The Harvard–Oxford Atlas 2.0 subcortical protocol encoded as landmark-defined rules: Reference manual, v1.0

This document specifies a geometric encoding of the Harvard–Oxford Atlas 2.0 (HOA2.0) subcortical segmentation protocol based on 16 landmarks, 21 planes and 16 structure-specific rules. Where the HOA2.0 manual places a border by an operational convention tied to an anatomical landmark (an operational border), the landmark is encoded as a single voxel, the convention as a plane through it, and the admissible extent of each structure as a rule on these planes. The landmarks of a subject thus determine the planes and the admissible zone of every structure. Each rule is given with the definition of the manual on which it is based and illustrated on a reference segmentation, together with the placement of each landmark. The document also lists the choices that go beyond the manual and describes how the encoding is used to measure and enforce compliance with the protocol.