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 <fischl@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 <fischl@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
>       >
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