A comparison of manual and automated neural architecture search for white matter tract segmentation
File version
Version of Record (VoR)
Author(s)
Zhu, Yanming
Zhang, Fan
O'Donnell, Lauren J
Song, Yang
Meijering, Erik
Griffith University Author(s)
Primary Supervisor
Other Supervisors
Editor(s)
Date
Size
File type(s)
Location
Abstract
Segmentation of white matter tracts in diffusion magnetic resonance images is an important first step in many imaging studies of the brain in health and disease. Similar to medical image segmentation in general, a popular approach to white matter tract segmentation is to use U-Net based artificial neural network architectures. Despite many suggested improvements to the U-Net architecture in recent years, there is a lack of systematic comparison of architectural variants for white matter tract segmentation. In this paper, we evaluate multiple U-Net based architectures specifically for this purpose. We compare the results of these networks to those achieved by our own various architecture changes, as well as to new U-Net architectures designed automatically via neural architecture search (NAS). To the best of our knowledge, this is the first study to systematically compare multiple U-Net based architectures for white matter tract segmentation, and the first to use NAS. We find that the recently proposed medical imaging segmentation network UNet3+ slightly outperforms the current state of the art for white matter tract segmentation, and achieves a notably better mean Dice score for segmentation of the fornix (+ 0.01 and + 0.006 mean Dice increase for left and right fornix respectively), a tract that the current state of the art model struggles to segment. UNet3+ also outperforms the current state of the art when little training data is available. Additionally, manual architecture search found that a minor segmentation improvement is observed when an additional, deeper layer is added to the U-shape of UNet3+. However, all networks, including those designed via NAS, achieve similar results, suggesting that there may be benefit in exploring networks that deviate from the general U-Net paradigm.
Journal Title
Scientific Reports
Conference Title
Book Title
Edition
Volume
13
Issue
Thesis Type
Degree Program
School
Publisher link
Patent number
Funder(s)
Grant identifier(s)
Rights Statement
Rights Statement
© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Item Access Status
Note
Access the data
Related item(s)
Subject
Biomedical imaging
Neural networks
Science & Technology
Multidisciplinary Sciences
Science & Technology - Other Topics
Persistent link to this record
Citation
Tchetchenian, A; Zhu, Y; Zhang, F; O'Donnell, LJ; Song, Y; Meijering, E, A comparison of manual and automated neural architecture search for white matter tract segmentation, Scientific Reports, 2023, 13, pp. 1617