External Email - Use Caution Hi Bruce,
what I mean is that, two of the main outputs of recon-all are T1.mgz (which has the skull) and brain.mgz (which has been skull stripped). For a group of patients, I lost the brain.mgz file and I still have the T1.mgz. I was wondering if there was a way, given T1.mgz as input, to get brain.mgz (avoiding the whole segmentation procedure again). Thank you BW Marianna ________________________________ Da: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> per conto di Bruce Fischl <fis...@nmr.mgh.harvard.edu> Inviato: mercoledì 16 ottobre 2019 17:40 A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Oggetto: Re: [Freesurfer] R: recon-all skull stripping 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: > > External Email - Use Caution > > 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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> per conto di Bruce Fischl > <fis...@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 > > > > > > > >
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