Hello all.

I am having a problem with skull stripping that I can't figure out a way around.  One subject out of 10 is having the problem.  The intensity normalization works fine and all values hover around 110 just like in the other 9 subjects.  However, during skull stripping the pons is very neatly cut out in this one subject.  Of course this causes problems later when WMFill can't find the pons.

I tried to change the flood height, but that didn't change anything (actually it changed NOTHING which kind of suprised me).  I tried adding a seed point, but that didn't change the segmentation either.  I even tried to add a seed point in Volume Index and Volume RAS coords just in case I was doing something wrong with the coord system expected by the routine.  I also tried not using the watershed.  But no matter what I try the pons is always neatly chopped out so I can't get past WMFill on this subject.

Does anyone have any ideas on what I might be able to do to allow the pons to be left during RmSkull?

Thanks for any ideas.