afni.nimh.nih.gov

Hi, Edwin-

Have you tried using the 'A' and 'B' buttons at the top of the controller, just to the right of 'Thr'? These provide "alpha" and "boxed" functionality when thresholding-- it is described in this AFNI Academy/Bootcamp video here (should be at about 16:20 in the video):
[youtu.be]
... in the description of thresholding over the next couple of minutes there, does that accomplish what you want?

And see Ex 5 here:
[afni.nimh.nih.gov]
(and any others with 'alpha' in them) to see how to control this same features in automatic image generation with @chauffeur_afni.

--pt