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Dear Freesurfer's experts,
I have run recon-all on one subject and it stopped with a "XL defect detected..." (please see below the log):
/#@# Fix Topology lh Sat Feb 16 08:22:31 CET 2019// // // mris_fix_topology -rusage /FS6.0.1/awellv3s013/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 awellv3s013 lh // // //reading spherical homeomorphism from 'qsphere.nofix'// //using genetic algorithm with optimized parameters// //setting seed for random number genererator to 1234// // //*************************************************************// //Topology Correction Parameters// //retessellation mode: genetic search// //number of patches/generation : 10// //number of generations : 10// //surface mri loglikelihood coefficient : 1.0// //volume mri loglikelihood coefficient : 10.0// //normal dot loglikelihood coefficient : 1.0// //quadratic curvature loglikelihood coefficient : 1.0// //volume resolution : 2// //eliminate vertices during search : 1// //initial patch selection : 1// //select all defect vertices : 0// //ordering dependant retessellation: 0// //use precomputed edge table : 0// //smooth retessellated patch : 2// //match retessellated patch : 1// //verbose mode : 0// // //*************************************************************// //INFO: assuming .mgz format// //$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $// // $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $// //before topology correction, eno=-112 (nv=135382, nf=270988, ne=406482, g=57)// //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 10 iterations// //marking ambiguous vertices...// //39303 ambiguous faces found in tessellation// //segmenting defects...// //22 defects found, arbitrating ambiguous regions...// //analyzing neighboring defects...// // -merging segment 16 into 2// //21 defects to be corrected // //0 vertices coincident// //reading input surface FS6.0.1/awellv3s013/surf/lh.qsphere.nofix...// //reading brain volume from brain...// //reading wm segmentation from wm...// //Computing Initial Surface Statistics// // -face loglikelihood: -9.1744 (-4.5872)// // -vertex loglikelihood: -6.3047 (-3.1523)// // -normal dot loglikelihood: -3.6091 (-3.6091)// // -quad curv loglikelihood: -5.8524 (-2.9262)// // Total Loglikelihood : -24.9405// // //CORRECTING DEFECT 0 (vertices=41, convex hull=76, v0=1825)// //After retessellation of defect 0 (v0=1825), euler #=-4 (114791,342427,227632) : difference with theory (-18) = -14 // // //CORRECTING DEFECT 1 (vertices=22, convex hull=53, v0=6219)// //After retessellation of defect 1 (v0=6219), euler #=-3 (114805,342485,227677) : difference with theory (-17) = -14 // // //CORRECTING DEFECT 2 (vertices=19736, convex hull=2755, v0=16117)// //normal vector of length zero at vertex 115020 with 0 faces// //vertex 115020 has 0 face// //XL defect detected...// //No such file or directory// //Linux hpc1.cyceron.fr 3.10.0-693.11.6.el7.x86_64 #1 SMP Thu Jan 4 01:06:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux// // //recon-all -s awellv3s013 exited with ERRORS at Sat Feb 16 10:17:17 CET 2019/
I looked at the ?h.orig.nofix but didn't see anything wrong, despite the fact that these surfaces are very not smooth.
What could I do ?
Best,
Matthieu