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
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