How can I more easily control the initial colors in the functional overlays?
There are two ways to control this, both of which involve setup files. The first is to set some values in your .Xdefault (or .Xresources) file in your home directory, which is read by the X11 graphics server when you login. When AFNI starts, it will query the server for resource values that start with the string AFNI. The full list of values that the program looks for is given in the sample file AFNI.Xdefaults, which is distributed with the AFNI source code. The second (and better) method is described in detail in README.setup.
