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A Decoupled Uncertainty Model for MRI Segmentation Quality Estimation


Sep 06, 2021
Richard Shaw, Carole H. Sudre, Sebastien Ourselin, M. Jorge Cardoso, Hugh G. Pemberton

* Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA) https://melba-journal.org. arXiv admin note: substantial text overlap with arXiv:2001.11927 

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Distinguishing Healthy Ageing from Dementia: a Biomechanical Simulation of Brain Atrophy using Deep Networks


Aug 18, 2021
Mariana Da Silva, Carole H. Sudre, Kara Garcia, Cher Bass, M. Jorge Cardoso, Emma C. Robinson

* MLCN 2021 

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Estimating MRI Image Quality via Image Reconstruction Uncertainty


Jun 21, 2021
Richard Shaw, Carole H. Sudre, Sebastien Ourselin, M. Jorge Cardoso


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The Medical Segmentation Decathlon


Jun 10, 2021
Michela Antonelli, Annika Reinke, Spyridon Bakas, Keyvan Farahani, AnnetteKopp-Schneider, Bennett A. Landman, Geert Litjens, Bjoern Menze, Olaf Ronneberger, Ronald M. Summers, Bram van Ginneken, Michel Bilello, Patrick Bilic, Patrick F. Christ, Richard K. G. Do, Marc J. Gollub, Stephan H. Heckers, Henkjan Huisman, William R. Jarnagin, Maureen K. McHugo, Sandy Napel, Jennifer S. Goli Pernicka, Kawal Rhode, Catalina Tobon-Gomez, Eugene Vorontsov, Henkjan Huisman, James A. Meakin, Sebastien Ourselin, Manuel Wiesenfarth, Pablo Arbelaez, Byeonguk Bae, Sihong Chen, Laura Daza, Jianjiang Feng, Baochun He, Fabian Isensee, Yuanfeng Ji, Fucang Jia, Namkug Kim, Ildoo Kim, Dorit Merhof, Akshay Pai, Beomhee Park, Mathias Perslev, Ramin Rezaiifar, Oliver Rippel, Ignacio Sarasua, Wei Shen, Jaemin Son, Christian Wachinger, Liansheng Wang, Yan Wang, Yingda Xia, Daguang Xu, Zhanwei Xu, Yefeng Zheng, Amber L. Simpson, Lena Maier-Hein, M. Jorge Cardoso


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Common Limitations of Image Processing Metrics: A Picture Story


Apr 13, 2021
Annika Reinke, Matthias Eisenmann, Minu D. Tizabi, Carole H. Sudre, Tim Rädsch, Michela Antonelli, Tal Arbel, Spyridon Bakas, M. Jorge Cardoso, Veronika Cheplygina, Keyvan Farahani, Ben Glocker, Doreen Heckmann-Nötzel, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Jens Kleesiek, Tahsin Kurc, Michal Kozubek, Bennett A. Landman, Geert Litjens, Klaus Maier-Hein, Bjoern Menze, Henning Müller, Jens Petersen, Mauricio Reyes, Nicola Rieke, Bram Stieltjes, Ronald M. Summers, Sotirios A. Tsaftaris, Bram van Ginneken, Annette Kopp-Schneider, Paul Jäger, Lena Maier-Hein

* This is a dynamic paper on limitations of commonly used metrics. The current version discusses segmentation metrics only, while future versions will also include metrics for classification and detection. For missing use cases, comments or questions, please contact [email protected] or [email protected]. Substantial contributions to this document will be acknowledged with a co-authorship 

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An MRF-UNet Product of Experts for Image Segmentation


Apr 12, 2021
Mikael Brudfors, Yaël Balbastre, John Ashburner, Geraint Rees, Parashkev Nachev, Sébastien Ourselin, M. Jorge Cardoso

* Accepted at MIDL 2021 

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Multi-Atlas Based Pathological Stratification of d-TGA Congenital Heart Disease


Apr 05, 2021
Maria A. Zuluaga, Alex F. Mendelson, M. Jorge Cardoso, Andrew M. Taylor, Sébastien Ourselin

* In: IEEE International Symposium on Biomedical Imaging 2014 

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Unsupervised Brain Anomaly Detection and Segmentation with Transformers


Feb 23, 2021
Walter Hugo Lopez Pinaya, Petru-Daniel Tudosiu, Robert Gray, Geraint Rees, Parashkev Nachev, Sebastien Ourselin, M. Jorge Cardoso

