I just took a look at it, and I think it's still running. How long has it been? There looks like there is a very large topological defect, that will take a long time to correct. The correction has complexity that is quadratic in the convex hull of the largest defect, so large ones can take a *long* time. Usually when there is one this big though it means something failed. Check the rh.inflated.nofix and rh.orig.nofix files to see if there is a connection to the skull or something else. If you have trouble fixing this, upload the subject and we'll take a look.
cheers Bruce On Thu, 20 Oct 2011, Kenichiro Tanaka wrote: > Dear Bruce, > > I emailed you the recon-all.log. > Please check it and tell me how wrong something is? > > Thanks, > > Kenichiro Tanaka. > > (2011/10/19 21:26), Bruce Fischl wrote: >> ok, why don't you tar and gzip the subject and put it on our ftp site. You >> can also just email me the recon-all.log and I'll take a look >> Bruce >> On Wed, 19 Oct 2011, Kenichiro Tanaka wrote: >> >> > Dear Bruce, >> > >> > I think they are error. >> > The number of output files is not complete. >> > For example, there are only lh.aparc.a2009s.stats, lh.aparc.stats and >> > lh.curv.stats on stats directory. >> > >> > Thanks, >> > >> > Kenichiro Tanaka. >> > >> > >> > >> > (2011/10/18 21:30), Bruce Fischl wrote: >> > Are you sure they are errors? We see this mysterious message >> > sometimes, but I don't think it is really an error, and usually >> > things are fine >> > >> > cheers >> > Bruce >> > >> > On Tue, 18 Oct 2011, Kenichiro Tanaka wrote: >> > >> > Hello All, >> > >> > While processing a brain image data(.mgz) through >> > ver5.0.0, I got the >> > following errors. >> > I have no idea how to resolve them. >> > I need outputs in stats directory, there are only >> > lh.aparc.a2009s.stats, >> > lh.aparc.stats, and lh.curv.stats. >> > What caused them? >> > How should I resolve them? >> > >> > IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF >> > ROUTINE MCSRCH ERROR >> > RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: >> > FUNCTION OR GRADIENT ARE >> > INCORRECT OR INCORRECT TOLERANCESoutof >> > QuasiNewtonEMA: 005: -log(p) = >> > 10318.1 tol 0.000010 >> > . >> > . >> > . >> > inflating to sphere (rms error < 2.00) >> > 000: dt: 0.0000, rms radial error=175.699, avgs=0 >> > 005/300: dt: 0.9000, rms radial error=175.446, >> > avgs=0 >> > 010/300: dt: 0.9000, rms radial error=174.904, >> > avgs=0 >> > 015/300: dt: 0.9000, rms radial error=174.193, >> > avgs=0 >> > 020/300: dt: 0.9000, rms radial error=173.383, >> > avgs=0 >> > 025/300: dt: 0.9000, rms radial error=172.518, >> > avgs=0 >> > 030/300: dt: 0.9000, rms radial error=171.620, >> > avgs=0 >> > 035/300: dt: 0.9000, rms radial error=170.706, >> > avgs=0 >> > 040/300: dt: 0.9000, rms radial error=169.784, >> > avgs=0 >> > 045/300: dt: 0.9000, rms radial error=168.860, >> > avgs=0 >> > 050/300: dt: 0.9000, rms radial error=167.935, >> > avgs=0 >> > 055/300: dt: 0.9000, rms radial error=167.012, >> > avgs=0 >> > 060/300: dt: 0.9000, rms radial error=166.092, >> > avgs=0 >> > 065/300: dt: 0.9000, rms radial error=165.175, >> > avgs=0 >> > 070/300: dt: 0.9000, rms radial error=164.262, >> > avgs=0 >> > 075/300: dt: 0.9000, rms radial error=163.352, >> > avgs=0 >> > 080/300: dt: 0.9000, rms radial error=162.447, >> > avgs=0 >> > 085/300: dt: 0.9000, rms radial error=161.547, >> > avgs=0 >> > 090/300: dt: 0.9000, rms radial error=160.651, >> > avgs=0 >> > 095/300: dt: 0.9000, rms radial error=159.759, >> > avgs=0 >> > 100/300: dt: 0.9000, rms radial