Particle Filtering for Geometric Active Contours with Application to Tracking Moving and Deforming Objects. - Yogesh Rathi; Namrata Vaswani; Allen R. Tannenbaum; Anthony J. Yezzi (CVPR (2), 2005)

Tracking deformable objects with unscented Kalman filtering and geometric active contours. - Samuel Dambreville; Yogesh Rathi; Allen R. Tannenbaum (ACC, 2006)

Time-varying Finite Dimensional Basis for Tracking Contour Deformations. - Namrata Vaswani; Anthony J. Yezzi; Yogesh Rathi; Allen R. Tannenbaum (CDC, 2006)

Shape-Based Approach to Robust Image Segmentation using Kernel PCA. - Samuel Dambreville; Yogesh Rathi; Allen R. Tannenbaum (CVPR (1), 2006)

Comparative Analysis of Kernel Methods for Statistical Shape Learning. - Yogesh Rathi; Samuel Dambreville; Allen R. Tannenbaum (CVAMIA, 2006)

Particle Filters for Infinite (or Large) Dimensional State Spaces- Part 1. - Namrata Vaswani; Anthony J. Yezzi; Yogesh Rathi; Allen R. Tannenbaum (ICASSP (3), 2006)

A Shape-Based Approach to Robust Image Segmentation. - Samuel Dambreville; Yogesh Rathi; Allen R. Tannenbaum (ICIAR (1), 2006)

Particle Filtering with Dynamic Shape Priors. - Yogesh Rathi; Samuel Dambreville; Allen R. Tannenbaum (ICIAR (1), 2006)

Filtering for Closed Curves. - Yogesh Rathi (2006)

Tracking Through Clutter Using Graph Cuts. - James G. Malcolm; Yogesh Rathi; Allen R. Tannenbaum (BMVC, 2007)

A Graph Cut Approach to Image Segmentation in Tensor Space. - James G. Malcolm; Yogesh Rathi; Allen R. Tannenbaum (CVPR, 2007)

Segmenting Images on the Tensor Manifold. - Yogesh Rathi; Allen R. Tannenbaum; Oleg V. Michailovich (CVPR, 2007)

Multi-Object Tracking Through Clutter Using Graph Cuts. - James G. Malcolm; Yogesh Rathi; Allen R. Tannenbaum (ICCV, 2007)

Graph Cut Segmentation with Nonlinear Shape Priors. - James G. Malcolm; Yogesh Rathi; Allen R. Tannenbaum (ICIP (4), 2007)

Tracking Deforming Objects Using Particle Filtering for Geometric Active Contours. - Yogesh Rathi; Namrata Vaswani; Allen R. Tannenbaum; Anthony J. Yezzi (IEEE Trans. Pattern Anal. Mach. Intell., 2007)

Image Segmentation Using Active Contours Driven by the Bhattacharyya Gradient Flow. - Oleg V. Michailovich; Yogesh Rathi; Allen R. Tannenbaum (IEEE Trans. Image Process., 2007)

A Generic Framework for Tracking Using Particle Filter With Dynamic Shape Prior. - Yogesh Rathi; Namrata Vaswani; Allen R. Tannenbaum (IEEE Trans. Image Process., 2007)

Orientation distribution estimation for Q-ball imaging. - Yogesh Rathi; Oleg V. Michailovich; Sylvain Bouix; Martha Elizabeth Shenton (CVPR Workshops, 2008)

Label Space: A Multi-object Shape Representation. - James G. Malcolm; Yogesh Rathi; Allen R. Tannenbaum (IWCIA, 2008)

Label Space: A Coupled Multi-shape Representation. - James G. Malcolm; Yogesh Rathi; Martha Elizabeth Shenton; Allen R. Tannenbaum (MICCAI (2), 2008)

Fast approximate surface evolution in arbitrary dimension. - James G. Malcolm; Yogesh Rathi; Anthony J. Yezzi; Allen R. Tannenbaum (Image Processing, 2008)

Segmenting images analytically in shape space. - Yogesh Rathi; Samuel Dambreville; Marc Niethammer; James G. Malcolm; James J. Levitt; Martha Elizabeth Shenton; Allen R. Tannenbaum (Image Processing, 2008)

Fast approximate curve evolution. - James G. Malcolm; Yogesh Rathi; Anthony J. Yezzi; Allen R. Tannenbaum (Real-Time Image Processing, 2008)

A Framework for Image Segmentation Using Shape Models and Kernel Space Shape Priors. - Samuel Dambreville; Yogesh Rathi; Allen R. Tannenbaum (IEEE Trans. Pattern Anal. Mach. Intell., 2008)

Neural Tractography Using an Unscented Kalman Filter. - James G. Malcolm; Martha Elizabeth Shenton; Yogesh Rathi (IPMI, 2009)

Two-Tensor Tractography Using a Constrained Filter. - James G. Malcolm; Martha Elizabeth Shenton; Yogesh Rathi (MICCAI (1), 2009)

Directional functions for orientation distribution estimation. - Yogesh Rathi; Oleg V. Michailovich; Martha Elizabeth Shenton; Sylvain Bouix (Medical Image Anal., 2009)

Spatially regularized q-ball imaging using spherical ridgelets. - Oleg V. Michailovich; Yogesh Rathi (ISBI, 2010)

