It comes to me that using VBM8 toolbox has an advantage over the common SPM routine introduced by the 'Partial Volume Estimation' function. That means it can better segment GM-WM mixed classes such as thalamus and other subcortical structures. It turns out that most part of the thalamus and subcortical grey matter are designated as white matter as shown in the graph I appended to this email. I am currently doing a VBM on white matter between a cohort of patients and normal subjects. Significantly reduced WM volume was shown in red and overlapped on a representative WM segmentation map. I am wondering how much I can trust the result. The detected change in yellow box consist of thalamus, putaman, pallidum and caudate, those regions that shouldn't be classified as white matter. The detected change in green box seems nail some true white matter. Can I say change in green box reliable and change in yellow box not? Thank you for your comments in advance!