The overlays are shown with their voxel intensity. For my tools, I create statistical maps as z-scores (so you do not need to worry about the degrees of freedom), but many other tools (SPM and FSL) save images with the t-value. If you want to convert an image from a t-score to a z-score you could modify my script
  https://github.com/rordenlab/spmScripts/blob/master/nii_zeronan.m
using the spm command
  z = spm_t2z(t,df);

In sum, my software displays the color intensity in the scale used by the software that created the image.