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: > > -<no>motioncor < 5 min > > -<no>nuintensitycor 3 min > > -<no>talairach 4 min > > -<no>normalization 3 min > > -<no>skullstrip 1 min > > -<no>gcareg 8 min > > -<no>canorm 1 min > > -<no>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:: mri_label2label time:: 0:03.92 cmd:: mris_label2annot time:: 0:11.87 cmd:: mris_anatomical_stats time:: 0:18.34 cmd:: mri_label2label time:: 0:20.87 cmd:: mri_label2label time:: 0:18.25 cmd:: mri_label2label time:: 0:18.72 cmd:: mri_label2label time:: 0:20.02 cmd:: mri_label2label time:: 0:18.76 cmd:: mri_label2label time:: 0:26.54 cmd:: mri_label2label time:: 0:20.88 cmd:: mri_label2label time:: 0:19.55 cmd:: mri_label2label time:: 0:19.84 cmd:: mri_label2label time:: 0:25.21 cmd:: mri_label2label time:: 0:16.97 cmd:: mri_label2label time:: 0:03.51 cmd:: mris_label2annot time:: 0:11.84 cmd:: mris_anatomical_stats time:: 0:00.00 cmd:: ln time:: 0:18.73 cmd:: mris_spherical_average time:: 0:11.44 cmd:: mris_anatomical_stats time:: 0:00.00 cmd:: ln time:: 0:17.43 cmd:: mris_spherical_average time:: 0:11.49 cmd:: mris_anatomical_stats
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