Publications by Muhamed Barakovic

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Over the last decade microstructure imaging has become commonly endorsed to estimate quantitative features of neuronal tissue. However, those techniques estimate the microstructure only locally. Microstructure informed tractography was recently proposed to ...

Muhamed Barakovic

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The functional characterization of callosal connections

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

Model-informed machine learning for multi-component T2 relaxometry

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

DWI Simulation-Assisted Machine Learning Models for Microstructure Estimation

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

Towards quantitative brain connectomics: microstructure informed tractography via convex optimization

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

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

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

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

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

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

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

Reducing false positives in tractography with microstructural and anatomical priors

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

Voxel size matters: big voxels are required to generate realistic extra-axonal dMRI signals from Monte Carlo simulations

Non-parametric axon diameter distribution mapping with PGSE: reconstruction of uni- and multimodal distributions

Improving Graph-Based Tractography Plausibility Using Microstructure Information

In-vivo Bundle-Specific Axon Diameter Distributions Estimation across the Corpus Callosum