Computational Brain Connectivity Mapping

Connectivity–informed spatio–temporal MEG source reconstruction: Simulation results using a MARmodel

Author(s): Ivana Kojčić, Théodore Papadopoulo, Rachid Deriche, Samuel Deslauriers-Gauthier
Published in: Colloque Line Garnero, Issue 2019, 2019
Publisher: Colloque

A spherical convolutional neural network for white matter structure imaging via dMRI

Author(s): Sedlar Sara, Alimi Abib, Papadopoulo Théodore, Deriche Rachid, Deslauriers-Gauthier Samuel
Published in: MICCAI 2021 - 24th International Conference on Medical Image Computing and Computer Assisted Intervention, Sep 2021, Strasbourg / Virtual, France, 2021
Publisher: Springer Nature i- Lecture Notes in Computer Science (LNCS)

Brain Tissue Microstructure Characterization Using dMRI Based Autoencoder Neural-Networks

Author(s): Zucchelli Mauro, Deslauriers-Gauthier Samuel, Deriche Rachid
Published in: MICCAI 2021 International Workshop on Computational Diffusion MRI, 2021
Publisher: Springer Nature i- Lecture Notes in Computer Science (LNCS)

Multi Tissue Modelling of Diffusion MRI Signal Reveals Volume Fraction Bias

Author(s): Matteo Frigo, Rutger H. J. Fick, Mauro Zucchelli, Samuel Deslauriers-Gauthier, Rachid Deriche
Published in: 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), Issue 2020, 2020, Page(s) 991-994, ISBN 978-1-5386-9330-8
Publisher: IEEE
DOI: 10.1109/isbi45749.2020.9098649

A Paradigm Free Regularization Approach to Recover Brain Activations: Validation on Task fMRI

Author(s): Costantini Isa, Deslauriers-Gauthier Samuel, Deriche Rachid
Published in: 28th Annual Meeting & Exhibition of the International Society for Magnetic Resonance in Medicine, Issue 2020 ISMRM, 2020
Publisher: ISMRM

Quantitative assessment of multi-scale tractography: bridging the resolution gap with 3D-PLI

Author(s): Alimi Abib, Frigo Matteo, Deslauriers-Gauthier Samuel, Deriche Rachid
Published in: ISMRM Virtual Conference & Exhibition, Issue 2020 ISMRM, 2020
Publisher: ISMRM

Diffusion MRI fiber orientation distribution function estimation using voxel-wise spherical U-net

Author(s): Sedlar Sara, Papadopoulo, Théodore, Deriche Rachid;
Published in: International MICCAI Workshop 2020 - Computational Diffusion MRI, Issue 2020 CDMRI, 2020
Publisher: MICCAI

Multi-compartment modelling of diffusion MRI signal shows TE-based volume fraction bias

Author(s): Frigo Matteo. Zucchelli Mauro, Fick, Rutger, Deslauriers-Gauthier, Samuel, Deriche, Rachid
Published in: 26th meeting of the Organization of Human Brain Mapping, Issue 2020 OHBM, 2020
Publisher: OHBM

Spatially Varying Monte Carlo Sure for the Regularization of Biomedical Images

Author(s): Marco Pizzolato, Rachid Deriche, Erick Jorge Canales-Rodriguez, Jean-Philippe Thiran
Published in: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), Issue 2019, 2019, Page(s) 1639-1642, ISBN 978-1-5386-3641-1
Publisher: IEEE
DOI: 10.1109/isbi.2019.8759338

Fully-Connected Neural Network and Spherical-Harmonics Rotation Invariant Features improve the estimation of brain tissue microstructure in Diffusion MRI

Author(s): Zucchelli Mauro, Deslauriers-Gauthier Samuel, Deriche Rachid
Published in: SOPHI.A Summit 2020, Issue 2020 SOPHI.A Summit, 2020
Publisher: Inria

A Unified Model for Structure-function Mapping Based on Eigenmodes

Author(s): Deslauriers-Gauthier Samuel, Deriche Rachid
Published in: 26th meeting of the Organisation for Humain Brain Mappin, Issue 2020 OHBM, 2020
Publisher: OHBM

Predicting brain functional connectivity from structural connectivity using fully connected neural networks

Author(s): Samuel Deslauriers-Gauthier, Mauro Zucchelli, Rachid Deriche
Published in: SophIA Summit, 2020
Publisher: Inria

Groupwise Structural Parcellation of the Cortex: A Sound Approach Based on Logistic Models

Author(s): Guillermo Gallardo, Rutger Fick, William Wells, Rachid Deriche, Demian Wassermann
Published in: MICCAI 2016: Computational Diffusion MRI, Issue Part of the Mathematics and Visualization book series (MATHVISUAL), 2016, Page(s) 99-112, ISBN 978-3-319-54129-7
Publisher: Springer, Cham
DOI: 10.1007/978-3-319-54130-3_8

