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...
#@# 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?