External Email - Use Caution Hi Bruce,
shall I do that with my original T1 as input or the T1.mgz? 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 17:58 A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Oggetto: Re: [Freesurfer] R: R: R: recon-all skull stripping Hi Marianna I think you can just run recon-all -s <subject> -skullstrip and it will run it for you as it normally does cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote: > > External Email - Use Caution > > Dear all, > > from this: > > (...) Removes the skull from mri/T1.mgz and stores the result in > mri/brainmask.auto.mgz and mri/brainmask.mgz. Runs the mri_watershed > program. If the strip fails, users can specify seed points (-wsseed) or > change the threshold (-wsthresh, -wsmore, -wsless). The -autorecon1 stage > ends here. > > i guess the function I need is mri_watershed. Now the question is: does > recon-all add optional flagged arguments to this function while running > recon-all? and which of them? > > 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 17:52 > A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Oggetto: Re: [Freesurfer] R: R: recon-all skull stripping > that will do a bit more than just the skullstripping > On Wed, 16 Oct 2019, > Krieger, Donald N. wrote: > > > External Email - Use Caution > > > > Please pardon me for jumping in here. > > I looks like recon-all -autorecon1 will do it, yes? > > > > Best - Don > > > > -----Original Message----- > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl > > Sent: Wednesday, October 16, 2019 12:48 PM > > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > > Subject: Re: [Freesurfer] R: R: recon-all skull stripping > > > > oh, sure, you can just run that part of recon-all. You don't need to rerun > the whole thing cheers Bruce On Wed, 16 Oct 2019, Inglese, Marianna wrote: > > > >> > >> 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 > >>>> > >>>> > >>>> > >>> > >>> > >> > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > >
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