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Thank you Bruce. 
I thought it was something similar to the FSL bet function, which extracts the brain using a fractional intensity threshold (0.5 for example). 
So I guess I won't be able to replicate the same exact skull stripping of freesurfer's recon-all.

BW
Marianna
Da: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> per conto di Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Inviato: mercoledì 16 ottobre 2019 17:23
A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Oggetto: Re: [Freesurfer] recon-all skull stripping
 
Hi Marianna

the skull stripping is a hybrid procedure that uses both a watershed
algorithm and a deformable surface. There is no single intensity threshold
in it. Maybe I'm misunderstanding your question? There are parameters you
can change (for example the preflooding height), but there is no intensity
thresholding

cheers
Bruce


On Wed, 16 Oct 2019, Inglese, Marianna
wrote:

>
>         External Email - Use Caution        
>
> To whom it may concern,
>
> I am using recon-all to segment many T1s. As I can see, one of the automatic
> step performed by recon-all is the skull stripping. Would it be possible to
> know the threshold used for the stripping? I guess it is the same threshold
> everytime. I would like to apply the skull stripping only on other T1s and
> need to get the same result.
>
> Thank you very much for the help.
>
> Yours faithfully,
>
> Marianna Inglese
>
> Research fellow, Imperial College London
> Department of Surgery and Cancer
>
>
>