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_freeview?highlight=%28topology%29%7C%28tutorial%29


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:

>
>         External Email - Use Caution        
>
> 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
>       >
>       >
>
>
>