Inference and Visualization of Information Flow in the Visual Pathway Using dMRI and EEG

Author(s): Samuel Deslauriers-Gauthier, Jean-Marc Lina, Russell Butler, Pierre-Michel Bernier, Kevin Whittingstall, Rachid Deriche, Maxime Descoteaux
Published in: International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2017), Issue LNCS, vol 10433, 2017, Page(s) 505-512, ISBN 978-3-319-66181-0
Publisher: Springer, Cham
DOI: 10.1007/978-3-319-66182-7_58

Large brain effective network from EEG/MEG data and dMR information

Author(s): Brahim Belaoucha, Theodore Papadopoulo
Published in: 2017 International Workshop on Pattern Recognition in Neuroimaging (PRNI), 2017, Page(s) 1-4, ISBN 978-1-5386-3159-1
Publisher: IEEE
DOI: 10.1109/PRNI.2017.7981511

Spatial regularization based on dMRI to solve EEG/MEG inverse problem

Author(s): Brahim Belaoucha, Theodore Papadopoulo
Published in: 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Issue 39th, 2017, Page(s) 3608-3611, ISBN 978-1-5090-2809-2
Publisher: IEEE
DOI: 10.1109/EMBC.2017.8037638

Assessing the feasibility of estimating axon diameter using diffusion models and machine learning

Author(s): Rutger H.J. Fick, Neda Sepasian, Marco Pizzolato, Andrada Ianus, Rachid Deriche
Published in: 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), Issue 14th, 2017, Page(s) 766-769, ISBN 978-1-5090-1172-8
Publisher: IEEE
DOI: 10.1109/ISBI.2017.7950631

Multi-Spherical Diffusion MRI: Exploring Diffusion Time Using Signal Sparsity

Author(s): Rutger H. J. Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stephane Lehericy, Rachid Deriche, Demian Wassermann
Published in: Computational Diffusion MRI. MICCAI 2016, Issue Mathematics and Visualization, 2016, Page(s) 71-83, ISBN 978-3-319-54129-7
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-54130-3_6

Mipy: An Open-Source Framework to improve reproducibility in Brain Microstructure Imaging

Author(s): Rutger Fick, Demian Wassermann, Rachid Deriche
Published in: Organization for Human Brain Mapping, Issue 2018 OHBM, 2018
Publisher: Organization for Human Brain Mapping

Reducing false positive connection in tractograms using joint structure-function filtering

Author(s): Matteo Frigo, Guillermo Gallardo, Isa Constantini, Alessandro Daducci, Demian Wassermann, Rachid Deriche, Samuel Deslauriers-Gauthier
Published in: Organization for Human Brain Mapping, Issue 2018 OHBM, 2018
Publisher: Organization for Human Brain Mapping

Effects of tractography filtering on the topology and interpretability of connectomes

Author(s): Frigo Matteo, Deslauriers-Gauthier Samuel, Parker Drew, Aziz Abdol, Ismail Ould, Kim John, Verma Ragini, Deriche Rachid
Published in: The Organization for Human Brain Mapping (OHBM), Issue 2019 OHBM, 2019
Publisher: OHBM

Regularizing the ODF estimate with the Laplace-Beltrami operator in 3D Polarized Light Imaging

Author(s): Alimi Abib O. Y., Deslauriers-Gauthier Samuel, Deriche Rachid
Published in: CoBCoM 2017 - Computational Brain Connectivity Mapping Winter School Workshop, Issue 2017 CoBCoM, 2017
Publisher: Inria

Towards the assessment of myelination using time-dependent diffusion MRI indices}

Author(s): Alimi Abib, Petiet Alexandra , Santin Mathieu, Philippe Anne-Charlotte, Leh{\'e}ricy St{\'e}phane. Deriche Rachid, Wassermann Demian
Published in: ISMRM 2018 - 26th International Society for Magnetic Resonance in Medicine, Issue 2018 ISMRM, 2018
Publisher: ISMRM

Solving the inclination sign ambiguity in three dimensional Polarized Light Imaging with a PDE-based method

Author(s): Abib Alimi, Marco Pizzolato, Rutger H.J. Fick, Rachid Deriche
Published in: 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), Issue 2017 ISBI, 2017, Page(s) 737-740, ISBN 978-1-5090-1172-8
Publisher: IEEE
DOI: 10.1109/isbi.2017.7950624

Analytical Fiber ODF Reconstruction in 3D Polarized Light Imaging: Performance Assessment

