Hi Gari
is it still running? The time it takes is square in the convex hull of the
largest defect, so that can take a long time. A 45K defect is too big and
typically means something is dramatically wrong, like the cerebellum or
skull is attached.
cheers
Bruce
On Sun, 5 Aug 2012, Garikoitz Lerma Usabiaga wrote:
Hi FS experts, I've run recon-all -i file -s subject -qcache -measure
thickness -all to:
- 18 subjects, session 1 T1
- same 18 subjects, session 2 T1
and everything went well.
Then I copied the <subject_id_session>/mri/orig/001.mgz-s to
<subject_id>/mri/orig/001.mgz and 002.mgz, and run the same command again:
recon-all -s <subject_id> -qcache -measure thickness -all
Half of the subjects are failing when trying to correct the topology. Please
find below the outputs of two of the subjects.
Should I use the -i and the original files instead of the already created
001.mgz files? What should I check in order to avoid this error or what
should I do in order to correct it?
thank you very much,
Gari
*************************************************************
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $
$Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $
before topology correction, eno=-956 (nv=167898, nf=337708, ne=506562,
g=479)
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...
127705 ambiguous faces found in tessellation
segmenting defects...
125 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 6 into 1
-merging segment 9 into 1
-merging segment 21 into 1
-merging segment 24 into 1
-merging segment 26 into 1
-merging segment 29 into 1
-merging segment 44 into 1
-merging segment 56 into 1
-merging segment 2 into 1
-merging segment 65 into 1
-merging segment 67 into 1
-merging segment 71 into 1
-merging segment 4 into 1
-merging segment 12 into 1
-merging segment 34 into 18
-merging segment 30 into 19
-merging segment 38 into 35
-merging segment 61 into 47
-merging segment 107 into 106
-merging segment 115 into 113
105 defects to be corrected
0 vertices coincident
reading input surface
/home/BCBL/glerma/freesurfer/subjects/BERTSO/B_16/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -7.9838 (-3.9919)
-vertex loglikelihood: -5.7349 (-2.8674)
-normal dot loglikelihood: -3.5106 (-3.5106)
-quad curv loglikelihood: -6.1770 (-3.0885)
Total Loglikelihood : -23.4063
CORRECTING DEFECT 0 (vertices=23, convex hull=21)
After retessellation of defect 0, euler #=-32 (96640,274187,177515) :
difference with theory (-102) = -70
CORRECTING DEFECT 1 (vertices=44927, convex hull=14482)
Topology Correction Parametersretessellation 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 1.44 2010/05/27 23:37:16 nicks Exp $
$Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $
before topology correction, eno=-600 (nv=159708, nf=320616, ne=480924,
g=301)
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...
115040 ambiguous faces found in tessellation
segmenting defects...
96 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 16 into 0
-merging segment 39 into 0
-merging segment 48 into 0
-merging segment 22 into 21
-merging segment 38 into 34
-merging segment 42 into 37
-merging segment 70 into 69
89 defects to be corrected
0 vertices coincident
reading input
surface/home/BCBL/glerma/freesurfer/subjects/BERTSO/B_11b/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -7.9998 (-3.9999)
-vertex loglikelihood: -5.5541 (-2.7771)
-normal dot loglikelihood: -3.5423 (-3.5423)
-quad curv loglikelihood: -6.1041 (-3.0520)
Total Loglikelihood : -23.2003
CORRECTING DEFECT 0 (vertices=41794, convex hull=12626)
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