Disease classification: a probabilistic approach. - Yogesh Rathi; James G. Malcolm; Sylvain Bouix; Robert W. McCarley; Larry J. Seidman; Jill M. Goldstein; Carl-Fredrik Westin; Martha Elizabeth Shenton (ISBI, 2010)

Fast and Accurate Reconstruction of HARDI Data Using Compressed Sensing. - Oleg V. Michailovich; Yogesh Rathi (MICCAI (1), 2010)

Biomarkers for Identifying First-Episode Schizophrenia Patients Using Diffusion Weighted Imaging. - Yogesh Rathi; James G. Malcolm; Oleg V. Michailovich; Jill M. Goldstein; Larry J. Seidman; Robert W. McCarley; Carl-Fredrik Westin; Martha Elizabeth Shenton (MICCAI (1), 2010)

A Geometry-Based Particle Filtering Approach to White Matter Tractography. - Peter Savadjiev; Yogesh Rathi; James G. Malcolm; Martha Elizabeth Shenton; Carl-Fredrik Westin (MICCAI (2), 2010)

Joint Generative Model for fMRI/DWI and Its Application to Population Studies. - Archana Venkataraman; Yogesh Rathi; Marek Kubicki; Carl-Fredrik Westin; Polina Golland (MICCAI (1), 2010)

Spatially regularized compressed sensing of diffusion MRI data - Oleg V. Michailovich; Yogesh Rathi; Sudipto Dolui (CoRR, 2010)

A filtered approach to neural tractography using the Watson directional function. - James G. Malcolm; Oleg V. Michailovich; Sylvain Bouix; Carl-Fredrik Westin; Martha Elizabeth Shenton; Yogesh Rathi (Medical Image Anal., 2010)

On Approximation of Orientation Distributions by Means of Spherical Ridgelets. - Oleg V. Michailovich; Yogesh Rathi (IEEE Trans. Image Process., 2010)

Deform PF-MT: Particle Filter With Mode Tracker for Tracking Nonaffine Contour Deformations. - Namrata Vaswani; Yogesh Rathi; Anthony J. Yezzi; Allen R. Tannenbaum (IEEE Trans. Image Process., 2010)

Filtered Multitensor Tractography. - James G. Malcolm; Martha Elizabeth Shenton; Yogesh Rathi (IEEE Trans. Medical Imaging, 2010)

White Matter Bundle Registration and Population Analysis Based on Gaussian Processes. - Demian Wassermann; Yogesh Rathi; Sylvain Bouix; Marek Kubicki; Ron Kikinis; Martha Elizabeth Shenton; Carl-Fredrik Westin (IPMI, 2011)

Compressed sensing of diffusion MRI data using spatial regularization and positivity constraints. - Sudipto Dolui; Oleg V. Michailovich; Yogesh Rathi (ISBI, 2011)

A swarm tracking approach for stochastic white matter tractography. - Yuanjing Feng; Peter Savadjiev; Yogesh Rathi; Meina Quan; Zhejin Wang; Carl-Fredrik Westin (ISBI, 2011)

Improving Registration Using Multi-channel Diffeomorphic Demons Combined with Certainty Maps. - Daniel Forsberg; Yogesh Rathi; Sylvain Bouix; Demian Wassermann; Hans Knutsson; Carl-Fredrik Westin (MBIA, 2011)

Sparse Multi-Shell Diffusion Imaging. - Yogesh Rathi; Oleg V. Michailovich; Kawin Setsompop; Sylvain Bouix; Martha Elizabeth Shenton; Carl-Fredrik Westin (MICCAI (2), 2011)

A full bi-tensor neural tractography algorithm using the unscented Kalman filter. - Stefan Lienhard; James G. Malcolm; Carl-Fredrik Westin; Yogesh Rathi (EURASIP J. Adv. Signal Process., 2011)

Spatially Regularized Compressed Sensing for High Angular Resolution Diffusion Imaging. - Oleg V. Michailovich; Yogesh Rathi; Sudipto Dolui (IEEE Trans. Medical Imaging, 2011)

Multi-scale Characterization of White Matter Tract Geometry. - Peter Savadjiev; Yogesh Rathi; Sylvain Bouix; Ragini Verma; Carl-Fredrik Westin (MICCAI (3), 2012)

Reconstruction of HARDI using compressed sensing and its application to contrast HARDI. - Sudipto Dolui; Iván C. Salgado Patarroyo; Oleg V. Michailovich; Yogesh Rathi (MMBIA, 2012)

Filtering in the Diffeomorphism Group and the Registration of Point Sets. - Yi Gao 002; Yogesh Rathi; Sylvain Bouix; Allen R. Tannenbaum (IEEE Trans. Image Process., 2012)

Joint Modeling of Anatomical and Functional Connectivity for Population Studies. - Archana Venkataraman; Yogesh Rathi; Marek Kubicki; Carl-Fredrik Westin; Polina Golland (IEEE Trans. Medical Imaging, 2012)

Comparing Simultaneous Multi-slice Diffusion Acquisitions. - Yogesh Rathi; Borjan A. Gagoski; Kawin Setsompop; Patricia Ellen Grant; Carl-Fredrik Westin (CDMRI/MMBC@MICCAI, 2013)