Author(s): A. Alimi, S. Deslauriers-Gauthier, F. Matuschke, D. Schmitz, M. Axer, R. Deriche
Published in: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), Issue 2019 ISBI, 2019, Page(s) 1652-1655, ISBN 978-1-5386-3641-1
Publisher: IEEE
DOI: 10.1109/isbi.2019.8759298

Towards validation of diffusion MRI tractography: bridging the resolution gap with 3D Polarized Light Imaging

Author(s): Abib Alimi, Samuel Deslauriers-Gauthier, Rachid Deriche
Published in: ISMRM 2019 - 27th International Society for Magnetic Resonance in Medicine}, Issue 2019 ISMRM, 2019
Publisher: ISMRM

White matter fiber bundles as a source model in the MEG inverse problem

Author(s): Kostiantyn Maksymenko, Th{\'e}odore Papadopoulo, Samuel Deslauriers-Gauthier
Published in: COBCOM 2017 - Computational Brain Connectivity Mapping, Winter School Workshop, Issue 2017 COBCOM, 2017
Publisher: Inria

Data-driven cortical clustering to provide a family of plausible solutions to M/EEG inverse problem

Author(s): Kostiantyn Maksymenko, Maureen Clerc, Th{\'e}odore Papadopoulo
Published in: iTWIST: international Traveling Workshop on Interactions between low-complexity data models and Sensing Techniques, Issue 2018 ITWIST, 2018
Publisher: iTWIST

Information Flow in the White Matter During a Motor Task: A Structural Connectivity Driven Approach

Author(s): Guillermo Gallardo, Demian Wassermann, Rachid Deriche, Maxime Descoteaux, Samuel Deslauriers-Gauthier
Published in: Organization for Human Brain Mapping ', Issue 2017 OHBM, 2017
Publisher: OHBM

Multi-Spherical Diffusion MRI: An in-vivo Test- Retest Study of Time-Dependent q-space Indices

Author(s): Rutger H. J. Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stephane Lehericy, Rachid Deriche, Demian Wassermann
Published in: ISMRM 2017: 25th International Society for Magnetic Resonance in Medicine, Issue 2017 ISMRM, 2017
Publisher: ISMRM

Spatio-Temporal dMRI Acquisition Design: Reducing the Number of Samples

Author(s): Patryk Filipiak , Rutger Fick , Alexandra Petiet , Mathieu Santin , Anne-Charlotte Philippe , Stéphane Lehéricy , Rachid Deriche , Demian Wassermann
Published in: ISMRM 2018: 26h International Society for Magnetic Resonance in Medicine, Issue 2018 ISMRM, 2018
Publisher: ISMRM

Diffusion Driven Label Fusion for White Matter Multi-Atlas Segmentation

Author(s): Guillermo Gallardo , Sylvain Bouix, Demian Wassermann
Published in: OHBM 2018 - Organization for Human Brain Mapping,, Issue 2018 OHBM, 2018
Publisher: OHBM

Solving the Cross-Subject Parcel Matching Problem using Optimal Transport

Author(s): Guillermo Gallardo , Nathalie Gayraud , Rachid Deriche , Maureen Clerc , Samuel Deslauriers-Gauthier , Demian Wassermann
Published in: International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2018), Issue 2018 MICCAI, 2018, ISBN 9783-030009281
Publisher: Springer International Publishing

A Novel Atlas of Human Cerebral Cortex based on Extrinsic Connectivity

Author(s): Guillermo Gallardo , Rachid Deriche , Demian Wassermann
Published in: OHBM 2017 - Organization for Human Brain Mapping 2017 Annual Meeting, Issue 2017 OHBM, 2017
Publisher: OHBM

Iterative two-stage approach to estimate sources and their interactions

Author(s): Brahim Belaoucha , Théodore Papadopoulo
Published in: 20th International Conference on Biomagnetism (BIOMAG2016),, Issue 2016 BIOMAG, 2016
Publisher: BIOMAG

fMRI Deconvolution via Temporal Regularization using a LASSO model and the LARS algorithm

Author(s): Isa Costantini , Patryk Filipiak , Kostiantyn Maksymenko , Samuel Deslauriers-Gauthier , Rachid Deriche
Published in: EMBC'18 - 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Issue 2018 EMBC, 2018
Publisher: EMBC

L1-Norm Regularized Deconvolution of Functional MRI BOLD Signal

Author(s): Isa Costantini , Patryk Filipiak , Kostiantyn Maksymenko , Samuel Deslauriers-Gauthier, Rachid Deriche
Published in: C@UCA, 2018
Publisher: UCA

Multi-Spherical MRI: Breaking the Boundaries of Diffusion Time

Author(s): Rutger Fick , Alexandra Petiet , Mathieu Santin , Anne-Charlotte Philippe , Stéphane Lehericy ,, Rachid Deriche , Demian Wassermann
Published in: ISMRM Workshop on: Breaking the Barriers of Diffusion MRI, Issue 2016 ISMRM, 2016
Publisher: ISMRM

