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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