Diffusion Propagator Estimation from Sparse Measurements in a Tractography Framework. - Yogesh Rathi; Borjan A. Gagoski; Kawin Setsompop; Oleg V. Michailovich; Patricia Ellen Grant; Carl-Fredrik Westin (MICCAI (3), 2013)

Diffusion Propagator Estimation Using Radial Basis Functions. - Yogesh Rathi; Marc Niethammer; Frederik B. Laun; Kawin Setsompop; Oleg V. Michailovich; Patricia Ellen Grant; Carl-Fredrik Westin (CDMRI/MMBC@MICCAI, 2013)

Combining Surface and Fiber Geometry: An Integrated Approach to Brain Morphology. - Peter Savadjiev; Yogesh Rathi; Sylvain Bouix; Alex R. Smith; Robert T. Schultz; Ragini Verma; Carl-Fredrik Westin (MICCAI (1), 2013)

On Describing Human White Matter Anatomy: The White Matter Query Language. - Demian Wassermann; Nikos Makris; Yogesh Rathi; Martha Elizabeth Shenton; Ron Kikinis; Marek Kubicki; Carl-Fredrik Westin (MICCAI (1), 2013)

Fiber feature map based landmark initialization for highly deformable DTI registration. - Aditya Gupta; Matthew Toews; Ravikiran Janardhana; Yogesh Rathi; John H. Gilmore; Maria L. Escolar; Martin Styner (Image Processing, 2013)

The Estimation of Free-Water Corrected Diffusion Tensors. - Ofer Pasternak; Klaus H. Maier-Hein; Christian F. Baumgartner; Martha Elizabeth Shenton; Yogesh Rathi; Carl-Fredrik Westin (Visualization and Processing of Tensors and Higher Order Descriptors for Multi-Valued Data, 2014)

Preliminary Findings in Diagnostic Prediction of Schizophrenia Using Diffusion Tensor Imaging. - Yogesh Rathi; Martha Elizabeth Shenton; Carl-Fredrik Westin (Visualization and Processing of Tensors and Higher Order Descriptors for Multi-Valued Data, 2014)

A generalized compressed sensing approach to high angular resolution diffusion imaging. - Oleg V. Michailovich; Yogesh Rathi (ISBI, 2014)

Maximum Entropy Estimation of Glutamate and Glutamine in MR Spectroscopic Imaging. - Yogesh Rathi; Lipeng Ning; Oleg V. Michailovich; HuiJun Liao; Borjan A. Gagoski; Patricia Ellen Grant; Martha Elizabeth Shenton; Robert Stern; Carl-Fredrik Westin; Alexander P. Lin (MICCAI (2), 2014)

A dual spherical model for multi-shell diffusion imaging. - Yogesh Rathi; Oleg V. Michailovich; Kawin Setsompop; Carl-Fredrik Westin (Image Processing, 2014)

Resolving complex fibre architecture by means of sparse spherical deconvolution in the presence of isotropic diffusion. - Quan Zhou; Oleg V. Michailovich; Yogesh Rathi (Image Processing, 2014)

Spatially regularized reconstruction of fibre orientation distributions in the presence of isotropic diffusion. - Quan Zhou; Oleg V. Michailovich; Yogesh Rathi (CoRR, 2014)

Multi-shell diffusion signal recovery from sparse measurements. - Yogesh Rathi; Oleg V. Michailovich; Frederik B. Laun; Kawin Setsompop; Patricia Ellen Grant; Carl-Fredrik Westin (Medical Image Anal., 2014)

Fusion of white and gray matter geometry: A framework for investigating brain development. - Peter Savadjiev; Yogesh Rathi; Sylvain Bouix; Alex R. Smith; Robert T. Schultz; Ragini Verma; Carl-Fredrik Westin (Medical Image Anal., 2014)

A Compressed-Sensing Approach for Super-Resolution Reconstruction of Diffusion MRI. - Lipeng Ning; Kawin Setsompop; Oleg V. Michailovich; Nikos Makris; Carl-Fredrik Westin; Yogesh Rathi (IPMI, 2015)

Harmonizing Diffusion MRI Data Across Multiple Sites and Scanners. - Hengameh Mirzaalian; Amicie de Pierrefeu; Peter Savadjiev; Ofer Pasternak; Sylvain Bouix; Marek Kubicki; Carl-Fredrik Westin; Martha Elizabeth Shenton; Yogesh Rathi (MICCAI (1), 2015)

Sparse deconvolution of higher order tensor for fiber orientation distribution estimation. - Yuanjing Feng; Ye Wu 001; Yogesh Rathi; Carl-Fredrik Westin (Artif. Intell. Medicine, 2015)

Sparse Reconstruction Challenge for diffusion MRI: Validation on a physical phantom to determine which acquisition scheme and analysis method to use? - Lipeng Ning; Frederik B. Laun; Yaniv Gur; Edward V. R. DiBella; Samuel Deslauriers-Gauthier; Thinhinane Megherbi; Aurobrata Ghosh; Mauro Zucchelli; Gloria Menegaz; Rutger Fick; Samuel St-Jean; Michael Paquette; et al. (Medical Image Anal., 2015)

Estimating Diffusion Propagator and Its Moments Using Directional Radial Basis Functions. - Lipeng Ning; Carl-Fredrik Westin; Yogesh Rathi (IEEE Trans. Medical Imaging, 2015)

