Hi,
I am processing the anatomical monkey brain now. When recon-all runs, it stops at the step of "mris_fix_topology"
I inserted the last part of my recon-all.log below:
It stops at "CORRECTING DEFECT 0 (vertices=65691, convex hull=4296)" for more than 12 hours. Does this step take that long? Or are there some problems in the data that make freesurfer idling?
Thanks,
Yang
#-------------------------------------------- #@# Fix Topology lh Sat Dec 4 17:01:16 EST 2010
cp ../surf/lh.orig.nofix ../surf/lh.orig
cp ../surf/lh.inflated.nofix ../surf/lh.inflated
/home/yang/091017Castor/scripts
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 091017Castor lh
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 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ before topology correction, eno=-810 (nv=213660, nf=428940, ne=643410, g=406) 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... 156279 ambiguous faces found in tessellation segmenting defects... 64 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 0 -merging segment 11 into 10 -merging segment 23 into 18 -merging segment 33 into 22 -merging segment 40 into 22 -merging segment 62 into 25 -merging segment 39 into 34 -merging segment 35 into 46 56 defects to be corrected 0 vertices coincident reading input surface /home/yang/091017Castor/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8048 (-4.4024) -vertex loglikelihood: -5.5855 (-2.7928) -normal dot loglikelihood: -3.4654 (-3.4654) -quad curv loglikelihood: -5.6070 (-2.8035) Total Loglikelihood : -23.4627
CORRECTING DEFECT 0 (vertices=65691, convex hull=4296)