External Email - Use Caution Hi Bruce,
I will send it you once I am in the lab. In relation to the tutorials, I know that there are tutorials and pdf documentation I have been consulting. But, just to start with editing, it would be helpful to see how another person is doing it in a video or explain it while he/she is doing it. Now I know Regards, Rosalia On Thu, Nov 15, 2018 at 9:35 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Rosalia > > there are some tutorials on our website. And can you send us the > recon-all.log where you have put a new brainmask.mgz into the subject's > dir and it gets overwritten? That shouldn't happen > > thanks > Bruce > On Thu, 15 Nov 2018, > Rosalia Dacosta Aguayo wrote: > > > > > 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 > > > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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