Hi Bruno

it looks to me like there is very little gray/white contrast, which is
the root of your problem. YOu could try limiting the intensity ranges in
the segmentation and surface deformation steps using expert options (e.g.
-wlo for mri_segment). We can also help improve the acquisition. If that is
an option it would be highly recommended - send us the details

cheers
Bruce


On Thu, 20 Feb 2020, Bruno Pastorello wrote:

>
>         External Email - Use Caution        
>
> Hi Nayan,Thanks for the reply. I already read this troubleshooting topics
> page, and I don't know if I correctly understood, it is to fix specific
> points where segmentation fails.  In the case of my subject, all brain
> surface is wrong. The all WM surface is located on pial, not specific
> points. 
> Is there another automatic way to fix this or just a "first quick" to force
> that major part of WM should be correctly located ? Could you see the
> screenshot attached?
> Best Bruno
> [gmaillogo1.png]
>
> Bruno Fraccini Pastorello
> Físico Médico | Ressonância Magnética | LIM44 
> Instituto de Radiologia do HCFMUSP
> Ramal: +55 11 2661-7619
> bruno.pastorello@hc.fm.usp.br
>
> Antes de imprimir pense em sua responsabilidade e compromisso com
> o AMBIENTE.
>
>
> Em qui., 20 de fev. de 2020 às 11:40, nayan wadhwani <nayanw775@gmail.com>
> escreveu:
>
>               External Email - Use Caution        
>
>       Hello,
>       You can follow https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.
>       0 to correct your defects.
>  
> Thanks and Regards
> Nayan Wadhwani
>
>
> On Thu, Feb 20, 2020 at 8:04 PM Bruno Pastorello
> <bruno.pastorello@hc.fm.usp.br> wrote:
>
>               External Email - Use Caution        
>
>       Dear freesurfer developers,I have a subject that the wm
>       surface is located where pial surface should be and pial
>       surface is located out of the brain. I tried to use -FLAIR
>       flag but the result is the same. Do you know what could be
>       happening? How to fix this problem? 
> thanks in advance
> Bruno
> [gmaillogo1.png]
>
> Bruno Fraccini Pastorello
> Físico Médico | Ressonância Magnética | LIM44 
> Instituto de Radiologia do HCFMUSP
> Ramal: +55 11 2661-7619
> bruno.pastorello@hc.fm.usp.br
>
> Antes de imprimir pense em sua responsabilidade e compromisso
> com o AMBIENTE.
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