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Dear Bram,

Thanks for your help, yes I tried to fix this issue following Bruce´s
suggestions and everything worked fine. I manually filled the brain lesions
in the wm.mgz and now the recon-all did not stop in the correcting defect.


Best regards,

El lun., 8 jul. 2019 a las 17:17, Diamond, Bram Ryder (<
brdiam...@mgh.harvard.edu>) escribió:

> Hi Miguel!
>
> I'll be happy to help with your issue, but I'm having trouble finding your
> subject's directory on our server. Could you please try and upload the data
> via FTP, again? Also, have you tried either of Bruce's suggestions?
>
> Thanks,
> Bram
>
> Bram R. Diamond, BSc
> Research Technician II
> Laboratory for Computational Neuroimaging
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street
> Charlestown, MA 02129
> (p): 617-726-6598
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas
> Fernández <miguelrivasf...@gmail.com>
> Sent: Wednesday, June 26, 2019 11:37 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] recon-all error: Correcting defect
>
>         External Email - Use Caution
>
> Hello Bruce,
>
> Ok, I have sent to you the subject via FileDrop if you want to take a
> look. Thanks.
>
> Best regards,
>
> El mié., 26 jun. 2019 a las 17:04, Bruce Fischl (<
> fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>) escribió:
> Hi Miguel
>
> depending on the lesions it may not be fixable (since they may change the
> topology of the cortex). If you upload the subject we will take a look, or
> you can try manually filling in the lesion in the wm.mgz (or marking it as
> lesion in the aseg.mgz) and seeing if that helps
>
> cheers
> Bruce
> On Wed, 26 Jun 2019, Miguel Ángel Rivas
> Fernández wrote:
>
> >
> >         External Email - Use Caution
> >
> >
> >  I ran the recon-all in one subject and and this process was stopped in
> the topology correction. In
> > particular during the
> >
> >  "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)".
> >
> > I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview
> and I noticed that the this
> > error would be located in the lh.inflated.nofix file. I am not
> completely sure but I suspect that
> > this error may be due to the fact that there is a large amount of brain
> lesion and this would
> > difficult the topology correction. How can I fix this problem?
> >
> > Thanks in advance.
> >
> > Best regards,
> >
> > --
> > Miguel Ángel Rivas Fernández
> >
> >_______________________________________________
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>
>
> --
> Miguel Ángel Rivas Fernández
>
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>


-- 
*Miguel Ángel Rivas Fernández*
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