Hi Gaurav,
From the afni GUI: Define Datamode -> Misc -> Save Layout.
With no name it would create .afni.startup_script in the current
directory, which would apply every time afni was later started
there.
If you specify a name, that can be passed via the -layout option.
If you put a .afni.startup_script file in your home directory, it
will be used for every afni session (unless a local one is).
- rick