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2020 – today
- 2025
[j7]Tim M. Tierney
, Nicholas Alexander, John Ashburner, Nicole Labra Avila, Yaël Balbastre, Gareth R. Barnes, Yulia Bezsudnova, Mikael Brudfors, Korbinian Eckstein, Guillaume Flandin, Karl J. Friston, Amirhossein Jafarian, Olivia S. Kowalczyk, Vladimir Litvak, Johan Medrano, Stephanie Mellor, George C. O'Neill, Thomas Parr, Adeel Razi, Ryan C. Timms, Peter Zeidman:
SPM 25: open source neuroimaging analysis software. J. Open Source Softw. 10(111): 8103 (2025)- [d1]Aaron Oliver-Taylor, Adam Li, Adam G. Thomas, Adeen Flinker, Adina S. Wagner, Agah Karakuzu, Agnese Zazio, Aki Nikolaidis, Alberto Lazari, Alejandro de la Vega, Alessio Giacomel, Alexander Rockhill, Alexander Jones, Alexander Li Cohen, Alexander von Lautz, Alexandre D'Astous, Alexandre Gramfort, Alexandre Hutton, Alexandre Routier, Alexandru Foias, Ali R. Khan, Alizee Wickenheiser, Alyssa Dai, Amber R. Hopkins, Ana Fouto, Anders Eklund, Andrea Pigorini, Andrew Hoopes, Andrew Jahn, Andrew Janke, Anibal Sólon, Anthony Galassi, Arianna Sala, Ariel Rokem, Arjen Stolk, Arman Jahanpour, Arnaud Delorme, Arnaud Marcoux, Arshitha Basavaraj, Ashley G. Gillman, Athanasia Monika Mowinckel, Augustijn Vrolijk, Aysegul Gunduz, Azeez Adebimpe, B. Nolan Nichols, Balint Kincses, Benjamin Beasley, Benjamin K. Dichter, Benjamin Gagl, Bertrand Thirion, Boris Clénet, Bradley Voytek, Brent McPherson, Brett L. Foster, Brian A. Wandell, Brian N. Lundstrom, Camille Maumet, Carlo Miniussi, Cecile Madjar, Chloé Pasturel, Chris Benjamin, Chris Gahnström, Chris Holdgraf, Chris J. Gorgolewski, Chris Rorden, Christian Büchel, Christian Horea, Christine Rogers, Christophe Phillips, Christopher G. Schwarz, Christopher J. Honey, Christopher J. Markiewicz, Christopher Lee-Messer, Clara Moreau, Clint Hansen, Cody C. Baker, Cyril R. Pernet, Cyrus Eierud, D. Sturgeon, Dan Levitas, Dan Lurie, Daniel A. Handwerker, Daniel McCloy, David C. Alsop, David A. Boas, David M. Groppe, David B. Keator, David McAlpine, David Thomas, Dejan Draschkow, Desmond J. Oathes, Dianne K. Patterson, Dimitri Papadopoulos Orfanos, Dmitry Petrov, Dora Hermes, Dorien Huijser, Dorota Jarecka, Douglas N. Greve, Duncan Macleod, Dung Truong, Dustin Moraczewski, Dylan Nielson, Eduard Ort, Eleonora Marcantoni, Elizabeth Bock, Elizabeth DuPre, Elke Warmerdam, Erdal Karaca, Eric A. Earl, Eric Achten, Eric Bridgeford, Erin W. Dickie, Ethan Blackwood, Eugene P. Duff, Ezequiel Mikulan, Federico Raimondo, Felipe Orihuela-Espina, Fidel Alfaro-Almagro, Filip Szczepankiewicz, Filippo Maria Castelli, Franco Pestilli, Franklin W. Feingold, François Tadel, Friederike Breuer, Gaia Rizzo, Gang Chen, Gaël Varoquaux, Ghislain Vaillant, Giacomo Bertazzoli, Giacomo Guidali, Giacomo Mazzamuto, Gilles de Hollander, Gio Piantoni, Giovanna Nordio, Gitte M. Knudsen, Giulio Castegnaro, Giuseppe Gallitto, Graham Searle, Granville J. Matheson, Gregory Kiar, Gregory Noack, Greydon Gilmore, Guillaume