Thickness-Mapping module should work well if you want to measure thickness along a certain axis.
Otherwise, I would recommend using the workflow described here:
You need to use a segmentation that contains the entire skull bone (not just the thin cortical surfaces but the internal cancellous bone as well).
You don’t need to use Shape Population Viewer to see the color overlay, just go to Models module and click “Visible” checkbox in Display / Scalars section (and select distance as active scalar, if it has not been selected already).