Bo,
It looks like control points will do the trick - in the wm. Your white
surfaces are missing some regions too. Control points will fix this and
subsequently fix your pial surfaces as well. Give them a try, but be sure
to get the control points in wm voxels, not too close to the wm/gm
boundary.
Jenni
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
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