The WM in the temporal lobe has intensities ranging [89-111] - hard to tell the average, but my estimate would be around ~95-100.
gray matter inside the pial surface ranges from 73-85, and outside the pial surface is approximately the same. WM in parietal lobe is generally 110. On Wed, 2006-08-16 at 15:50 -0400, Bruce Fischl wrote: > can you send an image without the aseg overlay? Is the wm darker there > than elsewhere (i.e. <110)? > On Wed, 16 Aug 2006, Bo Shi wrote: > > > Sorry, message cut off mid-write; > > > > We're having some trouble with the pial surface for the temporal lobes. > > All four datasets we've processed so far have temporal lobe pial > > surfaces that are significantly smaller than they should be (attached) > > > > I know there are control points for white matter - is there an > > equivalent for gray matter? > > > > > > 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 > >>>>> > >>>>> > >>>> > >>> > >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
