Andrew Hoopes

According to our database, Andrew Hoopes authored at least 19 papers between 2019 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2025

End-to-end Cortical Surface Reconstruction from Clinical Magnetic Resonance Images.

Jesper Duemose Nielsen, Karthik Gopinath, Andrew Hoopes, Adrian V. Dalca, Colin G. Magdamo, Steven E. Arnold, Sudeshna Das, Axel Thielscher, Juan Eugenio Iglesias, Oula Puonti

CoRR, May, 2025

MultiMorph: On-demand Atlas Construction.

S. Mazdak Abulnaga, Andrew Hoopes, Neel Dey, Malte Hoffmann, Marianne Rakic, Bruce Fischl, John V. Guttag, Adrian V. Dalca

CoRR, April, 2025

MultiMorph: On-demand Atlas Construction.

S. Mazdak Abulnaga, Andrew Hoopes, Neel Dey, Malte Hoffmann, Bruce Fischl, John V. Guttag, Adrian V. Dalca

Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2025

2024

The Brain Imaging Data Structure (BIDS) Specification.

Aaron Oliver-Taylor, Adam Li, Adam G. Thomas, Adeen Flinker, Adina S. Wagner, Agah Karakuzu, Aki Nikolaidis, Alberto Lazari, Alejandro de la Vega, Alessio Giacomel, Alexander Rockhill, Alexander Jones, Alexander Li Cohen, Alexander von Lautz, Alexandre Gramfort, Alexandre Hutton, Alexandre Routier, Alexandru Foias, Ali R. Khan, Alizee Wickenheiser, Ana Fouto, Anders Eklund, Andrea Pigorini, Andrew Hoopes, Andrew Jahn, Andrew Janke, Anibal Sólon, Anthony Galassi, Arianna Sala, Ariel Rokem, Arjen Stolk, Arnaud Delorme, Arnaud Marcoux, Arshitha Basavaraj, Ashley G. Gillman, Athanasia Monika Mowinckel, Aysegul Gunduz, Azeez Adebimpe, B. Nolan Nichols, Balint Kincses, Benjamin Beasley, Benjamin K. Dichter, Benjamin Gagl, Bertrand Thirion, Bradley Voytek, Brett L. Foster, Brian A. Wandell, Brian N. Lundstrom, Camille Maumet, Carlo Miniussi, Cecile Madjar, Chloé Pasturel, Chris Benjamin, Chris Gahnström, Chris Holdgraf, Chris Gorgolewski, Chris Rorden, Christian Büchel, Christian Horea, Christine Rogers, Christophe Phillips, Christopher J. Honey, Christopher J. Markiewicz, Christopher Lee-Messer, Clara Moreau, Clint Hansen, Cyril R. Pernet, Cyrus Eierud, D. Sturgeon, Dan Levitas, Dan Lurie, Daniel A. Handwerker, David C. Alsop, David A. Boas, David M. Groppe, David B. Keator, David McAlpine, David Thomas, Dejan Draschkow, Dianne K. Patterson, Dimitri Papadopoulos Orfanos, Dmitry Petrov, Dora Hermes, Dorien Huijser, Douglas N. Greve, Duncan Macleod, Dung Truong, 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, Felipe Orihuela-Espina, Fidel Alfaro-Almagro, Filip Szczepankiewicz, Filippo Maria Castelli, Franco Pestilli, Franklin W. Feingold, François Tadel, Gaia Rizzo, Gang Chen, Gaël Varoquaux, Ghislain Vaillant, Giacomo Bertazzoli, Giacomo Guidali, Giacomo Mazzamuto, Gilles de Hollander, Gio Piantoni, Gitte M. Knudsen, Giulio Castegnaro, Giuseppe Gallitto, Graham Searle, Granville J. Matheson, Gregory Kiar, Gregory Noack, Greydon Gilmore, Guillaume Flandin, 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, Isla Staden, Jaap von der Aar, Jakub Kaczmarzyk, James Gholam, James D. Kent, Jan-Mathijs Schoffelen, Jan Petr, Jean-Baptiste Poline, 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 Guiomar Niso Galán, Julia Sprenger, Julien Cohen-Adad, Julius Welzel, 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, Manjari Narayan, Manuel R. Mercier, Maqsood Yaqub, Marc Lalancette, Marco Castellaro, 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, Matt Sanderson, Matteo Tonietto, Matthias Günther, Matthias van Osch, Maureen J. Shader, Maurice Pasternak, Max A. van den Boom, Melanie Ganz-Benjaminsen, Michael Chappell, Michael Hanke, Michael P. Harms, Michael P. Milham, Michael P. Notter, Michael Schirner, Mikaël Naveau, Nader Pouratian, Natalia Petridou, National Institute of Mental Health, Nell Hardcastle, Nicholas Traut, Nick F. Ramsey, Nicole C. Swann, 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, R. Cameron Craddock, Rémi Gau, Richard Höchenberger, Richard N. Henson, Robert B. Innis, Robert E. Smith, Robert Knight, Robert Luke, Robert Oostenveld, Roberto Toro, Rohan Goyal, Ross W. Blair, Russell A. Poldrack, Rémi Adon, Samir Das, Samuel Garcia, Samuel Guay, Samuel A. Nastase, Sara Elgayar, Sasha D'Ambrosio, Satrajit S. Ghosh, Scott Makeig, Sein Jeung, Shashank Bansal, Sjoerd B. Vos, Soichi Hayashi, Stefan Appelhoff, 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 Salo, Teon L. Brooks, Thomas E. Nichols, Thomas Funck, Thomas Kirk, Thomas W. Okell, Tibor Auer, Timo Dickscheid, Timotheus Berg, Tobey Betthauser, Tobias Bengfort, Tom Hampshire, Tor Wager, Travis Riddle, Tristan Glatard, Tyler Collins, Ulrike Bingel, Vanessa Sochat, Vasudev Raguram, 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, Yoni Ashar, Yuan Wang, Zachary Michael, ezemikulan, josator2, monkeyman192, Étienne Bergeron

