mris_fix_topology -rusage /data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versuch_Pretess/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -g 1234 FJ_20170425_T1_Versuch_Pretess lh
reading spherical homeomorphism from 'qsphere.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
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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 1.50.2.1 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=-666 (nv=184736, nf=370804, ne=556206, g=334)
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 11 iterations
marking ambiguous vertices...
92297 ambiguous faces found in tessellation
segmenting defects...
151 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 3 into 2
-merging segment 32 into 12
-merging segment 94 into 12
-merging segment 45 into 36
-merging segment 53 into 37
-merging segment 62 into 60
-merging segment 81 into 70
-merging segment 88 into 70
-merging segment 144 into 132
-merging segment 141 into 138
-merging segment 150 into 147
140 defects to be corrected
0 vertices coincident
reading input surface /data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versuch_Pretess/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Computing Initial Surface Statistics
-face loglikelihood: -9.3516 (-4.6758)
-vertex loglikelihood: -6.1930 (-3.0965)
-normal dot loglikelihood: -3.5442 (-3.5442)
-quad curv loglikelihood: -6.0556 (-3.0278)
Total Loglikelihood : -25.1443
CORRECTING DEFECT 0 (vertices=9329, convex hull=1902, v0=235)
XL defect detected...
After retessellation of defect 0 (v0=235), euler #=-122 (135106,396534,261306) : difference with theory (-137) = -15
CORRECTING DEFECT 1 (vertices=47, convex hull=87, v0=788)
After retessellation of defect 1 (v0=788), euler #=-121 (135129,396640,261390) : difference with theory (-136) = -15
CORRECTING DEFECT 2 (vertices=1438, convex hull=465, v0=1311)
XL defect detected...
After retessellation of defect 2 (v0=1311), euler #=-119 (135552,398142,262471) : difference with theory (-135) = -16
CORRECTING DEFECT 3 (vertices=24, convex hull=64, v0=9358)
After retessellation of defect 3 (v0=9358), euler #=-118 (135563,398202,262521) : difference with theory (-134) = -16
CORRECTING DEFECT 4 (vertices=35, convex hull=54, v0=11845)
After retessellation of defect 4 (v0=11845), euler #=-117 (135574,398251,262560) : difference with theory (-133) = -16
CORRECTING DEFECT 5 (vertices=68, convex hull=94, v0=12131)
After retessellation of defect 5 (v0=12131), euler #=-116 (135584,398327,262627) : difference with theory (-132) = -16
CORRECTING DEFECT 6 (vertices=66, convex hull=29, v0=12470)
After retessellation of defect 6 (v0=12470), euler #=-115 (135586,398344,262643) : difference with theory (-131) = -16
CORRECTING DEFECT 7 (vertices=29, convex hull=34, v0=16888)
After retessellation of defect 7 (v0=16888), euler #=-114 (135587,398360,262659) : difference with theory (-130) = -16
CORRECTING DEFECT 8 (vertices=66, convex hull=79, v0=16899)
After retessellation of defect 8 (v0=16899), euler #=-113 (135625,398509,262771) : difference with theory (-129) = -16
CORRECTING DEFECT 9 (vertices=219, convex hull=64, v0=16932)
After retessellation of defect 9 (v0=16932), euler #=-112 (135644,398592,262836) : difference with theory (-128) = -16
CORRECTING DEFECT 10 (vertices=69, convex hull=58, v0=19570)
After retessellation of defect 10 (v0=19570), euler #=-111 (135659,398659,262889) : difference with theory (-127) = -16
CORRECTING DEFECT 11 (vertices=18978, convex hull=4487, v0=19837)
mri_pretess:
mbuerger@beo-05:/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1/mri $ rm /data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versuch_Pretess/scripts/IsRunning.lh+rh
rm: remove regular file `/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versuch_Pretess/scripts/IsRunning.lh+rh'?
mbuerger@beo-05:/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1/mri $ mri_pretess -keep wm.mgz wm127 norm.mgz wm.mgz
keeping edits
Ambiguous edge configurations...
Iteration Number : 1
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 1
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 1
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 0 (out of 16189883: 0.000000)
Searching for edits to keep ...
kept 0 WM ON voxels
kept 0 WM OFF voxels
mri_pretess done