Publications

2022
- A Riemannian revisiting of structure-function mapping based on eigenmodes
  Samuel Deslauriers-Gauthier, Mauro Zucchelli, Hiba Laghrissi, Rachid Deriche
  Frontiers in Neuroimaging – Brain Imaging Methods (2022)
- An Anisotropic 4D Filtering Approach to Recover Brain Activation From Paradigm-Free Functional MRI Data
  Isa Costantini, Rachid Deriche, Samuel Deslauriers-Gauthier
  Frontiers in Neuroimaging – Brain Imaging Methods (2022)
2021
- Brain Tissue Microstructure Characterization Using dMRI Based Autoencoder Neural-Networks
  Mauro Zucchelli, Samuel Deslauriers-Gauthier, Rachid Deriche
  MICCAI International Workshop on Computational Diffusion MRI (2021)
- A spherical convolutional neural network for white matter structure imaging via dMRI
  Sara Sedlar, Abib Alimi, Théodore Papadopoulo, Rachid Deriche, Samuel Deslauriers-Gauthier
  24th International Conference on Medical Image Computing and Computer Assisted Intervention (2021)
- Explainable 3D-CNN for Multiple Sclerosis patients stratification
  Federica Cruciani, Lorenza Brusini, Mauro Zucchelli, Gustavo Retuci Pinheiro, Francesco Setti, Ilaria Boscolo Galazzo, Rachid Deriche, Leticia Rittner, Massimiliano Calabrese, Gloria Menegaz
  Pattern Recognition. ICPR International Workshops and Challenges (2021)
- Interpretable Deep Learning as a mean for decrypting disease signature in Multiple Sclerosis
  Federica Cruciani, Lorenza Brusini, Mauro Zucchelli, Gustavo Retuci Pinheiro, Francesco Setti, Ilaria Boscolo Galazzo, Rachid Deriche, Leticia Rittner, Massimiliano Calabrese, Gloria Menegaz
  Journal of Neural Engineering (2021), 10.1088/1741-2552/ac0f4b
- 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, Daniel C Alexander, Markus Nilsson, Martijn Froeling, Geert-Jan Biessels, Mauro Zucchelli, Matteo Frigo, Enes Albay, Sara Sedlar, Abib Alimi, Samuel Deslauriers-Gauthier, Rachid Deriche, Rutger Fick, Maryam Afzali, Tomasz Pieciak, Fabian Bogusz, Santiago Aja-Fernández, Evren Ozarslan, Derek K Jones, Haoze Chan, Mingwu Jin, Zhijie Zhang, Fengxiang Wang, Vishwesh Nath, Prasanna Parvathaneni, Jan Morez, Jan Sijbers, Ben Jeurissen, Shreyas Fadnavis, Stefan Endres, Ariel Rokem, Eleftherios Garyfallidis, Irina Sanchez, Vesna Prchkovska, Paulo Rodrigues, Bennet A Landman, Kurt G Schilling
  NeuroImage (2021), 10.1016/j.neuroimage.2021.118367
- Network alignment and similarity reveal atlas-based topological differences in structural connectomes
  Matteo Frigo, Emilio Cruciani, David Coudert, Rachid Deriche, Emanuele Natale, Samuel Deslauriers-Gauthier
  Network Neuroscience (2021), 10.1162/netn_a_00199
- Investigating the effect of DMRI signal representation on fully-connected neural networks brain tissue microstructure estimation
  Mauro Zucchelli, Samuel Deslauriers-Gauthier, and Rachid Deriche
  IEEE International Symposium on Biomedical Imaging (ISBI) (2021)
- Incorporating transmission delays supported by diffusion MRI in MEG source reconstruction
  Ivana Kojčić, Théodore Papadopoulo, Rachid Deriche, and Samuel Deslauriers-Gauthier
  IEEE International Symposium on Biomedical Imaging (ISBI) (2021)
2020
- Paradigm Free Regularization for fMRI Brain Activation Recovery
  Isa Costantini
  These, Université Côte d’Azur
- Three-dimensional Polarized Light Imaging: Towards Multiscale and Multimodal Analysis with Diffusion Magnetic Resonance Imaging
  Abib Alimi
  These, Université Côte d’Azur
- A comprehensive study on electroencephalography and magnetoencephalography sensitivity to cortical and subcortical sources
  Maria Carla Piastra, Andreas Nüßing, Johannes Vorwerk, Maureen Clerc, Christian Engwer, and Carsten Wolters
  Human Brain Mapping (2020), 10.1002/hbm.25272
- Fully-Connected Neural Network and Spherical-Harmonics Rotation Invariant Features improve the estimation of brain tissue microstructure in Diffusion MRI
  Mauro Zucchelli, Samuel Deslauriers-Gauthier, and Rachid Deriche
  SophIA Summit (2020)
- Diffusion MRI tractography filtering techniques change the topology of structural connectomes
  Matteo Frigo, Samuel Deslauriers-Gauthier, Drew Parker, Abdol Aziz Ould Ismail, Junghoon John Kim, Ragini Verma, and Rachid Deriche
