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
