Is there a way to have the threshold values correspond to z-scores or p-values? I believe the default is voxel intensity, but I would like to be able to have my functional activations used as the colorbar scale. Is this possible? I have also tried this using Surf Ice, but it seems to produce the same issue.

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.