Dataset, September, 2024

VoxelPrompt: A Vision-Language Agent for Grounded Medical Image Analysis.

Andrew Hoopes, Victor Ion Butoi, John V. Guttag, Adrian V. Dalca

CoRR, 2024

2023

bids-specification.

Aaron Oliver-Taylor, Adam Li, Adam G. Thomas, Adeen Flinker, Adina S. Wagner, Agah Karakuzu, Aki Nikolaidis, Alberto Lazari, Alejandro de la Vega, Alessio Giacomel, Alexander Rockhill, Alexander Jones, Alexander Li Cohen, Alexander von Lautz, Alexandre Gramfort, Alexandre Hutton, Alexandre Routier, Alexandru Foias, Ali R. Khan, Alizee Wickenheiser, Ana Fouto, Anders Eklund, Andrea Pigorini, Andrew Hoopes, Andrew Jahn, Andrew Janke, Anibal Sólon, Anthony Galassi, Ariel Rokem, Arjen Stolk, Arnaud Delorme, Arnaud Marcoux, Arshitha Basavaraj, Ashley G. Gillman, Athanasia M. Mowinckel, Aysegul Gunduz, Azeez Adebimpe, B. Nolan Nichols, Balint Kincses, Benjamin Beasley, Benjamin K. Dichter, Benjamin Gagl, Bertrand Thirion, Bradley Voytek, Brett L. Foster, Brian A. Wandell, Brian N. Lundstrom, Camille Maumet, Carlo Miniussi, Cecile Madjar, Chloé Pasturel, Chris Benjamin, Chris Gahnström, Chris Holdgraf, Chris Gorgolewski, Chris Rorden, Christian Büchel, Christian Horea, Christine Rogers, Christophe Phillips, Christopher J. Honey, Christopher J. Markiewicz, Christopher Lee-Messer, Clara Moreau, Clint Hansen, Cyril R. Pernet, Cyrus Eierud, D. Sturgeon, Dan Levitas, Dan Lurie, Daniel A. Handwerker, David C. Alsop, David A. Boas, David M. Groppe, David B. Keator, David McAlpine, David Thomas, Dejan Draschkow, Dianne K. Patterson, Dimitri Papadopoulos Orfanos, Dmitry Petrov, Dora Hermes, Dorien Huijser, Douglas N. Greve, Duncan Macleod, Dung Truong, 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, Felipe Orihuela-Espina, Fidel Alfaro-Almagro, Filip Szczepankiewicz, Filippo Maria Castelli, Franco Pestilli, Franklin W. Feingold, François Tadel, Gaia Rizzo, Gang Chen, Gaël Varoquaux, Ghislain Vaillant, Giacomo Bertazzoli, Giacomo Guidali, Giacomo Mazzamuto, Gilles de Hollander, Gio Piantoni, Gitte M. Knudsen, Giulio Castegnaro, Giuseppe Gallitto, Graham Searle, Granville J. Matheson, Gregory Kiar, Gregory Noack, Greydon Gilmore, Guillaume Flandin, 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, Isla Staden, Jaap von der Aar, Jakub Kaczmarzyk, James Gholam, James D. Kent, Jan-Mathijs Schoffelen, Jan Petr, Jean-Baptiste Poline, 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, J. Guiomar Niso, Julia Sprenger, Julien Cohen-Adad, Julius Welzel, 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, Manjari Narayan, Manuel R. Mercier, Maqsood Yaqub, Marc Lalancette, Marco Castellaro, 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, Matt Sanderson, Matteo Tonietto, Matthias Günther, Matthias van Osch, Maureen J. Shader, Maurice Pasternak, Max A. van den Boom, Melanie Ganz-Benjaminsen, Michael Chappell, Michael Hanke, Michael P. Harms, Michael P. Milham, Michael P. Notter, Michael Schirner, Mikaël Naveau, Nader Pouratian, Natalia Petridou, National Institute of Mental Health, Nell Hardcastle, Nicholas Traut, Nick F. Ramsey, Nicole C. Swann, 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, R. Cameron Craddock, Rémi Gau, Richard Höchenberger, Richard N. Henson, Robert B. Innis, Robert E. Smith, Robert Knight, Robert Luke, Robert Oostenveld, Roberto Toro, Rohan Goyal, Ross W. Blair, Russell A. Poldrack, Rémi Adon, Samir Das, Samuel Garcia, Samuel A. Nastase, Sara Elgayar, Sasha D'Ambrosio, Satrajit S. Ghosh, Scott Makeig, Sein Jeung, Shashank Bansal, Sjoerd B. Vos, Soichi Hayashi, Stefan Appelhoff, 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 Salo, Teon L. Brooks, Thomas E. Nichols, Thomas Funck, Thomas Kirk, Thomas W. Okell, Tibor Auer, Timo Dickscheid, Timotheus Berg, Tobey Betthauser, Tobias Bengfort, Tom Hampshire, Tor Wager, Travis Riddle, Tristan Glatard, Tyler Collins, Ulrike Bingel, Vanessa V. Sochat, Vasudev Raguram, Vince D. Calhoun, Vittorio Iacovella, Vladimir Litvak, Wietske van der Zwaag, William Clarke, William Triplett, Wouter V. Potters, Xiangrui Li, Yaroslav O. Halchenko, Yoni Ashar, Yuan Wang, Zachary Michael, ezemikulan, josator2, monkeyman192, Étienne Bergeron