Corticospinal tract modeling for neurosurgical planning by tracking through regions of peritumoral edema and crossing fibers using two-tensor unscented Kalman filter tractography. - Zhenrui Chen; Yanmei Tie; Olutayo I. Olubiyi; Fan Zhang 013; Alireza Mehrtash; Laura Rigolo; Pegah Kahali; Isaiah Norton; Ofer Pasternak; Yogesh Rathi; Alexandra J. Golby; Lauren J. O'Donnell (Int. J. Comput. Assist. Radiol. Surg., 2016)

Inter-site and inter-scanner diffusion MRI data harmonization. - Hengameh Mirzaalian; Lipeng Ning; Peter Savadjiev; Ofer Pasternak; Sylvain Bouix; Oleg V. Michailovich; Gerald Grant; Christine E. Marx; Rajendra A. Morey; Laura A. Flashman; Marie St. George; Thomas W. McAllister; et al. (NeuroImage, 2016)

A joint compressed-sensing and super-resolution approach for very high-resolution diffusion imaging. - Lipeng Ning; Kawin Setsompop; Oleg V. Michailovich; Nikos Makris; Martha Elizabeth Shenton; Carl-Fredrik Westin; Yogesh Rathi (NeuroImage, 2016)

Corrigendum to "A joint compressed-sensing and super-resolution approach for very high-resolution diffusion imaging". - Lipeng Ning; Kawin Setsompop; Oleg V. Michailovich; Nikos Makris; Martha Elizabeth Shenton; Carl-Fredrik Westin; Yogesh Rathi (NeuroImage, 2016)

Automated connectivity-based groupwise cortical atlas generation: Application to data of neurosurgical patients with brain tumors for cortical parcellation prediction. - Fan Zhang 013; Pegah Kahali; Yannick Suter; Isaiah Norton; Laura Rigolo; Peter Savadjiev; Yang Song 001; Yogesh Rathi; Tom Weidong Cai; William M. Wells III; Alexandra J. Golby; Lauren J. O'Donnell (ISBI, 2017)

Application of probabilistically weighted graphs to image-based diagnosis of Alzheimer's disease using diffusion MRI. - Syeda Maryam; Laura McCrackin; Mark Crowley 001; Yogesh Rathi; Oleg V. Michailovich (Computer-Aided Diagnosis, 2017)

Dynamic Regression for Partial Correlation and Causality Analysis of Functional Brain Networks. - Lipeng Ning; Yogesh Rathi (MICCAI (1), 2017)

Supra-Threshold Fiber Cluster Statistics for Data-Driven Whole Brain Tractography Analysis. - Fan Zhang 013; Weining Wu; Lipeng Ning; Gloria McAnulty; Deborah P. Waber; Borjan A. Gagoski; Kiera Sarill; Hesham M. Hamoda; Yang Song 001; Weidong Cai 001; Yogesh Rathi; Lauren J. O'Donnell (MICCAI (1), 2017)

Precise Inference and Characterization of Structural Organization (PICASO) of tissue from molecular diffusion. - Lipeng Ning; Evren Özarslan; Carl-Fredrik Westin; Yogesh Rathi (NeuroImage, 2017)

Harmonizing Diffusion MRI Data Across Magnetic Field Strengths. - Suheyla Cetin Karayumak; Marek Kubicki; Yogesh Rathi (MICCAI (3), 2018)

Investigation into local white matter abnormality in emotional processing and sensorimotor areas using an automatically annotated fiber clustering in major depressive disorder. - Ye Wu 001; Fan Zhang 013; Nikos Makris; Yuping Ning; Isaiah Norton; Shenglin She; Hongjun Peng; Yogesh Rathi; Yuanjing Feng; Huawang Wu; Lauren J. O'Donnell (NeuroImage, 2018)

Whole brain white matter connectivity analysis using machine learning: An application to autism. - Fan Zhang 013; Peter Savadjiev; Weidong Cai 001; Yang Song 001; Yogesh Rathi; Birkan Tunç; Drew Parker; Tina Kapur; Robert T. Schultz; Nikos Makris; Ragini Verma; Lauren J. O'Donnell (NeuroImage, 2018)

Suprathreshold fiber cluster statistics: Leveraging white matter geometry to enhance tractography statistical analysis. - Fan Zhang 013; Weining Wu; Lipeng Ning; Gloria McAnulty; Deborah P. Waber; Borjan A. Gagoski; Kiera Sarill; Hesham M. Hamoda; Yang Song 001; Weidong Cai 001; Yogesh Rathi; Lauren J. O'Donnell (NeuroImage, 2018)

An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan. - Fan Zhang 013; Ye Wu 001; Isaiah Norton; Laura Rigolo; Yogesh Rathi; Nikos Makris; Lauren J. O'Donnell (NeuroImage, 2018)

A Dynamic Regression Approach for Frequency-Domain Partial Coherence and Causality Analysis of Functional Brain Networks. - Lipeng Ning; Yogesh Rathi (IEEE Trans. Medical Imaging, 2018)

Deep White Matter Analysis: Fast, Consistent Tractography Segmentation Across Populations and dMRI Acquisitions. - Fan Zhang 013; Nico Hoffmann; Suheyla Cetin Karayumak; Yogesh Rathi; Alexandra J. Golby; Lauren J. O'Donnell (MICCAI (3), 2019)

