Hi everyone, I'm using recon-all to flatten a number of scans from patients and controls. Most of them work fine, but there are 3 that do not reconstruct correctly. They all seem to share the same problem: Recon-all aborts during the automatic topology correction step, and there's a line in the log saying mrisDefectAnalysis : defect XXX overlap defect YYY. I've checked registration to talairach, skull strip and initial surfaces, the only thing I could see was that in some cases, bits of the superior sagittal sinus were wrongly included in the lh.orig.nofix, or small bits of dura, but nothing major. I'm attaching the relevant output from the topology fixer for two different cases. I would be grateful if someone could point me at other things to try. Is it possible to visualise the defects' locations, so I could find out which defect is actually causing the overlap message? Thanks for your help everyone, Johannes
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CASE 1 #@# Fix Topology lh Wed Jun 14 04:04:29 BST 2006 \n cp ../surf/lh.orig.nofix ../surf/lh.orig \n \n cp ../surf/lh.inflated.nofix ../surf/lh.inflated \n /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_2280/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga PAT_2280 lh \n 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=-656 (nv=197397, nf=396220, ne=594273, g=329) 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 9 iterations marking ambiguous vertices... 30743 ambiguous faces found in tessellation segmenting defects... defect 6 : 7 vertices have been added to the surface
[ ... ]
defect 314 : 2 vertices have been added to the surface total of 95 vertices has been added to the surface analyzing defects... mrisDefectAnalysis : defect 277 overlap defect 272 reading input surface /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_2280/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Darwin jalapeno6.fmrib.ox.ac.uk 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc
recon-all exited with ERRORS at Wed Jun 14 04:08:10 BST 2006
CASE 2 #@# Fix Topology rh Thu Jun 15 12:13:05 BST 2006 \n cp ../surf/rh.orig.nofix ../surf/rh.orig \n \n cp ../surf/rh.inflated.nofix ../surf/rh.inflated \n /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_3509/scripts \n mris_fix_topology -mgz -sphere qsphere.nofix -ga PAT_3509 rh \n 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=-2025 (nv=252518, nf=509180, ne=763723, g=1013) 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 13 iterations marking ambiguous vertices... 137391 ambiguous faces found in tessellation segmenting defects... defect 12 : 4 vertices have been added to the surface
[ ... ]
defect 440 : 4 vertices have been added to the surface total of 340 vertices has been added to the surface analyzing defects... mrisDefectAnalysis : defect 395 overlap defect 393 reading input surface /Volumes/JalapenoSAN/Scratch/natalie/schizophrenia/fs/PAT_3509/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Darwin jalapeno4.fmrib.ox.ac.uk 8.6.0 Darwin Kernel Version 8.6.0: Tue Mar 7 16:58:48 PST 2006; root:xnu-792.6.70.obj~1/RELEASE_PPC Power Macintosh powerpc
recon-all exited with ERRORS at Thu Jun 15 12:19:26 BST 2006