Andrew Hoopes
PhD Student, Computer Science & Artificial Intelligence Lab, EECS, MIT
Martinos Center for Biomedical Imaging, Massachusetts General Hospital
Publications
Automated EEG Classification to Track Levels of Consciousness (paper)
William H. Curley*, Andrew Hoopes*, David W. Zhou, Mary M. Conte, Jonathan D. Victor, Nicholas D. Schiff, Brian L. Edlow
medRxiv preprint. 2026.
Unified Brain Surface and Volume Registration (paper)
S. Mazdak Abulnaga, Andrew Hoopes, Malte Hoffmann, Robin Magnet, Maks Ovsjanikov, Lilla Zöllei, John Guttag, Bruce Fischl, Adrian Dalca
In proceedings of ICLR: International Conference on Learning Representations. 2026.
AtlasMorph: Learning Conditional Deformable Templates for Brain MRI (paper)
Marianne Rakic, Andrew Hoopes, S. Mazdak Abulnaga, Mert R. Sabuncu, John V. Guttag, Adrian V. Dalca
Medical Image Analysis 110, 103893. 2026.
MultiMorph: On-Demand Atlas Construction (paper, code)
S. Mazdak Abulnaga, Andrew Hoopes, Neel Dey, Malte Hoffmann, Marianne Rakic, Bruce Fischl, John Guttag, Adrian Dalca
In proceedings of CVPR: IEEE Conference on Computer Vision and Pattern Recognition. 2025.
VoxelPrompt: A Vision Agent for End-to-End Medical Image Analysis (paper)
Andrew Hoopes, Neel Dey, Victor Ion Butoi, John V. Guttag, Adrian V. Dalca
arXiv preprint arXiv:2410.08397. 2024.
Anatomy-Aware and Acquisition-Agnostic Joint Registration with SynthMorph (paper, website)
Malte Hoffmann, Andrew Hoopes, Douglas N. Greve, Bruce Fischl, Adrian V. Dalca
Imaging Neuroscience 2, 1-33. 2024.
Synthetic Data in Generalizable, Learning-Based Neuroimaging (paper)
Karthik Gopinath*, Andrew Hoopes*, et al.
Imaging Neuroscience 2. 2024.
An Open-Source Tool for Longitudinal Whole-Brain and White Matter Lesion Segmentation (paper, code)
Stefano Cerri, Douglas N. Greve, Andrew Hoopes, Henrik Lundell, Hartwig R. Siebner, Mark Mühlau, Koen Van Leemput
NeuroImage: Clinical 38, 103354. 2023.
Anatomy-Specific Acquisition-Agnostic Affine Registration Learned from Fictitious Images (paper, website)
Malte Hoffmann, Andrew Hoopes, Bruce Fischl, Adrian V. Dalca
In proceedings of SPIE Medical Imaging: Image Processing, 12464, 1246402. 2023.
SynthStrip: Skull-Stripping for Any Brain Image (paper, website)
Andrew Hoopes, Jocelyn S. Mora, Adrian V. Dalca, Bruce Fischl*, Malte Hoffmann*
NeuroImage 260, 119474. 2022.
Learning the Effect of Registration Hyperparameters with HyperMorph (paper, website, code)
Andrew Hoopes, Malte Hoffmann, Douglas Greve, John Guttag, Bruce Fischl, Adrian Dalca
MELBA: Journal of Machine Learning for Biomedical Imaging. 2022.
TopoFit: Rapid Reconstruction of Topologically-Correct Cortical Surfaces (paper, code)
Andrew Hoopes, Juan Eugenio Iglesias, Bruce Fischl, Douglas Greve*, Adrian Dalca*
In proceedings of MIDL: Medical Imaging with Deep Learning. 2022.
Hypermorph: Amortized Hyperparameter Learning for Image Registration (paper, website, code)
Andrew Hoopes, Malte Hoffmann, Bruce Fischl, John Guttag, and Adrian Dalca
In proceedings of IPMI: International Conference on Information Processing and Medical Imaging, 12729, pp. 3-17. 2021.
A Deep Learning Toolbox for Automatic Segmentation of Subcortical Limbic Structures from MRI Images (paper, code)
Douglas Greve, Benjamin Billot, Devani Cordero, Andrew Hoopes, Malte Hoffmann, Adrian Dalca, Bruce Fischl, Juan Eugenio Iglesias, Jean Augustinack
NeuroImage 244, 118610. 2021.
A Longitudinal Method for Simultaneous Whole-Brain and Lesion Segmentation in Multiple Sclerosis (paper)
Stefano Cerri, Andrew Hoopes, Douglas Greve, Mark Mühlau, Koen Van Leemput
Machine Learning in Clinical Neuroimaging and Radiogenomics in Neuro-oncology, pp. 119-128. 2020.