Hi Milène

did you edit in freeview? Or something else? If you load the wm.mgz on
top of the norm.mgz, does is still look to be in the same space? If so,
feel free to tar and gzip the entire subject dir and upload it and we will
take a look

cheers
Bruce



On Fri, 15
Feb 2019, Milene Buerger wrote:

>
>         External Email - Use Caution        
>
> Thank you Bruce for your answer!
> I figured out how to edit the wm.mgz. Indeed some parts of the skull were not properly removed from the
> brainmask and therefor considered as white matter. I manually removed voxels from the wm.mgz and then I
> tried to reintegrate the wm.mgz to the recon-all command by doing the mri_fill <inputvol> <outputvol>.
> Unfortunately I got this error:
>  
> mbuerger@beo-05:/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_2017042
> 5_T1/mri $ mri_fill wm.mgz filled.mgz
> reading input volume...done.
> searching for cutting planes...talairach transform
>  1.18336   0.13264   0.04891   10.53902;
> -0.11077   0.95044   0.09947  -11.50818;
> -0.00953  -0.18656   1.07681  -50.07034;
>  0.00000   0.00000   0.00000   1.00000;
> INFO: Modifying talairach volume c_(r,a,s) based on average_305
> voxel to talairach voxel transform
>  1.18336   0.04891  -0.13264  -14.02849;
> -0.00953   1.07681   0.18656   15.85732;
>  0.11077  -0.09947   0.95044   6.22865;
>  0.00000   0.00000   0.00000   1.00000;
> mri_fill: could not find valid seed for the cc
> Looking for area (min, max) = (350, 1400)
> area[0] = 9142 (min = 350, max = 1400), aspect = 0.54 (min = 0.10, max = 0.75)
> need search nearby
> using +/- offset search region where offset is 3.....
> using +/- offset search region where offset is 6.....
> using +/- offset search region where offset is 9.....
> using +/- offset search region where offset is 12.....
> area[0] = 597 (min = 350, max = 1400), aspect = 0.56 (min = 0.10, max = 0.75)
> min_slice = -1, min_area = 65536
> Looking for area (min, max) = (350, 1400)
> area[0] = 1874 (min = 350, max = 1400), aspect = 0.53 (min = 0.10, max = 0.75)
> need search nearby
> using +/- offset search region where offset is 3.....
> using +/- offset search region where offset is 6.....
> using +/- offset search region where offset is 9.....
> using +/- offset search region where offset is 12.....
> using +/- offset search region where offset is 15.....
> using +/- offset search region where offset is 18.....
> using +/- offset search region where offset is 21.....
> using +/- offset search region where offset is 24.....
> using +/- offset search region where offset is 27.....
> using +/- offset search region where offset is 30.....
> using +/- offset search region where offset is 33.....
> using +/- offset search region where offset is 36.....
> using +/- offset search region where offset is 39.....
> using +/- offset search region where offset is 42.....
> using +/- offset search region where offset is 45.....
> using +/- offset search region where offset is 48.....
> mri_fill: could not find corpus callosum
>  
>  
> Do you have any ideas?
>  
> Milène
>  
>  
> Gesendet: Mittwoch, 13. Februar 2019 um 16:01 Uhr
> Von: "Bruce Fischl" <fischl@nmr.mgh.harvard.edu>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Betreff: Re: [Freesurfer] Fix topology correcting defect
> Hi Milène
>
> a couple of things. First, to view a surface in freeview you have to
> specify that it is a surface with -f before the surface file name. So,
> from the mri dir you could do:
>
> freeview -v norm.mgz -f ../surf/lh.orig.nofix ../surf/lh.inflated.nofix
>
> Second, how long did you wait? Big defects take a long time. You should
> definitely look at your inflated and orig surfaces though to make sure that
> some dramatic isn't wrong (like skull attached, or hemispheres not
> separated) as your defect is probably too large to be an ordinary one that
> the topo fixer will correct successfully.
>
> cheers
> Bruce
>
> On Wed, 13 Feb 2019, "Milene Bürger" wrote:
>
> >
> >         External Email - Use Caution        
> >
> > Hi Freesurfers,  
> > I tried to run the recon-all command for several subjects of my study. It worked out for all of them
> > except for one. This one froze at fixing topology „Correcting defect“ 11 out of 140 defects. 
> > I looked for advises in the mailing list but I can’t find any major problems in the images that
> > Freesurfer processed so far. The last correct file that I can open in freeview, is filled.mgz (the
> > skull and cerebellum are properly removed and it shows the two hemispheres with 127 for rh and 255
> > for lh). I can’t find the file "filled-pretess255.mgz“ which should be the output, but I do have the
> > files lh.orig.nofix and rh.orig.nofix for example. I tried to look at these files, but freeview
> > can't open them (failed to load MRI) so that I can’t see if there are topological defects to correct
> > as you described on one of the FsTutorials. I already tried to run only the autorecon2 command, but
> > the same freezing problem appeared at one point. I also tried to only use the mri_pretess command
> > with different options, but it didn’t work.
> >  
> > I copied you the fix topology and what I tried with mri_pretess. I use freesurfer version 6.0.1.
> >  
> > Thanks a lot!
> >  
> > Milène
> >  
> >  mris_fix_topology-rusage/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Vers
> u
> > ch_Pretess/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -g 1234
> > FJ_20170425_T1_Versuch_Pretess 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 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $
> >   $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $
> > before topology correction, eno=-666 (nv=184736, nf=370804, ne=556206, g=334)
> > 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 11 iterations
> > marking ambiguous vertices...
> > 92297 ambiguous faces found in tessellation
> > segmenting defects...
> > 151 defects found, arbitrating ambiguous regions...
> > analyzing neighboring defects...
> >       -merging segment 3 into 2
> >       -merging segment 32 into 12
> >       -merging segment 94 into 12
> >       -merging segment 45 into 36
> >       -merging segment 53 into 37
> >       -merging segment 62 into 60
> >       -merging segment 81 into 70
> >       -merging segment 88 into 70
> >       -merging segment 144 into 132
> >       -merging segment 141 into 138
> >       -merging segment 150 into 147
> > 140 defects to be corrected 
> > 0 vertices coincident
> > reading inputsurface/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Vers
> u
> > ch_Pretess/surf/lh.qsphere.nofix...
> > reading brain volume from brain...
> > reading wm segmentation from wm...
> > Computing Initial Surface Statistics
> >       -face       loglikelihood: -9.3516  (-4.6758)
> >       -vertex     loglikelihood: -6.1930  (-3.0965)
> >       -normal dot loglikelihood: -3.5442  (-3.5442)
> >       -quad curv  loglikelihood: -6.0556  (-3.0278)
> >       Total Loglikelihood : -25.1443
> >  
> > CORRECTING DEFECT 0 (vertices=9329, convex hull=1902, v0=235)
> > XL defect detected...
> > After retessellation of defect 0 (v0=235), euler #=-122 (135106,396534,261306) : difference with
> > theory (-137) = -15 
> > CORRECTING DEFECT 1 (vertices=47, convex hull=87, v0=788)
> > After retessellation of defect 1 (v0=788), euler #=-121 (135129,396640,261390) : difference with
> > theory (-136) = -15 
> > CORRECTING DEFECT 2 (vertices=1438, convex hull=465, v0=1311)
> > XL defect detected...
> > After retessellation of defect 2 (v0=1311), euler #=-119 (135552,398142,262471) : difference with
> > theory (-135) = -16 
> > CORRECTING DEFECT 3 (vertices=24, convex hull=64, v0=9358)
> > After retessellation of defect 3 (v0=9358), euler #=-118 (135563,398202,262521) : difference with
> > theory (-134) = -16 
> > CORRECTING DEFECT 4 (vertices=35, convex hull=54, v0=11845)
> > After retessellation of defect 4 (v0=11845), euler #=-117 (135574,398251,262560) : difference with
> > theory (-133) = -16 
> > CORRECTING DEFECT 5 (vertices=68, convex hull=94, v0=12131)
> > After retessellation of defect 5 (v0=12131), euler #=-116 (135584,398327,262627) : difference with
> > theory (-132) = -16 
> > CORRECTING DEFECT 6 (vertices=66, convex hull=29, v0=12470)
> > After retessellation of defect 6 (v0=12470), euler #=-115 (135586,398344,262643) : difference with
> > theory (-131) = -16 
> > CORRECTING DEFECT 7 (vertices=29, convex hull=34, v0=16888)
> > After retessellation of defect 7 (v0=16888), euler #=-114 (135587,398360,262659) : difference with
> > theory (-130) = -16 
> > CORRECTING DEFECT 8 (vertices=66, convex hull=79, v0=16899)
> > After retessellation of defect 8 (v0=16899), euler #=-113 (135625,398509,262771) : difference with
> > theory (-129) = -16 
> > CORRECTING DEFECT 9 (vertices=219, convex hull=64, v0=16932)
> > After retessellation of defect 9 (v0=16932), euler #=-112 (135644,398592,262836) : difference with
> > theory (-128) = -16 
> > CORRECTING DEFECT 10 (vertices=69, convex hull=58, v0=19570)
> > After retessellation of defect 10 (v0=19570), euler #=-111 (135659,398659,262889) : difference with
> > theory (-127) = -16 
> > CORRECTING DEFECT 11 (vertices=18978, convex hull=4487, v0=19837)
> >  
> >  
> >  
> > mri_pretess:
> > mbuerger@beo-05:/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_2
> > 0170425_T1/mri $
> rm/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versu
> > ch_Pretess/scripts/IsRunning.lh+rh
> > rm: remove regular
> file`/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Vers
> > uch_Pretess/scripts/IsRunning.lh+rh'? 
> > mbuerger@beo-05:/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_2
> > 0170425_T1/mri $ mri_pretess -keep wm.mgz wm127 norm.mgz wm.mgz
> > keeping edits
> > Ambiguous edge configurations... 
> > Iteration Number : 1
> > pass   1 (xy+):   0 found -   0 modified     |    TOTAL:   0
> > pass   1 (xy-):   0 found -   0 modified     |    TOTAL:   0
> > pass   1 (yz+):   0 found -   0 modified     |    TOTAL:   0
> > pass   1 (yz-):   0 found -   0 modified     |    TOTAL:   0
> > pass   1 (xz+):   0 found -   0 modified     |    TOTAL:   0
> > pass   1 (xz-):   0 found -   0 modified     |    TOTAL:   0
> > Iteration Number : 1
> > pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
> > pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
> > pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
> > pass   1 (+++):   0 found -   0 modified     |    TOTAL:   0
> > Iteration Number : 1
> > pass   1 (++):   0 found -   0 modified     |    TOTAL:   0
> > pass   1 (+-):   0 found -   0 modified     |    TOTAL:   0
> > pass   1 (--):   0 found -   0 modified     |    TOTAL:   0
> > pass   1 (-+):   0 found -   0 modified     |    TOTAL:   0
> > Total Number of Modified Voxels = 0 (out of 16189883: 0.000000)
> > Searching for edits to keep ...
> >   kept 0 WM ON voxels
> >   kept 0 WM OFF voxels
> > mri_pretess done
> >  
> >  
> >
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>
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