Hi again,
We have had some suboptimal results from FreeSurfer's skullstripping algorithm,
even after iteratively trying different watershed thresholds and after checking
the quality of Talairach registration. The results are pretty good, but often
leave some dura matter and bits of neck
you can use
mri_convert -rl ...
to reslice the output of bet so that it has the same geometry as the rest
of our stream
cheers
Bruce
On Wed, 6 Mar 2013, Winter, Warren wrote:
Hi again,
We have had some suboptimal results from FreeSurfer's skullstripping algorithm,
even after iteratively
I would check the mri_em_register registrations of the step that
immediately precedes mri_watershed (and produces
talairach_with_skull.lta). We found that most of the variability and
failures occurred in this step, and mri_watershed itself is a very robust
brain extraction algorithm when it is
