Publications by Jonathan Rafael Patino Lopez

Cellular EXchange Imaging (CEXI): Evaluation of a diffusion model including water exchange in cells using numerical phantoms of permeable spheres

Jean-Philippe Thiran, Ileana Ozana Jelescu, Gabriel Girard, Jonathan Rafael Patino Lopez, Erick Jorge Canales Rodriguez, Rémy Marc M Gardier, Juan Luis Villarreal Haro

Purpose Biophysical models of diffusion MRI have been developed to characterize microstructure in various tissues, but existing models are not suitable for tissue composed of permeable spherical cells. In this study we introduce Cellular Exchange Imaging ( ...

Wiley2023

Molecular Imaging with Aquaporin-Based Reporter Genes: Quantitative Considerations from Monte Carlo Diffusion Simulations

Jean-Philippe Thiran, Jonathan Rafael Patino Lopez, Rémy Marc M Gardier

Aquaporins provide a unique approach for imaging genetic activity in deep tissues by increasing the rate of cellular water diffusion, which generates a magnetic resonance contrast. However, distinguishing aquaporin signals from the tissue background is cha ...

Amer Chemical Soc2023

Microstructure estimation from diffusion-MRI: Compartmentalized models in permeable cellular tissue

Jean-Philippe Thiran, Gabriel Girard, Jonathan Rafael Patino Lopez, Erick Jorge Canales Rodriguez, Rémy Marc M Gardier, Juan Luis Villarreal Haro

Diffusion-weighted magnetic resonance imaging (DW-MRI) is used to characterize brain tissue microstructure employing tissue-specific biophysical models. A current limitation, however, is that most of the proposed models are based on the assumption of negli ...

2022

Insights from the IronTract challenge: Optimal methods for mapping brain pathways from multi-shell diffusion MRI

Jean-Philippe Thiran, Elda Fischi Gomez, Gabriel Girard, Gaëtan Olivier D Rensonnet, Jonathan Rafael Patino Lopez, Erick Jorge Canales Rodriguez, Marco Pizzolato, Thomas Yu

Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI da ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2022

Simulation-based Microstructure Imaging: From Forward Signal Modeling to Machine Learning

Jonathan Rafael Patino Lopez

This thesis focuses on the signal modelling of Diffusion-Weighted Magnetic Resonance Imaging (DW-MRI) in the brain's white matter (WM). DW-MRI a non-invasive technique with enormous potential for the study of the brain's microstructure by measuring the dif ...

EPFL2021

Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?

Jonathan Rafael Patino Lopez, Thomas Yu

White matter bundle segmentation using diffusion MRI fiber tractography has become the method of choice to identify white matter fiber pathways in vivo in human brains. However, like other analyses of complex data, there is considerable variability in segm ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2021

Multi-Compartment Diffusion Mri, T2 Relaxometry And Myelin Water Imaging As Neuroimaging Descriptors For Anomalous Tissue Detection

Jean-Philippe Thiran, Elda Fischi Gomez, Gian Franco Piredda, Jonathan Rafael Patino Lopez, Erick Jorge Canales Rodriguez, Marco Pizzolato

Multiple sclerosis (MS) is an inflammatory and neurodegenerative disease characterized by diffuse and focal areas of tissue loss. Conventional MRI techniques such as T1-weighted and T2-weighted scans are generally used in the diagnosis and prognosis of the ...

IEEE2021

A Signal Peak Separation Index for axisymmetric B-tensor encoding

Jean-Philippe Thiran, Benoît Macq, Gabriel Girard, Gaëtan Olivier D Rensonnet, Jonathan Rafael Patino Lopez, Marco Pizzolato

Diffusion-weighted MRI (DW-MRI) has recently seen a rising interest in planar, spherical and general B-tensor encodings. Some of these sequences have aided traditional linear encoding in the estimation of white matter microstructural features, generally by ...

Springer2021

The Microstructural Features of the Diffusion-Simulated Connectivity (DiSCo) Dataset

Jean-Philippe Thiran, Gabriel Girard, Jonathan Rafael Patino Lopez, Marco Pizzolato

We present a detailed description of the structural characteristics of the MICCAI 2021 Diffusion Simulated Connectivity (DiSCo) Challenge synthetic dataset. The DiSCo dataset are one of a kind numerical phantoms for the simulation of the diffusion-weighted ...

