Automated, open-source segmentation of the Hippocampus and amygdala with the open Vanderbilt archive of the temporal lobe

Andrew J Plassard; Shunxing Bao; Maureen McHugo; Lori Beason-Held; Jennifer U Blackford; Stephan Heckers; Bennett A Landman

doi:10.1016/j.mri.2021.04.011

Automated, open-source segmentation of the Hippocampus and amygdala with the open Vanderbilt archive of the temporal lobe

Magn Reson Imaging. 2021 Sep:81:17-23. doi: 10.1016/j.mri.2021.04.011. Epub 2021 Apr 24.

Authors

Andrew J Plassard¹, Shunxing Bao², Maureen McHugo³, Lori Beason-Held⁴, Jennifer U Blackford⁵, Stephan Heckers⁶, Bennett A Landman⁷

Affiliations

¹ Vanderbilt University, Computer Science, 2301 Vanderbilt Place, Nashville, TN 37235, USA. Electronic address: andrew.j.plassard@vanderbilt.edu.
² Vanderbilt University, Computer Science, 2301 Vanderbilt Place, Nashville, TN 37235, USA. Electronic address: shunxing.bao@vanderbilt.edu.
³ Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, 1601 23rd Avenue South, Nashville, TN 37212, USA. Electronic address: maureen.mchugo@vanderbilt.edu.
⁴ Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, 31 Center Dr, #5C27 MSC 2292, Building 31, Room 5C27, Bethesda, Maryland, 20892-0001, USA. Electronic address: heldlo@grc.nia.nih.gov.
⁵ Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, 1601 23rd Avenue South, Nashville, TN 37212, USA. Electronic address: jenni.blackford@vumc.org.
⁶ Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, 1601 23rd Avenue South, Nashville, TN 37212, USA. Electronic address: stephan.heckers@vanderbilt.edu.
⁷ Vanderbilt University, Computer Science, 2301 Vanderbilt Place, Nashville, TN 37235, USA; Vanderbilt University, Electrical Engineering, 2301 Vanderbilt Place, Nashville, TN 37235, USA. Electronic address: bennett.landman@vanderbilt.edu.

Abstract

Examining volumetric differences of the amygdala and anterior-posterior regions of the hippocampus is important for understanding cognition and clinical disorders. However, the gold standard manual segmentation of these structures is time and labor-intensive. Automated, accurate, and reproducible techniques to segment the hippocampus and amygdala are desirable. Here, we present a hierarchical approach to multi-atlas segmentation of the hippocampus head, body and tail and the amygdala based on atlases from 195 individuals. The Open Vanderbilt Archive of the temporal Lobe (OVAL) segmentation technique outperforms the commonly used FreeSurfer, FSL FIRST, and whole-brain multi-atlas segmentation approaches for the full hippocampus and amygdala and nears or exceeds inter-rater reproducibility for segmentation of the hippocampus head, body and tail. OVAL has been released in open-source and is freely available.

Keywords: Amygdala; Hippocampus; Multi-atlas segmentation; Temporal lobe.

Publication types

Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Amygdala / diagnostic imaging
Hippocampus / diagnostic imaging
Humans
Image Processing, Computer-Assisted*
Magnetic Resonance Imaging*
Reproducibility of Results
Temporal Lobe / diagnostic imaging

Abstract

Publication types

MeSH terms

Grants and funding