it will figure out the input and output for you
On Wed, 16 Oct 2019,
Inglese, Marianna wrote:
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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