Gray Matter Segmentation in Ultra High Resolution 7 Tesla ex vivo T2w MRI of Human Brain Hemispheres
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Abstract (arXiv)
Ex vivo MRI of the brain provides remarkable advantages over in vivo MRI for visualizing and characterizing detailed neuroanatomy. However, automated cortical segmentation methods in ex vivo MRI are not well developed, primarily due to limited availability of labeled datasets, and heterogeneity in scanner hardware and acquisition protocols. In this work, we present a high resolution 7 Tesla dataset of 32 ex vivo human brain specimens. We benchmark the cortical mantle segmentation performance of nine neural network architectures, trained and evaluated using manually-segmented 3D patches sampled from specific cortical regions, and show excellent generalizing capabilities across whole brain hemispheres in different specimens, and also on unseen images acquired at different magnetic field strength and imaging sequences. Finally, we provide cortical thickness measurements across key regions in 3D ex vivo human brain images. Our code and processed datasets are publicly available at https://github.com/Pulkit-Khandelwal/picsl-ex-vivo-segmentation.
Key facts. Cited by 1 paper in the map (data through 14 Oct 2026). Builds on 7 of its 18 references that are in the map. First posted on arXiv 14 Oct 2021.
Builds on
7 of 18 references.
References · 7
- 2016V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentationcited by 2,292
- 2018Attention U-Net: Learning Where to Look for the Pancreascited by 1,435
- 2019FastSurfer -- A fast and accurate deep learning based neuroimaging pipelinecited by 112
- 2018AnatomyNet: Deep Learning for Fast and Fully Automated Whole-volume Segmentation of Head and Neck Anatomycited by 54
- 2020Domain Generalizer: A Few-shot Meta Learning Framework for Domain Generalization in Medical Imagingcited by 18
- 2019`Project & Excite' Modules for Segmentation of Volumetric Medical Scanscited by 7
- 2020Convolutional Neural Networks for cytoarchitectonic brain mapping at large scalecited by 3
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