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Hi Bruce,
I don't see major thing that could be wrong.
I uploaded on the FileDrop the subject directory compressed. Could you
have a look at it and tell me what you think ?
Best,
Matthieu
On 18/02/2019 15:56, Bruce Fischl wrote:
Hi Matthieu
have you looked at the lh.inflated.nofix to see if anything major is
wrong? The code doesn't exit when it detects an XL defect - it just
warns you and doesn't search as thoroughly for solutions (which would
take forever). It sounds like the 0 faces error is your problem, but
they are likely related. Take a look at the inflated.nofix and see if
you can identify the XL defect. It is probably near the back of the
brain since it is one of the first defects encountered.
cheers
Bruce
On Mon, 18 Feb 2019, Matthieu VANHOUTTE wrote:
External Email - Use Caution
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
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