Hello,
> We're working using vbm8 (that uses DARTEL for normalizing) in order to segment human 3D T1-weighted images.
> Looking at the results we notice that the subcortical structures (thalamus, caudate nucleus) are oddly hyperintense, i.e. the probability of these structures to belong GM is much higher than the cortical ones.
> Is there a known problem with the segmentation process?
There may be an issue (subcortical structures are notoriously difficult
to segment), but I would guess that you wrote out modulated (whichever
way :) normalized images, in which the effect of stretching and
compressing is more visible, especially following extensive non-linear
normalization (as in DARTEL). If this is the problem, the images should
look much "better" if you write them without modulation or in native
space. If the problem persists, it is something else.
Cheers,
Marko
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PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
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http://www.medizin.uni-tuebingen.de/kinder/epn
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