Publications by Muhamed Barakovic

Pore size estimation in axon-mimicking microfibers with diffusion-relaxation MRI

Jean-Philippe Thiran, Muhamed Barakovic, Erick Jorge Canales Rodriguez, Marco Pizzolato, Tim Bjørn Dyrby

Purpose: This study aims to evaluate two distinct approaches for fiber radius estimation using diffusion-relaxation MRI data acquired in biomimetic microfiber phantoms that mimic hollow axons. The methods considered are the spherical mean power-law approac ...

Wiley2024

A Multicenter Longitudinal MRI Study Assessing LeMan-PV Software Accuracy in the Detection of White Matter Lesions in Multiple Sclerosis Patients

Meritxell Bach Cuadra, Bénédicte Marie Maréchal, Tobias Kober, Cristina Granziera, Po-Jui Lu, Ricardo Alberto Corredor Jerez, Muhamed Barakovic, Lester Melie Garcia

BackgroundDetecting new and enlarged lesions in multiple sclerosis (MS) patients is needed to determine their disease activity. LeMan-PV is a software embedded in the scanner reconstruction system of one vendor, which automatically assesses new and enlarge ...

WILEY2023

Estimating axon radius using diffusion-relaxation MRI: calibrating a surface-based relaxation model with histology

Jean-Philippe Thiran, Muhamed Barakovic, Erick Jorge Canales Rodriguez

Axon radius is a potential biomarker for brain diseases and a crucial tissue microstructure parameter that determines the speed of action potentials. Diffusion MRI (dMRI) allows non-invasive estimation of axon radius, but accurately estimating the radius o ...

FRONTIERS MEDIA SA2023

The functional characterization of callosal connections

Giorgio Innocenti, Muhamed Barakovic

The brain operates through the synaptic interaction of distant neurons within flexible, often heterogeneous, distributed systems. Histological studies have detailed the connections between distant neurons, but their functional characterization deserves fur ...

PERGAMON-ELSEVIER SCIENCE LTD2022

Bundle-Specific Axon Diameter Index as a New Contrast to Differentiate White Matter Tracts

Jean-Philippe Thiran, Giorgio Innocenti, David Paul Roger Romascano, Cristina Granziera, Alessandro Daducci, Muhamed Barakovic, Gabriel Girard, Maxime Descoteaux

In the central nervous system of primates, several pathways are characterized by different spectra of axon diameters. In vivo methods, based on diffusion-weighted magnetic resonance imaging, can provide axon diameter index estimates non-invasively. However ...

2021

CLaiMS-Net: cortical lesions assessment in multiple sclerosis patients via a convolutional neural network and a single 3T MRI acquisition

Jean-Philippe Thiran, Meritxell Bach Cuadra, Cristina Granziera, Po-Jui Lu, Muhamed Barakovic, Francesco La Rosa

SAGE PUBLICATIONS LTD2021

An assessment of intra-scanner reproducibility of myelin-sensitive MRI measures

Meritxell Bach Cuadra, Cristina Granziera, Po-Jui Lu, Muhamed Barakovic, Lester Melie Garcia, Francesco La Rosa, Yi Wang

SAGE PUBLICATIONS LTD2021

Comparison of diffusion MRI and CLARITY fiber orientation estimates in both gray and white matter regions of human and primate brain

Jean-Philippe Thiran, Giorgio Innocenti, Muhamed Barakovic

Diffusion MRI (dMRI) represents one of the few methods for mapping brain fiber orientations non-invasively. Unfortunately, dMRI fiber mapping is an indirect method that relies on inference from measured diffusion patterns. Comparing dMRI results with other ...

2021

Measuring compartmental T-2-orientational dependence in human brain white matter using a tiltable RF coil and diffusion-T-2 correlation MRI

Muhamed Barakovic

The anisotropy of brain white matter microstructure manifests itself in orientational-dependence of various MRI contrasts, and can result in significant quantification biases if ignored. Understanding the origins of this orientation-dependence could enhanc ...

2021

Multiple sclerosis cortical and WM lesion segmentation at 3T MRI: a deep learning method based on FLAIR and MP2RAGE

Jean-Philippe Thiran, Meritxell Bach Cuadra, Ahmed Abdulkadir, Cristina Granziera, Mario Joao Fartaria de Oliveira, Po-Jui Lu, Muhamed Barakovic, Francesco La Rosa

The presence of cortical lesions in multiple sclerosis patients has emerged as an important biomarker of the disease. They appear in the earliest stages of the illness and have been shown to correlate with the severity of clinical symptoms. However, cortic ...

2020

Resolving bundle-specific intra-axonal T2 values within a voxel using diffusion-relaxation tract-based estimation

Jean-Philippe Thiran, Cristina Granziera, Alessandro Daducci, Muhamed Barakovic, Erick Jorge Canales Rodriguez

At the typical spatial resolution of MRI in the human brain, approximately 60–90% of voxels contain multiple fiber populations. Quantifying microstructural properties of distinct fiber populations within a voxel is therefore challenging but necessary. Whil ...

2020

Model-informed machine learning for multi-component T2 relaxometry

Jean-Philippe Thiran, Meritxell Bach Cuadra, Tobias Kober, Elda Fischi Gomez, Cristina Granziera, Tom Hilbert, Muhamed Barakovic, Gian Franco Piredda, Erick Jorge Canales Rodriguez, Marco Pizzolato, Thomas Yu

Recovering the distribution from multi-echo magnetic resonance (MR) signals is challenging but has high potential as it provides biomarkers characterizing the tissue micro-structure, such as the myelin water fraction (MWF). In this work, we propose to comb ...

2020

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

Tractostorm: The what, why, and how of tractography dissection reproducibility

David Paul Roger Romascano, Alessandro Daducci, Muhamed Barakovic, Gabriel Girard, Maxime Descoteaux

Investigative studies of white matter (WM) brain structures using diffusion MRI (dMRI) tractography frequently require manual WM bundle segmentation, often called "virtual dissection." Human errors and personal decisions make these manual segmentations har ...

Wiley2020

A new method for accurate in vivo mapping of human brain connections using microstructural and anatomical information

Jean-Philippe Thiran, Alessandro Daducci, Muhamed Barakovic, Maxime Descoteaux

Diffusion magnetic resonance imaging is a noninvasive imaging modality that has been extensively used in the literature to study the neuronal architecture of the brain in a wide range of neurological conditions using tractography. However, recent studies h ...

AMER ASSOC ADVANCEMENT SCIENCE2020

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

Towards quantitative brain connectomics: microstructure informed tractography via convex optimization

Muhamed Barakovic

Tractography is the only non-invasive technique which is used to reconstruct the white mat- ter structural connectivity of the human brain. It relies on a specific Magnetic Resonance Imaging (MRI) acquisition, called diffusion MRI, which is sensitive to th ...

EPFL2019

Improving Graph-Based Tractography Plausibility Using Microstructure Information

Jean-Philippe Thiran, Alessandro Daducci, Muhamed Barakovic, Gabriel Girard

2019

Realistic 3D Fiber Crossing Phantom Models for Monte Carlo Diffusion Simulations

Jean-Philippe Thiran, David Paul Roger Romascano, Alessandro Daducci, Muhamed Barakovic, Gabriel Girard, Gaëtan Olivier D Rensonnet, Jonathan Rafael Patino Lopez

2018