Automated landmark-based symmetric and standard alignment of skull base structures on CT

Justin A Cramer; Trevor Huff; Sean Kelly; Daniel Welch; Devin DeLuna; Conner Beyersdorf; Robin High; Matthew White

doi:10.1016/j.ynirp.2025.100260

Automated landmark-based symmetric and standard alignment of skull base structures on CT

Neuroimage Rep. 2025 Apr 4;5(2):100260. doi: 10.1016/j.ynirp.2025.100260. eCollection 2025 Jun.

Authors

Justin A Cramer¹, Trevor Huff², Sean Kelly³, Daniel Welch³, Devin DeLuna³, Conner Beyersdorf⁴, Robin High³, Matthew White³

Affiliations

¹ Mayo Clinic Arizona, 5711 E Mayo Blvd, Phoenix, AZ, 85054, USA.
² University of Arizona, 1501 N. Campbell, Tucson, AZ, 85724, USA.
³ University of Nebraska Medical Center, 42nd and Emile, Omaha, NE, 68198, USA.
⁴ University Hospitals, 11100 Euclid Avenue, Cleveland, OH, 44106, USA.

Abstract

Introduction: Symmetry and standard alignment are crucial in both clinical interpretation and research on head CT studies. Registration to a standard template is the traditional method for alignment, yet registration does not guarantee precise alignment of any given structure. This study introduces a method for aligning skull base structures while still achieving a standard anterior commissure-posterior commissure (AC-PC)-like orientation on head CT studies using landmarks, specifically the cochleas and nasal bridge.

Methods: A retrospective study was conducted using head CTs from various General Electric scanners. Landmarks were manually annotated, and a 3D U-Net was trained for landmark identification. Landmark-based alignment was then performed on a test dataset and assessed in two different ways: whole head and skull base alignment. Whole head alignment was assessed quantitatively by expert review. Skull base alignment was then assessed at the cochleas, comparing their alignment between this landmark-based technique and registration to a template.

Results: This landmark-based technique significantly improved whole head and skull base alignment of head CT studies. Whole head alignment reduced average deviations of 5, 11, and 4° in the axial, sagittal, and coronal planes to 1, 5, and 2° respectively. Meanwhile, skull base alignment assessed via the cochlea was also improved relative to traditional registration. For the landmark technique, the cochleas were deviated from perfect by a mean of 0.552 and 0.511 mm along the y and z axes compared to 2.110 and 2.506 mm with registration.

Conclusion: This study demonstrates a simple landmark-based technique for aligning the cochleas on head CT studies while approximating whole head AC-PC orientation, which has applications in both clinical and research settings, particularly for studies focused on the skull base.

Keywords: AC-PC line; Alignment; Head CT; Landmark; Registration; U-Net.