A Family of Principal Component Analyses for Dealing with Outliers. - Juan Eugenio Iglesias; Marleen de Bruijne; Marco Loog; François Lauze; Mads Nielsen (MICCAI (2), 2007)

Tracking medication information across medical records. - Juan Eugenio Iglesias; Krupa Rocks; Neda Jahanshad; Enrique Frías-Martínez; Lewellyn P. Andrada; Alex A. T. Bui (AMIA, 2009)

Robust Initial Detection of Landmarks in Film-Screen Mammograms Using Multiple FFDM Atlases. - Juan Eugenio Iglesias; Nico Karssemeijer (IEEE Trans. Medical Imaging, 2009)

Discretizing stochastic tractography: a fast implementation. - Juan Eugenio Iglesias; Paul M. Thompson; Cheng-Yi Liu; Zhuowen Tu (ISBI, 2010)

Fusing adaptive atlas and informative features for robust 3D brain image segmentation. - Cheng-Yi Liu; Juan Eugenio Iglesias; Arthur W. Toga; Zhuowen Tu (ISBI, 2010)

Synthetic MRI Signal Standardization: Application to Multi-atlas Analysis. - Juan Eugenio Iglesias; Ivo D. Dinov; Jaskaran Singh; Gregory Tong; Zhuowen Tu (MICCAI (3), 2010)

Agreement-Based Semi-supervised Learning for Skull Stripping. - Juan Eugenio Iglesias; Cheng-Yi Liu; Paul M. Thompson; Zhuowen Tu (MICCAI (3), 2010)

Combining Generative and Discriminative Models for Semantic Segmentation of CT Scans via Active Learning. - Juan Eugenio Iglesias; Ender Konukoglu; Albert Montillo; Zhuowen Tu; Antonio Criminisi (IPMI, 2011)

Entangled Decision Forests and Their Application for Semantic Segmentation of CT Images. - Albert Montillo; Jamie Shotton; John M. Winn; Juan Eugenio Iglesias; Dimitris N. Metaxas; Antonio Criminisi (IPMI, 2011)

Classification of Alzheimer's Disease Using a Self-Smoothing Operator. - Juan Eugenio Iglesias; Jiayan Jiang; Cheng-Yi Liu; Zhuowen Tu (MICCAI (3), 2011)

Robust Skull Stripping of Clinical Glioblastoma Multiforme Data. - William Speier; Juan Eugenio Iglesias; Leila El-Kara; Zhuowen Tu; Corey W. Arnold (MICCAI (3), 2011)

Robust Brain Extraction Across Datasets and Comparison With Publicly Available Methods. - Juan Eugenio Iglesias; Cheng-Yi Liu; Paul M. Thompson; Zhuowen Tu (IEEE Trans. Medical Imaging, 2011)

A generative model for multi-atlas segmentation across modalities. - Juan Eugenio Iglesias; Mert R. Sabuncu; Koen Van Leemput (ISBI, 2012)

A Generative Model for Probabilistic Label Fusion of Multimodal Data. - Juan Eugenio Iglesias; Mert R. Sabuncu; Koen Van Leemput (MBIA, 2012)

Incorporating Parameter Uncertainty in Bayesian Segmentation Models: Application to Hippocampal Subfield Volumetry. - Juan Eugenio Iglesias; Mert R. Sabuncu; Koen Van Leemput (MICCAI (3), 2012)

Pictorial multi-atlas segmentation of brain MRI. - Cheng-Yi Liu; Juan Eugenio Iglesias; Zhuowen Tu (MMBIA, 2012)

Fast Approximate Stochastic Tractography. - Juan Eugenio Iglesias; Paul M. Thompson; Cheng-Yi Liu; Zhuowen Tu (Neuroinformatics, 2012)

Is Synthesizing MRI Contrast Useful for Inter-modality Analysis? - Juan Eugenio Iglesias; Ender Konukoglu; Darko Zikic; Ben Glocker; Koen Van Leemput; Bruce Fischl (MICCAI (1), 2013)

A Probabilistic, Non-parametric Framework for Inter-modality Label Fusion. - Juan Eugenio Iglesias; Mert R. Sabuncu; Koen Van Leemput (MICCAI (3), 2013)

Fast, Sequence Adaptive Parcellation of Brain MR Using Parametric Models. - Oula Puonti; Juan Eugenio Iglesias; Koen Van Leemput (MICCAI (1), 2013)

Improved inference in Bayesian segmentation using Monte Carlo sampling: Application to hippocampal subfield volumetry. - Juan Eugenio Iglesias; Mert R. Sabuncu; Koen Van Leemput (Medical Image Anal., 2013)

A unified framework for cross-modality multi-atlas segmentation of brain MRI. - Juan Eugenio Iglesias; Mert Rory Sabuncu; Koen Van Leemput (Medical Image Anal., 2013)

Deformable Templates Guided Discriminative Models for Robust 3D Brain MRI Segmentation. - Cheng-Yi Liu; Juan Eugenio Iglesias; Zhuowen Tu (Neuroinformatics, 2013)

N3 Bias Field Correction Explained as a Bayesian Modeling Method. - Christian Thode Larsen; Juan Eugenio Iglesias; Koen Van Leemput (BAMBI, 2014)

