Hi Marianna
I'm not sure what you mean by "replicate". The procedure should be the same for all inputs unless you change something explicitly
cheers Bruce
On Wed, 16 Oct 2019, Inglese, Marianna wrote:
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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:
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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