I see that in the AFNI GUI we can define the value that will be mapped to the highest color (i.e. to 1), but is there a way to map a user-specified value X to zero? I’d like to be able to use the full color-scale after I set a threshold, but I cannot find a way to do that other than using 3dcalc to remove the values below X.
I feel like I’m missing something obvious here…
No, there’s no interactive way to do that. However, you could use InstaCalc inside AFNI to avoid having to create a temporary dataset with 3dcalc.
Also consider setting AFNI_PBAR_THREE to YES. You can try that out with “afni -DAFNI_PBAR_THREE=YES”. That allows you to remap the Overlay sub-brick display to have lower and upper limits. The colorbar will have “sashes” attached to drag. Left click on the solid bands of color above and below the colorbar for options on whether to color with the ends of the color scale or not.