Thank you two for your suggestions. I have gotten the overlay to work with both your suggestions.

As for my atlas, it was a custom made using the allen brain atlas for the ROIs. I see many papers claiming they are using an atlas from the Allen brain atlas, but they don't have an actual atlas file to download when I checked.

Thank you for the codes as it helped me learn more on how to use afni. It seems using NN creates a blocky image with cubic being very smoothed. wsinc5 seems to be the best mix.

And thank you Daniel for the Define Datamode tip. It's a quick way to see the atlas over my images. You helped me on my first question here and I looked at animal_warper per your suggestion, but it seems to best work with anatomical images. I'll give it a try with your settings that you suggest.