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 Freesurfer@nmr.mgh.harvard.edu 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@nmr.mgh.harvard.edu
-
Bruce Fischl