Re: [Freesurfer] mris_fix_topology stuck running

Hi Soichi

look at the inflated.nofix in the 3D view, not the orig.nofix. You can check out our tutorial here:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freev...

although there may be a better one (hopefully someone else will chime in if so)

cheers Bruce

On Tue, 26 Mar 2019, Soichi Hayashi wrote:

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Bruce, Thank you for your help. I'd very much appreciate it.

I've looked at rh.orig.nofix / rh.inflated.nofix, but I couldn't really find anything out of ordinary.. from my layman's eyes.

Screenshot from 2019-03-26 10-35-42.png

Could you point me to the wiki you mentioned?

Soichi

On Sun, Mar 24, 2019 at 4:37 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Soichi

  that is too big a defect to expect it to fix - more than half the number
  of vertices in a typical hemisphere. It means something is badly wrong
  that you need to correct prior to the topo fixer. You can look at our
  wiki for this kind of thing, but I would start by looking at the
  rh.orig.nofix and the rh.inflated.nofix. Something big is wrong, like large
  parts of the skull attached to the surface or something like that

  cheers
  Bruce


  On Sun, 24 Mar 2019, Soichi Hayashi wrote:

  >
  >         External Email - Use Caution        
  >
  > 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.
  >
  > Does anyone have any suggestion on how to troubleshoot this problem?
  >
  > Thank you,
  >
  > Soichi Hayashi
  > Indiana University
  >
  >