Emmanuel Caruyer homepage

Journal articles

2024

• Thomas Durantel, Gabriel Girard, Emmanuel Caruyer, Olivier Commowick, Julie Coloigner. A Riemannian framework for incorporating white matter bundle priors in ODF-based tractography algorithms.. PLoS ONE, In press, pp.1-10. ⟨hal-04246380⟩

2023

• Haykel Snoussi, Julien Cohen-Adad, Benoît Combès, Élise Bannier, Slimane Tounekti, et al.. Effectiveness of regional diffusion MRI measures in distinguishing multiple sclerosis abnormalities within the cervical spinal cord. Brain and Behavior, 2023, 13 (11), pp.e3159. ⟨10.1002/brb3.3159⟩. ⟨inserm-04313206⟩

• Gabriel Girard, Jonathan Rafael-Patiño, Raphaël Truffet, Dogu Baran Aydogan, Nagesh Adluru, et al.. Tractography passes the test: Results from the diffusion-simulated connectivity (disco) challenge. NeuroImage, 2023, 277, pp.1-11. ⟨10.1016/j.neuroimage.2023.120231⟩. ⟨hal-04390592⟩

2021

• Balazs Aczel, Barnabas Szaszi, Gustav Nilsonne, Olmo van den Akker, Casper Albers, et al.. Consensus-based guidance for conducting and reporting multi-analyst studies. eLife, 2021, 10, pp.e72185. ⟨10.7554/eLife.72185⟩. ⟨inserm-03431812⟩

• Jonathan Rafael-Patino, Gabriel Girard, Raphaël Truffet, Marco Pizzolato, Emmanuel Caruyer, et al.. The diffusion-simulated connectivity (DiSCo) dataset. Data in Brief, 2021, 38, pp.1-7. ⟨10.1016/j.dib.2021.107429⟩. ⟨inserm-03366969⟩

2020

• Alice Bates, Alessandro Daducci, Parastoo Sadeghi, Emmanuel Caruyer. A 4D Basis and Sampling Scheme for the Tensor Encoded Multi-Dimensional Diffusion MRI Signal. IEEE Signal Processing Letters, 2020, 27, pp.790-794. ⟨10.1109/LSP.2020.2991832⟩. ⟨inserm-02881980⟩

• Drew Parker, Abdol Aziz Ould Ismail, Ronald Wolf, Steven Brem, Simon Alexander, et al.. Freewater estimatoR using iNtErpolated iniTialization (FERNET): Characterizing peritumoral edema using clinically feasible diffusion MRI data. PLoS ONE, 2020, 15 (5), pp.e0233645. ⟨10.1371/journal.pone.0233645⟩. ⟨inserm-02884608⟩

2017

• Klaus H Maier-Hein, Peter F. Neher, Christophe Houde, Marc-Alexandre Côté, Eleftherios Garyfallidis, et al.. The challenge of mapping the human connectome based on diffusion tractography. Nature Communications, 2017, 8 (1), ⟨10.1038/s41467-017-01285-x⟩. ⟨hal-01631578⟩

2016

• Rutger H.J. Fick, Demian Wassermann, Emmanuel Caruyer, Rachid Deriche. MAPL: Tissue Microstructure Estimation Using Laplacian-Regularized MAP-MRI and its Application to HCP Data. NeuroImage, 2016, 134, pp.365-385. ⟨10.1016/j.neuroimage.2016.03.046⟩. ⟨hal-01291929⟩

• Oscar Esteban, Emmanuel Caruyer, Alessandro Daducci, Meritxell Bach-Cuadra, María Ledesma-Carbayo, et al.. Diffantom: Whole-Brain Diffusion MRI Phantoms Derived from Real Datasets of the Human Connectome Project. Frontiers in Neuroinformatics, 2016, 10, pp.4. ⟨10.3389/fninf.2016.00004⟩. ⟨inserm-03219764⟩

2015

• Emmanuel Caruyer, Ragini Verma. On facilitating the use of HARDI in population studies by creating rotation-invariant markers. Medical Image Analysis, 2015, 20 (1), pp.87-96. ⟨10.1016/j.media.2014.10.009⟩. ⟨hal-01090154⟩

• Farshid Sepehrband, Jeiran Choupan, Emmanuel Caruyer, Nyoman D. Kurniawan, Yaniv Gal, et al.. lop-DWI: A Novel Scheme for Pre-Processing of Diffusion Weighted Images in the Gradient Direction Domain. Frontiers in Neurology, 2015, 5 (290), ⟨10.3389/fneur.2014.00290⟩. ⟨hal-01103577⟩

