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
