why do you think there are defects? If you have run recon-all there are
pretty much guaranteed not wo be any. You can't really see this visually,
but mris_euler_number will tell you if there are any

cheers
Bruce
On Tue, 26 Sep 2017,
Fereshte wrote:

> Dear Experts,
> I checked the topology corrected surfaces in recon-all pipeline however i found it didn't do well as
> still there are many topology defects in the pial surfaces. I know how to correct them manually in
> freeview but are there any commands to recorrect these topological defects with for example
> variables ? ( shall i use mris_fix_topology or? ) 
> Thank you. 
>
> On Sat, Sep 23, 2017 at 7:16 PM Fereshte <fereshte.ramezani@gmail.com> wrote:
>       Thank you. 
> Cheers 
>
> On Sat, Sep 23, 2017 at 7:13 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>       Segonne, F., Pacheco, J., Fischl, B., 2007. Geometrically accurate
>       topology-correction of cortical surfaces using nonseparating loops. IEEE
>       Trans Med Imaging 26, 518-529.
>
>       Fischl, B., Liu, A., Dale, A.M., 2001. Automated manifold surgery:
>       constructing geometrically accurate and topologically correct models of
>       the human cerebral cortex. IEEE Trans Med Imaging 20, 70-80.
>
>       Florent Ségonne,Eric GrimsonBruce Fischl, 2003. Topological Correction of
>       Subcortical Segmentation
>       MICCAI 2003: Medical Image Computing and Computer-Assisted Intervention -
>       MICCAI 2003 pp 695-702
>
>       On Sat, 23 Sep
>       2017, Fereshte wrote:
>
>       > Where can i find the details? 
>       > Thank you.
>       >
>       > On Sat, Sep 23, 2017 at 6:59 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
>       >       Yes, that is part of the recon-all pipeline (actually we have 3 separate
>       >       topology correction procedures, two for the surface and one for the
>       >       volume)
>       >
>       >       cheers
>       >       Bruce
>       >       On Sat, 23 Sep 2017, Fereshte wrote:
>       >
>       >       > Dear FreeSurfer Developers Is it possible to correct topological defects
>       automatically
>       >       in
>       >       > FreeSurfer? ( not correcting manually with Recon Edit)
>       >       > Thank you.
>       >       >
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