Publications
Recent research papers and articles
Dipy, a library for the analysis of diffusion MRI data
Eleftherios Garyfallidis and Matthew Brett and Bagrat Amirbekian and Ariel Rokem and Stefan Van Der Walt and Maxime Descoteaux and Ian Nimmo-Smith and Dipy Contributors
Tractometer: towards validation of tractography pipelines
Marc-Alexandre Côté and Gabriel Girard and Arnaud Boré and Eleftherios Garyfallidis and Jean-Christophe Houde and Maxime Descoteaux
Quickbundles, a method for tractography simplification
Eleftherios Garyfallidis and Matthew Brett and Marta Morgado Correia and Guy B Williams and Ian Nimmo-Smith
Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI
Alessandro Daducci and Erick Jorge Canales-Rodrı and Maxime Descoteaux and Eleftherios Garyfallidis and Yaniv Gur and Ying-Chia Lin and Merry Mani and Sylvain Merlet and Michael Paquette and Alonso Ramirez-Manzanares and Marco Reisert and Paulo Reis Rodrigues and Farshid Sepehrband and Emmanuel Caruyer and Jeiran Choupan and Rachid Deriche and Mathews Jacob and Gloria Menegaz and Vesna Prčkovska and Mariano Rivera and Yves Wiaux and Jean-Philippe Thiran
Extracting biomarkers of autism from MEG resting-state functional connectivity networks
Vassilis Tsiaras and Panagiotis G Simos and Roozbeh Rezaie and Bhavin R Sheth and Eleftherios Garyfallidis and Eduardo M Castillo and Andrew C Papanicolaou
Reduced brain white matter integrity in trichotillomania: a diffusion tensor imaging study
Samuel R Chamberlain and Adam Hampshire and Lara A Menzies and Eleftherios Garyfallidis and Jon E Grant and Brian L Odlaug and Kevin Craig and Naomi Fineberg and Barbara J Sahakian
Dipy–a novel software library for diffusion MR and tractography
Eleftherios Garyfallidis and Matthew Brett and Bagrat Amirbekian and Christopher Nguyen and Fang-Cheng Yeh and Y Halchenko and I Nimmo-Smith
Robust and efficient linear registration of white-matter fascicles in the space of streamlines
Eleftherios Garyfallidis and Omar Ocegueda and Demian Wassermann and Maxime Descoteaux
Localizing and characterizing single fiber populations throughout the brain
Chantal MW Tax and Dmitry S Novikov and Eleftherios Garyfallidis and Max A Viergever and Maxime Descoteaux and Alexander Leemans
The approximation of the dissimilarity projection
Emanuele Olivetti and Thien Bao Nguyen and Eleftherios Garyfallidis
Fast clustering for interactive tractography segmentation
Emanuele Olivetti and Thien Bao Nguyen and Eleftherios Garyfallidis and Nivedita Agarwal and Paolo Avesani
Cleaning up the mess: tractography outlier removal using hierarchical QuickBundles clustering
Marc-Alexandre Côté and Eleftherios Garyfallidis and Hugo Larochelle and Maxime Descoteaux
Fast dimensionality reduction for brain tractography clustering
Eleftherios Garyfallidis and Matthew Brett and Ian Nimmo-Smith
Tractography-based connectomes are dominated by false-positive connections. bioRxiv
Klaus Maier-Hein and Peter Neher and Jean-Christophe Houde and Marc-Alexandre Cote and Eleftherios Garyfallidis and Jidan Zhong and Maxime Chamberland and Fang-Cheng Yeh and Ying Chia Lin and Qing Ji
Tractography-based connectomes are dominated by false-positive connections