  Journal of Neural Engineering (2020), 10.1088/1741-2552/abc29b
- Diffusion MRI fiber orientation distribution function estimation using voxel-wise spherical U-net
  Sara Sedlar, Théodore Papadopoulo, Rachid Deriche, Samuel Deslauriers-Gauthier
  MICCAI Workshop on Computational Diffusion MRI (2020)
- Quantitative assessment of multi-scale tractography: bridging the resolution gap with 3D-PLI
  Abib Alimi, Matteo Frigo, Samuel Deslauriers-Gauthier, and Rachid Deriche
  International Society for Magnetic Resonance in Medicine (ISMRM) (2020)
- A Paradigm Free Regularization Approach to Recover Brain Activations: Validation on Task fMRI
  Isa Costantini, Samuel Deslauriers-Gauthier, and Rachid Deriche
  International Society for Magnetic Resonance in Medicine (ISMRM) (2020)
- Multi-compartment modelling of diffusion MRI signal shows TE-based volume fraction bias
  Matteo Frigo, Mauro Zucchelli, Rutger Fick, Samuel Deslauriers-Gauthier, and Rachid Deriche
  Organization of Human Brain Mapping (OHBM) (2020)
- Analytical and fast fiber orientation distribution reconstruction in 3d-polarized light imaging
  Abib Alimi, Samuel Deslauriers-Gauthier, Felix Matuschke, Andreas Müller, Sascha EA Muenzing, Markus Axer, and Rachid Deriche
  Medical image analysis (2020), 10.1016/j.media.2020.101760
- Connectivity-informed M/EEG inverse problem
  Ivana Kojčić, Théodore Papadopoulo, Rachid Deriche, and Samuel Deslauriers-Gauthier
  MICCAI Workshop on GRaphs in biomedicAl Image anaLysis (2020)
- A Unified Framework for Multimodal Structure-function Mapping Based on Eigenmodes
  Samuel Deslauriers-Gauthier, Mauro Zucchelli, Matteo Frigo, and Rachid Deriche
  Medical Image Analysis (2020), 10.1016/j.media.2020.101799
- A Unified Model for Structure–function Mapping Based on Eigenmodes
  Samuel Deslauriers-Gauthier and Rachid Deriche
  Organisation for Humain Brain Mapping (OHBM) (2020)
- Non-invasive inference of information flow using diffusion MRI, functional MRI, and MEG
  Samuel Deslauriers-Gauthier, Isa Costantini, and Rachid Deriche
  Journal of Neural Engineering (2020), 10.1088/1741-2552/ab95ec
- Multi Tissue Modelling of Diffusion MRI Signal Reveals Volume Fraction Bias
  Matteo Frigo, Rutger H. J. Fick, Mauro Zucchelli, Samuel Deslauriers-Gauthier, and Rachid Deriche
  IEEE 17th International Symposium on Biomedical Imaging (2020), 10.1109/isbi45749.2020.9098649
- A Computational Framework For Generating Rotation Invariant Features And Its Application In Diffusion MRI
  Mauro Zucchelli, Samuel Deslauriers-Gauthier, and Rachid Deriche
  Medical Image Analysis (2020), 10.1016/j.media.2019.101597
2019
- Nouvelles approches algorithmiques pour les problèmes directs et inverses en M/EEG
  Kostiantyn Maksymenko
  These, Université Côte d’Azur
- Spatially Varying Monte Carlo Sure for the Regularization of Biomedical Images
  Marco Pizzolato, Rachid Deriche, Erick Jorge Canales-Rodriguez, Jean-Philippe Thiran
  IEEE 16th International Symposium on Biomedical Imaging (2019), 10.1109/isbi.2019.8759338
- Connectivity–informed spatio–temporal MEG source reconstruction: Simulation results using a MAR model
  Ivana Kojčić, Théodore Papadopoulo, Rachid Deriche, and Samuel Deslauriers-Gauthier
  Colloque Line Garnero (2019)
- Connectivity-informed solution for spatio-temporal M/EEG source reconstruction
  Ivana Kojčić, Théodore Papadopoulo, Rachid Deriche, and Samuel Deslauriers-Gauthier
  First meeting of the NeuroMod Institute (2019)
- Spherical convolutional neural network for diffusion MRI analysis
  Sara Sedlar, Abib Alimi, Théodore Papadopoulo, Rachid Deriche, and Samuel Deslauriers-Gauthier
  SophIA Summit (2020)
- Adaptive phase correction of diffusion-weighted images
  Marco Pizzolato, Guillaume Gilbert, Jean-Philippe Thiran, Maxime Descoteaux, and Rachid Deriche
  NeuroImage (2019)
- The Dmipy Toolbox: Diffusion MRI Multi-Compartment Modeling and Microstructure Recovery Made Easy
  Rutger H. J. Fick, Demian Wassermann, and Rachid Deriche
  Frontiers in Neuro Informatics (2019), 10.3389/fninf.2019.00064
- Fast Approximation of EEG Forward Problem and Application to Tissue Conductivity Estimation
  Kostiantyn Maksymenko, Maureen Clerc, and Théodore Papadopoulo
