External Email - Use Caution Dear Bram,
Thanks for your help, yes I tried to fix this issue following Bruce´s suggestions and everything worked fine. I manually filled the brain lesions in the wm.mgz and now the recon-all did not stop in the correcting defect. Best regards, El lun., 8 jul. 2019 a las 17:17, Diamond, Bram Ryder (< brdiam...@mgh.harvard.edu>) escribió: > Hi Miguel! > > I'll be happy to help with your issue, but I'm having trouble finding your > subject's directory on our server. Could you please try and upload the data > via FTP, again? Also, have you tried either of Bruce's suggestions? > > Thanks, > Bram > > Bram R. Diamond, BSc > Research Technician II > Laboratory for Computational Neuroimaging > Martinos Center for Biomedical Imaging > Massachusetts General Hospital > 149 13th Street > Charlestown, MA 02129 > (p): 617-726-6598 > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Miguel Ángel Rivas > Fernández <miguelrivasf...@gmail.com> > Sent: Wednesday, June 26, 2019 11:37 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all error: Correcting defect > > External Email - Use Caution > > Hello Bruce, > > Ok, I have sent to you the subject via FileDrop if you want to take a > look. Thanks. > > Best regards, > > El mié., 26 jun. 2019 a las 17:04, Bruce Fischl (< > fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>>) escribió: > Hi Miguel > > depending on the lesions it may not be fixable (since they may change the > topology of the cortex). If you upload the subject we will take a look, or > you can try manually filling in the lesion in the wm.mgz (or marking it as > lesion in the aseg.mgz) and seeing if that helps > > cheers > Bruce > On Wed, 26 Jun 2019, Miguel Ángel Rivas > Fernández wrote: > > > > > External Email - Use Caution > > > > > > I ran the recon-all in one subject and and this process was stopped in > the topology correction. In > > particular during the > > > > "CORRECTING DEFECT 36 (vertices=19847, convex hull=5892, v0=94733)". > > > > I reviewed the lh.inflated.nofix and the lh.orig.nofix files in Freeview > and I noticed that the this > > error would be located in the lh.inflated.nofix file. I am not > completely sure but I suspect that > > this error may be due to the fact that there is a large amount of brain > lesion and this would > > difficult the topology correction. How can I fix this problem? > > > > Thanks in advance. > > > > Best regards, > > > > -- > > Miguel Ángel Rivas Fernández > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Miguel Ángel Rivas Fernández > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- *Miguel Ángel Rivas Fernández*
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