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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