External Email - Use Caution
Hi Bruce,
Thanks!! I did find some skull attaching brain on wm.mgz/norma.mgz. So is the next step just fixing wm.mgz and running recon-all -autorecon2-wm -autorecon3 as suggested in correcting topological defects?
Best, Yi-Fang ᐧ
Bruce Fischl fischl@nmr.mgh.harvard.edu 於 2019年2月16日 週六 下午11:37寫道：
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 CautionI 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
#@# 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...
#@# 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 thewm.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 andwe 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 theskull were not properly
removed from the > brainmask and therefor considered as white matter. I manuallyremoved voxels from the wm.mgz
and then I > tried to reintegrate the wm.mgz to the recon-all command bydoing 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 youhave to
> specify that it is a surface with -f before the surface filename. 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. Youshould
> definitely look at your inflated and orig surfaces though tomake sure that
> some dramatic isn't wrong (like skull attached, or hemispheresnot
> separated) as your defect is probably too large to be anordinary 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 ofmy study. It worked out for
all of them > > except for one. This one froze at fixing topology „Correctingdefect“ 11 out of 140
defects. > > I looked for advises in the mailing list but I can’t find anymajor problems in the images
that > > Freesurfer processed so far. The last correct file that I canopen in freeview, is
filled.mgz (the > > skull and cerebellum are properly removed and it shows the twohemispheres with 127 for rh
and 255 > > for lh). I can’t find the file "filled-pretess255.mgz“ whichshould be the output, but I
do have the > > files lh.orig.nofix and rh.orig.nofix for example. I tried tolook at these files,
but freeview > > can't open them (failed to load MRI) so that I can’t see ifthere are topological defects
to correct > > as you described on one of the FsTutorials. I already tried torun only the autorecon2
command, but > > the same freezing problem appeared at one point. I also triedto only use the mri_pretess
command > > with different options, but it didn’t work. > > > > I copied you the fix topology and what I tried withmri_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 22:25:58zkaufman 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 corticalsurface...
> > > > 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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