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

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:

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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:
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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

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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