Flandin, Guiomar Niso, Gunnar Schaefer, Gustav Nilsonne, Hamish Innes-Brown, Hanne D. Hansen, Hanzhang Lu, Hao-Ting Wang, Helena Cockx, Henk Mutsaerts, Hernando Ombao, Hugo Boniface, Ayse Ilkay Isik, Ilona Lipp, International Neuroinformatics Coordinating Facility, Iris I. A. Groen, Isaac To, Isla Staden, Jaap von der Aar, Jacob Sanz-Robinson, Jakub Kaczmarzyk, James Gholam, James D. Kent, Jan-Mathijs Schoffelen, Jan Petr, Jan Valosek, Jean-Baptiste Poline, Jean-Charles Mariani, Jean-Christophe Houde, Jean-Dominique Gallezot, Jean-Philippe Lachaux, Jeanette Mumford, Jefferson Casimir, Jeffrey G. Ojemann, Jeffrey S. Grethe, JegouA, Jelle R. Dalenberg, Jeremy T. Moreau, Jessica A. Turner, Jochem W. Rieger, John A. Detre, John Pellman, John T. Wodder, Joke Durnez, Jon Haitz Legarreta Gorrono, Jonathan C. Lau, Jonathan Winawer, Joost P. A. Kuijer, Jose Manuel Saborit, Joseph Wexler, Joseph G. Woods, Julia Sprenger, Julia-Katharina Pfarr, Julien Cohen-Adad, Julio C. Hernandez-Pavon, Julius Welzel, Jérémie Fouquet, Kabilar Gunalan, Kai J. Miller, Kangjoo Lee, Katja Heuer, Kay Robbins, Kevin Larcher, Kimberly L. Ray, Kirstie J. Whitaker, Klara Gregorova, Klaus Gramann, Kris Thielemans, Kristofer E. Bouchard, Kurt Schilling, Laetitia Fesselier, Laura & John Arnold Foundation, Leandro Beltrachini, Lee Kamentsky, Lennart Walger, Lennart Wittkuhn, Liberty S. Hamilton, Luca Pollonini, Luis Hernandez-Garcia, Luke J. Edwards, Lyuba Zehl, Mainak Jas, Mana Biabani, Manjari Narayan, Manuel R. Mercier, Maqsood Yaqub, Marc Lalancette, Marco Castellaro, Margaret E. Heafield, Maria Ermolova, Maria de la Iglesia, Marie-Hélène Bourget, Mark Mikkelsen, Markus Morawski, Marta Bortoletto, Martin Craig, Martin Nørgaard, Martin Szinte, Martin Wilson, Martina Bulgari, Mateusz Pawlik, Mathias Goncalves, Mathieu Boudreau, Mathieu Dugré, Mathieu Guay-Paquet, Matt Cieslak, Matt Sanderson, Matt Stead, Matteo Tonietto, Matthias Günther, Matthias van Osch, Matthieu Chourrout, Mattia Veronese, Maureen J. Shader, Maurice Pasternak, Max A. van den Boom, Melanie Ganz-Benjaminsen, Melissa Kline Struhl, Michael Chappell, Michael J. Firbank, Michael Hanke, Michael P. Harms, Michael P. Milham, Michael P. Notter, Michael Schirner, Michelle Wang, Mikaël Naveau, Mohammad Torabi, Monique Denissen, Murat Bilgel, Nader Pouratian, Natalia Petridou, Natalie Rotstein, National Institute of Mental Health, Nell Hardcastle, Nicholas P. Holmes, Nicholas Traut, Nick F. Ramsey, Nick Guenther, Nicole C. Swann, Nigel C. Rogasch, Nikhil Bhagwat, Nikita Beliy, Nima Bigdely Shamlo, Olivier David, Orrin Devinsky, Oscar Esteban, Pamela LaMontagne, Parul Sethi, Patricia Clement, Patrick Park, Paule-Joanne Toussaint, Peer Herholz, Petra Ritter, Pierre Rioux, Pieter Vandemaele, Pradeep Reddy Raamana, Qian Chu, R. Cameron Craddock, Rémi Gau, Richard Höchenberger, Richard N. Henson, Robert B. Innis, Robert E. Smith, Robert Knight, Robert Luke, Robert Oostenveld, Roberto Guidotti, Roberto Toro, Rohan