  IEEE Transactions on Medical Imaging (2019), 10.1109/TMI.2019.2936921
- White matter information flow mapping from diffusion MRI and EEG
  Samuel Deslauriers-Gauthier, Jean-Marc Lina, Russell Butler, Kevin Whittingstall, Guillaume Gilbert, Pierre-Michel Bernier, Rachid Deriche, and Maxime Descoteaux
  NeuroImage, vol. 201 (2019), 10.1016/j.neuroimage.2019.116017
- Deconvolution of fMRI Data using a Paradigm Free Iterative Approach based on Partial Differential Equations
  Isa Costantini, Samuel Deslauriers-Gauthier, and Rachid Deriche
  Organization for Human Brain Mapping Annual Meeting (2019) Italy
- Novel 4-D Algorithm for Functional MRI Image Regularization using Partial Differential Equations
  Isa Costantini, Samuel Deslauriers-Gauthier, Rachid Deriche
  International Society for Magnetic Resonance in Medicine Annual Meeting and Exhibition (2019) Canada
- Towards validation of diffusion MRI tractography: bridging the resolution gap with 3D Polarized Light Imaging
  Abib Alimi, Samuel Deslauriers-Gauthier, and Rachid Deriche
  International Society for Magnetic Resonance in Medicine Annual Meeting and Exhibition (2019)
- A Novel Characterization of Traumatic Brain Injury in White Matter with Diffusion MRI Spherical-Harmonics Rotation Invariants
  Mauro Zucchelli, Drew Parker, Samuel Deslauriers-Gauthier, Junghoon Joh Kim, J Ragini Verma, and Rachid Deriche
  International Society for Magnetic Resonance in Medicine Annual Meeting and Exhibition (2019)
- Coarse-Grained Spatiotemporal Acquisition Design for Diffusion MRI
  Patryk Filipiak, Rutger Fick, A. Petiet, M. Santin, A.-C. Philippe, S. Lehericy, Rachid Deriche, Demian Wassermann
  Proceedings of The IEEE International Symposium on Biomedical Imaging (2019), 10.1109/isbi.2019.8759195
- Estimation of Axonal Conduction Speed and the Inter Hemispheric Transfer Time using Connectivity Informed Maximum Entropy on the Mean
  Samuel Deslauriers-Gauthier and Rachid Deriche
  SPIE Medical Imaging (2019), 10.1117/12.2511736
- Estimation of Axon Conduction Delay, Conduction Speed, and Diameter from Information Flow using Diffusion MRI and MEG
  Samuel Deslauriers-Gauthier and Rachid Deriche
  International Society for Magnetic Resonance in Medicine (2019)
- Effects of tractography filtering on the topology and interpretability of connectomes
  Matteo Frigo, Samuel Deslauriers-Gauthier, Drew Parker, Abdol Aziz, Ould Ismail, Junghoon John Kim, Ragini Verma, and Rachid Deriche
  Organisation for Human Brain Mapping Annual Meeting (2019) Italy
- Analytical Fiber ODF Reconstruction in 3D Polarized Light Imaging: Performance Assessment
  Abib Alimi, Samuel Deslauriers-Gauthier, Felix Matuschke, Daniel Schmitz, Markus Axer, and Rachid Deriche
  IEEE International Symposium on Biomedical Imaging (2019), 10.1109/isbi.2019.8759298
- Fiber orientation distribution function from non-negative sparse recovery with quantitative analysis of local fiber orientations and tractography using DW-MRI datasets
  Thinhinane Megherbi, Gabriel Girard, Aurobrata Ghosh, Fatima Oulebsir-Boumghar, and Rachid Deriche
  Magnetic Resonance Imaging 57 (2019) 218-234, 10.1016/j.mri.2018.10.003
- Solving the inclination sign ambiguity in three dimensional polarized light imaging with a pde-based method
  Abib Alimi, Marco Pizzolato, Rutger Fick, Rachid Deriche
  IEEE 14th International Symposium on Biomedical Imaging (2017), 10.1109/isbi.2017.7950624
2018
- OpenMEEG software for forward problems, coping with non-nested geometries
  Clerc Maureen, Gramfort Alexandre, Papadopoulo Théodore
  21st International Conference on Biomagnetism (2018)
- Investigating Diffusion-MRI based neurite density estimation model dependency: an in-vivo study on the HCP dataset
  Mauro Zucchelli, Maxime Descoteaux, Gloria Menegaz
  BIOMAG (2018)
- Spatio-Temporal dMRI Acquisition Design: Reducing the Number of Samples
  Patryk Filipiak, Rutger Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stéphane Lehéricy, Rachid Deriche, Demian Wassermann
  International Society for Magnetic Resonance in Medicine (2018)
- Spatio-Temporal dMRI Acquisition Design: Reducing the Number of Samples