2014

• Alessandro Daducci, Erick Canales Rodgriguez, Maxime Descoteaux, Eleftherios Garyfallidis, Yaniv Gur, et al.. Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI. IEEE Transactions on Medical Imaging, 2014, 99, pp.384-399. ⟨10.1109/TMI.2013.2285500⟩. ⟨hal-00908289⟩

2013

• Sylvain L. Merlet, Emmanuel Caruyer, Aurobrata Ghosh, Rachid Deriche. A computational diffusion MRI and parametric dictionary learning framework for modeling the diffusion signal and its features. Medical Image Analysis, 2013, pp.MEDIMA779. ⟨10.1016/j.media.2013.04.011⟩. ⟨hal-00820817⟩

• Emmanuel Caruyer, Christophe Lenglet, Guillermo Sapiro, Rachid Deriche. Design of multishell sampling schemes with uniform coverage in diffusion MRI. Magnetic Resonance in Medicine, 2013, 69 (6), pp.1534-1540. ⟨10.1002/mrm.24736⟩. ⟨hal-00821688⟩

• Emmanuel Caruyer, Iman Aganj, Christophe Lenglet, Guillermo Sapiro, Rachid Deriche. Motion Detection in Diffusion MRI via Online ODF Estimation. International Journal of Biomedical Imaging, 2013, 2013 (Article ID 84936), pp.1-8. ⟨10.1155/2013/849363⟩. ⟨hal-00798582⟩

2012

• Emmanuel Caruyer, Rachid Deriche. Diffusion MRI Signal Reconstruction with Continuity Constraint and Optimal Regularization. Medical Image Analysis, 2012, 16 (6), pp.1113-1120. ⟨10.1016/j.media.2012.06.011⟩. ⟨hal-00711883⟩

Conference papers

2024

• Constance Bocquillon, Juan Luis Villarreal Haro, Jonathan Rafael Patino Lopez, Jean-Philippe Thiran, Isabelle Corouge, et al.. Orientation dispersion estimated from multidimensional diffusion MRI: does it match simulated realistic microstructure?. ESMRMB 2024 - 40th Annual Meeting cientific European Society for Magnetic Resonance in Medecine and Biology, Oct 2024, Barcelone, Spain. pp.1-5. ⟨hal-04795839⟩

• Marie Poirier, Aymeric Stamm, Emmanuel Caruyer. Atlases and generic priors for multi-compartment mapping with diffusion MRI. ESMRMB 2024 - 40th Annual Meeting cientific European Society for Magnetic Resonance in Medecine and Biology, ESMRMB, Oct 2024, Barcelona, Spain. ⟨hal-04843311⟩

2023

• Emmanuel Caruyer. A piecewise-polynomial basis for generalized diffusion encoding gradient waveforms. ISMRM & ISMRT Annual Meeting & Exhibition, The International Society for Magnetic Resonance in Medicine (ISMRM), Jun 2023, Toronto ( CA ), Canada. ⟨inserm-04313189⟩

2022

• Nolwenn Jégou, Elise Bannier, Emmanuel Caruyer, Isabelle Corouge. Chaînes de traitement de données d'une tâche motrice en NIRS et comparaison avec l'IRM sur des sujets sains. Workshop "Acquisition multimodale et analyse des données", Dec 2022, Rennes, France. pp.28. ⟨hal-04308694⟩

• Haykel Snoussi, Benoit Combès, Olivier Commowick, Elise Bannier, Anne Kerbrat, et al.. Reproducibility and evolution of diffusion MRI measurements within the cervical spinal cord in multiple sclerosis. ISBI 2022 - IEEE International Symposium on Biomedical Imaging, Mar 2022, Kolkata, India. pp.1-5. ⟨inserm-03639907⟩

2021

• Jonathan Rafael-Patino, Gabriel Girard, Raphaël Truffet, Marco Pizzolato, Jean-Philippe Thiran, et al.. The Microstructural Features of the Diffusion-Simulated Connectivity (DiSCo) Dataset. CDMRI 2021 - International Workshop on Computational Diffusion MRI, Oct 2021, Strasbourg, France. pp.159-170, ⟨10.1007/978-3-030-87615-9_14⟩. ⟨inserm-03366318⟩