Estimation of axonal conduction speed and the inter hemispheric transfer time using connectivity informed maximum entropy on the mean

Author(s): Samuel Deslauriers-Gauthier, Rachid Deriche
Published in: Medical Imaging 2019: Biomedical Applications in Molecular, Structural, and Functional Imaging, Issue 2019 - SPIE MI, 2019, Page(s) 12, ISBN 9781-510625549
Publisher: SPIE
DOI: 10.1117/12.2511736

Estimation of Axon Conduction Delay, Conduction Speed, and Diameter from Information Flow using Diffusion MRI and MEG

Author(s): Samuel Deslauriers-Gauthier, Rachid Deriche
Published in: ISMRM 2019 - 27th International Society for Magnetic Resonance in Medicine Annual Meeting and Exhibition, Issue 2019 ISMRM, 2019
Publisher: ISMRM

Edema-informed anatomically constrained particle filter tractography

Author(s): Samuel Deslauriers-Gauthier, Drew Parker, François Rheault, Rachid Deriche, Steven Brem, Maxime Descoteaux, and Ragini Verma
Published in: MICCAI 2018 - 21st International Conference, Medical Image Computing and Computer Assisted Intervention, Issue LNCS 11072, 2018, Page(s) 375-382
Publisher: Springer

Coarse-Grained Spatiotemporal Acquisition Design for Diffusion MRI

Author(s): P. Filipiak, R. Fick, A. Petiet, M. Santin, A.-C. Philippe, S. Lehericy, R. Deriche, D. Wassermann
Published in: 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), Issue 2019 ISBI, 2019, Page(s) 155-158, ISBN 978-1-5386-3641-1
Publisher: IEEE
DOI: 10.1109/isbi.2019.8759195

Novel 4-D Algorithm for Functional MRI Image Regularization using Partial Differential Equations

Author(s): Isa Costantini, Samuel Deslauriers-Gauthier, Rachid Deriche
Published in: ISMRM 2019 - 27th International Society for Magnetic Resonance in Medicine Annual Meeting and Exhibition, Issue 2019 ISMRM, 2019
Publisher: ISMRM

Deconvolution of fMRI BOLD signal in time-domain using an exponential operator and Lasso optimization

Author(s): Isa Costantini, Patryk Filipiak, Kostiantyn Maksymenko, Rachid Deriche, Samuel Deslauriers-Gauthier
Published in: COBCOM 2017 - Computational Brain Connectivity Mapping, Winter School Workshop, Issue 2017 COBCOM, 2017
Publisher: Inria

Deconvolution of fMRI Data using a Paradigm Free Iterative Approach based on Partial Differential Equations

Author(s): Isa Costantini, Samuel Deslauriers-Gauthier, Rachid Deriche
Published in: OHBM 2019 - Organization for Human Brain Mapping 2019 Annual Meeting, Issue 2019 OHBM, 2019
Publisher: OHBM

Connectivity-informed solution for spatio-temporal M/EEG source reconstruction

Author(s): Ivana Kojčić, Théodore Papadopoulo, Rachid Deriche, Samuel Deslauriers-Gauthier
Published in: First meeting of the NeuroMod Institute, Issue 2019 NeuroMod, 2019
Publisher: NeuroMod

A Novel Characterization of Traumatic Brain Injury in White Matter with Diffusion MRI Spherical-Harmonics Rotation Invariants

Author(s): Zucchelli Mauro, Parker Drew, Deslauriers-Gauthier Samuel, Kim Junghoon, Verma Ragini, Deriche Rachid
Published in: ISMRM 2019 - 27th Annual Meeting International Society for Magnetic Resonance in Medicine, Issue 2019 ISMRM, 2019
Publisher: ISMRM

Data-driven cortical clustering to provide a family of plausible solutions to the M/EEG inverse problem

Author(s): Kostiantyn Maksymenko, Maureen Clerc, Théodore Papadopoulo
Published in: BIOMAG 2018, Aug 2018, Philadelphia, United States., Issue 2018 BIOMAG, 2018
Publisher: BIOMAG

Solving the Cross-Subject Parcel Matching Problem using Optimal Transport

Author(s): Guillermo Gallardo, Nathalie Gayraud, Rachid Deriche, Maureen Clerc, Samuel Deslauriers-Gauthier, Demian Wassermann
Published in: International Conference on Medical Image Computing and Computer-Assisted Intervention 2018,, Issue 2018 MICCAI, 2018
Publisher: Springer