Mid-Space-Independent Symmetric Data Term for Pairwise Deformable Image Registration. - Iman Aganj; Juan Eugenio Iglesias; Martin Reuter 001; Mert R. Sabuncu; Bruce Fischl (MICCAI (2), 2015)

Multi-atlas segmentation of biomedical images: A survey. - Juan Eugenio Iglesias; Mert R. Sabuncu (Medical Image Anal., 2015)

A computational atlas of the hippocampal formation using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation of in vivo MRI. - Juan Eugenio Iglesias; Jean C. Augustinack; Khoa Nguyen; Christopher M. Player; Allison Player; Michelle Wright; Nicole Roy; Matthew P. Frosch; Ann C. McKee; Lawrence L. Wald; Bruce Fischl; Koen Van Leemput (NeuroImage, 2015)

Bayesian segmentation of brainstem structures in MRI. - Juan Eugenio Iglesias; Koen Van Leemput; Priyanka Bhatt; Christen Casillas; Shubir Dutt; Norbert Schuff; Diana Truran-Sacrey; Adam L. Boxer; Bruce Fischl (NeuroImage, 2015)

An algorithm for optimal fusion of atlases with different labeling protocols. - Juan Eugenio Iglesias; Mert Rory Sabuncu; Iman Aganj; Priyanka Bhatt; Christen Casillas; David H. Salat; Adam L. Boxer; Bruce Fischl; Koen Van Leemput (NeuroImage, 2015)

Quantitative comparison of 21 protocols for labeling hippocampal subfields and parahippocampal subregions in in vivo MRI: Towards a harmonized segmentation protocol. - Paul A. Yushkevich; Robert S. C. Amaral; Jean C. Augustinack; Andrew R. Bender; Jeffrey D. Bernstein; Marina Boccardi; Martina Bocchetta; Alison C. Burggren; Valerie A. Carr; M. Mallar Chakravarty; Gaël Chételat; Ana M. Daugherty; et al. (NeuroImage, 2015)

Simultaneous Bayesian correction of slab boundary artifacts and bias field for high resolution ex vivo MRI. - Juan Eugenio Iglesias; Pedro M. Paz-Alonso; Garikoitz Lerma-Usabiaga; Ricardo Insausti; Karla L. Miller; César Caballero-Gaudes (ISBI, 2016)

Correction of Fat-Water Swaps in Dixon MRI. - Ben Glocker; Ender Konukoglu; Ioannis Lavdas; Juan Eugenio Iglesias; Eric O. Aboagye; Andrea G. Rockall; Daniel Rueckert (MICCAI (3), 2016)

Bayesian longitudinal segmentation of hippocampal substructures in brain MRI using subject-specific atlases. - Juan Eugenio Iglesias; Koen Van Leemput; Jean Augustinack; Ricardo Insausti; Bruce Fischl; Martin Reuter 001 (NeuroImage, 2016)

Fast and sequence-adaptive whole-brain segmentation using parametric Bayesian modeling. - Oula Puonti; Juan Eugenio Iglesias; Koen Van Leemput (NeuroImage, 2016)

Heritability and reliability of automatically segmented human hippocampal formation subregions. - Christopher D. Whelan; Derrek P. Hibar; Laura S. van Velzen; Anthony S. Zannas; Tania Carrillo-Roa; Katie McMahon; Gautam Prasad; Sinead Kelly; Joshua Faskowitz; Greig I. de Zubicaray; Juan Eugenio Iglesias; Theo G. M. van Erp; et al. (NeuroImage, 2016)

Part-to-Whole Registration of Histology and MRI Using Shape Elements. - Jonas Pichat; Juan Eugenio Iglesias; Sotiris Nousias; Tarek A. Yousry (ICCV Workshops, 2017)

Globally Optimal Coupled Surfaces for Semi-automatic Segmentation of Medical Images. - Juan Eugenio Iglesias (IPMI, 2017)

Template-Free Estimation of Intracranial Volume: A Preterm Birth Animal Model Study. - Juan Eugenio Iglesias; Sebastiano Ferraris; Marc Modat; Willy Gsell; Jan Deprest; Johannes L. van der Merwe; Tom Vercauteren (FIFI/OMIA@MICCAI, 2017)

Retrospective Head Motion Estimation in Structural Brain MRI with 3D CNNs. - Juan Eugenio Iglesias; Garikoitz Lerma-Usabiaga; Luis C. García-Peraza-Herrera; Sara Martinez; Pedro M. Paz-Alonso (MICCAI (2), 2017)

Part-to-whole Registration of Histology and MRI using Shape Elements. - Jonas Pichat; Juan Eugenio Iglesias; Sotiris Nousias; Tarek A. Yousry; Sébastien Ourselin; Marc Modat (CoRR, 2017)

Mid-space-independent deformable image registration. - Iman Aganj; Juan Eugenio Iglesias; Martin Reuter 001; Mert Rory Sabuncu; Bruce Fischl (NeuroImage, 2017)

High-resolution magnetic resonance imaging reveals nuclei of the human amygdala: manual segmentation to automatic atlas. - Zeynep M. Saygin; Dorit Kliemann; Juan Eugenio Iglesias; André J. W. van der Kouwe; Ellen Boyd; Martin Reuter 001; Allison Stevens; Koenraad Van Leemput; Alexis McKee; Matthew P. Frosch; Bruce Fischl; Jean C. Augustinack (NeuroImage, 2017)

A Probabilistic Model Combining Deep Learning and Multi-atlas Segmentation for Semi-automated Labelling of Histology. - Alessia Atzeni; Marnix Jansen; Sébastien Ourselin; Juan Eugenio Iglesias (MICCAI (2), 2018)

Model-Based Refinement of Nonlinear Registrations in 3D Histology Reconstruction. - Juan Eugenio Iglesias; Marco Lorenzi; Sebastiano Ferraris; Loïc Peter; Marc Modat; Allison Stevens; Bruce Fischl; Tom Vercauteren (MICCAI (2), 2018)

Large-Scale Mammography CAD with Deformable Conv-Nets. - Stephen Morrell; Zbigniew Wojna; Can Son Khoo; Sébastien Ourselin; Juan Eugenio Iglesias (RAMBO+BIA+TIA@MICCAI, 2018)

Technical note: probabilistic visual and electromagnetic data fusion for robust drift-free sequential mosaicking. Application to fetoscopy. - Marcel Tella-Amo; Loïc Peter; Dzhoshkun I. Shakir; Jan Deprest; Danail Stoyanov; Juan Eugenio Iglesias; Tom Vercauteren; Sébastien Ourselin (Image-Guided Procedures, 2018)

A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. - Juan Eugenio Iglesias; Ricardo Insausti; Garikoitz Lerma-Usabiaga; Martina Bocchetta; Koen Van Leemput; Douglas N. Greve; André J. W. van der Kouwe; Bruce Fischl; César Caballero-Gaudes; Pedro M. Paz-Alonso (CoRR, 2018)

A Statistically Representative Atlas for Mapping Neuronal Circuits in the Drosophila Adult Brain. - Ignacio Arganda-Carreras; Tudor Manoliu; Nicolas Mazuras; Florian Schulze; Juan Eugenio Iglesias; Katja Bühler; Arnim Jenett; François Rouyer; Philippe Andrey (Frontiers Neuroinformatics, 2018)

Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections. - Juan Eugenio Iglesias; Marc Modat; Loïc Peter; Allison Stevens; Roberto Annunziata; Tom Vercauteren; Ed S. Lein; Bruce Fischl; Sébastien Ourselin (Medical Image Anal., 2018)

A Survey of Methods for 3D Histology Reconstruction. - Jonas Pichat; Juan Eugenio Iglesias; Tarek A. Yousry; Sébastien Ourselin; Marc Modat (Medical Image Anal., 2018)

A magnetic resonance multi-atlas for the neonatal rabbit brain. - Sebastiano Ferraris; Johannes L. van der Merwe; Lennart Van Der Veeken; Ferran Prados; Juan Eugenio Iglesias; Andrew Melbourne; Marco Lorenzi; Marc Modat; Willy Gsell; Jan Deprest; Tom Vercauteren (NeuroImage, 2018)

A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology. - Juan Eugenio Iglesias; Ricardo Insausti; Garikoitz Lerma-Usabiaga; Martina Bocchetta; Koen Van Leemput; Douglas N. Greve; André J. W. van der Kouwe; Bruce Fischl; César Caballero-Gaudes; Pedro M. Paz-Alonso (NeuroImage, 2018)

Joint Inference on Structural and Diffusion MRI for Sequence-Adaptive Bayesian Segmentation of Thalamic Nuclei with Probabilistic Atlases. - Juan Eugenio Iglesias; Koen Van Leemput; Polina Golland; Anastasia Yendiki (IPMI, 2019)

Hierarchical Joint Registration of Tissue Blocks With Soft Shape Constraints For Large-Scale Histology of The Human Brain. - Matteo Mancini; Shauna Crampsie; David L. Thomas; Zane Jaunmuktane; Janice L. Holton; Juan Eugenio Iglesias (ISBI, 2019)

Unsupervised Deep Learning for Bayesian Brain MRI Segmentation. - Adrian V. Dalca; Evan M. Yu; Polina Golland; Bruce Fischl; Mert R. Sabuncu; Juan Eugenio Iglesias (MICCAI (3), 2019)

Compensatory Brain Connection Discovery in Alzheimer's Disease. - Iman Aganj; Aina Frau-Pascual; Juan Eugenio Iglesias; Anastasia Yendiki; Jean C. Augustinack; David H. Salat; Bruce Fischl (ISBI, 2020)

Partial Volume Segmentation of Brain MRI Scans of Any Resolution and Contrast. - Benjamin Billot; Eleanor D. Robinson; Adrian V. Dalca; Juan Eugenio Iglesias (MICCAI (7), 2020)

3D Reconstruction and Segmentation of Dissection Photographs for MRI-Free Neuropathology. - Henry F. J. Tregidgo; Adrià Casamitjana; Caitlin Latimer; Mitchell Kilgore; Eleanor D. Robinson; Emily Blackburn; Koen Van Leemput; Bruce Fischl; Adrian V. Dalca; Christine L. Mac Donald; Dirk Keene; Juan Eugenio Iglesias (MICCAI (5), 2020)

A Learning Strategy for Contrast-agnostic MRI Segmentation. - Benjamin Billot; Douglas N. Greve; Koen Van Leemput; Bruce Fischl; Juan Eugenio Iglesias; Adrian V. Dalca (MIDL, 2020)

An Auto-Encoder Strategy for Adaptive Image Segmentation. - Evan M. Yu; Juan Eugenio Iglesias; Adrian V. Dalca; Mert R. Sabuncu (MIDL, 2020)

Learning Multi-Modal Image Registration without Real Data. - Malte Hoffmann; Benjamin Billot; Juan Eugenio Iglesias; Bruce Fischl; Adrian V. Dalca (CoRR, 2020)

Joint Frequency- and Image-Space Learning for Fourier Imaging. - Nalini M. Singh; Juan Eugenio Iglesias; Elfar Adalsteinsson; Adrian V. Dalca; Polina Golland (CoRR, 2020)

Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast. - Juan Eugenio Iglesias; Benjamin Billot; Yaël Balbastre; Azadeh Tabari; John Conklin; Daniel C. Alexander; Polina Golland; Brian L. Edlow; Bruce Fischl (CoRR, 2020)

Active Annotation of Informative Overlapping Frames in Video Mosaicking Applications. - Loïc Peter; Marcel Tella-Amo; Dzhoshkun Ismail Shakir; Jan Deprest; Sébastien Ourselin; Juan Eugenio Iglesias; Tom Vercauteren (CoRR, 2020)

DeepReg: a deep learning toolkit for medical image registration. - Yunguan Fu; Nina Montaña Brown; Shaheer U. Saeed; Adrià Casamitjana; Zachary Baum; Rémi Delaunay; Qianye Yang; Alexander Grimwood; Zhe Min; Stefano B. Blumberg; Juan Eugenio Iglesias; Dean C. Barratt; et al. (J. Open Source Softw., 2020)

Automated segmentation of the hypothalamus and associated subunits in brain MRI. - Benjamin Billot; Martina Bocchetta; Emily Todd; Adrian V. Dalca; Jonathan D. Rohrer; Juan Eugenio Iglesias (NeuroImage, 2020)

Test-retest reliability of FreeSurfer automated hippocampal subfield segmentation within and across scanners. - Emma M. Brown; Meghan E. Pierce; Dustin C. Clark; Bruce R. Fischl; Juan Eugenio Iglesias; William P. Milberg; Regina E. McGlinchey; David H. Salat (NeuroImage, 2020)

Infant FreeSurfer: An automated segmentation and surface extraction pipeline for T1-weighted neuroimaging data of infants 0-2 years. - Lilla Zöllei; Juan Eugenio Iglesias; Yangming Ou; Patricia Ellen Grant; Bruce Fischl (NeuroImage, 2020)

DeepReg: a deep learning toolkit for medical image registration. - Yunguan Fu; Nina Montaña Brown; Shaheer U. Saeed; Adrià Casamitjana; Zachary M. C. Baum; Rémi Delaunay; Qianye Yang; Alexander Grimwood; Zhe Min; Stefano B. Blumberg; Juan Eugenio Iglesias; Dean C. Barratt; et al. (Zenodo, 2020)

Joint Segmentation Of Multiple Sclerosis Lesions And Brain Anatomy In MRI Scans Of Any Contrast And Resolution With CNNs. - Benjamin Billot; Stefano Cerri; Koen Van Leemput; Adrian V. Dalca; Juan Eugenio Iglesias (ISBI, 2021)

Learning Mri Contrast-Agnostic Registration. - Malte Hoffmann; Benjamin Billot; Juan Eugenio Iglesias; Bruce Fischl; Adrian V. Dalca (ISBI, 2021)

Synth-by-Reg (SbR): Contrastive Learning for Synthesis-Based Registration of Paired Images. - Adrià Casamitjana; Matteo Mancini; Juan Eugenio Iglesias (SASHIMI@MICCAI, 2021)

SynthSeg: Domain Randomisation for Segmentation of Brain MRI Scans of any Contrast and Resolution. - Benjamin Billot; Douglas N. Greve; Oula Puonti; Axel Thielscher; Koen Van Leemput; Bruce Fischl; Adrian V. Dalca; Juan Eugenio Iglesias (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)

Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast. - Juan Eugenio Iglesias; Benjamin Billot; Yaël Balbastre; Azadeh Tabari; John Conklin; R. Gilberto González; Daniel C. Alexander; Polina Golland; Brian L. Edlow; Bruce Fischl (NeuroImage, 2021)

Quantification of volumetric morphometry and optical property in the cortex of human cerebellum at micrometer resolution. - Chao J. Liu; William Ammon; Viviana Siless; Morgan Fogarty; Ruopeng Wang; Alessia Atzeni; Iman Aganj; Juan Eugenio Iglesias; Lilla Zöllei; Bruce Fischl; Jeremy D. Schmahmann; Hui Wang 060 (NeuroImage, 2021)

Reliability and sensitivity of two whole-brain segmentation approaches included in FreeSurfer - ASEG and SAMSEG. - Donatas Sederevicius; Dídac Vidal-Piñeiro; Øystein Sørensen; Koenraad Van Leemput; Juan Eugenio Iglesias; Adrian V. Dalca; Douglas N. Greve; Bruce Fischl; Atle Bjørnerud; Kristine B. Walhovd; Anders M. Fjell (NeuroImage, 2021)

Uncertainty-Aware Annotation Protocol to Evaluate Deformable Registration Algorithms. - Loïc Peter; Daniel C. Alexander; Caroline Magnain; Juan Eugenio Iglesias (IEEE Trans. Medical Imaging, 2021)

Robust Segmentation of Brain MRI in the Wild with Hierarchical CNNs and No Retraining. - Benjamin Billot; Colin G. Magdamo; Steven E. Arnold; Sudeshna Das 001; Juan Eugenio Iglesias (MICCAI (5), 2022)

SVoRT: Iterative Transformer for Slice-to-Volume Registration in Fetal Brain MRI. - Junshen Xu; Daniel Moyer; Patricia Ellen Grant; Polina Golland; Juan Eugenio Iglesias; Elfar Adalsteinsson (MICCAI (6), 2022)

TopoFit: Rapid Reconstruction of Topologically-Correct Cortical Surfaces. - Andrew Hoopes; Juan Eugenio Iglesias; Bruce Fischl; Douglas N. Greve; Adrian V. Dalca (MIDL, 2022)

SuperWarp: Supervised Learning and Warping on U-Net for Invariant Subvoxel-Precise Registration. - Sean I. Young; Yaël Balbastre; Adrian V. Dalca; William M. Wells III; Juan Eugenio Iglesias; Bruce Fischl (WBIR, 2022)

SUD: Supervision by Denoising for Medical Image Segmentation. - Sean I. Young; Adrian V. Dalca; Enzo Ferrante; Polina Golland; Bruce Fischl; Juan Eugenio Iglesias (CoRR, 2022)

Accurate super-resolution low-field brain MRI. - Juan Eugenio Iglesias; Riana Schleicher; Sonia Laguna; Benjamin Billot; Pamela Schaefer; Brenna McKaig; Joshua N. Goldstein; Kevin N. Sheth; Matthew S. Rosen; W. Taylor Kimberly (CoRR, 2022)

Robust Segmentation of Brain MRI in the Wild with Hierarchical CNNs and no Retraining. - Benjamin Billot; Colin G. Magdamo; Sean E. Arnold; Sudeshna Das 001; Juan Eugenio Iglesias (CoRR, 2022)

Robust machine learning segmentation for large-scale analysis of heterogeneous clinical brain MRI datasets. - Benjamin Billot; Colin G. Magdamo; Steven E. Arnold; Sudeshna Das 001; Juan Eugenio Iglesias (CoRR, 2022)

A Domain-specific Perceptual Metric via Contrastive Self-supervised Representation: Applications on Natural and Medical Images. - Hongwei Bran Li; Chinmay Prabhakar; Suprosanna Shit; Johannes C. Paetzold; Tamaz Amiranashvili; Jianguo Zhang 001; Daniel Rueckert; Juan Eugenio Iglesias; Benedikt Wiestler; Bjoern H. Menze (CoRR, 2022)

Deep active learning for suggestive segmentation of biomedical image stacks via optimisation of Dice scores and traced boundary length. - Alessia Atzeni; Loïc Peter; Eleanor D. Robinson; Emily Blackburn; Juri Althonayan; Daniel C. Alexander; Juan Eugenio Iglesias (Medical Image Anal., 2022)

Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas. - Adrià Casamitjana; Marco Lorenzi; Sebastiano Ferraris; Loïc Peter; Marc Modat; Allison Stevens; Bruce Fischl; Tom Vercauteren; Juan Eugenio Iglesias (Medical Image Anal., 2022)

High-resolution atlasing and segmentation of the subcortex: Review and perspective on challenges and opportunities created by machine learning. - Adrià Casamitjana; Juan Eugenio Iglesias (NeuroImage, 2022)

How Machine Learning is Powering Neuroimaging to Improve Brain Health. - Nalini M. Singh; Jordan B. Harrod; Sandya Subramanian; Mitchell B. Robinson; Ken Chang; Suheyla Cetin Karayumak; Adrian Vasile Dalca; Simon B. Eickhoff; Michael Fox; Loraine Franke; Polina Golland; Daniel Haehn; et al. (Neuroinformatics, 2022)

SynthMorph: Learning Contrast-Invariant Registration Without Acquired Images. - Malte Hoffmann; Benjamin Billot; Douglas N. Greve; Juan Eugenio Iglesias; Bruce Fischl; Adrian V. Dalca (IEEE Trans. Medical Imaging, 2022)

Cortical Analysis of Heterogeneous Clinical Brain MRI Scans for Large-Scale Neuroimaging Studies. - Karthik Gopinath; Douglas N. Greve; Sudeshna Das 001; Steven E. Arnold; Colin G. Magdamo; Juan Eugenio Iglesias (MICCAI (8), 2023)

Robust and Generalisable Segmentation of Subtle Epilepsy-Causing Lesions: A Graph Convolutional Approach. - Hannah Spitzer; Mathilde Ripart; Abdulah Fawaz; Logan Z. J. Williams; Emma C. Robinson; Juan Eugenio Iglesias; Sophie Adler; Konrad Wagstyl (MICCAI (8), 2023)

Domain-Agnostic Segmentation of Thalamic Nuclei from Joint Structural and Diffusion MRI. - Henry F. J. Tregidgo; Sonja Soskic; Mark D. Olchanyi; Juri Althonayan; Benjamin Billot; Chiara Maffei; Polina Golland; Anastasia Yendiki; Daniel C. Alexander; Martina Bocchetta; Jonathan D. Rohrer; Juan Eugenio Iglesias (MICCAI (8), 2023)