• Simona Schiavi, Mario Ocampo-Pineda, Raphaël Truffet, Emmanuel Caruyer, Alessandro Daducci, et al.. SANDI-AMICO: an open-source toolbox for fast Soma And Neurite Density Imaging (SANDI) with AMICO. 27th annual meeting of the Organization for Human Brain Mapping (OHBM), Jun 2021, Virtual, Singapore. ⟨inserm-03783770⟩

2020

• Raphaël Truffet, Jonathan Rafael-Patino, Gabriel Girard, Marco Pizzolato, Christian Barillot, et al.. An evolutionary framework for microstructure-sensitive generalized diffusion gradient waveforms. MICCAI 2020 - 23rd International Conference on Medical Image Computing and Computer Assisted Intervention, Oct 2020, Lima, Peru. pp.1-11. ⟨inserm-02910086⟩

2019

• Raphaël Truffet, Christian Barillot, Emmanuel Caruyer. Optimal selection of diffusion-weighting gradient waveforms using compressed sensing and dictionary learning. ISMRM 2019 - 27th Annual Meeting & Exhibition, May 2019, Montréal, Canada. pp.1-3. ⟨inserm-02015394v2⟩

• Alice Bates, Alessandro Daducci, Emmanuel Caruyer. Multi-Dimensional Diffusion MRI Sampling Scheme: B-tensor Design and Accurate Signal Reconstruction. ISMRM 2019 - 27th Annual Meeting & Exhibition, May 2019, Montréal, Canada. pp.1-4. ⟨inserm-02065830⟩

• Haykel Snoussi, Emmanuel Caruyer, Julien Cohen-Adad, Olivier Commowick, Benoit Combes, et al.. Geometric evaluation of distortion correction methods in diffusion MRI of the spinal cord. ISBI 2019 - 16th IEEE International Symposium on Biomedical Imaging, Apr 2019, Venice, Italy. pp.1696-1699, ⟨10.1109/ISBI.2019.8759196⟩. ⟨inserm-01986723⟩

2018

• Abdol Aziz Ould Ismail, Drew Parker, Moises Hernandez-Fernandez, Steven Brem, Simon Alexander, et al.. Characterizing Peritumoral Tissue Using Free Water Elimination in Clinical DTI. MICCAI 2018 - 21st International Conference on Medical Image Computing and Computer Assisted Intervention ; Workshop : Brain Lesion, Sep 2018, Granada, Spain. pp.1-9. ⟨inserm-01867347⟩

2017

• Haykel Snoussi, Emmanuel Caruyer, Olivier Commowick, Elise Bannier, Anne Kerbrat, et al.. Comparison of inhomogeneity distortion correction methods in diffusion MRI of the spinal cord. ESMRMB - 34th Annual Scientific Meeting European Society for Magnetic Resonance in Medecine and Biology, Oct 2017, Barcelone, Spain. ⟨inserm-01579134v2⟩

• Olivier Commowick, Renaud Hédouin, Emmanuel Caruyer, Christian Barillot. L2 Similarity Metrics for Diffusion Multi-Compartment Model Images Registration. 20th International Conference on Medical Image Computing and Computer Assisted Intervention - MICCAI, Sep 2017, Québec, Canada. pp.257-265, ⟨10.1007/978-3-319-66182-7_30⟩. ⟨inserm-01556476⟩

2014

• Jérémy Lecoeur, Emmanuel Caruyer, Mark Elliott, Steven Brem, Luke Macyszyn, et al.. Addressing the Challenge of Edema in Fiber Tracking. MICCAI 2014 DTI Tractography Challenge, Sep 2014, Boston, United States. ⟨hal-01072222⟩

• Emmanuel Caruyer, Alessandro Daducci, Maxime Descoteaux, Jean-Christophe Houde, Jean-Philippe Thiran, et al.. Phantomas: a flexible software library to simulate diffusion MR phantoms. ISMRM, May 2014, Milan, Italy. ⟨hal-00944644⟩

• Emmanuel Caruyer, Ragini Verma. Rotation-invariant measures for population study in HARDI. ISMRM, May 2014, Milan, Italy. ⟨hal-00944646⟩

• Emmanuel Caruyer, Luke Bloy, Birkan Tunç, Jérémy Lecoeur, Varsha Shankar, et al.. A comparative study of 16 tractography algorithms for the corticospinal tract: reproducibility and subject-specificity. ISMRM, May 2014, Milan, Italy. ⟨hal-00944649⟩

• Jean-Christophe Houde, Emmanuel Caruyer, Alessandro Daducci, Maxime Descoteaux. How should tractography go forward? A Tractometer evaluation of local reconstruction and tracking. ISMRM, May 2014, Milan, Italy. pp.6470. ⟨hal-01033816⟩

