visually is the only way. Do you think it is white matter?
On Mon, 29 Apr
2013, Claudia Dacquino wrote:
Yes it's my doubt too, but how can I check this?
2013/4/29 Bruce Fischl <fis...@nmr.mgh.harvard.edu>
then it's not rerunning the -cp. And is it really wm if it's
that dark?
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
Bruce,no the intensity is lesser then 110 at those voxels,
it's like 60-70.
Claudia
2013/4/29 Bruce Fischl <fis...@nmr.mgh.harvard.edu>
is the intensity at those voxels 110 after you have
processed
with autorecon2-cp?
On Mon, 29 Apr 2013, Claudia Dacquino wrote:
The problem is that after editng manually WM
by
adding control points, I
still have some WM and GM areas not included
in
either the pial or WM
boundaries, but I can see that there are
control
points added (green
cosses), but they seem not to be processed by
the
autorecon2-cp autorecon3.
Thanks
Claudia
2013/4/29 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
Hi Claudia
can you describe the problems? And cc
the list
so that others
can help?
thanks
Bruce
On Mon, 29 Apr 2013, Claudia Dacquino
wrote:
Hi Bruce,I think wm.mgz it's accurate
enough,
but what you
mean?
I'm trying to upload data, but I've
problems
with your
server.
Cheers,
Claudia
2013/4/29 Bruce Fischl
<fis...@nmr.mgh.harvard.edu>
Hi Claudia
it really depends on the
individual case
and what's
causing the
exclusion. Does the wm.mgz look
accurate? If so, you
may have a
topological defect that is being
fixed
incorrectly.
Usually we
focus on fixing the white boundary
and
that will
also correct
the pial. You can set the expected
gray
matter
intensities in
the xopts file, but that is rarely
necessary and
only if your
gray matter looks very different
than
the sequences
we are used
to.
If you can't sort it out feel free
to
upload you
data.
cheers
Bruce
On Mon, 29 Apr 2013, Claudia
Dacquino
wrote:
Hi Freesurfers,I have a
question
about pial
editing.
I have some reconructions in
which
there's a
lot of
grey matter excluded,
and consequently white
metter too.
I did
correct
these images manually by
control points editing, and
then
autorecon2-cp
autorecon3, but some
cortical
grey matter continues to not
be
included in
the pial
surface, and I have
white matter areas that are
still
not included
in
either the pial or white
matter boundaries.
Is there anyother ethods for
adding grey
matter in
the pial surfeces other
than editing control points
(such
as by
editing
voxels to add grey matter),
or something like that?
Thanks for your help.
Claudia
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