Klaus Maier-Hein and Peter Neher and Jean-Christophe Houde and Marc-Alexandre Cote and Eleftherios Garyfallidis and Jidan Zhong and Maxime Chamberland and Fang-Cheng Yeh and Ying Chia Lin and Qing Ji and Wilburn E Reddick and John O Glass and David Qixiang Chen and Yuanjing Feng and Chengfeng Gao and Ye Wu and Jieyan Ma and He Renjie and Qiang Li and Carl-Fredrik Westin and Samuel Deslauriers-Gauthier and J Omar Ocegueda Gonzalez and Michael Paquette and Samuel St-Jean and Gabriel Girard and Francois Rheault and Jasmeen Sidhu and Chantal MW Tax and Fenghua Guo and Hamed Y Mesri and Szabolcs David and Martijn Froeling and Anneriet M Heemskerk and Alexander Leemans and Arnaud Bore and Basile Pinsard and Christophe Bedetti and Matthieu Desrosiers and Simona Brambati and Julien Doyon and Alessia Sarica and Roberta Vasta and Antonio Cerasa and Aldo Quattrone and Jason Yeatman and Ali R Khan and Wesley Hodges and Simon Alexander and Darcvi Romascano and Muhamed Barakovic and Anna Auria and Oscar Esteban and Alia Lemkaddem and Jean-Philippe Thiran and H Ertan Cetingul and Benjamin L Odry and Boris Mailhe and Mariappan Nadar and Fabrizio Pizzagalli and Gautam Prasad and Julio Villalon-Reina and Justin Galvis and Paul Thompson and Francisco Requejo and Pedro Laguna and Luis Lacerda and Rachel Barrett and Flavio Dell'Acqua and Marco Catani and Laurent Petit and Emmanuel Caruyer and Alessandro Daducci and Tim Dyrby and Tim Holland-Letz and Claus Hilgetag and Bram Stieltjes and Maxime Descoteaux
Tract-profiling and bundle statistics: a test-retest validation study
Martin Cousineau and Eleftherios Garyfallidis and Marc-Alexandre Côté and Pierre-Marc Jodoin and Maxime Descoteaux
Tractome: a visual data mining tool for brain connectivity analysis
Diana Porro-Muñoz and Emanuele Olivetti and Nusrat Sharmin and Thien Bao Nguyen and Eleftherios Garyfallidis and Paolo Avesani
Comparison between discrete and continuous propagator indices from cartesian q-space dsi sampling
Mauro Zucchelli and Eleftherios Garyfallidis and Michael Paquette and Sylvain Merlet and Gloria Menegaz and Maxime Descoteaux
Semi-Automatic Segmentation of Optic Radiations and LGN, and Their Relationship to EEG Alpha Waves
Emmanuelle Renauld and Maxime Descoteaux and Michaël Bernier and Eleftherios Garyfallidis and Kevin Whittingstall
A hybrid approach for optimal automatic segmentation of white matter tracts in hardi
Amira Chekir and Maxime Descoteaux and Eleftherios Garyfallidis and Marc-Alexandre Côté and Fatima Oulebsir Boumghar
QuickBundlesX: sequential clustering of millions of streamlines in multiple levels of detail at record execution time
Eleftherios Garyfallidis and Marc-Alexandre Côté and François Rheault and Maxime Descoteaux
Dynamic changes in white matter abnormalities correlate with late improvement and deterioration following TBI: a diffusion tensor imaging study
Virginia FJ Newcombe and Marta M Correia and Christian Ledig and Maria G Abate and Joanne G Outtrim and Doris Chatfield and Thomas Geeraerts and Anne E Manktelow and Eleftherios Garyfallidis and John D Pickard and Barbara J Sahakian and Peter JA Hutchinson and Daniel Rueckert and Jonathan P Coles and Guy B Williams and David K Menon
Direct native-space fiber bundle alignment for group comparisons
Eleftherios Garyfallidis and Demian Wassermann and Maxime Descoteaux
Constrained spherical deconvolution on signal and ODF values
