ACPC-MAP: A protocol for manually aligning structural T1-weighted Magnetic Resonance Images to the Anterior Commissure - Posterior Commissure plane according to clinical standards.

Realigning structural MR images to stereotactic AC-PC space is a standard procedure that enhances anatomical consistency both within and across neuroimaging studies, allowing for precise spatial localization and reliable cross-subject comparisons in both clinical and research contexts. However, different versions of AC-PC spaces, stemming from varying definitions of the AC-PC axis as outlined in common stereotactic atlases like Talairach and Schaltenbrand, often lead to discrepancies between the neurosurgical and neuroimaging communities. Manual realignment of structural MR images to the clinically used version of the AC-PC plane is often necessary to validate the results of automated methods or to realign the image when these methods fail. Furthermore, manual realignment provides a critical ground truth for the development of new automated tools. However, such manual interventions are typically performed in a non-standardised manner by domain experts who possess the specialized knowledge of neuroanatomy and neuroimaging required to ensure accurate alignment. To address these challenges, we have developed and validated a standardized protocol for manually realigning structural MR images to the clinically used Schaltenbrand AC-PC plane, using a set of visual criteria to ensure accurate realignment. This protocol can be used to manually align images, verify results, validate existing automated methods, or generate ground truth data for developing new automated techniques.