Retrospective harmonization of multi-site diffusion MRI data acquired with different acquisition parameters. - Suheyla Cetin Karayumak; Sylvain Bouix; Lipeng Ning; Anthony James; Tim J. Crow; Martha Shenton; Marek Kubicki; Yogesh Rathi (NeuroImage, 2019)

TRAKO: Efficient Transmission of Tractography Data for Visualization. - Daniel Haehn; Loraine Franke; Fan Zhang 013; Suheyla Cetin Karayumak; Steve Pieper 001; Lauren J. O'Donnell; Yogesh Rathi (MICCAI (7), 2020)

Deep white matter analysis (DeepWMA): Fast and consistent tractography segmentation. - Fan Zhang 013; Suheyla Cetin Karayumak; Nico Hoffmann; Yogesh Rathi; Alexandra J. Golby; Lauren J. O'Donnell (Medical Image Anal., 2020)

Cross-scanner and cross-protocol multi-shell diffusion MRI data harmonization: Algorithms and results. - Lipeng Ning; Elisenda Bonet-Carne; Francesco Grussu; Farshid Sepehrband; Enrico Kaden; Jelle Veraart; Stefano B. Blumberg; Can Son Khoo; Marco Palombo; Iasonas Kokkinos; Daniel C. Alexander; Jaume Coll-Font; et al. (NeuroImage, 2020)

Creation of a novel trigeminal tractography atlas for automated trigeminal nerve identification. - Fan Zhang 013; Guoqiang Xie; Laura Leung; Michael A. Mooney; Lorenz Epprecht; Isaiah Norton; Yogesh Rathi; Ron Kikinis; Ossama Al-Mefty; Nikos Makris; Alexandra J. Golby; Lauren J. O'Donnell (NeuroImage, 2020)

Joint RElaxation-Diffusion Imaging Moments to Probe Neurite Microstructure. - Lipeng Ning; Borjan A. Gagoski; Filip Szczepankiewicz; Carl-Fredrik Westin; Yogesh Rathi (IEEE Trans. Medical Imaging, 2020)

FiberStars: Visual Comparison of Diffusion Tractography Data between Multiple Subjects. - Loraine Franke; Daniel Karl I. Weidele; Fan Zhang 013; Suheyla Cetin Karayumak; Steve Pieper 001; Lauren J. O'Donnell; Yogesh Rathi; Daniel Haehn (PacificVis, 2021)

Deep Fiber Clustering: Anatomically Informed Unsupervised Deep Learning for Fast and Effective White Matter Parcellation. - Yuqian Chen; Chaoyi Zhang; Yang Song 001; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Fan Zhang 013; Lauren J. O'Donnell (MICCAI (7), 2021)

A review of deep learning methods for MRI reconstruction. - Arghya Pal; Yogesh Rathi (CoRR, 2021)

Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset? - Kurt G. Schilling; François Rheault; Laurent Petit; Colin B. Hansen; Vishwesh Nath; Fang-Cheng Yeh; Gabriel Girard; Muhamed Barakovic; Jonathan Rafael-Patino; Thomas Yu; Elda Fischi Gomez; Marco Pizzolato; et al. (NeuroImage, 2021)

Model and Predict Age and Sex in Healthy Subjects Using Brain White Matter Features: A Deep Learning Approach. - Hao He; Fan Zhang 013; Steve Pieper 001; Nikos Makris; Yogesh Rathi; William M. Wells III; Lauren J. O'Donnell (ISBI, 2022)

Supwma: Consistent and Efficient Tractography Parcellation of Superficial White Matter with Deep Learning. - Tengfei Xue; Fan Zhang 013; Chaoyi Zhang; Yuqian Chen; Yang Song 001; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Lauren J. O'Donnell (ISBI, 2022)

White Matter Tracts are Point Clouds: Neuropsychological Score Prediction and Critical Region Localization via Geometric Deep Learning. - Yuqian Chen; Fan Zhang 013; Chaoyi Zhang; Tengfei Xue; Leo R. Zekelman; Jianzhong He; Yang Song 001; Nikos Makris; Yogesh Rathi; Alexandra J. Golby; Weidong Cai 001; Lauren J. O'Donnell (MICCAI (1), 2022)

TractoFormer: A Novel Fiber-Level Whole Brain Tractography Analysis Framework Using Spectral Embedding and Vision Transformers. - Fan Zhang 013; Tengfei Xue; Weidong Cai 001; Yogesh Rathi; Carl-Fredrik Westin; Lauren J. O'Donnell (MICCAI (1), 2022)

DFC: Anatomically Informed Fiber Clustering with Self-supervised Deep Learning for Fast and Effective Tractography Parcellation. - Yuqian Chen; Chaoyi Zhang; Tengfei Xue; Yang Song 001; Nikos Makris; Yogesh Rathi; Tom Weidong Cai; Fan Zhang 013; Lauren J. O'Donnell (CoRR, 2022)

A Deep Learning Approach Using Masked Image Modeling for Reconstruction of Undersampled K-spaces. - Kyler Larsen; Arghya Pal; Yogesh Rathi (CoRR, 2022)

