Hello Zhongming
1. Freesurfer can do this, though it is not perfect. It is my
understanding that the best (at least here at the NMR center) BEM
segmentations can be obtained when running special pulse sequences
called FLASH5 in the MRI to better visualize the skull boundaries. Matti
can probably provide additional details.
2. The BEMs outputted are in the appropriate form for EEG/MEG source
modeling.
3. The downsampling is a very serious issue that many people have
brought up. If you are looking for a first approximation, you will have
no problem at all. The freesurfer surfaces can simply be downsampled.
However, the spacing between vertices is not uniform. Therefore,
downsampling a non-uniformly spaced surface will result in another
similarly non-uniformly spaced surface. If you downsample by a large
number, you will become acutely aware of the problem. Conversely, if you
downsample by a small number, the surface will still look very much like
a surface, so perhaps you won't mind.
Another possible solution to this problem, which is still not correct
but may be closer, would be to establish a set of points that are
uniformly distributed around a sphere, and then pick those points from
the cortical surface in spherical coordinates. This solution will suffer
from distortions inherent in the spherical morph.
I have been in touch with the makers of SUMA, who are considering
developing an option to prepare correctly down-sampled surface vertices
based on surfaces Euclidean distances, and our own Doug Greve (also
CCed) has also be considering options within the freesurfer environment.
If you consider this issue important enough to solve, and are able to
solve it, I encourage you to share it with others, because I have found
that a number of people would like the correct solution available to
them (myself included).
Daniel
On Tue, 9 Aug 2005, Zhongming Liu wrote:
I am a new user of Freesurfer. My questions are related to the head
modeling
and MEG/EEG source modeling.
1. Can freesurfer generate the 3-shell boundary element model
(BEM): 3
triangulated interfaces of air-scalp, scalp-skull, skull-brain?
2. Is it possible to generate a closed and folded cortical surface
after the segmentation on MR images? Freesurfer seems to output two
splitted
hemispheres of cortex. I am particularly concerning this, because I
will use
the cortical surface to constrain the MEG/EEG source location and
direction.
3. Is it possible to evenly (or nearly evenly) down-sample the
vertices
of a fine cortical surface into around 6,000 points, onto which the
elementary dipole will be placed? Freesurfer generates the cortical
surface
with a huge number of triangles, which makes it impossible for MEG-based
source imaging.
Looking forward to your reply.
Best regards,
Zhongming Liu
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Daniel Goldenholz
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"Mavet v'chaim b'yad halashon"
"Life and death are in the hands of language"
- Proverbs 18:21
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