it helps detect cases in which the deformation is too big (e.g. when the surface deforms all the way into the cerebellum), and can thus recover from e.g. cerebellum chopping.
On Wed, 28 Jun 2006 dasoscia@buffalo.edu wrote:
I am currently in the process of manual editing...just curious though, what exatly does adding an atlas do to the skullstrip process?
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
First have a look at the troubleshooting wiki pages at:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
In particular, Subject 1 has a skull strip problem, and the fix info is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
I'm guessing you have seen this page since you have already attempted one type of fix (adjusting the watershed parameters). The alternative fix is the slice-by-slice manual editing.
You could also try adding the wsatlas flag:
recon-all -s (subject) -skullstrip -wsatlas
which will use an atlas to help with the skull-strip.
Does the contrast of your image look good? That is, comparing your orig.mgz to that of the sample subject 'bert' included with freesurfer?
Nick
On Wed, 2006-06-28 at 10:09 -0400, dasoscia@buffalo.edu wrote:
I am having trouble with one of my skull strips, and getting very extreme results. When I re-run the skullstrip using different
watershed
values, anything at 56% or below takes 75%+ of the brain out, and
as
soon as I jump to 57% or higher, it leaves on almost all of the
skull,
except for maybe 5% of it. Is this indicative of a more
complicated
problem, and what is my next step (other than manually taking off
the
skull), if any? Thanks _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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