Dear Ariadna,
The glassbrain image looks a bit noisy, which doesn't have to mean anything though. Based on the location, the MRI image seems to indicate GM differences in the caudate nucleus and the basal ganglia more generally. Please note that parts of the basal ganglia and the thalamus are quite difficult to identify in certain templates due to poor GM-WM contrast.
Did you use the Dartel or Shoot template as included in CAT12 for the high-dimensional registration part? In that case, it might be wise to overlay the results onto the corresponding template (GM-WM contrast for basal ganglia should be better), or even better, create a mean image of the normalised (bias corrected) structural volumes of your study, or alternatively, of the normalised modulated or unmodulated GM files as obtained from CAT12 preprocessing. IMO it's always preferable to map results on some image derived from your own data. If there were some issues during the segmentation-normalisation, resulting in enlarged ventricles relative to the templates / priors, it would obviously be misleading to rely on a mapping onto those templates.
Best regards
Helmut
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