd:: talairach_afd
time:: 5:26.60 cmd:: mri_normalize
time:: 1:02:34 cmd:: mri_em_register
time:: 2:10.99 cmd:: mri_watershed
time:: 1:11.88 cmd:: mri_gcut
time:: 53:11.75 cmd:: mri_em_register
time:: 4:00.77 cmd:: mri_ca_normalize
time:: 9:15:42 cmd:: mri_ca_register
time:: 2:26.80 cmd:: mri_ca_register
time:: 2:41.19 cmd:: mri_remove_neck
time:: 49:59.14 cmd:: mri_em_register
time:: 42:13.88 cmd:: mri_ca_label
time:: 1:29.74 cmd:: mri_cc
time:: 8:22.76 cmd:: mri_normalize
time:: 0:06.26 cmd:: mri_mask
time:: 2:15.52 cmd:: mri_segment
time:: 1:08.39 cmd:: mri_edit_wm_with_aseg
time:: 0:14.25 cmd:: mri_pretess
time:: 1:47.44 cmd:: mri_fill
time:: 0:07.82 cmd:: mri_pretess
time:: 0:06.26 cmd:: mri_tessellate
time:: 0:05.53 cmd:: mris_extract_main_component
time:: 0:08.82 cmd:: mris_smooth
time:: 1:32.37 cmd:: mris_inflate
time:: 11:54.58 cmd:: mris_sphere
time:: 32:29.24 cmd:: mris_fix_topology
time:: 0:06.86 cmd:: mris_remove_intersection
time:: 27:53.18 cmd:: mris_make_surfaces
time:: 0:00.17 cmd:: mris_calc
time:: 0:00.07 cmd:: mris_calc
time:: 0:00.10 cmd:: mris_calc
time:: 0:08.37 cmd:: mris_smooth
time:: 1:44.29 cmd:: mris_inflate
time:: 2:53.10 cmd:: mris_curvature
time:: 0:12.38 cmd:: mris_curvature_stats
time:: 2:59:01 cmd:: mris_sphere
time:: 1:42:58 cmd:: mris_register
time:: 0:04.70 cmd:: mris_jacobian
time:: 0:03.92 cmd:: mrisp_paint
time:: 2:34.75 cmd:: mris_ca_label
time:: 1:33.53 cmd:: mris_anatomical_stats
time:: 2:49.94 cmd:: mris_ca_label
time:: 1:54.05 cmd:: mris_anatomical_stats
time:: 0:09.09 cmd:: mri_pretess
time:: 0:06.06 cmd:: mri_tessellate
time:: 0:05.07 cmd:: mris_extract_main_component
time:: 0:08.84 cmd:: mris_smooth
time:: 1:41.04 cmd:: mris_inflate
time:: 11:16.03 cmd:: mris_sphere
time:: 43:49.82 cmd:: mris_fix_topology
time:: 0:08.65 cmd:: mris_remove_intersection
time:: 27:23.40 cmd:: mris_make_surfaces
time:: 0:00.43 cmd:: mris_calc
time:: 0:00.07 cmd:: mris_calc
time:: 0:00.10 cmd:: mris_calc
time:: 0:08.76 cmd:: mris_smooth
time:: 1:21.45 cmd:: mris_inflate
time:: 2:51.19 cmd:: mris_curvature
time:: 0:12.80 cmd:: mris_curvature_stats
time:: 2:10:09 cmd:: mris_sphere
time:: 1:48:06 cmd:: mris_register
time:: 0:04.58 cmd:: mris_jacobian
time:: 0:04.08 cmd:: mrisp_paint
time:: 2:34.42 cmd:: mris_ca_label
time:: 1:54.71 cmd:: mris_anatomical_stats
time:: 2:50.40 cmd:: mris_ca_label
time:: 2:04.81 cmd:: mris_anatomical_stats
time:: 34:49.65 cmd:: mris_volmask
time:: 18:39.54 cmd:: mri_segstats
time:: 7:07.57 cmd:: mri_aparc2aseg
time:: 7:02.38 cmd:: mri_aparc2aseg
time:: 16:53.63 cmd:: mri_aparc2aseg
time:: 28:07.75 cmd:: mri_segstats
time:: 0:00.02 cmd:: ln
time:: 0:18.98 cmd:: mri_label2label
time:: 0:22.28 cmd:: mri_label2label
time:: 0:18.37 cmd:: mri_label2label
time:: 0:20.10 cmd:: mri_label2label
time:: 0:19.96 cmd:: mri_label2label
time:: 0:18.64 cmd:: mri_label2label
time:: 0:29.49 cmd:: mri_label2label
time:: 0:18.81 cmd:: mri_label2label
time:: 0:17.79 cmd:: mri_label2label
time:: 0:19.80 cmd:: mri_label2label
time:: 0:23.95 cmd:: mri_label2label
time:: 0:16.81 cmd:: mr