A detailed manual segmentation procedure for the hypothalamus for 3T T1-weighted MRI.

The hypothalamus is a small grey matter structure which plays a crucial role in many physiological functions. Some studies have found an association between hypothalamic volume and psychopathology, which stresses the need for a standardized method to maximize segmentation accuracy. Here, we provide a detailed step-by-step method outlining the procedures to manually segment the hypothalamus using anatomical T1w images from 3T scanners, which many neuroimaging studies collect as a standard anatomical reference image. We compared volumes generated by manual segmentation and those generated by an automatic algorithm, observing a significant difference between automatically and manually segmented hypothalamus volumes on both sides (left: U = 222842, p-value < 2.2e-16; right: U = 218520, p- value < 2.2e-16).•Significant difference exists between existing automatic segmentation methods and the manual segmentation procedure.•We discuss potential drift effects, segmentation quality issues, and suggestions on how to mitigate them.•We demonstrate that the present manual segmentation procedure using standard T1-weighted MRI may be significantly more accurate than automatic segmentation outputs.
Competing Interests: Dr. Milev has received research grants from CAN-BIND, CIHR, Janssen, Lallemand, Lundbeck, Nubiyota, OBI and OMHF. Additionally, Dr. Milev has received speaking and consulting honoraria from AbbVie, Allergan, Janssen, KYE, Lundbeck, Otsuka, and Sunovion. Dr. Lam has received honoraria or research funds from Allergan, Asia-Pacific Economic Cooperation, BC Leading Edge Foundation, CIHR, CANMAT, Canadian Psychiatric Association, Hansoh, Healthy Minds Canada, Janssen, Lundbeck, Lundbeck Institute, Michael Smith Foundation for Health Research, MITACS, Ontario Brain Institute, Otsuka, Pfizer, St. Jude Medical, University Health Network Foundation, and VGH-UBCH Foundation. Dr. Strother is the Chief Scientific Officer of ADMdx, Inc., which receives NIH funding, and currently has research grants from Brain Canada, CIHR, the Ontario Brain Institute in Canada. Dr. Kennedy has received research funding or honoraria from the following sources: Abbott, Alkermes, Allergan, BMS, Brain Canada, Canadian Institutes for Health Research (CIHR), Janssen, Lundbeck, Lundbeck Institute, Ontario Brain Institute, Ontario Research Fund (ORF), Otsuka, Pfizer, Servier, Sunovion and Xian-Janssen. All other authors have no conflict of interest.
(© 2022 The Author(s). Published by Elsevier B.V.)