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Muhamed Barakovic

Cette personne a quitté l’EPFL

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Publications associées (27)

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The functional characterization of callosal connections

Muhamed Barakovic, Giorgio Innocenti

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

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

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

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

Model-informed machine learning for multi-component T2 relaxometry

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

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

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

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

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

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

DWI Simulation-Assisted Machine Learning Models for Microstructure Estimation

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

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

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

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

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

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, Cristina Granziera, 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

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

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

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

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

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

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

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

Jean-Philippe Thiran, Muhamed Barakovic, Giorgio Innocenti

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

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

Tobias Kober, Meritxell Bach Cuadra, Cristina Granziera, Bénédicte Marie Maréchal, Muhamed Barakovic, Ricardo Alberto Corredor Jerez, 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

Orientation invariant and non-parametric Axon Diameter Distribution mapping using PGSE and regularized discrete linear modeling

Jean-Philippe Thiran, Alessandro Daducci, David Paul Roger Romascano, Muhamed Barakovic, Anna Auria Rasclosa

Axon Diameter Distributions (ADDs) change during brain development and are altered in several brain pathologies. Mapping ADDs non-invasively using dMRI could provide a useful biomarker, but existing methods are either parametric, orientation dependent, sur ...

2017

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

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

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

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

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

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

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

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

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

When does a volume of a bundle achieve saturation? A microstructure informed tractography study

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

Volumetric analysis of bundles derived from tractography is a popular statistical measure used in neurological disorder studies. Recent research performed by Gauvin shows that different bundles saturate with different tractography parameters, however, to a ...

2017

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

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

SAGE PUBLICATIONS LTD2021

Reducing false positives in tractography with microstructural and anatomical priors

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

Tractography has proven particularly effective for studying noninvasively the neuronal architecture of the brain but recent studies have showed that the high incidence of false positives can significantly bias any connectivity analysis. We present a novel ...

2018