Matching parcellations using Optimal Transport: a proof of concept

Author(s): Guillermo Gallardo, Nathalie Thérèse Hélène Gayraud, Maureen Clerc, Demian Wassermann
Published in: Computational Brain Connectivity Mapping – Winter School Workshop 2017, Nov 2017, Juan-les-Pins, France., Issue 2017 CoBCoM, 2017
Publisher: CoBCoM

Connectivity-informed M/EEG inverse problem

Author(s): Ivana Kojčić, Théodore Papadopoulo, Rachid Deriche, Samuel Deslauriers-Gauthier
Published in: MICCAI Workshop on GRaphs in biomedicAl Image anaLysis (2020), Issue 2020 MICCAI, 2020
Publisher: Springer

Spherical convolutional neural network for diffusion MRI analysis

Author(s): Sedlar Sara, Alimi Abib, Papadopoulo Théodore, Deriche Rachid
Published in: Soph.IA Summit 2019, Issue 2019 Soph.IA Summit, 2019
Publisher: Inria

OpenMEEG software for forward problems, coping with non-nested geometries

Author(s): Clerc Maureen, Gramfort Alexandre, Papadopoulo Théodore
Published in: 21st International Conference on Biomagnetism, Issue 2018 Biomagnetism, 2018
Publisher: BIOMAG

Investigating The Effect Of Dmri Signal Representation On Fully-Connected Neural Networks Brain Tissue Microstructure Estimation

Author(s): Mauro Zucchelli, Samuel Deslauriers-Gauthier, Rachid Deriche
Published in: 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), 2021, Page(s) 725-728, ISBN 978-1-6654-1246-9
Publisher: IEEE
DOI: 10.1109/isbi48211.2021.9434046

Investigating Diffusion-MRI based neurite density estimation modeL dependency: an in-vivo study on the HCP dataset

Author(s): Mauro Zucchelli, Maxime Descoteaux, Gloria Menegaz
Published in: ISMRM 2018 - International Society for Magnetic Resonance in Medicine,, Issue 2018 ISMRM, 2018
Publisher: ISMRM

Incorporating Transmission Delays Supported By Diffusion Mri In Meg Source Reconstruction

Author(s): Ivana Kojcic, Theodore Papadopoulo, Rachid Deriche, Samuel Deslauriers-Gauthier
Published in: 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI), 2021, Page(s) 64-68, ISBN 978-1-6654-1246-9
Publisher: IEEE
DOI: 10.1109/isbi48211.2021.9433861

Novel algorithmic approaches for the forward and inverse M/EEG problems

Author(s): Maksymenko, Kostiantyn
Published in: Université Côte d'Azur, Issue 2019 Ph.D, 2019
Publisher: Université Côte d'Azur

Paradigm Free Regularization for fMRI Brain Activation Recovery

Author(s): Costantini, Isa
Published in: Université Côte d'Azur, Issue 2020 Ph.D, 2020
Publisher: Université Côte d'Azur

Three-dimensional Polarized Light Imaging: Towards Multiscale and Multimodal Analysis with Diffusion Magnetic Resonance Imaging

Author(s): Alimi, Abib
Published in: Université Côte d'Azur, Issue 2020 Ph.D, 2020
Publisher: Université Côte d'Azur

Advanced dMRI signal modeling for tissue microstructure characterization

Author(s): Rutger Fick
Published in: Université Côte d'Azur, Issue 2017, 2017
Publisher: Université Côte d'Azur

A unified framework for multimodal structure–function mapping based on eigenmodes

Author(s): Samuel Deslauriers-Gauthier, Mauro Zucchelli, Matteo Frigo, Rachid Deriche
Published in: Medical Image Analysis, Issue 66, 2020, Page(s) 101799, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2020.101799

Interpretable Deep Learning as a means for decrypting disease signature in Multiple Sclerosis

Author(s): Federica Cruciani, Lorenza Brusini, Mauro Zucchelli, Gustavo Retuci Pinheiro, Francesco Setti, Ilaria Boscolo Galazzo, Rachid Deriche, Leticia Rittner, Massimiliano Calabrese, Gloria Menegaz
Published in: Journal of Neural Engineering, 2021, ISSN 1741-2560
Publisher: Institute of Physics Publishing
DOI: 10.1088/1741-2552/ac0f4b

Analytical and fast Fiber Orientation Distribution reconstruction in 3D-Polarized Light Imaging

Author(s): Abib Alimi, Samuel Deslauriers-Gauthier, Felix Matuschke, Andreas Müller, Sascha E.A. Muenzing, Markus Axer, Rachid Deriche
Published in: Medical Image Analysis, Issue 65, 2020, Page(s) 101760, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2020.101760

Network alignment and similarity reveal atlas-based topological differences in structural connectomes

