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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