Suzanne,
You could try running different watershed thresholds to see if it fixes
the problem without having to clone it in:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix
Allison
--
On Fri, 19 Nov 2010, suzanne oosterwijk wrote:
> Hi,
>
> I have been running recon1 recently and I have noticed that for some of my
> participants big chunks are missing in the brainmask.mgz. Out of 20
> participants, five participants have this problem. The pattern is similar
> across participants: the missing parts start around slice 70-50 at the
> bottom (cerebellum) and then move upward. The data can be found in:
>
> /autofs/space/boggart_001/users/oosterwi/construct_struc
>
> It concerns constr011 (which I corrected using the clone method), and
> constr012, constr016, constr019 and constr020 (which still show the
> problem).
>
> I think it can be solved by cloning the T1 (aux volume) as is explained in
> the Freesurfer tutorial. Still, I wonder whether this is the best solution,
> and why this is happening in the first place.
>
> I appreciate any help or feedback on this. Thanks in advance!
> kind regards,
> Suzanne Oosterwijk
>
>