> Bruce
> I used the following
> version: freesurfer-x86_64-redhat-linux-gnu-stable5-20110522
>
> Is that the same as the one you are using or are you referring to an
> internal development version?
>
> I will try Nick's suggestion as well.
>
> Darren
>
> On Wed, Sep 5, 2012 at 4:05 PM, Bruce Fischl <
fischl@nmr.mgh.harvard.edu>
> wrote:
> I'm running it now with the current dev version and it's passed
> the skull
> stripping stage and it seems to have worked fine...
>
> On Wed,
> 5 Sep 2012, Nick Schmansky wrote:
>
> > Darren,
> >
> > I forgot to mention that you'll need to add
> >
> > -clean-bm
> >
> > after the -no-wsgcaatlas flag, otherwise the prior
> brainmask.mgz will be
> > retained and the new one will be saved as brainmask.auto.mgz.
> >
> > Nick
> >
> >
> > On Wed, 2012-09-05 at 09:54 -0500, Darren Gitelman wrote:
> >> Nick, List:
> >>
> >>
> >>
> >> Still no luck with this data. See attached as an example.
> >>
> >>
> >>
> >> To get to this point I had run:
> >>
> >>
> >>
> >> recon-all -all
> >>
> >>
> >>
> >> This ran to the error: mri_watershed Error: GLOBAL region of the
> >> brain empty !
> >>
> >>
> >>
> >> Then I followed your recommendation below
> >>
> >>
> >>
> >> recon-all -s <subjid> -skullstrip -no-wsgcaatlas, which had no
> errors
> >> and then
> >>
> >> recon-all -s <subjid> -autorecon2 -autorecon3
> >>
> >>
> >>
> >> This produced the result attached.
> >>
> >>
> >>
> >> I then deleted this directory and re-imported all the dicom data
> for
> >> this subject. Looked at the images, which look fine.
> >>
> >> Then I ran recon-all -s <subjid> -autorecon1
> >>
> >>
> >>
> >> This fails with the mri_watershed error.
> >>
> >>
> >>
> >> Then I ran recon-all -s <subjid> -skullstrip -no-wsgcaatlas.
> >>
> >>
> >>
> >> This runs without error but when I look at the brainmask.mgz it
> looks
> >> just like the attached image.
> >>
> >>
> >>
> >> Is there some way to set the thresholds differently? The T1 image
> >> looks fine to me although perhaps the intensity is slightly less
> than
> >> usual, but it doesn't seem particularly noisy.
> >>
> >>
> >>
> >> Darren
> >>
> >>
> >>
> >> _______________________________________________
> >> Freesurfer mailing list
> >>
Freesurfer@nmr.mgh.harvard.edu
> >>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > _______________________________________________
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> >
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> >
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> >
> >
> >
>
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