2013

• Jérémy Lecoeur, Emmanuel Caruyer, Luke Macyszyn, Ragini Verma. Improving White Matter Tractography by Resolving the Challenges of Edema. MICCAI 2013 DTI Tractography Challenge, Sep 2013, Nagoya, Japan. ⟨hal-00850496⟩

2012

• Emmanuel Caruyer, Rachid Deriche. A Computational Framework for Experimental Design in Diffusion MRI. CDMRI - MICCAI Workshop on Computational Diffusion MRI, Oct 2012, Nice, France. ⟨hal-00747700⟩

• Sylvain Merlet, Emmanuel Caruyer, Rachid Deriche. Parametric dictionary learning for modeling EAP and ODF in diffusion MRI. Medical Image Computing and Computer Assisted Intervention (MICCAI), Oct 2012, Nice, France. 8 p. ⟨hal-00728067⟩

• Emmanuel Caruyer, Rachid Deriche. Optimal Regularization for MR Diffusion Signal Reconstruction. ISBI - 9th IEEE International Symposium on Biomedical Imaging, May 2012, Barcelona, Spain. ⟨hal-00660635⟩

• Sylvain Merlet, Emmanuel Caruyer, Aurobrata Ghosh, Rachid Deriche. Parametric Dictionary Learning in Diffusion MRI. HARDI reconstruction workshop - ISBI - International Symposium on Biomedical Imaging, Alessandro Daducci and Jean-Philippe Thiran and Yves Wiaux, May 2012, Barcelona, Spain. ⟨hal-00697102⟩

2011

• Emmanuel Caruyer, Jian Cheng, Christophe Lenglet, Guillermo Sapiro, Tianzi Jiang, et al.. Optimal Design of Multiple Q-shells experiments for Diffusion MRI. MICCAI Workshop on Computational Diffusion MRI - CDMRI'11, Sep 2011, Toronto, Canada. ⟨inria-00617663⟩

• Jian Cheng, Sylvain Merlet, Emmanuel Caruyer, Aurobrata Ghosh, Tianzi Jiang, et al.. Compressive Sensing Ensemble Average Propagator Estimation via L1 Spherical Polar Fourier Imaging. MICCAI Workshop on Computational Diffusion MRI - CDMRI'11, Sep 2011, Toronto, Canada. ⟨inria-00615434⟩

• Sylvain Merlet, Emmanuel Caruyer, Rachid Deriche. Impact of radial and angular sampling on multiple shells acquisition in diffusion MRI. MICCAI 2011, Sep 2011, Toronto, Canada. pp.113-121. ⟨hal-00614387⟩

• Emmanuel Caruyer, Christophe Lenglet, Guillermo Sapiro, Rachid Deriche. Incremental gradient table for multiple Q-shells diffusion MRI. HBM 17th Annual Meeting, Jun 2011, Québec, Canada. ⟨inria-00617957⟩

• Emmanuel Caruyer, Iman Aganj, Christophe Lenglet, Guillermo Sapiro, Rachid Deriche. On Line Reconstruction and Motion Detection in HARDI. 19th ISMRM annual meeting, May 2011, Montréal, Canada. ⟨inria-00560899⟩

• Jian Cheng, Sylvain Merlet, Aurobrata Ghosh, Emmanuel Caruyer, Tianzi Jiang, et al.. Compressive Sensing Ensemble Average Propagator Estimation via L1 Spherical Polar Fourier Imaging. ISMRM, May 2011, Montréal, Canada. ⟨inria-00615437⟩

• Emmanuel Caruyer, Iman Aganj, Christophe Lenglet, Guillermo Sapiro, Rachid Deriche. Online Motion Detection in High Angular Resolution Diffusion Imaging. International Symposium on Biomedical Imaging: From Nano to Macro, Mar 2011, Chicago, United States. ⟨inria-00559904v2⟩

2010

• Emmanuel Caruyer, Iman Aganj, Ryan Muetzel, Christophe Lenglet, Guillermo Sapiro, et al.. Online orientation distribution function reconstruction in constant solid angle and its application to motion detection in HARDI. International Symposium on Biomedical Imaging: From Nano to Macro, Apr 2010, Rotterdam, Netherlands. ⟨inria-00559884⟩

2009

• Emmanuel Caruyer, Rachid Deriche. Adaptive Design of Sampling Directions in Diffusion Tensor MRI and Validation on Human Brain Images. MICCAI Workshop on Diffusion Modelling and the Fiber Cup, Sep 2009, Londres, United Kingdom. ⟨inria-00560054⟩

