Hi Cara the time it takes is quadratic in the convex hull of the largest defect. This means that if the defects are all small it will fly along and finish in under an hour. But if the defects are huge it can take forever. That said, you really should never have a defect larger than a couple of thousand vertices (and even that is quite large). If you do it typically means something else went wrong, like large pieces of the skull being left around
cheers Bruce On Thu, 24 Aug 2017, Cara Bohon wrote: > This is the first time I have had the message that it exited with errors. The > first times I ran it, it just stopped and the log file ended without a > summary statement of why the job stopped. I assumed that time was because I > was running it on a cluster with a 24 hour time limit, so I extended the job > to 48 hours and started the job again - this time I got the error described > below. > > How long is reasonable to be stuck on fix topology for one hemisphere? I > guess my fear was that if it hadn't finished in 48 hours, there was something > wrong. > > >> does this happen every time you run it? The message said that the job >> was killed, which suggests something outside of recon-all (eg, if you >> were running it on a cluster, sometimes a job will get killed if it runs >> out of memory or runs too long). >> >> >> On 08/23/2017 02:30 PM, Cara Bohon wrote: >>> I have a couple of subjects "exited with ERRORS" after running almost 48 >>> hours (when my others all took about 13-15 hours on the same server). Both >>> exited during Fix Topology lh. >>> >>> The only time "error" appears is in this line: IFLAG= -1 LINE SEARCH >>> FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: >>> INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT >>> TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 - which >>> prior messages to this list suggest is not meaningful or problematic. >>> >>> I am brand new to Freesurfer, so I'm not quite sure where to start in >>> troubleshooting. The orig.mgz file looks fine to me, but maybe I'm missing >>> something. Any other tips for things to check? I'm attaching a >>> recon-all.log file in case that is helpful. I am running Freesurfer 5.3.0 >>> on Linux. >>> >>> Thanks for any tips on addressing the error! >>> >>> -Cara > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
