try running it with -use-new-fixer
cheers,
Bruce
On Mon, 4 Feb 2008, Bill Monaco wrote:
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
#--------------------------------------------
[EMAIL PROTECTED] 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
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