External Email - Use Caution        

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.pastore...@hc.fm.usp.br <xxxx...@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 <
fis...@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.pastore...@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 <
> nayanw...@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.pastore...@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.pastore...@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
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Reply via email to