The ASNR-MICCAI Brain Tumor Segmentation (BraTS) Challenge 2023: Intracranial Meningioma. - Dominic LaBella; Maruf Adewole; Michelle Alonso-Basanta; Talissa Altes; Syed Muhammad Anwar; Ujjwal Baid; Timothy Bergquist; Radhika Bhalerao; Sully F. Chen; Verena Chung; Gian Marco Conte; Farouk Dako; et al. (CoRR, 2023)

The Brain Tumor Segmentation (BraTS) Challenge 2023: Local Synthesis of Healthy Brain Tissue via Inpainting. - Florian Kofler; Felix Meissen; Felix Steinbauer; Robert Graf; Eva Oswald; Ezequiel de la Rosa; Hongwei Bran Li; Ujjwal Baid; Florian A. Hölzl; Özgün Turgut; Izabela Horvath; Diana Waldmannstetter; et al. (CoRR, 2023)

The Brain Tumor Segmentation (BraTS) Challenge 2023: Brain MR Image Synthesis for Tumor Segmentation (BraSyn). - Hongwei Bran Li; Gian Marco Conte; Syed Muhammad Anwar; Florian Kofler; Koen Van Leemput; Marie Piraud; Ivan Ezhov; Felix Meissen; Maruf Adewole; Anastasia Janas; Anahita Fathi Kazerooni; Dominic LaBella; et al. (CoRR, 2023)

The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs). - Anahita Fathi Kazerooni; Nastaran Khalili; Xinyang Liu; Debanjan Haldar; Zhifan Jiang; Syed Muhammad Anwar; Jake Albrecht; Maruf Adewole; Udunna Anazodo; Hannah Anderson; Sina Bagheri; Ujjwal Baid; et al. (CoRR, 2023)

The Brain Tumor Segmentation (BraTS) Challenge 2023: Glioma Segmentation in Sub-Saharan Africa Patient Population (BraTS-Africa). - Maruf Adewole; Jeffrey D. Rudie; Anu Gbadamosi; Oluyemisi Toyobo; Raymond Confidence; Dong Zhang 009; Olubukola Omidiji; Rachel Akinola; Mohammad Abba Suwaid; Adaobi Emegoakor; Nancy Ojo; Kenneth Aguh; et al. (CoRR, 2023)

Robust and Generalisable Segmentation of Subtle Epilepsy-causing Lesions: a Graph Convolutional Approach. - Hannah Spitzer; Mathilde Ripart; Abdulah Fawaz; Logan Z. J. Williams; MELD project; Emma C. Robinson; Juan Eugenio Iglesias; Sophie Adler; Konrad Wagstyl (CoRR, 2023)

Diffeomorphic Multi-Resolution Deep Learning Registration for Applications in Breast MRI. - 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 (CoRR, 2023)

USLR: an open-source tool for unbiased and smooth longitudinal registration of brain MR. - Adrià Casamitjana; Roser Sala-Llonch; Karim Lekadir; Juan Eugenio Iglesias (CoRR, 2023)

Brain-ID: Learning Robust Feature Representations for Brain Imaging. - Peirong Liu; Oula Puonti; Xiaoling Hu 002; Daniel C. Alexander; Juan Eugenio Iglesias (CoRR, 2023)

Challenges of implementing computer-aided diagnostic models for neuroimages in a clinical setting. - Matthew Leming; Esther E. Bron; Rose Bruffaerts; Yangming Ou; Juan Eugenio Iglesias; Randy L. Gollub; Hyungsoon Im (npj Digit. Medicine, 2023)

SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining. - Benjamin Billot; Douglas N. Greve; Oula Puonti; Axel Thielscher; Koen Van Leemput; Bruce Fischl; Adrian V. Dalca; Juan Eugenio Iglesias (Medical Image Anal., 2023)

NeSVoR: Implicit Neural Representation for Slice-to-Volume Reconstruction in MRI. - Junshen Xu; Daniel Moyer; Borjan A. Gagoski; Juan Eugenio Iglesias; Patricia Ellen Grant; Polina Golland; Elfar Adalsteinsson (IEEE Trans. Medical Imaging, 2023)

Accurate Bayesian segmentation of thalamic nuclei using diffusion MRI and an improved histological atlas. - Henry F. J. Tregidgo; Sonja Soskic; Juri Althonayan; Chiara Maffei; Koen Van Leemput; Polina Golland; Ricardo Insausti; Garikoitz Lerma-Usabiaga; César Caballero-Gaudes; Pedro M. Paz-Alonso; Anastasia Yendiki; Daniel C. Alexander; et al. (NeuroImage, 2023)

Fully Convolutional Slice-to-Volume Reconstruction for Single-Stack MRI. - Sean I. Young; Yaël Balbastre; Bruce Fischl; Polina Golland; Juan Eugenio Iglesias (CVPR, 2024)

Brain-ID: Learning Contrast-Agnostic Anatomical Representations for Brain Imaging. - Peirong Liu; Oula Puonti; Xiaoling Hu 002; Daniel C. Alexander; Juan Eugenio Iglesias (ECCV (12), 2024)

Jump: A Joint Multimodal Registration Pipeline for Neuroimaging with Minimal Preprocessing. - Adrià Casamitjana; Juan Eugenio Iglesias; Raúl Tudela; Aida Niñerola-Baizan; Roser Sala-Llonch (ISBI, 2024)