Eleftherios Garyfallidis and Samuel St-Jean and Michael Paquette and Pierrick Coupé and Maxime Descoteaux
Identification of corresponding tracks in diffusion MRI tractographies
Eleftherios Garyfallidis and Matthew Brett and Vassilis Tsiaras and George Vogiatzis and Ian Nimmo-Smith
On the computation of integrals over fixed-size rectangles of arbitrary dimension
Omar Ocegueda and Oscar Dalmau and Eleftherios Garyfallidis and Maxime Descoteaux and Mariano Rivera
False positive bundles in tractography
Maxime Descoteaux and Jasmeen Sidhu and Eleftherios Garyfallidis and Jean-Christophe Houde and Peter Neher and Bram Stieltjes and Klaus H Maier-Hein
Deconvolution enhanced Generalized Q-Sampling 2 and DSI deconvolution
Eleftherios Garyfallidis and Michael Paquette and Samuel St-Jean and Pierrick Coupé and Maxime Descoteaux
Recognition of white matter bundles using local and global streamline-based registration and clustering
Eleftherios Garyfallidis and Marc-Alexandre Côté and Francois Rheault and Jasmeen Sidhu and Janice Hau and Laurent Petit and David Fortin and Stephen Cunanne and Maxime Descoteaux
3D-SSF: A bio-inspired approach for dynamic multi-subject clustering of white matter tracts
A Chekir and Salima Hassas and Maxime Descoteaux and M Côté and Eleftherios Garyfallidis and Fatima Oulebsir-Boumghar
To appear in: Computers in Biology and Medicine
A Chekir and S Hassas and M Descoteaux and M Côté and E Garyfallidis and F Oulebsir-Boumghar
[Re] Optimization of a free water elimination two-compartment model for diffusion tensor imaging.
Rafael Neto Henriques and Ariel Rokem and Eleftherios Garyfallidis and Samuel St-Jean and Eric Thomas Peterson and Marta Correia
NeuroView: a customizable browser-base utility
Anibal Sólon Heinsfeld and Alexandre Rosa Franco and Augusto Buchweitz and Felipe Meneguzzi
2015 Brainhack Proceedings
R Cameron Craddock and Pierre Bellec and Daniel S Margules and B Nolan Nichols and Jörg P Pfannmöller and AmanPreet Badhwar and David Kennedy and Jean-Baptiste Poline and Roberto Toro and Ben Cipollini and Ariel Rokem and Daniel Clark and Krzysztof J Gorgolewski and Daniel J Clark and Samir Das and Cécile Madjar and Ayan Sengupta and Zia Mohades and Sebastien Dery and Weiran Deng and Eric Earl and Damion V Demeter and Kate Mills and Glad Mihai and Luka Ruzic and Nick Ketz and Andrew Reineberg and Marianne C Reddan and Anne-Lise Goddings and Javier Gonzalez-Castillo and Caroline Froehlich and Gil Dekel and Daniel S Margulies and Ben D Fulcher and Tristan Glatard and Reza Adalat and Natacha Beck and Rémi Bernard and Najmeh Khalili-Mahani and Pierre Rioux and Marc-Étienne Rousseau and Alan C Evans and Yaroslav O Halchenko and Matteo Visconti di Oleggio Castello and Raúl Hernández-Pérez and Edgar A Morales and Laura V Cuaya and Kaori L Ito and Sook-Lei Liew and Hans J Johnson and Erik Kan and Julia Anglin and Michael Borich and Neda Jahanshad and Paul Thompson and Marcel Falkiewicz and Julia M Huntenburg and David O’Connor and Michael P Milham and Ramon Fraga Pereira and Anibal Sólon Heinsfeld and Alexandre Rosa Franco and Augusto Buchweitz and Felipe Meneguzzi and Rickson Mesquita and Luis CT Herrera and Daniela Dentico and Vanessa Sochat and Julio E Villalon-Reina and Eleftherios Garyfallidis