A Novel Supervised Contrastive Regression Framework for Prediction of Neurocognitive Measures Using Multi-Site Harmonized Diffusion MRI Tractography. - Tengfei Xue; Fan Zhang 013; Leo R. Zekelman; Chaoyi Zhang; Yuqian Chen; Suheyla Cetin Karayumak; Steven D. Pieper; William M. Wells III; Yogesh Rathi; Nikos Makris; Weidong Cai 001; Lauren J. O'Donnell (CoRR, 2022)

Age Prediction Performance Varies Across Deep, Superficial, and Cerebellar White Matter Connections. - Yuxiang Wei 004; Tengfei Xue; Yogesh Rathi; Nikos Makris; Fan Zhang 013; Lauren J. O'Donnell (CoRR, 2022)

Cross-site harmonization of multi-shell diffusion MRI measures based on rotational invariant spherical harmonics (RISH). - Alberto De Luca; Suheyla Cetin Karayumak; Alexander Leemans; Yogesh Rathi; Stephan P. Swinnen; Jolien Gooijers; Amanda Clauwaert; Roald Bahr; Stian Bahr Sandmo; Nir A. Sochen; David Kaufmann; Marc Muehlmann; et al. (NeuroImage, 2022)

White matter association tracts underlying language and theory of mind: An investigation of 809 brains from the Human Connectome Project. - Leo R. Zekelman; Fan Zhang 013; Nikos Makris; Jianzhong He; Yuqian Chen; Tengfei Xue; Daniela Liera; Daniel L. Drane; Yogesh Rathi; Alexandra J. Golby; Lauren J. O'Donnell (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)

Tractgraphcnn: Anatomically Informed Graph CNN for Classification Using Diffusion MRI Tractography. - Yuqian Chen; Fan Zhang 013; Leo R. Zekelman; Tengfei Xue; Chaoyi Zhang; Yang Song 001; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Lauren J. O'Donnell (ISBI, 2023)

A Deep-Learning Framework for Estimating the Posterior Distribution of the Standard Model of Diffusion Mri. - Hazhar Sufi Karimi; Lipeng Ning; Yogesh Rathi (ISBI, 2023)

DEEPRGVP: A novel microstructure-informed supervised contrastive learning framework for automated identification of the retinogeniculate pathway using dMRI tractography. - Sipei Li; Jianzhong He; Tengfei Xue; Guoqiang Xie; Shun Yao; Yuqian Chen; Erickson F. Torio; Yuanjing Feng; Dhiego Chaves de Almeida Bastos; Yogesh Rathi; Nikos Makris; Ron Kikinis; et al. (ISBI, 2023)

In-Vivo Estimation of Axon Radii From Clinical Scanners. - Debdut Mandal; Lipeng Ning; Yogesh Rathi (ISBI, 2023)

Tractography-Based Parcellation of Cerebellar Dentate Nuclei via a Deep Nonnegative Matrix Factorization Clustering Method. - Xiao Xu; Yuqian Chen; Leo R. Zekelman; Yogesh Rathi; Nikos Makris; Fan Zhang 013; Lauren J. O'Donnell (ISBI, 2023)

A Deep Learning Framework for Estimating Multi-Fiber PICASO Model Parameters of Tissue Microstructure Using Diffusion MRI. - Tengfei Xue; Hazhar Sufi Karimi; William Consagra; Fan Zhang 013; Weidong Cai 001; Lauren J. O'Donnell; Lipeng Ning; Yogesh Rathi (ISBI, 2023)

A Deep Network for Explainable Prediction of Non-imaging Phenotypes Using Anatomical Multi-view Data. - Yuxiang Wei 004; Yuqian Chen; Tengfei Xue; Leo R. Zekelman; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Fan Zhang 013; Lauren J. O'Donnell (CDMRI@MICCAI, 2023)

TractCloud: Registration-Free Tractography Parcellation with a Novel Local-Global Streamline Point Cloud Representation. - Tengfei Xue; Yuqian Chen; Chaoyi Zhang; Alexandra J. Golby; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Fan Zhang 013; Lauren J. O'Donnell (MICCAI (8), 2023)

Fiber Tract Shape Measures Inform Prediction of Non-Imaging Phenotypes. - Wan Liu 001; Yuqian Chen; Chuyang Ye; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Fan Zhang 013; Lauren J. O'Donnell (CoRR, 2023)

SlicerTMS: Interactive Real-time Visualization of Transcranial Magnetic Stimulation using Augmented Reality and Deep Learning. - Loraine Franke; Tae Young Park; Jie Luo 003; Yogesh Rathi; Steve Pieper 001; Lipeng Ning; Daniel Haehn (CoRR, 2023)

Reconstructing the somatotopic organization of the corticospinal tract remains a challenge for modern tractography methods. - Jianzhong He; Fan Zhang 013; Yiang Pan; Yuanjing Feng; Jarrett Rushmore; Erickson Torio; Yogesh Rathi; Nikos Makris; Ron Kikinis; Alexandra J. Golby; Lauren J. O'Donnell (CoRR, 2023)

Superficial white matter analysis: An efficient point-cloud-based deep learning framework with supervised contrastive learning for consistent tractography parcellation across populations and dMRI acquisitions. - Tengfei Xue; Fan Zhang 013; Chaoyi Zhang; Yuqian Chen; Yang Song 001; Alexandra J. Golby; Nikos Makris; Yogesh Rathi; Weidong Cai 001; Lauren J. O'Donnell (Medical Image Anal., 2023)

