Hi,

I've been sourcing the stable3 version of freesurfer and getting an error in the -fix step of recon-all for the lh. I'm running the command line:

recon-all -subjid <SUBJID> -fix -hemi lh

and I get the following output in scripts/recon-all.log

#-------------------------------------------- #@# Fix Topology lh Mon Feb 4 08:44:46 EST 2008

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

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

/autofs/space/biggs_011/users/PRECREST_MEMPRAGE_nrecon/VESS80_nrecon_vb15_MEMPRAGE/scripts

mris_fix_topology -mgz -sphere qsphere.nofix -ga VESS80_nrecon_vb15_MEMPRAGE lh

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

************************************************************* 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 1.441.2.1 2006/03/06 21:12:31 greve Exp $ before topology correction, eno=-24 (nv=134720, nf=269504, ne=404248, g=13) 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 8 iterations marking ambiguous vertices... 3903 ambiguous faces found in tessellation segmenting defects... defect 12 : 5 vertices have been added to the surface total of 5 vertices has been added to the surface analyzing defects... mrisDefectAnalysis : defect 12 overlap defect 11 reading input surface /autofs/space/biggs_011/users/PRECREST_MEMPRAGE_nrecon/VESS80_nrecon_vb15_MEMPRAGE/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Linux windu 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:48:03 EST 2007 i686 i686 i386 GNU/Linux

recon-all exited with ERRORS at Mon Feb 4 08:45:28 EST 2008

Any suggestions as to how to fix this or info as to what the problem may be?

Thanks,

Bill