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

Abstract

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.

Keywords

• Manual Segmentation of the Hypothalamus using standard 3T anatomical T1w images