Recon is still running. I started the process on 2/21/2013. Its been 4 days.
I ran this command, and viewed the aseg file, and that looks reasonable tkmedit ./ brainmask.mgz -aux T1.mgz -surfs -aseg Currently it is at this stage: Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 13 iterations marking ambiguous vertices... 124766 ambiguous faces found in tessellation segmenting defects... ...... 61 defects to be corrected 0 vertices coincident ...... ...... CORRECTING DEFECT 31 (vertices=244, convex hull=142) After retessellation of defect 31, euler #=-6 (59502,172495,112987) : difference with theory (-27) = -21 CORRECTING DEFECT 32 (vertices=44865, convex hull=8969) On Fri, Feb 22, 2013 at 5:33 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > I don't think either one of these are errors, just warnings that occur > pretty frequently and I don't think should impact the results. Does the > recon finish? Do the results look ok? > > > On Fri, 22 Feb 2013, Blessy M wrote: > > >> I am getting the bottom two sets of errors while doing a simple recon-all. >> >> More specifically while running this command: >> recon-all -subjid . -noskullstrip -autorecon1 -notal-check -autorecon2 >> -autorecon3 >> >> Has someone encountered this kind of errors? Is there a fix? >> >> 1) >> Computing MAP estimate using 2772 samples... >> ********************************************** >> IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR >> RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE >> INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = >> 7296.5 tol 0.000010 >> ... >> ... >> >> 2) >> unfolding failed - restoring original position -------------------- >> 0146: dt=13.779160, rms=0.814 (0.000%), neg=0, invalid=766 >> blurring input image with Gaussian with sigma=0.500... >> 0000: dt=0.000, rms=0.814, neg=0, invalid=766 >> gcamFindOptimalTimeStep: Complete in 101542.133 ms >> iter 0, gcam->neg = 801 >> >> ...................... >> >> unfolding failed - restoring original position -------------------- >> 0158: dt=13.828393, rms=0.814 (-0.069%), neg=0, invalid=766 >> blurring input image with Gaussian with sigma=0.500... >> 0000: dt=0.000, rms=0.814, neg=0, invalid=766 >> gcamFindOptimalTimeStep: Complete in 100610.148 ms >> >> >> >> > > 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<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. >
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