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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas Fernández <miguelrivasfdez@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 (<fischl@nmr.mgh.harvard.edu<mailto:fischl@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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