Hi Bruce, Thanks for the tips. I tried playing around with the files for a bit but didn’t make much progress.
Here’s a link to the full tar/gz’ed subject dir: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=4ej948sa49s Thanks! Dan On Fri Jun 24 22:22:17 EDT 2016, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Dan > > that defect is too big, there must be something wrong. Check to see if the > surface is connected to dura or across the hemis or something. You can look > at the lh.inflated.nofix and/or the lh.orig.nofix to see where the defects > are. Then you'll need to correct something once you've figured out why > there is such a huge defect. > > cheers > Bruce > > p.s. if you can't sort this out you can tar and gzip your whole subject dir > and we will take a look > > On Fri, Jun 24, 2016 at 9:15 PM, Dan Loewenherz > <daniel.loewenh...@aya.yale.edu> wrote: >> >> Hi freeserver folks, >> >> First time poster here. First off, thanks so much to the folks who >> work on and make this software available to the public. It seems like >> pretty incredible tech, from what little I understand of it. :) >> >> My problem is that the freesurfer process appears to be stuck on the >> recon-all command. It’s been sitting at ”CORRECTING DEFECT 0 >> (vertices=96285, convex hull=13916)” for about 10 hours now. Any way >> to cut that number down or should I just let it keep doing its thing? >> I’ve pasted all of the output pasted at end of the message. >> >> Thanks so much! >> >> Dan >> >> ************************************************************* >> INFO: assuming .mgz format >> $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ >> $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ >> before topology correction, eno=-684 (nv=141228, nf=283824, >> ne=425736, g=343) >> using quasi-homeomorphic spherical map to tessellate cortical surface... >> >> Correction of the Topology >> Finding true center and radius of Spherical Surface...done >> Surface centered at (0,0,0) with radius 100.0 in 14 iterations >> marking ambiguous vertices... >> 190731 ambiguous faces found in tessellation >> segmenting defects... >> 40 defects found, arbitrating ambiguous regions... >> analyzing neighboring defects... >> -merging segment 2 into 0 >> -merging segment 5 into 0 >> -merging segment 8 into 0 >> -merging segment 14 into 0 >> -merging segment 25 into 0 >> -merging segment 28 into 0 >> -merging segment 20 into 17 >> -merging segment 29 into 17 >> -merging segment 36 into 35 >> 31 defects to be corrected >> 0 vertices coincident >> reading input surface >> /Applications/freesurfer/subjects/Dan/surf/lh.qsphere.nofix... >> reading brain volume from brain... >> reading wm segmentation from wm... >> Computing Initial Surface Statistics >> -face loglikelihood: -8.8790 (-4.4395) >> -vertex loglikelihood: -7.4039 (-3.7020) >> -normal dot loglikelihood: -3.5029 (-3.5029) >> -quad curv loglikelihood: -6.1567 (-3.0783) >> Total Loglikelihood : -25.9425 >> >> CORRECTING DEFECT 0 (vertices=96285, convex hull=13916) _______________________________________________ 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.