  Patryk Filipiak, Rutger Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stéphane Lehéricy, Rachid Deriche, Demian Wassermann
  International Society for Magnetic Resonance in Medicine (2018)
- Towards the assessment of myelination using time-dependent diffusion MRI indices
  Abib Alimi, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stéphane Lehéricy, Rachid Deriche, and Demian Wassermann
  International Society for Magnetic Resonance in Medicine (2018)
- Dmipy, a Diffusion Microstructure Imaging toolbox in Python to improve research reproducibility
  Abib Alimi, Rutger Fick, Demian Wassermann, and Rachid Deriche
  Computational Diffusion MRI (2018), 10.1007/978-3-030-05831-9_5
- Data-driven cortical clustering to provide a family of plausible solutions to M/EEG inverse problem
  Kostiantyn Maksymenko, Maureen Clerc, and Théodore Papadopoulo
  International Traveling Workshop on Interactions between low-complexity data models and Sensing Techniques (2018)
- L1-Norm Regularized Deconvolution of Functional MRI BOLD Signal
  Isa Costantini , Patryk Filipiak , Kostiantyn Maksymenko , Samuel Deslauriers-Gauthier, and Rachid Deriche
  C@UCA (2018) France
- A Closed-Form Solution of Rotation Invariant Spherical Harmonic Features in Diffusion MRI
  Mauro Zucchelli, Samuel Deslauriers-Gauthier, Rachid Deriche
  Computational Diffusion MRI (2018), 10.1007/978-3-030-05831-9_7
- Resolving the crossing/kissing fiber ambiguity using Functionally Informed COMMIT
  Matteo Frigo, Isa Costantini, Rachid Deriche, and Samuel Deslauriers-Gauthier
  Computational Diffusion MRI 2018 (2018), 10.1007/978-3-030-05831-9_26
- Edema-informed anatomically constrained particle filter tractography
  Samuel Deslauriers-Gauthier, Drew Parker, François Rheault, Rachid Deriche, Steven Brem, Maxime Descoteaux, and Ragini Verma
  International Conference on Medical Image Computing and Computer-Assisted Intervention (2018) Spain 375-382
- Solving the Cross-Subject Parcel Matching Problem using Optimal Transport
  Guillermo Gallardo, Nathalie TH Gayraud, Rachid Deriche, Maureen Clerc, Samuel Deslauriers-Gauthier, and Demian Wassermann
  International Conference on Medical Image Computing and Computer-Assisted Intervention (2018) 836-843
- Reducing the number of samples in spatiotemporal dMRI acquisition design
  Patryk Filipiak, Rutger Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stephane Lehericy, Philippe Ciuciu, Rachid Deriche, and Demian Wassermann
  Magnetic Resonance in Medicine (2018) 1-16, 10.1002/mrm.27601
- fMRI Deconvolution via Temporal Regularization using a LASSO model and the LARS algorithm
  Isa Costantini, Patryk Filipiak, Kostiantyn Maksymenko, Samuel Deslauriers-Gauthier, and Rachid Deriche
  In 40th International Engineering in Medicine and Biology Conference (2018) USA
- Reducing false positive connection in tractograms using joint structure-function filtering
  Matteo Frigo, Guillermo Gallardo, Isa Constantini, Alessandro Daducci, Demian Wassermann, Rachid Deriche, and Samuel Deslauriers-Gauthier
  Organization for Human Brain Mapping Annual Meeting (2018) Singapore
- Mipy: An Open-Source Framework to improve reproducibility in Brain Microstructure Imaging
  Rutger Fick, Demian Wassermann, and Rachid Deriche
  Organization for Human Brain Mapping Annual Meeting (2018) Singapore
- Non-parametric graphnet-regularized representation of dMRI in space and time
  Rutger H.J. Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stephane Lehericy, Rachid Deriche, and Demian Wassermann
  Medical Image Analysis 43 (2018) 37-53, 10.1016/j.media.2017.09.002
- Rational Invariants of Even Ternary Forms Under the Orthogonal Group
  Paul Görlach, Evelyne Hubert, and Théo Papadopoulo
  Foundations of Computational Mathematics (2018) 1-47, 10.1007/s10208-018-9404-1
- Diffusion Driven Label Fusion for White Matter Multi-Atlas Segmentation
  Guillermo Gallardo , Sylvain Bouix, and Demian Wassermann
  Organization for Human Brain Mapping Annual Meeting (2018)
2017
- Matching parcellations using Optimal Transport: a proof of concept
  Guillermo Gallardo, Nathalie Thérèse Hélène Gayraud, Maureen Clerc, Demian Wassermann
  Computational Brain Connectivity Mapping Winter School Workshop (2017)

