Hi FSLers,
I've been trying to use FAST to get a good grey/white segmentation of
some monkey brains and having been running into some difficulties.
FAST does a nice job with the ventral half of the brain but more
dorsally, it is classifying most voxels as white matter. Although by
eye, there is a clear grey-white demarcation, in the more dorsal
areas the grey matter values appear to be closer to WM values,
especially WM values in the ventral part of the brain. I thought
this might be a bias field issue, but the bias field outputted by
FAST definitely does not show a ventral-dorsal gradient. To be
honest, I'm not sure how this is generated, so I'm not certain what
to make of that.
Regardless, the information necessary to successfully segment GM from
WM appears to be present in the image -- at least to my eye, the
differences are clear and robust throughout the entire
image. Nonetheless, I can't seem to find a way to robustly extract
this with FAST and would welcome any suggestions.
Thanks, in advance.
Joe
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