I am visualizing a binary map with values of 1, 2, or 3.  I need a discrete colour scale (voxels of 1 = orange, 2=blue, 3=red), similar to what I can do in the AFNI viewer (see attached). 

Is this possible in MRIcroGL? Currently I can only use the default continuous scales, without the ability to customize. 

Thank you!!

1. In the "Options" pulldown of the layers menu, make sure that "Load Smooth Overlays" is Unchecked. This will ensure that values stay discrete, e.g. a partial volume at the boundary of "2" and "3" should not get the value 2.5
2. From the color pulldown table choose a scheme with many hues, for example "Viridis", "Plasma" and "Magma" look distinct but also work with common forms of color blindness.
3. Set the "Darkest and Brightest" values to bound the values of interest.

When I uncheck "Load smooth overlays", it doesn't seem to really affect the outcome? 

I have a map of voxels with values of either 1's, 2's, or 3's... I was wondering if, similar to AFNI, I could manually set the colours of each discrete value? 

What I've done so far is find a colour scheme in MRIcroGL (NIH, for example) and set the darkest/brightest values to adjust the scale so that 1, 2, and 3 fall on colours that are different from each other. Gives me enough flexibility that I can find one that works :D.

This option determines how future images are loaded - you can load different images with or without smoothingg (nearest neighbor vs trilinear interpolation).

Try Scripting/Templates/jagged to see one overlay loaded with smoothing and the other without.