hmmm, sounds quite pathological as it allows up to 1,000 faces to intersect (which we thought would never happen). Can you look at the lh.inflated.nofix surface and see if there is a huge problem (skull attached? cerebellum attached? etc...)

cheers, Bruce On Mon, 4 Dec 2006, Bum Seok Jeong wrote:

During Fix topology, error message showed. Would you please let me know what happened?

Thanks for advance

#-------------------------------------------- #@# Fix Topology lh Fri Dec 1 22:06:19 EST 2006

cp ../surf/lh.orig.nofix ../surf/lh.orig

cp ../surf/lh.inflated.nofix ../surf/lh.inflated

/gr/caseD00916/scripts

mris_fix_topology -mgz -sphere qsphere.nofix -ga caseD00916 lh

reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters

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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 1.41 2006/02/06 19:41:59 nicks Exp $ $Id: mrisurf.c,v 1.453 2006/04/21 17:14:26 segonne Exp $ before topology correction, eno=-974 (nv=172934, nf=347844, ne=521752, g=488) 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 12 iterations marking ambiguous vertices... Too many intersected faces for face 142725 (71953, 71952, 70394) reading input surface /gr/caseD00916/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Linux b2_tm128.bwh.harvard.edu 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22:53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Fri Dec 1 22:07:15 EST 2006

<210> /gr% ls 3T_spgr.nii caseD00916/ <211> gr% cat caseD0091 6/scripts/recon-all-status.log status file for recon-all Thu Nov 30 14:50:29 EST 2006 #@# MotionCor Thu Nov 30 14:51:05 EST 2006 #@# Nu Intensity Correction Thu Nov 30 14:51:55 EST 2006 #@# Talairach Thu Nov 30 14:53:33 EST 2006 #@# Intensity Normalization Thu Nov 30 14:54:02 EST 2006 #@# Skull Stripping Thu Nov 30 14:57:30 EST 2006 recon-all finished without error at Thu Nov 30 14:58:57 EST 2006

New invocation of recon-all

status file for recon-all Thu Nov 30 15:04:52 EST 2006 #@# EM Registration Thu Nov 30 15:04:52 EST 2006 #@# CA Normalize Thu Nov 30 15:09:12 EST 2006 #@# CA Reg Thu Nov 30 15:10:26 EST 2006 #@# CA Reg Inv Fri Dec 1 00:12:14 EST 2006 #@# Remove Neck Fri Dec 1 00:13:14 EST 2006 #@# SkullLTA Fri Dec 1 00:14:49 EST 2006 #@# SubCort Seg Fri Dec 1 00:22:05 EST 2006 #@# ASeg Stats Fri Dec 1 01:06:04 EST 2006 #@# Intensity Normalization2 Fri Dec 1 01:19:19 EST 2006 #@# Mask BFS Fri Dec 1 01:24:25 EST 2006 #@# WM Segmentation Fri Dec 1 01:24:31 EST 2006 #@# Fill Fri Dec 1 01:32:10 EST 2006 #@# Tessellate lh Fri Dec 1 01:33:53 EST 2006 #@# Smooth1 lh Fri Dec 1 01:34:00 EST 2006 #@# Inflation1 lh Fri Dec 1 01:34:13 EST 2006 #@# QSphere lh Fri Dec 1 01:38:05 EST 2006 #@# Fix Topology lh Fri Dec 1 02:08:50 EST 2006 Linux 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22 :53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Fri Dec 1 02:09:39 EST 2006 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer