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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 xxxxxxx@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

Bruno Fraccini Pastorello Físico Médico | Ressonância Magnética | LIM44 Instituto de Radiologia do HCFMUSP Ramal: +55 11 2661-7619 bruno.pastorello@hc.fm.usp.br xxxxxxx@hc.fm.usp.br

*Antes de imprimir* pense em sua responsabilidade e compromisso com o *AMBIENTE*. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Hi Bruce, Thanks for the reply. What are the commands should I try?

mri_segment brainmask.mgz wm.mgz -wlo 90

and after:

recon-all -autorecon2-wm -autorecon3 -subjid <subject_name>

???

The images are scanned in a GE PETMR 3T. MR hardware configuration are limited because PET detection system.

3D Fast SPGR with IR Prepared TI/TR/TE=600/3.1/7.6 ms FA=8 Nex=0.8 Acquisition Matrix = 256x256 Reconstruction matrix=512x512 FOV=256x256 mm2 slice thickness = 1 mm ASSET=2

Bruno Fraccini Pastorello Físico Médico | Ressonância Magnética | LIM44 Instituto de Radiologia do HCFMUSP Ramal: +55 11 2661-7619 bruno.pastorello@hc.fm.usp.br xxxxxxx@hc.fm.usp.br

*Antes de imprimir* pense em sua responsabilidade e compromisso com o *AMBIENTE*.

Em qui., 20 de fev. de 2020 às 12:22, Bruce Fischl < fischl@nmr.mgh.harvard.edu> escreveu:

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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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