External Email - Use Caution
Hi Yi-Fang
the topology fixing time complexity is square in the convex hull of the
largest defect. So small defects are quick and big ones take forever. That
said, for any defects that can be fixed reliably the run time isn't too
bad. Almost always if it is taking this long it means something
catastrophic has happened - skull is attached to brain, or the hemis are
connected or some such. It is usually immediately obvious if you look at
the ?h.inflated.nofix and/or the ?h.orig.nofix over the wm.mgz/norm.mgz
cheers
Bruce
On Sat, 16 Feb 2019, Yi-Fang Chuang wrote:
>
> External Email - Use Caution
>
> I would like to follow-up this thread.
> I've encountered similar problem about the recon-all process is stuck at fix topology for a long time (10+
> hours) [Centos 6, Freesurfer 6.0.0]
> I can't see any problem from log files, just as follows
> 1.
>
> #@# Fix Topology Copy rh Fri Feb 15 00:34:11 CST 2019
>
> /home/yfc/subjects/BK036/scripts
>
>
> cp ../surf/rh.orig.nofix ../surf/rh.orig
>
>
>
> cp ../surf/rh.inflated.nofix ../surf/rh.inflated
>
>
> #@# Fix Topology lh Fri Feb 15 00:34:11 CST 2019
>
>
> mris_fix_topology -rusage /home/yfc/subjects/BK036/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere
> qsphere.nofix -ga -seed 1234 BK036 lh
>
>
> #@# Fix Topology rh Fri Feb 15 00:34:11 CST 2019
>
>
> mris_fix_topology -rusage /home/yfc/subjects/BK036/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere
> qsphere.nofix -ga -seed 1234 BK036 rh
>
>
> Waiting for PID 15635 of (15635 15638) to complete...
>
>
> 2.
>
>
> #@# Fix Topology Copy rh Fri Feb 15 21:23:50 CST 2019
>
> /home/yfc/subjects/BK151/scripts
>
>
> cp ../surf/rh.orig.nofix ../surf/rh.orig
>
>
>
> cp ../surf/rh.inflated.nofix ../surf/rh.inflated
>
>
> #@# Fix Topology lh Fri Feb 15 21:23:50 CST 2019
>
>
> mris_fix_topology -rusage /home/yfc/subjects/BK151/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere
> qsphere.nofix -ga -seed 1234 BK151 lh
>
>
> #@# Fix Topology rh Fri Feb 15 21:23:50 CST 2019
>
>
> mris_fix_topology -rusage /home/yfc/subjects/BK151/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere
> qsphere.nofix -ga -seed 1234 BK151 rh
>
>
> Waiting for PID 16471 of (16471 16474) to complete...
>
>
>
> Intriguingly, I've run through these subjects before on MacOS, Freesurfer 5.3.0 without error or being
> stuck.
>
> What's the problem here?
>
> Yi-Fang
>
>
> Bruce Fischl <fischl@nmr.mgh.harvard.edu> 於 2019年2月15日 週五 下午11:13寫道：
> 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/F
> J_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
> > > readinginputsurface/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
> > >
> > >
> > >
> > >_______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
> Yi-Fang Chuang (莊宜芳), M.D., Ph.D.
> Assistant Professor
> Institute of Public Health, National Yang-Ming University
> No. 155, Sec. 2, Linong Street, Taipei, 11221 Taiwan (R.O.C)
> +886-2-28267000#7981
> chuangy@ym.edu.tw
> Attending physician
> Department of Psychiatry, Far Eastern Memorial Hospital
> No.21, Sec. 2, Nanya S. Rd,. Banqiao Dist., New Taipei City 220, Taiwan (R.O.C)
> Special Volunteer
> NIA-Laboratory of Behavioral Neuroscience-Unit of Clinical and Translational Neuroscience
> BRC-Biomedical Research Center, 04C316
> 251 Bayview Blvd. Baltimore, MD
> chuangy@mail.nih.gov
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> 9ad622ca8] ᐧ
>
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