Howdy-

There is an AFNI environment variable to set for this behavior:

Variable: AFNI_GRAPH_FADE
-------------------------
If this variable is set to YES, then the 'threshold fade' feature
of the AFNI graph window is turned on for all graph viewers when
they open. Otherwise, you have to turn this feature on via the
'F' key or the toggle control in the Opt menu.

So, you can put a line like this in your ~/.afnirc file to set it whenever you open up afni:

AFNI_GRAPH_FADE = YES

To get this functionality, I think you need to have both 1) an olay (overlay) dataset selected, and 2) a nonzero threshold set.

Even if your mask is set and loaded as an olay, if condition #2 is not set, you won't get the white/gray differentiation in the graph viewer.

That all being said, this wasn't working on my laptop at the moment (with the latest version of AFNI), so it might be that something is a-broken at the moment. Will investigate a bit more next week.

--pt