Hello.
I am trying to troubleshoot an issue where recon_all is not finishing after >24 hours. It's getting stuck when it tries to run the following command.
$ mris_fix_topology -rusage ./output/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 output rh
INFO: assuming .mgz format
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
*************************************************************
$Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
$Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
reading input surface /home/hayashis/Downloads/output/surf/rh.qsphere.nofix...
before topology correction, eno=-696 (nv=191488, nf=384368, ne=576552, g=349)
reading brain volume from brain...
reading wm segmentation from wm...
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...
133741 ambiguous faces found in tessellation
segmenting defects...
63 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 16 into 0
-merging segment 23 into 0
-merging segment 48 into 0
-merging segment 32 into 22
-merging segment 49 into 47
-merging segment 54 into 51
57 defects to be corrected
0 vertices coincident
Computing Initial Surface Statistics
-face loglikelihood: -9.3123 (-4.6561)
-vertex loglikelihood: -6.5427 (-3.2713)
-normal dot loglikelihood: -3.5794 (-3.5794)
-quad curv loglikelihood: -6.0564 (-3.0282)
Total Loglikelihood : -25.4907
CORRECTING DEFECT 0 (vertices=65141, convex hull=8287, v0=517)
After displaying the last line, the process seems to be stuck running with 100% cpu (single core) for >24 hours until our batch scheduler kills it. I think the issue is with my input data, but it looks clean and well ACPC aligned, and I don't know what's wrong with it. The input image dimensions are 182 x 218 x 182.