Extracting biomarkers of autism from MEG resting-state functional connectivity networks. - Vassilis Tsiaras; Panagiotis G. Simos; Roozbeh Rezaie; Bhavin R. Sheth; Eleftherios Garyfallidis; Eduardo M. Castillo; Andrew C. Papanicolaou (Comput. Biol. Medicine, 2011)

The Approximation of the Dissimilarity Projection. - Emanuele Olivetti; Thien Bao Nguyen; Eleftherios Garyfallidis (PRNI, 2012)

Fast Clustering for Interactive Tractography Segmentation. - Emanuele Olivetti; Thien Bao Nguyen; Eleftherios Garyfallidis; Nivedita Agarwal; Paolo Avesani (PRNI, 2013)

Tractometer: Towards validation of tractography pipelines. - Marc-Alexandre Côté; Gabriel Girard; Arnaud Boré; Eleftherios Garyfallidis; Jean-Christophe Houde; Maxime Descoteaux (Medical Image Anal., 2013)

Dipy, a library for the analysis of diffusion MRI data. - Eleftherios Garyfallidis; Matthew Brett; Bagrat Amirbekian; Ariel Rokem; Stéfan van der Walt; Maxime Descoteaux; Ian Nimmo-Smith (Frontiers Neuroinformatics, 2014)

Quantitative Comparison of Reconstruction Methods for Intra-Voxel Fiber Recovery From Diffusion MRI. - Alessandro Daducci; Erick Jorge Canales-Rodríguez; Maxime Descoteaux; Eleftherios Garyfallidis; Yaniv Gur; Ying-Chia Lin; Merry Mani; Sylvain Merlet; Michael Paquette; Alonso Ramirez-Manzanares; Marco Reisert; Paulo Reis Rodrigues; et al. (IEEE Trans. Medical Imaging, 2014)

Tractome: a visual data mining tool for brain connectivity analysis. - Diana Porro-Muñoz; Emanuele Olivetti; Nusrat Sharmin; Thien Bao Nguyen; Eleftherios Garyfallidis; Paolo Avesani (Data Min. Knowl. Discov., 2015)

Robust and efficient linear registration of white-matter fascicles in the space of streamlines. - Eleftherios Garyfallidis; Omar Ocegueda; Demian Wassermann; Maxime Descoteaux (NeuroImage, 2015)

On the computation of integrals over fixed-size rectangles of arbitrary dimension. - Omar Ocegueda; Oscar Dalmau Cedeño; Eleftherios Garyfallidis; Maxime Descoteaux; Mariano Rivera (Pattern Recognit. Lett., 2016)

3D-SSF: A bio-inspired approach for dynamic multi-subject clustering of white matter tracts. - A. Chekir; Salima Hassas; Maxime Descoteaux; Marc-Alexandre Côté; Eleftherios Garyfallidis; Fatima Oulebsir-Boumghar (Comput. Biol. Medicine, 2017)

Recognition of white matter bundles using local and global streamline-based registration and clustering. - Eleftherios Garyfallidis; Marc-Alexandre Côté; Francois Rheault; Jasmeen Sidhu; Janice Hau; Laurent Petit; David Fortin; Stephen Cunanne; Maxime Descoteaux (NeuroImage, 2018)

Fitting IVIM with Variable Projection and Simplicial Optimization. - Shreyas Fadnavis; Hamza Farooq; Maryam Afzali; Christophe Lenglet; Tryphon T. Georgiou; Hu Cheng; Sharlene D. Newman; Shahnawaz Ahmed; Rafael Neto Henriques; Eric Peterson; Serge Koudoro; Ariel Rokem; et al. (CoRR, 2019)

Identifying Vulnerable Brain Networks in Mouse Models of Genetic Risk Factors for Late Onset Alzheimer's Disease. - Alexandra Badea; Wenlin Wu; Jordan Shuff; Michele Wang; Robert J. Anderson; Yi Qi; G. Allan Johnson; Joan G. Wilson; Serge Koudoro; Eleftherios Garyfallidis; Carol A. Colton; David B. Dunson (Frontiers Neuroinformatics, 2019)

nipy/nibabel: 2.4.0. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; Demian Wassermann; et al. (Zenodo, 2019)

nipy/nibabel: 2.4.1. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; Demian Wassermann; et al. (Zenodo, 2019)

nipy/nibabel: 2.5.0. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; Demian Wassermann; et al. (Zenodo, 2019)

nipy/nibabel: 2.5.1. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; Demian Wassermann; et al. (Zenodo, 2019)

nipy/nibabel: 3.0.0rc1. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; Demian Wassermann; et al. (Zenodo, 2019)

nipy/nibabel: 3.0.0rc2. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; Demian Wassermann; et al. (Zenodo, 2019)

nipy/nibabel: 3.0.0. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; Demian Wassermann; et al. (Zenodo, 2019)