Quantifying White Matter Hyperintensity and Brain Volumes in Heterogeneous Clinical and Low-Field Portable MRI. - Pablo Laso; Stefano Cerri; Annabel Sorby-Adams; Jennifer Guo; Farrah Mateen; Philipp Goebl; Jiaming Wu; Peirong Liu; Hongwei Bran Li; Sean I. Young; Benjamin Billot; Oula Puonti; et al. (ISBI, 2024)

Resolution- and Stimulus-Agnostic Super-Resolution of Ultra-High-Field Functional MRI: Application to Visual Studies. - Hongwei Bran Li; Matthew S. Rosen; Shahin Nasr; Juan Eugenio Iglesias (ISBI, 2024)

P-Count: Persistence-Based Counting of White Matter Hyperintensities in Brain MRI. - Xiaoling Hu 002; Annabel Sorby-Adams; Frederik Barkhof; W. Taylor Kimberly; Oula Puonti; Juan Eugenio Iglesias (TGI3@MICCAI, 2024)

PEPSI: Pathology-Enhanced Pulse-Sequence-Invariant Representations for Brain MRI. - Peirong Liu; Oula Puonti; Annabel Sorby-Adams; W. Taylor Kimberly; Juan Eugenio Iglesias (MICCAI (12), 2024)

Pseudo-rendering for Resolution and Topology-Invariant Cortical Parcellation. - Pablo Blasco Fernandez; Karthik Gopinath; John Williams-Ramirez; Rogeny Herisse; Lucas J. Deden-Binder; Dina Zemlyanker; Theressa Connors; Liana Kozanno; Derek H. Oakley; Bradley T. Hyman; Sean I. Young; Juan Eugenio Iglesias (MLMI@MICCAI (2), 2024)

Registration by Regression (RbR): A Framework for Interpretable and Flexible Atlas Registration. - Karthik Gopinath; Xiaoling Hu 002; Malte Hoffmann; Oula Puonti; Juan Eugenio Iglesias (WBIR, 2024)

H-SynEx: Using synthetic images and ultra-high resolution ex vivo MRI for hypothalamus subregion segmentation. - Lívia Rodrigues 001; Martina Bocchetta; Oula Puonti; Douglas N. Greve; Ana Carolina Londe; Marcondes França; Simone Appenzeller; Juan Eugenio Iglesias; Letícia Rittner (CoRR, 2024)

PEPSI: Pathology-Enhanced Pulse-Sequence-Invariant Representations for Brain MRI. - Peirong Liu; Oula Puonti; Annabel Sorby-Adams; William T. Kimberly; Juan Eugenio Iglesias (CoRR, 2024)

The Brain Tumor Segmentation in Pediatrics (BraTS-PEDs) Challenge: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs). - Anahita Fathi Kazerooni; Nastaran Khalili; Deep Gandhi; Xinyang Liu; Zhifan Jiang; Syed Muhammed Anwar; Jake Albrecht; Maruf Adewole; Udunna Anazodo; Hannah Anderson; Sina Bagheri; Ujjwal Baid; et al. (CoRR, 2024)

Analysis of the BraTS 2023 Intracranial Meningioma Segmentation Challenge. - Dominic LaBella; Ujjwal Baid; Omaditya Khanna; Shan McBurney-Lin; Ryan McLean; Pierre Nedelec; Arif Rashid; Nourel Hoda Tahon; Talissa Altes; Radhika Bhalerao; Yaseen Dhemesh; Devon Godfrey; et al. (CoRR, 2024)

Probabilistic Contrastive Learning with Explicit Concentration on the Hypersphere. - Hongwei Bran Li; Cheng Ouyang; Tamaz Amiranashvili; Matthew S. Rosen; Bjoern H. Menze; Juan Eugenio Iglesias (CoRR, 2024)

The 2024 Brain Tumor Segmentation (BraTS) Challenge: Glioma Segmentation on Post-treatment MRI. - Maria Correia de Verdier; Rachit Saluja; Louis Gagnon; Dominic LaBella; Ujjwal Baid; Nourel Hoda Tahon; Martha Foltyn-Dumitru; Jikai Zhang; Maram Alafif; Saif Baig; Ken Chang; Gennaro D'Anna; et al. (CoRR, 2024)

High-resolution segmentations of the hypothalamus and its subregions for training of segmentation models. - Lívia Rodrigues 001; Martina Bocchetta; Oula Puonti; Douglas N. Greve; Ana Carolina Londe; Marcondes França; Simone Appenzeller; Letícia Rittner; Juan Eugenio Iglesias (CoRR, 2024)

BraTS-PEDs: Results of the Multi-Consortium International Pediatric Brain Tumor Segmentation Challenge 2023. - Anahita Fathi Kazerooni; Nastaran Khalili; Xinyang Liu; Debanjan Haldar; Zhifan Jiang; Anna Zapaishchykova; Julija Pavaine; Lubdha M. Shah; Blaise V. Jones; Nakul Sheth; Sanjay P. Prabhu; Aaron S. McAllister; et al. (CoRR, 2024)

TV-based Deep 3D Self Super-Resolution for fMRI. - Fernando Pérez-Bueno; Hongwei Bran Li; Shahin Nasr; César Caballero-Gaudes; Juan Eugenio Iglesias (CoRR, 2024)

A Constrast-Agnostic Method for Ultra-High Resolution Claustrum Segmentation. - Chiara Mauri; Ryan Fritz; Jocelyn Mora; Benjamin Billot; Juan Eugenio Iglesias; Koen Van Leemput; Jean Augustinack; Douglas N. Greve (CoRR, 2024)