* 22 pages, 9 figures, submitted to MIDL 2021, OpenReview https://openreview.net/forum?id=Z1tlNqbCpp_ 

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Scale factor point spread function matching: Beyond aliasing in image resampling


Jan 16, 2021
M. Jorge Cardoso, Marc Modat, Tom Vercauteren, Sebastien Ourselin

* Published in MICCAI 2015 

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Biomechanical modelling of brain atrophy through deep learning


Dec 14, 2020
Mariana da Silva, Kara Garcia, Carole H. Sudre, Cher Bass, M. Jorge Cardoso, Emma Robinson

* Submitted to Medical Imaging Meets NeurIPS 2020 

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Test-time Unsupervised Domain Adaptation


Oct 05, 2020
Thomas Varsavsky, Mauricio Orbes-Arteaga, Carole H. Sudre, Mark S. Graham, Parashkev Nachev, M. Jorge Cardoso

* Accepted at MICCAI 2020 

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Hierarchical brain parcellation with uncertainty


Sep 16, 2020
Mark S. Graham, Carole H. Sudre, Thomas Varsavsky, Petru-Daniel Tudosiu, Parashkev Nachev, Sebastien Ourselin, M. Jorge Cardoso

* To be published in the MICCAI 2020 workshop: Uncertainty for Safe Utilization of Machine Learning in Medical Imaging 

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Combining multimodal information for Metal Artefact Reduction: An unsupervised deep learning framework


Apr 20, 2020
Marta B. M. Ranzini, Irme Groothuis, Kerstin Kläser, M. Jorge Cardoso, Johann Henckel, Sébastien Ourselin, Alister Hart, Marc Modat

* Accepted at IEEE International Symposium on Biomedical Imaging (ISBI) 2020 

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Automatic Right Ventricle Segmentation using Multi-Label Fusion in Cardiac MRI


Apr 05, 2020
Maria A. Zuluaga, M. Jorge Cardoso, Sébastien Ourselin

* Workshop on RV Segmentation Challenge in Cardiac MRI in conjunction with Medical Image Computing and Computer-Assisted Intervention 2012 

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The Future of Digital Health with Federated Learning


Mar 18, 2020
Nicola Rieke, Jonny Hancox, Wenqi Li, Fausto Milletari, Holger Roth, Shadi Albarqouni, Spyridon Bakas, Mathieu N. Galtier, Bennett Landman, Klaus Maier-Hein, Sebastien Ourselin, Micah Sheller, Ronald M. Summers, Andrew Trask, Daguang Xu, Maximilian Baust, M. Jorge Cardoso


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Neuromorphologicaly-preserving Volumetric data encoding using VQ-VAE


Feb 13, 2020
Petru-Daniel Tudosiu, Thomas Varsavsky, Richard Shaw, Mark Graham, Parashkev Nachev, Sebastien Ourselin, Carole H. Sudre, M. Jorge Cardoso


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A Heteroscedastic Uncertainty Model for Decoupling Sources of MRI Image Quality


Jan 31, 2020
Richard Shaw, Carole H. Sudre, Sebastien Ourselin, M. Jorge Cardoso


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On the Initialization of Long Short-Term Memory Networks


Dec 22, 2019
Mostafa Mehdipour Ghazi, Mads Nielsen, Akshay Pai, Marc Modat, M. Jorge Cardoso, Sebastien Ourselin, Lauge Sorensen


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Privacy-preserving Federated Brain Tumour Segmentation


Oct 02, 2019
Wenqi Li, Fausto Milletarì, Daguang Xu, Nicola Rieke, Jonny Hancox, Wentao Zhu, Maximilian Baust, Yan Cheng, Sébastien Ourselin, M. Jorge Cardoso, Andrew Feng

* MICCAI MLMI 2019 

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Multi-Domain Adaptation in Brain MRI through Paired Consistency and Adversarial Learning


Sep 17, 2019
Mauricio Orbes-Arteaga, Thomas Varsavsky, Carole H. Sudre, Zach Eaton-Rosen, Lewis J. Haddow, Lauge Sørensen, Mads Nielsen, Akshay Pai, Sébastien Ourselin, Marc Modat, Parashkev Nachev, M. Jorge Cardoso

* Accepted at 1st International Workshop on Domain Adaptation and Representation Transfer held at MICCAI 2019 