Patch2Self: Denoising Diffusion MRI with Self-Supervised Learning​. - Shreyas Fadnavis; Joshua Batson; Eleftherios Garyfallidis (NeurIPS, 2020)

nipy/nibabel: 3.0.1. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; Demian Wassermann; et al. (Zenodo, 2020)

nipy/nibabel: 3.0.2. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; Demian Wassermann; et al. (Zenodo, 2020)

nipy/nibabel: 2.5.2. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; Demian Wassermann; et al. (Zenodo, 2020)

nipy/nibabel: 3.1.0. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; et al. (Zenodo, 2020)

nipy/nibabel: 3.1.1. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; Eric Larson; et al. (Zenodo, 2020)

nipy/nibabel: 3.2.0. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Eric Larson; Satrajit S. Ghosh; et al. (Zenodo, 2020)

nipy/nibabel: 3.2.1. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Eric Larson; Satrajit S. Ghosh; et al. (Zenodo, 2020)

Fast Tractography Streamline Search. - Etienne St-Onge; Eleftherios Garyfallidis; D. Louis Collins (CDMRI@MICCAI, 2021)

ThetA - fast and robust clustering via a distance parameter. - Eleftherios Garyfallidis; Shreyas Fadnavis; Jong Sung Park; Bramsh Qamar Chandio; Javier Guaje; Serge Koudoro; Nasim Anousheh (CoRR, 2021)

FURY: advanced scientific visualization. - Eleftherios Garyfallidis; Serge Koudoro; Javier Guaje; Marc-Alexandre Côté; Soham Biswas; David Reagan; Nasim Anousheh; Filipi N. Silva; Geoffrey C. Fox; FURY Contributors (J. Open Source Softw., 2021)

On the generalizability of diffusion MRI signal representations across acquisition parameters, sequences and tissue types: Chronicles of the MEMENTO challenge. - Alberto De Luca; Andrada Ianus; Alexander Leemans; Marco Palombo; Noam Shemesh; Hui Zhang 005; Daniel C. Alexander; Markus Nilsson; Martijn Froeling; Geert Jan Biessels; Mauro Zucchelli; Matteo Frigo; et al. (NeuroImage, 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)

Pandora: 4-D White Matter Bundle Population-Based Atlases Derived from Diffusion MRI Fiber Tractography. - Colin B. Hansen; Qi Yang 004; Ilwoo Lyu; Francois Rheault; Cailey I. Kerley; Bramsh Qamar Chandio; Shreyas Fadnavis; Owen A. Williams; Andrea T. Shafer; Susan M. Resnick; David H. Zald; Laurie E. Cutting; et al. (Neuroinformatics, 2021)

FURY: advanced scientific visualisation. - Eleftherios Garyfallidis; Serge Koudoro; Javier Guaje; Marc-Alexandre Côté; Soham Biswas; David Reagan; Nasim Anousheh; Filipi N. Silva; Geoffrey C. Fox; FURY Contributors (Zenodo, 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)

NUQ: A Noise Metric for Diffusion MRI via Uncertainty Discrepancy Quantification. - Shreyas Fadnavis; Jens Sjölund; Anders Eklund 002; Eleftherios Garyfallidis (CoRR, 2022)

EVC-Net: Multi-scale V-Net with Conditional Random Fields for Brain Extraction. - Jong Sung Park; Shreyas Fadnavis; Eleftherios Garyfallidis (CoRR, 2022)

What's new and what's next in diffusion MRI preprocessing. - Chantal M. W. Tax; Matteo Bastiani; Jelle Veraart; Eleftherios Garyfallidis; M. Okan Irfanoglu (NeuroImage, 2022)

