Well, I figured out what my problem is. The skull strip only took off about a quarter of the skull on the top. Any suggestions on how to correct this?
Quoting Bruce Fischl <[EMAIL PROTECTED]>: > You must have a number of *huge* defects: > > > 163949 ambiguous faces found in tessellation > > segmenting defects... > > 93 defects found, arbitrating ambiguous regions... > > usually the # of defective vertices is less than 1/10 of this. Try > loading > the ?h.defect_labels (with tksurfer->file->load curv) onto the > ?h.inflated.nofix surface to visualize them. Something is badly > wrong. Is > the cerebellum attached? The skull? > > Bruce > > On Fri, 23 Jun 2006 > [EMAIL PROTECTED] wrote: > > > I think my fix topology sequence froze...I typed "top" in another > > terminal and this is what came up... > > > > ID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND > > 899 surf 25 0 2169m 1.6g 1984 R 99.1 43.1 1042:33 > mris_fix_topolo > > 18609 root 15 0 457m 196m 8616 S 0.7 5.3 23:08.06 X > > 18768 tinnitus 16 0 7088 2920 856 S 0.3 0.1 18:04.16 > gam_server > > 1453 surf 17 0 6148 1000 752 R 0.3 0.0 0:00.42 top > > > > According to this, my mris_fix_topogy has been running for over 17 > > hours, and I have a brand new, extremely fast computer. Here's > what the > > other terminal says... > > > > [EMAIL PROTECTED] Fix Topology lh Thu Jun 22 15:08:24 EDT 2006 > > > > cp ../surf/lh.orig.nofix ../surf/lh.orig > > > > > > cp ../surf/lh.inflated.nofix ../surf/lh.inflated > > > > /home/surf/freesurfer/subjects/DOD16-11-1-05/scripts > > > > mris_fix_topology -mgz -sphere qsphere.nofix -ga DOD16-11-1-05 lh > > > > 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 1.441.2.3 2006/04/12 02:03:02 nicks Exp $ > > before topology correction, eno=-1199 (nv=137208, nf=276936, > ne=415343, > > g=600) > > 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 17 iterations > > marking ambiguous vertices... > > 163949 ambiguous faces found in tessellation > > segmenting defects... > > 93 defects found, arbitrating ambiguous regions... > > analyzing neighboring defects... > > -merging segment 2 into 0 > > -merging segment 8 into 0 > > -merging segment 24 into 0 > > -merging segment 27 into 0 > > -merging segment 31 into 0 > > -merging segment 29 into 7 > > -merging segment 34 into 7 > > -merging segment 37 into 7 > > -merging segment 38 into 7 > > -merging segment 43 into 7 > > -merging segment 55 into 7 > > -merging segment 57 into 7 > > -merging segment 63 into 7 > > -merging segment 78 into 7 > > -merging segment 80 into 7 > > -merging segment 82 into 7 > > -merging segment 87 into 7 > > -merging segment 90 into 7 > > -merging segment 91 into 7 > > -merging segment 92 into 7 > > -merging segment 18 into 15 > > -merging segment 56 into 47 > > -merging segment 72 into 64 > > -merging segment 77 into 73 > > -merging segment 7 into 89 > > 68 defects to be corrected > > 0 vertices coincident > > vertex 43773: degenerate normal > > vertex 88884: degenerate normal > > vertex 90911: degenerate normal > > vertex 43773: degenerate normal > > vertex 88884: degenerate normal > > vertex 90911: degenerate normal > > vertex 43773: degenerate normal > > vertex 88884: degenerate normal > > vertex 90911: degenerate normal > > Computing Initial Surface Statistics > > -face loglikelihood: -9.4721 (-4.7360) > > -vertex loglikelihood: -7.7263 (-3.8632) > > -normal dot loglikelihood: -3.5502 (-3.5502) > > -quad curv loglikelihood: -6.2319 (-3.1159) > > Total Loglikelihood : -26.9804 > > > > CORRECTING DEFECT 0 (vertices=32525, convex hull=4561) > > > > > > > > Does it look like its frozen? And if so, could I just run > autorecon > > from the fix topology part, so I dont have to re-run the whole > thing? > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