error=158.871, >> > avgs=0 >> > 105/300: dt: 0.9000, rms radial error=157.989, >> > avgs=0 >> > 110/300: dt: 0.9000, rms radial error=157.110, >> > avgs=0 >> > 115/300: dt: 0.9000, rms radial error=156.236, >> > avgs=0 >> > 120/300: dt: 0.9000, rms radial error=155.367, >> > avgs=0 >> > 125/300: dt: 0.9000, rms radial error=154.502, >> > avgs=0 >> > 130/300: dt: 0.9000, rms radial error=153.642, >> > avgs=0 >> > 135/300: dt: 0.9000, rms radial error=152.786, >> > avgs=0 >> > 140/300: dt: 0.9000, rms radial error=151.934, >> > avgs=0 >> > 145/300: dt: 0.9000, rms radial error=151.087, >> > avgs=0 >> > 150/300: dt: 0.9000, rms radial error=150.245, >> > avgs=0 >> > 155/300: dt: 0.9000, rms radial error=149.407, >> > avgs=0 >> > 160/300: dt: 0.9000, rms radial error=148.573, >> > avgs=0 >> > 165/300: dt: 0.9000, rms radial error=147.744, >> > avgs=0 >> > 170/300: dt: 0.9000, rms radial error=146.919, >> > avgs=0 >> > 175/300: dt: 0.9000, rms radial error=146.098, >> > avgs=0 >> > 180/300: dt: 0.9000, rms radial error=145.282, >> > avgs=0 >> > 185/300: dt: 0.9000, rms radial error=144.470, >> > avgs=0 >> > 190/300: dt: 0.9000, rms radial error=143.663, >> > avgs=0 >> > 195/300: dt: 0.9000, rms radial error=142.860, >> > avgs=0 >> > 200/300: dt: 0.9000, rms radial error=142.061, >> > avgs=0 >> > 205/300: dt: 0.9000, rms radial error=141.266, >> > avgs=0 >> > 210/300: dt: 0.9000, rms radial error=140.476, >> > avgs=0 >> > 215/300: dt: 0.9000, rms radial error=139.693, >> > avgs=0 >> > 220/300: dt: 0.9000, rms radial error=138.914, >> > avgs=0 >> > 225/300: dt: 0.9000, rms radial error=138.140, >> > avgs=0 >> > 230/300: dt: 0.9000, rms radial error=137.370, >> > avgs=0 >> > 235/300: dt: 0.9000, rms radial error=136.604, >> > avgs=0 >> > 240/300: dt: 0.9000, rms radial error=135.842, >> > avgs=0 >> > 245/300: dt: 0.9000, rms radial error=135.085, >> > avgs=0 >> > 250/300: dt: 0.9000, rms radial error=134.332, >> > avgs=0 >> > 255/300: dt: 0.9000, rms radial error=133.583, >> > avgs=0 >> > 260/300: dt: 0.9000, rms radial error=132.838, >> > avgs=0 >> > 265/300: dt: 0.9000, rms radial error=132.098, >> > avgs=0 >> > 270/300: dt: 0.9000, rms radial error=131.362, >> > avgs=0 >> > 275/300: dt: 0.9000, rms radial error=130.629, >> > avgs=0 >> > 280/300: dt: 0.9000, rms radial error=129.901, >> > avgs=0 >> > 285/300: dt: 0.9000, rms radial error=129.177, >> > avgs=0 >> > 290/300: dt: 0.9000, rms radial error=128.456, >> > avgs=0 >> > 295/300: dt: 0.9000, rms radial error=127.740, >> > avgs=0 >> > 300/300: dt: 0.9000, rms radial error=127.028, >> > avgs=0 >> > >> > spherical inflation complete. >> > . >> > . >> > . >> > epoch 4 (K=1280.0), pass 1, starting sse = 541.21 >> > taking momentum steps... >> > taking momentum steps... >> > taking momentum steps... >> > pass 1 complete, delta sse/iter = 0.32/19 = 0.01710 >> > finalwriting spherical brain to >> > ../surf/lh.qsphere.nofix >> > spherical transformation took 0.10 hours >> > distance error %100000.00 >> > . >> > . >> > . >> > pass 1: epoch 1 of 3 starting distance error %21.36 >> > pass 1: epoch 2 of 3 starting distance error %21.04 >> > unfolding complete - removing small folds... >> > starting distance error %20.80 >> > removing remaining folds... >> > final distance error %20.81 >> > 364: 0 negative triangles >> > . >> > . >> > . >> > >> > >> > Thanks, >> > >> > Kenichiro Tanaka. >> > >> > _______________________________________________ >> > 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. >> > >> > >> > >> > >> > >> > > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
