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)