A deep learning toolbox for automatic segmentation of subcortical limbic structures from MRI images

Douglas N. Greve; Benjamin Billot; Devani Cordero; Andrew Hoopes; Malte Hoffmann; Adrian V. Dalca; Bruce Fischl; Juan Eugenio Iglesias; Jean C. Augustinack

NeuroImage (Dec 2021)

A deep learning toolbox for automatic segmentation of subcortical limbic structures from MRI images

Douglas N. Greve,
Benjamin Billot,
Devani Cordero,
Andrew Hoopes,
Malte Hoffmann,
Adrian V. Dalca,
Bruce Fischl,
Juan Eugenio Iglesias,
Jean C. Augustinack

Affiliations

Douglas N. Greve: Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Radiology Department, Boston, MA, USA; Corresponding author at: Radiology, Massachusetts General Hospital, 149 13th Street, Room 2301, Charlestown, Massachusetts 02129, United States.
Benjamin Billot: Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, UK
Devani Cordero: Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
Andrew Hoopes: Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
Malte Hoffmann: Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Radiology Department, Boston, MA, USA
Adrian V. Dalca: Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Radiology Department, Boston, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Boston, USA
Bruce Fischl: Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Radiology Department, Boston, MA, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Boston, USA
Juan Eugenio Iglesias: Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Radiology Department, Boston, MA, USA; Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, UK; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Boston, USA
Jean C. Augustinack: Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Boston, MA, USA; Harvard Medical School, Radiology Department, Boston, MA, USA

Journal volume & issue: Vol. 244
p. 118610

Abstract

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A tool was developed to automatically segment several subcortical limbic structures (nucleus accumbens, basal forebrain, septal nuclei, hypothalamus without mammillary bodies, the mammillary bodies, and fornix) using only a T1-weighted MRI as input. This tool fills an unmet need as there are few, if any, publicly available tools to segment these clinically relevant structures. A U-Net with spatial, intensity, contrast, and noise augmentation was trained using 39 manually labeled MRI data sets. In general, the Dice scores, true positive rates, false discovery rates, and manual-automatic volume correlation were very good relative to comparable tools for other structures. A diverse data set of 698 subjects were segmented using the tool; evaluation of the resulting labelings showed that the tool failed in less than 1% of cases. Test-retest reliability of the tool was excellent. The automatically segmented volume of all structures except mammillary bodies showed effectiveness at detecting either clinical AD effects, age effects, or both. This tool will be publicly released with FreeSurfer (surfer.nmr.mgh.harvard.edu/fswiki/ScLimbic). Together with the other cortical and subcortical limbic segmentations, this tool will allow FreeSurfer to provide a comprehensive view of the limbic system in an automated way.

Published in NeuroImage

ISSN: 1053-8119 (Print); 1095-9572 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Medicine: Internal medicine: Neurosciences. Biological psychiatry. Neuropsychiatry
Website: https://www.journals.elsevier.com/neuroimage

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