You can set up the windows the way you like them, then use the button Datamode->Misc->Save Layout to save a script that will restore them to approximately the way you want. The default script name is .afni.startup_script. If this file exists in the directory you are in when you start AFNI, then the commands in it will be executed. If it doesn't exist there, but does exist in your home directory, then that file will be used instead.

If you save to a different filename, the Run Script menu button will read in a script file and execute it.

Here is a sample file, generated in just this way:

// AFNI startup script, from Datamode->Misc->Save Layout
ADD_OVERLAY_COLOR #990000 darkred
OPEN_WINDOW A geom=+54+76
SET_THRESHOLD A.0000 0
SET_PBAR_ALL A.-99 1.000000 Color_circle_AJJ
SET_FUNC_VISIBLE A.+
SET_FUNC_RESAM A.Li.Li
SET_FUNC_RANGE A.0.004000
OPEN_WINDOW A.axialimage geom=+491+529 ifrac=0.8 opacity=5
OPEN_WINDOW A.sagittalimage geom=+50+586 ifrac=0.8 opacity=5

The AFNI driver/scripting capability is somewhat further documented in the file http://afni.nimh.nih.gov/pub/dist/src/README.driver.

One thing that is not saved in Save Layout is which datasets are current for each controller. You can manually edit the .afni.startup_script to add this option, if you want. For example, the line

SWITCH_ANATOMY zorkon

will switch the underlay anatomical dataset to be a dataset whose prefix-name is "zorkon", if such a dataset exists in the current directory.

This capability isn't exactly what you asked for, but it is close, and already exists on the AFNI you have on your machines now.

bob cox