List of regions in atlas are to large to be able to see the name of all regions in the screen. How can I make it so I can scroll down or up this window?
There is a bit of a trick to getting scrollable menus from the GUI, rather than (potentially giant) menu fields, as you are currently seeing.
Instead of left-clicking on the button that makes the menu (which is the normal thing to do), try right-clicking on the label next to it. That should open the menu with a scrollbar that you can navigate.
A couple more tips. You can use the instructions here for a video on the steps Paul mentioned.
If you view the atlas directly in the AFNI GUI, you will want to start AFNI to allow showing of color scales with more possible colors for the overlay.
afni -XXXnpane 1024