Author(s): Matteo Frigo, Emilio Cruciani, David Coudert, Rachid Deriche, Emanuele Natale, Samuel Deslauriers-Gauthier
Published in: Network Neuroscience, 2021, Page(s) 1-23, ISSN 2472-1751
Publisher: MIT Press Direct
DOI: 10.1162/netn_a_00199

The Dmipy Toolbox: Diffusion MRI Multi-Compartment Modeling and Microstructure Recovery Made Easy

Author(s): Rutger H. J. Fick, Demian Wassermann, Rachid Deriche
Published in: Frontiers in Neuroinformatics, Issue 13, 2019, ISSN 1662-5196
Publisher: Frontiers Research Foundation
DOI: 10.3389/fninf.2019.00064

Diffusion MRI tractography filtering techniques change the topology of structural connectomes

Author(s): Matteo Frigo, Samuel Deslauriers-Gauthier, Drew Parker, Abdol Aziz Ould Ismail, Junghoon John Kim, Ragini Verma, Rachid Deriche
Published in: Journal of Neural Engineering, Issue 17/6, 2020, Page(s) 065002, ISSN 1741-2560
Publisher: Institute of Physics Publishing
DOI: 10.1088/1741-2552/abc29b

A comprehensive study on electroencephalography and magnetoencephalography sensitivity to cortical and subcortical sources

Author(s): Maria Carla Piastra, Andreas Nüßing, Johannes Vorwerk, Maureen Clerc, Christian Engwer, Carsten H. Wolters
Published in: Human Brain Mapping, Issue 42/4, 2021, Page(s) 978-992, ISSN 1065-9471
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/hbm.25272

A computational Framework for generating rotation invariant features and its application in diffusion MRI

Author(s): Mauro Zucchelli, Samuel Deslauriers-Gauthier, Rachid Deriche
Published in: Medical Image Analysis, Issue 60, 2020, Page(s) 101597, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2019.101597

Computational brain connectivity mapping: A core health and scientific challenge

Author(s): Rachid Deriche
Published in: Medical Image Analysis, Issue 33, 2016, Page(s) 122-126, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2016.06.003

AxTract: Toward microstructure informed tractography

Author(s): Gabriel Girard, Alessandro Daducci, Laurent Petit, Jean-Philippe Thiran, Kevin Whittingstall, Rachid Deriche, Demian Wassermann, Maxime Descoteaux
Published in: Human Brain Mapping, Issue 38/11, 2017, Page(s) 5485-5500, ISSN 1065-9471
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/hbm.23741

Groupwise structural parcellation of the whole cortex: A logistic random effects model based approach

Author(s): Guillermo Gallardo, William Wells, Rachid Deriche, Demian Wassermann
Published in: NeuroImage, Issue Available online 1 February 2017, 2017, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2017.01.070

Non-parametric graphnet-regularized representation of dMRI in space and time

Author(s): Rutger H.J. Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stephane Lehericy, Rachid Deriche, Demian Wassermann
Published in: Medical Image Analysis, Issue 43, 2018, Page(s) 37-53, ISSN 1361-8415
Publisher: Elsevier BV
DOI: 10.1016/j.media.2017.09.002

Using diffusion MRI to discriminate areas of cortical grey matter

Author(s): Tharindu Ganepola, Zoltan Nagy, Aurobrata Ghosh, Theodore Papadopoulo, Daniel C. Alexander, Martin I. Sereno
Published in: NeuroImage, Issue 17, 2017, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2017.12.046

Diffusion MRI microstructure models with in vivo human brain Connectome data: results from a multi-group comparison

Author(s): Uran Ferizi, Benoit Scherrer, Torben Schneider, Mohammad Alipoor, Odin Eufracio, Rutger H.J. Fick, Rachid Deriche, Markus Nilsson, Ana K. Loya-Olivas, Mariano Rivera, Dirk H.J. Poot, Alonso Ramirez-Manzanares, Jose L. Marroquin, Ariel Rokem, Christian Pötter, Robert F. Dougherty, Ken Sakaie, Claudia Wheeler-Kingshott, Simon K. Warfield, Thomas Witzel, Lawrence L. Wald, José G. Raya, Daniel C. Al
Published in: NMR in Biomedicine, Issue 30/9, 2017, Page(s) e3734, ISSN 0952-3480
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/nbm.3734

Adaptive Waveform Learning: A Framework for Modeling Variability in Neurophysiological Signals

Author(s): Sebastian Hitziger, Maureen Clerc, Sandrine Saillet, Christian Benar, Theodore Papadopoulo
Published in: IEEE Transactions on Signal Processing, Issue 65/16, 2017, Page(s) 4324-4338, ISSN 1053-587X
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/TSP.2017.2698415

