Hello Ed,
> I am resending this in case someone missed it and can help us with
> this.
I did not miss it the first time, but I did fail to understand the
question... let me still try.
> I know how to perform the regular segmentation procedure as part of
> my processing. (1) However, I am trying to "perform tissue
> classification and set everything outside the cortex, to eg, black,
> and everything inside to, eg, white."
Well, that is pretty much what the segmented images represent... high
values (close to 1) for GM, low (close to 0) for everything else. Or do
you want to exclude subcortical regions? In that case, you would have to
do some kind of masking, either using standard masks (if your results
are already normalized), or some form of manual editing (e.g., using
MRIcron).
> (2) Also, I need to get the SPM Brain Surface Extraction procedure
> using the render> extract surface procedure. This does not work.
It is difficult to say what went wrong, but the first thing to check is,
what images did you use? The brain extraction expects you to use the
segmented GM and WM images, and ususally does a pretty decent job about
it. If the segmentation is suboptimal, then the brain extraction is not
going to work either.
Hope this helps,
Marko
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Marko Wilke (Dr.med./M.D.)
[log in to unmask]
Universitäts-Kinderklinik University Children's Hospital
Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
Hoppe-Seyler-Str. 1, D - 72076 Tübingen
Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
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