Hi All, I am running recon-all on a set of Diff images since last 2 days and it looks like FS stopped working.It says correcting defect 0 since yesterday afternoon. Any way to figure whats going on? Many Thanks Chikku
#@# Fix Topology lh Tue Apr 16 14:47:22 CEST 2013 \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n /Applications/freesurfer/subjects/Diff1/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Diff1 lh \n 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 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ before topology correction, eno=-340 (nv=73648, nf=147976, ne=221964, g=171) 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 12 iterations marking ambiguous vertices... 82800 ambiguous faces found in tessellation segmenting defects... 41 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 10 into 0 -merging segment 32 into 15 -merging segment 19 into 16 -merging segment 38 into 40 36 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/Diff1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8449 (-4.4225) -vertex loglikelihood: -7.8841 (-3.9420) -normal dot loglikelihood: -3.5035 (-3.5035) -quad curv loglikelihood: -6.1723 (-3.0862) Total Loglikelihood : -26.4048
CORRECTING DEFECT 0 (vertices=30266, convex hull=4754)
Hi Chikku
a 30,000 vertex defect means something is dramatically wrong - that's about 1/4 of the whole cortex. Check your filled.mgz or lh.orig.nofix and see if the skull is attached or the cerebellum or something. The computational complexity of the topology fixing is quadratic in the convex hull of the defect, so small ones are fast and big ones take the lifetime of the universe :)
cheers Bruce On Wed, 17 Apr 2013, Varghese Chikku wrote:
Hi All,I am running recon-all on a set of Diff images since last 2 days and it looks like FS stopped working.It says correcting defect 0 since yesterday afternoon. Any way to figure whats going on? Many Thanks Chikku
#@# Fix Topology lh Tue Apr 16 14:47:22 CEST 2013 \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n /Applications/freesurfer/subjects/Diff1/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Diff1 lh \n 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 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.4 2012/11/07 22:38:00 nicks Exp $ before topology correction, eno=-340 (nv=73648, nf=147976, ne=221964, g=171) 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 12 iterations marking ambiguous vertices... 82800 ambiguous faces found in tessellation segmenting defects... 41 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 10 into 0 -merging segment 32 into 15 -merging segment 19 into 16 -merging segment 38 into 40 36 defects to be corrected 0 vertices coincident reading input surface /Applications/freesurfer/subjects/Diff1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8449 (-4.4225) -vertex loglikelihood: -7.8841 (-3.9420) -normal dot loglikelihood: -3.5035 (-3.5035) -quad curv loglikelihood: -6.1723 (-3.0862) Total Loglikelihood : -26.4048
CORRECTING DEFECT 0 (vertices=30266, convex hull=4754)
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Varghese Chikku