Goyal, Ross W. Blair, Russell A. Poldrack, Rémi Adon, Samir Das, Samuel Garcia, Samuel Guay, Samuel Le Meur-Diebolt, Samuel A. Nastase, Sara Elgayar, Sasha D'Ambrosio, Satrajit S. Ghosh, Scott Makeig, Sebastian Urchs, Sein Jeung, Seyed Yahya Shirazi, Shashank Bansal, Silvia Isabella, Sjoerd B. Vos, Soichi Hayashi, Stefan Appelhoff, Stefanie De Smet, Stephan Bickel, Steven L. Meisler, Suyash Bhogawar, Sylvain Baillet, Sylvain Takerkart, Sébastien Tourbier, Sören Grothkopp, Tal Pal Attia, Tal Yarkoni, Tamás Spisák, Tamás Józsa, Taylor Khuhn, Taylor Salo, Teon L. Brooks, Thomas Deffieux, Thomas E. Nichols, Thomas Funck, Thomas Kirk, Thomas W. Okell, Tibor Auer, Til Ole Bergmann, Timo Dickscheid, Timotheus Berg, Tobey Betthauser, Tobias Bengfort, Tom Hampshire, Tor Wager, Torsten Stöter, Travis Riddle, Tristan Glatard, Tyler Collins, Ulrike Bingel, Vanessa V. Sochat, Vasudev Raguram, Victor H. Souza, Vince D. Calhoun, Vittorio Iacovella, Viviana Siless, Vladimir Litvak, Wietske van der Zwaag, William Clarke, William Triplett, Wouter V. Potters, Xiangrui Li, Yaroslav O. Halchenko, Yaël Balbastre, Yoni Ashar, Yuan Wang, Zachary Michael, Zhi-De Deng, ezemikulan, josator2, monkeyman192, patrick-g-h, Étienne Bergeron:
The Brain Imaging Data Structure (BIDS) Specification. Version 1.10.1. Zenodo, 2025 [all versions]
- [i23]Kyriaki-Margarita Bintsi, Yaël Balbastre, Jingjing Wu, Julia F. Lehman, Suzanne N. Haber, Anastasia Yendiki:
Fully Automated Segmentation of Fiber Bundles in Anatomic Tracing Data. CoRR abs/2508.12942 (2025) - 2024
- [c14]Sean I. Young, Yaël Balbastre, Bruce Fischl, Polina Golland, Juan Eugenio Iglesias:
Fully Convolutional Slice-to-Volume Reconstruction for Single-Stack MRI. CVPR 2024: 11535-11545 - [i22]Etienne Chollet, Yaël Balbastre, Caroline Magnain, Bruce Fischl, Hui Wang:
A label-free and data-free training strategy for vasculature segmentation in serial sectioning OCT data. CoRR abs/2405.13757 (2024) - [i21]Etienne Chollet, Yaël Balbastre, Chiara Mauri, Caroline Magnain, Bruce Fischl, Hui Wang:
Neurovascular Segmentation in sOCT with Deep Learning and Synthetic Training Data. CoRR abs/2407.01419 (2024) - [i20]Xiaoling Hu, Oula Puonti, Juan Eugenio Iglesias, Bruce Fischl, Yaël Balbastre:
Learn2Synth: Learning Optimal Data Synthesis Using Hypergradients. CoRR abs/2411.16719 (2024) - 2023
- [j6]Alessa Hering, Lasse Hansen, Tony C. W. Mok, Albert C. S. Chung, Hanna Siebert, Stephanie Häger, Annkristin Lange, Sven Kuckertz, Stefan Heldmann, Wei Shao, Sulaiman Vesal, Mirabela Rusu, Geoffrey A. Sonn, Théo Estienne, Maria Vakalopoulou, Luyi Han, Yunzhi Huang, Pew-Thian Yap, Mikael Brudfors, Yaël Balbastre, Samuel Joutard, Marc Modat, Gal Lifshitz, Dan Raviv, Jinxin Lv, Qiang Li, Vincent Jaouen, Dimitris Visvikis, Constance Fourcade, Mathieu Rubeaux, Wentao Pan, Zhe Xu, Bailiang Jian, Francesca De Benetti, Marek Wodzinski, Niklas Gunnarsson, Jens Sjölund, Daniel Grzech, Huaqi Qiu, Zeju Li, Alexander Thorley, Jinming Duan, Christoph Großbröhmer, Andrew Hoopes, Ingerid Reinertsen, Yiming Xiao, Bennett A. Landman, Yuankai Huo, Keelin Murphy, Nikolas Lessmann, Bram van Ginneken, Adrian V. Dalca, Mattias P. Heinrich:
Learn2Reg: Comprehensive Multi-Task Medical Image Registration Challenge, Dataset and Evaluation in the Era of Deep Learning. IEEE Trans. Medical Imaging 42(3): 697-712 (2023) - [i19]Matthew G. French, Gonzalo D. Maso Talou, Thiranja P. Babarenda Gamage, Martyn P. Nash, Poul M. F. Nielsen, Anthony J. Doyle, Juan Eugenio Iglesias, Yaël Balbastre, Sean I. Young:
Diffeomorphic Multi-Resolution Deep Learning Registration for Applications in Breast MRI. CoRR abs/2309.13777 (2023) - [i18]Sean I. Young, Yaël Balbastre, Bruce Fischl, Polina Golland, Juan Eugenio Iglesias:
Fully Convolutional Slice-to-Volume Reconstruction for Single-Stack MRI. CoRR abs/2312.03102 (2023) - 2022
- [j5]Jiarui Yang, Shuaibin Chang, Ichun Anderson Chen, Sreekanth Kura, Grace A. Rosen, Nicole A. Saltiel, Bertrand R. Huber, Divya Varadarajan, Yaël Balbastre, Caroline Magnain, Shih-Chi Chen, Bruce Fischl, Ann C. McKee, David A. Boas, Hui Wang:
Volumetric Characterization of Microvasculature in Ex Vivo Human Brain Samples By Serial Sectioning Optical Coherence Tomography. IEEE Trans. Biomed. Eng. 69(12): 3645-3656 (2022) - [c13]Mikael Brudfors, Yaël Balbastre, John Ashburner, Geraint Rees, Parashkev Nachev, Sébastien Ourselin, M. Jorge Cardoso:
Fitting Segmentation Networks on Varying Image Resolutions Using Splatting. MIUA 2022: 271-282 - [c12]Sean I. Young, Yaël Balbastre, Adrian V. Dalca, William M. Wells III, Juan Eugenio Iglesias, Bruce Fischl:
SuperWarp: Supervised Learning and Warping on U-Net for Invariant Subvoxel-Precise Registration. WBIR 2022: 103-115 - [i17]Sean I. Young, Yaël Balbastre, Adrian V. Dalca, William M. Wells III, Juan Eugenio Iglesias, Bruce Fischl:
SuperWarp: Supervised Learning and Warping on U-Net for Invariant Subvoxel-Precise Registration. CoRR abs/2205.07399 (2022) - [i16]Mikael Brudfors, Yaël Balbastre, John Ashburner, Geraint Rees, Parashkev Nachev, Sébastien Ourselin, M. Jorge Cardoso:
Fitting Segmentation Networks on Varying Image Resolutions using Splatting. CoRR abs/2206.06445 (2022) - 2021
- [j4]Yaël Balbastre, Mikael Brudfors, Michela Azzarito, Christian Lambert, Martina F. Callaghan, John Ashburner:
Model-based multi-parameter mapping. Medical Image Anal. 73: 102149 (2021) - [j3]Juan Eugenio Iglesias, Benjamin Billot, Yaël Balbastre, Azadeh Tabari, John Conklin, R. Gilberto González, Daniel C. Alexander, Polina Golland, Brian L. Edlow, Bruce Fischl:
Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast. NeuroImage 237: 118206 (2021) - [c11]Mikael Brudfors, Yaël Balbastre, John Ashburner, Geraint Rees, Parashkev Nachev, Sébastien Ourselin, M. Jorge Cardoso:
An MRF-UNet Product of Experts for Image Segmentation. MIDL 2021: 48-59 - [i15]Yaël Balbastre, Mikael Brudfors, Michela Azzarito, Christian Lambert, Martina F. Callaghan, John Ashburner:
Model-based multi-parameter mapping. CoRR abs/2102.01604 (2021) - [i14]Mikael Brudfors, Yaël Balbastre, John Ashburner, Geraint Rees, Parashkev Nachev, Sébastien Ourselin, M. Jorge Cardoso:
An MRF-UNet Product of Experts for Image Segmentation. CoRR abs/2104.05495 (2021) - [i13]Yaël Balbastre, Ali Aghaeifar, Nadège Corbin, Mikael Brudfors, John Ashburner, Martina F. Callaghan:
Correcting inter-scan motion artefacts in quantitative R1 mapping at 7T. CoRR abs/2108.10943 (2021) - [i12]Yu Yan, Yaël Balbastre, Mikael Brudfors, John Ashburner:
Factorisation-based Image Labelling. CoRR abs/2111.10326 (2021) - [i11]Alessa Hering, Lasse Hansen, Tony C. W. Mok, Albert C. S. Chung, Hanna Siebert, Stephanie Häger, Annkristin Lange, Sven Kuckertz, Stefan Heldmann, Wei Shao, Sulaiman Vesal, Mirabela Rusu, Geoffrey A. Sonn, Théo Estienne, Maria Vakalopoulou, Luyi Han, Yunzhi Huang, Mikael Brudfors, Yaël Balbastre, Samuel Joutard, Marc Modat, Gal Lifshitz, Dan Raviv, Jinxin Lv, Qiang Li, Vincent Jaouen, Dimitris Visvikis, Constance Fourcade, Mathieu Rubeaux, Wentao Pan, Zhe Xu, Bailiang Jian, Francesca De Benetti, Marek Wodzinski, Niklas Gunnarsson, Huaqi Qiu, Zeju Li, Christoph Großbröhmer, Andrew Hoopes, Ingerid Reinertsen, Yiming Xiao, Bennett A. Landman, Yuankai Huo, Keelin Murphy, Bram van Ginneken, Adrian V. Dalca, Mattias P. Heinrich:
Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning. CoRR abs/2112.04489 (2021) - 2020
- [c10]Yaël Balbastre, Mikael Brudfors, Michela Azzarito, Christian Lambert, Martina F. Callaghan, John Ashburner:
Joint Total Variation ESTATICS for Robust Multi-parameter Mapping. MICCAI (2) 2020: 53-63 - [c9]Mikael Brudfors, Yaël Balbastre, Guillaume Flandin, Parashkev Nachev, John Ashburner:
Flexible Bayesian Modelling for Nonlinear Image Registration. MICCAI (3) 2020: 253-263 - [c8]Mikael Brudfors, Yaël Balbastre, John Ashburner:
Groupwise Multimodal Image Registration Using Joint Total Variation. MIUA 2020: 184-194 - [i10]Mikael Brudfors, Yaël Balbastre, John Ashburner:
Groupwise Multimodal Image Registration using Joint Total Variation. CoRR abs/2005.02933 (2020) - [i9]Yaël Balbastre, Mikael Brudfors, Michela Azzarito, Christian Lambert, Martina F. Callaghan, John Ashburner:
Joint Total Variation ESTATICS for Robust Multi-Parameter Mapping. CoRR abs/2005.14247 (2020) - [i8]Mikael Brudfors, Yaël Balbastre, Guillaume Flandin, Parashkev Nachev, John Ashburner:
Flexible Bayesian Modelling for Nonlinear Image Registration. CoRR abs/2006.02338 (2020) - [i7]Juan Eugenio Iglesias, Benjamin Billot, Yaël Balbastre, Azadeh Tabari, John Conklin, Daniel C. Alexander, Polina Golland, Brian L. Edlow, Bruce Fischl:
Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast. CoRR abs/2012.13340 (2020)
2010 – 2019
- 2019
- [j2]John Ashburner, Mikael Brudfors, Kevin Bronik, Yaël Balbastre:
An algorithm for learning shape and appearance models without annotations. Medical Image Anal. 55: 197-215 (2019) - [c7]Mikael Brudfors, Yaël Balbastre, John Ashburner:
Nonlinear Markov Random Fields Learned via Backpropagation. IPMI 2019: 805-817 - [c6]Mikael Brudfors, John Ashburner, Parashkev Nachev, Yaël Balbastre:
Empirical Bayesian Mixture Models for Medical Image Translation. SASHIMI@MICCAI 2019: 1-12 - [i6]Mikael Brudfors, Yaël Balbastre, John Ashburner:
Nonlinear Markov Random Fields Learned via Backpropagation. CoRR abs/1902.10747 (2019) - [i5]Mikael Brudfors, John Ashburner, Parashkev Nachev, Yaël Balbastre:
Empirical Bayesian Mixture Models for Medical Image Translation. CoRR abs/1908.05926 (2019) - [i4]Mikael Brudfors, Yaël Balbastre, Parashkev Nachev, John Ashburner:
A Tool for Super-Resolving Multimodal Clinical MRI. CoRR abs/1909.01140 (2019) - 2018
- [c5]Yaël Balbastre, Mikael Brudfors, Kevin Bronik, John Ashburner:
Diffeomorphic Brain Shape Modelling Using Gauss-Newton Optimisation. MICCAI (1) 2018: 862-870 - [c4]Mikael Brudfors, Yaël Balbastre, Parashkev Nachev, John Ashburner:
MRI Super-Resolution Using Multi-channel Total Variation. MIUA 2018: 217-228 - [i3]Yaël Balbastre, Mikael Brudfors, Kevin Bronik, John Ashburner:
Diffeomorphic brain shape modelling using Gauss-Newton optimisation. CoRR abs/1806.07109 (2018) - [i2]John Ashburner, Mikael Brudfors, Kevin Bronik, Yaël Balbastre:
An Algorithm for Learning Shape and Appearance Models without Annotations. CoRR abs/1807.10731 (2018) - [i1]Mikael Brudfors, Yaël Balbastre, Parashkev Nachev, John Ashburner:
MRI Super-Resolution using Multi-Channel Total Variation. CoRR abs/1810.03422 (2018) - 2017
- [j1]Yaël Balbastre, Denis Rivière, Nicolas Souedet, Clara Fischer, Anne-Sophie Hérard, Susannah Williams, Michel E. Vandenberghe, Julien Flament, Romina Aron-Badin, Philippe Hantraye, Jean-François Mangin, Thierry Delzescaux:
Primatologist: A modular segmentation pipeline for macaque brain morphometry. NeuroImage 162: 306-321 (2017) - 2016
- [b1]Yaël Balbastre:
Développement et validation d'outils pour l'analyse morphologique du cerveau de Macaque. (Morphometry Analysis Tools for the Macaque Brain : Development and Validation). University of Paris-Saclay, France, 2016 - [c3]Zhenzhen You, Michel E. Vandenberghe, Yaël Balbastre, Nicolas Souedet, Philippe Hantraye, Caroline Jan, Anne-Sophie Hérard, Thierry Delzescaux:
Automated cell individualization and counting in cerebral microscopic images. ICIP 2016: 3389-3393 - 2015
- [c2]Michel E. Vandenberghe, Yaël Balbastre, Nicolas Souedet, Anne-Sophie Hérard, Marc Dhenain, Frédérique Frouin, Thierry Delzescaux:
Robust supervised segmentation of neuropathology whole-slide microscopy images. EMBC 2015: 3851-3854 - [c1]Yaël Balbastre, Michel E. Vandenberghe, Anne-Sophie Hérard, Pauline Gipchtein, Caroline Jan, Anselme L. Perrier, Philippe Hantraye, Romina Aron-Badin, Jean-François Mangin, Thierry Delzescaux:
A Quantitative Approach to Characterize MR Contrasts with Histology. Brainles@MICCAI 2015: 104-115
Coauthor Index
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