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Let's agree to disagree: learning highly debatable multirater labelling


Sep 04, 2019
Carole H. Sudre, Beatriz Gomez Anson, Silvia Ingala, Chris D. Lane, Daniel Jimenez, Lukas Haider, Thomas Varsavsky, Ryutaro Tanno, Lorna Smith, Sébastien Ourselin, Rolf H. Jäger, M. Jorge Cardoso

* Accepted at MICCAI 2019 

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Stochastic Filter Groups for Multi-Task CNNs: Learning Specialist and Generalist Convolution Kernels


Aug 26, 2019
Felix J. S. Bragman, Ryutaro Tanno, Sebastien Ourselin, Daniel C. Alexander, M. Jorge Cardoso

* Accepted for oral presentation at ICCV 2019 

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Robust parametric modeling of Alzheimer's disease progression


Aug 14, 2019
Mostafa Mehdipour Ghazi, Mads Nielsen, Akshay Pai, Marc Modat, M. Jorge Cardoso, Sébastien Ourselin, Lauge Sørensen


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As easy as 1, 2... 4? Uncertainty in counting tasks for medical imaging


Jul 25, 2019
Zach Eaton-Rosen, Thomas Varsavsky, Sebastien Ourselin, M. Jorge Cardoso

* Early Accept to MICCAI 2019 

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Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities and Results of the WMH Segmentation Challenge


Apr 01, 2019
Hugo J. Kuijf, J. Matthijs Biesbroek, Jeroen de Bresser, Rutger Heinen, Simon Andermatt, Mariana Bento, Matt Berseth, Mikhail Belyaev, M. Jorge Cardoso, Adrià Casamitjana, D. Louis Collins, Mahsa Dadar, Achilleas Georgiou, Mohsen Ghafoorian, Dakai Jin, April Khademi, Jesse Knight, Hongwei Li, Xavier Lladó, Miguel Luna, Qaiser Mahmood, Richard McKinley, Alireza Mehrtash, Sébastien Ourselin, Bo-yong Park, Hyunjin Park, Sang Hyun Park, Simon Pezold, Elodie Puybareau, Leticia Rittner, Carole H. Sudre, Sergi Valverde, Verónica Vilaplana, Roland Wiest, Yongchao Xu, Ziyue Xu, Guodong Zeng, Jianguo Zhang, Guoyan Zheng, Christopher Chen, Wiesje van der Flier, Frederik Barkhof, Max A. Viergever, Geert Jan Biessels

* Accepted for publication in IEEE Transactions on Medical Imaging 

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Training recurrent neural networks robust to incomplete data: application to Alzheimer's disease progression modeling


Mar 17, 2019
Mostafa Mehdipour Ghazi, Mads Nielsen, Akshay Pai, M. Jorge Cardoso, Marc Modat, Sebastien Ourselin, Lauge Sørensen

* Medical Image Analysis, Volume 53, Pages 39-46, 2019 
* arXiv admin note: substantial text overlap with arXiv:1808.05500 

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A large annotated medical image dataset for the development and evaluation of segmentation algorithms


Feb 25, 2019
Amber L. Simpson, Michela Antonelli, Spyridon Bakas, Michel Bilello, Keyvan Farahani, Bram van Ginneken, Annette Kopp-Schneider, Bennett A. Landman, Geert Litjens, Bjoern Menze, Olaf Ronneberger, Ronald M. Summers, Patrick Bilic, Patrick F. Christ, Richard K. G. Do, Marc Gollub, Jennifer Golia-Pernicka, Stephan H. Heckers, William R. Jarnagin, Maureen K. McHugo, Sandy Napel, Eugene Vorontsov, Lena Maier-Hein, M. Jorge Cardoso


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3D multirater RCNN for multimodal multiclass detection and characterisation of extremely small objects


Dec 21, 2018
Carole H. Sudre, Beatriz Gomez Anson, Silvia Ingala, Chris D. Lane, Daniel Jimenez, Lukas Haider, Thomas Varsavsky, Lorna Smith, H. Rolf Jäger, M. Jorge Cardoso


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Elastic Registration of Geodesic Vascular Graphs


Sep 14, 2018
Stefano Moriconi, Maria A. Zuluaga, H. Rolf Jager, Parashkev Nachev, Sebastien Ourselin, M. Jorge Cardoso

* Medical Image Computing and Computer Assisted Intervention -- MICCAI 2018 

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