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

Mohammad Ali¹, Jee Su Suh², Milita Ramonas³, Stefanie Hassel⁴, Stephen R Arnott⁵, Stephen C Strother⁵, Luciano Minuzzi^{2

6}, Roberto B Sassi⁷, Raymond W Lam⁷, Roumen Milev⁸, Daniel J Müller^{9

10}, Valerie H Taylor⁴, Sidney H Kennedy¹¹, Benicio N Frey^{2

6}; CAN-BIND Investigator Team

Affiliations

¹ Neuroscience Graduate Program, McMaster University, Hamilton, ON, Canada.
² Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada.
³ Juravinski Hospital and Cancer Centre, Hamilton Health Sciences, Hamilton, ON, Canada.
⁴ Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
⁵ Rotman Research Institute, Baycrest, Toronto, ON, Canada.
⁶ Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada.
⁷ Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada.
⁸ Departments of Psychiatry and Psychology, Queen's University, and Providence Care Hospital, Kingston, ON, Canada.
⁹ Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
¹⁰ Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.
¹¹ Centre for Depression and Suicide Studies, St. Michael's Hospital, Toronto ON, Canada.

PMID: 36193115
PMCID: PMC9526169
DOI: 10.1016/j.mex.2022.101864

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

Mohammad Ali et al. MethodsX. 2022.

. 2022 Sep 17:9:101864.

doi: 10.1016/j.mex.2022.101864. eCollection 2022.

Authors

Affiliations

¹ Neuroscience Graduate Program, McMaster University, Hamilton, ON, Canada.
² Mood Disorders Program, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada.
³ Juravinski Hospital and Cancer Centre, Hamilton Health Sciences, Hamilton, ON, Canada.
⁴ Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
⁵ Rotman Research Institute, Baycrest, Toronto, ON, Canada.
⁶ Women's Health Concerns Clinic, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada.
⁷ Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada.
⁸ Departments of Psychiatry and Psychology, Queen's University, and Providence Care Hospital, Kingston, ON, Canada.
⁹ Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
¹⁰ Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada.
¹¹ Centre for Depression and Suicide Studies, St. Michael's Hospital, Toronto ON, Canada.

PMID: 36193115
PMCID: PMC9526169
DOI: 10.1016/j.mex.2022.101864

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: Algorithm; Hypothalamus segmentation; MRI.

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Conflict of interest statement

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.

Figures

Image, graphical abstract — **Graphical abstract**

Fig 1: — **Fig. 1**
Diagram of the surrounding area of the hypothalamus

Fig 2 — **Fig. 2**
Schematic of a full manual hypothalamic segmentation. Blue = Right Hypothalamus; Red = Left Hypothalamus

Fig 3 — **Fig. 3**
Drift effects of manual segmentations performed at timepoints 1 and 2 (6-month test-retest interval)

Fig 4 — **Fig. 4**
Visual illustration of superimposed automatic and manual segmentation. Blue/red = manual segmentation; turquoise/brown= automatic segmentation

See this image and copyright information in PMC

References

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

LinkOut - more resources

Full Text Sources