Deep fiber clustering: Anatomically informed fiber clustering with self-supervised deep learning for fast and effective tractography parcellation. - Yuqian Chen; Chaoyi Zhang; Tengfei Xue; Yang Song 001; Nikos Makris; Yogesh Rathi; Tom Weidong Cai; Fan Zhang 013; Lauren J. O'Donnell (NeuroImage, 2023)

A Novel Deep Clustering Framework for Fine-Scale Parcellation of Amygdala Using DMRI Tractography. - Haolin He; Ce Zhu; Le Zhang 001; Yipeng Liu 001; Xiao Xu; Yuqian Chen; Leo R. Zekelman; Jarrett Rushmore; Yogesh Rathi; Nikos Makris; Lauren J. O'Donnell; Fan Zhang 013 (ISBI, 2024)

Estimating Neural Orientation Distribution Fields on High Resolution Diffusion MRI Scans. - Mohammed Munzer Dwedari; William Consagra; Philip Müller; Özgün Turgut; Daniel Rueckert; Yogesh Rathi (MICCAI (7), 2024)

SlicerTMS: Real-Time Visualization of Transcranial Magnetic Stimulation for Mental Health Treatment. - Loraine Franke; Jie Luo 003; Tae Young Park; Nam Wook Kim; Yogesh Rathi; Steven D. Pieper; Lipeng Ning; Daniel Haehn (MICCAI (6), 2024)

Cross-Domain Fiber Cluster Shape Analysis for Language Performance Cognitive Score Prediction. - Yui Lo; Yuqian Chen; Dongnan Liu; Wan Liu 001; Leo R. Zekelman; Fan Zhang 013; Yogesh Rathi; Nikos Makris; Alexandra J. Golby; Weidong Cai 001; Lauren J. O'Donnell (CDMRI@MICCAI, 2024)

Introducing QuantConn: Overcoming Challenging Diffusion Acquisitions with Harmonization. - Nancy Newlin; Kurt Schilling; Serge Koudoro; Bramsh Qamar Chandio; Praitayini Kanakaraj; Daniel Moyer; Claire E. Kelly; Sila Genc; Joseph Yuan-Mou Yang; Ye Wu 001; Nagesh Adluru; Vishwesh Nath; et al. (CDMRI@MICCAI, 2024)

TractGraphFormer: Anatomically Informed Hybrid Graph CNN-Transformer Network for Classification from Diffusion MRI Tractography. - Yuqian Chen; Fan Zhang 013; Meng Wang; Leo R. Zekelman; Suheyla Cetin Karayumak; Tengfei Xue; Chaoyi Zhang; Yang Song 001; Nikos Makris; Yogesh Rathi; Tom Weidong Cai; Lauren J. O'Donnell (CoRR, 2024)

Deep multimodal saliency parcellation of cerebellar pathways: linking microstructure and individual function through explainable multitask learning. - Ari Tchetchenian; Leo R. Zekelman; Yuqian Chen; Jarrett Rushmore; Fan Zhang 013; Edward H. Yeterian; Nikos Makris; Yogesh Rathi; Erik Meijering; Yang Song 001; Lauren J. O'Donnell (CoRR, 2024)

White Matter Geometry-Guided Score-Based Diffusion Model for Tissue Microstructure Imputation in Tractography Imaging. - Yui Lo; Yuqian Chen; Fan Zhang 013; Dongnan Liu; Leo R. Zekelman; Suheyla Cetin Karayumak; Yogesh Rathi; Tom Weidong Cai; Lauren J. O'Donnell (CoRR, 2024)

EVENet: Evidence-based Ensemble Learning for Uncertainty-aware Brain Parcellation Using Diffusion MRI. - Chenjun Li; Dian Yang; Shun Yao; Shuyue Wang; Ye Wu 001; Le Zhang 001; Qiannuo Li; Kang Ik Kevin Cho; Johanna Seitz-Holland; Lipeng Ning; Jon Haitz Legarreta; Yogesh Rathi; et al. (CoRR, 2024)

The shape of the brain's connections is predictive of cognitive performance: an explainable machine learning study. - Yui Lo; Yuqian Chen; Dongnan Liu; Wan Liu 001; Leo R. Zekelman; Jarrett Rushmore; Fan Zhang 013; Yogesh Rathi; Nikos Makris; Alexandra J. Golby; Weidong Cai 001; Lauren J. O'Donnell (CoRR, 2024)

MICCAI-CDMRI 2023 QuantConn Challenge Findings on Achieving Robust Quantitative Connectivity through Harmonized Preprocessing of Diffusion MRI. - Nancy R. Newlin; Kurt Schilling; Serge Koudoro; Bramsh Qamar Chandio; Praitayini Kanakaraj; Daniel Moyer; Claire E. Kelly; Sila Genc; Jian Chen; Joseph Yuan-Mou Yang; Ye Wu; Yifei He; et al. (CoRR, 2024)

TractGeoNet: A geometric deep learning framework for pointwise analysis of tract microstructure to predict language assessment performance. - Yuqian Chen; Leo R. Zekelman; Chaoyi Zhang; Tengfei Xue; Yang Song 001; Nikos Makris; Yogesh Rathi; Alexandra J. Golby; Weidong Cai 001; Fan Zhang 013; Lauren J. O'Donnell (Medical Image Anal., 2024)

