The idea predates modern usage, back to 1967: https://en.wikipedia.org/wiki/Talairach_coordinates, where they were trying to define a common way of referring to structures.

In this freesurfer sense it is the result of a training set, where an expert has delineated cortical and/or subcortical structure on a set of one or more images. If you have multiple images and you map them all into the same atlas space, you can derive a probabilistic model from this, or collapse it to a highest likelihood map or whatever you want.

The cortical and subcortical labeling algorithms used in freesurfer use such a (probabilistic) atlas as one of the inputs. GP is wishing that they could replace this with a new, presumably improved, version.