SPRINGER INTERNATIONAL PUBLISHING AG2021

The diffusion-simulated connectivity (DiSCo) dataset

Jean-Philippe Thiran, Gabriel Girard, Jonathan Rafael Patino Lopez, Marco Pizzolato

The methodological development in the mapping of the brain structural connectome from diffusion-weighted mag-netic resonance imaging (DW-MRI) has raised many hopes in the neuroscientific community. Indeed, the knowledge of the connections between different ...

ELSEVIER2021

Axon morphology is modulated by the local environment and impacts the noninvasive investigation of its structure-function relationship

Jean-Philippe Thiran, Jonathan Rafael Patino Lopez, Tim Bjørn Dyrby

Axonal conduction velocity, which ensures efficient function of the brain network, is related to axon diameter. Noninvasive, in vivo axon diameter estimates can be made with diffusion magnetic resonance imaging, but the technique requires three-dimensional ...

National Academy of Sciences2020

ActiveAx(ADD): Toward non-parametric and orientationally invariant axon diameter distribution mapping using PGSE

Jean-Philippe Thiran, David Paul Roger Romascano, Alessandro Daducci, Muhamed Barakovic, Jonathan Rafael Patino Lopez, Tim Bjørn Dyrby

Purpose Non-invasive axon diameter distribution (ADD) mapping using diffusion MRI is an ill-posed problem. Current ADD mapping methods require knowledge of axon orientation before performing the acquisition. Instead, ActiveAx uses a 3D sampling scheme to e ...

Wiley2020

Robust Monte-Carlo Simulations in Diffusion-MRI: Effect of the Substrate Complexity and Parameter Choice on the Reproducibility of Results

Jean-Philippe Thiran, David Paul Roger Romascano, Gabriel Girard, Jonathan Rafael Patino Lopez, Erick Jorge Canales Rodriguez, Alonso Ramirez Manzanares

Monte-Carlo Diffusion Simulations (MCDS) have been used extensively as a ground truth tool for the validation of microstructure models for Diffusion-Weighted MRI. However, methodological pitfalls in the design of the biomimicking geometrical configurations ...

2020

DWI Simulation-Assisted Machine Learning Models for Microstructure Estimation

Jean-Philippe Thiran, Muhamed Barakovic, Gabriel Girard, Jonathan Rafael Patino Lopez, Erick Jorge Canales Rodriguez, Marco Pizzolato, Thomas Yu

Diffusion MRI (DW-MRI) allows for the detailed exploration of the brain white matter microstructure, with applications in both research and the clinic. However, state-of-the-art methods for microstructure estimation suffer from known limitations, such as t ...

Springer Nature2020

Sparse wars: A survey and comparative study of spherical deconvolution algorithms for diffusion MRI

Jean-Philippe Thiran, David Paul Roger Romascano, Alessandro Daducci, Muhamed Barakovic, Gabriel Girard, Gaëtan Olivier D Rensonnet, Jonathan Rafael Patino Lopez, Erick Jorge Canales Rodriguez, Marco Pizzolato

Spherical deconvolution methods are widely used to estimate the brain's white-matter fiber orientations from diffusion MRI data. In this study, eight spherical deconvolution algorithms were implemented and evaluated. These included two model selection tech ...

2019

Robust Biophysical Parameter Estimation with a Neural Network Enhanced Hamiltonian Markov Chain Monte Carlo Sampler

Jean-Philippe Thiran, Gabriel Girard, Jonathan Rafael Patino Lopez, Erick Jorge Canales Rodriguez, Marco Pizzolato, Thomas Yu

Probabilistic parameter estimation in model fitting runs the gamut from maximum likelihood or maximum a posteriori point estimates from optimization to Markov Chain Monte Carlo (MCMC) sampling. The latter, while more computationally intensive, generally pr ...

SPRINGER INTERNATIONAL PUBLISHING AG2019

Assessing feasibility and reproducibility of a bundle-specific framework on in vivo axon diameter estimates at 300mT/m

Jean-Philippe Thiran, Giorgio Innocenti, David Paul Roger Romascano, Alessandro Daducci, Muhamed Barakovic, Gabriel Girard, Maxime Descoteaux, Jonathan Rafael Patino Lopez

In vivo quantitative estimation of axon diameter in the white matter could bring new tools to study the structural and functional architecture of the brain. Recently, the feasibility of axon diameter estimation with diffusion-weighted MRI (DW-MRI) has been ...

2018