Fast implementations of contextual PDE's for HARDI data processing in DIPY
SPL Meesters and GR Sanguinetti and Eleftherios Garyfallidis and JM Portegies and Remco Duits
Cleaning output of tractography via fiber to bundle coherence, a new open source implementation
SPL Meesters and GR Sanguinetti and Eleftherios Garyfallidis and JM Portegies and PPW Ossenblok and Remco Duits
Particle Swarm Optimization in Multi-Tensor Imaging
Micheal Paquette and Eleftherios Garyfallidis and Samuel St-Jean and Pierrick Coupé and Maxime Descoteaux
D21 Manual Segmentation of Fiber Tracts with Bundles of Interest
Paolo Avesani and Eleftherios Garyfallidis and Emanuele Olivetti and Stephan Gerhard
Robustness of diffusion scalar metrics when estimated with Generalized Q-Sampling Imaging acquisition schemes
MM Correia and GB Williams and F Yeh and I Nimmo-Smith and E Garyfallidis
Multiple-scale Visualization of Large Data based on Hierarchical Clustering
Thien Bao Nguyen and Emanuele Olivetti and Eleftherios Garyfallidis and Nivedita Agarwal and Paolo Avesani
brainhack
Julio E Villalon-Reina and Eleftherios Garyfallidis
Cartesian 3D-SHORE with Laplacian Regularization
Gonzalo Sanguinetti and Samuel St-Jean and Eleftherios Garyfallidis and Maxime Descoteaux
An algorithm and quantitative evaluation framework for registration of multi-modal brain MRI
Omar Ocegueda and Eleftherios Garyfallidis and Maxime Descoteaux and Mariano Rivera
Spherical Deconvolution on single shell and multishell combined with denoising
Samuel St-Jean and Michael Paquette and Eleftherios Garyfallidis and Maxime Descoteaux
Cartesian 3D-SHORE with Laplacian Regularization
Michael Paquette and Gonzalo Sanguinetti and Samuel St-Jean and Eleftherios Garyfallidis and Maxime Descoteaux
The challenge of mapping the human connectome based on diffusion tractography
Klaus H. Maier-Hein, Peter F. Neher, Jean-Christophe Houde, Marc-Ale Marc-Alexandre Côté, Eleftherios Garyfallidis, Jidan Zhong, Maxime Chamberland, [...] ,Maxime Descoteaux
MicroLearn: Framework for machine learning, reconstruction, optimization and microstructure modeling
Shreyas Fadnavis , Marco Reisert , Hamza Farooq , Maryam Afzali , Cheng Hu , Bago Amirbekian , and Eleftherios Garyfallidis
Bundle analytics, a computational framework for investigating the shapes and profiles of brain pathways across populations
Bramsh Qamar Chandio, Shannon Leigh Risacher, Franco Pestilli, Daniel Bullock, Fang-Cheng Yeh, Serge Koudoro, Ariel Rokem, Jaroslaw Harezlak & Eleftherios Garyfallidis
StND: Streamline-based Non-rigid partial-Deformation Tractography Registration
Bramsh Qamar Chandio & Eleftherios Garyfallidis
Brainhack: Developing a culture of open, inclusive, community-driven neuroscience
Rémi Gau, Stephanie Noble, Katja Heuer, Katherine L Bottenhorn, Isil P Bilgin, Yu-Fang Yang, Julia M Huntenburg, Johanna MM Bayer, Richard AI Bethlehem, Shawn A Rhoads, Christoph Vogelbacher, Valentin
Pandora: 4-D White Matter Bundle Population-Based Atlases Derived from Diffusion MRI Fiber Tractography
Colin B Hansen, Qi Yang, Ilwoo Lyu, Francois Rheault, Cailey Kerley, Bramsh Qamar Chandio, Shreyas Fadnavis, Owen Williams, Andrea T Shafer, Susan M Resnick, David H Zald, Laurie E Cutting, Warren D T
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