A detailed manual segmentation procedure for the hypothalamus for 3T T1-weighted MRI
Mohammad Ali,
Jee Su Suh,
Milita Ramonas,
Stefanie Hassel,
Stephen R. Arnott,
Stephen C. Strother,
Luciano Minuzzi,
Roberto B. Sassi,
Raymond W. Lam,
Roumen Milev,
Daniel J. Müller,
Valerie H. Taylor,
Sidney H. Kennedy,
Benicio N. Frey
Affiliations
Mohammad Ali
Neuroscience Graduate Program, McMaster University, Hamilton, ON, Canada
Jee Su Suh
Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
Milita Ramonas
Juravinski Hospital and Cancer Centre, Hamilton Health Sciences, Hamilton, ON, Canada
Stefanie Hassel
Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
Stephen R. Arnott
Rotman Research Institute, Baycrest, Toronto, ON, Canada
Stephen C. Strother
Rotman Research Institute, Baycrest, Toronto, ON, Canada
Luciano Minuzzi
Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada; Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
Roberto B. Sassi
Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
Raymond W. Lam
Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
Roumen Milev
Departments of Psychiatry and Psychology, Queen's University, and Providence Care Hospital, Kingston, ON, Canada
Daniel J. Müller
Department of Psychiatry, University of Toronto, Toronto, ON, Canada; Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
Valerie H. Taylor
Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
Sidney H. Kennedy
Centre for Depression and Suicide Studies, St. Michael's Hospital, Toronto ON, Canada; Corresponding authors.
Benicio N. Frey
Corresponding authors.; Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada; Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
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.
