MRI segmentation of the human brain: challenges, methods, and applications

I Despotović, B Goossens… - … mathematical methods in …, 2015 - Wiley Online Library
Image segmentation is one of the most important tasks in medical image analysis and is
often the first and the most critical step in many clinical applications. In brain MRI analysis …

SynthSR: A public AI tool to turn heterogeneous clinical brain scans into high-resolution T1-weighted images for 3D morphometry

JE Iglesias, B Billot, Y Balbastre, C Magdamo… - Science …, 2023 - science.org
Every year, millions of brain magnetic resonance imaging (MRI) scans are acquired in
hospitals across the world. These have the potential to revolutionize our understanding of …

SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining

B Billot, DN Greve, O Puonti, A Thielscher… - Medical image …, 2023 - Elsevier
Despite advances in data augmentation and transfer learning, convolutional neural
networks (CNNs) difficultly generalise to unseen domains. When segmenting brain scans …

Robust machine learning segmentation for large-scale analysis of heterogeneous clinical brain MRI datasets

B Billot, C Magdamo, Y Cheng, SE Arnold… - Proceedings of the …, 2023 - pnas.org
Every year, millions of brain MRI scans are acquired in hospitals, which is a figure
considerably larger than the size of any research dataset. Therefore, the ability to analyze …

Partial volume correction strategies in PET

O Rousset, A Rahmim, A Alavi, H Zaidi - PET clinics, 2007 - Elsevier
In the early days of PET, the partial volume effect (PVE) was identified as a serious factor
affecting image quality and limiting the accuracy of quantitative analysis. Because of the …

[HTML][HTML] A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI

JE Iglesias, JC Augustinack, K Nguyen, CM Player… - Neuroimage, 2015 - Elsevier
Automated analysis of MRI data of the subregions of the hippocampus requires
computational atlases built at a higher resolution than those that are typically used in current …

SynthMorph: learning contrast-invariant registration without acquired images

M Hoffmann, B Billot, DN Greve… - IEEE transactions on …, 2021 - ieeexplore.ieee.org
We introduce a strategy for learning image registration without acquired imaging data,
producing powerful networks agnostic to contrast introduced by magnetic resonance …

X-ray imaging and analysis techniques for quantifying pore-scale structure and processes in subsurface porous medium systems

D Wildenschild, AP Sheppard - Advances in Water resources, 2013 - Elsevier
We report here on recent developments and advances in pore-scale X-ray tomographic
imaging of subsurface porous media. Our particular focus is on immiscible multi-phase fluid …

An Open Source Multivariate Framework for n-Tissue Segmentation with Evaluation on Public Data

BB Avants, NJ Tustison, J Wu, PA Cook, JC Gee - Neuroinformatics, 2011 - Springer
We introduce Atropos, an ITK-based multivariate n-class open source segmentation
algorithm distributed with ANTs (http://www. picsl. upenn. edu/ANTs). The Bayesian …

Generalized overlap measures for evaluation and validation in medical image analysis

WR Crum, O Camara, DLG Hill - IEEE transactions on medical …, 2006 - ieeexplore.ieee.org
Measures of overlap of labelled regions of images, such as the Dice and Tanimoto
coefficients, have been extensively used to evaluate image registration and segmentation …