Learn2Synth: Learning Optimal Data Synthesis Using Hypergradients. - Xiaoling Hu 002; Oula Puonti; Juan Eugenio Iglesias; Bruce Fischl; Yaël Balbastre (CoRR, 2024)

Unraveling Normal Anatomy via Fluid-Driven Anomaly Randomization. - Peirong Liu; Ana Lawry Aguila; Juan Eugenio Iglesias (CVPR, 2025)

Hierarchical Uncertainty Estimation for Learning-based Registration in Neuroimaging. - Xiaoling Hu 002; Karthik Gopinath; Peirong Liu; Malte Hoffmann; Koen Van Leemput; Oula Puonti; Juan Eugenio Iglesias (ICLR, 2025)

TV-Based Deep 3D Self Super-Resolution for FMRI. - Fernando Pérez-Bueno; Hongwei B. Li; Shahin Nasr; César Caballero-Gaudes; Juan Eugenio Iglesias (ISBI, 2025)

USLR: An open-source tool for unbiased and smooth longitudinal registration of brain MRI. - Adrià Casamitjana; Roser Sala-Llonch; Karim Lekadir; Juan Eugenio Iglesias (Medical Image Anal., 2025)

"Recon-all-clinical": Cortical surface reconstruction and analysis of heterogeneous clinical brain MRI. - Karthik Gopinath; Douglas N. Greve; Colin G. Magdamo; Steven E. Arnold; Sudeshna Das 001; Oula Puonti; Juan Eugenio Iglesias (Medical Image Anal., 2025)

Brain Tumor Sequence Registration (BraTS-Reg) Challenge Dataset. - Bhakti Baheti; Satrajit Chakrabarty; Hamed Akbari; Michel Bilello; Benedikt Wiestler; Julian Schwarting; Evan Calabrese; Jeffrey D. Rudie; Syed Amaan Abidi; Mina Mousa; Javier E. Villanueva-Meyer; Brandon K. K. Fields; et al. (Zenodo, 2025)

Reference-Free 3D Reconstruction of Brain Dissection Photographs with Machine Learning. - Lin Tian; Sean I. Young; Jonathan Williams Ramirez; Dina Zemlyanker; Lucas J. Deden-Binder; Rogeny Herisse; Theresa R. Connors; Derek H. Oakley; Bradley T. Hyman; Oula Puonti; Matthew S. Rosen; Juan Eugenio Iglesias (CoRR, 2025)

From Low Field to High Value: Robust Cortical Mapping from Low-Field MRI. - Karthik Gopinath; Annabel Sorby-Adams; Jonathan Williams Ramirez; Dina Zemlyanker; Jennifer Guo; David Hunt; Christine L. Mac Donald; C. Dirk Keene; Timothy S. Coalson; Matthew F. Glasser; David C. Van Essen; Matthew S. Rosen; et al. (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)

Scalable Segmentation for Ultra-High-Resolution Brain MR Images. - Xiaoling Hu 002; Peirong Liu; Dina Zemlyanker; Jonathan Williams Ramirez; Oula Puonti; Juan Eugenio Iglesias (CoRR, 2025)

UNSURF: Uncertainty Quantification for Cortical Surface Reconstruction of Clinical Brain MRIs. - Raghav Mehta; Karthik Gopinath; Ben Glocker; Juan Eugenio Iglesias (CoRR, 2025)

Conditional diffusion models for guided anomaly detection in brain images using fluid-driven anomaly randomization. - Ana Lawry Aguila; Peirong Liu; Oula Puonti; Juan Eugenio Iglesias (CoRR, 2025)

BraTS orchestrator : Democratizing and Disseminating state-of-the-art brain tumor image analysis. - Florian Kofler; Marcel Rosier; Mehdi Astaraki; Ujjwal Baid; Hendrik Kristian Möller; Josef A. Buchner; Felix Steinbauer; Eva Oswald; Ezequiel de la Rosa; Ivan Ezhov; Constantin von See; Jan Kirschke; et al. (CoRR, 2025)

A large-scale heterogeneous 3D magnetic resonance brain imaging dataset for self-supervised learning. - Asbjørn Munk; Stefano Cerri; Jakob Ambsdorf; Julia Machnio; Sebastian Nørgaard Llambias; Vardan Nersesjan; Christian Hedeager Krag; Peirong Liu; Pablo Rocamora-García; Mostafa Mehdipour-Ghazi; Mikael Boesen; Michael Eriksen Benros; et al. (CoRR, 2025)

Automated Segmentation of Coronal Brain Tissue Slabs for 3D Neuropathology. - Jonathan Williams Ramirez; Dina Zemlyanker; Lucas J. Deden-Binder; Rogeny Herisse; Erendira Garcia Pallares; Karthik Gopinath; Harshvardhan Gazula; Christopher Mount; Liana Kozanno; Michael S. Marshall; Theresa R. Connors; Matthew P. Frosch; et al. (CoRR, 2025)

Supervision by Denoising. - Sean I. Young; Adrian V. Dalca; Enzo Ferrante; Polina Golland; Christopher A. Metzler; Bruce Fischl; Juan Eugenio Iglesias (IEEE Trans. Pattern Anal. Mach. Intell., 2025)