PSACNN: Pulse sequence adaptive fast whole brain segmentation. - Amod Jog; Andrew Hoopes; Douglas N. Greve; Koen Van Leemput; Bruce Fischl (NeuroImage, 2019)

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 (MLCN/RNO-AI@MICCAI, 2020)

HyperMorph: Amortized Hyperparameter Learning for Image Registration. - Andrew Hoopes; Malte Hoffmann; Bruce Fischl; John V. Guttag; Adrian V. Dalca (IPMI, 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 008; Sulaiman Vesal; Mirabela Rusu; et al. (CoRR, 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)

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)

TopoFit: Rapid Reconstruction of Topologically-Correct Cortical Surfaces. - Andrew Hoopes; Juan Eugenio Iglesias; Bruce Fischl; Douglas N. Greve; Adrian V. Dalca (MIDL, 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)

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)

SynthStrip: skull-stripping for any brain image. - Andrew Hoopes; Jocelyn S. Mora; Adrian V. Dalca; Bruce Fischl; Malte Hoffmann (NeuroImage, 2022)

Anatomy-specific acquisition-agnostic affine registration learned from fictitious images. - Malte Hoffmann; Andrew Hoopes; Bruce Fischl; Adrian V. Dalca (Image Processing, 2023)

Anatomy-aware and acquisition-agnostic joint registration with SynthMorph. - Malte Hoffmann; Andrew Hoopes; Douglas N. Greve; Bruce Fischl; Adrian V. Dalca (CoRR, 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 008; Sulaiman Vesal; Mirabela Rusu; et al. (IEEE Trans. Medical Imaging, 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; et al. (Zenodo, 2023)

VoxelPrompt: A Vision-Language Agent for Grounded Medical Image Analysis. - Andrew Hoopes; Victor Ion Butoi; John V. Guttag; Adrian V. Dalca (CoRR, 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; et al. (Zenodo, 2024)

MultiMorph: On-demand Atlas Construction. - S. Mazdak Abulnaga; Andrew Hoopes; Neel Dey; Malte Hoffmann; Bruce Fischl; John V. Guttag; Adrian V. Dalca (CVPR, 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, 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 001; Axel Thielscher; Juan Eugenio Iglesias; Oula Puonti (CoRR, 2025)