FiberNET: An Ensemble Deep Learning Framework for Clustering White Matter Fibers. - Vikash Gupta; Sophia I. Thomopoulos; Faisal Rashid; Paul M. Thompson (MICCAI (1), 2017)

FIBERNET 2.0: An automatic neural network based tool for clustering white matter fibers in the brain. - Vikash Gupta; Sophia I. Thomopoulos; Conor K. Corbin; Faisal Rashid; Paul M. Thompson (ISBI, 2018)

Multi-Shell Diffusion MRI Measures of Brain Aging: A Preliminary Comparison From ADNI3. - Talia M. Nir; Sophia I. Thomopoulos; Julio E. Villalon-Reina; Artemis Zavaliangos-Petropulu; Emily L. Dennis; Robert I. Reid; Matt A. Bernstein; Bret J. Borowski; Clifford R. Jack; Michael W. Weiner; Neda Jahanshad; Paul M. Thompson (ISBI, 2019)

Support Vector Based Autoregressive Mixed Models of Longitudinal Brain Changes and Corresponding Genetics in Alzheimer's Disease. - Qifan Yang; Sophia I. Thomopoulos; Linda Ding; Wesley Surento; Paul M. Thompson; Neda Jahanshad (PRIME@MICCAI, 2019)

Diffusion MRI Indices and Their Relation to Cognitive Impairment in Brain Aging: The Updated Multi-protocol Approach in ADNI3. - Artemis Zavaliangos-Petropulu; Talia M. Nir; Sophia I. Thomopoulos; Robert I. Reid; Matt A. Bernstein; Bret J. Borowski; Clifford R. Jack Jr.; Michael W. Weiner; Neda Jahanshad; Paul M. Thompson (Frontiers Neuroinformatics, 2019)

A Deep Transfer Learning Framework for 3D Brain Imaging Based on Optimal Mass Transport. - Ling-Li Zeng; Christopher R. K. Ching; Zvart Abaryan; Sophia I. Thomopoulos; Kai Gao 011; Alyssa H. Zhu; Anjanibhargavi Ragothaman; Faisal Rashid; Marc Harrison; Lauren E. Salminen; Brandalyn C. Riedel; Neda Jahanshad; et al. (MLCN/RNO-AI@MICCAI, 2020)

Predicting Progression from Mild Cognitive Impairment to Alzheimer's Disease using MRI-based Cortical Features and a Two-State Markov Model. - Eleonora Ficiarà; Valentino Crespi; Shruti Prashant Gadewar; Sophia I. Thomopoulos; Joshua Boyd; Paul M. Thompson; Neda Jahanshad; Fabrizio Pizzagalli (ISBI, 2021)

Region Specific Automatic Quality Assurance For MRI-Derived Cortical Segmentations. - Shruti Gadewar; Alyssa H. Zhu; Sophia I. Thomopoulos; Zhuocheng Li; Iyad Ba Gari; Piyush Maiti; Paul M. Thompson; Neda Jahanshad (ISBI, 2021)

Style Transfer Using Generative Adversarial Networks for Multi-site MRI Harmonization. - Mengting Liu; Piyush Maiti; Sophia I. Thomopoulos; Alyssa H. Zhu; Yaqiong Chai; Hosung Kim; Neda Jahanshad (MICCAI (3), 2021)

FiberNeat: Unsupervised White Matter Tract Filtering. - Bramsh Qamar Chandio; Tamoghna Chattopadhyay; Conor Owens-Walton; Julio E. Villalon-Reina; Leila Nabulsi; Sophia I. Thomopoulos; Eleftherios Garyfallidis; Paul M. Thompson (EMBC, 2022)

A comparison of methods to harmonize cortical thickness measurements across scanners and sites. - Delin Sun; Gopalkumar Rakesh; Courtney C. Haswell; Mark W. Logue; C. Lexi Baird; Erin O'Leary; Andrew S. Cotton; Hong Xie; Marijo B. Tamburrino; Tian Chen; Emily L. Dennis; Neda Jahanshad; et al. (NeuroImage, 2022)

ENIGMA + COINSTAC: Improving Findability, Accessibility, Interoperability, and Re-usability. - Jessica A. Turner; Vince D. Calhoun; Paul M. Thompson; Neda Jahanshad; Christopher R. K. Ching; Sophia I. Thomopoulos; Eric Verner; Gregory P. Strauss; Anthony O. Ahmed; Matthew D. Turner; Sunitha Basodi; Judith M. Ford; et al. (Neuroinformatics, 2022)

The Influence of Brain MRI Defacing Algorithms on Brain-Age Predictions via 3D Convolutional Neural Networks. - Ryan J. Cali; Ravi R. Bhatt; Sophia I. Thomopoulos; Shruti Gadewar; Iyad Ba Gari; Tamoghna Chattopadhyay; Neda Jahanshad; Paul M. Thompson (EMBC, 2023)

Efficiently Training Vision Transformers on Structural MRI Scans for Alzheimer's Disease Detection. - Nikhil J. Dhinagar; Sophia I. Thomopoulos; Emily Laltoo; Paul M. Thompson (EMBC, 2023)

Variational Autoencoders for Generating Synthetic Tractography-Based Bundle Templates in a Low-Data Setting. - Yixue Feng 001; Bramsh Qamar Chandio; Sophia I. Thomopoulos; Tamoghna Chattopadhyay; Paul M. Thompson (EMBC, 2023)

A Comprehensive Corpus Callosum Segmentation Tool for Detecting Callosal Abnormalities and Genetic Associations from Multi Contrast MRIs. - Shruti Prashant Gadewar; Elnaz Nourollahimoghadam; Ravi R. Bhatt; Abhinaav Ramesh; Shayan Javid; Iyad Ba Gari; Alyssa H. Zhu; Sophia I. Thomopoulos; Paul M. Thompson; Neda Jahanshad (EMBC, 2023)

Predictive Modeling Of Alzheimer's Disease Prognosis Using Anatomical & Diffusion MRI. - Nikita Goel; Sophia I. Thomopoulos; Tamoghna Chattopadhyay; Paul M. Thompson (EMBC, 2023)

BundleCleaner: Unsupervised Denoising and Subsampling of Diffusion MRI-Derived Tractography Data. - Yixue Feng 001; Bramsh Qamar Chandio; Julio E. Villalon-Reina; Sophia I. Thomopoulos; Himanshu Joshi; Gauthami Nair; Anand A. Joshi; Ganesan Venkatasubramanian; John P. John; Paul M. Thompson (CDMRI@MICCAI, 2023)

Normative Aging for an Individual's Full Brain MRI Using Style GANs to Detect Localized Neurodegeneration. - Shruti Prashant Gadewar; Alyssa H. Zhu; Sunanda Somu; Abhinaav Ramesh; Iyad Ba Gari; Sophia I. Thomopoulos; Paul M. Thompson; Talia M. Nir; Neda Jahanshad (MLMI@MICCAI (2), 2023)

Medial Tractography Analysis (MeTA) for White Matter Population Analyses Across Datasets. - Iyad Ba Gari; Abhinaav Ramesh; Shayan Javid; Shruti Prashant Gadewar; Elnaz Nourollahimoghadam; Sophia I. Thomopoulos; Paul M. Thompson; Talia M. Nir; Neda Jahanshad (NER, 2023)

Can Structural MRIs be used to Detect Amyloid Positivity using Deep Learning? - Tamoghna Chattopadhyay; Dheeraj Komandur; Jayati Naik; Ketaki Buwa; Saket Ozarkar; Sophia I. Thomopoulos; Paul M. Thompson (SIPAIM, 2023)

Along-Tract Parameterization of White Matter Microstructure using Medial Tractography Analysis (MeTA). - Iyad Ba Gari; Shayan Javid; Alyssa H. Zhu; Shruti Prashant Gadewar; Siddharth Narula; Abhinaav Ramesh; Sophia I. Thomopoulos; Lachlan T. Strike; Greig I. de Zubicaray; Katie L. McMahon; Margaret J. Wright; Paul M. Thompson; et al. (SIPAIM, 2023)

Predicting Decline in Clinical Assessments of Alzheimer's Disease With Machine Learning and 3D Brain MRI. - Nikita Goel; Sophia I. Thomopoulos; Paul M. Thompson (SIPAIM, 2023)

Unsupervised harmonization of brain MRI using 3D CycleGANs and its effect on brain age prediction. - Dheeraj Komandur; Umang Gupta; Tamoghna Chattopadhyay; Nikhil J. Dhinagar; Sophia I. Thomopoulos; Jiu-Chiuan Chen; Dan Beavers; Greg Ver Steeg; Paul M. Thompson (SIPAIM, 2023)

Large-scale Normative Modeling of Brain Microstructure. - Julio E. Villalon-Reina; Alyssa H. Zhu; Talia M. Nir; Sophia I. Thomopoulos; Emily Laltoo; Leila Kushan; Carrie E. Bearden; Neda Jahanshad; Paul M. Thompson (SIPAIM, 2023)

Video and Synthetic MRI Pre-training of 3D Vision Architectures for Neuroimage Analysis. - Nikhil J. Dhinagar; Amit Singh; Saket Ozarkar; Ketaki Buwa; Sophia I. Thomopoulos; Conor Owens-Walton; Emily Laltoo; Yao-Liang Chen; Philip A. Cook; Corey McMillan; Chih-Chien Tsai; Jiun-Jie Wang; et al. (CoRR, 2023)

DenseNet and Support Vector Machine classifications of major depressive disorder using vertex-wise cortical features. - Vladimir Belov; Tracy Erwin-Grabner; Ling-Li Zeng; Christopher R. K. Ching; André Aleman; Alyssa R. Amod; Zeynep Basgoze; Francesco Benedetti; Bianca Besteher; Katharina Brosch; Robin Bülow; Romain Colle; et al. (CoRR, 2023)

Neuroimaging-based classification of PTSD using data-driven computational approaches: A multisite big data study from the ENIGMA-PGC PTSD consortium. - Xi Zhu; Yoojean Kim; Orren Ravid; Xiaofu He; Benjamin Suarez-Jimenez; Sigal Zilcha-Mano; Amit Lazarov; Seonjoo Lee; Chadi G. Abdallah; Michael Angstadt; Christopher L. Averill; C. Lexi Baird; et al. (NeuroImage, 2023)

Deep Normative Tractometry for Identifying Joint White Matter Macro- and Micro-structural Abnormalities in Alzheimer's Disease. - Yixue Feng 001; Bramsh Qamar Chandio; Julio E. Villalon-Reina; Sebastian M. Benavidez; Tamoghna Chattopadhyay; Sasha Chehrzadeh; Emily Laltoo; Sophia I. Thomopoulos; Himanshu Joshi; Ganesan Venkatasubramanian; John P. John; Neda Jahanshad; et al. (EMBC, 2024)

Bundle Analytics based Data Harmonization for Multi-Site Diffusion MRI Tractometry. - Bramsh Qamar Chandio; Julio E. Villalon-Reina; Talia M. Nir; Sophia I. Thomopoulos; Yixue Feng 001; Sebastian M. Benavidez; Neda Jahanshad; Jaroslaw Harezlak; Eleftherios Garyfallidis; Paul M. Thompson (EMBC, 2024)

Brain Age Analysis and Dementia Classification using Convolutional Neural Networks trained on Diffusion MRI: Tests in Indian and North American Cohorts. - Tamoghna Chattopadhyay; Neha Ann Joshy; Saket Ozarkar; Ketaki Buwa; Yixue Feng 001; Emily Laltoo; Sophia I. Thomopoulos; Julio Villalon; Himanshu Joshi; Ganesan Venkatasubramanian; John P. John; Paul M. Thompson (EMBC, 2024)

Counterfactual MRI Generation with Denoising Diffusion Models for Interpretable Alzheimer's Disease Effect Detection. - Nikhil J. Dhinagar; Sophia I. Thomopoulos; Emily Laltoo; Paul M. Thompson (EMBC, 2024)

Synthesizing Study-Specific Controls Using Generative Models on Open Access Datasets for Harmonized Multi-Study Analyses. - Shruti Prashant Gadewar; Alyssa H. Zhu; Iyad Ba Gari; Sunanda Somu; Sophia I. Thomopoulos; Paul M. Thompson; Talia M. Nir; Neda Jahanshad (ISBI, 2024)

Comparison of Explainable AI Models for MRI-Based Alzheimer's Disease Classification. - Tamoghna Chattopadhyay; Neha Ann Joshy; Chirag Jagad; Emma J. Gleave; Sophia I. Thomopoulos; Yixue Feng 001; Julio E. Villalon-Reina; Emily Laltoo; Himanshu Joshi; Ganesan Venkatasubramanian; John P. John; Greg Ver Steeg; et al. (SIPAIM, 2024)

Diffusion Bridge Models for 3D Medical Image Translation. - Shaorong Zhang; Tamoghna Chattopadhyay; Sophia I. Thomopoulos; José Luis Ambite; Paul M. Thompson; Greg Ver Steeg (CoRR, 2025)