2016

Extracting the Core Structural Connectivity Network: Guaranteeing Network Connectedness Through a Graph-Theoretical Approach
Demian Wassermann, Dorian Mazauric, Guillermo Gallardo-Diez, and Rachid Deriche
Medical Image Computing and Computer-Assisted Intervention (2016) 89-96, 10.1007/978-3-319-46720-7_11

Multi-Spherical Diffusion MRI: Exploring Diffusion Time Using Signal Sparsity
Rutger H. J. Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stephane Lehericy, Rachid Deriche, and Demian Wassermann
MICCAI Workshop on computational diffusion MRI (2016) 71-83, 10.1007/978-3-319-54130-3_6

Groupwise Structural Parcellation of the Cortex: A Sound Approach Based on Logistic Models
Guillermo Gallardo, Rutger Fick, William Wells, Rachid Deriche, and Demian Wassermann
MICCAI Workshop on Computational Diffusion MRI (2016) 99-112, 10.1007/978-3-319-54130-3_8

Iterative two-stage approach to estimate sources and their interactions
Brahim Belaoucha and Théodore Papadopoulo
20th International Conference on Biomagnetism (2016)

Multi-Spherical MRI: Breaking the Boundaries of Diffusion Time
Rutger Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stéphane Lehericy, Rachid Deriche, and Demian Wassermann
ISMRM Workshop on: Breaking the Barriers of Diffusion MRI (2016)

Computational Brain Connectivity Mapping: A Core Health and Scientific Challenge
Rachid Deriche
Medical Image Analysis 33 (2016) 122–126, 10.1016/j.media.2016.06.003

Preprints

Improving Auto-Encoders’ self-supervised image classification using pseudo-labelling via data augmentation and the perceptual loss
Aymene Mohammed Bouayed, Karim Atif, Rachid Deriche, and Abdelhakim Saim

Multi-Tissue Multi-Compartment Models of Diffusion MRI
Matteo Frigo, Rutger Fick, Mauro Zucchelli, Samuel Deslauriers-Gauthier, Rachid Deriche

Funded by