Good to hear - but On Wed, 2006-08-16 at 14:44 -0400, Bruce Fischl wrote: > no - we don't really use the cortex labels from the aseg for this reason > (and others). Instead we use the surfaces (?h.white and ?h.pial) for > computing cortical properties, so you should be all set. > > cheers, > Bruce > > > On Wed, 16 Aug 2006, Bo Shi wrote: > > > Hi Bruce, > > > > The pial surface for the top regions of the brain do fairly well in > > ignoring the marrow, however, the unwanted regions still get classified > > as gray matter (image attached). > > > > This will adversely affect the reported cortex volume no? > > > > > > Thanks, > > Bo > > > > On Wed, 2006-08-16 at 14:14 -0400, Bruce Fischl wrote: > >> Hi Bo, > >> > >> does it affect your pial surface? You may be fine with just leaving it > >> in. > >> > >> cheers, > >> Bruce > >> On Wed, 16 Aug 2006, Bo Shi wrote: > >> > >>> Howdy - > >>> > >>> It seems that the skullstripping step is having some trouble removing > >>> bone marrow (see attached image). > >>> > >>> Adjusting watershed values (I've tried as low as 5) does not make any > >>> significant improvement. > >>> > >>> Does anyone else have this issue? Can anyone provide any hints as to > >>> how I might get a better automated skull-strip? I've been manually > >>> removing the marrow but it's getting real old. > >>> > >>> Any thoughts would be much appreciated. > >>> > >>> Bo > >>> > >>> > >> > > >
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