Rational Invariants of Even Ternary Forms Under the Orthogonal Group

Author(s): Paul Görlach, Evelyne Hubert, Théo Papadopoulo
Published in: Foundations of Computational Mathematics, Issue 2018 FCM, 2018, Page(s) 1-47, ISSN 1615-3375
Publisher: Springer Verlag
DOI: 10.1007/s10208-018-9404-1

Fiber orientation distribution function from non-negative sparse recovery with quantitative analysis of local fiber orientations and tractography using DW-MRI datasets

Author(s): Thinhinane Megherbi, Gabriel Girard, Aurobrata Ghosh, Fatima Oulebsir-Boumghar, Rachid Deriche
Published in: Magnetic Resonance Imaging, Issue 57, 2019, Page(s) 218-234, ISSN 0730-725X
Publisher: Elsevier BV
DOI: 10.1016/j.mri.2018.10.003

Reducing the number of samples in spatiotemporal dMRI acquisition design

Author(s): Patryk Filipiak, Rutger Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stephane Lehericy, Philippe Ciuciu, Rachid Deriche, Demian Wassermann
Published in: Magnetic Resonance in Medicine, Issue 81/5, 2019, Page(s) 3218-3233, ISSN 0740-3194
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/mrm.27601

Fast Approximation of EEG Forward Problem and Application to Tissue Conductivity Estimation

Author(s): Kostiantyn Maksymenko, Maureen Clerc, Theodore Papadopoulo
Published in: IEEE Transactions on Medical Imaging, Issue 2019 IEEE TMI, 2019, Page(s) 1-1, ISSN 0278-0062
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/TMI.2019.2936921

Non–invasive inference of information flow using diffusion MRI, functional MRI, and MEG

Author(s): Samuel Deslauriers-Gauthier, Isa Costantini, Rachid Deriche
Published in: Journal of Neural Engineering, Issue 17/4, 2020, Page(s) 045003, ISSN 1741-2552
Publisher: Wiley
DOI: 10.1088/1741-2552/ab95ec

On the generalizability of diffusion MRI signal representations across acquisition parameters, sequences and tissue types: Chronicles of the MEMENTO challenge

Author(s): 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 Özarslan, Derek K. Jones, Haoz
Published in: NeuroImage, Issue 240, 2021, Page(s) 118367, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2021.118367

Structural connectivity to reconstruct brain activation and effective connectivity between brain regions

Author(s): Brahim Belaoucha, Théodore Papadopoulo
Published in: Journal of Neural Engineering, Issue 17/3, 2020, Page(s) 035006, ISSN 1741-2552
Publisher: IOPScience
DOI: 10.1088/1741-2552/ab8b2b

White matter information flow mapping from diffusion MRI and EEG

Author(s): Samuel Deslauriers-Gauthier, Jean-Marc Lina, Russell Butler, Kevin Whittingstall, Guillaume Gilbert, Pierre-Michel Bernier, Rachid Deriche, Maxime Descoteaux
Published in: NeuroImage, Issue 201, 2019, Page(s) 116017, ISSN 1053-8119
Publisher: Academic Press
DOI: 10.1016/j.neuroimage.2019.116017

Multi-Tissue Multi-Compartment Models of Diffusion MRI

Author(s): Matteo Frigo, Rutger Fick, Mauro Zucchelli, Samuel Deslauriers-Gauthier, Rachid Deriche
Published in: 2021, Issue 2021, 2021
Publisher: Inria

Network alignment and similarity reveal atlas-based topological differences in structural connectomes

Author(s): Matteo Frigo, Emilio Cruciani, David Coudert, Rachid Deriche, Emanuele Natale, Samuel Deslauriers-Gauthier
Published in: 2020, Issue 2020, 2020
Publisher: Inria

Interpretable Deep Learning as a mean for decrypting disease signature in Multiple Sclerosis

Author(s): Federica Cruciani, Lorenza Brusini, Mauro Zucchelli, Gustavo Retuci Pinheiro, Francesco Setti, Ilaria Boscolo Galazzo, Rachid Deriche, Leticia Rittner, Massimiliano Calabrese, Gloria Menegaz
Published in: 2020, Issue 2020, 2020
Publisher: Inria

Improving Auto-Encoders' self-supervised image classification using pseudo-labelling via data augmentation and the perceptual loss

Author(s): Bouayed, Aymene Mohammed; Atif, Karim; Deriche, Rachid; saim, abdelhakim
Published in: 2020, Issue 2020, 2020
Publisher: Inria

Explainable 3D-CNN for Multiple Sclerosis patients stratification

Author(s): Federica Cruciani, Lorenza Brusini, Mauro Zucchelli, Gustavo Retuci Pinheiro, Francesco Setti, Ilaria Boscolo Galazzo, Rachid Deriche, Leticia Rittner, Massimiliano Calabrese, Gloria Menegaz
Published in: 2020, Issue 2020, 2020
Publisher: Inria