Book sections

2022

• Emmanuel Caruyer. Imagerie par résonance magnétique de diffusion. Le corps en images, pp.1-8, 2022. ⟨inserm-03798395⟩

Habilitation à diriger des recherches

2022

• Emmanuel Caruyer. Numerical methods for white matter microstructure and brain structural connectivity in diffusion MRI. Computer science. Université de Rennes 1, 2022. ⟨tel-03894045⟩

Master thesis

2007

• Emmanuel Caruyer. Signal and Noise in Diffusion Magnetic Resonance Images. Medical Imaging. 2007. ⟨dumas-00880381⟩

Books

2022

• Laure Blanc-Féraud, Emmanuel Caruyer, Christian Jutten, Herve Liebgott (Dir.). Le corps en images. CNRS, 2022, ISBN 9782271143280. ⟨inserm-03798417⟩

Poster communications

2023

• Nolwenn Jégou, Elise Bannier, Nora Erhart, Hector H Garcia, Emmanuel Caruyer, et al.. Reproductibilité d'une tâche motrice en NIRS et comparaison à l'IRMf BOLD sur des sujets adultes sains. SFRMBM 2023 - 6ème Congrès Scientifique de la Société Française de Résonance Magnétique en Biologie et Médecine, Mar 2023, Paris, France. pp.1-1. ⟨hal-04032802⟩

• Constance Bocquillon, Marc Lapert, Elise Bannier, Isabelle Corouge, Emmanuel Caruyer. Étude de l’effet du bruit sur l'estimation de l'anisotropie microscopique en IRM de diffusion. SFRMBM 2023 - Sixième congrès de la Société Française de Résonance Magnétique en Biologie et Médecine, Mar 2023, Paris, France. ⟨hal-04072656⟩

2022

• Nolwenn Jégou, Elise Bannier, Nora Erhart, Hector H Garcia, Emmanuel Caruyer, et al.. Reproducibility of motor task-based fNIRS and comparison with functional MRI in healthy adults. Biennial meeting of the Society for functional Near-Infrared Spectroscopy (fNIRS 2022), Oct 2022, Boston, MA, United States. . ⟨hal-03783898⟩

2018

• Raphaël Truffet, Emmanuel Caruyer. Optimal selection of diffusion-weighting gradient waveforms using compressed sensing and dictionary learning. AI days 2018, Apr 2018, Rennes, France. pp.1. ⟨inserm-01939066v2⟩

Reports

2009

• Emmanuel Caruyer, Iman Aganj, Christophe Lenglet, Guillermo Sapiro, Rachid Deriche. Online orientation distribution function reconstruction in constant solid angle and its application to motion detection in high angular resolution diffusion imaging. [Research Report] RR-7102, INRIA. 2009, pp.12. ⟨inria-00432959⟩

Theses

2012

• Emmanuel Caruyer. IRM de diffusion du Q-space : Acquisition et pré-traitements. Medical Imaging. Université Nice Sophia Antipolis, 2012. English. ⟨NNT : ⟩. ⟨tel-00750144⟩

Preprints, Working Papers, ...

2025

• Alex Mcsweeney-Davis, Chengran Fang, Emmanuel Caruyer, Anne Kerbrat, Jing-Rebecca Li. Alpha Mesh Swc: automatic and robust surface mesh generation from the skeleton description of brain cells. 2025. ⟨hal-04913819⟩

2024

• Meryem Ayşe Yücel, Robert Luke, Rickson Coelho Mesquita, Alexander von Lühmann, David Marc Anton Mehler, et al.. The fNIRS Reproducibility Study Hub (FRESH): Exploring Variability and Enhancing Transparency in fNIRS Neuroimaging Research. 2024. ⟨inserm-05047351⟩

2019

• Abdol Aziz Ould Ismail, Drew Parker, Moises Hernandez-Fernandez, Ronald Wolf, Steven Brem, et al.. Freewater EstimatoR using iNtErpolated iniTialization (FERNET): Toward Accurate Estimation of Free Water in Peritumoral Region Using Single-Shell Diffusion MRI Data. 2019. ⟨inserm-02309753⟩

2016

• Klaus H Maier-Hein, Peter Neher, Jean-Christophe Houde, Marc-Alexandre Côté, Eleftherios Garyfallidis, et al.. Tractography-based connectomes are dominated by false-positive connections. 2016. ⟨hal-03007290⟩