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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