Neural orientation distribution fields for estimation and uncertainty quantification in diffusion MRI. - William Consagra; Lipeng Ning; Yogesh Rathi (Medical Image Anal., 2024)

DDParcel: Deep Learning Anatomical Brain Parcellation From Diffusion MRI. - Fan Zhang 013; Kang Ik Kevin Cho; Johanna Seitz-Holland; Lipeng Ning; Jon Haitz Legarreta; Yogesh Rathi; Carl-Fredrik Westin; Lauren J. O'Donnell; Ofer Pasternak (IEEE Trans. Medical Imaging, 2024)

TractShapeNet: Efficient Multi-Shape Learning with 3D Tractography Point Clouds. - Yui Lo; Yuqian Chen; Dongnan Liu; Jon Haitz Legarreta; Leo R. Zekelman; Fan Zhang 013; Jarrett Rushmore; Yogesh Rathi; Nikos Makris; Alexandra J. Golby; Tom Weidong Cai; Lauren J. O'Donnell (ISBI, 2025)

A Novel Deep Learning Tractography Fiber Clustering Framework for Functionally Consistent White Matter Parcellation Using Multimodal Diffusion MRI and Functional MRI. - Jin Wang; Bocheng Guo; Yijie Li; Junyi Wang; Yuqian Chen; Jarrett Rushmore; Nikos Makris; Yogesh Rathi; Lauren J. O'Donnell; Fan Zhang 013 (ISBI, 2025)

DDEvENet: Evidence-based ensemble learning for uncertainty-aware brain parcellation using diffusion MRI. - Chenjun Li; Dian Yang; Shun Yao; Shuyue Wang; Ye Wu 001; Le Zhang 001; Qiannuo Li; Kang Ik Kevin Cho; Johanna Seitz-Holland; Lipeng Ning; Jon Haitz Legarreta; Yogesh Rathi; et al. (Comput. Medical Imaging Graph., 2025)

TractGraphFormer: Anatomically informed hybrid graph CNN-transformer network for interpretable sex and age prediction from diffusion MRI tractography. - Yuqian Chen; Fan Zhang 013; Meng Wang; Leo R. Zekelman; Suheyla Cetin Karayumak; Tengfei Xue; Chaoyi Zhang; Yang Song 001; Jarrett Rushmore; Nikos Makris; Yogesh Rathi; Weidong Cai 001; et al. (Medical Image Anal., 2025)

A deep learning approach to multi-fiber parameter estimation and uncertainty quantification in diffusion MRI. - William Consagra; Lipeng Ning; Yogesh Rathi (Medical Image Anal., 2025)

DeepNuParc: A novel deep clustering framework for fine-scale parcellation of brain nuclei using diffusion MRI tractography. - Haolin He; Ce Zhu; Le Zhang 001; Yipeng Liu 001; Xiao Xu; Yuqian Chen; Leo R. Zekelman; Jarrett Rushmore; Yogesh Rathi; Nikos Makris; Lauren J. O'Donnell; Fan Zhang 013 (NeuroImage, 2025)

Rapid Whole Brain Mesoscale In-vivo MR Imaging using Multi-scale Implicit Neural Representation. - Jun Lyu; Lipeng Ning; William Consagra; Qiang Liu; Richard J. Rushmore; Berkin Bilgic; Yogesh Rathi (CoRR, 2025)

TractCloud-FOV: Deep Learning-based Robust Tractography Parcellation in Diffusion MRI with Incomplete Field of View. - Yuqian Chen; Leo R. Zekelman; Yui Lo; Suheyla Cetin Karayumak; Tengfei Xue; Yogesh Rathi; Nikos Makris; Fan Zhang 013; Tom Weidong Cai; Lauren J. O'Donnell (CoRR, 2025)

DDCSR: A Novel End-to-End Deep Learning Framework for Cortical Surface Reconstruction from Diffusion MRI. - Chengjin Li; Yuqian Chen; Nir A. Sochen; Wei Zhang; Carl-Fredrik Westin; Yogesh Rathi; Lauren J. O'Donnell; Ofer Pasternak; Fan Zhang 013 (CoRR, 2025)

A Multimodal Deep Learning Approach for White Matter Shape Prediction in Diffusion MRI Tractography. - Yui Lo; Yuqian Chen; Dongnan Liu; Leo R. Zekelman; Jarrett Rushmore; Yogesh Rathi; Nikos Makris; Alexandra J. Golby; Fan Zhang 013; Tom Weidong Cai; Lauren J. O'Donnell (CoRR, 2025)

AGFS-Tractometry: A Novel Atlas-Guided Fine-Scale Tractometry Approach for Enhanced Along-Tract Group Statistical Comparison Using Diffusion MRI Tractography. - Ruixi Zheng; Wei Zhang; Yijie Li; Xi Zhu; Zhou Lan; Jarrett Rushmore; Yogesh Rathi; Nikos Makris; Lauren J. O'Donnell; Fan Zhang 013 (CoRR, 2025)

DDTracking: A Deep Generative Framework for Diffusion MRI Tractography with Streamline Local-Global Spatiotemporal Modeling. - Yijie Li; Wei Zhang; Xi Zhu; Ye Wu 001; Yogesh Rathi; Lauren J. O'Donnell; Fan Zhang 013 (CoRR, 2025)