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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)
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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.
Does anyone have any suggestion on how to troubleshoot this problem?
Thank you,
Soichi Hayashi Indiana University