Multi-Tissue Multi-Compartment models of diffusion MRI

Author(s): Matteo Frigo, Rutger Fick, Mauro Zucchelli, Samuel Deslauriers-Gauthier, Rachid, Deriche
Published in: bioRxiv, 2021
Publisher: bioRxiv
DOI: 10.1101/2021.01.29.428843

Resolving the Crossing/Kissing Fiber Ambiguity Using Functionally Informed COMMIT

Author(s): Matteo Frigo, Isa Costantini, Rachid Deriche, Samuel Deslauriers-Gauthier
Published in: Computational Diffusion MRI - International MICCAI Workshop, Granada, Spain, September 2018, Issue 2019 CDMRI, 2019, Page(s) 335-343, ISBN 978-3-030-05830-2
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-05831-9_26

Dmipy, A Diffusion Microstructure Imaging Toolbox in Python to Improve Research Reproducibility

Author(s): Abib Alimi, Rutger Fick, Demian Wassermann, Rachid Deriche
Published in: Computational Diffusion MRI - International MICCAI Workshop, Granada, Spain, September 2018, Issue 2019 CDMRI, 2019, Page(s) 55-67, ISBN 978-3-030-05830-2
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-05831-9_5

A Closed-Form Solution of Rotation Invariant Spherical Harmonic Features in Diffusion MRI

Author(s): Mauro Zucchelli, Samuel Deslauriers-Gauthier, Rachid Deriche
Published in: Computational Diffusion MRI - International MICCAI Workshop, Granada, Spain, September 2018, Issue 2019 CDMRI, 2019, Page(s) 77-89, ISBN 978-3-030-05830-2
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-05831-9_7

Spatio-Temporal dMRI Acquisition Design: Reducing the Number of qτ Samples Through a Relaxed Probabilistic Model

Author(s): Patryk Filipiak, Rutger Fick, Alexandra Petiet, Mathieu Santin, Anne-Charlotte Philippe, Stephane Lehericy, Rachid Deriche, Demian Wassermann
Published in: Computational Diffusion MRI, Issue 2018 CDMRI, 2018, Page(s) 37-49, ISBN 978-3-319-73838-3
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-73839-0_3

Extracting the Groupwise Core Structural Connectivity Network: Bridging Statistical and Graph-Theoretical Approaches

Author(s): Nahuel Lascano, Guillermo Gallardo-Diez, Rachid Deriche, Dorian Mazauric, Demian Wassermann
Published in: Information Processing in Medical Imaging, Issue 10265, 2017, Page(s) 373-384, ISBN 978-3-319-59049-3
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-59050-9_30

Diffusion MRI Anisotropy: Modeling, Analysis and Interpretation

Author(s): Rutger H. J. Fick, Marco Pizzolato, Demian Wassermann, Rachid Deriche
Published in: Modeling, Analysis, and Visualization of Anisotropy, 2017, Page(s) 203-228, ISBN 978-3-319-61357-4
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-61358-1_9

Extracting the Core Structural Connectivity Network: Guaranteeing Network Connectedness Through a Graph-Theoretical Approach

Author(s): Demian Wassermann, Dorian Mazauric, Guillermo Gallardo-Diez, Rachid Deriche
Published in: Medical Image Computing and Computer-Assisted Intervention – MICCAI 2016, Issue 9900, 2016, Page(s) 89-96, ISBN 978-3-319-46719-1
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-46720-7_11

Comparison of Biomarkers in Transgenic Alzheimer Rats Using Multi-Shell Diffusion MRI

Author(s): Rutger H. J. Fick, Madelaine Daianu, Marco Pizzolato, Demian Wassermann, Russell E. Jacobs, Paul M. Thompson, Terrence Town, Rachid Deriche
Published in: Computational Diffusion MRI, Issue 2017 CDMRI, 2017, Page(s) 187-199, ISBN 978-3-319-54129-7
Publisher: Springer International Publishing
DOI: 10.1007/978-3-319-54130-3_16

Explainable 3D-CNN for Multiple Sclerosis Patients Stratification

Author(s): Federica Cruciani, Lorenza Brusini, Mauro Zucchelli, Gustavo Retuci Pinheiro, Francesco Setti, Ilaria Boscolo Galazzo, Rachid Deriche, Leticia Rittner, Massimiliano Calabrese, Gloria Menegaz
Published in: Pattern Recognition. ICPR International Workshops and Challenges - Virtual Event, January 10–15, 2021, Proceedings, Part III, Issue 12663, 2021, Page(s) 103-114, ISBN 978-3-030-68795-3
Publisher: Springer International Publishing
DOI: 10.1007/978-3-030-68796-0_8

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