Hi Claudianow I'm confused. Did you put control points in those voxels? You definitely, definitely must avoid putting them in voxels that contain anything other than WM. The pial surface will usually be incorrect if the white surface is incorrect, so the first thing to do is make sure it is right
Bruce On Mon, 29 Apr 2013, Claudia Dacquino wrote:
But in "brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white
-segmentation aseg.mgz" it's labeled as white matter, could it be possible?
2013/4/29 Claudia Dacquino <claudia.dacqu...@gmail.com>
Actually it could not be WM, but I'm quite sure that there is
grey matter excluded by pial bounaries as well, how can I add
that?
2013/4/29 Bruce Fischl <fis...@nmr.mgh.harvard.edu>
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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