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.