External Email - Use Caution HI Bruce,
I have to run recon-all -autorecon1, then substitute the brainmask for my brainmask, changing the brainmask from FS to brainmask.original.FS and labelling my betted image brainmask.mgz and then run recon-all -autorecon2 becuase if I do as you say, FS is generating again its own brainmask and it is being hard. I have been looking as well for a video or something I can have to see how you edit the errors with FS and I have not found anything. Any help with this would be much appreciated. Yours sincerely, Rosalia On Thu, Nov 15, 2018 at 7:42 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Rosalia > > yes, editing and rerunning recon-all should work. Or update the > brainmask.mgz with your own version if you want. We should detect that and > retain it. > > cheers > Bruce > > On Wed, 14 Nov 2018, > Rosalia Dacosta Aguayo wrote: > > > > > External Email - Use Caution > > > > Dear Free Surfer team, > > > > Sorry for double posting but I would like to explain well so it will be > > easier to understand what I am looking for. > > > > 1. I have run recon-all -all in a participant > > 2. The skull stripped image has skull and dura behind. > > 3. I can manual edit or I can do -autorecon1 and then supply the > > brainmask.nii.gz generated from my betted image. > > 4. Questions: > > > > a) If I run -autorecon1 and make the substitution of the brainmask: I am > > afraid this is not going to improve the grey matter and white matter > > segmentation. So, if this first step is not well solved, I think that > then, > > no matter if I change my brainmask for a better one, that I will have the > > same problems with -autorecon2 and -autorecon3, is that correct? > > > > b) If I do manual edition, then I will have to run -autorecon1 > again...not > > sure if this would be the best solution. > > > > As I am new to this, I would greatly appreciate your experience. > > > > Best wishes, > > Rosalia > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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