Re: [Freesurfer] Fix topology correcting defect
ls from the wm.mgz > and then I > > tried to reintegrate the wm.mgz to the recon-all command by doing the mri_fill > . > > Unfortunately I got this error: > > > >mbuerger@beo-05:/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170 42 > > > 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; > > 0.0 0.0 0.0 1.0; > > 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; > > 0.0 0.0 0.0 1.0; > > 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" > > An: "Freesurfer support list" > > 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: > >
Re: [Freesurfer] Fix topology correcting defect
nsform > > > 1.18336 0.13264 0.04891 10.53902; > > > -0.11077 0.95044 0.09947 -11.50818; > > > -0.00953 -0.18656 1.07681 -50.07034; > > > 0.0 0.0 0.0 1.0; > > > 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; > > > 0.0 0.0 0.0 1.0; > > > 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" > > > An: "Freesurfer support list" > > > 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 > > >
Re: [Freesurfer] Fix topology correcting defect
+/- 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"
> An: "Freesurfer support list"
> 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 ve
Re: [Freesurfer] Fix topology correcting defect
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" > > An: "Freesurfer support list" > > 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
Re: [Freesurfer] Fix topology correcting defect
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 . 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; 0.0 0.0 0.0 1.0; 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; 0.0 0.0 0.0 1.0; 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" An: "Freesurfer support list" 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
Re: [Freesurfer] Fix topology correcting defect
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 . Unfortunately I got this error: mbuerger@beo-05:/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_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; 0.0 0.0 0.0 1.0; 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; 0.0 0.0 0.0 1.0; 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" An: "Freesurfer support list" 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_Versu > ch
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_Versu 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 input surface/data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versu 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)
[Freesurfer] Fix topology correcting defect
External Email - Use CautionHi 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_Versuch_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 input surface /data/projects/pediatric_mr_myelin/Evaluation_Milene/processed_with_freesurfer/FJ_20170425_T1_Versuch_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 def