Dataset, November, 2023

Learn2Reg: Comprehensive Multi-Task Medical Image Registration Challenge, Dataset and Evaluation in the Era of Deep Learning.

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

IEEE Trans. Medical Imaging, March, 2023

Anatomy-aware and acquisition-agnostic joint registration with SynthMorph.

Malte Hoffmann, Andrew Hoopes, Douglas N. Greve, Bruce Fischl, Adrian V. Dalca

CoRR, 2023

Anatomy-specific acquisition-agnostic affine registration learned from fictitious images.

Malte Hoffmann, Andrew Hoopes, Bruce Fischl, Adrian V. Dalca

Proceedings of the Medical Imaging 2023: Image Processing, 2023

2022

SynthStrip: skull-stripping for any brain image.

Andrew Hoopes, Jocelyn S. Mora, Adrian V. Dalca, Bruce Fischl, Malte Hoffmann

NeuroImage, 2022

An Open-Source Tool for Longitudinal Whole-Brain and White Matter Lesion Segmentation.

Stefano Cerri, Douglas N. Greve, Andrew Hoopes, Henrik Lundell, Hartwig R. Siebner, Mark Mühlau, Koen Van Leemput

CoRR, 2022

Learning the Effect of Registration Hyperparameters with HyperMorph.

Andrew Hoopes, Malte Hoffmann, Douglas N. Greve, Bruce Fischl, John V. Guttag, Adrian V. Dalca

CoRR, 2022

TopoFit: Rapid Reconstruction of Topologically-Correct Cortical Surfaces.

Andrew Hoopes, Juan Eugenio Iglesias, Bruce Fischl, Douglas N. Greve, Adrian V. Dalca

Proceedings of the International Conference on Medical Imaging with Deep Learning, 2022

2021

A deep learning toolbox for automatic segmentation of subcortical limbic structures from MRI images.

Douglas N. Greve, Benjamin Billot, Devani Cordero, Andrew Hoopes, Malte Hoffmann, Adrian V. Dalca, Bruce Fischl, Juan Eugenio Iglesias, Jean C. Augustinack

NeuroImage, 2021

Hypernet-Ensemble Learning of Segmentation Probability for Medical Image Segmentation with Ambiguous Labels.

Sungmin Hong, Anna K. Bonkhoff, Andrew Hoopes, Martin Bretzner, Markus D. Schirmer, Anne-Katrin Giese, Adrian V. Dalca, Polina Golland, Natalia S. Rost

CoRR, 2021

Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning.

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

CoRR, 2021

HyperMorph: Amortized Hyperparameter Learning for Image Registration.

Andrew Hoopes, Malte Hoffmann, Bruce Fischl, John V. Guttag, Adrian V. Dalca

Proceedings of the Information Processing in Medical Imaging, 2021

2020

A Longitudinal Method for Simultaneous Whole-Brain and Lesion Segmentation in Multiple Sclerosis.

Stefano Cerri, Andrew Hoopes, Douglas N. Greve, Mark Mühlau, Koen Van Leemput

Proceedings of the Machine Learning in Clinical Neuroimaging and Radiogenomics in Neuro-oncology, 2020

2019

PSACNN: Pulse sequence adaptive fast whole brain segmentation.

Amod Jog, Andrew Hoopes, Douglas N. Greve, Koen Van Leemput, Bruce Fischl

NeuroImage, 2019