Katy-
  Please look at section 7 of the PDF manual included with MRIcroGL. You can adjust the minimum and maximum ranges of your overlay by adjusting the 'min' and 'max' values in the Overlay panel, so in Figure 7.1 the red overlay hides values darker than 2 and scales the intensity of red from 2 to 4. In contrast, the green overlay hides values with less extreme values than -2 and linearly scales the green intenstiy from -2 to -4. The intensity of your overlay will depend on the software that generated the statistical map, for example NiiStat saves maps as Z-scores, whereas SPM typically saves T-scores. The software that generated your map will generally suggest a threshold for your map. If you open an overlay in MRIcroGL and choose Display/Multiplanar you will see crosshairs on top of your image, as you click to select different locations of the image, the intensity of the overlay is shown in the title bar. 
 In sum, the "meaning" of your map depends on the software that created the overlay. It might be a T-score, a Z-score, a binary mask, etc. So in your case I would look at the SnPM tools for more details.