[Freesurfer] Creating and using an atlas from scratch

Hello, I'm trying to create a canine atlas to use in freesurfers recon-all pipeline. I want to be able to perform cortical thickness measurements. I have manually skull-stripped 10 beagle brains. I have used fsl's FLIRT and FNIRT to make an averaged image of these 10 brain images in nifti format. As an alternative I have also used mri_robust_template to create an average template .mgz file to replace the talairach atlas. Could someone tell me what else is needed to replace the standard atlas and templates in the recon-all pipeline for what I need? Also where to replace the standard atlas and template files to be able to run recon-all?

Any help is much appreciated, Jeff Thompson