Fast Streamline Search: An Exact Technique for Diffusion MRI Tractography. - Etienne St-Onge; Eleftherios Garyfallidis; D. Louis Collins (Neuroinformatics, 2022)

nipy/nibabel: 3.2.2. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Eric Larson; Satrajit S. Ghosh; et al. (Zenodo, 2022)

nipy/nibabel: 4.0.0rc0. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Eric Larson; Satrajit S. Ghosh; et al. (Zenodo, 2022)

nipy/nibabel. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Eric Larson; Satrajit S. Ghosh; et al. (Zenodo, 2022)

Clinical validation of rapid GPU-enabled DTI tractography of the brain. - Felix Liu; Vanitha Sankaranarayanan; Javier E. Villanueva-Meyer; Shawn Hervey-Jumper; James Hawkins; Pablo F. Damasceno; Mauro Bisson; Joshua Romero; Thorsten Kurth; Massimiliano Fatica; Eleftherios Garyfallidis; Ariel Rokem; et al. (High Performance Computing for Imaging, 2023)

brainlife.io: A decentralized and open source cloud platform to support neuroscience research. - Soichi Hayashi; Bradley Caron; Anibal Sólon Heinsfeld; Sophia Vinci-Booher; Brent C. McPherson; Daniel N. Bullock; Giulia Berto; J. Guiomar Niso; Sandra Hanekamp; Daniel Levitas; Lindsey Kitchell; Josiah Leong; et al. (CoRR, 2023)

Denoising of diffusion MRI in the cervical spinal cord - effects of denoising strategy and acquisition on intra-cord contrast, signal modeling, and feature conspicuity. - Kurt G. Schilling; Shreyas Fadnavis; Joshua Batson; Mereze Visagie; Anna J. E. Combes; Samantha By; Colin D. Mcknight; Francesca Bagnato; Eleftherios Garyfallidis; Bennett A. Landman; Seth A. Smith; Kristin P. O'Grady (NeuroImage, 2023)

nipy/nibabel: 5.0.0. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Eric Larson; Satrajit S. Ghosh; et al. (Zenodo, 2023)

nipy/nibabel: 5.0.1. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Eric Larson; Satrajit S. Ghosh; et al. (Zenodo, 2023)

nipy/nibabel: 5.1.0. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Yaroslav O. Halchenko; Michiel Cottaar; Eric Larson; Satrajit S. Ghosh; et al. (Zenodo, 2023)

nipy/nibabel: 5.2.0. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Eric Larson; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; et al. (Zenodo, 2023)

Patch2Self2: Self-Supervised Denoising on Coresets via Matrix Sketching. - Shreyas Fadnavis; Agniva Chowdhury; Joshua Batson; Petros Drineas; Eleftherios Garyfallidis (CVPR, 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)

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)

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)

nipy/nibabel: 5.2.1. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Eric Larson; Yaroslav O. Halchenko; Michiel Cottaar; Satrajit S. Ghosh; et al. (Zenodo, 2024)

DeepN4: Learning N4ITK Bias Field Correction for T1-weighted Images. - Praitayini Kanakaraj; Tianyuan Yao; Leon Y. Cai; Ho Hin Lee; Nancy R. Newlin; Michael E. Kim; Chenyu Gao; Kimberly R. Pechman; Derek B. Archer; Timothy J. Hohman; Angela L. Jefferson; Lori L. Beason-Held; et al. (Neuroinformatics, 2024)

nipy/nibabel: 5.3.0. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Dimitri Papadopoulos Orfanos; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Eric Larson; Yaroslav O. Halchenko; Michiel Cottaar; et al. (Zenodo, 2024)

nipy/nibabel: 5.3.1. - Matthew Brett; Christopher J. Markiewicz; Michael Hanke; Marc-Alexandre Côté; Ben Cipollini; Dimitri Papadopoulos Orfanos; Paul McCarthy; Dorota Jarecka; Christopher P. Cheng; Eric Larson; Yaroslav O. Halchenko; Michiel Cottaar; et al. (Zenodo, 2024)

Multi-Resolution Guided 3D GANs for Medical Image Translation. - Juhyung Ha; Jong Sung Park; David Crandall; Eleftherios Garyfallidis; Xuhong Zhang 001 (WACV, 2025)

Skull stripping with purely synthetic data. - Jong Sung Park; Juhyung Ha; Siddhesh P. Thakur; Alexandra Badea; Spyridon Bakas; Eleftherios Garyfallidis (CoRR, 2025)

ResPlan: A Large-Scale Vector-Graph Dataset of 17,000 Residential Floor Plans. - Mohamed Abouagour; Eleftherios Garyfallidis (CoRR, 2025)